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https://www.readbyqxmd.com/read/28443498/the-overexpression-of-rabl3-is-associated-with-pathogenesis-and-clinicopathologic-variables-in-hepatocellular-carcinoma
#1
Yuhang Pan, Zhiyong Liu, Zhiying Feng, Dayang Hui, Xiangqi Huang, Dayue Tong, Yi Jin
Overexpression of Rabl3 is associated with some malignancies. However, their relationship with hepatocellular carcinoma remains unclear. In this study, the expression of Rabl3 in hepatocellular carcinoma cell lines, and four pairs of matched hepatocellular carcinoma tissues and their adjacent normal hepatic tissues were detected by quantitative reverse transcription polymerase chain reaction and western blot. In addition, the protein expression of Rabl3 was examined in 162 cases of hepatocellular carcinoma by immunohistochemistry...
April 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28442386/arginine-deiminase-pathway-provides-atp-and-boosts-growth-of-the-gas-fermenting-acetogen-clostridium-autoethanogenum
#2
Kaspar Valgepea, Kim Q Loi, James B Behrendorff, Renato de S P Lemgruber, Manuel Plan, Mark P Hodson, Michael Köpke, Lars K Nielsen, Esteban Marcellin
Acetogens are attractive organisms for the production of chemicals and fuels from inexpensive and non-food feedstocks such as syngas (CO, CO2 and H2). Expanding their product spectrum beyond native compounds is dictated by energetics, particularly ATP availability. Acetogens have evolved sophisticated strategies to conserve energy from reduction potential differences between major redox couples, however, this coupling is sensitive to small changes in thermodynamic equilibria. To accelerate the development of strains for energy-intensive products from gases, we used a genome-scale metabolic model (GEM) to explore alternative ATP-generating pathways in the gas-fermenting acetogen Clostridium autoethanogenum...
April 22, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28440619/collagen-membranes-with-ribonuclease-inhibitors-for-long-term-stability-of-electrochemical-aptamer-based-sensors-employing-rna
#3
Mirelis Santos-Cancel, Ryan J White
Electrochemical aptamer-based (E-AB) sensors offer advantageous analytical detection abilities on account of their rapid response time (sec to min), specificity to a target, and selectivity to function in complex media. Ribonucleic acid (RNA) aptamers employed in this class of sensor offer favorable binding characteristics resulting from the ability of RNA to form stable tertiary folds aided by long-range intermolecular interactions. As a result, RNA aptamers can fold into more complex three-dimensional structures than their DNA counterparts, and consequently, exhibit better binding ability to target analytes...
April 25, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28440443/microrna-expression-in-esophageal-squamous-cell-carcinoma-novel-diagnostic-and-prognostic-biomarkers
#4
Yan Wang, Jinnan Zhang, Wei Zhao, Donglin Wang, Wenduan Ma, Shengtao Shang, Chao Feng, Haixin Yu
The aim of the present study was to identify more effective molecular diagnostic biomarkers for esophageal squamous cell carcinoma (ESCC). The non‑coding RNA profile GSE43732, generated from 238 paired frozen tissues from 119 patients, was analyzed. Raw data were preprocessed and the differentially expressed miRNAs were screened by limma package with log2 fold change >2. Prognosis‑associated miRNAs were identified using receiver operating characteristic (ROC) and Kaplan-Meier (KM) curve analysis. miRNAs with an area under the ROC curve of ≥0...
April 13, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28440422/variable-terra-abundance-and-stability-in-cervical-cancer-cells
#5
Bong-Kyeong Oh, Ponnarath Keo, Jaeman Bae, Jung Hwa Ko, Joong Sub Choi
Telomeres are transcribed into long non-coding RNA, referred to as telomeric repeat-containing RNA (TERRA), which plays important roles in maintaining telomere integrity and heterochromatin formation. TERRA has been well characterized in HeLa cells, a type of cervical cancer cell. However, TERRA abundance and stability have not been examined in other cervical cancer cells, at least to the best of our knowledge. Thus, in this study, we measured TERRA levels and stability, as well as telomere length in 6 cervical cancer cell lines, HeLa, SiHa, CaSki, HeLa S3, C-33A and SNU-17...
