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REMOVAL OF NITROGEN FROM MUNICIPAL WASTEWATER - THE EFFECT
OF THE ADDITION OF CARBON SOURCES ON BIOLOGICAL
DENITRIFICATION
Jasmina Ibrahimpašić1, Merima Toromanović1, Tibela Landeka Dragičević2
1
2
University of Bihać, Biotechnical Faculty, Bihać, Bosnia and Herzegovina
University of Zagreb, Faculty of Food Technology and Biotechnology, Zagreb, Croatia
jasmina.ibrahimpasic@btf.unbi.ba, toromanovic_merima@hotmail.com
ABSTRACT
In this work was used activated sludge from the WWTP (wastewater treatment plant), in
which with technique accumulation nitrificants and denitrificants, were prepared mixed
bacterial cultures which showed the ability nitrification of ammonia- nitrogen to nitrate, as
well as the ability of denitrification of nitrate nitrogen to gaseous nitrogen in municipal
wastewater. As carbon source in the process of biological denitrification was used sodium
acetate, in the ratio C/N=1 and C/N=2. Activity of mixed microbial cultures for removal
components with nitrogen was determined by measuring the concentration of organic matter,
expressed as COD, ammonia-nitrogen, nitrite, nitrate, pH, concentration dissolved oxygen,
and the concentration of microbial biomass.
Keywords: municipal water, activated sludge, nitrogen removal
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INTRODUCTION
The most widely used procedure for the treatment of municipal wastewater is an aerobic
process with activated sludge. The activated sludge system with balance between different
types of bacteria is essential to ensure effective removal of pollutants, good sedimentation of
sludge and low levels of suspended particulate matter (Mesquita et al. 2009). Biological
nitrogen removal from wastewater is achieved by applying the process of aerobic ammonia
oxidation, or autotrophic aerobic nitrification and anoxic (facultative-anaerobic)
denitrification. Ammonia oxidizing bacteria (AOB), such as Nitrosomonas, Nitrosospira and
Nitrosococcus, converted ammonia to nitrite.
Nitrate oxidizing bacteria (NOB), such as Nitrobacter, Nitrosospira, Nitrococcus and
Nitrospina, further converted nitrite to nitrate (Henze et al. 2002). During denitrification
process nitrates are exceeding into the nitrogen gas. Nitrogen gas is released into the air, and
in this way removed from the wastewater. These two processes depend on several factors,
such as temperature, pH, dissolved oxygen, alkalinity, toxicity, etc. (Metcalf & Eddy, 2003;
Jeyanayaga, 2005; Gerardi, 2002).
The main objective of this study was to define the working conditions of removal nitrogen
compounds process of nitrification and denitrification in municipal wastewater, with the
addition of heterotrophic carbon source, and to determine the conditions for quality water
treatment in accordance with current regulations.
MATERIAL AND METHODS
In the research was used activated sludge from the WWTP (wastewater treatment plant). In
the activated sludge is, with a technique accumulation nitrificants and denitrificants, prepared
mixed bacterial cultures, which showed the ability of nitrification ammonia nitrogen to
nitrate, and the ability of denitrification of nitrate nitrogen to nitrogen gas. The enrichment of
mixed microbial culture was performed in Erlenmeyer flasks (500 mL, with working volume
of 100 mL) on rotary shaker and room temperature, with municipal wastewater as a source
of ammonium nitrogen (15-147 mg NH4+-N L–1). After of cultivation, the biomass as
inoculum was prepared and used in all experiments.
Activity of the microbial culture for the removal of nitrogen compounds was determined by
measuring the concentration of ammonia nitrogen, nitrite, nitrate, pH, dissolved oxygen
concentration and the concentration of the microbial biomass. Nitrogen removal in oxy/anoxia
conditions, as well as all the experiments that preceded: autotrophic and heterotrophic
nitrification with adding an external carbon source for nitrification, were conducted in a
laboratory reactor working volume of 2 liters. Denitrification is carried out in conditions
without aeration, with stirring the reactor contents with the help of the mixer placed in the
reactor. The reactor is equipped with gauges of pH, dissolved oxygen and temperature.
All analytical data were determined by the methods prescribed by APHA (APHA, 1998): the
concentration of organic substances, expressed as COD-value, BOD, NH4-N, NO3-N, NO2-N,
pH, temperature, dissolved oxygen concentration, dry matter, suspended solids and biomass
concentration.
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RESULTS
Experiments were carried out by gradually increasing the concentration of NH4-N, 15 mg/L to
147 mg/L, which is the same concentration of ammonia in municipal wastewater. In
experiments was monitored microbial activity with the addition of sodium acetate as a carbon
source in an external ratios C:N=1:1, C:N=2:1. Once the technique of enrichment and
adaptation prepared microbial cultures which showed the ability of biodegradation, in
experiments is added municipal wastewater and is accompanied by its biodegradation. Below
are shown the most important results.
Table 1. Chemical and physical indicators of quality of municipal wastewater
Parameter
Value
Color
Smell
Temperature (°C)
pH
Conductivity (µS)
Oxygen saturation (%)
Dissolved oxygen (mg/L)
Sediment matter (ml of sediment)
Evaporated residue (mg/L)
Annealed rest (mg/L)
Suspended solids (mg/L)
Nitrites (mg/L)
Nitrates (mg/L)
Ammonia (mg/L)
COD (mgO2/L)
BOD5 (mgO2/L)
gray-brown
typical
14,7
8
816
7,2
3,4
5
754,48
231
1014
0,41
1,1
147
284
245
Sludge from the treatment of wastewater NaAc was added as an external carbon source in the
ratio of C:N=2:1, and the concentration of NH4-N addition to the initial 50 mg/L. The total
volume of the reactor is 2L.
Figure 1. NH4-N, NO3-N, NO2-N and dissolved oxygen concentration, pH and temperature
determined during the process of nitrification
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Figure 2. The concentration of organic substances, expressed as COD
In the enriched microbial culture was added a municipal wastewater in an amount so that the
concentration of NH4-N is set to the initial 70 mg/L. As an external carbon source was added
sodium acetate at a ratio of C:N=1:1. The experiment was carried out with alternating
nitrification and denitrification. Nitrification is carried out in the oxy and denitrification in
anoxia conditions, with stirring. Oxy/anoxia conditions during the process of alternating
nitrification/denitrification maintained by the dynamics: 0.5 hours of anoxia conditions, then 1
hour oxy conditions, then again 0.5 hours of anoxia conditions and again oxy conditions. The
total volume of the reactor is 2L.
Figure 3. NO3-N, NO2-N and dissolved oxygen concentration and pH value determined
during the biodegradation process of wastewater
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Figure 4. The concentration of organic substances, expressed as COD and NH4-N during the
biodegradation of wastewater
After the technique of adaptation and enrichment, it was prepared microbial culture capable of
biological degradation, and in the sludge is added municipal wastewater and the NH4-N
concentration of 147 mg/L. The total volume of the reactor is 2L.
Dissolved oxygen
Nitrites
Nitrates
Figure 5. NO3-N, NO2-N, dissolved oxygen concentration and pH during the biodegradation
process of wastewater
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Figure 6. The concentration of organic substances, expressed as COD, NH4-N, and the
temperature
All previous nitrification processes were carried out under aerobic conditions. After nitrite
nitrogen completely oxidized, after 6 hours, into nitrate nitrogen, investigate the ability of
microbial cultures for the denitrification. Denitrification is carried out under anoxic conditions,
only by stirring. As a carbon source was used municipal wastewater. Parameters were
monitored every 3 hours, and 24 hours. The volume of the reactor is 2L.
Figure 7. NH4-N, NO3-N, NO2-N and the concentration of dissolved oxygen, pH and
temperature during the process of denitrification
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Figure 8. The concentration of organic substances, expressed as COD
DISCUSSION
In the experiment in the heterotrophic nitrification, where the organic compound as a source
of added sodium acetate in a 2:1 ratio, and the initial concentration of NH4-N 50 mg / l,
nitrification is done for five hours (Figure 1). Oxidation of ammonia (ammonia converted into
NO3 -N and NO 2-N) is followed by decomposition of organic matter (COD) in the beginning
of the process, as well as the accumulation of nitrite and nitrate (see Figures 1 and 2).
Extended aeration for a further three hours, all the NO2-N is converted to NO3-N. From the
first hour until the end of the process, NO3-N has accumulated (Figure 1). In the experiment,
heterotrophic nitrification rate of oxidation of ammonia was 19.4 mg NH4-N removed/L,h.
The highest concentration of nitrite of 8 mg/L was determined after two hours of nitrification,
when all the NH4-N was converted to NO3-N and NO2-N (Figure 1) and the pH of the lowest
point is reached, known as "ammonium valley" (7, 6). This "valley ammonia" pH profile can
be used as an indicator of the end of nitrification - accumulation of nitrite. For a further three
hours of aeration nitrite is oxidized to nitrate, and the pH is slowly started to rise (7.8 and 7.9),
(Figure 2). It was observed a decrease of pH during nitrification due to reduced buffering
capacity as well as reaching the lowest value of pH in point of nitrification and dissolved
oxygen. These profiles of pH (decrease of pH during nitrification due to reduced buffering
capacity as well as reaching the lowest pH in point of nitrification) and dissolved oxygen
(oxidation of ammonia during the process of low dissolved oxygen concentrations and a
progressive increase in dissolved oxygen concentration when ammonia is almost completely
oxidized) during the removal process nitrogen described by other authors (Chang & Hao,
1996; Paul et al. 1998).
Experiment alternating nitrification/denitrification was carried out at an initial concentration
of NH4-N 70 mg/L NO3-N 4.9 mg/L and COD 205 mg O2/L, with the addition of NaAc in a
ratio C:N=1:1 (Figure 3 and 4). Oxy/anoxia conditions during the process of alternating
nitrification/denitrification maintained by the dynamics: 0.5 hours of anoxia conditions, one
hour of oxy conditions, 0.5 hours of anoxia conditions, then again oxy conditions. In the
experiment was added sodium acetate at a ratio of C:N= 1:1 as the source of the carbon for
denitrification. Oxy conditions are achieved airing content in the reactor (air intake) and
denitrification is carried out in conditions without ventilation (auto aeration) but stirring the
contents of the reactor (by using the mixer). In experiments is added municipal wastewater.
During the first 0.5 hours of anoxic conditions increases the pH and reduces the concentration
of organic substances, expressed as COD value (see Figures 3 and 4). During denitrification
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reduces the concentration of NO3-N and slightly decreases the concentration of NH4-N (see
Figures 3 and 4). The concentration of dissolved oxygen in the denitrification ranged was
from 1.9 ± 0.2 mg/L. After completing the first stage of denitrification (0.5 hours anoxia
conditions) the aeration is included and under the oxy conditions nitrification is carried out for
one hour. In doing so, it reduces the pH value with the accumulation of NO3-N and NO2-N.
Then follows the second denitrification, which caused a significant reduction in COD values.
And this follows the denitrification reduction of NO3-N and a slight decrease in residual NH4N (see Figures 3 and 4). Denitrification again accompanied by an increase in pH (Figure 3).
After finishing second denitrification, aeration was included and conducted the experiment
nitrification. Over the next two and half hours, a process of nitrification was through
accumulation of NO3-N and NO2-N in the first three and a half hours the process, followed
by further aeration oxidation of NO2-N to NO3-N. In these experiments of nitrification it was
observed a decrease in pH value, which achieved the lowest value in the point of nitritation,
after which the pH value increases slightly by the end of the process. COD value does not
change significantly during the process of nitrification. In the experiment of alternating
nitrification/denitrification, dissolved oxygen concentration is reached 2 mg O2/L during the
first half hour of anoxia conditions; 2.6 mg O2/L during the first hour of the oxy conditions
and 2.2 mg O2/L in the next half hour anoxia conditions. During the last phase of nitrification
in this experiment, there was a slight increase in the concentration of dissolved oxygen
(Figure 3). Rate of oxidation of ammonia in the experiment alternating
nitrification/denitrification is 11.95 NH4-N/L,h. Rate of accumulation of nitrate in the
experiment alternating nitrification/denitrification was 2.2 mg NO3-N/L,h during all phases of
the observed processes. The experiment of removing substances with nitrogen from municipal
wastewater was carried out with a previously prepared mixed microbial culture and municipal
wastewater. NH4-N concentration is reached 147 mg/L (see Figures 5 and 6). Complete
nitrification was achieve d for six hours. In this work the oxidation of the ammonia is
achieved for five hours, and to the accumulation of nitrate and nitrite. Extended aeration for
one hour nitrite is completely converted into nitrate. The rate of removal of ammonia was
28.82 mg NH4-N/L, h. The highest concentration of nitrite was 5.5 mg/L. In the fifth hour all
the NH4-N is converted to NO3-N and NO2-N. The concentration of dissolved oxygen in the
course of these experiments (Figure 5) shows a pronounced oxygen consumption during the
oxidation of NH4-N with accumulation and NO3-N and NO2-N. Shortly after graduating
nitritation (accumulation of nitrite) concentration of dissolved oxygen begins to grow until the
end of the experiment. After complete nitrification concentration of NO3-N amounted 11.1
mg/L The experiment was conducted under conditions of temperature 26±2. Concentration of
organic ingredients is expressed as COD value, and the speed of decomposition of organic
substances, expressed as COD value was 22.16 mg/L,h. Concentration of sludge dry matter
amounted to 3.5 g/L.
All previous nitrification processes were carried out under aerobic conditions. After nitrite
nitrogen completely oxidized, or after six hours passed into nitrate nitrogen, experiment was
set out to investigate the ability of microbial cultures for the implementation of denitrification.
Denitrification was carried out under anaerobic conditions, only stirring. Parameters were
monitored every three hours, and 24 hours. Dry matter was 3 g/L. The concentration of NH4N during denitrification process has not changed, and amounted to 0 mg/L. The concentration
of nitrite and nitrate is reduced during the process of denitrification. Nitrates are from the
initial 11.3 mg/L after 24 hours of completely oxidized to nitrogen gas. Dissolved oxygen is
consumed in the process of denitrification, and after 24 hours the dissolved oxygen
concentration was 0.7 mg/L. The process of denitrification, nitrate reduction, follow the
increase in pH. The pH of the initial value of 8.1 after 24 hours the process was 9.3. Speed
degradation of organic substances, expressed as COD value was 1.95 mg/L,h (see Figures 7
and 8).
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CONCLUSION
Based on the obtained results and conducting discussion may be adopted the following
conclusions:
Biological processes with activated sludge achieved very efficiently removal of
nitrogen from wastewater.
Wastewater investigated in this work is a municipal wastewater in which the
ingredients are organic biodegradable, as evidenced by the results of research.
The activated sludge from the WWTP (wastewater treatment plant), which is used
in research, with technique of accumulation nitrificants and denitrificants, was
prepared as a mixed microbial culture that has the ability to process simultaneous
nitrification and denitrification of nitrogen compounds in municipal wastewater.
Removal of nitrogen from wastewater is achieved by the process of denitrification,
where the process must ensure the existence of anoxic conditions. Many studies
have confirmed that controled nitrogen in the used water can be achieved in the
most efficient processes with a combined nitrification and denitrification
(Stefancic, 2003, Dong et al. 2006).
In the experiment of heterotrophic nitrification, with addition of sodium acetate as
an external carbon source at a ratio of 2:1 and a pH of 7.8, the rate of oxidation of
ammonia was 16.4 mg NH4-N removed/L,h.
Rate of oxidation ammonia in the experiment alternating nitrification/denitrification
amounted to 11.95 mg NH4-N/L,h.
Mixed culture has shown the ability for a higher degree of nitrification at higher pH
values from 7.7 to 8.8 and a temperature of 27-30°C in municipal wastewater in
which is presented ammonia nitrogen source.
REFERENCES
APHA (1998). Standard Methods for the Examination of Wastewater and Wastewater Treatment. 20. Edition
American Public Health Association. American Water Works Association and Water Pollution Control
Federation, Washington, D.C.
Gerardi, M. H. (2002). Nitrification and Denitrification in the Activated Sludge Process. New York: John Wiley
& Sons, Inc.
Henze, M., Harremoës, P., La Cour Jansen, J., Arvin, E. (2002). Wastewater Treatement. Biological and
Chemical Processes. 3. Ed. pp 89-108.
Jeyanayaga, S. (2005). True Confessions of the Biological Nutrient Removal Process. Florida Water Resources
Journal. pp 37-46.
Mesquita, D.P., Dias, O., Amaral, A.L., and Ferreira, E.C. (2009). Monitoring of activated sludge settling ability
through image analysis: validation on full-scale wastewater treatment plants. Bioprocess and Biosystems
Engineering Vol. 32 Issue 3, pp 361–367.
Metcalf & Eddy (2003). Wastewater Engineering - Treatment and Reuse. 4th edition. New York: McGraw-Hill.
pp 60, 749.
Wang, K. (2012). Enhanced Biological Nitrogen Removal by Increasing Wastewater Temperature in An
Activated Sludge System. Industrial Ecology, Royal Institute of Technology. Stocholm. pp 3–16.
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Title
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REMOVAL OF NITROGEN FROM MUNICIPAL WASTEWATER - THE EFFECT OF THE ADDITION OF CARBON SOURCES ON BIOLOGICAL DENITRIFICATION
Author
Author
IBRAHIMPAŠIĆ, Jasmina
TOROMANOVIĆ, Merima
LANDEKA DRAGIČEVIĆ, Tibela
Abstract
A summary of the resource.
In this work was used activated sludge from the WWTP (wastewater treatment plant), in which with technique accumulation nitrificants and denitrificants, were prepared mixed bacterial cultures which showed the ability nitrification of ammonia- nitrogen to nitrate, as well as the ability of denitrification of nitrate nitrogen to gaseous nitrogen in municipal wastewater. As carbon source in the process of biological denitrification was used sodium acetate, in the ratio C/N=1 and C/N=2. Activity of mixed microbial cultures for removal components with nitrogen was determined by measuring the concentration of organic matter, expressed as COD, ammonia-nitrogen, nitrite, nitrate, pH, concentration dissolved oxygen, and the concentration of microbial biomass. Keywords: municipal water, activated sludge, nitrogen removal
Publisher
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International Burch University
Date
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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
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https://omeka.ibu.edu.ba/files/original/fef42c0f2e365d343ab6b0407d044617.pdf
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DIAGNOSING SLEEP APNEA VIA FEATURE SELECTION ON SINGLE
CHANNEL ECG
Huseyin Guruler1, Abdullah Ferikoglu 2
1
Mugla Sitki Kocman University, Faculty of Technology, Department of Information Systems
Engineering, Mugla-Turkey
hguruler@mu.edu.tr
2
Sakarya University, Faculty of Technology, Department of Electrical & Electronics
Engineering, Sakarya-Turkey
af@sakarya.edu.tr
1
Corresponding Author
ABSTRACT
This article is based on a combination of time-frequency domain functions, and nonlinear
techniques in the analysis of heart rate variability (HRV) for diagnosing obstructive sleep
apnea (OSA) using only single-lead electrocardiography (ECG) signals. The contribution of
the presented study to earlier ones is that it enables numerically determining what type of
HRV features better represent the aforementioned target by using correlation matrices and
neural networks (NNs).
