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https://www.readbyqxmd.com/read/29036990/-drug-resistance-and-dissemination-of-new-delhi-metallo-%C3%AE-lactamase-1-positive-bacteria-in-a-patient
#1
X F Zhao, M Yuan, X Chen, X F Liu, D S Yu, J Li
Objective: The aim of this work was to report the surveillance and dissemination of NDM-1 positive bacteria in a patient and ward environment. Methods: In 2010, during the therapy for a 51 years old patient, clinical and environmental samples were collected for carbapenem resistant bacterial culture, according to the clinical microbiological examination. Strains identification and antibiotic susceptibility were tested by VITEK Compact 2 system and E-test. The bla(NDM-1) was detected by PCR and analyzed by sequencing...
October 6, 2017: Zhonghua Yu Fang Yi Xue za Zhi [Chinese Journal of Preventive Medicine]
https://www.readbyqxmd.com/read/29036938/reactive-oxygen-species-and-nox-enzymes-are-emerging-as-key-players-in-cutaneous-wound-repair
#2
REVIEW
Dominik André-Lévigne, Ali Modarressi, Michael S Pepper, Brigitte Pittet-Cuénod
Our understanding of the role of oxygen in cell physiology has evolved from its long-recognized importance as an essential factor in oxidative metabolism to its recognition as an important player in cell signaling. With regard to the latter, oxygen is needed for the generation of reactive oxygen species (ROS), which regulate a number of different cellular functions including differentiation, proliferation, apoptosis, migration, and contraction. Data specifically concerning the role of ROS-dependent signaling in cutaneous wound repair are very limited, especially regarding wound contraction...
October 15, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29036923/environmental-impact-and-relative-invasiveness-of-free-roaming-domestic-carnivores-a-north-american-survey-of-governmental-agencies
#3
Ana Lepe, Valerie Kaplan, Alirio Arreaza, Robert Szpanderfer, David Bristol, M Scott Sinclair
A survey of the United States and Canadian governmental agencies investigated the environmental impact and relative invasiveness of free-roaming domestic non-native carnivores-dogs, cats, and ferrets. Agencies represented wildlife, fish, game, natural or environmental resources, parks and recreation, veterinary and human health, animal control, and agriculture. Respondents were asked to document the number and frequency of sightings of unconfined animals, evidence for environmental harm, and the resulting "degree of concern" in their respective jurisdictions...
October 14, 2017: Animals: An Open Access Journal From MDPI
https://www.readbyqxmd.com/read/29036705/chalcogenozidovudine-derivatives-with-antitumor-activity-comparative-toxicities-in-cultured-human-mononuclear-cells
#4
Assis Ecker, Pauline Christ Ledur, Rafael S da Silva, Daniela Bitencourt Rosa Leal, Oscar E D Rodrigues, Daniel Ardisson-Araújo, Emily Pansera Waczuk, João Batista Teixeira da Rocha, Nilda Vargas Barbosa
Considering a novel series of zidovudine (AZT) derivatives encompassing selenoaryl moieties promising candidates as therapeutics, we examined the toxicities elicited by AZT and derivatives 5'-(4-Chlorophenylseleno)zidovudine (SZ1); 5'-(Phenylseleno)zidovudine (SZ2); and 5'-(4-Methylphenylseleno)zidovudine (SZ3) in healthy cells and in mice. Resting and stimulated cultured human peripheral blood mononuclear cells (PBMCs) were treated with the compounds at concentrations ranging from 10 to 200 µM for 24 and/or 72 h...
July 28, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/29036698/chromosomal-context-affects-the-molecular-evolution-of-sex-linked-genes-and-their-autosomal-counterparts-in-turtles-and-other-vertebrates
#5
Srihari Radhakrishnan, Nicole Valenzuela
Sex chromosomes evolve differently from autosomes because natural selection acts distinctly on them given their reduced recombination and smaller population size. Various studies of sex-linked genes compared to different autosomal genes within species support these predictions. Instead, here we take a novel alternative approach comparing the rate of evolution between subsets of genes that are sex-linked in selected reptiles/vertebrates and the same genes located in autosomes in other amniotes. We report for the first time the faster evolution of Z-linked genes in a turtle (the Chinese soft-shell turtle Pelodiscus sinensis) relative to autosomal orthologs in other taxa, including turtles with temperature-dependent sex determination (TSD)...
