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https://www.readbyqxmd.com/read/29149532/exploitation-of-micrornas-by-japanese-encephalitis-virus-in-human-microglial-cells
#1
Meghana Rastogi, Neha Srivastava, Sunit K Singh
JEV infection in CNS leads to the JE neuroinflammation. Children and old age individual have been reported to be more prone to JEV infection. MicroRNAs are endogenous, small non-coding RNAs, which regulate the gene expression. These are ∼22 nucleotide long, conserved RNA sequence that binds at the 3'UTR of a target mRNA and regulate the post-transcriptional gene expression. The role of microRNAs has been reported in several diseases like cancer, viral infection, neuro-degeneration, diabetes etc. In the present study, the human microglial cells were infected with JEV (JaOAr strain)...
November 17, 2017: Journal of Medical Virology
https://www.readbyqxmd.com/read/29147886/peromyscus-leucopus-mouse-brain-transcriptome-response-to-powassan-virus-infection
#2
Luwanika Mlera, Kimberly Meade-White, Eric Dahlstrom, Rachel Baur, Kishore Kanakabandi, Kimmo Virtaneva, Stephen F Porcella, Marshall E Bloom
Powassan virus (POWV) is a tick-borne Flavivirus responsible for life-threatening encephalitis in North America and some regions of Russia. The ticks that have been reported to transmit the virus belong to the Ixodes species, and they feed on small-to-medium-sized mammals, such as Peromyscus leucopus mice, skunks, and woodchucks. We previously developed a P. leucopus mouse model of POWV infection, and the model is characterized by a lack of clinical signs of disease following intraperitoneal or intracranial inoculation...
November 16, 2017: Journal of Neurovirology
https://www.readbyqxmd.com/read/29147650/mitochondria-associated-microrna-expression-profiling-of-heart-failure
#3
Xiaoxia Wang, Chun Song, Xiao Zhou, Xiaorui Han, Jun Li, Zengwu Wang, Haibao Shang, Yuli Liu, Huiqing Cao
Heart failure (HF) is associated with mitochondrial dysfunction and energy metabolism impairment. MicroRNAs are implicated in the development of heart failure. However, the mitochondria enriched microRNA during heart failure remains elusive. Here, we generated a pressure overload-induced early and late stage heart failure model at 4 weeks and 8 weeks following transverse aortic constriction (TAC) in mice. We found that expression of mitochondrion protein COX4 was highly enriched in isolated mitochondria from cardiac tissues while GAPDH could hardly be detected...
2017: BioMed Research International
https://www.readbyqxmd.com/read/29144729/an-optical-nanoantenna-for-single-molecule-based-detection-of-zika-virus-nucleic-acids-without-molecular-multiplication
#4
Sarah Elisabeth Ochmann, Carolin Vietz, Kateryna Trofymchuk, Guillermo P Acuna, Birka Lalkens, Philip Tinnefeld
Due to the limited signal-to-background ratio, molecular diagnostics requires molecular amplification of the target molecules or molecular signal amplification after target recognition. For direct molecular detection, we demonstrate a purely physical fluorescence enhancement process which can elevate the fluorescence signal of single fluorescent dyes by several orders of magnitude. To this end, DNA origami-based optical antennas with a height of around 125 nm are used, which utilize metallic nanoparticles to create a hotspot where fluorescence signals are enhanced by plasmonic effects...
November 16, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29144434/the-role-of-non-coding-rnas-in-cytoplasmic-male-sterility-in-flowering-plants
#5
REVIEW
Helena Štorchová
The interactions between mitochondria and nucleus substantially influence plant development, stress response and morphological features. The prominent example of a mitochondrial-nuclear interaction is cytoplasmic male sterility (CMS), when plants produce aborted anthers or inviable pollen. The genes responsible for CMS are located in mitochondrial genome, but their expression is controlled by nuclear genes, called fertility restorers. Recent explosion of high-throughput sequencing methods enabled to study transcriptomic alterations in the level of non-coding RNAs under CMS biogenesis...
November 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29142136/size-composition-and-evolution-of-hiv-dna-populations-during-early-antiretroviral-therapy-and-intensification-with-maraviroc
#6
Antoine Chaillon, Sara Gianella, Steven M Lada, Josué Perez-Santiago, Parris Jordan, Caroline Ignacio, Maile Karris, Douglas Richman, Sanjay R Mehta, Susan J Little, Joel O Wertheim, Davey M Smith
Residual viremia is common during antiretroviral therapy (ART), and could be caused by ongoing low-level virus replication or by release of viral particles from infected cells. ART Intensification should impact ongoing viral propagation but not virion release. Eighteen acutely infected men were enrolled in a randomized controlled trial, and followed for a median of 107 weeks. Participants started ART with (n=9) or without (n=9) intensification with maraviroc (MVC) within 90 days of infection. Levels of HIV DNA and cell-free RNA were quantified by droplet digital PCR...