Keywords: Diagnosing disease, neural network, sleep apnea, heart rate variability, feature
selection, correlation matrices
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1. INTRODUCTION
Study on variations in the instantaneous heart rate (HR) time series using the beat-to-beat RR
intervals are known as HRV analysis. HR increases with sympathetic activity and decreases
with parasympathetic (vagal) activity. The balance between the effects of the sympathetic and
the parasympathetic systems, the two opposite acting branches of the autonomic nervous
system (ANS), is referred to as the sympathovagal balance (SB) (Acharya, Joseph, Kannathal,
Lim, & Suri, 2006).
Spectral analysis is typically used to estimate the effect of the sympathetic and
parasympathetic modulation of the RR intervals. The two main frequency bands of interest
are referred to as the low frequency (LF) band and the high frequency (HF) band.
Sympathetic tone is believed to influence the LF component, whereas both sympathetic and
parasympathetic activities have an effect on the HF component. The ratio of the power
contained in the LF and HF components has been used as a measure of the SB (Jos & Spaan,
2007).
OSA is a serious disorder caused by intermittent airway obstruction in sleep (Abdullah,
Maddage, Cosic, & Cvetkovic, 2010), (Lado, et al., 2009). OSA causes changes in cardiac
and neuronal activity and discontinuities in sleep pattern when observed via ECG and
electroencephalogram (EEG). OSA is usually diagnosed using polysomnography (PSG)
conducted in sleep laboratories (Roche, Celle, Pichot, Barthélémy, & Sforza, 2007). PSG is
utilized to define physiological sleep and its different stages, to assess sleep quality and to
diagnose many types of sleep disorders such as insomnia, OSA, restless legs syndrome and
periodic leg movement disorders. However, PSG is very expensive and the technology
requires not only the connection of various sensors and electrodes (e.g. EEG,
Electrooculogram (EOG) and Electromyogram (EMG), and ECG etc.) but also spending the
night in a bed (Yilmaz, Asyali, Arikan, Yetkin, & Ozgen, 2010).
Detection of OSA can be performed and significantly improved through HRV analysis, since
fluctuations of oxygen saturation in blood accompanied by apnea, cause variations in the HR
(Quiceno-Manrique, Alonso-Hernandez, Travieso-Gonzalez, Ferrer-Ballester, & CastellanosDominguez, 2009), (Al-Abed, Manry, Burk, Lucas, & Behbehani, 2009). SB has been used
for detection of OSA in many studies. The review (Penzel, et al., 2002), presents systematic
comparison of studies using different algorithms for OSA detection based on the same ECG
recordings (Moody, Mark, Goldberger, & Penzel, 2000). In these researches, HRV with or
without respiratory signals are generally analyzed in three main areas: Time, Frequency and
Non-linear Analysis. Each analysis technic produces some features, which are usually
numerical values. These values are used in decision-making algorithms or mathematical
models that may involve neural networks (NNs), support vector machines (SVMs), wavelet
etc. So far, many combinations of time, frequency and non-linear domain features of HRV
obtained from ECG have been used with different type of classification methods. Although
high accuracies of OSA detection and significant successes on apnea classification can be
achieved, it is still unclear which feature parameters are more effective for classification.
This study aims to classify pre-collected sleep data into one of the three basic types; apnea,
hypopnea, and healthy episodes, with fewer parameters obtained from single-lead ECG
recordings. Besides that, it determines numerically what features of HRV better represent the
classification.
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2. MATERIALS and METHODS
The present study uses a variety of significant and relevant characteristic features include
morphological information, duration and complexity details of the ECG to classification.
Table 1. summarize all the HRV measures.
Table 1. Summary of the HRV Measures
Nonlinear
Frequency
Time-Domain
Measures
RR
SDNN
HR
STD HR
RMSSD
NN50
pNN50
HRV
triangular
index
TINN
Peak frequencies
Absolute powers
Relative powers
Normalized
powers
SD1,
SD2
ApEn
SampEn
D2
DFA
Alfa 1
Alfa 2
RPA
Lmean
Lmax
REC
DET
ShanEn
Description
The mean of RR intervals
Standard deviation of RR intervals
The mean of HR
Standard deviation of instantaneous HR values
Square root of the mean squared differences between successive RR
intervals
Number of successive RR interval pairs that differ more than 50 ms
NN50 divided by the total number of RR intervals
The integral of the RR interval histogram divided by the height of the
histogramwidth of the RR interval histogram
Baseline
VLF, LF, and HF band peak frequencies
Absolute powers of VLF, LF, and HF bands
Relative powers of VLF, LF, and HF bands
Powers of LF and HF bands in normalized units
The standard deviation of the Poincare plot perpendicular to (SD1) and
along (SD2) the
line-of-identity
Approximate
entropy
Sample entropy
Correlation dimension
Detrended fluctuation analysis
Short term fluctuation slope
Long term fluctuation slope
Recurrence plot analysis
Mean line length
Maximum line length
Recurrence rate
Determinism
Shannon entropy
The feature sets obtained from analysis methods those are time-domain, frequency-domain
and non-linear methods. Time domain analysis involved statistical and geometrical
calculations. Frequency domain analysis was performed using fast Fourier transform (FFT)
and autoregressive (AR) modelings. Non-linear methods including Poincaré and recurrence
plots, approximate and sample entropies, detrended fluctuations and correlation dimensions
were used.
WFDB (WaveForm Databases) software package used for viewing, analyzing, and creating
recordings of physiologic signals. “Kubios HRV” software used for HRV analysis (Niskanen,
Tarvainen, Ranta-Aho, & Karjalainen, 2004). Matlab NN toolbox was used for classification.
Classification of OSA was realized on Apnea-ECG Database in PhysioBank (Penzel, Moody,
Mark, Goldberger, & Peter, 2000). Table 2 shows Demographic and Clinical Features of the
dataset. The data consists of 70 records, divided into learning and test sets equally. Learning
and test recordings involves three classes namely Apnea, Hypopnea, and Healthy depending
on apnea-hypopnea index (AHI) (Ruehland, et al., 2009).
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Table 2. Demographic and clinical features of apnea-ECG dataset
Subjects (n)
Age (years)
Males (n)
BMI (kg/m2)
Records (h)
AHI (e/h)
All subjects
70
45.6±10.6
57
28.1±6.5
8.2±0.5
-
Apnea
40
51.5±7.6
38
30.8±4.6
8.4±0.4
45.4±22.5
Hypopnea
10
47.2±5.9
8
30.4±9.2
8.0±0.6
12.1±12.0
Healthy
20
32.9±5.4
11
21.3±1.9
7.9±0.4
0.0±0.0
p-value
NS
p<0.01
NS
NS
p<0.01
Data are presented as mean ± SD or n; BMI: Body mass index; NS: no significant statistical difference
Depending of AHI: Apnea: Recordings with clear occurrence of sleep apnea (100 min or more). 40 recordings fulfilled this criterion.
Hypopnea: Recordings with some degree of sleep apnea (between 5 and 99 min). The recordings revealed either mild apnea, up to an
apnea index of 10 events per hour, or obstructive snoring in otherwise healthy subjects. 10 recordings fulfilled this criterion. Healthy:
Recordings of healthy subjects with neither sleep apnea (fewer than 5 min) nor habitual snoring. 20 recordings fulfilled this criterion.
Figure 1 describes the classification process.
Figure 1. OSA Classification Process
Feature extraction was realized on HRV by time, frequency and non-linear techniques. Due to
the feature extraction involves number of parameters having various degrees of importance
for classification, CMs were used to select the parameters, which are preferred for neural
networks (NNs) as an input. Better correlation provides better classification ability for NNs.
CMs are simply tables, in which correlation coefficients “see (1)” for every single column in
relation to target column take place.
(1)
Feed forward back propagation NNs can give high accuracy results with small number of
hidden layers. Hence, the classification process was realized with feed forward back
propagation NNs.
3. RESULTS
Table 3 and Figure 2 shows the classification and iteration results for 6 methods. Here, only
highly correlated parameters in each methods were noticed. CMs helps to find lower
correlated parameters, which could be eliminated by looking their correlation coefficients.
Methods 1 to 4 indicates classification ability of parameters belonging to each HRV analysis
method individually. Methods 5 and 6, on the other hand, involves mixed parameters from
methods 1 to 4. Method 6 use only high correlated parameters in its groups.
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Table 3. Classification results
Classes
1
Method
Accuracy
Iterations
2
Method
Accuracy
Iterations
3
Method
Accuracy
Iterations
4
Method
Accuracy
Iterations
5
Method
Accuracy
Iterations
6
Method
Accuracy
Iterations
A, B, C
(A+B), C
Temporal parameters
0.63
0.85
100
60
FFT spectral parameters
0.78
0.93
500
300
AR spectral parameters
0.78
0.93
300
70
Non-Linear parameters
0.72
0.96
400
100
All parameters from 1 to 4 methods
0.78
0.96
600
50
High correlated parameters from 1 to 4 methods
0.82
0.96
600
30
*
Three Classes are A, B, C and two classes are (A+B), C (A:Apnea B:Hypopnea C:Healthy)
Classification Accuracy
Iterations
Figure 2. Classification and Iteration Results
Series 1 the results for two classes (A+B) and C, Series 2 the results for three classes A, B and C
Accuracy was high using the parameters of non-linear, frequency and time domain respectively. The accuracy was
found 96.42% for the classification to A and C (A- Apnea C- Healthy) and 82% for the classification to A, B and C (AApnea B- Hypopnea C- Healthy) respectively. When certain parameters selected only higher correlated from 1 to 4
methods, highest accuracy observed with minimum iteration numbers using NNs.
4. CONCLUSIONS
This work offers a method for feature selection and regularization of classifier parameters that
were used to optimize classifier performance. The accuracy of the results with the dimension
reduction on the feature sets clearly shows that correlation matrices can be focused on
minimizing the feature sets used for sleep classification. Classification performance was
highest with non-linear equations and lowest with time domain features, with frequency
features at midpoint on OSA diagnosis. On the other hand, computational works were in
opposite direction in terms of iterations, which required to obtain reasonable results on NN
structures.
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5. ACKNOWLEDGMENTS
We would like to acknowledge the funding support for this project from The Scientific and
Technological Research Council of Turkey (TÜBİTAK), (2214) International Research
Fellowship Program, December 2010-December 2011.
6. REFERENCES
Abdullah, H., Maddage, N. C., Cosic, I., & Cvetkovic, D. (2010). Cross-correlation of EEG frequency bands and
heart rate variability for sleep apnoea classification. Medical & biological engineering & computing, 48(12),
1261-1269.
Acharya, U. R., Joseph, K. P., Kannathal, N., Lim, C. M., & Suri, J. S. (2006). Heart rate variability: A review.
Medical and Biological Engineering and Computing, 44(1), 1031-1051.
Al-Abed, M. A., Manry, M., Burk, J. R., Lucas, E. A., & Behbehani, K. (2009). Sleep disordered breathing
detection using heart rate variability and R-peak envelope spectrogram. IEEE Engineering in Medicine and
Biology Society, EMBC 2009, (pp. 7106-7109).
Jos, S. M., & Spaan, A. E. (2007). Advances in Cardiac Signal Processing. Berlin Heidelberg: Springer-Verlag.
Lado, M. J., Vila, X. A., Rodriguez-Linares, L., Mendez, A. J., Olivieri, D. N., & Felix, P. (2009). Detecting
Sleep Apnea by Heart Rate Variability Analysis: Assessing the Validity of Databases and Algorithms. Journal of
medical systems, 35(4), 473-481.
Moody, G. B., Mark, R. G., Goldberger, A. L., & Penzel, T. (2000). Stimulating rapid research advances via
focused competition: the computers in cardiology challenge 2000. IEEE Computers in Cardiology 2000, (pp.
207-210). Cambridge, MA, USA.
Niskanen, J. P., Tarvainen, M. P., Ranta-Aho, P. O., & Karjalainen, P. A. (2004). Software for advanced HRV
analysis. Computer methods and programs in biomedicine, 76(1), 73-81.
Penzel, T., McNames, J., Murray, A., de Chazal, P., Moody, G., & Raymond, B. (2002). Systematic comparison
of different algorithms for apnoea detection based on electrocardiogram recordings. Medical and Biological
Engineering and Computing, 40(4), 402-407.
Penzel, T., Moody, G. B., Mark, R. G., Goldberger, A. L., & Peter, J. H. (2000). Apnea-ECG database. IEEE
Computers in Cardiology 2000, (pp. 255-258). Cambridge, MA, USA.
Quiceno-Manrique, A. F., Alonso-Hernandez, J. B., Travieso-Gonzalez, C. M., Ferrer-Ballester, M. A., &
Castellanos-Dominguez, G. (2009). Detection of obstructive sleep apnea in ECG recordings using timefrequency distributions and dynamic features. IEEE Engineering in Medicine and Biology Society, EMBC 2009,
(pp. 5559-5562).
Roche, F., Celle, S., Pichot, V., Barthélémy, C., & Sforza, E. (2007). Analysis of the interbeat interval increment
to detect obstructive sleep apnoea/hypopnoea. European Respiratory Journal, 29(6), 1206-1211.
Ruehland, W. R., Rochford, P. D., O'Donoghue, F. J., Pierce, R. J., Singh, P., & Thornton, A. T. (2009). The
new AASM criteria for scoring hypopneas: impact on the apnea hypopnea index. Sleep, 32(2), 150-157.
Yilmaz, B., Asyali, M. H., Arikan, E., Yetkin, S., & Ozgen, F. (2010). Sleep stage and obstructive apneaic epoch
classification using single-lead ECG. Biomedical engineering online, 9, 39.
Huseyin Guruler is academic staff in the Department of Information Systems Engineering in
Mugla Sitki Kocman University, Turkey. His bachelor's degree is in the field of electronics
and computer from Marmara University. MSc is in the field of statistics and computer in
Mugla Sitki Kocman University. PhD is in the field of electronics and computer in Sakarya
University. PhD thesis is about diagnosing sleep apnea using ECG signals. His research
interests merge in data mining and knowledge discovery besides dealing with computational
biology and multi-user computers architecture.
164 | P a g e
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Title
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DIAGNOSING SLEEP APNEA VIA FEATURE SELECTION ON SINGLE CHANNEL ECG
Author
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GURULER, Huseyin
FERIKOGLU, Abdullah
Abstract
A summary of the resource.
This article is based on a combination of time-frequency domain functions, and nonlinear techniques in the analysis of heart rate variability (HRV) for diagnosing obstructive sleep apnea (OSA) using only single-lead electrocardiography (ECG) signals. The contribution of the presented study to earlier ones is that it enables numerically determining what type of HRV features better represent the aforementioned target by using correlation matrices and neural networks (NNs). Keywords: Diagnosing disease, neural network, sleep apnea, heart rate variability, feature selection, correlation matrices
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International Burch University
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2014-05-15
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ISSN 978-9958-834-36-3
Q Science (General),QH301 Biology,QH426 Genetics
-
https://omeka.ibu.edu.ba/files/original/5db2b35e0acf5a572566d74cb85a975c.pdf
356cf588575d8deb79b4bc7349b4a620
PDF Text
Text
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RETROTRANSPOSON BASED MARKERS AND THEIR APPLICATIONS
IN BARLEY (Hordeum vulgare L.cvs.) TISSUE CULTURE
Nermin Gozukirmizi
Istanbul University, Department of Molecular Biology and Genetics, 34134 Vezneciler,
Istanbul/Turkey
E-mail: nermin@istanbul.edu.tr
Abstract
Barley has economical value and it is an important model plant. Transposons cover more than
80% of barley genome. More than 40 retrotransposons were characterized in barley genome.
This type of transposons replicate via RNA and move in the genome. As a result of these
movements, mutations and genome enlargements are occurred. During the recent years, active
transcripts and protein products of some retrotransposons have been determined. Somaclonal
variations are spontaneously occurred variations in tissue culture conditions. These variations
could be produced by genetic and/or epigenetic mechanisms and result in problems in gen
transfer applications. We investigated the retrotransposon movements in barley tissue culture
and regenerated plantlets using inter retrotransposon amplified polymorphism (IRAP), inter
primer binding side (iPBS) and analytical techniques (DNA and RNA levels) and determined
the relationship between retrotransposon movements, changes in copy number and
differention in culture conditions. For these purposes BARE1, NIKITA, BAGY2 and
SUKKULA retrotransposons were analyzed. Our research results show that tissue culture
conditions and time increase the transposon based variation and copy numbers of
retrotransposons and thus, cause genome enlargements. This research will be contribute the
understanding of basic mechanisms related to plant development and differentiation in
cultured material and also restriction of variations in applications.
Keywords: Barley, Tissue Culture, Retrotransposon markers, Somaclonal variation
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1. Introduction
Hordeum vulgare L. (barley) is an important cereal crop and is also an excellent model
organism for biochemists, physiologists, geneticists and molecular biologists. In addition,
barley provides a reference to the genomes of other Triticeae crops such as wheat, rye and
some forage grasses. H. vulgare cvs. have been used as a model system for more than 40
years at the Istanbul University Molecular Biology and Genetics (former Biology)
Department. The first studies on experimental mutagenesis were followed by tissue culture,
gene transfers, DNA marker applications, DNA arrays finally epigenetic studies which,
progressed further after the 1990 - 2005 when collaboration was established with the Plant
Biotechnology group at the TUBITAK Research Institute for Genetic Engineering and
Biotechnology in Gebze, Kocaeli-Turkey (Gozukirmizi, 2003). Since 2011, we focused on the
roles of retrotransposons on tissue culture grown barley material since transposons cover
more than 80% of the barley genome. More than 40 retrotransposons were characterized in
barley genome (http://www.ncbi.nlm.nih.gov/). These types of transposons replicate via RNA
and move in the genome. As a result of these movements, mutations and genome
enlargements occur. Recently, active transcripts and protein products of some
retrotransposons were determined. They use an RNA intermediate mechanism for
transposition. Because of their copy–paste transposition, they cause genome expansion
(Shirasu, Schulman, Lahaye, & Schulze-Lefert, 2000; Vitte & Panaud, 2005; Grzebelus,
2006). Considering their transposition mechanism and structure, they are thought to resemble
retroviruses (Kalendar, Tanskanen, Immonen, Nevo, & Schulman, 2000; Sabot & Schulman,
2006; Sabot et al., 2006). Their new copies can insert themselves into near or within genes in
a head-to-head, tail-to-tail or head-to-tail orientation.
