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https://www.readbyqxmd.com/read/28719060/drug-use-and-phylogenetic-clustering-of-hepatitis-c-virus-infection-among-people-who-use-drugs-in-vancouver-canada-a-latent-class-analysis-approach
#1
Brendan Jacka, Bethany Bray, Tanya L Applegate, Brandon Dl Marshall, Viviane Dias Lima, Kanna Hayashi, Kora DeBeck, Jayna Raghwani, P Richard Harrigan, Mel Krajden, Julio Montaner, Jason Grebely
BACKGROUND: This study estimated latent classes (i.e., unobserved subgroups in a population) of people who use drugs in Vancouver, Canada and examined how these classes relate to phylogenetic clustering of hepatitis C virus (HCV) infection. METHODS: HCV antibody positive people who use drugs from two cohorts in Vancouver, Canada (1996-2012) with a Core-E2 sequence were included. Time-stamped phylogenetic trees were inferred and phylogenetic clustering was determined by time to most common recent ancestor...
July 18, 2017: Journal of Viral Hepatitis
https://www.readbyqxmd.com/read/28718764/crispr-mediated-genetic-interaction-profiling-identifies-rna-binding-proteins-controlling-metazoan-fitness
#2
Adam D Norris, Xicotencatl Gracida, John Calarco
<span style="font-size: 12pt; font-family: 'Times';">Genetic interaction screens have aided our understanding of complex genetic traits,</span><span style="font-size: 11.000000pt; font-family: 'Calibri';"> </span><span style="font-size: 12pt; font-family: 'Times';">diseases, and biological pathways. However, approaches for synthetic genetic analysis with</span><span style="font-size: 11.000000pt; font-family: 'Calibri';"> </span><span style="font-size: 12pt; font-family: 'Times';">null-alleles in metazoans have not been feasible...
July 18, 2017: ELife
https://www.readbyqxmd.com/read/28718434/undercover-agents-targeting-tumours-with-modified-platelets
#3
REVIEW
Stephanie R Hyslop, Emma C Josefsson
Platelets have long been recognised to colocalise with tumour cells throughout haematogenous metastasis. Interactions between these cells contribute to tumour cell survival and motility through the vasculature into other tissues. Now, the research focus is shifting towards developing means to exploit this relationship to provide accurate diagnostics and therapies. Alterations to platelet count, RNA profile, and platelet ultrastructure are associated with the presence of certain malignancies, and may be used for cancer detection...
March 2017: Trends in Cancer
https://www.readbyqxmd.com/read/28717649/circular-rna-profiling-and-bioinformatic-modeling-identify-its-regulatory-role-in-hepatic-steatosis
#4
Xing-Ya Guo, Chong-Xin He, Yu-Qin Wang, Chao Sun, Guang-Ming Li, Qing Su, Qin Pan, Jian-Gao Fan
Circular RNAs (circRNAs) exhibit a wide range of physiological and pathological activities. To uncover their role in hepatic steatosis, we investigated the expression profile of circRNAs in HepG2-based hepatic steatosis induced by high-fat stimulation. Differentially expressed circRNAs were subjected to validation using QPCR and functional analyses using principal component analysis, hierarchical clustering, target prediction, gene ontology (GO), and pathway annotation, respectively. Bioinformatic integration established the circRNA-miRNA-mRNA regulatory network so as to identify the mechanisms underlying circRNAs' metabolic effect...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28717530/comparative-and-integrative-analysis-of-rna-structural-profiling-data-current-practices-and-emerging-questions
#5
Krishna Choudhary, Fei Deng, Sharon Aviran
BACKGROUND: Structure profiling experiments provide single-nucleotide information on RNA structure. Recent advances in chemistry combined with application of high-throughput sequencing have enabled structure profiling at transcriptome scale and in living cells, creating unprecedented opportunities for RNA biology. Propelled by these experimental advances, massive data with ever-increasing diversity and complexity have been generated, which give rise to new challenges in interpreting and analyzing these data...
