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https://www.readbyqxmd.com/read/27913887/transcriptomics-analysis-of-hulless-barley-during-grain-development-with-a-focus-on-starch-biosynthesis
#1
Yawei Tang, Xingquan Zeng, Yulin Wang, Lijun Bai, Qijun Xu, Zexiu Wei, Hongjun Yuan, Tashi Nyima
Hulless barley, with its unique nutritional value and potential health benefits, has increasingly attracted attentions in recent years. However, the transcription dynamics during hulless barley grain development is not well understood. In the present study, we investigated the transcriptome changes during barley grain development using Illumina paired-end RNA-sequencing. Two datasets of the developing grain transcriptomes from two barley landraces with the differential seed starch synthesis traits were generated, and comparative transcriptome approach in both genotypes was performed...
December 2, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27913643/biogenesis-and-transcriptional-regulation-of-long-noncoding-rnas-in-the-human-immune-system
#2
REVIEW
Charles F Spurlock, Philip S Crooke, Thomas M Aune
The central dogma of molecular biology states that DNA makes RNA makes protein. Discoveries over the last quarter of a century found that the process of DNA transcription into RNA gives rise to a diverse array of functional RNA species, including genes that code for protein and noncoding RNAs. For decades, the focus has been on understanding how protein-coding genes are regulated to influence protein expression. However, with the completion of the Human Genome Project and follow-up ENCODE data, it is now appreciated that only 2-3% of the genome codes for protein-coding gene exons and that the bulk of the transcribed genome, apart from ribosomal RNAs, is at the level of noncoding RNA genes...
December 15, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/27913571/snord126-promotes-hcc-and-crc-cell-growth-by-activating-the-pi3k-akt-pathway-through-fgfr2
#3
Xianlong Fang, Dongmei Yang, Hongping Luo, Shuai Wu, Wenjie Dong, Jing Xiao, Sujing Yuan, Aimin Ni, Kang-Jian Zhang, Xin-Yuan Liu, Liang Chu
Small nucleolar RNA (snoRNA) dysfunctions have been associated with cancer development. SNORD126 is an orphan C/D box snoRNA that is encoded within introns 5-6 of its host gene, cyclin B1-interacting protein 1 (CCNB1IP1) The cancer-associated molecular mechanisms triggered by SNORD126 are not fully understood. Here, we demonstrate that SNORD126 is highly expressed in hepatocellular carcinoma (HCC) and colorectal cancer (CRC) patient samples. SNORD126 increased Huh-7 and SW480 cell growth and tumorigenicity in nude mice...
December 2, 2016: Journal of Molecular Cell Biology
https://www.readbyqxmd.com/read/27913414/distinct-anaerobic-bacterial-consumers-of-cellobiose-derived-carbon-in-boreal-fens-differing-in-ch4-vs-co2-production-ratio
#4
Heli Juottonen, Alexander Eiler, Christina Biasi, Eeva-Stiina Tuittila, Kim Yrjälä, Hannu Fritze
: Northern peatlands in general have high methane (CH4) emissions, but individual peatlands show considerable variation as CH4 sources. Particularly in nutrient poor peatlands, CH4 production can be low and exceeded by carbon dioxide (CO2) production from unresolved anaerobic processes. To clarify the role anaerobic bacterial degraders play in this variation, we compared consumers of cellobiose-derived carbon in two fens differing in nutrient status and the ratio of CH4 and CO2 produced...
December 2, 2016: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27913256/rapid-upregulation-of-the-hippocampal-connexins-36-and-45-mrna-levels-during-memory-consolidation
#5
Siamak Beheshti, Reyhaneh Zeinali, Abolghasem Esmaeili
Gap junction channels are implicated in learning and memory process. However, their role on each of the particular stages of memory formation have been studied less. In this study, the time profile of the expression levels of hippocampal connexins 36 and 45 (Cx36 and Cx45) mRNAs was measured during memory consolidation, in a passive avoidance paradigm. Totally 36 adult male rats were distributed into 5 groups of each 6. At different times profiles (30min, 3, 6 and 24h) following training, rats were decapitated and their hippocampi were immediately removed and frozen in liquid nitrogen...
