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Ribosomal rna

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https://www.readbyqxmd.com/read/28441441/a-novel-multiplexed-probe-based-quantitative-pcr-assay-for-the-soybean-root-and-stem-rot-pathogen-phytophthora-sojae-utilizes-its-transposable-element
#1
James S Haudenshield, Jeong Y Song, Glen L Hartman
Phytophthora root rot of soybean [Glycine max (L.) Merr.] is caused by the oomycete Phytophthora sojae (Kaufm. & Gerd.). P. sojae has a narrow host range, consisting primarily of soybean, and it is a serious pathogen worldwide. It exists in root and stem tissues as mycelium, wherein it can form oospores which subsequently germinate to release motile, infectious zoospores. Molecular assays detecting DNA of P. sojae are useful in disease diagnostics, and for determining the presence of the organism in host tissues, soils, and runoff or ponded water from potentially infested fields...
2017: PloS One
https://www.readbyqxmd.com/read/28439036/reclassification-of-the-specialized-metabolite-producer-pseudomonas-mesoacidophila-atcc-31433-as-a-member-of-the-burkholderia-cepacia-complex
#2
E Joel Loveridge, Cerith Jones, Matthew J Bull, Suzy C Moody, Małgorzata W Kahl, Zainab Khan, Louis Neilson, Marina Tomeva, Sarah E Adams, Andrew C Wood, Daniel Rodriguez-Martin, Ingrid Pinel, Julian Parkhill, Eshwar Mahenthiralingam, John Crosby
Pseudomonas mesoacidophila ATCC 31433 is a Gram-negative bacterium, first isolated from Japanese soil samples, which produces the monobactam isosulfazecin and the β-lactam potentiating bulgecins. To characterize the biosynthetic potential of P. mesoacidophila ATCC 31433 its complete genome was determined using single molecule real time DNA sequence analysis. The 7.8 Mb genome comprised four replicons: three chromosomal, each encoding ribosomal RNA, and one plasmid. Phylogenetic analysis demonstrated that P...
April 24, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28439016/astrocytes-locally-translate-transcripts-in-their-peripheral-processes
#3
Kristina Sakers, Allison M Lake, Rohan Khazanchi, Rebecca Ouwenga, Michael J Vasek, Adish Dani, Joseph D Dougherty
Local translation in neuronal processes is key to the alteration of synaptic strength necessary for long-term potentiation, learning, and memory. Here, we present evidence that regulated de novo protein synthesis occurs within distal, perisynaptic astrocyte processes. Astrocyte ribosomal proteins are found adjacent to synapses in vivo, and immunofluorescent detection of peptide elongation in acute slices demonstrates robust translation in distal processes. We have also developed a biochemical approach to define candidate transcripts that are locally translated in astrocyte processes...
April 24, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28438192/chryseobacterium-gleum-in-a-man-with-prostatectomy-in-senegal-a-case-report-and-review-of-the-literature
#4
O Arouna, F Deluca, M Camara, B Fall, B Fall, A Ba Diallo, J D Docquier, S Mboup
BACKGROUND: Here we report a rare case of a urinary tract infection due to Chryseobacterium gleum. This widely distributed Gram-negative bacillus is an uncommon human pathogen and is typically associated with health care settings. CASE PRESENTATION: We describe a case of urinary tract infection caused by Chryseobacterium gleum in a 68-year-old man of Wolof ethnicity (an ethnic group in Senegal, West Africa) who presented to our Department of Urology in a university teaching hospital (Hôpital Aristide Le Dantec) in Dakar, Senegal, 1 month after prostatectomy...
April 24, 2017: Journal of Medical Case Reports
https://www.readbyqxmd.com/read/28436820/srna-mediated-activation-of-gene-expression-by-inhibition-of-5-3-exonucleolytic-mrna-degradation
#5
Sylvain Durand, Frédérique Braun, Anne-Catherine Helfer, Pascale Romby, Ciarán Condon
Post-transcriptional control by small regulatory RNA (sRNA) is critical for rapid adaptive processes. sRNAs can directly modulate mRNA degradation in Proteobacteria without interfering with translation. However, Firmicutes have a fundamentally different set of ribonucleases for mRNA degradation and whether sRNAs can regulate the activity of these enzymes is an open question. We show that Bacillus subtilis RoxS, a major trans-acting sRNA shared with Staphylococus aureus, prevents degradation of the yflS mRNA, encoding a malate transporter...
