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https://www.readbyqxmd.com/read/28651357/using-viral-gene-sequences-to-compare-and-explain-the-heterogeneous-spatial-dynamics-of-virus-epidemics
#1
Simon Dellicour, Rebecca Rose, Nuno Rodrigues Faria, Luiz Fernando Pereira Vieira, Hervé Bourhy, Marius Gilbert, Philippe Lemey, Oliver G Pybus
Rabies is an important zoonotic disease distributed worldwide. A key question in rabies epidemiology is the identification of factors that impact virus dispersion. Here we apply new analytical methods, based on phylogeographic reconstructions of viral lineage movement, to undertake a comparative evolutionary-epidemiological study of the spatial dynamics of rabies virus (RABV) epidemics in different hosts and habitats. We have compiled RABV data sets from skunk, raccoon, bat and domestic dog populations in order to investigate the viral diffusivity of different RABV epidemics, and detect and compare those environmental factors that impact the velocity of viral spread in continuous spatial landscapes...
June 23, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28651020/the-nervous-system-of-the-adult-ascidian-ciona-intestinalis-type-a-ciona-robusta-insights-from-transgenic-animal-models
#2
Tomohiro Osugi, Yasunori Sasakura, Honoo Satake
The nervous system of ascidians is an excellent model system to provide insights into the evolutionary process of the chordate nervous system due to their phylogenetic positions as the sister group of vertebrates. However, the entire nervous system of adult ascidians has yet to be functionally and anatomically investigated. In this study, we have revealed the whole dorsal and siphon nervous system of the transgenic adult ascidian of Ciona intestinalis Type A (Ciona robusta) in which a Kaede reporter gene is expressed in a pan-neuronal fashion...
2017: PloS One
https://www.readbyqxmd.com/read/28650999/an-ancestral-haplotype-of-the-human-period2-gene-associates-with-reduced-sensitivity-to-light-induced-melatonin-suppression
#3
Tokiho Akiyama, Takafumi Katsumura, Shigeki Nakagome, Sang-Il Lee, Keiichiro Joh, Hidenobu Soejima, Kazuma Fujimoto, Ryosuke Kimura, Hajime Ishida, Tsunehiko Hanihara, Akira Yasukouchi, Yoko Satta, Shigekazu Higuchi, Hiroki Oota
Humans show various responses to the environmental stimulus in individual levels as "physiological variations." However, it has been unclear if these are caused by genetic variations. In this study, we examined the association between the physiological variation of response to light-stimulus and genetic polymorphisms. We collected physiological data from 43 subjects, including light-induced melatonin suppression, and performed haplotype analyses on the clock genes, PER2 and PER3, exhibiting geographical differentiation of allele frequencies...
2017: PloS One
https://www.readbyqxmd.com/read/28650986/evolutionary-history-and-phylogeographic-relationships-of-shrews-from-sorex-araneus-group
#4
Paweł Mackiewicz, Magdalena Moska, Heliodor Wierzbicki, Przemysław Gagat, Dorota Mackiewicz
Shrews of the Sorex genus are an evolutionarily successful group that includes more than 77 species widely distributed in Eurasia and North America. The genus is one of the rare cases where karyotypic changes reflect well the evolutionary relationships among its species. The taxa showing the greatest variation in karyotype are usually classified into the Sorex araneus group. Its evolution was associated with chromosomal rearrangements, which could have promoted fast diversification of this group into many chromosomal races and species...
2017: PloS One
https://www.readbyqxmd.com/read/28650938/outbreak-caused-by-escherichia-coli-o18-k1-h7-sequence-type-95-in-a-neonatal-intensive-care-unit-in-barcelona-spain
#5
Emma Sáez-López, Jordi Bosch, Maria Dolors Salvia, Dietmar Fernández-Orth, Virginio Cepas, Mario Ferrer-Navarro, Josep Figueras-Aloy, Jordi Vila, Sara M Soto
BACKGROUND: Escherichia coli is one of the most frequent causes of late-onset neonatal sepsis. The aim of this study was to characterize an outbreak of neonatal sepsis occurring in the neonatal intensive care unit (NICU) of the Hospital Clinic of Barcelona from April to August 2013. METHODS: After presentation of the index case, all E. coli isolates from previously hospitalized neonates, health care workers, and neonates admitted to the NICU from April to October 2013 were tested for K1 antigen positivity and epidemiologically compared by pulse-field gel electrophoresis...
