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Ribosome profiling

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https://www.readbyqxmd.com/read/28735410/rhizosphere-sampling-protocols-for-microbiome-16s-18s-its-rrna-library-preparation-and-enrichment-for-the-isolation-of-drought-tolerance-promoting-microbes
#1
Venkatachalam Lakshmanan, Prasun Ray, Kelly D Craven
Natural plant microbiomes are abundant and have a remarkably robust composition, both as epiphytes on the plant surface and as endophytes within plant tissues. Microbes in the former "habitat" face limited nutrients and harsh environmental conditions, while those in the latter likely lead a more sheltered existence. The most populous and diverse of these microbiomes are associated with the zone around the plant roots, commonly referred to as the rhizosphere. A majority of recent studies characterize these plant-associated microbiomes by community profiling of bacteria and fungi, using amplicon-based marker genes and next-generation sequencing (NGS)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28735396/isolation-of-polysomal-rna-for-analyzing-stress-responsive-genes-regulated-at-the-translational-level-in-plants
#2
Yong-Fang Li, Ramamurthy Mahalingam, Ramanjulu Sunkar
Alteration of gene expression is an essential mechanism, which allows plants to respond and adapt to adverse environmental conditions. Transcriptome and proteome analyses in plants exposed to abiotic stresses revealed that protein levels are not correlated with the changes in corresponding mRNAs, indicating regulation at translational level is another major regulator for gene expression. Analysis of translatome, which refers to all mRNAs associated with ribosomes, thus has the potential to bridge the gap between transcriptome and proteome...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28729959/shot-gun-proteome-and-transcriptome-mapping-of-the-jujube-floral-organ-and-identification-of-a-pollen-specific-s-locus-f-box-gene
#3
Ruihong Chen, Guoliang Chen, Jian Huang
The flower is a plant reproductive organ that forms part of the fruit produced as the flowering season ends. While the number and identity of proteins expressed in a jujube (Ziziphus jujuba Mill.) flower is currently unknown, integrative proteomic and transcriptomic analyses provide a systematic strategy of characterizing the floral biology of plants. We conducted a shotgun proteomic analysis on jujube flowers by using a filter-aided sample preparation tryptic digestion, followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS)...
2017: PeerJ
https://www.readbyqxmd.com/read/28729000/airway-microbiota-signals-anabolic-and-catabolic-remodeling-in-the-transplanted-lung
#4
Stéphane Mouraux, Eric Bernasconi, Céline Pattaroni, Angela Koutsokera, John-David Aubert, Johanna Claustre, Christophe Pison, Pierre-Joseph Royer, Antoine Magnan, Romain Kessler, Christian Benden, Paola M Soccal, Benjamin J Marsland, Laurent P Nicod
BACKGROUND: Homeostatic turnover of the extracellular matrix conditions the structure and function of the healthy lung. In lung transplantation, long-term management remains limited by Chronic Lung Allograft Dysfunction (CLAD), an umbrella term used for a heterogeneous entity ultimately associated with pathological airway and/or parenchyma remodeling. OBJECTIVE: To assess whether the local cross-talk between the pulmonary microbiota and host cells is a key determinant in the control of lower airway remodeling post-transplantation...
July 17, 2017: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28723662/acetyl-lupeolic-acid-inhibits-akt-signaling-and-induces-apoptosis-in-chemoresistant-prostate-cancer-cells-in-vitro-and-in-vivo
#5
Claudia Schmidt, Cornelia Loos, Lu Jin, Michael Schmiech, Christoph Q Schmidt, Menna El Gaafary, Tatiana Syrovets, Thomas Simmet
The triterpenoid acetyl-lupeolic acid (ac-LA) isolated from the oleogum resin of Boswellia carterii reduced the viability of a panel of cancer cell lines more efficiently than lupeol. There was no detectable intracellular conversion of ac-LA to lupeol and vice versa. In contrast to docetaxel, ac-LA did not induce selection of treatment-resistant cancer cells. By various parameters including DNA fragmentation, ac-LA was shown to induce apoptosis in androgen-independent PC-3 cells, whereas in MDA-MB-231 breast cancer cells, ac-LA led to cell accumulation in the G2/M phase of the cell cycle, but not to apoptosis...
