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https://www.readbyqxmd.com/read/28434202/distribution-of-norovirus-genotypes-and-subtypes-in-river-water-by-ultra-deep-sequencing-based-analysis
#1
M Boonchan, K Motomura, K Inoue, H Ode, P Y Chu, M Lin, Y Iwatani, K Ruchusatsawat, R Guntapong, R Tacharoenmuang, S Chantaroj, M Tatsumi, N Takeda, S Sangkitporn
To determine the distribution of NoV genotypes in natural river water in Thailand, we conducted a genome analysis using a next-generation sequencer. Twenty-five river water samples were collected at five different sites of the Khlong Klon River in the suburbs of Bangkok between August 2013 and December 2014. The partial genome of NoV was detected in 15 of the 25 samples (60.0%). Seven of these 15 samples (46.7%) contained multiple NoV GII genotypes: GII.4, GII.6, and GII.17. Our data showed that GII.17 had already emerged in August 2013 as a minor population, and it became a major genotype in December 2014...
April 23, 2017: Letters in Applied Microbiology
https://www.readbyqxmd.com/read/28434151/cbf2a-cbf4b-genomic-region-copy-numbers-alongside-the-circadian-clock-play-key-regulatory-mechanisms-driving-expression-of-fr-h2-cbfs
#2
Taniya Dhillon, Kengo Morohashi, Eric J Stockinger
The C-Repeat Binding Factors (CBFs) are DNA-binding transcriptional activators that were identified using Arabidopsis thaliana. In barley, Hordeum vulgare, a cluster of CBF genes reside at FROST RESISTANCE-H2, one of two loci having major effects on winter-hardiness. FR-H2 was revealed in a population derived from the winter barley 'Nure' and the spring barley 'Trèmois'. 'Nure' harbors two to three copies of CBF2A and CBF4B as a consequence of tandem iteration of the genomic region encompassing these genes whereas 'Trèmois' harbors single copies, and these copy number differences are associated with their transcript level differences...
April 22, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28434100/complete-genome-sequence-of-jacquemontia-yellow-vein-virus-a-novel-begomovirus-infecting-jacquemontia-tamnifolia-in-venezuela
#3
Elvira Fiallo-Olivé, Dorys T Chirinos, Francis Geraud-Pouey, Jesús Navas-Castillo
Wild plants of the family Convolvulaceae are hosts for a few New World begomoviruses (genus Begomovirus, family Geminiviridae). In this work, we report the complete genome sequence of a new begomovirus infecting the wild convolvulaceous plant Jacquemontia tamnifolia in Venezuela. The cloned bipartite genome showed the organization of typical New World begomoviruses and was found to be phylogenetically related to those of begomoviruses from Venezuela and other Caribbean countries. Several recombination events have been shown to have occurred involving genome fragment exchange with related begomoviruses infecting crops such as tomato and cucurbits and wild plants, including Jacquemontia sp...
April 22, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28434099/the-complete-genome-sequence-of-a-novel-virus-bellflower-veinal-mottle-virus-suggests-the-existence-of-a-new-genus-within-the-family-potyviridae
#4
Jang-Kyun Seo, Hae-Ryun Kwak, Mi-Kyeong Kim, Jeong-Soo Kim, Hong-Soo Choi
A new virus was isolated from a bellflower (Campanula takesimana) plant showing veinal mottle symptoms, and its complete genome sequence was determined. The viral genome consists of a positive-sense single-stranded RNA of 8,259 ribonucleotides. Electron microscopic observation revealed that the viral genome is packaged as a filamentous particle with an average length of approximately 760 nm. BLAST searches of protein databases showed that the encoded polyprotein has a maximum amino acid sequence identity of 34...
April 22, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28434044/faulty-rna-splicing-consequences-and-therapeutic-opportunities-in-brain-and-muscle-disorders
#5
REVIEW
Vittoria Pagliarini, Piergiorgio La Rosa, Claudio Sette
Alternative splicing is a powerful mechanism that largely expands the coding potential of eukaryotic genomes. Indeed, its complex and flexible regulation is exploited by cells to adapt to various environmental conditions, through production of protein variants displaying different functions. Such flexibility, however, is accompanied by high risk of errors, and dysregulation of splicing is now recognized as an important factor in human diseases. Notably, the RNA-based nature of splicing, which involves high specificity through base pair recognition, offers a remarkable therapeutic opportunity by allowing design of tools with elevated target selectivity...