April 20, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28439823/high-throughput-rt-qpcr-for-the-analysis-of-circulating-micrornas
#6
Geok Wee Tan, Lu Ping Tan
Reverse transcription followed by real-time or quantitative polymerase chain reaction (RT-qPCR) is the gold standard for validation of results from transcriptomic profiling studies such as microarray and RNA sequencing. The current need for most studies, especially biomarker studies, is to evaluate the expression levels or fold changes of many transcripts in a large number of samples. With conventional low to medium throughput qPCR platforms, many qPCR plates would have to be run and a significant amount of RNA input per sample will be required to complete the experiments...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439731/il-10-improves-cardiac-remodeling-after-myocardial-infarction-by-stimulating-m2-macrophage-polarization-and-fibroblast-activation
#7
Mira Jung, Yonggang Ma, Rugmani Padmanabhan Iyer, Kristine Y DeLeon-Pennell, Andriy Yabluchanskiy, Michael R Garrett, Merry L Lindsey
Inflammation resolution is important for scar formation following myocardial infarction (MI) and requires the coordinated actions of macrophages and fibroblasts. In this study, we hypothesized that exogenous interleukin-10 (IL-10), an anti-inflammatory cytokine, promotes post-MI repair through actions on these cardiac cell types. To test this hypothesis, C57BL/6J mice (male, 3- to 6-month old, n = 24/group) were treated with saline or IL-10 (50 μg/kg/day) by osmotic mini-pump infusion starting at day (d) 1 post-MI and sacrificed at d7 post-MI...
May 2017: Basic Research in Cardiology
https://www.readbyqxmd.com/read/28438458/an-efficient-cumate-inducible-system-for-procyclic-and-bloodstream-form-trypanosoma-brucei
#8
Feng-Jun Li, Zhi-Shen Xu, Htay Mon Aye, Anaïs Brasseur, Zhao-Rong Lun, Kevin S W Tan, Cynthia Y He
In Trypanosoma brucei, the tetracycline-inducible system enables tightly-regulated, highly-efficient expression of recombinant proteins or double-stranded RNA in both procyclic and bloodstream form cells, providing useful molecular genetic tools to study gene functions. An alternative, vanillic acid-inducible system is recently described for procyclic T. brucei, providing ∼18-fold increase in GFP reporter expression upon induction (Sunter JD. Mol Biochem Parasitol. 2016, 207:45-48). Here we describe a cumate-inducible system that allows efficient, tunable gene expression showing >300-fold increase in GFP expression upon induction...
April 21, 2017: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/28437675/whole-blood-sequencing-reveals-circulating-microrna-associations-with-high-risk-traits-in-non-st-segment-elevation-acute-coronary-syndrome
#9
Alice Wang, Lydia Coulter Kwee, Elizabeth Grass, Megan L Neely, Simon G Gregory, Keith A A Fox, Paul W Armstrong, Harvey D White, E Magnus Ohman, Matthew T Roe, Svati H Shah, Mark Y Chan
BACKGROUND AND AIMS: Although circulating microRNA (miRNAs) have emerged as biomarkers predicting mortality in acute coronary syndrome (ACS), more data are needed to understand these mechanisms. Mapping miRNAs to high-risk traits may identify miRNAs involved in pathways conferring risk for poor outcome in ACS. We aim to investigate the relationship between circulating miRNAs and high-risk traits in non-ST-segment elevation acute coronary syndrome (NSTE-ACS). METHODS: Whole-genome miRNA sequencing was performed on RNA extracted from whole blood of 199 patients with NSTE-ACS...
March 30, 2017: Atherosclerosis
https://www.readbyqxmd.com/read/28437108/design-of-a-toolbox-of-rna-thermometers
#10
Shaunak Sen, Divyansh Apurva, Rohit Satija, Dan Siegal, Richard M Murray
Biomolecular temperature sensors can be used for efficient control of large-volume bioreactors, for spatiotemporal imaging and control of gene expression, and to engineer robustness to temperature in biomolecular circuit design. While RNA-based sensors, called 'thermometers', have been investigated in both natural and synthetic contexts, an important challenge is to design diverse responses to temperature, differing in sensitivities and thresholds. We address this issue by constructing a library of RNA thermometers, based on thermodynamic computations, and experimentally measuring their activities in cell-free biomolecular 'breadboards'...
