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Ribosomal rna

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https://www.readbyqxmd.com/read/29776339/differential-gene-transcription-across-the-life-cycle-in-daphnia-magna-using-a-new-all-genome-custom-made-microarray
#1
Bruno Campos, Danielle Fletcher, Benjamín Piña, Romà Tauler, Carlos Barata
BACKGROUND: Unravelling the link between genes and environment across the life cycle is a challenging goal that requires model organisms with well-characterized life-cycles, ecological interactions in nature, tractability in the laboratory, and available genomic tools. Very few well-studied invertebrate model species meet these requirements, being the waterflea Daphnia magna one of them. Here we report a full genome transcription profiling of D. magna during its life-cycle. The study was performed using a new microarray platform designed from the complete set of gene models representing the whole transcribed genome of D...
May 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29774288/molecular-analysis-of-giardia-duodenalis-isolates-from-symptomatic-and-asymptomatic-children-from-la-habana-cuba
#2
Luis Enrique Jerez Puebla, Fidel A Núñez, Lissette Pérez Santos, Lázara Rojas Rivero, Isabel Martínez Silva, Lucía Ayllón Valdés, Iraís Atencio Millán, Norbert Müller
Giardiasis is considered the most common intestinal parasitic disease in humans worldwide. In Cuba, this infection has particularly a strong clinical impact on the child population. Giardia duodenalis is a highly diverse protozoan, which comprises a complex of eight morphologically identical genetic assemblages, further divided into sub-assemblages. The present study used triose phosphate isomerase ( tpi ) and small-subunit ribosomal RNA (SSU rRNA) genes as genetic markers for the identification of G. duodenalis assemblages and sub-assemblages in correlation with clinical and epidemiological data in children attended at the Paediatric Hospital "William Soler" and at Pedro Kouri Institute, between 2015 and 2016...
August 2017: Parasite Epidemiology and Control
https://www.readbyqxmd.com/read/29771354/methylation-guide-rna-evolution-in-archaea-structure-function-and-genomic-organization-of-110-c-d-box-srna-families-across-six-pyrobaculum-species
#3
Lauren M Lui, Andrew V Uzilov, David L Bernick, Andrea Corredor, Todd M Lowe, Patrick P Dennis
Archaeal homologs of eukaryotic C/D box small nucleolar RNAs (C/D box sRNAs) guide precise 2'-O-methyl modification of ribosomal and transfer RNAs. Although C/D box sRNA genes constitute one of the largest RNA gene families in archaeal thermophiles, most genomes have incomplete sRNA gene annotation because reliable, fully automated detection methods are not available. We expanded and curated a comprehensive gene set across six species of the crenarchaeal genus Pyrobaculum, particularly rich in C/D box sRNA genes...
May 16, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29771278/a-pelota-like-gene-regulates-root-development-and-defence-responses-in-rice
#4
Wona Ding, Jing Wu, Jin Ye, Wenjuan Zheng, Shanshan Wang, Xinni Zhu, Jiaqin Zhou, Zhichong Pan, Botao Zhang, Shihua Zhu
Background and Aims: Pelota (Pelo) are evolutionarily conserved genes reported to be involved in ribosome rescue, cell cycle control and meiotic cell division. However, there is little known about their function in plants. The aim of this study was to elucidate the function of an ethylmethane sulphonate (EMS)-derived mutation of a Pelo-like gene in rice (named Ospelo). Methods: A dysfunctional mutant was used to characterize the function of OsPelo. Analyses of its expression and sub-cellular localization were performed...
May 16, 2018: Annals of Botany
https://www.readbyqxmd.com/read/29769341/mutational-analysis-of-the-bovine-hepacivirus-internal-ribosome-entry-site
#5
A L Baron, A Schoeniger, P Becher, C Baechlein
In recent years, hepatitis C virus (HCV)-related viruses were identified in several species including dogs, horses, bats and rodents. Additionally, a novel virus of the genus Hepacivirus has been discovered in bovine samples and was termed bovine hepacivirus (BovHepV). Prediction of the BovHepV IRES (internal ribosome entry site) structure revealed strong similarities to the HCV IRES structure comprising domains II, IIIabcde, pseudoknot IIIf and domain IV with the initiation codon AUG. Unlike HCV, only one microRNA-122 (miR-122) binding site could be identified in the BovHepV 5' NTR...
