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https://www.readbyqxmd.com/read/28340337/structural-basis-of-rna-polymerase-i-transcription-initiation
#1
Christoph Engel, Tobias Gubbey, Simon Neyer, Sarah Sainsbury, Christiane Oberthuer, Carlo Baejen, Carrie Bernecky, Patrick Cramer
Transcription initiation at the ribosomal RNA promoter requires RNA polymerase (Pol) I and the initiation factors Rrn3 and core factor (CF). Here, we combine X-ray crystallography and cryo-electron microscopy (cryo-EM) to obtain a molecular model for basal Pol I initiation. The three-subunit CF binds upstream promoter DNA, docks to the Pol I-Rrn3 complex, and loads DNA into the expanded active center cleft of the polymerase. DNA unwinding between the Pol I protrusion and clamp domains enables cleft contraction, resulting in an active Pol I conformation and RNA synthesis...
March 23, 2017: Cell
https://www.readbyqxmd.com/read/28339458/rapid-surveillance-for-vector-presence-rsvp-development-of-a-novel-system-for-detecting-aedes-aegypti-and-aedes-albopictus
#2
Brian L Montgomery, Martin A Shivas, Sonja Hall-Mendelin, Jim Edwards, Nicholas A Hamilton, Cassie C Jansen, Jamie L McMahon, David Warrilow, Andrew F van den Hurk
BACKGROUND: The globally important Zika, dengue and chikungunya viruses are primarily transmitted by the invasive mosquitoes, Aedes aegypti and Aedes albopictus. In Australia, there is an increasing risk that these species may invade highly urbanized regions and trigger outbreaks. We describe the development of a Rapid Surveillance for Vector Presence (RSVP) system to expedite presence- absence surveys for both species. METHODOLOGY/PRINCIPAL FINDINGS: We developed a methodology that uses molecular assays to efficiently screen pooled ovitrap (egg trap) samples for traces of target species ribosomal RNA...
March 24, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28335556/trm5-and-trmd-two-enzymes-from-distinct-origins-catalyze-the-identical-trna-modification-m%C3%A2-g37
#3
REVIEW
Sakurako Goto-Ito, Takuhiro Ito, Shigeyuki Yokoyama
The N¹-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m¹G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome. Interestingly, Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. In this review, we describe the different strategies utilized by Trm5 and TrmD to recognize their substrate tRNAs, mainly based on their crystal structures complexed with substrate tRNAs...
March 21, 2017: Biomolecules
https://www.readbyqxmd.com/read/28335020/znhit3-is-defective-in-peho-syndrome-a-severe-encephalopathy-with-cerebellar-granule-neuron-loss
#4
Anna-Kaisa Anttonen, Anni Laari, Maria Kousi, Yawei J Yang, Tiina Jääskeläinen, Mirja Somer, Eija Siintola, Eveliina Jakkula, Mikko Muona, Saara Tegelberg, Tuula Lönnqvist, Helena Pihko, Leena Valanne, Anders Paetau, Melody P Lun, Johanna Hästbacka, Outi Kopra, Tarja Joensuu, Nicholas Katsanis, Maria K Lehtinen, Jorma J Palvimo, Anna-Elina Lehesjoki
Progressive encephalopathy with oedema, hypsarrhythmia, and optic atrophy (PEHO) syndrome is an early childhood onset, severe autosomal recessive encephalopathy characterized by extreme cerebellar atrophy due to almost total granule neuron loss. By combining homozygosity mapping in Finnish families with Sanger sequencing of positional candidate genes and with exome sequencing a homozygous missense substitution of leucine for serine at codon 31 in ZNHIT3 was identified as the primary cause of PEHO syndrome. ZNHIT3 encodes a nuclear zinc finger protein previously implicated in transcriptional regulation and in small nucleolar ribonucleoprotein particle assembly and thus possibly to pre-ribosomal RNA processing...
