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https://www.readbyqxmd.com/read/28550524/cop9-signalosome-subunit-pfcsne-regulates-secondary-metabolism-and-conidial-formation-in-pestalotiopsis-fici
#1
Yanjing Zheng, Xiuna Wang, Xiaoling Zhang, Wei Li, Gang Liu, Shihua Wang, Xiufeng Yan, Huixi Zou, Wen-Bing Yin
The COP9 signalosome (CSN) is a highly conserved multiprotein complex in all eukaryotes and involved in regulation of organism development. In filamentous fungi, several lines of evidence indicate that fungal development and secondary metabolism (SM) are mediated by the fifth subunit of CSN, called CsnE. Here we uncover a connection with CsnE and conidial formation as well as SM regulation in the plant endophytic fungus Pestalotiopsis fici. A homology search of the P. fici genome with CsnE, involved in sexual development and SM in Aspergillus nidulans, identified PfCsnE...
May 25, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28550410/different-exogenous-sugars-affect-the-hormone-signal-pathway-and-sugar-metabolism-in-red-globe-vitis-vinifera-l-plantlets-grown-in-vitro-as-shown-by-transcriptomic-analysis
#2
Juan Mao, Wenfang Li, Baoqin Mi, Mohammed Mujitaba Dawuda, Alejandro Calderón-Urrea, Zonghuan Ma, Yongmei Zhang, Baihong Chen
Exogenously applied 2% fructose is the most appropriate carbon source that enhances photosynthesis and growth of grape plantlets compared with the same concentrations of sucrose and glucose. The role of the sugars was regulated by the expression of key candidate genes related to hormones, key metabolic enzymes, and sugar metabolism of grape plantlets ( Vitis vinifera L.) grown in vitro. The addition of sugars including sucrose, glucose, and fructose is known to be very helpful for the development of grape (V...
May 26, 2017: Planta
https://www.readbyqxmd.com/read/28550284/multiple-viral-infections-in-agaricus-bisporus-characterisation-of-18-unique-rna-viruses-and-8-orfans-identified-by-deep-sequencing
#3
Gregory Deakin, Edward Dobbs, Julie M Bennett, Ian M Jones, Helen M Grogan, Kerry S Burton
Thirty unique non-host RNAs were sequenced in the cultivated fungus, Agaricus bisporus, comprising 18 viruses each encoding an RdRp domain with an additional 8 ORFans (non-host RNAs with no similarity to known sequences). Two viruses were multipartite with component RNAs showing correlative abundances and common 3' motifs. The viruses, all positive sense single-stranded, were classified into diverse orders/families. Multiple infections of Agaricus may represent a diverse, dynamic and interactive viral ecosystem with sequence variability ranging over 2 orders of magnitude and evidence of recombination, horizontal gene transfer and variable fragment numbers...
May 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28550087/transcriptional-networks-in-rodent-models-support-a-role-for-gut-brain-communication-in-neurogenic-hypertension-a-review-of-the-evidence
#4
Jasenka Zubcevic, Ashley Baker, Christopher J Martyniuk
Hypertension (HTN) is the most prevalent condition observed in primary health care. Hypertension shows complex etiology, and neuroinflammation, overactive sympathetic drive, and the microbiome are associated with the disease. To obtain mechanistic perspective into neurogenic HTN, we first constructed a framework for transcriptional regulators of the disease using the Comparative Toxicogenomics Database. This approach yielded a core group of 178 transcripts that are prevalent in HTN, including leptin and neuropeptide Y...
May 26, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28549990/early-transcriptome-responses-of-the-bovine-midcycle-corpus-luteum-to-prostaglandin-f2%C3%AE-includes-cytokine-signaling
#5
Heather Talbott, Xiaoying Hou, Fang Qiu, Pan Zhang, Chittibabu Guda, Fang Yu, Robert A Cushman, Jennifer R Wood, Cheng Wang, Andrea S Cupp, John S Davis
In ruminants, prostaglandin F2alpha (PGF2α)-mediated luteolysis is essential prior to estrous cycle resumption, and is a target for improving fertility. To deduce early PGF2α-provoked changes in the corpus luteum a short time-course (0.5-4 h) was performed on cows at midcycle. A microarray-determined transcriptome was established and examined by bioinformatic pathway analysis. Classic PGF2α effects were evident by changes in early response genes (FOS, JUN, ATF3) and prediction of active pathways (PKC, MAPK)...