July 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28720757/integrative-analyses-of-translatome-and-transcriptome-reveal-important-translational-controls-in-brown-and-white-adipose-regulated-by-micrornas
#6
David W Reid, Dan Xu, Peng Chen, Hongyuan Yang, Lei Sun
The epidemic of obesity and diabetes has markedly spurred the research interest in adipocyte biology. Brown adipocytes are specialized for energy expenditure and of therapeutic interest for treatment of metabolic diseases, but how brown adipocytes are distinguished from white adipocytes at the level of translational regulation remains poorly understood. To systemically determine the translational control of gene expression in adipose tissue, we performed ribosome profiling and RNA-seq in parallel to depict the translatome and transcriptome changes during primary brown and white adipogenesis, and between brown and white adipose tissue...
July 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28713914/systematic-identification-of-human-housekeeping-genes-possibly-useful-as-references-in-gene-expression-studies
#7
Maria Caracausi, Allison Piovesan, Francesca Antonaros, Pierluigi Strippoli, Lorenza Vitale, Maria Chiara Pelleri
The ideal reference, or control, gene for the study of gene expression in a given organism should be expressed at a medium‑high level for easy detection, should be expressed at a constant/stable level throughout different cell types and within the same cell type undergoing different treatments, and should maintain these features through as many different tissues of the organism. From a biological point of view, these theoretical requirements of an ideal reference gene appear to be best suited to housekeeping (HK) genes...
September 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28710887/elfamycins-inhibitors-of-elongation-factor-tu
#8
REVIEW
Samantha M Prezioso, Nicole E Brown, Joanna B Goldberg
Elfamycins are a relatively understudied group of antibiotics that target the essential process of translation through impairment of EF-Tu function. For the most part, the utility of these compounds has been as laboratory tools for the study of EF-Tu and the ribosome, as their poor pharmacokinetic profile and solubility has prevented implementation as therapeutic agents. However, due to the slowing of the antibiotic pipeline and the rapid emergence of resistance to approved antibiotics, this group is being reconsidered...
July 15, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28710588/identification-and-molecular-characterization-of-a-trans-acting-small-interfering-rna-producing-locus-regulating-leaf-rust-responsive-gene-expression-in-wheat-triticum-aestivum-l
#9
Summi Dutta, Dhananjay Kumar, Shailendra Jha, Kumble Vinod Prabhu, Manish Kumar, Kunal Mukhopadhyay
A novel leaf rust responsive ta-siRNA-producing locus was identified in wheat showing similarity to 28S rRNA and generated four differentially expressing ta-siRNAs by phasing which targeted stress responsive genes. Trans-acting-small interfering RNAs (Ta-siRNAs) are plant specific molecules generally involved in development and are also stress responsive. Ta-siRNAs identified in wheat till date are all responsive to abiotic stress only. Wheat cultivation is severely affected by rusts and leaf rust particularly affects grain filling...
July 14, 2017: Planta
https://www.readbyqxmd.com/read/28708998/profiling-ssb-nascent-chain-interactions-reveals-principles-of-hsp70-assisted-folding
#10
Kristina Döring, Nabeel Ahmed, Trine Riemer, Harsha Garadi Suresh, Yevhen Vainshtein, Markus Habich, Jan Riemer, Matthias P Mayer, Edward P O'Brien, Günter Kramer, Bernd Bukau
The yeast Hsp70 chaperone Ssb interacts with ribosomes and nascent polypeptides to assist protein folding. To reveal its working principle, we determined the nascent chain-binding pattern of Ssb at near-residue resolution by in vivo selective ribosome profiling. Ssb associates broadly with cytosolic, nuclear, and hitherto unknown substrate classes of mitochondrial and endoplasmic reticulum (ER) nascent proteins, supporting its general chaperone function. Ssb engages most substrates by multiple binding-release cycles to a degenerate sequence enriched in positively charged and aromatic amino acids...
July 13, 2017: Cell
https://www.readbyqxmd.com/read/28708522/itraq-based-proteomic-profiling-of-granulosa-cells-from-lamb-and-ewe-after-superstimulation
#11
Jiapeng Lin, Yangsheng Wu, Bing Han, Ying Chen, Liqin Wang, Xiaolin Li, Mingjun Liu, Juncheng Huang
The number of oocytes obtained from lambs after FSH treatment is far greater than those acquired from adult ewes. However, these oocytes typically have reduced viability in comparison with adult ewe oocytes. However, the molecular mechanisms of differences in viability between lamb and ewe oocytes remain unknown. In the present research, we applied iTRAQ coupled with LC-MS/MS proteomic analysis in order to investigate the proteomic expression profile of granulosa cells from lambs and ewes following stimulation with FSH...
