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Transcriptome pathway

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https://www.readbyqxmd.com/read/28330331/identification-and-quantification-of-novel-rna-isoforms-in-horn-cancer-of-bos-indicus-by-comprehensive-rna-seq
#1
Subhash J Jakhesara, Prakash G Koringa, Neelam M Nathani, Chaitanya G Joshi
Horn cancer (HC) is a squamous cell carcinoma of horn, commonly observed in Bos indicus of the Asian countries. To elucidate the complexity of alternative splicing present in the HC, high-throughput sequencing and analysis of HC and matching horn normal (HN) tissue were carried out. A total of 535,067 and 849,077 reads were analysed after stringent quality filtering for HN and HC, respectively. Cufflinks pipeline for transcriptome analysis revealed 4786 novel splice isoforms comprising 2432 exclusively in HC, 2055 exclusively in HN and 298 in both the conditions...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330322/de-novo-transcriptome-sequencing-in-monsonia-burkeana-revealed-putative-genes-for-key-metabolic-pathways-involved-in-tea-quality-and-medicinal-value
#2
Adugna A Woldesemayat, Khayalethu Ntushelo, David M Modise
Monsonia (Monsonia burkeana Planch. ex Harv) is one of the most valuable tea and traditional medicinal plants used in Southern Africa. In spite of this, there is no sequence information regarding this plant in literature. To provide understanding of the naturally occurring tea and drug-specific products and the key pathways for the biosynthesis of these molecules, we sequenced the leaf transcriptome using Illumina MiSeq platform and generated 2,590,652 paired-end reads that were assembled de novo into 45,450 high-quality transcripts...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329862/the-transcriptome-of-the-zebrafish-embryo-after-chemical-exposure-a-meta-analysis
#3
Andreas Schüttler, Kristin Reiche, Rolf Altenburger, Wibke Busch
Numerous studies have been published in the past years investigating the transcriptome of the zebrafish embryo (ZFE) upon being subjected to chemical stress. Aiming at a more mechanistic understanding of the results of such studies, knowledge about commonalities of transcript regulation in response to chemical stress is needed. Thus, our goal in this study was to identify and interpret genes and gene sets constituting a general response to chemical exposure. Therefore, we aggregated and reanalyzed published toxicogenomics data obtained with the ZFE...
February 27, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/28329151/caloric-restriction-and-rapamycin-differentially-alter-energy-metabolism-in-yeast
#4
Kyung-Mi Choi, Seok-Jin Hong, Jan M van Deursen, Sooah Kim, Kyoung Heon Kim, Cheol-Koo Lee
Rapamycin (RM), a drug that inhibits the mechanistic target of rapamycin (mTOR) pathway and responds to nutrient availability, seemingly mimics the effects of caloric restriction (CR) on healthy life span. However, the extent of the mechanistic overlap between RM and CR remains incompletely understood. Here, we compared the impact of CR and RM on cellular metabolic status. Both regimens maintained intracellular ATP through the chronological aging process and showed enhanced mitochondrial capacity. Comparative transcriptome analysis showed that CR had a stronger impact on global gene expression than RM...
March 8, 2017: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/28328945/mirnas-in-the-vitreous-humor-of-patients-affected-by-idiopathic-epiretinal-membrane-and-macular-hole
#5
Andrea Russo, Marco Ragusa, Cristina Barbagallo, Antonio Longo, Teresio Avitabile, Maurizio G Uva, Vincenza Bonfiglio, Mario D Toro, Rosario Caltabiano, Cesare Mariotti, Francesco Boscia, Mario Romano, Cinzia Di Pietro, Davide Barbagallo, Michele Purrello, Michele Reibaldi
PURPOSE: The aim of the present study was to assess the expression of miRNAs in the Vitreous Humor (VH) of patients with Macular Hole (MH) and Epiretinal Membrane (ERM) compared to a control group. METHODS: In this prospective, comparative study, 2-ml of VH was extracted from the core of the vitreous chamber in consecutive patients who underwent standard vitrectomy for ERM and MH. RNA was extracted and TaqMan® Low Density Arrays (TLDAs) were used to profile the transcriptome of 754 miRNAs...
