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Metabolism and RNA

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https://www.readbyqxmd.com/read/30546887/identification-of-key-genes-and-pathways-by-bioinformatics-analysis-with-tcga-rna-sequencing-data-in-hepatocellular-carcinoma
#1
Qiandong Zhu, Yunpeng Sun, Qingqing Zhou, Qikuan He, Haixin Qian
Improved insight into the molecular characteristics of hepatocellular carcinoma (HCC) is required to predict prognosis and to develop a new rationale for targeted therapeutic strategy. Bioinformatics methods, including functional enrichment and network analysis combined with survival analysis, are required to process a large volume of data to obtain further information on differentially expressed genes (DEGs). The RNA sequencing data related to HCC in The Cancer Genome Atlas (TCGA) database were analyzed to screen DEGs, which were separately submitted to perform gene enrichment analysis to identify gene sets and signaling pathways, and to construct a protein-protein interaction (PPI) network...
December 2018: Molecular and Clinical Oncology
https://www.readbyqxmd.com/read/30546110/intron-containing-rna-from-the-hiv-1-provirus-activates-type-i-interferon-and-inflammatory-cytokines
#2
Sean Matthew McCauley, Kyusik Kim, Anetta Nowosielska, Ann Dauphin, Leonid Yurkovetskiy, William Edward Diehl, Jeremy Luban
HIV-1-infected people who take drugs that suppress viremia to undetectable levels are protected from developing AIDS. Nonetheless, HIV-1 establishes proviruses in long-lived CD4+ memory T cells, and perhaps other cell types, that preclude elimination of the virus even after years of continuous antiviral therapy. Here we show that the HIV-1 provirus activates innate immune signaling in isolated dendritic cells, macrophages, and CD4+ T cells. Immune activation requires transcription from the HIV-1 provirus and expression of CRM1-dependent, Rev-dependent, RRE-containing, unspliced HIV-1 RNA...
December 13, 2018: Nature Communications
https://www.readbyqxmd.com/read/30546088/exosome-circrna-secreted-from-adipocytes-promotes-the-growth-of-hepatocellular-carcinoma-by-targeting-deubiquitination-related-usp7
#3
Haiyang Zhang, Ting Deng, Shaohua Ge, Ying Liu, Ming Bai, Kegan Zhu, Qian Fan, Jialu Li, Tao Ning, Fei Tian, Hongli Li, Wu Sun, Guoguang Ying, Yi Ba
Hepatocellular carcinoma (HCC), the major form of liver cancer, has shown increasing incidence and poor prognosis. Adipose tissue is known to function in energy storage and metabolism regulation by the secretion of adipokines. Circular RNAs (circRNAs), a novel type of noncoding RNA, have recently been recognized as key factors in tumor development, but the role of exosome circRNAs derived from adipose tissues has not been defined yet. Here, adipose-secreted circRNAs were found to regulate deubiquitination in HCC, thus facilitating cell growth...
December 13, 2018: Oncogene
https://www.readbyqxmd.com/read/30545311/identification-and-characteristics-of-muscle-growth-related-microrna-in-the-pacific-abalone-haliotis-discus-hannai
#4
Jianfang Huang, Xuan Luo, Miaoqin Huang, Guangmou Liu, Weiwei You, Caihuan Ke
BACKGROUND: The Pacific abalone, Haliotis discus hannai, is the most important cultivated abalone in China. Improving abalone muscle growth and increasing the rate of growth are important genetic improvement programs in this industry. MicroRNAs are important small noncoding RNA molecules that regulate post-transcription gene expression. However, no miRNAs have been reported to regulate muscle growth in H. discus hannai. RESULTS: we profiled six small RNA libraries for three large abalone individuals (L_HD group) and three small individuals (S_HD group) using RNA sequencing technology...
December 13, 2018: BMC Genomics
https://www.readbyqxmd.com/read/30545291/the-transcription-factor-pro44-and-the-histone-chaperone-asf1-regulate-distinct-aspects-of-multicellular-development-in-the-filamentous-fungus-sordaria-macrospora
#5
David Immanuel Schumacher, Ramona Lütkenhaus, Florian Altegoer, Ines Teichert, Ulrich Kück, Minou Nowrousian
BACKGROUND: Fungal fruiting bodies are complex three-dimensional structures that are formed to protect and disperse the sexual spores. Their morphogenesis requires the concerted action of numerous genes; however, at the molecular level, the spatio-temporal sequence of events leading to the mature fruiting body is largely unknown. In previous studies, the transcription factor gene pro44 and the histone chaperone gene asf1 were shown to be essential for fruiting body formation in the ascomycete Sordaria macrospora...