June 10, 2017: Theriogenology
https://www.readbyqxmd.com/read/28705956/rapid-recovery-gene-downregulation-during-excess-light-stress-and-recovery-in-arabidopsis
#12
Peter Alexander Crisp, Diep Ganguly, Aaron B Smith, Kevin D Murray, Gonzalo M Estavillo, Iain R Searle, Ethan Ford, Ozren Bogdanović, Ryan Lister, Justin O Borevitz, Steven R Eichten, Barry J Pogson
Stress recovery may prove to be a promising approach to increase plant performance, and theoretically, mRNA instability may facilitate faster recovery. Transcriptome (RNA-seq, qPCR, sRNA-seq, PARE) and methylome profiling during repeated excess-light stress and recovery was performed at intervals as short as three minutes. We demonstrate that 87% of the stress-upregulated mRNAs analysed exhibit very rapid recovery. For instance, HSP101 abundance declined two-fold every 5.1 minutes. We term this phenomenon Rapid Recovery Gene Downregulation (RRGD), whereby mRNA abundance rapidly decreases promoting transcriptome resetting...
July 13, 2017: Plant Cell
https://www.readbyqxmd.com/read/28699725/evaluation-of-candidate-reference-genes-for-quantitative-expression-studies-in-asian-seabass-lates-calcarifer-during-ontogenesis-and-in-tissues-of-healthy-and-infected-fishes
#13
Anutosh Paria, Jie Dong, P P Suresh Babu, M Makesh, Aparna Chaudhari, A R Thirunavukkarasu, C S Purushothaman, K V Rajendran
Quantitative real-time PCR (qRT-PCR), used to determine the gene expression profile, is an important tool in functional genomic research, including fishes. To obtain more robust and meaningful result, the best possible normalization of the data is of utmost significance. In the present study, we have evaluated the potential of five commonly used housekeeping genes i.e., elongation factor 1-α (EF1A), β-Actin (ACTB), 18S ribosomal RNA (18S), glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and β-2-Microglobulin (B2M) in normal physiological conditions, developmental stages and in response to bacterial infection in Asian seabass, Lates calcarifer (Bloch), an important food fish cultured in the Asia-Pacific region...
September 2016: Indian Journal of Experimental Biology
https://www.readbyqxmd.com/read/28698797/new-technologies-accelerate-the-exploration-of-non-coding-rnas-in-horticultural-plants
#14
REVIEW
Degao Liu, Ritesh Mewalal, Rongbin Hu, Gerald A Tuskan, Xiaohan Yang
Non-coding RNAs (ncRNAs), that is, RNAs not translated into proteins, are crucial regulators of a variety of biological processes in plants. While protein-encoding genes have been relatively well-annotated in sequenced genomes, accounting for a small portion of the genome space in plants, the universe of plant ncRNAs is rapidly expanding. Recent advances in experimental and computational technologies have generated a great momentum for discovery and functional characterization of ncRNAs. Here we summarize the classification and known biological functions of plant ncRNAs, review the application of next-generation sequencing (NGS) technology and ribosome profiling technology to ncRNA discovery in horticultural plants and discuss the application of new technologies, especially the new genome-editing tool clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems, to functional characterization of plant ncRNAs...
2017: Horticulture Research
https://www.readbyqxmd.com/read/28698213/gene-expression-profiles-of-brain-endothelial-cells-during-embryonic-development-at-bulk-and-single-cell-levels
#15
Mike Hupe, Minerva Xueting Li, Susanne Kneitz, Daria Davydova, Chika Yokota, Julianna Kele-Olovsson, Belma Hot, Jan M Stenman, Manfred Gessler
The blood-brain barrier is a dynamic interface that separates the brain from the circulatory system, and it is formed by highly specialized endothelial cells. To explore the molecular mechanisms defining the unique nature of vascular development and differentiation in the brain, we generated high-resolution gene expression profiles of mouse embryonic brain endothelial cells using translating ribosome affinity purification and single-cell RNA sequencing. We compared the brain vascular translatome with the vascular translatomes of other organs and analyzed the vascular translatomes of the brain at different time points during embryonic development...