Therefore, they can cause altered gene products, frame-shift mutations, reduction of
transcription level or even silencing of genes (Fedoroff, 2000). Due to their dynamic feature,
they are accepted as an important reason for genome evolution and speciation (Bento et al.,
2008). Since retrotransposon insertions are irreversible, they are considered useful genetic
elements in phylogenetic studies (Kumar, Gupta, Misra, Modi, & Pandey, 2009). Due to their
variation capacity between species, retrotransposons are usually studied for detection of
genetic relationships between varieties and related species (Waugh et al., 1997; Alavi-Kia,
Mohammadi, Aharizad, & Moghaddam, 2008; Baumel, Ainouche, Kalendar, & Schulman,
2002; Saeidi, Rahiminejad, & Heslop-Harrison, 2008; Belyayev et al., 2010; Smykal et al.,
2011;). Our group has mainly been working on BARE1 (Evrensel, Yilmaz, Temel, &
Gozukirmizi, 2011), BAGY2 (Yilmaz, Marakli, & Gozukirmizi, 2014), NIKITA (Bayram,
Yilmaz, Hamat-Mecbur, Kartal-Alacam, & Gozukirmizi, 2012) and SUKKULA (KartalAlacam, Yilmaz, Marakli, & Gozukirmizi, 2014, in press) retrotransposon insertion patterns
in barley calli and regenerated shoots with retrotransposon-based marker techniques (IRAP
and iPBS) to determine the effect of retrotransposon movements in somaclonal variations.
This presentation outlines the results of retrotransposon research in barley tissue culture with
the intention of contributing to barley-breeding programmes with recent biotechnological
techniques.
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2. Materials and Methods
2.1. Tissue Culture and Plantlet Regeneration
Mature embryos were excised from seeds after surface sterilization as described previously.
Basal salts of Murashige and Skoog (MS) (Murashige & Skoog, 1962) were supplemented
with 3% (w/v) sucrose, 1ml of MS vitamin mixture and 0.9% agar supplemented with 4 mg/L
dicamba with a pH of 5.7. All cultures were kept in a growth chamber with standard
conditions [25± oC, 16/8-h day/night photoperiod with fluorescent lights at 7000 lux] and was
maintained on the same medium for different period of time. After different cultivation times,
each callus was cut into three pieces and each piece was numbered with the starting embryo’s
number. One of the callus pieces was used for genomic DNA isolation, the second for shoot
regeneration in MS medium supplemented with 0.5 mg/L zeatin, and the third was
subcultured under the same callus culture conditions for aging. One of the pieces was used for
shoot regeneration and the other for DNA isolation. At the end of the tissue culture, we
obtained four experimental plant materials (calli with different aging times and their
regenerated shoots) from one embryo; these were considered a single group. IRAP was
performed with three different groups. Genomic DNA was isolated from those three groups
and three control groups using Tri Reagent (Sigma T9424) according to the manufacturer’s
instructions. The control groups consisted of noncultured mature embryos.
2.2. IRAP
IRAP was performed with forward and reverse primers designed for LTR sequences of
BARE1 (Yilmaz & Gozukirmizi, 2013) and BAGY2 (Yilmaz et al., 2014) retrotransposon.
Amplification was carried out in a 20 μL reaction volume containing 3.5 μL nuclease-free
dH2O, 0.5 μL dNTP mixture (10 mM), 2 μL of each primer (10 nmol/μL), 2 μL template
genomic DNA (10 ng/μL), and 10 μL 2× Sapphire enzyme mix. PCR conditions were an
initial denaturation step at 94°C for 3 min; followed by 30 cycles at 94°C for 20 s, 52°C for
20 s, and 72°C for 2 min; and a final extension step at 72°C for 10 min.
2.3. Evaluation of PCR Products
PCR products were loaded to 6% non-denature polyacrylamide gel (29:1 Acrylamide:Bis) and
gel was run at 200 V for 4 h in 1X TBE buffer. A molecular weight marker (GeneRuler™ 1
kb DNA Ladder, SM0312, Fermentas) was also loaded to determine the size of amplicons.
Gel was stained and photographed on a UV transilluminator. Well-resolved bands were
scored with a binary value, (1) for presence and (0) for absence. The binary matrix (1/0) was
used to calculate the similarity between embryo, 40 and 80 day-old calli. Jaccard’s similarity
index was calculated using the formula: NAB / (NAB + NB + NA); where NAB is the number of
bands shared by 2 samples, NA represents amplified fragments in sample A, and NB represents
amplified fragments in sample B (Jaccard, 1908).
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3. Results and Discussion
Our results showed that calli which have different culturing time can have different IRAP
band patterns although they originated from the same embryo (Figure 1).
Figure 1. IRAP profiles for BARE1. 1-3; mature embryo (control), 4-9; first group [4, 5, 6;
calli originated from the same embryo (30, 60, 90 day-old respectively), and 7, 8, 9;
regenerated shoot originated from these calli respectively)], 10-15; second group [10, 11, 12;
calli originated from another embryo (30, 60, 90 day-old respectively), and 13, 14, 15;
regenerated shoot originated from the second group’s calli)]. Arrows indicate the polymorphic
bands (Yilmaz & Gozukirmizi, 2013).
We also performed studies on NIKITA and SUKKULA retrotransposons on aging calli
materials (Bayram et al., 2012; Kartal-Alacam et al., 2014). We were able to observe
polymorphisms in cultured materials. Finally, we studied BAGY2 retrotransposon (Figure 2).
We observed that BARE1 and BAGY2 are the most active retrotransposons (with
polymorphism rates; up to 25% and 20% respectively) during callus culture (Evrensel et al.,
2011, Yilmaz et al., 2014). We also observed NIKITA polymorphisms at different ages in old
barley calli but the polymorphism rates were lower than BARE1 and BAGY2 (Bayram et al.,
2012).
Figure 2. IRAP profiles of calli and shoots for BAGY2. 1, non-cultured embryo; 2-13, tissue
culture materials (2, 6, 10 45-days-old calli; 3, 7, 11 shoots regenerated from 45-days-old calli;
4, 8, 12 90-days-old calli; 5, 9, 13 shoots regenerated from 90-days-old calli) (Yilmaz et al.,
2014).
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In addition to retrotransposon-based marker techniques, we also analyzed the copy number
alterations of BAGY2 internal domains (GAG, PR, RT, RH, INT) by real-time PCR (qPCR).
qPCR results proved that all internal domains have copy number variations between different
aged calli (Yilmaz et al., 2014). These findings show that tissue culture conditions and
culturing time cause insertional activation of some barley retrotransposons.
These findings may prove that tissue culture conditions and duration of cultivation period do
not cause the same effect on calli. This research will contribute to the understanding
of scientific mechanisms related to plant development and differentiation and also restriction
of variations in applications (Evrensel et al., 2011; Bayram et al., 2012; Yilmaz &
Gozukirmizi, 2013; Yilmaz et al., 2014; Kartal-Alacam et al., 2014).
Hirochika (1993) published one of the pioneer studies showing transposon activity changes in
tobacco protoplast culture. Afterward many studies were published for tissue culture effect on
transposon activations. Liu et al. (2004) demonstrated that Tos17 retrotransposon has been
activated during rice tissue culture. Somaclonal variations were also studied at banana by
IRAP technique (Muhammad & Othman 2005). Retrotransposon-derived polymorphisms
were also reported at tissue culture of a wild barley species (Hordeum brevisubulatum) by
various marker systems (Li et al., 2007). Campbell et al. (2011) also showed that BARE1
retrotransposon was activated in barley tissue culture.
We need more detailed studies on transposons, and their effects on epigenetic and genetic
mechanisms. Our data will be helpful for the understanding of their behavior during tissue
culture. We briefly conclude that barley retrotransposons, both autonomous and nonautonomous, are very active during tissue culture procedure and we still do not have an
opinion if these movements are randomly or partly directed according to the cultural
development of the plants.
4. References
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phylogenetic relationships in Crocus genus of Iran using inter-retrotransposon amplified polymorphism.
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Baumel, A., Ainouche, M., Kalendar, R., & Schulman, A.H. (2002). Retrotransposons and genomic stability in
populations of the young allopolyploid species Spartina anglica C.E. Hubbard (Poaceae). Molecular Biology
and Evolution, 19(8), 1218-1227.
Bayram, E., Yilmaz, S., Hamat-Mecbur, H., Kartal-Alacam, G. & Gozukirmizi, N. (2012). Nikita
retrotransposon movements in callus cultures of barley (Hordeum vulgare L.). Plant Omics, 5, 211-215.
Belyayev, A., Kalendar, R., Brodsky, L., Nevo, E., Schulman, A.H. & Raskina, O. (2010). Transposable
elements in a marginal plant population: temporal fluctuations provide new insights into genome evolution of
wild diploid wheat. Mobile DNA, 1, 1-16.
Bento, M., Pereira, H. S., Rocheta, M., Gustafson, P., Viegas, W., & Silva, M. (2008). Polyploidization as a
retraction force in plant genome evolution: Sequence rearrangements in Triticale. PLoS One, 3, 1-11.
Campbell, B. C., LeMare, S., Piperidis, G., & Godwin, I. D. (2011). IRAP, a retrotransposon-based marker
system for the detection of somaclonal variation in barley. Molecular Breeding, 27, 193-206.
Evrensel, C., Yilmaz, S., Temel, A., & Gozukirmizi, N. (2011). Variations in BARE-1 insertion patterns in barley
callus cultures. Genetics and Molecular Biology Research, 10, 980-987.
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Fedoroff, N. (2000). Transposons and genome evolution in plants. Proceedings of the National Academy of
Sciences of the United States of America, 97(13), 7002-7007.
Gozukirmizi, N. (2003). Pioneering biotechnological works on Hordeum vulgare L. cvs performed in
collaboration with the Istanbul University Biology Department and the TUBITAK Research Institute for Genetic
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Grzebelus, D. (2006). Transposon insertion polymorphism as a new source of molecular markers. Journal of
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Hirochika, H. (1993). Activation of tobacco retrotransposons during tissue culture. The EMBO Journal, 12,
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Jaccard, P. (1908). Nouvelles recherches sur la distribution florale. Bulletin de la Societe Vaudoise des Sciences
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Kalendar, R., Tanskanen, J., Immonen, S., Nevo, E., & Schulman, A.H. (2000). Genome evolution of wild
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divergence. Proceedings of the National Academy of Sciences of the United States of America, 97, 6603-6607.
Kartal-Alacam, G., Yilmaz, S., Marakli, S., & Gozukirmizi, N. (2014). Sukkula retrotransposon insertion
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Liu, Z. L., Han, F. P., Tan, M., Shan, X. H., Dong, Y. Z., Wang, X. Z., Fedak, G., Hao, S., & Liu, B. (2004).
Activation of a rice endogenous retrotransposon Tos17 in tissue culture is accompanied by cytosine
demethylation and causes heritable alteration in methylation pattern of flanking genomic regions. Theoretical
and Applied Genetics, 109, 200–209.
Muhammad, A. J., & Othman, R. Y. (2005). Characterization of Fusarium wilt-resistant and Fusarium wiltsusceptible somaclones of banana cultivar rastali (Musa AAB) by random amplified polymorphic DNA and
retrotransposon markers. Plant Molecular Biology Reporter, 23, 241-249.
Murashige, T. & Skoog, F. (1962). A revised medium for rapid growth and bio assays with tobacco tissue
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metaparasites and agents of genome evolution. Israel Journal of Ecology & Evolution, 52, 319-330.
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Saeidi, H., Rahiminejad, M. R., & Heslop-Harrison, J. S. (2008). Retroelement insertional polymorphisms,
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sequence provides evidence for reversible genome expansion. Genome Research, 10, 908-915.
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Genetic diversity of cultivated flax (Linum usitatissimum L.) germplasm assessed by retrotransposonbased markers. Theoretical and Applied Genetics, 122(7), 1385-1397.
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Waugh, R., McLean, K., Flavell, A. J., Pearce, S. R., Kumar, A., Thomas, B. B., & Powell, W. (1997). Genetic
distribution of Bare-1-like retrotransposable elements in the barley genome revealed by sequence-specific
amplification polymorphisms (S-SAP). Molecular and General Genetics, 253(6), 687-694.
Vitte, C., & Panaud, O. (2005). LTR retrotransposons and flowering plant genome size: emergence of the
increase/decrease model. Cytogenetic and Genome Research, 110, 91-107.
Yilmaz, S., & Gozukirmizi, N. (2013). Variation of retrotransposon movement in callus culture and regenerated
shoots of barley. Biotechnology and Biotechnological Equipment, 27, 4227-4230.
Yilmaz, S., Marakli, S., & Gozukirmizi, N. (2014). BAGY2 retrotransposon analyses in barley calli cultures and
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Prof.Dr. Nermin Gozukirmizi is a scientist from Istanbul University, Molecular Biology and
Genetics Department, Istanbul-Turkey. She took part for Establishment of Plant
Biotechnology Research Unit at Marmara Research Centre, Research Institute of Genetic
Engineering and Biotechnology, 1992-2006. She also had an active role for the establishment
of Molecular Biology and Genetics Department at Istanbul University. Her areas of research
include molecular biology, tissue culture and gene transfers, somatic variations, GMO and
biotechnology. She is an author or co-author of numerous scientific papers and several boks.
Her recent internationally published scientific papers are related to retrotransposons, gene
transfers and salt tolerance.
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Title
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RETROTRANSPOSON BASED MARKERS AND THEIR APPLICATIONS IN BARLEY (Hordeum vulgare L.cvs.) TISSUE CULTURE
Author
Author
GOZUKIRMIZI, Nermin
Abstract
A summary of the resource.
Barley has economical value and it is an important model plant. Transposons cover more than 80% of barley genome. More than 40 retrotransposons were characterized in barley genome. This type of transposons replicate via RNA and move in the genome. As a result of these movements, mutations and genome enlargements are occurred. During the recent years, active transcripts and protein products of some retrotransposons have been determined. Somaclonal variations are spontaneously occurred variations in tissue culture conditions. These variations could be produced by genetic and/or epigenetic mechanisms and result in problems in gen transfer applications. We investigated the retrotransposon movements in barley tissue culture and regenerated plantlets using inter retrotransposon amplified polymorphism (IRAP), inter primer binding side (iPBS) and analytical techniques (DNA and RNA levels) and determined the relationship between retrotransposon movements, changes in copy number and differention in culture conditions. For these purposes BARE1, NIKITA, BAGY2 and SUKKULA retrotransposons were analyzed. Our research results show that tissue culture conditions and time increase the transposon based variation and copy numbers of retrotransposons and thus, cause genome enlargements. This research will be contribute the understanding of basic mechanisms related to plant development and differentiation in cultured material and also restriction of variations in applications. Keywords: Barley, Tissue Culture, Retrotransposon markers, Somaclonal variation
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International Burch University
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2014-05-15
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ISSN 978-9958-834-36-3
Q Science (General),QH301 Biology,QH426 Genetics
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https://omeka.ibu.edu.ba/files/original/ef1c94fb2cf3124a1f10e538eeab8b18.pdf
b80bc04b43e184d7d7e81c2b01a2b315
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Text
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CAN CONCRETE BE GREEN IN BOSNIA AND HERZEGOVINA?
Sanin Džidić
International BURCH University Sarajevo
Faculty of Engineering and Information Technologies
Department of Architecture
Francuske revolucije bb, 71210 Ilidža, Sarajevo
e-mail: sanin.dzidic@ibu.edu.ba
SUMMARY
Bosnia and Herzegovina ratified the United Nations Framework Convention on Climate
Change (UNFCCC) on May 17, 2000. The Kyoto Protocol was signed and ratified by the
governments of 192 states and territories in the world. The Kyoto Protocol was ratified by
Bosnia and Herzegovina on April 22, 2007, after completion of ratification procedures of all
government levels. The First National Report of Bosnia and Herzegovina in accordance to the
UNFCCC was issued in 2009 and the Second National Report of Bosnia and Herzegovina in
accordance to the UNFCCC was adopted by B&H Council of Ministers in July 2013. The
main goal of the Kyoto Protocol is to reduce greenhouse gas emissions to environment what
caused many to focus on CO2 emissions as the most critical environment impact indicator.
Concrete is by far the most widely used construction material worldwide. One of its major
components is Portland cement as a binder. Total production of cement in Bosnia and
Herzegovina is about 850,000 tons in 2012, while fresh concrete production and concrete
products amount approximately to 1,300,000 tons in 2012. Taking in consideration that
production of every ton of cement yields to approximately 0.9 tons of CO2 and every cubic
meter of concrete contains about ten percent by weight of cement, significant quantity of CO2
is produced by cement industry in Bosnia and Herzegovina. It is estimation in 2001, that
cement industry emissions of CO2 represented around 4 percent of total CO2 emissions by
energy and industry in Bosnia and Herzegovina. However, substituting significant amounts of
cement in concrete mixture with industrial by-products such as silica fume, fly ash and blast
furnace slag also leads to minimization of cement consumption, even producing more durable
concrete. This paper discuss possibilities in decreasing CO2 emissions in cement and concrete
industry, as well as necessity of following directions of green and sustainable building in
Bosnia and Herzegovina.
Key Words: CO2 emission, cement, concrete, green buildings
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Introduction
The essence of the Kyoto Protocol invites nations to commit themselves in reducing
greenhouse gas (GHG) emissions. The Kyoto Protocol was adopted in Kyoto, Japan,
December 11, 1997, but enacted or enforced on February 16, 2005. The goal of this protocol
is to cope with the adverse effects of climate change, or global warming. The UNFCCC
(United Nations Framework Convention on Climate Change), states the goal of the Kyoto
Protocol is "stabilization of greenhouse gas concentrations in the atmosphere at a level that
would prevent dangerous anthropogenic interference with the climate system."
Many countries have agreed to legally bind limitations/reductions in their emissions of
greenhouse gases, as part of the Kyoto Protocol. These binding limitations/reductions are tight
in two commitments periods. The first commitment period is related to emissions between
2008-2012, and the second commitment period for emissions between 2013-2020.
The Kyoto Protocol considers emissions of six greenhouse gases:
carbon dioxide (CO2);
methane (CH4);
nitrous oxide (N2O);
hydrofluorocarbons (HFCs);
perfluorocarbons (PFCs);
sulphur hexafluoride (SF6).
There are 192 parties committed to the Kyoto Protocol. This includes 191 states (all the UN
members except Andorra, Canada, South Sudan and the United States) and the European
Union. The United States signed but did not ratify the Protocol. Canada withdrew from
Protocol in 2011.
