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https://www.readbyqxmd.com/read/28335556/trm5-and-trmd-two-enzymes-from-distinct-origins-catalyze-the-identical-trna-modification-m%C3%A2-g37
#1
REVIEW
Sakurako Goto-Ito, Takuhiro Ito, Shigeyuki Yokoyama
The N¹-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m¹G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome. Interestingly, Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. In this review, we describe the different strategies utilized by Trm5 and TrmD to recognize their substrate tRNAs, mainly based on their crystal structures complexed with substrate tRNAs...
March 21, 2017: Biomolecules
https://www.readbyqxmd.com/read/28335502/catechins-and-their-therapeutic-benefits-to-inflammatory-bowel-disease
#2
REVIEW
Fei-Yan Fan, Li-Xuan Sang, Min Jiang
Catechins are natural polyphenolic phytochemicals that exist in food and medicinal plants, such as tea, legume and rubiaceae. An increasing number of studies have associated the intake of catechins-rich foods with the prevention and treatment of chronic diseases in humans, such as inflammatory bowel disease (IBD). Some studies have demonstrated that catechins could significantly inhibit the excessive oxidative stress through direct or indirect antioxidant effects and promote the activation of the antioxidative substances such as glutathione peroxidases (GPO) and glutathione (GSH), reducing the oxidative damages to the colon...
March 19, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28335409/the-formyl-peptide-receptors-diversity-of-ligands-and-mechanism-for-recognition
#3
REVIEW
Hui-Qiong He, Richard D Ye
The formyl peptide receptors (FPRs) are G protein-coupled receptors that transduce chemotactic signals in phagocytes and mediate host-defense as well as inflammatory responses including cell adhesion, directed migration, granule release and superoxide production. In recent years, the cellular distribution and biological functions of FPRs have expanded to include additional roles in homeostasis of organ functions and modulation of inflammation. In a prototype, FPRs recognize peptides containing N-formylated methionine such as those produced in bacteria and mitochondria, thereby serving as pattern recognition receptors...
March 13, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28335391/new-metabolites-and-bioactive-chlorinated-benzophenone-derivatives-produced-by-a-marine-derived-fungus-pestalotiopsis-heterocornis
#4
Hui Lei, Xiuping Lin, Li Han, Jian Ma, Qingjuan Ma, Jialiang Zhong, Yonghong Liu, Tiemin Sun, Jinhui Wang, Xueshi Huang
Four new compounds, including two isocoumarins, pestaloisocoumarins A and B (1, 2), one sesquiterpenoid degradation, isopolisin B (4), and one furan derivative, pestalotiol A (5), together with one known isocoumarin, gamahorin (3), and three chlorinated benzophenone derivatives, pestalachloride B (6), pestalachloride E (7) and a mixture of pestalalactone atropisomers (8a/8b), were isolated from a culture of the fungus Pestalotiopsis heterocornis associated with sponge Phakellia fusca. These new chemical structures were established using NMR and MS spectroscopic data, as well as single-crystal X-ray crystallographic analysis and CD Cotton effects...
March 13, 2017: Marine Drugs
https://www.readbyqxmd.com/read/28335201/size-and-shape-dependent-antibacterial-studies-of-silver-nanoparticles-synthesized-by-wet-chemical-routes
#5
Muhammad Akram Raza, Zakia Kanwal, Anum Rauf, Anjum Nasim Sabri, Saira Riaz, Shahzad Naseem
Silver nanoparticles (AgNPs) of different shapes and sizes were prepared by solution-based chemical reduction routes. Silver nitrate was used as a precursor, tri-sodium citrate (TSC) and sodium borohydride as reducing agents, while polyvinylpyrrolidone (PVP) was used as a stabilizing agent. The morphology, size, and structural properties of obtained nanoparticles were characterized by scanning electron microscopy (SEM), UV-visible spectroscopy (UV-VIS), and X-ray diffraction (XRD) techniques. Spherical AgNPs, as depicted by SEM, were found to have diameters in the range of 15 to 90 nm while lengths of the edges of the triangular particles were about 150 nm...
