43 research outputs found

    A Moving Landscape for Comparative Genomics in Mammals

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    Today we count some 62,000 species of vertebrates (half are fishes) including some 550 species of mammals on earth. The genome sequencing of non-laboratory species in recent years is expanding our breadth and understanding of genetic bases of adaptation and evolution in varied and amazing ways. Recent completion and inspection of whole genome sequence and assembly for over 200 species of mammals, from platypus to panda to human, offer the prospect of a better view of the patterns of changes within genome organization across the mammalian radiations. In 2009 my colleagues and I have created Genome-10K, an international consortium of scientist who have set a goal of gathering, sequencing, assembling, and annotating to high quality some 10,000 vertebrate genomes with 2nd and 3rd generation sequencing technology within the coming five years. These activities and advances provide an enormous Bioinformatics challenge whose solution will provide future zoologists of every persuasion a genome sequence resource for their favorite study animal. The applications and potential for the genome sequence in several research questions will be discussed

    Gene Discovery and Data Sharing in Genome Wide Association Analyses: Lessons Form AIDS Genetic Restriction Genes

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    As genome wide association studies plus whole genome sequence analyses for complex human disease determinants are expanding, it seems useful to develop strategies to facilitate large data sharing, rapid replication and validation of provocative statistical associations that straddle the threshold for genome wide significance. At this conference, we shall announce GWATCH, (Genome Wide Association Tracks Chromosome Highway) a web based data release platform that can freely display and inspect unabridged genome tracked association data without compromising privacy or Informed Consent constrictions, allowing for rapid discovery and replication opportunities. We illustrate the utility with HIV-AIDS resistance genes screened in combined large multicenter cohort studies GWAS (MACS, HGDS, MHGS, ALLIVE, LSOCA HOMER) developed and studied over the last decades

    Super-soft and super-elastic dry gels

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    Molecular combs and bottlebrushes are a new class of polymer architecture allowing for anomalously low density of entanglements in polymer melts. The conformations and rheological properties of melts of these branched macromolecule composed of a flexible backbone and side chains densely tethered to it are investigated theoretically, experimentally and by computer simulations.1,2 We develop the rule for dialing in the desired value of the melt plateau modulus of these molecules as low as 1000 times below the conventional values for linear polymer melts and experimentally verify the validity of our theory. The theory also predicts that elastomers made from these melts should be super-elastic and reversibly stretch up to ten times more than elastomers made from linear polymers. Hybrid networks with both permanent and reversible bonds made with this novel architecture are predicted to be super-tough and self-healing. References W.F.M. Daniel, J. Burdynska, M. Vatankhah-Varnoosfaderani, K. Matyjaszewski, J. Paturej, M. Rubinstein, A.V. Dobrynin and S.S. Sheiko, Nature Materials, 2016, 15, 183-190. L.H Cai, T.E. Kodger, R.E. Guerra, A.F. Pegoraro, M. Rubinstein, and D.A. Weitz, Advanced Materials 2015, 27, 5132–5140

    Genome Sequencing and Comparative Analysis of Saccharomyces cerevisiae Strains of the Peterhof Genetic Collection