Figure 1 – Kyoto Protocol Participation
The Kyoto Protocol was ratified by Bosnia and Herzegovina on April 22, 2007, after
completion of ratification procedures of all government levels. The First National Report of
Bosnia and Herzegovina in accordance to the UNFCCC was issued in 2009 and the Second
National Report of Bosnia and Herzegovina in accordance to the UNFCCC was adopted by
B&H Council of Ministers in July 2013.
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New Construction Paradigm
Construction industry is important part of the economy of each country. The old paradigm of
construction took in consideration costs, schedule and quality. This paradigm was often
presented as a triangle or a pyramid with cost supported by schedule and quality in each angle.
This was very well known to each construction or project manager. There was attention in
achieving the desired quality in a scheduled period of time for a minimal particular cost. New
principles of green and sustainable approach to all aspects of human life introduced
modifications of this paradigm in construction sector too. The Paradigm has changed and
become much more comprehensive.
Figure 2 – New Construction Paradigm
The new paradigm involves additional factors beyond above mentioned. The decision making
model in designing a project in order to achieve sustainability requires the balance of the old
factors, plus human health, safety and comfort as it relates to the environment. Instead of a
triangle or pyramid shape, depicting the decision model, the shape of the decision making
model for sustainability construction looks like much more comprehensive.
The new EU Construction Products Regulation (CPR 305/2011/EU), published by the
European Parliament on March 9, 2011, completely replaced the Construction Products
Directive (CPD 89/106/EEC) officially on July 1, 2013 and took in consideration this new
approach. In its definitions, CPR 305/2011/EU defines construction product as any product or
kit which is produced and placed on the market for incorporation in a permanent manner in
construction works or parts thereof and the performance of which has an effect on the
performance of the construction works with respect to the basic requirements for construction
works. “Kit” means a construction product placed on the market by a single manufacturer as
a set of at least two separate components that need to be put together to be incorporated in the
construction works. CPR 305/2011/EU defines term “construction works” buildings and civil
engineering works.
According to the CPR 305/2011/EU ANNEX I - Basic Requirements for Construction Works,
Construction works as a whole and in their separate parts must be fit for their intended use,
taking into account in particular the health and safety of persons involved throughout the life
cycle of the works. Subject to normal maintenance, construction works must satisfy these
basic requirements for construction works for an economically reasonable working life as
follows:
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1. Mechanical resistance and stability
The construction works must be designed and built in such a way that the loadings that are
liable to act on them during their constructions and use will not lead to any of the following:
collapse of the whole or part of the work;
major deformations to an inadmissible degree;
damage to other parts of the construction works or to fittings or installed equipment as
a result of major deformation of the load-bearing construction;
damage by an event to an extent disproportionate to the original cause.
2. Safety in case of fire
The construction works must be designed and built in such a way that in the event of an
outbreak of fire:
the load-bearing capacity of the construction can be assumed for a specific period of
time;
the generation and spread of fire and smoke within the construction works are limited;
the spread of fire to neighboring construction works is limited;
occupants can leave the construction works or be rescued by other means;
the safety of rescue teams is taken into consideration.
3. Hygiene, health and the environment
The construction works must be designed and built in such a way that they will, throughout
their life cycle, not be a threat to the hygiene or health and safety of workers, occupants or
neighbors, nor have an exceedingly high impact, over their entire life cycle, on the
environmental quality or on the climate during their construction, use and demolition, in
particular as a result of any of the following:
the giving-off of toxic gas;
the emissions of dangerous substances, volatile organic compounds (VOC),
greenhouse gases or dangerous particles into indoor or outdoor air;
the emission of dangerous radiation;
the release of dangerous substances into ground water, marine waters, surface waters
or soil;
the release of dangerous substances into drinking water or substances which have an
otherwise negative impact on drinking water;
faulty discharge of waste water, emission of flue gases or faulty disposal of solid or
liquid waste;
dampness in parts of the construction works or on surfaces within the construction
works.
4. Safety and accessibility in use
The construction works must be designed and built in such a way that they do not present
unacceptable risks of accidents or damage in service or in operation such as slipping, falling,
collision, burns, electrocution, injury from explosion and burglaries. In particular,
construction works must be designed and built taking into consideration accessibility and use
for disabled persons.
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5. Protection against noise
The construction works must be designed and built in such a way that noise perceived by the
occupants or people nearby is kept to a level that will not threaten their health and will allow
them to sleep, rest and work in satisfactory conditions.
6. Energy economy and heat retention
The construction works and their heating, cooling, lighting and ventilation installations must
be designed and built in such a way that the amount of energy they require in use shall be low,
when account is taken of the occupants and of the climatic conditions of the location.
Construction works must also be energy-efficient, using as little energy as possible during
their construction and dismantling.
7. Sustainable use of natural resources
The construction works must be designed, built and demolished in such a way that the use of
natural resources is sustainable and in particular ensure the following:
reuse or recyclability of the construction works, their materials and parts after
demolition;
durability of the construction works;
use of environmentally compatible raw and secondary materials in the construction
works.
While the parties will ultimately always consider the cost of the design in construction, they
now have to take into account the human factors as well as the environment and how the
ecology of the design relates to the overall environment.
Engineers and architects have choices of the material and products they use to design projects.
Considering structure, the typical choice is among concrete, steel and wood. For roads and
highways, the choice is generally between concrete and asphalt. Choice of the material
depends on many factors including cost, characteristics, maintenance and performance for
specific application. Today, engineers and architects are motivated more than ever before to
select materials that are more sustainable due to increased interest in sustainable development.
Discussing the term green building technology, it considers structures that are environmental
friendly and resource-efficient throughout a building service life, from design to construction.
Green approach to design of buildings assumes reducing overall impact on the natural
environment by efficient use of energy, water and other resources as well as reducing waste,
pollution and environmental degradation.
Right now it is assumed that about thirty percent of total CO2 emissions in the world belong
to the human activities related to the construction sector. The Tables 1 and 2 show total CO2
emissions per sectors in twenty-seven EU countries in period 1990-2007.
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Table 1 - CO2 emissions by sector in EU 27 in millions of tones
3.
Concrete and Cement
Concrete is by far the most widely used construction material worldwide. In this regard,
sustainable development of concrete and concrete design needs to be foundation of all
construction activity in this millennium. For concrete production, the billions of tons of
natural materials have been mined and processed worldwide and leave substantial mark on the
environment. However, the most damaging aspect to the environment is huge quantity of
energy used for production of Portland cement. In this process, large quantities of CO2 are
also released into atmosphere. So, cement and concrete may have an important role to play in
enabling reducing the total CO2 emissions from cement and concrete production.
Table 2 - CO2 emissions by sector in EU 27 in shares (%)
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Though “cement” and “concrete” are often used interchangeably, concrete is actually the final
product made from cement. The primary component of cement is limestone. To produce
cement, limestone and other clay-like materials are heated in a kiln at 1400°C and then
ground to form a lumpy, solid substance called clinker; clinker is then combined with gypsum
to form cement.
Cement manufacturing is highly energy and emissions intensive because of the extreme heat
required to produce it. Producing a ton of cement requires 4.7 million BTU of energy,
equivalent to about 200 kilo of coal, and generates nearly a ton of CO2. Given its high
emissions and critical importance to society, cement is an obvious place to look to reduce
greenhouse gas emissions.
A single industry of cement accounts for around five percent of global carbon dioxide (CO2)
emissions. It produces a material so ubiquitous it is nearly invisible: cement. Cement is the
primary ingredient in concrete, which in turn forms the foundations and structures of the
buildings we live and work in, and the roads and bridges we drive on. Concrete is the second
most consumed substance on Earth after water. On average, each year, three tons of concrete
are consumed by every person on the planet.
Concrete is used globally to build buildings, bridges, roads, runways, sidewalks, and dams.
Cement is indispensable for construction activity, so it is tightly linked to the global economy.
Cement production is growing by percent annually, and is expected to rise from 2.55 billion
tons in 2006 to 3.7 - 4.4 billion tons by 2050.
The production of cement releases greenhouse gas emissions both directly and indirectly: the
heating of limestone releases CO2 directly, while the burning of fossil fuels to heat the kiln
indirectly results in CO2 emissions.
The direct emissions of cement occur through a chemical process called calcination.
Calcination occurs when limestone, which is made of calcium carbonate, is heated, breaking
down into calcium oxide and CO2. This process accounts for approximately fifty percent of all
emissions from cement production.
Indirect emissions are produced by burning fossil fuels to heat the kiln. Kilns are usually
heated by coal, natural gas, or oil, and the combustion of these fuels produces additional CO2
emissions, just as they would in producing electricity. This represents around forty percent of
cement emissions. Finally, the electricity used to power additional plant machinery, and the
final transportation of cement, represents another source of indirect emissions and account for
five to ten percent of the industry’s emissions.
According to the First and Second BIH National Reports according to the UNFCCC, cement
production industry in BiH produces the biggest amount of CO2 in industrial sector after the
industry of steel and iron. It represents three percent of total CO2 emission in BiH.
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Figure 3 – CO2 Emission in BiH in 2001
The following table shows the quantity of cement produced in BiH made according to the data
by Thematic Reports on Industrial Production in BiH in years 2009-2012 by Agency for
Statistics BiH.
2009
1,073,762
Cement Production in BiH in Tonnes
2010
2011
948,513
893,017
2012
845,657
Table 3 - Cement Production in BiH 2009-2012
Table 4 is made based upon data from the same source as previous table and represents
production of concrete in BiH in period 2009-2012.
Concrete Products
Fresh Concrete Mix
TOTAL
2009
282,496
807,675
1,090,171
Concrete Production in BiH in Tonnes
2010
2011
330,194
408,732
1,019,618
1,175,035
1,349,812
1,583,767
2012
328,788
1,270,725
1,599,513
Table 4 - Concrete Production in BiH 2009-2012
Analyzing these two last tables, it is obvious that cement production in BiH is reduced in
period 2009-2012 by twenty-one percent, while concrete and concrete products production
increased by almost forty-seven percent, which is very interesting comparison. Most possibly,
it is a result of cement import in BiH from neighboring countries, while increase in concrete
production is result of intensified efforts in construction on Highway-Corridor Vc, in period
of time considered. However, as much as such trends are favorable to emissions of CO2,
economical effects for economy of BiH are questionable. We will be happy to conclude that
such trends are result of introducing green technologies in cement production, but
unfortunately this was probably not a case.
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Opportunities for Reducing CO2 Emissions in Concrete Production in BiH
A primary goal is a reduction in use of Portland cement, which is possible to archive by
partially replacing it with various cementitious materials. Most preferably are byproducts of
different industrial processes in which way double goal is scored. One of such materials is fly
ash, actually a residue of coal combustion which can be excellent substitution. The use of fly
ash has a number of advantages but some disadvantages as well. Fly ash can improve specific
properties of concrete, such as durability. The fly ash is less expensive than Portland cement
and since it is a waste product, it should be disposed at great cost. However, there is a
relatively slow rate of concrete strength development, but it is irrelevant in applications where
high early strength is not required.
Another excellent cementitious material is ground granulated blast furnace slag. It is
byproduct by steel industry. As fly ash, the ground granulated blast furnace slug can improve
some mechanical and durability properties of concrete, while the cost of slag is comparable to
Portland cement.
Replacing cement with silica fume which is a byproduct of semiconductor industry is
additional option, although there is no such industry in Bosnia and Herzegovina. This
siliceous material improves both strength and durability of concrete and it is already part of
concrete mix for high strength concretes. The silica fume is difficult to handle due to its
extreme fineness and is much more expensive than cement. It also reduces the concrete fire
resistance.
The other aspect to make green concrete is substitution of virgin aggregate material with
concrete debris, especially taking in consideration that vast amounts of material are needed
for aggregate in concrete. Using such debris to produce new concrete conserves natural
resources and reduces valuable landfill capacity at the same time.
Additional possibility is material excavated from the construction of tunnels such as current
construction of the tunnels at the Highway Corridor Vc, which may very well be suitable as
aggregate to produce concrete for tunnel lining. In absolute terms, it may render unnecessary
mining of hundreds of thousand tons of virgin materials for concrete aggregate. According to
findings of the author of this paper, it is currently done exactly on the construction of the
Highway Corridor Vc.
Except the possibility discussed in last paragraph, Bosnia and Herzegovina did not do much
about production of green concrete. However, further research developments abroad and in
Bosnia and Herzegovina and different analysis should highlight the direction in reducing
GHGs emissions in concrete and cement production, as well as other environmental aspects of
the concrete production. So, the answer to the question from the title of this paper is not
simple, but definite conclusion is – “concrete can be greener, than it is now”. This paper just
highlights some possibilities and directions, but future research and analysis will provide the
answer.
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Conclusion
In general, the construction industry consumes forty percent of the total energy and about one
half of the world’s major resources. It is estimation that production of concrete produces
seven percent of total CO2 emissions in the world. Every one ton of cement produced, leads to
about 0.9 tons of CO2 emissions and typical cubic meter of concrete contains about ten
percent of cement. In the other hand, available sources of suitable virgin aggregates are
depleted and opening new sources of virgin materials is getting increasingly difficult, because
of environmental concerns. The water requirements for concrete production in the world are
almost four trillion liters of water each year worldwide, and this does not include wash water
and curing water. So, the possibilities for production of green concrete in Bosnia and
Herzegovina are more or less the same as in the other countries and lead in two major
directions:
Increased use of supplementary cementitious material, especially those that are
byproducts of industrial processes; and
Increased reliance on recycled materials. Since aggregate constitutes the bulk of
concrete, en effective recycling strategy will lesson the demand for virgin materials
and diminish landfill areas capacities.
6.
References
1. European Commission, Directorate General for Energy and Transportation, “EU Energy in Figures
2010, CO2 Emissions by Sector”;
2.M. J. Backer Esq, “The New Paradigm in Construction…no Longer It Is Simply Cost, Quality and
Budget”, CMAA, Southern California Chapter, 2009;
3. L.S. da Silva, “A Course on Design of Steel Structures”; ECCS, CECM, EKS, Stockholm; April
2013;
4. Goran Vukmir i dr, “Prvi nacionalni izvještaj Bosne i Hercegovine u skladu sa okvirnom
konvencijom Ujedinjenih nacija o klimatskim promjenama”, Banja Luka, BiH, 2009;
5. Svjetlana Radusin i dr, “Drugi nacionalni izvještaj Bosne i Hercegovine u skladu sa okvirnom
konvencijom Ujedinjenih”, juni 2013;
6. Tematski bilten TB 05, “Industrijska proizvodnja u Bosni i Hercegovini 2009”, Agencija za statistiku
Bosne i Hercegovine, Zelenih beretki 26, Sarajevo, BiH, 2010, ISSN 1840 – 104X;
7.Tematski bilten TB 05, “Industrijska proizvodnja u Bosni i Hercegovini 2010”, Agencija za statistiku
Bosne i Hercegovine, Zelenih beretki 26, Sarajevo, BiH, 2011, ISSN 1840 – 104X;
8. “Industrijska proizvodnja u Bosni i Hercegovini 2011”, Agencija za statistiku Bosne i Hercegovine,
Zelenih beretki 26, Sarajevo, BiH, 2012;
9. “Industrijska proizvodnja u Bosni i Hercegovini 2012”, Agencija za statistiku Bosne i Hercegovine,
Zelenih beretki 26, Sarajevo, BiH, 2013;
10.C. Meyer, “Concrete as a Green Building Material”, Columbia University; New York, NY 10027,
USA;
11. K. H. Obla, “What is Green Concrete”, Concrete in Focus, May/June 2009;
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12.L. Yang, “Sustainability and Innovative Construction: Green Building with Concrete”, Civil and
Enviromental Engineering 2012, Volume 2, Issue 5, ISSN 2165-784X JCEE;
13. M Glavind, C. Munch-Petersen; “Green Concrete in Denmark”, Structural Concrete, 2000, 1, No.
1M
14. K. Edvardsen, K. Tollose, “Envoromentally Green Concrete Structures”, featured at the proceedings
FIB-symposium “Concrete and Enviroment” in Berlin, October 2001.
15. http://unfccc.int/kyoto_protocol/items/2830.php
16. http://www.cop17-cmp7durban.com/en/frequently-asked-questions/what-is-the- kyotoprotocol.html
17. http://en.wikipedia.org/wiki/Kyoto_Protocol
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Title
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CAN CONCRETE BE GREEN IN BOSNIA AND HERZEGOVINA?
Author
Author
DŽIDIĆ, Sanin
Abstract
A summary of the resource.
Bosnia and Herzegovina ratified the United Nations Framework Convention on Climate Change (UNFCCC) on May 17, 2000. The Kyoto Protocol was signed and ratified by the governments of 192 states and territories in the world. The Kyoto Protocol was ratified by Bosnia and Herzegovina on April 22, 2007, after completion of ratification procedures of all government levels. The First National Report of Bosnia and Herzegovina in accordance to the UNFCCC was issued in 2009 and the Second National Report of Bosnia and Herzegovina in accordance to the UNFCCC was adopted by B&H Council of Ministers in July 2013. The main goal of the Kyoto Protocol is to reduce greenhouse gas emissions to environment what caused many to focus on CO2 emissions as the most critical environment impact indicator. Concrete is by far the most widely used construction material worldwide. One of its major components is Portland cement as a binder. Total production of cement in Bosnia and Herzegovina is about 850,000 tons in 2012, while fresh concrete production and concrete products amount approximately to 1,300,000 tons in 2012. Taking in consideration that production of every ton of cement yields to approximately 0.9 tons of CO2 and every cubic meter of concrete contains about ten percent by weight of cement, significant quantity of CO2 is produced by cement industry in Bosnia and Herzegovina. It is estimation in 2001, that cement industry emissions of CO2 represented around 4 percent of total CO2 emissions by energy and industry in Bosnia and Herzegovina. However, substituting significant amounts of cement in concrete mixture with industrial by-products such as silica fume, fly ash and blast furnace slag also leads to minimization of cement consumption, even producing more durable concrete. This paper discuss possibilities in decreasing CO2 emissions in cement and concrete industry, as well as necessity of following directions of green and sustainable building in Bosnia and Herzegovina. Key Words: CO2 emission, cement, concrete, green buildings
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/730719527e5578fd3d43ba30f199617d.pdf
3d79986ea43502148cc1dca1e5cfe0dc
PDF Text
Text
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COMPARISON OF CODON USAGE IN MITOCHONDRIAL GENOMES OF
RHINOLOPHID AND HIPPOSIDERID BATS
Semir Dorić1 and Lada Lukić Bilela1,2#
1
Dept. of Biology, Faculty of Science, University of Sarajevo, Zmaja od Bosne 33-35, 71 000
Sarajevo, Bosnia and Herzegovina; semir.doric@gmail.com; llbilela@gmail.com
2
Biospeleological Society in Bosnia and Herzegovina, Avde Jabučice 30, 71 000 Sarajevo,
Bosnia and Herzegovina; biospeld2008@gmail.com
# Corresponding author
Abstract
According to current phylogenetic hypotheses, the bats of the families Rhinolophidae and
Hipposideridae are sister groups nested within the clade of Pteropodiformes. The
Hipposideridae are family of bats commonly known as the Old World leaf-nose bats. While
this family has long been considered as a rhinolophid subfamily Hipposiderinae, it is now
more generally classified as its own family. The Hipposideridae contain 10 living genera and
more than 70 species, mostly in the widespread genus Hipposideros. This study is an attempt
to confirm a distinction between these two families by a codon usage comparison of a
complete set of mitochondrial protein-coding genes from currently available mitochondrial
(mt) genomes of rhinolophid and hiposiderid bats. The INCA 2.1 and GCUA 2.0 were used
for the codon usage computing. Measure Independent of Length and Composition (MILC),
was used to estimate the codon usage of 13 mt protein-coding genes from five species of
genus Rhinolophus and one species of Hipposideros (while only four genes were available
from H. larvatus). Large randomly generated sequence sets were used to test for dependence
on (i) sequence length, (ii) overall amount of codon bias and (iii) codon bias discrepancy in
the sequences. Our findings suggest no significant differences in codon usage bias, among
analyzed rhinolophid species, by statistical estimation of absolute frequency values despite
the changed MILC values for nd1 and nd3 from Hipposideros armiger.
