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https://www.readbyqxmd.com/read/28821546/a-supervised-statistical-learning-approach-for-accurate-legionella-pneumophila-source-attribution-during-outbreaks
#1
Andrew H Buultjens, Kyra Y L Chua, Sarah L Baines, Jason Kwong, Wei Gao, Zoe Cutcher, Stuart Adcock, Susan Ballard, Mark B Schultz, Takehiro Tomita, Nela Subasinghe, Glen P Carter, Sacha J Pidot, Lucinda Franklin, Torsten Seemann, Anders Gonçalves Da Silva, Benjamin P Howden, Timothy P Stinear
Public health agencies are increasingly relying on genomics during Legionnaires' disease investigations. However, the causative bacterium (Legionella pneumophila) has an unusual population structure with extreme temporal and spatial genome sequence conservation. Furthermore, Legionnaires' disease outbreaks can be caused by multiple L. pneumophila genotypes in a single source. These factors can confound cluster identification using standard phylogenomic methods. Here, we show that a statistical learning approach based onL...
August 18, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28818574/antimicrobial-resistance-determinants-and-susceptibility-profiles-of-pneumococcal-isolates-recovered-in-trinidad-and-tobago
#2
Paulina A Hawkins, Patrick E Akpaka, Michele Nurse-Lucas, Rebecca Gladstone, Stephen D Bentley, Robert F Breiman, Lesley McGee, William H Swanston
INTRODUCTION: In Latin America and the Caribbean, pneumococcal infections were estimated to account for 12,000-18,000 deaths, 327,000 cases of pneumonia, 4,000 cases of meningitis and 1,229 cases of sepsis each year in children under five years old. Resistance of pneumococci to antimicrobial agents has evolved into a worldwide health problem in the last few decades. OBJECTIVE: The aim of this study was to determine the antimicrobial susceptibility profiles of 98 pneumococcal isolates collected in Trinidad and Tobago and associated genetic determinants...
August 14, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28818331/molecular-epidemiology-of-epizootic-haematopoietic-necrosis-virus-ehnv
#3
Paul M Hick, Kuttichantran Subramaniam, Patrick M Thompson, Thomas B Waltzek, Joy A Becker, Richard J Whittington
Low genetic diversity of Epizootic haematopoietic necrosis virus (EHNV) was determined for the complete genome of 16 isolates spanning the natural range of hosts, geography and time since the first outbreaks of disease. Genomes ranged from 125,591-127,487 nucleotides with 97.47% pairwise identity and 106-109 genes. All isolates shared 101 core genes with 121 potential genes predicted within the pan-genome of this collection. There was high conservation within 90,181 nucleotides of the core genes with isolates separated by average genetic distance of 3...
August 14, 2017: Virology
https://www.readbyqxmd.com/read/28817683/genome-wide-association-analysis-of-cold-tolerance-at-germination-in-temperate-japonica-rice-oryza-sativa-l-varieties
#4
Ester Sales, Juan Viruel, Concha Domingo, Luis Marqués
A pool of 200 traditional, landraces and modern elite and old cultivars of rice, mainly japonica varieties adapted to temperate regions, have been used to perform a genome wide association study to detect chromosome regions associated to low temperature germination (LTG) regulation using a panel of 1672 SNP markers. Phenotyping was performed by determining growth rates when seeds were germinated at 25° and 15°C in order to separate the germination vigorousness from cold tolerance effects. As expected, the ability to produce viable seedlings varied widely among rice cultivars and also depended greatly on temperature...