March 1, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28334881/random-pseuoduridylation-in-vivo-reveals-critical-region-of-escherichia-coli-23s-rrna-for-ribosome-assembly
#5
Margus Leppik, Aivar Liiv, Jaanus Remme
Pseudouridine is the most common modified nucleoside in RNA, which is found in stable RNA species and in eukaryotic mRNAs. Functional analysis of pseudouridine is complicated by marginal effect of its absence. We demonstrate that excessive pseudouridines in rRNA inhibit ribosome assembly. Ten-fold increase of pseudouridines in the 16S and 23S rRNA made by a chimeric pseudouridine synthase leads to accumulation of the incompletely assembled large ribosome subunits. Hyper modified 23S rRNA is found in the r-protein assembly defective particles and are selected against in the 70S and polysome fractions showing modification interference...
March 7, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334864/coordination-among-tertiary-base-pairs-results-in-an-efficient-frameshift-stimulating-rna-pseudoknot
#6
Yu-Ting Chen, Kai-Chun Chang, Hao-Teng Hu, Yi-Lan Chen, You-Hsin Lin, Chiung-Fang Hsu, Cheng-Fu Chang, Kung-Yao Chang, Jin-Der Wen
Frameshifting is an essential process that regulates protein synthesis in many viruses. The ribosome may slip backward when encountering a frameshift motif on the messenger RNA, which usually contains a pseudoknot structure involving tertiary base pair interactions. Due to the lack of detailed molecular explanations, previous studies investigating which features of the pseudoknot are important to stimulate frameshifting have presented diverse conclusions. Here we constructed a bimolecular pseudoknot to dissect the interior tertiary base pairs and used single-molecule approaches to assess the structure targeted by ribosomes...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334682/phytochemical-induced-nucleolar-stress-results-in-the-inhibition-of-breast-cancer-cell-proliferation
#7
Anna Lewinska, Diana Bednarz, Jagoda Adamczyk-Grochala, Maciej Wnuk
The nucleolus is a stress sensor and compromised nucleolar activity may be considered as an attractive anticancer strategy. In the present study, the effects of three plant-derived natural compounds, i.e., sulforaphane (SFN), ursolic acid (UA) and betulinic acid (BA) on nucleolar state were investigated in breast cancer cell lines of different receptor status, namely MCF-7, MDA-MB-231 and SK-BR-3 cells. Cytostatic action of phytochemicals against breast cancer cells was observed at low micromolar concentration window (5-20µM) and mediated by elevated p21 levels, and cell proliferation of SFN-, UA- and BA-treated normal human mammary epithelial cells (HMEC) was unaffected...
March 14, 2017: Redox Biology
https://www.readbyqxmd.com/read/28334396/quantifying-circular-rna-expression-from-rna-seq-data-using-model-based-framework
#8
Musheng Li, Xueying Xie, Jing Zhou, Mengying Sheng, Xiaofeng Yin, Eun-A Ko, Tong Zhou, Wanjun Gu
Motivation: Circular RNAs (circRNAs) are a class of non-coding RNAs that are widely expressed in various cell lines and tissues of many organisms. Although the exact function of many circRNAs is largely unknown, the cell type- and tissue-specific circRNA expression has implicated their crucial functions in many biological processes. Hence, the quantification of circRNA expression from high-throughput RNA-seq data is becoming important to ascertain. Although many model-based methods have been developed to quantify linear RNA expression from RNA-seq data, these methods are not applicable to circRNA quantification...
March 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28333060/can-dna-sequencing-show-differences-between-microbial-communities-in-polish-and-danish-wastewater-treatment-plants
#9
A Miłobędzka, A Muszyński
The microbial populations in the activated sludge of two Polish wastewater treatment plants (WWTPs) were identified and quantified using Illumina sequencing of 16S ribosomal RNA amplicons over a 2-year period. Their dynamics over time were compared to Danish WWTPs (data collected in previous studies by Center for Microbial Communities, Aalborg University). The bacterial communities in Polish and Danish WWTPs were similar to each other, but the microbial diversity in Polish WWTPs was lower. The dominant genera in Polish WWTPs were more abundant than in Danish WWTPs; 30 of them constituted more than half the of activated sludge community...