Keywords: MILC, MELP, bats, codon usage, codon frequencies
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1. Introduction
Rhinolophidae split from their sister family, the Hipposideridae, towards the end of the
Eocene (Maree and Grant, 1997; McKenna and Bell, 1997; Teeling et al., 2003; Eick et al.,
2005). This estimate of divergence is congruent with the fossil data, with fossils of extinct
Rhinolophus and Hipposideros species first occurring in middle Eocene deposits (ca. 49–37
MYA; Simmons and Geisler, 1998). The family Rhinolophidae Gray, 1825 consists of a
single genus Rhinolophus Lacépéde, 1799. The taxon is exclusively Old World, with at least
77 species (Simmons, 2005) occurring in both temperate and tropical areas throughout the
Afrotropical, Australian, Indomalayan, Oceanian and Palaearctic regions (Csorba et al., 2003).
A previous classifications imply two subfamilies, the Hipposiderinae and the Rhinolophinae,
of the family Rhinolophidae according to Koopman, 1993, 1994; McKenna and Bell, 1997;
Simmons and Geisler, 1998; Teeling et al., 2002, while contemporaneously the hipposiderids
excluded from this family following Corbet and Hill (1992), Bates and Harrison (1997) and
Simmons (2005). Interestingly, Rhynolophus monoceros (used in our study) is often treated
as a Taiwanese endemic, and very similar to R. pusillus of the mainland in terms of body size,
echolocation call frequency and mitochondrial gene sequences (Li et al. 2006). It is perhaps
best treated as a synonym of R. pusillus, especially given that the Taiwanese Hipposideros
terasensis considered synonymous with H. armiger of the mainland according to Simmons
(2005).
Besides, in more recent studies of deep rhinolophid phylogeny based on analysis of
cytochrome b and the three nuclear introns: thyrotropin, thyroglobulin and protein-kinase
(PRKC1) the hipposiderid bats were used as outgroup (Stoffberg et al., 2010) A
multidisciplinary approach: morphometric measurements (Bogdanowicz, 1992), recording
and analysis of echolocation signals, karyotypic variation (Koubínová et al, 2010), D-loop
sequence analysis) contribute in resolving t1he correct phylogenetic position of the species
within these two families (Stoffberg et al, 2010). According to current phylogenetic
hypotheses, the bats of the families Rhinolophidae and Hipposideridae are sister groups
nested within the clade of Pteropodiformes (Koubínová et al, 2010). Rhinolophidae form a
monophyletic group and can be divided into at least two major clades – the predominantly
African and the predominantly Oriental clades – based on the current biogeographical
distributions of the majority of species within each clade. Morphological (Bogdanowicz, 1992)
and cytochrome b (Guillén-Servent et al., 2003) analyses also suggest that the African
rhinolophids form a monophyletic clade. The typical metazoan mitochondrial (mt) genome
comprises a single circular, double-stranded DNA molecule with a size between 14 and 18 kb
that contains a uniform set of 37 genes (Boore, 1999). Mitochondrial genomes are powerful
tool in phylogenetic analyses to elucidate the complex relationships among taxa. More rapidly
evolving mitochondrial genes may distinguish even closely related species and thus they have
been employed in conservation genetic studies (Avise, 1995). Thus, generation of full mtgenome sequences is important for both evolutionary studies and conservation management of
endangered species.
The aim of this study was a codon usage comparison of mitochondrial genes and
identification of possible differences in codon frequency values from rhinolophid and
hipposiderid bats as a contribution to phylogeny elucidation between these two families.
2. Materials and methods
The nucleotide sequences of 13 (nd1, nd2, nd3, nd4, nd4l, nd5, nd6, cox1, cox2, cytb, cox3,
atp6, atp8) mitochondrial protein-coding genes from five species of the family Rhinolophidae
and Hipposideros armiger (Hodgson, 1835) as well as four genes (nd1, nd2, cox1, cytb) from
H. larvatus (Horsfield, 1823) were obtained from GenBank (NCBI) (Table 1).
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Table 1. Selected species of the families Rhinolophidae and Hipposideridae used for
sequence analysis, with a mitochondrial genome accession number in GenBank database.
Selected species
Accession number
Rhinolophus ferrumequinum (Schreber, 1774)
NC_020326.1
R. pumilus K. Andersen, 1905
NC_005434.1
R. monoceros K. Andersen, 1905
NC_005433.1
R. formosae (Sanborn, 1939)
NC_011304.1
R. luctus (Temminck, 1834)
NC_018539.1
Hipposideros armiger (Hodgson, 1835)
H. larvatus (Horsfield, 1823)
H. larvatus (nd1)
H. larvatus (nd2)
H. larvatus (cox1)
H. larvatus (cytb)
NC_018540.1
JX861075.1
DQ888653.1
JQ915493.1
JQ365642.1
EU434949.1
INCA 2.1 (Supek and Vlahoviček, 2006) and GCUA 2.0 (Fuhrmann et. all., 2004) were used
for codon usage computing. Measure Independent of Length and Composition (MILC), was
used to estimate the codon usage of thirteen mtDNA genes of selected species within genera
Rhinolophus and Hipposideros. Large randomly generated sequence sets were used to test for
dependence on (i) sequence length, (ii) overall amount of codon bias and (iii) codon bias
discrepancy in the sequences. MILC Based Expression Level Predictor (MELP) was used as a
measurement to quantitatively predict the levels of selected mitochondrial gene expression.
3. Results and discussion
Calculations of MILC and MELP values for thirteen and four protein-coding genes of selected
species, six and seven respectively, were carried out in INCA 2.1. (Table 2). Reference MILC
values were used as absolute frequencies of codon usage for selected genes (Fo). Estimation of
the percentage difference of codon usage bias among selected species followed trough χ2
statistical observations as well as GCUA 2.0.
Table 2. MILC and MELP average values for 13 (from five rhinolophid and one hipposiderid
bat) (A) as well as four protein coding genes from Hipposideros larvatus (B).
Selected species
Rhinolophus ferrumequinum
R. pumilus
R. monoceros
R. formosae
R. luctus
Hipposideros armiger
MILC
0.631
0.627
0.635
0.615
0.633
0.666
MELP
1.011
1.009
1.015
1.030
1.021
1.007
A
Selected species
Rhinolophus ferrumequinum
R. pumilus
R. monoceros
R. formosae
R. luctus
Hipposideros armiger
Hipposideros larvatus
MILC
0.516
0.525
0.527
0.511
0.527
0.509
0.522
MELP
1.057
1.050
1.054
1.043
1.043
1.030
1.022
B
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Absolute differences between the theoretical (Ft) and observed (Fo) values of codon
frequencies were less than 1%, comparing thirteen and four protein-coding genes from six and
seven selected species, respectively (Graph. 1).
Graph 1. Absolute difference of Ft and Fo for MILC values for 13 (from five rhinolophid and
one hipposiderid bat) (A) and four protein-coding genes from Hipposideros larvatus (B).
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The obtained value of χ2 was 0.00218 with p=0.01 and n=5 (six species) and 0.0096 with p=
0.009 and n=6 (seven species). In both cases p value was <0.5 which indicates no significant
difference. However, analysis mediated by GCUA 2.0 revealed important differences in
codon usage frequencies. Absolute differences in codon usage frequency between
Hipposideros armiger and Rhinolophus ferrumequinum were 8.19% , H. armiger and R.
monoceros 8.17%, H. armiger and R. pumilus 9.89%, H. armiger and R. luctus 8.3%.
The typical deviation from the universal genetic code observed in mitochondrial genomes of
rhinolophid and hipposiderid bats are similar to that already found in other vertebrates, with
TGA coding for tryptophan, instead of being a stop codon. Hipposideros armiger prefers
TGG (Trp) with the absolute frequency of 0.154 related to five species of genus Rhinolophus
with frequencies of 0.05-0.65.
Among the terminations codons, UAA was the most preferred by all analyzed species, then
AGA while the codon AGG is found neither in mitochondrial genes of five rhinolophid
species nor in H. armiger and H. larvatus. AGA and AGG were thought to have become
mitochondrial stop codons early in vertebrate evolution (Osawa, et al., 1989). However, at
least in humans it has now been shown that AGA and AGG sequences are not recognized as
termination codons. UAG codon is rather preferred by H. armiger than rhinolophid bats with
a difference of 4.04%. Actually, the UGA Stop-to-Trp is the change is the most frequently
occurring reassignment known. Disappearance of UAG would be favored by mutation
pressure increasing the AU content. The reason UAG is reassigned less frequently than UGA
may be because of the relative difficulty of the required change in the tRNA. In the case of
UGA, the existing tRNA-Trp can simply mutate its anticodon (Sengupta et al., 2007).
Synonymous codons are not used with equal frequencies, so based on a multivariate analysis
of codon usage data from unicellular organisms, Grantham et al. (1980) proposed the genome
hypothesis implying some relationship between codon usage and taxonomic distance. A long
time ago was noticed a correlation between taxonomic divergence and the similarity of the
codon dialect (Ikemura, 1985; Maruyama et al. 1986).
4. Concluding remarks
During the last decade, analyses of the mitochondrial genome became a powerful tool to
resolve the phylogenetic relationships among the various eukaryotic lineages and to elucidate
the early events during evolution of multicellularity. MILC and MELP algorithms have
proved to be excellent tools for mitogenomic phylogeny and molecular evolution studies.
The codon usage comparison of 13 mt protein-coding genes from five species of genus
Rhinolophus and one species of Hipposideros has shown 8.17 to 9.89% differences of codon
frequency values using GCUA 2.0. However, our results mediated by INCA 2.1., without any
statistically significant difference in codon usage among selected species could be explained
by the estimation based on the only one complete mitochondrial protein-coding gene set (H.
armiger) and four genes (from H. larvatus) from hipposiderid bats. Furthermore, MILC
algorithm has proved to be very sensitive, discriminating genes by their length, alternative
stop codons and nucleotide composition. MILC values for nd1 and nd3 genes from
hipposiderid bats differ from genes of selected rhinolophid species due to the nucleotide
composition. This could indicate possible further differences on complete mtDNA sequences
which can help in elucidation of phylogenetic relationships within these two chiropteran
families.
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5. References
Agnarsson, I., Zambrana-Torrelio, C., M., Flores-Saldana, N., P., & May-Collado, LJ. (2011). A time-calibrated
species-level phylogeny of bats (Chiroptera, Mammalia). PLOS Currents, 10, 13-71.
Avise, J.C. (1995). Mitochondrial DNA polymorphism and a connection between genetics and demography of
relevance to conservation. Conservation Biology, 9, 686–690.
Bogdanowicz, W. (1992). Phenetic relationships among bats of the family Rhinolophidae. Acta Theriologica, 37,
213–240.
Boore, J.L. (1999). Animal mitochondrial genomes. Nucleic Acids Research, 27, 1767–1780.
Csorba, G., Ujhelyi, P., & Thomas, N. (2003). Horseshoe Bats of the World (Chiroptera: Rhinolophidae). Alana
Books, Shropshire. p. 160.
Eick, G.N., Jacobs, D.S., & Matthee, C.A. (2005). A nuclear DNA phylogenetic perspective on the evolution of
echolocation and historical biogeography of extant bats (Chiroptera). Molecular Biology and Evolution, 22,
1869–1886.
Fuhrmann, M., Hausherr, A., Ferbitz, L., Schödl, T., Heitzer, M., & Hegemann, P. (2004). Monitoring dynamic
expression of nuclear genes in Chlamydomonas reinhardtii by using a synthetic luciferase reporter gene. Plant
Molecular Biologie, 55(6), 869-81.
Grantham, R., Gautier, C., Gouy, M., Mercier, R., & Pave, A. (1980). Codon catalog usage and the genome
hypothesis. Nucleic Acids Research, 8, 49-62.
Guillén-Servent, A., Francis, C.M., & Ricklefs, R.E. (2003). Phylogeny and biogeography of the horseshoe bats.
In: Csorba, G., Ujhelyi, P., & Thomas, N. (Eds.), Horseshoe Bats of the World. Alana Books, p. 160.
Ikemura, T. (1985). Codon usage and tRNA content in unicellular and multicelular organisms. Molecular
Biology and Evolution, 2, 13-34.
Koubínová, D., Sreepada, K. S., Koubek, P., & Zima, J. (2010). Karyotypic Variation in Rhinolophid and
Hipposiderid Bats (Chiroptera: Rhinolophidae, Hipposideridae). Acta Chiropterologica, 12(2), 393-400.
Li, G., Jones, G., Rossiter, S.J., Chen, S.F., Parsons, S. & Zhang, S. (2006). Phylogenetics of small horseshoe
bats from East Asia based on mitochondrial DNA sequence variation. Journal of Mammalogy, 87, 1234-1240.
Maree, S., & Grant, W.S. (1997). Origins of horseshoe bats (Rhinolophus, Rhinolophidae) in southern Africa:
evidence from allozyme variability. Journal of Mammalian Evolution, 4, 195–214.
Maruyama, T., Gojobori, T., Aota, S.I., & Ikemura, T. (1986). Codon usage tabulated from the GenBank genetic
sequence data. Nucleic Acids Research, 14, l51-197.
McKenna, M.C., & Bell, S.K. (1997). Classification of Mammals above the Species Level. Columbia University
Press. p. 631.
Osawa, S., Ohama, T., Jukes, T.H., & Watanabe, K. (1989). Evolution of the mitochondrial genetic code. I.
Origin of AGR serine and stop codons in metazoan mitochondria. 29(3), 202-207.
Sengupta, S., Yang, X., & Higgs, P. G. (2007). The Mechanisms of Codon Reassignments in Mitochondrial
Genetic Codes. Journal of Molecular Evolution, 64, 662-688.
Simmons, N.B., & Geisler, J.H. (1998). Phylogenetic relationships of Icaronycteris, Archaeonyteris,
Hassianycteris and Palaeochiropteryx to extant bat lineages, with comments on the evolution of echolocation and
foraging strategies in Microchiroptera. The Bulletin of the American Museum of Natural History, 235, 1–182.
Simmons, N.B. (2005). Order Chiroptera. In: Wilson, D.E., & Reeder, D.M. (Eds.), Mammal Species of the
World: A Taxonomic and Geographic Reference, third ed. Smithsonian Institution Press, pp. 312–529.
Stoffberg, S., Jacobs, D.S., Mackie, I.J., & Matthee, C.A. (2010). Molecular phylogenetics and historical
biogeography of Rhinolophus bats. Molecular Phylogenetics and Evolution, 54, 1–9.
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Supek, F., & Vlahoviček, K. (2005). Comparison of codon usage measures and their applicability in prediction
of microbial gene expressivity. BMC Bioinformatics, 6, 182.
Supek, F., & Vlahoviček, K. (2006). INCA: synonymous codon usage analysis and clustering by means of selforganizing maps. BMC Bioinformatics, 20(14), 2329-2330.
Teeling, E.C., Madeson, O., Van Den Bussche, R.A., De Jong, W.W., Stanhope, M.J., & Springer, M.S., (2002).
Microbat paraphyly and the convergent evolution of a key innovation in Old World rhinolophoid microbats.
PNAS USA, 99, 1431–1436.
Teeling, E.C., Madsen, O., Murphy, W.J., Springer, M.S., & O’Brien, S.J. (2003). Nuclear gene sequences
confirm ancient link between New Zealand’s short-tailed bat and South American noctilionoid bats. Molecular
Phylogenetic and Evolution, 28, 308–319.
Vaughan, T., Ryan, J., & Czaplewski, N. (2000). Mammalogy, 4th Edition. Toronto: Brooks Cole Press.
Wilson, D., & Reeder, D. (2005). Mammal Species of the World, 3rd edition. Baltimore: Johns Hopkins
University Press.
Semir Dorić is postgraduate student at Faculty of Science, University of Sarajevo
(Department of biology) with a special interest in field of molecular biology and
bioinformatics. In diploma thesis has analyzed a codon usage in selected representatives of
family Rhinolophidae (Chiroptera) with a dedication to implement different software
packages towards improving the quality of his investigations.
Lada Lukić Bilela is associated professor of Molecular biology and Genomics at Faculty of
Science, University of Sarajevo (Department of biology). She received her BSc in Biology
(Faculty of Science, Sarajevo) MS and PhD in Mitochondrial genomics of Porifera at (Faculty
of Science, Zagreb; field: molecular and cell biology). She was employed in Ruđer Bošković
Institute at Laboratory of molecular genetics and performed her postdoctoral training at
Johannes Gutenberg University of Mainz (Marie Curries Training Network fellowship).
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COMPARISON OF CODON USAGE IN MITOCHONDRIAL GENOMES OF RHINOLOPHID AND HIPPOSIDERID BATS
Author
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DORIĆ, Semir
LUKIĆ BILELA, Lada
Abstract
A summary of the resource.
