46 10 3494 https://omeka.ibu.edu.ba/files/original/607da21842ba6a92dcd60e42c1f88966.pdf df457c175f9db3cd3d16ca1d651d1a4c PDF Text Text 1st International Syposium on Sustainable Development, June 9-10 2009, Sarajevo Biodegradable Modified Corn Starch and Its Electroreological Properties M ustafa Yavuz, Suleyman Demirel University,Isparta, Turkey yavuz@fef.sdu.edu.tr Tahir Tilki Süleyman Demirel University,Isparta, Turkey Meh met Çabuk Mus Alparslan University, Mus, Turkey Meh met Ulutürk Süleyman Demirel University,Isparta, Turkey Abstract: In this study an electrorheological (ER) effect of the suspensions containing both native starch (S) and modified starch (MS) particles in corn oil under various externally applied electric field strengths are reported. To prepare an ER active material, biodegradable starch was partially hydrolyzed and converted to its Li+ salt. Both biopolymers were characterized by 13C-NMR, Scanning Electron Microscopy (SEM), Energy Dispersive Spectroscopy (EDS) and Thermogravimetric Analysis (TGA). Suspensions of Starch and modified Starch particles were prepared in corn oil at concentrations ranging from 5-40% by mass. Rheological measurements were carried out via a rotational rheometer with a high voltage generator to investigate the effects of electric field strength and particle concentration on ER performance. Effects of various parameters such as sedimentation stability, dispersed particle concentration, electric field strength, shear rate, frequency and temperature onto ER activity were investigated. Modified starch suspension was accepted as a biodegradable anhydrous ER fluid. Introduction Biodegradation is the process by which organic substances are broken down by the enzymes and microorganisms. The term is often used in relation to ecology. Starch is a linear polymer (polysaccaride) made up of repeating glucose groups linked by glucosidic linkages in the 1-4 carbon positions. Biodegradation of starch based polymers is a result of enzymatic attack (Ogungbenle 2007) at the glucosidic linkages between the sugar groups leading to a reduction in chain length and the splitting of sugar units (monosaccharides, disaccharides and oligosaccharides)(Kato et al. 2003). ER fluids can potentially be used as a smart materialfor active devices, which transform electric energy to mechanical energy. They are composed of a suspension of polarization solid particles dispersed in a nonconducting liquid media (Block & Kelly 1988). When an electricfieldisimposed,the rheological properties of the fluid vary, showing a characteristic fibrillation (Winslow 1949);the strings of the particles are oriented along the direction ofthe electricfield. This structureis known to be induced by a mismatch ofthe dielectric constants and conductivity ofthe suspended particles and theinsulating oil(Parthasarathy & Klingenberg 1996). ER fluids are divided into two categories (Tao et al. 2001): one is called dry-base ER system (or anhydrous, which shows ER activity without adding any polar promoter) the other one is called wet-base ER systems (or hydrous, which needs a polar promoterto be added to show ER activity). In this study, we investigate native starch and modified starch as a vigorous nominee for anhydrous particles in high performance dry-base systems by analyzing the effect of particle concentration, electric field strength, shear rate and frequency via sheartests. 50 �1st International Syposium on Sustainable Development, June 9-10 2009, Sarajevo Experimental 1. Material The chemicals were Aldrich, Acros and Merck products, with analytical grade. The base fluid used was corn oil with a density ρ= 0.936 g/cm3, viscosity η = 45 mPa s, dielectric constant ε = 3.34, and conductivity (E = 1 kV/mm) σ = 4X10-11 S/m at 25 o C. The starch was (used as dispersed phase) produced by Acros Organics products. 2. Modification Of Native Starch Suspensions of the air-dried corn starch (50 g) in distilled water (500 mL) were supplemented with ammonium vanadate (NH4 VO 3). A marine blue color was appeared. The pH of each suspension was adjusted to 9.0 by adding 10% NaOH(aq). Each suspension was continuously stirred for 48 h at a constant temperature of 35–40o C, under atmospheric conditions. After the reaction was completed, its color turned to yellowish. The reaction mixture was filtered through a sintered glass and the filtrate washed with cold water to remove any impurities present. The products were dried in desiccators over molecular sieves. The dried products were dispersed in 0.1 M LiOH(aq) and the lithium-salt of partially modified starch was obtained. The final product was also dried under the same conditions. The modification reaction mechanism of the native starch is given in Scheme 1. H CH2OH OH NH4VO3 10% NaOH O H H H H O H pH: 9 OH OH LiOH COOH OH H OH OH OH H OH Scheme 1. Oxidation reaction mechanism and chemical structure of modified starch. 3. Electrorheological Measurements Suspensions of starch derivative particles were prepared in corn oil at a series of concentration (c = 5– 40% m/m). Suspensions were mechanically stirred before each measurement against sedimentation. Rheological properties ofthe suspensions were determined with a Termo-Haake RS600 parallel plateElectro-rheometer (Germany). The gap between the paralel plates was 1.0 mm and the diameters ofthe upper and lower plates were 35 mm. Allthe experiments were carried out at a controlled rate (CR) mode and at various temperatures (25–125 ◦ C, with 25 ◦ C increments.). The voltage used in these experiments was also supplied by a 0–12.5 kV (with 0.5 kV increments) dc electric field generator (Fug Electronics,HCL 14, Germany), which enabled resistivity to be created during the experiments. Scheme 2. Mechanism of ER behavior. Results and Discussion 1. Characterizations Both native starch and modified starch were subjected to the following characterizations before ER measurements to be carried out; The 13 C-N MR spectra were obtained in D MSO-d6 and CDCl3 at ambient 51 �1st International Syposium on Sustainable Development, June 9-10 2009, Sarajevo temperature using a 400 MHz Bruker DPX Avonce Nuclear Magnetic Resonance Spectrometer atthe Scientific and Technical Research Council of Turkey (TUBITAK), Ankara Test and Analysis Laboratory (ATAL). Modified starch showed similar 13 C-N MR spectratothat of the native starch,indicating that modification did not have an effect on the molecular packing of the double helices in the crystalline regions but a new additional signal of the carbonyl carbons in ester groups formed by the formulation at 176.15 ppm is clearly visible; some differences exist also in C6 region. The samples were scanned by Scanning electron micrographs (SE M) with an extra of ED A X analyzer ( Jeol JSM-6360 LV, Japan ).The study of EDAX analysis revealthat reactions of modification were completed positively. EDAX analysis evaluated the extent of ionic types (Mi et al. 2003). Spectra (a) is shown energy profiles coming from starch as oxygen and carbon but spectra (b) shows that one more energy profile became the Li+. (a) (b) Figure 1. EDAX analysis of energy positions (a) starch (b)modified starch. Thermal analysis data of particles were obtained using a Setaram 8ET8 V8 Evolution 1760 model thermogravimetric analyzer(TG A) inthe presence of nitrogen atmosphere up to 600o C, ata heating rate of 10 o C / min. The results from TGA are compared for starch and modified starch as a thermogram. Starch has two decomposition stages with one beginning at 250 o C and another beginning at 450 o C. Thermal result of starch and modified starch is similar. There aretwo weightlosses for samples consistat 245 o C and 440 o C. The weight loss is approximately 100% for starch and 85% for modified starch at 600 o C. as a result, modified starch was appeared about 15% end ofthe analysis( Vijaya et al. 2008). Figure 2. Thermogravimetriccurve of (a) starch and (b) modified starch. 52 �1st International Syposium on Sustainable Development, June 9-10 2009, Sarajevo 2. Electrorheology 2.1.Effect Of Dispersed Particle Concentration Effect of dispersed particle concentration on viscosity of S and MS suspensions was investigated using five different concentrations (5%–40% m/m) and results obtained are shown in Figure 3. Suspension concentration exerts principle effect on the ER activity (Wu & Shen 1996). The viscosities of both S and MS suspensions were shown increase with rising particle concentration up to c = 30 (%, m/m) and then leveled off. The maximum electric field induced viscosities (ηE) of Starch and Modified Starch were observed to be 1976 Pas and 3170 Pas,respectively under E = 2 kV/mm and shown a typical strong ER effect. Figure 3. The change in viscosity with concentration, T = 20o C and E = 2 kV/mm. 2.2. Effect Of Electric Field Strength Shear stress is one of the critical design parameter in ER phenomenon and has attracted considerable attention both theoretically and experimentally. Figure 4 also shows the changes in the shear stress (τ) and viscosity (� of S and MS in Corn Oil suspensions under various electric field values. Increase in electric field causesincreasein τ and � Thisis due tothe formation of chain-like structure caused by the polarized particlesin suspensions under E electric field strength ( Choi et al. 1997). Figure 4. The change of viscosity and shear stress with electric field strength, T = 20o C, c = 30% m/m,�= 0.2 s−1 2.3. Effect Of Temperature The temperature dependence of the shear stress is shown in Figure5. The results were investigated at 53 �1st International Syposium on Sustainable Development, June 9-10 2009, Sarajevo temperatures between 25-80°C. It was observed that,for S/Corn Oil system, τ decreased with increasing T and a shear stress loss of ∆τ = 118 Pa was measured. An interesting curve was obtained for MS/Corn Oil suspension, showing a decrease in τ up to T = 50 °C, then gave an increase with rising T. This may be attributed to the loss of moistureinthe MS/Corn Oilsuspension and the increased kinetic energy of Li+ ionsinsertedintothe structure of starch withthe modification process, which gave risetoincreased mobility and polarizability ofthe suspended modified starch. Although shear stress changes withincreasing temperature reported inthe literature ( Unal et al. 2006;Liu & Shaw 2001 ) Figure 5. Effect oftemperature on the shear stress for starch and modified starch suspension, c =30% m/m, � = 0.2 s–1, E = 2.0 kV/mm. 2.4. Effect of frequency The effect of frequency (f) on the shear modulus (G’) for S and MS suspension is shown Fig.6. Up to f = 50 Hz, viscoelastic properties of both Starch and Modified Starch were not much changed. After f = 50 Hz, a sharpincrease was observed for each sample as atypical characteristic of a viscoelastic material, which indicates a vibration damping property. The increase in G’ with increasing external f was also reported in the literature( Zhao et al. 2008). Figure 6. The change of Gı with frequency, c= 30% m/m, T=20o C, γ = 10 Pa, E=2kV/mm . 2.5. Sedimentation stability Sedimentation ratio curves as a function of time for S and M S suspension at 20% concentration at room temperature are shown in figure 7 that, prepared polymer suspensions exhibited colloidal stability against sedimentation, which the sedimentation ratio is 58 % end of 30 days. The sedimentation stability of modified starch suspension is betterthan that of starch. Thisis possibly because starch is easily congregation foritsflakelike structure, greatly modifies its dispersal ability so as to increase its anti-sedimentation ability (Xiang & Zhao 2006). 54 �1st International Syposium on Sustainable Development, June 9-10 2009, Sarajevo Figure 7. Sedimentation stability of starch and modified starch depend on time, c = 20% m/m, T= 20o C Conclusions In presentstudy we have shown thatthe native starch can successfully be partially modified and converted to ER active Li salt. The results showed that, S and MS suspension exhibited ER behavior under electric field strength. The conductivities of S (10-9 S/m) and MS (10-5 S/m) were in the range of ER active materials. Sedimentation stabilities of S and MS suspension were found to be 58% and suitable for potential industrial applications. Optimum particle concentration of the both suspensions was determined to be 30% by mass. The shear stresses of the both materials were shown a linear increase with increasing E. S and MS suspension showed Newtonian behavior when E = 0 kV and Bingham behavior when E ≠ 0 kV. The viscosities of S and MS suspension decreased with increasing shear rate and given a typical of viscoelastic behavior by means of shear thinning. Electric field induced viscosities of the both materials were observed to increase linearly. Temperature was observed to be effective on the both materials and caused shear stress losses on S and shear stress increase on M S, especially at elevated temperatures. Our results revealed that, wet-base ER active S/corn oil suspension system become dry-base ER active after the modification, and shown 3 times stronger ER strength; which is extremely important from industrial point of view. Acknowledgements We are grateful for financial support by The Scientific and Technical Research Council of Turkey (Project no: 107T628 ) References Block H. and Kelly J.P. (1988). Electro-rheology. Journal of Physics D: Applied Physics, 21, 1661-1667. Choi, H. J., M. S. Cho, and M. S. Jhon. (1997). Electrorheological properties of poly(acene quinone) radical suspensions. Polym. Adv. Tech. 8, 697–700. F.-L. Mi, H.-W. Sung, C.-C. Su, C.-K. Peng (2003). Synthesis and characterization of biodegradable TPP/genipin cocrosslinked chitosan gel beads. Polymer 44 6521-6530. Kato Y., Matsuo R., Isogai A. (2003). Oxidation process of water-soluble starch in TEMPO-mediated system. Carbohydrate Polymers, 5, 1 69–75. Liu, B.; Shaw, M. T. (2001). Electrorheology of filled silicone elastomers. J. Rheol., 45, 641-657. Ogungbenle H. N. (2007). Effect of chemical modification in starch of some legume flours. Pakistan Journal of Nutrition, 6 (2), 167-171. Parthasarathy, M. and Klingenberg, D.J. (1996). Electrorheology : mechanisms and models. Mater. Sci. Eng., R17:57–103. 55 �1st International Syposium on Sustainable Development, June 9-10 2009, Sarajevo Tao, R., Zhang, J., Shiroyanagi, Y., Tang, X. and Zhang, X. (2001). Electrorheological Fluidsunder Shear. Int. J. Mod. Phys. B, 15:918–929. Unal, H. I.; Agirbas, O.; Yilmaz, H. (2006). Electrorheological properties of poly(Li-2-hydroxyethylmethacrylate) suspensions Coll. and Surf. A: Physicochem. Eng. Asp., 274, 77-84. Winslow, W.. M. (1953). Field Controlled Hydraulic Device. U.S., Pat. No: 2661596. Wu, S. and Shen, J., 1996. Electrorheological properties of chitin suspensions. J.Appl.Polymer Sci., 60:2159-2164. Xiang, L.; Zhao, X. (2006). Preparation of montmorillonite/titania nanocomposite and enhanced electrorheological activity. J. Coll. Inter. Sci., 296, 131–140. Vijaya, Y., Popuri, S.R., Boddu, V.M. and Krishnaiah, A. (2008), Modified chitosan and calcium alginate biopolymer sorbents for removal of nickel(II) through adsorption. Carbohydrate Polymers, 72 (2), 261-271. Zhao,Y.; Wang, B.; Ding, C.; Zhao, X. (2008). Nano Titanium Oxide Organosol: Synthesis, Characterization, and Application for Electrorheological Fluid. J.Appl.Polym.Sci.,110, 3763-3769. 56 � Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Extent The size or duration of the resource. 471 Title A name given to the resource Biodegradable Modified Corn Starch and Its Electroreological Properties Author Author Yavuz, Mustafa Tilki, Tahir Çabuk, Mehmet Ulutürk, Mehmet Abstract A summary of the resource. In this study an electrorheological (ER) effect of the suspensions containing both native starch (S) and modified starch (MS) particles in corn oil under various externally applied electric field strengths are reported. To prepare an ER active material, biodegradable starch was partially hydrolyzed and converted to its Li+ salt. Both biopolymers were characterized by 13C-NMR, Scanning Electron Microscopy (SEM), Energy Dispersive Spectroscopy (EDS) and Thermogravimetric Analysis (TGA). Suspensions of Starch and modified Starch particles were prepared in corn oil at concentrations ranging from 5-40% by mass. Rheological measurements were carried out via a rotational rheometer with a high voltage generator to investigate the effects of electric field strength and particle concentration on ER performance. Effects of various parameters such as sedimentation stability, dispersed particle concentration, electric field strength, shear rate, frequency and temperature onto ER activity were investigated. Modified starch suspension was accepted as a biodegradable anhydrous ER fluid. Date A point or period of time associated with an event in the lifecycle of the resource 2009-06 Keywords Keywords. Conference or Workshop Item PeerReviewed Q Science (General) https://omeka.ibu.edu.ba/files/original/c3eb050f80218247ff9cd4ccd39a5010.pdf 163f53eadbed66102cc912a8361002ba PDF Text Text 3rd International Symposium on Sustainable Development, May 31 - June 01 2012, Sarajevo Biodiversity for sustinable agriculture: Common bean genetic diversity Nemli Seda , Tanyolac M.Bahattin Department of Bioengineering, Ege University Izmir, Turkey E-mail: eryilmazseda@hotmail.com Abstract The immense genetic diversity of genotypes of crops is the most directly useful and economically valuable part of biodiversity. Genetic diversity is a key factor enabling adaptation, and therefore survival, of natural populations in changing environments. And also genetic diversity is essential tool for any breeding program. Leguminous plants, after cereals, include the most economically important species of agricultural interest, considering area cultivated and total production. Among the grain legumes,soybean, peanuts and common beans are the most important commercial crops. Common bean (Phaseolus vulgaris L.) and its related species are important protein sources for the world population. In 2006, the bean industry was valued at $1.2 billion and $180 million in USA and Canada, respectively. The average yield of bean varieties cropped in developing countries is still very low. The analysis of genetic diversity and relationships among different individuals, species, or populations is an important topic in genetics and plant breeding. Since morphological charactersin plants effect from environmental condition, DNA markers provide the most precise tool for measuring genetic relationships, because they are potentially unlimited in number Among the DNA techniques, Amplified Fragment Length Polymorphism (AFLP) is intense and provides a powerful tool for genotype identification, phylogeny The AFLP technique is based on the amplification of short restriction endonuclease digested genomic DNA fragments onto which adaptors have been ligated at both ends.For this purpose common bean genomes were analyzed using AFLP fingerprinting to examine the genetic variation within and among genotypes.. A total of 86 common bean accessions collected from different countries were used in this study. For the AFLP analysis,12 primer combination were used. Acrylamide gels from primer combination were scored according to presence (1) or absence (0) of amplified fragments.The molecular data were analyzed using the NTSYs program. A dendrogram was generated using JMP software (version 3.1, SAS Institute, 1995) based on the UPGMA (unweighted pair-group method of arithmetic average). The eightysix genotypes represented seven different clusters as revealed by AFLP primers. The minimum variation was detected between sample 20, Turkey and sample 24, Turkey (GD = 0.09), and the maximum was found between samples 34 and 28 (GD = 0.80). Keywords: Biodiversity, Common bean, AFLP 22 �3rd International Symposium on Sustainable Development, May 31 - June 01 2012, Sarajevo 1.INTRODUCTION Common bean (Phaseolus vulgaris) is an important economic food legume and is widely grown in North, Middle and South America, Eastern Africa, Europe and China. The bean seed is rich in protein, fiber, carbohydrates, minerals and vitamins. Beans provide a good source of protein for rural and urban poor in many developing countries. (Pachico,1989) Common bean originated and was domesticated in the New World and has two major gene pools, The Andean and The Mesoamerican, based on their centers of origin in South and Central America, respectively. (gebts and debouck 1991). Common bean is a diploid (2n=22) legume with a relatively small genome. A few species show an aneuploid reduction to 20 chromosomes. The genome of common bean is one of the smallest in the legume family at 625 Mbp per haploid genome. DNA markers provide the most precise tool for measuring genetic relationships, because they are potentially unlimited in number and are not affected by the environment (Maciel et al., 2003). During the last two decades, DNA-based molecular markers have been extensively used for a variety of purposes in many animal and plant systems. Among the DNA techniques, amplified fragment length polymorphism (AFLP) is robust and provides a powerful tool for studies of genetic variation, genotype identification, phylogeny (Kafkas 2006), and molecular linkage mapping (Hurtado and Ramstedt 2002). The AFLP analysis provides a higher level of polymorphism than random amplified polymorphism DNA (RAPD) or restriction fragment length polymorphism (RFLP) (Pejic et al., 1998).Amplified fragment length polymorphisms are based on selective and semiquantitative PCR amplification of restriction fragments digested from total genomic DNA. Fragments generated by digestion of DNA with a combination of two restriction endonucleases are linked to suitable adapters and, thereafter, linked DNA fragments are amplified selectively with different primer combinations (Vos et al., 1995). The RFLPs (Becerra-Vela´ squez and Gepts, 1994; Duarte et al., 1999; Metais et al., 2000; Maciel et al., 2001), RAPDs (Haley et al., 1994; Nienhuis et al., 1995; Moura-Duarte et al., 1999; Beebe et al. 2000; Metais et al., 2000), inter simple sequence repeats (ISSRs) (Rosales-Serna et al., 2003), and more recently, AFLPs (Tohme et al., 1996; Caicedo et al., 1999; Maciel et al., 2003; Pallottiniet al., 2004) have been successfully used for the description of diversity in common bean. In the present paper, AFLP analysis was used to investigate genetic variability at the DNA level in 86 common bean collected from different countries. 2.MATERIAL-METOD A total of 86 common bean accessions were used in this study (Table 1), including 45 Turkey accessions, 5 Netherlands accessions, 4 Germany accessions,, 3 China accessions, 17 England accessions,11 USA accessions, 1 Bulgaria accessions. Table 1: A list of 86 P. vulgaris accessions used in AFLP analysis 23 �3rd International Symposium on Sustainable Development, May 31 - June 01 2012, Sarajevo Genotip Number Genotip Number Location 1 Turkey 20 Turkey 2 Netherlands 21 Turkey 3 Germany 22 Turkey 4 Germany 23 Turkey 5 Germany 24 Turkey 6 Turkey 25 Turkey 7 Netherlands 26 Turkey 8 Netherlands 27 Turkey 9 Netherlands 28 USA 10 Turkey 29 USA 11 Turkey 30 USA 12 Turkey 31 England 13 China 32 England 14 China 33 England 15 Turkey 34 England 16 Turkey 35 England 17 Turkey 36 England 18 Turkey 37 England 19 Turkey 38 England 39 England 63 Turkey 40 England 64 Turkey 41 England 65 USA 42 Turkey 66 England 43 Turkey 67 Turkey 44 Turkey 68 Turkey 45 Turkey 69 Turkey 46 Turkey 70 Turkey 47 Turkey 71 Turkey 48 Turkey 72 Turkey 49 Netherlands 73 India 50 USA 74 USA 51 USA 75 England 52 USA 76 England 53 Turkey 77 England 54 Turkey 78 England 24 Location �3rd International Symposium on Sustainable Development, May 31 - June 01 2012, Sarajevo 55 Turkey 79 England 56 Turkey 80 Turkey 57 Bulgaria 81 Turkey 58 Turkey 82 USA 59 Turkey 83 USA 60 China 84 USA 61 Turkey 85 Turkey 62 Turkey 86 Turkey 2.1. DNA extraction Young leaves from plants collected were harvested and placed in an aluminum foil and kept in liquid nitrogen. Leaf tissue from each individual was ground to a fine powder in liquid nitrogen with a mortar and pestle. Total genomic DNA was extracted following the procedure as described by Doyle & Doyle. The purified DNA was quantified with ND-1000 (Nanodrop, Thermo Co.) spectrophotometer. The DNA quality was also assessed and the concentration determined by visualization under UV light, on 1% agarose gels in TAE (Tris-acetic acid-EDTA) buffer and then agarose gel–stained. 2.2. AFLP analysis Li-Cor AFLP Kit (catalog number: 830-06195 AFLP 2-DYE Selective Amplification Kit) was used according to the manufacturer’s recommendations. According to the kit, 200 ng pure DNA was digested with EcoR I and Mse I restriction enzymes. The enzyme adaptors were ligate to the digested DNA. Selective amplification of restriction fragments was conducted using primers with three selective nucleotide extensions, RD700/800 dyes. Twenty-two primer combinations were used to screen for polymorphism among samples. Amplification products were resolved on 8% acrylamide gel in 1 9 TBE (Trisborate-EDTA) buffer under 1500 V and 40 mA conditions. Li-Cor 4300s DNA Analyzer machine was used to image, analyze, and screen the bands profile 2.3. Band scoring and data analysis Each polymorphic AFLP bands were scored manually as present(1) or absent (0) across all 33 genotypes for each primer-paircombination and the values were used to compile binary datamatrix.Onlybright, clearly distinguishable bands were usedin the genetic analysis. Genetic disimilarity estimates were calculated using Jaccard’scoefficient of disimilarity (Jaccard, 1908). JMP software (version 3.1, SAS Institute, 1995) was used to calculate distances and a dendrogram was generated. The accessions were grouped by cluster analysis using the unweighted pair-group method (UPGMA).PIC (polymorphism information content) was calculated from the 1/0 datum matrix. The PIC value refers to the relative value of each marker with respect to the amount of polymorphism it exhibits. PIC was also calculated by 1- Σpi2: , where i= indiviual p and pi = the allele frequencies of the loci. (De Riek,2001). 