April 22, 2017: Human Genetics
https://www.readbyqxmd.com/read/28434033/the-gut-microbiome-as-a-target-for-prevention-and-treatment-of-hyperglycaemia-in-type-2-diabetes-from-current-human-evidence-to-future-possibilities
#6
REVIEW
Louise Brunkwall, Marju Orho-Melander
The totality of microbial genomes in the gut exceeds the size of the human genome, having around 500-fold more genes that importantly complement our coding potential. Microbial genes are essential for key metabolic processes, such as the breakdown of indigestible dietary fibres to short-chain fatty acids, biosynthesis of amino acids and vitamins, and production of neurotransmitters and hormones. During the last decade, evidence has accumulated to support a role for gut microbiota (analysed from faecal samples) in glycaemic control and type 2 diabetes...
April 22, 2017: Diabetologia
https://www.readbyqxmd.com/read/28434019/recent-developments-in-olive-olea-europaea-l-genetics-and-genomics-applications-in-taxonomy-varietal-identification-traceability-and-breeding
#7
REVIEW
L Sebastiani, M Busconi
The latest results in DNA markers application and genomic studies in olive. Olive (Olea europaea L.) is among the most ancient tree crops worldwide and the source of oil beneficial for human health. Despite this, few data on olive genetics are available in comparison with other cultivated plant species. Molecular information is mainly linked to molecular markers and their application to the study of DNA variation in the Olea europaea complex. In terms of genomic research, efforts have been made in sequencing, heralding the era of olive genomic...
April 22, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28433992/the-aachen-minipig-phenotype-genotype-hematological-and-biochemical-characterization-and-comparison-to-the-g%C3%A3-ttingen-minipig
#8
Kerstin Pawlowsky, Lisa Ernst, Julia Steitz, Thaddäus Stopinski, Babette Kögel, Anna Henger, Reinhart Kluge, René Tolba
BACKGROUND: The pig is one of the most frequently used large animal models for biomedical research, especially in the field of translational research and surgical models. While standard livestock breeds are used in short-term and acute studies, minipig breeds are the preferred breeds in long-term and chronic studies due to their limited growth and body weight. OBJECTIVE: In consideration of the 3R principle (refinement, reduction, replacement) and the increasing demand, the aim of this study was to generate a new, robust, non-specific-pathogen-free minipig breed, the Aachen minipig...
April 22, 2017: European Surgical Research. Europäische Chirurgische Forschung. Recherches Chirurgicales Européennes
https://www.readbyqxmd.com/read/28433800/chromosomal-alterations-and-gene-expression-changes-associated-with-the-progression-of-leukoplakia-to-advanced-gingivobuccal-cancer
#9
Priyanka G Bhosale, Simona Cristea, Srikant Ambatipudi, Rajiv S Desai, Rajiv Kumar, Asawari Patil, Shubhada Kane, Anita M Borges, Alejandro A Schäffer, Niko Beerenwinkel, Manoj B Mahimkar
We present an integrative genome-wide analysis that can be used to predict the risk of progression from leukoplakia to oral squamous cell carcinoma (OSCC) arising in the gingivobuccal complex (GBC). We find that the genomic and transcriptomic profiles of leukoplakia resemble those observed in later stages of OSCC and that several changes are associated with this progression, including amplification of 8q24.3, deletion of 8p23.2, and dysregulation of DERL3, EIF5A2, ECT2, HOXC9, HOXC13, MAL, MFAP5 and NELL2. Comparing copy number profiles of primary tumors with and without lymph-node metastasis, we identify alterations associated with metastasis, including amplifications of 3p26...
April 20, 2017: Translational Oncology
https://www.readbyqxmd.com/read/28433741/loss-of-the-neurodevelopmental-gene-zswim6-alters-striatal-morphology-and-motor-regulation
#10
David J Tischfield, Dave K Saraswat, Andrew Furash, Stephen C Fowler, Marc V Fuccillo, Stewart A Anderson
The zinc-finger SWIM domain-containing protein 6 (ZSWIM6) is a protein of unknown function that has been associated with schizophrenia and limited educational attainment by three independent genome-wide association studies. Additionally, a putatively causal point mutation in ZSWIM6 has been identified in several cases of acromelic frontonasal dysostosis with severe intellectual disability. Despite the growing number of studies implicating ZSWIM6 as an important regulator of brain development, its role in this process has never been examined...
