keyword
MENU ▼
Read by QxMD icon Read
search

Small rna

keyword
https://www.readbyqxmd.com/read/29228423/cd44v6-regulates-gastric-carcinoma-occurrence-and-development-through-up-regulating-vegf-expression
#1
S Liang, H-L Li, G-Y Han, J-H Cui
OBJECTIVE: Gastric carcinoma (GC) is one of the most common malignant tumors around the world. It is featured as high morbidity, poor prognosis, and short survival, thus seriously threats to the quality of life. The mechanism of GC is still unclear, leading to a difficulty in the treatment. CD44V6 plays an important role in tumorigenesis and progression, while its role in GC still needs further elucidation. PATIENTS AND METHODS: GC tissue and para-carcinoma tissue were collected from patients in different tumor-mode-metastasis (TNM) stages...
November 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/29228364/age-dependent-changes-in-mean-and-variance-of-gene-expression-across-tissues-in-a-twin-cohort
#2
Ana Viñuela, Andrew A Brown, Alfonso Buil, Pei-Chien Tsai, Matthew N Davies, Jordana T Bell, Emmanouil T Dermitzakis, Timothy D Spector, Kerrin S Small
Changes in mean and variance of gene expression with age have consequences for healthy aging and disease development. Age-dependent changes in phenotypic variance have been associated to a decline in regulatory functions leading to increase in disease risk. Here we investigate age-related mean and variance changes in gene expression measured by RNA-seq of fat, skin, whole blood and derived lymphoblastoid cell lines (LCLs) expression from 855 adult female twins. We see evidence of up to 60% of age effects on transcription levels shared across tissues, and 47% of those on splicing...
December 8, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/29228327/most-m6a-rna-modifications-in-protein-coding-regions-are-evolutionarily-unconserved-and-likely-nonfunctional
#3
Zhen Liu, Jianzhi Zhang
Methylation of the adenosine base at the nitrogen-6 position (m6A) is the most prevalent internal posttranscriptional modification of mRNAs in many eukaryotes. Despite the rapid progress in the transcriptome-wide mapping of m6As, identification of proteins responsible for writing, reading, and erasing m6As, and elucidation of m6A functions in splicing, RNA stability, translation, and other processes, it is unknown whether most observed m6A modifications are functional. To address this question, we respectively analyze the evolutionary conservation of yeast and human m6As in protein-coding regions...
December 8, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29228301/targeted-inhibition-of-janus-kinases-abates-interfon-gamma-induced-invasive-behaviour-of-fibroblast-like-synoviocytes
#4
Thomas Karonitsch, Denise Beckmann, Karolina Dalwigk, Birgit Niederreiter, Paul Studenic, Ruth A Byrne, Johannes Holinka, Florian Sevelda, Adelheid Korb-Pap, Günter Steiner, Josef S Smolen, Thomas Pap, Hans P Kiener
Objectives: The aim was to explore the function of the T-cell cytokine IFNγ for mesenchymal tissue remodelling in RA and to determine whether IFNγ signalling controls the invasive potential of fibroblast-like synoviocytes (FLS). Methods: To assess architectural responses, FLS were cultured in three-dimensional micromasses. FLS motility was analysed in migration and invasion assays. Signalling events relevant to cellular motility were defined by western blots. Baricitinib and small interfering RNA pools were used to suppress Janus kinase (JAK) functions...
December 7, 2017: Rheumatology
https://www.readbyqxmd.com/read/29228294/accurate-mapping-of-trna-reads
#5
Anne Hoffmann, Jörg Fallmann, Mario Mörl, Peter F Stadler, Fabian Amman
Motivation: Many repetitive DNA elements are transcribed at appreciable expression levels. Mapping the corresponding RNA sequencing reads back to a reference genome is notoriously difficult and error-prone task, however. This is in particular true if chemical modifications introduce systematic mismatches, while at the same time the genomic loci are only approximately identical, as in the case of tRNAs. Results: We therefore developed a dedicated mapping strategy to handle RNA-seq reads that map to tRNAs relying on a modified target genome in which known tRNA loci are masked and instead intronless tRNA precursor sequences are appended as artificial "chromosomes"...
December 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29225734/pdrg1-at-the-interface-between-intermediary-metabolism-and-oncogenesis
#6
REVIEW
María Ángeles Pajares
PDRG1 is a small oncogenic protein of 133 residues. In normal human tissues, the p53 and DNA damage-regulated gene 1 (PDRG1) gene exhibits maximal expression in the testis and minimal levels in the liver. Increased expression has been detected in several tumor cells and in response to genotoxic stress. High-throughput studies identified the PDRG1 protein in a variety of macromolecular complexes involved in processes that are altered in cancer cells. For example, this oncogene has been found as part of the RNA polymerase II complex, the splicing machinery and nutrient sensing machinery, although its role in these complexes remains unclear...
