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https://www.readbyqxmd.com/read/29351302/extension-of-the-viral-ecology-in-humans-using-viral-profile-hidden-markov-models
#1
Zurab Bzhalava, Emilie Hultin, Joakim Dillner
When human samples are sequenced, many assembled contigs are "unknown", as conventional alignments find no similarity to known sequences. Hidden Markov models (HMM) exploit the positions of specific nucleotides in protein-encoding codons in various microbes. The algorithm HMMER3 implements HMM using a reference set of sequences encoding viral proteins, "vFam". We used HMMER3 analysis of "unknown" human sample-derived sequences and identified 510 contigs distantly related to viruses (Anelloviridae (n = 1), Baculoviridae (n = 34), Circoviridae (n = 35), Caulimoviridae (n = 3), Closteroviridae (n = 5), Geminiviridae (n = 21), Herpesviridae (n = 10), Iridoviridae (n = 12), Marseillevirus (n = 26), Mimiviridae (n = 80), Phycodnaviridae (n = 165), Poxviridae (n = 23), Retroviridae (n = 6) and 89 contigs related to described viruses not yet assigned to any taxonomic family)...
2018: PloS One
https://www.readbyqxmd.com/read/29349904/lysosome-remodelling-and-adaptation-during-phagocyte-activation
#2
REVIEW
Victoria E B Hipolito, Erika Ospina-Escobar, Roberto J Botelho
Lysosomes are acidic and hydrolytic organelles responsible for receiving and digesting cargo acquired during endocytosis, phagocytosis, and autophagy. For macrophages and dendritic cells, the lysosome is kingpin, playing a direct role in microbe killing and antigen processing for presentation. Strikingly, the historic view that lysosomes are homogeneous and static organelles is being replaced with a more elegant paradigm, in which lysosomes are heterogeneous, dynamic and respond to cellular needs. For example, lysosomes are signaling platforms that integrate stress detection and molecular decision hubs like mTORC1 and AMPK to modulate cellular activity...
January 19, 2018: Cellular Microbiology
https://www.readbyqxmd.com/read/29349441/association-between-sn-2-fatty-acid-profiles-of-breast-milk-and-development-of-the-infant-intestinal-microbiome
#3
Tiemin Jiang, Bin Liu, Jufang Li, Xueyan Dong, Man Lin, Minghui Zhang, Junying Zhao, Yaohua Dai, Lijun Chen
Increasing evidence shows that host diet and gut microbes are related. Previous studies have shown the effects of specific dietary fatty acids (FAs) on intestinal microbiota, but little is known about the effect of the stereospecifically numbered sn-2 position in triglycerides (TG) of human milk on the gut microbiome of infants. This study aimed at examining possible effects of sn-2 FAs of human milk on the gut microbial development of breastfeeding babies. Sn-2 FAs and intestinal microbiota were assessed by GC-MS and high-throughput 16S rRNA sequencing, respectively...
January 19, 2018: Food & Function
https://www.readbyqxmd.com/read/29349359/resensitization-of-methicillin-resistant-staphylococcus-aureus-by-amoxapine-an-fda-approved-antidepressant
#4
Tyler J Wilson, Meghan S Blackledge, Patrick A Vigueira
The rapid increase in bacterial resistance to antibiotics is a global healthcare crisis. Non-antibiotic pharmaceuticals that have attained approval by the United States Food and Drug Administration have the potential to be repurposed as bacterial resistance-modifying agents and therefore could become valuable resources in our battle against antibiotic-resistant microbes. Amoxapine is a tetracyclic antidepressant used in the treatment of major depressive disorder. Here we demonstrate the ability of amoxapine to resensitize methicillin-resistant Staphylococcus aureus strain ATCC 43300 to oxacillin in both agar diffusion and broth microdilution assays...
