keyword
MENU ▼
Read by QxMD icon Read
search

Ribosomal rna

keyword
https://www.readbyqxmd.com/read/28212567/ribosomal-dna-status-inferred-from-dna-cloud-assays-and-mass-spectrometry-identification-of-agarose-squeezed-proteins-interacting-with-chromatin-aspic-ms
#1
Kamil Krol, Justyna Jendrysek, Janusz Debski, Marek Skoneczny, Anna Kurlandzka, Joanna Kaminska, Michal Dadlez, Adrianna Skoneczna
Ribosomal RNA-encoding genes (rDNA) are the most abundant genes in eukaryotic genomes. To meet the high demand for rRNA, rDNA genes are present in multiple tandem repeats clustered on a single or several chromosomes and are vastly transcribed. To facilitate intensive transcription and prevent rDNA destabilization, the rDNA-encoding portion of the chromosome is confined in the nucleolus. However, the rDNA region is susceptible to recombination and DNA damage, accumulating mutations, rearrangements and atypical DNA structures...
February 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28209895/seagrass-ecosystems-reduce-exposure-to-bacterial-pathogens-of-humans-fishes-and-invertebrates
#2
Joleah B Lamb, Jeroen A J M van de Water, David G Bourne, Craig Altier, Margaux Y Hein, Evan A Fiorenza, Nur Abu, Jamaluddin Jompa, C Drew Harvell
Plants are important in urban environments for removing pathogens and improving water quality. Seagrass meadows are the most widespread coastal ecosystem on the planet. Although these plants are known to be associated with natural biocide production, they have not been evaluated for their ability to remove microbiological contamination. Using amplicon sequencing of the 16S ribosomal RNA gene, we found that when seagrass meadows are present, there was a 50% reduction in the relative abundance of potential bacterial pathogens capable of causing disease in humans and marine organisms...
February 17, 2017: Science
https://www.readbyqxmd.com/read/28209552/detection-of-giardia-duodenalis-assemblage-e-infections-at-the-tibetan-plateau-area-yaks-are-suitable-hosts
#3
Wang Guang-Hua, Wang Ge-Ping, Li Xiu-Ping, Ma Li-Qing, Gabriele Karanis, Eleni Christodoulou-Vafeiadou, Panagiotis Karanis
The prevalence of Giardia duodenalis (G. duodenalis) assemblages in yaks is poorly known. The present study examined 297 fecal samples from weaned yak, 4 to 7 months of age, from 3 different farms, in Tibetan Plateau Area (TPA) of the Qinghai Province in Western China. The prevalence of infection was determined by light and immunofluorescence microscopy, and nested-PCR. PCR was performed for the small subunit ribosomal RNA (SSU) amplified 16 positive for G. duodenalis products. The prevalence of Giardia species was 5...
February 13, 2017: Acta Tropica
https://www.readbyqxmd.com/read/28208788/next-generation%C3%A2-sequencing-based%C3%A2-ribomethseq%C3%A2-protocol%C3%A2-for%C3%A2-analysis%C3%A2-of%C3%A2-trna%C3%A2-2-o-methylation
#4
Virginie Marchand, Florian Pichot, Kathrin Thüring, Lilia Ayadi, Isabel Freund, Alexander Dalpke, Mark Helm, Yuri Motorin
Analysis of RNA modifications by traditional physico-chemical approaches is labor  intensive,  requires  substantial  amounts  of  input  material  and  only  allows  site-by-site  measurements.  The  recent  development  of  qualitative  and  quantitative  approaches  based  on   next-generation sequencing (NGS) opens new perspectives for the analysis of various cellular RNA  species.  The  Illumina  sequencing-based  RiboMethSeq  protocol  was  initially  developed  and  successfully applied for mapping of ribosomal RNA (rRNA) 2'-O-methylations...
February 9, 2017: Biomolecules
https://www.readbyqxmd.com/read/28208653/molecular-characterization-of-mycolactone-producing-mycobacteria-from-aquatic-environments-in-buruli-ulcer-non-endemic-areas-in-c%C3%A3-te-d-ivoire
#5
Marcellin B Tano, Christelle Dassi, Lydia Mosi, Marina Koussémon, Bassirou Bonfoh
Non-tuberculous mycobacteria (NTM), particularly mycolactone producing mycobacteria (MPM), are bacteria found in aquatic environments causing skin diseases in humans like Buruli ulcer (BU). Although the causative agent for BU, Mycobacterium ulcerans has been identified and associated with slow-moving water bodies, the real transmission route is still unknown. This study aimed to characterize MPMs from environmental aquatic samples collected in a BU non-endemic community, Adiopodoumé, in Côte d'Ivoire. Sixty samples were collected in four types of matrices (plant biofilms, water filtrate residues, plant detritus and soils) from three water bodies frequently used by the population...