November 26, 2017: World Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29224736/a-natural-small-molecule-inhibitor-corilagin-blocks-hcv-replication-and-modulates-oxidative-stress-to-reduce-liver-damage
#7
B Uma Reddy, Ranajoy Mullick, Anuj Kumar, Geetika Sharma, Paromita Bag, Chaitrali Laha Roy, Govindarajan Sudha, Himani Tandon, Pratik Dave, Asutosh Shukla, Priyanka Srinivasan, Madhusudhan Nandhitha, Narayanaswamy Srinivasan, Saumitra Das
Hepatitis C virus (HCV) infection causes chronic liver disease, which often leads to hepatocellular carcinoma. Earlier, we have demonstrated anti-HCV property of the methanolic extract of Phyllanthus amarus, an age-old folk-medicine against viral hepatitis. Here, we report identification of a principal bioactive component 'corilagin', which showed significant inhibition of the HCV key enzymes, NS3 protease and NS5B RNA-dependent-RNA-polymerase. This pure compound could effectively inhibit viral replication in the infectious cell culture system, displayed strong antioxidant activity by blocking HCV induced generation of reactive oxygen species and suppressed up-regulation of NOX4 and TGF-β mRNA levels...
December 7, 2017: Antiviral Research
https://www.readbyqxmd.com/read/29224277/-clinicopathologic-analysis-of-micronodular-thymoma-with-lymphoid-stroma
#8
X Y Wang, M Xu, L G Shi, Y Z Ding, Q Cheng, Y W Zhao
Objective: To investigate the clinicopathologic features of micronodular thymoma with lymphoid stroma(MNT). Methods: Five cases of MNT diagnosed from January 2007 to December 2016 in Henan Provincial People's Hospital were collected.Hematoxylin-Eosin staining and immunohistochemistry were used to evaluate the histological and immunophenotypic characteristics in 5 MNT cases. Epstein-Barr virus (EBV) status was detected by in situ hybridization for EBV-encoded small RNA (EBER). Polymerase chain reaction was used to detect the rearrangement of immunoglobulin genes...
December 8, 2017: Zhonghua Bing Li Xue za Zhi Chinese Journal of Pathology
https://www.readbyqxmd.com/read/29224073/cleantag-adapters-improve-small-rna-next-generation-sequencing-library-preparation-by-reducing-adapter-dimers
#9
Sabrina Shore, Jordana M Henderson, Anton P McCaffrey
Next-generation small RNA sequencing is a valuable tool which is increasing our knowledge regarding small noncoding RNAs and their function in regulating genetic information. Library preparation protocols for small RNA have thus far been restricted due to higher RNA input requirements (>10 ng), long workflows, and tedious manual gel purifications. Small RNA library preparation methods focus largely on the prevention or depletion of a side product known as adapter dimer that tends to dominate the reaction...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29223746/bcap-promotes-osteoclast-differentiation-through-regulation-of-the-p38-dependent-creb-signaling-pathway
#10
Jung Ha Kim, Kabsun Kim, Inyoung Kim, Semun Seong, Keun-Bae Lee, Nacksung Kim
Many studies have determined that PI3K-Akt signaling pathways play important roles in osteoclast differentiation and function. In the present study, we investigated the roles of B-cell adaptor for PI3K (BCAP), which is a PI3K binding molecule, in osteoclasts. Overexpression of BCAP in osteoclast precursor cells enhanced osteoclast differentiation induced by tumor necrosis factor alpha (TNF-α) as well as receptor activator of nuclear factor-κB ligand (RANKL). Conversely, osteoclast differentiation mediated by both cytokines was attenuated when BCAP expression was downregulated using small interfering RNA...
December 6, 2017: Bone
https://www.readbyqxmd.com/read/29223657/the-evolutionary-field-hypothesis-non-mendelian-transgenerational-inheritance-mediates-diversification-and-evolution
#11
REVIEW
Corrado Spadafora
Epigenetics is increasingly regarded as a potential contributing factor to evolution. Building on apparently unrelated results, here I propose that RNA-containing nanovesicles, predominantly small regulatory RNAs, are released from somatic tissues in the bloodstream, cross the Weismann barrier, reach the epididymis, and are eventually taken up by spermatozoa; henceforth the information is delivered to oocytes at fertilization. In the model, a LINE-1-encoded reverse transcriptase activity, present in spermatozoa and early embryos, plays a key role in amplifying and propagating these RNAs as extrachromosomal structures...