November 15, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29141604/genome-wide-identification-of-mirnas-and-lncrnas-in-cajanus-cajan
#7
Chandran Nithin, Amal Thomas, Jolly Basak, Ranjit Prasad Bahadur
BACKGROUND: Non-coding RNAs (ncRNAs) are important players in the post transcriptional regulation of gene expression (PTGR). On one hand, microRNAs (miRNAs) are an abundant class of small ncRNAs (~22nt long) that negatively regulate gene expression at the levels of messenger RNAs stability and translation inhibition, on the other hand, long ncRNAs (lncRNAs) are a large and diverse class of transcribed non-protein coding RNA molecules (> 200nt) that play both up-regulatory as well as down-regulatory roles at the transcriptional level...
November 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29140695/rna-g-quadruplexes-in-kirsten-ras-kras-oncogene-as-targets-for-small-molecules-inhibiting-translation
#8
Giulia Miglietta, Susanna Cogoi, Jessica Marinello, Giovanni Capranico, Alexander S Tikhomirov, Andrey E Shchekotikhin, Luigi E Xodo
The human KRAS transcript contains a G-rich 5'-UTR sequence (77 % GC) harbouring several G4 motifs capable to form stable RNA G-quadruplex (RG4) structures that can serve as targets for small molecules. A biotin-streptavidin pull-down assay showed that 4,11-bis(2-aminoethylamino)anthra[2,3-b]furan-5,10-dione (2a) binds to RG4s in the KRAS transcript under low-abundance cellular conditions. Dual-luciferase assays demonstrated that 2a and its analogue 4,11-bis(2-aminoethylamino)anthra[2,3-b]thiophene-5,10-dione 2b) repress translation in a dose-dependent manner...
November 15, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29138809/microrna-expression-profiles-in-non%C3%A2-epithelial-ovarian-tumors
#9
Roger K Chang, Xidan Li, Ninni Mu, Olga Hrydziuszko, Beatriz Garcia-Majano, Catharina Larsson, Weng-Onn Lui
Ovarian germ cell tumors (OGCTs) and sex cord stromal tumors (SCSTs) are rare gynecologic tumors that are derived from germ and stromal cells, respectively. Unlike their epithelial counterparts, molecular pathogenesis of these tumor types is still poorly understood. Here, we characterized microRNA (miRNA) expression profiles of 9 OGCTs (2 malignant and 7 benign) and 3 SCSTs using small RNA sequencing. We observed significant miRNA expression variations among the three tumor groups. To further demonstrate the biological relevance of our findings, we selected 12 miRNAs for validation in an extended cohort of 16 OGCTs (9 benign and 7 malignant) and 7 SCSTs by reverse transcription-quantitative polymerase chain reaction...
November 10, 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/29138211/transcriptome-sequencing-of-the-naked-mole-rat-heterocephalus-glaber-and-identification-of-hypoxia-tolerance-genes
#10
Bang Xiao, Li Li, Chang Xu, Shanmin Zhao, Lifang Lin, Jishuai Cheng, Wenjing Yang, Wei Cong, Guanghan Kan, Shufang Cui
The naked mole rat (NMR; Heterocephalus glaber) is a small rodent species found in regions of Kenya, Ethiopia and Somalia. It has a high tolerance for hypoxia and is thus, considered one of the most important natural models for studying hypoxia tolerance mechanisms. The various mechanisms underlying the NMR's hypoxia tolerance are beginning to be understood at different levels of organization, and next-generation sequencing methods promise to expand this understanding to the level of gene expression. In this study, we examined the sequence and transcript abundance data of the muscle transcriptome of NMRs exposed to hypoxia using the Illumina HiSeq 2500 system to clarify the possible genomic adaptive responses to the hypoxic underground surroundings...
