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https://www.readbyqxmd.com/read/29351633/evolutionary-genetics-of-cytoplasmic-incompatibility-genes-cifa-and-cifb-in-prophage-wo-of-wolbachia
#1
Amelia R I Lindsey, Danny W Rice, Sarah R Bordenstein, Andrew W Brooks, Seth R Bordenstein, Irene L G Newton
The bacterial endosymbiont Wolbachia manipulates arthropod reproduction to facilitate its maternal spread through host populations. The most common manipulation is cytoplasmic incompatibility (CI): Wolbachia-infected males produce modified sperm that cause embryonic mortality, unless rescued by embryos harboring the same Wolbachia. The genes underlying CI, cifA and cifB, were recently identified in the eukaryotic association module of Wolbachia's prophage WO. Here, we use transcriptomic and genomic approaches to address three important evolutionary facets of the cif genes...
January 17, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29351600/gtc-how-to-maintain-huge-genotype-collections-in-a-compressed-form
#2
Agnieszka Danek, Sebastian Deorowicz
Motivation: Nowadays, genome sequencing is frequently used in many research centers. In projects, such as the Haplotype Reference Consortium or the Exome Aggregation Consortium, huge databases of genotypes in large populations are determined. Together with the increasing size of these collections, the need for fast and memory frugal ways of representation and searching in them becomes crucial. Results: We present GTC, a novel compressed data structure for representation of huge collections of genetic variation data...
January 16, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29351563/a-consensus-linkage-map-of-lentil-based-on-dart-markers-from-three-ril-mapping-populations
#3
Duygu Ates, Secil Aldemir, Ahmad Alsaleh, Semih Erdogmus, Seda Nemli, Abdullah Kahriman, Hakan Ozkan, Albert Vandenberg, Bahattin Tanyolac
BACKGROUND: Lentil (Lens culinaris ssp. culinaris Medikus) is a diploid (2n = 2x = 14), self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes. MATERIALS AND METHODS: A consensus map of lentil (Lens culinaris ssp. culinaris Medikus) was constructed using three different lentils recombinant inbred line (RIL) populations, including "CDC Redberry" x "ILL7502" (LR8), "ILL8006" x "CDC Milestone" (LR11) and "PI320937" x "Eston" (LR39)...
2018: PloS One
https://www.readbyqxmd.com/read/29351172/a-systematic-review-and-meta-analysis-of-genetic-risk-factors-for-neuropathic-pain
#4
Abirami Veluchamy, Harry L Hébert, Weihua Meng, Colin N A Palmer, Blair H Smith
Neuropathic pain (NP) is an increasingly common chronic pain state and a major health burden, affecting approximately 7-10% of the general population. Emerging evidence suggests that genetic factors could partially explain individual susceptibility to NP and the estimated heritability in twins is 37%. The aim of this study was to systematically review and summarize the studies in humans that have investigated the influence of genetic factors associated with NP. We conducted a comprehensive literature search and performed meta-analyses of all the potential genetic variants associated with NP...
January 18, 2018: Pain
https://www.readbyqxmd.com/read/29351011/a-migratory-divide-in-the-painted-bunting-passerina-ciris
#5
C J Battey, Ethan B Linck, Kevin L Epperly, Cooper French, David L Slager, Paul W Sykes, John Klicka
In the painted bunting (Passerina ciris), a North American songbird, populations on the Atlantic coast and interior southern United States are known to be allopatric during the breeding season, but efforts to map connectivity with wintering ranges have been largely inconclusive. Using genomic and morphological data from museum specimens and banded birds, we found evidence of three genetically differentiated painted bunting populations with distinct wintering ranges and molt-migration phenologies. In addition to confirming that the Atlantic coast population remains allopatric throughout the annual cycle, we identified an unexpected migratory divide within the interior breeding range...
February 2018: American Naturalist
https://www.readbyqxmd.com/read/29350701/genetic-testing-how-genetics-and-genomics-can-affect-healthcare-disparities%C3%A2
#6
Deborah Allen
Advances in oncology care have transformed treatment approaches as genetics and genomics analyses promote implementation of personalized medicine. Genetics and genomics research in TP53 have demonstrated that some mutations are prevalent in minority populations. This has implications on personalized treatment approaches, particularly in early disease stages. The purpose of this article is to describe oncology nurses' role in applying these findings in practice to reduce disparities observed in cancer and survivorship care...
February 1, 2018: Clinical Journal of Oncology Nursing
https://www.readbyqxmd.com/read/29350137/multiplex-pcr-based-next-generation-sequencing-and-global-diversity-of-seoul-virus-in-humans-and-rats
#7
Won-Keun Kim, Jin Sun No, Seung-Ho Lee, Dong Hyun Song, Daesang Lee, Jeong-Ah Kim, Se Hun Gu, Sunhye Park, Seong Tae Jeong, Heung-Chul Kim, Terry A Klein, Michael R Wiley, Gustavo Palacios, Jin-Won Song
Seoul virus (SEOV) poses a worldwide public health threat. This virus, which is harbored by Rattus norvegicus and R. rattus rats, is the causative agent of hemorrhagic fever with renal syndrome (HFRS) in humans, which has been reported in Asia, Europe, the Americas, and Africa. Defining SEOV genome sequences plays a critical role in development of preventive and therapeutic strategies against the unique worldwide hantavirus. We applied multiplex PCR-based next-generation sequencing to obtain SEOV genome sequences from clinical and reservoir host specimens...