November 29, 2016: Behavioural Brain Research
https://www.readbyqxmd.com/read/27913250/identification-of-non-coding-and-coding-rnas-in-porcine-endometrium
#6
Yueying Wang, Tao Hu, Lihang Wu, Xiaoran Liu, Songyi Xue, Minggang Lei
One of the most critical periods of embryonic loss in pig is day 12 of pregnancy, when implantation begins. Here, we analyzed the gene expression on day 12 of pregnancy and non-pregnancy in the porcine endometrium using RNA sequencing (RNA-seq). 237 mRNAs, 34 lncRNAs and 1 miRNA were significantly differentially expressed between the two groups. Further functional analyses were conducted to identify these differentially expressed transcripts. The results demonstrated that they participate in various biological processes, such as cell adhesion, binding, nucleic and metabolic processes...
November 29, 2016: Genomics
https://www.readbyqxmd.com/read/27913212/vcp-cooperates-with-ubxd1-to-degrade-mitochondrial-outer-membrane-protein-mcl1-in-model-of-huntington-s-disease
#7
Xing Guo, Xin Qi
Proteasome-dependent turnover of mitochondrial outer membrane (OMM)-associated proteins is one of the mechanisms for maintaining proper mitochondrial quality and function. However, the underlying pathways and their implications in human disease are poorly understood. Huntington's disease (HD) is a fatal, inherited neurodegenerative disorder caused by expanded CAG repeats in the N terminal of the huntingtin gene (mutant Huntingtin, mtHtt). In this study, we show an extensive degradation of the OMM protein MCL1 (Myeloid cell leukemia sequence 1) in both HD mouse striatal cells and HD patient fibroblasts...
November 29, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27912752/a-comparison-of-microrna-expression-profiles-from-splenic-hemangiosarcoma-splenic-nodular-hyperplasia-and-normal-spleens-of-dogs
#8
Janet A Grimes, Nripesh Prasad, Shawn Levy, Russell Cattley, Stephanie Lindley, Harry W Boothe, Ralph A Henderson, Bruce F Smith
BACKGROUND: Splenic masses are common in older dogs; yet diagnosis preceding splenectomy and histopathology remains elusive. MicroRNAs (miRNAs) are short, non-coding RNAs that play a role in post-transcriptional regulation, and differential expression of miRNAs between normal and tumor tissue has been used to diagnose neoplastic diseases. The objective of this study was to determine differential expression of miRNAs by use of RNA-sequencing in canine spleens that were histologically confirmed as hemangiosarcoma, nodular hyperplasia, or normal...
December 3, 2016: BMC Veterinary Research
https://www.readbyqxmd.com/read/27912056/conflict-resolution-in-the-genome-how-transcription-and-replication-make-it-work
#9
REVIEW
Stephan Hamperl, Karlene A Cimprich
The complex machineries involved in replication and transcription translocate along the same DNA template, often in opposing directions and at different rates. These processes routinely interfere with each other in prokaryotes, and mounting evidence now suggests that RNA polymerase complexes also encounter replication forks in higher eukaryotes. Indeed, cells rely on numerous mechanisms to avoid, tolerate, and resolve such transcription-replication conflicts, and the absence of these mechanisms can lead to catastrophic effects on genome stability and cell viability...
December 1, 2016: Cell
https://www.readbyqxmd.com/read/27911875/autophagy-flux-induced-by-ginsenoside-rg3-attenuates-human-prion-protein-mediated-neurotoxicity-and-mitochondrial-dysfunction
#10
Ji-Hong Moon, Ju-Hee Lee, You-Jin Lee, Sang-Youel Park
Mitochondrial quality control is a process by which mitochondria undergo successive rounds of fusion and fission with dynamic exchange of components to segregate functional and damaged elements. Removal of mitochondrion that contains damaged components is accomplished via autophagy. In this study, we investigated whether ginsenoside Rg3, an active ingredient of the herbal medicine ginseng that is used as a tonic and restorative agent, could attenuate prion peptide, PrP (106-126)-induced neurotoxicity and mitochondrial damage...
