<p>Pairwise genetic distance matrix based on the <i>R</i><sub><i>st... more <p>Pairwise genetic distance matrix based on the <i>R</i><sub><i>st</i></sub> and <i>P</i> values between the five major ethnic groups from Northern Iraq and representative nearby and distant populations<sup><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0187408#t003fn001" target="_blank">†</a></sup>.</p
The Southwest Asian, circum-Mediterranean, and Southern European populations (collectively, SWAMS... more The Southwest Asian, circum-Mediterranean, and Southern European populations (collectively, SWAMSE) together with Northern European populations form one of five "continental" groups of global populations in many analyses of population relationships. This region is of great anthropologic and forensic interest but relationships of large numbers of populations within the region have not been able to be cleanly resolved with autosomal genetic markers. To examine the genetic boundaries to the SWAMSE region and whether internal structure can be detected we have assembled data for a total of 151 separate autosomal genetic markers on populations in this region and other parts of the world for a global set of 95 populations. The markers include 83 ancestry informative SNPs as singletons and 68 microhaplotype loci defined by 204 SNPs. The 151 loci are ancestry informative on a global scale, identifying at least five biogeographic clusters. One of those clusters is a clear grouping of 37 populations containing the SWAMSE plus northern European populations to the exclusion of populations in South Central Asia and populations from farther East. A refined analysis of the 37 populations shows the northern European populations clustering separately from the SWAMSE populations. Within Southwest Asia the Samaritans and Shabaks are distinct outliers. The Yemenite Jews, Saudi, Kuwaiti, Palestinian Arabs, and Southern Tunisians cluster together loosely while the remaining populations from Northern Iraq, Mediterranean Europe, the Caucasus region, and Iran cluster in a more complex graded fashion. The majority of the SWAMSE populations from the mainland of Southwest Asia form a cluster with little internal structure reflecting a very complex history of endogamy and migrations. The set of 151 DNA polymorphisms not only distinguishes major geographical regions globally but can distinguish ancestry to a small degree within geographical regions such as SWAMSE. We discuss forensic characteristics of the polymorphisms and also identify those that rank highest by Rosenberg's In measure for the SWAMSE region populations and for the global set of populations analyzed. DATA AVAILABILITY: Genotypes on all 151 markers for all 3790 individuals typed in the Kidd Lab on the 72 Kidd lab populations have been deposited in the Zenodo archive and can be freely accessed at https://doi.org/10.5281/zenodo.4658892. Some of the data has been made public previously as supplemental files appended to publications. Data for the additional individuals included in the analyses was taken from already public datasets as indicated in the text.
Y-chromosomal haplogroups are sets of ancestrally related paternal lineages, traditionally assign... more Y-chromosomal haplogroups are sets of ancestrally related paternal lineages, traditionally assigned by the use of Y-chromosomal single nucleotide polymorphism (Y-SNP) markers. An increasingly popular and a less labor-intensive alternative approach has been Y-chromosomal haplogroup assignment based on already available Y-STR data using a variety of different algorithms. In the present study, such in silico haplogroup assignments were made based on 23-loci Y-STR data for 100 unrelated male individuals from the Tuzla Canton, Bosnia and Herzegovina (B&H) using the following four different algorithms: Whit Athey's Haplogroup Predictor, Jim Cullen's World Haplogroup & Haplogroup-I Subclade Predictor, Vadim Urasin's YPredictor and the NevGen Y-DNA Haplogroup Predictor. Prior in-house assessment of these four different algorithms using a previously published dataset (n=132) from B&H with both Y-STR (12-loci) and Y-SNP data suggested haplogroup misassignment rates between 0.76% and 3.02%. Subsequent analyses with the Tuzla Canton population sample revealed only a few differences in the individual haplogroup assignments when using different algorithms. Nevertheless, the resultant Y-chromosomal haplogroup distribution by each method was very similar, where the most prevalent haplogroups observed were I, R and E with their sublineages I2a, R1a and E1b1b, respectively, which is also in accordance with the previously published Y-SNP data for the B&H population. In conclusion, results presented herein not only constitute a concordance study on the four most popular haplogroup assignment algorithms, but they also give a deeper insight into the inter-population differentiation in B&H on the basis of Y haplogroups for the first time.
Since the introduction of the term low copy number DNA, also referred as low template DNA, touch ... more Since the introduction of the term low copy number DNA, also referred as low template DNA, touch DNA or trace DNA analysis, it has quickly become focal point of forensic DNA testing as well as other DNA based studies. Low template DNA (ltDNA) samples can be described as the samples which involve single source samples with template DNA in concentrations below 100 picograms (pg). Due to sensitivity of ltDNA samples to contamination, it is of great importance to optimize performance of the multiplex STR systems and existing protocols to increase chance of successful analysis. The main objective of this study was analysis of 20 challenging samples (skeletal remains, cigarette buts, chewing gum, poorly collected buccal swabs etc.) mostly low template DNA samples, preliminarily profiled by PowerPlex ® 16 multiplex STR systems and additionally processed with new generation multiplex STR kit PowerPlex ® Fusion. Sample isolation was done using a standard phenol-chloroform method for bone samples and DNeasy ® Blood and Tissue Kit for other forensic samples. PowerPlex ® 16 (PP16), multiplex STR system and PowerPlex ® Fusion (PP Fusion) were used for co-amplification of 15 and 24 autosomal STR loci respectively. Results of this preliminary study suggest that PP Fusion primer set is better optimized for the analysis of ltDNA samples, and it is more robust regarding presence of the potential PCR inhibitors.