May 16, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29767361/making-and-sequencing-heavily-multiplexed-high-throughput-16s-ribosomal-rna-gene-amplicon-libraries-using-a-flexible-two-stage-pcr-protocol
#6
Ankur Naqib, Silvana Poggi, Weihua Wang, Marieta Hyde, Kevin Kunstman, Stefan J Green
Deep sequencing of polymerase chain reaction (PCR)-amplified small subunit (16S or 18S) ribosomal RNA (rRNA) genes fragments is commonly employed to characterize the composition and structure of microbial communities. Preparing genomic DNA for sequencing of such gene fragments on Illumina sequencers can be performed in a straightforward, two-stage PCR method, described herein. The protocol described allows for up to 384 samples to be sequenced simultaneously, and provides great flexibility in choice of primers...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29767358/sureselect-xt-rna-direct-a-technique-for-expression-analysis-through-sequencing-of-target-enriched-ffpe-total-rna
#7
Jennifer Carter Jones, Alex P Siebold, Carolina Becker Livi, Anne Bergstrom Lucas
Gene expression profiling of samples from biobanks requires a method that can be used with intact as well as partially degraded RNA. High throughput applications can benefit from reducing the number of processing steps including eliminating the poly(A) selection and ribosomal depletion steps. When performing targeted capture, we have found that we can eliminate the upfront poly(A) selection/ribosomal depletion steps that cause bias in standard mRNA-Seq workflows. This target enrichment solution allows for whole transcriptome or customized content to characterize differential gene expression patterns (especially for mid/low level transcripts)...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29766661/structure-based-design-of-a-eukaryote-selective-antiprotozoal-fluorinated-aminoglycoside
#8
Hiroki Kanazawa, Oscar M Saavedra, Juan Pablo Maianti, Simon A Young, Luis Izquierdo, Terry K Smith, Stephen Hanessian, Jiro Kondo
Aminoglycosides (AG) are antibiotics that lower the accuracy of protein synthesis by targeting a highly-conserved RNA helix of the ribosomal A-site. The discovery of AGs that selectively target the eukaryotic ribosome, but lack activity in prokaryotes, are promising as antiprotozoals for the treatment of neglected tropical diseases, and as therapies to read-through point-mutation genetic diseases. However, a single nucleobase change A1408G in the eukaryotic A-site leads to negligible affinity for most AGs. Herein we report the synthesis of 6'-fluoro sisomicin, the first 6'-fluorinated aminoglycoside, which specifically interacts with the protozoal cytoplasmic rRNA A-site, but not the bacterial A-site, as evidenced by X-ray co-crystal structures...
May 15, 2018: ChemMedChem
https://www.readbyqxmd.com/read/29765956/transcriptomic-profiling-of-zebrafish-hair-cells-using-ribotag
#9
Maggie S Matern, Alisha Beirl, Yoko Ogawa, Yang Song, Nikhil Paladugu, Katie S Kindt, Ronna Hertzano
The zebrafish inner ear organs and lateral line neuromasts are comprised of a variety of cell types, including mechanosensitive hair cells. Zebrafish hair cells are evolutionarily homologous to mammalian hair cells, and have been particularly useful for studying normal hair cell development and function. However, the relative scarcity of hair cells within these complex organs, as well as the difficulty of fine dissection at early developmental time points, makes hair cell-specific gene expression profiling technically challenging...
2018: Frontiers in Cell and Developmental Biology
https://www.readbyqxmd.com/read/29763665/selection-and-paucity-of-phylogenetic-signal-challenge-the-utility-of-alpha-tubulin-in-reconstruction-of-evolutionary-history-of-free-living-litostomateans-protista-ciliophora
#10
Ľubomír Rajter, Peter Vďačný
The class Litostomatea represents a highly diverse but monophyletic group, uniting both free-living and endosymbiotic ciliates. Ribosomal RNA genes and ITS-region sequences helped to recognize and define the main litostomatean lineages, but did not provide enough phylogenetic signal to unambiguously resolve their interrelationships. In this study, we attempted to improve the resolution among main free-living predatory lineages by adding the gene coding for alpha-tubulin. However, our phylogenetic analyses challenged the performance of alpha-tubulin in reconstruction of evolutionary history of free-living litostomateans...
