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Ribosome profiling

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https://www.readbyqxmd.com/read/28228255/can1-arginine-permease-deficiency-extends-yeast-replicative-lifespan-via-translational-activation-of-stress-response-genes
#1
Carine Beaupere, Brian M Wasko, Jared Lorusso, Brian K Kennedy, Matt Kaeberlein, Vyacheslav M Labunskyy
Transcriptional regulation plays an important role in the control of gene expression during aging. However, translation efficiency likely plays an equally important role in determining protein abundance, but it has been relatively understudied in this context. Here, we used RNA sequencing (RNA-seq) and ribosome profiling to investigate the role of translational regulation in lifespan extension by CAN1 gene deletion in yeast. Through comparison of the transcriptional and translational changes in cells lacking CAN1 with other long-lived mutants, we were able to identify critical regulatory factors, including transcription factors and mRNA-binding proteins, that coordinate transcriptional and translational responses...
February 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/28213609/gut-microbial-profile-is-altered-in-primary-biliary-cholangitis-and-partially-restored-after-udca-therapy
#2
Ruqi Tang, Yiran Wei, Yanmei Li, Weihua Chen, Haoyan Chen, Qixia Wang, Fan Yang, Qi Miao, Xiao Xiao, Haiyan Zhang, Min Lian, Xiang Jiang, Jun Zhang, Qin Cao, Zhuping Fan, Maoying Wu, Dekai Qiu, Jing-Yuan Fang, Aftab Ansari, M Eric Gershwin, Xiong Ma
OBJECTIVE: A close relationship between gut microbiota and some chronic liver disorders has recently been described. Herein, we systematically performed a comparative analysis of the gut microbiome in primary biliary cholangitis (PBC) and healthy controls. DESIGN: We first conducted a cross-sectional study of 60 ursodeoxycholic acid (UDCA) treatment-naïve patients with PBC and 80 matched healthy controls. Second, an independent cohort composed of 19 treatment-naïve patients and 34 controls was used to validate the results...
February 17, 2017: Gut
https://www.readbyqxmd.com/read/28213379/slowed-decay-of-mrnas-enhances-platelet-specific-translation
#3
Eric W Mills, Rachel Green, Nicholas T Ingolia
Platelets are anucleate cytoplasmic fragments that lack genomic DNA, but continue to synthesize protein using a pool of mRNAs, ribosomes, and regulatory small RNAs inherited from the precursor megakaryocyte (MK). The regulatory processes that shape the platelet transcriptome and the full scope of platelet translation have remained elusive. Using RNA-Seq and ribosome profiling of primary human platelets, we show the platelet transcriptome encompasses a subset of transcripts detected by RNA-Seq analysis of in vitro derived MK cells and these platelet-enriched transcripts are broadly occupied by ribosomes...
February 17, 2017: Blood
https://www.readbyqxmd.com/read/28212626/a-global-characterization-of-the-translational-and-transcriptional-programs-induced-by-methionine-restriction-through-ribosome-profiling-and-rna-seq
#4
Ke Zou, Qi Ouyang, Hao Li, Jiashun Zheng
BACKGROUND: Among twenty amino acids, methionine has a special role as it is coded by the translation initiation codon and methionyl-tRNAi (Met-tRNAi) is required for the assembly of the translation initiation complex. Thus methionine may play a special role in global gene regulation. Methionine has also been known to play important roles in cell growth, development, cancer, and aging. In this work, we characterize the translational and transcriptional programs induced by methionine restriction (MetR) and investigate the potential mechanisms through which methionine regulates gene expression, using the budding yeast S...