Bosnia and Herzegovina is located in the South-Eastern Europe, characterized by numerous historic... more Bosnia and Herzegovina is located in the South-Eastern Europe, characterized by numerous historical influences, massive migration processes and complex population structure. For that reason, the aim of this study is to provide an accurate and precise update of the population genetics data of allele frequencies on 23 Y-STR loci in Bosnia and Herzegovina using larger sample size. For this purpose, 480 adult male individuals from the general population have been genotyped over 23 Y-STR loci contained in the PowerPlex Y23 system. Population genetics parameters have been calculated, namely allele and haplotype frequencies, gene and haplotype diversity, as well as Rst and P values for the assessment of interpopulation differences. The obtained results are in close agreement with previously published data for Bosnian-Herzegovinian population, as well as for local subpopulations. This study offers significantly increased resolution and information content, with 454 unique haplotypes. Popula...
The relationship between genetic risk factors of thrombophilia and pregnancy loss (PL) is being d... more The relationship between genetic risk factors of thrombophilia and pregnancy loss (PL) is being discussed. The focus has been on F5 1691G>A, F2 20210G>A, and MTHFR 677C>T polymorphisms that may predispose women to microthrombosis during the stages of embryo implantation and placentation. Although, the frequencies of these polymorphisms were reported in different populations, such studies have not yet been performed in Bosnian population. In this study, we determined the prevalence of F5 G>A (rs6025), F2 G>A (rs1799963) and MTHFR C>T (rs1801133) polymorphisms in Bosnian women. A total of 154 women with PL, mean age 33 (±5.4) years, were enrolled in the study. As a control group, 154 mothers [mean age 31.4 (±6.7) years] with at least one live-born child were included. We used real-time polymerase chain reaction (PCR) to determine the frequencies of F5 G>A and F2 G>A genotypes, and PCRrestriction fragment length polymorphism (RFLP) for analyzing MTHFR C>T genotypes. The frequency of heterozygotes for F5 and F2 was significantly higher in women with venous thrombosis (VT) compared to women without VT (p = 0.047 and p = 0.001, respectively). There was no significant difference in the distribution of MTHFR genotypes and alleles between these two groups. In addition, we observed no significant differences in the genotype and allele frequencies between the group with PL and control group, for all investigated polymorphisms. The allele frequencies for 1691A (F5), 20210A (F2), and 677T (MTHFR) reported in this study are consistent with the data obtained for other European countries, however, we were not able to confirm the association between the three polymorphisms and PL in Bosnian women.
Analysis of Y-chromosome haplogroup distribution is widely used when investigating geographical c... more Analysis of Y-chromosome haplogroup distribution is widely used when investigating geographical clustering of different populations, which is why it plays an important role in population genetics, human migration patterns and even in forensic investigations. Individual determination of these haplogroups is mostly based on the analysis of single nucleotide polymorphism (SNP) markers located in the non-recombining part of Y-chromosome (NRY). On the other hand, the number of forensic and anthropology studies investigating short tandem repeats on the Y-chromosome (Y-STRs) increases rapidly every year. During the last few years, these markers have been successfully used as haplogroup prediction methods, which is why they have been used in this study. Previously obtained Y-STR haplotypes (23 loci) from 100 unrelated Turkish males recently settled in Sarajevo were used for the determination of haplogroups via 'Whit Athey's Haplogroup Predictor' software. The Bayesian probabilit...
Short tandem repeats (STRs) located on the Y-chromosome are a useful tool for various scientific ... more Short tandem repeats (STRs) located on the Y-chromosome are a useful tool for various scientific fields, such as forensic investigation, but also for the investigation of population structure and molecular history. In this study, population data based on 23 Y-STR loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) from 23 European human populations were compared. All haplotype data for this research were gathered from previously published articles. Arlequin v3.5.1.2, POPTREE2, and MEGA 5.1 software packages were used for the calculation of allelic frequencies and genetic distance, and the construction of the European, as well as worldwide phylogenetic trees. Obtained results indicate a formation of several distinct sub-clusters within European population cluster. Observed sub-clusters were mostly recognized within geographically closer population...
Widely considered as one of the cradles of human civilization, Mesopotamia is largely situated in... more Widely considered as one of the cradles of human civilization, Mesopotamia is largely situated in the Republic of Iraq, which is also the birthplace of the Sumerian, Akkadian, Assyrian and Babylonian civilizations. These lands were subsequently ruled by the Persians, Greeks, Romans, Arabs, Mongolians, Ottomans and finally British prior to the independence. As a direct consequence of this rich history, the contemporary Iraqi population comprises a true mosaic of different ethnicities, which includes Arabs, Kurds, Turkmens, Assyrians, and Yazidis among others. As such, the genetics of the contemporary Iraqi populations are of anthropological and forensic interest. In an effort to contribute to a better understanding of the genetic basis of this ethnic diversity, a total of 500 samples were collected from Northern Iraqi volunteers belonging to five major ethnic groups, namely: Arabs (n = 102), Kurds (n = 104), Turkmens (n = 102), Yazidis (n = 106) and Syriacs (n = 86). 17-loci Y-STR an...
The region of Western Balkans has been inhabited since the Paleolithic era and was the route of t... more The region of Western Balkans has been inhabited since the Paleolithic era and was the route of the spread of farming from the Middle East to Europe during the Neolithic era. In the present study, Y-STR data from European populations have been used to construct median-joining networks. The study was performed using Whit Athey’s Haplogroup Predictor, Y Utility and Network 4 software packages to predict Y haplogroups, construct networks, perform clustering of closely related Y chromosomes and calculate time estimates between individual nodes. The results of the study imply that geographically close populations cluster together at both Balkan and European levels. It was observed that an elevated number of study populations and individual haplogroups increases the possibility that individuals of different ethnic background cluster within the same or neighboring clades of network. Subsequent time estimates, performed based on the mutation frequency between the ancestral node and its desc...
