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https://www.readbyqxmd.com/read/29782991/beneficial-and-paradoxical-roles-of-selenium-at-nutritional-levels-of-intake-in-healthspan-and-longevity
#1
REVIEW
Li Zhang, Huawei Zeng, Wen-Hsing Cheng
Accumulation of genome and macromolecule damage is a hallmark of aging, age-associated degeneration, and genome instability syndromes. Although processes of aging are irreversible, they can be modulated by genome maintenance pathways and environmental factors such as diet. Selenium (Se) confers its physiological functions mainly through selenoproteins, but Se compounds and other proteins that incorporate Se nonspecifically also impact optimal health. Bruce Ames proposed that the aging process could be mitigated by a subset of low-hierarchy selenoproteins whose levels are preferentially reduced in response to Se deficiency...
May 18, 2018: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/29782933/whole-genome-sequencing-and-analyses-identify-high-genetic-heterogeneity-and-diversity-of-rotavirus-genotype-p-6-strains-circulating-in-africa
#2
Martin M Nyaga, Yi Tan, Mapaseka L Seheri, Rebecca A Halpin, Asmik Akopov, Karla M Stucker, Nadia B Fedorova, Susmita Shrivastava, A Duncan Steele, Jason M Mwenda, Brett E Pickett, Suman R Das, M Jeffery Mphahlele
Rotavirus A (RVA) exhibits a wide genotype diversity globally. Little is known about the genetic composition of genotype P[6] from Africa. This study investigated possible evolutionary mechanisms leading to genetic diversity of genotype P[6] VP4 sequences. Phylogenetic analyses on 167 P[6] VP4 full-length sequences were conducted, which included six porcine-origin sequences. Of the 167 sequences, 57 were newly acquired through whole genome sequencing as part of this study. The other 110 sequences were all publicly-available global P[6] VP4 full-length sequences downloaded from GenBank...
May 18, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29781797/from-plants-to-nematodes-serratia-grimesii-bxf1-genome-reveals-an-adaptation-to-the-modulation-of-multi-species-interactions
#3
Francisco Nascimento, Cláudia Vicente, Peter Cock, Maria Tavares, Márcio Rossi, Koichi Hasegawa, Manuel Mota
Serratia grimesii BXF1 is a bacterium with the ability to modulate the development of several eukaryotic hosts. Strain BXF1 was isolated from the pinewood nematode, Bursaphelenchus xylophilus, the causative agent of pine wilt disease affecting pine forests worldwide. This bacterium potentiates Bursaphelenchus xylophilus reproduction, acts as a beneficial pine endophyte, and possesses fungal and bacterial antagonistic activities, further indicating a complex role in a wide range of trophic relationships. In this work, we describe and analyse the genome sequence of strain BXF1, and discuss several important aspects of its ecological role...
May 21, 2018: Microbial Genomics
https://www.readbyqxmd.com/read/29780362/characterization-and-genomic-study-of-phage-vb_ecos-b2-infecting-multidrug-resistant-escherichia-coli
#4
Yue Xu, Xinyan Yu, Yu Gu, Xu Huang, Genyan Liu, Xiaoqiu Liu
The potential of bacteriophage as an alternative antibacterial agent has been reconsidered for control of pathogenic bacteria due to the widespread occurrence of multi-drug resistance bacteria. More and more lytic phages have been isolated recently. In the present study, we isolated a lytic phage named vB_EcoS-B2 from waste water. VB_EcoS-B2 has an icosahedral symmetry head and a long tail without a contractile sheath, indicating that it belongs to the family Siphoviridae . The complete genome of vB_EcoS-B2 is composed of a circular double stranded DNA of 44,283 bp in length, with 54...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29780036/revised-phylogeny-of-the-cellulose-synthase-gene-superfamily-insights-into-cell-wall-evolution
#5
Alan Little, Julian G Schwerdt, Neil J Shirley, Shi F Khor, Kylie Neumann, Lisa A O'Donovan, Jelle Lahnstein, Helen M Collins, Marilyn Henderson, Geoffrey B Fincher, Rachel A Burton
Cell walls are crucial for the integrity and function of all land plants, and are of central importance in human health, livestock production, and as a source of renewable bioenergy. Many enzymes that mediate the biosynthesis of cell wall polysaccharides are encoded by members of the large cellulose synthase (CesA) gene superfamily. Here, we analyzed 29 sequenced genomes and 17 transcriptomes to revise the phylogeny of the CesA gene superfamily in angiosperms. Our results identify ancestral gene clusters that predate the monocot-eudicot divergence and reveal several novel evolutionary observations, including the expansion of the Poaceae-specific cellulose synthase-like CslF family to the graminids and restiids and the characterisation of a previously unreported eudicot lineage, CslM, that forms a reciprocally monophyletic eudicot-monocot grouping with the CslJ clade...
