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https://read.qxmd.com/read/30785788/the-biospecimen-preanalytical-variables-program-a-multiassay-comparison-of-effects-of-delay-to-fixation-and-fixation-duration-on-nucleic-acid-quality
#1
Latarsha J Carithers, Rachana Agarwal, Ping Guan, Hana Odeh, Michael C Sachs, Kelly B Engel, Sarah R Greytak, Mary Barcus, Conrado Soria, Chih-Jian Jason Lih, P Mickey Williams, Philip A Branton, Leslie Sobin, Benjamin Fombonne, Therese Bocklage, Chris Andry, Elizabeth R Duffy, Gabriel Sica, Rajiv Dhir, Scott Jewell, Nancy Roche, Helen M Moore
CONTEXT.—: Despite widespread use of formalin-fixed, paraffin-embedded (FFPE) tissue in clinical and research settings, potential effects of variable tissue processing remain largely unknown. OBJECTIVE.—: To elucidate molecular effects associated with clinically relevant preanalytical variability, the National Cancer Institute initiated the Biospecimen Preanalytical Variables (BPV) program. DESIGN.—: The BPV program, a well-controlled series of systematic, blind and randomized studies, investigated whether a delay to fixation (DTF) or time in fixative (TIF) affects the quantity and quality of DNA and RNA isolated from FFPE colon, kidney, and ovarian tumors in comparison to case-matched snap-frozen controls...
February 20, 2019: Archives of Pathology & Laboratory Medicine
https://read.qxmd.com/read/30785516/waiting-daas-list-mortality-impact-in-hcv-cirrhotic-patients
#2
Giovanni Faria Silva, Vanessa Gutierrez de Andrade, Alecsandro Moreira
BACKGROUND: The infection for the hepatitis C virus (HCV) is a leading cause of liver-related morbidity and mortality through its evolution to liver cirrhosis, end-stage liver complications and hepatocellular carcinoma. Currently, the new drugs for the HCV infection, based on direct antiviral agents, have changed the outcomes in this setting. OBJECTIVE: To assess death incidence, during the wait for the treatment with the new drugs, and to analyze which independent variable (age, sex, ascite, HDA, albumin, α-fetoprotein, platelets and Meld score) had relation with death...
October 2018: Arquivos de Gastroenterologia
https://read.qxmd.com/read/30785446/comparative-genomics-and-transcriptomics-insights-into-the-c1-metabolic-model-of-a-formaldehyde-degrading-strain-methylobacterium-sp-xjlw
#3
Yunhai Shao, Jun Li, Yanxin Wang, Fengmei Yi, Yanan Zhang, Peiwu Cui, Weihong Zhong
A formaldehyde-degrading strain Methylobacterium sp. XJLW was isolated and exhibited a special phenotype for formaldehyde utilization. The accumulation of formic acid in large quantities and lower cell growth was detected when XJLW utilized formaldehyde as the sole carbon source, suggesting XJLW has a potentially novel pathway to transfer formaldehyde to methanol and then enter the serine cycle for C1 metabolism. This mechanism requires exploration via molecular omics. Thus, the complete genome of XJLW was sequenced, and the transcriptome difference was also analyzed based on the RNA-seq data of strain XJLW cultivated with methanol and glucose, respectively...
February 20, 2019: Molecular omics
https://read.qxmd.com/read/30784585/rig-i-selectively-discriminates-against-5-monophosphate-rna
#4
Xiaoming Ren, Melissa M Linehan, Akiko Iwasaki, Anna Marie Pyle
The innate immune sensor RIG-I must sensitively detect and respond to viral RNAs that enter the cytoplasm, while remaining unresponsive to the abundance of structurally similar RNAs that are the products of host metabolism. In the case of RIG-I, these viral and host targets differ by only a few atoms, and a molecular mechanism for such selective differentiation has remained elusive. Using a combination of quantitative biophysical and immunological studies, we show that RIG-I, which is normally activated by duplex RNAs containing a 5'-tri- or diphosphate (5'-ppp or 5'-pp RNAs), is actively antagonized by RNAs containing 5'-monophosphates (5'-p RNAs)...
February 19, 2019: Cell Reports
https://read.qxmd.com/read/30784293/treatment-of-surface-plasmon-resonance-spr-background-in-total-internal-reflection-ellipsometry-characterization-of-rna-polymerase-ii-film-formation
#5
Dušan Hemzal, Yu Ri Kang, Jan Dvořák, Tomasz Kabzinski, Karel Kubíček, Young Dong Kim, Josef Humlíček
To deal with the general problem of biomolecule specific binding analysis, we have applied the technique of difference spectra to the surface plasmon resonance (SPR)-enhanced total internal reflection ellipsometry measurement. We suggest a three-step treatment of the SPR background that can easily be integrated with the usual measurement routine. First, making use of the difference spectrum in ellipsometric angle Δ, single peak footprints of the topmost layer are obtained that facilitate its sensitive detection during film growth...
