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https://www.readbyqxmd.com/read/28317896/use-of-rna-seq-data-to-identify-and-validate-rt-qpcr-reference-genes-for-studying-the-tomato-pseudomonas-pathosystem
#1
Marina A Pombo, Yi Zheng, Zhangjun Fei, Gregory B Martin, Hernan G Rosli
The agronomical relevant tomato-Pseudomonas syringae pv. tomato pathosystem is widely used to explore and understand the underlying mechanisms of the plant immune response. Transcript abundance estimation, mainly through reverse transcription-quantitative PCR (RT-qPCR), is a common approach employed to investigate the possible role of a candidate gene in certain biological process under study. The accuracy of this technique relies heavily on the selection of adequate reference genes. Initially, genes derived from other techniques (such as Northern blots) were used as reference genes in RT-qPCR experiments, but recent studies in different systems suggest that many of these genes are not stably expressed...
March 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28296577/genome-wide-identification-and-characterization-of-small-rnas-in-rhodobacter-capsulatus-and-identification-of-small-rnas-affected-by-loss-of-the-response-regulator-ctra
#2
Marc P Grüll, Lourdes Peña-Castillo, Martin E Mulligan, Andrew S Lang
Small non-coding RNAs (sRNAs) are involved in the control of numerous cellular processes through various regulatory mechanisms, and in the past decade many studies have identified sRNAs in a multitude of bacterial species using RNA sequencing (RNA-seq). Here, we present the first genome-wide analysis of sRNA sequencing data in Rhodobacter capsulatus, a purple nonsulfur photosynthetic alphaproteobacterium. Using a recently developed bioinformatics approach, sRNA-Detect, we detected 422 putative sRNAs from R...
March 15, 2017: RNA Biology
https://www.readbyqxmd.com/read/28286035/identification-and-characterization-of-two-putative-micrornas-encoded-by-bombyx-mori-cypovirus
#3
Zhong-Hua Pan, Ping Wu, Kun Gao, Cheng-Xiang Hou, Guang-Xing Qin, Tao Geng, Xi-Jie Guo
Viral microRNAs (miRNAs) have been demonstrated to play important roles in virus-host interactions. Some RNA virus-encoded miRNAs have been reported to promote viral replication and may be used as potential drug targets. Bombyx mori cypovirus (BmCPV), an important pathogen of silkworm, is a double-stranded RNA virus frequently causing serious damages in sericulture. Research on miRNA encoded by BmCPV may be useful to elucidate the BmCPV-host interaction and to develop new anti-viral methods. In our previous study, small RNA libraries of the midgut of BmCPV-infected silkworm have been generated by deep sequencing and several BmCPV-encoded putative miRNAs were predicted...
March 7, 2017: Virus Research
https://www.readbyqxmd.com/read/28283798/serological-dynamics-and-risk-factors-of-besnoitia-besnoiti-infection-in-breeding-bulls-from-an-endemically-infected-purebred-beef-herd
#4
Alessia Libera Gazzonis, Gema Alvarez Garcia, Andrea Maggioni, Sergio Aurelio Zanzani, Emanuela Olivieri, Riccardo Compiani, Giuseppe Sironi, Luis Miguel Ortega Mora, Maria Teresa Manfredi
Bovine besnoitiosis has been deemed a re-emerging disease in Western Europe and considered endemic in Spain, Portugal, France and in some areas of Northern Italy. This report refers to an infection outbreak in a purebred beef herd from Northern Italy involving a large number of bulls. In October 2013, 544 animals were serologically tested with an in-house ELISA followed by a confirmatory Western blot to evaluate Besnoitia besnoiti seroprevalence. A year later, 461 animals were then serologically re-tested together with imported animals (n = 268)...
March 10, 2017: Parasitology Research
https://www.readbyqxmd.com/read/28256563/the-alr-groel1-operon-in-mycobacterium-tuberculosis-an-interplay-of-multiple-regulatory-elements
#5
Aadil H Bhat, Deepika Pathak, Alka Rao
Threonylcarbamoyladenosine is a universally conserved essential modification of tRNA that ensures translational fidelity in cellular milieu. TsaD, TsaB and TsaE are identified as tRNA-A37-threonylcarbamoyl (t(6)A)-transferase enzymes that have been reconstituted in vitro, in few bacteria recently. However, transcriptional organization and regulation of these genes are not known in any of these organisms. This study describes the intricate architecture of a complex multicistronic alr-groEL1 operon, harboring essential genes, namely tsaD, tsaB, tsaE, groES, groEL1, and alr (required for cell wall synthesis), and rimI encoding an N-α- acetyltransferase in Mycobacterium tuberculosis...