February 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28201982/transcriptome-profile-of-rat-genes-in-injured-spinal-cord-at-different-stages-by-rna-sequencing
#5
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/28198673/diversity-and-enterotype-in-gut-bacterial-community-of-adults-in-taiwan
#6
Chao Liang, Han-Chi Tseng, Hui-Mei Chen, Wei-Chi Wang, Chih-Min Chiu, Jen-Yun Chang, Kuan-Yi Lu, Shun-Long Weng, Tzu-Hao Chang, Chao-Hsiang Chang, Chen-Tsung Weng, Hwei-Ming Wang, Hsien-Da Huang
BACKGROUND: Gastrointestinal microbiota, particularly gut microbiota, is associated with human health. The biodiversity of gut microbiota is affected by ethnicities and environmental factors such as dietary habits or medicine intake, and three enterotypes of the human gut microbiome were announced in 2011. These enterotypes are not significantly correlated with gender, age, or body weight but are influenced by long-term dietary habits. However, to date, only two enterotypes (predominantly consisting of Bacteroides and Prevotella) have shown these characteristics in previous research; the third enterotype remains ambiguous...
January 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28194024/regnase-1-a-rapid-response-ribonuclease-regulating-inflammation-and-stress-responses
#7
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/28193672/translation-of-poly-a-tails-leads-to-precise-mrna-cleavage
#8
Nicholas R Guydosh, Rachel Green
Translation of poly(A) tails leads to mRNA cleavage but the mechanism and global pervasiveness of this "nonstop/no-go" decay process is not understood. Here we performed ribosome profiling (in a yeast strain lacking exosome function) of short 15-18 nt mRNA footprints to identify ribosomes stalled at 3' ends of mRNA decay intermediates. In this background, we found mRNA cleavage extending hundreds of nucleotides upstream of ribosome stalling in poly(A) and predominantly in one reading frame. These observations suggest that decay-triggering endonucleolytic cleavage is closely associated with the ribosome...
February 13, 2017: RNA
https://www.readbyqxmd.com/read/28183172/dynamic-changes-of-yak-bos-grunniens-gut-microbiota-during-growth-revealed-by-pcr-dgge-and-metagenomics
#9
Yuanyang Nie, Zhiwei Zhou, Jiuqiang Guan, Baixue Xia, Xiaolin Luo, Yang Yang, Yu Fu, Qun Sun
Objective: To understand the dynamic structure, function, and influence on nutrient metabolism in hosts, it was crucial to assess the genetic potential of gut microbial community in yaks of different ages. Method: The denaturing gradient gel electrophoresis (DGGE) profiles and Illumina-based metagenomic sequencing on colon content of 15 semi-domestic yaks were investigated. Unweighted pairwise grouping method with mathematical averages (UPGMA) clustering and principal component analysis (PCA) were used to analize the DGGE fingerprint...
January 26, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28178033/social-influences-on-prevotella-and-the-gut-microbiome-of-young-monkeys
#10
Wellington Z Amaral, Gabriele R Lubach, Alexandra Proctor, Mark Lyte, Gregory J Phillips, Christopher L Coe
OBJECTIVE: Our aim was to evaluate the bacterial profiles of young monkeys as they were weaned into peer groups with a particular focus on Prevotella, an important taxon in both human and nonhuman primates. The weaning of infants and increased social contact with peers is a developmental stage that is likely to affect the gut microbiome. METHODS: Gut bacteria were assessed in 63 rhesus monkeys living in social groups comprised of 4-7 individuals. Two groups were assessed prospectively on Day 1 and 2 weeks after rehousing away from the mother and group formation...
February 7, 2017: Psychosomatic Medicine
https://www.readbyqxmd.com/read/28174421/streptomyces-euryhalinus-sp-nov-a-new-actinomycete-isolated-from-a-mangrove-forest
#11
Kaushik Biswas, Jayanta D Choudhury, Riddhi Mahansaria, Malay Saha, Joydeep Mukherjee
A Gram-positive, aerobic, non-motile actinomycete (strain MS 3/20(T)) was isolated from the sediment of the Sundarbans mangrove forest in India. On International Streptomyces Project (ISP) medium 2, the isolate produced yellowish brown to red aerial hyphae that carried spiny-surfaced spores in a retinaculum-apertum arrangement. Whole-cell hydrolysate of the strain contained LL-diaminopimelic acid and galactose. Predominant menaquinones were MK-9(H8) and MK-9(H6). Diagnostic polar lipids were glycolipid, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, unidentified phospholipid and unidentified amino lipid...