Allele frequencies of 15 STRs included in the PowerPlex 16 System (D3S1358, TH01, D21S11, D18S51,... more Allele frequencies of 15 STRs included in the PowerPlex 16 System (D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, VWA, D8S1179, TPOX and FGA) were calculated from the referent sample of 100 unrelated individuals of both sexes from Turkish student population living in Sarajevo, Bosnia and Herzegovina. Buccal swab, as a source of DNA, was collected from the volunteers from whom the informed consent form was obtained. DNA extraction was performed using QIAamp DNA Micro kit by Qiagen. DNA template ranging from 0.5 to 2 ng was used to amplify 15 STR loci by PCR multiplex amplification which was performed by using the PowerPlex 16 kit (Promega Corp., Madison, WI, USA) according to the manufacturer's protocol. The amplifications were carried out in a PE Gene Amp PCR System thermal cycler (Applied Biosystems) and capillary electrophoresis was carried out in an ABI PRISM 310 Genetic Analyzer (Applied Biosystems) in accordance with the manufactu...
Background: The human angiotensin I converting enzyme 1 (ACE1) gene insertion/deletion (I/D) poly... more Background: The human angiotensin I converting enzyme 1 (ACE1) gene insertion/deletion (I/D) polymorphism is classified based on the presence or absence of a 287 bp Alu sequence. The ACE1 D allele is associated with higher ACE1 concentrations in tissues. Previous research has shown that susceptibility to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is primarily determined by the affinity between the viral receptor-binding domain and the host human receptor angiotensin-converting enzyme 2 (hACE2) receptor. In the human genome, ACE2 is identified as a homolog to ACE1. Objective: The purpose of this study was to characterize the ACE1 D allele distribution in Bosnia and Herzegovina (B&H), so as to compare it to population data from other European countries and to investigate the potential correlation between D allele frequencies and coronavirus disease 2019 (COVID-19) epidemiological findings in selected European populations. Methods: The ACE1 D allele frequencies in 18 selected European populations were analyzed and compared with COVID-19 prevalence, mortality, and severity using multivariate linear regression analysis. Results and Discussion: The ACE1 D allele distribution within the B&H population was similar to its distribution in other European populations. Regression analysis showed no significant correlation between the D allele frequency and the incidence of infections between the examined populations, nor with the rates of fatality and severe cases. Conclusion: There is no clear statistical evidence that the ACE1 D allele is associated with increased or decreased COVID-19 incidence, mortality, and case severity within the investigated populations.
The region of Western Balkans has been inhabited since the Paleolithic era and was the route of t... more The region of Western Balkans has been inhabited since the Paleolithic era and was the route of the spread of farming from the Middle East to Europe during the Neolithic era. In the present study, Y-STR data from European populations have been used to construct median-joining networks. The study was performed using Whit Athey's Haplogroup Predictor, Y Utility and Network 4 software packages to predict Y haplogroups, construct networks, perform clustering of closely related Y chromosomes and calculate time estimates between individual nodes. The results of the study imply that geographically close populations cluster together at both Balkan and European levels. It was observed that an elevated number of study populations and individual haplogroups increases the possibility that individuals of different ethnic background cluster within the same or neighboring clades of network. Subsequent time estimates, performed based on the mutation frequency between the ancestral node and its descendant nodes, revealed that I2a haplogroup within the Western Balkan region has the most compact clustering (age, estimated at 3109 years), followed by Hg E1b1b which has the second most compact clustering (4896 years). The obtained results are nonetheless in accordance with previously published research investigating the frequency of Y haplogroups based on Y-SNP variant frequencies, indicating that Western Balkan countries are mainly represented by I2a subclade (average for six countries 32.3%), followed by E1b1b and R1a (average for six countries of 21.5% and 17%, respectively).
This study was conducted to confirm preliminary anthropological research indicating the specifici... more This study was conducted to confirm preliminary anthropological research indicating the specificity of isolated Selška Valley populations and implement clear mapping of genetic distances between neighboring populations and similar "inland island" populations from the region. The sample consisted of 86 unrelated individuals born in the Selška Valley from the lowland villages (Bukovica, Ševlje, Dolenja Vas, Selca, Železniki and Zali Log) and the mountain villages (Podlonk, Prtovč, Spodnje Danje, Zgornja Sorica and Spodnja Sorica). The for mentioned 15 STR loci (D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, vWA, D8S1179, TPOX and FGA) were analyzed and statistical analysis was applied to determine population-genetics and forensic parameters. The frequencies of 15 STR loci from isolated populations of Slovenian villages, Slovenia, Bosnian mountain villages and Bosnia and Herzegovina were analyzed to calculate genetic distances between them. Our results confirmed a similar genetic pattern between the Selška Valley mountain villages and Slovenian general population as well as Bosnian mountain villages and general Bosnian population. Even if the sample size was relatively small and examined populations were geographically isolated, observed genetic variation within the whole population was relatively high and comparable with neighboring populations. Additional analysis proved that the Selška Valley population is genetically closest to the Slovenian and Austrian populations. On the other hand, comparison with similarly patterned populations confirmed that this population could be recognized as "inland island" population in genetic terms.
