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https://www.readbyqxmd.com/read/28545149/persistence-of-lineage-iv-peste-des-petits-ruminants-virus-within-israel-since-1993-an-evolutionary-perspective
#1
Brian Clarke, Mana Mahapatra, Orly Friedgut, Velizar Bumbarov, Satya Parida
Peste-des-petits ruminants (PPR) is one of the most important infectious diseases of domesticated small ruminants. From the initial identification in 1942 in West Africa, PPR virus (PPRV) has spread throughout much of the developing world. PPRV is now considered endemic throughout Africa, with the notable exception of South Africa, the Middle-East and Israel, as well as South-, East-, and Central Asia. Despite this widespread dispersal, the evolution and transmission of PPRV in endemic populations is not well understood...
2017: PloS One
https://www.readbyqxmd.com/read/28545090/neotropical-bats-that-co-habit-with-humans-function-as-dead-end-hosts-for-dengue-virus
#2
Amanda Vicente-Santos, Andres Moreira-Soto, Claudio Soto-Garita, Luis Guillermo Chaverri, Andrea Chaves, Jan Felix Drexler, Juan Alberto Morales, Alejandro Alfaro-Alarcón, Bernal Rodríguez-Herrera, Eugenia Corrales-Aguilar
Several studies have shown Dengue Virus (DENV) nucleic acids and/or antibodies present in Neotropical wildlife including bats, suggesting that some bat species may be susceptible to DENV infection. Here we aim to elucidate the role of house-roosting bats in the DENV transmission cycle. Bats were sampled in households located in high and low dengue incidence regions during rainy and dry seasons in Costa Rica. We captured 318 bats from 12 different species in 29 households. Necropsies were performed in 205 bats to analyze virus presence in heart, lung, spleen, liver, intestine, kidney, and brain tissue...
May 18, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28545083/simultaneous-inference-of-phylogenetic-and-transmission-trees-in-infectious-disease-outbreaks
#3
Don Klinkenberg, Jantien A Backer, Xavier Didelot, Caroline Colijn, Jacco Wallinga
Whole-genome sequencing of pathogens from host samples becomes more and more routine during infectious disease outbreaks. These data provide information on possible transmission events which can be used for further epidemiologic analyses, such as identification of risk factors for infectivity and transmission. However, the relationship between transmission events and sequence data is obscured by uncertainty arising from four largely unobserved processes: transmission, case observation, within-host pathogen dynamics and mutation...
May 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28544882/inference-and-evolutionary-analysis-of-genome-scale-regulatory-networks-in-large-phylogenies
#4
Christopher Koch, Jay Konieczka, Toni Delorey, Ana Lyons, Amanda Socha, Kathleen Davis, Sara A Knaack, Dawn Thompson, Erin K O'Shea, Aviv Regev, Sushmita Roy
Changes in transcriptional regulatory networks can significantly contribute to species evolution and adaptation. However, identification of genome-scale regulatory networks is an open challenge, especially in non-model organisms. Here, we introduce multi-species regulatory network learning (MRTLE), a computational approach that uses phylogenetic structure, sequence-specific motifs, and transcriptomic data, to infer the regulatory networks in different species. Using simulated data from known networks and transcriptomic data from six divergent yeasts, we demonstrate that MRTLE predicts networks with greater accuracy than existing methods because it incorporates phylogenetic information...
May 24, 2017: Cell Systems
https://www.readbyqxmd.com/read/28544878/evolutionary-context-improves-regulatory-network-predictions
#5
Jonathan L Gordon, Brigida Gallone, Steven Maere, Kevin J Verstrepen
A novel algorithm harnesses phylogenetic information and facilitates a better understanding of the evolutionary divergence of gene regulation between species.
May 24, 2017: Cell Systems
https://www.readbyqxmd.com/read/28544607/spotted-gar-and-the-evolution-of-innate-immune-receptors
#6
Dustin J Wcisel, Tatsuya Ota, Gary W Litman, Jeffrey A Yoder
The resolution of the gar genome affords an opportunity to examine the diversification and functional specialization of immune effector molecules at a distant and potentially informative point in phylogenetic development. Although innate immunity is effected by a particularly large number of different families of molecules, the focus here is to provide detailed characterization of several families of innate receptors that are encoded in large multigene families, for which orthologous forms can be identified in other species of bony fish but not in other vertebrate groups as well as those for which orthologs are present in other vertebrate species...
