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https://www.readbyqxmd.com/read/29334679/the-il20-genetic-polymorphism-is-associated-with-altered-clinical-outcome-in-septic-shock
#1
Taka-Aki Nakada, Petch Wacharasint, James A Russell, John H Boyd, Emiri Nakada, Simone A Thair, Tadanaga Shimada, Keith R Walley
BACKGROUND: The IL10 family of genes includes crucial immune regulators. We tested the hypothesis that single nucleotide polymorphisms (SNPs) in IL10, IL19, IL20, and IL24 of the IL10 family gene cluster alter the clinical outcome of septic shock. METHODS: Patients with septic shock (n = 1,193) were genotyped for 13 tag SNPs of IL10, IL19, IL20, and IL24. IL20 gene expression was measured in genotyped lymphoblastoid cells in vitro. Cardiac surgical ICU patients (n = 981) were genotyped for IL20 rs2981573 A/G...
January 16, 2018: Journal of Innate Immunity
https://www.readbyqxmd.com/read/29334376/positively-selected-enhancer-elements-endow-osteosarcoma-cells-with-metastatic-competence
#2
James J Morrow, Ian Bayles, Alister P W Funnell, Tyler E Miller, Alina Saiakhova, Michael M Lizardo, Cynthia F Bartels, Maaike Y Kapteijn, Stevephen Hung, Arnulfo Mendoza, Gursimran Dhillon, Daniel R Chee, Jay T Myers, Frederick Allen, Marco Gambarotti, Alberto Righi, Analisa DiFeo, Brian P Rubin, Alex Y Huang, Paul S Meltzer, Lee J Helman, Piero Picci, Henri Versteeg, John Stamatoyannopolus, Chand Khanna, Peter C Scacheri
Metastasis results from a complex set of traits acquired by tumor cells, distinct from those necessary for tumorigenesis. Here, we investigate the contribution of enhancer elements to the metastatic phenotype of osteosarcoma. Through epigenomic profiling, we identify substantial differences in enhancer activity between primary and metastatic human tumors and between near isogenic pairs of highly lung metastatic and nonmetastatic osteosarcoma cell lines. We term these regions metastatic variant enhancer loci (Met-VELs)...
January 15, 2018: Nature Medicine
https://www.readbyqxmd.com/read/29333753/comparative-performance-of-different-scale-down-simulators-of-substrate-gradients-in-penicillium-chrysogenum-cultures-the-need-of-a-biological-systems-response-analysis
#3
Guan Wang, Junfei Zhao, Cees Haringa, Wenjun Tang, Jianye Xia, Ju Chu, Yingping Zhuang, Siliang Zhang, Amit T Deshmukh, Walter van Gulik, Joseph J Heijnen, Henk J Noorman
In a 54 m3 large-scale penicillin fermentor, the cells experience substrate gradient cycles at the timescales of global mixing time about 20-40 s. Here, we used an intermittent feeding regime (IFR) and a two-compartment reactor (TCR) to mimic these substrate gradients at laboratory-scale continuous cultures. The IFR was applied to simulate substrate dynamics experienced by the cells at full scale at timescales of tens of seconds to minutes (30 s, 3 min and 6 min), while the TCR was designed to simulate substrate gradients at an applied mean residence time (τc) of 6 min...
January 15, 2018: Microbial Biotechnology
https://www.readbyqxmd.com/read/29333087/antioxydation-and-cell-migration-genes-are-identified-as-potential-therapeutic-targets-in-basal-like-and-brca1-mutated-breast-cancer-cell-lines
#4
Maud Privat, Justine Rudewicz, Nicolas Sonnier, Christelle Tamisier, Flora Ponelle-Chachuat, Yves-Jean Bignon
Basal-like breast cancers are among the most aggressive cancers and effective targeted therapies are still missing. In order to identify new therapeutic targets, we performed Methyl-Seq and RNA-Seq of 10 breast cancer cell lines with different phenotypes. We confirmed that breast cancer subtypes cluster the RNA-Seq data but not the Methyl-Seq data. Basal-like tumor hypermethylated phenotype was not confirmed in our study but RNA-Seq analysis allowed to identify 77 genes significantly overexpressed in basal-like breast cancer cell lines...
2018: International Journal of Medical Sciences
https://www.readbyqxmd.com/read/29332168/efficient-crispr-cas9-based-genome-editing-in-carrot-cells
#5
Magdalena Klimek-Chodacka, Tomasz Oleszkiewicz, Levi G Lowder, Yiping Qi, Rafal Baranski
The first report presenting successful and efficient carrot genome editing using CRISPR/Cas9 system. Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated (Cas9) is a powerful genome editing tool that has been widely adopted in model organisms recently, but has not been used in carrot-a model species for in vitro culture studies and an important health-promoting crop grown worldwide. In this study, for the first time, we report application of the CRISPR/Cas9 system for efficient targeted mutagenesis of the carrot genome...