April 24, 2017: ELife
https://www.readbyqxmd.com/read/28433562/characterization-of-the-complete-mitochondrial-genome-of-khawia-sinensis-belongs-among-platyhelminths-cestodes
#6
Yan Feng, Han-Li Feng, Yi-Hui Fang, Ying-Bing Su
Khawia sinensis is an important species in freshwater fish causing considerable economic losses to the breeding industry. This is the first mt genome of a caryophyllidean cestode characterised. The entire mt genome of K. sinensis is 13,759 bp in length. This mt genome contains 12 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and two non-coding regions. The arrangement of the K. sinensis mt genome is the same as other tapeworms, however, the incomplete stop codon (A) is more frequent that other species...
April 20, 2017: Experimental Parasitology
https://www.readbyqxmd.com/read/28433538/the-ns1-protein-from-influenza-virus-stimulates-translation-initiation-by-enhancing-ribosome-recruitment-to-mrnas
#7
Baptiste Panthu, Olivier Terrier, Coralie Carron, Aurélien Traversier, Antoine Corbin, Laurent Balvay, Bruno Lina, Manuel Rosa-Calatrava, Théophile Ohlmann
The non-structural protein NS1 of influenza A viruses exerts pleiotropic functions during infection. Amongst these functions, NS1 was shown to be involved both in the control of viral and cellular translation; however the mechanism by which this occurs remains to be determined. Thus, we have revisited the role of NS1 in translation by using a combination of influenza infection, mRNA reporter transfection, in vitro functional and biochemical assays. Our data show that the NS1 protein is able to enhance translation of virtually all tested mRNAs with the exception of constructs bearing the Dicistroviruses IRESes (DCV and CrPV), suggesting a role at the level of translation initiation...
April 19, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28431265/nucleolar-reorganization-in-response-to-rdna-damage
#8
REVIEW
Marjolein van Sluis, Brian McStay
Nucleoli, sites of ribosome biogenesis, form around nucleolar organizer regions (NORs) comprising rDNA arrays, located on human acrocentric chromosome p-arms. NORs provide an opportunity to investigate the DNA double strand break (DSB) response at highly transcribed, repetitive, essential loci. Targeted introduction of DSBs into rDNA results in ATM-dependent inhibition of RNA-polymerase I transcription, coupled with movement of rDNA from the nucleolar interior to anchoring points at the periphery. Reorganization renders rDNA accessible to repair factors, normally excluded from nucleoli...
April 18, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/28429321/euglena-transcript-processing
#9
David C McWatters, Anthony G Russell
RNA transcript processing is an important stage in the gene expression pathway of all organisms and is subject to various mechanisms of control that influence the final levels of gene products. RNA processing involves events such as nuclease-mediated cleavage, removal of intervening sequences referred to as introns and modifications to RNA structure (nucleoside modification and editing). In Euglena, RNA transcript processing was initially examined in chloroplasts because of historical interest in the secondary endosymbiotic origin of this organelle in this organism...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28428795/non-canonical-translation-in-plant-rna-viruses
#10
REVIEW
Manuel Miras, W Allen Miller, Verónica Truniger, Miguel A Aranda
Viral protein synthesis is completely dependent upon the host cell's translational machinery. Canonical translation of host mRNAs depends on structural elements such as the 5' cap structure and/or the 3' poly(A) tail of the mRNAs. Although many viral mRNAs are devoid of one or both of these structures, they can still translate efficiently using non-canonical mechanisms. Here, we review the tools utilized by positive-sense single-stranded (+ss) RNA plant viruses to initiate non-canonical translation, focusing on cis-acting sequences present in viral mRNAs...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28428565/small-methyltransferase-rlmh-assembles-a-composite-active-site-to-methylate-a-ribosomal-pseudouridine