November 30, 2016: Oncotarget
https://www.readbyqxmd.com/read/27911846/dna-methylome-of-the-20-gigabase-norway-spruce-genome
#11
Israel Ausin, Suhua Feng, Chaowei Yu, Wanlu Liu, Hsuan Yu Kuo, Elise L Jacobsen, Jixian Zhai, Javier Gallego-Bartolome, Lin Wang, Ulrika Egertsdotter, Nathaniel R Street, Steven E Jacobsen, Haifeng Wang
DNA methylation plays important roles in many biological processes, such as silencing of transposable elements, imprinting, and regulating gene expression. Many studies of DNA methylation have shown its essential roles in angiosperms (flowering plants). However, few studies have examined the roles and patterns of DNA methylation in gymnosperms. Here, we present genome-wide high coverage single-base resolution methylation maps of Norway spruce (Picea abies) from both needles and somatic embryogenesis culture cells via whole genome bisulfite sequencing...
November 28, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27911841/high-performance-multiplexed-fluorescence-in-situ-hybridization-in-culture-and-tissue-with-matrix-imprinting-and-clearing
#12
Jeffrey R Moffitt, Junjie Hao, Dhananjay Bambah-Mukku, Tian Lu, Catherine Dulac, Xiaowei Zhuang
Highly multiplexed single-molecule FISH has emerged as a promising approach to spatially resolved single-cell transcriptomics because of its ability to directly image and profile numerous RNA species in their native cellular context. However, background-from off-target binding of FISH probes and cellular autofluorescence-can become limiting in a number of important applications, such as increasing the degree of multiplexing, imaging shorter RNAs, and imaging tissue samples. Here, we developed a sample clearing approach for FISH measurements...
November 22, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27911772/c-terminal-domain-ctd-phosphatase-links-rho-gtpase-signaling-to-pol-ii-ctd-phosphorylation-in-arabidopsis-and-yeast
#13
Bo Zhang, Guohua Yang, Yu Chen, Yihong Zhao, Peng Gao, Bo Liu, Haiyang Wang, Zhi-Liang Zheng
Rho GTPases, including the Rho, Cdc42, Rac, and ROP subfamilies, act as pivotal signaling switches in various growth and developmental processes. Compared with the well-defined role of cytoskeletal organization in Rho signaling, much less is known regarding transcriptional regulation. In a mutant screen for phenotypic enhancers of transgenic Arabidopsis plants expressing a constitutively active form of ROP2 (designated CA1-1), we identified RNA polymerase II (Pol II) C-terminal domain (CTD) phosphatase-like 1 (CPL1) as a transcriptional regulator of ROP2 signaling...
November 28, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27911744/dysregulation-of-mrna-localization-and-translation-in-genetic-disease
#14
Eric T Wang, J Matthew Taliaferro, Ji-Ann Lee, Indulekha P Sudhakaran, Wilfried Rossoll, Christina Gross, Kathryn R Moss, Gary J Bassell
RNA-binding proteins (RBPs) acting at various steps in the post-transcriptional regulation of gene expression play crucial roles in neuronal development and synaptic plasticity. Genetic mutations affecting several RBPs and associated factors lead to diverse neurological symptoms, as characterized by neurodevelopmental and neuropsychiatric disorders, neuromuscular and neurodegenerative diseases, and can often be multisystemic diseases. We will highlight the physiological roles of a few specific proteins in molecular mechanisms of cytoplasmic mRNA regulation, and how these processes are dysregulated in genetic disease...
November 9, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27911729/polyadenylation-and-degradation-of-rna-in-the-mitochondria
#15
REVIEW
Shiri Levy, Gadi Schuster
Mitochondria have their own gene expression machinery and the relative abundance of RNA products in these organelles in animals is mostly dictated by their rate of degradation. The molecular mechanisms regulating the differential accumulation of the transcripts in this organelle remain largely elusive. Here, we summarize the present knowledge of how RNA is degraded in human mitochondria and describe the coexistence of stable poly(A) tails and the nonabundant tails, which have been suggested to play a role in the RNA degradation process...
