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https://www.readbyqxmd.com/read/28716126/the-effects-of-potato-virus-y-derived-virus-small-interfering-rnas-of-three-biologically-distinct-strains-on-potato-solanum-tuberosum-transcriptome
#1
Lindani Moyo, Shunmugiah V Ramesh, Madhu Kappagantu, Neena Mitter, Vidyasagar Sathuvalli, Hanu R Pappu
BACKGROUND: Potato virus Y (PVY) is one of the most economically important pathogen of potato that is present as biologically distinct strains. The virus-derived small interfering RNAs (vsiRNAs) from potato cv. Russet Burbank individually infected with PVY-N, PVY-NTN and PVY-O strains were recently characterized. Plant defense RNA-silencing mechanisms deployed against viruses produce vsiRNAs to degrade homologous viral transcripts. Based on sequence complementarity, the vsiRNAs can potentially degrade host RNA transcripts raising the prospect of vsiRNAs as pathogenicity determinants in virus-host interactions...
July 17, 2017: Virology Journal
https://www.readbyqxmd.com/read/28715413/zika-virus-alters-the-microrna-expression-profile-and-elicits-an-rnai-response-in-aedes-aegypti-mosquitoes
#2
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/28713909/effects-of-lentiviral-vector%C3%A2-mediated-shrna-silencing-of-tgf%C3%AE-1-on-the-expression-of-col1a1-in-rat-hepatic-stellate-cells
#3
Gan-Ping Bai, Guo-He Yan, Guo-Jian Wang, Ping Wan, Xiao-Fei Liu, Heng Wang, Rong-Hua Zhang
The present study aimed to construct a lentiviral RNA interference (RNAi) vector targeting the transforming growth factor β1 (TGFβ1) gene of rats, in order to examine its effect on silencing of the TGFβ1 gene and on the expression of collagen type 1 α1 (Col1a1) in HSC‑T6 rat hepatic stellate cells. Three RNAi sites of the TGFβ1 gene were selected according to its CDs sequence. Three pairs of small interfering RNA (siRNA) of these RNAi sites were synthesized and then transfected into HSC‑T6 cells, respectively, to confirm the optimal siRNA sequence via reverse transcription‑polymerase chain reaction analysis...
July 6, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28713857/a-new-clade-of-insect-specific-flaviviruses-from-australian-anopheles-mosquitoes-displays-species-specific-host-restriction
#4
Agathe M G Colmant, Jody Hobson-Peters, Helle Bielefeldt-Ohmann, Andrew F van den Hurk, Sonja Hall-Mendelin, Weng Kong Chow, Cheryl A Johansen, Jelke Fros, Peter Simmonds, Daniel Watterson, Chris Cazier, Kayvan Etebari, Sassan Asgari, Benjamin L Schulz, Nigel Beebe, Laura J Vet, Thisun B H Piyasena, Hong-Duyen Nguyen, Ross T Barnard, Roy A Hall
Flaviviruses are arthropod-borne viruses found worldwide and are responsible for significant human and veterinary diseases, including dengue, Zika, and West Nile fever. Some flaviviruses are insect specific and replicate only in mosquitoes. We report a genetically divergent group of insect-specific flaviviruses from Anopheles mosquitoes that do not replicate in arthropod cell lines or heterologous Anopheles species, exhibiting unprecedented specialization for their host species. Determination of the complete sequences of the RNA genomes of three of these viruses, Karumba virus (KRBV), Haslams Creek virus, and Mac Peak virus (McPV), that are found in high prevalence in some Anopheles mosquito populations and detection of virus-specific proteins, replicative double-stranded RNA, and small interfering RNA responses in the host mosquito species provided strong evidence of a functional replicating virus in the mosquito midgut...