December 13, 2018: BMC Genetics
https://www.readbyqxmd.com/read/30545217/changes-in-fruit-firmness-cell-wall-composition-and-transcriptional-profile-in-the-yellow-fruited-tomato-1-yft1-mutant
#6
Ling Li, Weihua Zhao, Xuechao Feng, Lulu Chen, Lida Zhang, Lingxia Zhao
Fruit firmness is an important trait in tomato (Solanum lycopersicum), associated with shelf life and economic value; however, the precise mechanism determining fruit softening remains elusive. A yellow fruit tomato 1(yft1) mutant, harbors a genetic lesion in the YFT1 gene, and has significantly firmer fruit than those of the cv. M82 wild type at a red ripe stage, 54 dpa (days post anthesis). When softening was further dissected, it was found that the yft1 firm fruit phenotype correlated with a difference in cellulose, hemicellulose and pectin deposition in the primary cell wall (PCW) compared to cv...
December 13, 2018: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/30545132/proteogenomic-analysis-of-burkholderia-species-strains-25-and-46-isolated-from-uraniferous-soils-reveals-multiple-mechanisms-to-cope-with-uranium-stress
#7
Meenakshi Agarwal, Ashish Pathak, Rajesh Singh Rathore, Om Prakash, Rakesh Singh, Rajneesh Jaswal, John Seaman, Ashvini Chauhan
Two Burkholderia spp. (strains SRS-25 and SRS-46) were isolated from high concentrations of uranium (U) from the U.S. Department of Energy (DOE)-managed Savannah River Site (SRS). SRS contains soil gradients that remain co-contaminated by heavy metals from previous nuclear weapons production activities. Uranium (U) is one of the dominant contaminants within the SRS impacted soils, which can be microbially transformed into less toxic forms. We established microcosms containing strains SRS-25 and SRS-46 spiked with U and evaluated the microbially-mediated depletion with concomitant genomic and proteomic analysis...
December 12, 2018: Cells
https://www.readbyqxmd.com/read/30545084/transcriptome-sequencing-and-biochemical-analysis-of-perianths-and-coronas-reveal-flower-color-formation-in-narcissus-pseudonarcissus
#8
Xi Li, Dongqin Tang, Hui Du, Yimin Shi
Narcissus pseudonarcissus is an important bulbous plant with white or yellow perianths and light yellow to orange-red coronas, but little is known regarding the biochemical and molecular basis related to flower color polymorphisms. To investigate the mechanism of color formation, RNA-Seq of flower of two widely cultured cultivars ('Slim Whitman' and 'Pinza') with different flower color was performed. A total of 84,463 unigenes were generated from the perianths and coronas. By parallel metabolomic and transcriptomic analyses, we provide an overview of carotenoid biosynthesis, degradation, and accumulation in N...
December 12, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/30544995/global-expression-profiling-identifies-a-novel-hyaluronan-synthases-2-gene-in-the-pathogenesis-of-lower-extremity-varicose-veins
#9
Chia-Shan Hsieh, Chia-Ti Tsai, Yau-Hung Chen, Sheng-Nan Chang, Juey-Jen Hwang, Eric Y Chuang, I-Hui Wu
Lower extremities varicose veins (VV) are among the most easily recognized venous abnormalities. The genetic mechanism of VV is largely unknown. In this study, we sought to explore the global expressional change of VV and identify novel genes that might play a role in VV. We used next-generation ribonucleic acid (RNA) sequence (RNA seq) technology to study the global messenger RNA expressional change in the venous samples of five diseased and five control patients. We identified several differentially expressed genes, which were further confirmed by conventional reverse transcription polymerase chain reaction (RT-PCR)...
December 11, 2018: Journal of Clinical Medicine
https://www.readbyqxmd.com/read/30544876/mitochondrial-rna-expression-and-single-nucleotide-variants-in-association-with-clinical-parameters-in-primary-breast-cancers
#10
Marjolein J A Weerts, Marcel Smid, John A Foekens, Stefan Sleijfer, John W M Martens
The human mitochondrial DNA (mtDNA) encodes 37 genes, including thirteen proteins essential for the respiratory chain, and RNAs functioning in the mitochondrial translation apparatus. The total number of mtDNA molecules per cell (mtDNA content) is variable between tissue types and also between tumors and their normal counterparts. For breast cancer, tumors tend to be depleted in their mtDNA content compared to adjacent normal mammary tissue. Various studies have shown that primary breast tumors harbor somatic mtDNA variants...