2017: PloS One
https://www.readbyqxmd.com/read/28328794/hcv-drives-increased-type-i-ifn-associated-impairments-associated-to-fibrosis-severity-in-art-treated-hiv-1-hcv-coinfected-individuals
#6
Morgane Griesbeck, Marc-Antoine Valantin, Karine Lacombe, Assia Samri-Hassimi, Julie Bottero, Catherine Blanc, Zineb Sbihi, Rima Zoorob, Christine Katlama, Marguerite Guiguet, Marcus Altfeld, Brigitte Autran
BACKGROUND: Viral coinfections might contribute to the increased immune activation and inflammation that persist in ART-treated HIV-1 patients. We investigated whether the HCV co-infection contributes to such alterations by impairing the pDC IFNα/TLR7 pathway in a highly homogeneous group of ART-treated HIV-1-HCV co-infected patients. METHODS: Twenty nine HIV-1-infected patients with fully suppressive ART were included, fifteen of whom being HCV co-infected with mild to moderate fibrosis and matched for their HIV-1 disease, and thirteen control healthy donors...
March 21, 2017: AIDS
https://www.readbyqxmd.com/read/28327625/early-metabolic-and-transcriptional-variations-in-fruit-of-natural-white-fruited-fragaria-vesca-genotypes
#7
Katja Härtl, Alisandra Denton, Katrin Franz-Oberdorf, Thomas Hoffmann, Melanie Spornraft, Björn Usadel, Wilfried Schwab
Strawberry fruits (Fragaria vesca) are valued for their sweet fruity flavor, juicy texture, and characteristic red color caused by anthocyanin pigments. To gain a deeper insight into the regulation of anthocyanin biosynthesis, we performed comparative metabolite profiling and transcriptome analyses of one red-fruited and two natural white-fruited strawberry varieties in two tissues and three ripening stages. Developing fruit of the three genotypes showed a distinctive pattern of polyphenol accumulation already in green receptacle and achenes...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28327132/simultaneous-analysis-of-mirna-mrna-in-human-meningiomas-by-integrating-transcriptome-a-relationship-between-ptx3-and-mir-29c
#8
Altay Burak Dalan, Sukru Gulluoglu, Emre Can Tuysuz, Aysegul Kuskucu, Cumhur Kaan Yaltirik, Oguz Ozturk, Ugur Ture, Omer Faruk Bayrak
BACKGROUND: Although meningioma is a common disease, there is a lack of understanding of the underlying molecular mechanisms behind its initiation and progression. We used combined miRNA-mRNA transcriptome analysis to discover dysregulated genes and networks in meningiomas. METHODS: Fourteen fresh-frozen meningioma samples and one human meningeal cell line were analyzed by using miRNA and whole transcriptome microarray chips. Data was filtered and analyzed. Candidate miRNAs and mRNAs were selected for validation in fifty-eight patient samples...
March 21, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28327131/transcriptome-analysis-of-pancreatic-cells-across-distant-species-highlights-novel-important-regulator-genes
#9
Estefania Tarifeño-Saldivia, Arnaud Lavergne, Alice Bernard, Keerthana Padamata, David Bergemann, Marianne L Voz, Isabelle Manfroid, Bernard Peers
BACKGROUND: Defining the transcriptome and the genetic pathways of pancreatic cells is of great interest for elucidating the molecular attributes of pancreas disorders such as diabetes and cancer. As the function of the different pancreatic cell types has been maintained during vertebrate evolution, the comparison of their transcriptomes across distant vertebrate species is a means to pinpoint genes under strong evolutionary constraints due to their crucial function, which have therefore preserved their selective expression in these pancreatic cell types...
March 21, 2017: BMC Biology
https://www.readbyqxmd.com/read/28327084/a-transcriptome-multi-tissue-analysis-identifies-biological-pathways-and-genes-associated-with-variations-in-feed-efficiency-of-growing-pigs
#10
Florence Gondret, Annie Vincent, Magalie Houée-Bigot, Anne Siegel, Sandrine Lagarrigue, David Causeur, Hélène Gilbert, Isabelle Louveau
BACKGROUND: Animal's efficiency in converting feed into lean gain is a critical issue for the profitability of meat industries. This study aimed to describe shared and specific molecular responses in different tissues of pigs divergently selected over eight generations for residual feed intake (RFI). RESULTS: Pigs from the low RFI line had an improved gain-to-feed ratio during the test period and displayed higher leanness but similar adiposity when compared with pigs from the high RFI line at 132 days of age...
