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https://www.readbyqxmd.com/read/29342270/whole-genome-analysis-reveals-the-evolution-and-transmission-of-an-mdr-dh-nap11-106-clostridium-difficile-clone-in-a-paediatric-hospital
#1
Larry K Kociolek, Egon A Ozer, Dale N Gerding, David W Hecht, Sameer J Patel, Alan R Hauser
Background: Clostridium difficile strain DH/NAP11/106, a relatively antibiotic-susceptible strain, is now the most common cause of C. difficile infection (CDI) among adults in the USA. Objectives: To identify mechanisms underlying the evolution and transmission of an MDR DH/NAP11/106 clone. Methods: WGS (Illumina MiSeq), restriction endonuclease analysis (REA) and antibiotic susceptibility testing were performed on 134 C. difficile isolates collected from paediatric patients with CDI over a 2 year period...
January 12, 2018: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29342136/clonal-evolution-mechanisms-in-nt5c2-mutant-relapsed-acute-lymphoblastic-leukaemia
#2
Gannie Tzoneva, Chelsea L Dieck, Koichi Oshima, Alberto Ambesi-Impiombato, Marta Sánchez-Martín, Chioma J Madubata, Hossein Khiabanian, Jiangyan Yu, Esme Waanders, Ilaria Iacobucci, Maria Luisa Sulis, Motohiro Kato, Katsuyoshi Koh, Maddalena Paganin, Giuseppe Basso, Julie M Gastier-Foster, Mignon L Loh, Renate Kirschner-Schwabe, Charles G Mullighan, Raul Rabadan, Adolfo A Ferrando
Relapsed acute lymphoblastic leukaemia (ALL) is associated with resistance to chemotherapy and poor prognosis. Gain-of-function mutations in the 5'-nucleotidase, cytosolic II (NT5C2) gene induce resistance to 6-mercaptopurine and are selectively present in relapsed ALL. Yet, the mechanisms involved in NT5C2 mutation-driven clonal evolution during the initiation of leukaemia, disease progression and relapse remain unknown. Here we use a conditional-and-inducible leukaemia model to demonstrate that expression of NT5C2(R367Q), a highly prevalent relapsed-ALL NT5C2 mutation, induces resistance to chemotherapy with 6-mercaptopurine at the cost of impaired leukaemia cell growth and leukaemia-initiating cell activity...
January 17, 2018: Nature
https://www.readbyqxmd.com/read/29342134/chromosomal-instability-drives-metastasis-through-a-cytosolic-dna-response
#3
Samuel F Bakhoum, Bryan Ngo, Ashley M Laughney, Julie-Ann Cavallo, Charles J Murphy, Peter Ly, Pragya Shah, Roshan K Sriram, Thomas B K Watkins, Neil K Taunk, Mercedes Duran, Chantal Pauli, Christine Shaw, Kalyani Chadalavada, Vinagolu K Rajasekhar, Giulio Genovese, Subramanian Venkatesan, Nicolai J Birkbak, Nicholas McGranahan, Mark Lundquist, Quincey LaPlant, John H Healey, Olivier Elemento, Christine H Chung, Nancy Y Lee, Marcin Imielenski, Gouri Nanjangud, Dana Pe'er, Don W Cleveland, Simon N Powell, Jan Lammerding, Charles Swanton, Lewis C Cantley
Chromosomal instability is a hallmark of cancer that results from ongoing errors in chromosome segregation during mitosis. Although chromosomal instability is a major driver of tumour evolution, its role in metastasis has not been established. Here we show that chromosomal instability promotes metastasis by sustaining a tumour cell-autonomous response to cytosolic DNA. Errors in chromosome segregation create a preponderance of micronuclei whose rupture spills genomic DNA into the cytosol. This leads to the activation of the cGAS-STING (cyclic GMP-AMP synthase-stimulator of interferon genes) cytosolic DNA-sensing pathway and downstream noncanonical NF-κB signalling...
