Analysis of mitochondrial DNA variability of residents of the Republic of Serbia : population genetics, phylogenetic and phylogeographic perspectives.

савременим људским популацијама Европе резултат су веома комплексних еволуционих, демографских и културолошких процеса који су се одвијали на простору Европе током више хиљада година. Међу најважнијим процесима издвајају се пост-глацијална реколонизација Европе, ширење пољопривреде током неолита (неолитска транзиција) и бројне миграције људских популација, попут миграција индоевропских народа током бронзаног доба и Велике сеобе народа у раном средњем веку. Балканско полуострво је имало важну улогу током целокупне историје људске врсте на евроазијском континенту због тога што је представљало важан миграцијски коридор преко којег су се одвијале миграције од праисторије па све до савременог доба. Такође, током последњег леденог максимума Балканско полуострво је представљало један од глацијaлних рефугијума са којег је отпочела пост-глацијaлна реколонизација Европе. Имајући у виду да српска популација насељава централни део Балканског полуострва, у овој популацији се могу очекивати генетички трагови комплексних демографских процеса. Предмет истраживања ове докторске дисертације било је испитивање варијабилности митохондријске ДНК (мтДНК) у савременој популацији Србије са популационо генетичког, филогенетског и филогеографског аспекта. У ту сврху анализирана је варијабилност првог и другог хиперваријабилног сегмента (HVS-I и HVS-II) и полиморфизми кодирајућег региона мтДНК код 172 испитаника чији су преци по женској линији из последње две генерације декларисаног српског етницитета. Поред тога, одабрано је и комплетно секвенцирано 58 митогенома који су анализирани у циљу бољег разумевања еволуције појединих мтДНК хаплогрупа, као и утврђивања доприноса различитих миграција у обликовању садашњег обрасца варијабилности митохондријског генског пула српске популације. У српској популацији заступљене су већином мтДНК хаплогрупе/подхаплогрупе карактеристичне за европске популације, а њихове учесталости и параметри генетичке разноврсности налазе сe у распону вредности детектованих у осталим европским популацијама. Српска популација није генетички диференцирана у односу на друге јужнословенске популације и у свим анализама заузима централну позицију између јужнословенских популација источног и западног дела Балканског полуострва. Највећи проценат HVS-I и HVS-I/HVS-II хаплотипова становништво Србије дели са географски блиским популацијама Балканског полуострва из јужнословенске групе, где су детектовани и потенцијално приватни хаплотипови...Genetic structure and clinal distribution of genetic variation in contemporary human populations in Europe are the results of interplay between exceptionally complex evolutionary, demographic and cultural processes which took place in Europe during several thousand years. Among the most important processes are post-glacial recolonization of Europe, spread of farming during the Neolithic period (Neolithic transition) and numerous migrations of human populations such as Bronze Age migrations of Indo-Europeans and migrations during the Migration Period that occurred in the Early Middle Ages. The Balkan Peninsula played an important role during the entire history of humankind in Europe and Asia because it served as an important migration corridor starting from prehistoric to present days. Furthermore, during the last glacial maximum, this region was one of the glacial refugia from which the post-glacial recolonization of Europe was initiated. Since Serbian population inhabits the central part of the Balkan Peninsula, this population may harbour genetic traces of past complex demographic processes that were occurring in the Balkans over time. The subject of this doctoral thesis was the study of the mitochondrial DNA (mtDNA) variability in a contemporary population of Serbia from population genetics, phylogenetic and phylogeographic aspects. For that purpose, the variability of HVS-I and HVS-II regions and polymorphisms within the coding region of mtDNA have been assessed in 172 individuals whose Serbian maternal ancestry was confirmed for at least two generations. Furthermore, 58 selected mitogenomes were completely sequenced in order to provide new insights into the evolution of particular mtDNA haplogroups and to assess the contribution of various human migrations in modelling contemporary maternal gene pool of the Serbian population. Serbian population comprises mainly mtDNA haplogroups/subhaplogroups typical for European populations and their frequencies and levels of genetic diversity are mostly in the range of those detected in other European populations. Serbian population is not genetically differentiated from other south-Slavic populations and in all analyses it occupies a central position among south-Slavic populations from the eastern and western part of the Balkan Peninsula. The highest percentage of HVS-I and HVS-I/HVS-II haplotypes Serbian population shares with south-Slavic populations from the Balkan Peninsula, where potential private haplotypes have been observed as well. In general, European populations were grouped in a manner reflecting their geographic distribution. Furthermore, Slavic populations were grouped according to their linguistic affiliation. Rather high values of all parameters of genetic diversity of rare mtDNA subhaplogroups in the Balkan Peninsula are concordant with the previously demonstrated refugial character of this region..