March 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28326315/genomewide-expression-and-functional-interactions-of-genes-under-drought-stress-in-maize
#11
Nepolean Thirunavukkarasu, Rinku Sharma, Nidhi Singh, Kaliyugam Shiriga, Sweta Mohan, Swati Mittal, Shikha Mittal, Mallana Gowdra Mallikarjuna, Atmakuri Ramakrishna Rao, Prasanta Kumar Dash, Firoz Hossain, Hari Shanker Gupta
A genomewide transcriptome assay of two subtropical genotypes of maize was used to observe the expression of genes at seedling stage of drought stress. The number of genes expressed differentially was greater in HKI1532 (a drought tolerant genotype) than in PC3 (a drought sensitive genotype), indicating primary differences at the transcriptional level in stress tolerance. The global coexpression networks of the two genotypes differed significantly with respect to the number of modules and the coexpression pattern within the modules...
2017: International Journal of Genomics
https://www.readbyqxmd.com/read/28326294/the-eukaryote-like-serine-threonine-kinase-stk-regulates-the-growth-and-metabolism-of-zoonotic-streptococcus-suis
#12
Chunyan Zhang, Wen Sun, Meifang Tan, Mengmeng Dong, Wanquan Liu, Ting Gao, Lu Li, Zhuofei Xu, Rui Zhou
Like eukaryotes, bacteria express one or more serine/threonine kinases (STKs) that initiate diverse signaling networks. The STK from Streptococcus suis is encoded by a single-copy stk gene, which is crucial in stress response and virulence. To further understand the regulatory mechanism of STK in S. suis, a stk deletion strain (Δstk) and its complementary strain (CΔstk) were constructed to systematically decode STK characteristics by applying whole transcriptome RNA sequencing (RNA-Seq) and phosphoproteomic analysis...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28325815/neuropathic-pain-promotes-adaptive-changes-in-gene-expression-in-brain-networks-involved-in-stress-and-depression
#13
Giannina Descalzi, Vasiliki Mitsi, Immanuel Purushothaman, Sevasti Gaspari, Kleopatra Avrampou, Yong-Hwee Eddie Loh, Li Shen, Venetia Zachariou
Neuropathic pain is a complex chronic condition characterized by various sensory, cognitive, and affective symptoms. A large percentage of patients with neuropathic pain are also afflicted with depression and anxiety disorders, a pattern that is also seen in animal models. Furthermore, clinical and preclinical studies indicate that chronic pain corresponds with adaptations in several brain networks involved in mood, motivation, and reward. Chronic stress is also a major risk factor for depression. We investigated whether chronic pain and stress affect similar molecular mechanisms and whether chronic pain can affect gene expression patterns that are involved in depression...
March 21, 2017: Science Signaling
https://www.readbyqxmd.com/read/28323865/the-microrna-302b-inhibited-insulin-like-growth-factor-binding-protein-2-signaling-pathway-induces-glioma-cell-apoptosis-by-targeting-nuclear-factor-ia
#14
Chin-Cheng Lee, Peng-Hsu Chen, Kuo-Hao Ho, Chwen-Ming Shih, Chia-Hsiung Cheng, Cheng-Wei Lin, Kur-Ta Cheng, Ann-Jeng Liu, Ku-Chung Chen
MicroRNAs are small noncoding RNAs that post-transcriptionally control the expression of genes involved in glioblastoma multiforme (GBM) development. Although miR-302b functions as a tumor suppressor, its role in GBM is still unclear. Therefore, this study comprehensively explored the roles of miR-302b-mediated gene networks in GBM cell death. We found that miR-302b levels were significantly higher in primary astrocytes than in GBM cell lines. miR-302b overexpression dose dependently reduced U87-MG cell viability and induced apoptosis through caspase-3 activation and poly(ADP ribose) polymerase degradation...
2017: PloS One
https://www.readbyqxmd.com/read/28322828/metabolic-characterization-of-human-aqueous-humor-in-relation-to-high-myopia
#15
Yinghong Ji, Jun Rao, Xianfang Rong, Shang Lou, Zhi Zheng, Yi Lu
High myopia is the common eye disorder worldwide, which may contribute to increase the risk of serious disorders including glaucoma and cataract. Although various studies including genomics, transcriptomics, and proteomics have been implicated to identify potential biomarkers (genes or proteins) for predicting high myopia and to reveal the underlying mechanisms, the comprehensive metabolomics in relation to high myopia is very limited. In this study, we identified 242 metabolites in aqueous humor (AH) from a set of 40 patients (including 20 with high myopia and 20 for controls), using a non-targeted metabolomic technology, gas chromatography coupled to time-of-flight mass spectrometer (GC/TOF MS)...