September 27, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29036693/icg-a-wiki-driven-knowledgebase-of-internal-control-genes-for-rt-qpcr-normalization
#6
Jian Sang, Zhennan Wang, Man Li, Jiabao Cao, Guangyi Niu, Lin Xia, Dong Zou, Fan Wang, Xingjian Xu, Xiaojiao Han, Jinqi Fan, Ye Yang, Wanzhu Zuo, Yang Zhang, Wenming Zhao, Yiming Bao, Jingfa Xiao, Songnian Hu, Lili Hao, Zhang Zhang
Real-time quantitative PCR (RT-qPCR) has become a widely used method for accurate expression profiling of targeted mRNA and ncRNA. Selection of appropriate internal control genes for RT-qPCR normalization is an elementary prerequisite for reliable expression measurement. Here, we present ICG (http://icg.big.ac.cn), a wiki-driven knowledgebase for community curation of experimentally validated internal control genes as well as their associated experimental conditions. Unlike extant related databases that focus on qPCR primers in model organisms (mainly human and mouse), ICG features harnessing collective intelligence in community integration of internal control genes for a variety of species...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036691/nuclear-localized-c9orf72-associated-arginine-containing-dipeptides-exhibit-age-dependent-toxicity-in-c-elegans
#7
Paige Rudich, Carley Snoznik, Simon C Watkins, John Monaghan, Udai Bhan Pandey, Todd Lamitina
A hexanucleotide repeat expansion mutation in the C9orf72 gene represents a prevalent genetic cause of several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Non-canonical translation of this repeat gives rise to several distinct dipeptide protein species that could play pathological roles in disease. Here, we show in the model system C. elegans that expression of the arginine-containing dipeptides, but not alanine-containing dipeptides, produces toxic phenotypes in multiple cellular contexts, including motor neurons...
September 27, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/29036681/intra-specific-trends-of-lumen-and-wall-resistivities-of-vessels-within-the-stem-xylem-vary-among-three-woody-plants
#8
Hiroki Ooeda, Ichiro Terashima, Haruhiko Taneda
Water flow through xylem vessels encounters hydraulic resistance when passing through the vessel lumen and end wall. Comparative studies have reported that lumen and end wall resistivities co-limit water flow through stem xylem in several angiosperm woody species that have vessels of different average diameter and length. This study examined the intra-specific relationship between the lumen and end wall resistivities (Rlumen and Rwall) for vessels within the stem xylem using three deciduous angiosperm woody species found in temperate forest...
September 23, 2017: Tree Physiology
https://www.readbyqxmd.com/read/29036674/detecting-and-characterizing-micrornas-of-diverse-genomic-origins-via-mirvial
#9
Jing Xia, Lun Li, Tiantian Li, Zhiwei Fang, Kevin Zhang, Junfei Zhou, Hai Peng, Weixiong Zhang
MicroRNAs form an essential class of post-transcriptional gene regulator of eukaryotic species, and play critical parts in development and disease and stress responses. MicroRNAs may originate from various genomic loci, have structural characteristics, and appear in canonical or modified forms, making them subtle to detect and analyze. We present miRvial, a robust computational method and companion software package that supports parameter adjustment and visual inspection of candidate microRNAs. Extensive results comparing miRvial and six existing microRNA finding methods on six model organisms, Mus musculus, Drosophila melanogaste, Arabidopsis thaliana, Oryza sativa, Physcomitrella patens and Chlamydomonas reinhardtii, demonstrated the utility and rigor of miRvial in detecting novel microRNAs and characterizing features of microRNAs...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036648/coarse-roots-prevent-declines-in-whole-tree-non-structural-carbohydrate-pools-during-drought-in-an-isohydric-and-an-anisohydric-species
#10
Steven A Kannenberg, Kimberly A Novick, Richard P Phillips
Predicted increases in the frequency and severity of droughts have led to a renewed focus on how plants physiologically adjust to low water availability. A popular framework for understanding plant responses to drought characterizes species along a spectrum from isohydry to anisohydry based on their regulation of gas exchange and leaf water potential under drying conditions. One prediction that arises from this theory is that plant drought responses may hinge, in part, on their usage of non-structural carbohydrate (NSC) pools...