May 12, 2018: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/29763437/postnatal-colonization-with-human-infant-type-bifidobacterium-species-alters-behavior-of-adult-gnotobiotic-mice
#11
Berkley Luk, Surabi Veeraragavan, Melinda Engevik, Miriam Balderas, Angela Major, Jessica Runge, Ruth Ann Luna, James Versalovic
Accumulating studies have defined a role for the intestinal microbiota in modulation of host behavior. Research using gnotobiotic mice emphasizes that early microbial colonization with a complex microbiota (conventionalization) can rescue some of the behavioral abnormalities observed in mice that grow to adulthood completely devoid of bacteria (germ-free mice). However, the human infant and adult microbiomes vary greatly, and effects of the neonatal microbiome on neurodevelopment are currently not well understood...
2018: PloS One
https://www.readbyqxmd.com/read/29762668/benchmarking-taxonomic-assignments-based-on-16s-rrna-gene-profiling-of-the-microbiota-from-commonly-sampled-environments
#12
Alexandre Almeida, Alex L Mitchell, Aleksandra Tarkowska, Robert D Finn
Background: Taxonomic profiling of ribosomal RNA (rRNA) sequences has been the accepted norm for inferring the composition of complex microbial ecosystems. QIIME and mothur have been the most widely used taxonomic analysis tools for this purpose, with MAPseq and QIIME 2 being two recently released alternatives. However, no independent and direct comparison between these four main tools has been performed. Here, we compared the default classifiers of MAPseq, mothur, QIIME, and QIIME 2 using synthetic simulated datasets comprised of some of the most abundant genera found in the human gut, ocean and soil environments...
May 11, 2018: GigaScience
https://www.readbyqxmd.com/read/29760477/functional-interplay-between-e2f7-and-ribosomal-rrna-gene-transcription-regulates-protein-synthesis
#13
Amanda S Coutts, Shonagh Munro, Nicholas B La Thangue
A prerequisite for protein synthesis is the transcription of ribosomal rRNA genes by RNA polymerase I (Pol I), which controls ribosome biogenesis. UBF (upstream binding factor) is one of the main Pol I transcription factors located in the nucleolus that activates rRNA gene transcription. E2F7 is an atypical E2F family member that acts as a transcriptional repressor of E2F target genes, and thereby contributes to cell cycle arrest. Here, we describe an unexpected role for E2F7 in regulating rRNA gene transcription...
May 14, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29760415/rbm24-stabilizes-hepatitis-b-virus-pregenomic-rna-but-inhibits-core-protein-translation-by-targeting-the-terminal-redundancy-sequence
#14
Yongxuan Yao, Bo Yang, Huang Cao, Kaitao Zhao, Yifei Yuan, Yingshan Chen, Zhenhua Zhang, Yun Wang, Rongjuan Pei, Jizheng Chen, Xue Hu, Yuan Zhou, Mengji Lu, Chunchen Wu, Xinwen Chen
The terminal redundancy (TR) sequence of the 3.5-kb hepatitis B virus (HBV) RNA contains sites that govern many crucial functions in the viral life cycle, including polyadenylation, translation, RNA packaging, and DNA synthesis. In the present study, RNA-binding motif protein 24 (RBM24) is shown to be involved in the modulation of HBV replication by targeting the TR of HBV RNA. In HBV-transfected hepatoma cell lines, both knockdown and overexpression of RBM24 led to decreased HBV replication and transcription...
May 14, 2018: Emerging Microbes & Infections
https://www.readbyqxmd.com/read/29760298/a-newly-designed-primer-revealed-high-phylogenetic-diversity-of-endozoicomonas-in-coral-reefs
#15
Jia-Ho Shiu, Jiun-Yan Ding, Ching-Hung Tseng, Shueh-Ping Lou, Takuma Mezaki, Yu-Ting Wu, Hsiang-Iu Wang, Sen-Lin Tang
Endozoicomonas bacteria are commonly regarded as having a potentially symbiotic relationship with their coral hosts. However, their diversity and phylogeny in samples collected from various sources remain unclear. Therefore, we designed an Endozoicomonas-specific primer paired with a bacterial universal primer to detect the 16S ribosomal RNA (rRNA) genes of this taxon and conducted an in-depth investigation of the Endozoicomonas community structure in reef-building corals. The primer had high specificity in the V3-V4 region (95...
