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https://www.readbyqxmd.com/read/28209211/comparative-expression-profile-of-micrornas-in-anopheles-anthropophagus-midgut-after-blood-feeding-and-plasmodium-infection
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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...
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
#11
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
#12
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
#13
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
#14
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
https://www.readbyqxmd.com/read/28060253/a-method-for-measuring-rna-n-6-methyladenosine-modifications-in-cells-and-tissues
#15
Chao-Yung Wang, Mei-Hsiu Lin, Hui-Ting Su
N(6)-Methyladenosine (m(6)A) modifications of RNA are diverse and ubiquitous amongst eukaryotes. They occur in mRNA, rRNA, tRNA, and microRNA. Recent studies have revealed that these reversible RNA modifications affect RNA splicing, translation, degradation, and localization. Multiple physiological processes, like circadian rhythms, stem cell pluripotency, fibrosis, triglyceride metabolism, and obesity are also controlled by m(6)A modifications. Immunoprecipitation/sequencing, mass spectrometry, and modified northern blotting are some of the methods commonly employed to measure m(6)A modifications...
December 5, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28056764/temperature-dependent-srna-transcriptome-of-the-lyme-disease-spirochete
#16
Niko Popitsch, Ivana Bilusic, Philipp Rescheneder, Renée Schroeder, Meghan Lybecker
BACKGROUND: Transmission of Borrelia burgdorferi from its tick vector to a vertebrate host requires extensive reprogramming of gene expression. Small regulatory RNAs (sRNA) have emerged in the last decade as important regulators of bacterial gene expression. Despite the widespread observation of sRNA-mediated gene regulation, only one sRNA has been characterized in the Lyme disease spirochete B. burgdorferi. We employed an sRNA-specific deep-sequencing approach to identify the small RNA transcriptome of B...
January 5, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28052459/functional-analysis-of-brassica-napus-phloem-protein-and-ribonucleoprotein-complexes
#17
Anna Ostendorp, Steffen Pahlow, Lena Krüßel, Patrizia Hanhart, Marcel Y Garbe, Jennifer Deke, Patrick Giavalisco, Julia Kehr
Phloem sap contains a large number of macromolecules, including proteins and RNAs from different classes. Proteome analyses of phloem samples from different plant species under denaturing conditions identified hundreds of proteins potentially involved in diverse processes. Surprisingly, these studies also found a significant number of ribosomal and proteasomal proteins. This led to the suggestion that active ribosome and proteasome complexes might be present in the phloem, challenging the paradigm that protein synthesis and turnover are absent from the enucleate sieve elements of angiosperms...
January 4, 2017: New Phytologist
https://www.readbyqxmd.com/read/28035599/functional-characterization-of-the-cuti-gene-for-the-transcription-of-carbon-monoxide-dehydrogenase-genes-in-mycobacterium-sp-strain-jc1-dsm-3803
#18
Jae Ho Lee, Sae Woong Park, Young Min Kim, Jeong-Il Oh
Carbon monoxide dehydrogenase (CO-DH) in Mycobacterium sp. strain JC1 is a key enzyme for the carboxydotrophic growth, when carbon monoxide (CO) is supplied as a sole source of carbon and energy. This enzyme is also known to act as nitric oxide dehydrogenase (NO-DH) for the detoxification of NO. Several accessory genes such as cutD, cutE, cutF, cutG, cutH, and cutI, are clustered together with two copies of the CO-DH structural genes (cutB1C1A1 and cutB2C2A2) in Mycobacterium sp. strain JC1 and are well conserved in carboxydotrophic mycobacteria...
January 2017: Journal of Microbiology / the Microbiological Society of Korea
https://www.readbyqxmd.com/read/28005933/differential-regulation-of-rrna-and-trna-transcription-from-the-rrna-trna-composite-operon-in-escherichia-coli
#19
Hiraku Takada, Tomohiro Shimada, Debashish Dey, M Zuhaib Quyyum, Masahiro Nakano, Akira Ishiguro, Hideji Yoshida, Kaneyoshi Yamamoto, Ranjan Sen, Akira Ishihama
Escherichia coli contains seven rRNA operons, each consisting of the genes for three rRNAs (16S, 23S and 5S rRNA in this order) and one or two tRNA genes in the spacer between 16S and 23S rRNA genes and one or two tRNA genes in the 3' proximal region. All of these rRNA and tRNA genes are transcribed from two promoters, P1 and P2, into single large precursors that are afterward processed to individual rRNAs and tRNAs by a set of RNases. In the course of Genomic SELEX screening of promoters recognized by RNA polymerase (RNAP) holoenzyme containing RpoD sigma, a strong binding site was identified within 16S rRNA gene in each of all seven rRNA operons...
2016: PloS One
https://www.readbyqxmd.com/read/27998862/-expression-of-mir-106b-in-esophageal-squamous-cell-carcinoma
#20
Chang-Yan Xiao, Zi-Jian Guo, Lei Cao, Xiao-Wen Ding, Qiang Liu, Xiao-Chun Wang
OBJECTIVE: To investigate the expression of mir-106b in esophageal squamous cell carcinoma (ESCC) tissue and analyze its correlation with the clinicopathologic features of ESCC. METHODS: A total of 200 fresh surgical specimens of ESCC and adjacent tissues collected between 2001 and 2007 were examined for expressions of mir-106b using real-time PCR (RT-PCR). Northern blot analysis for mir-106b was performed in 4 pairs of samples to confirm the RT-PCR results. The relationship between mir-106b expression and clinicopathological features and prognosis of the patients were analyzed...
December 20, 2016: Nan Fang Yi Ke da Xue Xue Bao, Journal of Southern Medical University
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