December 6, 2017: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/29223394/islet-%C3%AE-cell-an-endocrine-cell-secreting-mirnas
#12
Aisen Zhang, Dameng Li, Yucheng Liu, Jing Li, Yujing Zhang, Chen-Yu Zhang
The pancreas is an important endocrine organ. Pancreatic beta (β) cells secrete insulin to regulate the metabolism of glucose and maintain the stability of blood glucose. MicroRNAs (miRNAs), small (20-25 nt) non-coding RNA molecules, function in target gene silencing through post-transcriptional patterns, and multiple miRNAs regulate insulin secretion, insulin signaling pathways in pancreatic β cells and islet activity. In recent years, it has been found that many types of cells can secrete regulatory miRNA, but whether islet cells can secrete miRNA has not been clarified yet...
December 6, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29222952/accumulation-of-the-coumarin-scopolin-under-abiotic-stress-conditions-is-mediated-by-the-arabidopsis-thaliana-tho-trex-complex
#13
Stefanie Döll, Markus Kuhlmann, Twan Rutten, Michael Florian Mette, Sarah Scharfenberg, Antonios Petridis, Dorothee-Carina Berreth, Hans-Peter Mock
Secondary metabolites are involved in plant stress response. Among these are scopolin and its active form scopoletin, which are coumarin-derivatives associated with reactive oxygen species scavenging and pathogen defence. Here we show that scopolin accumulation can be induced in the root by osmotic stress and in the leaf by low temperature stress in Arabidopsis thaliana. A genetic screen for altered scopolin levels in A. thaliana revealed a mutant compromised in scopolin accumulation in response to stress; the lesion was present in a homologue of THO1 coding for a subunit of the THO/TREX complex...
December 9, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29222441/robust-rna-based-in-situ-mutation-detection-delineates-colorectal-cancer-subclonal-evolution
#14
Ann-Marie Baker, Weini Huang, Xiao-Ming Mindy Wang, Marnix Jansen, Xiao-Jun Ma, Jeffrey Kim, Courtney M Anderson, Xingyong Wu, Liuliu Pan, Nan Su, Yuling Luo, Enric Domingo, Timon Heide, Andrea Sottoriva, Annabelle Lewis, Andrew D Beggs, Nicholas A Wright, Manuel Rodriguez-Justo, Emily Park, Ian Tomlinson, Trevor A Graham
Intra-tumor heterogeneity (ITH) is a major underlying cause of therapy resistance and disease recurrence, and is a read-out of tumor growth. Current genetic ITH analysis methods do not preserve spatial context and may not detect rare subclones. Here, we address these shortfalls by developing and validating BaseScope-a novel mutation-specific RNA in situ hybridization assay. We target common point mutations in the BRAF, KRAS and PIK3CA oncogenes in archival colorectal cancer samples to precisely map the spatial and morphological context of mutant subclones...
December 8, 2017: Nature Communications
https://www.readbyqxmd.com/read/29222167/cytoplasmic-linker-protein-clip170-negatively-regulates-tlr4-signaling-by-targeting-the-tlr-adaptor-protein-tirap
#15
Padmaja Jakka, Bindu Bhargavi, Swapna Namani, Subathra Murugan, Gary Splitter, Girish Radhakrishnan
Cytoplasmic linker protein 170 (CLIP170) is a CAP-Gly domain-containing protein that is associated with the plus end of growing microtubules and implicated in various cellular processes, including the regulation of microtubule dynamics, cell migration, and intracellular transport. Our studies revealed a previously unrecognized property and role of CLIP170. We identified CLIP170 as one of the interacting partners of Brucella effector protein TcpB that negatively regulates TLR2 and TLR4 signaling. In this study, we demonstrate that CLIP170 interacts with the TLR2 and TLR4 adaptor protein TIRAP...
December 8, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/29222062/evolutionary-history-of-the-cobalamin-independent-methionine-synthase-gene-family-across-the-land-plants
#16
Hugo Vianna Silva Rody, Luiz Orlando de Oliveira
Plants are successful paleopolyploids. The wide diversity of land plants is driven strongly by their gene duplicates undergoing distinct evolutionary fates after duplication. We used genomic resources from 35 model plant species to unravel the evolutionary fate of gene copies (paralogs) of the cobalamin-independent methionine synthase (metE) gene family across the land plants. To explore genealogical relationships and characterize positive selection as a driving force in the evolution of metE paralogs within a single species, we carried out complementary analyses on genomic data of 32 genotypes of soybean...