January 2018: Heliyon
https://www.readbyqxmd.com/read/29348523/antibiotic-resistance-mutations-induced-in-growing-cells-of-bacillus-related-thermophiles
#5
Hirokazu Suzuki, Tatsunari Taketani, Jyumpei Kobayashi, Takashi Ohshiro
Stress-induced mutagenesis can assist pathogens in generating drug-resistant cells during antibiotic therapy; however, if and how antibiotics induce mutagenesis in microbes remains poorly understood. A non-pathogenic thermophile, Geobacillus kaustophilus HTA426, efficiently produces derivative cells resistant to rifampicin and streptomycin via rpoB and rpsL mutations, respectively. Here, we examined this phenomenon to suggest a novel mutagenic mode induced by antibiotics. Fluctuation analysis indicated that mutations occurred via spontaneous mutations during culture...
January 18, 2018: Journal of Antibiotics
https://www.readbyqxmd.com/read/29348236/a-global-atlas-of-the-dominant-bacteria-found-in-soil
#6
Manuel Delgado-Baquerizo, Angela M Oliverio, Tess E Brewer, Alberto Benavent-González, David J Eldridge, Richard D Bardgett, Fernando T Maestre, Brajesh K Singh, Noah Fierer
The immense diversity of soil bacterial communities has stymied efforts to characterize individual taxa and document their global distributions. We analyzed soils from 237 locations across six continents and found that only 2% of bacterial phylotypes (~500 phylotypes) consistently accounted for almost half of the soil bacterial communities worldwide. Despite the overwhelming diversity of bacterial communities, relatively few bacterial taxa are abundant in soils globally. We clustered these dominant taxa into ecological groups to build the first global atlas of soil bacterial taxa...
January 19, 2018: Science
https://www.readbyqxmd.com/read/29348167/thiosulfate-sulfurtransferase-like-domain-containing-1-protein-interacts-with-thioredoxin
#7
Marouane Libiad, Nicole Motl, David L Akey, Naoya Sakamoto, Eric R Fearon, Janet L Smith, Ruma Banerjee
Rhodanese domains are structural modules present in the sulfurtransferase superfamily. These domains can exist as single units, in tandem repeats or fused to domains with other activities. Despite their prevalence across species, the specific physiological roles of most sulfurtransferases are not known. Mammalian rhodanese and mercaptopyruvate sulfurtransferase are perhaps the best-studied members of this protein superfamily and are involved in hydrogen sulfide metabolism. The relatively unstudied human thiosulfate sulfurtransferase like domain-containing 1 (TSTD1) protein, a single-domain cytoplasmic sulfurtransferase, was also postulated to play a role in the sulfide oxidation pathway using thiosulfate to form glutathione persulfide, for subsequent processing in the mitochondrial matrix...
January 18, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29348087/phytochemical-screening-and-antibacterial-activity-of-different-solvent-extracted-samples-of-arisaema-jacquemontii
#8
Madiha Iqbal, Jehan Bakht, Mohammad Shafi
The current research was carried out to assess the antibacterial activities and phytochemical analysis of the methanol, n-hexane, ethyl acetate, n-butanol soluble fractions and aqueous extracts of the tubers of Arisaema jacquemontii. All the extracts were tested for their antibacterial potential at 1, 2 and 3 mg disc-1 concentrations against 6 bacterial strains through disc diffusion suseptibility assay. The data suggested that different extracts showed varying degree of growth inhibition against the tested microbes...
January 2018: Pakistan Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/29346530/bacterioplankton-composition-in-tropical-high-elevation-lakes-of-the-andean-plateau
#9
Pablo Aguilar, Cristina Dorador, Irma Vila, Ruben Sommaruga
High-elevation lakes in the tropics are subject to extreme environmental fluctuations and microbes may harbour a unique genomic repertoire, but their composition and diversity are largely unknown. Here we compared the planktonic bacterial community composition (BCC) and diversity of three tropical lakes located in the high Andean plateau (???4400 m above sea level) during the dry and wet season. Diversity in these lakes was higher in the cool and wet season than in the warm and dry one. OTUs composition was significantly different among lakes and between seasons...
January 16, 2018: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29346373/reconciling-pasteur-and-darwin-to-control-infectious-diseases
#10
Samuel Alizon, Pierre-Olivier Méthot
The continual emergence of new pathogens and the increased spread of antibiotic resistance in bacterial populations remind us that microbes are living entities that evolve at rates that impact public health interventions. Following the historical thread of the works of Pasteur and Darwin shows how reconciling clinical microbiology, ecology, and evolution can be instrumental to understanding pathology, developing new therapies, and prolonging the efficiency of existing ones.