April 15, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28335198/gold-nanoparticles-an-efficient-antimicrobial-agent-against-enteric-bacterial-human-pathogen
#6
Shahzadi Shamaila, Noshin Zafar, Saira Riaz, Rehana Sharif, Jawad Nazir, Shahzad Naseem
Enteric bacterial human pathogens, i.e., Escherichia coli, Staphylococcus aureus, Bacillus subtilis and Klebsiella pneumoniae, are the major cause of diarrheal infections in children and adults. Their structure badly affects the human immune system. It is important to explore new antibacterial agents instead of antibiotics for treatment. This project is an attempt to explain how gold nanoparticles affect these bacteria. We investigated the important role of the mean particle size, and the inhibition of a bacterium is dose-dependent...
April 14, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28334934/a-pseudaminic-acid-or-a-legionaminic-acid-derivative-transferase-is-strain-specifically-implicated-in-the-general-protein-o-glycosylation-system-of-the-periodontal-pathogen-tannerella-forsythia
#7
Markus B Tomek, Bettina Janesch, Daniel Maresch, Markus Windwarder, Friedrich Altmann, Paul Messner, Christina Schäffer
The occurrence of nonulosonic acids in bacteria is wide-spread and linked to pathogenicity. However, the knowledge of cognate nonulosonic acid transferases is scarce. In the periodontopathogen Tannerella forsythia, several proposed virulence factors carry strain-specifically either a pseudaminic or a legionaminic acid derivative as terminal sugar on an otherwise structurally identical, protein-bound oligosaccharide. This study aims to shed light on the transfer of either nonulosonic acid derivative on a proximal N-acetylmannosaminuronic acid residue within the O-glycan structure, exemplified with the bacterium's abundant S-layer glycoproteins...
March 16, 2017: Glycobiology
https://www.readbyqxmd.com/read/28334797/molecular-mechanism-governing-ratio-dependent-transcription-regulation-in-the-ccdab-operon
#8
Alexandra Vandervelde, Igor Drobnak, San Hadži, Yann G-J Sterckx, Thomas Welte, Henri De Greve, Daniel Charlier, Rouslan Efremov, Remy Loris, Jurij Lah
Bacteria can become transiently tolerant to several classes of antibiotics. This phenomenon known as persistence is regulated by small genetic elements called toxin-antitoxin modules with intricate yet often poorly understood self-regulatory features. Here, we describe the structures of molecular complexes and interactions that drive the transcription regulation of the ccdAB toxin-antitoxin module. Low specificity and affinity of the antitoxin CcdA2 for individual binding sites on the operator are enhanced by the toxin CcdB2, which bridges the CcdA2 dimers...
February 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334743/comparative-genomic-analysis-of-translation-initiation-mechanisms-for-genes-lacking-the-shine-dalgarno-sequence-in-prokaryotes
#9
So Nakagawa, Yoshihito Niimura, Takashi Gojobori
In prokaryotes, translation initiation is believed to occur through an interaction between the 3΄ tail of a 16S rRNA and a corresponding Shine-Dalgarno (SD) sequence in the 5΄ untranslated region (UTR) of an mRNA. However, some genes lack SD sequences (non-SD genes), and the fraction of non-SD genes in a genome varies depending on the prokaryotic species. To elucidate non-SD translation initiation mechanisms in prokaryotes from an evolutionary perspective, we statistically examined the nucleotide frequencies around the initiation codons in non-SD genes from 260 prokaryotes (235 bacteria and 25 archaea)...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334702/in-vitro-antibacterial-activity-of-7-substituted-6-fluoroquinolone-and-7-substituted-6-8-difluoroquinolone-derivatives
#10
Socorro Leyva-Ramos, Denisse de Loera, Jaime Cardoso-Ortiz
BACKGROUND: Fluoroquinolones are widely prescribed synthetic antimicrobial agents. Quinolones act by converting their targets, gyrase and topoisomerase IV, into toxic enzymes that fragment the bacterial chromosome; the irreversible DNA damage eventually causes the killing of bacteria. Thorough knowledge of the structure-activity relationship of quinolones is essential for the development of new drugs with improved activity against resistant strains. METHODS: The compounds were screened for their antibacterial activity against 4 representing strains using the Kirby-Bauer disk diffusion method...