January 17, 2018: Nature
https://www.readbyqxmd.com/read/29341390/building-a-new-research-framework-for-social-evolution-intralocus-caste-antagonism
#4
Tanya M Pennell, Luke Holman, Edward H Morrow, Jeremy Field
The breeding and non-breeding 'castes' of eusocial insects provide a striking example of role-specific selection, where each caste maximises fitness through different morphological, behavioural and physiological trait values. Typically, queens are long-lived egg-layers, while workers are short-lived, largely sterile foragers. Remarkably, the two castes are nevertheless produced by the same genome. The existence of inter-caste genetic correlations is a neglected consequence of this shared genome, potentially hindering the evolution of caste dimorphism: alleles that increase the productivity of queens may decrease the productivity of workers and vice versa, such that each caste is prevented from reaching optimal trait values...
January 16, 2018: Biological Reviews of the Cambridge Philosophical Society
https://www.readbyqxmd.com/read/29340796/the-complete-plastome-of-macaw-palm-acrocomia-aculeata-jacq-lodd-ex-mart-and-extensive-molecular-analyses-of-the-evolution-of-plastid-genes-in-arecaceae
#5
Amanda de Santana Lopes, Túlio Gomes Pacheco, Tabea Nimz, Leila do Nascimento Vieira, Miguel P Guerra, Rubens O Nodari, Emanuel Maltempi de Souza, Fábio de Oliveira Pedrosa, Marcelo Rogalski
The plastome of macaw palm was sequenced allowing analyses of evolution and molecular markers. Additionally, we demonstrated that more than half of plastid protein-coding genes in Arecaceae underwent positive selection. Macaw palm is a native species from tropical and subtropical Americas. It shows high production of oil per hectare reaching up to 70% of oil content in fruits and an interesting plasticity to grow in different ecosystems. Its domestication and breeding are still in the beginning, which makes the development of molecular markers essential to assess natural populations and germplasm collections...
January 16, 2018: Planta
https://www.readbyqxmd.com/read/29340581/gene-turnover-and-diversification-of-the-%C3%AE-and-%C3%AE-globin-gene-families-in-sauropsid-vertebrates
#6
Federico G Hoffmann, Michael W Vandewege, Jay F Storz, Juan C Opazo
The genes that encode the α- and β-chain subunits of vertebrate hemoglobin have served as a model system for elucidating general principles of gene family evolution, but little is known about patterns of evolution in amniotes other than mammals and birds. Here we report a comparative genomic analysis of the α- and β-globin gene clusters in sauropsids (archosaurs and nonavian reptiles). The objectives were to characterize changes in the size and membership composition of the α- and β-globin gene families within and among the major sauropsid lineages, to reconstruct the evolutionary history of the sauropsid α- and β-globin genes, to resolve orthologous relationships, and to reconstruct evolutionary changes in the developmental regulation of gene expression...
January 11, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29340252/positive-selection-on-human-gamete-recognition-genes
#7
Michael W Hart, Daryn A Stover, Vanessa Guerra, Sahar V Mozaffari, Carole Ober, Carina F Mugal, Ingemar Kaj
Coevolution of genes that encode interacting proteins expressed on the surfaces of sperm and eggs can lead to variation in reproductive compatibility between mates and reproductive isolation between members of different species. Previous studies in mice and other mammals have focused in particular on evidence for positive or diversifying selection that shapes the evolution of genes that encode sperm-binding proteins expressed in the egg coat or zona pellucida (ZP). By fitting phylogenetic models of codon evolution to data from the 1000 Genomes Project, we identified candidate sites evolving under diversifying selection in the human genes ZP3 and ZP2...
