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https://www.readbyqxmd.com/read/28647881/alterations-in-soil-microbial-communities-caused-by-treatments-with-penicillin-or-neomycin
#1
Qichun Zhang, Ouyang Kang, Salma Jabeen, Warren A Dick
Antibiotic residues in soils can lead to serious health risk and ecological hazards. In this study, the effects of penicillin and neomycin, two antibiotics widely used in animal production, were investigated on soil bacterial communities. Changes in the community structure were monitored using three 16S ribosomal DNA (rDNA) polymerase chain reaction-based approaches, including denaturing gradient gel electrophoresis (DGGE), amplified rDNA restriction analysis (ARDRA), and terminal-restriction fragment length polymorphism (T-RFLP) analysis...
June 25, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28647582/comparison-of-sequencing-the-d2-region-of-the-large-subunit-ribosomal-rna-gene-microseq%C3%A2-versus-the-internal-transcribed-spacer-its-regions-using-two-public-databases-for-identification-of-common-and-uncommon-clinically-relevant-fungal-species
#2
S Arbefeville, A Harris, P Ferrieri
CONTEXT: Fungal infections cause considerable morbidity and mortality in immunocompromised patients. Rapid and accurate identification of fungi is essential to guide accurately targeted antifungal therapy. With the advent of molecular methods, clinical laboratories can use new technologies to supplement traditional phenotypic identification of fungi. OBJECTIVE: The aims of the study were to evaluate the sole commercially available MicroSEQ® D2 LSU rDNA Fungal Identification Kit compared to the in-house developed internal transcribed spacer (ITS) regions assay in identifying moulds, using two well-known online public databases to analyze sequenced data...
June 21, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28647331/combination-of-histidine-lysine-methionine-and-leucine-promotes-%C3%AE-casein-synthesis-via-the-mechanistic-target-of-rapamycin-signaling-pathway-in-bovine-mammary-epithelial-cells
#3
H N Gao, S G Zhao, N Zheng, Y D Zhang, S S Wang, X Q Zhou, J Q Wang
The ratio of different AA in the diets of cows is vital to improve milk protein yield. β-Casein is one of the important milk proteins with high nutritive value. However, the suitable ratio of essential amino acids (EAA) for the expression of β-casein in the immortalized bovine mammary epithelial cell line is not fully characterized. This study employed response surface methodology to determine the optimal ratio of His, Lys, Met, and Leu on β-casein expression level in vitro and clarified the effect of the 4 EAA on β-casein via the mechanistic target of rapamycin (mTOR) signaling pathway...
June 21, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28646896/detection-of-the-plasmodium-falciparum-kelch-13-gene-p553l-mutation-in-sporozoites-isolated-from-mosquito-salivary-glands-in-south-central-vietnam
#4
Yoshimasa Maeno, Nguyen Tuyen Quang, Richard Culleton, Satoru Kawai, Gaku Masuda, Kaoru Hori, Shusuke Nakazawa, Ron P Marchand
BACKGROUND: Plasmodium falciparum has developed resistance against artemisinin in Southeast Asia. Mutations in the P. falciparum Kelch-13 (Pfk13) gene are associated with artemisinin resistance in vitro and in vivo. We investigated the prevalence of mutations in PfK13 from sporozoite-stage parasites isolated from the salivary glands of Anopheles dirus mosquitoes. METHODS: Mosquitoes were caught by human-landing catches at two locations within the Khanh Phu commune, South-Central Vietnam...
June 24, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28646679/hypoxia-induced-adam-17-expression-is-mediated-by-rsk1-dependent-c-ebp%C3%AE-activation-in-human-lung-fibroblasts
#5
Jing-Yun Chen, Chien-Huang Lin, Bing-Chang Chen
Hypoxia was identified as a mediator of lung fibrosis in patients with chronic obstructive asthma (COA). Overexpression of a disintegrin and metalloproteinase 17 (ADAM 17) and connective tissue growth factor (CTGF) leads to development of tissue fibrosis. However, the signaling pathway in hypoxia-induced ADAM 17 expression remains poorly defined. In this study, we investigated the roles that ribosomal S-6 kinase 1 (RSK1)/CCAAT/enhancer-binding protein β (C/EBPβ)-dependent ADAM 17 expression plays in hypoxia-induced CTGF expression in human lung fibroblasts...
