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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
#1
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/28434148/advancing-chimeric-antigen-receptor-t-cell-therapy-with-crispr-cas9
#2
REVIEW
Jiangtao Ren, Yangbing Zhao
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (CRISPR/Cas9) system, an RNA-guided DNA targeting technology, is triggering a revolution in the field of biology. CRISPR/Cas9 has demonstrated great potential for genetic manipulation. In this review, we discuss the current development of CRISPR/Cas9 technologies for therapeutic applications, especially chimeric antigen receptor (CAR) T cell-based adoptive immunotherapy. Different methods used to facilitate efficient CRISPR delivery and gene editing in T cells are compared...
April 22, 2017: Protein & Cell
https://www.readbyqxmd.com/read/28433796/genetic-diversity-and-virulence-genes-of-salmonella-enterica-subspecies-enterica-serotype-enteritidis-isolated-from-meats-and-eggs
#3
Fatemeh Fardsanei, Mohammad Mehdi Soltan Dallal, Masoumeh Douraghi, Taghi Zahraei Salehi, Mahmood Mahmoodi, Hamed Memariani, Farhad Nikkhahi
Salmonella enterica subspecies enterica serotype Enteritidis (S. Enteritidis) is one of the leading causes of food-borne gastroenteritis associated with the consumption of contaminated food products of animal origin. Little is known about the genetic diversity and virulence content of S. Enteritidis isolated from poultry meats and eggs in Iran. A total of 34 S. Enteritidis strains were collected from different food sources of animal origin in Tehran from May 2015 to July 2016. All of the S. Enteritidis strains were serotyped, antimicrobial susceptibility tested, and characterized for virulence genes...
April 19, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28433772/mesenchymal-stem-cells-induce-epithelial-to-mesenchymal-transition-in-colon-cancer-cells-through-direct-cell-to-cell-contact
#4
Hidehiko Takigawa, Yasuhiko Kitadai, Kei Shinagawa, Ryo Yuge, Yukihito Higashi, Shinji Tanaka, Wataru Yasui, Kazuaki Chayama
We previously reported that in an orthotopic nude mouse model of human colon cancer, bone marrow-derived mesenchymal stem cells (MSCs) migrated to the tumor stroma and promoted tumor growth and metastasis. Here, we evaluated the proliferation and migration ability of cancer cells cocultured with MSCs to elucidate the mechanism of interaction between cancer cells and MSCs. Proliferation and migration of cancer cells increased following direct coculture with MSCs but not following indirect coculture. Thus, we hypothesized that direct contact between cancer cells and MSCs was important...
April 20, 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/28433662/iron-and-thiol-redox-signaling-in-cancer-an-exquisite-balance-to-escape-ferroptosis
#5
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/28433422/postnatal-choline-supplementation-selectively-attenuates-hippocampal-microrna-alterations-associated-with-developmental-alcohol-exposure
#6
Sridevi Balaraman, Nirelia M Idrus, Rajesh C Miranda, Jennifer D Thomas
Prenatal alcohol exposure can result in a range of physical, neuropathological, and behavioral alterations, collectively termed fetal alcohol spectrum disorders (FASD). We have shown that supplementation with the nutrient choline reduces the severity of developmental alcohol-associated deficits in hippocampal-dependent behaviors and normalizes some aspects of hippocampal cholinergic development and DNA methylation patterns. Alcohol's developmental effects may also be mediated, in part, by altering microRNAs (miRNAs) that serve as negative regulators of gene translation...
January 3, 2017: Alcohol
https://www.readbyqxmd.com/read/28433382/applications-of-the-crispr-cas9-system-in-kidney-research
#7
REVIEW
Yoshiki Higashijima, Seiichi Hirano, Masaomi Nangaku, Osamu Nureki
The recently discovered clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated protein 9 (Cas9) is an RNA-guided DNA nuclease, and has been harnessed for the development of simple, efficient, and relatively inexpensive technologies to precisely manipulate the genomic information in virtually all cell types and organisms. The CRIPSR-Cas9 systems have already been effectively used to disrupt multiple genes simultaneously, create conditional alleles, and generate reporter proteins, even in vivo...
