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Ribosomal rna

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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/28733876/human-papillomavirus-type-8-e7-protein-binds-nuclear-myosin-1c-and-downregulates-the-expression-of-pre-rrna
#3
Evelyn Oswald, Eileen Reinz, Renate Voit, François Aubin, Angel Alonso, Eeva Auvinen
Our aim was to search for new cellular binding partners for the E6 and E7 oncogenes of beta human papillomaviruses (HPV), whose direct role in skin carcinogenesis has not been thoroughly investigated. By employing glutathione S-transferase pulldown and coimmunoprecipitation, we identified nuclear myosin 1c as a binding partner of HPV 8 E7 protein. As nuclear myosin 1c is an essential component of the RNA polymerase I transcription complex, we studied the effects of HPV 8 E7 protein expression on ribosomal RNA (rRNA) expression...
July 21, 2017: Virus Genes
https://www.readbyqxmd.com/read/28733652/deficient-glutamate-biosynthesis-triggers-a-concerted-upregulation-of-ribosomal-protein-genes-in-arabidopsis
#4
Tamara Muñoz-Nortes, José Manuel Pérez-Pérez, Raquel Sarmiento-Mañús, Héctor Candela, José Luis Micol
Biomass production requires the coordination between growth and metabolism. In a large-scale screen for mutants affected in leaf morphology, we isolated the orbiculata1 (orb1) mutants, which exhibit a pale green phenotype and reduced growth. The combination of map-based cloning and next-generation sequencing allowed us to establish that ORB1 encodes the GLUTAMATE SYNTHASE 1 (GLU1) enzyme, also known as FERREDOXIN-DEPENDENT GLUTAMINE OXOGLUTARATE AMINOTRANSFERASE 1 (Fd-GOGAT1). We performed an RNA-seq analysis to identify global gene expression changes in the orb1-3 mutant...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28733601/anti-tubercular-activity-of-pyrazinamide-is-independent-of-trans-translation-and-rpsa
#5
Nicholas A Dillon, Nicholas D Peterson, Heather A Feaga, Kenneth C Keiler, Anthony D Baughn
Pyrazinamide (PZA) is a first line anti-tubercular drug for which the mechanism of action remains unresolved. Recently, it was proposed that the active form of PZA, pyrazinoic acid (POA), disrupts the ribosome rescue process of trans-translation in Mycobacterium tuberculosis. This model suggested that POA binds within the carboxy-terminal domain of ribosomal protein S1 (RpsA) and inhibits trans-translation leading to accumulation of stalled ribosomes. Here, we demonstrate that M. tuberculosis RpsA interacts with single stranded RNA, but not with POA...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28733463/tlr4-and-c5ar-crosstalk-in-dendritic-cells-induces-a-core-regulatory-network-of-rsk2-pi3k%C3%AE-sgk1-and-foxo-transcription-factors
#6
Anouk Zaal, Benjamin Nota, Kat S Moore, Miranda Dieker, S Marieke van Ham, Anja Ten Brinke
Crosstalk between complement component 5a receptors (C5aRs) and TLRs in dendritic cells (DCs) occurs upon pathogen invasion; however, studies on C5aR and TLR crosstalk mainly focused on the modulating effect of C5a on TLR-induced cytokine production. To elucidate the breadth of C5aR and TLR4 crosstalk, the effect of simultaneous treatment with C5a and LPS was investigated in human monocyte-derived DCs (moDCs) 2 h after stimulation using whole transcriptome sequencing analysis. Although the effect of C5a on hallmark genes defining TLR4-induced DC maturation was limited at this time point, RNA sequencing analysis revealed a great variety of novel C5a targets, of which many interfere with TLR4-mediated immune activation...
July 21, 2017: Journal of Leukocyte Biology
https://www.readbyqxmd.com/read/28732596/structural-and-functional-insights-into-human-re-initiation-complexes
#7
Melanie Weisser, Tanja Schäfer, Marc Leibundgut, Daniel Böhringer, Christopher Herbert Stanley Aylett, Nenad Ban
After having translated short upstream open reading frames, ribosomes can re-initiate translation on the same mRNA. This process, referred to as re-initiation, controls the translation of a large fraction of mammalian cellular mRNAs, many of which are important in cancer. Key ribosomal binding proteins involved in re-initiation are the eukaryotic translation initiation factor 2D (eIF2D) or the homologous complex of MCT-1/DENR. We determined the structures of these factors bound to the human 40S ribosomal subunit in complex with initiator tRNA positioned on an mRNA start codon in the P-site using a combination of cryoelectron microscopy and X-ray crystallography...