May 20, 2018: Plant Physiology
https://www.readbyqxmd.com/read/29779790/a-hyperthermophilic-phage-decoration-protein-suggests-common-evolutionary-origin-with-herpesvirus-triplex-proteins-and-an-anti-crispr-protein
#6
Nicholas P Stone, Brendan J Hilbert, Daniel Hidalgo, Kevin T Halloran, Jooyoung Lee, Erik J Sontheimer, Brian A Kelch
Virus capsids are protein shells that protect the viral genome from environmental assaults, while maintaining the high internal pressure of the tightly packaged genome. To elucidate how capsids maintain stability under harsh conditions, we investigated the capsid components of the hyperthermophilic phage P74-26. We determined the structure of capsid protein gp87 and show that it has the same fold as decoration proteins in many other phages, despite lacking significant sequence homology. We also find that gp87 is significantly more stable than mesophilic homologs...
April 26, 2018: Structure
https://www.readbyqxmd.com/read/29779780/on-sunspots-click-science-and-molecular-iconography
#7
Igor Mokrousov
CRISPR-spoligotyping and MIRU-VNTR typing, SITVIT_WEB and MIRU-VNTRplus are the methods and online resources most widely used for Mycobacterium tuberculosis genotype family assignment and clustering analysis. They have been proven invaluable for molecular epidemiological studies of this important human pathogen in setting up the terminology and classification framework. However, they are inherently limited by insufficient knowledge of evolution of the targeted genome loci (especially, CRISPR). The situation is aggravated by the dogmatic, iconographic perception of these increasingly user-friendly online tools...
May 2018: Tuberculosis
https://www.readbyqxmd.com/read/29778766/first-genetic-characterization-of-usutu-virus-from-culex-pipiens-mosquitoes-serbia-2014
#8
Gábor Kemenesi, Dóra Buzás, Brigitta Zana, Kornélia Kurucz, Bosiljka Krtinic, Anett Kepner, Fanni Földes, Ferenc Jakab
Since its first appearance in Europe, Usutu virus (USUV) diverged to several different genetic lineages. The virus was reported to date from multiple countries across Europe (Hungary, Italy, Switzerland, Spain, Germany, Czech Republic and Belgium). Considering the more frequently published impact of the virus on humans it is crucial to investigate locally circulating genetic variants and trace its evolution. We retrospectively analyzed mosquito samples from Serbia Vojvodina region, collected during 2014. In this study we report the results of the screening of 23,753 female mosquitoes (753 pools) for USUV-specific nucleic-acid...
May 17, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29778722/phylogenomics-resolves-evolutionary-relationships-and-provides-insights-into-floral-evolution-in-the-tribe-shoreeae-dipterocarpaceae
#9
Jacqueline Heckenhauer, Rosabelle Samuel, Peter S Ashton, Kamariah Abu Salim, Ovidiu Paun
A supra-annual, community-level synchronous flowering prevails in several parts of the tropical forests of Southeast Asia and its evolution has been hypothesized to be linked to pollinator shifts. The aseasonal Southeast Asian lowland rainforests are dominated by Dipterocarpaceae, which exhibit great floral diversity, a range of pollination syndromes and include species with annual and supra-annual gregarious flowering. Phylogenetic relationships within this family are still unclear, especially in the tribe Shoreeae...