According to current phylogenetic hypotheses, the bats of the families Rhinolophidae and Hipposideridae are sister groups nested within the clade of Pteropodiformes. The Hipposideridae are family of bats commonly known as the Old World leaf-nose bats. While this family has long been considered as a rhinolophid subfamily Hipposiderinae, it is now more generally classified as its own family. The Hipposideridae contain 10 living genera and more than 70 species, mostly in the widespread genus Hipposideros. This study is an attempt to confirm a distinction between these two families by a codon usage comparison of a complete set of mitochondrial protein-coding genes from currently available mitochondrial (mt) genomes of rhinolophid and hiposiderid bats. The INCA 2.1 and GCUA 2.0 were used for the codon usage computing. Measure Independent of Length and Composition (MILC), was used to estimate the codon usage of 13 mt protein-coding genes from five species of genus Rhinolophus and one species of Hipposideros (while only four genes were available from H. larvatus). Large randomly generated sequence sets were used to test for dependence on (i) sequence length, (ii) overall amount of codon bias and (iii) codon bias discrepancy in the sequences. Our findings suggest no significant differences in codon usage bias, among analyzed rhinolophid species, by statistical estimation of absolute frequency values despite the changed MILC values for nd1 and nd3 from Hipposideros armiger. Keywords: MILC, MELP, bats, codon usage, codon frequencies
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International Burch University
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2014-05-15
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ISSN 978-9958-834-36-3
Q Science (General),QH301 Biology,QH426 Genetics
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https://omeka.ibu.edu.ba/files/original/04e9c57a1c75ceadebc426947295337f.pdf
c8c684fec162e6320f0bf40e2fb6f70b
PDF Text
Text
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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
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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).
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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:
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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
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Picture 1. Satellite record of Sarajevo
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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
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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
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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
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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.
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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.
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2447
Title
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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
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International Burch University
Date
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2014-05-15
Keywords
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Article
PeerReviewed
Identifier
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ISSN 978-9958-834-36-3
Q Science (General),QH301 Biology,QH426 Genetics
-
https://omeka.ibu.edu.ba/files/original/6dc4d8c961b54d0b44a2e23bc04947ac.pdf
74a72576e5c99d4b050e1834196041c6
PDF Text
Text
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EFFECTS OF DIFFERENT TYPES FERTILIZERS ON GRAIN YIELD IN
DIFFERENT SORTS OF FLAX
Dervišević Selma, Veladžić Mirsad, Jogić Vildana
University of Bihac
Biotechnical Faculty
Abstract
A few years ago began the re-cultivation of flax in the area of the northwestern part of Bosnia
and Herzegovina with the ultimate aim of producing seeds and fibers. Flax seed contains
about 57 % alpha linolenic acid known by multiple medical effects as the guardian of
cardiovascular health, and which the current way of nutrition we take into the organism in
about ten times smaller quantity than those recommended by the World Health Organization.
In addition to the seed of the flax are obtained with high quality fibers that are
environmentally acceptable and for which there is a great need in the area of the European
Union. In order to achieve higher yields have been conducted research on the effects of
fertilization on seed yield. For this purpose, the experiment was conducted under field
conditions at two locations (Cojluk and Ostruznica) in a split-plot design. In the research were
used three varieties (Mikael, Belstar and variety X) with five fertilization treatments: T1 control, T2 - mineral fertilizers T3 - organic fertilization, T4 - bacterial fertilizer (Azoter) and
T5 - bacterial+organic fertilizer. Based on the obtained results, the two-year investigation of
morphological and phenological traits was found that there were differences between the
studied varieties and fertilizer on the basis of treatment. Statistical significance of highest
yield at both locations was obtained by variety Belstar with fertilization treatment T5 (1600
kg/ha Ostruznica and 1900 kg/ha Cojluk). With the aid of the Kruskal-Wallis test revealed
significant differences in fertilization treatments, which had an impact on all the
characteristics of the flax plant, the statistical differences between the varieties studied traits
less significant. After the research, as the best variety for cultivation, and on the basis of the
yield level, recommended varieties Belstar with the aforementioned method of fertilization
(T5).
Keywords: flax, omega 3 fatty acids, fertilization, yield.
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1. Introduction
Flax cultivation in Bosnia and Herzegovina is unjustified neglected, and in recent years has
started cultivation again, because every day the growing demand for flax, both on domestic
and on the foreign markets (Šimetić, 2008). To satisfy the market need for seed of these
culture it is necessary to increase the yield of flax, which can be achieved by sowing high
yielding varieties and optimizing agricultural activities (Khourang et al. 2012). Flax is a
culture that is relatively small/symbolic grown in the area of the northwestern part of Bosnia
and Herzegovina, and therefore the results will form the basis for its further cultivation, as
well as key plants that the physico-chemical characteristics, has a great impact on human
health, and as such should is an indispensable food and nutrition an integral part of every
inhabitant. The aim of the research is to determine the level of influence of different types of
fertilizers (organic, bacterial, organic-bacterial, mineral and cultivation without fertilizers) on
grain yield of different varieties of flax.
2. Materials and Methods
At the locality Cojluk, and the locality Ostruznica, Bosanska Krupa in 2012 and 2013, has
been set an experiment with three varieties of flax: Mikael, Belstar and variety X. The
experiments were set by scheme randomized block design with four replications, and five
variants of fertilization: T1 - control (without fertilizer application), T2 - T3 and mineral
fertilizers - organic fertilization (bovine manure), T4 - bacterial fertilizer (Azoter) and T5 organic + bacterial fertilizer. Size plot was 10 m2, and the sowing is done in the third week of
April on the basis of 1200 germinable seeds per m2. A common technology of growing flax is
applied. Analysis of soil substrate was performed by standard methods that are applied in
scientific institutions (AOAC, 1995). Measurements of quantitative traits and qualitative traits
were performed in the laboratory of Biotechnical Faculty, University of Bihac, and the results
were analyzed by using statistical software PAST (2013) and XL STAT (2011). During the
growing season are followed morphological and phenological properties: time of germination,
increase flax during the growing season, beginning of flowering and full maturity, number of
capsules per plant and number of seeds in the capsule.
3. Results and Discussion
Before setting the experiment for the vegetation period in 2012 and the 2013th year was made
the control of soil fertility. The results are shown in graph 1.
Graph 1. Results of soil fertility control in the studied locations
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Results of the analysis indicate that investigated soil of location Cojluk has a very high
content of humus, very good presence of nitrogen, but extremely weak content of potassium
and phosphorus, and in addition to other treatments applied fertilizer NPK fertilizer
formulation (5:10:20), while the plot on the location Ostruznica significantly poorer quality
when it comes to the content of humus, potassium and nitrogen, and a little higher percentage
of phosphorus (NPK = 20:10:20). Previous studies (Butorac et al. 2006a & 2006b; Easson &
Long, 1992; Padlock, 1994; Zedan et al. 1999) indicate that large amounts of nitrogen
affecting the formation of finer flax fiber, less hardness, but lead to increased risk of lodging,
and thus to a loss in yield. There have been many significant research on the effects of
fertilization on the quality of the fiber, but not on the quality and yield of seeds, and the
results will be of great importance to future farmers of this culture.
Table 1. Variance analysis of investigated morphological characteristics of flax
St. anal
Cojluk
Ostruzn
ica
Plant height
Sum of squares Mean squares
1293,600
128,869
F
Pr > F
10,078 *
0,002
Sum of squares Mean squares
14777,600
3694,40
F
Pr > F
65,026 *
00,00185
Length branching
Sum of squares
2683,240
F
37,180
Sum of squares
1968,480
F
24,617 *
Mean squares
70,96
Pr > F
0,1726
Mean squares
420,120
Pr > F
0,016
Number of seeds
Sum of squares
102,010
F
47,463*
Sum of squares
750,720
F
41,345 *
Mean
2,149
Pr > F
0,0366
Mean
187,687
Pr > F
0,01309
* Significant at the level of 0.05%
Table 1 shows the statistical analysis of observed traits of flax monitored during the
experiment, which significantly affect on seed yield. After processing the data collected for
both the test locations, there was a statistically significant difference between the samples of
plants on the basis of fertilization treatments and examined varieties, where as the best way of
fertilization, with all three varieties, location Cojluk showed T5 (a combination of bacterial
and organic fertilizers).
Analysis of variance showed a statistically significant difference (P <0.05) on the basis of
plant height where the tallest stalks of flax varieties Mikael recorded at 89 cm, and the lowest
in the stems of the variety X, the same treatment fertilization, height 71 cm. By statistical
analysis the significance of the results it can be concluded that the differences in plant height
caused by variety, but the method of fertilization, where the lowest stems measured at variety
X, T1 = 47 cm, then sort Belstar, T1 = 53 cm and a variety Mikael T1 = 68 cm. On the
location of Ostružnica, due to significantly lower soil quality were achieved significant
differences measured value, but as best variety, when a measurement of the height of the
plants, showed Mikael variety, fertilization treatment T5 = 79 cm, as the worst sort X, T3 =
45 cm, while the fertilization treatment T5 achieved height was 65 cm. Further measurements
were found statistical differences in other traits investigated. After established the presence of
a statistical difference, with the help of the Kruskal-Wallis test was determined statistical
significance of differences in both locations (Table 2).
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Table 2. Kruskal - Wallis test
Cojluk
T1
T2
T3
T4
Height
NS
×
×
×
Number of seeds ×
×
×
×
Branching
NS
×
×
×
Ostruznica
T1
T2
T3
T4
Height
NS
×
NS
×
Number of seeds ×
×
×
×
Branching
NS
×
NS
NS
Note: NS = nonsignificant difference, × = significant difference.
T5
×
×
×
T5
×
×
×
With the help of the Kruskal-Wallis test (Table 2) revealed significant differences in
fertilization treatments, which had an impact on all the features of the flax plant, which is the
height, number of seeds and branching, while the statistical differences between the varieties
studied traits less significant. The harvest of flax was performed in the first week of August
when the flax was on the turn from yellow to full maturity, the leaves are down, stalk got dark
color, and the capsules began to shoot. After separating the seeds from the remains of plants
was determined the height of yield on the basis of the test varieties and fertilizer treatments.
Table 3. Variance analysis of seed yield the examined flax varieties
St. anal
Yield
Cojluk
Sum of squares
1742233,333
Mean squares
435583
Fisher’s t
4,659*
PF
0,0022
Ostruznica
Sum of squares
2095506,667
Mean squares
523886,667
Fisher’s t
5,866 *
PF
0,011
From Table 3 are visible statistical differences in both studied locations. After analysis of
variance was done using Kruskal-Wallis test which showed us (Table 4) that are statistically
significant differences in the yields using a different fertilization treatments, while statistical
differences in the yields of those varieties are not considered so significant.
Table 4. Kruskal-Wallis test
Table of groups: Sum of ranks
Ostruznica
Cojluk
15
30
Groups
A
B
Cojluk
Ostruznica
sort
NS
NS
treatments
×
×
Note: NS = nonsignificant difference, × = significant difference.
Pospišil and colleagues (2010) performed the research seed yield in eight varieties of flax oil
(Atlanta, Flanders, Biltstar, Altess, Mikael, Princess, Niagara, Eole), and the results showed
that the highest yield was sort Altess (1644 kg/ha). Comparing their results and yield varieties
Belstar the location Cojluk, with organic fertilizer + bacterial treatment more than good (1900
kg/ha). In contrast to locations Cojluk, and due to much lower soil quality, conditioned
significantly lower percentage of humus and microelements, there has been a lower yield that
was statistically significantly different at different fertilization treatments, so for example the
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variety Belstar was: control (300 kg/ha), mineral fertilizers (900 kg/ha), organic manure (1200
kg/ha), bacterial fertilizer (950 kg/ha) and the highest yield with organic + bacterial fertilizer
treatment (1600 kg/ha).
4. Conclusion
On the basis of the study of morphological and phenological characteristics of flax at two
locations, it can be concluded the following:
All varieties are grown consistently to the end of vegetation.
The results show that there are no statistically significant differences between the
varieties in terms of seed yield.
There are statistically significant differences in seed yield based on the fertilization
treatments.
The highest yield was achieved at fertilization treatment T5 (organic+bacterial
fertilizer) in all tested cultivars in both locations.
According to the results, we can conclude that it is the best Belstar variety for growing
flax and because achieves the highest seed yield.
The area of the Unsko-Sanski Canton is relatively underdeveloped area, when in is the
question mentioned farming culture. The development of farming and cultivation of flax, as a
branch of agriculture, until now was not followed by scientific research and achievements.
Therefore it can be concluded that this work is a contribution to science.
5. References
AOAC (1995). Offical Method of analysis (16 th ed.). Washington DC. Association of Offical Chemists.
Butorac, J., Pospišil, M., Mustapić, Z., Zorić, D. (2006a). Procjena važnijih agronosmkih i morfoloških svojstava
sorti lana pri različitoj gustoći sjetve. Sjemenarstvo. 23. 437 - 445.
Butorac, J., Pospišil, M., Mustapić, Z. (2006b). Utjecaj gustoće sjetve na neka morfološka i fenološka svojstva
sorti predivog lana. Sjemenarstvo. 23. 447 - 456.
Easson, D.L., & Long, F.N. (1992). The effect of time sowing, seed rate and nitrogen level on the fibre yield and
quality of flax (Linum usitatissimum L.). Irish Agric and Food Res. 31. 163 - 172.
Khourang, M., Brumand, P., Omidbaigi, R. (2012). Effect of some chemical and biological fertilizers on
productivity of medicinal flax (Linum usitatissimum L.) plant. International journal of Agronomy and Plant
Production. 3. 78 - 83.
Padlock, A. (1994). The effect of long-term fertilizer application in a crop rotation on yield and quality of fiber
flax. Agrokhimiya. 4. 55 - 60.
Pospišil, M., Pospišil, A., Butorac, J., Škevin, D., Kraljić, K., Obranović, M., Brčić, M. (2010). Prinos i
sastavnice prinosa istraživanih sorti uljnog lana u sjeverozapadnoj Hrvatskoj. International Symposium on
Agriculture. 624 - 627.
Šimetić, S. (2008). Lan u proizvodnji i upotrebi. Sjemenarstvo. 25 (3-4). 217 - 221.
Zedan, S.Z., Kineber, M.E., Mostafa, S.H. (1999). Response of flax to potassium and nitrogen fertilitation under
sandy soil conditions. Egyp J Agric Res. 77. 729 - 743.
107 | P a g e
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2491
Title
A name given to the resource
EFFECTS OF DIFFERENT TYPES FERTILIZERS ON GRAIN YIELD IN DIFFERENT SORTS OF FLAX
Author
Author
DERVIŠEVIĆ, Selma
VELADŽIĆ, Mirsad
JOGIĆ, Vildana
Abstract
A summary of the resource.
A few years ago began the re-cultivation of flax in the area of the northwestern part of Bosnia and Herzegovina with the ultimate aim of producing seeds and fibers. Flax seed contains about 57 % alpha linolenic acid known by multiple medical effects as the guardian of cardiovascular health, and which the current way of nutrition we take into the organism in about ten times smaller quantity than those recommended by the World Health Organization. In addition to the seed of the flax are obtained with high quality fibers that are environmentally acceptable and for which there is a great need in the area of the European Union. In order to achieve higher yields have been conducted research on the effects of fertilization on seed yield. For this purpose, the experiment was conducted under field conditions at two locations (Cojluk and Ostruznica) in a split-plot design. In the research were used three varieties (Mikael, Belstar and variety X) with five fertilization treatments: T1 - control, T2 - mineral fertilizers T3 - organic fertilization, T4 - bacterial fertilizer (Azoter) and T5 - bacterial+organic fertilizer. Based on the obtained results, the two-year investigation of morphological and phenological traits was found that there were differences between the studied varieties and fertilizer on the basis of treatment. Statistical significance of highest yield at both locations was obtained by variety Belstar with fertilization treatment T5 (1600 kg/ha Ostruznica and 1900 kg/ha Cojluk). With the aid of the Kruskal-Wallis test revealed significant differences in fertilization treatments, which had an impact on all the characteristics of the flax plant, the statistical differences between the varieties studied traits less significant. After the research, as the best variety for cultivation, and on the basis of the yield level, recommended varieties Belstar with the aforementioned method of fertilization (T5). Keywords: flax, omega 3 fatty acids, fertilization, yield.
Publisher
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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
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ISSN 978-9958-834-36-3
Q Science (General),QH301 Biology,QH426 Genetics
-
https://omeka.ibu.edu.ba/files/original/a7059052cf255353e1893a0ef78b7746.pdf
b664bd6b097e1938cd385887cea6d7e9
PDF Text
Text
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EFFECT OF DIFFERENT FERTILIZERS TYPES ON FLAX FIBRES
CHARACTERISTICS
IN DIFFERENT CULTIVARS OF FLAX
Dervišević Selma, Veladžić Mirsad, Jogić Vildana
University of Bihac
Biotechnical Faculty
Abstract
This work presents the results of research on the impact of organic, minerals, organic and
microbiological fertilizers on characteristics of flax fibers in three different varieties of flax.
The experiment was performed in the municipality of Bosanska Krupa in 2012. The parcel
was set up in randomized block of design with four replications, and the size of the
assessment parcel was 10 m2. All three varieties are sown on the basis of 1000 germinable
seeds per m2. They represented two foreign sorts: Michael, Belstar and domestic sort X. In the
autumn mineral fertilizers were entered in soil in the scale of NPK = 15:15:15, 250 g/20m2, 3
kg/20m2 of manure and 10 l/ha of microbiological fertilizers ''Azoter''. The different
combinations of fertilizers were used: organic fertilizer, microbiological fertilizer,
organic+microbiological fertilizer and control (without fertilization) - for each tested sort. The
research was a multi-factorial (cultivar and method of fertilization). According to the results
obtained during the one-year research, Michael and Belstar varieties have achieved the best
results with organic+bacteriological fertilizer. Fibers got out of Michael and Belstar variety
have better quality, they are longer and harder, which makes them suitable for use in technical
textiles where even coarser fibres get more important. X sort fibres are the shortest and the
thickest, so they give better results with bacteriological fertilizers.
Keywords: flax, sort, morphological characteristics, phenological characteristics, fiber,
fertilizer.
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1. Introduction
In addition to the elastic properties of which have, flax fibers are characterized by high
strength which reinforces their component (Kocjan & Rijavec, 2010). According to EU
guidelines by summer 2012, 95% of all new vehicles must be able to be recycled, which is the
recommended use of natural fibers, especially flax. There is increasing interest in the use of
flax fibers in the field of technical textiles where the coarse fibers gaining increasing
importance of (bio-composites), and therefore hards now considered very valuable component
of the insulating material (Šurina et al. 2006 & 2009b).
Length and fineness of the fibers are the most important characteristics that determine the
quality and suitability of flax fibers as raw material for the production of textile yarn and
fabrics (Butorac et al. 2008). Hann (2005) considers that the wetting stems is most demanding
stage in the production of flax fibers, usually it is the natural way, with the help of enzymes
produced by microorganisms. Biological process takes 8 to 14 day in cold water, but 3 to 4
days at a temperature of 30 to 40 ° C, with a regular change of the water.
With proper selection of varieties and production technology (eg optimum nitrogen
fertilization) and processing would ensure the natural fibers from own production for the
textile industry, but also the raw material for other industries with minimal environmental
pollution.
