Evolution of major histocompatibility complex class I and class II genes in the brown bear

International audienceBackground: Major histocompatibility complex (MHC) proteins constitute an essential component of the vertebrate immune response, and are coded by the most polymorphic of the vertebrate genes. Here, we investigated sequence variation and evolution of MHC class I and class II DRB, DQA and DQB genes in the brown bear Ursus arctos to characterise the level of polymorphism, estimate the strength of positive selection acting on them, and assess the extent of gene orthology and trans-species polymorphism in Ursidae . Results: We found 37 MHC class I, 16 MHC class II DRB, four DQB and two DQA alleles. We confirmed the expression of several loci: three MHC class I, two DRB, two DQB and one DQA. MHC class I also contained two clusters of non-expressed sequences. MHC class I and DRB allele frequencies differed between northern and southern populations of the Scandinavian brown bear. The rate of nonsynonymous substitutions (d N ) exceeded the rate of synonymous substitutions (d S ) at putative antigen binding sites of DRB and DQB loci and, marginally significantly, at MHC class I loci. Models of codon evolution supported positive selection at DRB and MHC class I loci. Both MHC class I and MHC class II sequences showed orthology to gene clusters found in the giant panda Ailuropoda melanoleuca. Conclusions: Historical positive selection has acted on MHC class I, class II DRB and DQB, but not on the DQA locus. The signal of historical positive selection on the DRB locus was particularly strong, which may be a general feature of caniforms. The presence of MHC class I pseudogenes may indicate faster gene turnover in this class through the birth-and-death process. South - north population structure at MHC loci probably reflects origin of the populations from separate glacial refugia

REPRODUCTIVE ABILITY DIFFERENT LINES COWS OF RRYKARPATTYA INTERBREED OF UKRAINIAN RED-AND-WHITE DAIRY CATTLE

Досліджено відтворювальну здатність корів різних ліній прикарпатського внутрішньопородного типу української червоно-рябої молочної породи. Встановлено, що вік І осіменіння корів в середньому по стаду становив 18,6 місяця, тривалість сервіс-періоду, залежно від лактації, знаходилася в межах 91,3–106,2, сухостійного періоду – в межах 71,8–73,4 та міжотельного періоду – в межах 371,9–390,6 дня. Серед тварин шести досліджуваних ліній найменшими віком І осіменіння (561,8 дня або 18,5 місяця), тривалістю сервіс- (ІІ, ІІІ та краща лактації), сухостійного (ІІ та краща лактації) і міжотельного (ІІ, ІІІ та краща лактації) періодів характеризувалися корови лінії Рігела 352882. Коефіцієнт мінливості віку І осіменіння, залежно від лінії, знаходився в межах 11,5–13,4, живої маси при І осіменінні – в межах 7,6–10,7 %, тривалості сервіс-періоду, залежно від лактації та лінії, –  в межах 9,5–27,0, сухостійного періоду – в межах 11,3–31,0 та міжотельного періоду – в межах 12,3–22,8 %. Гіршими за відтворювальною здатністю виявилися корови лінії Астронавта 1458744.Исследовано воспроизводительную способность коров разных линий прикарпатского внутрипородного типа украинской красно-пестрой молочной породы. Установлено, что возраст первого осеменения коров в среднем по стаду составлял 18,6 месяца, продолжительность сервис-периода, в зависимости от лактации, находилась в пределах 91,3–106,2, сухостойного периода – в пределах 71,8–73,4 и межотельного периода – в пределах 371,9-390,6 дня. Среди животных шести исследуемых линий самыми меньшими возрастом первого осеменения (561,8 дня или 18,5 месяца), продолжительностью сервис- (II, III и лучшая лактации), сухостойного (II и лучшая лактации) и межотельного (II, III и лучшая лактации) периодов характеризовались коровы линии Ригела 352882. Коэффициент изменчивости возраста первого осеменения, в зависимости от линии, находился в пределах 11,5–13,4, живой массы при первом осеменении – в пределах 7,6–10,7 %, продолжительности сервис-периода, в зависимости от лактации и линии – в пределах 9,5–27,0,, сухостойного периода – в пределах 11,3–31,0 и межотельного периода – в пределах 12,3-22,8 %. Худшая воспроизведеная способность отмечена у коров линии Астронавта 1458744.There were studied reproductive ability of cows of different lines interbreed type of Ukrainian Prykarpattya red-white dairy cattle. The average age of insemination was 18.6 months, the length of service period, depending on the lactation is within 91,3–106,2, dry period - within 71,8-73,4 and inter-calving - within 371,9–390,6 days. The cows of Rigel line 352882 had the shortest duration of insemination (day 561.8 or 18.5 months), service-lasting (II, III and better lactation), dry (second lactation and better) and inter-calving (II, III and better lactation) periods among three lines of breed. The coefficient of variability of age and insemination, as the line was within 11,5–13,4, live weight at insemination and – within 7,6–10,7 % the length of service period depends on lactation and lines – within 9,5–27,0,, dry period – within 11,3–31,0 and inter-calving period – within 12,3–22,8 %. The cows of Astronauts line 1458744 had worse reproductive ability

