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https://www.readbyqxmd.com/read/28340372/shotgun-metagenomic-sequencing-reveals-freshwater-beach-sands-as-reservoir-of-bacterial-pathogens
#1
Mahi M Mohiuddin, Yasser Salama, Herb E Schellhorn, G Brian Golding
Recreational waters and adjacent beach sands harbor complex microbial communities which may contain human pathogens that cannot be detected by conventional methods. Here, we investigate the diversity of bacterial populations inhabiting four freshwater beaches of the Great Lakes region using shotgun metagenomic sequencing approach. Our analysis suggests that average taxonomic richness and alpha diversity are significantly higher (P < 0.001) in beach sands compared to the corresponding water environments...
March 1, 2017: Water Research
https://www.readbyqxmd.com/read/28339466/in-silico-search-for-modifier-genes-associated-with-pancreatic-and-liver-disease-in-cystic-fibrosis
#2
Pascal Trouvé, Emmanuelle Génin, Claude Férec
Cystic Fibrosis is the most common lethal autosomal recessive disorder in the white population, affecting among other organs, the lung, the pancreas and the liver. Whereas Cystic Fibrosis is a monogenic disease, many studies reveal a very complex relationship between genotype and clinical phenotype. Indeed, the broad phenotypic spectrum observed in Cystic Fibrosis is far from being explained by obvious genotype-phenotype correlations and it is admitted that Cystic Fibrosis disease is the result of multiple factors, including effects of the environment as well as modifier genes...
2017: PloS One
https://www.readbyqxmd.com/read/28335808/potential-for-hydrogen-oxidizing-chemolithoautotrophic-and-diazotrophic-populations-to-initiate-biofilm-formation-in-oligotrophic-deep-terrestrial-subsurface-waters
#3
Xiaofen Wu, Karsten Pedersen, Johanna Edlund, Lena Eriksson, Mats Åström, Anders F Andersson, Stefan Bertilsson, Mark Dopson
BACKGROUND: Deep terrestrial biosphere waters are separated from the light-driven surface by the time required to percolate to the subsurface. Despite biofilms being the dominant form of microbial life in many natural environments, they have received little attention in the oligotrophic and anaerobic waters found in deep bedrock fractures. This study is the first to use community DNA sequencing to describe biofilm formation under in situ conditions in the deep terrestrial biosphere. RESULTS: In this study, flow cells were attached to boreholes containing either "modern marine" or "old saline" waters of different origin and degree of isolation from the light-driven surface of the earth...
March 23, 2017: Microbiome
https://www.readbyqxmd.com/read/28334273/gwas-summary-based-pathway-analysis-correcting-for-the-genetic-confounding-impact-of-environmental-exposures
#4
Qianrui Fan, Feng Zhang, Wenyu Wang, Jiawen Xu, Jingcan Hao, Awen He, Yan Wen, Ping Li, Xiao Liang, Yanan Du, Li Liu, Cuiyan Wu, Sen Wang, Xi Wang, Yujie Ning, Xiong Guo
Genome-wide association study (GWAS)-based pathway association analysis is a powerful approach for the genetic studies of human complex diseases. However, the genetic confounding effects of environment exposure-related genes can decrease the accuracy of GWAS-based pathway association analysis of target diseases. In this study, we developed a pathway association analysis approach, named Mendelian randomization-based pathway enrichment analysis (MRPEA), which was capable of correcting the genetic confounding effects of environmental exposures, using the GWAS summary data of environmental exposures...
March 8, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28333069/environmental-enrichment-in-kennelled-pit-bull-terriers-canis-lupus-familiaris
#5
Jenna Kiddie, Anna Bodymore, Alex Dittrich
Although social enrichment can be considered beneficial in helping dogs cope with the kennel environment, when taking individual needs into account, it places a large demand on the carers and may not be appropriate in under-resourced kennels. Some kennels are also designed in such a way that there is too much social interaction, in that individuals cannot choose to distance themselves from conspecifics. This study therefore aimed to assess the effects of easily accessible enrichment on the behaviour of kennelled Pit Bull Terrier type dogs rescued from a dog-fighting ring in the Philippines...
