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https://www.readbyqxmd.com/read/28103286/mirnas-do-not-regulate-circadian-protein-synthesis-in-the-dinoflagellate-lingulodinium-polyedrum
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
https://www.readbyqxmd.com/read/27981548/expression-of-long-non-coding-rna-lncrna-h19-in-immunodeficient-mice-induced-with-human-colon-cancer-cells
#9
Q Hu, Y-B Wang, P Zeng, G-Q Yan, L Xin, X-Y Hu
OBJECTIVE: To study the expression of long non-coding RNA (lncRNA) H19 in immunodeficient mice induced with human colon cancer cells. Long non-coding RNAs (lncRNA) have a vital and regulatory role, in almost all cancers including colon cancer. In the present study, the prominent regulatory role of IncH19 RNA in immunodeficient mice induced with human colon cancer cells was identified. Interestingly, the lncH19 RNA was up-regulated in human colon cancer cells induced immunodeficient mice colon cancer samples...
December 2016: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/27932586/nup100-regulates-saccharomyces-cerevisiae-replicative-life-span-by-mediating-the-nuclear-export-of-specific-trnas
#10
Christopher L Lord, Ophir Ospovat, Susan R Wente
Nuclear pore complexes (NPCs), which are composed of nucleoporins (Nups) and regulate transport between the nucleus and cytoplasm, significantly impact the replicative life span (RLS) of Saccharomyces cerevisiae We previously reported that deletion of the non-essential gene NUP100 increases RLS, although the molecular basis for this effect was unknown. In this study, we find that nuclear tRNA accumulation contributes to increased longevity in nup100Δ cells. Fluorescence in situ hybridization (FISH) experiments demonstrate several specific tRNAs accumulate in the nuclei of nup100Δ mutants...
December 8, 2016: RNA
https://www.readbyqxmd.com/read/27929395/deficiency-in-the-ubiquitin-conjugating-enzyme-ube2a-in-alzheimer-s-disease-ad-is-linked-to-deficits-in-a-natural-circular-mirna-7-sponge-circrna-cirs-7
#11
Yuhai Zhao, Peter N Alexandrov, Vivian Jaber, Walter J Lukiw
Our understanding of the highly specialized functions for small non-coding single-stranded RNA (ssRNA) in the transcriptome of the human central nervous system (CNS) continues to evolve. Circular RNAs (circRNAs), a recently discovered class of ssRNA enriched in the brain and retina, are extremely stable and intrinsically resilient to degradation by exonuclease. Conventional methods of ssRNA, microRNA (miRNA), or messenger RNA (mRNA) detection and quantitation requiring free ribonucleotide ends may have considerably underestimated the quantity and significance of CNS circRNA in the CNS...
December 5, 2016: Genes
https://www.readbyqxmd.com/read/27913725/in-vivo-expression-technology-and-5-end-mapping-of-the-borrelia-burgdorferi-transcriptome-identify-novel-rnas-expressed-during-mammalian-infection
#12
Philip P Adams, Carlos Flores Avile, Niko Popitsch, Ivana Bilusic, Renée Schroeder, Meghan Lybecker, Mollie W Jewett
Borrelia burgdorferi, the bacterial pathogen responsible for Lyme disease, modulates its gene expression profile in response to the environments encountered throughout its tick-mammal infectious cycle. To begin to characterize the B. burgdorferi transcriptome during murine infection, we previously employed an in vivo expression technology-based approach (BbIVET). This identified 233 putative promoters, many of which mapped to un-annotated regions of the complex, segmented genome. Herein, we globally identify the 5' end transcriptome of B...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27902342/functional-analysis-of-a-viroid-rna-motif-mediating-cell-to-cell-movement-in-nicotiana-benthamiana
#13
Dongmei Jiang, Meng Wang, Shifang Li
Cell-to-cell trafficking through different cellular layers is a key process for various RNAs including those of plant viruses and viroids, but the regulatory mechanisms involved are still not fully elucidated and good model systems are important. Here, we analyze the function of a simple RNA motif (termed "loop19") in Potato spindle tuber viroid (PSTVd) which is required for trafficking in Nicotiana benthamiana leaves. Northern blotting, RT-PCR and in situ hybridization analyses demonstrated that unlike wild type PSTVd, which was present in the nuclei in all cell types, the trafficking-defective loop19 mutants were visible only in the nuclei of upper epidermal and palisade mesophyll cells, which shows that PSTVd loop19 plays a role in mediating RNA trafficking from palisade to spongy mesophyll cells in Nicotiana benthamiana leaves...
October 14, 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27899677/the-mouse-gene-expression-database-gxd-2017-update
#14
Jacqueline H Finger, Constance M Smith, Terry F Hayamizu, Ingeborg J McCright, Jingxia Xu, Meiyee Law, David R Shaw, Richard M Baldarelli, Jon S Beal, Olin Blodgett, Jeff W Campbell, Lori E Corbani, Jill R Lewis, Kim L Forthofer, Pete J Frost, Sharon C Giannatto, Lucie N Hutchins, Dave B Miers, Howie Motenko, Kevin R Stone, Janan T Eppig, James A Kadin, Joel E Richardson, Martin Ringwald
The Gene Expression Database (GXD; www.informatics.jax.org/expression.shtml) is an extensive and well-curated community resource of mouse developmental expression information. Through curation of the scientific literature and by collaborations with large-scale expression projects, GXD collects and integrates data from RNA in situ hybridization, immunohistochemistry, RT-PCR, northern blot and western blot experiments. Expression data from both wild-type and mutant mice are included. The expression data are combined with genetic and phenotypic data in Mouse Genome Informatics (MGI) and made readily accessible to many types of database searches...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27887986/isolation-of-bacterial-compartments-to-track-movement-of-protein-synthesis-factors
#15
Hanchao Zhao, Susan A Martinis
Aminoacyl-tRNA synthetases (AARSs) comprise an enzyme family that generates and maintains pools of aminoacylated tRNAs, which serve as essential substrates for protein synthesis. Many protein synthesis factors, including tRNA and AARSs also have non-canonical functions. Particularly in mammalian cells, alternate functions of AARSs have been associated with re-distribution in the cell to sites that are removed from translation. Sub-fractionation methods for E. coli were designed and optimized to carefully investigate re-localization of bacterial AARSs and tRNA that might aid in conferring alternate activities...