June 23, 2017: Pediatric Infectious Disease Journal
https://www.readbyqxmd.com/read/28650824/computing-manhattan-path-difference-mediantrees-a-practical-local-search-approach
#6
Alexey Markin, Oliver Eulenstein
Median tree problems are powerful tools for inferring large-scale phylogenetic trees that hold enormous promise for society at large. Such problems seek a median tree for a given collection of input trees under some problem-specific distance. Here, we introduce a median tree problem under the classic Manhattan path-difference distance. We show that this problem is NP-hard, devise an ILP formulation, and provide an effective local search heuristic that is based on solving a local search problem exactly. Our algorithm for the local search problem improves asymptotically by a factor of n on the best-known (naive) solution, where n is the overall number of taxa in the input trees...
June 22, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28650314/natrinema-soli-sp-nov-a-novel-halophilic-archaeon-isolated-from-a-hypersaline-wetland
#7
Mehrnoosh Rasooli, Ali Naghoni, Mohammad Ali Amoozegar, Leila Mirfeizi, Mahdi Moshtaghi Nikou, Seyed Abolhassan Shahzadeh Fazeli, Hiroaki Minegishi, Antonio Ventosa
An extremely halophilic archaeon, designated strain 5-3T, was isolated from a soil sample of Meighan wetland in Iran. Strain 5-3T was strictly aerobic, catalase-positive and oxidase-negative. Cells were Gram-stain-negative, non-motile and ovoid. Colonies of strain 5-3T were cream-coloured. The isolate showed optimum growth at 4.0 M NaCl, 40 °C and pH 7.0. The major polar lipids of the strain were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, two unknown phospholipids and three glycolipids (including one that was chromatographically identical to S2-DGD)...
June 26, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28649989/an-l-threonine-transaldolase-is-required-for-l-threo-%C3%AE-hydroxy-%C3%AE-amino-acid-assembly-during-obafluorin-biosynthesis
#8
Thomas A Scott, Daniel Heine, Zhiwei Qin, Barrie Wilkinson
β-Lactone natural products occur infrequently in nature but possess a variety of potent and valuable biological activities. They are commonly derived from β-hydroxy-α-amino acids, which are themselves valuable chiral building blocks for chemical synthesis and precursors to numerous important medicines. However, despite a number of excellent synthetic methods for their asymmetric synthesis, few effective enzymatic tools exist for their preparation. Here we report cloning of the biosynthetic gene cluster for the β-lactone antibiotic obafluorin and delineate its biosynthetic pathway...
June 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28649982/structural-and-regulatory-diversity-shape-hla-c-protein-expression-levels
#9
Gurman Kaur, Stephanie Gras, Jesse I Mobbs, Julian P Vivian, Adrian Cortes, Thomas Barber, Subita Balaram Kuttikkatte, Lise Torp Jensen, Kathrine E Attfield, Calliope A Dendrou, Mary Carrington, Gil McVean, Anthony W Purcell, Jamie Rossjohn, Lars Fugger
Expression of HLA-C varies widely across individuals in an allele-specific manner. This variation in expression can influence efficacy of the immune response, as shown for infectious and autoimmune diseases. MicroRNA binding partially influences differential HLA-C expression, but the additional contributing factors have remained undetermined. Here we use functional and structural analyses to demonstrate that HLA-C expression is modulated not just at the RNA level, but also at the protein level. Specifically, we show that variation in exons 2 and 3, which encode the α1/α2 domains, drives differential expression of HLA-C allomorphs at the cell surface by influencing the structure of the peptide-binding cleft and the diversity of peptides bound by the HLA-C molecules...
June 26, 2017: Nature Communications
https://www.readbyqxmd.com/read/28649733/composition-of-the-root-mycorrhizal-community-associated-with-coffea-arabica-in-fifa-mountains-jazan-region-saudi-arabia
#10
Mosbah Mahdhi, Taieb Tounekti, Turki Ali Al-Turki, Habib Khemira
Arbuscular mycorrhizal fungi (AMF) constitute a key functional group of soil biota that can greatly contribute to crop productivity and ecosystem sustainability. They improve nutrient uptake and enhance the ability of plants to cope with abiotic stresses. The presence of AMF in coffee (Coffea arabica L.) plant roots have been reported in several locations but not in Saudi Arabia despite the fact that coffee has been in cultivation here since ancient times. The objective of the present study was to investigate the diversity of AMF communities colonizing the roots of coffee trees growing in two sites of Fifa Mountains (south-west Saudi Arabia): site 1 at 700 m altitude and site 2 at 1400 m...