July 12, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28732463/common-and-phylogenetically-widespread-coding-for-peptides-by-bacterial-small-rnas
#8
Robin C Friedman, Stefan Kalkhof, Olivia Doppelt-Azeroual, Stephan A Mueller, Martina Chovancová, Martin von Bergen, Benno Schwikowski
BACKGROUND: While eukaryotic noncoding RNAs have recently received intense scrutiny, it is becoming clear that bacterial transcription is at least as pervasive. Bacterial small RNAs and antisense RNAs (sRNAs) are often assumed to be noncoding, due to their lack of long open reading frames (ORFs). However, there are numerous examples of sRNAs encoding for small proteins, whether or not they also have a regulatory role at the RNA level. METHODS: Here, we apply flexible machine learning techniques based on sequence features and comparative genomics to quantify the prevalence of sRNA ORFs under natural selection to maintain protein-coding function in 14 phylogenetically diverse bacteria...
July 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28731470/a-genomic-perspective-on-stoichiometric-regulation-of-soil-carbon-cycling
#9
Wyatt H Hartman, Rongzhong Ye, William R Horwath, Susannah G Tringe
Similar to plant growth, soil carbon (C) cycling is constrained by the availability of nitrogen (N) and phosphorus (P). We hypothesized that stoichiometric control over soil microbial C cycling may be shaped by functional guilds with distinct nutrient substrate preferences. Across a series of rice fields spanning 5-25% soil C (N:P from 1:12 to 1:70), C turnover was best correlated with P availability and increased with experimental N addition only in lower C (mineral) soils with N:P⩽16. Microbial community membership also varied with soil stoichiometry but not with N addition...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28730353/an-exploration-into-the-bacterial-community-under-different-pasteurization-conditions-during-substrate-preparation-composting-phase-ii-for-agaricus-bisporus-cultivation
#10
Fabricio Rocha Vieira, John Andrew Pecchia
Substrate preparation (i.e., composting) for Agaricus bisporus cultivation is the most critical point of mushroom production. Among many factors involved in the composting process, the microbial ecology of the system is the underlying drive of composting and can be influenced by composting management techniques. Pasteurization temperature at the beginning of phase II, in theory, may influence the bacterial community and subsequently the "selectivity" and nutrition of the final substrate. Therefore, this hypothesis was tested by simulation in bioreactors under different pasteurization conditions (57 °C/6 h, 60 °C/2 h, and 68 °C/2 h), simulating conditions adopted by many producers...
July 20, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28729142/nocardia-farcinica-brain-abscess-report-of-3-cases
#11
Ana Galacho-Harriero, Pedro D Delgado-López, Maria P Ortega-Lafont, Javier Martín-Alonso, José M Castilla-Díez, Belen Sánchez-Borge
BACKGROUND: Central nervous system nocardial infection is a rarely reported disease that usually affects patients with predisposing and debilitating conditions but also the immunocompetent population. The most common variant affecting the brain is Nocardia farcinica. Management of brain nocardiosis is troublesome and requires consideration of the severity of the underlying systemic disease, the difficulties in identifying the bacterium and the frequent delay in initiating adequate therapy...
July 17, 2017: World Neurosurgery
https://www.readbyqxmd.com/read/28729000/airway-microbiota-signals-anabolic-and-catabolic-remodeling-in-the-transplanted-lung
#12
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/28728127/is-bacterial-luminescence-response-to-low-dose-radiation-associated-with-mutagenicity
#13
T V Rozhko, O A Guseynov, V E Guseynova, A A Bondar, A N Devyatlovskaya, N S Kudryasheva
Luminous marine bacteria are widely used in bioassays with luminescence intensity being a physiological parameter tested. The purpose of the study was to determine whether bacterial genetic alteration is responsible for bioluminescence kinetics change under low-dose radiation exposure. The alpha-emitting radionuclide (241)Am and beta-emitting radionuclide (3)H were used as the sources of low-dose ionizing radiation. Changes of bioluminescence kinetics of Photobacterium phosphoreum in solutions of (241)Am(NO3)3, 7 kBq/L, and tritiated water, 100 MBq/L, were studied; bioluminescence kinetics stages (absence of effect, activation, and inhibition) were determined...
July 17, 2017: Journal of Environmental Radioactivity
https://www.readbyqxmd.com/read/28727769/small-subunit-ribosomal-metabarcoding-reveals-extraordinary-trypanosomatid-diversity-in-brazilian-bats
#14
Maria Augusta Dario, Ricardo Moratelli Mendonça da Rocha, Philipp Schwabl, Ana Maria Jansen, Martin S Llewellyn
BACKGROUND: Bats are a highly successful, globally dispersed order of mammals that occupy a wide array of ecological niches. They are also intensely parasitized and implicated in multiple viral, bacterial and parasitic zoonosis. Trypanosomes are thought to be especially abundant and diverse in bats. In this study, we used 18S ribosomal RNA metabarcoding to probe bat trypanosome diversity in unprecedented detail. METHODOLOGY/PRINCIPAL FINDINGS: Total DNA was extracted from the blood of 90 bat individuals (17 species) captured along Atlantic Forest fragments of Espírito Santo state, southeast Brazil...