November 23, 2016: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/27880931/an-xist-related-small-rna-regulates-kras-g-quadruplex-formation-beyond-x-inactivation
#16
Yuli C Chang, Chien-Chih Chiu, Chung-Yee Yuo, Wen-Ling Chan, Ya-Sian Chang, Wen-Hsin Chang, Shou-Mei Wu, Han-Lin Chou, Ta-Chih Liu, Chi-Yu Lu, Wen-Kuang Yang, Jan-Gowth Chang
X-inactive-specific transcript (XIST), a long non-coding RNA, is essential for the initiation of X-chromosome inactivation. However, little is known about other roles of XIST in the physiological process in eukaryotic cells. In this study, the bioinformatics approaches revealed XIST could be processed into a small non-coding RNA XPi2. The XPi2 RNA was confirmed by a northern blot assay; its expression was gender-independent, suggesting the role of XPi2 was beyond X-chromosome inactivation. The pull-down assay combined with LC-MS-MS identified two XPi2-associated proteins, nucleolin and hnRNP A1, connected to the formation of G-quadruplex...
November 17, 2016: Oncotarget
https://www.readbyqxmd.com/read/27867378/improved-pathogenicity-of-a-beet-black-scorch-virus-variant-by-low-temperature-and-co-infection-with-its-satellite-rna
#17
Jin Xu, Deshui Liu, Yongliang Zhang, Ying Wang, Chenggui Han, Dawei Li, Jia-Lin Yu, Xian-Bing Wang
Co-infection of none-coding satellite RNAs (sat-RNAs) usually inhibits replication and attenuates disease symptoms of helper viruses. However, we find that the sat-RNA of Beet black scorch virus (BBSV) and low temperature (18°C) additively enhance the systemic infection of BBSV in Nicotiana benthamiana. Northern blotting hybridization revealed a relatively reduced accumulation of BBSV-derived small interfering RNAs (siRNAs) in presence of sat-RNA as compared to that of BBSV alone. Cloning and sequencing of total small RNAs showed that more than 50% of the total small RNAs sequenced from BBSV-infected plants were BBSV-siRNAs, whereas the abundance of sat-siRNAs were higher than BBSV-siRNAs in the sat-RNA co-infected plants, indicating that the sat-RNA occupies most of the silencing components and possibly relieves the RNA silencing-mediated defense against BBSV...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27863521/seroprevalence-of-bovine-theileriosis-in-northern-china
#18
Yaqiong Li, Zhijie Liu, Junlong Liu, Jifei Yang, Qian Li, Pengfei Guo, Guiquan Guan, Guangyuan Liu, Jianxun Luo, Hong Yin, Youquan Li
BACKGROUND: Bovine theileriosis is a common disease transmitted by ticks, and can cause loss of beef and dairy cattle worldwide. Here, an indirect enzyme-linked immunosorbent assay (iELISA) based on Theileria luwenshuni surface protein (TlSP) was developed and used to carry out a seroepidemiological survey of bovine theileriosis in northern China. METHODS: We used the BugBuster Ni-NTA His•Bind Purification Kit to purify recombinant TlSP (rTlSP), which was subsequently analyzed by Western Blotting to evaluate cross-reactivity with other pathogen-positive sera...
November 18, 2016: Parasites & Vectors
https://www.readbyqxmd.com/read/27832540/determining-if-an-mrna-is-a-substrate-of-nonsense-mediated-mrna-decay-in-saccharomyces-cerevisiae
#19
Marcus J O Johansson
Nonsense-mediated mRNA decay (NMD) is a conserved eukaryotic quality control mechanism which triggers decay of mRNAs harboring premature translation termination codons. In this chapter, I describe methods for monitoring the influence of NMD on mRNA abundance and decay rates in Saccharomyces cerevisiae. The descriptions include detailed methods for growing yeast cells, total RNA isolation, and Northern blotting. Although the chapter focuses on NMD, the methods can be easily adapted to assess the effect of other mRNA decay pathways...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27802286/variation-analysis-of-physiological-traits-in-betula-platyphylla-overexpressing-talea-thbzip-gene-under-salt-stress
#20
Xiyang Zhao, Tangchun Zheng, Longting Shao, Zhenhai Xiao, Fuwei Wang, Shuchun Li, Lina Zang, Mi Zheng, Ying Li, Guan-Zheng Qu
The aim of this study was to determine whether transgenic birch (Betula platyphylla) ectopic overexpressing a late embryogenesis abundant (LEA) gene and a basic leucine zipper (bZIP) gene from the salt-tolerant genus Tamarix (salt cedar) show increased tolerance to salt (NaCl) stress. Co-transfer of TaLEA and ThbZIP in birch under the control of two independent CaMV 35S promoters significantly enhanced salt stress. PCR and northern blot analyses indicated that the two genes were ectopically overexpressed in several dual-gene transgenic birch lines...
2016: PloS One
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