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Ribosome profiling

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https://www.readbyqxmd.com/read/28522455/psa3-a-protein-on-the-stromal-face-of-the-thylakoid-membrane-promotes-photosystem-i-accumulation-in-cooperation-with-the-assembly-factor-pyg7
#1
Jie Shen, Rosalind Williams-Carrier, Alice Barkan
Photosystem I (PSI) is a large protein-pigment complex located in the thylakoid membrane in cyanobacteria, plants, and algae. Although the structure and components of PSI are well characterized, mechanisms that orchestrate its assembly are poorly understood. In this study, we discovered a novel nucleus-encoded protein, Photosystem I Assembly 3 (PSA3), that is required for PSI accumulation. PSA3 is conserved among green photosynthetic eukaryotes but is lacking in cyanobacteria. Mutations in the psa3 gene cause the specific loss of PSI in Arabidopsis and maize...
May 18, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28520920/methylation-of-human-eukaryotic-elongation-factor-alpha-eef1a-by-a-member-of-a-novel-protein-lysine-methyltransferase-family-modulates-mrna-translation
#2
Magnus E Jakobsson, Jedrzej Malecki, Benedikt S Nilges, Anders Moen, Sebastian A Leidel, Pål Ø Falnes
Many cellular proteins are methylated on lysine residues and this has been most intensively studied for histone proteins. Lysine methylations on non-histone proteins are also frequent, but in most cases the functional significance of the methylation event, as well as the identity of the responsible lysine (K) specific methyltransferase (KMT), remain unknown. Several recently discovered KMTs belong to the so-called seven-β-strand (7BS) class of MTases and we have here investigated an uncharacterized human 7BS MTase currently annotated as part of the endothelin converting enzyme 2, but which should be considered a separate enzyme...
May 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28516123/polysome-fractionation-to-analyze-mrna-distribution-profiles
#3
Amaresh C Panda, Jennifer L Martindale, Myriam Gorospe
Eukaryotic cells adapt to changes in external or internal signals by precisely modulating the expression of specific gene products. The expression of protein-coding genes is controlled at the transcriptional and post-transcriptional levels. Among the latter steps, the regulation of translation is particularly important in cellular processes that require rapid changes in protein expression patterns. The translational efficiency of mRNAs is altered by RNA-binding proteins (RBPs) and noncoding (nc)RNAs such as microRNAs (Panda et al...
February 5, 2017: Bio-protocol
https://www.readbyqxmd.com/read/28515355/translational-reprogramming-of-colorectal-cancer-cells-induced-by-5-fluorouracil-through-a-mirna-dependent-mechanism
#4
Bash-Imam Zeina, Thérizols Gabriel, Vincent Anne, Lafôrets Florian, Polay Espinoza Micaela, Pion Nathalie, Macari Françoise, Pannequin Julie, David Alexandre, Saurin Jean-Christophe, Hichem C Mertani, Textoris Julien, Auboeuf Didier, Catez Frédéric, Dalla Venezia Nicole, Dutertre Martin, Marcel Virginie, Diaz Jean-Jacques
5-Fluorouracil (5-FU) is a widely used chemotherapeutic drug in colorectal cancer. Previous studies showed that 5-FU modulates RNA metabolism and mRNA expression. In addition, it has been reported that 5-FU incorporates into the RNAs constituting the translational machinery and that 5-FU affects the amount of some mRNAs associated with ribosomes. However, the impact of 5-FU on translational regulation remains unclear. Using translatome profiling, we report that a clinically relevant dose of 5-FU induces a translational reprogramming in colorectal cancer cell lines...
May 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28514447/global-translational-reprogramming-is-a-fundamental-layer-of-immune-regulation-in-plants
#5
Guoyong Xu, George H Greene, Heejin Yoo, Lijing Liu, Jorge Marqués, Jonathan Motley, Xinnian Dong
In the absence of specialized immune cells, the need for plants to reprogram transcription to transition from growth-related activities to defence is well understood. However, little is known about translational changes that occur during immune induction. Using ribosome footprinting, here we perform global translatome profiling on Arabidopsis exposed to the microbe-associated molecular pattern elf18. We find that during this pattern-triggered immunity, translation is tightly regulated and poorly correlated with transcription...
