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https://www.readbyqxmd.com/read/29054116/t-cell-epitope-content-comparison-epicc-of-swine-h1-influenza-a-virus-hemagglutinin
#1
Andres H Gutiérrez, Vicki Rapp-Gabrielson, Frances E Terry, Crystal Loving, Leonard Moise, William D Martin, Anne S De Groot
BACKGROUND: Predicting vaccine efficacy against emerging pathogen strains is a significant problem in human and animal vaccine design. T cell epitope cross-conservation may play an important role in cross-strain vaccine efficacy. While influenza A virus (IAV) hemagglutination inhibition (HI) antibody titers are widely used to predict protective efficacy of one IAV vaccine against new strains, no similar correlate of protection has been identified for T cell epitopes. OBJECTIVE: We developed a computational method (EpiCC) that facilitates pairwise comparison of protein sequences based on an immunological property - T cell epitope content - rather than sequence identity, and evaluated its ability to classify swine IAV strain relatedness to estimate cross-protective potential of a vaccine strain for circulating viruses...
October 20, 2017: Influenza and Other Respiratory Viruses
https://www.readbyqxmd.com/read/29054112/human-parainfluenza-virus-infection-in-severe-acute-respiratory-infection-cases-in-beijing-2014-2016-a-molecular-epidemiological-study
#2
Yang Pan, Yi Zhang, Shi Weixian, Xiaomin Peng, Shujuan Cui, Daitao Zhang, Guilan Lu, Yimeng Liu, Shuangsheng Wu, Peng Yang, Quanyi Wang
BACKGROUND: Severe Acute Respiratory Infection (SARI) threatens human health and even survival, causing a huge number of hospitalized patients every year. However, as one of the most common respiratory viruses circulated worldwide, the epidemiological and phylogenetic characteristics of human parainfluenza virus (HPIV) in these cases were not well known. METHODS: A molecular epidemiological study against HPIVs infection in SARIs was performed from Sep. 2014 to Aug...
October 20, 2017: Influenza and Other Respiratory Viruses
https://www.readbyqxmd.com/read/29054108/increase-in-pro-apoptotic-activity-of-inhibitory-pas-domain-protein-via-phosphorylation-by-mk2
#3
Shuya Kasai, Mary Jane Elizabeth Richardson, Satoru Torii, Ken-Ichi Yasumoto, Hiroki Shima, Kazuhiko Igarashi, Ken Itoh, Kazuhiro Sogawa, Kazutaka Murayama
Inhibitory PAS domain protein (IPAS) is a bifunctional protein that downregulates hypoxic gene expression and exerts pro-apoptotic activity by preventing pro-survival activity of Bcl-xL and its related factors. Pro-apoptotic activity of IPAS is attenuated by the activation of the PINK1-Parkin pathway, and involved in neuronal degeneration in an experimental mouse model of Parkinson's disease. The current study shows that phosphorylation of IPAS at Ser184 by MAPK-activated protein kinase 2 (MK2 or MAPKAPK2) enhances the pro-apoptotic function of IPAS...
October 20, 2017: FEBS Journal
https://www.readbyqxmd.com/read/29053985/rapid-cultivation-of-free-living-planktonic-anammox-cells
#4
Lei Zhang, Satoshi Okabe
Despite that anaerobic ammonium oxidizing (anammox) bacteria are key players in the global nitrogen cycle, no pure cultures are still available. Planktonic cell culture with high purity is, therefore, essential for physiological and biochemical studies of anammox bacteria. However, development of such planktonic cell cultures requires an enormous amount of time and effort. Here we developed a novel rapid method for cultivating free-living planktonic anammox cells. First, anammox granules were physically dispersed, immobilized in 6% polyvinyl alcohol-4% sodium alginate (PVA-SA) gel beads, and then pre-cultured in an up-flow column reactor...