January 13, 2018: Plant Cell Reports
https://www.readbyqxmd.com/read/29331522/nanos3-not-nanos1-and-nanos2-is-a-germ-cell-marker-gene-in-large-yellow-croaker-during-embryogenesis
#6
Kunhuang Han, Shihai Chen, Mingyi Cai, Yonghua Jiang, Ziping Zhang, Yilei Wang
In this study, three nanos gene subtypes (Lcnanos1, Lcnanos2 and Lcnanos3) from Larimichthys crocea, were cloned and characterized. We determined the spatio-temporal expression patterns of each subtype in tissues as well as the cellular localization of mRNA in embryos. Results showed that deduced Nanos proteins have two main homology domains: N-terminal CCR4/NOT1 deadenylase interaction domain and highly conserved carboxy-terminal region bearing two conserved CCHC zinc-finger motifs. The expression levels of Lcnanos1 in testis were significantly higher than other tissues, followed by heart, brain, eye, and ovary...
January 10, 2018: Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology
https://www.readbyqxmd.com/read/29331085/verification-of-dna-motifs-in-arabidopsis-using-crispr-cas9-mediated-mutagenesis
#7
Chenlong Li, Chen Chen, Huhui Chen, Suikang Wang, Xuemei Chen, Yuhai Cui
Transcription factors (TFs) and chromatin-modifying factors (CMFs) access chromatin by recognizing specific DNA motifs in their target genes. Chromatin Immunoprecipitation followed by next generation sequencing (ChIP-seq) has been widely used to discover the potential DNA binding motifs for both TFs and CMFs. Yet, an in vivo method for verifying DNA motifs captured by ChIP-seq is lacking in plants. Here, we describe the use of clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated 9 (Cas9) to verify DNA motifs in their native genomic context in Arabidopsis...
January 13, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29331077/optimized-paired-sgrna-cas9-cloning-and-expression-cassette-triggers-high-efficiency-multiplex-genome-editing-in-kiwifruit
#8
Zupeng Wang, Shuaibin Wang, Dawei Li, Qiong Zhang, Li Li, Caihong Zhong, Yifei Liu, Hongwen Huang
Kiwifruit is an important fruit crop; however, technologies for its functional genomic and molecular improvement are limited. The clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system has been successfully applied to genetic improvement in many crops, but its editing capability is variable depending on the different combinations of the synthetic guide RNA (sgRNA) and Cas9 protein expression devices. Optimizing conditions for its use within a particular species is therefore needed to achieve highly efficient genome editing...
January 13, 2018: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29330722/location-of-low-copy-genes-in-chromosomes-of-brachiaria-spp
#9
Thaís Furtado Nani, James C Schnable, Jacob D Washburn, Patrice Albert, Welison Andrade Pereira, Fausto Souza Sobrinho, James A Birchler, Vânia Helena Techio
Repetitive DNA sequences have been widely used in cytogenetic analyses. The use of gene sequences with a low-copy-number, however, is little explored especially in plants. To date, the karyotype details in Brachiaria spp. are limited to the location of rDNA sites. The challenge lies in developing new probes based on incomplete sequencing data for the genus or complete sequencing of related species, since there are no model species with a sequenced genome in Brachiaria spp. The present study aimed at the physical location of conserved genes in chromosomes of Brachiaria ruziziensis, Brachiaria brizantha, and Brachiaria decumbens using RNAseq data, as well as sequences of Setaria italica and Sorghum bicolor through the fluorescent in situ hybridization technique...
January 12, 2018: Molecular Biology Reports
https://www.readbyqxmd.com/read/29330647/absence-of-the-nitrous-oxide-reductase-gene-cluster-in-commercial-alfalfa-inoculants-is-probably-due-to-the-extensive-loss-of-genes-during-rhizobial-domestication
#10
Silvina Brambilla, Romina Frare, Gabriela Soto, Cintia Jozefkowicz, Nicolás Ayub
As other legume crops, alfalfa cultivation increases the emission of the greenhouse gas nitrous oxide (N2O). Since legume-symbiotic nitrogen-fixing bacteria play a crucial role in this emission, it is important to understand the possible impacts of rhizobial domestication on the evolution of denitrification genes. In comparison with the genomes of non-commercial strains, those of commercial alfalfa inoculants exhibit low total genome size, low number of ORFs and high numbers of both frameshifted genes and pseudogenes, suggesting a dramatic loss of genes during bacterial domestication...