July 20, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28726822/ribosomes-are-optimized-for-autocatalytic-production
#15
Shlomi Reuveni, Måns Ehrenberg, Johan Paulsson
Many fine-scale features of ribosomes have been explained in terms of function, revealing a molecular machine that is optimized for error-correction, speed and control. Here we demonstrate mathematically that many less well understood, larger-scale features of ribosomes-such as why a few ribosomal RNA molecules dominate the mass and why the ribosomal protein content is divided into 55-80 small, similarly sized segments-speed up their autocatalytic production.
July 19, 2017: Nature
https://www.readbyqxmd.com/read/28724659/human-milk-microbial-community-structure-is-relatively-stable-and-related-to-variations-in-macronutrient-and-micronutrient-intakes-in-healthy-lactating-women
#16
Janet E Williams, Janae M Carrothers, Kimberly A Lackey, Nicola F Beatty, Mara A York, Sarah L Brooker, Bahman Shafii, William J Price, Matthew L Settles, Mark A McGuire, Michelle K McGuire
Background: The human milk microbiome has been somewhat characterized, but little is known about changes over time and relations with maternal factors such as nutrient intake.Objective: We sought to characterize the human milk microbiome and described associations with maternal nutrient intake, time postpartum, delivery mode, and body mass index (BMI; in kg/m(2)).Methods: Milk samples (n = 104) and 24-h diet recalls were collected 9 times from 21 healthy lactating women from day 2 to 6 mo postpartum. Women were classified by BMI as healthy weight (<25) or overweight or obese (≥25)...
July 19, 2017: Journal of Nutrition
https://www.readbyqxmd.com/read/28722181/historical-biome-distribution-and-recent-human-disturbance-shape-the-diversity-of-arbuscular-mycorrhizal-fungi
#17
Meelis Pärtel, Maarja Öpik, Mari Moora, Leho Tedersoo, Robert Szava-Kovats, Søren Rosendahl, Matthias C Rillig, Ylva Lekberg, Holger Kreft, Thorunn Helgason, Ove Eriksson, John Davison, Francesco de Bello, Tancredi Caruso, Martin Zobel
The availability of global microbial diversity data, collected using standardized metabarcoding techniques, makes microorganisms promising models for investigating the role of regional and local factors in driving biodiversity. Here we modelled the global diversity of symbiotic arbuscular mycorrhizal (AM) fungi using currently available data on AM fungal molecular diversity (small subunit (SSU) ribosomal RNA (rRNA) gene sequences) in field samples. To differentiate between regional and local effects, we estimated species pools (sets of potentially suitable taxa) for each site, which are expected to reflect regional processes...
July 19, 2017: New Phytologist
https://www.readbyqxmd.com/read/28721505/distinct-bloom-dynamics-of-toxic-and-non-toxic-microcystis-cyanobacteria-subpopulations-in-hoedong-reservoir-korea
#18
Bum Soo Park, Zhun Li, Yoon-Ho Kang, Hyeon Ho Shin, Jae-Hyoung Joo, Myung-Soo Han
Despite the importance of understanding the bloom mechanisms that influence cyanobacterial toxin production, the dynamics of toxic Microcystis subpopulations are largely unknown. Here, we quantified both toxic and entire (i.e., toxic and non-toxic) Microcystis populations based on the microcystin synthetase E (mcyE) and 16S ribosomal RNA genes. Samples were collected from pelagic water and sediments twice per week from October to December 2011, and we investigated the effects of physicochemical factors (pH, water temperature, dissolved oxygen, nutrients, etc...
July 19, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28721504/microbial-community-structure-and-function-decoupling-across-a-phosphorus-gradient-in-streams
#19
Erick S LeBrun, Ryan S King, Jeffrey A Back, Sanghoon Kang
Phosphorus (P) is a key biological element with important and unique biogeochemical cycling in natural ecosystems. Anthropogenic phosphorus inputs have been shown to greatly affect natural ecosystems, and this has been shown to be especially true of freshwater systems. While the importance of microbial communities in the P cycle is widely accepted, the role, composition, and relationship to P of these communities in freshwater systems still hold many secrets. Here, we investigated combined bacterial and archaeal communities utilizing 16S ribosomal RNA (rRNA) gene sequencing and computationally predicted functional metagenomes (PFMs) in 25 streams representing a strong P gradient...
July 18, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28720757/integrative-analyses-of-translatome-and-transcriptome-reveal-important-translational-controls-in-brown-and-white-adipose-regulated-by-micrornas
#20
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
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