2017: PloS One
https://www.readbyqxmd.com/read/28815532/hepatitis-c-virus-replication
#5
Tetsuro Suzuki
Viruses use synthetic mechanism and organelles of the host cells to facilitate their replication and make new viruses. Host's ATP provides necessary energy. Hepatitis C virus (HCV) is a major cause of liver disease. Like other positive-strand RNA viruses, the HCV genome is thought to be synthesized by the replication complex, which consists of viral- and host cell-derived factors, in tight association with structurally rearranged vesicle-like cytoplasmic membranes. The virus-induced remodeling of subcellular membranes, which protect the viral RNA from nucleases in the cytoplasm, promotes efficient replication of HCV genome...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28812736/the-evolution-and-population-diversity-of-human-specific-segmental-duplications
#6
Megan Y Dennis, Lana Harshman, Bradley J Nelson, Osnat Penn, Stuart Cantsilieris, John Huddleston, Francesca Antonacci, Kelsi Penewit, Laura Denman, Archana Raja, Carl Baker, Kenneth Mark, Maika Malig, Nicolette Janke, Claudia Espinoza, Holly A F Stessman, Xander Nuttle, Kendra Hoekzema, Tina A Lindsay-Graves, Richard K Wilson, Evan E Eichler
Segmental duplications contribute to human evolution, adaptation and genomic instability but are often poorly characterized. We investigate the evolution, genetic variation and coding potential of human-specific segmental duplications (HSDs). We identify 218 HSDs based on analysis of 322 deeply sequenced archaic and contemporary hominid genomes. We sequence 550 human and nonhuman primate genomic clones to reconstruct the evolution of the largest, most complex regions with protein-coding potential (N = 80 genes from 33 gene families)...
February 17, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812021/association-analysis-of-arsenic-induced-straighthead-in-rice-oryza-sativa-l-based-on-the-selected-population-with-a-modified-model
#7
Xiaobai Li, Biaolin Hu, Xuhao Pan, Ning Zhang, Dianxing Wu
A rice physiological disorder makes mature panicle keep erect with empty grains termed as "straighthead." Straighthead causes yield losses and is a serious threat to rice production worldwide. Here, a new study of association mapping was conducted to identify QTL involved in straighthead. A subset of 380 accessions was selected from the USDA rice core collection and genotyped with 72 genome-wide SSR markers. An optimal model implemented with principle components (PCs) was used in this association mapping. As a result, five markers were identified to be significantly associated with straighthead...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28811666/the-essential-kinase-atr-ensuring-faithful-duplication-of-a-challenging-genome
#8
REVIEW
Joshua C Saldivar, David Cortez, Karlene A Cimprich
One way to preserve a rare book is to lock it away from all potential sources of damage. Of course, an inaccessible book is also of little use, and the paper and ink will continue to degrade with age in any case. Like a book, the information stored in our DNA needs to be read, but it is also subject to continuous assault and therefore needs to be protected. In this Review, we examine how the replication stress response that is controlled by the kinase ataxia telangiectasia and Rad3-related (ATR) senses and resolves threats to DNA integrity so that the DNA remains available to read in all of our cells...
August 16, 2017: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/28811569/transcriptional-response-to-stress-is-pre-wired-by-promoter-and-enhancer-architecture
#9
Anniina Vihervaara, Dig Bijay Mahat, Michael J Guertin, Tinyi Chu, Charles G Danko, John T Lis, Lea Sistonen
Programs of gene expression are executed by a battery of transcription factors that coordinate divergent transcription from a pair of tightly linked core initiation regions of promoters and enhancers. Here, to investigate how divergent transcription is reprogrammed upon stress, we measured nascent RNA synthesis at nucleotide-resolution, and profiled histone H4 acetylation in human cells. Our results globally show that the release of promoter-proximal paused RNA polymerase into elongation functions as a critical switch at which a gene's response to stress is determined...
August 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/28810827/validation-of-%C3%AE-lactam-minimum-inhibitory-concentration-predictions-for-pneumococcal-isolates-with-newly-encountered-penicillin-binding-protein-pbp-sequences
#10
Yuan Li, Benjamin J Metcalf, Sopio Chochua, Zhongya Li, Robert E Gertz, Hollis Walker, Paulina A Hawkins, Theresa Tran, Lesley McGee, Bernard W Beall
BACKGROUND: Genomic sequence-based deduction of antibiotic minimum inhibitory concentration (MIC) has great potential to enhance the speed and sensitivity of antimicrobial susceptibility testing. We previously developed a penicillin-binding protein (PBP) typing system and two methods (Random Forest (RF) and Mode MIC (MM)) that accurately predicted β-lactam MICs for pneumococcal isolates carrying a characterized PBP sequence type (phenotypic β-lactam MICs known for at least one isolate of this PBP type)...