May 17, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29778329/the-kinetoplast-dna-of-the-australian-trypanosome-trypanosoma-copemani-shares-features-with-trypanosoma-cruzi-and-trypanosoma-lewisi
#10
Adriana Botero, Irit Kapeller, Crystal Cooper, Peta L Clode, Joseph Shlomai, R C Andrew Thompson
Kinetoplast DNA (kDNA) is the mitochondrial genome of trypanosomatids. It consists of a few dozen maxicircles and several thousand minicircles, all catenated topologically to form a two-dimensional DNA network. Minicircles are heterogeneous in size and sequence among species. They present one or several conserved regions that contain three highly conserved sequence blocks (CSBs). CSB-1 (10 bp sequence) and CSB-2 (8 bp sequence) present lower interspecies homology, while CSB-3 (12 bp sequence) or the Universal Minicircle Sequence (UMS) is conserved within most trypanosomatids...
May 17, 2018: International Journal for Parasitology
https://www.readbyqxmd.com/read/29778197/genetic-analysis-and-biological-characteristics-of-different-internal-gene-origin-h5n6-reassortment-avian-influenza-virus-in-china-in-2016
#11
Wenqiang Sun, Jiaxin Li, Jiao Hu, Daxiu Jiang, Chaonan Xing, Tiansong Zhan, Xiufan Liu
Clade 2.3.4.4 of H5N6 subtype Avian Influenza Viruses (AIVs) has become dominant clade in South-East Asia. So far, a total of 16 cases of human infection, including 6 deaths, have been confirmed since 2014. In this study, we systematically investigated the genetic evolution and biological characteristics of these viruses. We first carried out phylogenetic and statistical analysis of all H5N6 viruses that were downloaded from Influenza Research Database, GISAID and isolates from our lab. We found that H5N6 AIVs continued to reassort with other AIVs subtypes since 2014...
June 2018: Veterinary Microbiology
https://www.readbyqxmd.com/read/29777775/genome-analysis-of-the-ancient-tracheophyte-selaginella-tamariscina-reveals-evolutionary-features-relevant-to-the-acquisition-of-desiccation-tolerance
#12
Zhichao Xu, Tianyi Xin, Dorothea Bartels, Ying Li, Wei Gu, Hui Yao, Sai Liu, Haoying Yu, Xiangdong Pu, Jianguo Zhou, Jiang Xu, Caicai Xi, Hetian Lei, Jingyuan Song, Shilin Chen
Resurrection plants, which are the "gifts" of natural evolution, are ideal models for studying genetic basis of plant desiccation tolerance. Here, we report a high-quality genome assembly of 301 Mb for the diploid spike moss Selaginella tamariscina, a primitive vascular resurrection plant. We predicated 27,761 protein-coding genes from the assembled S. tamariscina genome, 11.38% (2363) of which showed significant expression changes in response to desiccation. Approximately 60.58% of the S. tamariscina genome was annotated as repetitive DNA, which is almost 2-fold increase of that in the genome of desiccation-sensitive S...
May 16, 2018: Molecular Plant
https://www.readbyqxmd.com/read/29777493/transgenic-mice-carrying-glud2-as-a-tool-for-studying-the-expressional-and-the-functional-adaptation-of-this-positive-selected-gene-in-human-brain-evolution
#13
Andreas Plaitakis, Dimitra Kotzamani, Zoe Petraki, Maria Delidaki, Vagelis Rinotas, Ioannis Zaganas, Eleni Douni, Kyriaki Sidiropoulou, Cleanthe Spanaki
Human evolution is characterized by brain expansion and up-regulation of genes involved in energy metabolism and synaptic transmission, including the glutamate signaling pathway. Glutamate is the excitatory transmitter of neural circuits sub-serving cognitive functions, with glutamate-modulation of synaptic plasticity being central to learning and memory. GLUD2 is a novel positively-selected human gene involved in glutamatergic transmission and energy metabolism that underwent rapid evolutionary adaptation concomitantly with prefrontal cortex enlargement...