June 21, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/28646313/domestic-wastewater-treatment-by-constructed-wetlands-enhanced-with-bioremediating-rhizobacteria
#6
Irina Salgado, Herlen Cárcamo, María Elena Carballo, Mario Cruz, María Del Carmen Durán
Constructed wetlands (CWs) offer several advantages for treating waters; however, the successful application of these systems remains a challenge. Practical solutions to pollution through CWs remain incipient because wetlands are still studied as "black boxes"; further studies are required regarding the involvement of rhizosphere bacteria in the removal of pollutants. This research focused on increasing the performance of CWs treatment systems for the removal of inorganic and organic pollutants from domestic wastewater, by the application of native bioremediating rhizobacteria...
June 23, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28646175/ribosome-rna-profiling-to-quantify-ovarian-development-and-identify-sex-in-fish
#7
Zhi-Gang Shen, Hong Yao, Liang Guo, Xiao-Xia Li, Han-Ping Wang
Terminologies of ovary development, by somewhat subjective describing and naming main changes of oocytes, have been criticized for confusing and inconsistency of terms and classifications, and the incurred consequences impede communication among researchers. In the present work, we developed regression between ovary development and three ribosome RNA (rRNA) indexes, namely 5S rRNA percent, 18S rRNA percent, and 5S-18S rRNA ratio, using close relationship between volume percent of primary growth stage oocytes or gonadosomatic index and rRNA content, demonstrating species-specific quantification of ovary development can be established in species with either synchronous and asynchronous oogenesis...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28646134/complete-mitochondrial-genome-of-clistocoeloma-sinensis-brachyura-grapsoidea-gene-rearrangements-and-higher-level-phylogeny-of-the-brachyura
#8
Zhao-Zhe Xin, Yu Liu, Dai-Zhen Zhang, Xin-Yue Chai, Zheng-Fei Wang, Hua-Bin Zhang, Chun-Lin Zhou, Bo-Ping Tang, Qiu-Ning Liu
Deciphering the animal mitochondrial genome (mitogenome) is very important to understand their molecular evolution and phylogenetic relationships. In this study, the complete mitogenome of Clistocoeloma sinensis was determined. The mitogenome of C. sinensis was 15,706 bp long, and its A+T content was 75.7%. The A+T skew of the mitogenome of C. sinensis was slightly negative (-0.020). All the transfer RNA genes had the typical cloverleaf structure, except for the trnS1 gene, which lacked a dihydroxyuridine arm...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28646031/metabolism-and-acetylation-contribute-to-leucine-mediated-inhibition-of-cardiac-glucose-uptake
#9
Edith Renguet, Audrey Ginion, Roselle Gélinas, Laurent Bultot, Julien Auquier, Isabelle Robillard Frayne, Caroline Daneault, Jean-Louis Vanoverschelde, Christine Des Rosiers, Louis Hue, Sandrine Horman, Christophe Beauloye, Luc Bertrand
High plasma leucine levels strongly correlate with type 2 diabetes. Studies of muscle cells suggest that leucine alters the insulin response for glucose transport by activating an insulin-negative feedback loop driven by the mammalian target of rapamycin/p70 ribosomal S6 kinase (mTOR/p70S6K) pathway. Here, we examined the molecular mechanism involved in leucine's action on cardiac glucose uptake. Leucine was indeed able to curb glucose uptake after insulin stimulation in both cultured cardiomyocytes and perfused hearts...
June 23, 2017: American Journal of Physiology. Heart and Circulatory Physiology
https://www.readbyqxmd.com/read/28646020/mcam-mediates-chemoresistance-in-small-cell-lung-cancer-via-the-pi3k-akt-sox2-signaling-pathway
#10
Satyendra C Tripathi, Johannes F Fahrmann, Muge Celiktas, Mitzi Aguilar, Kieren D Marini, Mohit Kumar Jolly, Hiroyuki Katayama, Hong Wang, Eunice N Murage, Jennifer B Dennison, D Neil Watkins, Herbert Levine, Edwin J Ostrin, Ayumu Taguchi, Samir M Hanash
Despite favorable responses to initial therapy, small cell lung cancer (SCLC) relapse occurs within a year and exhibits resistance to multiple drugs. Due to limited accessibility of patient tissues for research purposes, SCLC-patient derived xenografts (PDX) have provided the best opportunity to address this limitation. Here we sought to identify novel mechanisms involved in SCLC chemoresistance. Through in-depth proteomic profiling, we identified MCAM as a markedly upregulated surface receptor in chemoresistant SCLC cell lines and in chemoresistant PDX compared to matched treatment-naïve tumors...