The set of 55 ancestry informative SNPs (AISNPs) originally developed by the Kidd Lab has been st... more The set of 55 ancestry informative SNPs (AISNPs) originally developed by the Kidd Lab has been studied on a large number of populations and continues to be applied to new population samples. The existing reference database of population samples allows the relationships of new population samples to be inferred on a global level. Analyses show that these autosomal markers constitute one of the better panels of AISNPs. Continuing to build this reference database enhances its value. Because more than half of the 25 ethnic groups recently studied with these AISNPs are from Southwest Asia and the Mediterranean region, we present here various analyses focused on populations from these regions along with selected reference populations from nearby regions where genotype data are available. Many of these ethnic groups have not been previously studied for forensic markers. Data on populations from other world regions have also been added to the database but are not included in these focused analyses. The new population samples added to ALFRED and FROG-kb increase the total to 164 population samples that have been studied for all 55 AISNPs.
Stress is a part of human life, especially for urban citizens. Stress is inseparable characterist... more Stress is a part of human life, especially for urban citizens. Stress is inseparable characteristics of student life, especially exam days. Stress management is one of the first steps which can affect students success during the exams, especially in universities. Blood pressure is the first stress observation symptom to understand its level. Therefore, to understand the stress impact of university students during the exam weeks, a conditional experiment has been designed. 200 students were selected from Bosnian and Turkish female and male. The students` blood systolic, diastolic and heart rate were measured to detect the differences between non-exams days and exam days. The blood pressure measurement has been done 3 times in specific times, non-exam days, midterm and final days. Since non-exam days were taken as stress off days, they were supposed that these days were control data to compare with exam days to see the differences. As a result of the measurements, Bosnian females showed the highest increasing, systolic 13.2%, diastolic 9.3% and heart rate 8.5% during the midterm exam days. The group has been followed by Bosnian males, systolic 6.9%, diastolic 6.1% and heart rate 6.63 increased during the midterm days. Although Turkish students blood pressure and heart rate increased, the values were less than Bosnian students. Moreover, high correlation significance results belonged to Bosnian females and males, 0.722 and 0.698 respectively. Finally, it was concluded that if students have scholarship they have more blood pressure during the exams. While 95% of Bosnian females and 90% of Bosnian males have some scholarship, no Turkish students have scholarship demonstrated the differences between Bosnian and Turkish students blood measurements.
Angiotensin I converting enzyme (ACE) gene, as a component of Renin-Angiotensin System (RAS), reg... more Angiotensin I converting enzyme (ACE) gene, as a component of Renin-Angiotensin System (RAS), regulates blood pressure as it converts somatic isozyme Angiotensin I into physiologically active peptide Angiotensin II and simultaneously brakes down bradykinins. Over 100 polymorphisms are reported for ACE gene. Most of these polymorphisms having no phenotypic effect relay the attention towards polymorphisms based on insertions (I) or deletions (D) of a 287 bp Alu repeat sequence in 16th intron. There are three possible genotypes for the stated polymorphism: DD, DI or II. There have been a lot of studies searching for direct associations between ACE polymorphisms and performance phenotypes along different sports requiring power or endurance. The previous experiments are based on the performance criteria but direct associations of ACE polymorphisms are not fully understood until today. We believe different approaches may aid scientist to plot the big picture. A sample population of 101 individuals from Bosnia and Herzegovina contributed to sample pool of the initial project. Buccal swabs from 101 samples were collected along with a phenotypic structure and environmental characteristic survey which was filled by each individual himself/herself. Genotypes of the individuals were obtained after isolation, amplification and gel electrophoresis of biological samples collected as buccal swabs. A total of 165 artificial neural network (ANN) models were developed considering the input parameters, possible genotype outputs, applied algorithm and sample size. The aim of developing various ANNs was to validate a possible ACE polymorphism genotype prediction algorithm based on phenotypic and environmental characteristics of individuals, in other words, without any biological testing. A two-layered feed-forward network, with sigmoid hidden neurons was designed to perform the classification of input data. Trainscg (Scaled Conjugate Gradient) activation function was used in hidden layer since classification of data was non-linear. All ANN models were trained with scaled conjugate gradient backpropagation. ANN models differing in the parameters has shown different accuracy in the results. Most outstanding result was observed in the ANN build composed of 2 distinctive layers with 500 neurons in the first and 3 neurons in the second layer. Trained with 70% of samples and verified with 15% of samples and validated with an additional 50 samples. Training set was composed of the following subject parameters; gender, eye color, hair color, height, weight, presence of hypertension in family and presence of cardiovascular diseases in family. The highest prediction accuracy was obtained as 86,6 % training score, 78,6 % testing score and 80,2 % overall score in genotype prediction for ACE polymorphisms. With further development of data collection and high resolution analysis, overall score could be boosted. Also, phenotypical data can be applied as markers of genotypes in ACE polymorphisms.
β-Glucosidase (β-D-glucoside glucohydrolase, EC 3.2.1.21) is a catalytic enzyme present in both p... more β-Glucosidase (β-D-glucoside glucohydrolase, EC 3.2.1.21) is a catalytic enzyme present in both prokaryotes and eukaryotes that selectively catalyzes either the linkage between two glycone residues or between glycone and aryl or alkyl aglycone residue. Growing edible mushrooms in the soil with increased cellulose content can lead to the production of glucose, which is a process dependent on β-glucosidase. In this study, β-glucosidase was isolated from Agaricus bisporus (white button mushroom) using ammonium sulfate precipitation and hydrophobic interaction chromatography, giving 10.12-fold purification. Biochemical properties of the enzyme were investigated and complete characterization was performed. The enzyme is a dimer with two subunits of approximately 46 and 62 kDa. Optimum pH for the enzyme is 4.0, while the optimum temperature is 55 °C. The enzyme was found to be exceptionally thermostable. The most suitable commercial substrate for this enzyme is p-NPGlu with Km and Vmax va...
