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https://www.readbyqxmd.com/read/29054886/the-ssu-processome-interactome-in-saccharomyces-cerevisiae-reveals-potential-new-protein-subcomplexes
#1
Nicholas G Vincent, J Michael Charette, Susan J Baserga
Ribosome assembly is an evolutionarily conserved and energy intensive process required for cellular growth, proliferation, and maintenance. In yeast, assembly of the small ribosomal subunit (SSU) requires approximately 75 assembly factors that act in coordination to form the SSU processome, a 6 MDa ribonucleoprotein complex. The SSU processome is required for processing, modifying, and folding the pre-ribosomal RNA (rRNA) to prepare it for incorporation into the mature SSU. Although the protein composition of the SSU processome has been known for some time, the interaction network of the proteins required for its assembly has remained poorly defined...
October 20, 2017: RNA
https://www.readbyqxmd.com/read/29054869/estimating-population-turnover-rates-from-relative-quantification-methods-reveals-microbial-dynamics-in-marine-sediment
#2
Richard Kevorkian, Jordan T Bird, Alexander Shumaker, Karen G Lloyd
Difficulty quantifying biogeochemically significant microbes in marine sediments limits our ability to assess interspecific interactions, population turnover times, and niches of uncultured taxa. We incubated surface sediments from Cape Lookout Bight, North Carolina USA, anoxically at 21°C for 122 days. Sulfate decreased until day 68, after which methane increased, with hydrogen concentration consistent with predicted values of an electron donor exerting thermodynamic control. We measured turnover times using two relative quantification methods, quantitative PCR (qPCR) and the product of 16S gene read abundance and total cell abundance (FRAxC, for fraction of read abundance times cells), to estimate population turnover rates of uncultured clades...
October 20, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29054663/characterization-of-bacterial-diversity-in-contaminated-groundwater-using-matrix-assisted-laser-desorption-ionization-time-of-flight-mass-spectrometry
#3
Misty S Martin, Inês C Santos, Doug D Carlton, Paula Stigler-Granados, Zacariah L Hildenbrand, Kevin A Schug
Groundwater is a major source for drinking water in the United States, and therefore, its quality and quantity is of extreme importance. One major concern that has emerged is the possible contamination of groundwater due to the unconventional oil and gas extraction activities. As such, the impacts of exogenous contaminants on microbial ecology is an area to be explored to understand what are the chemical and physical conditions that allow the proliferation of pathogenic bacteria and to find alternatives for water treatment by identifying organic-degrading bacteria...
October 17, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29054657/feed-additives-shift-gut-microbiota-and-enrich-antibiotic-resistance-in-swine-gut
#4
Yi Zhao, Jian-Qiang Su, Xin-Li An, Fu-Yi Huang, Christopher Rensing, Kristian Koefoed Brandt, Yong-Guan Zhu
Antibiotic resistance genes (ARGs) are emerging environmental contaminants posing a threat to public health. Antibiotics and metals are widely used as feed additives and could consequently affect ARGs in swine gut. In this study, high-throughput quantitative polymerase chain reaction (HT-qPCR) based ARG chip and next-generation 16S rRNA gene amplicon sequencing data were analyzed using multiple statistical approaches to profile the antibiotic resistome and investigate its linkages to antibiotics and metals used as feed additives and to the microbial community composition in freshly collected swine manure samples from three large-scale Chinese pig farms...
October 17, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29054650/vitamin-b12-effects-on-chlorinated-methanes-degrading-microcosms-dual-isotope-and-metabolically-active-microbial-populations-assessment
#5
Diana Rodríguez-Fernández, Clara Torrentó, Miriam Guivernau, Marc Viñas, Daniel Hunkeler, Albert Soler, Cristina Domènech, Mònica Rosell
Field-derived anoxic microcosms were used to characterize chloroform (CF) and carbon tetrachloride (CT) natural attenuation to compare it with biostimulation scenarios in which vitamin B12 was added (B12/pollutant ratio of 0.01 and 0.1) by means of by-products, carbon and chlorine compound-specific stable-isotope analysis, and the active microbial community through 16S rRNA MiSeq high-throughput sequencing. Autoclaved slurry controls discarded abiotic degradation processes. B12 catalyzed CF and CT biodegradation without the accumulation of dichloromethane, carbon disulphide, or CF...