Direct PCR amplification of the HVSI region in mitochondrial DNA from buccal cell swabs

Amplification of human mitochondrial DNA (mtDNA) has been widely used in population genetics, human evolutionary and molecular anthropology studies. mtDNA hypervariable segments I and II (HVSI and HVSII) were shown to be a suitable tool in genetic analyses due to the unique properties of mtDNA, such as the lack of recombination, maternal mode of inheritance, rapid evolutionary rate and high population-specific polymorphisms. Here we present a rapid and low-cost method for direct PCR amplification of a 330 bp fragment of HVSI from buccal cell samples. Avoiding the DNA isolation step makes this method appropriate for the analysis of a large number of samples in a short period of time. Since the transportation of samples and fieldwork conditions can affect the quality of samples and subsequent DNA analysis, we tested the effects of long-term storage of buccal cell swabs on the suitability of such samples for direct PCR amplification. We efficiently amplified a 330 bp fragment of HVSI even after the long-term storage of buccal cells at room temperature, +4°C or at -20°C, for up to eight months. All examined PCR products were successfully sequenced, regardless of sample storage time and conditions. Our results suggest that the direct PCR amplification of the HVSI region from buccal cells is a method well suited for large-scale mtDNA population studies

Influence of different factors on the RAID 0 paired magnetic disk arrays

The rapid technological progress has led to a growing need for more data storage space. The appearance of big data requires larger storage space, faster access and exchange of data as well as data security. RAID (Redundant Array of Independent Disks) technology is one of the most cost-effective ways to satisfy needs for larger storage space, data access and protection. However, the connection of multiple secondary memory devices in RAID 0 aims to improve the secondary memory system in a way to provide greater storage capacity, increase both read data speed and write data speed but it is not fault-tolerant or error-free. This paper provides an analysis of the system for storing the data on the paired arrays of magnetic disks in a RAID 0 formation, with different number of queue entries for overlapped I/O, where queue depth parameter has the value of 1 and 4. The paper presents a range of test results and analysis for RAID 0 series for defined workload characteristics. The tests were carried on in Microsoft Windows Server 2008 R2 Standard operating system, using 2, 3, 4 and 6 paired magnetic disks and controlled by Dell PERC 6/i hardware RAID controller. For the needs of obtaining the measurement results, ATTO Disk Benchmark has been used. The obtained results have been analyzed and compared to the expected behavior

Popliteal artery injury following traumatic knee joint dislocation in a 14-year-old boy: A case report and review of the literature

Introduction. Posterior knee joint dislocation associated with injury of the popliteal artery in children is an extremely rare condition. Rapid diagnosis and treatment are essential for limb salvage and function. Case report. We reported a 14-year-old boy who suffered traumatic displacement of the right knee and contusion of the popliteal artery during motorcycle accident. The diagnosis was confirmed using Doppler and duplex ultrasonography and digital substraction transfemoral arteriography. The urgent surgical procedure was performed using posterior approach to the popliteal artery. During the surgical exploration, rupture of the posterior cruciate ligament associated with thrombosed popliteal artery have been found. The damaged popliteal artery was resected and replaced with autologous saphenous vein graft. The last stage of the procedure was a transosseous femoral fixation of posterior circuate ligament. A 3-year-follow-up after the surgery demonstrated intact arterial perfusion and very good function of the knee with a minimal difference as compared with the contralateral knee. Conclusion. Combined orthopedic and vascular injuries are very rare in children. They require combined treatment. [Projekat Ministarstva nauke Republike Srbije, br. 175008