<p>Pairwise genetic distance matrix based on the <i>R</i><sub><i>st... more <p>Pairwise genetic distance matrix based on the <i>R</i><sub><i>st</i></sub> and <i>P</i> values between the five major ethnic groups from Northern Iraq and representative nearby and distant populations<sup><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0187408#t003fn001" target="_blank">†</a></sup>.</p
The Southwest Asian, circum-Mediterranean, and Southern European populations (collectively, SWAMS... more The Southwest Asian, circum-Mediterranean, and Southern European populations (collectively, SWAMSE) together with Northern European populations form one of five "continental" groups of global populations in many analyses of population relationships. This region is of great anthropologic and forensic interest but relationships of large numbers of populations within the region have not been able to be cleanly resolved with autosomal genetic markers. To examine the genetic boundaries to the SWAMSE region and whether internal structure can be detected we have assembled data for a total of 151 separate autosomal genetic markers on populations in this region and other parts of the world for a global set of 95 populations. The markers include 83 ancestry informative SNPs as singletons and 68 microhaplotype loci defined by 204 SNPs. The 151 loci are ancestry informative on a global scale, identifying at least five biogeographic clusters. One of those clusters is a clear grouping of 37 populations containing the SWAMSE plus northern European populations to the exclusion of populations in South Central Asia and populations from farther East. A refined analysis of the 37 populations shows the northern European populations clustering separately from the SWAMSE populations. Within Southwest Asia the Samaritans and Shabaks are distinct outliers. The Yemenite Jews, Saudi, Kuwaiti, Palestinian Arabs, and Southern Tunisians cluster together loosely while the remaining populations from Northern Iraq, Mediterranean Europe, the Caucasus region, and Iran cluster in a more complex graded fashion. The majority of the SWAMSE populations from the mainland of Southwest Asia form a cluster with little internal structure reflecting a very complex history of endogamy and migrations. The set of 151 DNA polymorphisms not only distinguishes major geographical regions globally but can distinguish ancestry to a small degree within geographical regions such as SWAMSE. We discuss forensic characteristics of the polymorphisms and also identify those that rank highest by Rosenberg's In measure for the SWAMSE region populations and for the global set of populations analyzed. DATA AVAILABILITY: Genotypes on all 151 markers for all 3790 individuals typed in the Kidd Lab on the 72 Kidd lab populations have been deposited in the Zenodo archive and can be freely accessed at https://doi.org/10.5281/zenodo.4658892. Some of the data has been made public previously as supplemental files appended to publications. Data for the additional individuals included in the analyses was taken from already public datasets as indicated in the text.
Y-chromosomal haplogroups are sets of ancestrally related paternal lineages, traditionally assign... more Y-chromosomal haplogroups are sets of ancestrally related paternal lineages, traditionally assigned by the use of Y-chromosomal single nucleotide polymorphism (Y-SNP) markers. An increasingly popular and a less labor-intensive alternative approach has been Y-chromosomal haplogroup assignment based on already available Y-STR data using a variety of different algorithms. In the present study, such in silico haplogroup assignments were made based on 23-loci Y-STR data for 100 unrelated male individuals from the Tuzla Canton, Bosnia and Herzegovina (B&H) using the following four different algorithms: Whit Athey's Haplogroup Predictor, Jim Cullen's World Haplogroup & Haplogroup-I Subclade Predictor, Vadim Urasin's YPredictor and the NevGen Y-DNA Haplogroup Predictor. Prior in-house assessment of these four different algorithms using a previously published dataset (n=132) from B&H with both Y-STR (12-loci) and Y-SNP data suggested haplogroup misassignment rates between 0.76% and 3.02%. Subsequent analyses with the Tuzla Canton population sample revealed only a few differences in the individual haplogroup assignments when using different algorithms. Nevertheless, the resultant Y-chromosomal haplogroup distribution by each method was very similar, where the most prevalent haplogroups observed were I, R and E with their sublineages I2a, R1a and E1b1b, respectively, which is also in accordance with the previously published Y-SNP data for the B&H population. In conclusion, results presented herein not only constitute a concordance study on the four most popular haplogroup assignment algorithms, but they also give a deeper insight into the inter-population differentiation in B&H on the basis of Y haplogroups for the first time.
Since the introduction of the term low copy number DNA, also referred as low template DNA, touch ... more Since the introduction of the term low copy number DNA, also referred as low template DNA, touch DNA or trace DNA analysis, it has quickly become focal point of forensic DNA testing as well as other DNA based studies. Low template DNA (ltDNA) samples can be described as the samples which involve single source samples with template DNA in concentrations below 100 picograms (pg). Due to sensitivity of ltDNA samples to contamination, it is of great importance to optimize performance of the multiplex STR systems and existing protocols to increase chance of successful analysis. The main objective of this study was analysis of 20 challenging samples (skeletal remains, cigarette buts, chewing gum, poorly collected buccal swabs etc.) mostly low template DNA samples, preliminarily profiled by PowerPlex ® 16 multiplex STR systems and additionally processed with new generation multiplex STR kit PowerPlex ® Fusion. Sample isolation was done using a standard phenol-chloroform method for bone samples and DNeasy ® Blood and Tissue Kit for other forensic samples. PowerPlex ® 16 (PP16), multiplex STR system and PowerPlex ® Fusion (PP Fusion) were used for co-amplification of 15 and 24 autosomal STR loci respectively. Results of this preliminary study suggest that PP Fusion primer set is better optimized for the analysis of ltDNA samples, and it is more robust regarding presence of the potential PCR inhibitors.