January 12, 2018: Microbial Ecology
https://www.readbyqxmd.com/read/29330624/functional-transcriptomic-annotation-and-protein-protein-interaction-network-analysis-identify-nek2-birc5-and-top2a-as-potential-targets-in-obese-patients-with-luminal-a-breast-cancer
#11
Miriam Nuncia-Cantarero, Sandra Martinez-Canales, Fernando Andrés-Pretel, Gabriel Santpere, Alberto Ocaña, Eva Maria Galan-Moya
PURPOSE: Although obesity is a risk factor for breast cancer, little effort has been made in the identification of druggable molecular alterations in obese-breast cancer patients. Tumors are controlled by their surrounding microenvironment, in which the adipose tissue is a main component. In this work, we intended to describe molecular alterations at a transcriptomic and protein-protein interaction (PPI) level between obese and non-obese patients. METHODS AND RESULTS: Gene expression data of 269 primary breast tumors were compared between normal-weight (BMI < 25, n = 130) and obese (IMC > 30, n = 139) patients...
January 12, 2018: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/29330484/single-cell-rna-sequencing-resolves-self-antigen-expression-during-mtec-development
#12
Ricardo J Miragaia, Xiuwei Zhang, Tomás Gomes, Valentine Svensson, Tomislav Ilicic, Johan Henriksson, Gozde Kar, Tapio Lönnberg
The crucial capability of T cells for discrimination between self and non-self peptides is based on negative selection of developing thymocytes by medullary thymic epithelial cells (mTECs). The mTECs purge autoreactive T cells by expression of cell-type specific genes referred to as tissue-restricted antigens (TRAs). Although the autoimmune regulator (AIRE) protein is known to promote the expression of a subset of TRAs, its mechanism of action is still not fully understood. The expression of TRAs that are not under the control of AIRE also needs further characterization...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330297/characterization-and-evidence-of-the-mir-888-cluster-as-a-novel-cancer-network-in-prostate
#13
Tsuyoshi Hasegawa, Garrison Glavich, Mary Pahuski, Aleena M Short, Oliver John Semmes, Lifang Yang, Vitold Galkin, Richard R Drake, Aurora Esquela-Kerscher
Prostate cancer afflicts 1 in 7 men and is the second leading cause of male cancer-related deaths in the United States. MicroRNAs (miRNAs), an extensive class of ~22 nucleotide non-coding RNAs, are often aberrantly expressed in tissues and fluids from prostate cancer patients but the mechanism of how specific miRNAs regulate prostate tumorigenesis and metastasis are poorly understood. Here, miR-888 was identified as a novel prostate factor that promotes proliferation and migration. miR-888 resides within a genomic cluster of 7 miRNA genes (mir-892c, mir-890, mir-888, mir-892a, mir-892b, mir-891b, mir-891a) on human chromosome Xq27...
January 12, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29330288/epigenetically-regulated-chromosome-14q32-mirna-cluster-induces-metastasis-and-predicts-poor-prognosis-in-lung-adenocarcinoma-patients
#14
Margarita Gonzalez-Vallinas, Manuel Rodriguez-Paredes, Marco Albrecht, Carsten Sticht, Damian Stichel, Julian Gutekunst, Adriana Pitea, Steffen Sass, Francisco J Sánchez-Rivera, Justo L Bermejo, Jennifer Schmitt, Carolina De La Torre, Arne Warth, Fabian Theis, Nikola Mueller, Norbert Gretz, Thomas Muley, Michael Meister, Darjus F Tschaharganeh, Peter Schirmacher, Franziska Matthäus, Kai Breuhahn
Most lung cancer deaths are related to metastases, which indicates the necessity of detecting and inhibiting tumor cell dissemination. Here, we aimed to identify microRNAs (miRNAs) involved in metastasis of lung adenocarcinoma as prognostic biomarkers and therapeutic targets. To that end, lymph node metastasis-associated miRNAs were identified in The Cancer Genome Atlas (TCGA) lung adenocarcinoma patient cohort (sequencing data; n=449) and subsequently validated by RT-qPCR in an independent clinical cohort (n=108)...
January 12, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29330189/targeted-synthesis-and-characterization-of-a-gene-cluster-encoding-nad-p-h-dependent-3%C3%AE-3%C3%AE-and-12%C3%AE-hydroxysteroid-dehydrogenases-from-eggerthella-cag-298-a-gut-metagenomic-sequence
#15
Sean M Mythen, Saravanan Devendran, Celia Méndez-García, Isaac Cann, Jason M Ridlon
Gut metagenomic sequences provide a rich source of microbial genes, the majority of which are annotated by homology or unknown. Genes and gene pathways that encode enzymes catalyzing biotransformation of host bile acids are important to identify in gut metagenomic sequences due to the importance of bile acids on gut microbiome structure and host physiology. Hydroxysteroid dehydrogenases (HSDH) are pyridine nucleotide-dependent enzymes with stereo-specificity and regio-specificity for bile acid and steroid hydroxyl groups...
