prediction of overall survival with 2nd line l2os chemotherapy ct in patients with advanced biliary tract cancer abtc ageo ct2bil cohort update and international multicenter external validations

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Analysis of BAC-end sequences in rainbow trout: Content characterization and assessment of synteny between trout and other fish genomes

<p>Abstract</p> <p>Background</p> <p>Rainbow trout (<it>Oncorhynchus mykiss</it>) are cultivated worldwide for aquaculture production and are widely used as a model species to gain knowledge of many aspects of fish biology. The common ancestor of the salmonids experienced a whole genome duplication event, making extant salmonids such as the rainbow trout an excellent model for studying the evolution of tetraploidization and re-diploidization in vertebrates. However, the lack of a reference genome sequence hampers research progress for both academic and applied purposes. In order to enrich the genomic tools already available in this species and provide further insight on the complexity of its genome, we sequenced a large number of rainbow trout BAC-end sequences (BES) and characterized their contents.</p> <p>Results</p> <p>A total of 176,485 high quality BES, were generated, representing approximately 4% of the trout genome. BES analyses identified 6,848 simple sequence repeats (SSRs), of which 3,854 had high quality flanking sequences for PCR primers design. The first rainbow trout repeat elements database (INRA RT rep1.0) containing 735 putative repeat elements was developed, and identified almost 59.5% of the BES database in base-pairs as repetitive sequence. Approximately 55% of the BES reads (97,846) had more than 100 base pairs of contiguous non-repetitive sequences. The fractions of the 97,846 non-repetitive trout BES reads that had significant BLASTN hits against the zebrafish, medaka and stickleback genome databases were 15%, 16.2% and 17.9%, respectively, while the fractions of the non-repetitive BES reads that had significant BLASTX hits against the zebrafish, medaka, and stickleback protein databases were 10.7%, 9.5% and 9.5%, respectively. Comparative genomics using paired BAC-ends revealed several regions of conserved synteny across all the fish species analyzed in this study.</p> <p>Conclusions</p> <p>The characterization of BES provided insights on the rainbow trout genome. The discovery of specific repeat elements will facilitate analyses of sequence content (e.g. for SNPs discovery and for transcriptome characterization) and future genome sequence assemblies. The numerous microsatellites will facilitate integration of the linkage and physical maps and serve as valuable resource for fine mapping QTL and positional cloning of genes affecting aquaculture production traits. Furthermore, comparative genomics through BES can be used for identifying positional candidate genes from QTL mapping studies, aid in future assembly of a reference genome sequence and elucidating sequence content and complexity in the rainbow trout genome.</p

Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals

peer-reviewedH.D.D., A.J.C., P.J.B. and B.J.H. would like to acknowledge the Dairy Futures Cooperative Research Centre for funding. H.P. and R.F. acknowledge funding from the German Federal Ministry of Education and Research (BMBF) within the AgroClustEr ‘Synbreed—Synergistic Plant and Animal Breeding’ (grant 0315527B). H.P., R.F., R.E. and K.-U.G. acknowledge the Arbeitsgemeinschaft Süddeutscher Rinderzüchter, the Arbeitsgemeinschaft Österreichischer Fleckviehzüchter and ZuchtData EDV Dienstleistungen for providing genotype data. A. Bagnato acknowledges the European Union (EU) Collaborative Project LowInputBreeds (grant agreement 222623) for providing Brown Swiss genotypes. Braunvieh Schweiz is acknowledged for providing Brown Swiss phenotypes. H.P. and R.F. acknowledge the German Holstein Association (DHV) and the Confederación de Asociaciones de Frisona Española (CONCAFE) for sharing genotype data. H.P. was financially supported by a postdoctoral fellowship from the Deutsche Forschungsgemeinschaft (DFG) (grant PA 2789/1-1). D.B. and D.C.P. acknowledge funding from the Research Stimulus Fund (11/S/112) and Science Foundation Ireland (14/IA/2576). M.S. and F.S.S. acknowledge the Canadian Dairy Network (CDN) for providing the Holstein genotypes. P.S. acknowledges funding from the Genome Canada project entitled ‘Whole Genome Selection through Genome Wide Imputation in Beef Cattle’ and acknowledges WestGrid and Compute/Calcul Canada for providing computing resources. J.F.T. was supported by the National Institute of Food and Agriculture, US Department of Agriculture, under awards 2013-68004-20364 and 2015-67015-23183. A. Bagnato, F.P., M.D. and J.W. acknowledge EU Collaborative Project Quantomics (grant 516 agreement 222664) for providing Brown Swiss and Finnish Ayrshire sequences and genotypes. A.C.B. and R.F.V. acknowledge funding from the public–private partnership ‘Breed4Food’ (code BO-22.04-011- 001-ASG-LR) and EU FP7 IRSES SEQSEL (grant 317697). A.C.B. and R.F.V. acknowledge CRV (Arnhem, the Netherlands) for providing data on Dutch and New Zealand Holstein and Jersey bulls.Stature is affected by many polymorphisms of small effect in humans1. In contrast, variation in dogs, even within breeds, has been suggested to be largely due to variants in a small number of genes2,3. Here we use data from cattle to compare the genetic architecture of stature to those in humans and dogs. We conducted a meta-analysis for stature using 58,265 cattle from 17 populations with 25.4 million imputed whole-genome sequence variants. Results showed that the genetic architecture of stature in cattle is similar to that in humans, as the lead variants in 163 significantly associated genomic regions (P < 5 × 10−8) explained at most 13.8% of the phenotypic variance. Most of these variants were noncoding, including variants that were also expression quantitative trait loci (eQTLs) and in ChIP–seq peaks. There was significant overlap in loci for stature with humans and dogs, suggesting that a set of common genes regulates body size in mammals