May 24, 2017: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/28544594/diversity-of-aromatic-hydroxylating-dioxygenase-genes-in-mangrove-microbiome-and-their-biogeographic-patterns-across-global-sites
#7
Sanderson T P de Sousa, Lucélia Cabral, Gileno Vieira Lacerda Júnior, Valéria M Oliveira
Aromatic hydrocarbons (AH), such as polycyclic aromatic hydrocarbons, are compounds largely found in nature. Aromatic-ring-hydroxylating dioxygenases (ARHD) are proteins involved in AH degradation pathways. We used ARHD functional genes from an oil-impacted mangrove area and compared their diversity with other sites around the world to understand the ARHD biogeographic distribution patterns. For this, a comprehensive database was established with 166 operational protein families (OPFs) from 1,758 gene sequences obtained from 15 different sites worldwide, of which twelve are already published studies and three are unpublished...
May 23, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28544438/genome-wide-identification-characterization-and-evolution-of-cuticular-protein-genes-in-the-malaria-vector-anopheles-sinensis-diptera-culicidae
#8
Bai-Qi Liu, Liang Qiao, Qi-Yi He, Yong Zhou, Shuang Ren, Bin Chen
Thirteen cuticular proteins (CPs) families have been recognized in arthropods. In this study, 250 Anopheles sinensis CP genes were identified and named based on genome and transcriptome sequences. They were classified into 10 families based on motifs and phylogenetic analyses. In 11 other insect species, 9 had CP numbers > 150 while Apis mellifera and Tribolium castaneum had CP numbers less than 52. The CPs of 8 species occupied > 1.4% of the total genomic gene number whereas in 3 species the CPs occupied < 1%...
May 24, 2017: Insect Science
https://www.readbyqxmd.com/read/28544395/morphology-and-molecular-phylogeny-of-a-new-hypotrich-ciliate-pseudourostyla-guizhouensis-sp-nov-from-southern-china-with-notes-on-a-chinese-population-of-hemicycliostyla-franzi-foissner-1987-paiva-et%C3%A2-al-2012-ciliophora-hypotricha
#9
REVIEW
Yanbo Li, Zhao Lyu, Alan Warren, Kexin Zhou, Fengchao Li, Xumiao Chen
The morphology and molecular phylogeny of a soil hypotrich ciliate, Pseudourostyla guizhouensis sp. nov., collected from southern China, were investigated. Pseudourostyla guizhouensis sp. nov. has an elongate elliptical body measuring 180-310 × 65-85 μm in vivo; invariably two right and three or four left marginal rows; six or seven dorsal kineties; adoral zone consisting of 57-70 membranelles; 12-16 frontal cirri, one buccal cirrus, 13-20 midventral pairs, two frontoterminal cirri, two pre-transverse ventral cirri, and five to seven transverse cirri...
May 22, 2017: Journal of Eukaryotic Microbiology
https://www.readbyqxmd.com/read/28544099/genetic-signatures-coupled-with-lineage-shift-characterize-endemic-evolution-of-dengue-virus-serotype-2-during-2015-outbreak-in-delhi-india
#10
Manish Chandra Choudhary, Ekta Gupta, Shvetank Sharma, Nadeem Hasnain, Pragya Agarwala
OBJECTIVE: In 2015 New Delhi witnessed a massive outbreak of Dengue virus (DENV) resulting in high morbidity and mortality. We report the molecular characterization of the dominant circulating DENV strain to understand its evolution and dispersal. MATERIALS AND METHODS: DENV infections were diagnosed by detection of IgM/NS1 antigen and serotyping was performed by C-PrM PCR. Envelope gene was amplified and variation(s) in envelope gene were analyzed. Phylogenetic tree construction, time-based phylogeny and origin of DENV were analyzed...