February 8, 2017: Journal of Antibiotics
https://www.readbyqxmd.com/read/28173612/expression-profile-of-mammalian-target-of-rapamycin-related-proteins-in-graft-biopsy-specimens-significance-for-predicting-interstitial-fibrosis-after-kidney-transplantation
#12
Satoshi Ogawa, Takeshi Ishimura, Hideaki Miyake, Masato Fujisawa
OBJECTIVE: To investigate the influence of the expression profile of mammalian target of rapamycin-related proteins on the development of interstitial fibrosis after kidney transplantation. METHODS: Immunohistochemical staining was carried out to evaluate the expression of five mammalian target of rapamycin-related proteins (phosphorylated-Akt, Ras homolog enriched in brain, phosphorylated-mammalian target of rapamycin, phosphorylated-p70 ribosomal S6 kinase and phosphorylated-4E binding protein 1) in graft biopsy specimens obtained from 77 patients at 3 months after kidney transplantation...
February 7, 2017: International Journal of Urology: Official Journal of the Japanese Urological Association
https://www.readbyqxmd.com/read/28169522/entropy-and-enzyme-catalysis
#13
Johan Åqvist, Masoud Kazemi, Geir Villy Isaksen, Bjørn Olav Brandsdal
The role played by entropy for the enormous rate enhancement achieved by enzymes has been debated for many decades. There are, for example, several confirmed cases where the activation free energy is reduced by around 10 kcal/mol due to entropic effects, corresponding to a rate enhancement of ∼10(7) compared to the uncatalyzed reaction. However, despite substantial efforts from both the experimental and theoretical side, no real consensus has been reached regarding the origin of such large entropic contributions to enzyme catalysis...
February 7, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28166799/toll-like-receptor-3-activation-selectively-reverses-hiv-latency-in-microglial-cells
#14
David Alvarez-Carbonell, Yoelvis Garcia-Mesa, Stephanie Milne, Biswajit Das, Curtis Dobrowolski, Roxana Rojas, Jonathan Karn
BACKGROUND: Multiple toll-like receptors (TLRs) are expressed in cells of the monocytic lineage, including microglia, which constitute the major reservoir for human immunodeficiency virus (HIV) infection in the brain. We hypothesized that TLR receptor mediated responses to inflammatory conditions by microglial cells in the central nervous system (CNS) are able to induce latent HIV proviruses, and contribute to the etiology of HIV-associated neurocognitive disorders. RESULTS: Newly developed human microglial cell lines (hµglia), obtained by immortalizing human primary microglia with simian virus-40 (SV40) large T antigen and the human telomerase reverse transcriptase, were used to generate latently infected cells using a single-round HIV virus carrying a green fluorescence protein reporter (hµglia/HIV, clones HC01 and HC69)...
February 6, 2017: Retrovirology
https://www.readbyqxmd.com/read/28166707/isolation-and-partial-characterization-of-streptococcus-suis-from-clinical-cases-in-cattle
#15
Ogi Okwumabua, Hanna Peterson, Hui-Min Hsu, Phil Bochsler, Melissa Behr
Sixteen isolates of gram-positive, coccoid bacteria were obtained from clinical cases of diverse conditions in cattle and identified as Streptococcus suis using 16S ribosomal DNA gene sequencing and other bacterial identification methods. None of the isolates could be assigned to any of the known S. suis capsular types. Virulence-associated gene profiling that targeted muramidase-released protein, extracellular protein factor, suilysin, 89-kb pathogenicity island, and arginine deiminase ( arcA) genes were negative except for 1 isolate that was arcA positive...