February 20, 2019: Applied Spectroscopy
https://read.qxmd.com/read/30784285/zonula-occludens-1-associated-nucleic-acid-binding-protein-plays-an-invasion-promoting-role-in-bladder-cancer
#6
X Xu, K You, B Wu
Cancer cell invasion is an important characteristic of malignant tumors. Cancer cells overcome the constraints of tight junctions (TJ) to invade other tissues, but less is known about the regulating role of tight junction on bladder cancer (BC) invasion. In order to identify the invasion-regulating function of tight junction component, we investigated the oncogenetic features of zonula occludens-1 associated nucleic acid binding protein (ZONAB), a TJ protein that is usually highly expressed in solid cancers...
February 20, 2019: Neoplasma
https://read.qxmd.com/read/30784073/transfusion-of-hiv-infected-blood-products-despite-highly-sensitive-nucleic-acid-testing
#7
Pierre Cappy, Valérie Barlet, Quentin Lucas, Xavier Tinard, Josiane Pillonel, Sylvie Gross, Pierre Tiberghien, Syria Laperche
BACKGROUND: In France, the risk of HIV transmission by transfusion was reduced by implementing pooled nucleic acid testing (NAT) in 2001 and individual NAT in 2010. We report here the first case in France of transfusion of human immunodeficiency virus (HIV)-infected blood donated during HIV pre-ramp-up phase that tested individual NAT negative. METHODS: Blood donations are screened for HIV antibodies and HIV RNA (ProcleixUltrio, Grifols; limit of detection at 95%, 23 copies/mL)...
February 19, 2019: Transfusion
https://read.qxmd.com/read/30783970/in-situ-hybridization-for-detection-of-aav-mediated-gene-expression
#8
Jacqueline E Hunter, Brittney L Gurda, Sea Young Yoon, Michael J Castle, John H Wolfe
Techniques to localize vector transgenes in cells and tissues are essential in order to fully characterize gene therapy outcomes. In situ hybridization (ISH) uses synthesized complementary RNA or DNA nucleotide probes to localize and detect sequences of interest in fixed cells, tissue sections, or whole tissue mounts. Variations in techniques include adding labels to probes, such as fluorophores, which can allow for the simultaneous visualization of multiple targets. Here we provide the steps necessary to: (1) label probes for colorimetric visualization and (2) perform ISH on OCT cryo-preserved fixed frozen tissues...
2019: Methods in Molecular Biology
https://read.qxmd.com/read/30783653/the-r-package-rsubread-is-easier-faster-cheaper-and-better-for-alignment-and-quantification-of-rna-sequencing-reads
#9
Yang Liao, Gordon K Smyth, Wei Shi
We present Rsubread, a Bioconductor software package that provides high-performance alignment and read counting functions for RNA-seq reads. Rsubread is based on the successful Subread suite with the added ease-of-use of the R programming environment, creating a matrix of read counts directly as an R object ready for downstream analysis. It integrates read mapping and quantification in a single package and has no software dependencies other than R itself. We demonstrate Rsubread's ability to detect exon-exon junctions de novo and to quantify expression at the level of either genes, exons or exon junctions...
February 20, 2019: Nucleic Acids Research
https://read.qxmd.com/read/30783480/microrna-144-attenuates-cardiac-ischemia-reperfusion-injury-by-targeting-foxo1
#10
Lusha E, Hong Jiang, Zhibing Lu
Cardiovascular ischemic disease refers to a large class of conditions that are harmful to human health. A number of previous studies have demonstrated that microRNAs (miRs) have notable roles in regulating cardiac injury. miR-144 is influential in the differentiation, growth, and metastatic processes of cells; however, the impact of miR-144 in cardiac ischemia/reperfusion (I/R) injury has not been thoroughly elucidated to date. In the present study, reverse transcription quantitative polymerase chain reaction was used to evaluate RNA expression...
March 2019: Experimental and Therapeutic Medicine
https://read.qxmd.com/read/30783451/correlation-of-the-expression-of-inflammatory-factors-with-expression-of-apoptosis-related-genes-bax-and-bcl-2-in-burned-rats
#11
Zhixue Wang, Jifeng Fang, Jizhou Xiao
Correlation of the expression of inflammatory factors with expression of apoptosis-related genes, B-cell lymphoma 2 ( Bcl-2 ) and Bcl-2 associated X protein ( Bax ), in burned rats was investigated. Forty healthy Sprague-Dawley rats were selected and randomly divided into SHAM group (n=10), I° burn group (n=10), II° burn group (n=10) and III° burn group (n=10). Changes in tumor necrosis factor-α (TNF-α), Bax messenger ribonucleic acid (mRNA), Bcl-2 mRNA, Bax protein and Bcl-2 protein expression levels were detected...
