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https://www.readbyqxmd.com/read/29786967/developmental-chromatin-restriction-of-pro-growth-gene-networks-acts-as-an-epigenetic-barrier-to-axon-regeneration-in-cortical-neurons
#1
Ishwariya Venkatesh, Vatsal Mehra, Zimei Wang, Ben Califf, Murray G Blackmore
Axon regeneration in the central nervous system is prevented in part by a developmental decline in the intrinsic regenerative ability of maturing neurons. This loss of axon growth ability likely reflects widespread changes in gene expression, but the mechanisms that drive this shift remain unclear. Chromatin accessibility has emerged as a key regulatory mechanism in other cellular contexts, raising the possibility that chromatin structure may contribute to the age-dependent loss of regenerative potential. Here we establish an integrated bioinformatic pipeline that combines analysis of developmentally dynamic gene networks with transcription factor regulation and genome-wide maps of chromatin accessibility...
May 22, 2018: Developmental Neurobiology
https://www.readbyqxmd.com/read/29786918/novel-genes-and-insights-in-complete-asthma-remission
#2
Judith M Vonk, Maartje A E Nieuwenhuis, F Nicole Dijk, Anne Boudier, Valerie Siroux, Emmanuelle Bouzigon, Nicole Probst-Hensch, Medea Imboden, Dirk Keidel, Don Sin, Yohan Bossé, Ke Hao, Maarten van den Berge, Alen Faiz, Gerard H Koppelman, Dirkje S Postma
BACKGROUND: Asthma is a chronic respiratory disease without a cure, though there exists spontaneous remission. Genome wide association(GWA) studies have pinpointed genes associated with asthma development, but did not investigate asthma remission. OBJECTIVES: We performed a GWA study to develop insights in asthma remission. METHODS: Clinical remission (ClinR) was defined by absence of asthma treatment and wheezing in the last year and asthma attacks in the last 3 years, and complete remission (ComR) similarly but additionally with normal lung function and absence of bronchial hyperresponsiveness (BHR)...
May 22, 2018: Clinical and Experimental Allergy: Journal of the British Society for Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29786812/the-microrna-expression-profile-in-rat-lung-tissue-early-after-burn-injury
#3
Donghai Zhang, Yang Chang, Shaofang Han, Longlong Yang, Quan Hu, Yonghui Yu, Lingying Liu, Jiake Chai
BACKGROUND: Severe burn causes acute lung injury in many victims, but the related mechanisms have been barely investigated. microRNAs (miRNAs) important regulators in numerous physiological and pathophysiological process. However, the roles of miRNAs in burn lung injury are untested. METHODS: Six healthy male Sprague-Dawley rats were randomly assigned into burn and sham groups. Lung injury was evaluated by hematoxylin and eosin (HE) staining at 24 h after injury...
May 2018: Ulusal Travma Ve Acil Cerrahi Dergisi, Turkish Journal of Trauma & Emergency Surgery: TJTES
https://www.readbyqxmd.com/read/29786746/luteolin-induces-myelodysplastic-syndrome%C3%A2-derived-cell-apoptosis-via-the-p53%C3%A2-dependent-mitochondrial-signaling-pathway-mediated-by-reactive-oxygen-species
#4
Weimin Dong, Yan Lin, Yang Cao, Yue Liu, Xiaobao Xie, Weiying Gu
Luteolin, a common dietary flavonoid, induces the apoptosis of cells in several types of cancer. However, its role in myelodysplastic syndrome (MDS) and the potential underlying mechanisms remain to be elucidated. To evaluate the potential benefit and underlying mechanisms of luteolin in MDS cells, the viability of SKM‑1 cells and primary bone marrow (PBM) mononuclear cells from patients with intermediate‑ or high‑risk MDS were assessed using a Cell Counting Kit‑8 assay. The apoptotic features of cell morphology were assessed using Wright‑Giemsa staining, DNA fragmentation was analyzed by agarose gel electrophoresis, and the extent of apoptosis was quantified by flow cytometry (FCM)...
May 18, 2018: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29786687/genome-wide-analysis-of-circular-rnas-in-bovine-cumulus-cells-treated-with-bmp15-and-gdf9
#5
Yao Fu, Hao Jiang, Jian-Bo Liu, Xu-Lei Sun, Zhe Zhang, Sheng Li, Yan Gao, Bao Yuan, Jia-Bao Zhang
Circular RNAs (circRNAs) are important members of the non-coding RNA family, and those relating to animal physiologies have been widely studied in recent years. This study aimed to explore the roles of circRNAs in the regulation of follicular development. We constructed four bovine cumulus cell cDNA libraries, including a negative control group (NC) and groups treated with BMP15, GDF9 and BMP15 + GDF9, and we sequenced the libraries on the Illumina HiSeq Xten platform. We identified 1706 circRNAs and screened for differential circRNA expression...