December 9, 2018: Cancers
https://www.readbyqxmd.com/read/30544755/rna-modification-level-estimation-with-pulser
#11
Etienne Boileau, Christoph Dieterich
RNA modifications regulate the complex life of transcripts. An experimental approach called LAIC-seq was developed to characterize modification levels on a transcriptome-wide scale. In this method, the modified and unmodified molecules are separated using antibodies specific for a given RNA modification (e.g., m⁶A). In essence, the procedure of biochemical separation yields three fractions: Input, eluate, and supernatent, which are subjected to RNA-seq. In this work, we present a bioinformatics workflow, which starts from RNA-seq data to infer gene-specific modification levels by a statistical model on a transcriptome-wide scale...
December 10, 2018: Genes
https://www.readbyqxmd.com/read/30544636/itraq-based-quantitative-proteomics-analysis-reveals-the-mechanism-underlying-the-weakening-of-carbon-metabolism-in-chlorotic-tea-leaves
#12
Fang Dong, Yuanzhi Shi, Meiya Liu, Kai Fan, Qunfeng Zhang, Jianyun Ruan
To uncover mechanism of highly weakened carbon metabolism in chlorotic tea ( Camellia sinensis ) plants, iTRAQ (isobaric tags for relative and absolute quantification)-based proteomic analyses were employed to study the differences in protein expression profiles in chlorophyll-deficient and normal green leaves in the tea plant cultivar "Huangjinya". A total of 2110 proteins were identified in "Huangjinya", and 173 proteins showed differential accumulations between the chlorotic and normal green leaves...
December 7, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/30544626/rna-sequencing-provides-insights-into-the-regulation-of-solanesol-biosynthesis-in-nicotiana-tabacum-induced-by-moderately-high-temperature
#13
Ning Yan, Yongmei Du, Hongbo Zhang, Zhongfeng Zhang, Xinmin Liu, John Shi, Yanhua Liu
Solanesol is a terpene alcohol composed of nine isoprene units that mainly accumulates in solanaceous plants, especially tobacco ( Nicotiana tabacum ). The present study aimed to investigate the regulation of solanesol accumulation in tobacco leaves induced by moderately high temperature (MHT). Exposure to MHT resulted in a significant increase in solanesol content, dry weight, and net photosynthetic rate in tobacco leaves. In MHT-exposed tobacco leaves, 492 and 1440 genes were significantly up- and downregulated, respectively, as revealed by RNA-sequencing...
December 7, 2018: Biomolecules
https://www.readbyqxmd.com/read/30544592/hibernation-leads-to-altered-gut-communities-in-bumblebee-queens-bombus-terrestris
#14
Lien Bosmans, María I Pozo, Christel Verreth, Sam Crauwels, Felix Wäckers, Hans Jacquemyn, Bart Lievens
Many reptiles, amphibians, mammals, and insects practice some form of hibernation during which their metabolic rate is drastically reduced. This allows them to conserve energy and survive the harsh winter conditions with little or no food. While it can be expected that a reduction in host metabolism has a substantial influence on the gut microbial community, little is known about the effects of hibernation on the composition of the microbial gut community, especially for insects. In this study, we assessed and compared the bacterial gut community composition within the midgut and ileum of indoor-reared queens of Bombus terrestris before and after an artificial hibernation period of 16 weeks...
December 7, 2018: Insects
https://www.readbyqxmd.com/read/30543425/kinetic-model-of-translational-autoregulation
#15
Vivian Tyng, Michael E Kellman
We investigate dynamics of a kinetic model of inhibitory autoregulation as exemplified when a protein inhibits its own production by interfering with its messenger RNA, known in molecular biology as translational autoregulation. We first show how linear models without feedback set the stage with a nonequilibrium steady state that constitutes the target of the regulation. However, regulation in the simple linear model is far from optimal. The negative feedback mechanism whereby the protein ``jams" the mRNA greatly enhances the effectiveness of the control, with response to perturbation that is targeted, rapid, and metabolically efficient...