September 26, 2017: Tree Physiology
https://www.readbyqxmd.com/read/29036646/de-novo-deleterious-sequence-variants-that-alter-the-transcriptional-activity-of-the-homeoprotein-pbx1-are-associated-with-intellectual-disability-and-pleiotropic-developmental-defects
#11
Anne Slavotinek, Maurizio Risolino, Marta Losa, Megan T Cho, Kristin G Monaghan, Dina Schneidman-Duhovny, Sarah Parisotto, Johanna C Herkert, Alexander P A Stegmann, Kathryn Miller, Natasha Shur, Jacqueline Chui, Eric Muller, Suzanne DeBrosse, Justin O Szot, Gavin Chapman, Nicholas S Pachter, David S Winlaw, Bryce A Mendelsohn, Joline Dalton, Kyriakie Sarafoglou, Peter I Karachunski, Jane M Lewis, Helio Pedro, Sally L Dunwoodie, Licia Selleri, Joseph Shieh
We present eight patients with de novo, deleterious sequence variants in the PBX1 gene. PBX1 encodes a three amino acid loop extension (TALE) homeodomain transcription factor that forms multimeric complexes with TALE and HOX proteins to regulate target gene transcription during development. As previously reported, Pbx1 homozygous mutant mice (Pbx1-/-) develop malformations and hypoplasia or aplasia of multiple organs, including the craniofacial skeleton, ear, branchial arches, heart, lungs, diaphragm, gut, kidneys, and gonads...
September 22, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/29036599/carbon-allocation-and-partitioning-in-populus-tremuloides-are-modulated-by-ectomycorrhizal-fungi-under-phosphorus-limitation
#12
Shalaka Shinde, Dhiraj Naik, Jonathan R Cumming
The fate of carbon (C) captured by forest trees during photosynthesis is influenced by the supply of other resources. Fixed C may be partitioned among biomolecules within the leaf and/or allocated throughout the tree to growth, storage and maintenance activities. Phosphorus (P) availability often limits tree productivity due to its high biological demand and strong interactions with soil minerals. As ectomycorrhizal (ECM) fungi play critical roles in enhancing phosphate (Pi) acquisition by their hosts, these symbioses will influence the fate of C within trees and forested ecosystems...
September 28, 2017: Tree Physiology
https://www.readbyqxmd.com/read/29036594/impaired-defense-reactions-in-apple-replant-disease-affected-roots-of-malus-domestica-m26
#13
Stefan Weiß, Benye Liu, Dennis Reckwell, Ludger Beerhues, Traud Winkelmann
A soil- and site-dependent complex of diverse microbial populations causes apple replant disease (ARD), which leads to economic losses for tree nurseries and apple producers due to reduced plant growth and diminished fruit yields. Soil fumigation has been widely used to mitigate ARD, but the application of these chemicals is restricted in the European Union. Hence, other counteractions have to be developed. Genomics-based breeding may be used to select ARD-tolerant genotypes; however, molecular responses of ARD are not well understood...
September 19, 2017: Tree Physiology
https://www.readbyqxmd.com/read/29036592/gain-and-loss-of-small-rna-classes-characterization-of-small-rnas-in-the-parasitic-nematode-family-strongyloididae
#14
Anja Holz, Adrian Streit
The nematode family Strongyloididae is of particular interest because it contains important parasites of medical and veterinary relevance. In addition, species of this family can form parasitic and free-living generations and it also occupies an interesting phylogenetic position within the nematodes. Nematodes differ in several ways from other taxa with respect to their small non-coding RNAs. Recent comparative studies revealed that there is also considerable variability within the nematodes. However, no Strongyloididae species or close relative was included in these studies...
