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Transcriptomics

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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
#1
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/28432216/embryonic-cholecystitis-and-defective-gallbladder-contraction-in-the-sox17-haploinsufficient-model-of-biliary-atresia
#2
Hiroki Higashiyama, Aisa Ozawa, Hiroyuki Sumitomo, Mami Uemura, Ko Fujino, Hitomi Igarashi, Kenya Imaimatsu, Naoki Tsunekawa, Yoshikazu Hirate, Masamichi Kurohmaru, Yukio Saijoh, Masami Kanai-Azuma, Yoshiakira Kanai
The gallbladder excretes cytotoxic bile acids to the duodenum through the cystic duct and common bile duct system. Sox17 haploinsufficiency causes the biliary atresia-like phenotypes and hepatitis in late organogenesis mouse embryos. However, the molecular and cellular mechanisms in the Sox17-haploinsufficient gallbladder and liver in the etiology of biliary atresia remain unclear. In this study, transcriptomic analyses revealed the early onset of cholecystitis in the Sox17(+/-) embryos, together with the appearance of ectopic cystic duct-like epithelia in their gallbladders...
April 21, 2017: Development
https://www.readbyqxmd.com/read/28432092/a-genome-wide-investigation-on-biofilm-formation-in-bacillus-cereus
#3
Fang Yan, Yiyang Yu, Kevin Gozzi, Yun Chen, Jian-Hua Guo, Yunrong Chai
Bacillus cereus is a soil-dwelling Gram-positive bacterium capable of forming structured multicellular communities, or biofilms. However, the regulatory pathways controlling biofilm formation are less well understood in B. cereus In this work, we developed a method to study B. cereus biofilms formed at the air-liquid interface. We applied two genome-wide approaches, random transposon insertion mutagenesis to identify genes that are potentially important for biofilm formation, and transcriptome analyses by RNA-seq to characterize genes that are differentially expressed in B...
April 21, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28431977/transcriptome-comparison-reveals-insights-into-muscle-response-to-hypoxia-in-blunt-snout-bream-megalobrama-amblycephala
#4
Bo-Xiang Chen, Shao-Kui Yi, Wei-Feng Wang, Yan He, Yan Huang, Ze-Xia Gao, Hong Liu, Wei-Min Wang, Huan-Ling Wang
The economic and biological significance of blunt snout bream (Megalobrama amblycephala) makes this species important to explore the underlying molecular mechanism of hypoxia response. In the present study, we compared the transcriptional responses to serious hypoxia in skeletal muscle among hypoxia tolerant (MT), sensitive (MS) and control (without hypoxia treatment, MC) M. amblycephala obtained according to the time difference of losing balance after hypoxia treatment. A total of 88,200,889 clean reads were generated and assembled into 44,493 unigenes...
April 18, 2017: Gene
https://www.readbyqxmd.com/read/28431938/selective-inhibition-of-ezh2-by-a-small-molecule-inhibitor-regulates-microglial-gene-expression-essential-for-inflammation
#5
Sarder Arifuzzaman, Amitabh Das, Sun Hwa Kim, Taeho Yoon, Young Seek Lee, Kyoung Hwa Jung, Young Gyu Chai
Multiple studies have documented that Enhancer of zeste homolog 2 (EZH2) could play a role in inflammation and a wide range of malignancies; however, the underlying mechanisms remain largely unaddressed. Microglial activation is a key process in the production and release of numerous pro-inflammatory mediators that play important roles in inflammation and neurodegeneration in the central nervous system (CNS). Therefore, our aim was to investigate whether inhibition of EZH2 with the selective small molecule inhibitor EPZ-6438 protects against neonatal microglial activation...