March 2019: Experimental and Therapeutic Medicine
https://read.qxmd.com/read/30782707/a-prospective-cohort-for-the-investigation-of-alteration-in-temporal-transcriptional-and-microbiome-trajectories-preceding-preterm-birth-a-study-protocol
#12
Tobias Brummaier, Basirudeen Syed Ahamed Kabeer, Stephen Lindow, Justin C Konje, Sasithon Pukrittayaamee, Juerg Utzinger, Mohammed Toufiq, Antonios Antoniou, Alexandra K Marr, Sangrawee Suriyakan, Tomoshige Kino, Souhaila Al Khodor, Annalisa Terranegra, François Nosten, Daniel H Paris, Rose McGready, Damien Chaussabel
INTRODUCTION: Preterm birth (PTB) results from heterogeneous influences and is a major contributor to neonatal mortality and morbidity that continues to have adverse effects on infants beyond the neonatal period. This protocol describes the procedures to determine molecular signatures predictive of PTB through high-frequency sampling during pregnancy, at delivery and the postpartum period. METHODS AND ANALYSIS: Four hundred first trimester pregnant women from either Myanmar or Thailand of either Karen or Burman ethnicity, with a viable, singleton pregnancy will be enrolled in this non-interventional, prospective pregnancy birth cohort study and will be followed through to the postpartum period...
January 15, 2019: BMJ Open
https://read.qxmd.com/read/30782362/specific-and-simultaneous-detection-of-micro-rna-21-and-let-7a-by-rolling-circle-amplification-combined-with-lateral-flow-strip
#13
Mengdi Yao, Xuefei Lv, Yulin Deng, Madiha Rasheed
Owing to the pivotal function in post transcriptional gene modification, miRNA biomarkers are playing crucial role in tracking and diagnosing various forms of tumors in a short time period. Hence, the need to develop simple, sensitive and specific detection of miRNAs for precise diagnosis arises. This current study is aimed to develop a detecting platform by combining rolling circle amplification with AuNps-based lateral flow strip (LFS-RCA) for simultaneous detection of miRNA 21 and miRNA let-7a. The current methodology is simple, sensitive, specific and selective for miRNA let-7a and miRNA 21 with the limits of detection (LOD) as low as 20 pM and 40 pM, respectively...
May 9, 2019: Analytica Chimica Acta
https://read.qxmd.com/read/30782188/a-novel-lncrna-mcm3ap-as1-promotes-the-growth-of-hepatocellular-carcinoma-by-targeting-mir-194-5p-foxa1-axis
#14
Yufeng Wang, Liu Yang, Tianxiang Chen, Xin Liu, Yang Guo, Qiaojuan Zhu, Xiangmin Tong, Wei Yang, Qiuran Xu, Dongsheng Huang, Kangsheng Tu
BACKGROUND: Hepatocellular carcinoma (HCC) is the most common malignant liver tumor with poor clinical outcomes. Increasing amount of long non-coding RNAs (lncRNAs) have been revealed to be implicated in the carcinogenesis and progression of HCC. However, the expressions, clinical significances, and roles of most lncRNAs in HCC are still unknown. METHODS: The expression of lncRNA MCM3AP antisense RNA 1 (MCM3AP-AS1) in HCC tissues and cell lines was detected by qRT-PCR and fluorescence in situ hybridization...
February 19, 2019: Molecular Cancer
https://read.qxmd.com/read/30782157/circular-rna-ctfrc-acts-as-the-sponge-of-microrna-107-to-promote-bladder-carcinoma-progression
#15
Hongwei Su, Tao Tao, Zhao Yang, Xing Kang, Xu Zhang, Danyue Kang, Song Wu, Chong Li
BACKGROUND: Circular RNA (circRNA) represents a broad and diverse endogenous RNAs that can regulate gene expression in cancer. However, the regulation and function of bladder cancer (BC) circRNAs remain largely unknown. METHODS: Here we generated circRNA microarray data from three BC tissues and paired non-cancerous matched tissues, and detected circular RNA-cTFRC up-regulated and correlated with tumor grade and poor survival rate of BC patients. We subsequently performed functional analyses in cell lines and an animal model to support clinical findings...