June 26, 2017: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/28649712/cross-platform-compatibility-of-de-novo-aligned-snps-in-a-non-model-butterfly-genus
#11
Erin O Campbell, Corey S Davis, Julian R Dupuis, Kevin Muirhead, Felix A H Sperling
High-throughput sequencing methods for genotyping genome-wide markers are being rapidly adopted for phylogenetics of non-model organisms in conservation and biodiversity studies. However, the reproducibility of SNP genotyping and degree of marker overlap or compatibility between datasets from different methodologies have not been tested in non-model systems. Using double-digest restriction site associated DNA sequencing, we sequenced a common set of 22 specimens from the butterfly genus Speyeria on two different Illumina platforms, using two variations of library preparation...
June 26, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28649585/data-on-the-genome-wide-identification-of-cnl-r-genes-in-setaria-italica-l-p-beauv
#12
Ethan J Andersen, Madhav P Nepal
We report data associated with the identification of 242 disease resistance genes (R-genes) in the genome of Setaria italica as presented in "Genetic diversity of disease resistance genes in foxtail millet (Setaria italica L.)" (Andersen and Nepal, 2017) [1]. Our data describe the structure and evolution of the Coiled-coil, Nucleotide-binding site, Leucine-rich repeat (CNL) R-genes in foxtail millet. The CNL genes were identified through rigorous extraction and analysis of recently available plant genome sequences using cutting-edge analytical software...
August 2017: Data in Brief
https://www.readbyqxmd.com/read/28649403/inter-personal-diversity-and-temporal-dynamics-of-dental-tongue-and-salivary-microbiota-in-the-healthy-oral-cavity
#13
Michael W Hall, Natasha Singh, Kester F Ng, David K Lam, Michael B Goldberg, Howard C Tenenbaum, Josh D Neufeld, Robert G Beiko, Dilani B Senadheera
Oral microbes form a complex and dynamic biofilm community, which is subjected to daily host and environmental challenges. Dysbiosis of the oral biofilm is correlated with local and distal infections and postulating a baseline for the healthy core oral microbiota provides an opportunity to examine such shifts during the onset and recurrence of disease. Here we quantified the daily, weekly, and monthly variability of the oral microbiome by sequencing the largest oral microbiota time-series to date, covering multiple oral sites in ten healthy individuals...
2017: NPJ Biofilms and Microbiomes
https://www.readbyqxmd.com/read/28649358/postglacial-dispersal-patterns-and-mitochondrial-genetic-structure-of-the-pyrenean-desman-galemys-pyrenaicus-in-the-northwestern-region-of-the-iberian-peninsula
#14
Marina Querejeta, Angel Fernández-González, Rafael Romero, Jose Castresana
The genetic structure of small semiaquatic animals may be influenced by dispersal across both rivers and land. The relative importance of these two modes of dispersal may vary across different species and with ecological conditions and evolutionary periods. The Pyrenean desman (Galemys pyrenaicus) is an endemic mammal of the Iberian Peninsula with a strong phylogeographic structure and semiaquatic habits, thus making it an ideal model to study the effects of river and overland dispersal on its genetic structure...
June 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28649355/resequencing-and-comparison-of-whole-mitochondrial-genome-to-gain-insight-into-the-evolutionary-status-of-the-shennongjia-golden-snub-nosed-monkey-snj-r-roxellana
#15
Yanyun Hong, Hairui Duo, Juyun Hong, Jinyuan Yang, Shiming Liu, Lianghui Yu, Tuyong Yi
Shennongjia Rhinopithecus roxellana (SNJ R. roxellana) is the smallest geographical population of R. roxellana. The phylogenetic relationships among its genera and species and the biogeographic processes leading to their current distribution are largely unclear. To address these issues, we resequenced and obtained a new, complete mitochondrial genome of SNJ R. roxellana by next-generation sequencing and standard Sanger sequencing. We analyzed the gene composition, constructed a phylogenetic tree, inferred the divergence ages based on complete mitochondrial genome sequences, and analyzed the genetic divergence of 13 functional mtDNA genes...