Data production models for the CDF experiment

The data production for the CDF experiment is conducted on a large Linux PC farm designed to meet the needs of data collection at a maximum rate of 40 MByte/sec. We present two data production models that exploits advances in computing and communication technology. The first production farm is a centralized system that has achieved a stable data processing rate of approximately 2 TByte per day. The recently upgraded farm is migrated to the SAM (Sequential Access to data via Metadata) data handling system. The software and hardware of the CDF production farms has been successful in providing large computing and data throughput capacity to the experiment.Comment: 8 pages, 9 figures; presented at HPC Asia2005, Beijing, China, Nov 30 - Dec 3, 200

Interspecific introgression of MHC genes in Triturus newts: evidence from multiple contact zones

The major histocompatibility complex (MHC) genes are central to the adaptive immune response in vertebrates. Selection generally maintains high MHC variation because the spectrum of recognized pathogens depends on MHC polymorphism. Novel alleles favoured by selection originate by interallelic recombination or de novo mutations but may also be acquired by introgression from related species. However, the extent and prevalence of MHC introgression remain an open question. In this study, we tested for MHC introgression in six hybrid zones formed by six Triturus newt species. We sequenced and genotyped the polymorphic second exons of the MHC class I and II genes and compared their interspecific similarity at various distances from the centre of the hybrid zone. We found evidence for introgression of both MHC classes in the majority of examined hybrid zones, with support for a more substantial class I introgression. Furthermore, the overall MHC allele sharing outside of hybrid zones was elevated between pairs of Triturus species with abutting ranges, regardless of the phylogenetic distance between them. No effect of past hybrid zone movement on MHC allele sharing was found. Finally, using previously published genome-wide data, we demonstrated that MHC introgression was more extensive than genome-wide introgression, supporting its adaptive potential. Our study thus provides evidence for the prevalence of MHC introgression across multiple Triturus hybrid zones, indicating that MHC introgression between divergent hybridizing species may be widespread and adaptive.Animal science

Data processing model for the CDF experiment

The data processing model for the CDF experiment is described. Data processing reconstructs events from parallel data streams taken with different combinations of physics event triggers and further splits the events into datasets of specialized physics datasets. The design of the processing control system faces strict requirements on bookkeeping records, which trace the status of data files and event contents during processing and storage. The computing architecture was updated to meet the mass data flow of the Run II data collection, recently upgraded to a maximum rate of 40 MByte/sec. The data processing facility consists of a large cluster of Linux computers with data movement managed by the CDF data handling system to a multi-petaByte Enstore tape library. The latest processing cycle has achieved a stable speed of 35 MByte/sec (3 TByte/day). It can be readily scaled by increasing CPU and data-handling capacity as required.Comment: 12 pages, 10 figures, submitted to IEEE-TN