November 14, 2017: Biology Open
https://www.readbyqxmd.com/read/29137313/rna-seq-reveals-distinctive-rna-profiles-of-small-extracellular-vesicles-from-different-human-liver-cancer-cell-lines
#11
Martina Berardocco, Annalisa Radeghieri, Sara Busatto, Marialucia Gallorini, Chiara Raggi, Clarissa Gissi, Igea D'Agnano, Paolo Bergese, Armando Felsani, Anna C Berardi
Liver cancer (LC) is one of the most common cancers and represents the third highest cause of cancer-related deaths worldwide. Extracellular vesicle (EVs) cargoes, which are selectively enriched in RNA, offer great promise for the diagnosis, prognosis and treatment of LC. Our study analyzed the RNA cargoes of EVs derived from 4 liver-cancer cell lines: HuH7, Hep3B, HepG2 (hepato-cellular carcinoma) and HuH6 (hepatoblastoma), generating two different sets of sequencing libraries for each. One library was size-selected for small RNAs and the other targeted the whole transcriptome...
October 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/29136092/microrpm-a-microrna-prediction-model-based-only-on-plant-small-rna-sequencing-data
#12
Kuan-Chien Tseng, Yi-Fan Chiang-Hsieh, Hsuan Pai, Chi-Nga Chow, Shu-Chuan Lee, Han-Qin Zheng, Po-Li Kuo, Guan-Zhen Li, Yu-Cheng Hung, Na-Sheng Lin, Wen-Chi Chang
Motivation: MicroRNAs (miRNAs) are endogenous non-coding small RNAs (of about 22 nucleotides), which play an important role in the post-transcriptional regulation of gene expression via either mRNA cleavage or translation inhibition. Several machine learning-based approaches have been developed to identify novel miRNAs from next generation sequencing (NGS) data. Typically, precursor/genomic sequences are required as references for most methods. However, the non-availability of genomic sequences is often a limitation in miRNA discovery in non-model plants...
November 9, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29135975/transcriptomic-profiling-of-human-breast-and-melanoma-cells-selected-by-migration-through-narrow-constraints
#13
Dominika A Rudzka, William Clark, Ann Hedley, Gabriela Kalna, Michael F Olson
The metastatic spread of cancer cells is a step-wise process that starts with dissociation from primary tumours and local invasion of adjacent tissues. The ability to invade local tissues is the product of several processes, including degradation of extracellular matrices (ECM) and movement of tumour cells through physically-restricting gaps. To identify properties contributing to tumour cells squeezing through narrow gaps, invasive MDA-MB-231 human breast cancer and MDA-MB-435 human melanoma cells were subjected to three successive rounds of selection using cell culture inserts with highly constraining 3 μm pores...
November 14, 2017: Scientific Data
https://www.readbyqxmd.com/read/29134713/comparative-ecological-transcriptomics-and-the-contribution-of-gene-expression-to-the-evolutionary-potential-of-a-threatened-fish
#14
Chris J Brauer, Peter J Unmack, Luciano B Beheregaray
Understanding whether small populations with low genetic diversity can respond to rapid environmental change via phenotypic plasticity is an outstanding research question in biology. RNA sequencing (RNA-seq) has recently provided the opportunity to examine variation in gene expression, a surrogate for phenotypic variation, in non-model species. We used a comparative RNA-seq approach to assess expression variation within and among adaptively divergent populations of a threatened freshwater fish, Nannoperca australis, found across a steep hydroclimatic gradient in the Murray-Darling Basin, Australia...
November 13, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/29134596/preparing-cdna-libraries-from-lytic-phage-infected-cells-for-whole-transcriptome-analysis-by-rna-seq
#15
Bob Blasdel, Pieter-Jan Ceyssens, Rob Lavigne
Whole genome wide analysis of transcription using RNA-Seq methods is a powerful way to elucidate differential expression of gene features in bacteria across different conditions as well as for discovering previously exotic RNA species. Indeed, RNA sequencing has revolutionized the study of bacterial transcription with the diversity and quantity of small noncoding RNA elements that have been found and its ability to clearly define operons, promoters , and terminators . We discuss our experience with applying RNA sequencing technology to analyzing the lytic cycle, including extraction, processing, and a guide to the customized statistical analysis necessary for analyzing differential host and phage transcription...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29133129/hbsag-mrna-degradation-induced-by-dihydroquinolizinone-molecule-depends-on-hbv-posttranscriptional-regulatory-element
#16
Tianlun Zhou, Timothy Block, Fei Liu, Andrew S Kondratowicz, Liren Sun, Siddhartha Rawat, Jeffrey Branson, Fang Guo, Hongyan Liang, Lauren Bailey, Chris Moore, Xiaohe Wang, Andy Cuconatti, Min Gao, Amy C H Lee, Troy Harasym, Tim Chiu, Dimitar Gotchev, Bruce Dorsey, Rene Rijnbrand, Michael J Sofia
In pursuit of novel therapeutics targeting the hepatitis B virus (HBV) infection, we evaluated a dihydroquinolizinone compound (DHQ-1) that possessed nanomolar activities against the production of virion and surface protein (HBsAg) in tissue culture. This compound also showed broad HBV genotype coverage and was inactive against a panel of DNA and RNA viruses of other species. Oral administration of DHQ-1 in the AAV-HBV mouse model resulted in a strong reduction of serum HBsAg as soon as 4 days following the commencement of treatment...