April 18, 2017: Biochemical Pharmacology
https://www.readbyqxmd.com/read/28431567/transcriptome-profiling-of-elymus-sibiricus-an-important-forage-grass-in-qinghai-tibet-plateau-reveals-novel-insights-into-candidate-genes-that-potentially-connected-to-seed-shattering
#6
Wengang Xie, Junchao Zhang, Xuhong Zhao, Zongyu Zhang, Yanrong Wang
BACKGROUND: Elymus sibiricus is an important forage grass in semi-arid regions, but it is difficult to grow for commercial seed production due to high seed shattering. To better understand the underlying mechanism and explore the putative genes related to seed shattering, we conducted a combination of morphological, histological, physiochemical and transcriptome analysis on two E. sibiricus genotypes (XH09 and ZhN03) that have contrasting seed shattering. RESULTS: The results show that seed shattering is generally caused by a degradation of the abscission layer...
April 21, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28431521/a-reference-floral-transcriptome-of-sexual-and-apomictic-paspalum-notatum
#7
Juan Pablo A Ortiz, Santiago Revale, Lorena A Siena, Maricel Podio, Luciana Delgado, Juliana Stein, Olivier Leblanc, Silvina C Pessino
BACKGROUND: Paspalum notatum Flügge is a subtropical grass native to South America, which includes sexual diploid and apomictic polyploid biotypes. In the past decade, a number of apomixis-associated genes were discovered in this species through genetic mapping and differential expression surveys. However, the scarce information on Paspalum sequences available in public databanks limited annotations and functional predictions for these candidates. RESULTS: We used a long-read 454/Roche FLX+ sequencing strategy to produce robust reference transcriptome datasets from florets of sexual and apomictic Paspalum notatum genotypes and delivered a list of transcripts showing differential representation in both reproductive types...
April 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28431510/delayed-response-to-cold-stress-is-characterized-by-successive-metabolic-shifts-culminating-in-apple-fruit-peel-necrosis
#8
Nigel E Gapper, Maarten L A T M Hertog, Jinwook Lee, David A Buchanan, Rachel S Leisso, Zhangjun Fei, Guiqin Qu, James J Giovannoni, Jason W Johnston, Robert J Schaffer, Bart M Nicolaï, James P Mattheis, Christopher B Watkins, David R Rudell
BACKGROUND: Superficial scald is a physiological disorder of apple fruit characterized by sunken, necrotic lesions appearing after prolonged cold storage, although initial injury occurs much earlier in the storage period. To determine the degree to which the transition to cell death is an active process and specific metabolism involved, untargeted metabolic and transcriptomic profiling was used to follow metabolism of peel tissue over 180 d of cold storage. RESULTS: The metabolome and transcriptome of peel destined to develop scald began to diverge from peel where scald was controlled using antioxidant (diphenylamine; DPA) or rendered insensitive to ethylene using 1-methylcyclopropene (1-MCP) beginning between 30 and 60 days of storage...
April 21, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28431227/membrane-lipids-speak-to-histones
#9
Yuxiang Zheng, Lewis C Cantley
In this issue of Molecular Cell, Ye et al. (2017) use a combination of genetic, metabolomic, and transcriptomic approaches to explore the potential for methionine metabolism to influence signal transduction and gene expression in budding yeast.
April 20, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28431016/somatic-transposition-and-meiotically-driven-elimination-of-an-active-helitron-family-in-pleurotus-ostreatus
#10
Alessandra Borgognone, Raúl Castanera, Elaia Muguerza, Antonio G Pisabarro, Lucía Ramírez
Helitrons constitute a superfamily of DNA transposons that were discovered in silico and are widespread in most eukaryotic genomes. They are postulated to mobilize through a "rolling-circle" mechanism, but the experimental evidence of their transposition has been described only recently. Here, we present the inheritance patterns of HELPO1 and HELPO2 helitron families in meiotically derived progeny of the basidiomycete Pleurotus ostreatus. We found distorted segregation patterns of HELPO2 helitrons that led to a strong under-representation of these elements in the progeny...