April 24, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28436444/transcriptome-profiling-of-sulfate-deprivation-responses-in-two-agarophytes-gracilaria-changii-and-gracilaria-salicornia-rhodophyta
#11
Wei-Kang Lee, Parameswari Namasivayam, Janna Ong Abdullah, Chai-Ling Ho
Seaweeds survive in marine waters with high sulfate concentration compared to those living at freshwater habitats. The cell wall polymer of Gracilaria spp. which supplies more than 50% of the world agar is heavily sulfated. Since sulfation reduces the agar quality, it is interesting to investigate the effects of sulfate deprivation on the sulfate contents of seaweed and agar, as well as the metabolic pathways of these seaweeds. In this study, two agarophytes G. changii and G. salicornia were treated under sulfate deprivation for 5 days...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28435892/dramatic-improvement-of-crispr-cas9-editing-in-candida-albicans-by-increased-single-guide-rna-expression
#12
Henry Ng, Neta Dean
The clustered regularly interspaced short palindromic repeat system with CRISPR-associated protein 9 nuclease (CRISPR/Cas9) has emerged as a versatile tool for genome editing in Candida albicans. Mounting evidence from other model systems suggests that the intracellular levels of single guide RNA (sgRNA) limit the efficiency of Cas9-dependent DNA cleavage. Here, we tested this idea and describe a new means of sgRNA delivery that improves previously described methods by ~10-fold. The efficiency of Cas9/sgRNA-dependent cleavage and repair of a single-copy yeast enhanced monomeric red fluorescent protein (RFP) gene was measured as a function of various parameters that are hypothesized to affect sgRNA accumulation, including transcriptional and posttranscriptional processing...
March 2017: MSphere
https://www.readbyqxmd.com/read/28433811/rapid-and-sensitive-detection-of-salmonid-alphavirus-using-taqman-real-time-pcr
#13
Wen Shi, Aochen Song, Shuai Gao, Yuting Wang, Lijie Tang, Yigang Xu, Tong Ren, Yijing Li, Min Liu
Salmonid alphavirus (SAV) infection has led to the spread of salmon pancreas disease (PD) and sleeping disease (SD) to salmonids in several countries in Europe, resulting in tremendous economic losses to the fish farming industry. Recently, with increases in the fish import trade, many countries in which SAV has been unreported, such as China, may be seriously threatened by these diseases. It is therefore necessary to develop efficient detection methods for the prevention and diagnosis of SAV infection. In this study, a rapid and sensitive TaqMan real-time PCR method was established and assessed for this purpose...
April 19, 2017: Molecular and Cellular Probes
https://www.readbyqxmd.com/read/28433606/in-silico-methods-for-co-transcriptional-rna-secondary-structure-prediction-and-for-investigating-alternative-rna-structure-expression
#14
REVIEW
Irmtraud M Meyer
RNA transcripts are the primary products of active genes in any living organism, including many viruses. Their cellular destiny not only depends on primary sequence signals, but can also be determined by RNA structure. Recent experimental evidence shows that many transcripts can be assigned more than a single functional RNA structure throughout their cellular life and that structure formation happens co-transcriptionally, i.e. as the transcript is synthesised in the cell. Moreover, functional RNA structures are not limited to non-coding transcripts, but can also feature in coding transcripts...
April 19, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28433422/postnatal-choline-supplementation-selectively-attenuates-hippocampal-microrna-alterations-associated-with-developmental-alcohol-exposure
#15
Sridevi Balaraman, Nirelia M Idrus, Rajesh C Miranda, Jennifer D Thomas
Prenatal alcohol exposure can result in a range of physical, neuropathological, and behavioral alterations, collectively termed fetal alcohol spectrum disorders (FASD). We have shown that supplementation with the nutrient choline reduces the severity of developmental alcohol-associated deficits in hippocampal-dependent behaviors and normalizes some aspects of hippocampal cholinergic development and DNA methylation patterns. Alcohol's developmental effects may also be mediated, in part, by altering microRNAs (miRNAs) that serve as negative regulators of gene translation...