March 2017: Quantitative Biology
https://www.readbyqxmd.com/read/28717421/isolation-of-membrane-vesicles-from-prokaryotes-a-technical-and-biological-comparison-reveals-heterogeneity
#6
Priscila Dauros Singorenko, Vanessa Chang, Alana Whitcombe, Denis Simonov, Jiwon Hong, Anthony Phillips, Simon Swift, Cherie Blenkiron
Prokaryotes release membrane vesicles (MVs) with direct roles in disease pathogenesis. MVs are heterogeneous when isolated from bacterial cultures so Density Gradient Centrifugation (DGC) is valuable for separation of MV subgroups from contaminating material. Here we report the technical variability and natural biological heterogeneity seen between DGC preparations of MVs for Mycobacterium smegmatis and Escherichia coli and compare these DGC data with size exclusion chromatography (SEC) columns. Crude preparations of MVs, isolated from cultures by ultrafiltration and ultracentrifugation were separated by DGC with fractions manually collected as guided by visible bands...
2017: Journal of Extracellular Vesicles
https://www.readbyqxmd.com/read/28716420/characterization-of-bdcbf-genes-and-genome-wide-transcriptome-profiling-of-bdcbf3-dependent-and-independent-cold-stress-responses-in-brachypodium-distachyon
#7
Jingjie Hao, Jinliang Yang, Jiangli Dong, Shui-Zhang Fei
Freezing stress substantially reduces crop yields and limits plant distribution. The identification of genes critical for cold acclimation is thus of great importance. C-repeat binding factors (CBFs) are transcription factors that play key regulatory roles in the cold acclimation process, which dramatically increases freezing tolerance in plants. We report here that B. distachyon can successfully cold acclimate and we identified a CBF gene family consisting of eight genes in a tandem array and are designated as BdCBF1-8...
September 2017: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/28716093/c-elegans-sup-46-an-hnrnpm-family-rna-binding-protein-that-prevents-paternally-mediated-epigenetic-sterility
#8
Wendy L Johnston, Aldis Krizus, Arun K Ramani, Wade Dunham, Ji Young Youn, Andrew G Fraser, Anne-Claude Gingras, James W Dennis
BACKGROUND: In addition to DNA, gametes contribute epigenetic information in the form of histones and non-coding RNA. Epigenetic programs often respond to stressful environmental conditions and provide a heritable history of ancestral stress that allows for adaptation and propagation of the species. In the nematode C. elegans, defective epigenetic transmission often manifests as progressive germline mortality. We previously isolated sup-46 in a screen for suppressors of the hexosamine pathway gene mutant, gna-2(qa705)...
July 17, 2017: BMC Biology
https://www.readbyqxmd.com/read/28715488/microrna-dependent-and-independent-deregulation-of-long-non-coding-rnas-by-an-oncogenic-herpesvirus
#9
Sunantha Sethuraman, Lauren Appleby Gay, Vaibhav Jain, Irina Haecker, Rolf Renne
Kaposi's sarcoma (KS) is a highly prevalent cancer in AIDS patients, especially in sub-Saharan Africa. Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiological agent of KS and other cancers like Primary Effusion Lymphoma (PEL). In KS and PEL, all tumors harbor latent KSHV episomes and express latency-associated viral proteins and microRNAs (miRNAs). The exact molecular mechanisms by which latent KSHV drives tumorigenesis are not completely understood. Recent developments have highlighted the importance of aberrant long non-coding RNA (lncRNA) expression in cancer...
July 17, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28715440/transcriptional-profiling-of-the-rat-nucleus-accumbens-after-modest-or-high-alcohol-exposure
#10
Julia Morud, Arghavan Ashouri, Erik Larsson, Mia Ericson, Bo Söderpalm
Alcohol use disorder is a chronic relapsing brain disorder and a global health issue. Prolonged high alcohol consumption increases the risk for dependence development, a complex state that includes progressive alterations in brain function. The molecular mechanisms behind these changes remain to be fully disclosed, but several genes show altered expression in various regions of the rat brain even after modest alcohol exposure. The present study utilizes whole-transcriptome sequencing (RNA-seq) to investigate expression changes in the brain nucleus accumbens (NAc), an area of particular interest in addictive disorders, of alcohol consuming rats...