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    The Peterhof genetic collection of Saccharomyces cerevisiae strains (PGC) is a large laboratory stock that has accumulated several thousands of strains for over than half a century. It originated independently of other common laboratory stocks from a distillery lineage (race XII). Several PGC strains have been extensively used in certain fields of yeast research but their genomes have not been thoroughly explored yet. Here we employed whole genome sequencing to characterize five selected PGC strains including one of the closest to the progenitor, 15V-P4, and several strains that have been used to study translation termination and prions in yeast (25-25-2V-P3982, 1B-D1606, 74-D694, and 6P-33G-D373). The genetic distance between the PGC progenitor and S288C is comparable to that between two geographically isolated populations. The PGC seems to be closer to two bakery strains than to S288C-related laboratory stocks or European wine strains. In genomes of the PGC strains, we found several loci which are absent from the S288C genome; 15V-P4 harbors a rare combination of the gene cluster characteristic for wine strains and the RTM1 cluster. We closely examined known and previously uncharacterized gene variants of particular strains and were able to establish the molecular basis for known phenotypes including phenylalanine auxotrophy, clumping behavior and galactose utilization. Finally, we made sequencing data and results of the analysis available for the yeast community. Our data widen the knowledge about genetic variation between Saccharomyces cerevisiae strains and can form the basis for planning future work in PGC-related strains and with PGC-derived alleles.PBD acknowledges the Russian Foundation for Basic Research (www.rfbr.ru) for grant 14-04-31265. OVT and SGIV acknowledge the Russian Foundation for Basic Research for grant 15-29-02526. JVS acknowledges the Russian Science Foundation (www.rscf.ru) for grant 14-50-00069 and the Saint-Petersburg State University for grant 1.38.426.2015. PBD, AGM, EAR, and JVS acknowledge the Saint-Petersburg State University for research grant 1.37.291.2015. PBD and OVT acknowledge the Saint-Petersburg City Committee on Science and High School (knvsh.gov.spb.ru/) for grants 15404 and 15919, respectively. PBD, AGM, JVS, and SGIV acknowledge the Saint-Petersburg State University for research grant 15.61.2218.2013. PBD acknowledges the Saint-Petersburg State University for research grant 1.42.1394.2015

    Genome-wide sequence analyses of ethnic populations across Russia

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    The Russian Federation is the largest and one of the most ethnically diverse countries in the world, however no centralized reference database of genetic variation exists to date. Such data are crucial for medical genetics and essential for studying population history. The Genome Russia Project aims at filling this gap by performing whole genome sequencing and analysis of peoples of the Russian Federation. Here we report the characterization of genome-wide variation of 264 healthy adults, including 60 newly sequenced samples. People of Russia carry known and novel genetic variants of adaptive, clinical and functional consequence that in many cases show allele frequency divergence from neighboring populations. Population genetics analyses revealed six phylogeographic partitions among indigenous ethnicities corresponding to their geographic locales. This study presents a characterization of population-specific genomic variation in Russia with results important for medical genetics and for understanding the dynamic population history of the world's largest country

    Pangolin genomes and the evolution of mammalian scales and immunity

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    Pangolins, unique mammals with scales over most of their body, no teeth, poor vision, and an acute olfactory system, comprise the only placental order (Pholidota) without a whole-genome map. To investigate pangolin biology and evolution, we developed genome assemblies of the Malayan (Manis javanica) and Chinese (M. pentadactyla) pangolins. Strikingly, we found that interferon epsilon (IFNE), exclusively expressed in epithelial cells and important in skin and mucosal immunity, is pseudogenized in all African and Asian pangolin species that we examined, perhaps impacting resistance to infection. We propose that scale development was an innovation that provided protection against injuries or stress and reduced pangolin vulnerability to infection. Further evidence of specialized adaptations was evident from positively selected genes involving immunity-related pathways, inflammation, energy storage and metabolism, muscular and nervous systems, and scale/hair development. Olfactory receptor gene families are significantly expanded in pangolins, reflecting their well-developed olfaction system. This study provides insights into mammalian adaptation and functional diversification, new research tools and questions, and perhaps a new natural IFNE-deficient animal model for studying mammalian immunity.University of Malaya and Ministry of Education, Malaysia [UM.C/HIR/MOHE/08]; UMRG grant from the University of Malaya and Ministry of Education, Malaysia [RG541-13HTM]; Russian Ministry of Science [11.G34.31.0068]; NIH-NHGRI grant [5U54HG00307907]SCI(E)[email protected]