March 2017: Water Science and Technology: a Journal of the International Association on Water Pollution Research
https://www.readbyqxmd.com/read/28331594/the-first-complete-mitogenome-of-the-south-china-deep-sea-giant-isopod-bathynomus-sp-crustacea-isopoda-cirolanidae-allows-insights-into-the-early-mitogenomic-evolution-of-isopods
#10
Yanjun Shen, Qi Kou, Zaixuan Zhong, Xinzheng Li, Lisheng He, Shunping He, Xiaoni Gan
In this study, the complete mitochondrial (mt) genome sequence of the South China deep-sea giant isopod Bathynomus sp. was determined, and this study is the first to explore in detail the mt genome of a deep-sea member of the order Isopoda. This species belongs to the genus Bathynomus, the members of which are saprophagous residents of the deep-sea benthic environment; based on their large size, Bathynomus is included in the "supergiant group" of isopods. The mt genome of Bathynomus sp. is 14,965 bp in length and consists of 13 protein-coding genes, two ribosomal RNA genes, only 18 transfer RNA genes, and a noncoding control region 362 bp in length, which is the smallest control region discovered in Isopoda to date...
March 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28329689/the-human-cchc-type-zinc-finger-nucleic-acid-binding-protein-binds-g-rich-elements-in-target-mrna-coding-sequences-and-promotes-translation
#11
Daniel Benhalevy, Sanjay K Gupta, Charles H Danan, Suman Ghosal, Hong-Wei Sun, Hinke G Kazemier, Katrin Paeschke, Markus Hafner, Stefan A Juranek
The CCHC-type zinc finger nucleic acid-binding protein (CNBP/ZNF9) is conserved in eukaryotes and is essential for embryonic development in mammals. It has been implicated in transcriptional, as well as post-transcriptional, gene regulation; however, its nucleic acid ligands and molecular function remain elusive. Here, we use multiple systems-wide approaches to identify CNBP targets and function. We used photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP) to identify 8,420 CNBP binding sites on 4,178 mRNAs...
March 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/28328981/dysbiosis-and-compositional-alterations-with-aging-in-the-gut-microbiota-of-patients-with-heart-failure
#12
Takehiro Kamo, Hiroshi Akazawa, Wataru Suda, Akiko Saga-Kamo, Yu Shimizu, Hiroki Yagi, Qing Liu, Seitaro Nomura, Atsuhiko T Naito, Norifumi Takeda, Mutsuo Harada, Haruhiro Toko, Hidetoshi Kumagai, Yuichi Ikeda, Eiki Takimoto, Jun-Ichi Suzuki, Kenya Honda, Hidetoshi Morita, Masahira Hattori, Issei Komuro
Emerging evidence has suggested a potential impact of gut microbiota on the pathophysiology of heart failure (HF). However, it is still unknown whether HF is associated with dysbiosis in gut microbiota. We investigated the composition of gut microbiota in patients with HF to elucidate whether gut microbial dysbiosis is associated with HF. We performed 16S ribosomal RNA gene sequencing of fecal samples obtained from 12 HF patients and 12 age-matched healthy control (HC) subjects, and analyzed the differences in gut microbiota...