Evaluating ND1 and Cytb mitochondrial genes as markers for diversity analysis of protected White-tailed eagle species from Serbia

White-tailed eagle is the biggest bird of prey in Central and Southeast Europe. In Serbia it inhabits the Vojvodina province and the valleys of Danube, Sava, Tisa and Tamiš. Anthropogenic pressure on its habitats in Europe caused a decline in its numbers, but due to the strict laws protecting both species and its habitats, birds’ numbers are now steady and increasing. In Serbia, as a strictly protected species it is a subject of different conservation programs. The available genetic data for this population are scarce and it is necessary to assess its genetic diversity to improve the existing conservation efforts. ND1 and Cytb mitochondrial genes can be used to estimate the populations’ adaptation to different environmental conditions and their variability can potentially be used to evaluate differentiation between populations. To assess the genetic diversity of White-tailed eagle in Serbia we used mitochondrial ND1 and Cytb nucleotide sequences from 40 unrelated birds collected in nests. ND1 and Cytb nucleotide sequences variability was evaluated using standard parameters of genetic diversity (PGD). Acquired values were compared with the available data for the variability of the D-loop region which showed that combined ND1/Cytb nucleotide sequences PGD provide comparable results. Using publicly available sequences we reconstructed haplotype networks for ND1, Cytb, ND1/Cytb and D-loop which further showed the applicability of ND1/ Cytb in population genetics analyses. Phylogeny reconstructed using combined ND1/Cytb sequences identified two branches in Serbian white-tailed eagles. Although the majority of substitutions were nonsynonymous, no selective pressure was detected. Our data suggest that combined ND1/Cytb sequence variability provides sufficient information to be used for population comparison, population differentiation analyses and phylogeny reconstruction, but also gives a tool to potentially identify adaptations to different environmental conditions.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202