May 18, 2018: Neurochemical Research
https://www.readbyqxmd.com/read/29777105/phenotypic-diversification-by-enhanced-genome-restructuring-after-induction-of-multiple-dna-double-strand-breaks
#14
Nobuhiko Muramoto, Arisa Oda, Hidenori Tanaka, Takahiro Nakamura, Kazuto Kugou, Kazuki Suda, Aki Kobayashi, Shiori Yoneda, Akinori Ikeuchi, Hiroki Sugimoto, Satoshi Kondo, Chikara Ohto, Takehiko Shibata, Norihiro Mitsukawa, Kunihiro Ohta
DNA double-strand break (DSB)-mediated genome rearrangements are assumed to provide diverse raw genetic materials enabling accelerated adaptive evolution; however, it remains unclear about the consequences of massive simultaneous DSB formation in cells and their resulting phenotypic impact. Here, we establish an artificial genome-restructuring technology by conditionally introducing multiple genomic DSBs in vivo using a temperature-dependent endonuclease TaqI. Application in yeast and Arabidopsis thaliana generates strains with phenotypes, including improved ethanol production from xylose at higher temperature and increased plant biomass, that are stably inherited to offspring after multiple passages...
May 18, 2018: Nature Communications
https://www.readbyqxmd.com/read/29776953/the-landscape-of-actionable-genomic-alterations-in-cell-free-circulating-tumor-dna-from-21-807-advanced-cancer-patients
#15
Oliver A Zill, Kimberly C Banks, Stephen R Fairclough, Stefanie Mortimer, James V Vowles, Reza Mokhtari, David R Gandara, Philip C Mack, Justin I Odegaard, Rebecca J Nagy, Arthur M Baca, Helmy Eltoukhy, Darya I Chudova, Richard B Lanman, AmirAli Talasaz
PURPOSE: Cell-free DNA (cfDNA) sequencing provides a non-invasive method for obtaining actionable genomic information to guide personalized cancer treatment, but the presence of multiple alterations in circulation related to treatment and tumor heterogeneity complicate the interpretation of the observed variants. Experimental Design: We describe the somatic mutation landscape of 70 cancer genes from cfDNA deep-sequencing analysis of 21,807 patients with treated, late-stage cancers across >50 cancer types...
May 18, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29776407/comparative-genomics-of-the-miniature-wasp-and-pest-control-agent-trichogramma-pretiosum
#16
Amelia R I Lindsey, Yogeshwar D Kelkar, Xin Wu, Dan Sun, Ellen O Martinson, Zhichao Yan, Paul F Rugman-Jones, Daniel S T Hughes, Shwetha C Murali, Jiaxin Qu, Shannon Dugan, Sandra L Lee, Hsu Chao, Huyen Dinh, Yi Han, Harsha Vardhan Doddapaneni, Kim C Worley, Donna M Muzny, Gongyin Ye, Richard A Gibbs, Stephen Richards, Soojin V Yi, Richard Stouthamer, John H Werren
BACKGROUND: Trichogrammatids are minute parasitoid wasps that develop within other insect eggs. They are less than half a millimeter long, smaller than some protozoans. The Trichogrammatidae are one of the earliest branching families of Chalcidoidea: a diverse superfamily of approximately half a million species of parasitoid wasps, proposed to have evolved from a miniaturized ancestor. Trichogramma are frequently used in agriculture, released as biological control agents against major moth and butterfly pests...