October 15, 2017: Water Research
https://www.readbyqxmd.com/read/29053983/conceptualizing-trust-in-community-academic-research-partnerships-using-concept-mapping-approach-a-multi-ctsa-study
#5
Gaurav Dave, Leah Frerichs, Jennifer Jones, Mimi Kim, Jennifer Schaal, Stefanie Vassar, Deepthi Varma, Catherine Striley, Corrine Ruktanonchai, Adina Black, Jennifer Hankins, Nakita Lovelady, Crystal Cene, Melissa Green, Tiffany Young, Shristi Tiwari, Ann Cheney, Linda Cottler, Greer Sullivan, Arleen Brown, Jessica Burke, Giselle Corbie-Smith
OBJECTIVES: Collaborations between communities, healthcare practices and academic institutions are a strategy to address health disparities. Trust is critical in the development and maintaining of effective collaborations. The aim of this pilot study was to engage stakeholders in defining determinants of trust in community academic research partnerships and to develop a framework for measuring trust. METHODS: The study was conducted by five collaborating National Institute of Health' Clinical and Translational Sciences Awardees...
October 12, 2017: Evaluation and Program Planning
https://www.readbyqxmd.com/read/29053977/suicidal-ideation-declines-with-improvement-in-the-subjective-symptoms-of-major-depression
#6
John G Keilp, Steven P Ellis, Marianne Gorlyn, Ainsley K Burke, Maria A Oquendo, J John Mann, Michael F Grunebaum
BACKGROUND: Suicidal ideation appears to be more strongly associated with subjective rather than neurovegetative symptoms of depression. Effective treatment, then, should produce reductions in suicidal ideation to the degree that these subjective symptoms are alleviated relative to treatment effects on other symptoms. METHODS: In a randomized clinical trial comparing paroxetine and bupropion for treatment of depression in patients with either suicidal ideation or past attempt, depression severity and suicidal ideation were assessed weekly during the 8-week study...
September 19, 2017: Journal of Affective Disorders
https://www.readbyqxmd.com/read/29053941/a-point-source-outbreak-of-coccidioidomycosis-among-a-highway-construction-crew
#7
Mark Nicas
Coccidioidomycosis is an infection caused by inhaling spores of the soil fungus Coccidioides immitis (hereafter termed Cocci). Cocci is endemic in certain areas of California. When soil containing the fungus is disturbed, as during earth-moving activities, respirable Cocci spores can become airborne and be inhaled by persons in the vicinity. This paper describes a cluster of seven Cocciodioidomycosis cases among a highway construction crew that occurred in June/July 2008 in Kern County, CA, which is among the most highly endemic regions for Cocci in California...
October 20, 2017: Journal of Occupational and Environmental Hygiene
https://www.readbyqxmd.com/read/29053911/investigating-the-minimal-clinically-important-difference-for-snot-22-symptom-domains-in-surgically-managed-chronic-rhinosinusitis
#8
Naweed I Chowdhury, Jess C Mace, Todd E Bodner, Jeremiah A Alt, Adam S Deconde, Joshua M Levy, Timothy L Smith
BACKGROUND: Prior work has described 5 domains within the 22-item Sino-Nasal Outcomes Test (SNOT-22) that allow for stratification of symptoms into similar clusters and that can be used to direct therapy. Although the outcomes of various interventions on these symptom domains have been reported, minimal clinically important difference (MCID) values have not been investigated, which has limited clinical interpretation of these results. METHODS: This study was designed as a secondary analysis of a prospective, multi-institutional, observational cohort...
October 20, 2017: International Forum of Allergy & Rhinology
https://www.readbyqxmd.com/read/29053853/genome-sequence-analysis-of-a-distinctive-italian-infectious-bursal-disease-virus
#9
V Felice, G Franzo, E Catelli, A Di Francesco, M Bonci, M Cecchinato, G Mescolini, D Giovanardi, P Pesente, C Lupini
In a recent study, an emerging infectious bursal disease virus (IBDV) genotype (ITA) was detected in IBDV-live vaccinated broilers without clinical signs of infectious bursal disease (IBD). VP2 sequence analysis showed that strains of the ITA genotype clustered separately from vaccine strains and from other IBDV reference strains, either classic or very virulent. In order to obtain a more exhaustive molecular characterization of the IBDV ITA genotype and speculate on its origin, genome sequencing of the field isolate IBDV/Italy/1829/2011, previously assigned to the ITA genotype, was performed, and the sequences obtained were compared to the currently available corresponding sequences...