July 2017: MSphere
https://www.readbyqxmd.com/read/28713413/identification-of-conserved-and-novel-micrornas-in-blueberry
#5
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/28713393/the-complete-chloroplast-genome-of-chinese-bayberry-morella-rubra-myricaceae-implications-for-understanding-the-evolution-of-fagales
#6
Lu-Xian Liu, Rui Li, James R P Worth, Xian Li, Pan Li, Kenneth M Cameron, Cheng-Xin Fu
Morella rubra (Myricaceae), also known as Chinese bayberry, is an economically important, subtropical, evergreen fruit tree. The phylogenetic placement of Myricaceae within Fagales and the origin of Chinese bayberry's domestication are still unresolved. In this study, we report the chloroplast (cp) genome of M. rubra and take advantage of several previously reported chloroplast genomes from related taxa to examine patterns of evolution in Fagales. The cp genomes of three M. rubra individuals were 159,478, 159,568, and 159...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28712318/phylogenetic-studies-and-comparative-chloroplast-genome-analyses-elucidate-the-basal-position-of-halophyte-nitraria-sibirica-nitrariaceae-in-the-sapindales
#7
Lu Lu, Xia Li, Zhaodong Hao, Liming Yang, Jingbo Zhang, Ye Peng, Haibin Xu, Ye Lu, Jin Zhang, Jisen Shi, Jinhui Chen, Tielong Cheng
Nitraria sibirica is a halophyte and belongs to the family Nitrariaceae. The chloroplast genome of Nitraria sibirica (159,466 bp) has a quadripartite structure, which consists of a large single-copy (87,914 bp) region, a small single-copy (18,316 bp) region, and a pair of inverted repeats (26,618 bp). Sequencing analyses indicate that the chloroplast genome contains 113 distinct genes, including 79 peptide-coding genes, 30 transfer RNA genes, and 4 ribosomal RNA genes. We also identified 105 perfect simple sequence repeats, 12 most divergent non-coding regions, and 6 most divergent coding regions when compared to the chloroplast genomes of the Sapindales plants...
July 15, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28711463/modulation-of-atlantic-salmon-mirnome-response-to-sea-louse-infestation
#8
REVIEW
Valentina Valenzuela-Muñoz, Beatriz Novoa, Antonio Figueras, Cristian Gallardo-Escárate
MicroRNAs are non-coding RNA that plays a crucial role in post-transcriptional regulation and immune system regulation. On other hand, sea lice are prevalent parasites that affect salmon farming, generating different degrees of immune suppression depending on the salmon and sea louse species. Caligus rogercresseyi for example, which affects the salmon industry in Chile, decreases Th1 response, macrophage activation, TLR-mediated response and iron regulation in infected fish. In this study, we explore Atlantic salmon miRNome during infestation by C...
July 12, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28710037/rna-editing-independently-occurs-at-three-mir-376a-1-sites-and-may-compromise-the-stability-of-the-microrna-hairpin
#9
Alicia Gallego, Diego A Hartasánchez, Marina Brasó-Vives, Eva Garcia-Ramallo, Maria Lopez-Valenzuela, Neus Baena, Miriam Guitart, Hugo Fernández-Bellon, Ivanela Kondova, Ronald Bontrop, Yukio Kawahara, Yolanda Espinosa-Parrilla
RNA editing is being recognized as an important post-transcriptional mechanism that may have crucial roles in introducing genetic variation and phenotypic diversity. Despite microRNA editing recurrence, defining its biological relevance is still under extended debate. To better understand microRNA editing function and regulation we performed an exhaustive characterization of the A-to-I site-specific patterns in mir-376a-1, a mammalian microRNA which RNA editing is involved in the regulation of development and in disease...
July 11, 2017: Gene
https://www.readbyqxmd.com/read/28709615/transcriptional-profiling-of-rickettsia-prowazekii-coding-and-non-coding-transcripts-during-in-vitro-host-pathogen-and-vector-pathogen-interactions
#10
Casey L C Schroeder, Hema P Narra, Abha Sahni, Kamil Khanipov, Jignesh Patel, Yuriy Fofanov, Sanjeev K Sahni
Natural pathogen transmission of Rickettsia prowazekii, the etiologic agent of epidemic typhus, to humans is associated with arthropods, including human body lice, ticks, and ectoparasites of eastern flying squirrel. Recently, we have documented the presence of small RNAs in Rickettsia species and expression of R. prowazekii sRNAs during infection of cultured human microvascular endothelial cells (HMECs), which represent the primary target cells during human infections. Bacterial noncoding transcripts are now well established as critical post-transcriptional regulators of virulence and adaptation mechanisms in varying host environments...