April 19, 2017: Kidney International
https://www.readbyqxmd.com/read/28432783/gene-structure-and-expression-characteristic-of-a-novel-odorant-receptor-gene-cluster-in-the-parasitoid-wasp-microplitis-mediator-hymenoptera-braconidae
#8
S-N Wang, S Shan, Y Zheng, Y Peng, Z-Y Lu, Y-Q Yang, R-J Li, Y-J Zhang, Y-Y Guo
Odorant receptors (ORs) expressed in the antennae of parasitoid wasps are responsible for detection of various lipophilic airborne molecules. In the present study, 107 novel OR genes were identified from Microplitis mediator antennal transcriptome data. Phylogenetic analysis of the set of OR genes from M. mediator and Microplitis demolitor revealed that M. mediator OR (MmedOR) genes can be classified into different subfamilies, and the majority of MmedORs in each subfamily shared high sequence identities and clear orthologous relationships to M...
April 22, 2017: Insect Molecular Biology
https://www.readbyqxmd.com/read/28432622/diversity-shift-in-bacterial-phenol-hydroxylases-driven-by-alkyl-phenols-in-oil-refinery-wastewaters
#9
Besma Harzallah, Hacène Bousseboua, Yves Jouanneau
Phenol hydroxylases (PHs) play a primary role in the bacterial degradation of phenol and alkylphenols. They are divided into two main classes, single-component and multi-component PHs, having distinctive catalytic subunits designated as PheA1 and LmPH, respectively. The diversity of these enzymes is still largely unexplored. Here, both LmPH and pheA1 gene sequences were examined in activated sludge from oil refinery wastewaters. Phenol, p-cresol, or 3,4-dimethylphenol (3,4-DMP) supplied as extra carbon sources were rapidly mineralized by the microbial community...
April 21, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28432562/increased-expression-of-the-microrna-106b-25-cluster-and-its-host-gene-mcm7-in-corticotroph-pituitary-adenomas-is-associated-with-tumor-invasion-and-crooke-s-cell-morphology
#10
Filip Garbicz, Dawid Mehlich, Beata Rak, Emir Sajjad, Maria Maksymowicz, Wiktor Paskal, Grzegorz Zieliński, Paweł K Włodarski
PURPOSE: MCM7 (minichromosome maintenance complex component 7), a DNA replication licensing factor, is a host gene for the oncogenic miR-106b~25 cluster. It has been recently revealed as a relevant prognostic biomarker in a variety of cancers, including pituitary adenomas. The purpose of this study was to assess whether miR-106b~25 and MCM7 levels correlate with tumor invasiveness in a cohort of ACTH-immunopositive adenomas. METHODS: Tissue samples were obtained intraoperatively from 25 patients with pituitary adenoma...
April 21, 2017: Pituitary
https://www.readbyqxmd.com/read/28432308/network-aided-bi-clustering-for-discovering-cancer-subtypes
#11
Guoxian Yu, Xianxue Yu, Jun Wang
Bi-clustering is a widely used data mining technique for analyzing gene expression data. It simultaneously groups genes and samples of an input gene expression data matrix to discover bi-clusters that relevant samples exhibit similar gene expression profiles over a subset of genes. The discovered bi-clusters bring insights for categorization of cancer subtypes, gene treatments and others. Most existing bi-clustering approaches can only enumerate bi-clusters with constant values. Gene interaction networks can help to understand the pattern of cancer subtypes, but they are rarely integrated with gene expression data for exploring cancer subtypes...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28432142/structural-similarities-between-neuregulin-1-3-isoforms-determine-their-subcellular-distribution-and-signaling-mode-in-central-neurons
#12
Detlef Vullhorst, Tanveer Ahmad, Irina Karavanova, Carolyn Keating, Andres Buonanno
The Neuregulin (NRG) family of ErbB ligands is comprised of numerous variants originating from the use of different genes, alternative promoters and splice variants. NRGs have generally been thought to be transported to axons and presynaptic terminals where they signal via ErbB3/4 receptors in paracrine or juxtacrine mode. However, we recently demonstrated that unprocessed pro-NRG2 accumulates on cell bodies and proximal dendrites, and that NMDAR activity is required for shedding of its ectodomain by metalloproteinases...