February 2018: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/29348500/myeloid-derived-suppressor-cells-coming-of-age
#8
REVIEW
Filippo Veglia, Michela Perego, Dmitry Gabrilovich
Myeloid-derived suppressor cells (MDSCs) are a heterogeneous population of cells generated during a large array of pathologic conditions ranging from cancer to obesity. These cells represent a pathologic state of activation of monocytes and relatively immature neutrophils. MDSCs are characterized by a distinct set of genomic and biochemical features, and can, on the basis of recent findings, be distinguished by specific surface molecules. The salient feature of these cells is their ability to inhibit T cell function and thus contribute to the pathogenesis of various diseases...
January 18, 2018: Nature Immunology
https://www.readbyqxmd.com/read/29348432/genome-wide-association-study-of-self-reported-food-reactions-in-japanese-identifies-shrimp-and-peach-specific-loci-in-the-hla-dr-dq-gene-region
#9
Seik-Soon Khor, Ryoko Morino, Kazuyuki Nakazono, Shigeo Kamitsuji, Masanori Akita, Maiko Kawajiri, Tatsuya Yamasaki, Azusa Kami, Yuria Hoshi, Asami Tada, Kenichi Ishikawa, Maaya Hine, Miki Kobayashi, Nami Kurume, Naoyuki Kamatani, Katsushi Tokunaga, Todd A Johnson
Food allergy is an increasingly important health problem in the world. Several genome-wide association studies (GWAS) focused on European ancestry samples have identified food allergy-specific loci in the HLA class II region. We conducted GWAS of self-reported reactivity with common foods using the data from 11011 Japanese women and identified shrimp and peach allergy-specific loci in the HLA-DR/DQ gene region tagged by rs74995702 (P = 6.30 × 10-17, OR = 1.91) and rs28359884 (P = 2.3 × 10-12, OR = 1...
January 18, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29348336/nine-whole-genome-assemblies-of-yersinia-pestis-subsp-microtus-bv-altaica-strains-isolated-from-the-altai-mountain-natural-plague-focus-no-36-in-russia
#10
Angelina A Kislichkina, Alexandr G Bogun, Lidiya A Kadnikova, Nadezhda V Maiskaya, Viktor I Solomentsev, Svetlana V Dentovskaya, Sergey V Balakhonov, Andrey P Anisimov
We report here the draft genome sequences of nine Yersinia pestis subsp. microtus bv. Altaica strains isolated from the Altai Mountain plague focus (no. 36), which represent the 0.PE4 phylogroup circulating in populations of Mongolian pika (Ochotona pallasi).
January 18, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29348298/a-review-of-prostate-cancer-genome-wide-association-studies-gwas
#11
Sarah Benafif, Zsofia Kote-Jarai, Rosalind A Eeles
Prostate cancer (PrCa) is the commonest cancer in men in Europe and the USA. The genetic heritability of PrCa is contributed to by both rarely occurring genetic variants with higher penetrance and moderate to commonly occurring variants conferring lower risks. The number of identified variants belonging to the latter category has increased dramatically in the last 10 years with the development of the genome wide association study (GWAS) and the collaboration of international consortia that have led to the sharing of large-scale genotyping data...
January 18, 2018: Cancer Epidemiology, Biomarkers & Prevention
https://www.readbyqxmd.com/read/29348143/detecting-polygenic-adaptation-in-admixture-graphs
#12
Fernando Racimo, Jeremy J Berg, Joseph K Pickrell
An open question in human evolution is the importance of polygenic adaptation: adaptive changes in the mean of a multifactorial trait due to shifts in allele frequencies across many loci. In recent years, several methods have been developed to detect polygenic adaptation using loci identified in genome-wide association studies (GWAS). Though powerful, these methods suffer from limited interpretability: they can detect which sets of populations have evidence for polygenic adaptation, but are unable to reveal where in the history of multiple populations these processes occurred...
January 18, 2018: Genetics
https://www.readbyqxmd.com/read/29347977/expansion-of-cytochrome-p450-and-cathepsin-genes-in-the-generalist-herbivore-brown-marmorated-stink-bug
#13
Raman Bansal, Andy Michel
BACKGROUND: The brown marmorated stink bug (Halyomorpha halys) is an invasive pest in North America which causes severe economic losses on tree fruits, ornamentals, vegetables, and field crops. The H. halys is an extreme generalist and this feeding behaviour may have been a major contributor behind its establishment and successful adaptation in invasive habitats of North America. To develop an understanding into the mechanism of H. halys' generalist herbivory, here we specifically focused on genes putatively facilitating its adaptation on diverse host plants...