April 19, 2017: Neurobiology of Disease
https://www.readbyqxmd.com/read/28433737/exploring-biochemical-pathways-for-mono-ethylene-glycol-meg-synthesis-from-synthesis-gas
#11
M Ahsanul Islam, Noushin Hadadi, Meric Ataman, Vassily Hatzimanikatis, Gregory Stephanopoulos
Mono-ethylene glycol (MEG) is an important petrochemical with widespread use in numerous consumer products. The current industrial MEG-production process relies on non-renewable fossil fuel-based feedstocks, such as petroleum, natural gas, and naphtha; hence, it is useful to explore alternative routes of MEG-synthesis from gases as they might provide a greener and more sustainable alternative to the current production methods. Technologies of synthetic biology and metabolic engineering of microorganisms can be deployed for the expression of new biochemical pathways for MEG-synthesis from gases, provided that such promising alternative routes are first identified...
April 19, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28433724/whole-genome-de-novo-sequencing-of-wood-rot-fungus-fomitopsis-palustris-atcc62978-with-both-a-cellulolytic-and-ligninolytic-enzyme-system
#12
Chang-Young Hong, Su-Yeon Lee, Sun-Hwa Ryu, Myungkil Kim
Fomitopsis palustris is a model brown rot fungus causing destructive wood decay based on the cellulase system. Endoglucanase secreted by F. palustris hydrolyzes cellulose in both the crystalline and amorphous form. In this study, whole-genome sequencing was conducted to identify genes related to F. palustris cellulose degradation and their functions. We determined the 43-Mb complete draft genome of F. palustris (ATCC 62978), comprising 14,592 predicted gene models. Gene annotation provided crucial information about the location and function of protein-encoding genes...
April 19, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28433723/elimination-of-the-cryptic-plasmid-in-leuconostoc-citreum-by-crispr-cas9-system
#13
Ye-Ji Jang, Seung-Oh Seo, Seul-Ah Kim, Ling Li, Tae-Jip Kim, Sun Chang Kim, Yong-Su Jin, Nam Soo Han
Leuconostoc spp. are important lactic acid bacteria for the fermentation of foods. In particular, L. citreum strains isolated from various foods have been used as host strains for genetic and metabolic engineering studies. In order to develop a food-grade genetic engineering system, L. citreum CB2567 was isolated from Kimchi. However, the isolated bacterium contained a cryptic plasmid which was difficult to eliminate. As the existence of the plasmid might hinder strain engineering, we eliminated the plasmid using an RNA-guided DNA endonuclease CRISPR/Cas9 system...
April 19, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28433722/high-precision-genome-sequencing-of-engineered-g-oxydans-621h-by-combining-long-nanopore-and-short-accurate-illumina-reads
#14
Angela Kranz, Alexander Vogel, Ursula Degner, Ines Kiefler, Michael Bott, Björn Usadel, Tino Polen
State of the art and novel high-throughput DNA sequencing technologies enable fascinating opportunities and applications in the life sciences including microbial genomics. Short high-quality read data already enable not only microbial genome sequencing, yet can be inadequately to solve problems in genome assemblies and for the analysis of structural variants, especially in engineered microbial cell factories. Single-molecule real-time sequencing technologies generating long reads promise to solve such assembly problems...
April 19, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28433665/advancing-the-science-of-myocardial-recovery-with-mechanical-circulatory-support-a-working-group-of-the-national-heart-lung-and-blood-institute
#15
Stavros G Drakos, Francis D Pagani, Martha S Lundberg, J Timothy Baldwin
The medical burden of heart failure (HF) has spurred interest in clinicians and scientists to develop therapies to restore the function of a failing heart. To advance this agenda, the National Heart Lung Blood Institute (NHLBI) convened a Working Group of experts on June 2-3, 2016 in Bethesda Maryland to develop recommendations for the NHLBI aimed at advancing the science of cardiac recovery in the setting of mechanical circulatory support (MCS). MSC devices effectively reduce volume and pressure overload that drives the cycle of progressive myocardial dysfunction, thereby triggering structural and functional reverse remodeling...