May 23, 2017: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/28549934/in-vitro-metabolomic-approaches-to-investigating-the-potential-biological-effects-of-phenolic-compounds-an-update
#6
REVIEW
Úrsula Catalán, Laura Barrubés, Rosa Maria Valls, Rosa Solà, Laura Rubió
Dietary phenolic compounds (PCs) have been receiving interest for their presumed roles in disease prevention. However, there is a lack of studies on the underlying molecular mechanisms. In this regard, in vitro metabolomic approaches are suitable for the investigation of the molecular changes in response to PC exposure. Up to date, the biological effects of PCs have only been examined for PCs from rosemary (Rosmarinus officinalis), olive oil, and resveratrol using cell-based metabolomic approach, although transcriptomic and/or proteomic studies have also been conducted in the same in vitro cell experiment in some cases...
May 23, 2017: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/28549856/three-decades-of-managing-tomato-spotted-wilt-virus-in-peanut-in-southeastern-united-states
#7
REVIEW
R Srinivasan, M R Abney, A K Culbreath, R C Kemerait, R S Tubbs, W S Monfort, H R Pappu
Southeastern states namely Georgia, Florida, and Alabama produce two-thirds of the peanuts in the United States. Thrips-transmitted Tomato spotted wilt virus (TSWV), which causes spotted wilt disease, has been a major impediment to peanut production for the past three decades. The cultivars grown in the 1980s were extremely susceptible to TSWV. Early yield losses extended to tens of millions of dollars each year (up to 100% loss in many fields). This situation led to the creation of an interdisciplinary team known as "SWAT: Spotted Wilt Action Team"...
May 23, 2017: Virus Research
https://www.readbyqxmd.com/read/28549855/multi-platform-analysis-reveals-a-complex-transcriptome-architecture-of-a-circovirus
#8
Norbert Moldován, Zsolt Balázs, Dóra Tombácz, Zsolt Csabai, Attila Szűcs, Michael Snyder, Zsolt Boldogkői
In this study, we used Pacific Biosciences RS II long-read and Illumina HiScanSQ short-read sequencing technologies for the characterization of porcine circovirus type 1 (PCV-1) transcripts. Our aim was to identify novel RNA molecules and transcript isoforms, as well as to determine the exact 5'- and 3'-end sequences of previously described transcripts with single base-pair accuracy. We discovered a novel 3'-UTR length isoform of the Cap transcript, and a non-spliced Cap transcript variant. Additionally, our analysis has revealed a 3'-UTR isoform of Rep and two 5'-UTR isoforms of Rep' transcripts, and a novel splice variant of the longer Rep' transcript...
May 23, 2017: Virus Research
https://www.readbyqxmd.com/read/28549776/methylome-and-transcriptome-profiling-in-myasthenia-gravis-monozygotic-twins
#9
Shimrat Mamrut, Nili Avidan, Frédérique Truffault, Elsebeth Staun-Ram, Tarek Sharshar, Bruno Eymard, Mélinée Frenkian, Jiri Pitha, Marc de Baets, Laurent Servais, Sonia Berrih-Aknin, Ariel Miller
OBJECTIVE: To identify novel genetic and epigenetic factors associated with Myasthenia gravis (MG) using an identical twins experimental study design. METHODS: The transcriptome and methylome of peripheral monocytes were compared between monozygotic (MZ) twins discordant and concordant for MG, as well as with MG singletons and healthy controls, all females. Sets of differentially expressed genes and differentially methylated CpGs were validated using RT-PCR for expression and target bisulfite sequencing for methylation on additional samples...
May 23, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/28549625/a-matter-of-maturity-the-impact-of-pre-mrna-processing-in-gene-expression-and-antigen-presentation
#10
Rodrigo Prado Martins, Robin Fåhraeus
RNA processing plays a pivotal role in the diversification of high eukaryotes transcriptome and proteome. The expression of gene products controlling a variety of cellular and physiological processes depends largely on a complex maturation process undergone by pre-mRNAs to become translation-competent mRNAs. Here we review the different mechanisms involved in the pre-mRNA processing and disclose their impact in the gene regulation process in eukaryotic cells. We describe some viral strategies targeting pre-mRNA processing to control gene expression and host immune response and discuss their relevance as tools for a better understanding of cell biology...