October 17, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29054074/temperature-dependence-of-bioelectrochemical-co2-conversion-and-methane-production-with-a-mixed-culture-biocathode
#6
Hou-Yun Yang, Bai-Ling Bao, Jing Liu, Yuan Qin, Yi-Ran Wang, Kui-Zu Su, Jun-Cheng Han, Yang Mu
This study evaluated the effect of temperature on methane production by CO2 reduction during microbial electrosynthesis (MES) with a mixed-culture biocathode. Reactor performance, in terms of the amount and rate of methane production, current density, and coulombic efficiency, was compared at different temperatures. The microbial properties of the biocathode at each temperature were also analyzed by 16S rRNA gene sequencing. The results showed that the optimum temperature for methane production from CO2 reduction in MES with a mixed-culture cathode was 50°C, with the highest amount and rate of methane production of 2...
October 2, 2017: Bioelectrochemistry
https://www.readbyqxmd.com/read/29053600/detection-and-management-of-mango-dieback-disease-in-the-united-arab-emirates
#7
Esam Eldin Saeed, Arjun Sham, Ayah AbuZarqa, Khawla A Al Shurafa, Tahra S Al Naqbi, Rabah Iratni, Khaled El-Tarabily, Synan F AbuQamar
Mango is affected by different decline disorders causing significant losses to mango growers. In the United Arab Emirates (UAE), the pathogen was isolated from all tissues sampled from diseased trees affected by Lasiodiplodia theobromae. Symptoms at early stages of the disease included general wilting appearance of mango trees, and dieback of twigs. In advanced stages, the disease symptoms were also characterized by the curling and drying of leaves, leading to complete defoliation of the tree and discolouration of vascular regions of the stems and branches...
October 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29053248/in-vitro-evolution-of-unmodified-16s-rrna-for-simple-ribosome-reconstitution
#8
Yoshiki Murase, Hiroki Nakanishi, Gakushi Tsuji, Takeshi Sunami, Norikazu Ichihashi
One of the largest challenges in the synthesis of artificial cell that can reproduce is in vitro assembly of ribosomes from in vitro synthesized rRNAs and proteins. In this study, to circumvent the chemical modification of 16S rRNA for reconstitution of fully active 30S subunit, we performed artificial evolution of 16S rRNA, which forms the functional 30S subunit without chemical modifications. We first established an in vitro selection scheme by combining the integrated synthesis, assembly, and translation (iSAT) system with the liposome sorting technique...
October 20, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29052043/biodegradation-and-chemotaxis-of-polychlorinated-biphenyls-biphenyls-and-their-metabolites-by-rhodococcus-spp
#9
Hui Wang, Jinxing Hu, Kai Xu, Xianjin Tang, Xinhua Xu, Chaofeng Shen
Two biphenyl-degrading bacterial strains, SS1 and SS2, were isolated from polychlorinated biphenyl (PCB)-contaminated soil. They were identified as Rhodococcus ruber and Rhodococcus pyridinivorans based on the 16S rRNA gene sequence, as well as morphological, physiological and biochemical characteristics. SS1 and SS2 exhibited tolerance to 2000 and 3000 mg/L of biphenyl. And they could degrade 83.2 and 71.5% of 1300 mg/L biphenyl within 84 h, respectively. In the case of low-chlorinated PCB congeners, benzoate and 3-chlorobenzoate, the degradation activities of SS1 and SS2 were also significant...
October 19, 2017: Biodegradation
https://www.readbyqxmd.com/read/29051756/genomic-gc-content-affects-the-accuracy-of-16s-rrna-gene-sequencing-based-microbial-profiling-due-to-pcr-bias
#10
Martin F Laursen, Marlene D Dalgaard, Martin I Bahl
Profiling of microbial community composition is frequently performed by partial 16S rRNA gene sequencing on benchtop platforms following PCR amplification of specific hypervariable regions within this gene. Accuracy and reproducibility of this strategy are two key parameters to consider, which may be influenced during all processes from sample collection and storage, through DNA extraction and PCR based library preparation to the final sequencing. In order to evaluate both the reproducibility and accuracy of 16S rRNA gene based microbial profiling using the Ion Torrent PGM platform, we prepared libraries and performed sequencing of a well-defined and validated 20-member bacterial DNA mock community on five separate occasions and compared results with the expected even distribution...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29050418/impact-of-egg-disinfection-of-hatching-eggs-on-the-eggshell-microbiome-and-bacterial-load
#11
R Olsen, E Kudirkiene, I Thøfner, S Pors, P Karlskov-Mortensen, L Li, S Papasolomontos, C Angastiniotou, J Christensen
Disinfection of hatching eggs is essential to ensure high quality production of broilers. Different protocols are followed in different hatcheries; however, only limited scientific evidence on how the disinfection procedures impact the microbiome is available. The aim of the present study was to characterize the microbiome and aerobic bacterial load of hatching eggs before disinfection and during the subsequent disinfection steps. The study included a group of visibly clean and a group of visibly dirty eggs...