    Genomic Legacy of the African Cheetah, Acinonyx jubatus

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    Background Patterns of genetic and genomic variance are informative in inferring population history for human, model species and endangered populations. Results Here the genome sequence of wild-born African cheetahs reveals extreme genomic depletion in SNV incidence, SNV density, SNVs of coding genes, MHC class I and II genes, and mitochondrial DNA SNVs. Cheetah genomes are on average 95 % homozygous compared to the genomes of the outbred domestic cat (24.08 % homozygous), Virunga Mountain Gorilla (78.12 %), inbred Abyssinian cat (62.63 %), Tasmanian devil, domestic dog and other mammalian species. Demographic estimators impute two ancestral population bottlenecks: one \u3e100,000 years ago coincident with cheetah migrations out of the Americas and into Eurasia and Africa, and a second 11,084–12,589 years ago in Africa coincident with late Pleistocene large mammal extinctions. MHC class I gene loss and dramatic reduction in functional diversity of MHC genes would explain why cheetahs ablate skin graft rejection among unrelated individuals. Significant excess of non-synonymous mutations in AKAP4 (p\u3c0.02), a gene mediating spermatozoon development, indicates cheetah fixation of five function-damaging amino acid variants distinct from AKAP4 homologues of other Felidae or mammals; AKAP4 dysfunction may cause the cheetah’s extremely high (\u3e80 %) pleiomorphic sperm. Conclusions The study provides an unprecedented genomic perspective for the rare cheetah, with potential relevance to the species’ natural history, physiological adaptations and unique reproductive disposition

    Coastal Erosion Variability at the Southern Laptev Sea Linked to Winter Sea Ice and the Arctic Oscillation

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    Arctic coastal erosion experiences pronounced effects from ongoing climate change. The Laptev Sea figures among the Arctic regions with the most severe erosion rates. Here, we use unprecedentedly long records of almost 30 years of annual in-situ coastal erosion rate measurements from Bykovsky Peninsula and Muostakh Island to separate the main modes of variability, which we attribute to large-scale drivers. The first (lower-frequency) and second (higher-frequency) modes are associated with winter sea-ice cover in the Laptev Sea and with the Arctic Oscillation, respectively, which together account for 85.1±24.1% of the total observed variance. Arctic coastal erosion has so far been neglected in Earth system models (ESMs). The proposed mechanisms set favorable conditions for coastal erosion at large scales (synoptic to planetary scales), compatible with those represented in modern ESMs

    An Example of Microwave Holography Investigation of an Old Orthodox Russian Icon Dated to 19th Century

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    The study, preservation and restoration of the cultural heritage objects of mankind are not only of great cultural importance but also have a significant economic component because cultural values of past centuries attract tourists from all over the world. The use of modern technical and scientific achievements in the field of non-destructive testing makes it possible to obtain new knowledge about cultural objects regarding their origin and dating, as well as to contribute to their better restoration and preservation. An important component of their use is additional opportunities to identify high quality fakes of original cultural objects that have historical significance. The capabilities of various non-destructive testing (NDT) methods used to examine cultural objects are characterized by their penetration depth, resolution, and sensitivity to material properties. Thus, in many cases, it is necessary to perform multi-sensor non-destructive testing and creating large data sets that require an efficient evaluation. This article considers an example of using microwave (MW) holographic sensors for the examining of an old Orthodox Russian Icon dated of the late 19th century. The paper describes the technology of microwave holography, which has recently been applied to the examination of art works. Unlike the well-studied X-ray method, MW holography makes it possible to examine objects with one-sided access. Its other advantages are the relative cheapness of the equipment and the safety of use due to the low level of radiation. The article describes a MW holograms reconstruction algorithm, as well as a method for improving the quality of obtained MW images. The data collected at MW research of the Icon are compared with the results of X-ray examination and confirmed by subsequent opening and visual examination performed by professional restorers

    Supercritical Antisolvent Processing of Nitrocellulose: Downscaling to Nanosize, Reducing Friction Sensitivity and Introducing Burning Rate Catalyst

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    A supercritical antisolvent process has been applied to obtain the nitrocellulose nanoparticles with an average size of 190 nm from the nitrocellulose fibers of 20 μm in diameter. Compared to the micron-sized powder, nano-nitrocellulose is characterized with a slightly lower decomposition onset, however, the friction sensitivity has been improved substantially along with the burning rate increasing from 3.8 to 4.7 mm·s−1 at 2 MPa. Also, the proposed approach allows the production of stable nitrocellulose composites. Thus, the addition of 1 wt.% carbon nanotubes further improves the sensitivity of the nano-nitrocellulose up to the friction-insensitive level. Moreover, the simultaneous introduction of carbon nanotubes and nanosized iron oxide catalyzes the combustion process evidenced by a high-speed filming and resulting in the 20% burning rate increasing at 12 MPa. The presented approach to the processing of energetic nanomaterials based on the supercritical fluid technology opens the way to the production of nitrocellulose-based nanopowders with improved performance
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