November 10, 2017: Antiviral Research
https://www.readbyqxmd.com/read/29133028/evolution-and-postglacial-colonization-of-seewis-hantavirus-with-sorex-araneus-in-finland
#17
Jiaxin Ling, Teemu Smura, Daniel Tamarit, Otso Huitu, Liina Voutilainen, Heikki Henttonen, Antti Vaheri, Olli Vapalahti, Tarja Sironen
Hantaviruses have co-existed with their hosts for millions of years. Seewis virus (SWSV), a soricomorph-borne hantavirus, is widespread in Eurasia, ranging from Central Siberia to Western Europe. To gain insight into the phylogeography and evolutionary history of SWSV in Finland, lung tissue samples of 225 common shrews (Sorex araneus) trapped from different parts of Finland were screened for the presence of SWSV RNA. Forty-two of the samples were positive. Partial small (S), medium (M) and large (L) segments of the virus were sequenced, and analyzed together with all SWSV sequences available in Genbank...
November 10, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29133016/dynamic-transcriptional-control-of-macrophage-mirna-signature-via-inflammation-responsive-enhancers-revealed-using-a-combination-of-next-generation-sequencing-based-approaches
#18
Zsolt Czimmerer, Attila Horvath, Bence Daniel, Gergely Nagy, Ixchelt Cuaranta-Monroy, Mate Kiss, Zsuzsanna Kolostyak, Szilard Poliska, Laszlo Steiner, Nikolas Giannakis, Tamas Varga, Laszlo Nagy
MicroRNAs are important components of the post-transcriptional fine-tuning of macrophage gene expression in physiological and pathological conditions. However, the mechanistic underpinnings and the cis-acting genomic factors of how macrophage polarizing signals induce miRNA expression changes are not well characterized. Therefore, we systematically evaluated the transcriptional basis underlying the inflammation-mediated regulation of macrophage microRNome using the combination of different next generation sequencing datasets...
November 10, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29131834/plasma-microrna-profiling-exploring-better-biomarkers-for-lymphoma-surveillance
#19
Drirh Khare, Neta Goldschmidt, Aya Bardugo, Devorah Gur-Wahnon, Iddo Z Ben-Dov, Batia Avni
Early detection of relapsed lymphoma improves response and survival. Current tools lack power for detection of early relapse, while being cumbersome and expensive. We searched for sensitive biomarkers that precede clinical relapse, and serve for further studies on therapy response and relapse. We recruited 20 healthy adults, 14 diffuse large B-cell lymphoma (DLBCL) patients and 11 Hodgkin lymphoma (HL) patients at diagnosis. Using small-RNA sequencing we identified in DLBCL patients increased plasma levels of miR-124 and miR-532-5p, and decreased levels of miR-425, miR-141, miR-145, miR-197, miR-345, miR-424, miR-128 and miR-122...
2017: PloS One
https://www.readbyqxmd.com/read/29131253/lncrna-snhg7-promotes-the-proliferation-and-inhibits-apoptosis-of-gastric-cancer-cells-by-repressing-the-p15-and-p16-expression
#20
M-W Wang, J Liu, Q Liu, Q-H Xu, T-F Li, S Jin, T-S Xia
OBJECTIVE: To investigate the relative expression of long non-coding small nucleolar RNA host gene 7 (lncRNA SNHG7) in gastric cancer tissues and cells, the effect of lncRNA SNHG7 on proliferation and apoptosis of gastric cancer cells in vivo and in vitro experiments, and the relevant mechanism. PATIENTS AND METHODS: Real-time quantitative polymerase chain reaction (qRT-PCR) experiment was performed to detect the relative expressions of SNHG7 in the gastric cancer tissues and cells...
October 2017: European Review for Medical and Pharmacological Sciences
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