January 18, 2018: PLoS Biology
https://www.readbyqxmd.com/read/29345309/microbial-mitigation-exacerbation-continuum-a-novel-framework-for-microbiome-effects-on-hosts-in-the-face-of-stress
#11
Aaron S David, Khum B Thapa-Magar, Michelle E Afkhami
A key challenge to understanding microbiomes and their role in ecological processes is contextualizing their effects on host organisms, particularly when faced with environmental stress. One influential theory, the Stress Gradient Hypothesis, might predict that the frequency of positive interactions increases with stressful conditions such that microbial taxa would mitigate harmful effects on host performance. Yet, equally plausible is that microbial taxa could exacerbate these effects. Here, we introduce the "Mitigation-Exacerbation Continuum" as a novel framework to conceptualize microbial mediation of stress...
January 18, 2018: Ecology
https://www.readbyqxmd.com/read/29343843/cathelicidin-oa1-a-novel-antioxidant-peptide-identified-from-an-amphibian-accelerates-skin-wound-healing
#12
Xiaoqing Cao, Ying Wang, Chunyun Wu, Xiaojie Li, Zhe Fu, Meifeng Yang, Wenxin Bian, Siyuan Wang, Yongli Song, Jing Tang, Xinwang Yang
Cathelicidins play pivotal roles in host defense. The discovery of novel cathelicidins is important research; however, despite the identification of many cathelicidins in vertebrates, few have been reported in amphibians. Here we identified a novel cathelicidin (named cathelicidin-OA1) from the skin of an amphibian species, Odorrana andersonii. Produced by posttranslational processing of a 198-residue prepropeptide, cathelicidin-OA1 presented an amino acid sequence of 'IGRDPTWSHLAASCLKCIFDDLPKTHN' and a molecular mass of 3038...
January 17, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29342973/biogenic-weathering-solubilization-of-iron-from-minerals-by-epilithic-freshwater-algae-and-cyanobacteria
#13
George E Mustoe
A sandstone outcrop exposed to freshwater seepage supports a diverse assemblage of photosynthetic microbes. Dominant taxa are two cyanophytes (Oscillatoria sp., Rivularia sp.) and a unicellular green alga (Palmellococcus sp.). Less abundant taxa include a filamentous green alga, Microspora, and the desmid Cosmarium. Biologic activity is evidenced by measured levels of chlorophyll and lipids. Bioassay methods confirm the ability of these microbes to dissolve and metabolize Fe from ferruginous minerals. Chromatographic analysis reveals citric acid as the likely chelating agent; this low molecular weight organic acid is detectable in interstitial fluid in the sandstone, measured as 0...
January 15, 2018: Microorganisms
https://www.readbyqxmd.com/read/29342414/bacilli-community-of-saline-alkaline-soils-from-the-ararat-plain-armenia-assessed-by-molecular-and-culture-based-methods
#14
Hovik Panosyan, Anna Hakobyan, Nils-Kåre Birkeland, Armen Trchounian
The bacterial community composition in the A horizon of a natural saline-alkaline soil located in Ararat Plain (Armenia) was studied using molecular and culture-based methods The sequence analysis of a 16S rRNA gene clone library and denaturing gradient gel electrophoresis (DGGE) profiles indicated dominance of Firmicutes populations. The majority of the sequences of the bacterial 16S rRNA gene library were close relatives of representatives belonging to the genera Halobacillus (41.2%), Piscibacillus (23.5%), Bacillus (23...
January 5, 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29342144/erratum-moving-beyond-microbiome-wide-associations-to-causal-microbe-identification
#15
Neeraj K Surana, Dennis L Kasper
This corrects the article DOI: 10.1038/nature25019.