January 3, 2017: Alcohol
https://www.readbyqxmd.com/read/28433053/the-envelope-proteins-of-the-bunyavirales
#16
Pablo Guardado-Calvo, Félix A Rey
The Bunyavirales Order encompasses nine families of enveloped viruses containing a single-stranded negative-sense RNA genome divided into three segments. The small (S) and large (L) segments encode proteins participating in genome replication in the infected cell cytoplasm. The middle (M) segment encodes the viral glycoproteins Gn and Gc, which are derived from a precursor polyprotein by host cell proteases. Entry studies are available only for a few viruses in the Order, and in each case they were shown to enter cells via receptor-mediated endocytosis...
2017: Advances in Virus Research
https://www.readbyqxmd.com/read/28432618/the-identification-of-key-genes-and-pathways-in-hepatocellular-carcinoma-by-bioinformatics-analysis-of-high-throughput-data
#17
Chaoyang Zhang, Li Peng, Yaqin Zhang, Zhaoyang Liu, Wenling Li, Shilian Chen, Guancheng Li
Liver cancer is a serious threat to public health and has fairly complicated pathogenesis. Therefore, the identification of key genes and pathways is of much importance for clarifying molecular mechanism of hepatocellular carcinoma (HCC) initiation and progression. HCC-associated gene expression dataset was downloaded from Gene Expression Omnibus database. Statistical software R was used for significance analysis of differentially expressed genes (DEGs) between liver cancer samples and normal samples. Gene Ontology (GO) term enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, based on R software, were applied for the identification of pathways in which DEGs significantly enriched...
June 2017: Medical Oncology
https://www.readbyqxmd.com/read/28432541/genome-characteristics-of-the-proteorhodopsin-containing-marine-flavobacterium-polaribacter-dokdonensis-dsw-5
#18
Kiyoung Yoon, Ju Yeon Song, Min-Jung Kwak, Soon-Kyeong Kwon, Jihyun F Kim
Bacteria in the genus Polaribacter, belonging to the family Flavobacteriaceae, are typically isolated from marine environments. Polaribacter dokdonensis DSW-5, the type strain of the species, is a Gram-negative bacterium isolated from the East Sea of Korea. Whole genome shotgun sequencing was performed with the HiSeq 2000 platform and paired-end reads were generated at 188-fold coverage. The sequencing reads were assembled into two contigs with a total length of 3.08 Mb. The genome sequences of DSW-5 contain 2,776 proteincoding sequences and 41 RNA genes...
April 22, 2017: Journal of Microbiology / the Microbiological Society of Korea
https://www.readbyqxmd.com/read/28432364/rrm-domain-of-als-ftd-causing-fus-characteristic-of-irreversible-unfolding-spontaneously-self-assembles-into-amyloid-fibrils
#19
Yimei Lu, Liangzhong Lim, Jianxing Song
526-residue FUS functions to self-assemble into reversible droplets/hydrogels, which could be further solidified into pathological fibrils. FUS is intrinsically prone to aggregation, composed of N-terminal low-sequence complexity (LC); RNA-recognition motif (RRM) and C-terminal LC domains. Intriguingly, previous in vivo studies revealed that its RRM is required for manifesting FUS cytotoxicity but the underlying mechanism remains unknown. Here, we characterized solution conformations of FUS and its five differentially dissected fragments, followed by detailed investigations on thermal unfolding, NMR dynamics and self-assembly of RRM...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28432348/white-spot-syndrome-virus-vp28-specific-double-stranded-rna-provides-protection-through-a-highly-focused-sirna-population
#20
Pål Nilsen, Marius Karlsen, Kallaya Sritunyalucksana, Siripong Thitamadee
Several studies have demonstrated that injection of double-stranded RNAs (dsRNA) homologous to mRNA for the white spot syndrome virus (WSSV) viral protein 28 (VP28) can induce protection in shrimp against WSSV through RNA interference (RNAi). In comparison to shrimp injected with either PBS or a green fluorescent protein (GFP) nonspecific dsRNA, we obtained nearly complete protection against WSSV infection in shrimp injected with VP28 dsRNA. Upregulation of host genes associated with small RNA silencing was measured 48 hours post treatment in groups injected with dsRNA, and although the VP28-treated group remained moderately upregulated after challenge with WSSV, many-fold higher induction was observed in both control groups reflecting the ongoing viral infection...
April 21, 2017: Scientific Reports
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