2017: PloS One
https://www.readbyqxmd.com/read/28715413/zika-virus-alters-the-microrna-expression-profile-and-elicits-an-rnai-response-in-aedes-aegypti-mosquitoes
#11
Miguel A Saldaña, Kayvan Etebari, Charles E Hart, Steven G Widen, Thomas G Wood, Saravanan Thangamani, Sassan Asgari, Grant L Hughes
Zika virus (ZIKV), a flavivirus transmitted primarily by Aedes aegypti, has recently spread globally in an unprecedented fashion, yet we have a poor understanding of host-microbe interactions in this system. To gain insights into the interplay between ZIKV and the mosquito, we sequenced the small RNA profiles in ZIKV-infected and non-infected Ae. aegypti mosquitoes at 2, 7 and 14 days post-infection. ZIKA induced an RNAi response in the mosquito with virus-derived short interfering RNAs and PIWI-interacting RNAs dramatically increased in abundance post-infection...
July 17, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28715379/detection-of-microrna-expression-in-peritoneal-membrane-of-rats-using-quantitative-real-time-pcr
#12
Keiji Hirai, Hiromichi Yoshizawa, Toshimi Imai, Yusuke Igarashi, Ichiro Hirahara, Susumu Ookawara, Kenichi Ishibashi, Yoshiyuki Morishita
MicroRNAs (miRNAs) are small noncoding RNAs that regulate messenger RNA expression post-transcriptionally. The miRNA expression profile has been investigated in various organs and tissues in rat. However, standard methods for the purification of miRNAs and detection of their expression in rat peritoneal membrane have not been well established. We have developed an effective and reliable method to purify and quantify miRNAs using quantitative real-time reverse-transcription polymerase chain reaction (qRT-PCR) in rat peritoneal membrane...
June 27, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28714520/genomic-profiling-of-long-non-coding-rna-and-mrna-expression-associated-with-acquired-temozolomide-resistance-in-glioblastoma-cells
#13
Huijun Zeng, Ningbo Xu, Yanting Liu, Boyang Liu, Zhao Yang, Zhao Fu, Changlin Lian, Hongbo Guo
Temozolomide (TMZ) is an alkylating chemotherapeutic agent widely used in anti-glioma treatment. However, acquired TMZ resistance represents a major clinical challenge that leads to tumor relapse or progress. This study investigated the genomic profiles including long non-coding RNA (lncRNA) and mRNA expression associated with acquired TMZ resistance in glioblastoma (GBM) cells in vitro. The TMZ-resistant (TR) of GBM sub-cell lines were established through repetitive exposure to increasing TMZ concentrations in vitro...
August 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/28714361/rna-editing-is-induced-by-type-i-interferon-in-esophageal-squamous-cell-carcinoma
#14
Jinyao Zhang, Zhaoli Chen, Zefang Tang, Jianbing Huang, Xueda Hu, Jie He
In recent years, abnormal RNA editing has been shown to play an important role in the development of esophageal squamous cell carcinoma, as such abnormal editing is catalyzed by ADAR (adenosine deaminases acting on RNA). However, the regulatory mechanism of ADAR1 in esophageal squamous cell carcinomas remains largely unknown. In this study, we investigated ADAR1 expression and its association with RNA editing in esophageal squamous cell carcinomas. RNA sequencing applied to esophageal squamous cell carcinoma clinical samples showed that ADAR1 expression was correlated with the expression of STAT1, STAT2, and IRF9...
July 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28713971/systematic-analysis-of-lncrnas-mirnas-and-mrnas-for-the-identification-of-biomarkers-for-osteoporosis-in-the-mandible-of-ovariectomized-mice
#15
Lingyu Hao, Jiayao Fu, Yawen Tian, Junhua Wu
Osteoporosis is a complex and multifactorial disease caused by an imbalance between bone formation and resorption. Post‑menopausal women with endogenous estrogen deficiency suffer from systemic bone loss and osteoporosis, and are at high risk of this affecting the jaw bones. MicroRNAs (miRNAs or miRs) have been implicated in the mechanisms of metabolic bone diseases and are expressed at differential levels in alveolar bone following ovariectomy. In the present study, we systematically analyzed the expression profiles of miRNAs, mRNAs and long non‑coding RNA (lncRNAs) in the mandible of ovariectomized (OVX) mice...