25 �3rd International Symposium on Sustainable Development, May 31 - June 01 2012, Sarajevo 3.Results and Discussion 3.1.AFLP Marker analysis The size of bands scored in all the 44 accessions were in the range of 50–450 bp. 86 genotypes were analyzed by AFLP-PCR using 13 selective primer combinations as listed in Table 2. A total of 245 polymorphic bands were generated, and the number of polymorphic bands per each primer combination ranged from 4 (MCAG-EAGG) to 32 (MCAC-EACA) with an average number of 18.8 bands. A representative gel obtained from the primer combination MCAA/E-ACG ( 700 ) is presented in Fig. 1. Polymorphic bands from 86 DNA samples, amplified by 13 AFLP primer combinations, are also listed in Table 2 . The maximum number of polymorphic bands obtained per primer confirmed the high polymorphism determination efficiency of AFLPs in comparison with other marker systems used for common bean such as RAPD (Haley et al., 1994; Maciel et al., 2001; Tiwari et al., 2005 ) and RFLP ( Sonnante et al., 1994; Stockton and Gepts, 2004 ). Table 2 Polymorphic bands from 86 DNA samples, amplified by 13 AFLP primer combinations Primer Number Primer Pairs 1 MCAC-EACA No. of bands 32 2 MCAA-EAAC 25 3 MCAA-EACA 15 4 MCTC-EAAG 15 5 MCAG-EACA 27 6 MCAT-EACA 14 7 MCTG-EACA 25 8 MCAC-EAGC 23 9 MCAA-EACG 12 10 MCAA-EAGC 15 11 MCTC-EACT 20 12 MCAG-EAGG 4 13 MCAT-EAGG 18 TOTAL 245 polymorphic 3.2. Genetic diversity analysis To determine the genetic relationships among the 86 genotypes, the scoring data (1 for presence and 0 for absence) resulting from the 13 primer combinations were used to compute the dissimilarity matrix according to Jaccard (1908). This dissimilarity matrix was used to generate a dendrogram using the UPGMA method. The 86 genotypes represented seven clades as revealed by AFLP primers 26 �3rd International Symposium on Sustainable Development, May 31 - June 01 2012, Sarajevo (Fig.2). Group I was the largest one containing 44 accessions that included twenty five Turkey varieties and seven England land races. As shown in Table 3, the minimum variation was detected between sample 20 Turkey, and sample 24 Turkey (GD= 0,0094) and the maximum was found between sample 34 England and samples 28 USA (GD = 0,80). 27 �3rd International Symposium on Sustainable Development, May 31 - June 01 2012, Sarajevo Fig.1. AFLP pattern of 1-48 common bean DNA samples. 28 �3rd International Symposium on Sustainable Development, May 31 - June 01 2012, Sarajevo Fig.1. AFLP pattern of 49-86 common bean DNA samples 29 �3rd International Symposium on Sustainable Development, May 31 - June 01 2012, Sarajevo Fig. 2 Dendrogram resulting from UPGMA cluster analysis of 86 common bean genotypes based on data derived from 13 AFLP primer combinations Studies of genetic diversity using molecular marker and DNA sequencing techniques are necessary if we are to understand a population’s genetic structure and phylogeography, identify the center of genetic diversity of a species, and develop effective conservation strategies (Gao, 2003).PCR-based molecular marker techniques play an important role in the analysis of genetic diversity and relatedness for crop plants, where most of the species involved are almost 30 �3rd International Symposium on Sustainable Development, May 31 - June 01 2012, Sarajevo unknown at the genetic level (Ilgin et al. 2009). In this study, the AFLP method generated large numbers of polymorphic bands. We detected a total of 284 polymorphic bands, and the number of polymorphic bands for each primer combination ranged from from 4 (MCAG-EAGG) to 32 (MCAC-EACA) with an average number of 18.8 bands. Our study shows that AFLP provided a large number of polymorphic bands and a large amount of genotypic information. Grilli Caiola et al. (2004) found the number of polymorphic bands per primer to be 2.01 in their RAPD study. In conclusion, we have shown that AFLP profiling techniques may provide useful information on the level of polymorphism and diversity in common bean, showing their utility in the characterization of germplasm accessions. AFLP marker systems have comparable accuracy in grouping genotypes of this species according to their gene pool of origin 31 �3rd International Symposium on Sustainable Development, May 31 - June 01 2012, Sarajevo 32 �3rd International Symposium on Sustainable Development, May 31 - June 01 2012, Sarajevo Table 33 3 Genetic distance matrix computed according to Jaccard (1908)’s coefficient based on AFLP data �3rd International Symposium on Sustainable Development, May 31 - June 01 2012, Sarajevo REFERENCES Becerra-Vela´ squez, V.L., and P. Gepts. 1994. RFLP diversity in common bean. Genome 37:256–263 Beebe, S., P.W. Sckroch, J. Tohme, M.C. Duque, F. Pedraza, and J. Nienhuis. 2000. Structure of genetic diversity among common bean landraces of Middle American origin based on correspondence analysis of RAPD. Crop Sci. 40:264–273. Caicedo, A.L., Gaitan, E., Duque, M.C., Torochica, O., Debouck, D.G., Thome,J., 1999. AFLP fingerprinting of Phaseolus lunatus L. and related wild species from S. America. Crop Sci. 39, 1497–1507 Duarte, J.M., J.B. Santos, and L.C. Melo. 1999. Genetic divergence among common bean cultivars from different races based on RAPD markers. Genet. Mol. Biol. 22:419–426 GAO LZ. 2003. The conservation of Chinese rice biodiversity:genetic erosion, ethnobotany and prospects. Genetic Resources and Crop Evolution 50: 17–32. Gepts P, Debouck D (1991) Origin, domestication, and evolution of the common bean (Phaseolus vulgaris L.). In: Schoonhoven AV(ed) Common beans: research for crop improvement. CIAT, Ca-li, pp 7–53 Hair JF, Ander Grilli Caiola M, Caputo P, Zanier R (2004) RAPD analysis in Crocus sativus L. accessions and related Crocus species. Biol Plant48:375–380 Haley, S.D., P.N. Miklas, L. Afanador, and J.D. Kelly. 1994. Random mplified polymorphic DNA (RAPD) marker variability between and within gene pools of common bean. J. Am. Soc. Hortic. 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Random amplified poly-morphic DNA (RAPD) markers variability among cultivars and landraces of common bean (P. vulgaris L.) of South Brazil. Euphytica 120, 257–263 Metais, I., C. Aubry, B. Hamon, R. Jalouzot, and D. Peltier. 2000. Description and analysis of genetic diversity between commercial bean lines (Phaseolus vulgarisL.). Theor. Appl. Genet. 101:1207–1214 34 �3rd International Symposium on Sustainable Development, May 31 - June 01 2012, Sarajevo Moura-Duarte, J., J. Bosco dos Santos, and L. Cunha Melo. 1999. Genetic divergence among common bean cultivars from different races based on RAPD markers. Genet. Mol. Biol. 22:419–426. Nienhuis, J., J. Tivang, P. Skroch, and J.B. Santos. 1995. Genetic relationships among cultivars and landraces of Lima bean (Phaseolus lunatus L.) as measured by RAPD markers. J. Am. Soc. Hortic Sci. 120:300–306. PACHICO, D.1989 Trends in world common bean production, pp. 1-8 in Bean Production Problems in the Tropics, edited by H. F. SCHWARTZ and M. A. PASTORCORRALES. CIAT Press, Cali, Colombia Pallottini, L., E. Garcia, J. Kami, G. Barcaccia, and P. Gepts. 2004. The genetic anatomy of a patented yellow bean. Crop Sci. 44:968–977 Pejic I, Ajmone-Marsan P, Morgante M, Kozumplick V, Castiglioni P, Taramino G, Motto M (1998). Comparative analysis of genetic similarity among maize inbred lines detected by RFLPs, RAPDs, SSRs, and AFLPs. Theor. Appl. Genet. 97: 1248-1255. Rosales-Serna R., Hernandez-Delgado S., Gonzalez-Paz M., Acosta-Gallegos J.A., Mayek-Perez N., 2005, Genetic relationships and diversity revealed by AFLP markers in Mexican common bean bred cultivars, Crop Sci. 45: 1951- 1957. Sonnante, G., Stockton, T., Nodari, R.O., Becerra, V., Gepts, P., 1994. Evolutionof genetic diversity during the domestication of common-bean ( Phaseolusvulgaris L.). Theor. Appl. Genet. 89, 629–635. Stockton, T., Gepts, P., 2004. Identification of DNA probes that reveal poly-morphisms among closely related Phaseolus vulgaris lines. Euphytica 76,177–183 Tiwari, M., Singh, N., Rathore, M., Kumar, N., 2005. RAPD markers in the analysis of genetic diversity among common bean germplasm from Central Himalaya. Genet. Res. Crop Evol. 52, 315–324 Tohme, J., Gonza ´ lez, O.D., Beebe, S., Duque, C., 1996. AFLP analysis of gene pools of a wild bean core collection. Crop Sci. 36, 1375–1384 Vos P., Hogers R., Bleeker M., Relijans M., Lee T., Hornes M., Frijers A., Pot J.,Peleman J., Kuiper M., Zabeau M., 1995, AFLP: A new technique for DNA fingerprinting, Nucleic Acids Research 23: 4407 – 4414. 35 � Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Extent The size or duration of the resource. 1223 Title A name given to the resource Biodiversity for sustinable agriculture: Common bean genetic diversity Author Author Nemli , Seda Abstract A summary of the resource. The immense genetic diversity of genotypes of crops is the most directly useful and economically valuable part of biodiversity. Genetic diversity is a key factor enabling adaptation, and therefore survival, of natural populations in changing environments. And also genetic diversity is essential tool for any breeding program. Leguminous plants, after cereals, include the most economically important species of agricultural interest, considering area cultivated and total production. Among the grain legumes,soybean, peanuts and common beans are the most important commercial crops. Common bean (Phaseolus vulgaris L.) and its related species are important protein sources for the world population. In 2006, the bean industry was valued at $1.2 billion and $180 million in USA and Canada, respectively. The average yield of bean varieties cropped in developing countries is still very low. The analysis of genetic diversity and relationships among different individuals, species, or populations is an important topic in genetics and plant breeding. Since morphological charactersin plants effect from environmental condition, DNA markers provide the most precise tool for measuring genetic relationships, because they are potentially unlimited in number Among the DNA techniques, Amplified Fragment Length Polymorphism (AFLP) is intense and provides a powerful tool for genotype identification, phylogeny The AFLP technique is based on the amplification of short restriction endonuclease digested genomic DNA fragments onto which adaptors have been ligated at both ends.For this purpose common bean genomes were analyzed using AFLP fingerprinting to examine the genetic variation within and among genotypes.. A total of 86 common bean accessions collected from different countries were used in this study. For the AFLP analysis,12 primer combination were used. Acrylamide gels from primer combination were scored according to presence (1) or absence (0) of amplified fragments.The molecular data were analyzed using the NTSYs program. A dendrogram was generated using JMP software (version 3.1, SAS Institute, 1995) based on the UPGMA (unweighted pair-group method of arithmetic average). The eightysix genotypes represented seven different clusters as revealed by AFLP primers. The minimum variation was detected between sample 20, Turkey and sample 24, Turkey (GD = 0.09), and the maximum was found between samples 34 and 28 (GD = 0.80). Keywords: Biodiversity, Common bean, AFLP Date A point or period of time associated with an event in the lifecycle of the resource 2012-05-31 Keywords Keywords. Conference or Workshop Item PeerReviewed S Agriculture (General) https://omeka.ibu.edu.ba/files/original/5a6220379fdbb063f4036eb11f77ebd2.pdf 3c35b51e209db25e4d76aff6984ce7d6 PDF Text Text PROCEEDINGS th ______ The 5 International Symposium on Sustainable Development_______ ISSD 2014 BIOINFORMATICS TOOLS FOR GENE LIST ANALYSIS Imer Muhović*, Larisa Bešić, Adna Ašić, Serkan Dogan, Osman Doluca International Burch University, Department of Genetics and Bioengineering *Corresponding author: imer91@gmail.com ABSTRACT The advent of the era of high-throughput sequencing has brought a wealth of biological data to researchers, but the vastness of the available data has created a demand for tools that could be used to analyze it. One such type of tools are gene set analysis tools, that take a list of genes that were found to be up or down regulated during an experiment. For the sake of simplicity this review focuses solely on freely available web based tools that have been published or have undergone significant updates in the last 5 years. This review is meant to assist tool developers to better understand the needs of the end-users, and in it we look at the currently available gene list analysis tools, their strengths and weaknesses, and offer suggestions for their improvement. Key words: microarray, gene set, systems biology, enrichment, gene ontology 29 | P a g e �ISSD 2014 th The 5 International Symposium on Sustainable Development_______ PROCEEDINGS INTRODUCTION Many modern molecular biology experiments result in the production of a list of important molecules. These molecules may be up/down regulated genes obtained from microarray or RNA-seq experiments, or a list of SNP – containing genes. The issue that is created by such lists is in the length of them. Your average co-expression experiment results in a list of hundreds or thousands of „interesting“ genes, and determining the biological significance of such a list is very difficult, as it requires either significant knowledge about the metabolic process being investigated, or it requires the researcher to conduct an extensive literature search to answer questions such as „What does this gene do? Where is it expressed? Does it interact with other genes? Is it linked to a particular disorder?“ Manually performing such a task would be time consuming and tedious, costing the researcher precious time and resources. To save the time and sanity of researchers undertaking such experiments various tools for annotation enrichment (also known as pathway analysis) have been developed. These tools map genes and proteins to their associated biological annotations (gene Ontology terms, or pathway membership) and then compare the frequency of such terms in the given gene list, with a background list to identify the over expressed, or under expressed terms in the list, following the assumption that such terms are important to the metabolic process that is being studied. As an example, imagine that in a list obtained by a microarray experiment, 20% of the genes are tumor suppressor genes, while in a „normal“ tissue only 5% are. By using standard statistical method we can determine that tumor suppressor genes are enriched in this list, and therefore play an important role in the biological process we are investigating. Most review articles in this field divide tools according to the statistical method that they use. There are three most common ones: Singular Enrichment Analysis (SEA), Gene set enrichment analysis (GSEA), and modular enrichment analysis (MEA).(Huang, Sherman, & Lempicki, 2009) SEA – compares annotation terms one by one with a list of interesting genes for enrichment. A p-value for enrichment is obtained by comparing the frequency of an annotation term with the frequency of that term appearing by chance. All terms that are beyond the cut-off value are said to be enriched. The drawback of this approach is that it ignores the hierarchical relationship between GO terms, and results in large lists of enriched terms due to the fact that it treats similar terms as though they were unique. GSEA – these methods take as an input not only the list of interesting (up or down regulated genes) but all of the genes obtained by an experiment. It functions best in experiments in which two tissue types are compared, because it requires a quantitative value (change in differential expression) for each gene in order to rank them by significant enrichment. A so called maximum enrichment score (MES) is calculated from the ranked list of genes in an annotation category, and enrichment p-values are determined by comparing the MES of the term to a randomly generated MES distribution. To put it in simpler terms, GSEA determines if genes that share a biological annotation (for example belong to the same pathway) are randomly distributed in the gene list (and therefore not significantly attributing to a change in phenotype), or if they are overrepresented in a part of the list (top or bottom, according to fold change, or differential expression), which would indicate that they play a role in the pathway that is being studied.(Subramanian et al., 2005) 30 | P a g e �PROCEEDINGS th ______ The 5 International Symposium on Sustainable Development_______ ISSD 2014 MEA – seeks to use the relationships between different annotation terms to remove the redundancy, or underrepresentation of important terms that may be caused by SEA and GSEA methods. They seek to improve sensitivity and specificity by using composite annotation terms. The issue with them may be found if they use only a single information source, usually GO. Most current tools seem to have switched to using MEA as opposed to SEA, as the link between different levels of annotation has become clearer, and the integration of different databases has become easier. Molecular interaction network present the easiest, most intuitive way of representing such large and complex datasets, and several curated databases already exist that link all known binary protein interactions, as well as enrichment data, whether extracted from literature of HT experiments. DATABASES To better study and keep track of all known pathway data several databases have been constructed. A key difference between databases lays in their data acquisition methods. We can separate curated databases from automatic ones; by the way the data are added in the database, either by trained experts or via automatic methods. Each has its own advantages, shallow curated databases have larger network coverage, while curated ones have higher quality of data, but still data capture errors such as false positives in the data still can't be excluded. Another difference is the data source, as some databases take their data from peer reviewed literature, while secondary databases look to integrate primary databases and thus become a one-stop shop for all your protein interaction needs. One we have a list of PPI interactions we need methods to visualize this data and extract the useful data from them. Due to the large number of PPIs in a possible network the results usually look like a giant ball of yarn that is difficult to interpret so visualization techniques offered by the tool play an important role. H-InvDB (http://www.h-invitational.jp/) is a human gene database first published in 2004.It contains 244,709 human DNA sequences, and provides the user with a broad variety of tools for genome analysis. According to the authors analysis 19,309 annotated genes were found to be specific to H-InvDB and not to be found in RefSeq or Ensembl.(Takeda et al., 2012) PINA (The Protein Interaction Network Analysis) is an integrative resource that combines data from six manually curated public databases, and offers a set of tools for network construction, filtering, analysis and visualization. It offers protein-protein interaction (PPI) network construction, by clustering approaches from an interactome constructed for six available model organisms. All identified terms are annotated using GO terms, KEGG pathways, Pfam domains and MsigDB data.(Cowley et al., 2011) 31 | P a g e �ISSD 2014 th The 5 International Symposium on Sustainable Development_______ PROCEEDINGS STRING is a database that seeks to provide biologists with a global perspective on as many interactions from as many organisms as possible. It scores both known and predicted interactions, and offers the users tools for statistical analysis and enrichment analysis of queried terms.(Franceschini et al., 2012) GeneSigDB (http://www.genesigdb.org or http://compbio.dfci.harvard.edu/genesigdb/) is a database of gene signatures collected manually from published literature, focusing on cancer studies, as well as immune cells, stem cells and lung disease. It is an excellent tool for prognostic analysis of cancer and related diseases, or use as an gene set enrichment tool. The visualization of enriched terms is performed via heatmap that provides us with publicationquality images, and GeneSigDB allows us to download data in .gmt file format that can be later used for additional gene set enrichment analysis.(Culhane et al., 2011) IntAct is an open-source, molecular interaction database that contains data manually curated from literature or raw depositions. It has two levels of curation, and contains around 275 000 interactions, collected from over 5000 publications. A recent upgrade has brought it a visual display of data, which are downloadable in multiple formats.(Kerrien et al., 2011) The MetaCyc database (http://metacyc.org/) is a freely accessible resource that contains data from metabolic pathways and enzymes from all domains of life. MetaCyc pathway data is obtained experimental and small-molecule metabolic pathways and are curated from the primary scientific literature. Currently there are more than 1800 pathways derived from over 30 000 publications, making MetaCyc the largest curated collection of metabolic pathways. (Caspi et al., 2011) IPAVS (Integrated Pathway Resources, Analysis and Visualization System) is a manually curated database of known protein pathways. It combines several publicly available pathway databases, and provides the tools to filter search and analyze biological pathways. It is freely available, interactive and integrated pathway database which is designed to address the needs of bench biologists, computational biologists and physicians. It offers biologists a single point of access to several manually curated pathway resources, in addition to its own expert-curated pathways that are in standard format. (Sreenivasaiah, Rani, Cayetano, Arul, & Kim, 2011) NETWORK CLUSTERING Proteins are usually represented as nodes, and interactions as vertices, giving us a ball and stick model of interactions. One of the main aims of pathway analysis strategies is to discover clusters of proteins that perform a similar function. This is mostly done by network topology as highly interconnected nodes form clusters, and the basic assumption is that clusters identify proteins that share a common function. Issues that may arise from analyzing pathways in this fashion is that large networks tend to resemble balls of yarn, due to having hundreds of nodes and vertices, thus making the inference of biological data from them very hard, and confusing. 32 | P a g e �PROCEEDINGS th ______ The 5 International Symposium on Sustainable Development_______ ISSD 2014 NETWORK ANNOTATION Annotation of nodes and edges is usually needed to make some sense of the information found in PPINs. The annotations may include info about the method by which the interaction was detected, some confidence scores and similar parameters. Gene Ontology project is the most widely used source of extra information that can be used in network analysis. It's creates a hierarchical list of terms called Ontologies that covers three independent biological domains: 1 - Cellular Components 2 - Biological Processes 3- Molecular Function.(Ashburner et al., 2000) This enables us to highlight the proteins that perform the same function, thus allowing a functional representation of a network, usually GO is combined with cluster detection to provide greater interpretation of a network. GENE LIST ANALYSIS TOOLS Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool Enrichr is a web based tool that takes in as an input a list of differentially expressed genes, and produces lists of enriched terms. The authors have solved the issues that arise when using only one source of enrichment data, by using 35 gene set libraries split into six groups, with each containing different data about different enrichment terms. It uses 1) ChEA (The ChIP-x Enrichment Analysis Database), it’s own resource of putative transcription factor targets created from publications that report experiments of profiling mammalian DNA binding transcription factors. ; 2) position weight matrices (PWMs) from TRANSFAC and JASPAR ; that were used to scan all promoter regions (-2000 to +500 from the start of transcription) of all human genes, they kept all 100% matches to the consensus sequence between a factor and a target gene. 3) target genes generated from PMWs downloaded from the UCSC genome browser , because it produces different results compared to the ones mentioned above 4) transcription factor targets extracted from the ENCODE project . In addition, the two other gene-set libraries in the transcription category are gene sets associated with: 5) histone modifications extracted from the Roadmap Epigenomics Project ; and 6) microRNAs targets computationally predicted by TargetScan . It provides three different statistical measures of the results, of which one is the Fischer exact test, the other an in-house variation and last a combination of the two. The authors performed a quality evaluation of these methods in their original paper. Enrichr provides many different options for visualizing the data, one of which is a grid of squares, with the most enriched elements being colored more brightly when compared to the rest. It also allows the visualization in the form of a list of enriched terms, bar graph, network and table. An advantage of Enrichr over other programs of the same type is it’s availability and modern design, it’s available as a mobile application for smartphones and tablets, and the webinterface is clear, and intuitive. The authors tested the software by comparing nine cancer cell lines and found an upregulation in the PRC2 polycomb group target genes.(Chen et al., 2013) 33 | P a g e �ISSD 2014 th The 5 International Symposium on Sustainable Development_______ PROCEEDINGS Network2Canvas is a network visualization program that makes it easier to visualize large protein-protein interaction networks, and enrichment terms. The most common issue with using ball and stick models of PPI networks is that larger networks tend to end up looking like balls of yarn, making it very difficult to visually analyze the properties of the network. Network2Canvas works around this issue by placing the nodes on a square toroidal canvas, the nodes are then clustered on the canvas via simulated annealing in order to have the maximum number of local connections, and their brightness is set to correspond to the local fitness of the node. This software takes as input a list of differentially expressed genes, or a list of drugs and outputs a set of enriched terms including drug side effects, common pathways etc. The website is accompanied by a video tutorial on how to use the program, and offers a variety of possible canvases, for example Kinase Enrichment Analysis or KEGG pathways, and more. Overall N2C is a very useful and intuitive tool for molecular data analysis, especially for larger lists of genes or drugs.