May 17, 2017: Nature
https://www.readbyqxmd.com/read/28514446/identification-of-preoptic-sleep-neurons-using-retrograde-labelling-and-gene-profiling
#6
Shinjae Chung, Franz Weber, Peng Zhong, Chan Lek Tan, Thuc Nghi Nguyen, Kevin T Beier, Nikolai Hörmann, Wei-Cheng Chang, Zhe Zhang, Johnny Phong Do, Shenqin Yao, Michael J Krashes, Bosiljka Tasic, Ali Cetin, Hongkui Zeng, Zachary A Knight, Liqun Luo, Yang Dan
In humans and other mammalian species, lesions in the preoptic area of the hypothalamus cause profound sleep impairment, indicating a crucial role of the preoptic area in sleep generation. However, the underlying circuit mechanism remains poorly understood. Electrophysiological recordings and c-Fos immunohistochemistry have shown the existence of sleep-active neurons in the preoptic area, especially in the ventrolateral preoptic area and median preoptic nucleus. Pharmacogenetic activation of c-Fos-labelled sleep-active neurons has been shown to induce sleep...
May 17, 2017: Nature
https://www.readbyqxmd.com/read/28504349/polysome-profiling-of-mab-producing-cho-cell-lines-links-translational-control-of-cell-proliferation-and-recombinant-mrna-loading-onto-ribosomes-with-global-and-recombinant-protein-synthesis
#7
Charlotte L Godfrey, Emma J Mead, Olalekan Daramola, Sarah Dunn, Diane Hatton, Ray Field, Gary Pettman, C Mark Smales
mRNA translation is a key process determining growth, proliferation and duration of a Chinese hamster ovary (CHO) cell culture and influences recombinant protein synthesis rate. During bioprocessing, CHO cells can experience stresses leading to reprogramming of translation and decreased global protein synthesis. Here we apply polysome profiling to determine reprogramming and translational capabilities in host and recombinant monoclonal antibody-producing (mAb) CHO cell lines during batch culture. Recombinant cell lines with the fastest cell specific growth rates were those with the highest global translational efficiency...
May 15, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28490664/inhibiting-the-oncogenic-translation-program-is-an-effective-therapeutic-strategy-in-multiple-myeloma
#8
Salomon Manier, Daisy Huynh, Yu J Shen, Jia Zhou, Timur Yusufzai, Karma Z Salem, Richard Y Ebright, Jiantao Shi, Jihye Park, Siobhan V Glavey, William G Devine, Chia-Jen Liu, Xavier Leleu, Bruno Quesnel, Catherine Roche-Lestienne, John K Snyder, Lauren E Brown, Nathanael Gray, James Bradner, Luke Whitesell, John A Porco, Irene M Ghobrial
Multiple myeloma (MM) is a frequently incurable hematological cancer in which overactivity of MYC plays a central role, notably through up-regulation of ribosome biogenesis and translation. To better understand the oncogenic program driven by MYC and investigate its potential as a therapeutic target, we screened a chemically diverse small-molecule library for anti-MM activity. The most potent hits identified were rocaglate scaffold inhibitors of translation initiation. Expression profiling of MM cells revealed reversion of the oncogenic MYC-driven transcriptional program by CMLD010509, the most promising rocaglate...
May 10, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28490220/solithromycin-cem-101-a-new-fluoroketolide-antibiotic-and-its-role-in-the-treatment-of-gonorrhea
#9
Alexandra M Mancuso, Mona A Gandhi, Judianne Slish
Solithromycin is a macrolide antibiotic that has undergone review for the treatment of community-acquired bacterial pneumonia. Solithromycin is also being investigated and has shown promise for the treatment of gonorrhea. With increasing antibiotic resistance, the development of novel antibiotics to combat infections is essential. The unique ribosome-binding stability of solithromycin and mild side effect profile make this a promising new antibiotic. This article will provide an overview on the mechanism of action, clinical efficacy, and safety of this drug for the treatment of gonorrhea...
January 1, 2017: Journal of Pharmacy Practice
https://www.readbyqxmd.com/read/28483825/replication-of-ribosomal-dna-in-arabidopsis-occurs-both-inside-and-outside-of-the-nucleolus-during-s-phase-progression
#10
Martina Dvořáčková, Berta Raposo, Petr Matula, Joerg Fuchs, Veit Schubert, Vratislav Peška, Bénédicte Desvoyes, Crisanto Gutierrez, Jiří Fajkus
Ribosomal RNA genes (rDNA) have been used as valuable experimental systems in numerous studies. Here we focus on elucidating the spatio-temporal organisation of rDNA replication in Arabidopsis thaliana. To determine the subnuclear distribution of rDNA and the progression of its replication during S phase, we apply a 5-ethynyl-2'-deoxyuridine (EdU) labelling, fluorescence-activated cell sorting, fluorescence in situ hybridization, and structured illumination microscopy. We show that rDNA is replicated inside and outside the nucleolus where active transcription occurs at the same time...