May 23, 2017: Tropical Medicine & International Health: TM & IH
https://www.readbyqxmd.com/read/28544059/objective-assessment-of-the-evolutionary-action-equation-for-the-fitness-effect-of-missense-mutations-across-cagi-blinded-contests
#11
Panagiotis Katsonis, Olivier Lichtarge
A major challenge in genome interpretation is to estimate the fitness effect of coding variants of unknown significance (VUS). Labor, limited understanding of protein functions, and lack of assays generally limit direct experimental assessment of VUS, and make robust and accurate computational approaches a necessity. Often, however, algorithms that predict mutational effect disagree amongst themselves and with experimental data, slowing their adoption for clinical diagnostics. To objectively assess such methods, the Critical Assessment of Genome Interpretation (CAGI) community organizes contests to predict unpublished experimental data, available only to CAGI assessors...
May 23, 2017: Human Mutation
https://www.readbyqxmd.com/read/28544006/morphology-and-phylogeny-of-two-novel-ciliates-arcanisutura-chongmingiensis-n-gen-n-sp-and-naxella-paralucida-n-sp-from-shanghai-china
#12
Wanying Liao, Xinpeng Fan, Qianqian Zhang, Yuan Xu, Fukang Gu
The morphologies of two novel ciliates, Arcanisutura chongmingiensis n. gen., n. sp. and Naxella paralucida n. sp., collected from Shanghai, China, have been investigated using live observation and silver staining methods. Arcanisutura n. gen. can be easily distinguished from related genera by its inconspicuous, oblique anterior suture. Arcanisutura chongmingiensis n. sp. is mainly recognized by its elongated body with a tail-like posterior end, 25-33 somatic kineties, and 4-11 excretory pores. Naxella paralucida n...
May 25, 2017: Journal of Eukaryotic Microbiology
https://www.readbyqxmd.com/read/28543995/the-effects-of-restoring-logged-tropical-forests-on-avian-phylogenetic-and-functional-diversity
#13
Cindy C P Cosset, David P Edwards
Selective logging is the most prevalent land-use change in the tropics. Despite the resulting degradation of forest structure, selectively logged forests still harbour a substantial amount of biodiversity leading to suggestions that their protection is the next best alternative to conserving primary, old-growth forests. Restoring carbon stocks under Reducing Emissions from Deforestation and Forest Degradation (REDD+) schemes is a potential method for obtaining funding to protect logged forests, via enrichment planting and liberation cutting of vines...
May 24, 2017: Ecological Applications: a Publication of the Ecological Society of America
https://www.readbyqxmd.com/read/28543631/a-three-dimensional-placoderm-stem-group-gnathostome-pharyngeal-skeleton-and-its-implications-for-primitive-gnathostome-pharyngeal-architecture
#14
Martin D Brazeau, Matt Friedman, Anna Jerve, Robert C Atwood
The pharyngeal skeleton is a key vertebrate anatomical system in debates on the origin of jaws and gnathostome (jawed vertebrate) feeding. Furthermore, it offers considerable potential as a source of phylogenetic data. Well-preserved examples of pharyngeal skeletons from stem-group gnathostomes remain poorly known. Here, we describe an articulated, nearly complete pharyngeal skeleton in an Early Devonian placoderm fish, Paraplesiobatis heinrichsi Broili, from Hunsrück Slate of Germany. Using synchrotron light tomography, we resolve and reconstruct the three-dimensional gill arch architecture of Paraplesiobatis and compare it with other gnathostomes...
May 23, 2017: Journal of Morphology
https://www.readbyqxmd.com/read/28543439/metagenomic-profiling-of-the-microbial-freshwater-communities-in-two-bulgarian-reservoirs
#15
Ivan Iliev, Galina Yahubyan, Mariana Marhova, Elena Apostolova, Mariyana Gozmanova, Gana Gecheva, Sonya Kostadinova, Angelina Ivanova, Vesselin Baev
Microorganisms inhabiting freshwater environments are an integral part of the aquatic ecosystems. Very few data are available regarding the profiles of the microbial communities in the reservoirs in Bulgaria, despite their key role in the biogeochemical processes. In the present study, we provide the first comprehensive metagenomic analysis on the planktonic bacterial diversity of two large and economically important Bulgarian reservoirs (Batak and Tsankov Kamak) using next-generation sequencing of 16S ribosomal RNA gene (16S rRNA)...