March 24, 2017: Chemotherapy
https://www.readbyqxmd.com/read/28334274/interactive-effects-of-multiple-climate-change-factors-on-ammonia-oxidizers-and-denitrifiers-in-a-temperate-steppe
#11
Cuijing Zhang, Jupei Shen, Yifei Sun, Juntao Wang, Limei Zhang, Zhongling Yang, Hongyan Han, Shiqiang Wan, Jizheng He
Global climate change could have profound effects on belowground microbial communities and subsequently affect soil biogeochemical processes. The interactive effects of multiple co-occurring climate change factors on microbially-mediated processes are not well understood. A four-factorial field experiment with elevated CO2, watering, nitrogen (N) addition and night warming was conducted in a temperate steppe of northern China. Real-time polymerase chain reaction and terminal-restriction fragment length polymorphism, combined with clone library techniques were applied to examine the effects of those climate change factors on N-related microbial abundance and community composition...
March 15, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28334087/microbial-community-structure-and-biodiversity-of-size-fractionated-granules-in-a-partial-nitritation-anammox-process
#12
Jinghuan Luo, Hui Chen, Xiaoyu Han, Yanfang Sun, Zhiguo Yuan, Jianhua Guo
The performance of a granule-based partial nitritation-anammox process is expected to be affected by the granular size distribution, but little is known about impacts of granule sizes on the microbial community structure and diversity. To reveal how the microbial composition and diversity vary with granular sizes, granules from a partial nitritation-anammox reactor were size-fractionated into five classes (i.e. <0.2, 0.2-0.5, 0.5-0.8, 0.8-1.0, >1.0 mm). Microbial communities and diversity in these five size-fractionated granules were investigated using 16S rRNA gene high-throughput sequencing...
February 18, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28334005/multi-scale-model-of-drug-induced-adaptive-resistance-of-gram-negative-bacteria-to-polymyxin-b
#13
Wojciech Krzyzanski, Gauri G Rao
The purpose of this report is to apply multi-scale modeling using the theory of physiologically structured populations (PSP) to develop a mathematical model for antimicrobial resistance based on a heterogeneous distribution of receptors and affinities among bacterial cells. The theory has been tested on data obtained from an in vitro static time-kill infection model analyzing the pharmacodynamics of polymyxin B against Gram-negative bacteria. The drug binding parameter KD (dissociation equilibrium constant) is assumed to vary between the bacterial cells...
2017: PloS One
https://www.readbyqxmd.com/read/28333237/new-paenibacillus-strain-produces-a-family-of-linear-and-cyclic-antimicrobial-lipopeptides-cyclization-is-not-essential-for-their-antimicrobial-activity
#14
En Huang, Xu Yang, Liwen Zhang, Sun Hee Moon, Ahmed E Yousef
A new bacterial isolate, Paenibacillus sp. OSY-N, showed potent antimicrobial activity against Gram-negative and Gram-positive bacteria. Antimicrobials produced by this strain were purified by reverse-phase high performance liquid chromatography (HPLC). Structural analysis, using mass spectrometry (MS), of a single active HPLC fraction revealed two known cyclic lipopeptides, BMY-28160 and permetin A, a new cyclic lipopeptide, and the linear counterparts of these cyclic compounds. The latter were designated as paenipeptin A, B and C, respectively...
February 25, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28333060/can-dna-sequencing-show-differences-between-microbial-communities-in-polish-and-danish-wastewater-treatment-plants
#15
A Miłobędzka, A Muszyński
The microbial populations in the activated sludge of two Polish wastewater treatment plants (WWTPs) were identified and quantified using Illumina sequencing of 16S ribosomal RNA amplicons over a 2-year period. Their dynamics over time were compared to Danish WWTPs (data collected in previous studies by Center for Microbial Communities, Aalborg University). The bacterial communities in Polish and Danish WWTPs were similar to each other, but the microbial diversity in Polish WWTPs was lower. The dominant genera in Polish WWTPs were more abundant than in Danish WWTPs; 30 of them constituted more than half the of activated sludge community...