March 23, 2017: Animals: An Open Access Journal From MDPI
https://www.readbyqxmd.com/read/28328870/the-effect-of-early-life-experience-environment-and-genetic-factors-on-spontaneous-home-cage-aggression-related-wounding-in-male-c57bl-6-mice
#6
Brianna N Gaskill, Aurora M Stottler, Joseph P Garner, Christina W Winnicker, Guy B Mulder, Kathleen R Pritchett-Corning
Aggression is a major welfare issue in mice, particularly when mice unfamiliar to each other are first placed in cages, as happens on receipt from a vendor, and following cage cleaning. Injuries from aggression are the second leading cause of unplanned euthanasia in mice, following ulcerative dermatitis. Commonly employed strategies for reducing aggression-related injury are largely anecdotal, and may even be counterproductive. Here we report a series of experiments testing potential explanations and interventions for post-shipping aggression-related injuries in C57BL/6 mice...
March 22, 2017: Lab Animal
https://www.readbyqxmd.com/read/28328175/preparation-and-application-of-epitope-magnetic-molecularly-imprinted-polymers-for-enrichment-of-sulfonamide-antibiotics-in-water
#7
Yufeng Hu, Cheng Wang, Xiangdao Li, Lifen Liu
Sulfonamides, which are widely used synthetic antibiotics, are hydrophilic and stable. They can easily migrate into the environment and aquatic animals, and increase the risk of cancer, drug resistance, and allergic symptoms if consumed by humans. Here, we developed an epitope magnetic imprinting approach to enrich multiple sulfonamide antibiotics from a water sample. Epitope magnetic molecularly imprinted polymers (EMMIPs) were prepared by free-radical polymerization using vinyl-functioned Fe3 O4 as a core, sulfanilamide (SA) as a dummy template, methacrylic acid as a functional monomer, and ethylene glycol dimethacrylate as a cross-linker...
March 22, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28326069/different-bacterial-communities-involved-in-peptide-decomposition-between-normoxic-and-hypoxic-coastal-waters
#8
Shuting Liu, Boris Wawrik, Zhanfei Liu
Proteins and peptides are key components of the labile dissolved organic matter pool in marine environments. Knowing which types of bacteria metabolize peptides can inform the factors that govern peptide decomposition and further carbon and nitrogen remineralization in marine environments. A (13)C-labeled tetrapeptide, alanine-valine-phenylalanine-alanine (AVFA), was added to both surface (normoxic) and bottom (hypoxic) seawater from a coastal station in the northern Gulf of Mexico for a 2-day incubation experiment, and bacteria that incorporated the peptide were identified using DNA stable isotope probing (SIP)...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28323889/towards-a-critical-evaluation-of-an-empirical-and-volume-based-solvation-function-for-ligand-docking
#9
Heloisa S Muniz, Alessandro S Nascimento
Molecular docking is an important tool for the discovery of new biologically active molecules given that the receptor structure is known. An excellent environment for the development of new methods and improvement of the current methods is being provided by the rapid growth in the number of proteins with known structure. The evaluation of the solvation energies outstands among the challenges for the modeling of the receptor-ligand interactions, especially in the context of molecular docking where a fast, though accurate, evaluation is ought to be achieved...
2017: PloS One
https://www.readbyqxmd.com/read/28321213/cd161-tconv-and-cd161-treg-share-a-transcriptional-and-functional-phenotype-despite-limited-overlap-in-tcr%C3%AE-repertoire
#10
Chantal L Duurland, Chrysothemis C Brown, Ryan F L O'Shaughnessy, Lucy R Wedderburn
Human regulatory T cells (Treg) are important in immune regulation, but can also show plasticity in specific settings. CD161 is a lectin-like receptor and its expression identifies an effector-like Treg population. Here, we determined how CD161(+) Treg relate to CD161(+) conventional T cells (Tconv). Transcriptional profiling identified a shared transcriptional signature between CD161(+) Tconv and CD161(+) Treg, which is associated with T helper (Th)1 and Th17 cells, and tissue homing, including high expression of gut-homing receptors...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28320881/lpto-pg0027-is-required-for-lipid-a-1-phosphatase-activity-in-porphyromonas-gingivalis-w50
#11
Minnie Rangarajan, Joseph Aduse-Opoku, Ahmed Hashim, Graham McPhail, Zofia Luklinska, M Florencia Haurat, Mario F Feldman, Michael A Curtis
Porphyromonas gingivalis produces outer-membrane vesicles (OMVs) rich in virulence factors including cysteine-proteases and A-LPS, one of the two lipopolysaccharides (LPS) produced by this organism. Previous studies had suggested that A-LPS together with PG0027, an outer-membrane (OM) protein, may be involved in OMV-formation. Their roles in this process were examined using parent W50 and mutant ΔPG0027 strains. Inactivation of PG0027 caused a reduction in yield of OMVs. Lipid A from cells and OMVs of P. gingivalis W50 and ΔPG0027 strains were analysed by matrix-assisted laser-desorption-ionisation-time of flight mass spectrometry (MALDI-TOF- MS)...