May 21, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29786565/modelling-non-alcoholic-fatty-liver-disease-in-human-hepatocyte-like-cells
#6
Marcus J Lyall, Jessy Cartier, John P Thomson, Kate Cameron, Jose Meseguer-Ripolles, Eoghan O'Duibhir, Dagmara Szkolnicka, Baltasar Lucendo Villarin, Yu Wang, Giovanny Rodriguez Blanco, Warwick B Dunn, Richard R Meehan, David C Hay, Amanda J Drake
Non-alcoholic fatty liver disease (NAFLD) is the most common cause of liver disease in developed countries. An in vitro NAFLD model would permit mechanistic studies and enable high-throughput therapeutic screening. While hepatic cancer-derived cell lines are a convenient, renewable resource, their genomic, epigenomic and functional alterations mean their utility in NAFLD modelling is unclear. Additionally, the epigenetic mark 5-hydroxymethylcytosine (5hmC), a cell lineage identifier, is rapidly lost during cell culture, alongside expression of the Ten-eleven-translocation ( TET ) methylcytosine dioxygenase enzymes, restricting meaningful epigenetic analysis...
July 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29786556/assessment-of-stem-cell-differentiation-based-on-genome-wide-expression-profiles
#7
REVIEW
Patricio Godoy, Wolfgang Schmidt-Heck, Birte Hellwig, Patrick Nell, David Feuerborn, Jörg Rahnenführer, Kathrin Kattler, Jörn Walter, Nils Blüthgen, Jan G Hengstler
In recent years, protocols have been established to differentiate stem and precursor cells into more mature cell types. However, progress in this field has been hampered by difficulties to assess the differentiation status of stem cell-derived cells in an unbiased manner. Here, we present an analysis pipeline based on published data and methods to quantify the degree of differentiation and to identify transcriptional control factors explaining differences from the intended target cells or tissues. The pipeline requires RNA-Seq or gene array data of the stem cell starting population, derived 'mature' cells and primary target cells or tissue...
July 5, 2018: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
https://www.readbyqxmd.com/read/29786122/complete-genomic-sequence-of-a-novel-macluravirus-alpinia-oxyphylla-mosaic-virus-alomv-identified-in-alpinia-oxyphylla
#8
Weiyao Hu, Zengping Li, Xiaoye Wang, Wenbo Liu, Chaohao Huang, Weiguo Miao, Hongguang Cui
A macluravirus, tentatively named alpinia oxyphylla mosaic virus (AloMV), was identified in Alpinia oxyphylla, and its complete genomic sequence determined. The positively single-stranded RNA genome is comprised of 8213 nucleotides excluding the poly (A) tail, and contains one large open reading frame encoding a polyprotein of 2,626 amino acids. Blastp search showed that the polyprotein of AloMV shared 48%~68% aa sequence identities with other reported macluraviruses. Phylogenetic analysis based on the nucleotide sequence of the polyprotein showed that AloMV, together with all other macluraviruses, clustered into the same group most closely related to cardamom mosaic virus, sharing 66...
May 21, 2018: Archives of Virology
https://www.readbyqxmd.com/read/29786120/identification-and-characterization-of-a-tombusvirus-isolated-from-japanese-gentian
#9
Koki Fujisaki, Chika Tateda, Asuka Shirakawa, Mari Iwai, Yoshiko Abe
The DECS (dsRNA isolation, exhaustive amplification, cloning and sequencing) analysis technique for viral diagnosis detected a tombusvirus in Japanese gentian not displaying severe symptoms. We tentatively named this virus "gentian virus A" (GeVA). GeVA systemically but inefficiently infected Japanese gentian without causing visible symptoms, while it led to severe symptoms in some other plants. The complete genome sequence of GeVA indicated a typical tombusvirus-like structure. Phylogenetic analysis of the deduced amino acid sequences of four tombusvirus-encoded proteins did not reveal other known tombusviruses that were closely-related to GeVA, suggesting that it is a novel tombusvirus...