(Tan, Chen, Dannenfelser, Clark, & Ma’ayan, 2013) Genes2FAN: Proteins interaction studies are mostly done by analyzing binary protein interactions, but these are not the only ways two genes, or their protein products can interact. The authors of this program used knowledge on the shared properties of genes from diverse sources to create functional association networks (FANs), to allow researchers to identify additional interactions between groups of genes, which are not immediately obvious from PPI networks. G2F uses a database of 14 FANs, and large scale PPI networks to create subnetworks that can connect lists of human and mouse genes. Lists of genes are taken as an input to produce a subnetwork, using a ranked list of intermediate genes that connect the genes from the queried list. This web application offers a powerful new approach to analyzing gene associations, as it can find the intermediate parts of a pathway, and thus allow us to observe a greater, clearer picture of a molecular process.(Dannenfelser, Clark, & Ma’ayan, 2012) Sets2Network is a tool created to allow the creation of interaction networks by analyzing the co-occurrence of entities in related sets. It gives us a general method for inferring networks by repeated observation of sets of related terms. It interprets the frequency of the occurrence of the link as the probability that it is present in the real-world network. This tool has usages outside the realm of biology, as it can create a network from any file given in the GMT (Gene Matrix Transpose) format, for example it can be used to create a network of co-authorship by taking in a GMT file of publications and authors, or predict direct PPI from HT MS data. (Clark, Dannenfelser, Tan, Komosinski, & Ma’ayan, 2012, p. 2) S2N can output the data in various formats, so subsequent analysis can be performed on the data, using additional visualization tools such as yEd. DAVID (Database for Annotation, Visualization and Integrated Discovery, available at http://david.abcc.ncifcrf.gov/) is one of the oldest and most well-known web-based bioinformatics resources for the functional interpretation of gene/protein lists. It has been cited over 6000 times since its initial publication. It takes inputs in list form and allows the user to perform gene-term enrichment analysis, visualization of the gene-term relationships, search for related genes, pathway analysis and much more. They have recently published DAVID-WS (Web service) an API (application programming interface) which allows for the programmatic automation of requests to DAVID, and thus the easier automation of tasks, without the need for human interactions.(Jiao et al., 2012) 34 | P a g e �PROCEEDINGS th ______ The 5 International Symposium on Sustainable Development_______ ISSD 2014 EnrichNet is a web-based tool created in order to address the current limitations of gene set analysis tools. Most GSA tools use the over-representation-based enrichment analysis method which uses the overrepresentation of a gene list of interest in a reference list via a statistical test (usually Fisher’s exact test) as proof of biological significance. The issue with this approach is that it low power of discrimination, and significant variance with changes in overlap size, among others. EnrichNet uses an graph-based statistic approach to analyze gene sets, via exploiting information from molecular network structures of, and offers interactive visualization of network sub-structures. It offers integrated data sources (molecular interaction data, pathway and tissue-specific gene expression data) and uses graph-based statistical analysis and forced – directed layout generation to provide a clearer and more detailed understanding of the gene set interactions. It uses a minimalist interface, with clear output, and we refer the reader to the paper for more information.(Glaab, Baudot, Krasnogor, Schneider, & Valencia, 2012) GeneCodis is a tool for enrichment analysis, available since 2007, its newest version offers a more concise output and removes some redundancy, via summarizing of significantly enriched terms, they also expanded the original application, by adding new sources of information, such as genetic diseases, gene-drug interactions and PUBMED information. GeneCodis offers a very customizable input, as it integrates data from several organisms, which is rather rare as most of the enrichment analysis tools focus only on humans. Its capable of filtering the output.(Tabas-Madrid, Nogales-Cadenas, & Pascual-Montano, 2012) GeneMANIA (http://www.genemania.org) is a web-app for gene list analysis. Given a list, it will extend it with functionally similar genes, obtained from genomics and proteomics databases. It’s capable of finding genes of similar function, and those that are most likely to interact with the ones in the list. It supports multiple organisms, and integrates hundreds of datasets from GEO, BioGRID, IRefIndex and I2D.(Zuberi et al., 2013) Graphite Web: A new web-app for pathway analysis and visualization, that takes as input gene lists from microarray or RNA-seq experiments. It combines topological methods with multivariate pathway analyses and provides a clear network visualization tool, for efficient interpretation of expression experiment results. It works with three model organisms, and integrates two pathway databases.(Sales, Calura, Martini, & Romualdi, 2013) CONCLUSION While new tools are constantly arriving they individually don’t see too much use or recognition, this may be due to low popularity, or just being hard to find. This lack of visibility makes it hard for researchers to test out new tools, as they rarely know that they even exist, and this leads to a lack of feedback for the tool makers, which in turn leads to a lack of improvement in the available tools. The usage of targeted internet marketing to possible users should be considered by future tool makers as a way of reaching out to new users, and obtaining feedback on their work. The current focus of enrichment analysis should probably be turned over to better visualization of datasets, as the ball and stick models are prone to looking like a ball of yarn if the input list is too large. Better visualization of data will allow for much easier analysis, and comprehension of experimental results. API support is another issue, as most of the tools listed in this review rely on manual input of data, DAVID-WS is a nice exception to the rule. APIs could allow for easier testing and automation of enrichment analysis tools, thus simplifying and speeding up a biologist’s workflow. 35 | P a g e �ISSD 2014 th The 5 International Symposium on Sustainable Development_______ PROCEEDINGS Standardization is another issue encountered in the use of these tools, as few of them support multiple formats of output files, while exception do exist, they are few and mostly consist of older, more established tools. While some tools do offer advantages over others, there exists no gold standard for enrichment analysis, with labs using whichever tools they prefer, this makes it hard to gauge the effectiveness of an approach, as only by repeat usage do the advantages of a tool become clearly apparent. 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GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics. Nucleic Acids Research, 40(W1), W478–W483. doi:10.1093/nar/gks402 Takeda, J. -i., Yamasaki, C., Murakami, K., Nagai, Y., Sera, M., Hara, Y., … Imanishi, T. (2012). H-InvDB in 2013: an omics study platform for human functional gene and transcript discovery. Nucleic Acids Research, 41(D1), D915–D919. doi:10.1093/nar/gks1245 Tan, C. M., Chen, E. Y., Dannenfelser, R., Clark, N. R., & Ma’ayan, A. (2013). Network2Canvas: network visualization on a canvas with enrichment analysis. Bioinformatics, 29(15), 1872–1878. doi:10.1093/bioinformatics/btt319 Zuberi, K., Franz, M., Rodriguez, H., Montojo, J., Lopes, C. T., Bader, G. D., & Morris, Q. (2013). GeneMANIA Prediction Server 2013 Update. Nucleic Acids Research, 41(W1), W115–W122. doi:10.1093/nar/gkt533 Imer Muhović is a MSc student at the International Burch University. His main interests lie in bioinformatics and systems biology, and he is currently in the process of constructing a novel bioinformatics tool for sequence analysis, which will form his Master’s thesis. 37 | P a g e � Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Extent The size or duration of the resource. 2450 Title A name given to the resource BIOINFORMATICS TOOLS FOR GENE LIST ANALYSIS Author Author MUHOVIĆ, Imer BEŠIĆ, Larisa AŠIĆ, Adna DOGAN, Serkan DOLUCA, Osman Abstract A summary of the resource. The advent of the era of high-throughput sequencing has brought a wealth of biological data to researchers, but the vastness of the available data has created a demand for tools that could be used to analyze it. One such type of tools are gene set analysis tools, that take a list of genes that were found to be up or down regulated during an experiment. For the sake of simplicity this review focuses solely on freely available web based tools that have been published or have undergone significant updates in the last 5 years. This review is meant to assist tool developers to better understand the needs of the end-users, and in it we look at the currently available gene list analysis tools, their strengths and weaknesses, and offer suggestions for their improvement. Key words: microarray, gene set, systems biology, enrichment, gene ontology Publisher An entity responsible for making the resource available International Burch University Date A point or period of time associated with an event in the lifecycle of the resource 2014-05-15 Keywords Keywords. Article PeerReviewed Identifier An unambiguous reference to the resource within a given context ISSN 978-9958-834-36-3 Q Science (General),QH301 Biology,QH426 Genetics https://omeka.ibu.edu.ba/files/original/b07ea9e57cba6ae337bfd4515469085d.pdf 1aead1a15145473c159b69bbe91031a6 PDF Text Text Journal of Natural Sciences and Engineering, Vol. 2, (2020) DOI number: 10.14706/JONSAE2020213 Biometrics Based Access Control System Mujo Hadžimehanović1, Dino Kečo1, Demir Korać1 1 International Burch University, Sarajevo, Bosnia and Herzegovina mujo.hadzimehanovic@stu.ibu.edu.ba dino.keco@ibu.edu.ba demir.korac@stu.ibu.edu.ba Abstract – Access control includes attendance checking and intrusion prevention. It is used to protect property, employees and other assets of a company or institution. Since attendance checking and intrusion detection are important segments of many educational institutions and other businesses as well, it is important to make these processes faster, easier and as convenient as possible. Lots of institutions are suffering from unreliable attendance checking methods, so we have decided to use biometrics, more precisely face recognition to automate and improve this overall process. As part of this study the full system has been implemented for recognition of people. As an example of usage in an educational institutions multiple photos will be recorded during the class session, so that in case of students leave class after the first shot, they will be removed from the attendance sheet. All recognized people will be stored in Mongo database as an array of features and later read from database and processed by using Python script for face recognition. All educational institutions are going to have benefits from this study. Benefits would be improving attendance management and security. Keywords - attendance, face, images, recognition 1. Introduction Technology is rapidly improving nowadays and everyday activities are adopting these improvements. Point is to automate these activities and not to lose time performing them. Attendance is a really important part in most organizations such as schools, faculties, companies etc. Today, attendance is performed in various ways. Best way to do it is biometrics. Biometrics is a bioengineering area which is an automated method for person recognition based on its physiological or behavioural characteristics. There are many biometric templates such as fingerprints, face, hand geometry, iris, voice or signature. System is going to use face biometric template because it is the fastest approach and requires no human intervention. This method is better than other biometric methods because these methods are time consuming. There are also lots of systems which are using RFID cards, location based attendance tracking systems, signature based etc. Negative things about these methods are that they can be faked. In RFID and location based systems employees are carrying RFID cards or GPS locators. So, other people can check instead of other employees. There are two main stages of face recognition process and they are face detection and face identification [1]. Recording employees' work hours and their activities, attendance of students in schools are really important components of every company or school. This process is maintained by using signature, fingerprint, iris, RFID or face recognition. System is going to use a camera which captures images of people entering the company or school building. Detected faces will be compared with pictures which are already in the database. If a person's picture is in the database attendance �Journal of Natural Sciences and Engineering, Vol. 2, (2020) DOI number: 10.14706/JONSAE2020213 will be checked automatically. Otherwise, the security system is going to be informed that an unrecognized person entered the building. So, this system can also be used as an intrusion detection system. 2. Literature Review Following section contains a presentation of all related work and their methods. Since they have large-scale data with massive noisy labels, X. Wu, R. He, Z. Sun, and T. Tan used a Light CNN framework [2]. Their Light CNN architecture contains Max-Feature-Map to suppress low activation neurons in all layers. Their model was trained on Celeb-1M dataset. In order to handle noisy labeled images, they proposed a semantic bootstrapping method to automatically re-label training data via pre-trained deep networks. For training purposes they used five types of databases. First type is commonly used Labeled Faces in the Wild which consists of ~13,250 images of ~5,750 people. At VR@FAR=0 for Light CNN-29, they achieved 97.50%, while results from all other methods were lower than 70%. Next type of the database are collections of images extracted from Youtube videos which contain YouTube Celebrities (YTC) and Celebrity1000 database. Precision achieved for these datasets is 94.18%. Third type are MegaFace, IJB-A and IJB-B datasets which are challenging and they got 85.13% precision. Cross-domain databases are the fourth type of database. It includes CACD - VS, Multi - PIE and the CASIA NIR - VIS 2.0 database. They achieved 98.55% on CACD, 95.0% on Multi-PIE and on CASIA VR@FAR=0.1% result is further improved from 94.03% to 94.77%. M. Arsenovic, S. Sladojevic, A. Anderla, and D. Stefanovic use Convolutional Neural Networks (CNNs) cascade to detect faces and CNN to generate embeddings of each face [3]. Fact is the best results for larger datasets are achieved by using CNNs, but in their production environment that was not the case. CNN gave the best results for smaller datasets. Accuracy of 95.02% was achieved on a dataset created by authors in the realtime environment. Five employees of the company took pictures of themselves and they used these pictures as a dataset. Model was trained with these 5 pictures. Active annotation and learning framework was used by H. Ye et al [4]. They are starting with face image training set without labels and train a deep neural network iteratively model created was used to choose examples for further manual annotation. After following active learning strategy, Value of Information criterion is derived to actively select candidate annotation images. This model reaches the coverage of 70.7% with a precision of 95%. MSR Image Recognition Challenge by J. Li et al introduces a knowledge base which has an idea to assign each face unique entity key and provide large dataset consisting of about 100,000 famous persons with around 100 images per person (MsCeleb) [5]. Method achieved coverage of 46.1% at 95% precision on the random dataset and 33% at 95% precision on the hard set of their challenge. Authors proposed a method consisting of two stages to learn robust human face representations for effective recognition of human faces. First stage in the training set is cleaning the noisy data because dataset is taken from the internet so images without faces can appear. In order to do so, a deep neural network was trained on existing dataset. �Journal of Natural Sciences and Engineering, Vol. 2, (2020) DOI number: 10.14706/JONSAE2020213 S. Chintalapati and M. V. Raghunadh used SVM and Bayesian classifier for automated attendance system based on face detection and recognition [6]. They proved that these classifiers are better when compared to other distance classifiers. This system automatically detects the student which enters the classroom and marks the attendance if recognizes him. One of the failures of the system is recognizing faces only up to 30 degrees angle variations. 3. Methods and Materials Dataset to be used is Labeled Faces in the Wild [7] which is a database of face photographs designed for studying the problem of unconstrained face recognition. It contains more than 13,000 pictures collected from the web. Each image has been labeled with the name of the person on it. There are 1680 different persons in images. Fig.1 shows samples from LFW dataset. Fig.1. Samples from dataset These images need to be processed in order to get numerical representation of faces which is called feature vector. Feature vector consists of various numbers in a specific order which can be: height or width of face, width of lips, nose height etc… Final output of processed image needs to be an array with features which is shown in Fig.2. All features are stored in the mongo database for speed improvement. Python script iterates in a folder which has dataset images and stores one by one in a database with image name and features. Face Recognition library with deep learning is going to be used for this project. Deep learning model has an accuracy of 99.38% on Labeled Faces in Wild dataset. Features of face recognition library are finding faces in pictures, finding facial features in pictures and identifying faces in pictures. Once installed face recognition gives us two command line programs: ● face_recognition - recognize face on image ● face_detection - detect face in image Face recognition process consists of two stages. This includes taking and preparing training dataset and integration into existing system. For testing purposes, data was collected at the university. These are images of students which were taken in the first year. Images are preprocessed and inserted into the mongo database by �Journal of Natural Sciences and Engineering, Vol. 2, (2020) DOI number: 10.14706/JONSAE2020213 using python script for inserting images. After insertion, facebook images of the same people were taken and tested by using python script for face recognition. Fig.2. Array of features 3.1 Data preprocessing Implemented system is going to use monitoring cameras at the entrance. It means that we could have some kind of network or other problems and taken images could be blurry, so we have to include such images in training dataset, Fig.3. Persons entering the building can be photographed from different angles, so these kind of photos should be included also in training dataset, Fig 4. �Journal of Natural Sciences and Engineering, Vol. 2, (2020) DOI number: 10.14706/JONSAE2020213 Fig.3. Original and Blurred image Fig.3 shows an example of original and blurred images. If we have perfect conditions we would have a picture like the original one, but if the system experiences network issues we might have a blurry image like the one represented. System has to be ready to respond accordingly to these kinds of issues. Python script was written using OpenCV [8] interface to generate blurry images out of the original ones. Fig.4. Image from front and side In Fig.5 we can see facial features drawn on picture of Pep Guardiola. Most important features are shown: eyes, nose, mouth and chin location. These features are used when recognizing people on images. Face recognition library contains script face_landmarks for detecting facial landmarks and positioning the face based on them. Fig.5. Facial features �Journal of Natural Sciences and Engineering, Vol. 2, (2020) DOI number: 10.14706/JONSAE2020213 3.2 Usage Workflow Application usage workflow is represented on Fig.6. Images need to be collected into a single folder, so that insertion helper scripts can be run. For multiple insertions we need to pass a folder of images to script, which iterates through these images, creates encodings and inserts them into database. Single insertion script accepts an image as a parameter, encodes it and inserts into a database. Last step is recognizing images, the script accepts an image which needs to be recognized and iterates through mongoDB collection and looks for matching images. Fig.6. Usage workflow 3.3 Face Recognition Library Face recognition library which we are using is built using dlib’s face recognition with deep learning. We can install library by using a python package installer. Once installed we are provided with two command-line programs : face_recognition and face_detection. Face recognition recognizes faces in a photograph or in a folder of photos. There should be two folders, one containing known people and second which contains photos of people which we want to recognize. Face recognition program is run with two parameters which are the names of these folders. Face detection program finds pixel coordinates of faces. It takes a folder with images as parameter and at the end prints one line for each face that was detected. There is also an option to speed up the overall process by doing a recognition with multiple CPU cores. For example if we have 8 core CPU, we can process 8 times as many images in the same amount of time. Dlib is a toolkit written in C++ and contains ML algorithms and tools for solving real world problems. The most important thing is that dlib is an open source library which enables anyone to use it anywhere, free of any charge. Some of the dlib’s features are Deep Learning, Multiclass SVM, Image Processing etc.. Our library uses Image Processing tool for face recognition built by using deep learning tools from dlib. �Journal of Natural Sciences and Engineering, Vol. 2, (2020) DOI number: 10.14706/JONSAE2020213 3.4 Helper Scripts There are multiple helper scripts which enable user to insert multiple or single image into database and recognize faces. The most important parts of scripts are represented in the following lines. insertMultiple.py for image in images: current_image = face_recognition.load_image_file("images/" + image) encodings = face_recognition.face_encodings(current_image) if len(encodings) > 0: current_image_encoded = encodings[0] num_of_images+=1 else: print("No faces found in the image " + image) num_of_not_found+=1 continue mydict = { "image": image, "encoding": current_image_encoded.tolist() } x = mycol.insert_one(mydict) print(image + " inserted") Code snippet above loads images from the folder, encodes them and inserts them into mongoDB. We have to provide the name of the folder which contains images and simply run the script. �Journal of Natural Sciences and Engineering, Vol. 2, (2020) DOI number: 10.14706/JONSAE2020213 faceRecognition.py unknown_image = face_recognition.load_image_file("image.jpg") unknown_face_encoding = face_recognition.face_encodings(unknown_image)[0] known_faces = [] names = [] for x in mycol.find(): known_faces.append(x['encoding']) names.append(x['image']) results = face_recognition.compare_faces(known_faces, unknown_face_encoding) for x in range(len(known_faces)): if results[x] == True: print("Recognized: " + names[x]) else: print("Failed: " + names[x]) Code represented above does face recognition. It takes an image of the person which we want to recognize, encodes it, loops through face encodings from the database and checks if a person exists in the database. 4. Results By using a custom dataset which was collected from our university. Students' images were taken and tested on created scripts. From these tests we have obtained accuracy of 90.9% when testing on images found on Facebook. There were some problems when recognizing people from different angles, but this can be material for further study. Images of people are not shown because they did not agree to publish their images. Since face_recognition python library has a pre-trained model there is no need for additional training. Improvement is that all images are inserted in mongoDB with image name and face encodings array. Fig.5 shows one part of mongoDB record. Python script for inserting images in mongoDB is written and it takes a folder with images and inserts one by one in the database. In our testing environment LFW dataset is used and all images are collected into a single folder. Number of images inserted in the database is 4014. There are also images on which faces are not recognized. Unrecognized images number is 21. So, if we take into consideration that 4014 images are inserted and 21 are unrecognized which means that more than 99% images were recognized. Example of such an image is shown in Fig.6. Execution time of the script is about 35 minutes for LFW Dataset. Final result of this research would be access control application. Application can be installed on Raspberry Pi which has a camera installed. All assets that are necessary for access control application to be fully functional can be installed on Raspberry. These are mongoDB, python and python libraries. Overall process is not so challenging, so that we do not need anything better than Raspberry Pi 3 B+ which is a model that we used while testing the application. �Journal of Natural Sciences and Engineering, Vol. 2, (2020) DOI number: 10.14706/JONSAE2020213 5. Conclusion The aim of this study was to make the attendance checking process a lot easier for companies and schools by using biometrics. Every employee or student would be recorded by camera at the entrance and recorded in the system. For educational institutions cameras will be installed in classrooms so that the system can make multiple shots during lessons. This research was successful because it made the recognition process faster by using a document based database which is really fast. This study will bring benefits for multiple groups. Benefit for schools is easier attendance recording and reducing waste of time at the beginning of the classes. Also students will not have a chance to avoid coming to classes because this system will not allow them to cheat. Similar benefit is for companies to track their employees coming and leaving time. Future research suggestions in this field are solving problems if a person is recorded from the side and possibly getting blurry images because of internet connection issues. REFERENCES [1] B. T. Liyew and P. Hazari, “A Survey on Face Recognition based Students Attendance System.” [2] X. Wu, R. He, Z. Sun, and T. Tan, “A Light CNN for Deep Face Representation With Noisy Labels,” IEEE Transactions on Information Forensics and Security, vol. 13, no. 11. pp. 2884–2896, 2018, doi: 10.1109/tifs.2018.2833032. [3] M. Arsenovic, S. Sladojevic, A. Anderla, and D. Stefanovic, “FaceTime — Deep learning based face recognition attendance system,” 2017 IEEE 15th International Symposium on Intelligent Systems and Informatics (SISY). 