keyword
MENU ▼
Read by QxMD icon Read
search

rna processing

keyword
https://www.readbyqxmd.com/read/28813689/large-scale-machine-learning-of-media-outlets-for-understanding-public-reactions-to-nation-wide-viral-infection-outbreaks
#1
Sungwoon Choi, Jangho Lee, Min-Gyu Kang, Hyeyoung Min, Yoon-Seok Chang, Sungroh Yoon
From May to July 2015, there was a nation-wide outbreak of Middle East respiratory syndrome (MERS) in Korea. MERS is caused by MERS-CoV, an enveloped, positive-sense, single stranded RNA virus belonging to the family Coronaviridae. Despite expert opinions that the danger of MERS might be exaggerated, there was an overreaction by the public according to the Korean mass media, which led to a noticeable reduction in social and economic activities during the outbreak. To explain this phenomenon, we presumed that machine learning-based analysis of media outlets would be helpful and collected a number of Korean mass media articles and short-text comments produced during the 10-week outbreak...
August 13, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28813466/comprehensive-comparison-of-neonate-and-adult-human-platelet-transcriptomes
#2
Eva Caparrós-Pérez, Raúl Teruel-Montoya, Mª José López-Andreo, Mª Carmen Llanos, José Rivera, Verónica Palma-Barqueros, Jose E Blanco, Vicente Vicente, Constantino Martínez, Francisca Ferrer-Marín
Understanding the underlying mechanisms of the well-substantiated platelet hyporeactivity in neonates is of interest given their implications for the clinical management of newborns, a population at higher bleeding risk than adults (especially sick and preterm infants), as well as for gaining insight into the regulatory mechanisms of platelet biology. Transcriptome analysis is useful in identifying mRNA signatures affecting platelet function. However, human fetal/neonatal platelet transcriptome analysis has never before been reported...
2017: PloS One
https://www.readbyqxmd.com/read/28812395/current-research-on-circular-rnas-associated-with-colorectal-cancer
#3
Penghui Wang, Xiaodong He
Representing a novel type of endogenous noncoding RNAs, circular RNAs (circRNAs) have recently gained much attention for their involvement in multiple biological processes. CircRNAs are ubiquitously expressed in eukaryotic cells and modulate gene expression by acting as sponges of microRNAs (miRNAs) or other proteins, such as RNA-binding proteins (RBPs). Due to their unique structure, circRNAs are more stable than linear RNAs. Expression profiles of circRNAs are associated with clinicopathological characteristics of colorectal cancer patients, such as differentiation, TNM classification and distant metastasis...
August 16, 2017: Scandinavian Journal of Gastroenterology
https://www.readbyqxmd.com/read/28811863/long-noncoding-rnas-and-rna-binding-proteins-in-oxidative-stress-cellular-senescence-and-age-related-diseases
#4
REVIEW
Chongtae Kim, Donghee Kang, Eun Kyung Lee, Jae-Seon Lee
Cellular senescence is a complex biological process that leads to irreversible cell-cycle arrest. Various extrinsic and intrinsic insults are associated with the onset of cellular senescence and frequently accompany genomic or epigenomic alterations. Cellular senescence is believed to contribute to tumor suppression, immune response, and tissue repair as well as aging and age-related diseases. Long noncoding RNAs (lncRNAs) are >200 nucleotides long, poorly conserved, and transcribed in a manner similar to that of mRNAs...
2017: Oxidative Medicine and Cellular Longevity
https://www.readbyqxmd.com/read/28811754/comparative-genome-analysis-of-rathayibacter-tritici-ncppb-1953-with-rathayibacter-toxicus-strains-can-facilitate-studies-on-mechanisms-of-nematode-association-and-host-infection
#5
Jungwook Park, Pyeong An Lee, Hyun-Hee Lee, Kihyuck Choi, Seon-Woo Lee, Young-Su Seo
Rathayibacter tritici, which is a Gram positive, plant pathogenic, non-motile, and rod-shaped bacterium, causes spike blight in wheat and barley. For successful pathogenesis, R. tritici is associated with Anguina tritici, a nematode, which produces seed galls (ear cockles) in certain plant varieties and facilitates spread of infection. Despite significant efforts, little research is available on the mechanism of disease or bacteria-nematode association of this bacterium due to lack of genomic information. Here, we report the first complete genome sequence of R...