May 23, 2017: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/28549623/standardising-rna-profiling-based-biomarker-application-in-cancer-the-need-for-robust-control-of-technical-variables
#11
REVIEW
James P Stewart, Susan Richman, Tim Maughan, Mark Lawler, Philip D Dunne, Manuel Salto-Tellez
Histopathology-based staging of colorectal cancer (CRC) has utility in assessing the prognosis of patient subtypes, but as yet cannot accurately predict individual patient's treatment response. Transcriptomics approaches, using array based or next generation sequencing (NGS) platforms, of formalin fixed paraffin embedded tissue can be harnessed to develop multi-gene biomarkers for predicting both prognosis and treatment response, leading to stratification of treatment. While transcriptomics can shape future biomarker development, currently <1% of published biomarkers become clinically validated tests, often due to poor study design or lack of independent validation...
May 23, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28549454/genomic-adaptation-to-agricultural-environments-cabbage-white-butterflies-pieris-rapae-as-a-case-study
#12
Kristin L Sikkink, Megan E Kobiela, Emilie C Snell-Rood
BACKGROUND: Agricultural environments have long presented an opportunity to study evolution in action, and genomic approaches are opening doors for testing hypotheses about adaptation to crops, pesticides, and fertilizers. Here, we begin to develop the cabbage white butterfly (Pieris rapae) as a system to test questions about adaptation to novel, agricultural environments. We focus on a population in the north central United States as a unique case study: here, canola, a host plant, has been grown during the entire flight period of the butterfly over the last three decades...
May 26, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28549198/de-novo-transcriptome-assembly-of-sugarcane-leaves-submitted-to-prolonged-water-deficit-stress
#13
A A Belesini, F M S Carvalho, B R Telles, G M de Castro, P F Giachetto, J S Vantini, S D Carlin, J O Cazetta, D G Pinheiro, M I T Ferro
Sugarcane production is strongly influenced by drought, which is a limiting factor for agricultural productivity in the world. In this study, the gene expression profiles obtained by de novo assembly of the leaf transcriptome of two sugarcane cultivars that differ in their physiological response to water deficit were evaluated by the RNA-Seq method: drought-tolerant cultivar (SP81-3250) and drought-sensitive cultivar (RB855453). For this purpose, plants were grown in a greenhouse for 60 days and were then submitted to three treatments: control (-0...
May 25, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28549159/a-non-photosynthetic-diatom-reveals-early-steps-of-reductive-evolution-in-plastids
#14
Ryoma Kamikawa, Daniel Moog, Stefan Zauner, Goro Tanifuji, Ken-Ichiro Ishida, Hideaki Miyashita, Shigeki Mayama, Tetsuo Hashimoto, Uwe-G Maier, John M Archibald, Yuji Inagaki
Non-photosynthetic plastids retain important biological functions and are indispensable for cell viability. However, the detailed processes underlying the loss of plastidal functions other than photosynthesis remain to be fully understood. In this study, we used transcriptomics, subcellular localization, and phylogenetic analyses to characterize the biochemical complexity of the non-photosynthetic plastids of the apochlorotic diatom Nitzschia sp. NIES-3581. We found that these plastids have lost isopentenyl pyrophosphate (IPP) biosynthesis and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO)-based carbon fixation but have retained various proteins for other metabolic pathways, including amino acid biosynthesis, and a portion of the Calvin-Benson cycle comprised only of glycolysis/gluconeogenesis, and the reductive pentose phosphate pathway (rPPP)...
May 26, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28548993/muscle-metabolism
#15
Nicolas Tardif, Jonathan Grip, Olav Rooyackers
PURPOSE OF REVIEW: To review the recent findings on metabolic derangements leading to loss of muscle mass and function. RECENT FINDINGS: Several recent studies investigated methods to assess muscle mass and function and its clinical relevance. These are also included. A few studies confirm that a low muscle mass is related to a worse outcome but also a compromised muscle function at discharge is related to long-term survival. A low quality of muscle assessed by the density of muscle from a computed tomography scan is related to mortality...