August 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28810713/co-opted-megasatellite-dna-drives-evolution-of-secondary-night-vision-in-azara-s-owl-monkey
#11
Akihiko Koga, Hideyuki Tanabe, Yuriko Hirai, Hiroo Imai, Masanori Imamura, Takao Oishi, Roscoe Stanyon, Hirohisa Hirai
Owl monkeys (genus Aotus) are the only taxon in simian primates that consists of nocturnal or otherwise cathemeral species. Their night vision is superior to that of other monkeys, apes, and humans but not as good as that of typical nocturnal mammals. This incomplete night vision has been used to conclude that these monkeys only secondarily adapted to a nocturnal lifestyle, or to their cathemeral lifestyle that involves high night-time activity. It is known that the rod cells of many nocturnal mammals possess a unique nuclear architecture in which heterochromatin is centrally located...
July 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28809852/the-snp-set-based-association-study-identifies-itga1-as-a-susceptibility-gene-of-attention-deficit-hyperactivity-disorder-in-han-chinese
#12
L Liu, L Zhang, H M Li, Z R Wang, X F Xie, J P Mei, J L Jin, J Shi, L Sun, S C Li, Y L Tan, L Yang, J Wang, H M Yang, Q J Qian, Y F Wang
Genome-wide association studies, which detect the association between single-nucleotide polymorphisms (SNPs) and disease susceptibility, have been extensively applied to study attention-deficit/hyperactivity disorder (ADHD), but genome-wide significant associations have not been found yet. Genetic heterogeneity and insufficient genomic coverage may account for the missing heritability. We performed a two-stage association study for ADHD in the Han Chinese population. In the discovery stage, 1033 ADHD patients and 950 healthy controls were genotyped using both the Affymetrix Genome-Wide Human SNP Array 6...
August 15, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28809022/enhancer-analyses-using-chicken-embryo-electroporation
#13
Masanori Uchikawa, Naoko Nishimura, Makiko Iwafuchi-Doi, Hisato Kondoh
Chicken embryo electroporation is a powerful tool used to identify and analyze enhancers involved in developmental gene regulation. In this chapter, the basic procedures and underlying principles of enhancer analysis using chicken embryo electroporation are described in the following steps: (1) identification of enhancers in a wide genomic region, (2) determination of the full enhancer region, (3) definition of the core enhancer regions, and (4) analysis of a functional transcription factor binding sequences in the core region...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28808230/environmental-drivers-of-a-microbial-genomic-transition-zone-in-the-ocean-s-interior
#14
Daniel R Mende, Jessica A Bryant, Frank O Aylward, John M Eppley, Torben Nielsen, David M Karl, Edward F DeLong
The core properties of microbial genomes, including GC content and genome size, are known to vary widely among different bacteria and archaea (1,2) . Several hypotheses have been proposed to explain this genomic variability, but the fundamental drivers that shape bacterial and archaeal genomic properties remain uncertain (3-7) . Here, we report the existence of a sharp genomic transition zone below the photic zone, where bacterial and archaeal genomes and proteomes undergo a community-wide punctuated shift...
August 14, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28807931/identification-of-novel-growth-regulators-in-plant-populations-expressing-random-peptides
#15
Zhilong Bao, Maureen A Clancy, Raquel F Carvalho, Kiona Elliott, Kevin M Folta
The use of chemical genomics approaches allows the identification of small molecules that integrate into biological systems, thereby changing discrete processes that influence growth, development or metabolism. Libraries of chemicals are applied to living systems, and changes in phenotype are observed, potentially leading to the identification of new growth regulators. This work describes an approach that is the nexus of chemical-genomics and synthetic biology. Here each plant in an extensive population synthesizes a unique small peptide arising from a transgene composed of a randomized nucleic acid sequence core, flanked by translational start, stop, and cysteine-encoding (for disulfide cyclization) sequences...