July 10, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28713413/identification-of-conserved-and-novel-micrornas-in-blueberry
#16
Junyang Yue, Xiaohui Lu, Huan Zhang, Jiao Ge, Xueling Gao, Yongsheng Liu
MicroRNAs (miRNAs) are a class of small endogenous RNAs that play important regulatory roles in cells by negatively affecting gene expression at both transcriptional and post-transcriptional levels. There have been extensive studies aiming to identify miRNAs and to elucidate their functions in various plant species. In the present study, we employed the high-throughput sequencing technology to profile miRNAs in blueberry fruits. A total of 9,992,446 small RNA tags with sizes ranged from 18 to 30 nt were obtained, indicating that blueberry fruits have a large and diverse small RNA population...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28713408/transcriptome-analyses-shed-new-insights-into-primary-metabolism-and-regulation-of-blumeria-graminis-f-sp-tritici-during-conidiation
#17
Fan-Song Zeng, Fabrizio Menardo, Min-Feng Xue, Xue-Jiang Zhang, Shuang-Jun Gong, Li-Jun Yang, Wen-Qi Shi, Da-Zhao Yu
Conidia of the obligate biotrophic fungal pathogen Blumeria graminis f. sp. tritici (Bgt) play a vital role in its survival and rapid dispersal. However, little is known about the genetic basis for its asexual reproduction. To uncover the primary metabolic and regulatory events during conidiation, we sequenced the transcriptome of Bgt epiphytic structures at 3 (vegetative hyphae growth), 4 (foot cells initiation), and 5 (conidiophore erection) days post-inoculation (dpi). RNA-seq analyses identified 556 and 404 (combined 685) differentially expressed genes (DEGs) at 4 and 5 dpi compared with their expression levels at 3 dpi, respectively...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28711945/the-molecular-characterization-of-porcine-egg-precursor-cells
#18
Te-Sha Tsai, Jacqueline Johnson, Yvonne White, Justin C St John
Female-factor infertility can be caused by poor oocyte quality and depleted ovarian reserves. Egg precursor cells (EPCs), isolated from the ovarian cortex, have the potential to be used to overcome female infertility. We aimed to define the origins of EPCs by analyzing their gene expression profiles and mtDNA content using a mini-pig model. We characterized FAC-sorted DDX4+-derived porcine EPCs by performing RNA-sequencing and determined that they utilize pathways important for cell cycle and proliferation, which supports the existence of adult mitotically active oogonial cells...
June 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28711944/analysis-of-long-non-coding-rna-expression-profiles-identifies-novel-lncrna-biomarkers-in-the-tumorigenesis-and-malignant-progression-of-gliomas
#19
Gang Chen, Yanfei Cao, Lina Zhang, Hongxing Ma, Chao Shen, Jiang Zhao
Long non-coding RNAs have been shown to be associated with cancer development and progression, demonstrating potential applications as novel diagnostic or prognostic molecular markers in clinical management and treatment. However, the functional significance of lncRNAs in the development and malignant progression of gliomas is still unclear and needed to be further explored. we first obtained genome-wide lncRNA expression profiles in a large cohort of patients with gliomas from the Gene Expression Omnibus database using microarray probes repurposing method and investigated the lncRNA expression patterns during the tumorigenesis and malignant progression of gliomas...
June 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28711684/folding-of-the-silver-aptamer-in-a-dnazyme-probed-by-2-aminopurine-fluorescence
#20
Runjhun Saran, Lu Yao, Peter Hoang, Juewen Liu
The RNA-cleaving Ag10c DNAzyme was recently isolated via in vitro selection and it can bind two Ag(+) ions for activity. The Ag10c contains a well-defined Ag(+) binding aptamer as indicated by DMS footprinting. Since aptamer binding is often accompanied with conformational changes, we herein used 2-aminopurine (2AP) to probe its folding in the presence of Ag(+). The Ag10c was respectively labeled with 2AP at three different positions, both in the substrate strand and in the enzyme strand. Ag(+)-induced folding was observed at the substrate cleavage junction and the A9 position of the enzyme strand, consistent with aptamer binding...
July 12, 2017: Biochimie
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