March 20, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28318465/lunch-at-the-library-examination-of-a-community-based-approach-to-addressing-summer-food-insecurity
#12
Janine S Bruce, Monica M De La Cruz, Gala Moreno, Lisa J Chamberlain
OBJECTIVE: To examine a library-based approach to addressing food insecurity through a child and adult summer meal programme. The study examines: (i) risk of household food insecurity among participants; (ii) perspectives on the library meal programme; and (iii) barriers to utilizing other community food resources. DESIGN: Quantitative surveys with adult participants and qualitative semi-structured interviews with a sub-sample of adult participants. SETTING: Ten libraries using public and private funding to serve meals to children and adults for six to eight weeks in low-income Silicon Valley communities (California, USA) during summer 2015...
March 20, 2017: Public Health Nutrition
https://www.readbyqxmd.com/read/28316900/influence-of-environmental-factors-on-biodegradation-of-quinalphos-by-bacillus-thuringiensis
#13
Venkata Subba Reddy Gangireddygari, Praveen Kumar Kalva, Khayalethu Ntushelo, Manjunatha Bangeppagari, Arnaud Djami Tchatchou, Rajasekhar Reddy Bontha
BACKGROUND: The extensive and intensive uses of organophosphorus insecticide-quinalphos in agriculture, pose a health hazard to animals, humans, and environment because of its persistence in the soil and crops. However, there is no much information available on the biodegradation of quinalphos by the soil micro-organisms, which play a significant role in detoxifying pesticides in the environment; so research is initiated in biodegradation of quinalphos. RESULTS: A soil bacterium strain, capable of utilizing quinalphos as its sole source of carbon and energy, was isolated from soil via the enrichment method on minimal salts medium (MSM)...
2017: Environmental Sciences Europe
https://www.readbyqxmd.com/read/28314792/comparative-profiling-of-small-rnas-of-pig-seminal-plasma-and-ejaculated-and-epididymal-sperm
#14
Cai Chen, Han Wu, Dan Shen, Saisai Wang, Li Zhang, Xiaoyan Wang, Bo Gao, Tianwen Wu, Bichun Li, Kui Li, Chengyi Song
The similarities and differences of small RNAs in seminal plasma, epididymal sperm and ejaculated sperm remain largely undefined. We conducted a systematic comparative analysis of small RNA profiles in pig ejaculated sperm, epididymal sperm and seminal plasma and found that the diversity distribution of small RNA species was generally similar, whereas the abundance of small RNAs is dramatically different across the three libraries; miRNAs and small RNAs derived from rRNA, tRNA, small nuclear RNA, 7SK RNA, NRON RNA and cis-regulatory RNA were enriched in the three libraries, but piRNA was absent...
March 17, 2017: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/28299401/sodium-lauryl-ether-sulfate-sles-degradation-by-nitrate-reducing-bacteria
#15
Ana M S Paulo, Rozelin Aydin, Mauricio R Dimitrov, Harm Vreeling, Ana J Cavaleiro, Pedro A García-Encina, Alfons J M Stams, Caroline M Plugge
The surfactant sodium lauryl ether sulfate (SLES) is widely used in the composition of detergents and frequently ends up in wastewater treatment plants (WWTPs). While aerobic SLES degradation is well studied, little is known about the fate of this compound in anoxic environments, such as denitrification tanks of WWTPs, nor about the bacteria involved in the anoxic biodegradation. Here, we used SLES as sole carbon and energy source, at concentrations ranging from 50 to 1000 mg L(-1), to enrich and isolate nitrate-reducing bacteria from activated sludge of a WWTP with the anaerobic-anoxic-oxic (A(2)/O) concept...