August 2017: Plant Pathology Journal
https://www.readbyqxmd.com/read/28811565/iss-pc-identifying-splicing-sites-via-physical-chemical-properties-using-deep-sparse-auto-encoder
#6
Zhao-Chun Xu, Peng Wang, Wang-Ren Qiu, Xuan Xiao
Gene splicing is one of the most significant biological processes in eukaryotic gene expression, such as RNA splicing, which can cause a pre-mRNA to produce one or more mature messenger RNAs containing the coded information with multiple biological functions. Thus, identifying splicing sites in DNA/RNA sequences is significant for both the bio-medical research and the discovery of new drugs. However, it is expensive and time consuming based only on experimental technique, so new computational methods are needed...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811496/genome-wide-expression-differences-in-anti-vegf-and-dexamethasone-treatment-of-inflammatory-angiogenesis-in-the-rat-cornea
#7
Pierfrancesco Mirabelli, Anthony Mukwaya, Anton Lennikov, Maria Xeroudaki, Beatrice Peebo, Mira Schaupper, Neil Lagali
Angiogenesis as a pathological process in the eye can lead to blindness. In the cornea, suppression of angiogenesis by anti-VEGF treatment is only partially effective while steroids, although effective in treating inflammation and angiogenesis, have broad activity leading to undesirable side effects. In this study, genome-wide expression was investigated in a suture-induced corneal neovascularization model in rats, to investigate factors differentially targeted by dexamethasone and anti-Vegf. Topical treatment with either rat-specific anti-Vegf, dexamethasone, or normal goat IgG (sham) was given to sutured corneas for 48 hours, after which in vivo imaging, tissue processing for RNA microarray, and immunofluorescence were performed...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811374/recruitment-of-crispr-cas-systems-by-tn7-like-transposons
#8
Joseph E Peters, Kira S Makarova, Sergey Shmakov, Eugene V Koonin
A survey of bacterial and archaeal genomes shows that many Tn7-like transposons contain minimal type I-F CRISPR-Cas systems that consist of fused cas8f and cas5f, cas7f, and cas6f genes and a short CRISPR array. Several small groups of Tn7-like transposons encompass similarly truncated type I-B CRISPR-Cas. This minimal gene complement of the transposon-associated CRISPR-Cas systems implies that they are competent for pre-CRISPR RNA (precrRNA) processing yielding mature crRNAs and target binding but not target cleavage that is required for interference...
August 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28811159/implementing-and-scaling-up-hcv-treatment-services-for-people-who-inject-drugs-and-other-high-risk-groups-in-ukraine-an-evaluation-of-programmatic-and-treatment-outcomes
#9
Alyona Mazhnaya, Anna Meteliuk, Tetiana Barnard, Alexei Zelenev, Sergii Filippovych, Frederick L Alticec
BACKGROUND: HCV prevalence estimates among people who inject drugs (PWID) in Ukraine is high (60-90%), yet barriers to HCV treatment and care remain substantial including limited access to direct acting antiviral (DAA) medications. A feasibility scale-up project implemented HCV treatment in community-based settings to improve access to DAA treatment for key populations in this context. METHODS: Using program-level data and verified medical records, we describe the development, implementation processes and outcomes for HCV treatment for PWID and other risks groups...
August 12, 2017: International Journal on Drug Policy
https://www.readbyqxmd.com/read/28811015/multiple-targeted-graphene-based-nanocarrier-for-intracellular-imaging-of-mrnas
#10
Ying Wang, Zhaohui Li, Misha Liu, Jinjin Xu, Dehong Hu, Yuehe Lin, Jinghong Li
Simultaneous detection and imaging of multiple intracellular messenger RNA (mRNAs) hold great significant for early cancer diagnostics and preventive medicine development. Herein, we propose a multiple-targeted graphene oxide (GO) nanocarrier that can simultaneously detect and image different type mRNAs in living cells. First of all, in vitro detection of multiple targets have been realized successfully based on the multiple-targeted GO nanocarrier with linear relationship ranging from 3 nM to 200 nM, as well as sensitive detection limit of 1...