April 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28431015/large-scale-collection-of-full-length-cdna-and-transcriptome-analysis-in-hevea-brasiliensis
#11
Yuko Makita, Kiaw Kiaw Ng, G Veera Singham, Mika Kawashima, Hideki Hirakawa, Shusei Sato, Ahmad Sofiman Othman, Minami Matsui
Natural rubber has unique physical properties that cannot be replaced by products from other latex-producing plants or petrochemically produced synthetic rubbers. Rubber from Hevea brasiliensis is the main commercial source for this natural rubber that has a cis-polyisoprene configuration. For sustainable production of enough rubber to meet demand elucidation of the molecular mechanisms involved in the production of latex is vital. To this end, we firstly constructed rubber full-length cDNA libraries of RRIM 600 cultivar and sequenced around 20,000 clones by the Sanger method and over 15,000 contigs by Illumina sequencer...
April 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28430642/immunocompetent-mouse-allograft-models-for-development-of-therapies-to-target-breast-cancer-metastasis
#12
Yuan Yang, Howard H Yang, Ying Hu, Peter H Watson, Huaitian Liu, Thomas R Geiger, Miriam R Anver, Diana C Haines, Philip Martin, Jeffrey E Green, Maxwell P Lee, Kent W Hunter, Lalage M Wakefield
Effective drug development to combat metastatic disease in breast cancer would be aided by the availability of well-characterized preclinical animal models that (a) metastasize with high efficiency, (b) metastasize in a reasonable time-frame, (c) have an intact immune system, and (d) capture some of the heterogeneity of the human disease. To address these issues, we have assembled a panel of twelve mouse mammary cancer cell lines that can metastasize efficiently on implantation into syngeneic immunocompetent hosts...
February 25, 2017: Oncotarget
https://www.readbyqxmd.com/read/28430144/a-systems-biology-approach-using-transcriptomic-data-reveals-genes-and-pathways-in-porcine-skeletal-muscle-affected-by-dietary-lysine
#13
Taiji Wang, Jean M Feugang, Mark A Crenshaw, Naresh Regmi, John R Blanton, Shengfa F Liao
Nine crossbred finishing barrows (body weight 94.4 ± 6.7 kg) randomly assigned to three dietary treatments were used to investigate the effects of dietary lysine on muscle growth related metabolic and signaling pathways. Muscle samples were collected from the longissimus dorsi of individual pigs after feeding the lysine-deficient (4.30 g/kg), lysine-adequate (7.10 g/kg), or lysine-excess (9.80 g/kg) diet for five weeks, and the total RNA was extracted afterwards. Affymetrix Porcine Gene 1.0 ST Array was used to quantify the expression levels of 19,211 genes...
April 21, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28430122/a-comprehensive-diverse-omics-approach-to-better-understanding-the-molecular-pathomechanisms-of-down-syndrome
#14
REVIEW
Keiichi Ishihara, Satoshi Akiba
Diverse '-omics' technologies permit the comprehensive quantitative profiling of a variety of biological molecules. Comparative '-omics' analyses, such as transcriptomics and proteomics, are powerful and useful tools for unraveling the molecular pathomechanisms of various diseases. As enhanced oxidative stress has been demonstrated in humans and mice with Down syndrome (DS), a redox proteomic analysis is useful for understanding how enhanced oxidative stress aggravates the state of individuals with oxidative stress-related disorders...
April 21, 2017: Brain Sciences
https://www.readbyqxmd.com/read/28429829/molecular-adaptation-in-the-world-s-deepest-living-animal-insights-from-transcriptome-sequencing-of-the-hadal-amphipod-hirondellea-gigas
#15
Yi Lan, Jin Sun, Renmao Tian, Douglas H Bartlett, Runsheng Li, Yue Him Wong, Weipeng Zhang, Jian-Wen Qiu, Ting Xu, Li-Sheng He, Harry G Tabata, Pei-Yuan Qian
The Challenger Deep in the Mariana Trench is the deepest point in the oceans of our planet. Understanding how animals adapt to this harsh environment characterized by high hydrostatic pressure, food-limited, dark, and cold is of great scientific interest. Of the animals dwelling in the Challenger Deep, amphipods have been captured using baited traps. In the present study, we sequenced the transcriptome of the amphipod Hirondellea gigas collected at a depth of 10,929 m from the East Pond of the Challenger Deep...