May 22, 2017: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/28543388/environmental-constraints-on-the-compositional-and-phylogenetic-beta-diversity-of-tropical-forest-snake-assemblages
#16
Mario R Moura, Henrique C Costa, Antônio J S Argôlo, Walter Jetz
The ongoing biodiversity crisis increases the importance and urgency of studies addressing the role of environmental variation on the composition and evolutionary history of species assemblages, but especially the tropics and ectotherms remain understudied. In regions with rainy summers, coexistence of ectothermic species may be determined by the partitioning of the climatic niche, since ectotherms can rely on water availability and thermoregulatory behaviour to buffer constraints along their climatic niche...
May 22, 2017: Journal of Animal Ecology
https://www.readbyqxmd.com/read/28543189/rapid-radiations-of-both-kiwifruit-hybrid-lineages-and-their-parents-shed-light-on-a-two-layer-mode-of-species-diversification
#17
Yifei Liu, Dawei Li, Qiong Zhang, Chi Song, Caihong Zhong, Xudong Zhang, Ying Wang, Xiaohong Yao, Zupeng Wang, Shaohua Zeng, Ying Wang, Yangtao Guo, Shuaibin Wang, Xinwei Li, Li Li, Chunyan Liu, Honour C McCann, Weiming He, Yan Niu, Min Chen, Liuwen Du, Junjie Gong, Paul M Datson, Elena Hilario, Hongwen Huang
Reticulate speciation caused by interspecific hybridization is now recognized as an important mechanism in the creation of biological diversity. However, depicting the patterns of phylogenetic networks for lineages that have undergone interspecific gene flow is challenging. Here we sequenced 25 taxa representing natural diversity in the genus Actinidia with an average mapping depth of 26× on the reference genome to reconstruct their reticulate history. We found evidence, including significant gene tree discordance, cytonuclear conflicts, and changes in genome-wide heterozygosity across taxa, collectively supporting extensive reticulation in the genus...
May 25, 2017: New Phytologist
https://www.readbyqxmd.com/read/28543058/shallow-size-density-relations-within-mammal-clades-suggest-greater-intra-guild-ecological-impact-of-large-bodied-species
#18
R Ø Pedersen, S Faurby, J-C Svenning
1.Population densities of species have a predictable relationship to their body mass on a global scale. This relationship is known as the size-density relationship. The relationship was originally found to be directly opposite of metabolic rate scaling, which led to the hypothesis of energetic equivalence. However, recent studies have suggested that the size-density relationship varies between clades. Specifically, the size-density relationship for certain mammal clades has been found to be less negative than the relationship across all mammals...
May 24, 2017: Journal of Animal Ecology
https://www.readbyqxmd.com/read/28543056/cloning-and-analysis-of-the-glwc-1-and-glwc-2-genes-encoding-putative-blue-light-photoreceptor-from-ganoderma-lucidum
#19
Xinran Xu, Xiangdong Chen, Wumengxiao Yu, Yu Liu, Weiwei Zhang, Jin Lan
Blue light plays an important role during the growth of Ganoderma lucidum, one of the best-known medicinal macrofungi in China. In the present study, we cloned Glwc-1 and Glwc-2, the homologue of the blue light photoreceptors Ncwc-1 and Ncwc-2 of Neurospora crassa, from G. lucidum. The deduced amino acid sequence of Glwc-1 contained the similar function domains as NcWC-1 including LOV, PAS B, PAS C, and PAC domains. The deduced amino acid sequence of Glwc-2 contained PAS domain and GATA-type zinc finger (Znf) domain as well as NcWC-2...
May 23, 2017: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/28543028/correlated-evolution-between-colouration-and-ambush-site-in-predators-with-visual-prey-lures
#20
F M Gawryszewski, M A Calero-Torralbo, R G Gillespie, M A Rodríguez-Gironés, M E Herberstein
The evolution of a visual signal will be affected by signaller and receiver behaviour, and by the physical properties of the environment where the signal is displayed. Crab spiders are typical sit-and-wait predators found in diverse ambush sites, such as tree bark, foliage and flowers. Some of the flower-dweller species present a UV(+) -white visual lure that makes them conspicuous and attractive to their prey. We hypothesised that UV(+) -white colouration was associated with the evolution of a flower-dwelling habit...
May 23, 2017: Evolution; International Journal of Organic Evolution
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