February 11, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28204512/ribosomal-rna-genes-contribute-to-the-formation-of-pseudogenes-and-junk-dna-in-the-human-genome
#6
Brent M Robicheau, Edward Susko, Amye M Harrigan, Marlene Snyder
No abstract text is available yet for this article.
February 15, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28202229/requirement-of-the-rna-binding-protein-smpb-during-intracellular-growth-of-listeria-monocytogenes
#7
Mobarak Abu Mraheil, Renate Frantz, Lisa Teubner, Heiko Wendt, Uwe Linne, Jessica Wingerath, Thomas Wirth, Trinad Chakraborty
Bacterial trans-translation is the main quality control mechanism employed to relieve stalled ribosomes. Trans-translation is mediated by the small protein B (SmpB) and transfer-mRNA (tmRNA) ribonucleoprotein complex, which interacts with translational complexes stalled at the 3' end of non-stop mRNAs to release the stalled ribosomes thereby targeting the nascent polypeptides and truncated mRNAs for degradation. The trans-translation system exists with a few exceptions in all bacteria. In the present study, we assessed the contribution of SmpB to the growth and virulence of Listeria monocytogenes, a human intracellular food-borne pathogen that colonizes host tissues to cause severe invasive infections...
February 1, 2017: International Journal of Medical Microbiology: IJMM
https://www.readbyqxmd.com/read/28201982/transcriptome-profile-of-rat-genes-in-injured-spinal-cord-at-different-stages-by-rna-sequencing
#8
Ling-Ling Shi, Nan Zhang, Xiu-Mei Xie, Yue-Juan Chen, Rui Wang, Lin Shen, Jian-Sheng Zhou, Jian-Guo Hu, He-Zuo Lü
BACKGROUND: Spinal cord injury (SCI) results in fatal damage and currently has no effective treatment. The pathological mechanisms of SCI remain unclear. In this study, genome-wide transcriptional profiling of spinal cord samples from injured rats at different time points after SCI was performed by RNA-Sequencing (RNA-Seq). The transcriptomes were systematically characterized to identify the critical genes and pathways that are involved in SCI pathology. RESULTS: RNA-Seq results were obtained from total RNA harvested from the spinal cords of sham control rats and rats in the acute, subacute, and chronic phases of SCI (1 day, 6 days and 28 days after injury, respectively; n = 3 in every group)...
February 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28197340/phenotypic-and-genotypic-analysis-of-multidrug-resistant-mycobacterium-tuberculosis-isolates-from-sudanese-patients
#9
Solima M A Sabeel, Mohamed Ahmed Salih, Manasik Ali, Salah-Eldin El-Zaki, Nadir Abuzeid, Zeinab Abubaker Mohammed Elgadi, Hisham N Altayb, Asrar M A Elegail, Nuha Y Ibrahim, Bahaeldin K Elamin
Background. Currently, mutations in rpoB, KatG, and rrs genes and inhA promoter were considered to be involved in conferring resistance to rifampicin, isoniazid, and streptomycin in Mycobacterium tuberculosis (MTB). Objective. The aims of this study were to detect the prevalence of first-line tuberculosis (TB) drug resistance among a group of previously treated and newly detected TB patients, to determine the association between prevalence of multidrug resistance (MDR) and demographic information (age and sex), to explain genes correlated with MDR Mycobacterium tuberculosis, and to characterize MTB via 16S ribosomal RNA (16S rRNA) analysis...
2017: Tuberculosis Research and Treatment
https://www.readbyqxmd.com/read/28196664/new-records-of-ornithodoros-puertoricensis-fox-1947-ixodida-argasidae-parasitizing-humans-in-rural-and-urban-dwellings-panama
#10
Sergio E Bermúdez, Eduardo Castillo, Tyler D Pohlenz, Alexander Kneubehl, Aparna Krishnavajhala, Lillian Domínguez, Antonio Suárez, Job E López
The presence of ticks inside human constructions was evaluated in two localities from Colon province (Charco La Piedra and Espinar) and one from Panama province (Ancon, City of Panama). In two of houses, eight people from Charco La Piedra and one from Ancón reported "insect bites," which produced blisters for several weeks. The investigation resulted in the collection of argasid ticks, which were identified by morphology and sequencing the 16s ribosomal RNA gene, and later evaluated for the presence of relapsing fever Borrelia DNA...