April 21, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28432094/the-use-of-synthetic-hybrid-strains-to-determine-the-role-of-replicon-3-in-virulence-of-the-burkholderia-cepacia-complex
#13
Kirsty Agnoli, Roman Freitag, Margarida C Gomes, Christian Jenul, Angela Suppiger, Olga Mannweiler, Carmen Frauenknecht, Daniel Janser, Annette C Vergunst, Leo Eberl
The Burkholderia cepacia complex (Bcc) displays a wealth of metabolic diversity with great biotechnological potential, but the utilisation of these bacteria is limited by their opportunistic pathogenicity to humans. The third replicon of the Bcc, megaplasmid pC3 (0.5 to 1.4 Mb, previously chromosome 3), is important for various phenotypes, including virulence, antifungal and proteolytic activities, and the utilization of certain substrates. Approximately half of plasmid pC3 is well-conserved throughout sequenced Bcc members, while the other half is not...
April 21, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28431974/unique-mitochondrial-localization-of-arginase-1-and-2-in-hepatocytes-of-air-breathing-walking-catfish-clarias-batrachus-and-their-differential-expression-patterns-under-hyper-ammonia-stress
#14
Bodhisattwa Banerjee, Debaprasad Koner, Priyanka Lal, Nirmalendu Saha
Arginase (ARG) catalyzes the final step of ornithine-urea cycle (OUC) leading to a conversion of L-arginine to L-ornithine and urea. Several isoforms of ARG have been reported in vertebrates, out of which the two predominant isoforms are the cytosolic ARG1 and the mitochondrial ARG2. The air-breathing walking catfish (Clarias batrachus) is frequently being challenged by different environmental insults such as hyper-ammonia, dehydration and osmotic stresses in their natural habitats throughout the year. The present study investigated the active presence of ARG1 and ARG2 isoforms in hepatocytes along with unique localization of both the isoforms inside the mitochondria, and also their specific expression patterns under hyper-ammonia stress (5mM NH4Cl) in isolated hepatocytes of walking catfish...
April 18, 2017: Gene
https://www.readbyqxmd.com/read/28431945/in-vitro-fermentation-behaviors-of-fucosylated-chondroitin-sulfate-from-pearsonothuria-graeffei-by-human-gut-microflora
#15
Chao-Yang Wei, Ning-Bo Liao, Yu Zhang, Xing-Qian Ye, Shan Li, Ya-Qin Hu, Dong-Hong Liu, Robert J Linhardt, Xin Wang, Shi-Guo Chen
A fucosylated chondroitin sulfate (FCS-pg) with highly repeated structure from Pearsonothuria graeffei was subjected to a in vitro fermentation model to investigate its fermentability and effects on human gut microflora. High performance liquid chromatography (HPLC) measurement found FCS-pg can be fermented to short chain fatty acids (SCFAs) by gut microflora from partial human fecal samples. 16S rRNA gene-based polymerase chain reaction-based denaturing gradient gel electrophoresis (PCR-DGGE) profiling and real-time quantitative PCR analysis showed that FCS-pg mainly increased the proportions of Clostridium cluster XI, Bacteriodes prevotella group, Bifidobacterium genus, Clostridium cluster I and Clostridium cluster XIVab, whereas the numbers of the Enterobacteriaceae and Lactobacillus decreased...
April 18, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28431529/hirbin-high-resolution-identification-of-differentially-abundant-functions-in-metagenomes
#16
Tobias Österlund, Viktor Jonsson, Erik Kristiansson
BACKGROUND: Gene-centric analysis of metagenomics data provides information about the biochemical functions present in a microbiome under a certain condition. The ability to identify significant differences in functions between metagenomes is dependent on accurate classification and quantification of the sequence reads (binning). However, biological effects acting on specific functions may be overlooked if the classes are too general. METHODS: Here we introduce High-Resolution Binning (HirBin), a new method for gene-centric analysis of metagenomes...
