Forensic botany refers to the application of plant biology disciplines in crime investigations. Since plants are widespread in most habitats, they often provide valuable clues in criminal investigations. Hence, the primary role of forensic botany is to establish a connection between the victim or suspect and the crime scene. The forensic applications of forensic botany include many aspects including recognition of plant evidence at the crime scene, collection and preservation of plant evidence, maintenance of the chain of custody, and a testimony for the admissibility of this evidence in court. For the development of new efficient methods for plant identification and individualization, the initial step is optimization of DNA isolation from plant material. The aim of this work is to optimize the DNA isolation protocol of different leaf and non-leaf plant tissues, including pollen grains, using the salting out method from Taraxacum officinale, a species of the Asteraceae family. Since the species is very common in ecosystems with antropogenic influence, the need to optimize the DNA isolation protocol is of high importance. The efficiency of the isolation protocol was evaluated using spectrophotometry (concentration and purity) and gel electrophoresis. The results demonstrate that salting out can be used for the isolation of DNA from Taraxacum officinale. However, optimization is required, depending on the part of the plant from which DNA is extracted.

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 probability of 90 of the studied haplotypes is greater than 92.2% and ranges from 51.4% to 84.3% for the remaining 10 haplotypes. A distribution of 17 different haplogroups was found, with the Y- haplogroup J2a being most prevalent, having been found in 26% of all the samples, whereas R1b, G2a and R1a were less prevalent, covering a range of 10% to 15% of all the samples. Together, these four haplogroups account for 63% of all Y-chromosomes. Eleven haplogroups (E1b1b, G1, I1, I2a, I2b, J1, J2b, L, Q, R2, and T) range from 2% to 5%, while E1b1a and N are found in 1% of all samples. Obtained results indicate that a large majority of the Turkish paternal line belongs to West Asia, Europe Caucasus, Western Europe, Northeast Europe, Middle East, Russia, Anatolia, and Black Sea Y-chromosome lineages. As the distribution of Y-chromosome haplogroups is consistent with the previously published data for the Turkish population residing in Turkey, it was concluded that the analyzed population could also be recognized as a representative sample of the Turkish population residing in Turkey.

Short tandem repeats (STRs) located on the Y- chromosome are a useful tool for the study of population structure and history. In this study, 23 Y-STR loci from 50 populations were compared (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, GATAH4, DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643). The allele frequencies were calculated using Arlequin v3.5.1.2, while the haplotype data for these calculations were gathered from previously published articles. Furthermore, a worldwide phylogenetic tree was generated, and genetic distance values were calculated using POPTREE2 and MEGA 5.1 software. The results illustrate formation of several distinct clusters and sub clusters within them and indicate that this was mostly due to geographical proximity, which in turn resulted in neighboring populations becoming part of the same cluster. While the obtained results were in accordance with previously published research on autosomal STR analysis, the Y-STRs analyzed in the current study were more informative since they enabled regional clustering in addition to the continental one. Lastly, the use of a larger number of loci yielded clustering that is more specific than what has been calculated to date.

In previous population studies of Serbian human population, 15 STR loci included in the Identifiler were used. For further development of this dataset, we analyzed the new ESS loci and the SE33 locus. We tested 197 unrelated healthy individuals born in Serbia. Qiagen MicroTM Tissue Kit was used for DNA extraction from whole blood, Quantifiler assay for quantification and PowerPlex ESI 17 System for amplification and detection. Electrophoresis of the amplification products was preformed on an ABI PRISM 310. Numerical allele designations of the profiles were obtained by processing with Gene Mapper1 IDv 3.2 Software. Arlequin software, version 3.5.1.2, was used to calculate allele frequencies, observed heterozygosity (Ho), expected heterozygosity (He) and Pvalues of the Hardy-Weinberg equilibrium (HWE). Also, the same software was used for the exact population differentiation tests using allele frequencies. Matching probability (MP), power of discrimination (PD), polymorphism information content (PIC), probability of exclusion (PE) and typical paternity index (TPI) were determined by Powerstats, version 1.2. No statistically significant deviation (p < 0.05) from HWE was found, except for the D2S441 locus (0.0306), which was rejected after Bonferroni correction. Also, we have compared Serbian data with the data obtained from geographically closer (neighboring) European populations. Nei’s genetic distances among 10 European populations including this study were computed and a NJphylogenetic tree of 5 ESS STR loci for compared populations was built. It could be seen that, even using only 6 STR loci, “neighboring clustering” of the data could be recognized.

Aim To present the results obtained in the identification of human remains from World War II found in two mass graves in Ljubuški, Bosnia and Herzegovina. Methods Samples from 10 skeletal remains were collected. Teeth and femoral fragments were collected from 9 skeletons and only a femoral fragment from 1 skeleton. DNA was isolated from bone and teeth samples using an optimized phenol/chloroform DNA extraction procedure. All samples required a pre-extraction decalcification with EDTA and additional post-extraction DNA purification using filter columns. Additionally, DNA from 12 reference samples (buccal swabs from potential living relatives) was extracted using the Qiagen DNA extraction method. QuantifilerTM Human DNA Quantification Kit was used for DNA quantification. PowerPlex ESI kit was used to simultaneously amplify 15 autosomal short tandem repeat (STR) loci, and PowerPlex Y23 was used to amplify 23 Y chromosomal STR loci. Matching probabilities were estimated using a standard statistical approach. Results A total of 10 samples were processed, 9 teeth and 1 femoral fragment. Nine of 10 samples were profiled using autosomal STR loci, which resulted in useful DNA profiles for 9 skeletal remains. A comparison of established victims' profiles against a reference sample database yielded 6 positive identifications. Conclusion DNA analysis may efficiently contribute to the identification of remains even seven decades after the end of the World War II. The significant percentage of positively identified remains (60%), even when the number of the examined possible living relatives was relatively small (only 12), proved the importance of cooperation with the members of the local community, who helped to identify the closest missing persons’ relatives and collect referent samples from them.