May 21, 2018: Archives of Virology
https://www.readbyqxmd.com/read/29786090/crispr-off-target-analysis-in-genetically-engineered-rats-and-mice
#10
Keith R Anderson, Maximilian Haeussler, Colin Watanabe, Vasantharajan Janakiraman, Jessica Lund, Zora Modrusan, Jeremy Stinson, Qixin Bei, Andrew Buechler, Charles Yu, Sobha R Thamminana, Lucinda Tam, Michael-Anne Sowick, Tuija Alcantar, Natasha O'Neil, Jinjie Li, Linda Ta, Lisa Lima, Merone Roose-Girma, Xin Rairdan, Steffen Durinck, Søren Warming
Despite widespread use of CRISPR, comprehensive data on the frequency and impact of Cas9-mediated off-targets in modified rodents are limited. Here we present deep-sequencing data from 81 genome-editing projects on mouse and rat genomes at 1,423 predicted off-target sites, 32 of which were confirmed, and show that high-fidelity Cas9 versions reduced off-target mutation rates in vivo. Using whole-genome sequencing data from ten mouse embryos, treated with a single guide RNA (sgRNA), and from their genetic parents, we found 43 off-targets, 30 of which were predicted by an adapted version of GUIDE-seq...
May 21, 2018: Nature Methods
https://www.readbyqxmd.com/read/29785904/identification-of-an-immune-modulation-locus-utilising-a-bovine-mammary-gland-infection-challenge-model
#11
Mathew D Littlejohn, Sally-Anne Turner, Caroline G Walker, Sarah D Berry, Kathryn Tiplady, Ric G Sherlock, Greg Sutherland, Simon Swift, Dorian Garrick, S Jane Lacy-Hulbert, Scott McDougall, Richard J Spelman, Russell G Snell, J Eric Hillerton
Inflammation of the mammary gland following bacterial infection, commonly known as mastitis, affects all mammalian species. Although the aetiology and epidemiology of mastitis in the dairy cow are well described, the genetic factors mediating resistance to mammary gland infection are not well known, due in part to the difficulty in obtaining robust phenotypic information from sufficiently large numbers of individuals. To address this problem, an experimental mammary gland infection experiment was undertaken, using a Friesian-Jersey cross breed F2 herd...
May 2018: Journal of Dairy Research
https://www.readbyqxmd.com/read/29785674/assembly-of-a-complete-genome-sequence-for-gemmata-obscuriglobus-reveals-a-novel-prokaryotic-rrna-operon-gene-architecture
#12
Josef D Franke, Wilson R Blomberg, Robert T Todd, Robert W Thomas, Anna M Selmecki
Gemmata obscuriglobus is a Gram-negative bacterium with several intriguing biological features. Here, we present a complete, de novo whole genome assembly for G. obscuriglobus which consists of a single, circular 9 Mb chromosome, with no plasmids detected. The genome was annotated using the NCBI Prokaryotic Genome Annotation pipeline to generate common gene annotations. Analysis of the rRNA genes revealed three interesting features for a bacterium. First, linked G. obscuriglobus rrn operons have a unique gene order, 23S-5S-16S, compared to typical prokaryotic rrn operons (16S-23S-5S)...
May 21, 2018: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29785670/polymorphic-imprinting-of-slc38a4-gene-in-bovine-placenta
#13
Da Xu, Cui Zhang, Junliang Li, Guannan Wang, Weina Chen, Dongjie Li, Shijie Li
Imprinted genes are characterized by monoallelic expression that is dependent on parental origin. Comparative analysis of imprinted genes between species is a powerful tool for understanding the biological significance of genomic imprinting. The slc38a4 gene encodes a neutral amino acid transporter and is identified as imprinted in mice. In this study, the imprinting status of SLC38A4 was assessed in bovine adult tissues and placenta using a polymorphism-based approach. Results indicate that SLC38A4 is not imprinted in eight adult bovine tissues including heart, liver, spleen, lung, kidney, muscle, fat, and brain...
May 21, 2018: Biochemical Genetics
https://www.readbyqxmd.com/read/29785615/molecular-characterization-of-proton-beam-induced-mutations-in-soybean-using-genotyping-by-sequencing
#14
Woon Ji Kim, Jaihyunk Ryu, Juhyun Im, Sang Hun Kim, Si-Yong Kang, Jeong-Hee Lee, Sung-Hwan Jo, Bo-Keun Ha
Proton beam irradiation is a next-generation technique to develop mutant crop varieties. The mutagenic effects and molecular mechanisms of radiation are important multi-disciplinary research subjects. This study was conducted to investigate the types of mutations induced in the soybean genome by proton beam irradiation. In total, 22 plants, including 10 M2 plants treated with proton beam irradiation at 118 and 239 Gy, each, and two wild-type plants (Daepung) were sequenced by genotyping-by-sequencing (GBS)...