June 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28649351/new-insights-into-the-genetic-composition-and-phylogenetic-relationship-of-wolves-and-dogs-in-the-iberian-peninsula
#16
Ana Elisabete Pires, Isabel R Amorim, Carla Borges, Fernanda Simões, Tatiana Teixeira, Andreia Quaresma, Francisco Petrucci-Fonseca, José Matos
This study investigates the gene pool of Portuguese autochthonous dog breeds and their wild counterpart, the Iberian wolf subspecies (Canis lupus signatus), using standard molecular markers. A combination of paternal and maternal molecular markers was used to investigate the genetic composition, genetic differentiation and genetic relationship of native Portuguese dogs and the Iberian wolf. A total of 196 unrelated dogs, including breed and village dogs from Portugal, and other dogs from Spain and North Africa, and 56 Iberian wolves (wild and captive) were analyzed for nuclear markers, namely Y chromosome SNPs, Y chromosome STR loci, autosomal STR loci, and a mitochondrial fragment of the control region I...
June 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28649349/stochastic-losses-of-fire-dependent-endemic-herbs-revealed-by-a-65-year-chronosequence-of-dispersal-limited-woody-plant-encroachment
#17
John Stephen Brewer
The factors responsible for maintaining diverse groundcover plant communities of high conservation value in frequently burned wet pine savannas are poorly understood. While most management involves manipulating extrinsic factors important in maintaining species diversity (e.g., fire regimes), most ecological theory (e.g., niche theory and neutral theory) examines how traits exhibited by the species promote species coexistence. Furthermore, although many ecologists focus on processes that maintain local species diversity, conservation biologists have argued that other indices (e...
June 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28649347/factors-restricting-the-range-expansion-of-the-invasive-green-anole-anolis-carolinensis-on-okinawa-island-japan
#18
Yukari Suzuki-Ohno, Kenjiro Morita, Nobuaki Nagata, Hideaki Mori, Shintaro Abe, Takashi Makino, Masakado Kawata
The green anole Anolis carolinensis invaded the Ogasawara Islands in Japan, drove various native species to extinction, and its distribution expanded 14 years after initial establishment. A. carolinensis invaded Okinawa Island, but it has not expanded its distribution in more than 25 years, although its density is extremely high in the southern region. To determine whether A. carolinensis has the potential to expand its distribution on Okinawa Island, we performed phylogenetic analysis of mitochondrial ND2 DNA sequences to study the origin of A...
June 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28649306/decreasing-prevalence-of-transmitted-drug-resistance-among-art-naive-hiv-1-infected-patients-in-iceland-1996-2012
#19
Malik Sallam, Gülşen Özkaya Şahin, Hlynur Indriðason, Joakim Esbjörnsson, Arthur Löve, Anders Widell, Magnus Gottfreðsson, Patrik Medstrand
Introduction: Resistance to antiretroviral drugs can complicate the management of HIV-1 infection and impair control of its spread. The aim of the current study was to investigate the prevalence and transmission of HIV-1 drug resistance among 106 antiretroviral therapy (ART)-naïve patients diagnosed in Iceland (1996-2012). Methods: HIV-1 polymerase sequences were analysed using the Calibrated Population Resistance tool. Domestic spread of transmitted drug resistance (TDR) was investigated through maximum likelihood and Bayesian approaches...
2017: Infection Ecology & Epidemiology
https://www.readbyqxmd.com/read/28649271/effect-of-electrochemotherapy-on-human-herpesvirus-8-kinetics-in-classic-kaposi-sarcoma
#20
Noemy Starita, Gianluca Di Monta, Andrea Cerasuolo, Ugo Marone, Anna Maria Anniciello, Gerardo Botti, Luigi Buonaguro, Franco M Buonaguro, Maria Lina Tornesello
BACKGROUND: Electrochemotherapy (ECT) has shown to be an effective treatment for cutaneous and subcutaneous Kaposi sarcoma (KS) lesions. However, no study has investigated the impact of ECT treatment on the kinetics of human herpesvirus type 8 (HHV8), which is considered the necessary causal agent of KS. We aimed to evaluate HHV8 viral load and expression levels in patients affected by classic KS who received one or more ECT treatments and have been followed semi annually for up to four years...
2017: Infectious Agents and Cancer
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