2017, doi: 10.1109/sisy.2017.8080587. [4] H. Ye et al., “Face Recognition via Active Annotation and Learning,” Proceedings of the 2016 ACM on Multimedia Conference - MM ’16. 2016, doi: 10.1145/2964284.2984059. [5] J. Li et al., “Robust Face Recognition with Deep Multi-View Representation Learning,” Proceedings of the 2016 ACM on Multimedia Conference - MM ’16. 2016, doi: 10.1145/2964284.2984061. [6] S. Chintalapati and M. V. Raghunadh, “Automated attendance management system based on face recognition algorithms,” 2013 IEEE International Conference on Computational Intelligence and Computing Research. 2013, doi: 10.1109/iccic.2013.6724266. [7] “LFW Face Database : Main.” [Online]. Available: http://vis-www.cs.umass.edu/lfw/. [Accessed: 19-Jan-2019]. [8] “OpenCV library.” [Online]. Available: https://opencv.org/. [Accessed: 09-Jan-2019]. � Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Title A name given to the resource Journal of Natural Sciences and Engineering Identifier An unambiguous reference to the resource within a given context 2637-2835 DOI Digital object identifier 10.14706 Publisher An entity responsible for making the resource available International Burch University Description An account of the resource Journal of Natural Sciences and Engineering (JONSAE) is a peer-reviewed, biannually published international journal focusing on empirical and theoretical research in all branches of Engineering and Natural Sciences. It is published on the behalf of Faculty of Engineering and Natural Sciences of International Burch University and aims to provide the best content regarding by publishing original research papers, review articles, special issues, feature articles, and book reviews. All manuscript submissions are subject to initial appraisal by the Editor, and, if found suitable for further consideration, to peer review by independent, anonymous referees. All peer review is double-blind and submission is online. The journal welcomes theoretical, applied, interdisciplinary and methodological work, with preference on empirical research, critical approach and problem-solving methods in manuscripts. Language A language of the resource English Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Title A name given to the resource Biometrics Based Access Control System Author Author Mujo Hadžimehanović, ​Dino Kečo,​ ​Demir Korać​ Abstract A summary of the resource. ​Access control includes attendance checking and intrusion prevention. It is used to protect property, employees and other assets of a company or institution. Since attendance checking and intrusion detection are important segments of many educational institutions and other businesses as well, it is important to make these processes faster, easier and as convenient as possible. Lots of institutions are suffering from unreliable attendance checking methods, so we have decided to use biometrics, more precisely face recognition to automate and improve this overall process. As part of this study the full system has been implemented for recognition of people. As an example of usage in an educational institutions multiple photos will be recorded during the class session, so that in case of students leave class after the first shot, they will be removed from attendance sheet. All recognized people will be stored in Mongo database as an array of features and later read from database and processed by using Python script for face recognition. All educational institutions are going to have benefits from this study. Benefits would be improving attendance management and security. Keywords Keywords. Keywords - attendance, face, images, recognition Identifier An unambiguous reference to the resource within a given context 2637-2835 Publisher An entity responsible for making the resource available International Burch University, Sarajevo, Bosnia and Herzegovina Source A related resource from which the described resource is derived Journal of Natural Sciences and Engineering Date A point or period of time associated with an event in the lifecycle of the resource January, 2020 https://omeka.ibu.edu.ba/files/original/04e9c57a1c75ceadebc426947295337f.pdf c8c684fec162e6320f0bf40e2fb6f70b PDF Text Text PROCEEDINGS th ______ The 5 International Symposium on Sustainable Development_______ ISSD 2014 BIOMONITORING OF LEAD POLLUTION ON THE URBAN FLORA Mustafa Dogan1, Zlatko Nedić2, Rifet Terzić3 1 International School of Zenica, Bosnia and Herzegovina; mustafadogan74@hotmail.com 2 High School Orasje, Bosnia and Herzegovina; zlatko8679@hotmail.com 2 University of Tuzla, Bosnia and Herzegovina; rifet.terzic@untz.ba ABSTRACT In this study, the first aim was to find out the measures of lead (Pb) as the heavy metal pollution in Sarajevo, Bosnia and Herzegovina. The second aim was to test if chicory, Cichorium intybus L., can be used as a biomonitor of heavy metal pollution. Twenty-eight sites (urban, suburban and rural) in Sarajevo were investigated during the summer period in 2010. Concentrations of Pb were determined in leaves and roots of Cichorium intybus L. and also in soils collected from a wide range of sites with different degrees of metal pollution. As a result of measurements, the highest values of lead accumulations in plants have been observed in roots as expected. The highest values were detected as 30.10 mgkg-1 dry weight in roots and as 28.20 mgkg-1 dry weight in leaves in the PMF garden in Pofalici. On the other hand, the highest value of lead was detected as 450.05 mgkg-1 dry weight in soil in Museum Garden. Theoretically it is expected to observe highest accumulation in soils, roots and leaves, respectively. After getting results, it is observed the relationship of lead accumulation among soils, roots and leaves as expected. Cichorium intybus L. was found to be a useful biomonitor in the determination of lead pollution. Key words: Cichorium intybus L., lead pollution, biomonitoring, Sarajevo 17 | P a g e �ISSD 2014 th The 5 International Symposium on Sustainable Development_______ PROCEEDINGS INTRODUCTION One of the common worldwide plants is the common chicory. It is also known as succory, blue sailors, cornflower, and coffee weed. Cichorium intybus L., also known as common chicory, is a bushy perennial herbaceous plant. It has blue, lavender, or sometimes white flowers. It lives as a wild plant on roadsides in many countries of its native Europe, Asia, North America and Australia (Davis, 1975). Various varieties are cultivated for salad leaves, chicons (blanched buds), or for roots (var. sativum), which are baked, ground, and used as a coffee substitute and additive. It is also grown as a forage crop for livestock. When flowering, Cichorium intybus L. has tough, grooved, and some hairy stem, from 25 to 100 centimeters tall. The leaves are stalked, lanceolate and unlobed. The flower heads are 2 to 4 centimeters wide, and bright blue. There are two rows of involucral bracts - the inner are longer and erect, the outer are shorter and spreading. It flowers from July until October. The achenes have no pappus (feathery hairs), but do have toothed scales on top. (Rose & Francis, 1981) Lower plants, especially mosses and lichens, in view of their higher capacity for metal accumulation are probably the organisms most frequently used for monitoring metal pollution in urban environments (Markert, 1993; Al-Shayeb et al., 1995 & Aksoy et al., 1999). During the past few decades there has been an increase in the use of higher plant leaves as biomonitor of heavy metal pollution in the terrestrial environment (Aksoy & Ozturk, 1996, 1997; Aksoy & Demirezen, 2006). Wild chicory is a leafy vegetable and it has several characteristics for biomonitoring purposes which are worldwide cosmopolitan distribution, ability to tolerate a broad range of climatic and soil conditions, and ability to grow as a weed so it can be used as a biological indicator of heavy metal contamination (Simon et al., 1984). Also, it is a perennial plant that could be another convenient characteristic for biomonitoring purposes. Numerous organisms have been used to monitor heavy metal pollutions (Augusto et al., 2007). These include invertebrates, vertebrates, cyanobacteria, lichens, mosses, and many parts of plants (tree barks, tree rings, pine needles, grasses and leaves) (Lovett et al., 1997; Aksoy & Öztürk, 1996; Sakurai et al., 2000; Augusto et al., 2007; Aksoy, 2008; Atiq-UrRehman and Iqbal, 2008). Some plant species have more ability of uptaking high levels of metals and other toxic elements, without showing any visible injury. These are later denominated as accumulator or biomonitor plants (De Temmerman et al., 2004). The term biomonitor is defined as an organism that provides quantitative information on the quality of the environment around it. Therefore, a good biomonitor will indicate the presence of the pollutant and also attempt to provide additional information about the amount and intensity of the exposure (Wolterbeek, 2002). With proper selection of organisms, the general advantage of the biomonitoring approach is related primarily to the permanent and common occurrence of the organism in the field, even in remote areas, the ease of sampling, and the absence of any necessary expensive technical equipment (Wittig, 1993; Wolterbeek, 2002). Many studies on the accumulation of heavy metals by various plant species have been reported (Peterson et al., 1979; Lepp, 1981; Page et al., 1981; Nasu & Kugimoto, 1984; De Temmerman & Hoenig, 2004; Finster et al., 2004; Augusto et al., 2007). Although it is consumed enormously, there are only few data available on heavy metal accumulation of wild chicory in contaminated areas (Simon et al., 1984; Turkan, 1986; Del Rio-Celestino et al., 2006; Aksoy & Demirezen, 2006; Aksoy, 2008). 18 | P a g e �PROCEEDINGS th ______ The 5 International Symposium on Sustainable Development_______ ISSD 2014 MATERIALS AND METHODS Method: Lead (Pb) concentrations were investigated in the samples of soil, roots and aerial parts of chicory. The analyses were done by Federal Institute of Agriculture in Sarajevo. Concentrations of lead were measured in terms of mg/kg in twenty eight localities. 1. Sample Collection and Identification: The soil, roots and aerial parts of chicory were handpicked carefully into plastic bags at the each locality. All samples were labeled with respect to their localities. 2. Sample Processing: In the laboratory, all samples were exposed to air dry for 5 days. Then the dried samples were grounded to have fine powder. 3. Sample Analysis by ICP-AES (Inductively Coupled Plasma – Atomic Emission Spectrometry): After sample processing, the last step was analytical procedures of ICP-AES analysis. Perkin Elmer Plasma 400 ICP-AES operating in sequential mode was used for all analyses. Atomic spectrometer is very useful for element analysis because every element has its own characteristic set of energy level. By the use of atomic spectrometer, the set of emission wavelengths were measured. Table 1 Comparison of heavy metal concentrations (mg kg-1 dry wt) considered toxic or contaminated, taken from the literature (adapted from Ross, 1994), with values from this study. Concentrations in soil Concentration in Present results Element Considered toxic contaminated plants Soil Plants Pb 100-400 30-300 4.80 - 450.05 0.60 - 30.10 Study Areas In this study, Sarajevo City center and around are studied. Twenty eight localities are investigated for heavy metal pollution. These locations are: 19 | P a g e �ISSD 2014 th The 5 International Symposium on Sustainable Development_______ Table 2 localities and gps values Latitude: Longitude: L1: Pofalići - PMF garden 43°51'17.40"N 18°23'44.03"E L2: Grbavica 43°51'9.63"N 18°24'5.55"E L3: Tranzit road - Vraca 43°50'52.00"N 18°23'53.00"E L4: Tranzit road - A.S. 43°50'48.38"N 18°23'57.99"E L5: Vraca - Memorial park 43°50'40.02"N 18°23'59.81"E L6: Trebević 43°50'20.04"N 18°24'49.01"E L7: Trebević II 43°50'35.79"N 18°24'57.50"E L8: Skenderija V.P. 43°51'21.36"N 18°24'45.90"E L9: Ćumurija 43°51'24.48"N 18°25'36.78"E L10: Bentbaša 43°51'34.24"N 18°26'12.60"E L11: Holiday Inn tram line 43°51'19.77"N 18°24'7.66"E L12: Tranzit road - Soukbunar 43°51'8.84"N 18°24'53.04"E L13: Bistrik church 43°51'20.79"N 18°25'54.62"E L14: Museum garden 43°51'18.58"N 18°24'11.37"E L15: Bakije 43°52'2.40"N 18°26'30.21"E L16: Babina bašta 43°51'32.76"N 18°26'5.68"E L17: Tranzit road - Bistrik 43°51'14.43"N 18°25'25.95"E L18: Pofalići – tram line 43°51'15.95"N 18°23'35.94"E L19: Otoka 43°50'51.77"N 18°21'37.50"E L20: Stup 43°50'36.40"N 18°19'47.08"E L21: Kobilja Glava 43°53'0.56"N 18°23'5.30"E L22: Ilidža 43°49'53.69"N 18°18'32.10"E L23: Faletići 43°52'15.03"N 18°27'11.27"E L24: Semizovac 43°55'15.55"N 18°18'59.09"E L25: Ćevljanovići 44° 3'8.92"N 18°28'37.14"E L26: Olovo 44° 7'36.75"N 18°36'50.06"E L27: Kladanj 44°14'28.91"N 18°42'20.61"E L28: Museum garden II 43°51'18.24"N 18°24'6.56"E 20 | P a g e PROCEEDINGS �PROCEEDINGS th ______ The 5 International Symposium on Sustainable Development_______ ISSD 2014 Picture 1. Satellite record of Sarajevo 21 | P a g e �ISSD 2014 th The 5 International Symposium on Sustainable Development_______ PROCEEDINGS RESULTS Table 3 Results of lead analysis Localities L1: Pofalići-PMF garden L2: Grbavica L3: Tranzit road-Vraca L4: Tranzit road -A.S. L5: Vraca-Memorial park L6: Trebević L7: Trebević II L8: Skenderija V.P. L9: Ćumurija L10: Bentbaša L11: Holiday Inn tram line L12: Tranzit road -Soukbunar L13: Bistrik church L14: Museum garden L15: Bakije L16: Babina bašta L17: Tranzit road -Bistrik L18: Pofalići -tram line L19: Otoka L20: Stup L21: Kobilja Glava L22: Ilidža L23: Faletići L24: Semizovac L25: Ćevljanovići L26: Olovo L27: Kladanj L28: Museum garden II SOIL Results of lead (mg/kg) 206.64 49.00 103.32 25.83 77.00 50.10 4.80 77.49 99.80 77.50 154.98 31.00 97.30 542.43 69.70 25.83 70.34 129.16 73.34 136.68 51.66 18.33 65.50 25.00 30.60 73.00 5.00 450.05 ROOT Results of lead (mg/kg) 30.10 9.40 11.90 8.70 5.60 1.70 0.90 8.50 9.70 7.00 11.00 5.80 8.90 28.00 5.20 3.80 4.20 10.00 3.80 3.30 6.20 4.20 2.10 8.70 3.00 10.10 6.40 10.30 LEAF Results of lead (mg/kg) 28.20 8.38 15.70 8.50 6.80 1.10 0.60 4.30 7.60 6.40 5.10 7.50 7.20 22.00 4.80 4.10 3.00 5.80 1.75 2.20 2.80 3.30 2.50 5.60 2.00 13.20 4.10 9.80 A- DESCRIPTIVE ANALYSIS OF LEAD Table 4 Descriptive analysis of lead LEAD Mean Median max. min. st dev 22 | P a g e SOIL Results of lead (mg/kg) 100.76 71.67 542.43 4.80 121.60 ROOT Results of lead (mg/kg) 8.16 6.70 30.10 0.90 6.65 LEAF Results of lead (mg/kg) 6.94 5.35 28.20 0.60 6.26 �PROCEEDINGS th ______ The 5 International Symposium on Sustainable Development_______ ISSD 2014 B- DESCRIPTIVE ANALYSIS WITH RESPECT TO URBAN, SUBURBAN AND RURAL AREAS Table 5 Results with respect to urban, suburban and rural areas SOIL - Results of lead (mg/kg) ROOT - Results of lead (mg/kg) LEAF - Results of lead (mg/kg) Urban Suburban Rural 152.75 61.79 31.42 10.57 6.21 5.13 8.30 6.45 4.43 SOIL Results of lead (mg/kg) Graph 1 Distribution of lead concentration in urban, suburban and rural areas (mg/kg) C- REGRESSIVE ANALYSIS OF LEAD Table 6: Regressive analysis of lead – soil Dependent Variable: SOIL_PB Method: Least Squares Date: 05/14/14 Time: 21:35 Sample: 1 28 Included observations: 28 Variable Coefficient Std. Error t-Statistic Prob. LEAF_PB -6,680899 ROOT_PB 16,24043 8,115762 -0,8232 0,4185 7,899495 2,055882 0,0508 LOCATION 50,69459 C -10,7494 40,2297 1,260128 0,2197 28,31497 -0,379637 0,7076 R-squared Adjusted R-squared S.E. of regression Sum squared resid Log likelihood F-statistic Prob(F-statistic) 0,507033 0,445412 90,55576 196808,3 -163,7392 8,228267 0,000612 Mean dependent var S.D. dependent var Akaike info criterion Schwarz criterion Hannan-Quinn criter. Durbin-Watson stat 100,7636 121,5993 11,98137 12,17169 12,03955 1,481338 23 | P a g e �ISSD 2014 th The 5 International Symposium on Sustainable Development_______ PROCEEDINGS Table 7: Regressive analysis of lead - root Dependent Variable: ROOT_PB Method: Least Squares Date: 05/14/14 Time: 21:32 Sample: 1 28 Included observations: 28 Variable Coefficient Std. Error t-Statistic LEAF_PB 0,866314 0,084729 10,22457 0 SOIL_PB 0,00922 0,004485 2,055882 0,0508 LOCATION 0,680752 0,979956 0,694676 0,4939 C 0,878754 0,652479 1,346794 R-squared Adjusted R-squared S.E. of regression Sum squared resid Log likelihood F-statistic Prob(F-statistic) 0,906412 0,894713 2,15768 111,734 -59,10511 77,48062 0 Mean dependent var S.D. dependent var Akaike info criterion Schwarz criterion Hannan-Quinn criter. Durbin-Watson stat Prob. 0,1906 8,160714 6,649664 4,507508 4,697823 4,565689 2,401098 Table 8: Regressive analysis of lead - leaf Dependent Variable: LEAF_PB Method: Least Squares Variable Coefficient ROOT_PB SOIL_PB LOCATION C R-squared Adjusted R-squared S.E. of regression Sum squared resid Log likelihood F-statistic Prob(F-statistic) 0,938794 -0,00411 -0,118226 -0,247595 0,885385 0,871058 2,24613 121,0824 -60,23001 61,79893 0 Date: 05/14/14 Time: 21:29 Sample: 28 Included observations: 28 Std. Error t-Statistic 0,091818 10,22457 0,004993 -0,8232 1,03005 -0,114777 0,70261 -0,352393 Mean dependent var S.D. dependent var Akaike info criterion Schwarz criterion Hannan-Quinn criter. Durbin-Watson stat Prob. 0 0,4185 0,9096 0,7276 6,940357 6,255153 4,587858 4,778173 4,646039 2,201968 DISCUSSION and CONCLUSION Especially the first half of the previous century has high lead (Pb) emission into the environment because lead has been used as an antiknock agent in gasoline. According to Olendrzynski et al. (1995), about 70% of the total emissions in Europe were related to traffic, 15% to industrial production, 5%-10% to power generation, and 2% to waste burning. Another research concludes that the major source of human lead accumulation in developing countries was found to be airborne lead, 90 percent of which comes from leaded gasoline (MECA, 2003). Similar results indicating lead in the atmosphere mainly emitted from automobiles were investigated by several other researches (Foner, 1987; Gratani et al., 1992; Bahemuka & Mubofu, 1999; Renberg et al., 2000; Yaman et al., 2000; Andrews & Sutherland, 2004; Finster et al., 2004). Aksoy & Sahin, (1999) indicated that sampling of soil and different parts of plants is useful to determine the source and location of lead contamination. Table 1 represents a comparison of the toxic heavy metal concentrations (Ross, 1994). Because concentrations of lead in Cichorium intybus L. do not exceed generally the upper limit, studied sites of Sarajevo are not highly polluted by lead. 24 | P a g e �PROCEEDINGS th ______ The 5 International Symposium on Sustainable Development_______ ISSD 2014 The concentrations of lead as heavy metal found in soil, roots and aerial parts of Cichorium intybus L. in different sites are presented in the Table 3. The lead concentrations in different localities show differences. Especially lead concentrations in soil show some excessive amounts in some localities. In terms of root and leaf, results are in the acceptable range. Only two sites exceed the upper limits which are located in the museum garden. Two different localities in museum garden show high pollution levels. Moreover, especially urban samples show values in which the upper limit is higher than the minimum levels of contamination. Aerial deposition of lead over a long time period might cause to that high concentration. Based on the results of a previous study carried out by Aksoy (2008), It is expected soil lead concentration should be higher than that of roots and leaves. It is clear that the concentrations of lead in soil were significantly higher than that of in roots and aerial parts of plants. Therefore, the concentrations of lead in the soils support Cichorium intybus L. in the same areas. The descriptive analysis with respect to urban, suburban and rural areas shows the practical results as expected theoretically. The mean lead concentrations in soil in the urban samples are significantly higher than that of suburban and rural samples. On the other hand, the mean lead concentrations in root and leaf samples are significantly higher than that of rural and are slightly higher than that of suburban samples. The similar correlation can be found vertically in the same table. The mean lead concentrations in urban, suburban and rural areas show decreasing relations in soils, roots and leaves, respectively. These results are also expected theoretical results because of exposure time interval to lead pollution. Because soil is exposed to lead pollution more years than root and leaves, more lead is accumulated in soil. Basically, there are two ways whereby plants get contaminated by lead, which are one from soil sources via root absorption (Yaman et al., 2000; Finster et al., 2004; Wong & Li, 2004; Del Rio-Celestino et al., 2006), and the second from aerial deposition onto plant leaves (Aydinalp & Marinova, 2004). It can be said that the high lead content in urban soils and plant samples is mostly because of the traffic density. Traffic density is considered as one of the major source of heavy metal contamination, especially in terms of lead. Different lead pollution levels among plants are because of the different levels of deposition airborne lead and from soil sources. Lead can increase high elevations after emitted from exhausts so it is very difficult to find lead free plants. When airborne lead precipitates, it accumulates on soil and plants. Consequently, high pollution levels of soil in urban sites are more likely due to the deposition of airborne lead and exposure interval. This study shows that there is no significant pollution level in roots and leaves of Cichorium intybus L. at the collected sites. It is clear that with an increase in the lead concentration in soil due to percolation, the uptake of heavy metals by Cichorium intybus L. also increases. So it can be concluded that Cichorium intybus L. can be used as biomonitor of heavy metal pollution because it shows the criteria for a species as a biomonitor. Furthermore, because it is common in Europe, Asia and Australia it may be very useful biomonitor in these areas. As a result this study shows that an immediate action is required to provide sustainable traffic, to use ecological methods to have a sustainable development in the area. 25 | P a g e �ISSD 2014 th The 5 International Symposium on Sustainable Development_______ PROCEEDINGS REFERENCES Aksoy, A. 2008. Chicory (Cichorium intybus L.): Possible biomonitor of metal pollution. Pak. J. Bot., 40(2): 791-797. Aksoy, A. and D. Demirezen. 2006. 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Frederick Warne & Co. pp. 390–391. ISBN 0-7232-2419-6. Ross, M.S. 1994. Sources and form of potentially toxic metals in soil-plant systems. In: Toxic Metals in SoilPlant Systems (Ed.): M.S. Ross. pp.3-25. John Wiley, Chichester. Sakurai T., J. Kim, N. Suzuki, T. Matsuo, D. Li, Y. Yao. 2000. Polychlorinated dibenzo-p-dioxins and dibenzofurans in sediment, soil, fish, shellfish and crab samples from Tokyo Bay area, Japan, Chemosphere, 40:627–40. Sawidis, T., A. Marnasidis, G. Zachariadis and J. Stratis. 1995. A study of air pollution with heavymetals in Thessaloniki city (Greece) using trees as biological indicators. Archives Environ. Cont. Toxicol., 28: 118-124. Simon JE, Chadwick AF & Craker LE (1984). Herbs: An Indexed Bibliography 1971-1980. The Scientific Literature on Selected Herbs and Aromatic and Medicinal Plants of the Temperature Zone . Archon Books, Hamden, CT, USA. Tam, N.F.Y., W.K. Liu, M.H. Wang and Y.S. Wong. 1987. Heavy metal pollution in roadside, urban parks and gardens in Hong Kong. Sci. Total Environ., 59: 325-328. Turkan I (1986). Izmir ili merkezi ve çevre yollari kenarinda yetisen bitkilerde kursun, çinko ve kadmiyum kirlenmesinin arastirilmasi. Doga Dergisi 10: 116-120. Tyler, G. 1981. Heavy Metal in Soil Biology and Biochemistry. In: (Eds.): E.A. Paul & J.N. Ladd. Soil Biochem., 5: 371-414. Wittig, R. 1993.General aspects of biomonitoring heavy metals by plants. In: Plants as Biomonitors/Indicator for Heavy Metals in the Terrestial Environment. Markert B., VCH Publisher, Weinheim, 3-28. Wolterbeek B. 2002. Biomonitoring of trace element air pollution: principles, possibilities and perspectives. Environ. Poll., 120: 11–21. Wong CSC & Li XD (2004). Pb contamination and isotopic composition of urban soils in Hong Kong. Sci Total Environ 319: 185-195. Yakupoglu, Guray, Sarica and Kaya. Determination of Airborne Lead Contamination in Cichorium intybus L. in an Urban Environment. Turk J Bot 32 (2008) 319-324 27 | P a g e �ISSD 2014 th The 5 International Symposium on Sustainable Development_______ PROCEEDINGS Yaman M, Dilgin Y & Gucer S (2000). Speciation of lead in soils and relation with its concentration in fruits. Anal Chim Acta 410: 119125. http://www.innvista.com/HEALTH/foods/vegetables/chicory.htm http://plantanswers.tamu.edu/vegetables/endive.html http://dolcevitadiaries.co.uk/2009/05/19/wild-chicory-spaghetti/ GPS information of Localities, 2013. Googleearth, Accessed on January 2013. 