January 12, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29330183/campylobacter-jejuni-colonization-in-the-crow-gut-involves-high-deletion-within-the-cytolethal-distending-toxin-gene-cluster
#16
Keya Sen, Jingrang Lu, Piyali Mukherjee, Tanner Berglund, Eunice Varughese, Asish K Mukhopadhyay
Campylobacter spp. are major causes of gastroenteritis worldwide. The virulence potential of Campylobacter shed in crow feces obtained from a roost area in Bothell, Washington, was studied and compared with isolates from other parts of Washington, and from a different crow spp., 7000 miles away, in Kolkata, India. Campylobacter was isolated from 61% and 69 % of the fecal samples obtained from Washington and Kolkata, respectively and were confirmed to be C. jejuni The cytolethal distending toxin (CDT) gene cluster from these isolates revealed a truncated sequence of about 1400 bp...
January 12, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29330178/development-of-an-efficient-genome-editing-tool-in-bacillus-licheniformis-using-crispr-cas9-nickase
#17
Kaifeng Li, Dongbo Cai, Zhangqian Wang, Zhili He, Shouwen Chen
Bacillus strains are important industrial bacteria that can produce various biochemical products. However, low transformation efficiencies and a lack of effective genome editing tools have hindered its widespread application. Recently, clustered regularly interspaced short palindromic repeat (CRISPR)/cas9 techniques have been utilized in many organisms as genome editing tools because of their high efficiency and easy manipulation. In this study, an efficient genome editing method was developed for Bacillus licheniformis using a CRISPR-Cas9 nickase integrated into the genome of B...
January 12, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29329927/systems-biomarkers-in-psoriasis-integrative-evaluation-of-computational-and-experimental-data-at-transcript-and-protein-levels
#18
Tuba Sevimoglu, Beste Turanli, Ceyhun Bereketoglu, Kazim Yalcin Arga, Ayse Serap Karadag
Psoriasis is a complex autoimmune disease with multiple genes and proteins being involved in its pathogenesis. Despite the efforts performed to understand mechanisms of psoriasis pathogenesis and to identify diagnostic and prognostic targets, disease-specific and effective biomarkers were still not available. This study is compiled regarding clinical validation of computationally proposed biomarkers at gene and protein expression levels through qRT-PCR and ELISA techniques using skin biopsies and blood plasma...
January 9, 2018: Gene
https://www.readbyqxmd.com/read/29329560/overexpression-of-the-double-homeodomain-protein-dux4c-interferes-with-myofibrillogenesis-and-induces-clustering-of-myonuclei
#19
Céline Vanderplanck, Alexandra Tassin, Eugénie Ansseau, Sébastien Charron, Armelle Wauters, Céline Lancelot, Kelly Vancutsem, Dalila Laoudj-Chenivesse, Alexandra Belayew, Frédérique Coppée
BACKGROUND: Facioscapulohumeral muscular dystrophy (FSHD) is associated with DNA hypomethylation at the 4q35 D4Z4 repeat array. Both the causal gene DUX4 and its homolog DUX4c are induced. DUX4c is immunodetected in every myonucleus of proliferative cells, while DUX4 is present in only 1/1000 of myonuclei where it initiates a gene deregulation cascade. FSHD primary myoblasts differentiate into either atrophic or disorganized myotubes. DUX4 expression induces atrophic myotubes and associated FSHD markers...
January 12, 2018: Skeletal Muscle
https://www.readbyqxmd.com/read/29329366/delineating-differential-regulatory-signatures-of-the-human-transcriptome-in-the-choriodecidua-and-myometrium-at-term-labor
#20
Sylvia Lui, Cyntia Duval, Farkhondeh Farrokhnia, Sylvie Girard, Lynda K Harris, Clare L Tower, Adam Stevens, Rebecca L Jones
Background: Preterm deliveries remain the leading cause of neonatal morbidity and mortality. Current therapies target only myometrial contractions and are largely ineffective. As labor involves multiple coordinated events across maternal and fetal tissues, identifying fundamental regulatory pathways of normal term labor is vital to understanding successful parturition and consequently labor pathologies. We aimed to identify transcriptomic signatures of human normal term labor of two tissues: in the fetal-facing choriodecidua and the maternal myometrium...
January 10, 2018: Biology of Reproduction
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