December 13, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/30542341/glycogen-synthase-kinase-3%C3%AE-enhances-hepatitis-c-virus-replication-by-supporting-mir-122
#16
Maged Saleh, Sabrina Rüschenbaum, Christoph Welsch, Stefan Zeuzem, Darius Moradpour, Jérôme Gouttenoire, Christian M Lange
Hepatitis C virus (HCV) infection is associated with alterations in host lipid and insulin signaling cascades, which are partially explained by a dependence of the HCV life cycle on key molecules in these metabolic pathways. Yet, little is known on the role in the HCV life cycle of glycogen synthase kinase 3 (GSK3), one of the most important kinases in cellular metabolism. Therefore, the impact of GSK3 on the HCV life cycle was assessed in human hepatoma cell lines harboring subgenomic genotype 1b and 2a replicons or producing cell culture-derived HCV genotype 2a by exposure to synthetic GSK3 inhibitors, GSK3 gene silencing, overexpression of GSK3 constructs and immunofluorescence analyses...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/30542335/dual-rna-seq-uncovers-metabolic-amino-acids-dependency-of-the-intracellular-bacterium-piscirickettsia-salmonis-infecting-atlantic-salmon
#17
Diego Valenzuela-Miranda, Cristian Gallardo-Escárate
High-throughput sequencing technologies have offered the possibility to understand the complexity of the transcriptomic responses of an organism during a wide variety of biological scenarios, such as the case of pathogenic infections. Recently, the simultaneous sequencing of both pathogen and host transcriptomes (dual RNA-seq) during the infection has become a promising approach to uncover the complexity of the host-pathogen interactions. In this study, through a double rRNA depletion and RNA sequencing protocols, we simultaneously analyzed the transcriptome of the intracellular bacterium Piscirickettsia salmonis and its host the Atlantic salmon ( Salmo salar ) during the course of the infection...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/30542328/rare-earth-elements-alter-redox-balance-in-methylomicrobium-alcaliphilum-20z-r
#18
Ilya R Akberdin, David A Collins, Richard Hamilton, Dmitry Y Oshchepkov, Anil K Shukla, Carrie D Nicora, Ernesto S Nakayasu, Joshua N Adkins, Marina G Kalyuzhnaya
Background: Rare Earth Elements (REEs) control methanol utilization in both methane- and methanol-utilizing microbes. It has been established that the addition of REEs leads to the transcriptional repression of MxaFI-MeDH [a two-subunit methanol dehydrogenase (MeDH), calcium-dependent] and the activation of XoxF-MeDH (a one-subunit MeDH, lanthanum-dependent). Both enzymes are pyrroquinoline quinone-dependent alcohol dehydrogenases and show significant homology; however, they display different kinetic properties and substrate specificities...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/30541556/-omics-data-integration-and-functional-analyses-link-enoyl-coa-hydratase-short-chain-1-to-drug-refractory-dilated-cardiomyopathy
#19
Nzali V Campbell, David A Weitzenkamp, Ian L Campbell, Ronald F Schmidt, Chindo Hicks, Michael J Morgan, David C Irwin, John J Tentler
BACKGROUND: Large-scale "omics" datasets have not been leveraged and integrated with functional analyses to discover potential drivers of cardiomyopathy. This study addresses the knowledge gap. METHODS: We coupled RNA sequence (RNA-Seq) variant detection and transcriptome profiling with pathway analysis to model drug refractory dilated cardiomyopathy (drDCM) using the BaseSpace sequencing hub and Ingenuity Pathway Analysis. We used RNA-Seq case-control datasets (n = 6 cases, n = 4 controls), exome sequence familial DCM datasets (n = 3 Italians, n = 5 Italians, n = 5 Chinese), and controls from the HapMap project (n = 5 Caucasians, and n = 5 Asians) for disease modeling and putative mutation discovery...
December 12, 2018: BMC Medical Genomics
https://www.readbyqxmd.com/read/30541135/functional-expansion-of-a-tca-cycle-operon-mrna-by-a-3-end-derived-small-rna
#20
Masatoshi Miyakoshi, Gianluca Matera, Kanako Maki, Yasuhiro Sone, Jörg Vogel
Global RNA profiling studies in bacteria have predicted the existence of many of small noncoding RNAs (sRNAs) that are processed off mRNA 3' ends to regulate other mRNAs via the RNA chaperones Hfq and ProQ. Here, we present targets of SdhX (RybD), an Hfq-dependent sRNA that is generated by RNase E mediated 3' processing of the ∼10 000-nt mRNA of the TCA cycle operon sdhCDAB-sucABCD in enteric bacteria. An in silico search predicted ackA mRNA, which encodes acetate kinase, as a conserved primary target of SdhX...
December 12, 2018: Nucleic Acids Research
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