January 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29347168/quantifying-the-entropic-cost-of-cellular-growth-control
#14
Daniele De Martino, Fabrizio Capuani, Andrea De Martino
Viewing the ways a living cell can organize its metabolism as the phase space of a physical system, regulation can be seen as the ability to reduce the entropy of that space by selecting specific cellular configurations that are, in some sense, optimal. Here we quantify the amount of regulation required to control a cell's growth rate by a maximum-entropy approach to the space of underlying metabolic phenotypes, where a configuration corresponds to a metabolic flux pattern as described by genome-scale models...
July 2017: Physical Review. E
https://www.readbyqxmd.com/read/29346759/nf-%C3%AE%C2%BAb-chromatin-interactions-drive-diverse-phenotypes-by-modulating-transcriptional-noise
#15
Victor C Wong, Victor L Bass, M Elise Bullock, Arvind K Chavali, Robin E C Lee, Walther Mothes, Suzanne Gaudet, Kathryn Miller-Jensen
Noisy gene expression generates diverse phenotypes, but little is known about mechanisms that modulate noise. Combining experiments and modeling, we studied how tumor necrosis factor (TNF) initiates noisy expression of latent HIV via the transcription factor nuclear factor κB (NF-κB) and how the HIV genomic integration site modulates noise to generate divergent (low-versus-high) phenotypes of viral activation. We show that TNF-induced transcriptional noise varies more than mean transcript number and that amplification of this noise explains low-versus-high viral activation...
January 16, 2018: Cell Reports
https://www.readbyqxmd.com/read/29346646/the-evolutionary-history-of-nebraska-deer-mice-local-adaptation-in-the-face-of-strong-gene-flow
#16
Susanne P Pfeifer, Stefan Laurent, Vitor C Sousa, Catherine R Linnen, Matthieu Foll, Laurent Excoffier, Hopi E Hoekstra, Jeffrey D Jensen
The interplay of gene flow, genetic drift, and local selective pressure is a dynamic process that has been well studied from a theoretical perspective over the last century. Wright and Haldane laid the foundation for expectations under an island-continent model, demonstrating that an island-specific beneficial allele may be maintained locally if the selection coefficient is larger than the rate of migration of the ancestral allele from the continent. Subsequent extensions of this model have provided considerably more insight...
January 15, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29346644/genome-wide-analysis-of-disease-progression-in-age-related-macular-degeneration
#17
Qi Yan, Ying Ding, Yi Liu, Tao Sun, Lars G Fritsche, Traci Clemons, Rinki Ratnapriya, Michael L Klein, Richard J Cook, Yu Liu, Ruzong Fan, Lai Wei, Gonçalo R Abecasis, Anand Swaroop, Emily Y Chew, Daniel E Weeks, Wei Chen
Family- and population-based genetic studies have successfully identified multiple disease-susceptibility loci for Age-related Macular Degeneration (AMD), one of the first batch and most successful examples of genome-wide association study (GWAS). However, most genetic studies to date have focused on case-control studies of late AMD (choroidal neovascularization [CNV] or geographic atrophy [GA]). The genetic influences on disease progression are largely unexplored. We assembled unique resources to perform a genome-wide bivariate time-to-event analysis to test for association of time-to-late-AMD with ∼9 million variants on 2,721 Caucasians from a large multi-center randomized clinical trial, the Age-Related Eye Disease Study...
January 15, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29346601/accumulation-of-mutational-load-at-the-edges-of-a-species-range
#18
Yvonne Willi, Marco Fracassetti, Stefan Zoller, Josh Van Buskirk
Why species have geographically restricted distributions is an unresolved question in ecology and evolutionary biology. Here we test a new explanation, that mutation accumulation due to small population size or a history of range expansion can contribute to restricting distributions by reducing population growth rate at the edge. We examined genomic diversity and mutational load across the entire geographic range of the North American plant Arabidopsis lyrata, including old, isolated populations predominantly at the southern edge and regions of postglacial range expansion at the northern and southern edges...
January 15, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29346589/urban-evolutionary-ecology-and-the-potential-benefits-of-implementing-genomics
#19
Christopher J Schell
Urban habitats are quickly becoming exceptional models to address adaptation under rapid environmental change, given the expansive temporal and spatial scales with which anthropogenic landscape conversion occurs. Urban ecologists in the last 10-15 years have done an extraordinary job of highlighting phenotypic patterns that correspond with urban living, as well as delineating urban population structure using traditional genetic markers. The underpinning genetic mechanisms that govern those phenotypic patterns, however, are less well established...
January 13, 2018: Journal of Heredity
https://www.readbyqxmd.com/read/29346588/genome-sequencing-of-museum-specimens-reveals-rapid-changes-in-the-genetic-composition-of-honey-bees-in-california
#20
Julie M Cridland, Santiago R Ramirez, Cheryl A Dean, Amber Sciligo, Neil D Tsutsui
The western honey bee, Apis mellifera, is an enormously influential pollinator in both natural and managed ecosystems. In North America, this species has been introduced numerous times from a variety of different source populations in Europe and Africa. Since then, feral populations have expanded into many different environments across their broad introduced range. Here, we used whole genome sequencing of historical museum specimens and newly collected modern populations from California (USA) to analyze the impact of demography and selection on introduced populations during the past 105 years...
January 15, 2018: Genome Biology and Evolution
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