May 21, 2018: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/29785479/ngspanpipe-a-pipeline-for-pan-genome-identification-in-microbial-strains-from-experimental-reads
#15
Umay Kulsum, Arti Kapil, Harpreet Singh, Punit Kaur
Recent advancements in sequencing technologies have decreased both time span and cost for sequencing the whole bacterial genome. High-throughput Next-Generation Sequencing (NGS) technology has led to the generation of enormous data concerning microbial populations publically available across various repositories. As a consequence, it has become possible to study and compare the genomes of different bacterial strains within a species or genus in terms of evolution, ecology and diversity. Studying the pan-genome provides insights into deciphering microevolution, global composition and diversity in virulence and pathogenesis of a species...
2018: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29785397/whole-genome-sequencing-of-greater-amberjack-seriola-dumerili-for-snp-identification-on-aligned-scaffolds-and-genome-structural-variation-analysis-using-parallel-resequencing
#16
Kazuo Araki, Jun-Ya Aokic, Junya Kawase, Kazuhisa Hamada, Akiyuki Ozaki, Hiroshi Fujimoto, Ikki Yamamoto, Hironori Usuki
Greater amberjack ( Seriola dumerili ) is distributed in tropical and temperate waters worldwide and is an important aquaculture fish. We carried out de novo sequencing of the greater amberjack genome to construct a reference genome sequence to identify single nucleotide polymorphisms (SNPs) for breeding amberjack by marker-assisted or gene-assisted selection as well as to identify functional genes for biological traits. We obtained 200 times coverage and constructed a high-quality genome assembly using next generation sequencing technology...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29785349/novel-non-symbiotic-isolates-of-neorhizobium-from-a-dryland-agricultural-soil
#17
Amalia Soenens, Juan Imperial
Semi-selective enrichment, followed by PCR screening, resulted in the successful direct isolation of fast-growing Rhizobia from a dryland agricultural soil. Over 50% of these isolates belong to the genus Neorhizobium , as concluded from partial rpoB and near-complete 16S rDNA sequence analysis. Further genotypic and genomic analysis of five representative isolates confirmed that they form a coherent group within Neorhizobium , closer to N. galegae than to the remaining Neorhizobium species, but clearly differentiated from the former, and constituting at least one new genomospecies within Neorhizobium...
2018: PeerJ
https://www.readbyqxmd.com/read/29785339/identification-of-potential-crucial-genes-and-pathways-associated-with-vein-graft-restenosis-based-on-gene-expression-analysis-in-experimental-rabbits
#18
Qiang Liu, Xiujie Yin, Mingzhu Li, Li Wan, Liqiao Liu, Xiang Zhong, Zhuoqi Liu, Qun Wang
Occlusive artery disease (CAD) is the leading cause of death worldwide. Bypass graft surgery remains the most prevalently performed treatment for occlusive arterial disease, and veins are the most frequently used conduits for surgical revascularization. However, the clinical efficacy of bypass graft surgery is highly affected by the long-term potency rates of vein grafts, and no optimal treatments are available for the prevention of vein graft restenosis (VGR) at present. Hence, there is an urgent need to improve our understanding of the molecular mechanisms involved in mediating VGR...
2018: PeerJ
https://www.readbyqxmd.com/read/29785121/association-between-angiogenesis-and-cytotoxic-signatures-in-the-tumor-microenvironment-of-gastric-cancer
#19
Yi Feng, Ying Dai, Zhihua Gong, Jia-Nan Cheng, Longhui Zhang, Chengdu Sun, Xianghua Zeng, Qingzhu Jia, Bo Zhu
Background: A suppressive immune microenvironment and pathological angiogenesis are hallmarks of gastric cancer. Theoretically, immune checkpoint inhibitors (ICIs) stimulate pre-primed neoantigen-specific T cells, and antiangiogenic agents then facilitate their infiltration into the tumor niche by promoting vascular normalization. Currently, the interconnections of these two phenotypes and their relevance to the tumor microenvironment (TME) have not been fully characterized in gastric cancer...
2018: OncoTargets and Therapy
https://www.readbyqxmd.com/read/29785087/transcriptomic-impacts-of-rumen-epithelium-induced-by-butyrate-infusion-in-dairy-cattle-in-dry-period
#20
Ransom L Baldwin, Robert W Li, Yankai Jia, Cong-Jun Li
The purpose of this study was to evaluate the effects of butyrate infusion on rumen epithelial transcriptome. Next-generation sequencing (NGS) and bioinformatics are used to accelerate our understanding of regulation in rumen epithelial transcriptome of cattle in the dry period induced by butyrate infusion at the level of the whole transcriptome. Butyrate, as an essential element of nutrients, is a histone deacetylase (HDAC) inhibitor that can alter histone acetylation and methylation, and plays a prominent role in regulating genomic activities influencing rumen nutrition utilization and function...
2018: Gene Regulation and Systems Biology
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