September 25, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29036588/a-novel-data-structure-to-support-ultra-fast-taxonomic-classification-of-metagenomic-sequences-with-k-mer-signatures
#15
Xinan Liu, Ye Yu, Jinpeng Liu, Corrine F Elliott, Chen Qian, Jinze Liu
Motivation: Metagenomic read classification is a critical step in the identification and quantification of microbial species sampled by high-throughput sequencing. Although many algorithms have been developed to date, they suffer significant memory and/or computational costs. Due to the growing popularity of metagenomic data in both basic science and clinical applications, as well as the increasing volume of data being generated, efficient and accurate algorithms are in high demand. Results: We introduce MetaOthello, a probabilistic hashing classifier for metagenomic sequencing reads...
July 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036576/currbs-simple-and-robust-evaluation-of-enzyme-combinations-for-reduced-representation-approaches
#16
Daniel E Martin-Herranz, António J M Ribeiro, Felix Krueger, Janet M Thornton, Wolf Reik, Thomas M Stubbs
DNA methylation is an important epigenetic modification in many species that is critical for development, and implicated in ageing and many complex diseases, such as cancer. Many cost-effective genome-wide analyses of DNA modifications rely on restriction enzymes capable of digesting genomic DNA at defined sequence motifs. There are hundreds of restriction enzyme families but few are used to date, because no tool is available for the systematic evaluation of restriction enzyme combinations that can enrich for certain sites of interest in a genome...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036566/the-role-of-alternative-splicing-and-differential-gene-expression-in-cichlid-adaptive-radiation
#17
Pooja Singh, Christine Börger, Heather More, Christian Sturmbauer
Species diverge eco-morphologically through the continuous action of natural selection on functionally important structures, producing alternative adaptive morphologies. In cichlid fishes, the oral and pharyngeal jaws are such key structures. Adaptive variation in jaw morphology contributes to trophic specialisation, which is hypothesised to fuel their rapid speciation in the East African Great Lakes. Much is known about the genes involved in cichlid jaw and craniofacial development. However, it is still unclear what salient sources of variation gave rise to trophic-niche specialisation, facilitating adaptive radiation...
September 27, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29036529/itsonedb-a-comprehensive-collection-of-eukaryotic-ribosomal-rna-internal-transcribed-spacer-1-its1-sequences
#18
Monica Santamaria, Bruno Fosso, Flavio Licciulli, Bachir Balech, Ilaria Larini, Giorgio Grillo, Giorgio De Caro, Sabino Liuni, Graziano Pesole
A holistic understanding of environmental communities is the new challenge of metagenomics. Accordingly, the amplicon-based or metabarcoding approach, largely applied to investigate bacterial microbiomes, is moving to the eukaryotic world too. Indeed, the analysis of metabarcoding data may provide a comprehensive assessment of both bacterial and eukaryotic composition in a variety of environments, including human body. In this respect, whereas hypervariable regions of the 16S rRNA are the de facto standard barcode for bacteria, the Internal Transcribed Spacer 1 (ITS1) of ribosomal RNA gene cluster has shown a high potential in discriminating eukaryotes at deep taxonomic levels...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036515/the-jasmonate-zim-domain-gene-family-mediates-ja-signaling-and-stress-response-in-cotton
#19
Heng Sun, Lin Chen, Jianying Li, Meiling Hu, Abid Ullah, Xin He, Xiyan Yang, Xianlong Zhang
JASMONATE ZIM-domain (JAZ) family proteins are involved in regulating diverse biological processes in plants. However, their functions have not been well characterized in cotton (Gossypium spp.). In the present study, 13, 15, 25, and 30 JAZ genes were identified in Gossypium arboretum, Gossypium raimondii, Gossypium barbadense and Gossypium hirsutum respectively, based on gene homology. Selection and variation analyses showed that the SNP density of GhJAZ genes in wild species was much higher than that in domesticated species...
October 3, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29036466/insights-into-epigenome-evolution-from-animal-and-plant-methylomes
#20
Soojin V Yi
Evolutionary studies of DNA methylation begin to provide insights into the underlying forces governing the variation of genomic DNA methylation across different species. Comparisons of gross levels of DNA methylation between distantly related species indicate that the size of the genome and the level of genomic DNA methylation are positively correlated. In plant genomes, this can be reliably explained by the contents of repetitive sequences, while the underlying driver of this correlation is less clear in animal genomes...
September 25, 2017: Genome Biology and Evolution
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