Bosnia and Herzegovina is located in the South-Eastern Europe, characterized by numerous historic... more Bosnia and Herzegovina is located in the South-Eastern Europe, characterized by numerous historical influences, massive migration processes and complex population structure. For that reason, the aim of this study is to provide an accurate and precise update of the population genetics data of allele frequencies on 23 Y-STR loci in Bosnia and Herzegovina using larger sample size. For this purpose, 480 adult male individuals from the general population have been genotyped over 23 Y-STR loci contained in the PowerPlex Y23 system. Population genetics parameters have been calculated, namely allele and haplotype frequencies, gene and haplotype diversity, as well as Rst and P values for the assessment of interpopulation differences. The obtained results are in close agreement with previously published data for Bosnian-Herzegovinian population, as well as for local subpopulations. This study offers significantly increased resolution and information content, with 454 unique haplotypes. Popula...
The relationship between genetic risk factors of thrombophilia and pregnancy loss (PL) is being d... more The relationship between genetic risk factors of thrombophilia and pregnancy loss (PL) is being discussed. The focus has been on F5 1691G>A, F2 20210G>A, and MTHFR 677C>T polymorphisms that may predispose women to microthrombosis during the stages of embryo implantation and placentation. Although, the frequencies of these polymorphisms were reported in different populations, such studies have not yet been performed in Bosnian population. In this study, we determined the prevalence of F5 G>A (rs6025), F2 G>A (rs1799963) and MTHFR C>T (rs1801133) polymorphisms in Bosnian women. A total of 154 women with PL, mean age 33 (±5.4) years, were enrolled in the study. As a control group, 154 mothers [mean age 31.4 (±6.7) years] with at least one live-born child were included. We used real-time polymerase chain reaction (PCR) to determine the frequencies of F5 G>A and F2 G>A genotypes, and PCRrestriction fragment length polymorphism (RFLP) for analyzing MTHFR C>T genotypes. The frequency of heterozygotes for F5 and F2 was significantly higher in women with venous thrombosis (VT) compared to women without VT (p = 0.047 and p = 0.001, respectively). There was no significant difference in the distribution of MTHFR genotypes and alleles between these two groups. In addition, we observed no significant differences in the genotype and allele frequencies between the group with PL and control group, for all investigated polymorphisms. The allele frequencies for 1691A (F5), 20210A (F2), and 677T (MTHFR) reported in this study are consistent with the data obtained for other European countries, however, we were not able to confirm the association between the three polymorphisms and PL in Bosnian women.
Analysis of Y-chromosome haplogroup distribution is widely used when investigating geographical c... more Analysis of Y-chromosome haplogroup distribution is widely used when investigating geographical clustering of different populations, which is why it plays an important role in population genetics, human migration patterns and even in forensic investigations. Individual determination of these haplogroups is mostly based on the analysis of single nucleotide polymorphism (SNP) markers located in the non-recombining part of Y-chromosome (NRY). On the other hand, the number of forensic and anthropology studies investigating short tandem repeats on the Y-chromosome (Y-STRs) increases rapidly every year. During the last few years, these markers have been successfully used as haplogroup prediction methods, which is why they have been used in this study. Previously obtained Y-STR haplotypes (23 loci) from 100 unrelated Turkish males recently settled in Sarajevo were used for the determination of haplogroups via 'Whit Athey's Haplogroup Predictor' software. The Bayesian probabilit...
Short tandem repeats (STRs) located on the Y-chromosome are a useful tool for various scientific ... more Short tandem repeats (STRs) located on the Y-chromosome are a useful tool for various scientific fields, such as forensic investigation, but also for the investigation of population structure and molecular history. In this study, population data based on 23 Y-STR loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643) from 23 European human populations were compared. All haplotype data for this research were gathered from previously published articles. Arlequin v3.5.1.2, POPTREE2, and MEGA 5.1 software packages were used for the calculation of allelic frequencies and genetic distance, and the construction of the European, as well as worldwide phylogenetic trees. Obtained results indicate a formation of several distinct sub-clusters within European population cluster. Observed sub-clusters were mostly recognized within geographically closer population...
Widely considered as one of the cradles of human civilization, Mesopotamia is largely situated in... more Widely considered as one of the cradles of human civilization, Mesopotamia is largely situated in the Republic of Iraq, which is also the birthplace of the Sumerian, Akkadian, Assyrian and Babylonian civilizations. These lands were subsequently ruled by the Persians, Greeks, Romans, Arabs, Mongolians, Ottomans and finally British prior to the independence. As a direct consequence of this rich history, the contemporary Iraqi population comprises a true mosaic of different ethnicities, which includes Arabs, Kurds, Turkmens, Assyrians, and Yazidis among others. As such, the genetics of the contemporary Iraqi populations are of anthropological and forensic interest. In an effort to contribute to a better understanding of the genetic basis of this ethnic diversity, a total of 500 samples were collected from Northern Iraqi volunteers belonging to five major ethnic groups, namely: Arabs (n = 102), Kurds (n = 104), Turkmens (n = 102), Yazidis (n = 106) and Syriacs (n = 86). 17-loci Y-STR an...
The region of Western Balkans has been inhabited since the Paleolithic era and was the route of t... more The region of Western Balkans has been inhabited since the Paleolithic era and was the route of the spread of farming from the Middle East to Europe during the Neolithic era. In the present study, Y-STR data from European populations have been used to construct median-joining networks. The study was performed using Whit Athey’s Haplogroup Predictor, Y Utility and Network 4 software packages to predict Y haplogroups, construct networks, perform clustering of closely related Y chromosomes and calculate time estimates between individual nodes. The results of the study imply that geographically close populations cluster together at both Balkan and European levels. It was observed that an elevated number of study populations and individual haplogroups increases the possibility that individuals of different ethnic background cluster within the same or neighboring clades of network. Subsequent time estimates, performed based on the mutation frequency between the ancestral node and its desc...