June 29, 2017: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/28706993/high-frequency-of-intestinal-th17-cells-correlates-with-microbiota-alterations-and-disease-activity-in-multiple-sclerosis
#11
Ilaria Cosorich, Gloria Dalla-Costa, Chiara Sorini, Roberto Ferrarese, Maria Josè Messina, Jayashree Dolpady, Elisa Radice, Alberto Mariani, Pier Alberto Testoni, Filippo Canducci, Giancarlo Comi, Vittorio Martinelli, Marika Falcone
T helper 17 (TH17) cells are key players in multiple sclerosis (MS), and studies in animal models demonstrated that effector TH17 cells that trigger brain autoimmunity originate in the intestine. We validate in humans the crucial role of the intestinal environment in promoting TH17 cell expansion in MS patients. We found that increased frequency of TH17 cells correlates with high disease activity and with specific alterations of the gut mucosa-associated microbiota in MS patients. By using 16S ribosomal RNA sequencing, we analyzed the microbiota isolated from small intestinal tissues and found that MS patients with high disease activity and increased intestinal TH17 cell frequency showed a higher Firmicutes/Bacteroidetes ratio, increased relative abundance of Streptococcus, and decreased Prevotella strains compared to healthy controls and MS patients with no disease activity...
July 2017: Science Advances
https://www.readbyqxmd.com/read/28706437/comparison-of-two-neurotrophic-serpins-reveals-a-small-fragment-with-cell-survival-activity
#12
Paige N Winokur, Preeti Subramanian, Jeanee L Bullock, Veronique Arocas, S Patricia Becerra
PURPOSE: Protease nexin-1 (PN-1), a serpin encoded by the SERPINE2 gene, has serine protease inhibitory activity and neurotrophic properties in the brain. PN-1 inhibits retinal angiogenesis; however, PN-1's neurotrophic capacities in the retina have not yet been evaluated. Pigment epithelium-derived factor (PEDF) is a serpin that exhibits neurotrophic and antiangiogenic activities but lacks protease inhibitory properties. The aim of this study is to compare PN-1 and PEDF. METHODS: Sequence comparisons were performed using computer bioinformatics programs...
2017: Molecular Vision
https://www.readbyqxmd.com/read/28705399/monoblepharidomycetes-diversity-includes-new-parasitic-and-saprotrophic-species-with-highly-intronized-rdna
#13
Sergey A Karpov, Karomat S Mamanazarova, Olga V Popova, Vladimir V Aleoshin, Timothy Y James, Maria A Mamkaeva, Victoria S Tcvetkova, Andrey E Vishnyakov, Joyce E Longcore
The Monoblepharidomycetes is the sister class to the Chytridiomycetes in the phylum Chytridiomycota. The six known genera have thalli that are either monocentric and without rhizoids or produce hyphae with an independent evolutionary origin from the hyphae of higher fungi. On the basis of morphological characters and phylogenetic evidence from the small and large subunits of nuclear ribosomal RNA, we established two new genera, Sanchytrium and Telasphaerula, each with a single species. We re-analyzed intergeneric relationships within the monoblephs, and established two new families...
August 2017: Fungal Biology
https://www.readbyqxmd.com/read/28704716/transcriptional-consequences-of-xpa-disruption-in-human-cell-lines
#14
Mandira Manandhar, Megan G Lowery, Karen S Boulware, Kevin H Lin, Yue Lu, Richard D Wood
Nucleotide excision repair (NER) in mammalian cells requires the xeroderma pigmentosum group A protein (XPA) as a core factor. Remarkably, XPA and other NER proteins have been detected by chromatin immunoprecipitation at some active promoters, and NER deficiency is reported to influence the activated transcription of selected genes. However, the global influence of XPA on transcription in human cells has not been determined. We analyzed the human transcriptome by RNA sequencing (RNA-Seq). We first confirmed that XPA is confined to the cell nucleus even in the absence of external DNA damage, in contrast to previous reports that XPA is normally resident in the cytoplasm and is imported following DNA damage...
June 29, 2017: DNA Repair
https://www.readbyqxmd.com/read/28703803/micu1-protects-against-myocardial-ischemia-reperfusion-injury-and-its-control-by-the-importer-receptor-tom70
#15
Qiang Xue, Haifeng Pei, Qinshe Liu, Mingjun Zhao, Jing Sun, Erhe Gao, Xinliang Ma, Ling Tao
Mitochondrial Ca(2+) overload is a main contributor to mitochondrial damage hence cardiomyocyte death in myocardial ischemia/reperfusion (MI/R) injury. MICU1 has been recently identified as an important regulator of mitochondrial Ca(2+) homeostasis. Here we try to identify the role of MICU1 in MI/R, and to investigate whether the mitochondrial importer receptor Tom70 possesses critical roles in the mitochondrial translocation of MICU1 and MI/R. Specific small interfering RNA (20 μg) against MICU1 and Tom70, and lentivirus vectors carrying the Tom70a sequences (3...