#11
Cha San Koh, Rohini Madireddy, Timothy J Beane, Phillip D Zamore, Andrei A Korostelev
Eubacterial ribosomal large-subunit methyltransferase H (RlmH) methylates 23S ribosomal RNA pseudouridine 1915 (Ψ1915), which lies near the ribosomal decoding center. The smallest member of the SPOUT superfamily of methyltransferases, RlmH lacks the RNA recognition domain found in larger methyltransferases. The catalytic mechanism of RlmH enzyme is unknown. Here, we describe the structures of RlmH bound to S-adenosyl-methionine (SAM) and the methyltransferase inhibitor sinefungin. Our structural and biochemical studies reveal catalytically essential residues in the dimer-mediated asymmetrical active site...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28426418/first-report-on-molecular-evidence-of-tylodelphys-cerebralis-diplostomulum-cerebralis-chakrabarti-1968-digenea-diplostomidae-from-snakehead-fish-channa-punctata
#12
Anshu Chaudhary, Richa Tripathi, Shivi Gupta, Hridaya Shanker Singh
Freshwater snakehead fish, Channa punctata (Perciformes: Channidae) from Meerut (U.P.), India were screened for infection with metacercaria from the eye (vitreous humor) and brain (cranial cavity) and were analyzed by molecular methods using PCR and sequencing of the complete internal transcribed spacers (ITS1-5.8S-ITS2) of the ribosomal RNA gene. Recovered metacercariae from sites, vitreous humor and cranial cavity were previously diagnosed as Diplostomulum cerebralis Chakrabarti, 1968 on the basis of morphological characteristics...
June 1, 2017: Acta Parasitologica
https://www.readbyqxmd.com/read/28425179/resilience-of-the-prokaryotic-microbial-community-of-acropora-digitifera-to-elevated-temperature
#13
Andrian P Gajigan, Leomir A Diaz, Cecilia Conaco
The coral is a holobiont formed by the close interaction between the coral animal and a diverse community of microorganisms, including dinoflagellates, bacteria, archaea, fungi, and viruses. The prokaryotic symbionts of corals are important for host fitness but are also highly sensitive to changes in the environment. In this study, we used 16S ribosomal RNA (rRNA) sequencing to examine the response of the microbial community associated with the coral, Acropora digitifera, to elevated temperature. The A. digitifera microbial community is dominated by operational taxonomic unit (OTUs) affiliated with classes Alphaproteobacteria and Gammaproteobacteria...
April 20, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28423325/rapid-genome-wide-recruitment-of-rna-polymerase-ii-drives-transcription-splicing-and-translation-events-during-t-cell-responses
#14
Kathrin Davari, Johannes Lichti, Christian Gallus, Franziska Greulich, N Henriette Uhlenhaut, Matthias Heinig, Caroline C Friedel, Elke Glasmacher
Activation of immune cells results in rapid functional changes, but how such fast changes are accomplished remains enigmatic. By combining time courses of 4sU-seq, RNA-seq, ribosome profiling (RP), and RNA polymerase II (RNA Pol II) ChIP-seq during T cell activation, we illustrate genome-wide temporal dynamics for ∼10,000 genes. This approach reveals not only immediate-early and posttranscriptionally regulated genes but also coupled changes in transcription and translation for >90% of genes. Recruitment, rather than release of paused RNA Pol II, primarily mediates transcriptional changes...
April 18, 2017: Cell Reports
https://www.readbyqxmd.com/read/28422071/comparative-analysis-of-the-complete-chloroplast-genome-of-four-endangered-herbals-of-notopterygium
#15
Jiao Yang, Ming Yue, Chuan Niu, Xiong-Feng Ma, Zhong-Hu Li
Notopterygium H. de Boissieu (Apiaceae) is an endangered perennial herb endemic to China. A good knowledge of phylogenetic evolution and population genomics is conducive to the establishment of effective management and conservation strategies of the genus Notopterygium. In this study, the complete chloroplast (cp) genomes of four Notopterygium species (N. incisum C. C. Ting ex H. T. Chang, N. oviforme R. H. Shan, N. franchetii H. de Boissieu and N. forrestii H. Wolff) were assembled and characterized using next-generation sequencing...