August 29, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28810930/sex-differences-in-microrna-mrna-networks-examination-of-novel-epigenetic-programming-mechanisms-in-the-sexually-dimorphic-neonatal-hypothalamus
#11
Christopher P Morgan, Tracy L Bale
BACKGROUND: Sexual differentiation of the male brain, and specifically the stress circuitry in the hypothalamus, is primarily driven by estrogen exposure during the perinatal period. Surprisingly, this single hormone promotes diverse programs of sex-specific development that vary widely between different cell types and across the developing male brain. The complexity of this phenomenon suggests that additional layers of gene regulation, including microRNAs (miRNAs), must act downstream of estrogen to mediate this specificity...
August 15, 2017: Biology of Sex Differences
https://www.readbyqxmd.com/read/28810905/omni-polya-a-method-and-tool-for-accurate-recognition-of-poly-a-signals-in-human-genomic-dna
#12
Arturo Magana-Mora, Manal Kalkatawi, Vladimir B Bajic
BACKGROUND: Polyadenylation is a critical stage of RNA processing during the formation of mature mRNA, and is present in most of the known eukaryote protein-coding transcripts and many long non-coding RNAs. The correct identification of poly(A) signals (PAS) not only helps to elucidate the 3'-end genomic boundaries of a transcribed DNA region and gene regulatory mechanisms but also gives insight into the multiple transcript isoforms resulting from alternative PAS. Although progress has been made in the in-silico prediction of genomic signals, the recognition of PAS in DNA genomic sequences remains a challenge...
August 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28810896/silencing-the-girdin-gene-enhances-radio-sensitivity-of-hepatocellular-carcinoma-via-suppression-of-glycolytic-metabolism
#13
Li Yu, Yifan Sun, Jingjing Li, Yan Wang, Yuxing Zhu, Yong Shi, Xiaojun Fan, Jianda Zhou, Ying Bao, Jie Xiao, Ke Cao, Peiguo Cao
BACKGROUND: Radiotherapy has been used increasingly to treat primary hepatocellular carcinoma. Clinically, the main cause of radiotherapy failure is cellular radioresistance, conferred via glycolytic metabolism. Our previous study demonstrated that Girdin is upregulated in primary hepatocellular carcinoma and promotes the invasion and metastasis of tumor cells. However, whether Girdin underlies the radio-sensitivity of hepatocellular carcinoma remains unclear. METHODS: A short hairpin RNA (shRNA) was used to silence CCDC88A (encoding Girdin), and real-time PCR was performed to determine CCDC88A mRNA expression...
August 15, 2017: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/28810650/glutathione-s-transferase-a1-mediates-nicotine-induced-lung-cancer-cell-metastasis-by-promoting-epithelial-mesenchymal-transition
#14
Wei Wang, Feiyu Liu, Chaoyang Wang, Chengde Wang, Yijun Tang, Zhongmin Jiang
The present study aimed to investigate the effect of glutathione S-transferase A1 (GSTA1) on lung cancer cell viability, invasion and adhesion in the presence of nicotine in vitro. Furthermore, the effect of GSTA1 on the epithelial-mesenchymal transition (EMT), a process strongly associated with lung cancer metastasis, was examined. Human lung carcinoma A549 cells were treated with various concentrations of nicotine (0.01, 0.1, 1 and 10 µM) and levels of GSTA1 mRNA and protein were measured by reverse transcription-quantitative polymerase chain reaction and western blot analysis, respectively...
August 2017: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28810637/binding-of-line-1-rna-to-psf-transcriptionally-promotes-gage6-and-regulates-cell-proliferation-and-tumor-formation-in-vitro
#15
Jiao Lv, Ziyi Zhao
Hepatocellular carcinoma (HCC) has one of the highest mortality rates among numerous types of cancer. It has been demonstrated that in hepatitis B (HBV)-associated HCC, the expression of chimeric fusion transcript HBx-long interspersed nuclear element-1 (LINE-1) initiated by HBV integration is correlated with hepatocarcinogenesis and poor patient survival rates. Furthermore, increased rates of LINE-1 hypomethylation have been detected in HCC tissues compared with adjacent tissues. This suggests that individual LINE-1 RNA (L1 RNA) serves an important role in the processes of hepatocarcinogenesis...