June 23, 2017: Cancer Research
https://www.readbyqxmd.com/read/28645916/structures-and-dynamics-of-hibernating-ribosomes-from-staphylococcus-aureus-mediated-by-intermolecular-interactions-of-hpf
#11
Iskander Khusainov, Quentin Vicens, Rustam Ayupov, Konstantin Usachev, Alexander Myasnikov, Angelita Simonetti, Shamil Validov, Bruno Kieffer, Gulnara Yusupova, Marat Yusupov, Yaser Hashem
In bacteria, ribosomal hibernation shuts down translation as a response to stress, through reversible binding of stress-induced proteins to ribosomes. This process typically involves the formation of 100S ribosome dimers. Here, we present the structures of hibernating ribosomes from human pathogen Staphylococcus aureus containing a long variant of the hibernation-promoting factor (SaHPF) that we solved using cryo-electron microscopy. Our reconstructions reveal that the N-terminal domain (NTD) of SaHPF binds to the 30S subunit as observed for shorter variants of HPF in other species...
June 23, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28645570/quantitative-proteomics-analysis-by-itraq-revealed-underlying-changes-in-thermotolerance-of-arthrospira-platensis
#12
Rong Chang, Bingxin Lv, Bosheng Li
Growth temperature is a critical factor that affects cultivation of Arthrospira platensis which is a type of cyanobacterium widely known as Spirulina that has significant commercial value. To investigate the molecular mechanism underlying the thermotolerance of Spirulina, differential protein expression profiling was carried out using iTRAQ-based quantitative proteomic analysis. This study only analyzed changes in thylakoids. Among the 2085 proteins quantified, 43 differentially expressed proteins were selected based on the fold change cutoff scores of ≥2 or ≤0...
June 20, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28644864/overexpression-and-characterization-of-two-types-of-nitrile-hydratases-from-rhodococcus-rhodochrous-j1
#13
Yao Lan, Xiaohuan Zhang, Zhongmei Liu, Li Zhou, Ruihua Shen, Xianping Zhong, Wenjing Cui, Zhemin Zhou
Nitrile hydratase (NHase) from Rhodococcus rhodochrous J1 is widely used for industrial production of acrylamide and nicotinamide. However, the two types of NHases (L-NHase and H-NHase) from R. rhodochrous J1 were only slightly expressed in E. coli by routine methods, which limits the comprehensive and systematic characterization of the enzyme properties. We successfully expressed the two types of recombinant NHases in E. coli by codon-optimization, engineering of Ribosome Binding Site (RBS) and spacer sequences...
2017: PloS One
https://www.readbyqxmd.com/read/28644475/post-translational-modification-of-ribosomally-synthesized-peptides-by-a-radical-sam-epimerase-in-bacillus-subtilis
#14
Alhosna Benjdia, Alain Guillot, Pauline Ruffié, Jérôme Leprince, Olivier Berteau
Ribosomally synthesized peptides are built out of L-amino acids, whereas D-amino acids are generally the hallmark of non-ribosomal synthetic processes. Here we show that the model bacterium Bacillus subtilis is able to produce a novel type of ribosomally synthesized and post-translationally modified peptide that contains D-amino acids, and which we propose to call epipeptides. We demonstrate that a two [4Fe-4S]-cluster radical S-adenosyl-L-methionine (SAM) enzyme converts L-amino acids into their D-counterparts by catalysing Cα-hydrogen-atom abstraction and using a critical cysteine residue as the hydrogen-atom donor...
July 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28644007/cyclotides-as-tools-in-chemical-biology
#15
Simon J de Veer, Joachim Weidmann, David J Craik
Among the various molecules that plants produce for defense against pests and pathogens, cyclotides stand out as exceptionally stable and structurally unique. These ribosomally synthesized peptides are around 30 amino acids in size, and are stabilized by a head-to-tail cyclic peptide backbone and three disulfide bonds that form a cystine knot. They occur in certain plants of the Rubiaceae, Violaceae, Cucurbitaceae, Fabaceae, and Solanaceae families, with an individual plant producing up to hundreds of different cyclotides...