February 5, 2017: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/28196591/nuclear-pkc%C3%AE-ect2-rac1-and-ribosome-biogenesis-a-novel-axis-in-lung-tumorigenesis
#11
Martin J Baker, Mariana Cooke, Marcelo G Kazanietz
The RhoGEF Ect2 controls cell division and exerts oncogenic functions in multiple cancers. In this issue of Cancer Cell, Justilien et al. report that Ect2 is required for lung tumorigenesis and identified a role for this GEF in ribosomal RNA (rRNA) synthesis that is mediated by Rac1 and PKCι-dependent phosphorylation.
February 13, 2017: Cancer Cell
https://www.readbyqxmd.com/read/28195221/transcriptome-analysis-around-the-onset-of-strawberry-fruit-ripening-uncovers-an-important-role-of-oxidative-phosphorylation-in-ripening
#12
Qing-Hua Wang, Cheng Zhao, Miao Zhang, Yu-Zhong Li, Yuan-Yue Shen, Jia-Xuan Guo
Although much progress has been made towards understanding the ripening of non-climacteric fruit using the strawberry as a model plant, the defined molecular mechanisms remain unclear. Here, RNA-sequencing was performed using four cDNA libraries around the onset of ripening, and a total of 31,793 unigenes and 335 pathways were annotated including the top five pathways, which were involved in ribosome, spliceosome, protein processing, plant-pathogen interaction and plant hormone signaling, and the important DEGs related to ripening were annotated to be mainly involved in protein translation and processing, sugar metabolism, energy metabolism, phytohormones, antioxidation, pigment and softening, especially finding a decreased trend of oxidative phosphorylation during red-coloring...
February 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28194024/regnase-1-a-rapid-response-ribonuclease-regulating-inflammation-and-stress-responses
#13
REVIEW
Renfang Mao, Riyun Yang, Xia Chen, Edward W Harhaj, Xiaoying Wang, Yihui Fan
RNA-binding proteins (RBPs) are central players in post-transcriptional regulation and immune homeostasis. The ribonuclease and RBP Regnase-1 exerts critical roles in both immune cells and non-immune cells. Its expression is rapidly induced under diverse conditions including microbial infections, treatment with inflammatory cytokines and chemical or mechanical stimulation. Regnase-1 activation is transient and is subject to negative feedback mechanisms including proteasome-mediated degradation or mucosa-associated lymphoid tissue 1 (MALT1) mediated cleavage...
February 13, 2017: Cellular & Molecular Immunology
https://www.readbyqxmd.com/read/28188847/pharmacological-inhibition-of-spinal-cord-injury-stimulated-ribosomal-biogenesis-does-not-affect-locomotor-outcome
#14
Ewa Kilanczyk, Kariena R Andres, Justin Hallgren, Sujata Saraswat Ohri, Marikki Laiho, Scott R Whittemore, Michal Hetman
After unresolved endoplasmic reticulum stress, recovery of protein synthesis including increased expression of ribosomal components and translation factors may induce cell death. Using a mouse model of moderate contusive spinal cord injury (SCI) at the T9 level, upregulation of ribosomal biogenesis was observed in the injury epicenter at 24h after trauma. Such upregulation coincided with endoplasmic reticulum stress response as previously reported in this model. It was also accompanied by changes in expression of many other genes associated with translational regulation...
February 7, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/28188182/unstable-inheritance-of-45s-rrna-genes-in-arabidopsis-thaliana
#15
Fernando A Rabanal, Viktoria Nizhynska, Terezie Mandáková, Polina Yu Novikova, Martin A Lysak, Richard Mott, Magnus Nordborg
The considerable genome size variation in Arabidopsis thaliana has been shown largely to be due to copy number variation (CNV) in 45S ribosomal RNA (rRNA) genes. Surprisingly, attempts to map this variation by means of genome-wide association studies (GWAS) failed to identify either of the two likely sources, namely the nucleolar organizer regions (NORs). Instead, GWAS implicated a trans-acting locus, as if rRNA CNV was a phenotype rather than a genotype. To explain these results, we investigated the inheritance and stability of rRNA gene copy number using the variety of genetic resources available in A...