May 12, 2018: Microbes and Environments
https://www.readbyqxmd.com/read/29758946/gut-microbiome-is-altered-in-patients-with-alzheimer-s-disease
#16
Zhen-Qian Zhuang, Lin-Lin Shen, Wei-Wei Li, Xue Fu, Fan Zeng, Li Gui, Yang Lü, Min Cai, Chi Zhu, Yin-Ling Tan, Peng Zheng, Hui-Yun Li, Jie Zhu, Hua-Dong Zhou, Xian-Le Bu, Yan-Jiang Wang
Previous studies suggest that gut microbiota is associated with neuropsychiatric disorders, such as Parkinson's disease, amyotrophic lateral sclerosis, and depression. However, whether the composition and diversity of gut microbiota is altered in patients with Alzheimer's disease (AD) remain largely unknown. In the present study, we collected fecal samples from 43 AD patients and 43 age- and gender-matched cognitively normal controls. 16S ribosomal RNA sequencing technique was used to analyze the microbiota composition in feces...
May 11, 2018: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/29756662/existence-of-diverse-modifications-in-16-28-nt-small-rnas
#17
Meng-Dan Lan, Jun Xiong, Xue-Jiao You, Xiao-Cheng Weng, Xiang Zhou, Bi-Feng Yuan, Yu-Qi Feng
RNA contains diverse modifications that exert important influences in a variety of cellular processes. So far more than 150 modifications have been identified in various RNA species, mainly in ribosomal RNA (rRNA), transfer RNA (tRNA), and messenger RNA (mRNA). In contrast to rRNA, tRNA and mRNA, the known modifications in small RNAs have been primarily limited to 2'-O-ribose methylations in plants and inosine in mammals. Methylation of small RNAs in mammals is still unclear. Current methods widely used in the characterization of small RNAs are mainly based on the strategy of nucleic acid hybridization and sequencing, which cannot characterize modifications in small RNAs...
May 14, 2018: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29753892/next-generation-sequencing-reveals-packaging-of-host-rnas-by-brome-mosaic-virus
#18
N Shrestha, P H Weber, S V Burke, W Wysocki, M R Duvall, J J Bujarski
Although RNA viruses evolved the mechanisms of specific encapsidation, miss-packaging of cellular RNAs has been reported in such RNA virus systems as flock house virus or cucumber necrosis virus. To find out if brome mosaic virus (BMV), a tripartite RNA virus, can package cellular RNAs, BMV was propagated in barley and in Nicotiana benthamiana hosts, purified by cesium chloride (CsCl) gradient ultracentrifugation followed by nuclease treatment to remove any contaminating cellular (host) RNAs. The extracted virion RNA was then sequenced by using next-generation sequencing (NGS RNA-Seq) with the Illumina protocol...
May 10, 2018: Virus Research
https://www.readbyqxmd.com/read/29752988/the-complete-mitochondrial-genome-of-parasesarma-pictum-brachyura-grapsoidea-sesarmidae-and-comparison-with-other-brachyuran-crabs
#19
Zhengfei Wang, Xuejia Shi, Yitao Tao, Qiong Wu, Yuze Bai, Huayun Guo, Dan Tang
Mitochondrial DNA (mtDNA) is an extrachromosomal genome which can provide important information for evolution and phylogenetic analysis. In this study, we assembled a complete mitogenome of a crab Parasesarma pictum (Brachyura: Grapsoidea: Sesarmidae) from next generation sequencing reads at the first time. P. pictum is a mudflat crab, belonging to the Sesarmidae family (subfamily Sesarminae), which is perched on East Asia. The 15,716 bp mitogenome covers 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), 2 ribosomal RNA genes (rRNAs), and one control region (CR)...
May 9, 2018: Genomics
https://www.readbyqxmd.com/read/29752494/morphological-observation-and-comparative-transcriptomic-analysis-of-clostridium-perfringens-biofilm-and-planktonic-cells
#20
Xiaofen Zhang, Yuhua Ma, Guisheng Ye
Bacterial biofilms can enhance survival in adverse environments and promote infection. However, little is known about biofilm formation by Clostridium perfringens. To better characterize this process, we used SEM to observe the surfaces of C. perfringens biofilms after 12, 24, 48, and 72 h of incubation. Biofilm cells appeared to be encased in a dense matrix material, and the total biomass of the biofilm increased with incubation time. To gain insight into the differentially expressed genes (DEGs) between biofilm and planktonic cells, we carried out comparative transcriptomic analysis using RNA sequencing...
May 11, 2018: Current Microbiology
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