2017: PloS One
https://www.readbyqxmd.com/read/28324847/species-identification-in-forensic-samples-using-the-spindel-approach-a-ghep-isfg-inter-laboratory-collaborative-exercise
#13
Cíntia Alves, Rui Pereira, Lourdes Prieto, Mercedes Aler, Cesar R L Amaral, Cristina Arévalo, Gabriela Berardi, Florencia Di Rocco, Mariela Caputo, Cristian Hernandez Carmona, Laura Catelli, Heloísa Afonso Costa, Pavla Coufalova, Sandra Furfuro, Óscar García, Anibal Gaviria, Ana Goios, Juan José Builes Gómez, Alexis Hernández, Eva Del Carmen Betancor Hernández, Luís Miranda, David Parra, Susana Pedrosa, Maria João Anjos Porto, Maria de Lurdes Rebelo, Matteo Spirito, María Del Carmen Villalobos Torres, António Amorim, Filipe Pereira
DNA is a powerful tool available for forensic investigations requiring identification of species. However, it is necessary to develop and validate methods able to produce results in degraded and or low quality DNA samples with the high standards obligatory in forensic research. Here, we describe a voluntary collaborative exercise to test the recently developed Species Identification by Insertions/Deletions (SPInDel) method. The SPInDel kit allows the identification of species by the generation of numeric profiles combining the lengths of six mitochondrial ribosomal RNA (rRNA) gene regions amplified in a single reaction followed by capillary electrophoresis...
March 7, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28321788/characteristics-of-aerococcus-viridans-isolated-from-bovine-subclinical-mastitis-and-its-effect-on-milk-scc-yield-and-composition
#14
Meng Sun, Jian Gao, Tariq Ali, Dan Yu, Shiyao Zhang, Saeed U Khan, Séamus Fanning, Bo Han
Aerococcus viridians (A. viridans), an environmental Gram-positive bacterium, has been documented to be associated with bovine mastitis. However, its exact role in bovine mastitis and the changes it brings about in milk characteristics are not yet known. The objectives of the current study were to describe the antibiotic resistance of A. viridans from bovine mastitis as well as the correlation between existence of this pathogen in udders and the somatic cell counts (SCC), daily milk yield, and composition of individual cow...
March 20, 2017: Tropical Animal Health and Production
https://www.readbyqxmd.com/read/28321487/benzene-degradation-in-a-denitrifying-biofilm-reactor-activity-and-microbial-community-composition
#15
Marcelle J van der Waals, Siavash Atashgahi, Ulisses Nunes da Rocha, Bas M van der Zaan, Hauke Smidt, Jan Gerritse
Benzene is an aromatic compound and harmful for the environment. Biodegradation of benzene can reduce the toxicological risk after accidental or controlled release of this chemical in the environment. In this study, we further characterized an anaerobic continuous biofilm culture grown for more than 14 years on benzene with nitrate as electron acceptor. We determined steady state degradation rates, microbial community composition dynamics in the biofilm, and the initial anaerobic benzene degradation reactions...
March 20, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28321119/notch1-mutated-chronic-lymphocytic-leukemia-cells-are-characterized-by-a-myc-related-overexpression-of-nucleophosmin-1-and-ribosome-associated-components
#16
F Pozzo, T Bittolo, E Vendramini, R Bomben, P Bulian, F M Rossi, A Zucchetto, E Tissino, M Degan, G D'Arena, F Di Raimondo, F Zaja, G Pozzato, D Rossi, G Gaidano, G Del Poeta, V Gattei, M Dal Bo
In chronic lymphocytic leukemia (CLL), the mechanisms controlling cell growth and proliferation in presence of NOTCH1 mutations remain largely unexplored. By performing a gene expression profile of NOTCH1 mutated (NOTCH1-mut) versus NOTCH1 wild type CLL, we identified a gene signature of NOTCH1-mut CLL characterized by upregulation of genes related to ribosome biogenesis, such as nucleophosmin1 (NPM1) and ribosomal proteins (RNPs). Activation of NOTCH1 signaling by EDTA or by co-culture with JAGGED1-expressing stromal cells increased NPM1 expression, and inhibition of NOTCH1 signaling by either NOTCH1-specific small interfering RNA (siRNA) or γ-secretase inhibitor reduced NPM1 expression...