28 | P a g e � Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Extent The size or duration of the resource. 2447 Title A name given to the resource BIOMONITORING OF LEAD POLLUTION ON THE URBAN FLORA Author Author DOGAN, Mustafa NEDIĆ, Zlatko TERZIĆ, Rifet Abstract A summary of the resource. In this study, the first aim was to find out the measures of lead (Pb) as the heavy metal pollution in Sarajevo, Bosnia and Herzegovina. The second aim was to test if chicory, Cichorium intybus L., can be used as a biomonitor of heavy metal pollution. Twenty-eight sites (urban, suburban and rural) in Sarajevo were investigated during the summer period in 2010. Concentrations of Pb were determined in leaves and roots of Cichorium intybus L. and also in soils collected from a wide range of sites with different degrees of metal pollution. As a result of measurements, the highest values of lead accumulations in plants have been observed in roots as expected. The highest values were detected as 30.10 mgkg-1 dry weight in roots and as 28.20 mgkg-1 dry weight in leaves in the PMF garden in Pofalici. On the other hand, the highest value of lead was detected as 450.05 mgkg-1 dry weight in soil in Museum Garden. Theoretically it is expected to observe highest accumulation in soils, roots and leaves, respectively. After getting results, it is observed the relationship of lead accumulation among soils, roots and leaves as expected. Cichorium intybus L. was found to be a useful biomonitor in the determination of lead pollution. Key words: Cichorium intybus L., lead pollution, biomonitoring, Sarajevo Publisher An entity responsible for making the resource available International Burch University Date A point or period of time associated with an event in the lifecycle of the resource 2014-05-15 Keywords Keywords. Article PeerReviewed Identifier An unambiguous reference to the resource within a given context ISSN 978-9958-834-36-3 Q Science (General),QH301 Biology,QH426 Genetics https://omeka.ibu.edu.ba/files/original/6a021d5b952e453ea45688ddb9d5aeca.pdf 5e68e537da16e051d84d3703963e05da PDF Text Text Biosecurity and Major Diseases in Shrimp Culture Gurel Turkmen Faculty of Fisheries, Ege University, Izmir, Turkey gurel.turkmen@ege.edu.tr Erol Toksen Faculty of Fisheries, Ege University, Izmir, Turkey erol.toksen@ege.edu.tr Abstract: The global shrimp aquaculture has passed its 30th year as a significant and rapidly growing and now represents a multi-billion dollar a year industry. More than half of the global shrimp supply now comes from farms. Recent statistics show that in 2008, 3,399,105 metric tons (MT) of the total world supply of 6,519,671 MT of shrimp (or 52%) were produced from aquaculture. However, shrimp farmers have suffered significant economic losses over the last decade, largely from viral diseases that have plagued the industry. In Asia, mortalities of cultured shrimp due to White Spot Syndrome Virus (WSSV) and Yellow Head Virus (YHV) have resulted in significant economic losses, and Taura syndrome virus (TSV) is now spreading throughout this region. Similarly, in the Western Hemisphere, both WSSV and TSV have caused catastrophic losses on shrimp farms. In Ecuador alone, WSSV was responsible for an estimated 53% decline in shrimp production from 1998 to 2000, resulting in a loss of export revenue in excess of $516 million. It is believed that these diseases are transferred between regions through the importation of hatchery broodstock, postlarvae and shrimp products. Once new pathogens are imported to an area, infection of wild stock appears to be inevitable, eliminating future possibilities of using uncontaminated wild stock to culture. Good biosecurity measures are vital to maintaining healthy animals, to reducing the risk of acquiring diseases in aquaculture facilities and to harvest high quality good yield. Thus, biosecurity measurements for a shrimp farming facility includes; disease prevention, disease monitoring, effectively managing disease outbreaks, cleaning and disinfection between production cycles and general security precautions. Key words: Shrimp, Culture, Biosecurity, Disease, Prevention, 1. Introduction The global shrimp farming industry has passed its 30th year as a significant and rapidly growing industry. More than half of the global penaeid shrimp supply now comes from farms. Recent statistics (FAO, 2010) show that in 2008, 3,399,105 metric tons (MT) of the total world supply of 6,519,671 MT of shrimp (or 52%) were produced from aquaculture. The huge scale of the shrimp farming industry represents fourteen of billions of dollars of physical assets and hundreds of thousands of jobs. Two species are dominant in the global shrimp farming industry. These are the black tiger shrimp Penaeus monodon and the Pacific white shrimp Litopenaeus vannamei. In Asia, the dominant species of choice was the Giant Tiger shrimp P. monodon native to tropical, coastal regions of the Indo-Pacific basin. In the West, the principal farmed species was P. vannamei, the Pacific White shrimp which is native to the tropical Pacific coast of Latin America. In the early 1990s, Asian shrimp farmers contributed more than 90% of total world production while farmers in the West contributed less than 10% of the total. Development of specific pathogen-free SPF stocks of P. vannamei in the U.S. in the early 1990s and their industry-wide use caused a doubling of U.S. industry production. Subsequent introduction of the domesticated non-native SPF P. vannamei to Asia in the late 90s, produced dramatic increases in shrimp production and rapid spread through Southeast Asia. Rapid and sustained increases in Asian shrimp production resulted from P. vannamei’s widespread adoption and these drove global shrimp production to double since 2000. By 2004, P. vannamei emerged as the leading shrimp species in worldwide production contributing more than 50% of total world farmed-shrimp production. In 2008, P. vannamei production accounted for more than 70% of total world production and was the dominant species farmed in China, Thailand, and Indonesia the world’s three leading production countries. 606 �The vast majority of shrimp culture in the world is conducted in outdoor earthen ponds that are typically located in coastal zones and exposed to a variety of pathogens. The worldwide experience of the shrimp farming industry is that pathogens, especially viruses, are a serious threat to the productivity and even survival of the industry. Although farmed shrimp now represent more than 50% of the global penaeid shrimp supply, farmers have suffered significant economic losses over the last decade, largely from viral diseases that have plagued the industry (Table 1. Lightner, 2005 ). In Asia, mortalities of cultured shrimp due to White spot syndrome virus (WSSV) and Yellow head virus (YHV) have resulted in significant economic losses (Flegel and Alday-Sanz 1998), and Taura syndrome virus (TSV) is now spreading throughout this region. Similarly, in the Western Hemisphere, both WSSV and TSV have caused catastrophic losses on shrimp farms (Lightner, 2003). In Ecuador alone, WSSV was responsible for an estimated 53% decline in shrimp production from 1998 to 2000, resulting in a loss of export revenue in excess of $516 million (Rosenberry, 2000). Virus WSSV - Asia WSSV - Americas TSV YHV IHHNV Year of emergence to 2001 1992 1999 1991-1992 1991 1981 Product loss (US dollars) 4-6 billion > 1 billion 1-2 billion 0.1-0.5 billion 0.5-1.0 billion Table 1. Estimated Economic Losses Since The Emergence of Certain Diseases in Penaeid Shrimp Aquaculture The pandemics due to the penaeid viruses WSSV and TSV, and to a lesser extent to IHHNV and Yellow Head Virus (YHV), have cost the penaeid shrimp industry billions of dollars in lost crops, jobs, and export revenue. In response to these viral pathogens, the global shrimp farming industry is changing the way shrimp aquaculture is practiced. The social and economic impacts of the pandemics caused by these pathogens in countries in which shrimp farming constitutes a significant industry have been profound. In the wake of the viral pandemics the shrimp culture industry has sought ways to restore the industry’s levels of production to the “previrus” years. The application of biosecurity to shrimp farming is central to those efforts (Lightner 2005). At the shrimp farm level, biosecurity refers to producing healthy shrimp in a well-controlled environment that excludes the introduction or propagation of unwanted organisms and includes the prevention or escape of organisms back into the natural environment. The primary goal of a biosecurity program in shrimp farming is to prevent the introduction of any infectious organism into a shrimp farming system. In this study a brief review was given of basic farm management strategies to improve the outlook for more biosecure production and control of disease in shrimp culture. A series of standard operating procedure recommendations was presented including farm location and design, pond preparation, stocking strategies, water exchange, feed management, health monitoring, and disease exclusion. 2. Biosecurity in Shrimp Farming Biosecurity, as it is being applied to shrimp aquaculture, may be defined as the practice of exclusion of specific pathogens from cultured aquatic stocks in broodstock facilities, hatcheries, and farms, or from entire regions or countries for the purpose of disease prevention (Lightner 2003). Lightner (2003), discussed ways of excluding pathogens from stock (i.e., post larvae and broodstock), especially through the use of quarantine and specific pathogen-free (SPF) certified stocks, and restricting imports of live and frozen shrimp. Excluding vectors and external sources of contamination and preventing internal cross contamination were suggested methods for excluding pathogens from hatcheries and farms. In the poultry industry, biosecurity has been defined as an essential group of tools for the prevention, control, and eradication of economically important infectious diseases. While biosecurity in this context may have many facets, central to its application in shrimp farming are the concepts of stock control and pathogen exclusion. This has been accomplished through the practice of stocking farms only with shrimp that are free of the diseases of concern into farms with controlled water sources. The latter issue of controlled water sources is being accomplished through better farm siting, farm design and water management through the use of such strategies as inland shrimp farming, “zero” water exchange, and the use of water treatment devices that remove potential vectors from the source water (Browdy et al. 2001). Horowitz and Horowitz (2003) described physical, chemical, and biological precautionary measures to be taken as well as a second line of defense against potential disease outbreaks. Physical measures are those that aim at preventing the intrusion of disease-carrying vectors to the farm site, and include physical barriers, water treatment, and quarantine. Chemical measures are those used to treat materials before they enter the facility. 607 �Chlorination and ozonization are often used to treat incoming water, and iodine and chlorine are used to treat other potential vectors such as tools, footwear, and clothing. Biological measures include the use of SPF shrimp, which are readily available commercially. A second line of defense for the shrimp industry is to use specific pathogen-resistant shrimp, which, in addition to being disease-free, are resistant to specific diseases. Since shrimp do not develop a specific immune response, common immunostimulants, such as β-1-3 glucan, lipopolysaccharides, and peptidoglycans are used to improve the ability of the shrimp to prevent infection. The pathogens WSSV and IHHNV are considered to have been introduced into the Americas from Asia with live shrimp or with frozen infected commodity shrimp (FAO 2003; Tang et al. 2003). Both WSSV and IHHNV have been demonstrated in wild penaeid shrimp in the Americas (Motte et al. 2003) and Asia (Fegan and Clifford 2001). The establishment of these and other pathogens in wild shrimp stocks in the Americas has changed the way shrimp are farmed. Gone are the days when broodstock and postlarvae could be collected from the wild without concern that they might be carrying disease. Also gone are the days when shrimp farms, in all but the most geographically isolated locations, could be designed and operated without a biosecurity program. In the decade following the emergence and spread of WSSV throughout Asia and into the Americas and the emergence and spread of TSV throughout the Americas and into Asia, the industry has begun to adopt a variety of biosecurity measures and programs as its best defense against these and other diseases. In some shrimp farming regions, the application of the principles of biosecurity has helped farms in those regions to reduce losses due to disease and to improve production (Fegan and Clifford 2001). If a disease presents itself at a particular pond, effective biosecurity measures should prevent the complete loss of the crop and the spread of disease to other ponds. Lightner (2003) recommended an approach to eliminating pathogens at the stock level and partial disinfection at the facility level. To eliminate pathogens in post-larvae and broodstock, affected tanks and ponds should be depopulated, disinfected, and restocked with SPF shrimp. It may, however, be necessary to depopulate the entire stock and to fallow the entire facility if partial disinfection (using lime, chlorine, or drying) is not successful. Horowitz and Horowitz (2003) suggested providing better environmental and biological conditions to the infected population to increase its ability to resist diseases. They discussed the following steps: a) effect physical measures (increase aeration, control temperature, improve the feeding regime, remove sludge and organic matter, and treat wastewater) to improve the environmental conditions, b) effect chemical measures, including control of pH and salinity, reduction of ammonia and nitrite, and application of antibiotics, and c) to use effective biological measures, consisting mainly of the use of probiotics containing a mix of bacterial species to establish beneficial microbial communities under culture conditions. 2.1. Control of Shrimp Stocks The single most important principle of biosecurity is stock control, which may be simply defined as the use of captive or domesticated stocks, cultured under controlled conditions, and which have been the subject of an active disease surveillance and control program (Lightner 2003). While numerous methods have been incorporated into the operational design and management of shrimp farms previously affected by TSV and WSSV to eradicate them and to insure that they are not reintroduced, none can be expected to provide much protection against crop losses in farms that use seed stock derived from wild stock sources. The use of only domesticated shrimp stocks that have a known history of being free of pathogens of concern can help to mitigate this risk. However, an SPF history comes only from a long-term captive breeding and disease surveillance program at a facility that has a fully functional and effective biosecurity plan (Fegan and Clifford 2001). The successful application of the SPF concept is dependent upon the absence of the pathogen(s) of concern in the stocks being reared (or that are present), on the availability of sensitive and accurate detection and diagnostic methods for the pathogen(s), and the presence of an effective barrier (i.e., facility design and geographic location, government mandated import restrictions, etc.) to prevent the introduction of the specific pathogen(s) intended to be excluded. The International Council for the Exploration of the Sea (ICES) Guidelines (Code of Practice to Reduce the Risks of Adverse Effects Arising from the Introduction on Nonindigenous Marine Species, 1973, as reviewed in Sindermann (1988, 1990) was followed for the development of these stocks (Table 2). Original ICES Guidelines 1. Conduct comprehensive disease study in native habitat 2. Transfer {founder stock} system in recipient area 3. Maintain and study closed system population 4. Develop broodstock in closed system Adapted to SPF Shrimp Development 1. Identify stock of interest (i.e., cultured or wild) 2. Evaluate stock's healtlddisease history. 3. Acquire and test samples for specific listed pathogens (SLPs) and pests. 4. Import and quarantine founder (F0) population; 608 �5. Grow isolated F1 individuals; destroyoriginal introductions 6. Introduce small lots to natural waters - continue disease study. monitor F0 stock. 5. Produce F1 generation from F0 stock. 6. Culture F1 stock through criticmonitor general health and test for SLPs. al stage(s); 7. If SLPs, pests, other significant pathologies are not detected, F-1 stock may be defined as SPF and released from quarantine. Table 2. Recommended Steps in The ICES Guidelines for Risk Reduction in Aquatic Species Introductions 2.2. SPF and SPR Shrimp Stocks Stock control requirements are being addressed in at least three ways. Where the industry has remained dependent upon wild (adult or postlarval = PL) stocks as its source of “seed,” routine polymerase chain reaction (PCR) testing of broodstock and PLs for important pathogens like WSSV, TSV, YHV, and IHHNV has been adopted. Other components of the industry have chosen to attempt to develop and use specific pathogen resistant stocks (SPR) when pathogen exclusion from other sources such as the water supply is not a practical option (Lightner and Redman 1998). Nonetheless, the development and use of “specific pathogen free” (SPF) stocks is emerging as perhaps the best management strategy for stock control in farms, regions or countries with biosecurity programs. Although marketers commonly use the term “disease-free” to describe the live shrimp products in commerce, they are in reality marketing shrimp that are free of specific disease causing agents. Because nothing that is living is completely free of some sort of disease, such “disease free shrimp” are more correctly referred to as being free of certain specific pathogens or SPF. The term SPF implies that the stock of interest is free of one or more specific pathogens (Fegan and Clifford 2001). To the USMSFP, SPF means the stock of interest has at least 2 yr of documented historical freedom of the disease agents listed on its working list of specific pathogens, that the stock has been cultured in biosecure facilities, and that the stock was either cultured under conditions where the listed disease agents would have produced recognizable disease if any were present and/or that the stock has been subjected to routine surveillance and testing for the listed pathogens. Those pathogens on the USMSFP SPF list have also met certain criteria including: 1) the pathogen(s) must be excludable; 2) adequate diagnostic and pathogen detection methods are available; and 3) the pathogen(s) poses significant threat of disease and production losses (Lotz et al. 1995; Lightner 2003), which are also among the criteria required for disease listing by the Office International des Epizooties, OIE (OIE 2003a, 2003b) Secondary Quarantine Facility Primary Quarantine of F0: test for pathogens/pests negative nenegati + = no nenegati Produce Produce negative adult F Generation nenegati 1 broodstock + = no (SPF/SPR) negative Breeding nenegati Center(s)& + = no hatcheries + = no nenegati nenegati negative nenegati FARMS Figure 2. Schematic of The Steps in Developing Specific Pathogen Free Breeding Lines. Specific pathogen free stocks developed by the USMSFP were developed in the spirit of the ICES Guidelines (Table 2; Fig. 1). To begin the process, each “SPF candidate population” of wild or cultured shrimpstocks of interest was identified. Samples of the stock were taken and tested using appropriate diagnostic and pathogen detection methods for the specific pathogens of concern. If none were found, a founder population (F,) of the “candidate SPF” stock was acquired and reared in primary quarantine. During primary quarantine, the F, stock was monitored for signs of disease, sampled, and tested periodically for specific pathogens. If any pathogens of concern were detected, the stock was destroyed. Those stocks that tested negative for pathogens of concern through primary quarantine (which ran from 30 d to as much as 1 yr for some stocks) were moved to a separate secondary quarantine facility for maturation, selection, mating, and production of a second (F,) 609 �generation. The F, stocks were maintained in quarantine for further testing for specific pathogens of concern. Those that tested negative were designated as SPF, and used to produce domesticated lines of SPF and “high health” shrimp (Wyban et al. 1992; Brock and Main 1994; Pruder et al. 1995; Lotz et al. 1995) 3. Major Diseases in Shrimp Culture Farmed shrimp are infected by a range of disease agents including bacteria, viruses, fungi and protozoa. This overview focuses mainly on viral and bacterial diseases that have had a significant impact on the shrimp farming industry. There are a number of viruses that infect shrimp, but not all of them cause fatal diseases. Infectious hypodermal and hematopoietic necrosis virus (IHHNV) has been observed in most commercially farmed shrimp species. It appears to be harmless in some species such as the Asian tiger shrimp, Penaeus monodon, but malicious in others causing mortality and growth retardation. There are a number of other viruses such as the monodon baculovirus (MBV), hepatopancreatic parvo-like virus (HPV), and baculovirus penaei (BP) that damage the cells of the hepatopancreas and make the shrimp susceptible to other disease agents. It is believed that infection by these viruses causes a reduction in growth rates. As noted earlier, the three viruses that cause acutely fatal diseases in shrimp farming are the white spot syndrome virus (WSSV), yellow head virus (YHV) and Taura syndrome virus (TSV). All three viruses can cause extensive mortality within a few days of the first clinical signs of the disease. As discussed below, the severity of a viral disease typically subsides in about two years after the first incidence of the given disease. This apparently indicates some type of an adaptive response to the disease agent. However, the viruses are never completely eliminated. They resurface periodically, particularly at times of stress, to cause large-scale mortalities. Furthermore, growth retardation often coincides with viral infections resulting in economic losses. The most important diseases of cultured penaeid shrimp, in terms of economic impact, in Asia, the Indo-Pacific, and the Americas have infectious agents as their cause (Tables 3, 4). Among the infectious diseases of cultured shrimp, certain viruscaused diseases stand out as the most significant. The impact of White Spot Disease (WSD) due to white spot syndrome virus (WSSV) has been particularly noteworthy. Rosenberry (2001) estimated that disease due to WSSV “robbed the industry” of approximately 200,000 MT of production in 2000 worth more than $1 billion. The viral disease pandemics caused by WSSV and Taura Syndrome Virus (TSV) that began in 1992 and caused billions in lost revenue have forever changed the shrimp farming industry (Table 1; Lightner 2005). The social and economic impacts of the pandemics caused by these pathogens in countries in which shrimp farming constitutes a significant industry have been profound. In the wake of the viral pandemics the shrimp culture industry has sought ways to restore the industry’s levels of production to the “pre-virus” years. The application of biosecurity to shrimp farming is central to those efforts. Some of the most important diseases (and their etiological agents) were once limited in distribution to either the Western or Eastern Hemisphere and many of the most significant shrimp pathogens were moved from the regions where they initially appeared to new regions even before the “new” pathogen had been recognized, named, proven to cause the disease, and before reliable diagnostic methods were developed. The diseases, due to the shrimp viruses IHHNV (infectious hypodermal and hematopoietic necrosis virus), TSV, and WSSV, were all transferred with live shrimp stocks from country to country and from one continent to another well before their etiology was understood (Lightner 2003). Viral diseases White Spot Syndrome Virus Yellow head Virus group Taura Syndrome Virus MBV group IHHNV HPV group RE0 group Bacterial and fungal diseases Vibriosis: -septic HP necrosis -hatchery vibriosis -luminescent vibrio Other bacteria: -Rickettsia Fungal: -Larval mycosis -Fusariosis Other diseases Epicommensals and parasites: -Leucothrix mucor -peritrich protozoans -gregarines -microsporidians Nutritional imbalances Toxic syndromes and environmental extremes Table 3. Major Diseases of IndoPacific and East Asian Penaeid Shrimp (Lightner, 2005) 610 �Viral diseases White Spot Syndrome Virus Taura Syndrome Virus IHHNV BP group HPV group IMNV RE0 III LOVV RPS Bacterial and fungal diseases Vibriosis: -Sindrome Gaviota” -hatchery vibriosis -luminescent vibrio -shell disease -septic HP necrosis Other bacteria: -NHP bacterium Fungal: -Larval Mycosis -Fusariosis Other diseases Epicommensals and parasites: -Leucothrix mucor -peritrich protozoans -gregarines -microsporidians Nutritional imbalances Toxic syndromes and environmental extremes Zoea II syndrome Table 4. Major Diseases of The American Penaeids (Lightner, 2005) 3.1. Yellow Head Virus Yellow head virus was first reported in Thailand in 1991. A related virus called Gill Associated Virus (GAV) was reported from Australia in 1996. Yellow head virus caused severe disease outbreaks in Thailand until 1994. The disease typically occurs in juveniles or sub-adults. A spurt in feed consumption followed by loss in appetite, lethargy and erratic swimming are the gross signs first observed. Pale yellow coloration of the gills and cephalothorax is often noted. Mortalities start within a few days and can reach as high as 100% in 3-5 days after the gross signs are observed. Sporadic disease outbreaks still occur, mainly in Asia, but the mortalities are less severe than past (Lightner, 2005). 