April 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28431213/genome-mining-unearths-a-hybrid-nonribosomal-peptide-synthetase-like-pteridine-synthase-biosynthetic-gene-cluster
#17
Hyun Bong Park, Corey E Perez, Karl W Barber, Jesse Rinehart, Jason M Crawford
Nonribosomal peptides represent a large class of metabolites with pharmaceutical relevance. Pteridines, such as pterins, folates, and flavins, are heterocyclic metabolites that often serve as redox-active cofactors. The biosynthetic machineries for construction of these distinct classes of small molecules operate independently in the cell. Here, we discovered an unprecedented nonribosomal peptide synthetase-like-pteridine synthase hybrid biosynthetic gene cluster in Photorhabdus luminescens using genome synteny analysis...
March 15, 2017: ELife
https://www.readbyqxmd.com/read/28430808/quantification-of-hypoxia-related-gene-expression-as-a-potential-approach-for-clinical-outcome-prediction-in-breast-cancer
#18
Abderrahim El Guerrab, Anne Cayre, Fabrice Kwiatkowski, Maud Privat, Jean-Marc Rossignol, Fabrice Rossignol, Frédérique Penault-Llorca, Yves-Jean Bignon
Breast cancers are solid tumors frequently characterized by regions with low oxygen concentrations. Cellular adaptations to hypoxia are mainly determined by "hypoxia inducible factors" that mediate transcriptional modifications involved in drug resistance and tumor progression leading to metastasis and relapse occurrence. In this study, we investigated the prognostic value of hypoxia-related gene expression in breast cancer. A systematic review was conducted to select a set of 45 genes involved in hypoxia signaling pathways and breast tumor progression...
2017: PloS One
https://www.readbyqxmd.com/read/28429995/new-insights-into-the-role-of-dietary-spermine-on-inflammation-immune-function-and-related-signalling-molecules-in-the-thymus-and-spleen-of-piglets
#19
Wei Cao, Xianjian Wu, Gang Jia, Hua Zhao, Xiaoling Chen, Caimei Wu, Jiayong Tang, Jing Wang, Jingyi Cai, Guangmang Liu
This study aimed to determine the effects of dietary spermine supplementation on the inflammatory response and immune function of the thymus and spleen in piglets. Eighty suckling piglets were randomly assigned to receive adequate nutrients supplemented with spermine (0.4 mmol/kg body weight) or restricted nutrient intake supplemented with normal saline for 7 h or 3, 6 and 9 days in pairs. Regardless of treatment time, spermine supplementation decreased (p < 0.05, compared with the controls) the following: (1) tumour necrosis factor α (TNF-α), interleukin (IL)-1β, 2 and 6, and interferon (IFN)-γ levels in serum; (2) gene expression of cluster of differentiation 8 and integrin beta-2 in the thymus and spleen and the lymphocyte function-associated antigen 1 in the thymus; (3) mRNA levels of TNF-α, IL 1β, 2, 6, and 12, IFN-γ and inducible nitric oxide synthase in the thymus and spleen, as well as IL-8 in the spleen; and (4) eukaryotic IF4E-binding protein 1, Janus kinase 2, signal transducer and activator of transcription 3, and nuclear factor-kappa B P65 gene transcriptions in the thymus and spleen...
June 2017: Archives of Animal Nutrition
https://www.readbyqxmd.com/read/28429739/a-large-scale-benchmark-of-gene-prioritization-methods
#20
Dimitri Guala, Erik L L Sonnhammer
In order to maximize the use of results from high-throughput experimental studies, e.g. GWAS, for identification and diagnostics of new disease-associated genes, it is important to have properly analyzed and benchmarked gene prioritization tools. While prospective benchmarks are underpowered to provide statistically significant results in their attempt to differentiate the performance of gene prioritization tools, a strategy for retrospective benchmarking has been missing, and new tools usually only provide internal validations...
April 21, 2017: Scientific Reports
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