January 1, 2017: Journal of Veterinary Diagnostic Investigation
https://www.readbyqxmd.com/read/28155666/ribotagger-fast-and-unbiased-16s-18s-profiling-using-whole-community-shotgun-metagenomic-or-metatranscriptome-surveys
#16
Chao Xie, Chin Lui Wesley Goi, Daniel H Huson, Peter F R Little, Rohan B H Williams
BACKGROUND: Taxonomic profiling of microbial communities is often performed using small subunit ribosomal RNA (SSU) amplicon sequencing (16S or 18S), while environmental shotgun sequencing is often focused on functional analysis. Large shotgun datasets contain a significant number of SSU sequences and these can be exploited to perform an unbiased SSU--based taxonomic analysis. RESULTS: Here we present a new program called RiboTagger that identifies and extracts taxonomically informative ribotags located in a specified variable region of the SSU gene in a high-throughput fashion...
December 22, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28148822/transcriptional-responses-to-hyperplastic-mrl-signalling-in-drosophila
#17
Vincent Jonchère, Nada Alqadri, John Herbert, Lauren Dodgson, David Mason, Giovanni Messina, Francesco Falciani, Daimark Bennett
Recent work has implicated the actin cytoskeleton in tissue size control and tumourigenesis, but how changes in actin dynamics contribute to hyperplastic growth is still unclear. Overexpression of Pico, the only Drosophila Mig-10/RIAM/Lamellipodin adapter protein family member, has been linked to tissue overgrowth via its effect on the myocardin-related transcription factor (Mrtf), an F-actin sensor capable of activating serum response factor (SRF). Transcriptional changes induced by acute Mrtf/SRF signalling have been largely linked to actin biosynthesis and cytoskeletal regulation...
February 2017: Open Biology
https://www.readbyqxmd.com/read/28147438/seminal-microbiome-in-men-with-and-without-prostatitis
#18
Reet Mändar, Margus Punab, Paul Korrovits, Silver Türk, Kristo Ausmees, Eleri Lapp, Jens-Konrad Preem, Kristjan Oopkaup, Andres Salumets, Jaak Truu
OBJECTIVES: To profile the seminal microbiome applying next generation sequencing. METHODS: Semen samples of 67 men were involved in the study (21 men with and 46 men without prostatitis). Seminal microbiomes were profiled applying the method that uses combinatorial sequence tags attached to polymerase chain reaction primers that amplify the ribosomal ribonucleic acid V6 region. Amplified polymerase chain reaction products were sequenced using an Illumina paired-end protocol on HiSeq2000 platform...
February 1, 2017: International Journal of Urology: Official Journal of the Japanese Urological Association
https://www.readbyqxmd.com/read/28145468/the-srnaome-mining-revealed-existence-of-unique-signature-small-rnas-derived-from-5-8srrna-from-piper-nigrum-and-other-plant-lineages
#19
Srinivasan Asha, E V Soniya
Small RNAs derived from ribosomal RNAs (srRNAs) are rarely explored in the high-throughput data of plant systems. Here, we analyzed srRNAs from the deep-sequenced small RNA libraries of Piper nigrum, a unique magnoliid plant. The 5' end of the putative long form of 5.8S rRNA (5.8SLrRNA) was identified as the site for biogenesis of highly abundant srRNAs that are unique among the Piperaceae family of plants. A subsequent comparative analysis of the ninety-seven sRNAomes of diverse plants successfully uncovered the abundant existence and precise cleavage of unique rRF signature small RNAs upstream of a novel 5' consensus sequence of the 5...
February 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28138069/ribosome-pausing-arrest-and-rescue-in-bacteria-and-eukaryotes
#20
REVIEW
Allen R Buskirk, Rachel Green
Ribosomes translate genetic information into polypeptides in several basic steps: initiation, elongation, termination and recycling. When ribosomes are arrested during elongation or termination, the cell's capacity for protein synthesis is reduced. There are numerous quality control systems in place to distinguish between paused ribosomes that need some extra input to proceed and terminally stalled ribosomes that need to be rescued. Here, we discuss similarities and differences in the systems for resolution of pauses and rescue of arrested ribosomes in bacteria and eukaryotes, and how ribosome profiling has transformed our ability to decipher these molecular events...
March 19, 2017: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences
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