3.2. White Spot Syndrome Virus White spot syndrome virus was first reported in Japan in 1993, although it might have originated in China. This virus has caused the most damage to the shrimp farming industry. It spread to almost all shrimp farming countries of Asia in a span of three years. It was reported in the United States in 1995, and spread to Central and South American countries in a span of four years. Almost all shrimp species have been affected. Further, most crustaceans can be infected with the virus and become carriers. The characteristic feature of WSSV infection is the presence of white spots or patches under the carapace, although this may not be present in all diseased shrimp. Soon after showing general signs of ill-health such as reduced feed intake and erratic swimming, mortalities occur. Mortality up to 100% may occur within seven days after the first sign of problems. The infection may occur at any stage in the life cycle of the shrimp. Stressful conditions such as sudden changes in environmental conditions, particularly lowered temperatures, trigger disease. Frequent WSSV disease outbreaks still occur worldwide, but there are more and more cases of shrimp populations escaping severe mortality in spite of WSSV infections (Lightner, 2005; Wyaban, 2009). 3.3. Taura Syndrome Virus Taura syndrome was reported first in 1992 in Ecuador. Presence of TSV was reported in 1995. TSV spread throughout the Pacific coast of Central and South America and mainly affected the Pacifc White Shrimp, P. vannamei. Distinguishable gross signs of TSV are pale reddish coloration of the body, red tail fans, necrosis of the cuticular epithelium, and soft shells. Mortality during molting is common. Sometimes, the shrimp are affected only transitionally: gross signs of the disease may occur, but the shrimp may behave and feed normally. While TSV still occurs, the catastrophic losses suffered in the early years of TSV infection are less common now. 3.4. Vibriosis Infection by Vibrio spp. is the most common bacterial disease problem in shrimp culture. Vibrio spp. are ubiquitous and naturally present in most aquatic ecosystems. Infections occur when shrimp are stressed or unhealthy. Infections may also occur as a result of high concentrations of Vibrio spp. in the culture system. Some species and strains, particularly V. harveyi, are more infectious than others. Shell lesions, black coloration of gills and discoloration of shells occur as a result of vibriosis. Severe mortalities may follow acute infections. 611 �Chronic infections may result in erratic swimming behavior, abnormal coloration, external fouling and less severe, but sustained mortalities (Lightner 2003, 2005). 4. Biosecurity Protocol for Shrimp Farming Biosecurity protocol for shrimp farming included three main management strategies focusing on: (a) pond bottom preparation and water management prior to stocking, (b) seed selection and stocking, and (c) poststocking management (Clifford and Cook, 2002; Wyaban 2009). 4.1. Pond Bottom Preparation and Water Management Prior to Stocking - Removal of bottom sludge, Particularly in ponds stocking higher densities (up to 8 PL/m2). - Plowing on wet soil if the sludge has not been removed completely. - Use of lime in pond preparation. - Disinfection of pond water - Fertilization reduces the risk of disease outbreak in lower stocking density farms. - Water filtration using twin bag filters of 250 µm mesh size. - Water conditioning for 10–15 days before stocking. 4.2. Seed Selection and Stocking - Uniform size and color post-larvae (PLs), actively swimming against the water current. Stocking of poor quality of seed (less active, more mortality during transportation and size of less than 16 mm in case of nursery reared juveniles increases the risk of shrimp disease outbreak. - Stocking Pathogen Free (SPF) Larvae (SPF shrimp stocks are avaible in some countries) - Longer transport time (>6 hours) of the seed from hatchery or nursery to the pond also increases the likelihood of a subsequent disease outbreak. - Weak PL elimination before stocking using formalin (100 ppm) stress for 15–20 minutes in continuously aerated water. - On-farm nursery rearing of PLs for 15–20 days. - Stocking into green water and avoiding transparent water during stocking. 4.3. Post Stocking Management - Perform a visual inspection of the pond on a daily basis. - Sampling for growth and survival - Monitor shrimp health and the appearance of disease using animals collected in the weekly growth and population samples - Gut content and their color. In general, 80% or more of the shrimp randomly sampled from a healthy, well nourished, recently fed pond should display the intestinal tract (mid-gut) running the length of the tail to be full of food. In addition to quantifying gut fullness and using it to detect under-feeding or predict the onset of disease, the color of the shrimp’s gut contents can also be very informative (Table 5). Gut Content Color Black, dark brown Light or golden brown Red, pinkish Green Pale, whitish Probable Food Item Benthic detritus, sediment Manufactured feed Cannibalized body parts from shrimp Benthic algae None (disease condition) Probable Cause(S) Under-feeding; inadequate feeding Normal dead Disease event in pond Under-feeding Gregarines, or some other disease Table 5. The Color of The Shrimp’s Gut Contents and Predict The Onset of Disease - Use of water reservoirs, and 10–15 days aging before use in grow out ponds. 612 �- Water filtration-ponds using water filter nets of fine mesh have better production. - Aeration-ponds using aeration tend to have higher shrimp production. - High salinity and pH (>8.5) have an affect on risk of disease outbreaks - Green water (pond color) ponds have better production and lower risk of disease outbreak. - Clear water with bentic and filamentous algae lead to lower production. - Regular use of agricultural lime, especially after water exchange and rain. - No use of any harmful/banned chemicals. - Use of feed check trays to ensure feeding based on shrimp demand. - Feeding across the pond using boat/floating device to avoid local waste accumulation. - Regular removal of benthic algae. - Water exchanges only during critical periods. - Weekly checking of pond bottom mud for blackish organic waste accumulation and unpleasant odor. - Regular shrimp health checks, and weekly health and growth monitoring using a cast net. - Removal and safe disposal of sick or dead shrimp. - Emergency harvesting after proper decision-making. - No draining or abandoning of disease-affected stock 4.4. A Biosecure Farm Model A drawing showing a 100-ha farm comprised of fifty 2.0-ha ponds with a centralized pumping and ozone contact facility is presented in Fig. 2. The gross farm area of 182 ha includes 18 ha of pond surface area committed to a series of sedimentation, aeration, and retention ponds (Schuur, 2003). The mechanical area includes a forebay or pumping basin that is accessed by gates for selecting water supply from either the treatment pond in a recirculation mode, or the raw water source in an exchange replenishment mode. From the forebay the water is pumped through an ozone injection device and then through a contact channel with sufficient volume to allow a minimum of 10 min retention time in a maximum flow situation. The effluent from the contact chamber is discharged into the primary supply channel that encircles the entire perimeter of the farm. The pump lift from the forebay is about 3 m in order to provide a sufficient hydraulic gradient for gravity distribution by the supply channel network to all of the ponds. The supply channel has cross-sectional area sufficient to carry peak flows to the furthermost ponds with only a minor loss of head. The nearly square configuration is optimal for reducing the farm perimeter to a minimum for biosecurity purposes. There is an all-weather dike-top roadway outside the supply channel encircling the farm perimeter of roughly 5.4 km. For security purposes the farm perimeter can be circuited in about 10 min at a modest vehicle speed. The external roadway traffic naturally inhibits plant growth and cover for terrestrial crabs that might seek access. A further barrier to intrusion inside the roadway is a short fence constructed with metal or plastic sheet material embedded in the ground and suspended by stakes. This barrier is a common feature of many intensive farms in combination with lime and pesticide application. The roadway also provides a ‘killing zone’ before the barrier where any potential carriers can be detected and eliminated. About 18% of the production pond surface is allocated to serial treatment ponds that provide sedimentation, aeration, and retention in order to improve water quality within the farm. The two sedimentation areas can be used in series or parallel flow, or in some cases one at time while the other is being dried and reconditioned. Additional retention time improves the water quality by providing additional area for autotrophic and/or heterotrophic processes to absorb and digest ammonia and organic matter. Mechanical aeration applied in the series provides more efficient oxygen transfer efficiency to the farm as a whole. This is due to the additional driving force provided by the difference between oxygen-depleted water from sedimentation ponds and the effluent concentration at the discharge of the aeration lagoon. References Brock, J. A., Main, K. (1994). A guide to the common problems and diseases of cultured Penaeus vannamei. The Oceanic Institute, Honolulu, Hawaii, USA. Browdy, C. L., D. Bratvold, A. D. Stokes, Mclntosh, R. P. (2001). Perspectives on the application of closed shrimp culture systems. p. 2-34 in C. L. Browdy and D. E. Jory, editors. The new wave, Proceedings of the Special Session on Sustainable Shrimp Culture. Aquaculture 2001. The World Aquaculture Society, Baton Rouge, Louisiana, USA. Clifford, H.C., Cook, H.L. (2002). Disease Management in Shrimp Culture Ponds. Aquaculture Magazine: 28(4): 18-26 613 �FAO (2003). Health management and biosecurity maintance in white shrimp (Penaeus vannamei) hatcheries in Latin America. FAO Fisheries Technical Paper 450. FAO, Rome. 62p. 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Poulos, J. Wang, R. M. Redman, H. -H. Shih, Lightner, D. V. (2003). Geographic variations among infectious hypodermal and hematopoietic necrosis virus (IHHNV) isolates and characteristics of their infection. Diseases of Aquatic Organisms, 53:91-99. 614 �Wyaban, J. (2009). World Shrimp Farming Revolution: Industry Impact of Domestication, Breeding and Widespread Use of Specific Pathogen Free Penaeus vannamei. Craig L. Browdy and Darryl E. Jory, editors. The Rising Tide, Proceedings of the Special Session on Sustainable Shrimp Farming, World Aquaculture 2009. The World Aquaculture Society, Baton Rouge Louisiana USA. 12-21p. Wyban J. A., J. Swingle, J. N. Sweeney, Pruder, G. D. (1992). Development and commercial performance of high health shrimp from SPF broodstock Penaeus vannamei. p. 254-260 in J. Wyban, editor. Proceedings of the Special Session on Shrimp Farming, Orlando, Florida, 22-25 May 1992. World Aquaculture Society, Baton Rouge, Louisiana, USA. 615 � Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Extent The size or duration of the resource. 608 Title A name given to the resource Biosecurity and Major Diseases in Shrimp Culture Author Author Turkmen, Gurel Toksen, Erol Abstract A summary of the resource. The global shrimp aquaculture has passed its 30th year as a significant and rapidly growing and now represents a multi-billion dollar a year industry. More than half of the global shrimp supply now comes from farms. Recent statistics show that in 2008, 3,399,105 metric tons (MT) of the total world supply of 6,519,671 MT of shrimp (or 52%) were produced from aquaculture. However, shrimp farmers have suffered significant economic losses over the last decade, largely from viral diseases that have plagued the industry. In Asia, mortalities of cultured shrimp due to White Spot Syndrome Virus (WSSV) and Yellow Head Virus (YHV) have resulted in significant economic losses, and Taura syndrome virus (TSV) is now spreading throughout this region. Similarly, in the Western Hemisphere, both WSSV and TSV have caused catastrophic losses on shrimp farms. In Ecuador alone, WSSV was responsible for an estimated 53% decline in shrimp production from 1998 to 2000, resulting in a loss of export revenue in excess of $516 million. It is believed that these diseases are transferred between regions through the importation of hatchery broodstock, postlarvae and shrimp products. Once new pathogens are imported to an area, infection of wild stock appears to be inevitable, eliminating future possibilities of using uncontaminated wild stock to culture. Good biosecurity measures are vital to maintaining healthy animals, to reducing the risk of acquiring diseases in aquaculture facilities and to harvest high quality good yield. Thus, biosecurity measurements for a shrimp farming facility includes; disease prevention, disease monitoring, effectively managing disease outbreaks, cleaning and disinfection between production cycles and general security precautions. Date A point or period of time associated with an event in the lifecycle of the resource 2010-06 Keywords Keywords. Conference or Workshop Item PeerReviewed Q Science (General) https://omeka.ibu.edu.ba/files/original/c643b98c1f965c25953c6a7bef893643.pdf ba9de6edd3133b17a98b469ef34fcb46 PDF Text Text Biotechnology and Aquaculture in Sustainable Development Altunok Muhammet, Peker Zerife, Serezli Ramazan, Tekinay Ahmet Adem, Kizak Volkan Izmir Katip Celebi University, Faculty of Fisheries, Izmir, Turkey, Tunceli University, Faculty of Fisheries, Tunceli, Turkey, E-mails: muhammet.altunok@hotmail.de,zerifesude@hotmail.com,ramazan.serezli@hotmail.de, aatekinay@yahoo.com, volkan.kizak@tunceli.edu.tr Abstract Aquaculture is the fastest growing food sector in the world with its increasing role for economy and safe food strategy of countries. Due to the continuing depletion of the fish stocks, farming of aquatic organisms such as fish, crustaceans, molluscs and aquatic plants, is now a substantial global industry supplying a significant proportion of the aquatic products consumed. Shortage in food supply and high prices are the possible important risks in the future, and aquatic products are the valuable sources of protein and essential nutrient components for global food security and eliminating malnutrition. Aquaculture also plays an important role in rural economies through the creation of new employments. In these cases, aquaculture outputs will need to be enhanced several fold in order to meet the rising demands for fish and other aquatic products in coming years. Biotechnology options seem to be good potential for increasing aquacultural productivity, food security and environmental quality worldwide. Biotechnology is offering valuable options such as protein expression, microsatellite, gene mapping and genomic, DNA vaccines, DNA chips, proteomics, transgenic technology and embryonic stem cell technology. This technology provides genetic manipulations, molecular cloning, embryo manipulation, genetically-engineered diagnostics, immunoprophylactic agents. All of these applications could help improve the selective breeding, hybridization, productivity, health, growth, nutrition, cryopreservation and conservation of genetic resources in aquacultural stocks for the benefit of mankind. However, there is need for the regulation of biotechnology activities in terms of the potential adverse impacts on the environment and human health. There is also increasing concern about the impact of biotechnology on sustainable development in various fields. The main environmental safety issue of these applications is the effects of genetically modified organisms (GMOs) on biodiversity and gene transfer in the environment. Therefore, this review discussed the integration of biotechnology and biosafety in aquaculture, and policies for the environmentally sound use and management of aquacultural biotechnology in sustainable development. Keywords: Biotechnology, Aquaculture, Sustainable Development, Food security, Public health 182 �1.INTRODUCTION Aquaculture is the farming of aquatic organisms such as fish, crustaceans, molluscs and aquatic plants under controlled conditions. Aquaculture is the fastest growing food sector in the world with its increasing role in the economic development and safe food strategy of countries. Recently aquaculture sector is faced with several challenges such as low productivity, low diversification of species, high competition in the market and environmental impacts that have resulted from the intensification and global development of aquaculture industry. Seasonal fluctuations in environmental conditions and in the supply of resources with good quality and stable costs such as feeds are also prevalent. Biotechnology is one tool that holds much promise towards addressing these aquacultural problems. The relatively new tools of biotechnology offer significant opportunities to improve aquacultural productivity and environmental quality worldwide. Today biotechnology has developed creative new methods to detect the gene liable for specific characteristics, such as disease resistance, nutrient composition, and insert them into another fish or aquatic organism (Fletcher et al., 2011). Biotechnology offers tremendous potential for improving production and it provides opportunities to reduce the need for additives in feeds and the use of chemicals (e.g. hormones). Advanced biotechnology in feed are rapidly evolving and promise to improve the composition, digestibility and bio-availability of feed towards high growth rate (Brinker and Reiter, 2011). All of these contribute to increase the intensity and produce more products at less economic and environmental cost, thereby helping to build global food security and more sustainable and environmentally friendly farming. Aquacultural biotechnology could generally be separated into techniques; biochemical and molecular markers, protein expression technology, microsatellite, RFLP and QTL analysis and applications (gene mapping, gene cloning, transgenesis, population genetics, chromosome (ploidy) manipulation, gynogenesis, androgenesis, sex reversal, proteomics, DNA chips technology and embryonic stem cell technology. Protein expression technology allows producing many bioactive molecules such as hormones, gonadotropins and enzymes. DNA fingerprinting and mapping technologies are principally used in stock idenfication, breeding selection and identification of genetic markers for significant traits such as growth enhancement and disease resistance in the genome (Hew and Fletcher, 2001). This technology is more effective and faster than traditional breeding techniques to develop new strains. 2.Sustainable development of aquaculture According to the current trends in food sectors, wild fisheries, natural stocks and demand for aquaculture products, it is awaited that aquaculture will become a major driving force to increase food production worldwide. Products from aquaculture will need to be increased several fold in order to meet the rising demands for fish and other aquatic foods in coming years (Figure 1). It was recently estimated that aquaculture provides about 50% of all the fish consumed by human today (FAO, 2010). On the other hand, the aquaculture industry will have to double its food produce with less land and water in the next decades, mainly because of growing pressures from urbanisation, industrialisation and climate change. Moreover, water scarcity that results in competition for water amongst local people, farmers and industry, is raising the potential for conflict. 183 �Figure 1. Projected supply of food fish originating from aquaculture and capture fisheries; based on assumed constant capture fisheries production, constant production of fish meal, constant demand for food fish and projected population increases. The line at 2015 represents the point where the food fish supply from aquaculture is projected to equal that from capture fisheries.(FAO, 2007): The intensification of aquaculture has led to concerns attached to environmental impacts, food safety, animal health and welfare, and socio-economic issues (Subasinghe et al., 2009). All of these factors influence the sustainability in development of current aquaculture system. As a principle for the sustainable development of aquaculture, it can be said that as the improvement of economic productivity for aquaculture is necessary and this must be environmentally acceptable. Therefore, the ecosystem where the aquaculture operation takes place has to be identified to control unwanted interactions. The identifying process includes a wide range of topics relevant to ecological equilibrium and biodiversity conservation. Hence, environmental acceptability is the most difficult component of the sustainable development. In addition to this, as an indicator, economic viability and improving the economic performance of the aquaculture practices are also critical to achieve the improvements in aquaculture efficiency and to meet the world's increasing demand for aquatic food. General trends in development of the aquaculture sector are the following (Subasinghe, 2007): (a) continuing intensification of aquaculture production; (b) continuing diversification of species use; (c) continuing diversification of production systems and practices; (d) increasing influence of markets, trade and consumers; (e) enhancing regulation and improving governance of the sector and (f ) increasing attention on better management of the sector. Aquaculture production increases but there is a question remains whether the industry grows in a sustainable manner and fast enough to meet the future projected demand while preserving the natural resources. To cope with this global uncertainity, biotechnology plays a key role in the sustainable development of aquaculture includes economic and social development as well as environmental protection throughout the world. Application of biotechnology to production 184 �of aquatic species has great potential to improve aquaculture and to meet demand for aquatic foods. Along with increasing production of aquatic food products, biological techniques should be applied to increase productivity and improve product quality. In parallel, there are several potential key contributions of biotechnology both to increase resistance against diseases and to increase growth rates of aquatic species. Biotechnology contributes to sustainable aquaculture by reducing the dependence on chemicals, particularly antibiotics, through the deployment of genes conferring resistance to diseases. Biotechnology also provides powerful tools for the enhancement and protection of wild and cultured aquatic species, particularly the improvement of fish stocks in commercial aquaculture production. Also, biotechnology allows the production of species in more quantities on the same area (intensification) at a lower cost, the support biodiversity and vital ecosystems, and the reduction of environmentally damaging aquacultural practices. 3.Aquacultural biotechnology Biotechnology has potential to affect aquaculture and can provide at least a partial solution to the problem of feeding the world‘s growing population because without dramatic increases in production this cannot be achieved. Exploiting more resources such as more water, fish for meal and oil, and heavy use of chemicals for aquacultural use is environmentally unsustainable. Modern biotechnology has also opened up opportunities to increase production and enhance the quality of fresh and processed farmed species. In addition, farmed species are now being developed to resist disease, and this will reduce losses and allows increased production on same area, and therefore bring possible benefits to rural areas. Finally biotechnology can contribute significantly to aquaculture industry, for example by helping to make more diversification in farmed species that will more attractive to consumers. Modern biotechnology will be a useful for the genetic improvement of aquacultured species and the protection and management of wild aquatic populations. 4.Genetically modified species (Transgenics) Recently, aquaculture sector is growing and developing in biotechonogy advance for genetic improvements in aquatic species. As a main application of modern biotechnology transgenics are new varieties of species have been bred by cross of two strains in order to transfer desirable traits from each into the new variety to improve the genetic traits of the species used in aquaculture. Transgenics involves the selective transfer of one or more genes for desired traits from one variety to another. These traits may include improvement of growth rates, larger size, more efficient feed convertion into muscle and control of sexuel maturation (Elzaeems, 2004). growth hormone genes from human or animal sources was successfully introduced into several fish species such as salmon, trout and tilapia, resulted several times faster growth than their natural counterparts. This is a faster and more accurate method of breeding new varieties. If desired traits cannot be achieved by traditional breeding, the transfer of genes between species also is possible. For exemple, better tolerance to environmental stresses and increasing of resistance to extreme environments are important applications to establish unique characteristics and produce a valuable biological product such as antifreeze protein gene (AFP) transfer in fish for adaptation to a freezing environment (Hew at al., 1992). In this regard, one more constraints should be the potential impacts of climate change on aquaculture. Biotechnology responsible for the practical response to climate change and can help to strengthen the adaptive capacity and resilience of the sector. Tolerant of low oxygen levels in the water is a desirable genetic trait that can also be 185 �developed in the aquatic organisms by using different transgenic techniques. Intensification and sustainable development of aquaculture will rely on disease prevention, and therefore, biotechnology is essential way for greater resistance to pathogens and improvement of farmed species health through selection for disease resistance (El-Zaeem and Aseem, 2004). Also, by using this technique disease transfer between cultured and wild populations can be reduced. New products and market opportunities can be developed related to aquatic species welfare. There are two main techniques to transfer genetic material in fish. These are micro-injection (injection of genetic material into newly fertilized fish eggs) and electroporation (transferring of DNA into embryos or directly into tissues through the use of an electrical current). RISK: However recent concerns about genetically modified species and food products derived from them may curtail their widespread use. GMOs have not gained worldwide acceptance. At this point, there is not enough independent scientific research to introduce their potential risks to human health. Horizontal gene transfer from genetically modified plants to microorganisms was shown in a previous study that genes from a transgenic crop move quickly into weedy population (Snow at all., 1999). Questions concerning the transfer of allergenic proteins and potential ecological impact of virus-resistant transgenic plants have been also raised (Tepfer, 2002). Transgenic fish is offered new species for aquaculture development but any escapes into the environment can threat wild populations and biodiversity8. 