Allele frequencies of 15 STRs included in the PowerPlex 16 System (D3S1358, TH01, D21S11, D18S51,... more Allele frequencies of 15 STRs included in the PowerPlex 16 System (D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, VWA, D8S1179, TPOX and FGA) were calculated from the referent sample of 100 unrelated individuals of both sexes from Turkish student population living in Sarajevo, Bosnia and Herzegovina. Buccal swab, as a source of DNA, was collected from the volunteers from whom the informed consent form was obtained. DNA extraction was performed using QIAamp DNA Micro kit by Qiagen. DNA template ranging from 0.5 to 2 ng was used to amplify 15 STR loci by PCR multiplex amplification which was performed by using the PowerPlex 16 kit (Promega Corp., Madison, WI, USA) according to the manufacturer's protocol. The amplifications were carried out in a PE Gene Amp PCR System thermal cycler (Applied Biosystems) and capillary electrophoresis was carried out in an ABI PRISM 310 Genetic Analyzer (Applied Biosystems) in accordance with the manufactu...
Background: The human angiotensin I converting enzyme 1 (ACE1) gene insertion/deletion (I/D) poly... more Background: The human angiotensin I converting enzyme 1 (ACE1) gene insertion/deletion (I/D) polymorphism is classified based on the presence or absence of a 287 bp Alu sequence. The ACE1 D allele is associated with higher ACE1 concentrations in tissues. Previous research has shown that susceptibility to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is primarily determined by the affinity between the viral receptor-binding domain and the host human receptor angiotensin-converting enzyme 2 (hACE2) receptor. In the human genome, ACE2 is identified as a homolog to ACE1. Objective: The purpose of this study was to characterize the ACE1 D allele distribution in Bosnia and Herzegovina (B&H), so as to compare it to population data from other European countries and to investigate the potential correlation between D allele frequencies and coronavirus disease 2019 (COVID-19) epidemiological findings in selected European populations. Methods: The ACE1 D allele frequencies in 18 selected European populations were analyzed and compared with COVID-19 prevalence, mortality, and severity using multivariate linear regression analysis. Results and Discussion: The ACE1 D allele distribution within the B&H population was similar to its distribution in other European populations. Regression analysis showed no significant correlation between the D allele frequency and the incidence of infections between the examined populations, nor with the rates of fatality and severe cases. Conclusion: There is no clear statistical evidence that the ACE1 D allele is associated with increased or decreased COVID-19 incidence, mortality, and case severity within the investigated populations.
The region of Western Balkans has been inhabited since the Paleolithic era and was the route of t... more The region of Western Balkans has been inhabited since the Paleolithic era and was the route of the spread of farming from the Middle East to Europe during the Neolithic era. In the present study, Y-STR data from European populations have been used to construct median-joining networks. The study was performed using Whit Athey's Haplogroup Predictor, Y Utility and Network 4 software packages to predict Y haplogroups, construct networks, perform clustering of closely related Y chromosomes and calculate time estimates between individual nodes. The results of the study imply that geographically close populations cluster together at both Balkan and European levels. It was observed that an elevated number of study populations and individual haplogroups increases the possibility that individuals of different ethnic background cluster within the same or neighboring clades of network. Subsequent time estimates, performed based on the mutation frequency between the ancestral node and its descendant nodes, revealed that I2a haplogroup within the Western Balkan region has the most compact clustering (age, estimated at 3109 years), followed by Hg E1b1b which has the second most compact clustering (4896 years). The obtained results are nonetheless in accordance with previously published research investigating the frequency of Y haplogroups based on Y-SNP variant frequencies, indicating that Western Balkan countries are mainly represented by I2a subclade (average for six countries 32.3%), followed by E1b1b and R1a (average for six countries of 21.5% and 17%, respectively).
This study was conducted to confirm preliminary anthropological research indicating the specifici... more This study was conducted to confirm preliminary anthropological research indicating the specificity of isolated Selška Valley populations and implement clear mapping of genetic distances between neighboring populations and similar "inland island" populations from the region. The sample consisted of 86 unrelated individuals born in the Selška Valley from the lowland villages (Bukovica, Ševlje, Dolenja Vas, Selca, Železniki and Zali Log) and the mountain villages (Podlonk, Prtovč, Spodnje Danje, Zgornja Sorica and Spodnja Sorica). The for mentioned 15 STR loci (D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSF1PO, Penta D, vWA, D8S1179, TPOX and FGA) were analyzed and statistical analysis was applied to determine population-genetics and forensic parameters. The frequencies of 15 STR loci from isolated populations of Slovenian villages, Slovenia, Bosnian mountain villages and Bosnia and Herzegovina were analyzed to calculate genetic distances between them. Our results confirmed a similar genetic pattern between the Selška Valley mountain villages and Slovenian general population as well as Bosnian mountain villages and general Bosnian population. Even if the sample size was relatively small and examined populations were geographically isolated, observed genetic variation within the whole population was relatively high and comparable with neighboring populations. Additional analysis proved that the Selška Valley population is genetically closest to the Slovenian and Austrian populations. On the other hand, comparison with similarly patterned populations confirmed that this population could be recognized as "inland island" population in genetic terms.