Aim To explore the distribution and polymorphisms of 23 short tandem repeat (STR) loci on the Y chromosome in the Turkish population recently settled in Sarajevo, Bosnia and Herzegovina and to investigate its genetic relationships with the homeland Turkish population and neighboring populations. Methods This study included 100 healthy unrelated male individuals from the Turkish population living in Sarajevo. Buccal swab samples were collected as a DNA source. Genomic DNA was extracted using the salting out method and amplification was performed using PowerPlex Y 23 amplification kit. The studied population was compared to other populations using pairwise genetic distances, which were represented with a multi-dimensional scaling plot. Results Haplotype and allele frequencies of the sample population were calculated and the results showed that all 100 samples had unique haplotypes. The most polymorphic locus was DYS458, and the least polymorphic DYS391. The observed haplotype diversity was 1.0000 ± 0.0014, with a discrimination capacity of 1.00 and the match probability of 0.01. Rst values showed that our sample population was closely related in both dimensions to the Lebanese and Iraqi populations, while it was more distant from Bosnian, Croatian, and Macedonian populations. Conclusion Turkish population residing in Sarajevo could be observed as a representative Turkish population, since our results were consistent with those previously published for the homeland Turkish population. Also, this study once again proved that geographically close populations were genetically more related to each other.

Abstract Although DNA genetic markers, including Y-chromosomal short tandem repeats (Y-STRs), are widely used in the analysis of population data, autosomal short tandem repeats (STRs) have a wide role in the investigation of human migration patterns throughout the history, genealogical research, and population genetics. In this review, allele frequencies of 13 autosomal STR loci (D3S1358, TH01, D21S11, D18S51, D5S818, D13S317, D7S820, D16S539, CSF1PO, vWA, D8S1179, TPOX, and FGA) have been reviewed in 64 different worldwide populations. Allele frequency data for 13 STR loci was collected from previously published scientific papers in the journal databases for each studied population and molecular genetic diversity among the 64 sample populations was compared. Further, a worldwide phylogenetic tree and genetic distance values were created using POPTREE2 software and UPGMA method. Results confirmed that the differences among local sub-populations are much smaller than the differences among geographically separated populations. The obtained results, as the researchers had expected, were in the compliance with previously published papers with the difference that the researchers used data on populations from all over the world and thus created a more detailed phylogenetic tree. In that way, the authors offer an insight into the global phylogenetic tree created on the basis of STR allele frequencies for the first time. The goal of this manuscript is to prove the usefulness of these 13 STR markers within the analysis of the genetic distance and its correlation with “geographically-based genetic clustering” among the worldwide populations.

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

The advent of the era of high-throughput sequencing has brought a wealth of biological data to researchers, but the vastness of the available data has created a demand for tools that could be used to analyze it. One such type of tools are gene set analysis tools, that take a list of genes that were found to be up or down regulated during an experiment. For the sake of simplicity this review focuses solely on freely available web based tools that have been published or have undergone significant updates in the last 5 years. This review is meant to assist tool developers to better understand the needs of the end-users, and in it we look at the currently available gene list analysis tools, their strengths and weaknesses, and offer suggestions for their improvement. Key words: microarray, gene set, systems biology, enrichment, gene ontology

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.

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 manufacturer's recommendations. The frequency of each locus was calculated from the numbers of each observed genotype. Deviation from Hardy-Weinberg equilibrium and observed heterozygosity were calculated. Data were analyzed by using Microsoft Excel workbook template--Powerstats V12 and the power of discrimination (PD), power of exclusion (PE), as well as other population genetic indices for the 15 STR loci were calculated. Obtained results contribute to existing Turkish DNA database, as well as insight of differences and similarities in comparison to population of Bosnia and Herzegovina. In addition, 13 autosomal STR loci frequencies (D3S1358, TH01, D21S11, D18S51, Penta E, D5S818, D13S317, D7S820, D16S539, CSFIPO, Penta D, VWA, D8S1 179, TPOX, and FGA) were studied in 15 different worldwide populations (Turkish, Bosnian, Croatian, Serbian, Montenegrin, Macedonian, Albanian, Kosovan, Greek, Russian, Japanese, Korean, Lithuanian, Iraqi, Belarusian). For the proof of corresponding data, two different Turkish population STR data obtained from previously published articles were compared with our data and this showed that our data correspond to these 2 previously published data. Further, STR allele frequency data for 13 loci for each population were obtained from previous scientific articles and the allele frequencies and genetic diversity among the 15 sample populations were compared. In addition, even though the populations are from different nationalities, the STR data are similar among the geographically close populations. The phylogenetic tree established among worldwide populations and genetic distance values show a great affinity among the 15populations. Our data is useful for anthropological and further comparative genetic studies of populations.

In this study a decision support system has been projected from the biochemistry blood parameters which will be very helpful and will make everything easier for the physicians in the diagnosis of Hyperthyroidi. The system operation is achieved via the association rules structure which is related as one of the data mining techniques. The basic characteristic of the thyroid hormone parameters that is, TSH, FT3, FT4, TT3 and TT4 parameters are used in the process of entering the system and finally Hyper(%) results have been evaluated at the end of this process. Data of 472 patients are evaluated in the projected system. The results of the decision support system have completely matched with those of the physicianspsila decisions.