Több-billentyűs redoműtét felnőtt betegen komplex pulmonalis atresiában

Absztrakt: A 30 éves, komplex pulmonalis atresiás betegnél csecsemőkorban az unifokalizálás eldönthetősége miatt exploratio, 10 éves korban rekonstrukciós műtét (kamrai sövényhiány zárása, unifokalizáció, jobb kamra–arteria pulmonalis folytonosságának kialakítása homografttal) történt. A mindkét kamra csökkent működését okozó aortabillentyű-elégtelenség és ascendenstágulat, illetve homograftelégtelenség miatt az aortabillentyű plasztikája, a pulmonalis billentyű, illetve az aorta ascendens és arteria pulmonalis törzs cseréje vált szükségessé. Magyarországon betegünk az első, akinél ilyen redoműtét történt. A műtét sikere igazolja, hogy megfelelő gondozás, diagnosztika (echokardiográfia, MR, CT) mellett az időben történt műtét jó korai és késői eredményt biztosíthat a komplex szívhibás, felnőttkorú betegek számára. Orv. Hetil., 2017, 158(14), 546–549. | Abstract: 30-year-old adult with complex pulmonary atresia (previous surgical procedures: in infancy: exploration, at age of 10: ventricular septal defect closing, unifocalization, homograft implantation between right ventricular outflow tract and pulmonary artery) has biventricular dysfunction because of aortic valve regurgitation, ascending aortic aneurysm, and homograft insufficienty. Multivalve surgery: aortic valve plasty, pulmonary homograft changes for homograft and ascending aortic reconstruction by graft were carried out successfully. In Hungary this was the first case of this type of surgery. Management of special problems (follow-up, correct diagnostics (echocardiography, MR, CT), indication and necessity of reoperation, optimal age) in adult patients with complex congenital heart defects produces excellent early and late surgical results. Orv. Hetil., 2017, 158(14), 546–549

Effect of axillary brachial plexus blockade on baroreflex-induced skin vasomotor responses: Assessing the effectiveness of sympathetic blockade

Background: The combination of laser Doppler flowmetry and non-invasive blood pressure monitoring allows the continuous observation of cutaneous vascular resistance (CVR). Continuous recording of unmodulated skin blood flow (SBF) is very sensitive to artefacts, rendering the method unreliable. In contrast, intermittent short lasting challenges of the CVR by cardiovascular autonomic reflexes may provide information about the responsiveness of the sympathetic nervous system in the skin. Methods: Eleven patients with below-wrist hand surgery (six males and five females; aged 35.2 ± 7.1 years) performed Valsalva maneuver following axillary blockade. Skin blood flow was continuously monitored on the forearm of the side axillary blockade, as well as on the contra-lateral forearm, which was used as the control. The responses were expressed as changes compared with the baseline level derived from a resting period of 30s. The maxima

ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence

Background: The possibilities offered by next generation sequencing (NGS) platforms are revolutionizing biotechnological laboratories. Moreover, the combination of NGS sequencing and affordable high-throughput genotyping technologies is facilitating the rapid discovery and use of SNPs in non-model species. However, this abundance of sequences and polymorphisms creates new software needs. To fulfill these needs, we have developed a powerful, yet easy-to-use application. Results: The ngs_backbone software is a parallel pipeline capable of analyzing Sanger, 454, Illumina and SOLiD (Sequencing by Oligonucleotide Ligation and Detection) sequence reads. Its main supported analyses are: read cleaning, transcriptome assembly and annotation, read mapping and single nucleotide polymorphism (SNP) calling and selection. In order to build a truly useful tool, the software development was paired with a laboratory experiment. All public tomato Sanger EST reads plus 14.2 million Illumina reads were employed to test the tool and predict polymorphism in tomato. The cleaned reads were mapped to the SGN tomato transcriptome obtaining a coverage of 4.2 for Sanger and 8.5 for Illumina. 23,360 single nucleotide variations (SNVs) were predicted. A total of 76 SNVs were experimentally validated, and 85% were found to be real. Conclusions: ngs_backbone is a new software package capable of analyzing sequences produced by NGS technologies and predicting SNVs with great accuracy. In our tomato example, we created a highly polymorphic collection of SNVs that will be a useful resource for tomato researchers and breeders. The software developed along with its documentation is freely available under the AGPL license and can be downloaded from http://bioinf. comav.upv.es/ngs_backbone/ or http://github.com/JoseBlanca/franklin.Blanca Postigo, JM.; Pascual Bañuls, L.; Ziarsolo Areitioaurtena, P.; Nuez Viñals, F.; Cañizares Sales, J. (2011). Ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using Next Generation Sequence. BMC Genomics. 12:1-8. doi:10.1186/1471-2164-12-285S1812Metzker ML: Sequencing technologies - the next generation. Nature Reviews Genetics. 2010, 11 (1): 31-46. 10.1038/nrg2626.454 sequencing. [ http://www.454.com/ ]Illumina Inc. [ http://www.illumina.com/ ]Flicek P, Birney E: Sense from sequence reads: methods for alignment and assembly (vol 6, pg S6, 2009). 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[ http://1000genomes.org/wiki/doku.php?id=1000_genomes:analysis:vcf4.0 ]The seqanswers internet forum. [ http://seqanswers.com/ ]Blankenberg D, Taylor J, Schenck I, He JB, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Ross CH, Nekrutenko A: A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly. Genome Research. 2007, 17 (6): 960-964. 10.1101/gr.5578007.CloVR Automated Sequence Analysis from Your Desktop. [ http://clovr.org/ ]Papanicolaou A, Stierli R, Ffrench-Constant RH, Heckel DG: Next generation transcriptomes for next generation genomes using est2assembly. Bmc Bioinformatics. 2009, 10:Applied Biosystems by life technologies. [ http://www.appliedbiosystems.com/absite/us/en/home/applications-technologies/solid-next-generation-sequencing.html ]Wall PK, Leebens-Mack J, Chanderbali AS, Barakat A, Wolcott E, Liang HY, Landherr L, Tomsho LP, Hu Y, Carlson JE, Ma H, Schuster SC, Soltis DE, Soltis PS, Altman N, dePamphilis CW: Comparison of next generation sequencing technologies for transcriptome characterization. Bmc Genomics. 2009, 10:Murchison EP, Tovar C, Hsu A, Bender HS, Kheradpour P, Rebbeck CA, Obendorf D, Conlan C, Bahlo M, Blizzard CA, Pyecroft S, Kreiss A, Kellis M, Stark A, Harkins TT, Marshall Graves JA, Woods GM, Hanon GJ, Papenfuss AT: The Tasmanian Devil Transcriptome Reveals Schwann Cell Origins of a Clonally Transmissible Cancer. Science. 2010, 327 (5961): 84-87. 10.1126/science.1180616.Parchman TL, Geist KS, Grahnen JA, Benkman CW, Buerkle CA: Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery. 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The distributions of the six species constituting the smooth newt species complex (Lissotriton vulgaris sensu lato and L. montandoni) – an addition to the New Atlas of Amphibians and Reptiles of Europe

The ‘smooth newt’, the taxon traditionally referred to as Lissotriton vulgaris, consists of multiple morphologically distinct taxa. Given the uncertainty concerning the validity and rank of these taxa, L. vulgaris sensu lato has often been treated as a single, polytypic species. A recent study, driven by genetic data, proposed to recognize five species, L. graecus, L. kosswigi, L. lantzi, L. schmidtleri and a more restricted L. vulgaris. The Carpathian newt L. montandoni was confirmed to be a closely related sister species. We propose to refer to this collective of six Lissotriton species as the smooth newt or Lissotriton vulgaris species complex. Guided by comprehensive genomic data from throughout the range of the smooth newt species complex we 1) delineate the distribution ranges, 2) provide a distribution database, and 3) produce distribution maps according to the format of the New Atlas of Amphibians and Reptiles of Europe, for the six constituent species. This allows us to 4) highlight regions where more research is needed to determine the position of contact zones

Coevolution between MHC class I and antigen-processing genes in salamanders

Animal sciencesNaturali