5.Hybridization Hybridization is a simple genetic technology that is the most practical way is the crosses in captivity of males of one species and females of the other. Inter-specific hybridisation have been practiced for aquaculture to increase growth rate, transfer or combine desirable traits of two species and increase resistance to culture conditions. Hybridization also produces monosex populations for the advantage of sexual dimorphism when the sex-determining mechanisms in the parental lines are different such as hybridisation of tilapias. It is also preferred for stocking programmes to reduce unwanted reproduction through production of sterile fish or mono-sex populations and increase environmental tolerances. It is widely practiced with many fish species throughout the world such as hybrid striped bass in the USA, hybrid clarid catfish in Thailand and salmonids in general. This helps diversification and to ensure a steady and consistent supply of fish to the market. The development of artificial breeding techniques and the improvements in reproductive technologies allows more domestication of aquatic species and mating many of them through artificial fertilization after hand striping eggs and milt from fish. In marine fish culture, sterile hybrid fish should be usefull because of the environmental concern (unwanted reproduction). Despite its widespread use, hybridization has still to cope with some problems depend on the genetic structure of the parents, particularly in the context of unexpected and undesirable results in hybrid progeny, such as failure to produce sterile fish, loss of color pattern, and reduced viability. RISK: Hybridization does represent a genetic modification wherein genes are moved between different species. Thus, escaped hybrids may be aquaculture industry's biggest environmental challenges regarding to the genetic resources and biodiversity. 6.Hormonal applications Biotechnological tools can be applied to induce breeding of fish and early development of aquatic species. Gonadotropin releasing hormone (GnRH) is the most used now in the induced breeding of fish and marked commercially throughout the world (Alok et al., 2000). 186 �Hormonal stimulation allows year-round production of gametes and fry of economically valuable species. Domestication of species for aquaculture is necessary and the number of domesticated aquatic species is still rising rapidly. Hormone therapy is applied to improve and control of reproductive cycles during the domestication. Similarly, this tool may provide techniques for improving the reproductive success and survival of endangered species, thereby helping to preserve the biodiversity in wild. Higher growth of species in aquaculture sector is one of the main goals for farmers, and therefore various types of growth hormone is applyed in fish and other aquatic animals. Hormone treatment also includes inducing sterility and triploidy. RISK: Hormones are issues of great public concern because they pose a serious threat to human and environment. The significance of these substances for the environment and human health is not yet fully understood but they accumulate in environment and play important role on sexsual dimorphism, fertility and toxicity in ecosystem. 7.Chromosome set manipulation Chromosome manipulations have been applied extensively in the improvement of fish breeding for gonadal sterilization, sex control and clonation. It is important practical way in cultured fish species to induce polyploidy and uniparental chromosome inheritance. There are two types of uniparental inheritance: gynogenesis that is the process of development with maternal inheritance and androgenesis that is paternal. Poliploidy used to induce triploids to produce sterile progenies. Induction of tetraploidy provides sterile triploids through interploidy crosses between tetraploids and diploids. The technique also can be used to generate homozygous lines in fish such as tilapias, cyprinids and salmonids. 8.Cryopreservation Cryopreservation is a process where biological material is long-term preserved by cooling to low temperatures usually at −196 °C in liquid nitrogen. As any physiological activities and biochemical reactions is tranquilized and effectively stopped at these low temperatures, therefore making it possible to keep them viable for long period. Cryoprotectant solutions are used in the process to prevent preserved cells from damage due to freezing during the cooling and thawing process. The development of cryopreservation technology provides short and long term storage of gametes, and thus the technology has been adapted to cryopreservation of fish spermatozoa. Application of the method to aquaculture increases the flexibility in breeding of species; specificly if the sexes mature at different times (in hybridization) or spawning season is very short. Cryopreservation overcomes problems of low amount of semen from males in photoperiod treatment. The resulting benefits could include year-round production of gametes and creation of new markets (cryopreservation of genetically improved or phenotypic sperm). Gene banking of cultivated and wild aquatic organisms is also essential and the technique may help to conserve genetic resources and biodiversity. 9.Aquatic species health and vaccines Disease has become a primary constraint to sustainable aquaculture production and improvements in aquatic animal health are coming from modern biotechnology. Biotechnological tools such as gene probes and polymerase chain reaction (PCR) has showed great potential in this area. Genetically engineered (DNA) vaccines are also being developed to protect fish against pathogens and are expected to replace other methods of vaccine 187 �production. In general, DNA vaccines contain only genes of the pathogen, which produce the antigen whereas conventional vaccines are made from live, weakened or killed pathogen. The cost of this technique is low compared to producing weakened live organisms and these vaccines more stable at normal temperatures. Previous studies showed that the non specific defense system can be stimulated using microbials such as lipopoliysacharides, peptidoglycans or glucans (Soltanian at al., 2009). This technology has been adopted for aquaculture to improve the health and well being of cultivated aquatic organisms. The development of new vaccines help the organisms recognize and fight diseases causing losses to millions of dollars annually throughout the world. It also prevents the using chemicals in aqauaculture, means preventing chemical pollution in environment and potential hazardaous effects to human health. RISK: However, genetically modified vaccines carry significant unpredictability and a number of inherent harmful potentials and hazards such as potential risks about the vaccine DNA to invade the host‘s genome and possibly trigger genes relating to tumour development. Effects of these vaccines on the non-targeted species, possible genetic recombinations with naturally occurring relatives and hybrid virus progenies are other unpredictable options. There is, therefore, a great deal of caution surrounding the development of DNA vaccines at this time. Feed production Nutrition is essential in maintaing a healthy stock in a sustainable and profitable aquaculture and still in the developing stage. As feed costs rise and markets become more competitive, biotechnological aplications are currently being used in the feed sources and the improvement of the feed composition. In the farming of aquatic species fish meal is the most common protein source in diets. However, wild fish stocks are declining and the available fish resources will not be enough to meet the increasing demand for fish meal and fish oil. Therefore, there are environmental concerns regarding fish feed such as conservation of wild stocks and waste dischargers into the water due to excess phosphorus in diets causing eutrophication. These are main limiting factors regarding to feed in sustainable development of aquaculture, thus biotechnology are used to produce alternative plant based protein sources because plants contain anti-nutritional compounds and requires processing to improve its quality. In this regard, biotechnology allows the producing feed enzymes that help to improve the utilization of plant-protein based feed by aquatic species. As another environmental concern regarding the problem of phosphorus pollution, modern biotechnology is working on the development of low environmental-loading feed. 10.CONCLUSION Aquacultural biotechnology is now evolving very rapidly and making a significant contribution to the development of sector. In general, the technology promises immense gains in food security, economic issues and environmental protection. Efforts are directed to: the improvement of fish feed quality; genetic engineering in order to improve the protein value of fishes; the reproduction of species; disease diagnoses; hybridization technology 188 �genetic engineering for the production of vaccines. the treatment of pollutants generated by aquaculture. All of these factors influence the sustainability of an aquaculture system and may play fundamental role in future aquacultural development policies. Improved productivity and the resulting increase in production would benefit the rural poor by providing more food, poverty reduction and through improved employment opportunities. Advances in biotechnology applied to aquaculture can be useful in understanding waste treatment and reducing pollution risks. To eliminate uncertainties and vulnerabilities in the risks, governmental support is the essential element in enhancing aquaculture development without any environmental impact. Thus, sustainable biotechnological applications in aquaculture have to be identified and developed according to the risk assessments of the product and method. There are some principles that aquacultural biotechnology must adhere to in order to be sustainable, namely; environmentally acceptable in terms of methods, improved species and discharges. safety for human health large scale and heavy restrictions for non-native and geneticly modified species (farming in land-based tanks) supporting the long-term economic and social well-being of local communities ensuring a strong healthy and welfare for farmed species economically feasable and sustainable more investment for biotechnology industry. achieving a sustainable feed resources promoting good menagment involving human resource development regulations of the modifications Biotechnology is almost becoming an industry but still there is no any knowledge what the impacts will be. Moreover, biotechnology has raised important ethical and morality issues which need to be carefully addressed before its application to aquaculture. Therefore, to ensure maximum social benefit at minimal risk is high on the policy agenda of the countries In addition development of biotechnology will need to be shared among diferent disciplines and stakeholders. In this regard, educating of decision-makers in food safety and biotechnology regulation will be also very important. In conclusion biotechnology is important key for aquaculture, but it might still be too early to judge the future impact of biotechnology on its sustainable development. REFERENCES Alok D., Talwar G.P., Garg L.C. 2000. In vivo activity of salmon gonadotropin releasing hormone (GnRH), its agonists with structural modifications at positions 6 and 9, mammalian GnRH agonists and native cGnRH-II on the spawning of an Indian catfish. Aquaculture International 7, 383-392. Brinker, A., Reiter, R. 2011. Fish meal replacement by plant protein substitution and guar gum addition in trout feed, Part I: effects on feed utilization and fish quality. Aquaculture 310:350-360. 189 �El-zaeems, S.Y. 2004. Alteration of the productive performance characteristics of Orechromis niloticus and Tilapia Zillii under the effect of foreign DNA injection. Egypt J. Aquat. Boil. Fish. 8(1): 261-278. El-Zaeem, S.Y., Aseem, S.S. 2004. Application of biotechnology in fish breeding: 1 – production of highly immune genetically modified Nile, tilapia Orechromis niloticus with accelerated growth by direct injection of Shark FAO. 2007. The role of aquaculture in sustainable development. Thirty-fourth Session. 17-24 November 2007, C 2007/INF/16 Rome. FAO. 10 pp. FAO. 2010. The State of World Fisheries and Aquaculture. Rome. 197 pp. Fletcher, G. L., Hobbs, R. S., Evans, R. P., Shears, M. A., Hahn, A. L., Hew, C. L. 2011. Lysozyme transgenic Atlantic salmon (Salmo salar L.). Aquaculture Research, 42: 427–440. Hew CL, Davies PL, Fletcher G. 1992. Antifreeze protein gene transfer in Atlantic salmon. Mol Mar Biol Biotechnol. 1(4-5):309-17. Hew, C.L., Fletcher, G.L. 2001. The role of aquatic biotechnology in aquaculture. Aquaculture 197, 191-204. Snow, A.A, Andersen, B, Jørgensen, R. 1999. Costs of transgenic herbicide resistance introgressed from Brassica napus into weedy B. rapa. Molecular Ecology 8:605–615. Soltanian, S., Stuyven, E., Cox, E., Sorgeloos, P., Bossier, P. 2009. Beta-glucans as immunostimulant in vertebrates and invertebrates. Critical Reviews in Microbiology , 35: 109–138. Subasinghe, R.P. 2007. Aquaculture: Status and Prospects. In ―Role of Aquaculture in Sustainable Development. FAO Department of Fisheries and Aquaculture, Rome, Italy. Subasinghe, R., Soto, D., Jia, J. 2009. Global aquaculture and its role in sustainable development. Reviews in Aquaculture, 1: 2–9. Tepfer, M. 2002. Risk assessment of virus-resistant transgenic plants. Annual Review of Phytopathology. 40, 467-491. Environmental Impact of Hydroelectric power plants (HPP) and Fishways Mehmet Kocabaş1, Nadir Başçinar2, Filiz Kutluyer3, Önder Aksu3 1 Karadeniz Technical University, Faculty of Forestry, Department of Wildlife Ecology & Management, 61080, Trabzon, Turkey 2Karadeniz Technical University, Faculty of Marine Sciences, Department of Fisheries Technology Engineering, 61530, Trabzon, Turkey 3Tunceli University, Fisheries Faculty, 62000, Tunceli Abstract Hydroelectric power plants (HPP), which are not cause environment pollution relatively and renewable, inexpensive, has increased importance. However, there are positive and negative impacts on the ecological balance of these systems. One of the main environmental impact of hydropower development is related to fish passage both upstream and downstream. 190 � Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Extent The size or duration of the resource. 1243 Title A name given to the resource Biotechnology and Aquaculture in Sustainable Development Author Author Altunok , Muhammet Abstract A summary of the resource. Aquaculture is the fastest growing food sector in the world with its increasing role for economy and safe food strategy of countries. Due to the continuing depletion of the fish stocks, farming of aquatic organisms such as fish, crustaceans, molluscs and aquatic plants, is now a substantial global industry supplying a significant proportion of the aquatic products consumed. Shortage in food supply and high prices are the possible important risks in the future, and aquatic products are the valuable sources of protein and essential nutrient components for global food security and eliminating malnutrition. Aquaculture also plays an important role in rural economies through the creation of new employments. In these cases, aquaculture outputs will need to be enhanced several fold in order to meet the rising demands for fish and other aquatic products in coming years. Biotechnology options seem to be good potential for increasing aquacultural productivity, food security and environmental quality worldwide. Biotechnology is offering valuable options such as protein expression, microsatellite, gene mapping and genomic, DNA vaccines, DNA chips, proteomics, transgenic technology and embryonic stem cell technology. This technology provides genetic manipulations, molecular cloning, embryo manipulation, genetically-engineered diagnostics, immunoprophylactic agents. All of these applications could help improve the selective breeding, hybridization, productivity, health, growth, nutrition, cryopreservation and conservation of genetic resources in aquacultural stocks for the benefit of mankind. However, there is need for the regulation of biotechnology activities in terms of the potential adverse impacts on the environment and human health. There is also increasing concern about the impact of biotechnology on sustainable development in various fields. The main environmental safety issue of these applications is the effects of genetically modified organisms (GMOs) on biodiversity and gene transfer in the environment. Therefore, this review discussed the integration of biotechnology and biosafety in aquaculture, and policies for the environmentally sound use and management of aquacultural biotechnology in sustainable development. Keywords: Biotechnology, Aquaculture, Sustainable Development, Food security, Public health Date A point or period of time associated with an event in the lifecycle of the resource 2012-05-31 Keywords Keywords. Conference or Workshop Item PeerReviewed H Social Sciences (General) https://omeka.ibu.edu.ba/files/original/e3999745e01af9f9602f835d37bbc282.pdf e0477d3369dd0bcb6788306c3755223f PDF Text Text Bir Bektâşî Şairin Diliyle Nevrûz Ve Çiçekler Melek DİKMEN Süleyman Demirel Üniversitesi, Isparta/Türkiye kahraman_melek@hotmail.com. Kamile ÇETİN Süleyman Demirel Üniversitesi, Isparta/Türkiye kamilecetin80@gmail.com. Özet: Toplum hayatını en çok etkileyen mevsimlerden biri olan baharın gelişi, tüm dünyada yapılan değişik törenlerle coşkulu bir biçimde kutlanır. Türklerde de baharın gelişi bir bayram kabul edilir ve bu bağlamda ilk akla gelen Nevruz Bayramı’dır. Nevrûz, Osmanlı döneminde de sayılı günlerden biri olarak kutlanmıştır. Bu durumun edebî hayattaki yansımalarından biri, baharın başlaması münasebetiyle kaside, gazel gibi nazım şekilleriyle kaleme alınan ve başta padişah olmak üzere devlet ricaline sunulan nevruziyye adlı şiirlerdir. Bu tebliğde, bir Bektâşî şairi olan Mehmet Ali Hilmi Dede Baba’nın ihtiva ettiği değişik çiçek adlarıyla dikkati çeken “Nevrûziyye” başlıklı şiiri değerlendirilmeye çalışılacaktır. Anahtar Kelimeler:Mehmet Ali Hilmi Dede Baba, Nevruz, Nevrûziyye, Çiçekler. Bahar, tabiatın canlanması, havaların ısınması gibi özellikleri ile toplum hayatını en çok etkileyen mevsimlerden biridir. Bu sebeple tüm dünyada baharın gelişi, yapılan değişik törenlerle coşkulu bir biçimde kutlanır. Bu bağlamda bahar, daha çok toprağa bağlı bir hayat sistemine sahip olan Türk milleti için de son derece önemlidir. Bu yüzden Türklerde baharın gelişi âdeta bir bayram olarak değerlendirilir. Bahar denilince ilk akla gelen ise Nevruz Bayramı’dır. Nevruz sözcüğü Farsça nev (yeni) ve ruz (gün) kelimelerinin birleşmesinden meydana gelmiş olup, “yeni gün” anlamına gelmektedir. Türk mûsikîsinde en eski makamlardan birinin adı da (Öztuna, 2000: 296) olan Nevruz, eski İran takvimine göre yılın ilk günüdür ve güneşin koç burcuna girmesi sebebiyle ilkbaharın başlangıcı sayılır. Farslara atfedilen bir bayram olan Nevruz, aslında Türkler için de birtakım manalar ve semboller içeren çok önemli bir gündür. Bunlardan en çok dikkati çekeni, Ergenekon Destanı’nda anlatıldığı üzere Göktürk Devleti’nin kurucusu olan Aşina ailelerinin Nevruz’da Ergenekon’dan çıktıklarına ve özgürlüklerine kavuştuklarına inanılmasıdır. (Çay, 1996: 10; Koca, 2002: 52) Bu yönüyle de Nevruz, Türk toplulukları için önemli bir fonksiyona sahiptir. İran geleneğinde öncelikle yılbaşı olarak kutlanan Nevruz, Türk kültüründe baharı, yaşama sevincini, su ve kutsal arınmayı, yenilenmeyi, uyanan doğa ile birlikte bolluk-bereketi ve üremeyi simgeleyen anlam ve öğelerle yüklüdür. (Altun, 2002: 17). Bütün Türklerde 21 Mart yılbaşı olarak kabul edilir. Nevruz Bayramı sırasında köy, kasaba ve şehir meydanlarında veya kırlarda toplu yemekler yapılır, hep birlikte kırlara çıkılarak eğlenilir; şölenler, yarışmalar, gösteriler, seyirlik oyunlar düzenlenir. (Pirverdioğlu: 44-48). Nevruz, Osmanlı döneminde de özel günlerden biri sayılmış, devlet kademelerinden başlayarak halka yansıyan bir şenlik havası ve hediyeleşme geleneği ile kutlanmıştır. (Halaçoğlu, 1996: 183-188; Köktürk, 2005) Baharın başlaması münasebetiyle kaside, gazel gibi nazım şekilleriyle kaleme alınan ve başta padişah olmak üzere devlet ricaline sunulan “nevruziyye” adlı şiirler Nevruz’un Osmanlılardaki önemine işaret etmektedir. Klâsik Türk edebiyatında Nef’î ile Rami Paşazâde Ref’et Bey’in nevruziyyeleri ünlüdür. (Cunbur, 1995: 37; Güzel, 1995: 98; Kılıç, 1999: 209) Alevî-Bektâşî geleneğinde de Nevrûz kutsal bir gün kabul edilmiştir. Zira inanışa göre Hz. Ali bugün doğmuştur. Bu sebeple Nevruz için “Sultan Nevruz” ve ““Mevlüd-i şah-ı velayettir bugün...” ifadeleri kullanılmıştır. Aynı zamanda Hz. Muhammed’e peygamberliğin bugün verildiği, gece gündüz eşitliğinden dolayı nübüvvet ve velayetin eşitlendiği, Hz. Ali ile Fâtıma’nın bugün evlendiği, Kerbela olayının da Nevruz günü gerçekleştiği diğer inanışlarıdır. (Temren, 1995: 152-155). Şi’â inancına göre ise bugün Hz. Ali, Hz. Peygamber tarafından halife ilan edilmiştir. (Çay, 1996: 9-10) Bazı bölgelerde yapılan Nevruz kutlamalarında halkın sabah kırlara gittiği, gidemeyenlere koklamaları için nevruz çiçeği getirildiği, Hz. Ali’nin kokusunu yaydığı şeklindeki inançtan dolayı kutsal kabul edildiği de kaydedilmektedir. (Uçkun, 2005: 165). Nevruziyye türü şiirlerin Bektaşîlerde de var olduğu, cem âyinlerinde, Nevrûz bayramı gecesinde dergâh bahçelerinde, kırlarda okunduğu bilinmektedir. Bu şiirlerde, tabiat sevgisi, Hz. Ali muhabbeti, yeni yıl gibi hususlar söz konusu edilmiştir. (Çay, 1996: 91). 421 �Bu çalışmada, XIX. yüzyıl şairi olan ve aynı zamanda Bektaşî geleneğine mensup bulunan Mehmet Ali Hilmi Dede Baba’nın38 (H.1258/H. 1287) Divanı’nda yer alan “Nevruziyye”si ele alınacaktır. Söz konusu şiir, 13 beyitten müteşekkil olup aruzun Mefâ’îlün Mefâ’îlün Mefâ’îlün Mefâ’îlün kalıbıyla kaleme alınmıştır. (Noyan: 1325/1907). Hilmi Dede-Baba, şiirine gam olarak nitelendirdiği kış aylarından sonra insanın gönlündeki sevinci, neşeyi arttıran Nevrûz’un gelişine şükrederek başlamıştır. Nevrûz’un gelişiyle birlikte her taraf rengârenk çiçeklerle bezenmiştir; elbette böyle bir görünüm insana keyif ve yaşama sevinci verecektir: Bi-hamdillâh gidüp gam geldi Nevruz-ı neşât-efzâ Bezendi sû-be-sû elvan çiçekle dâğ ile sahrâ Bahar geldiğine göre bu mevsimin vazgeçilmez çiçeği olan gülün sahneye çıkması kaçınılmazdır. Nitekim bu günlerde çeşitli süsler ve ziynetler ortaya koymak için gül bahçesinde birçok goncalar peyda olmuştur: Bahâr eyyâmı gûne zîb ü zînet bahş içün el-hak Oluptur gülsitânda gül bedenden goncalar peydâ Devam eden beyitte bir dadıya teşbih edilen yeryüzünün (dünya, toprak) nisan bulutu ile çemen çocuğunu emzirdiğinden bahsedilmektedir. Bu şerefe nâil olduğu için yeryüzü dadısı yeşil bir kaftanla ödüllendirilmiştir. Beyitte, baharın gelişiyle birlikte bilhassa Nisan ayında yağmurların yağması ve dünyanın yemyeşil bir görünüme kavuşması “dadı-bulut-çocuk-emzirmek” şeklindeki bir tablo ile ifade edilmiştir: Çemen tıflını emzirdikçe dâim ebr-i nisândan Giyüpdür dâye-i arz ol şerefle hil’at-i hadrâ Şairin bir sonraki beyitte pek çok bahar çiçeğini sahneye çıkardığı görülmektedir. Bu bağlamda ilk çiçekler olarak şebboy, zerrin ve nergis söz konusu edilmiştir. Şeb-bû (şebboy), pembe, kırmızı, krem, açık sarı, portakal renginde veya mor renkli çiçekler açan bir bitkidir. (Yücel, 2002: 98; Tırman, 1987: 212). Zerrin (fulya) ise ilkbaharda çiçek açan bir bitki olup sarı veya sarımsı-kahverengi renkte çiçekleri vardır. (Yücel, 2002: 230; Tırman, 1987: 169). Zerrin, eski toplum hayatımızda itibar görmüş çiçeklerdendir. (Polat, 2001: 187-189). Nergis ise, sarı veya beyaz renkli çiçekler açar. (Yücel, 2002: 228; Tırman, 1987: 169). Mitolojiye göre Narkissos adlı güzelliğine son derece mağrur bir perinin ölümüyle ortaya çıkmıştır. (Erhat, 2003: 211-212). Nergis, Klâsik Türk edebiyatında hastalık, mahmurluk ve şehlâlık sıfatlarının sembolü durumundadır. Şiirlerde çoğunlukla sevgilinin gözü ile mukayese edilir. (TDEA, “Nergis”: 14-15). Mehmet Ali Hilmi Dede Baba’nın tasavvuruna göre, güzellerin elbiseleri şebboy kokusu ile kokulanırken zerrinin gözü açılmış; şehlâ nergis de uykudan uyanmıştır. Klâsik şiirin genel anlayışına uygun olarak zerrin ile göz ve nergis ile de yine “tatlı şaşı; elâ göz” arasında münasebet kurulmuştur. Beyitte, baharda bilhassa gece vakitlerinde âdeta insanı sarhoş eden, baş döndürücü hoş kokulu çiçeklerin yer aldığı bir tablo çizilmiştir. Beyit “hoş koku” üzerinde şekillenmiştir: Muattar oldu hubânın libâsı ıtr-ı şebbûdan Açıldı dîde-i zerrîn uyandı nergis-i şehlâ Bir önceki beyitte birden çok çiçek adına yer veren şair, devam eden kısımda çiçekler kadrosuna zülf-i arûs ve sünbülü de eklemiştir. Zülf-i arûs (gelin perçemi), göz alıcı güzellikte ve beyaz, pembemsi mor, morumsu mavi, krem rengi ve sarı arasında değişen renklerde çiçekleri bulunan bir bitkidir. (http://www.killerplants.com/plant-of-the-week/20041206.asp) Sünbül (sümbül) bilindiği üzere, menekşe mavisi veya beyaz renkli olup çok güzel kokan bir çiçektir. (Yücel, 2002: 186; Tırman, 1987: 223). Klâsik edebiyatta sık rastlanan çiçeklerden olup şekli ve kokusu itibariyle sevgilinin saçına benzetilir. (Pala, 1998: 362). Beyitte sarılıcı bir bitki olan zülf-i arûs, sevgilinin boyuna dolanmış olarak tasvir edilmiştir. Sümbül ise istiâre yoluyla, sevgilinin kırmızı renkli yanağı üzerine dökülmüş hoş kokulu ve dağınık saçlarını karşılamaktadır. Bektaşî geleneğinde sümbül, Nevruz’un simgelerinden biridir. Günümüzde de Bektaşîlerce hazırlanan Nevruz sofralarında sümbül bulundurma geleneği vardır. Hz. Ali’yi anmak için her can, sümbülün kokusundan bir nefes çeker. Fakat beyitte sümbülün bu anlamı ve kullanımı ile ilgili bir husus söz konusu edilmemiştir. Sarıldıkça sarılmış zülf-i ‘arûs kadd-i dilcûya Yakıştıkça yakışmış rûy-i âle sünbül-i ra’nâ Devam eden beyitte bir gül bahçesi tablosu içinde şakayık, ortanca ve menekşe çiçeklerine yer verilmiştir. Şakâyık koyu kırmızı renkte çiçekleri bulunan, (Yücel, 2002: 248; Tırman, 1987: 76) ortanca beyaz, pembe, kırmızı ya da eflatun renkli, (Yücel, 2002: 186; Tırman, 1987: 207) menekşe ise mor, beyaz veya pembe renkli çiçekleri olan bitkilerdir. (Yücel, 2002: 340; Oğuz vd., 1987: 169; Tırman, 1987: 157). Beyitte şakayık, bahçede ortanca çiçeğiyle arkadaş olmuş iken menekşe, gül bahçesinin tenha bir köşesinde yalnız başına, boynu bükük bir vaziyette yatmış bir kimse olarak teşhis edilmiştir: 38 “Mehmet Ali Hilmi Dede 1842’de İstanbul’da doğmuş bir Bektâşî şairidir. Sultan Ahmed civarında Güngörmez Camii imamı Nuri Efendi ile Emine Bacı’nın oğludur. Ailesi Merdiven Köyü’nde Şahkulu Sultan Tekkesi post-nişini Hasan Baba’dan kendisi de Aşçı Baba’dan el almıştır. 