January 17, 2018: Nature
https://www.readbyqxmd.com/read/29342073/structure-elucidation-of-unknown-metabolites-in-metabolomics-by-combined-nmr-and-ms-ms-prediction
#16
Rene M Boiteau, David W Hoyt, Carrie D Nicora, Hannah A Kinmonth-Schultz, Joy K Ward, Kerem Bingol
We introduce a cheminformatics approach that combines highly selective and orthogonal structure elucidation parameters; accurate mass, MS/MS (MS²), and NMR into a single analysis platform to accurately identify unknown metabolites in untargeted studies. The approach starts with an unknown LC-MS feature, and then combines the experimental MS/MS and NMR information of the unknown to effectively filter out the false positive candidate structures based on their predicted MS/MS and NMR spectra. We demonstrate the approach on a model mixture, and then we identify an uncatalogued secondary metabolite in Arabidopsis thaliana...
January 17, 2018: Metabolites
https://www.readbyqxmd.com/read/29342065/diagnosis-of-periprosthetic-joint-infection-the-potential-of-next-generation-sequencing
#17
Majd Tarabichi, Noam Shohat, Karan Goswami, Abtin Alvand, Randi Silibovsky, Katherine Belden, Javad Parvizi
BACKGROUND: Next-generation sequencing is a well-established technique for sequencing of DNA and has recently gained attention in many fields of medicine. Our aim was to evaluate the accuracy of next-generation sequencing in identifying the causative organism(s) in patients with periprosthetic joint infection. METHODS: In this prospective study, samples were collected from 65 revision arthroplasties (39 knees and 26 hips) and 17 primary arthroplasties (9 hips and 8 knees)...
January 17, 2018: Journal of Bone and Joint Surgery. American Volume
https://www.readbyqxmd.com/read/29341934/advances-in-the-delivery-of-antisense-oligonucleotides-for-combating-bacterial-infectious-diseases
#18
REVIEW
Xiao-Yan Xue, Xing-Gang Mao, Ying Zhou, Zhou Chen, Yue Hu, Zheng Hou, Ming-Kai Li, Jing-Ru Meng, Xiao-Xing Luo
Discovery and development of new antibacterial drugs against multidrug resistant bacterial strains have become more and more urgent. Antisense oligonucleotides (ASOs) show immense potential to control the spread of resistant microbes due to its high specificity of action, little risk to human gene expression, and easy design and synthesis to target any possible gene. However, efficient delivery of ASOs to their action sites with enough concentration remains a major obstacle, which greatly hampers their clinical application...
January 13, 2018: Nanomedicine: Nanotechnology, Biology, and Medicine
https://www.readbyqxmd.com/read/29340928/microbiota-signaling-pathways-that-influence-neurologic-disease
#19
REVIEW
Laura M Cox, Howard L Weiner
Though seemingly distinct and autonomous, emerging evidence suggests there is a bidirectional interaction between the intestinal microbiota and the brain. This crosstalk may play a substantial role in neurologic diseases, including anxiety, depression, autism, multiple sclerosis, Parkinson's disease, and, potentially, Alzheimer's disease. Long hypothesized by Metchnikoff and others well over 100 years ago, investigations into the mind-microbe axis is now seeing a rapid resurgence of research. If specific pathways and mechanisms of interaction are understood, it could have broad therapeutic potential, as the microbiome is environmentally acquired and can be modified to promote health...
January 16, 2018: Neurotherapeutics: the Journal of the American Society for Experimental NeuroTherapeutics
https://www.readbyqxmd.com/read/29340060/assessment-of-antimicrobial-and-wound-healing-effects-of-brevinin-2ta-against-the-bacterium-klebsiella-pneumoniae-in-dermally-wounded-rats
#20
Siqin Liu, Qilin Long, Yang Xu, Jun Wang, Zhongwei Xu, Lei Wang, Mei Zhou, Yuxin Wu, Tianbao Chen, Chris Shaw
Antimicrobial peptides (AMPs) are regarded as promising alternatives for antibiotics due to their inherent capacity to prevent microbial drug resistance. Amphibians are rich source of bioactive molecules, which provide numerous AMPs with various structures as drug candidates. Here, we isolated and identified a novel AMP Brevinin-2Ta (B-2Ta) from the skin secretion of the European frog, Pelophylax kl. esculentus. In vitro studies revealed that it showed broad antimicrobial activities against S. aureus, E. coli and C...
December 19, 2017: Oncotarget
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