April 21, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28429720/noumeavirus-replication-relies-on-a-transient-remote-control-of-the-host-nucleus
#16
Elisabeth Fabre, Sandra Jeudy, Sébastien Santini, Matthieu Legendre, Mathieu Trauchessec, Yohann Couté, Jean-Michel Claverie, Chantal Abergel
Acanthamoeba are infected by a remarkable diversity of large dsDNA viruses, the infectious cycles of which have been characterized using genomics, transcriptomics and electron microscopy. Given their gene content and the persistence of the host nucleus throughout their infectious cycle, the Marseilleviridae were initially assumed to fully replicate in the cytoplasm. Unexpectedly, we find that their virions do not incorporate the virus-encoded transcription machinery, making their replication nucleus-dependent...
April 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28429538/finding-a-partner-in-the-ocean-molecular-and-evolutionary-bases-of-the-response-to-sexual-cues-in-a-planktonic-diatom
#17
Swaraj Basu, Shrikant Patil, Daniel Mapleson, Monia Teresa Russo, Laura Vitale, Cristina Fevola, Florian Maumus, Raffaella Casotti, Thomas Mock, Mario Caccamo, Marina Montresor, Remo Sanges, Maria Immacolata Ferrante
Microalgae play a major role as primary producers in aquatic ecosystems. Cell signalling regulates their interactions with the environment and other organisms, yet this process in phytoplankton is poorly defined. Using the marine planktonic diatom Pseudo-nitzschia multistriata, we investigated the cell response to cues released during sexual reproduction, an event that demands strong regulatory mechanisms and impacts on population dynamics. We sequenced the genome of P. multistriata and performed phylogenomic and transcriptomic analyses, which allowed the definition of gene gains and losses, horizontal gene transfers, conservation and evolutionary rate of sex-related genes...
April 21, 2017: New Phytologist
https://www.readbyqxmd.com/read/28429323/protein-targeting-to-the-plastid-of-euglena
#18
Dion G Durnford, Steven D Schwartzbach
The lateral transfer of photosynthesis between kingdoms through endosymbiosis is among the most spectacular examples of evolutionary innovation. Euglena, which acquired a chloroplast indirectly through an endosymbiosis with a green alga, represents such an example. As with other endosymbiont-derived plastids from eukaryotes, there are additional membranes that surround the organelle, of which Euglena has three. Thus, photosynthetic genes that were transferred from the endosymbiont to the host nucleus and whose proteins are required in the new plastid, are now faced with targeting and plastid import challenges...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28429320/euglena-gracilis-genome-and-transcriptome-organelles-nuclear-genome-assembly-strategies-and-initial-features
#19
ThankGod Echezona Ebenezer, Mark Carrington, Michael Lebert, Steven Kelly, Mark C Field
Euglena gracilis is a major component of the aquatic ecosystem and together with closely related species, is ubiquitous worldwide. Euglenoids are an important group of protists, possessing a secondarily acquired plastid and are relatives to the Kinetoplastidae, which themselves have global impact as disease agents. To understand the biology of E. gracilis, as well as to provide further insight into the evolution and origins of the Kinetoplastidae, we embarked on sequencing the nuclear genome; the plastid and mitochondrial genomes are already in the public domain...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28429252/analysis-of-global-gene-expression-profiles-during-the-flowering-initiation-process-of-lilium%C3%A2-%C3%A3-%C3%A2-formolongi
#20
Yu-Fan Li, Ming-Fang Zhang, Meng Zhang, Gui-Xia Jia
The onset of flowering is critical for the reproductive development of plants. Lilium × formolongi is a lily hybrid that flowers within a year after sowing. We successfully identified four important stages during vegetative growth and flowering initiation of L. × formolongi under long day conditions. The plant tissues from the four stages were used in a genome-wide transcriptional analysis to investigate stage-specific changes of gene expression in L. × formolongi. In total, the sequence reads of the four RNA-sequencing libraries were assembled into 52,824 unigenes, of which 37,031 (70...
April 20, 2017: Plant Molecular Biology
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