The set of 55 ancestry informative SNPs (AISNPs) originally developed by the Kidd Lab has been st... more The set of 55 ancestry informative SNPs (AISNPs) originally developed by the Kidd Lab has been studied on a large number of populations and continues to be applied to new population samples. The existing reference database of population samples allows the relationships of new population samples to be inferred on a global level. Analyses show that these autosomal markers constitute one of the better panels of AISNPs. Continuing to build this reference database enhances its value. Because more than half of the 25 ethnic groups recently studied with these AISNPs are from Southwest Asia and the Mediterranean region, we present here various analyses focused on populations from these regions along with selected reference populations from nearby regions where genotype data are available. Many of these ethnic groups have not been previously studied for forensic markers. Data on populations from other world regions have also been added to the database but are not included in these focused analyses. The new population samples added to ALFRED and FROG-kb increase the total to 164 population samples that have been studied for all 55 AISNPs.
Stress is a part of human life, especially for urban citizens. Stress is inseparable characterist... more Stress is a part of human life, especially for urban citizens. Stress is inseparable characteristics of student life, especially exam days. Stress management is one of the first steps which can affect students success during the exams, especially in universities. Blood pressure is the first stress observation symptom to understand its level. Therefore, to understand the stress impact of university students during the exam weeks, a conditional experiment has been designed. 200 students were selected from Bosnian and Turkish female and male. The students` blood systolic, diastolic and heart rate were measured to detect the differences between non-exams days and exam days. The blood pressure measurement has been done 3 times in specific times, non-exam days, midterm and final days. Since non-exam days were taken as stress off days, they were supposed that these days were control data to compare with exam days to see the differences. As a result of the measurements, Bosnian females showed the highest increasing, systolic 13.2%, diastolic 9.3% and heart rate 8.5% during the midterm exam days. The group has been followed by Bosnian males, systolic 6.9%, diastolic 6.1% and heart rate 6.63 increased during the midterm days. Although Turkish students blood pressure and heart rate increased, the values were less than Bosnian students. Moreover, high correlation significance results belonged to Bosnian females and males, 0.722 and 0.698 respectively. Finally, it was concluded that if students have scholarship they have more blood pressure during the exams. While 95% of Bosnian females and 90% of Bosnian males have some scholarship, no Turkish students have scholarship demonstrated the differences between Bosnian and Turkish students blood measurements.
Angiotensin I converting enzyme (ACE) gene, as a component of Renin-Angiotensin System (RAS), reg... more Angiotensin I converting enzyme (ACE) gene, as a component of Renin-Angiotensin System (RAS), regulates blood pressure as it converts somatic isozyme Angiotensin I into physiologically active peptide Angiotensin II and simultaneously brakes down bradykinins. Over 100 polymorphisms are reported for ACE gene. Most of these polymorphisms having no phenotypic effect relay the attention towards polymorphisms based on insertions (I) or deletions (D) of a 287 bp Alu repeat sequence in 16th intron. There are three possible genotypes for the stated polymorphism: DD, DI or II. There have been a lot of studies searching for direct associations between ACE polymorphisms and performance phenotypes along different sports requiring power or endurance. The previous experiments are based on the performance criteria but direct associations of ACE polymorphisms are not fully understood until today. We believe different approaches may aid scientist to plot the big picture. A sample population of 101 individuals from Bosnia and Herzegovina contributed to sample pool of the initial project. Buccal swabs from 101 samples were collected along with a phenotypic structure and environmental characteristic survey which was filled by each individual himself/herself. Genotypes of the individuals were obtained after isolation, amplification and gel electrophoresis of biological samples collected as buccal swabs. A total of 165 artificial neural network (ANN) models were developed considering the input parameters, possible genotype outputs, applied algorithm and sample size. The aim of developing various ANNs was to validate a possible ACE polymorphism genotype prediction algorithm based on phenotypic and environmental characteristics of individuals, in other words, without any biological testing. A two-layered feed-forward network, with sigmoid hidden neurons was designed to perform the classification of input data. Trainscg (Scaled Conjugate Gradient) activation function was used in hidden layer since classification of data was non-linear. All ANN models were trained with scaled conjugate gradient backpropagation. ANN models differing in the parameters has shown different accuracy in the results. Most outstanding result was observed in the ANN build composed of 2 distinctive layers with 500 neurons in the first and 3 neurons in the second layer. Trained with 70% of samples and verified with 15% of samples and validated with an additional 50 samples. Training set was composed of the following subject parameters; gender, eye color, hair color, height, weight, presence of hypertension in family and presence of cardiovascular diseases in family. The highest prediction accuracy was obtained as 86,6 % training score, 78,6 % testing score and 80,2 % overall score in genotype prediction for ACE polymorphisms. With further development of data collection and high resolution analysis, overall score could be boosted. Also, phenotypical data can be applied as markers of genotypes in ACE polymorphisms.
β-Glucosidase (β-D-glucoside glucohydrolase, EC 3.2.1.21) is a catalytic enzyme present in both p... more β-Glucosidase (β-D-glucoside glucohydrolase, EC 3.2.1.21) is a catalytic enzyme present in both prokaryotes and eukaryotes that selectively catalyzes either the linkage between two glycone residues or between glycone and aryl or alkyl aglycone residue. Growing edible mushrooms in the soil with increased cellulose content can lead to the production of glucose, which is a process dependent on β-glucosidase. In this study, β-glucosidase was isolated from Agaricus bisporus (white button mushroom) using ammonium sulfate precipitation and hydrophobic interaction chromatography, giving 10.12-fold purification. Biochemical properties of the enzyme were investigated and complete characterization was performed. The enzyme is a dimer with two subunits of approximately 46 and 62 kDa. Optimum pH for the enzyme is 4.0, while the optimum temperature is 55 °C. The enzyme was found to be exceptionally thermostable. The most suitable commercial substrate for this enzyme is p-NPGlu with Km and Vmax va...
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