2018: PeerJ
https://www.readbyqxmd.com/read/29340223/yabby3-orthologous-genes-in-wild-tomato-species-structure-variability-and-expression
#8
M A Filyushin, M A Slugina, A V Shchennikova, E Z Kochieva
Evolution of the genes encoding YABBY transcription factors is believed to be one of the key reasons for flat leaf emergence from the radially symmetrical stem and gynoecium diversity. YABBY genes determine the identity of the abaxial surface of all aboveground lateral organs in seed plants. In the present study, complete sequences of YABBY3-orthologous genes were identified and characterized in 13 accessions of cultivated and wild tomato species with diverse morphophysiology of leaves, flowers, and fruits...
October 2017: Acta Naturae
https://www.readbyqxmd.com/read/29339760/biochemical-and-genetic-characterization-of-a-novel-metallo-%C3%AE-lactamase-from-marine-bacterium-erythrobacter-litoralis-htcc-2594
#9
Xia-Wei Jiang, Hong Cheng, Ying-Yi Huo, Lin Xu, Yue-Hong Wu, Wen-Hong Liu, Fang-Fang Tao, Xin-Jie Cui, Bei-Wen Zheng
Metallo-β-lactamases (MBLs) are a group of enzymes that can inactivate most commonly used β-lactam-based antibiotics. Among MBLs, New Delhi metallo-β-lactamase-1 (NDM-1) constitutes an urgent threat to public health as evidenced by its success in rapidly disseminating worldwide since its first discovery. Here we report the biochemical and genetic characteristics of a novel MBL, ElBla2, from the marine bacterium Erythrobacter litoralis HTCC 2594. This enzyme has a higher amino acid sequence similarity to NDM-1 (56%) than any previously reported MBL...
January 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29339745/genomic-and-transcriptomic-analysis-of-the-asian-honeybee-apis-cerana-provides-novel-insights-into-honeybee-biology
#10
Qingyun Diao, Liangxian Sun, Huajun Zheng, Zhijiang Zeng, Shengyue Wang, Shufa Xu, Huoqing Zheng, Yanping Chen, Yuanyuan Shi, Yuezhu Wang, Fei Meng, Qingliang Sang, Lianfei Cao, Fang Liu, Yongqiang Zhu, Wenfeng Li, Zhiguo Li, Congjie Dai, Minjun Yang, Shenglu Chen, Runsheng Chen, Shaowu Zhang, Jay D Evans, Qiang Huang, Jie Liu, Fuliang Hu, Songkun Su, Jie Wu
The Asian honeybee Apis cerana is one of two bee species that have been commercially kept with immense economic value. Here we present the analysis of genomic sequence and transcriptomic exploration for A. cerana as well as the comparative genomic analysis of the Asian honeybee and the European honeybee A. mellifera. The genome and RNA-seq data yield new insights into the behavioral and physiological resistance to the parasitic mite Varroa the evolution of antimicrobial peptides, and the genetic basis for labor division in A...
January 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29339519/evidence-for-convergent-evolution-of-sine-directed-staufen-mediated-mrna-decay
#11
Bronwyn A Lucas, Eitan Lavi, Lily Shiue, Hana Cho, Sol Katzman, Keita Miyoshi, Mikiko C Siomi, Liran Carmel, Manuel Ares, Lynne E Maquat
Primate-specific Alu short interspersed elements (SINEs) as well as rodent-specific B and ID (B/ID) SINEs can promote Staufen-mediated decay (SMD) when present in mRNA 3'-untranslated regions (3'-UTRs). The transposable nature of SINEs, their presence in long noncoding RNAs, their interactions with Staufen, and their rapid divergence in different evolutionary lineages suggest they could have generated substantial modification of posttranscriptional gene-control networks during mammalian evolution. Some of the variation in SMD regulation produced by SINE insertion might have had a similar regulatory effect in separate mammalian lineages, leading to parallel evolution of the Staufen network by independent expansion of lineage-specific SINEs...