March 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28220142/absence-of-an-n-linked-glycosylation-motif-in-the-glycoprotein-of-the-live-attenuated-argentine-hemorrhagic-fever-vaccine-candid-1-results-in-its-improper-processing-and-reduced-surface-expression
#6
John T Manning, Alexey V Seregin, Nadezhda E Yun, Takaaki Koma, Cheng Huang, José Barral, Juan C de la Torre, Slobodan Paessler
Junin virus (JUNV), a highly pathogenic New World arenavirus, is the causative agent of Argentine hemorrhagic fever (AHF). The live-attenuated Candid #1 (Can) strain currently serves as a vaccine for at-risk populations. We have previously shown that the Can glycoprotein (GPC) gene is the primary gene responsible for attenuation in a guinea pig model of AHF. However, the mechanisms through which the GPC contributes to the attenuation of the Can strain remain unknown. A more complete understanding of the mechanisms underlying the attenuation and immunogenicity of the Can strain will potentially allow for the rational design of additional safe and novel vaccines...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28209211/comparative-expression-profile-of-micrornas-in-anopheles-anthropophagus-midgut-after-blood-feeding-and-plasmodium-infection
#7
Wenquan Liu, Zhenhua Hao, Liyang Huang, Lingzi Chen, Qimei Wei, Liya Cai, Shaohui Liang
BACKGROUND: Anopheles anthropophagus is one of the major vectors of malaria in Asia. MicroRNAs (miRNAs) play important roles in cell development and differentiation as well as in the cellular response to stress and infection. In a former study, we have investigated the global miRNA profiles in relation to sex in An. anthropophagus. However, the miRNAs contributing to the blood-feeding and infection with Plasmodium are still unknown. METHODS: High-throughput sequencing was performed to identify miRNA profiles of An...
February 16, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28203519/the-widespread-occurrence-of-trna-derived-fragments-in-saccharomyces-cerevisiae
#8
Kamilla Bąkowska-Żywicka, Anna M Mleczko, Marta Kasprzyk, Piotr Machtel, Marek Żywicki, Tomasz Twardowski
Short RNAs derived from the cleavage of tRNA molecules are observed in most organisms. Their occurrence seems to be induced by stress conditions, but still little is known about their biogenesis and functions. We find that the recovery of tRNA fragments depends on the RNA isolation method. Using an optimized RNA extraction protocol and northern blot hybridization technique, we show that the tRNA-derived fragments in yeast are widespread in 12 different growth conditions. We did not observe significant stress-dependent changes in the amounts of tRNA fragments pool...
December 2016: FEBS Open Bio
https://www.readbyqxmd.com/read/28203174/richter-s-syndrome-with-hypercalcemia-induced-by-tumor-associated-production-of-parathyroid-hormone-related-peptide
#9
Naoki Watanabe, Hajime Yasuda, Soji Morishita, Yasuo Aota, Junichi Tomomatsu, Masaru Tanaka, Akimichi Ohsaka, Norio Komatsu
Humoral hypercalcemia due to parathyroid hormone-related peptide (PTHrP) elevation is a well-known complication of various malignancies, but the situation is rare concerning hematological malignancies except for adult T-cell leukemia/lymphoma. We report a case of Richter's syndrome with humoral hypercalcemia, and demonstrate by reverse transcription polymerase chain reaction (RT-PCR) that peripheral blood PTHrP levels were 2,500-fold higher compared to healthy controls. PTHrP production by tumor cells in chronic lymphocytic leukemia (CLL) and Richter's syndrome has been previously demonstrated by nonquantitative methods such as immunohistochemistry and northern blot analysis, but this is the first report using the RT-PCR method...
January 2017: Case Reports in Oncology
https://www.readbyqxmd.com/read/28180294/removing-bias-against-short-sequences-enables-northern-blotting-to-better-complement-rna-seq-for-the-study-of-small-rnas
#10
Yun S Choi, Lanelle O Edwards, Aubrey DiBello, Antony M Jose
No abstract text is available yet for this article.