May 25, 2017: Current Opinion in Critical Care
https://www.readbyqxmd.com/read/28548969/transcriptome-profiling-in-preadipocytes-identifies-long-noncoding-rnas-as-sam68-targets
#16
Naomi Li, Steven Hébert, Jingwen Song, Claudia L Kleinman, Stéphane Richard
The KH-type RNA binding protein Sam68 is required for adipogenesis. We have previously shown that Sam68-deficient mice have a lean phenotype and are protected against dietary-induced obesity due to defects in mTOR and S6K1 alternative splicing. Herein we profiled the transcriptome of Sam68 wild type and deficient 3T3-L1 mouse preadipocytes. We identified 652 protein-coding genes and 9 ncRNAs that were significantly altered with the loss of Sam68. As expected, downregulated genes were significantly associated with GO terms linked to cell migration, motility, and fat cell differentiation, while upregulated genes were mostly associated with GO terms linked to neurogenesis...
May 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28548702/p16-loss-and-e2f-cell-cycle-deregulation-in-infant-posterior-fossa-ependymoma
#17
Seth C Lummus, Andrew M Donson, Katherine Gowan, Kenneth L Jones, Rajeev Vibhakar, Nicholas K Foreman, B K Kleinschmidt-DeMasters
BACKGROUND: Posterior fossa (PF) ependymomas (EPNs) in infants less than 1 year of age (iEPN-PF) have a poorer clinical outcome than EPNs in older children. While radiation therapy is the standard of care for the latter, it is withheld in infants to avoid neurotoxicity to immature brain. It is unknown whether the adverse outcome in iEPN-PFs is due to treatment differences or aggressive biology. We examined this question using molecular profiling. METHODS: Six anaplastic iEPN-PFs were subjected to transcriptomic analysis and FISH for p16 loss and gains of 1q, and compared with anaplastic PF EPNs from older children...
May 26, 2017: Pediatric Blood & Cancer
https://www.readbyqxmd.com/read/28548660/transcriptomic-and-micrornaomic-profiling-reveals-multi-faceted-mechanisms-to-cope-with-phosphate-stress-in-a-dinoflagellate
#18
Xinguo Shi, Xin Lin, Ling Li, Meizhen Li, Brian Palenik, Senjie Lin
Although gene regulation can occur at both transcriptional and epigenetic (microRNA) levels, combined transcriptomic and microRNAomic responses to environmental stress are still largely unexplored for marine plankton. Here, we conducted transcriptome and microRNAome sequencing for Prorocentrum donghaiense to understand the molecular mechanisms by which this dinoflagellate copes with phosphorus (P) deficiency. Under P-depleted conditions, G1/S specific cyclin gene was markedly downregulated, consistent with growth inhibition, and genes related to dissolved organic phosphorus (DOP) hydrolysis, carbon fixation, nitrate assimilation, glycolysis, and cellular motility were upregulated...
May 26, 2017: ISME Journal
https://www.readbyqxmd.com/read/28548655/an-n-acetylglucosamine-transporter-required-for-arbuscular-mycorrhizal-symbioses-in-rice-and-maize
#19
Marina Nadal, Ruairidh Sawers, Shamoon Naseem, Barbara Bassin, Corinna Kulicke, Abigail Sharman, Gynheung An, Kyungsook An, Kevin R Ahern, Amanda Romag, Thomas P Brutnell, Caroline Gutjahr, Niko Geldner, Christophe Roux, Enrico Martinoia, James B Konopka, Uta Paszkowski
Most terrestrial plants, including crops, engage in beneficial interactions with arbuscular mycorrhizal fungi. Vital to the association is mutual recognition involving the release of diffusible signals into the rhizosphere. Previously, we identified the maize no perception 1 (nope1) mutant to be defective in early signalling. Here, we report cloning of ZmNope1 on the basis of synteny with rice. NOPE1 encodes a functional homologue of the Candida albicans N-acetylglucosamine (GlcNAc) transporter NGT1, and represents the first plasma membrane GlcNAc transporter identified from plants...
May 26, 2017: Nature Plants
https://www.readbyqxmd.com/read/28548029/digital-assays-part-ii-digital-protein-and-cell-assays
#20
Amar S Basu
A digital assay is one in which the sample is partitioned into many containers such that each partition contains a discrete number of biological entities (0, 1, 2, 3, . . .). A powerful technique in the biologist's toolkit, digital assays bring a new level of precision in quantifying nucleic acids, measuring proteins and their enzymatic activity, and probing single-cell genotype and phenotype. Where part I of this review focused on the fundamentals of partitioning and digital PCR, part II turns its attention to digital protein and cell assays...
May 1, 2017: SLAS Technology
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