2. Materials and Methods
The study was conducted during the vegetation period of 2012. the location of Bosanska
Krupa, a sample plot is set in randomized block design with four replications. In the research
are used three varieties of flax: Michael, Belstar and variety X and 5 variants od fertilization:
T1 - control (without fertilizer application), T2 - mineral fertilizers, T3 - organic fertilization
(bovine manure), T4 - bacterial fertilizer (azoter) and T5 - organic+bacterial fertilizer.
Applied is a common technology growing of flax. During the vegetation were followed the
following features: time of emergence and growth of the plants, while the the harvest of flax
carried out in the second half of July. Selected samples of flax are wetted and dried fruits in
the river, where the does not have frequent visitors.
After immersion, the stems are washed and dried naturally in daily temperature which was
about 35 °C in the period of 10 days. The fibers were separated in the traditional way. Splint
was removed with hand-made crusher. Quality control of fiber, was performed in the
laboratory Saniteks - Velika Kladuša, and was examined length, thickness, weight and
elasticity of the fiber. Length and thickness of the fibers were determined using a micrometer,
brand Stoßgeschützt (Germany), the elasticity was determined by dynamometer brand Instron
1026 (USA), while the weight of the fibers was determined with the help of analytical
balances. In accordance with the applied research plan, for all the studied traits, was
conducted statistical analyzes of variance analysis using the statistical package SPSS version
16.0 trial.
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3. Results and Discussion
Attendees were statistically significant differences between the studied varieties for all the
characters (table 1-4). For the purposes of textile fiber length and finesse are the most
important characteristics that determine the quality of the fiber. It is recommended that the
technical stem length be longer than 60 cm (Butorac et al. 2009). During of our research the
resulting values were not lower.
By statistical analysis the significance of the results can be concluded that the differences in
stem length are conditioned with the variety and method of fertilization.
Table 1. The mean of stem length (cm) in three varieties in relation to the applied fertilizer
treatments and Levens' test
stem length
sort
Michael
Belstar
sort X
Michael
Belstar
Sort X
between var
fertilizer
T1
T2
T3
T4
T5
T1
T2
T3
T4
T5
T1
T2
T3
T4
T5
SD
N
60,13
5,20
30
77,00
0,98
30
68,03
4,50
30
80,96
2,26
30
70,63
5,33
30
60,23
6,78
30
65,66
1,47
30
68,40
1,54
30
50,43
2,12
30
72,73
4,57
30
47,00
4,14
30
51,63
1,75
30
45,06
1,11
30
50,43
1,45
30
66,53
3,85
30
Leven's test
level of significance
F
0.01
(F(4)=119.776, p< 0.01)
0.01
(F(4)=145.578, p<0.01)
0.01
(F(4)=279.548, p< 0.01)
0.01
(F(2)=201.85, p=0.000)
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Table 2. The mean of fiber length (cm) in three varieties in relation to the applied fertilizer
treatments and Levens' test
fiber length
sort
Michael
Belstar
sort X
Michael
Belstar
Sort X
between var
fertilizer
T1
T2
T3
T4
T5
T1
T2
T3
T4
T5
T1
T2
T3
T4
T5
SD
2,01
7,28
0,41
4,78
2,86
3,70
2,77
3,56
3,51
3,35
1,81
2,07
5,41
4,02
3,20
N
30
30
30
30
30
30
30
30
30
30
30
30
30
30
30
17,30
30,36
24,46
24,40
34,20
19,30
25,20
25,20
26,42
25,50
15,10
11,60
18,60
20,70
19,60
Leven's test
level of significance
F
0.01
(F(4)=11.791, p=0.000)
0.01
(F(4)=3.524, p=0.025)
0.01
(F(4)=5.492, p=0.004)
0.01
(F(2)=40.75, p=0.000).
Variety Michael fertilized with T5 has resulted with the longest fibers (34.20 cm), while the
shortest fibers were measured at T1. The hypothesis is rejected at the significance level of
0.01 (F (2) = 40.75, P = 0.000). Differences in the length of the fibers are random and sort
Michael has significantly longer fibers compared to the other two tested varieties and fertilizer
treatments T5 and T4 compared to other treatments. Kocjan and Rijavec (2010) in research
conducted in the area of Bijela Krajina reported that the average length of domestic technical
textile fiber flax was 19 cm. Based on this can be said that the results of this study agree with
the studies mentioned authors, and that the fibers are all tested varieties can be successfully
used in textile industry. The fineness of the fibers is primarily related to the thickness, weight
and elasticity of the fiber (table 3, 4 and 5).
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Table 3. The mean of fibers thickness (μ) in three varieties in relation to the applied fertilizer
treatments and Levens' test
fibers thickness
sort
Michael
Belstar
sort X
fertilizer
T1
T2
T3
T4
T5
T1
T2
T3
T4
T5
T1
T2
T3
T4
T5
Michael
Belstar
Sort X
between var.
SD
0,008
0,013
0,008
0,011
0,013
0,007
0,010
0,008
0,010
0,008
0,005
0,010
0,008
0,007
0,004
N
30
30
30
30
30
30
30
30
30
30
30
30
30
30
30
0,054
0,042
0,022
0,034
0,028
0,030
0,032
0,032
0,032
0,034
0,024
0,020
0,026
0,020
0,012
Leven's test
level of significance
F
0.01
(F(4)=11.791, p=0.000)
0.01
(F(4)=3.524, p=0.025)
0.01
(F(4)=5.492, p=0.004)
0.01
(F(2)=40.75, p=0.000).
Statistical analysis of the significance of differences among the varieties and treatments
(F(2)=40.75, p=0.000) shows that these differences were significant only at the level of
varieties.
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Table 4 Mean values of fibers elasticity (cN/dtex), with three varieties in relation to the
applied fertilizer treatments and Levens' test
fibers elasticity
sort
Michael
Belstar
sort X
fertilizer
T1
T2
T3
T4
T5
T1
T2
T3
T4
T5
T1
T2
T3
T4
T5
Michael
Belstar
Sort X
between var.
7,50
9,00
6,00
6,00
10,75
10,00
8,00
9,00
9,00
9,00
5,50
6,50
6,00
9,00
7,00
Leven's test
level of significance
0.01
0.01
0.01
0.05
SD
0,707
1,414
0,000
1,414
3,889
0,000
0,000
1,414
1,414
1,414
0,707
0,707
0,000
1,414
0,000
N
30
30
30
30
30
30
30
30
30
30
30
30
30
30
30
F
(F(2)=6.345, p=0.01)
After the statistical analysis, it is evident that the statistical differences are not random Ho is
rejected at the significance level of 0.05 and concluded that the variety Michael has elastic
fibers in comparison to other tested varieties of flax.
Table 5. Average values of fibers weight (g) in relation to the applied fertilizer treatments
fertilizer
T1
T2
T3
T4
T5
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Michael
0,0065
0,0059
0,0054
0,0058
0,0059
Belstar
0,0046
0,0043
0,0045
0,0058
0,0053
sort X
0,0025
0,0029
0,0034
0,0039
0,0021
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4. Conclusion
After the research and statistical processing of the obtained data, we can conclude that are
present statistically significant differences based on the characteristics of the studied varieties
and fertilizer treatments.
The best results were achieved with the fertilization treatment T5 (organic+bacterial fertilizer).
Based on the analysis of the length, thickness and elasticity of fibers, very good results were
obtained with the cultivar Michael and Belstar, and it can be concluded that these two
varieties are intended for the processing. The variety X has the most tender and shortest fibers,
and it can be concluded that gives better results with bacteriological fertilization.
Therefore, this work is a contribution to the improvement of fiber flax cultivation and
encouragement of this type of cultivation and production in the northwestern part of Bosnia
and Herzegovina, and beyond.
5. References
Butorac, J., Pospišil, M., Mustapić, Z., Duvnjak, I. (2009). Procjena agronomskih i morfoloških svojstava sorata
predivog lana bez prihrane i s prihranom dušikom. Sjemenarstvo. 26. 3 - 4.
Butorac, J., Šurina, R., Andrassy, M., Popišil, M., Augustinović, Z., Brčić, M. (2008). Utjecaj dužine vegetacije
kultivara predivog lana na morfološka tekstilno-tehnološka svojstva. International Symposium on agrisulture.
Opatija. 723 - 727.
Hann, M. A. (2005). Innovation in linen manufacturing. Textile progress. 37. 7 - 8.
Kocjan-Ačko, D., Rijavec, T. (2010). Gospodarsko pomembne latnosti domačega lana (Linum ustitassimum L.)
iz Bele krajine ter možnosti ponovne pridelave in predelave. Novi izzivi v poljedelstvu. Slovensko agronomsko
društvo. Rogaška Slatina. 160 - 167.
Šurina, R., Andrassy, M., Pezelj, E. (2006). Technical and Cottonised Flax Fibers - Comparison of Properties.
Book of abstracts of the 37 thInternational Symposium on Novelties in Textiles. Ljubljana. 52.
Šurina, R., Andrassy, M., Vujasinović, E. (2009b). Lan - biljka i vlakno kroz stoljeća. Tekstil 58. 625 - 639.
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2490
Title
A name given to the resource
EFFECT OF DIFFERENT FERTILIZERS TYPES ON FLAX FIBRES CHARACTERISTICS IN DIFFERENT CULTIVARS OF FLAX
Author
Author
DERVIŠEVIĆ, Selma
VELADŽIĆ, Mirsad
JOGIĆ, Vildana
Abstract
A summary of the resource.
This work presents the results of research on the impact of organic, minerals, organic and microbiological fertilizers on characteristics of flax fibers in three different varieties of flax. The experiment was performed in the municipality of Bosanska Krupa in 2012. The parcel was set up in randomized block of design with four replications, and the size of the assessment parcel was 10 m2. All three varieties are sown on the basis of 1000 germinable seeds per m2. They represented two foreign sorts: Michael, Belstar and domestic sort X. In the autumn mineral fertilizers were entered in soil in the scale of NPK = 15:15:15, 250 g/20m2, 3 kg/20m2 of manure and 10 l/ha of microbiological fertilizers ''Azoter''. The different combinations of fertilizers were used: organic fertilizer, microbiological fertilizer, organic+microbiological fertilizer and control (without fertilization) - for each tested sort. The research was a multi-factorial (cultivar and method of fertilization). According to the results obtained during the one-year research, Michael and Belstar varieties have achieved the best results with organic+bacteriological fertilizer. Fibers got out of Michael and Belstar variety have better quality, they are longer and harder, which makes them suitable for use in technical textiles where even coarser fibres get more important. X sort fibres are the shortest and the thickest, so they give better results with bacteriological fertilizers. Keywords: flax, sort, morphological characteristics, phenological characteristics, fiber, fertilizer.
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International Burch University
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2014-05-15
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ISSN 978-9958-834-36-3
Q Science (General),QH301 Biology,QH426 Genetics
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https://omeka.ibu.edu.ba/files/original/1d9974681b6c9bffe870a484904e374d.pdf
c4affc5a26cd0d0ad6ebcdb353c7fdfb
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Text
PROCEEDINGS
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LOW COST AND PORTABLE HEARTBEAT RATE MEASUREMENT
FROM THE FINGER
Bahadır Cömert, Ayhan İstanbullu, Uğur Turhal
Department of Computer Engineering, Balıkesir University
baha_c.84@hotmail.com, iayhan@balikesir.edu.tr, ugurturhal@balikesir.edu.tr
ABSTRACT
In this study, portable and low cost heart beat rate measurement device has been designed
with using PIC 16F877. It measures heart beat rates from finger using optical sensors and the
rate is then averaged and displayed on a text based LCD. The finger tip probe has been
selected from commercial products. The device works with 1 x 9V battery. Also it measures
ambient temperature and humidity in addition to heart beat. The measurement accuracy is
acceptable. The hardware that has been designed in this study is available for checking the
pulse with education purpose. The hardware can be improved adding wireless data transfer
devices in telemedicine applications. The device has the advantage that it can be used by nonprofessional people at home to measure the heart rate easily and safely. This paper report
describes how to build a digital heart-rate monitor using a PIC 16F877 microcontroller
(MCU). The heart beat rate per minute is displayed on an LCD.
Keywords: biomedical instrumentation, heart rate measurement, bio electronic, PIC 16F877
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I. INTRODUCTION
The heart is a strong pump which pumps between 5-35 litre blood to the body with changing
speed between 60-80 beats per minute and approximately 9000 litres in a day. The regular
control and the measurement of heart beat per minute (bpm) of an organ , active in body like
this, are quite important. One of the mostly used and certain methods for measuring the heart
rate is electro-cardiogram (ECG). ECG is an expensive device and it is not economical for
heart rate measurement. There are also some devices like wrist whatches which are low-cost.
These devices can give certain results but although they are low-cost, their price is very high
which makes them uneconomic.
There are many measurement methods valid for this. However, the use of digital sensors in
measurements makes having much certain and correct results possible. In fact, these
measurement sensors have started to being placed in smart phones in modern day. However,
this technology is getting more expensive as it is getting smaller.
Sport is in every step of life. Mostly, athletes have lower heart rates than people who move
relatively less. While the heart rates of older children are about 90, the heart rates of babies
are about 120. The heart rate gradually increases while doing exercises and it returns slowly
to the rest value after exercises. The revealing rate, when the pulse is normal, is the indicator
of how healthy the person is. The values below the normal heart rate are usually signs of
bradycardia; and the values above the normal heart rate are signs of tachycardia. However, the
sport can cause a heart attack when it is done unconsciously. The heart attack was the second
illness is stated 722,130 between 2000-2011. These results prove the importance of regular
cardiac rhythm control [10].
When the literature is reviewed for the studies made about this issue, it is possible to see some
other low cost more developed studies or like the present one.
In their study Hashem and his colleagues combine analogue and digital signal processing
techniques to keep the device simple and to efficiently suppress the disturbance in signals.
Their experimental studies show that the heart rate can be filtered and digitized so that it is
possible to calculate the accurate pulse rate.
In Laghrouche’s study, arterial oxygen saturation in the patient’s blood signal is measured
with an optical sensor and converted to digital data using a microcontroller system. Then the
digital data are sent to a receiver where it is in 433 MHz FM-FSK transmitter. At the receiver,
the digital data are reconverted to analog signal to be monitored and recorded on the PC.
In Mamun’s study, a measurement circuit is developed by using a low cost ATmega8
microcontroller system from ATMEL. This measurement circuit can be easily used by
families, hospitals, clinics and sports centre.
In Toral and his colleagues’ study, pulse, SpO2 and temperature signals are conveyed to
computer and displayed with LabVIEW program. In this study, wireless communication
technologies are not used.
The aim of this study is to design a low-cost and portable cardiac rhythm measuring
instrument and to make a critical measurement real. The designed device is working with
1x9V the ambient temperature and moisture. The design circuit and graphics (software
program) about the device are shared in this study.
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II. THE PULSE OXIMETRY DEVICE
The pulse oximetre are devices that measure the oxygenation of blood passing through tissue
bed which is between photodedector and light source that give out red and infrared light with
special probes placed on finger or ear. The block diagram of mentioned device is shown in
Figure 1. Actually, the device consist of infrared transmitter LED and infrared receiver
photodiode. The transmitter-sensors is fixed to finger of the subject. ( Figure 2)
Figure 1: Block diagram of the measurement device
Figure 2: Transmitter-sensors is fixed to finger of the subject
The LED sends infrared light to the finger. Photo-transistor detects this ray and measures the
change in blood amount from finger artery. This signal as pulse, then is increased, filtered and
sent to the low-cost microcontroller to analyze and show. The microcontroller counts the
number of pulses in certain intervals and therefore, the heart rate of the subject is obtained.
This input is collected for a while and averaged to see the heart rate accurately. The calculated
heart rate is displayed on LCD as beats per minute. The circuit diagram of measurement
device is shown in Figure 3 and printed circuit diagram is shown in Figure 4 and sample
measurement results are shown in Figures 5-6-7.
Figure 3: Circuit diagram of measurement device
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Figure 4: Printed circuit diagram
Figure 5: Sample measurement results
Figure 6: Sample measurement results
Figure 7: Sample measurement results
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III. THE STRUCTURE AND OPERATION OF CIRCUIT
The circuit basically consist of two functional amplifiers, a low-pass filter, a microcontroller
and an LCD. During the studies, it is determined to use low-pass filter in the circuit to filter
the high frequency noise coming from surroundings. The corner frequency of amplifier is
chosen as 1.6 Hz. The output of amplifier is connected to one of the digital inputs of
PIC16F877 version microcontroller via R4 resistance and RV1 trimpot. In order to decrease
the cost of circuit, the microcontroller is worked from 4 MHz resonator. The output ports of
microcontroller are connected to the LCD. The circuit starts when it is pressed on push-button
switch working with 9V battery.
When the structure of circuit is analysed; C5 (47 uF) capacitor functions as filter. R7 (10K)
resistance is a current limiting resistor that prevents the high current that will follow on D1
(IR LED) diode. D1 and D2 diodes in the circuit diagram consist of IR Led Transmitter and
photodiode receiver which form the internal structure of device called pulse oximeter. After
the pulse oximeter is fixed to the index finger, a signal is sent to zener diode by D1 (IR)
transmitter as to pressure of blood flowing through fingertip. This signal sent to the zener
diode starts to sway smoothly. D2 (Photodiode) receiver diode receives the signal sent by D1
(IR) transmitter diode and voltage is formed upon the amount of signal. This voltage is
enhanced with maximum lucrative LM358N (U5:A) op-amp. A signal is obtained in response
to the voltage enhanced by op-opamp.This signal is filtered from low pass filter consisting of
R6 resistance and C6 capacitor. After that, oscillation is decreased to minimum and is
implemented to the output of LM358N (U5:B) op-amp and the analogue input of
microcontroller (MCU). The implemented voltage is calibrated with RV1 trimpot. And this
calibrated voltage is transformed into an understandable numerical value with software
program and then it is conveyed to LCD screen via PORTB that is the output of
microcontroller. In addition to the pulse number, ambient temperature and moisture are also
conveyed to the LCD screen after being measured with the SHT11 heat and moisture sensor
connected to the PORTD output of MCU. This pulse oximeter device is low-cost and its
accuracy rating is not high enough, so it is quite important to place the finger’s plump point
properly into the device’s slot.
IV. THE SOFTWARE OF CIRCUIT IN COMPUTER LANGUAGE
The software is developed by using popular C basic compiler and CCS-C is used as program
description language. In Figure 8 below, the program listing of microcontroller is given.
When it is mentioned about the written program; at the beginning of the program, variables
used in program are referred. RB0-RB7 and RD0-RD1 pins of PORT B are used as outputs.