February 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28173863/structure-and-transcription-of-the-helicoverpa-armigera-densovirus-hadv2-genome-and-its-expression-strategy-in-ld652-cells
#11
Pengjun Xu, Robert I Graham, Kenneth Wilson, Kongming Wu
BACKGROUND: Densoviruses (DVs) are highly pathogenic to their hosts. However, we previously reported a mutualistic DV (HaDV2). Very little was known about the characteristics of this virus, so herein we undertook a series of experiments to explore the molecular biology of HaDV2 further. RESULTS: Phylogenetic analysis showed that HaDV2 was similar to members of the genus Iteradensovirus. However, compared to current members of the genus Iteradensovirus, the sequence identity of HaDV2 is less than 44% at the nucleotide-level, and lower than 36, 28 and 19% at the amino-acid-level of VP, NS1 and NS2 proteins, respectively...
February 7, 2017: Virology Journal
https://www.readbyqxmd.com/read/28173803/hypoxia-inducible-microrna-224-promotes-the-cell-growth-migration-and-invasion-by-directly-targeting-rassf8-in-gastric-cancer
#12
Chuan He, Libo Wang, Jiantao Zhang, Hong Xu
BACKGROUND: Hypoxia plays an important role in the development of various cancers. MicroRNAs (miRNAs) act as post-transcriptional regulators of gene expression and modulate the tumorigenesis, including gastric cancer. However, the roles and molecular mechanism of miR-224 in gastric cancer under hypoxia remain poorly understood. METHOD: Real-time PCR and Northern blot assay were used to examine the effects of hypoxia and HIF-1α on miR-224 expression. Luciferase and ChIP assays were performed to determine whether miR-224 was a transcriptional target of HIF-1α...
February 7, 2017: Molecular Cancer
https://www.readbyqxmd.com/read/28161629/gene-expression-analysis-of-enzymes-of-the-carotenoid-biosynthesis-pathway-involved-in-%C3%AE-cryptoxanthin-accumulation-in-wild-raspberry-rubus-palmatus
#13
Kouichi Mizuno, Tetsuo Tokiwano, Yuko Yoshizawa
β-cryptoxanthin (β-Cry), a xanthophyll, is unlike other abundant carotenoids, such as α-carotene, β-carotene, lycopene, lutein, and zeaxanthin. It is not found in most fruits or vegetables but is found only in specific fruits, such as hot chili pepper, persimmon, and citrus fruits. Because recent reports suggest that β-Cry intake is beneficial to human health, the xanthophyll requires further investigation. Although β-Cry accumulates in the fruit of wild raspberry, Rubus palmatus, it is not present in cultivated raspberry...
February 2, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28154810/genome-wide-transcriptional-start-site-mapping-and-srna-identification-in-the-pathogen-leptospira-interrogans
#14
Anna Zhukova, Luis Guilherme Fernandes, Perrine Hugon, Christopher J Pappas, Odile Sismeiro, Jean-Yves Coppée, Christophe Becavin, Christophe Malabat, Azad Eshghi, Jun-Jie Zhang, Frank X Yang, Mathieu Picardeau
Leptospira are emerging zoonotic pathogens transmitted from animals to humans typically through contaminated environmental sources of water and soil. Regulatory pathways of pathogenic Leptospira spp. underlying the adaptive response to different hosts and environmental conditions remains elusive. In this study, we provide the first global Transcriptional Start Site (TSS) map of a Leptospira species. RNA was obtained from the pathogen Leptospira interrogans grown at 30°C (optimal in vitro temperature) and 37°C (host temperature) and selectively enriched for 5' ends of native transcripts...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28154486/viral-effects-of-a-dsrna-mycovirus-pov-asi2792-on-the-vegetative-growth-of-the-edible-mushroom-pleurotus-ostreatus
#15
Ha-Yeon Song, Hyo-Jin Choi, Hansaem Jeong, Dahye Choi, Dae-Hyuk Kim, Jung-Mi Kim
A double-stranded RNA (dsRNA) mycovirus was detected in malformed fruiting bodies of Pleurotus ostreatus strain ASI2792, one of bottle cultivated commercial strains of the edible oyster mushroom. The partial RNA-dependent RNA polymerase (RdRp) gene of the P. ostreatus ASI2792 mycovirus (PoV-ASI2792) was cloned, and a cDNA sequences alignment revealed that the sequence was identical to the RdRp gene of a known PoSV found in the P. ostreatus strain. To investigate the symptoms of PoV-ASI2792 infection by comparing the isogenic virus-free P...