Mitochondrial gene pool variability of the residents of the Republic of Serbia

Mitohondrijska DNK (mtDNK) se odlikuje nizom osobina koje je čine pogodnom za istraživanja evolutivne istorije ljudskih populacija koja se zasniva na molekularnim markerima ženske linije nasleđivanja. Tokom poslednje decenije publikovano je više naučnih radova u kojima je analizirana varijabilnost mtDNK u populaciji Srbije primenom markera različite rezolucije uključujući i kompletne genome. U skladu sa očekivanjima zasnovanim na istorijskim, arheološkim i drugim izvorima koji govore u prilog veoma kompleksne istorije populacija na Balkanskom poluostrvu, mtDNK podaci su potvrdili da se srpska populacija odlikuje visokim nivoom raznovrsnosti mtDNK koji je posledica izuzetno složene dinamike ove populacije tokom vremena. Današnji mtDNK profil populacije Srbije ne odstupa od matrilinealnog profila karakterističnog za druge evropske populacije, a genetičke distance pokazuju da ova populacija zauzima centralnu poziciju unutar grupe južnoslovenskih populacija koje se odlikuju visokom heterogenošću. Srpska populacija deli najveći procenat mtDNK haplotipova sa geografski bliskim populacijama Balkanskog poluostrva koje pripadaju južnoslovenskoj grupi, gde su uočeni i potencijalno privatni haplotipovi. Na osnovu filogenetske i filogeografske analize kompletnih mitogenoma u srpskoj populaciji detektovane su retke mtDNK linije, karakteristične za druge regione, poput Bliskog istoka (N1b, HV2), istočne Azije (D4) i Afrike (L2a1), kao i one koje su potencijalno specifične za Balkansko poluostrvo, poput K1a13a1, U4c1b1 i H6a2b. Pored toga, srpska populacija deli određeni broj mtDNK podhaplogrupa sa istočno- i zapadnoslovenskim populacijama kao i sa germanskim populacijama severne i srednje Evrope. Istraživanja varijabilnosti mtDNK su pokazala da se izuzetno velika raznovrsnost mtDNK savremene populacije Srbije može objasniti genetičkim doprinosom kako slovenskih i germanskih, tako i pre-slovenskih populacija koje su naseljavale Balkansko poluostrvo pre Velike seobe naroda.The mitochondrial DNA (mtDNA) is characterized by a number of features that make it suitable for studying the evolutionary history of human populations based on molecular markers with the female-specific line of inheritance. During the last decade, several scientific papers were published in which the mtDNA variability in the population of Serbia was analyzed using markers of different resolution including complete mitogenomes. In accordance with expectations based on historical, archaeological and other sources that speak in favor of a very complex history of populations on the Balkan Peninsula, mtDNA data confirmed that Serbian population is characterized by a high level of mtDNA diversity, which is a consequence of the exceptionally complex dynamics of this population over time. Today’s mtDNA profile of the Serbian population does not differ from the matrilineal landscape characteristic of other European populations, and according to genetic distances, this population occupies a central position within the group of South- Slavic populations characterized by high heterogeneity. The Serbian population shares the highest percentage of mtDNA haplotypes with the geographically close populations of the Balkan Peninsula belonging to the South-Slavic group, where potentially private haplotypes were also observed. Phylogenetic and phylogeographic analysis of complete mitogenomes in the Serbian population revealed rare mtDNA lineages, characteristic of other regions, such as the Middle East (N1b, HV2), East Asia (D4) and Africa (L2a1), as well as those that are potentially specific for Balkan Peninsula, like K1a13a1, U4c1b1 and H6a2b. In addition, Serbian population shares a certain number of mtDNA subhaplogroups with East- and West-Slavic populations as well as with the Germanic populations of Northern and Central Europe. Studies of mtDNA variability have shown that the exceptionally high mtDNA diversity in contemporary Serbian population may be associated with the genetic contribution of both Slavic and Germanic, as well as pre- Slavic populations that inhabited the Balkan Peninsula before the Great Migration

Endovascular aortic repair: First twenty years

Endovascular aortic/aneurysm repair (EVAR) was introduced into clinical practice at the beginning of the nineties. Its fast development had a great influence on clinicians, vascular surgeons and interventional radiologists, educational curriculums, patients, industry and medical insurance. The aim of this paper is to present the contribution of clinicians and industry to the development and advancement of endovascular aortic repair over the last 20 years. This review article presents the development of EVAR by focusing on the contribution of physicians, surgeons and interventional radiologists in the creation of the new field of vascular surgery termed hybrid vascular surgery, and also the contribution of technological advancement by a significant help of industrial representatives – engineers and their counselors. This article also analyzes studies conducted in order to compare the successfulness of EVAR with up-to-now applied open surgical repair of aortic aneurysms, and some treatment techniques of other aortic diseases. During the first two decades of its development the EVAR method was rapidly progressing and was adopted concurrently with the expansion of technology. Owing to large randomized studies, early and long-term results indicate specific complications of this method, thus influencing further technological improvement and defining risk patients groups in whom the use of the technique should be avoided. Good results are insured only in centers, specialized in vascular surgery, which have on their disposal adequate conditions for solving all complications associated with this method

Comparative evaluation of antimutagenic and antimitotic effects of Morchella esculenta extracts and protocatechuic acid