October 10, 2017: Poultry Science
https://www.readbyqxmd.com/read/29053819/changes-in-immune-and-metabolic-gut-response-in-broilers-fed-%C3%AE-mannanase-in-%C3%AE-mannan-containing-diets
#10
R J Arsenault, J T Lee, R Latham, B Carter, M H Kogut
β-galactomannans found in soy-based broiler feed are known to cause physiological effects that are hypothesized to be related to gut inflammation. Previous studies have shown that the incorporation of β-mannanase in the diet or as a supplement results in improvements to certain performance parameters related to gut health and feed conversion. Using kinome analysis, we characterized the mechanism of β-galactomannan activity and supplementation with β-mannanase on the gut of commercial broilers to understand the mode of action...
September 14, 2017: Poultry Science
https://www.readbyqxmd.com/read/29053769/relationships-of-variations-in-the-tongue-microbiota-and-pneumonia-mortality-in-nursing-home-residents
#11
Shinya Kageyama, Toru Takeshita, Michiko Furuta, Mikiko Tomioka, Mikari Asakawa, Shino Suma, Kenji Takeuchi, Yukie Shibata, Yasuyuki Iwasa, Yoshihisa Yamashita
Background: Aspiration of oral debris, containing dense oral bacteria, is a major cause of pneumonia in elderly adults. This study investigated the relationship between tongue microbiota composition and incidence of pneumonia-related deaths, in nursing home residents. Methods: The subjects were assessed for health conditions, including their tongue microbiota, at baseline. We determined tongue microbiota profiles by 16S ribosomal RNA gene sequencing and clustering approach...
October 19, 2017: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/29053732/body-typing-of-children-and-adolescents-using-3d-body-scanning
#12
Henry Loeffler-Wirth, Mandy Vogel, Toralf Kirsten, Fabian Glock, Tanja Poulain, Antje Körner, Markus Loeffler, Wieland Kiess, Hans Binder
Three-dimensional (3D-) body scanning of children and adolescents allows the detailed study of physiological development in terms of anthropometrical alterations which potentially provide early onset markers for obesity. Here, we present a systematic analysis of body scanning data of 2,700 urban children and adolescents in the age range between 5 and 18 years with the special aim to stratify the participants into distinct body shape types and to describe their change upon development. In a first step, we extracted a set of eight representative meta-measures from the data...
2017: PloS One
https://www.readbyqxmd.com/read/29053730/assessment-of-intra-and-interregional-genetic-variation-in-the-eastern-red-backed-salamander-plethodon-cinereus-via-analysis-of-novel-microsatellite-markers
#13
Alexander C Cameron, Jeffry J Anderson, Robert B Page
The red-backed salamander (Plethodon cinereus) has long-served as a model system in ecology, evolution, and behavior, and studies surveying molecular variation in this species have become increasingly common over the past decade. However, difficulties are commonly encountered when extending microsatellite markers to populations that are unstudied from a genetic perspective due to high levels of genetic differentiation across this species' range. To ameliorate this issue, we used 454 pyrosequencing to identify hundreds of microsatellite loci...
2017: PloS One
https://www.readbyqxmd.com/read/29053724/accounting-for-the-complex-hierarchical-topology-of-eeg-phase-based-functional-connectivity-in-network-binarisation
#14
Keith Smith, Daniel Abásolo, Javier Escudero
Research into binary network analysis of brain function faces a methodological challenge in selecting an appropriate threshold to binarise edge weights. For EEG phase-based functional connectivity, we test the hypothesis that such binarisation should take into account the complex hierarchical structure found in functional connectivity. We explore the density range suitable for such structure and provide a comparison of state-of-the-art binarisation techniques, the recently proposed Cluster-Span Threshold (CST), minimum spanning trees, efficiency-cost optimisation and union of shortest path graphs, with arbitrary proportional thresholds and weighted networks...
2017: PloS One
https://www.readbyqxmd.com/read/29053714/atopic-asthmatic-immune-phenotypes-associated-with-airway-microbiota-and-airway-obstruction
#15
Benjamin A Turturice, Halvor S McGee, Brian Oliver, Melissa Baraket, Brian T Nguyen, Christian Ascoli, Ravi Ranjan, Asha Rani, David L Perkins, Patricia W Finn
BACKGROUND: Differences in asthma severity may be related to inflammation in the airways. The lower airway microbiota has been associated with clinical features such as airway obstruction, symptom control, and response to corticosteroids. OBJECTIVE: To assess the relationship between local airway inflammation, severity of disease, and the lower airway microbiota in atopic asthmatics. METHODS: A cohort of young adult, atopic asthmatics with intermittent or mild/moderate persistent symptoms (n = 13) were assessed via bronchoscopy, lavage, and spirometry...