March 21, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28320503/post-transcriptional-and-translational-regulation-of-mrna-like-long-non-coding-rnas-by-micrornas-in-early-developmental-stages-of-zebrafish-embryos
#17
Kyung-Tae Lee, Jin-Wu Nam
microRNA (miRNA) represses protein-coding gene via seed pairing to 3' untranslated reiongs (UTRs) of mRNA at the post-transcriptional and translational level. Although working models of miRNA-mediated gene silencing have been successfully established using miRNA transfections and knockouts, the regulatory interaction between miRNA and long non-coding RNA (lncRNA) remain unknown. In particular, how mRNA-resembling lncRNAs with 5' cap, 3' poly(A)-tail, or coding features are regulated by miRNA is yet to be examined...
March 21, 2017: BMB Reports
https://www.readbyqxmd.com/read/28319273/gastric-microbiota-features-associated-with-cancer-risk-factors-and-clinical-outcomes-a-pilot-study-in-gastric-cardia-cancer-patients-from-shanxi-china
#18
Guoqin Yu, Nan Hu, Lemin Wang, Chaoyu Wang, Xiao-You Han, Mike Humphry, Jacques Ravel, Christian C Abnet, Philip R Taylor, Alisa M Goldstein
Little is known about the link between gastric microbiota and the epidemiology of gastric cancer. In order to determine the epidemiologic and clinical relevance of gastric microbiota, we used 16S ribosomal RNA gene sequencing analysis to characterize the composition and structure of the gastric microbial community of 80 paired samples (non-malignant and matched tumor tissues) from gastric cardia adenocarcinoma (GCA) patients in Shanxi, China. We also used PICRUSt to predict microbial functional profiles. Compared to patients without family history of upper gastrointestinal (UGI) cancer in the non-malignant gastric tissue microbiota, patients with family history of UGI cancer had higher Helicobacter pylori (Hp) relative abundance (median: 0...
March 20, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28317538/families-genera-and-species-of-botryosphaeriales
#19
Tao Yang, Johannes Z Groenewald, Ratchadawan Cheewangkoon, Fahimeh Jami, Jafar Abdollahzadeh, Lorenzo Lombard, Pedro W Crous
Members of Botryosphaeriales are ecologically diverse, but most commonly associated with leaf spots, fruit and root rots, die-back or cankers of diverse woody hosts. Based on morphology and DNA sequence data, the Botryosphaeriales have to date been shown to contain eight families, with an additional two, Endomelanconiopsisaceae (Endomelanconiopsis) and Pseudofusicoccumaceae (Pseudofusicoccum) being newly described in this study. Furthermore, Oblongocollomyces is introduced as new genus, while Spencermartinsia is reduced to synonymy under Dothiorella...
April 2017: Fungal Biology
https://www.readbyqxmd.com/read/28316417/molecular-characterization-and-phylogenetic-analysis-of-plasmodium-vivax-plasmodium-falciparum-plasmodium-ovale-plasmodium-malariae-and-plasmodium-cynomolgi
#20
Soumendranath Chatterjee, Priyanka Mukhopadhyay, Raktima Bandyopadhyay, Paltu Dhal, Debraj Biswal, Prabir Kumar Bandyopadhyay
18S ribosomal RNA gene sequences of different species of Plasmodium were aligned and analyzed to determine the molecular diversity among different species of Plasmodium. AT content of P. cynomolgi, P. ovale, P. falciparum, P. vivax and P. malariae ranged from 62.30 to 63.15, 63.90 to 65.29, 66.67 to 68.40, 61.66 to 63.25 and 64.09 to 76.36 in case respectively. GC content of P. cynomolgi, P. ovale, P. falciparum, P. vivaxand P. malariae ranged from 36.85 to 37.70, 34.71 to 36.43, 31.60 to 33.27, 23.64 to 35...
March 2017: Journal of Parasitic Diseases: Official Organ of the Indian Society for Parasitology
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