RA2 pin of PORT A is set as input port. The Program starts when the key, which works with
9V battery, is on and after the pulse oximeter is fixed to fingertip. As the analogue-digital
converter pin of microcontroller, RA2 pin transforms the voltage that is transmitted from
finger into a numerical value. After that, the pulse value measured from finger is transmitted
to for loop and a sample of pulse value is obtained in every 50 ms. And this process is
repeated 30 times. The reason for this repetition is to reach the truest pulse value by obtaining
many samples. These 30 samples are averaged and divided by 60. The numerical value of
voltage coming from fingertip as a result of measurements is multiplied by 2, because the
response of this voltage gives the real pulse value. And this is the reason for dividing the
average by 60. If the device is not fixed to finger or the pulse value is lower than 50 or higher
than 140, pulse value will not be displayed and “WRONG MEASUREMENT” will be
displayed as a warning. And lastly; with the measure pulse value, ambient temperature and
moisture are also displayed on LCD screen.
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Program Software
#include <16F877A.h>
#device adc=10
#FUSES XT,PROTECT
#use delay(clock=4MHz)
#include <Port-B-LCD.c>
#include <sht11.c>
float restemp, truehumid;
float olcum;
int1 a;
int8 say;
long ort;
void main()
{
setup_adc_ports(ALL_ANALOG);
setup_adc(ADC_clock_div_32);
setup_psp(PSP_DISABLED);
setup_spi(SPI_SS_DISABLED);
setup_timer_0(RTCC_INTERNAL|
RTCC_DIV_1);
setup_timer_1(T1_DISABLED);
setup_timer_2(T2_DISABLED,0,1);
setup_comparator(NC_NC_NC_NC);
setup_vref(FALSE);
lcd_hazirla();
output_low(pin_b4);
set_adc_channel(2);
delay_ms(1);
sht_init();
while(TRUE)
{
ort=0;
for (say=0;say<30;say++)
{
olcum=read_adc();
ort=ort+olcum;
delay_ms(50)
}
sht_rd (restemp, truehumid);
olcum=ort/60;
imlec(1,1);
if(olcum>50&&olcum<140)
{
printf(lcd_veri,"NABIZ=%2.0f
" ,olcum);
}
else
{
a++;if (a==0) printf(lcd_veri,"HATALI OLCUM!");
if (a==1) printf(lcd_veri,".............");
}
imlec(2,1);
printf(lcd_veri,"T=%3.1f%cC", restemp,223);
imlec(2,10);
printf(lcd_veri,"Rh=%2.0f%% ", truehumid);
}
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V. CONCLUSION
In order to measure the heart rate, low-cost and microcontroller based device is described.
The device has an advantage that it can be used by any people who is not professional and it
makes it possible to measure the heart rate safely and easily.
The device can be developed in some areas as shown below:
Voice can be added to the device and therefore; voice output will be possible during the
pulse.
The highest and lowest heart rate numbers can be displayed after a while.
Serial output can be added to the device and therefore; heart beats can be sent to the PC
for online and offline analysis.
Warnings or abnormalities (as too high or too low heart beats) can be shown on the LCD or
with a LED or with a bell.
REFERENCES
[1]
Forerunner 201/301 User Guide, web site: http://www.grmin.com
[2]
Pulsar heart rate monitors, web site:http://www.heartratemonitor.co.uk
[3]
Cosy Communications web site: http://cosycommunications.com
[4] Johnston, W.S., Mendelson, Y. (2004). Extracting breathing rate information from a wearable reflectance
pulse oximeter sensor. In Engineering in Medicine and Biology Society - IEMBS '04 : 26th Annual International
Conference of the IEEE. Vol. 2, 5388-5391.
[5] Paradiso, R, Loriga, G., Taccini, N. (2005). A wearable health care system based on knitted integrated
sensors. IEEE Transactions on Information Technology in Biomedicine, 9, 337-344.
[6] D. Ibrahim and K. Buruncuk, "Heart Rate Measurement from the Finger Using a Low- Cost
Microcontroller," Near East University, Faculty Of Engineering, TRN, 2005.
[7] S. Kara, et al., "Low-cost compact ECG with graphic LCD and phonocardiogram system design," Journal
of Medical Systems, vol. 30, pp. 205-209, 2006.
[8] V. Jayasree, et al., "Design and Development Of a Simple Hardware Setup for Sensing Blood Volume
Pulse and a PIC Microcontroller Based Heart Rate Meter," in Biomedical and Pharmaceutical Engineering,
2006. ICBPE 2006. International Conference on, 2006, pp. 256-258.
[9] M. Laghrouche , S. Haddab, S. Lotmani, K. Mekdoud, S. Ameur, " Low-Cost Embedded Oximeter,"
Mouloud MAMMERI University, LAMPA Laboratory, Department of Electronics, Po Box 17 RP 15000.
[10]https://www.destatis.de/DE/ZahlenFakten/GesellschaftStaat/Gesundheit/Todesursachen/Tabellen/Sterbefaell
eInsgesamt.html.
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Bahadır Cömert was born in Samsun, Turkey in 1984. He graduated in 2011 from
Departmen of Electronic-Computer Science Education, Electronic and Communication
Teaching in Marmara University in İstanbul. He is having his post graduate in Balıkesir
University in Turkey. His current research interests include the investigation of information
technologies to support electronic and electronic engineering education, medical
instrumentation and medical informatic.
Ayhan Istanbullu was born in Kutahya, Turkey in 1972. He was awarded his Ph.D. degree in
2003 from Gazi University in Turkey. Between 2001 and 2006 he was an instructor at the
University of Mugla, Turkey in the Department of Electronic and Computer Science
Education. He is currently an Associated Professor in the Computer Engineering Department
of Balikesir University, Turkey. His current research interests include the investigation of
information technologies to support electronic and computer engineering education, medical
instrumentation and medical informatic.
Uğur TURHAL was born in Trabzon, Turkey in 1988. He was graduated with Bachelor’s
degree from Marmara University in 2011. He is a graduate student in the Computer
Engineering Department of Yalova University, Turkey. Also, He is working as a computer
specialist at Balikesir University, Turkey. Interested areas are; Bioinformatics, Signal
Processing, Microarray Datasets, Cancer Dieseases
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2528
Title
A name given to the resource
LOW COST AND PORTABLE HEARTBEAT RATE MEASUREMENT FROM THE FINGER
Author
Author
COMERT, Bahadir
ISTANBULLU, Ayhan
TURHAL, Ugur
Abstract
A summary of the resource.
In this study, portable and low cost heart beat rate measurement device has been designed with using PIC 16F877. It measures heart beat rates from finger using optical sensors and the rate is then averaged and displayed on a text based LCD. The finger tip probe has been selected from commercial products. The device works with 1 x 9V battery. Also it measures ambient temperature and humidity in addition to heart beat. The measurement accuracy is acceptable. The hardware that has been designed in this study is available for checking the pulse with education purpose. The hardware can be improved adding wireless data transfer devices in telemedicine applications. The device has the advantage that it can be used by nonprofessional people at home to measure the heart rate easily and safely. This paper report describes how to build a digital heart-rate monitor using a PIC 16F877 microcontroller (MCU). The heart beat rate per minute is displayed on an LCD. Keywords: biomedical instrumentation, heart rate measurement, bio electronic, PIC 16F877
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/f402afff9e7568a9e686f87462421fbb.pdf
18e418ffa08dc169fa40f1b0ee183fbe
PDF Text
Text
PROCEEDINGS
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OVERVIEW OF THE AUTOSOMAL STR CLUSTERING BETWEEN BALKAN
POPULATIONS
Adna Ašić1, *, Bea Bunjo1, Serkan Doğan1, Larisa Bešić1, Imer Muhović1, Damir Marjanović2
1
International Burch University, Department of Genetics and Bioengineering, Sarajevo,
Bosnia and Herzegovina,
2
University of Sarajevo, Institute for Genetic Engineering and Biotechnology, Sarajevo,
Bosnia and Herzegovina
adna.asic@gmail.com
ABSTRACT
Autosomal short tandem repeats (STRs) are the most widely used DNA markers in forensic
investigation of the population history, human migration patterns, and genealogical research.
In this study, the usefulness of 13 most widely used STR loci (D3S1358, TH01, D21S11,
D18S51, D5S818, D13S317, D7S820, D16S539, CSF1PO, vWA, D8S1179, TPOX, and FGA)
was examined along with the investigation of their application in the studies of the phylogeny
of human populations. We compared allele frequencies of STR loci of the populations from
the Balkan Peninsula to determine the similarities and differences among them and to
determine how informative they are when it comes to the human identity testing. We made
UPGMA phylogenetic tree using POPTREE2 software and Nei’s table of genetic distances
using MEGA5.21 software. Additionally, MDS (multidimensional scaling) plot was generated
using SPSS 20.0 software. The results implied that both geographical proximity and shared
history are determining the strong clustering of the populations on the Balkans. Another
conclusion drawn from this overview is that the studied STR markers are highly polymorphic
and thus, satisfyingly informative to be used for human identity testing and phylogenetic
research.
Keywords: Balkan Peninsula, autosomal STRs, phylogenetic tree, genetic distance, clustering,
population study
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INTRODUCTION
Short tandem repeats (STRs), also called microsatellites or simple sequence repeats (SSRs),
are the DNA sequences located in the non-coding region of the human genome and consist of
2-7 bp long repetitive units that are repeated 3-15 times, thus making STRs long up to
approximately 400 bp (Gunn, 2006, Goodwin, Linacre, Hadi, 2011). They occur on all 22
pairs of autosomal chromosomes, and on X and Y sex chromosomes (Gunn, 2006). Since they
are typically located between the genes, they can be of different size among the individuals
without affecting the genetic health of the person (Butler, 2010). These differences can be the
result of mutations, recombination, and independent chromosomal variation (Gunn, 2006),
and it makes STRs effective for the human identification purposes (Butler, 2010). STRs are
also used for studying the diversity among different populations, as well as for the
determination of similarity between closely related populations (Doğan, Kovačević,
Marjanović, 2013). 13 core STR loci that are most widely used are chosen to be the basis of
the CODIS national DNA database and they are: CSF1PO, FGA, TH01, TPOX, VWA,
D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, and D21S11 (Butler,
2011).
Data in the form of allele frequencies are useful for the studies of the phylogenetic
relationships between different species or populations. STRs are the markers of choice in the
modern phylogenetic analyses. They are providing genetic distance measures used for the
construction of the phylogenetic tree which shows similarities and differences between the
populations. Two most widely used methods for the construction of the phylogenetic tree are:
neighbor-joining (NJ) and un-weighted pair group method with arithmetic mean (UPGMA).
The latter one is used for showing the relationships among closely related populations and
usually produces a rooted tree (Takezaki, Nei, 1996).
In the present study, allele frequencies of 13 autosomal STR loci were compared for 14
populations originating from the area of the Balkan Peninsula and the phylogenetic tree was
constructed showing the relationships among these populations. The aim of the study was to
determine whether autosomal STR loci are informative enough to be used for human
identification purposes and in the population studies. Additionally, we wanted to explore the
similarities and differences among the populations on the Balkans.
MATERIALS AND METHODS
14 populations originating from the Balkan Peninsula were compared in this study: BosnianHerzegovinian, Croatian, Serbian, Montenegrin, Macedonian, Slovenian, Turkish (living in
Turkey), Turkish (living in Bosnia and Herzegovina), Albanian (living in Kosovo, Serbia),
Albanian (living in North-West Italy), Romanian, Hungarian, Greek, and the population from
Vojvodina, Serbia (Figure 1). Table 1 lists all populations along with the references for the
articles from which data were taken.
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Figure 1: Geographical location of the countries of origin of the populations compared in the
study (colored in grey)
Data on the allele frequencies was collected by searching through the journal databases. Only
the articles giving the details about the experimental procedure and using the adequate sample
size were included in the research. Additionally, studies which did not include all 13 STR loci
of interest were excluded from this research.
Table 1: The list of the populations compared in the present study
Population
Bosnian-Herzegovinian
Croatian
Serbian
Montenegrin
Macedonian
Slovenian
Turkish (Turkey)
Turkish (Bosnia and Herzegovina)
Albanian (Kosovo, Serbia)
Albanian (NW Italy)
Romanian
Hungarian
Greek
Vojvodina, Serbia
Reference
Marjanović et al. (2006)
Projić et al. (2007)
Keckarević et al. (2009)
Veselinović et al. (2004)
Havaš et al. (2007)
Drobnič et al. (2005)
Çakir et al. (2003)
Dogan et al. (2013)
Kubat et al. (2004)
Robino et al. (2001)
Barbarii et al. (2004)
Rak et al. (2010)
Kovatsi et al. (2006)
Petrić et al. (2012)
Phylogenetic tree showing the relationships between the populations was constructed using
POPTREE2 program (Takezaki, Nei, Tamura, 2010). The method of choice was UPGMA
method since it is the best option for showing the distances between closely related species or
populations and is giving the clearest results. The table of Nei’s genetic distances was
obtained using MEGA5.21 software (Tamura, Peterson, D., Peterson, N., Stecher, Nei, Kumar,
2011). Multidimensional scaling (MDS) analysis and plot generation were done using SPSS
20.0 software package (SPSS, Chicago, IL, USA).
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RESULTS AND DISCUSSION
The results of this study are presented in the rectangular (Figure 2) and the circular (Figure 3)
UPGMA phylogenetic trees and the Nei's table of genetic distances (Table 2). The results
imply that the populations from the Balkan Peninsula are genetically close to each other since
all of them clustered closely to each other in the phylogenetic trees. Also, large genetic
distances between the populations were not observed in the genetic distance table. All
populations from the Western Balkans, except Montenegro, are positioned close to each other
which is explained by the fact that they share the common origin and historical background.
Although it is on the opposite side of the phylogenetic tree when compared to the other
populations from the Western Balkans, Montenegrin population still seems to be very close to
these populations according to the Nei’s table. General population from Serbia is positioned
close to the population from Vojvodina province, which is also expected since these two
populations inhabit the same country.
Figure 2: Rectangular UPGMA phylogenetic tree showing the relationships between the
populations inhabiting the Balkan Peninsula
The similarity between the Balkan populations observed in this study is confirmed in a paper
by Projić et al. (2007), where the similar results were obtained with the smaller number of
populations from the Balkans. Marjanović et al. (2006) did not find any significant
differences between Bosnian-Herzegovinian and Croatian populations. Havaš et al. (2007) did
not find large genetic differences between Macedonians, on one side, and Serbians and
Greeks, on the other. In that study, minor differences were found only between Macedonians
and Romanians.
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Figure 3: Circular UPGMA phylogenetic tree showing the relationships between the
populations inhabiting the Balkan Peninsula
Turkish populations living in Turkey and in Bosnia and Herzegovina have clustered close to
each other, as well as Albanian populations living in Kosovo, Serbia and in North-West Italy,
which was expected since these are the same populations living in different countries. In this
way, it is shown that the common origin plays an important role in determining the genetic
similarity/difference between populations, apart from their geographical positions.
Table 2: Nei’s table of genetic distances for the populations from the Balkan Peninsula
VOJ
TUR,
B&H
B&H
CRO
SRB
MTN
MAC
ALB
GRE
ALB,
IT
HUN
SLO
ROM
TUR,
B&H
0,018
B&H
CRO
SRB
MTN
MAC
ALB
GRE
0,013
0,011
0,011
0,016
0,012
0,016
0,010
ALB,
IT
0,016
0,022
0,016
0,014
0,020
0,014
0,018
0,015
0,013
0,012
0,010
0,020
0,018
0,013
0,017
0,013
0,011
0,017
0,018
0,015
0,015
0,018
0,014
0,012
0,010
0,008
0,017
0,012
0,015
HUN
SLO
ROM
TUR
0,007
0,007
0,014
0,016
0,018
0,011
0,017
0,019
0,012
0,018
0,015
0,015
0,018
0,014
0,000
0,015
0,010
0,008
0,005
0,013
0,009
0,011
0,005
0,011
0,010
0,009
0,014
0,012
0,013
0,007
0,018
0,017
0,015
0,023
0,017
0,017
0,014
0,020
0,015
0,013
0,018
0,013
0,015
0,014
0,011
0,013
0,017
0,015
0,005
0,011
0,013
0,011
0,014
0,019
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The results of this study were confirmed with the multidimensional scaling (MDS) plot which
shows the distances between the compared populations in the two dimensions (Figure 4).
Figure 4: MDS plot which shows the relationships between the populations from the Balkan
Peninsula
When it comes to the properties of the individual loci, two most informative loci in the
populations from the Balkans are FGA with the average power of discrimination (PD) value
of 0.964 and D18S51 with the average PD value of 0.963. On the other hand, the least
informative loci are TPOX (average PD value of 0.809) and TH01 (average PD value of
0.921).
CONCLUSION
The general conclusion drawn from this research is that the populations inhabiting the Balkan
Peninsula are genetically very close to each other since important genetic differences based on
the allele frequencies of 13 autosomal STR loci between the populations were not observed.
Additionally, it is concluded that the STR loci tested are informative enough to be used for the
purposes of individualization and the population studies.
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REFERENCES
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PROCEEDINGS
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Dublin Core
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Extent
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2439
Title
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OVERVIEW OF THE AUTOSOMAL STR CLUSTERING BETWEEN BALKAN POPULATIONS
Author
Author
AŠIĆ, Adna
BUNJO, Bea
DOGAN, Serkan
BEŠIĆ, Larisa
MUHOVIĆ, Imer
MARJANOVIĆ, Damir
Abstract
A summary of the resource.
Autosomal short tandem repeats (STRs) are the most widely used DNA markers in forensic investigation of the population history, human migration patterns, and genealogical research. In this study, the usefulness of 13 most widely used STR loci (D3S1358, TH01, D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, CSF1PO, vWA, D8S1179, TPOX, and FGA) was examined along with the investigation of their application in the studies of the phylogeny of human populations. We compared allele frequencies of STR loci of the populations from the Balkan Peninsula to determine the similarities and differences among them and to determine how informative they are when it comes to the human identity testing. We made UPGMA phylogenetic tree using POPTREE2 software and Nei’s table of genetic distances using MEGA5.21 software. Additionally, MDS (multidimensional scaling) plot was generated using SPSS 20.0 software. The results implied that both geographical proximity and shared history are determining the strong clustering of the populations on the Balkans. Another conclusion drawn from this overview is that the studied STR markers are highly polymorphic and thus, satisfyingly informative to be used for human identity testing and phylogenetic research. Keywords: Balkan Peninsula, autosomal STRs, phylogenetic tree, genetic distance, clustering, population study
Publisher
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International Burch University
Date
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2014-05-15
Keywords
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Article
PeerReviewed
Identifier
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ISSN 978-9958-834-36-3
Q Science (General),QH301 Biology,QH426 Genetics