2017: PloS One
https://www.readbyqxmd.com/read/29053711/evaluation-of-spoligotyping-snps-and-customised-miru-vntr-combination-for-genotyping-mycobacterium-tuberculosis-clinical-isolates-in-madagascar
#16
Rondroarivelo Rasoahanitralisoa, Niaina Rakotosamimanana, David Stucki, Christophe Sola, Sebastien Gagneux, Voahangy Rasolofo Razanamparany
BACKGROUND: Combining different molecular typing methods for Mycobacterium tuberculosis complex (MTBC) can be a powerful tool for molecular epidemiology-based investigation of TB. However, the current standard method that provides high discriminatory power for such a combination, mycobacterial interspersed repetitive units-variable numbers of tandem repeats typing (MIRU-VNTR), is laborious, time-consuming and often too costly for many resource-limited laboratories. We aimed to evaluate a reduced set of loci for MIRU-VNTR typing in combination with spoligotyping and SNP-typing for routine molecular epidemiology of TB...
2017: PloS One
https://www.readbyqxmd.com/read/29053643/genome-wide-identification-and-analysis-of-mapk-and-mapkk-gene-families-in-bread-wheat-triticum-aestivum-l
#17
Haoshuang Zhan, Hong Yue, Xian Zhao, Meng Wang, Weining Song, Xiaojun Nie
The mitogen-activated protein kinase (MAPK) cascade is a universal signal transduction module that plays a vital role in regulating growth and development, as well as environmental stress responses in plants. Wheat is one of the most important crops worldwide. Although the MAPK kinase kinase (MAP3K) family in wheat has been investigated, the MAPK and MAPK kinase (MAP2K) gene families remain unknown at present. Here, 54 MAPK and 18 MAPKK genes were identified in wheat using recent genomic information. Phylogenetic analysis of Triticum aestivum L...
October 20, 2017: Genes
https://www.readbyqxmd.com/read/29053635/differential-interaction-of-antimicrobial-peptides-with-lipid-structures-studied-by-coarse-grained-molecular-dynamics-simulations
#18
Galo E Balatti, Ernesto E Ambroggio, Gerardo D Fidelio, M Florencia Martini, Mónica Pickholz
In this work; we investigated the differential interaction of amphiphilic antimicrobial peptides with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid structures by means of extensive molecular dynamics simulations. By using a coarse-grained (CG) model within the MARTINI force field; we simulated the peptide-lipid system from three different initial configurations: (a) peptides in water in the presence of a pre-equilibrated lipid bilayer; (b) peptides inside the hydrophobic core of the membrane; and (c) random configurations that allow self-assembled molecular structures...
October 20, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29053633/diversity-and-phylogenetic-analyses-of-bacterial-symbionts-in-three-whitefly-species-from-southeast-europe
#19
Marisa Skaljac, Surapathrudu Kanakala, Katja Zanic, Jasna Puizina, Ivana Lepen Pleic, Murad Ghanim
Bemisia tabaci (Gennadius), Trialeurodes vaporariorum (Westwood), and Siphoninus phillyreae (Haliday) are whitefly species that harm agricultural crops in many regions of the world. These insects live in close association with bacterial symbionts that affect host fitness and adaptation to the environment. In the current study, we surveyed the infection of whitefly populations in Southeast Europe by various bacterial symbionts and performed phylogenetic analyses on the different symbionts detected. Arsenophonus and Hamiltonella were the most prevalent symbionts in all three whitefly species...
October 20, 2017: Insects
https://www.readbyqxmd.com/read/29053464/co-expression-network-approach-to-studying-the-effects-of-botulinum-neurotoxin-a
#20
Kavitha Mukund, Samuel R Ward, Richard L Lieber, Shankar Subramaniam
Botulinum Neurotoxin A (BoNT-A) is a potent neurotoxin with several clinical applications.The goal of this study was to utilize co-expression network theory to analyze temporal transcriptional data from skeletal muscle after BoNT-A treatment. Expression data for 2000 genes (extracted using a ranking heuristic) served as the basis for this analysis. Using weighted gene co-expression network analysis (WGCNA), we identified 19 co-expressed modules, further hierarchically clustered into 5 groups. Quantifying average expression and co-expression patterns across these groups revealed temporal aspects of muscle's response to BoNT-A...
October 16, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
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