March 15, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28295189/unpacking-socio-economic-risks-for-reading-and-academic-self-concept-in-primary-school-differential-effects-and-the-role-of-the-preschool-home-learning-environment
#16
Alexandria Crampton, James Hall
BACKGROUND: Uncertainty remains concerning how children's reading and academic self-concept are related and how these are differentially affected by social disadvantage and home learning environments. AIMS: To contrast the impacts of early socio-economic risks and preschool home learning environments upon British children's reading abilities and academic self-concept between 7 and 10 years. SAMPLE: n = 3,172 British children aged 3-10 years and their families...
March 13, 2017: British Journal of Educational Psychology
https://www.readbyqxmd.com/read/28295020/lactobacillus-johnsonii-supplementation-attenuates-respiratory-viral-infection-via-metabolic-reprogramming-and-immune-cell-modulation
#17
W Fonseca, K Lucey, S Jang, K E Fujimura, A Rasky, H-A Ting, J Petersen, C C Johnson, H A Boushey, E Zoratti, D R Ownby, A M Levine, K R Bobbit, S V Lynch, N W Lukacs
Regulation of respiratory mucosal immunity by microbial-derived metabolites has been a proposed mechanism that may provide airway protection. Here we examine the effect of oral Lactobacillus johnsonii supplementation on metabolic and immune response dynamics during respiratory syncytial virus (RSV) infection. L. johnsonii supplementation reduced airway T helper type 2 cytokines and dendritic cell (DC) function, increased regulatory T cells, and was associated with a reprogrammed circulating metabolic environment, including docosahexanoic acid (DHA) enrichment...
March 15, 2017: Mucosal Immunology
https://www.readbyqxmd.com/read/28293193/isobaric-tags-for-relative-and-absolute-quantitation-itraq-based-proteomic-analysis-of-hugan-qingzhi-and-its-protective-properties-against-free-fatty-acid-induced-l02-hepatocyte-injury
#18
Fan Xia, Xiaorui Yao, Waijiao Tang, Chunxin Xiao, Miaoting Yang, Benjie Zhou
In previous research, Hugan Qingzhi, a traditional Chinese medicine, was shown to have protective effects against hepatic steatosis. However, its activity against non-alcoholic fatty liver disease (NAFLD) and the mechanisms by which it exerts its effects remain unknown. In the present study, the effects of Hugan Qingzhi on free fatty acid (FFA)-induced L02 cells were examined. The techniques of iTRAQ labeling, together with strong cation exchange-non-liquid chromatography-tandem mass spectrometry (SCX-non-LC-MS/MS) analysis and serum pharmacology, were used to evaluate the effects of Hugan Qingzhi-medicated serum on FFA-induced L02 hepatocyte injury...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28292322/revealing-large-metagenomic-regions-through-long-dna-fragment-hybridization-capture
#19
Cyrielle Gasc, Pierre Peyret
BACKGROUND: High-throughput DNA sequencing technologies have revolutionized genomic analysis, including the de novo assembly of whole genomes from single organisms or metagenomic samples. However, due to the limited capacity of short-read sequence data to assemble complex or low coverage regions, genomes are typically fragmented, leading to draft genomes with numerous underexplored large genomic regions. Revealing these missing sequences is a major goal to resolve concerns in numerous biological studies...
March 14, 2017: Microbiome
https://www.readbyqxmd.com/read/28290150/extracellular-matrix-modulation-is-driven-by-experience-dependent-plasticity-during-stroke-recovery
#20
Miriana Jlenia Quattromani, Mathilde Pruvost, Carla Guerreiro, Fredrik Backlund, Elisabet Englund, Anders Aspberg, Tomasz Jaworski, Jakob Hakon, Karsten Ruscher, Leszek Kaczmarek, Denis Vivien, Tadeusz Wieloch
Following stroke, complete cellular death in the ischemic brain area may ensue, with remaining brain areas undergoing tissue remodelling to various degrees. Experience-dependent brain plasticity exerted through an enriched environment (EE) promotes remodelling after central nervous system injury, such as stroke. Post-stroke tissue reorganization is modulated by growth inhibitory molecules differentially expressed within the ischemic hemisphere, like chondroitin sulfate proteoglycans found in perineuronal nets (PNNs)...
March 13, 2017: Molecular Neurobiology
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