Morchella esculenta (L.) Pers. methanolic extracts, obtained from fruiting bodies growing wild in Serbia and Portugal, were screened for their antimutagenic properties and compared to protocatechuic acid, previously identified in both species. Salmonella typhimurium TA100 reversion assay was used for the antimutagenic properties. Methanolic extracts expressed important antimutagenic potency towards S. typhimurium, which was documented by index of antimutagenicity (I). Sample from Serbia expressed slightly higher antimutagenic properties with inhibition rate of 58.7%. Sample from Portugal gave inhibition rate of 51.7%. Protocatechuic acid had inhibition rate I of his+ revertants of 72.4%. Cell viability in the presence of extracts was also documented. M. esculenta samples from Serbia and Portugal possessed novel biological potential for the studied species, as well as its phenolic compound – protocatechuic acid, identified in both samples. Genotoxic effect, regarding mitotic index and chromosomal aberration score, was also assessed by using Allium cepa L. assay. Protocatechuic acid showed the most significant decrease in mitotic index, as well as decrease in chromosomal aberration score.Serbian Ministry of Education, Science and Technological Development; FCT Portugal; COMPETE/QREN/EU, PTDC/AGR-ALI/110062/2009 PEst-OE/AGR/UI0690/201

Comparative evaluation of antimutagenic and antimitotic effects of Morchella esculenta extracts and protocatechuic acid

Morchella esculenta (L.) Pers. methanolic extracts, obtained from fruiting bodies growing wild in Serbia and Portugal, were screened for their antimutagenic properties and compared to protocatechuic acid, previously identified in both species. Salmonella typhimurium TA100 reversion assay was used for the antimutagenic properties. Methanolic extracts expressed important antimutagenic potency towards S. typhimurium, which was documented by index of antimutagenicity (I). A sample from Serbia expressed slightly higher antimutagenic properties with an inhibition rate of 58.7%. A sample from Portugal gave an inhibition rate of 51.7%. Protocatechuic acid had an inhibition rate I of his(+) revertants of 72.4%. Cell viability in the presence of extracts was also documented. M. esculenta samples from Serbia and Portugal possessed novel biological potential for the studied species, as well as its phenolic compound - protocatechuic acid, identified in both samples. Genotoxic effect, regarding mitotic index and chromosomal aberration score, was also assessed by using the Allium cepa L. assay. Protocatechuic acid showed the most significant decrease in mitotic index, as well as decrease in chromosomal aberration score

Chemical composition of the mushroom Meripilus giganteus Karst. and bioactive properties of its methanolic extract

Wild Meripilus giganteus Karst belongs to the order Polyporales, in which some members are known to possess a wide range of pharmacological properties. M. giganteus showed to be rich in carbohydrates (74.49 g/100 g) and proteins (15.94 g/100 g), presenting low fat content (1.51 g/100 g). Chemical composition was determined by using chromatographic techniques. Also, various bioactive compounds were detected including all four tocopherol isoforms with d- and ?-tocopherols being predominant (123.35 and 77.80 µg/100 g, respectively); five organic acids (oxalic, malic, quinic, citric and fumaric acids) with predominant malic acid (3.17 g/100 g); and three phenolic acids and related compounds (p-hydroxybenzoic, p-coumaric and cinnamic acids; 1010, 2420 and 340 µg/100 g, respectively). M. giganteus methanolic extract exhibited antioxidant activity tested by five different assays with the strongest potential in TBARS assay (EC 50 0.31 mg/mL); and antimicrobial activities (MIC/MBC 0.0125–5 mg/mL; MIC/MFC 0.025–0.4 mg/mL). Furthermore, treatment of cervical carcinoma cell line (HeLa) led to reduction in cell's viability in MTT assay (IC 50 0.41 mg/mL after 48 h), induced process of apoptosis and inhibited cell's migration in vitro. The analysed extract was not toxic for zebrafish embryos (at 0.5 mg/mL), indicating its biosafety and potential application as a dietary supplement in chemoprevention.This work was supported by the Ministry of Education, Science and Technological Development of the Republic of Serbia (grant numbers 173032, 173051 and 47025). Authors are grateful to the Foundation for Science and Technology (FCT, Portugal) for financial support to CIMO (Pest-OE/AGR/UI0690/2015) and L. Barros grant (SFRH/BPD/107855/2015). We would like to thank dr Jelena Dinic for help in performing DAPI/PI staining.info:eu-repo/semantics/publishedVersio