June 23, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28642991/extensive-overlap-of-tropical-rainforest-bacterial-endophytes-between-soil-plant-parts-and-plant-species
#16
Emmanuel Haruna, Noraziah M Zin, Dorsaf Kerfahi, Jonathan M Adams
The extent to which distinct bacterial endophyte communities occur between different plant organs and species is poorly known and has implications for bioprospecting efforts. Using the V3 region of the bacterial 16S ribosomal RNA (rRNA) gene, we investigated the diversity patterns of bacterial endophyte communities of three rainforest plant species, comparing leaf, stem, and root endophytes plus rhizosphere soil community. There was extensive overlap in bacterial communities between plant organs, between replicate plants of the same species, between plant species, and between plant organ and rhizosphere soil, with no consistent clustering by compartment or host plant species...
June 22, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28641603/molecular-detection-of-sarcocystis-lutrae-in-the-european-badger-meles-meles-in-scotland
#17
T Lepore, P M Bartley, F Chianini, A I Macrae, E A Innes, F Katzer
Neck samples from 54 badgers and 32 tongue samples of the same badgers (Meles meles), collected in the Lothians and Borders regions of Scotland, were tested using polymerase chain reactions (PCRs) directed against the 18S ribosomal DNA and the internal transcribed spacer (ITS1) region of protozoan parasites of the family Sarcocystidae. Positive results were obtained from 36/54 (67%) neck and 24/32 (75%) tongue samples using an 18S rDNA PCR. A 468 base pair consensus sequence that was generated from the 18S rDNA PCR amplicons (KX229728) showed 100% identity to Sarcocystis lutrae...
June 23, 2017: Parasitology
https://www.readbyqxmd.com/read/28641403/a-molasses-habitat-derived-fungus-aspergillus-tubingensis-xg21-with-high-%C3%AE-fructofuranosidase-activity-and-its-potential-use-for-fructooligosaccharides-production
#18
Yijia Xie, Huanxia Zhou, Caixia Liu, Jing Zhang, Ning Li, Zhanli Zhao, Guoyong Sun, Yaohua Zhong
The industrial microorganisms used for fructooligosaccharides (FOS) synthesis are generally fermented with sucrose as carbon source to induce the production of β-fructofuranosidase (FFase) having transfructosylation activity. Consequently, isolation of novel FFase producers from a sucrose-enriched biotope would help improve FOS productivity and reduce the process cost. Here, three fungi isolated from a unique sugarcane molasses habitat were found to possess FFase activity and one of them, XG21, exhibited a high capacity to synthesize FOS...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28640897/impact-of-selected-non-steroidal-anti-inflammatory-pharmaceuticals-on-microbial-community-assembly-and-activity-in-sequencing-batch-reactors
#19
Cong Jiang, Jinju Geng, Haidong Hu, Haijun Ma, Xingsheng Gao, Hongqiang Ren
This study covers three widely detected non-steroidal anti-inflammatory pharmaceuticals (NSAIDs), diclofenac (DCF), ibuprofen (IBP) and naproxen (NPX), as NSAIDs pollutants. The objective is to evaluate the impact of NSAIDs at their environmental concentrations on microbial community assembly and activity. The exposure experiments were conducted under three conditions (5 μg L-1 DCF, 5 μg L-1 DCF+5 μg L-1 IBP and 5 μg L-1 DCF+5 μg L-1 IBP+ 5 μg L-1 NPX) in sequencing batch reactors (SBRs) for 130 days...
2017: PloS One
https://www.readbyqxmd.com/read/28640831/ribosomal-dna-copy-number-loss-and-sequence-variation-in-cancer
#20
Baoshan Xu, Hua Li, John M Perry, Vijay Pratap Singh, Jay Unruh, Zulin Yu, Musinu Zakari, William McDowell, Linheng Li, Jennifer L Gerton
Ribosomal DNA is one of the most variable regions in the human genome with respect to copy number. Despite the importance of rDNA for cellular function, we know virtually nothing about what governs its copy number, stability, and sequence in the mammalian genome due to challenges associated with mapping and analysis. We applied computational and droplet digital PCR approaches to measure rDNA copy number in normal and cancer states in human and mouse genomes. We find that copy number and sequence can change in cancer genomes...
June 2017: PLoS Genetics
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