December 2016: Mycobiology
https://www.readbyqxmd.com/read/28148795/hepatitis-b-virus-encoded-mirna-controls-viral-replication
#16
Xi Yang, Hongfeng Li, Huahui Sun, Hongxia Fan, Yaqi Hu, Min Liu, Xin Li, Hua Tang
microRNAs (miRNAs) are a class of small single-stranded non-coding functional RNAs. Hepatitis B virus (HBV) is an enveloped DNA virus with virions and subviral forms of particles that lack a core. It was not known whether HBV encodes miRNAs. Here, we identified an HBV-encoded miRNA (called HBV-miR-3) by deep sequencing and northern blot. HBV-miR-3 is located at nts 373-393 of the HBV genome and was generated from 3.5Kb, 2,4Kb and 2.1Kb HBV in classic miRNA biogenesis (Drosha-Dicer dependent) manner. HBV-miR-3 was highly expressed in hepatoma cell lines with an integrated HBV genome and HBV (+) hepatoma tumors...
February 1, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28115465/targeted-crispr-disruption-reveals-a-role-for-rnase-mrp-rna-in-human-preribosomal-rna-processing
#17
Katherine C Goldfarb, Thomas R Cech
MRP RNA is an abundant, essential noncoding RNA whose functions have been proposed in yeast but are incompletely understood in humans. Mutations in the genomic locus for MRP RNA cause pleiotropic human diseases, including cartilage hair hypoplasia (CHH). Here we applied CRISPR-Cas9 genome editing to disrupt the endogenous human MRP RNA locus, thereby attaining what has eluded RNAi and RNase H experiments: elimination of MRP RNA in the majority of cells. The resulting accumulation of ribosomal RNA (rRNA) precursor-analyzed by RNA fluorescent in situ hybridization (FISH), Northern blots, and RNA sequencing-implicates MRP RNA in pre-rRNA processing...
January 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28115164/inhibition-of-glutathione-production-by-l-s-r-buthionine-sulfoximine-activates-hepatic-ascorbate-synthesis-a-unique-anti-oxidative-stress-mechanism-in-mice
#18
Miao Yu, Ying Liu, Yajun Duan, Yuanli Chen, Jihong Han, Lei Sun, Xiaoxiao Yang
Glutathione (GSH) and ascorbate, the cytoplasmic antioxidants, can regenerate and replace each other in scavenging reactive oxygen species reaction. Mice, but not guinea pigs, produce ascorbate endogenously. l-Buthionine-S,R-sulfoximine (L-S,R-BSO) substantially inhibited GSH production at a greater degree and caused a higher toxicity to guinea pigs than mice, implying that mice may have an additional protective mechanism against oxidative stress injury. Indeed, administration of L-S,R-BSO to mice inhibited tissue GSH production while increasing ascorbate levels...
January 20, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28103286/mirnas-do-not-regulate-circadian-protein-synthesis-in-the-dinoflagellate-lingulodinium-polyedrum
#19
Steve Dagenais-Bellefeuille, Mathieu Beauchemin, David Morse
Dinoflagellates have been shown to express miRNA by bioinformatics and RNA blot (Northern) analyses. However, it is not yet known if miRNAs are able to alter gene expression in this class of organisms. We have assessed the possibility that miRNA may mediate circadian regulation of gene expression in the dinoflagellate Lingulodinium polyedrum using the Luciferin Binding Protein (LBP) as a specific example. LBP is a good candidate for regulation by miRNA since mRNA levels are constant over the daily cycle while protein synthesis is restricted by the circadian clock to a period of several hours at the start of the night phase...
2017: PloS One
https://www.readbyqxmd.com/read/28086791/identification-of-functional-enolase-genes-of-the-silkworm-bombyx-mori-from-public-databases-with-a-combination-of-dry-and-wet-bench-processes
#20
Akira Kikuchi, Takeru Nakazato, Katsuhiko Ito, Yosui Nojima, Takeshi Yokoyama, Kikuo Iwabuchi, Hidemasa Bono, Atsushi Toyoda, Asao Fujiyama, Ryoichi Sato, Hiroko Tabunoki
BACKGROUND: Various insect species have been added to genomic databases over the years. Thus, researchers can easily obtain online genomic information on invertebrates and insects. However, many incorrectly annotated genes are included in these databases, which can prevent the correct interpretation of subsequent functional analyses. To address this problem, we used a combination of dry and wet bench processes to select functional genes from public databases. RESULTS: Enolase is an important glycolytic enzyme in all organisms...
January 13, 2017: BMC Genomics
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