March 17, 2017: Experimental Eye Research
https://www.readbyqxmd.com/read/28322583/interplay-between-genetic-and-epigenetic-mechanisms-in-rheumatoid-arthritis
#16
Mojca Frank-Bertoncelj, Kerstin Klein, Steffen Gay
Genetic and environmental factors contribute to the risk for rheumatoid arthritis (RA), with epigenetics serving as a possible interface through which risk factors contribute to RA. High-throughput technologies for interrogating genome and epigenome, and the availability of genetic and epigenetic datasets across a diversity of cell types, enable the identification of candidate causal genetic variants for RA to study their function in core RA processes. To date, RA risk variants were studied in the immune cells but not joint resident cells, for example, synovial fibroblasts...
March 21, 2017: Epigenomics
https://www.readbyqxmd.com/read/28322580/macrophage-kdm6b-controls-the-pro-fibrotic-transcriptome-signature-of-foam-cells
#17
Annette E Neele, Koen Hm Prange, Marten A Hoeksema, Saskia van der Velden, Tina Lucas, Stefanie Dimmeler, Esther Lutgens, Jan Van den Bossche, Menno Pj de Winther
AIM: In order to identify regulators of foam cells, we studied the H3K27 demethylase Kdm6b (also known as Jmjd3), a known regulator of macrophages, in controlling the transcriptional profile of foam cells. MATERIALS & METHODS: Foam cells from Kdm6b-deleted or Kdm6b wild-type mice were isolated and used for RNA-sequencing analysis. RESULTS: Pathway analysis revealed that pro-fibrotic pathways were strongly suppressed in Kdm6b-deleted foam cells...
March 21, 2017: Epigenomics
https://www.readbyqxmd.com/read/28322296/de-novo-sequencing-and-comparative-analysis-of-leaf-transcriptomes-of-diverse-condensed-tannin-containing-lines-of-underutilized-psophocarpus-tetragonolobus-l-dc
#18
Vinayak Singh, Ridhi Goel, Veena Pande, Mehar Hasan Asif, Chandra Sekhar Mohanty
Condensed tannin (CT) or proanthocyanidin (PA) is a unique group of phenolic metabolite with high molecular weight with specific structure. It is reported that, the presence of high-CT in the legumes adversely affect the nutrients in the plant and impairs the digestibility upon consumption by animals. Winged bean (Psophocarpus tetragonolobus (L.) DC.) is one of the promising underutilized legume with high protein and oil-content. One of the reasons for its underutilization is due to the presence of CT. Transcriptome sequencing of leaves of two diverse CT-containing lines of P...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28321286/crispr-cas9-mediated-heterozygous-knockout-of-the-autism-gene-chd8-and-characterization-of-its-transcriptional-networks-in-cerebral-organoids-derived-from-ips-cells
#19
Ping Wang, Ryan Mokhtari, Erika Pedrosa, Michael Kirschenbaum, Can Bayrak, Deyou Zheng, Herbert M Lachman
BACKGROUND: CHD8 (chromodomain helicase DNA-binding protein 8), which codes for a member of the CHD family of ATP-dependent chromatin-remodeling factors, is one of the most commonly mutated genes in autism spectrum disorders (ASD) identified in exome-sequencing studies. Loss of function mutations in the gene have also been found in schizophrenia (SZ) and intellectual disabilities and influence cancer cell proliferation. We previously reported an RNA-seq analysis carried out on neural progenitor cells (NPCs) and monolayer neurons derived from induced pluripotent stem (iPS) cells that were heterozygous for CHD8 knockout (KO) alleles generated using CRISPR-Cas9 gene editing...
2017: Molecular Autism
https://www.readbyqxmd.com/read/28321230/integrated-transcriptome-and-metabolic-analyses-reveals-novel-insights-into-free-amino-acid-metabolism-in-huangjinya-tea-cultivar
#20
Qunfeng Zhang, Meiya Liu, Jianyun Ruan
The chlorotic tea variety Huangjinya, a natural mutant, contains enhanced levels of free amino acids in its leaves, which improves the drinking quality of its brewed tea. Consequently, this chlorotic mutant has a higher economic value than the non-chlorotic varieties. However, the molecular mechanisms behind the increased levels of free amino acids in this mutant are mostly unknown, as are the possible effects of this mutation on the overall metabolome and biosynthetic pathways in tea leaves. To gain further insight into the effects of chlorosis on the global metabolome and biosynthetic pathways in this mutant, Huangjinya plants were grown under normal and reduced sunlight, resulting in chlorotic and non-chlorotic leaves, respectively; their leaves were analyzed using transcriptomics as well as targeted and untargeted metabolomics...
2017: Frontiers in Plant Science
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