October 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27911723/ribonucleoprotein-bodies-are-phased-in
#16
REVIEW
Aristeidis P Sfakianos, Alan J Whitmarsh, Mark P Ashe
Intracellular compartments are necessary for the regulation of many biochemical processes that ensure cell survival, growth and proliferation. Compartmentalisation is commonly achieved in organelles with defined lipid membranes, such as mitochondria, endoplasmic reticulum or the Golgi apparatus. While these organelles are responsible for many localised biochemical processes, recent evidence points to another class of compartments that lack membrane boundaries. The structure and content of these bodies depend on their function and subcellular localisation, but they mainly incorporate proteins and RNA...
October 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27911720/the-roles-of-the-exoribonucleases-dis3l2-and-xrn1-in-human-disease
#17
REVIEW
Amy L Pashler, Benjamin P Towler, Christopher I Jones, Sarah F Newbury
RNA degradation is a vital post-transcriptional process which ensures that transcripts are maintained at the correct level within the cell. DIS3L2 and XRN1 are conserved exoribonucleases that are critical for the degradation of cytoplasmic RNAs. Although the molecular mechanisms of RNA degradation by DIS3L2 and XRN1 have been well studied, less is known about their specific roles in the development of multicellular organisms or human disease. This review focusses on the roles of DIS3L2 and XRN1 in the pathogenesis of human disease, particularly in relation to phenotypes seen in model organisms...
October 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27911483/effects-of-dietary-heme-iron-and-exercise-training-on-abdominal-fat-accumulation-and-lipid-metabolism-in-high-fat-diet-fed-mice
#18
Masanori Katsumura, Shoko Takagi, Hana Oya, Shohei Tamura, Takaoki Saneyasu, Kazuhisa Honda, Hiroshi Kamisoyama
Animal by-products can be recycled and used as sources of essential nutrients. Water-soluble heme iron (WSHI), a functional food additive for supplementing iron, is produced by processing animal blood. In this study, we investigated the effects of dietary supplementation of 3% WSHI and exercise training for 4 weeks on the accumulation of abdominal fat and lipid metabolism in mice fed high-fat diet. Exercise-trained mice had significantly less perirenal adipose tissue, whereas WSHI-fed mice tended to have less epididymal adipose tissue...
December 2, 2016: Animal Science Journal, Nihon Chikusan Gakkaihō
https://www.readbyqxmd.com/read/27911186/rna-decay-evolution-and-the-testis
#19
Samantha H Jones, Miles Wilkinson
NMD is a highly conserved pathway that degrades specific subsets of RNAs. There is increasing evidence for roles of NMD in development. In this commentary, we focus on spermatogenesis, a process dramatically impeded upon loss or disruption of NMD. NMD requires strict regulation for normal spermatogenesis, as loss of a newly discovered NMD repressor, UPF3A, also causes spermatogenic defects, most prominently during meiosis. We discuss the unusual evolution of UPF3A, whose paralog, UPF3B, has the opposite biochemical function and acts in brain development...
December 2, 2016: RNA Biology
https://www.readbyqxmd.com/read/27910903/prostate-cancer-patients-negative-biopsy-controls-discrimination-by-untargeted-metabolomics-analysis-of-urine-by-lc-qtof-upstream-information-on-other-omics
#20
M A Fernández-Peralbo, E Gómez-Gómez, M Calderón-Santiago, J Carrasco-Valiente, J Ruiz-García, M J Requena-Tapia, M D Luque de Castro, F Priego-Capote
The existing clinical biomarkers for prostate cancer (PCa) diagnosis are far from ideal (e.g., the prostate specific antigen (PSA) serum level suffers from lack of specificity, providing frequent false positives leading to over-diagnosis). A key step in the search for minimum invasive tests to complement or replace PSA should be supported on the changes experienced by the biochemical pathways in PCa patients as compared to negative biopsy control individuals. In this research a comprehensive global analysis by LC-QTOF was applied to urine from 62 patients with a clinically significant PCa and 42 healthy individuals, both groups confirmed by biopsy...
December 2, 2016: Scientific Reports
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