May 8, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28481057/mapping-and-comparing-bacterial-microbiota-in-the-sinonasal-cavity-of-healthy-allergic-rhinitis-and-chronic-rhinosinusitis-subjects
#11
Devyani Lal, Paul Keim, Josie Delisle, Bridget Barker, Matthew A Rank, Nicholas Chia, James M Schupp, John D Gillece, Emily K Cope
BACKGROUND: The role of microbiota in sinonasal inflammation can be further understood by targeted sampling of healthy and diseased subjects. We compared the microbiota of the middle meatus (MM) and inferior meatus (IM) in healthy, allergic rhinitis (AR), and chronic rhinosinusitis (CRS) subjects to characterize intrasubject, intersubject, and intergroup differences. METHODS: Subjects were recruited in the office, and characterized into healthy, AR, and CRS groups...
May 8, 2017: International Forum of Allergy & Rhinology
https://www.readbyqxmd.com/read/28480290/group-b-streptococci-colonization-in-pregnant-guatemalan-women-prevalence-risk-factors-and-vaginal-microbiome
#12
Anne-Marie Rick, Angie Aguilar, Rosita Cortes, Remei Gordillo, Mario Melgar, Gabriela Samayoa-Reyes, Daniel N Frank, Edwin J Asturias
BACKGROUND: Infection causes 1 of every 5 neonatal deaths globally. Group B Streptococcus (GBS) is the most significant pathogen, although little is known about its epidemiology and risk in low-income countries. METHODS: A cross-sectional study in 2015 at a public hospital in Guatemala City enrolled women ≥35 weeks' gestation. Vaginal and rectal swabs were processed using Lim broth and GBS CHROMagar then agglutination testing. Risk factors were assessed using multivariate analysis...
2017: Open Forum Infectious Diseases
https://www.readbyqxmd.com/read/28472935/gene-expression-profile-during-proliferation-and-differentiation-of-rainbow-trout-adipocyte-precursor-cells
#13
Marta Bou, Jerôme Montfort, Aurélie Le Cam, Cécile Rallière, Véronique Lebret, Jean-Charles Gabillard, Claudine Weil, Joaquim Gutiérrez, Pierre-Yves Rescan, Encarnación Capilla, Isabel Navarro
BACKGROUND: Excessive accumulation of adipose tissue in cultured fish is an outstanding problem in aquaculture. To understand the development of adiposity, it is crucial to identify the genes which expression is associated with adipogenic differentiation. Therefore, the transcriptomic profile at different time points (days 3, 8, 15 and 21) along primary culture development of rainbow trout preadipocytes has been investigated using an Agilent trout oligo microarray. RESULTS: Our analysis identified 4026 genes differentially expressed (fold-change >3) that were divided into two major clusters corresponding to the main phases observed during the preadipocyte culture: proliferation and differentiation...
May 4, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28460071/interactive-microbial-distribution-analysis-using-bioatlas
#14
Jesper Beltoft Lund, Markus List, Jan Baumbach
Massive amounts of 16S rRNA sequencing data have been stored in publicly accessible databases, such as GOLD, SILVA, GreenGenes (GG), and the Ribosomal Database Project (RDP). Many of these sequences are tagged with geo-locations. Nevertheless, researchers currently lack a user-friendly tool to analyze microbial distribution in a location-specific context. BioAtlas is an interactive web application that closes this gap between sequence databases, taxonomy profiling and geo/body-location information. It enables users to browse taxonomically annotated sequences across (i) the world map, (ii) human body maps and (iii) user-defined maps...
April 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28460065/sbspksv2-structure-based-sequence-analysis-of-polyketide-synthases-and-non-ribosomal-peptide-synthetases
#15
Shradha Khater, Money Gupta, Priyesh Agrawal, Neetu Sain, Jyoti Prava, Priya Gupta, Mansi Grover, Narendra Kumar, Debasisa Mohanty
Genome guided discovery of novel natural products has been a promising approach for identification of new bioactive compounds. SBSPKS web-server has been a valuable resource for analysis of polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) gene clusters. We have developed an updated version - SBSPKSv2 which is based on comprehensive analysis of sequence, structure and secondary metabolite chemical structure data from 311 experimentally characterized PKS/NRPS gene clusters with known biosynthetic products...