January 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29339515/mers-cov-and-h5n1-influenza-virus-antagonize-antigen-presentation-by-altering-the-epigenetic-landscape
#12
Vineet D Menachery, Alexandra Schäfer, Kristin E Burnum-Johnson, Hugh D Mitchell, Amie J Eisfeld, Kevin B Walters, Carrie D Nicora, Samuel O Purvine, Cameron P Casey, Matthew E Monroe, Karl K Weitz, Kelly G Stratton, Bobbie-Jo M Webb-Robertson, Lisa E Gralinski, Thomas O Metz, Richard D Smith, Katrina M Waters, Amy C Sims, Yoshihiro Kawaoka, Ralph S Baric
Convergent evolution dictates that diverse groups of viruses will target both similar and distinct host pathways to manipulate the immune response and improve infection. In this study, we sought to leverage this uneven viral antagonism to identify critical host factors that govern disease outcome. Utilizing a systems-based approach, we examined differential regulation of IFN-γ-dependent genes following infection with robust respiratory viruses including influenza viruses [A/influenza/Vietnam/1203/2004 (H5N1-VN1203) and A/influenza/California/04/2009 (H1N1-CA04)] and coronaviruses [severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome CoV (MERS-CoV)]...
January 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29339406/genetic-diversity-molecular-phylogeny-and-selection-evidence-of-jinchuan-yak-revealed-by-whole-genome-resequencing
#13
Daoliang Lan, Xianrong Xiong, Tserang-Donko Mipam, Changxiu Fu, Qiang Li, Yi Ai, Dingchao Hou, Zhixin Chai, Jincheng Zhong, Jian Li
Jinchuan yak, a newly discovered yak breed, not only possesses a large proportion of multi-ribs but also exhibits many good characteristics, such as high meat production, milk yield and reproductive performance. However, information about their overall genetic structure, relationship with yaks in other areas, and possible origins and evolutionary processes is limited. In this study, 7,693,689 high-quality single-nucleotide polymorphisms were identified by resequencing the genome of Jinchuan yak. Principal component and population genetic structure analyses showed that Jinchuan yak was distinguished as an independent population among the domestic yak population...
January 16, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29339183/evolution-of-the-growth-hormone-prolactin-prolactin-2-and-somatolactin-family
#14
Daniel Ocampo Daza, Dan Larhammar
Growth hormone (GH), prolactin (PRL), prolactin 2 (PRL2) and somatolactin (SL) belong to the same hormone family and have a wide repertoire of effects including development, osmoregulation, metabolism and stimulation of growth. Both the hormone and the receptor family have been proposed to have expanded by gene duplications in early vertebrate evolution. A key question is how hormone-receptor preferences have arisen among the duplicates. The first step to address this is to determine the time window for these duplications...
January 12, 2018: General and Comparative Endocrinology
https://www.readbyqxmd.com/read/29338715/landscape-genomics-natural-selection-drives-the-evolution-of-mitogenome-in-penguins
#15
Barbara Ramos, Daniel González-Acuña, David E Loyola, Warren E Johnson, Patricia G Parker, Melanie Massaro, Gisele P M Dantas, Marcelo D Miranda, Juliana A Vianna
BACKGROUND: Mitochondria play a key role in the balance of energy and heat production, and therefore the mitochondrial genome is under natural selection by environmental temperature and food availability, since starvation can generate more efficient coupling of energy production. However, selection over mitochondrial DNA (mtDNA) genes has usually been evaluated at the population level. We sequenced by NGS 12 mitogenomes and with four published genomes, assessed genetic variation in ten penguin species distributed from the equator to Antarctica...
January 16, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29338642/functional-evolution-of-biosynthetic-enzymes-that-produce-plant-volatiles
#16
Takao Koeduka
Plants synthesize volatile compounds to attract pollinators. The volatiles emitted by flowers are often complex mixtures of organic compounds; pollinators are capable of distinctly recognizing different volatile compounds. Plants also produce volatile compounds to protect themselves against herbivores and pathogens. Some of the volatile compounds produced in floral and vegetative tissues are toxic to insects and microbes. To adapt changes in the environment, plants have evolved the ability to synthesize a unique set of volatiles...