September 1, 2017: Poultry Science
https://www.readbyqxmd.com/read/29050374/taxonomic-structure-and-functional-association-of-foxtail-millet-root-microbiome
#12
Tao Jin, Yayu Wang, Yueying Huang, Jin Xu, Pengfan Zhang, Nian Wang, Xin Liu, Haiyan Chu, Guang Liu, Honggang Jiang, Yuzhen Li, Jing Xu, Karsten Kristiansen, Liang Xiao, Yunzeng Zhang, Gengyun Zhang, Guohua Du, Houbao Zhang, Hongfeng Zou, Haifeng Zhang, Zhuye Jie, Suisha Liang, Huijue Jia, Jingwang Wan, Dechun Lin, Jinying Li, Guangyi Fan, Huanming Yang, Jian Wang, Yang Bai, Xun Xu
The root microbes play pivotal roles in plant productivity, nutrient uptakes, and disease resistance. The root microbial community structure has been extensively investigated by 16S/18S/ITS amplicons and metagenomic sequencing in crops and model plants. However, the functional associations between root microbes and host plant growth are poorly understood. This work investigates the root bacterial community of foxtail millet (Setaria italica) and its potential effects on host plant productivity. We determined the bacterial composition of 2882 samples from foxtail millet rhizoplane, rhizosphere and corresponding bulk soils from 2 well-separated geographic locations by 16S rRNA gene amplicon sequencing...
October 1, 2017: GigaScience
https://www.readbyqxmd.com/read/29050247/rnai-mediated-knockdown-of-parp1-does-not-improve-the-development-of-female-cloned-mouse-embryos
#13
Guang-Yu Bai, Si-Hang Song, Rui-Zhen Sun, Zi-Hui Zhang, Jingyu Li, Zhen-Dong Wang, Zhong-Hua Liu, Lei Lei
Somatic cell nuclear transfer is an important technique for life science research, but its efficiency is still extremely low, and most genes that are important during early development, such as X chromosome-linked genes, are not appropriately expressed during this process. Poly (ADP-ribose) polymerase (PARP) is an enzyme that transfers ADP ribose clusters to target proteins. PARP family members such as PARP1 participate in cellular signalling pathways through poly (ADP-ribosylation) (PARylation), which ultimately promotes changes in chromatin structure, gene expression, and the localization and activity of proteins that mediate signalling responses...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29049965/development-of-a-molecular-method-for-testing-the-effectiveness-of-uv-systems-on-site
#14
Limor Nizri, Dalit Vaizel-Ohayon, Hila Ben-Amram, Yehonatan Sharaby, Malka Halpern, Hadas Mamane
We established a molecular method for quantifying ultraviolet (UV) disinfection efficacy using total bacterial DNA in a water sample. To evaluate UV damage to the DNA, we developed the "DNA damage" factor, which is a novel cultivation-independent approach that reveals UV-exposure efficiency by applying a simple PCR amplification method. The study's goal was to prove the feasibility of this method for demonstrating the efficiency of UV systems in the field using flow-through UV reactors. In laboratory-based experiments using seeded bacteria, the DNA damage tests demonstrated a good correlation between PCR products and UV dose...
October 10, 2017: Water Research
https://www.readbyqxmd.com/read/29049321/determination-and-production-of-antimicrobial-compounds-by-aspergillus-clavatonanicus-strain-mj31-an-endophytic-fungus-from-mirabilis-jalapa-l-using-uplc-esi-ms-ms-and-td-gc-ms-analysis
#15
Vineet Kumar Mishra, Ajit Kumar Passari, Preeti Chandra, Vincent Vineeth Leo, Brijesh Kumar, Sivakumar Uthandi, Sugitha Thankappan, Vijai Kumar Gupta, Bhim Pratap Singh
Endophytic fungi associated with medicinal plants are reported as potent producers of diverse classes of secondary metabolites. In the present study, an endophytic fungi, Aspergillus clavatonanicus strain MJ31, exhibiting significant antimicrobial activity was isolated from roots of Mirabilis jalapa L., was identified by sequencing three nuclear genes i.e. internal transcribed spacers ribosomal RNA (ITS rRNA), 28S ribosomal RNA (28S rRNA) and translation elongation factor 1- alpha (EF 1α). Ethyl acetate extract of strain MJ31displayed significant antimicrobial potential against Bacillus subtilis, followed by Micrococccus luteus and Staphylococcus aureus with minimum inhibitory concentrations (MIC) of 0...