July 13, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28702216/hidden-biofilms-in-a-far-northern-lake-and-implications-for-the-changing-arctic
#16
Vani Mohit, Alexander Culley, Connie Lovejoy, Frédéric Bouchard, Warwick F Vincent
Shallow lakes are common across the Arctic landscape and their ecosystem productivity is often dominated by benthic, cyanobacterial biofilms. Many of these water bodies freeze to the bottom and are biologically inactive during winter, but full freeze-up is becoming less common with Arctic warming. Here we analyzed the microbiome structure of newly discovered biofilms at the deepest site of a perennially ice-covered High Arctic lake as a model of polar microbial communities that remain unfrozen throughout the year...
2017: NPJ Biofilms and Microbiomes
https://www.readbyqxmd.com/read/28702194/elevation-of-brain-enriched-mirnas-in-cerebrospinal-fluid-of-patients-with-acute-ischemic-stroke
#17
Sofie Sølvsten Sørensen, Ann-Britt Nygaard, Anting Liu Carlsen, Niels H H Heegaard, Mads Bak, Thomas Christensen
BACKGROUND: The purpose of this study was to investigate the potential of cerebrospinal fluid miRNAs as diagnostic biomarkers of acute ischemic stroke using three different profiling techniques in order to identify and bypass any influence from technical variation. METHODS: Cerebrospinal fluid (CSF) from patients with acute ischemic stroke (n = 21) and controls (n = 21) was collected by lumbar puncture. miRNA analysis was performed with three different methods: 1) Trizol RNA extraction followed by Illumina Next Generation Sequencing (NGS) on all small RNAs, 2) Exiqon RNA extraction protocol and miRNA qPCR assays, and 3) validation of 24 selected miRNAs with Norgen Biotek RNA extraction protocol and Applied Biosystems qPCR assays...
2017: Biomarker Research
https://www.readbyqxmd.com/read/28702050/circulating-micrornas-in-serum-from-cattle-challenged-with-bovine-viral-diarrhea-virus
#18
Tasia M Taxis, Fernando V Bauermann, Julia F Ridpath, Eduardo Casas
Bovine viral diarrhea virus (BVDV) is an RNA virus that is often associated with respiratory disease in cattle. MicroRNAs have been proposed as indicators of exposure to respiratory pathogens. The objective of this study was to identify microRNAs in cattle that had been challenged with a non-cytopathic field strain of BVDV. Five colostrum deprived neonate Holstein calves were inoculated with BVDV (challenged) and 4 were mock challenged (control). Serum from all calves was collected at four different times: prior to challenge (day 0) and at 4, 9, and 16 days post-challenge...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28701783/circulating-mir-323-3p-is-a-biomarker-for-cardiomyopathy-and-an-indicator-of-phenotypic-variability-in-friedreich-s-ataxia-patients
#19
M Seco-Cervera, D González-Rodríguez, J S Ibáñez-Cabellos, L Peiró-Chova, P González-Cabo, E García-López, J J Vílchez, I Sanz-Gallego, F V Pallardó, J L García-Giménez
MicroRNAs (miRNAs) are noncoding RNAs that contribute to gene expression modulation by regulating important cellular pathways. In this study, we used small RNA sequencing to identify a series of circulating miRNAs in blood samples taken from Friedreich's ataxia patients. We were thus able to develop a miRNA biomarker signature to differentiate Friedreich's ataxia (FRDA) patients from healthy people. Most research on FDRA has focused on understanding the role of frataxin in the mitochondria, and a whole molecular view of pathological pathways underlying FRDA therefore remains to be elucidated...
July 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28700597/differentially-expressed-micrornas-in-diapausing-versus-hcl-treated-bombyx-embryos
#20
Wentao Fan, Yangsheng Zhong, Mingyue Qin, Bimin Lin, Fangyan Chen, Huichao Yan, Wenchu Li, Jianrong Lin
Differentially expressed microRNAs were detected to explore the molecular mechanisms of diapause termination. The total small RNA of diapause-destined silkworm eggs and HCl-treated eggs was extracted and then sequenced using HiSeq high-throughput method. 44 novel miRNAs were discovered. Compared to those in the diapause-destined eggs, 61 miRNAs showed significant changes in the acid-treated eggs, with 23 being up-regulated and 38 being down-regulated. The potential target genes of differentially expressed miRNAs were predicted by miRanda...
2017: PloS One
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