July 11, 2017: Science Signaling
https://www.readbyqxmd.com/read/28697813/multilocus-sequence-typing-and-clonal-population-genetic-structure-of-cyclospora-cayetanensis-in-humans
#16
Junqiang Li, Yankai Chang, K E Shi, Rongjun Wang, Kanda Fu, Shan Li, Jinling Xu, Liting Jia, Zhenxin Guo, Longxian Zhang
To investigate the prevalence of Cyclospora cayetanensis in a longitudinal study and to conduct a population genetic analysis, fecal specimens from 6579 patients were collected during the cyclosporiasis - prevalent seasons in two urban areas of central China in 2011-2015. The overall incidence of C. cayetanensis infection was 1·2% (76/6579): 1·6% (50/3173) in Zhengzhou and 0·8% (26/3406) in Kaifeng (P 0·05). All the isolates clustered in the C. cayetanensis clade based on the small subunit ribosomal RNA gene sequence phylogenetic analysis...
July 12, 2017: Parasitology
https://www.readbyqxmd.com/read/28696283/suboptimal-t-cell-receptor-signaling-compromises-protein-translation-ribosome-biogenesis-and-proliferation-of-mouse-cd8-t-cells
#17
Thomas C J Tan, John Knight, Thomas Sbarrato, Kate Dudek, Anne E Willis, Rose Zamoyska
Global transcriptomic and proteomic analyses of T cells have been rich sources of unbiased data for understanding T-cell activation. Lack of full concordance of these datasets has illustrated that important facets of T-cell activation are controlled at the level of translation. We undertook translatome analysis of CD8 T-cell activation, combining polysome profiling and microarray analysis. We revealed that altering T-cell receptor stimulation influenced recruitment of mRNAs to heavy polysomes and translation of subsets of genes...
July 10, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28693133/overexpression-of-the-x-linked-ribosomal-protein-s4-predicts-poor-prognosis-in-patients-with-intrahepatic-cholangiocarcinoma
#18
Jie Kuang, Qin-Yu Li, Fei Fan, Ning-Jia Shen, Yong-Jie Zhan, Zhao-Hui Tang, Wen-Long Yu
X-linked ribosomal protein S4 (RPS4X) has previously been reported to be associated with cisplatin resistance and clinical outcome in bladder and ovarian cancer. However, the value of RPS4X as a diagnostic and prognostic marker in intrahepatic cholangiocarcinoma (ICC) has not yet been investigated. The present study evaluated the expression pattern, and diagnostic and prognostic value of RPS4X in patients with ICC. Retrospective analysis was performed for a total of 201 patients with intrahepatic cholangiocarcinoma, and 8 patients with inflammation of the bile duct...
July 2017: Oncology Letters
https://www.readbyqxmd.com/read/28690927/quantitative-proteome-level-analysis-of-paulownia-witches-broom-disease-with-methyl-methane-sulfonate-assistance-reveals-diverse-metabolic-changes-during-the-infection-and-recovery-processes
#19
Zhe Wang, Wenshan Liu, Guoqiang Fan, Xiaoqiao Zhai, Zhenli Zhao, Yanpeng Dong, Minjie Deng, Yabing Cao
Paulownia witches' broom (PaWB) disease caused by phytoplasma is a fatal disease that leads to considerable economic losses. Although there are a few reports describing studies of PaWB pathogenesis, the molecular mechanisms underlying phytoplasma pathogenicity in Paulownia trees remain uncharacterized. In this study, after building a transcriptome database containing 67,177 sequences, we used isobaric tags for relative and absolute quantification (iTRAQ) to quantify and analyze the proteome-level changes among healthy P...
2017: PeerJ
https://www.readbyqxmd.com/read/28683101/nutritional-and-reproductive-signaling-revealed-by-comparative-gene-expression-analysis-in-chrysopa-pallens-rambur-at-different-nutritional-statuses
#20
Benfeng Han, Shen Zhang, Fanrong Zeng, Jianjun Mao
BACKGROUND: The green lacewing, Chrysopa pallens Rambur, is one of the most important natural predators because of its extensive spectrum of prey and wide distribution. However, what we know about the nutritional and reproductive physiology of this species is very scarce. RESULTS: By cDNA amplification and Illumina short-read sequencing, we analyzed transcriptomes of C. pallens female adult under starved and fed conditions. In total, 71236 unigenes were obtained with an average length of 833 bp...
2017: PloS One
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