Jakość wód epizodycznej rzeki Bounamoussa w północnowschodniej Algierii: Statystyczna analiza wybranych parametrów fizycznych i chemicznych

Nowadays, problems with wastes constitute a danger increasingly important for the recipient environments. Indeed, the water is affected in an increasing way by mineral and organic materials from which some ones are pathogenic and thus dangerous for the ecosystem. It is in this context that the present study took place, it relates to the surface waters pollution of the Wadi Bounamoussa in the Algeria northeast. The study concerns the analysis of physical and chemical parameters of waters such as: temperature (T), pH, electrical conductivity (EC), Cl–, chemical oxygen demand (COD), total absorbance colour (TAC), total hardness (TH), PO4 3–, total phosphorus (Ptot) along the wadi in one year long survey (October 2013 to July 2014). Waters were sampled at ten study sites with a quarterly sampling. In order to establish a relationship between various physical and chemical parameters and for a better assessment the anthropogenic effect on the Wadi Bounamoussa's water quality, we have processed a statistical treatment by means of the Principal Component Analysis (PCA). PCA has revealed two gradients. The first reflects the eutrophication caused by chemical fertilizers used in agriculture and the intensive livestock farming development, while the second describes the resulting water mineralization of high rates of the Cl– and EC. Moreover, PCA has allowed discriminating the stations according to their physical and chemical data. This study has allowed us also to reveal the influence of seasonal variations.Odpady stwarzają obecnie rosnące zagrożenie dla środowisk, do których trafiają. Tak jest w przypadku wód w coraz większym stopniu zasilanych substancjami nieorganicznymi i materią organiczną, która może zawierać patogeny stanowiące zagrożenie środowiska. Realizowane w tym kontekście badania dotyczą zanieczyszczenia wód powierzchniowych epizodycznej rzeki Bounamoussa w północnowschodniej Algierii. Badania obejmowały analizę fizycznych i chemicznych parametrów wód takich jak: temperatura (T), pH, przewodnictwo elektrolityczne (EC), stężenie jonów chlorkowych (Cl–), chemiczne zapotrzebowanie na tlen (COD), zasadowość (TAC), całkowita twardość (TH), jonów fosforanowych (PO4 3–) i fosforu ogólnego (Ptot) mierzonych wzdłuż biegu rzeki od października 2013 do lipca 2014 r. Wody do analiz pobierano z dziesięciu stanowisk, co trzy miesiące. W celu ustalenia zależności pomiędzy różnymi parametrami fizycznymi i chemicznymi i lepszej oceny oddziaływań antropogenicznych na jakość wód rzeki przeprowadzono analizę statystyczną metodą głównych składowych (PCA). Analiza ta ujawniła dwa gradienty. Pierwszy odzwierciedla eutrofizację wywołaną dostawą nawozów z rolnictwa i intensywnego chowu zwierząt; drugi opisuje mineralizację wód, która przejawia się dużym stężeniem chlorków i dużym przewodnictwem. Analiza PCA pozwoliła ponadto wyodrębnić stanowiska według ich właściwości fizycznych i chemicznych. Wyniki badań umożliwiły także wykazanie sezonowej zmienności analizowanych parametrów

Improvement of RFLP-based identification of lactic acid bacteria isolated from healthy and diseased fish: differential diagnosis and practical issues

International audienc