August 2017: Experimental and Therapeutic Medicine
https://www.readbyqxmd.com/read/28810236/microrna-375-inhibits-growth-and-enhances-radiosensitivity-in-oral-squamous-cell-carcinoma-by-targeting-insulin-like-growth-factor-1-receptor
#16
Bin Zhang, Ying Li, Daorong Hou, Quan Shi, Shuo Yang, Qihong Li
BACKGROUND: MicroRNAs (miRNAs) have emerged as key players in various human biological processes, including tumorigenesis. Here, we investigated the roles of miR-375 in the pathogenesis of oral squamous cell carcinoma (OSCC). METHODS: We performed quantitative real-time PCR (qRT-PCR) to detect miR-375 expression in OSCC tissues and corresponding normal oral epithelial tissues and analyze the correlation of miR-375 expression with OSCC metastasis and patient's survival...
August 15, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28810078/discovery-of-key-physicochemical-structural-and-spatial-properties-of-rna-targeted-bioactive-ligands
#17
Brittany S Morgan, Jordan E Forte, Rebecca N Culver, Yuqi Zhang, Amanda E Hargrove
While myriad non-coding RNAs are known to be essential in cellular processes and misregulated in diseases, the development of RNA-targeted small molecule probes has met with limited success. To elucidate guiding principles for selective small molecule:RNA recognition, we analyzed cheminformatic and shape-based descriptors for 104 RNA-targeted ligands with demonstrated biological activity (RNA-targeted BIoactive ligaNd Database, RBIND). We then compared R-BIND to both FDA-approved small molecule drugs and RNA ligands without reported bioactivity...
August 15, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28809941/analysis-of-agoshrna-maturation-and-loading-into-ago2
#18
Alex Harwig, Zita Kruize, Zhenhuang Yang, Tobias Restle, Ben Berkhout
The RNA interference (RNAi) pathway was recently expanded by the discovery of multiple alternative pathways for processing of natural microRNA (miRNA) and man-made short hairpin RNA (shRNA) molecules. One non-canonical pathway bypasses Dicer cleavage and requires instead processing by Argonaute2 (Ago2), which also executes the subsequent silencing step. We named these molecules AgoshRNA, which generate only a single active RNA strand and thus avoid off-target effects that can be induced by the passenger strand of a regular shRNA...
2017: PloS One
https://www.readbyqxmd.com/read/28809853/rna-seq-analysis-of-amygdala-tissue-reveals-characteristic-expression-profiles-in-schizophrenia
#19
X Chang, Y Liu, C-G Hahn, R E Gur, P M A Sleiman, H Hakonarson
The amygdala brain region has been implicated in the pathophysiology of schizophrenia through emotion processing. However, transcriptome messages in the amygdala of schizophrenia patients have not been well studied. We used RNA sequencing to investigate gene-expression profiling in the amygdala tissues, and identified 569 upregulated and 192 downregulated genes from 22 schizophrenia patients and 24 non-psychiatric controls. Gene functional enrichment analysis demonstrated that the downregulated genes were enriched in pathways such as 'synaptic transmission' and 'behavior', whereas the upregulated genes were significantly over-represented in gene ontology pathways such as 'immune response' and 'blood vessel development'...
August 15, 2017: Translational Psychiatry
https://www.readbyqxmd.com/read/28809130/long-noncoding-rna-a-new-contributor-and-potential-therapeutic-target-in-fibrosis
#20
Xiaoying Jiang, Fujun Zhang
Fibrosis is the excess deposition of extracellular matrix components which occur in multiple organs and ultimately leads to organ failure. Long noncoding RNAs (lncRNAs) are a kind of noncoding RNAs longer than approximately 200 nucleotides with no protein-encoding capacity. A growing body of evidence suggests that lncRNAs are also involved in tissues fibrosis in several organs, such as lungs fibrosis, liver fibrosis, renal fibrosis and cardiac fibrosis. In this review, we summarized the current studies of lncRNAs in the process of fibrosis and hopefully aid in better understanding the molecular mechanism of fibrosis and provide a basis to explore new therapeutic targets of fibrosis...
August 15, 2017: Epigenomics
keyword
keyword
101436
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"