February 19, 2019: Molecular Cancer
https://read.qxmd.com/read/30782093/sphingosine-1-phosphate-s1p-increased-il-6-expression-and-cell-growth-in-endometriotic-cells
#16
Osamu Yoshino, Kaori Yamada-Nomoto, Kuniyuki Kano, Yosuke Ono, Mutsumi Kobayashi, Masami Ito, Satoshi Yoneda, Akitoshi Nakashima, Tomoko Shima, Takashi Onda, Yutaka Osuga, Junken Aoki, Shigeru Saito
OBJECTS: There is growing evidence that sphingosine 1-phosphate (S1P) is involved in inflammatory diseases. As endometriosis is known as an inflammatory disease, we investigated the role of S1P system in the development of endometriosis. METHODS: The expression of sphingosine kinase (SphK) 1 in endometriosis lesions was examined by immunohistochemistry. The cystic fluid of ovarian cysts/tumors were obtained to measure S1P concentrations. Endometriotic stromal cells (ESC) derived from endometrioma were used for in vitro experiments...
February 19, 2019: Reproductive Sciences
https://read.qxmd.com/read/30781720/cell-free-dna-variant-sequencing-using-ctc-depleted-blood-for-comprehensive-liquid-biopsy-testing-in-metastatic-breast-cancer
#17
Corinna Keup, Markus Storbeck, Siegfried Hauch, Peter Hahn, Markus Sprenger-Haussels, Mitra Tewes, Pawel Mach, Oliver Hoffmann, Rainer Kimmig, Sabine Kasimir-Bauer
Liquid biopsy analytes such as cell-free DNA (cfDNA) and circulating tumor cells (CTCs) exhibit great potential for personalized treatment. Since cfDNA and CTCs are considered to give additive information and blood specimens are limited, isolation of cfDNA and CTC in an "all from one tube" format is desired. We investigated whether cfDNA variant sequencing from CTC-depleted blood (CTC-depl. B; obtained after positive immunomagnetic isolation of CTCs (AdnaTest EMT-2/Stem Cell Select, QIAGEN)) impacts the results compared to cfDNA variant sequencing from matched whole blood (WB)...
February 18, 2019: Cancers
https://read.qxmd.com/read/30781658/transcriptome-analyses-provide-novel-insights-into-heat-stress-responses-in-chieh-qua-benincasa-hispida-cogn-var-chieh-qua-how
#18
Min Wang, Biao Jiang, Wenrui Liu, Yu'e Lin, Zhaojun Liang, Xiaoming He, Qingwu Peng
Temperature rising caused by global warming has imposed significant negative effects on crop qualities and yields. To get the well-known molecular mechanism upon the higher temperature, we carefully analyzed the RNA sequencing-based transcriptomic responses of two contrasting chieh-qua genotypes: A39 (heat-tolerant) and H5 (heat-sensitive). In this study, twelve cDNA libraries generated from A39 and H5 were performed with a transcriptome assay under normal and heat stress conditions, respectively. A total of 8705 differentially expressed genes (DEGs) were detected under normal conditions (3676 up-regulated and 5029 down-regulated) and 1505 genes under heat stress (914 up-regulated and 591 down-regulated), respectively...
February 18, 2019: International Journal of Molecular Sciences
https://read.qxmd.com/read/30781518/ebola-virus-isolation-using-huh-7-cells-has-methodological-advantages-and-similar-sensitivity-to-isolation-using-other-cell-types-and-suckling-balb-c-laboratory-mice
#19
James Logue, Walter Vargas Licona, Timothy K Cooper, Becky Reeder, Russel Byrum, Jing Qin, Nicole Deiuliis Murphy, Yu Cong, Amanda Bonilla, Jennifer Sword, Wade Weaver, Gregory Kocher, Gene G Olinger, Peter B Jahrling, Lisa E Hensley, Richard S Bennett
Following the largest Ebola virus disease outbreak from 2013 to 2016, viral RNA has been detected in survivors from semen and breast milk long after disease recovery. However, as there have been few cases of sexual transmission, it is unclear whether every RNA positive fluid sample contains infectious virus. Virus isolation, typically using cell culture or animal models, can serve as a tool to determine the infectivity of patient samples. However, the sensitivity of these methods has not been assessed for the Ebola virus isolate, Makona...
February 16, 2019: Viruses
https://read.qxmd.com/read/30779912/tirnas-as-a-novel-biomarker-for-cell-damage-assessment-in-in-vitro-ischemia-reperfusion-model-in-rat-neuronal-pc12-cells
#20
Alaa Elkordy, Sherif Rashad, Heba Shehabeldeen, Eikan Mishima, Kuniyasu Niizuma, Takaaki Abe, Teiji Tominaga
The disruption of appropriate cellular stress responses is implicated in the pathogenesis of different neurological disorders including ischemic injury. Early diagnosis and treatment are often associated with better prognosis in ischemic stroke patients. Thus, there is an urgent need to improve the speed and accuracy of stroke diagnosis by developing highly sensitive stroke biomarkers. We recently reported that transfer RNA (tRNA) was involved in cell stress response pathways. Under cell stress conditions, mature tRNA is cleaved by a specific ribonuclease, angiogenin, generating tRNA-derived stress-induced RNA (tiRNA)...
February 16, 2019: Brain Research
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