April 19, 2017: Genes
https://www.readbyqxmd.com/read/28421090/comparative-genomics-and-phylogenomics-of-east-asian-tulips-amana-liliaceae
#16
Pan Li, Rui-Sen Lu, Wu-Qin Xu, Tetsuo Ohi-Toma, Min-Qi Cai, Ying-Xiong Qiu, Kenneth M Cameron, Cheng-Xin Fu
The genus Amana Honda (Liliaceae), when it is treated as separate from Tulipa, comprises six perennial herbaceous species that are restricted to China, Japan and the Korean Peninsula. Although all six Amana species have important medicinal and horticultural uses, studies focused on species identification and molecular phylogenetics are few. Here we report the nucleotide sequences of six complete Amana chloroplast (cp) genomes. The cp genomes of Amana range from 150,613 bp to 151,136 bp in length, all including a pair of inverted repeats (25,629-25,859 bp) separated by the large single-copy (81,482-82,218 bp) and small single-copy (17,366-17,465 bp) regions...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28420964/identification-of-the-spinal-expression-profile-of-non-coding-rnas-involved-in-neuropathic-pain-following-spared-nerve-injury-by-sequence-analysis
#17
Jun Zhou, Qingming Xiong, Hongtao Chen, Chengxiang Yang, Youling Fan
Neuropathic pain (NP) is caused by damage to the nervous system, resulting in aberrant pain, which is associated with gene expression changes in the sensory pathway. However, the molecular mechanisms are not fully understood. A non-coding Ribose Nucleic Acid (ncRNA) is an RNA molecule that is not translated into a protein. NcRNAs are involved in many cellular processes, and mutations or imbalances of the repertoire within the body can cause a variety of diseases. Although ncRNAs have recently been shown to play a role in NP pathogenesis, the specific effects of ncRNAs in NP remain largely unknown...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28420090/toxins-of-prokaryotic-toxin-antitoxin-systems-with-sequence-specific-endoribonuclease-activity
#18
REVIEW
Hisako Masuda, Masayori Inouye
Protein translation is the most common target of toxin-antitoxin system (TA) toxins. Sequence-specific endoribonucleases digest RNA in a sequence-specific manner, thereby blocking translation. While past studies mainly focused on the digestion of mRNA, recent analysis revealed that toxins can also digest tRNA, rRNA and tmRNA. Purified toxins can digest single-stranded portions of RNA containing recognition sequences in the absence of ribosome in vitro. However, increasing evidence suggests that in vivo digestion may occur in association with ribosomes...
April 14, 2017: Toxins
https://www.readbyqxmd.com/read/28418308/chromosomal-16s-ribosomal-rna-methyltransferase-rmte1-in-escherichia-coli-sequence-type-448
#19
Bin Li, Marissa P Pacey, Yohei Doi
We identified rmtE1, an uncommon 16S ribosomal methyltransferase gene, in an aminoglycoside- and cephalosporin-resistant Escherichia coli sequence type 448 clinical strain co-harboring blaCMY-2. Long-read sequencing revealed insertion of a 101,257-bp fragment carrying both resistance genes to the chromosome. Our findings underscore E. coli sequence type 448 as a potential high-risk multidrug-resistant clone.
May 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28416566/structure-of-deah-rha-atpase-prp43p-bound-to-rna-implicates-a-pair-of-hairpins-and-motif-va-in-translocation-along-rna
#20
Yangzi He, Jonathan P Staley, Gregers Rom Andersen, Klaus H Nielsen
Three families of nucleic acid-dependent ATPases (DEAH/RHA, Ski2-like and NS3/NPH-II), termed the DExH ATPases, are thought to execute myriad functions by processive, ATP-dependent, 3' to 5' translocation along single-stranded nucleic acid. While the mechanism of translocation of the viral NS3/NPH-II family has been studied extensively, it has not been clear if or how the principles that have emerged for this family extend to the other two families. Here we report the crystal structure of the yeast DEAH/RHA family ATPase Prp43p, which functions in splicing and ribosome biogenesis, in complex with poly-uracil and a non-hydrolysable ATP analogue...
April 17, 2017: RNA
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