January 17, 2018: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/29337984/anteroposterior-axis-patterning-by-early-canonical-wnt-signaling-during-hemichordate-development
#17
Sébastien Darras, Jens H Fritzenwanker, Kevin R Uhlinger, Ellyn Farrelly, Ariel M Pani, Imogen A Hurley, Rachael P Norris, Michelle Osovitz, Mark Terasaki, Mike Wu, Jochanan Aronowicz, Marc Kirschner, John C Gerhart, Christopher J Lowe
The Wnt family of secreted proteins has been proposed to play a conserved role in early specification of the bilaterian anteroposterior (A/P) axis. This hypothesis is based predominantly on data from vertebrate embryogenesis as well as planarian regeneration and homeostasis, indicating that canonical Wnt (cWnt) signaling endows cells with positional information along the A/P axis. Outside of these phyla, there is strong support for a conserved role of cWnt signaling in the repression of anterior fates, but little comparative support for a conserved role in promotion of posterior fates...
January 16, 2018: PLoS Biology
https://www.readbyqxmd.com/read/29337961/how-the-evolution-of-multicellularity-set-the-stage-for-cancer
#18
REVIEW
Anna S Trigos, Richard B Pearson, Anthony T Papenfuss, David L Goode
Neoplastic growth and many of the hallmark properties of cancer are driven by the disruption of molecular networks established during the emergence of multicellularity. Regulatory pathways and molecules that evolved to impose regulatory constraints upon networks established in earlier unicellular organisms enabled greater communication and coordination between the diverse cell types required for multicellularity, but also created liabilities in the form of points of vulnerability in the network that when mutated or dysregulated facilitate the development of cancer...
January 16, 2018: British Journal of Cancer
https://www.readbyqxmd.com/read/29337419/evolution-of-resistance-to-chytridiomycosis-is-associated-with-a-robust-early-immune-response
#19
Laura F Grogan, Scott D Cashins, Lee F Skerratt, Lee Berger, Michael S McFadden, Peter Harlow, David A Hunter, Ben C Scheele, Jason Mulvenna
Potentiating the evolution of immunity is a promising strategy for addressing biodiversity diseases. Assisted selection for infection resistance may enable the recovery and persistence of amphibians threatened by chytridiomycosis; a devastating fungal skin disease threatening hundreds of species globally. However, knowledge of the mechanisms involved in the natural evolution of immunity to chytridiomycosis is limited. Understanding the mechanisms of such resistance may help speed assisted-selection. Using a transcriptomics approach we examined gene expression responses of endangered alpine tree frogs (Litoria verreauxii alpina) to subclinical infection, comparing two long-exposed populations with a naïve population...
January 16, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29337313/complete-genome-sequencing-of-the-luminescent-bacterium-vibrio-qinghaiensis-sp-q67-using-pacbio-technology
#20
Liang Gong, Yu Wu, Qijie Jian, Chunxiao Yin, Taotao Li, Vijai Kumar Gupta, Xuewu Duan, Yueming Jiang
Vibrio qinghaiensis sp.-Q67 (Vqin-Q67) is a freshwater luminescent bacterium that continuously emits blue-green light (485 nm). The bacterium has been widely used for detecting toxic contaminants. Here, we report the complete genome sequence of Vqin-Q67, obtained using third-generation PacBio sequencing technology. Continuous long reads were attained from three PacBio sequencing runs and reads >500 bp with a quality value of >0.75 were merged together into a single dataset. This resultant highly-contiguous de novo assembly has no genome gaps, and comprises two chromosomes with substantial genetic information, including protein-coding genes, non-coding RNA, transposon and gene islands...
January 16, 2018: Scientific Data
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