December 6, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29221985/hotair-mediated-reciprocal-regulation-of-ezh2-and-dnmt1-contribute-to-polyphyllin-i-inhibited-growth-of-castration-resistant-prostate-cancer-cells-in-vitro-and-in-vivo
#17
SongTao Xiang, PeiLiang Zou, Qing Tang, Fang Zheng, JingJing Wu, ZhiQiang Chen, Swei Sunny Hann
BACKGROUND: Polyphyllin I (PPI), one of the steroidal saponins in paris polyphylla, has been reported to exhibit antitumor effects. However, the detailed molecular mechanism underlying this has not been elucidated. METHODS: Cell viability and cell cycle distribution were measured using 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) and Flow cytometry assays, respectively. Cell invasion and migration were examined by Transwell invasion and wound healing assays...
December 5, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29221139/epstein-barr-virus-in-tumor-infiltrating-b-cells-of-myasthenia-gravis-thymoma-an-innocent-bystander-or-an-autoimmunity-mediator
#18
Paola Cavalcante, Stefania Marcuzzo, Sara Franzi, Barbara Galbardi, Lorenzo Maggi, Teresio Motta, Raffaella Ghislandi, Antonella Buzzi, Luisella Spinelli, Lorenzo Novellino, Fulvio Baggi, Carlo Antozzi, Fabio Conforti, Tommaso Martino De Pas, Massimo Barberis, Pia Bernasconi, Renato Mantegazza
The thymus plays a key role in myasthenia gravis (MG), a B cell-mediated autoimmune disorder affecting neuromuscular junction. Most MG patients have thymic abnormalities, including hyperplasia and thymoma, a neoplasm of thymic epithelial cells. Epstein-Barr virus (EBV) is associated with autoimmune diseases and tumors. Recently, we showed EBV persistence and reactivation in hyperplastic MG thymuses, suggesting that EBV might contribute to intra-thymic B cell dysregulation in MG patients. Here, we investigated EBV involvement in thymoma-associated MG, by searching for EBV markers in MG (n=26) and non-MG (n=14) thymomas...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29221117/inhibition-of-chemerin-cmklr1-axis-in-neuroblastoma-cells-reduces-clonogenicity-and-cell-viability-in-vitro-and-impairs-tumor-growth-in-vivo
#19
Conny Tümmler, Igor Snapkov, Malin Wickström, Ugo Moens, Linda Ljungblad, Lotta Helena Maria Elfman, Jan-Olof Winberg, Per Kogner, John Inge Johnsen, Baldur Sveinbjørnsson
Pro-inflammatory cells, cytokines, and chemokines are essential in promoting a tumor supporting microenvironment. Chemerin is a chemotactic protein and a natural ligand for the receptors CMKLR1, GPR1, and CCRL2. The chemerin/CMKLR1 axis is involved in immunity and inflammation, and it has also been implicated in obesity and cancer. In neuroblastoma, a childhood tumor of the peripheral nervous system we identified correlations between high CMKLR1 and GPR1 expression and reduced overall survival probability. CMKLR1, GPR1, and chemerin RNA and protein were detected in neuroblastoma cell lines and neuroblastoma primary tumor tissue...
November 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29220494/soapnuke-a-mapreduce-acceleration-supported-software-for-integrated-quality-control-and-preprocessing-of-high-throughput-sequencing-data
#20
Yuxin Chen, Yongsheng Chen, Chunmei Shi, Zhibo Huang, Yong Zhang, Shengkang Li, Yan Li, Jia Ye, Chang Yu, Zhuo Li, Xiuqing Zhang, Jian Wang, Huanming Yang, Lin Fang, Qiang Chen
Quality Control (QC) and preprocessing are essential steps for sequencing data analysis to ensure the accuracy of results. However, existing tools cannot provide a satisfying solution with integrated comprehensive functions, proper architectures and highly-scalable acceleration. In this article, we demonstrate SOAPnuke as a tool with abundant functions for a "QC-Preprocess-QC" workflow and MapReduce acceleration framework. Four modules with different preprocessing functions are designed for processing datasets from genomic, small RNA (sRNA), Digital Gene Expression (DGE) and metagenomic experiments respectively...
December 4, 2017: GigaScience
keyword
keyword
6911
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"