August 14, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28807899/pitx1-directly-modulates-the-core-limb-development-program-to-implement-hindlimb-identity
#16
Stephen Nemec, Maëva Luxey, Deepak Jain, Aurélie Huang Sung, Tomi Pastinen, Jacques Drouin
Forelimbs (FL) and hindlimbs (HL) develop complex musculoskeletal structures that rely on the deployment of a conserved developmental program. Pitx1, a transcription factor gene with expression restricted to HL and absent from FL, plays an important role in generating HL features. The genomic mechanisms by which Pitx1 effects HL identity remain poorly understood, however. Here, we use expression profiling and analysis of direct Pitx1 targets to characterize the HL- and FL-restricted genetic programs and situate the Pitx1-dependent gene network within the context of limb-specific gene regulation...
August 14, 2017: Development
https://www.readbyqxmd.com/read/28806924/essential-genome-of-campylobacter-jejuni
#17
Rabindra K Mandal, Tieshan Jiang, Young Min Kwon
BACKGROUND: Campylobacter species are a leading cause of bacterial foodborne illness worldwide. Despite the global efforts to curb them, Campylobacter infections have increased continuously in both developed and developing countries. The development of effective strategies to control the infection by this pathogen is warranted. The essential genes of bacteria are the most prominent targets for this purpose. In this study, we used transposon sequencing (Tn-seq) of a genome-saturating library of Tn5 insertion mutants to define the essential genome of C...
August 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28806616/parvovirus-b19-integration-into-human-cd36-erythroid-progenitor-cells
#18
Tyler Janovitz, Susan Wong, Neal S Young, Thiago Oliveira, Erik Falck-Pedersen
The pathogenic autonomous human parvovirus B19 (B19V) productively infects erythroid progenitor cells (EPCs). Functional similarities between B19V nonstructural protein (NS1), a DNA binding endonuclease, and the Rep proteins of Adeno-Associated Virus (AAV) led us to hypothesize that NS1 may facilitate targeted nicking of the human genome and B19 vDNA integration. We adapted an integration capture sequencing protocol (IC-Seq) to screen B19V infected human CD36+ EPCs for viral integrants, and discovered 40,000 unique B19V integration events distributed throughout the human genome...
August 11, 2017: Virology
https://www.readbyqxmd.com/read/28803908/comparative-analysis-of-basidiomycete-transcriptomes-reveals-a-core-set-of-expressed-genes-encoding-plant-biomass-degrading-enzymes
#19
Mao Peng, Maria Victoria Aguilar-Pontes, Matthieu Hainaut, Bernard Henrissat, Kristiina Hildén, Miia R Mäkelä, Ronald P de Vries
Basidiomycete fungi can degrade a wide range of plant biomass, including living and dead trees, forest litter, crops, and plant matter in soils. Understanding the process of plant biomass decay by basidiomycetes could facilitate their application in various industrial sectors such as food & feed, detergent, and biofuels, and also provide new insights into their essential biological role in the global carbon cycle. The fast expansion of basidiomycete genomic and functional genomics data (e.g. transcriptomics, proteomics) has facilitated exploration of key genes and regulatory mechanisms of plant biomass degradation...
August 10, 2017: Fungal Genetics and Biology: FG & B
https://www.readbyqxmd.com/read/28802715/elucidating-virus-entry-using-a-tetracysteine-tagged-virus
#20
REVIEW
Bjorn-Patrick Mohl, Polly Roy
Fluorescent tags constitute an invaluable tool in facilitating a deeper understanding of the mechanistic processes governing virus-host interactions. However, when selecting a fluorescent tag for in vivo imaging of cells, a number of parameters and aspects must be considered. These include whether the tag may affect and interfere with protein conformation or localization, cell toxicity, spectral overlap, photo-stability and background. Cumulatively, these constitute challenges to be overcome. Bluetongue virus (BTV), a member of the Orbivirus genus in the Reoviridae family, is a non-enveloped virus that is comprised of two architecturally complex capsids...
August 9, 2017: Methods: a Companion to Methods in Enzymology
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