April 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28460002/proteomic-analysis-of-polyribosomes-identifies-splicing-factors-as-potential-regulators-of-translation-during-mitosis
#16
Ranen Aviner, Sarah Hofmann, Tamar Elman, Anjana Shenoy, Tamar Geiger, Ran Elkon, Marcelo Ehrlich, Orna Elroy-Stein
Precise regulation of mRNA translation is critical for proper cell division, but little is known about the factors that mediate it. To identify mRNA-binding proteins that regulate translation during mitosis, we analyzed the composition of polysomes from interphase and mitotic cells using unbiased quantitative mass-spectrometry (LC-MS/MS). We found that mitotic polysomes are enriched with a subset of proteins involved in RNA processing, including alternative splicing and RNA export. To demonstrate that these may indeed be regulators of translation, we focused on heterogeneous nuclear ribonucleoprotein C (hnRNP C) as a test case and confirmed that it is recruited to elongating ribosomes during mitosis...
April 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28458086/effect-of-abattoir-and-cut-on-variations-in-microbial-communities-of-vacuum-packaged-beef
#17
Mandeep Kaur, John P Bowman, Bianca Porteus, Alison L Dann, Mark Tamplin
This report builds on the earlier studies of the shelf-life of chilled Australian vacuum packaged (VP) beef primals (striploin and cube roll), products distinguished in the global marketplace for unusually long shelf-life. Notable findings in those studies were a shelf-life of at least 26weeks at -0.5°C, low microbial counts, and relatively high sensory scores. However, growth rates for total viable counts (TVC) and lactic acid bacteria (LAB) varied among the different abattoirs. The present study adds to these findings, by providing greater definition about temporal changes in bacterial communities using terminal restriction fragment length polymorphism (TRFLP) and clone library analyses of 16S ribosomal RNA (16S rRNA) gene, and measuring statistical associations among abattoir, beef cut, storage time and sensory attributes...
April 22, 2017: Meat Science
https://www.readbyqxmd.com/read/28457515/terminal-restriction-fragment-length-polymorphism-profiling-of-bacterial-flora-derived-from-single-human-hair-shafts-can-discriminate-individuals
#18
Eiji Nishi, Kota Watanabe, Yukihiro Tashiro, Kenji Sakai
Human hairs are the trace evidence most commonly encountered at many crime scenes. However, they have not been effectively utilized for actual criminal investigations because of the low accuracy of their morphological inspection, low detection rate of short tandem repeat (STR) typing, and the problem of heteroplasmy in mitochondrial DNA analysis. Here, we examined the possibility of individual discrimination by comparing profiles of bacterial flora on hair. We carried out the profiling of terminal restriction fragment length polymorphisms (T-RFLP) of the amplified bacterial 16S ribosomal RNA (rRNA) gene from hair samples...
March 2017: Legal Medicine
https://www.readbyqxmd.com/read/28457228/differences-in-gut-microbial-composition-correlate-with-regional-brain-volumes-in-irritable-bowel-syndrome
#19
Jennifer S Labus, Emily B Hollister, Jonathan Jacobs, Kyleigh Kirbach, Numan Oezguen, Arpana Gupta, Jonathan Acosta, Ruth Ann Luna, Kjersti Aagaard, James Versalovic, Tor Savidge, Elaine Hsiao, Kirsten Tillisch, Emeran A Mayer
BACKGROUND: Preclinical and clinical evidence supports the concept of bidirectional brain-gut microbiome interactions. We aimed to determine if subgroups of irritable bowel syndrome (IBS) subjects can be identified based on differences in gut microbial composition, and if there are correlations between gut microbial measures and structural brain signatures in IBS. METHODS: Behavioral measures, stool samples, and structural brain images were collected from 29 adult IBS and 23 healthy control subjects (HCs)...
May 1, 2017: Microbiome
https://www.readbyqxmd.com/read/28454561/a-comprehensive-multi-omics-approach-uncovers-adaptations-for-growth-and-survival-of-pseudomonas-aeruginosa-on-n-alkanes
#20
Sarah L Grady, Stephanie A Malfatti, Thusitha S Gunasekera, Brian K Dalley, Matt G Lyman, Richard C Striebich, Michael B Mayhew, Carol L Zhou, Oscar N Ruiz, Larry C Dugan
BACKGROUND: Examination of complex biological systems has long been achieved through methodical investigation of the system's individual components. While informative, this strategy often leads to inappropriate conclusions about the system as a whole. With the advent of high-throughput "omic" technologies, however, researchers can now simultaneously analyze an entire system at the level of molecule (DNA, RNA, protein, metabolite) and process (transcription, translation, enzyme catalysis)...
April 28, 2017: BMC Genomics
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