February 10, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28187600/-i-eimeria-i-i-atlapetesi-i-nom-nov-a-replacement-name-for-i-eimeria-i-i-pileata-i-soriano-vargas-et-al-2015-apicomplexa-eimeriidae-preoccupied-by-i-eimeria-i-i-pileata-i-straneva-and-kelley-1979-apicomplexa-eimeriidae-with-observations-on-histopathology-and
#16
Edgardo Soriano-Vargas, Celene Salgado-Miranda, Andrea Paloma Zepeda-Velázquez, Juan Pablo Medina, Mariusz Krzysztof Janczur, Maricruz González-Gómez, Izanami Tereira Flores-Valle, Bruno Pereira Berto, Carlos Wilson Gomes Lopes
Eimeria pileata Soriano-Vargas, Medina, Salgado-Miranda, García-Conejo, Galindo-Sánchez, Janczur, Berto and Lopes, 2015 is a junior homonym of Eimeria pileata Straneva and Kelley, 1979 and needs to be replaced. This coccidium was described from a rufous-capped brush finch Atlapetes pileatus Wagler in the Nevado de Toluca Natural Protected Area, Mexico. Thus, to maintain the original intent of the specific epithet derived from the scientific name of the type-host, the name Eimeria atlapetesi nom. nov. is proposed as a replacement name...
January 31, 2017: Zootaxa
https://www.readbyqxmd.com/read/28187496/post-translational-modification-directs-nuclear-and-hyphal-tip-localization-of-c-albicans-mrna-binding-protein-slr1
#17
Chaiyaboot Ariyachet, Christian Beißel, Xiang Li, Selena Lorrey, Olivia Mackenzie, Patrick M Martin, Katharine O'Brien, Tossapol Pholcharee, Sue Sim, Heike Krebber, Anne E McBride
The morphological transition of the opportunistic fungal pathogen Candida albicans from budding to hyphal growth has been implicated in its ability to cause disease in animal models. Absence of SR-like RNA-binding protein Slr1 slows hyphal formation and decreases virulence in a systemic candidiasis model, suggesting a role for post-transcriptional regulation in these processes. SR (serine-arginine)-rich proteins influence multiple steps in mRNA metabolism and their localization and function are frequently controlled by modification...
February 10, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28186489/folding-behavior-of-a-t-shaped-ribosome-binding-translation-enhancer-implicated-in-a-wide-spread-conformational-switch
#18
My-Tra Le, Wojciech K Kasprzak, Taejin Kim, Feng Gao, Megan Yl Young, Xuefeng Yuan, Bruce A Shapiro, Joonil Seog, Anne E Simon
Turnip crinkle virus contains a T-shaped, ribosome-binding, translation enhancer (TSS) in its 3'UTR that serves as a hub for interactions throughout the region. The viral RNA-dependent RNA polymerase (RdRp) causes the TSS/surrounding region to undergo a conformational shift postulated to inhibit translation. Using optical tweezers (OT) and steered molecular dynamic simulations (SMD), we found that the unusual stability of pseudoknotted element H4a/Ψ3 required five upstream adenylates, and H4a/Ψ3 was necessary for cooperative association of two other hairpins (H5/H4b) in Mg(2+)...
February 10, 2017: ELife
https://www.readbyqxmd.com/read/28186172/appropriateness-of-reference-genes-for-normalizing-messenger-rna-in-mouse-2-4-dinitrobenzene-sulfonic-acid-dnbs-induced-colitis-using-quantitative-real-time-pcr
#19
Nour Eissa, Laëtitia Kermarrec, Hayam Hussein, Charles N Bernstein, Jean-Eric Ghia
2,4-Dinitrobenzene sulfonic acid (DNBS)-induced colitis is an experimental model that mimics Crohn's disease. Appropriateness of reference genes is crucial for RT-qPCR. This is the first study to determine the stability of reference gene expression (RGE) in mice treated with DNBS. DNBS experimental Colitis was induced in male C57BL/6 mice. RNA was extracted from colon tissue and comprehensive analysis of 13 RGE was performed according to predefined criteria. Relative colonic TNF-α and IL-1β mRNA levels were calculated...
February 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28185099/microbial-arsenite-oxidation-with-oxygen-nitrate-or-an-electrode-as-the-sole-electron-acceptor
#20
Van Khanh Nguyen, Huong T Tran, Younghyun Park, Jaecheul Yu, Taeho Lee
The purpose of this study was to identify bacteria that can perform As(III) oxidation for environmental bioremediation. Two bacterial strains, named JHS3 and JHW3, which can autotrophically oxidize As(III)-As(V) with oxygen as an electron acceptor, were isolated from soil and water samples collected in the vicinity of an arsenic-contaminated site. According to 16S ribosomal RNA sequence analysis, both strains belong to the ɤ-Proteobacteria class and share 99% sequence identity with previously described strains...
February 9, 2017: Journal of Industrial Microbiology & Biotechnology
keyword
keyword
28861
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"