46 research outputs found
Diversity of the cell-wall associated genomic island of the archaeon Haloquadratum walsbyi
Background: Haloquadratum walsbyi represents up to 80 % of cells in NaCl-saturated brines worldwide, but is
notoriously difficult to maintain under laboratory conditions. In order to establish the extent of genetic diversity in a
natural population of this microbe, we screened a H. walsbyi enriched metagenomic fosmid library and recovered
seven novel version of its cell-wall associated genomic island. The fosmid inserts were sequenced and analysed.
Results: The novel cell-wall associated islands delineated two major clades within H. walsbyi. The islands predominantly contained genes putatively involved in biosynthesis of surface layer, genes encoding cell surface glycoproteins and genes involved in envelope formation. We further found that these genes are maintained in the population and that the diversity of this region arises through homologous recombination but also through the action of mobile genetic elements, including viruses.
Conclusions: The population of H. walsbyi in the studied saltern brine is composed of numerous clonal lineages that differ in surface structures including the cell wall. This type of variation probably reflects a number of mechanisms that minimize the infection rate of predating virusesAll authors were supported by project MICROGEN (Programa CONSOLIDER-INGENIO 2010 CSD2009-00006) from the Spanish Ministerio de Ciencia e InnovaciĆ³n.FR-V and AMBC received support from MEDIMAX BFPU2013- 48007-P from the Spanish Ministerio de EconomĆa y CompetitividadMaCuMBA Project 311975 of the European Commission FP7ACOMP/2014/024, AORG 2014/032 and PROMETEO II/2014/012. LP received support from Ministry for School and Sports of the Republic of Slovenia under Slovenian Research Agency program P1-0198
Overview of Human Population-Genetic Studies in Bosnia and Herzegovina during the Last Three Centuries: History and Prospective
Modern Bosnia and Herzegovina is a multi-ethnic and multi-religion country, with a very stormy history. Certain archaeological
findings indicate continuous population of its territory since the Paleolithic. In time, vast number of different
factors jointly influenced fascinating diversity of local human populations. A great number of small, more or less isolated,
indigenous populations, make this area quite attractive for population-genetic surveys of different levels and
approaches. Austro-Hungarian military physicians conducted the very first known bio-anthropological analyses of
Bosnia-Herzegovina population at the end of the 19th century. Thus, the first step towards resolving the genetic structures
of local B&H human populations was made. The studies that followed (conducted throughout most of the 20th century)
were primarily based on the observation of various phenotypic traits. This stage was followed by the examination of various
cytogenetic and fundamental DNA based molecular markers. The efforts undertaken over the last three centuries revealed
Ā»human genetic treasureĀ« in Bosnia and Herzegovina. However, even now, after all the studies that were conducted,
many interesting features remain to be discovered and described within the existing local human populations
Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber
<p>Abstract</p> <p>Background</p> <p>Saturated brines are extreme environments of low diversity. <it>Salinibacter ruber </it>is the only bacterium that inhabits this environment in significant numbers. In order to establish the extent of genetic diversity in natural populations of this microbe, the genomic sequence of reference strain DSM 13855 was compared to metagenomic fragments recovered from climax saltern crystallizers and obtained with 454 sequencing technology. This kind of analysis reveals the presence of metagenomic islands, i.e. highly variable regions among the different lineages in the population.</p> <p>Results</p> <p>Three regions of the sequenced isolate were scarcely represented in the metagenome thus appearing to vary among co-occurring <it>S. ruber </it>cells. These metagenomic islands showed evidence of extensive genomic corruption with atypically low GC content, low coding density, high numbers of pseudogenes and short hypothetical proteins. A detailed analysis of island gene content showed that the genes in metagenomic island 1 code for cell surface polysaccharides. The strain-specific genes of metagenomic island 2 were found to be involved in biosynthesis of cell wall polysaccharide components. Finally, metagenomic island 3 was rich in DNA related enzymes.</p> <p>Conclusion</p> <p>The genomic organisation of <it>S. ruber </it>variable genomic regions showed a number of convergences with genomic islands of marine microbes studied, being largely involved in variable cell surface traits. This variation at the level of cell envelopes in an environment devoid of grazing pressure probably reflects a global strategy of bacteria to escape phage predation.</p
Incidence of horse meat in processed food on B&H market
Following the āhorse meat scandalā in 2013, European Union countries have conducted official control of EU market and unraveled food fraud which implicated a number of processed food products and food businesses. Five years after the breakout of the scandal, no official information on market surveillance in Bosnia and Herzegovina is available. Therefore, 73 randomly selected meat products from retail were collected and analyzed for the presence of horse DNA. Horse DNA was detected in 21 products (28.77%). Particularly disturbing for B&H consumers is high proportion of sujuk samples positive for horse DNA (46.15%) with lower incidence among the products of small manufactures. Also disturbing is the finding that 71.43% of the products that contain horse DNA were produced in B&H. According to our data there is a requirement for stricter surveillance of both import and internal market
Allele Frequencies for 15 Short Tandem Repeat Loci in Representative Sample of Croatian Population
Aim To study the distribution of allele frequencies of 15 short
tandem repeat (STR) loci in a representative sample of Croatian
population.
Methods A total of 195 unrelated Caucasian individuals born in
Croatia, from 14 counties and the City of Zagreb, were sampled
for the analysis. All the tested individuals were voluntary donors.
Buccal swab was used as the DNA source. AmpFlSTRĀ® IdentifilerĀ®
was applied to simultaneously amplify 15 STR loci. Total reaction
volume was 12.5 Ī¼L. The PCR amplification was carried out in PE
Gene Amp PCR System Thermal Cycler. Electrophoresis of the
amplification products was preformed on an ABI PRISM 3130
Genetic Analyzer. After PCR amplification and separation by
electrophoresis, raw data were compiled, analyzed, and numerical
allele designations of the profiles were obtained. Deviation from
Hardy-Weinberg equilibrium, observed and expected heterozygosity,
power of discrimination, and power of exclusion were calculated.