2017: PloS One
https://www.readbyqxmd.com/read/29048352/effects-of-short-term-probiotic-ingestion-on-immune-profiles-and-microbial-translocation-among-hiv-1-infected-vietnamese-children
#16
Azumi Ishizaki, Xiuqiong Bi, Lam Van Nguyen, Kazunori Matsuda, Hung Viet Pham, Chung Thi Thu Phan, Dung Thi Khanh Khu, Hiroshi Ichimura
Here, we investigated the effects of the probiotic strain Lactobacillus casei Shirota (LcS) on immune profiles and intestinal microbial translocation among children infected with human immunodeficiency virus (HIV). This prospective study included 60 HIV-infected children-including 31 without antiretroviral therapy (ART) (HIV(+)) and 29 who received ART for a median of 3.5 years (ART(+)) and 20 children without HIV infection (HIV(-)). Participants were recruited in Vietnam. All children were given fermented milk containing LcS (6...
October 19, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29047421/pedobacter-kyonggii-sp-nov-a-psychrotolerant-bacterium-isolated-from-forest-soil
#17
Dhiraj Kumar Chaudhary, Sang Don Lee, Jaisoo Kim
Strain K-4-11-1(T), a psychrotolerant, light salmon-coloured, Gram-stain-negative, non-motile and rod-shaped bacterium, was isolated from forest soil of Kyonggi University, Suwon, South Korea. It was able to grow at 0-32 °C, at pH 5.0-10.0 and with 0-1.5 % (w/v) NaCl. This strain was taxonomically characterized by a polyphasic approach. Based on 16S rRNA gene sequence analysis, strain K-4-11-1(T) belongs to the genus Pedobacter and is closely related to Pedobacter ginsenosidimutans THG-45(T) (98.75 % sequence similarity), Pedobacter borealis G-1(T) (98...
October 19, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29047380/population-genetics-of-enterocytozoon-bieneusi-in-captive-giant-pandas-of-china
#18
Wei Li, Yuan Song, Zhijun Zhong, Xiangming Huang, Chengdong Wang, Caiwu Li, Haidi Yang, Haifeng Liu, Zhihua Ren, Jingchao Lan, Kongju Wu, Guangneng Peng
BACKGROUND: Most studies on Enterocytozoon bieneusi are conducted based on the internal transcribed spacer (ITS) region of the rRNA gene, whereas some have examined E. bieneusi population structures. Currently, the population genetics of this pathogen in giant panda remains unknown. The objective of this study was to determine the E. bieneusi population in captive giant pandas in China. RESULTS: We examined 69 E. bieneusi-positive specimens from captive giant pandas in China using five loci (ITS, MS1, MS3, MS4 and MS7) to infer E...
October 18, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/29046663/reclassification-of-paenibacillus-riograndensis-as-a-genomovar-of-paenibacillus-sonchi-genome-based-metrics-improve-bacterial-taxonomic-classification
#19
Fernando H Sant'Anna, Adriana Ambrosini, Rocheli de Souza, Gabriela de Carvalho Fernandes, Evelise Bach, Eduardo Balsanelli, Valter Baura, Luciana F Brito, Volker F Wendisch, Fábio de Oliveira Pedrosa, Emanuel M de Souza, Luciane M P Passaglia
Species from the genus Paenibacillus are widely studied due to their biotechnological relevance. Dozens of novel species descriptions of this genus were published in the last couple of years, but few utilized genomic data as classification criteria. Here, we demonstrate the importance of using genome-based metrics and phylogenetic analyses to identify and classify Paenibacillus strains. For this purpose, Paenibacillus riograndensis SBR5(T), Paenibacillus sonchi X19-5(T), and their close relatives were compared through phenotypic, genotypic, and genomic approaches...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29046225/composition-and-influencing-factors-of-bacterial-communities-in-ballast-tank-sediments-implications-for-ballast-water-and-sediment-management
#20
Baoyi Lv, Yuxue Cui, Wen Tian, Daolun Feng
This study aims to reveal the composition and influencing factors of bacterial communities in ballast tank sediments. Nine samples were collected and their 16S rRNA gene sequences were analyzed by high-throughput sequencing. The analysis results showed the Shannon index in ballast tank sediments was in the range of 5.27-6.35, which was significantly higher than that in ballast water. Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi and Proteobacteria were the dominant phyla and accounted for approximately 80% of all 16S rRNA gene sequences of the samples...
October 12, 2017: Marine Environmental Research
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