1863’re posta oturan Hilmi Dede, aynı yıl Hacı Bektaş Dergâhı’na giderek icazetini almıştır. 1907’de vefatına kadar bu görevini sürdürmüştür. Mezarı tekkenin haziresindedir.”, Süleyman Solmaz, “Bir Bektaşi Şâiri Mehmed Ali Hilmi Dedebaba ve Divânı”, http://www.pau.edu.tr/pau20/asp_download.aspx?id=738 (30.04.2009). 422 �Şakayık hemdem olmuş bağçede ortanca dilberle Menekşe boynunu bükmüş yatur tenhâ gülzârda Bir sonraki beytin çiçekler kadrosu, hanımeli, civanperçemi, hüsnü Yusuf ve zerrinkadehten oluşmaktadır. Bahsi geçen çiçeklerden hanımelinin çiçekleri, beyaz ya da sarımsı beyazdır. (Tırman, 1987: 120; Yücel vd., 1995: 101-102). Civanperçeminin ise küçük ve beyaz renkli çiçekleri vardır. (Yücel, 2002: 32). Bir diğer çiçek olan hüsnüyusuf, pembe, kırmızı, beyaz ve menekşe renginde çiçekleri bulunan bir bitkidir. (Yücel, 2002: 128; Tırman, 1987: 140). Zerrîn-kadehin (sarı zerrin, zerren) ise altın sarısı renginde çiçekleri vardır. (Yücel, 2002: 228). Beyitte, hanım elinin hüsnü Yusuf’tan civanperçemini açtığı ve âşıklara zerrinkadehle kırmızı şarap sunduğu söylenilmektedir. Zerrinkadehi, altından yapılmış kadeh olarak anlamanın yanında, bir çiçek adı olarak değerlendirmek de mümkündür. Beyitte, hanımeli, civanperçemi, hüsnü Yusuf, zerrîn-kadeh şeklinde, pek çok bahar bitkisinin çiçek açmasından söz edilmektedir: Hanımeli civân perçemin açmış hüsn-i Yusuf’tan Sunar uşşâka hem zerrin kadehle bade-i hamrâ Akabinde sahneye kendisine çok yakışmış pembe renkli bir kıyafet giyen gelincik, yeşillenip çiçek açmış dilberdudağı ve fesleğen çıkmıştır. Gelinciğin parlak kırmızı, nadiren beyaz, sarı ve pembe renkli çiçekleri vardır. (Tırman, 1987: 100). Dilberdudağının (aslanağzı) çiçekleri dudak şeklinde olup kırmızı, pembe veya sarı gibi değişik renklerde olabilir. (Yücel, 2002: 52). Fesleğen hoş kokulu, otsu bir bitkidir; beyaz, pembe veya leylak renkli çiçekler açar. (Yücel, 2002: 238). Pembe kıyafeti kendisine çok yakışan gelinciğe nazar değmemesi için “maşallah” denildiği de dikkati çekmektedir: Gelincik penbe giymiş pek yaraşmış şimdi mâşallah Yeşillenmiş açup dilber dudağı fesleğen-âsâ Bahar, bilhassa eski toplum hayatımızda kır eğlencelerinin yapıldığı, bahçelerde güzellerin arz-ı endâm ettikleri bir mevsimdir. Beyitte bahsi geçen kadife, sarı veya portakal renginde çiçekleri olan bir bitkidir. (Yücel, 2002: 314). Bir başka çiçek olan atlasın parlak kırmızı renkli çiçekleri vardır. (Yücel, 2002: 142). Mine genellikle eflâtun, mavi, bazen de alaca ya da beyaz renkli çiçekler açar. (Tırman, 1987: 160; Yücel, 2002:332). Serv-i revân (salınan servi) istiâresiyle karşılanan sevgilinin gül bahçesine teşrif edip kadife, atlas ve mine gibi çiçekleri temaşa etme vakti gelmiştir. Salın serv-i hırâmânım temâşâ eyle ezhârı Döşenmiş sahn-ı gülşende kadife atlas u mînâ Bir sonraki beyitte ise karanfil, lale, nesrin, yasemin, zambak ve fulya çiçeklerine yer verilmiştir. Beyitte yer alan nahıl kelimesi, eskiden balmumundan veya gümüşten özel olarak hazırlanan ve gelinin önünde taşınan meyve, çiçek ve kıymetli taşlarla müzeyyen ağaç (Onay, 2000: 343) anlamındadır. (Arıkan, 2007; İnce: 89-96; (Nahılların İslam resim sanatındaki örnekleri hakkında örnek minyatürler için bkz. Tulum, 2007: 36, 420, 422). Karanfilin çiçekleri değişik renklerde ve güzel kokuludur. (Yücel, 2002: 130; Tırman, 1987: 140). Klâsik şiirde eskiden kavukla sarık, sarıkla fes arasına konulan ya da yakaya takılan çiçekler arasında yer alması, (Onay, 2000: 393-394) şarap kokusunu gidermek için yenmesi, (Onay, 2000: 417) birtakım macunların terkibinde bir baharat olarak kullanılması (Onay, 2000: 315) gibi özellikleriyle söz konusu edilen karanfil, bazen de kırmızı rengi sebebiyle sevgilinin yanağına teşbih edilmiştir. (Çavuşoğlu, 2001: 290). Lalenin ise çiçekleri çan biçiminde ve kırmızı başta olmak üzere çok değişik renklerdedir. (Yücel, 2002: 322; Tırman, 1987: 223). Renginden dolayı lale, klâsik şiirde kan, mum, şarap, yanak, âşığın gözyaşı, lâl, kâse-i mercan, çerâğ, kanlı kefen, al sancak vb. unsurlara teşbih edilmiş; şekil bakımından da genellikle kadeh olarak tasavvur edilmiştir. (Pala, 1998: 252). Lale kelimesindeki harflerin sırası değiştirildiğinde “Allah” ve “hilâl” sözcüklerinin elde edilebilmesi de bu çiçeğin sevilmesinde etkili olmuştur. (Ayvazoğlu, 1997: 109-110). Zambak beyaz-pembe-kırmızı renkte çiçekleri bulunan bir bitkidir. (Tırman, 1987: 223; Yücel, 2002: 210). Nesrin, Van gülü anlamındadır. Ancak “Van gülü” olarak ünlenen çeşidin hangi tür veya varyeteye sahip olduğu kesin olarak bilinmemektedir. (Baytop, 2001: 85). Yasemin, beyaz renkli ve güzel kokulu çiçekleri bulunan bir bitkidir. (Yücel vd., 1995: 92). Klâsik şiirde daha çok beyaz renkli olanlarının tercih edildiğini gördüğümüz yasemin, daha çok rengi, kokusu, yaprağı itibariyle anılır ve sevgilinin yanağı ya da gömleği olarak tahayyül edilir. (Pala, 1998: 415; Çavuşoğlu, 2001: 291; Polat, 2001: 197-199). Fulya çiçeği ise daha önce de bahsi geçen zerrindir. Şairin tasavvuruna göre Yüce Allah’ın kudretiyle her taraf karanfil, lale, nesrin, zambak, yasemin ve fulya çiçekleriyle tıpkı bir nahıl gibi donanmıştır. Beyit, renk renk çiçekleriyle çok canlı bir bahar ve bahçe manzarasını gözümüzde canlandırmaktadır: Nahıl gibi donanmış her taraf bâ-kudret-i Yezdân Karanfil lâle vü nesrin ü zanbak yasemen fulya Yine birden çok çiçeğin hep beraber yer aldıkları aşağıdaki beyitte, rengârenk bir tablo çizilmektedir. Nilüfer, güzel kokulu, beyaz, pembe, sarı, mavi renkli çiçekleri bulunan bir su bitkisidir. (Yücel, 2002: 236-238; Tırman, 1987: 173). Filbahri, beyaz renkli ve güzel kokulu çiçekleri bulunan bir bitkidir. (Yücel vd., 1995: 109). Beytin mana dünyasına göre nilüfer ve filbahri çiçekleriyle amber ve mercan ortaya çıkmış; bunu görünce sedef de ağzını açıp içinde bulunan inciyi gül bahçesine hediye etmiştir. Beyitte bahsi geçen sadef, deniz 423 �kaplumbağasına benzeyen, daha çok Hint ve Çin denizlerinde bulunduğu rivayet edilen bir çeşit istiridyedir. Nisan ayında (18 Nisan) denizin yüzüne veya sahile çıkarak ağzını açtığına, yağmur tanesini yuttuğuna ve böylece incinin oluştuğuna inanılır. (Pala, 1998: 337). Beyitte dikkat edilirse nilüfer, amber, mercan, sadef, inci kelimeleri suyla bağlantılıdır. Bu da herhalde ilkbaharda yağmurların yağmasıyla suların çoğalmasını ifade etmek üzere kullanılmış olmalıdır: Çıkınca nilüfer filbahriden hem anber ü mercan Sadef ağzın açup incüsin etmiş gülşene ihdâ Bahar mevsiminde düzenlenen, birtakım mezeler ve çiçeklerle donatılan, şaşaalı bir içki meclisi tasviri yapan aşağıdaki beyit, her biri birden çok çağrışıma sahip avize, ateş, balmumu çiçeklerini ihtiva etmektedir. Avize çiçeği, beyaz renkli çiçekleri bulunan bir bitkidir. (Yücel vd., 1995: 157). Ateş çiçeğinin kırmızı renkli çiçekleri vardır. (Yücel, 2002: 286). Bir başka çiçek olan balmumu (mum çiçeği) ise, beyaz renkli ve hoş kokulu çiçekleri ile dikkati çeker. (http://www.cicekcesitleri.com/Mum_Cicegi). Çiçek bahçesinde tertip edilen rintler meclisinde ateş çiçeği, parlak balmumunu yakıp avize ile hem meclisi hem de bahçeyi aydınlatmayı amaçlamıştır. Tevriyeli bir kullanıma sahip olan avize ve balmumunun aynı zamanda birer çiçek adı olduğu da hatırlanmalıdır: Şükûfistânı tenvîre etmeğe hem bezm-i rindânı Yakup âvizeden âteş çiçeği balmumun ra’nâ Nevrûziyyenin son beytinde gecesefası ve kahkaha çiçekleri yer almaktadır. Gecesefası, boyun kısımları beyaz, yukarı doğru genelde mor veya gökyüzü mavisi renginde çiçekleri olan bir bitkidir. (Yücel, 2002: 194). Kahkaha çiçeği, beyaz, nadiren açık pembe renkte taç yaprakları bulunan bir çiçektir. Yücel, 2002: 80). Bir önceki beyitte bir bahar gecesinde düzenlenen içki meclisi tasviri yapan şair, son beyitte buna paralel olarak “ay” istiaresiyle ifade ettiği sevgilinin rakipler ile mehtap gezintisine çıktığından bahsetmektedir. Sevgili, böyle bir gezintide kahkahalarla gecesefası yaparken, âşık-şair binlerce kez “ya sabır” çekmektedir. İkili bir anlam dünyasına sahip olan gece safası ve kahkaha aynı zamanda birer çiçek ismidir: O meh ağyâr ile gece safâda kahkahalarla Hezârân yâ sabur çekmekte şimdi Hilmi-i şeydâ Sonuç Bir Alevî-Bektâşî şeyhi olan Mehmet Ali Hilmi Dede Baba’nın “Nevruziyye” başlıklı şiirini konu alan bu çalışmada şu sonuçlara ulaşılmıştır: Alevî-Bektâşî geleneğinde son derece önemli bir yeri olan ve kutsal bir gün olarak kabul edilen Nevrûz, bu geleneğe mensup bir şairin kaleminde ifade bulmuştur. Şairin Alevî-Bektâşî geleneğine bağlı olmasından dolayı, şiirde Yezdân, çerâğ uyandırmak (mum yakmak) gibi bu geleneğe ait unsurlar da söz konusu edilmiştir. Klâsik şiir anlayışına uygun olarak Mehmet Ali Hilmi Dede Baba da kışı bir gam mevsimi, baharı ise insanın gönlüne ferahlık ve yaşama sevinci veren bir mevsim olarak takdim etmiştir. Nevruziyyede elvân çiçek, ezhâr, şükûfistan, gülşen gibi genel anlamda çiçek ve çiçek bahçesi anlamına gelen kelimeler kullanılmıştır. Bunların dışında gül, gonca, şeb-bû, zerrîn, nergis, zülf-i arûs, sünbül, şakayık, ortanca, benefşe, hanımeli, civanperçemi, hüsn-i Yusuf, zerrin-kadeh, gelincik, dilber dudağı, fesleğen, kadife, atlas, mina, karanfil, lale, nesrin, zambak, yasemin, fulya, nilüfer, filbahri, avize, ateş çiçeği, balmumu çiçeği, gece sefası ve kahkaha çiçeklerinden oluşan oldukça geniş bir çiçek kadrosu vardır. Görüldüğü üzere, çalışmaya konu olan Nevrûziyye, Klâsik Türk edebiyatının çok bilinen gül, sümbül, nergis, lale vb. çiçeklerinin yanında, değişik çiçekleri de ihtiva etmektedir. Şiir, bu yönüyle de ilgi çekicidir. Klâsik Türk şiirinde sıkça kullanılanların dışında çiçeklerin zikredilmesi, son dönemlerde kaleme alınan şiirlerde sesten ziyade müşahhaslığın ön plana çıkmış olmasına bağlanabilir. Mehmet Ali Hilmi Dede Baba, son dönem şairlerinden olduğu için şiirine yenilik ve farklılık getirme çabasında olduğu düşünülebilir. Her biri farklı renk ve kokulara sahip bu kadar çok çiçeğin bir arada yer aldığı bir şiirde Nevrûz ve dolayısıyla bahar oldukça renkli, bol çağrışımlı ve canlı tablolar hâlinde gözler önüne serilmiştir. Bir erkek şairin kaleminde bu kadar çok çiçeğin bir arada zikredilmesiyle, Alevî-Bektaşî geleneğinde Nevruz’un ve baharın önemi ortaya çıkmaktadır. Bibliyografya Altun, E. (2002). “Türk Halk Kültüründe Nevruz”, Türk Kültüründe Nevruz V. Uluslararası Bilgi Şöleni Bildirileri, Ankara. Arıkan, M., “Osmanlı Saray Düğünlerinde Yemekler”, http://turkoloji.cu.edu.tr/GENEL/murat_arikan_osmanli_saray_yemek.pdf (Erişim tarihi: 30.04.2009). 424 �Ayvazoğlu, B. (1997). Güller Kitabı Türk Çiçek Kültürü Üzerine Bir Deneme, Ötüken Yay., Ankara. Baytop T. (2001). Türkiye’de Eski Bahçe Gülleri, Kültür Bakanlığı Yay., Ankara. Cunbur, M. (1995). “Klâsik Edebiyatımızda Nevruz”, Türk Kültüründe Nevruz Uluslararası Bilgi Şöleni (Sempozyumu) Bildirileri, (Yayına Haz. Prof. Dr. Sadık Tural), AKM Yay., Ankara,. Çavuşoğlu, M. (2001) Necati Bey Divanı’nın Tahlili, Kitabevi Yay., İstanbul. Çay, A. M., (1996). Türk Ergenekon Bayramı Nevruz, Turan Kültür Vakfı, Ankara, 1996. Erhat, A. (2003). Mitoloji Sözlüğü, Remzi Kitabevi, İstanbul. Güzel, A. (1995). “XIV-XV. Yüzyıl Edebiyatında Nevruz ve Nevruziyeler”, Türk Kültüründe Nevruz Uluslararası Bilgi Şöleni (Sempozyumu) Bildirileri, (Ankara 20-22 Mart 1995), (Yayına Haz. Prof. Dr. Sadık Tural), AKM Yay., Ankara, 95104. Halaçoğlu, Y. (1996) “Osmanlılarda Nevruz Kutlamaları”, Nevruz ve Renkler, (Yayına Haz. Prof. Sadık Tural-Elmas Kılıç), AKM Yay., Ankara. http://www.cicekcesitleri.com/Mum_Cicegi (Erişim tarihi: 21 Ağustos 2007). http://www.killerplants.com/plant-of-the-week/20041206.asp (Erişim tarihi: 21 Ağustos 2007). İnce, A. (1988) “Divan Şiirinde Nahıl”, Türk Dünyası Araştırmaları, (54), 89-96. Kılıç, F. (1999). “Osmanlı Devleti’nde Klâsik Edebiyatımızda Nevruz”, Türk Dünyasında Nevruz Üçüncü Uluslararası Bilgi Şöleni. Koca, S. (2002) “Eski Türklerde Bayram ve Festivaller”, Türkler, Yeni Türkiye Yay., Ankara, (III), Noyan, B. (1907). Mehmet Ali Hilmi Dede-Baba Divanı, İstanbul. Oğuz, M. G. & Yayıntaş, A. (1987). Park ve Bahçelerimizin Süs Bitkileri, (Yardımcı Ders Kitabı), E.Ü. Fen-Fakültesi Baskı İşleri, İzmir. Onay, (2000). Eski Türk Edebiyatında Mazmunlar ve İzahı, (Haz. Cemâl Kurnaz), Akçağ Yay., Ankara. Öztuna, Y. (2000). “Nevrûz”, Türk Mûsikîsi Kavram ve Terimleri Ansiklopedisi, AKM Yay., Ankara. Pala, İ. (1998) Ansiklopedik Divân Şiiri Sözlüğü, Ötüken Yay., İstanbul. Pirverdioğlu A. (2002). “Türklerde Yılbaşı ve Bahar Geleneği”, Türkler, Yeni Türkiye Yay., Ankara, (III), 44-50. Polat, N. H. (2001). Türk Çiçek ve Ziraat Kültürü Üzerine Cevat Rüştü’den Bir Güldeste, Kitabevi Yay., İstanbul. Solmaz, S. “Bir Bektaşi Şâiri Mehmed Ali Hilmi Dedebaba ve Divânı”, http://www.pau.edu.tr/pau20/asp_download.aspx?id=738 (Erişim tarihi: 30.04.2009). TDEA, “Nergis”, (VII) 14-15, Dergâh Yay., İstanbul . Temren, B. (1995). “Bektaşi Geleneklerinde Nevruz Kutlamaları Kırklar Bayramı”, Foklor/Edebiyat, S. 3, Ankara. Tırman, F. (1987). Tabii Çiçekler Morfolojisi ve Yapma Çiçekçilikte Kullanılan Kalıplar, Selçuk Üniversitesi Yay., Konya. Uçkun, R. (2005) “Alevî-Bektaşî Geleneğinde Nevruz Kutlamaları”, Uluslararası Bektaşilik ve Alevilik Sempozyumu I, Isparta. Vehbî (2007). Surnâme, Sultan Ahmet’in Düğün Kitabı, Haz. Mertol Tulum, Kabalcı Yay., İstanbul. Yücel E. & Yaltırık F. & Öztürk M. (1995). Süs Bitkileri (Ağaçlar ve Çalılar), Anadolu Üniversitesi Yay., Eskişehir. Yücel, E.(2002). Çiçekler ve Yer Örtücüler, Etam Matbaa Tesisleri, Eskişehir. 425 � Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Extent The size or duration of the resource. 436 Title A name given to the resource Bir Bektâşî Şairin Diliyle Nevrûz Ve Çiçekler Author Author DİKMEN, Melek ÇETİN, Kamile Abstract A summary of the resource. Toplum hayatını en çok etkileyen mevsimlerden biri olan baharın gelişi, tüm dünyada yapılan değişik törenlerle coşkulu bir biçimde kutlanır. Türklerde de baharın gelişi bir bayram kabul edilir ve bu bağlamda ilk akla gelen Nevruz Bayramı’dır. Nevrûz, Osmanlı döneminde de sayılı günlerden biri olarak kutlanmıştır. Bu durumun edebî hayattaki yansımalarından biri, baharın başlaması münasebetiyle kaside, gazel gibi nazım şekilleriyle kaleme alınan ve başta padişah olmak üzere devlet ricaline sunulan nevruziyye adlı şiirlerdir. Bu tebliğde, bir Bektâşî şairi olan Mehmet Ali Hilmi Dede Baba’nın ihtiva ettiği değişik çiçek adlarıyla dikkati çeken “Nevrûziyye” başlıklı şiiri değerlendirilmeye çalışılacaktır. Date A point or period of time associated with an event in the lifecycle of the resource 2009-06 Keywords Keywords. Conference or Workshop Item PeerReviewed L Education (General) https://omeka.ibu.edu.ba/files/original/3186b7c139f78e2ff0577cfcc14b6b24.docx d7f719081cd447644da596fd17040313 https://omeka.ibu.edu.ba/files/original/9d1b70971d80ddfc4bff66cc9ae63eee.pdf 715350b4a88f868484a65722844358a7 PDF Text Text BİR DİLBİLİMCİ OLARAK ALİ ŞİR NEVAYÎ Mücahit AKKUŞ Hitit Üniversitesi, Fen-Edebiyat Fakültesi, Türk Dili ve Edebiyatı Bölümü, Çorum / Türkiye Anahtar Kelimeler: Dil, tarih, Ali Şir Nevayî, Dilbilim, Türkçe. ÖZET Dil; duygu, düşünce ve isteklerin aktarılmasını sağlayan doğal bir vasıtadır. İnsanoğlu, tarihin eski çağlarından beri bu vasıtayı kullanmıştır. Kimi zaman sesle, kimi zaman jest ve mimikle kimi zaman da yazıyla anlaşmaya çalışmıştır. Dil, yapısını bünyesinde koruyarak zamanla gelişir. Başka dillerle kelime alışverişinde bulunur. Bu alışveriş bazen yoğun bir şekilde bazen de göze çarpmayacak kadar az bir şekilde olur. Alınan kelimelerin de o dilde uzun zaman kalıp kalmamasına o dili kullanan insanlar karar verir. Tarih, din ve coğrafi ortamlar o dilin şekillenmesi için son derece önemli unsurlardır. Derin bir tarih olgusu, farklı coğrafyalarda yaşamış olmaları ve çeşitli dinlere bağlı olma durumu Türklerin de dilini oldukça şekillendiren konular olmuştur. Bu vasıtalarla dil zaman içinde lehçe dediğimiz çeşitli kollara ayrılmıştır. Bu kollarda farklı ses özellikleri, farklı yapılar ve farklı kelime birikimi oluşmaya başlamıştır. Bu farklı kollar içerisinde Çağatay Türkçesi diye bir kol oluşmuş ve Ali şir Nevayî diye de bir âlim çıkarak Türkçenin bu lehçesi ile çok değerli eserler meydana getirmiştir. Gerek sözlük çalışması yapmış, gerek divanlar hazırlamış gerekse de başka alanlarda birikimlerini gözler önüne sermeyi başarmıştır. Türk dünyasının en önemli şahsiyetlerinden biri olan Ali Şir Nevayî, Türk dilinin ve edebiyatının gelişmesinde önemli katkıları olmuş büyük bir ediptir. Hayatı boyunca Türkçenin diğer diller karşısındaki önemine dikkat çekmiş ve bu doğrultuda eserler meydana getirmiştir. Bu çalışmada dilbilim ve Ali Şir Nevayî üzerinde durulmuştur. Dilbilimin alt kolları olan, anlambilim, sözlükbilim, biçimbilim vb. konuları Ali Şir Navayî’nin eserleri göz önüne alınarak değerlendirilmeye çalışılmıştır. Bu değerli şahsiyetin belirli manzum parçaları anlam itibariyle değerlendirililmiş, yaptığı sözcük çalışması sözcükbilim ve sözlükbilim anlayışıyla irdelenmiş, eserleri günümüz dilbilim anlayışıyla tanzim edilmiştir. Bu çalışmalar yapılarak Ali Şir Nevayî eserlerinin de dilbilim konusunda ne derece önem arz ettiği gözler önüne serilmeye çalışılmıştır. � Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Extent The size or duration of the resource. 1999 Title A name given to the resource BİR DİLBİLİMCİ OLARAK ALİ ŞİR NEVAYÎ Author Author AKKUŞ, Mücahit Abstract A summary of the resource. Anahtar Kelimeler: Dil, tarih, Ali Şir Nevayî, Dilbilim, Türkçe. ÖZET Dil; duygu, düşünce ve isteklerin aktarılmasını sağlayan doğal bir vasıtadır. İnsanoğlu, tarihin eski çağlarından beri bu vasıtayı kullanmıştır. Kimi zaman sesle, kimi zaman jest ve mimikle kimi zaman da yazıyla anlaşmaya çalışmıştır. Dil, yapısını bünyesinde koruyarak zamanla gelişir. Başka dillerle kelime alışverişinde bulunur. Bu alışveriş bazen yoğun bir şekilde bazen de göze çarpmayacak kadar az bir şekilde olur. Alınan kelimelerin de o dilde uzun zaman kalıp kalmamasına o dili kullanan insanlar karar verir. Tarih, din ve coğrafi ortamlar o dilin şekillenmesi için son derece önemli unsurlardır. Derin bir tarih olgusu, farklı coğrafyalarda yaşamış olmaları ve çeşitli dinlere bağlı olma durumu Türklerin de dilini oldukça şekillendiren konular olmuştur. Bu vasıtalarla dil zaman içinde lehçe dediğimiz çeşitli kollara ayrılmıştır. Bu kollarda farklı ses özellikleri, farklı yapılar ve farklı kelime birikimi oluşmaya başlamıştır. Bu farklı kollar içerisinde Çağatay Türkçesi diye bir kol oluşmuş ve Ali şir Nevayî diye de bir âlim çıkarak Türkçenin bu lehçesi ile çok değerli eserler meydana getirmiştir. Gerek sözlük çalışması yapmış, gerek divanlar hazırlamış gerekse de başka alanlarda birikimlerini gözler önüne sermeyi başarmıştır. Türk dünyasının en önemli şahsiyetlerinden biri olan Ali Şir Nevayî, Türk dilinin ve edebiyatının gelişmesinde önemli katkıları olmuş büyük bir ediptir. Hayatı boyunca Türkçenin diğer diller karşısındaki önemine dikkat çekmiş ve bu doğrultuda eserler meydana getirmiştir. Bu çalışmada dilbilim ve Ali Şir Nevayî üzerinde durulmuştur. Dilbilimin alt kolları olan, anlambilim, sözlükbilim, biçimbilim vb. konuları Ali Şir Navayî’nin eserleri göz önüne alınarak değerlendirilmeye çalışılmıştır. Bu değerli şahsiyetin belirli manzum parçaları anlam itibariyle değerlendirililmiş, yaptığı sözcük çalışması sözcükbilim ve sözlükbilim anlayışıyla irdelenmiş, eserleri günümüz dilbilim anlayışıyla tanzim edilmiştir. Bu çalışmalar yapılarak Ali Şir Nevayî eserlerinin de dilbilim konusunda ne derece önem arz ettiği gözler önüne serilmeye çalışılmıştır. Publisher An entity responsible for making the resource available International Burch University Date A point or period of time associated with an event in the lifecycle of the resource 2013-05-17 Keywords Keywords. Article PeerReviewed Identifier An unambiguous reference to the resource within a given context ISSN 2203-4548 https://omeka.ibu.edu.ba/files/original/78132e906a85dc8aeae0e3824f97701c.docx d7f719081cd447644da596fd17040313 https://omeka.ibu.edu.ba/files/original/f5197950e75735d059c4f8ec0a1af78f.pdf 715350b4a88f868484a65722844358a7 PDF Text Text BİR DİLBİLİMCİ OLARAK ALİ ŞİR NEVAYÎ Mücahit AKKUŞ Hitit Üniversitesi, Fen-Edebiyat Fakültesi, Türk Dili ve Edebiyatı Bölümü, Çorum / Türkiye Anahtar Kelimeler: Dil, tarih, Ali Şir Nevayî, Dilbilim, Türkçe. ÖZET Dil; duygu, düşünce ve isteklerin aktarılmasını sağlayan doğal bir vasıtadır. İnsanoğlu, tarihin eski çağlarından beri bu vasıtayı kullanmıştır. Kimi zaman sesle, kimi zaman jest ve mimikle kimi zaman da yazıyla anlaşmaya çalışmıştır. Dil, yapısını bünyesinde koruyarak zamanla gelişir. Başka dillerle kelime alışverişinde bulunur. Bu alışveriş bazen yoğun bir şekilde bazen de göze çarpmayacak kadar az bir şekilde olur. Alınan kelimelerin de o dilde uzun zaman kalıp kalmamasına o dili kullanan insanlar karar verir. Tarih, din ve coğrafi ortamlar o dilin şekillenmesi için son derece önemli unsurlardır. Derin bir tarih olgusu, farklı coğrafyalarda yaşamış olmaları ve çeşitli dinlere bağlı olma durumu Türklerin de dilini oldukça şekillendiren konular olmuştur. Bu vasıtalarla dil zaman içinde lehçe dediğimiz çeşitli kollara ayrılmıştır. Bu kollarda farklı ses özellikleri, farklı yapılar ve farklı kelime birikimi oluşmaya başlamıştır. Bu farklı kollar içerisinde Çağatay Türkçesi diye bir kol oluşmuş ve Ali şir Nevayî diye de bir âlim çıkarak Türkçenin bu lehçesi ile çok değerli eserler meydana getirmiştir. Gerek sözlük çalışması yapmış, gerek divanlar hazırlamış gerekse de başka alanlarda birikimlerini gözler önüne sermeyi başarmıştır. Türk dünyasının en önemli şahsiyetlerinden biri olan Ali Şir Nevayî, Türk dilinin ve edebiyatının gelişmesinde önemli katkıları olmuş büyük bir ediptir. Hayatı boyunca Türkçenin diğer diller karşısındaki önemine dikkat çekmiş ve bu doğrultuda eserler meydana getirmiştir. Bu çalışmada dilbilim ve Ali Şir Nevayî üzerinde durulmuştur. Dilbilimin alt kolları olan, anlambilim, sözlükbilim, biçimbilim vb. konuları Ali Şir Navayî’nin eserleri göz önüne alınarak değerlendirilmeye çalışılmıştır. Bu değerli şahsiyetin belirli manzum parçaları anlam itibariyle değerlendirililmiş, yaptığı sözcük çalışması sözcükbilim ve sözlükbilim anlayışıyla irdelenmiş, eserleri günümüz dilbilim anlayışıyla tanzim edilmiştir. Bu çalışmalar yapılarak Ali Şir Nevayî eserlerinin de dilbilim konusunda ne derece önem arz ettiği gözler önüne serilmeye çalışılmıştır. � Dublin Core The Dublin Core metadata element set is common to all Omeka records, including items, files, and collections. For more information see, http://dublincore.org/documents/dces/. Extent The size or duration of the resource. 1957 Title A name given to the resource BİR DİLBİLİMCİ OLARAK ALİ ŞİR NEVAYÎ Author Author AKKUS, Mucahit Abstract A summary of the resource. Anahtar Kelimeler: Dil, tarih, Ali Şir Nevayî, Dilbilim, Türkçe. ÖZET Dil; duygu, düşünce ve isteklerin aktarılmasını sağlayan doğal bir vasıtadır. İnsanoğlu, tarihin eski çağlarından beri bu vasıtayı kullanmıştır. Kimi zaman sesle, kimi zaman jest ve mimikle kimi zaman da yazıyla anlaşmaya çalışmıştır. Dil, yapısını bünyesinde koruyarak zamanla gelişir. Başka dillerle kelime alışverişinde bulunur. Bu alışveriş bazen yoğun bir şekilde bazen de göze çarpmayacak kadar az bir şekilde olur. Alınan kelimelerin de o dilde uzun zaman kalıp kalmamasına o dili kullanan insanlar karar verir. Tarih, din ve coğrafi ortamlar o dilin şekillenmesi için son derece önemli unsurlardır. Derin bir tarih olgusu, farklı coğrafyalarda yaşamış olmaları ve çeşitli dinlere bağlı olma durumu Türklerin de dilini oldukça şekillendiren konular olmuştur. Bu vasıtalarla dil zaman içinde lehçe dediğimiz çeşitli kollara ayrılmıştır. Bu kollarda farklı ses özellikleri, farklı yapılar ve farklı kelime birikimi oluşmaya başlamıştır. Bu farklı kollar içerisinde Çağatay Türkçesi diye bir kol oluşmuş ve Ali şir Nevayî diye de bir âlim çıkarak Türkçenin bu lehçesi ile çok değerli eserler meydana getirmiştir. Gerek sözlük çalışması yapmış, gerek divanlar hazırlamış gerekse de başka alanlarda birikimlerini gözler önüne sermeyi başarmıştır. Türk dünyasının en önemli şahsiyetlerinden biri olan Ali Şir Nevayî, Türk dilinin ve edebiyatının gelişmesinde önemli katkıları olmuş büyük bir ediptir. Hayatı boyunca Türkçenin diğer diller karşısındaki önemine dikkat çekmiş ve bu doğrultuda eserler meydana getirmiştir. Bu çalışmada dilbilim ve Ali Şir Nevayî üzerinde durulmuştur. Dilbilimin alt kolları olan, anlambilim, sözlükbilim, biçimbilim vb. konuları Ali Şir Navayî’nin eserleri göz önüne alınarak değerlendirilmeye çalışılmıştır. Bu değerli şahsiyetin belirli manzum parçaları anlam itibariyle değerlendirililmiş, yaptığı sözcük çalışması sözcükbilim ve sözlükbilim anlayışıyla irdelenmiş, eserleri günümüz dilbilim anlayışıyla tanzim edilmiştir. Bu çalışmalar yapılarak Ali Şir Nevayî eserlerinin de dilbilim konusunda ne derece önem arz ettiği gözler önüne serilmeye çalışılmıştır. Publisher An entity responsible for making the resource available IBU Publishing Date A point or period of time associated with an event in the lifecycle of the resource 2013-05-03 Keywords Keywords. Article PeerReviewed