May 18, 2018: BMC Biology
https://www.readbyqxmd.com/read/29775788/complete-genome-sequence-of-achromobacter-spanius-type-strain-dsm-23806t-a-pathogen-isolated-from-human-blood
#17
Gengmi Li, Li Yang, Tao Zhang, Xiaojiao Guo, Jian Qin, Yingjiang Cao, Qianhua Yang, Shumei You, Guoliang Yuan, Xianqi Wan, Jing Luo, Zhaoxiang Li, Lei Gao, Ying Liu, Kaifeng Jiang, Jiakui Zheng
OBJECTIVES: Achromobacter spanius is a new described, non-fermenting Gram-negative and coccoid pathogen that isolated from patient blood. In order to investigate the pathogenesis of this strain in genomic level, whole genome sequencing was carried out on this strain. METHODS: In this study, complete genome of the type strain of this species DSM 23806T was sequenced using single-molecule real-time (SMRT) DNA sequencing. RESULTS: Complete genome of DSM 23806T consists of one circular DNA chromosome of 6,425,783bp with a GC content of 64...
May 15, 2018: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/29775755/whole-genome-sequencing-and-bioinformatics-analysis-of-two-egyptian-genomes
#18
Mahmoud ElHefnawi, Sungwon Jeon, Youngjune Bhak, Asmaa ElFiky, Ahmed Horaiz, JeHoon Jun, Hyunho Kim, Jong Bhak
We report two Egyptian male genomes (EGP1 and EGP2) sequenced at ~ 30× sequencing depths. EGP1 had 4.7 million variants, where 198,877 were novel variants while EGP2 had 209,109 novel variants out of 4.8 million variants. The mitochondrial haplogroup of the two individuals were identified to be H7b1 and L2a1c, respectively. We also identified the Y haplogroup of EGP1 (R1b) and EGP2 (J1a2a1a2 > P58 > FGC11). EGP1 had a mutation in the NADH gene of the mitochondrial genome ND4 (m.11778 G > A) that causes Leber's hereditary optic neuropathy...
May 15, 2018: Gene
https://www.readbyqxmd.com/read/29775460/genus-wide-comparison-of-pseudovibrio-bacterial-genomes-reveal-diverse-adaptations-to-different-marine-invertebrate-hosts
#19
Anoop Alex, Agostinho Antunes
Bacteria belonging to the genus Pseudovibrio have been frequently found in association with a wide variety of marine eukaryotic invertebrate hosts, indicative of their versatile and symbiotic lifestyle. A recent comparison of the sponge-associated Pseudovibrio genomes has shed light on the mechanisms influencing a successful symbiotic association with sponges. In contrast, the genomic architecture of Pseudovibrio bacteria associated with other marine hosts has received less attention. Here, we performed genus-wide comparative analyses of 18 Pseudovibrio isolated from sponges, coral, tunicates, flatworm, and seawater...
2018: PloS One
https://www.readbyqxmd.com/read/29774431/complete-genome-sequences-of-three-novel-cycloviruses-identified-in-a-dragonfly-odonata-anisoptera-from-china
#20
Saif Ul Islam, Wenzhong Lin, Ran Wu, Chen Lin, Waqar Islam, Muhammad Arif, Zhenguo Du, Zujian Wu
Three cycloviruses (genus Cyclovirus, family Circoviridae) were recovered from a dragonfly (Odonata: Anisoptera) captured in Fuzhou, China. The three cycloviruses, named dragonfly associated cyclovirus 9, 10 and 11 (DfCyV-9, -10, -11), respectively, show 56.1-79.6% genome-wide identity to known cycloviruses and 61.6-65.1% among themselves. Thus, according to the current species demarcation criteria, they represent three novel cycloviruses. Notably, DfCyV-10 has a predicted replication-associated protein (Rep) that is most similar to that of bat associated cyclovirus 2 (BatACyV-2), a cyclovirus discovered in China, with 79...
May 17, 2018: Archives of Virology
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