April 19, 2017: Journal of Cardiac Failure
https://www.readbyqxmd.com/read/28433662/iron-and-thiol-redox-signaling-in-cancer-an-exquisite-balance-to-escape-ferroptosis
#16
REVIEW
Shinya Toyokuni, Fumiya Ito, Kyoko Yamashita, Yasumasa Okazaki, Shinya Akatsuka
Epidemiological data indicate a constant worldwide increase in cancer mortality, although the age of onset is increasing. Recent accumulation of genomic data on human cancer via next-generation sequencing confirmed that cancer is a disease of genome alteration. In many cancers, the Nrf2 transcription system is activated via mutations either in Nrf2 or Keap1 ubiquitin ligase, leading to persistent activation of the genes with antioxidative functions. Furthermore, deep sequencing of passenger mutations is clarifying responsible cancer causative agent(s) in each case, including aging, APOBEC activation, smoking and UV...
April 19, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28433605/stability-of-patient-specific-features-of-altered-dna-replication-timing-in-xenografts-of-primary-human-acute-lymphoblastic-leukemia
#17
Takayo Sasaki, Juan Carlos Rivera-Mulia, Daniel Vera, Jared Zimmerman, Sunny Das, Michelle Padget, Naoto Nakamichi, Bill H Chang, Jeff Tyner, Brian J Druker, Andrew P Weng, Curt I Civin, Connie J Eaves, David M Gilbert
Genome-wide DNA replication timing (RT) profiles reflect the global 3D chromosome architecture of cells. They also provide a comprehensive and unique megabase-scale picture of the cellular epigenetic state. Thus normal differentiation involves reproducible changes in RT and transformation generally perturbs these, although the potential effects of altered RT on the properties of transformed cells remain largely unknown. A major challenge to interrogating these issues in human acute lymphoid leukemia (ALL) is the low proliferative activity of most of the cells, which may be further reduced in cryopreserved samples and difficult to overcome in vitro...
April 19, 2017: Experimental Hematology
https://www.readbyqxmd.com/read/28433562/characterization-of-the-complete-mitochondrial-genome-of-khawia-sinensis-belongs-among-platyhelminths-cestodes
#18
Yan Feng, Han-Li Feng, Yi-Hui Fang, Ying-Bing Su
Khawia sinensis is an important species in freshwater fish causing considerable economic losses to the breeding industry. This is the first mt genome of a caryophyllidean cestode characterised. The entire mt genome of K. sinensis is 13,759 bp in length. This mt genome contains 12 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and two non-coding regions. The arrangement of the K. sinensis mt genome is the same as other tapeworms, however, the incomplete stop codon (A) is more frequent that other species...
April 19, 2017: Experimental Parasitology
https://www.readbyqxmd.com/read/28433553/identification-and-validation-of-micrornas-directly-regulating-the-udp-glucuronosyltransferase-1a-subfamily-enzymes-by-a-functional-genomics-approach
#19
Ioannis Papageorgiou, Michael H Court
Posttranscriptional repression of UDP-glucuronosyltransferase (UGT) 1A expression by microRNAs (miRNAs) may be an important mechanism underlying interindividual variability in drug glucuronidation. Furthermore, the UGT1A 3'-UTR shared by all UGT1A enzymes is polymorphic, containing three linked SNPs (rs10929303, rs1042640, and rs8330) that could influence miRNA binding. The aim of this study was to identify the complete complement of miRNAs that could regulate UGT1A expression through binding to the reference and/or common variant UGT1A 3'-UTR...
April 19, 2017: Biochemical Pharmacology
https://www.readbyqxmd.com/read/28433529/antimicrobial-peptides-within-the-yellowtail-kingfish-seriola-lalandi
#20
Simon Muncaster, Kirsty Kraakman, Olivia Gibbons, Koen Mensink, Maria Forlenza, Gregory Jacobson, Steve Bird
A number of Seriola species are currently farmed or being investigated as future aquaculture species in countries around the world. However they face a number of issues and limitations which will need to be overcome to ensure future stability and growth, one of which are disease outbreaks. Despite this, very little has been done to understand the immune system of Seriola species and very few immune genes have been characterised. Antimicrobial peptides (AMP) are naturally occurring low molecular weight polypeptides that play a major role in an organism's immune system and act effectively as a first line of defence...
April 19, 2017: Developmental and Comparative Immunology
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