March 2017: Water Science and Technology: a Journal of the International Association on Water Pollution Research
https://www.readbyqxmd.com/read/28333044/effects-of-c-n-ratio-on-nitrous-oxide-production-from-nitrification-in-a-laboratory-scale-biological-aerated-filter-reactor
#16
Qiang He, Yinying Zhu, Leilei Fan, Hainan Ai, Xiaoliu Huangfu, Mei Chen
Emission of nitrous oxide (N2O) during biological wastewater treatment is of growing concern. This paper reports findings of the effects of carbon/nitrogen (C/N) ratio on N2O production rates in a laboratory-scale biological aerated filter (BAF) reactor, focusing on the biofilm during nitrification. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) and microelectrode technology were utilized to evaluate the mechanisms associated with N2O production during wastewater treatment using BAF...
March 2017: Water Science and Technology: a Journal of the International Association on Water Pollution Research
https://www.readbyqxmd.com/read/28331940/acute-thymic-involution-and-mechanisms-for-recovery
#17
REVIEW
Abdur Rahman Ansari, Huazhen Liu
Acute thymic involution (ATI) is usually regarded as a virulence trait. It is caused by several infectious agents (bacteria, viruses, parasites, fungi) and other factors, including stress, pregnancy, malnutrition and chemotherapy. However, the complex mechanisms that operate during ATI differ substantially from each other depending on the causative agent. For instance, a transient reduction in the size and weight of the thymus and depletion of populations of T cell subsets are hallmarks of ATI in many cases, whereas severe disruption of the anatomical structure of the organ is also associated with some factors, including fungal, parasitic and viral infections...
March 22, 2017: Archivum Immunologiae et Therapiae Experimentalis
https://www.readbyqxmd.com/read/28331079/characterization-and-vaccine-potential-of-membrane-vesicles-produced-by-francisella-noatunensis-sup-orientalis-in-an-adult-zebrafish-model
#18
Leidy Lagos, Julia I Tandberg, Urska Repnik, Preben Boysen, Erik Ropstad, Deepa Varkey, Ian T Paulsen, Hanne C Winther-Larsen
Vaccine development against extracellular bacteria has been important for the sustainability of the aquaculture industry. In contrast, infections with intracellular pathogens remain largely an unresolved problem. Francisella noatunensis subspecies orientalis (Fno) are Gram-negative, facultative intracellular bacteria that cause the disease francisellosis in fish. Francisellosis is commonly characterized as a chronic granulomatous disease with high morbidity and can result in high mortality depending on the host...
March 22, 2017: Clinical and Vaccine Immunology: CVI
https://www.readbyqxmd.com/read/28330987/architecture-and-mechanism-of-the-central-gear-in-an-ancient-molecular-timer
#19
REVIEW
Martin Egli
Molecular clocks are the product of natural selection in organisms from bacteria to human and their appearance early in evolution such as in the prokaryotic cyanobacterium Synechococcus elongatus suggests that these timers served a crucial role in genetic fitness. Thus, a clock allows cyanobacteria relying on photosynthesis and nitrogen fixation to temporally space the two processes and avoid exposure of nitrogenase carrying out fixation to high levels of oxygen produced during photosynthesis. Fascinating properties of molecular clocks are the long time constant, their precision and temperature compensation...
March 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/28330333/extraction-and-bioactive-profile-of-the-compounds-produced-by-rhodococcus-sp-vld-10
#20
Bokka Yellamanda, Muvva Vijayalakshmi, Alapati Kavitha, Dorigondla Kumar Reddy, Yenamandra Venkateswarlu
A potent actinobacterial strain isolated from the marine samples of Bheemunipatnam beach, Visakhapatnam, India, was identified as Rhodococcus sp. VLD-10 using the conventional and genomic (16S rRNA) approaches. Bioactive compounds responsible for the antimicrobial activity of the strain were elucidated by cultivating the strain VLD-10 in a modified yeast extract-malt extract-lactose broth followed by subsequent chromatographic and spectroscopic analyses. Extraction, purification, and structural confirmation of five compounds, viz...
December 2016: 3 Biotech
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