Bonferroniās correction was used before each comparative
analysis.
Results We compared Croatian data with those obtained from
geographically neighboring European populations. The significant
difference (at P<0.01) in allele frequencies was recorded only between
Croatian and Slovenian populations for vWA locus. There
was no significant deviation from Hardy-Weinberg equilibrium
for all the observed loci.
Conclusion Obtained population data concurred with the expected
āSTR data frameā for this part of Europe
Two Tales of Prokaryotic Genomic Diversity: Escherichia coli and Halophiles
Jedna je od opÄenitih znaÄajki prokariota velika raznolikost genoma, na Å”to utjeÄu mutacije, horizontalni prijenos gena, prisutnost bakteriocina i bakterijskih virusa. Iznimna se genomska raznolikost razvila kao posljedica izlaganja mikroorganizama stresu i njihove prilagodbe razliÄitim uvjetima okoliÅ”a. U radu su predstavljena dva primjera raznolikosti prokariota: genetska varijabilnost jedinki vrste Escherichia coli i raznolikost mikroorganizama prisutnih u slanim staniÅ”tima, praÄena raspravom o zdravstvenim problemima uzrokovanim unosom kontaminirane hrane i moguÄnosti primjene mikroorganizama u biotehnologiji.Prokaryotes are generally characterized by vast genomic diversity that has been shaped by mutations, horizontal gene transfer, bacteriocins and phage predation. Enormous genetic diversity has developed as a result of stresses imposed in harsh environments and the ability of microorganisms to adapt. Two examples of prokaryotic diversity are presented: on intraspecies level, exemplified by Escherichia coli, and the diversity of the hypersaline environment, with the discussion of food-related health issues and biotechnological potential
Contemporary Challenges and Solutions
CA18131
CP16/00163
NIS-3317
NIS-3318
decision 295741
C18/BM/12585940The human microbiome has emerged as a central research topic in human biology and biomedicine. Current microbiome studies generate high-throughput omics data across different body sites, populations, and life stages. Many of the challenges in microbiome research are similar to other high-throughput studies, the quantitative analyses need to address the heterogeneity of data, specific statistical properties, and the remarkable variation in microbiome composition across individuals and body sites. This has led to a broad spectrum of statistical and machine learning challenges that range from study design, data processing, and standardization to analysis, modeling, cross-study comparison, prediction, data science ecosystems, and reproducible reporting. Nevertheless, although many statistics and machine learning approaches and tools have been developed, new techniques are needed to deal with emerging applications and the vast heterogeneity of microbiome data. We review and discuss emerging applications of statistical and machine learning techniques in human microbiome studies and introduce the COST Action CA18131 āML4Microbiomeā that brings together microbiome researchers and machine learning experts to address current challenges such as standardization of analysis pipelines for reproducibility of data analysis results, benchmarking, improvement, or development of existing and new tools and ontologies.publishersversionpublishe
2020 consensus guideline for optimal approach to the diagnosis and treatment of HER2-positive breast cancer in Bosnia and Herzegovina
The HERe2Cure project, which involved a group of breast cancer experts, members of multidisciplinary tumor boards from healthcare institutions in Bosnia and Herzegovina, was initiated with the aim of defining an optimal approach to the diagnosis and treatment of HER2 positive breast cancer. After individual multidisciplinary consensus meetings were held in all oncology centers in Bosnia and Herzegovina, a final consensus meeting was held in order to reconcile the final conclusions discussed in individual meetings. Guidelines were adopted by consensus, based on the presentations and suggestions of experts, which were first discussed in a panel discussion and then agreed electronically between all the authors mentioned. The conclusions of the panel discussion represent the consensus of experts in the field of breast cancer diagnosis and treatment in Bosnia and Herzegovina. The objectives of the guidelines include the standardization, harmonization and optimization of the procedures for the diagnosis, treatment and monitoring of patients with HER2-positive breast cancer, all of which should lead to an improvement in the quality of health care of mentioned patients. The initial treatment plan for patients with HER2-positive breast cancer must be made by a multidisciplinary tumor board comprised of at least: a medical oncologist, a pathologist, a radiologist, a surgeon, and a radiation oncologist/radiotherapist
2020 consensus guideline for optimal approach to the diagnosis and treatment of HER2-positive breast cancer in Bosnia and Herzegovina.
The HERe2cure project, which involved a group of breast cancer experts, members of multidisciplinary tumor boards from healthcare institutions in Bosnia and Herzegovina, was initiated with the aim of defining an optimal approach to the diagnosis and treatment of HER2 positive breast cancer. After individual multidisciplinary consensus meetings were held in all oncology centers in Bosnia and Herzegovina, a final consensus meeting was held in order to reconcile the final conclusions discussed in individual meetings. Guidelines were adopted by consensus, based on the presentations and suggestions of experts, which were first discussed in a panel discussion and then agreed electronically between all the authors mentioned. The conclusions of the panel discussion represent the consensus of experts in the field of breast cancer diagnosis and treatment in Bosnia and Herzegovina. The objectives of the guidelines include the standardization, harmonization and optimization of the procedures for the diagnosis, treatment and monitoring of patients with HER2-positive breast cancer, all of which should lead to an improvement in the quality of health care of mentioned patients. The initial treatment plan for patients with HER2-positive breast cancer must be made by a multidisciplinary tumor board comprised of at least: a medical oncologist, a pathologist, a radiologist, a surgeon, and a radiation oncologist/radiotherapist