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https://www.readbyqxmd.com/read/29126101/prefmd-a-web-server-for-protein-structure-refinement-via-molecular-dynamics-simulations
#1
Lim Heo, Michael Feig
Summary: Refinement of protein structure models is a long-standing problem in structural bioinformatics. Molecular dynamics-based methods have emerged as an avenue to achieve consistent refinement. The PREFMD web server implements an optimized protocol based on the method successfully tested in CASP11. Validation with recent CASP refinement targets shows consistent and more significant improvement in global structure accuracy over other state-of-the-art servers. Availability: PREFMD is freely available as a web server at http://feiglab...
November 8, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29121073/diffslc-a-graph-centrality-method-to-detect-essential-proteins-of-a-protein-protein-interaction-network
#2
Divya Mistry, Roger P Wise, Julie A Dickerson
Identification of central genes and proteins in biomolecular networks provides credible candidates for pathway analysis, functional analysis, and essentiality prediction. The DiffSLC centrality measure predicts central and essential genes and proteins using a protein-protein interaction network. Network centrality measures prioritize nodes and edges based on their importance to the network topology. These measures helped identify critical genes and proteins in biomolecular networks. The proposed centrality measure, DiffSLC, combines the number of interactions of a protein and the gene coexpression values of genes from which those proteins were translated, as a weighting factor to bias the identification of essential proteins in a protein interaction network...
2017: PloS One
https://www.readbyqxmd.com/read/29115890/exploiting-bilosomes-for-delivering-bioactive-polysaccharide-isolated-from-enteromorpha-intestinalis-for-hacking-hepatocellular-carcinoma
#3
Azza Abdelmageed Matloub, Alaa Hamed Salama, Hadeer Ahmed Aglan, Mona Mahmoud AbouSamra, Sahar Salah Mohamed ElSouda, Hanaa Hamdy Ahmed
Bile salts containing vesicles (bilosomes) represent a portentous vesicular carrier that showed prosperous results in delivering active moieties in the gastrointestinal tract (GIT). In this study, bilosomes were exploited to deliver sulphated polysaccharide-protein complexes of Enteromorpha intestinalis (EHEM) and enhance its activity against hepatocellular carcinoma as well as resist harsh GIT conditions. Bilosomes were prepared using the sodium salt of three different bile acids (cholic, deoxycholic, taurodeoxycholic) and two different non-ionic surfactants (Span 40 and 65)...
November 8, 2017: Drug Development and Industrial Pharmacy
https://www.readbyqxmd.com/read/29110065/fungi-in-gastrointestinal-tracts-of-human-and-mice-from-community-to-functions
#4
REVIEW
Jiayan Li, Daiwen Chen, Bing Yu, Jun He, Ping Zheng, Xiangbing Mao, Jie Yu, Junqiu Luo, Gang Tian, Zhiqing Huang, Yuheng Luo
Fungi are often ignored in studies on gut microbes because of their low level of presence (making up only 0.1% of the total microorganisms) in the gastrointestinal tract (GIT) of monogastric animals. Recent studies using novel technologies such as next generation sequencing have expanded our understanding on the importance of intestinal fungi in humans and animals. Here, we provide a comprehensive review on the fungal community, the so-called mycobiome, and their functions from recent studies in humans and mice...
November 6, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/29077956/butyrate-presence-in-distinct-gastrointestinal-tract-segments-modifies-differentially-digestive-processes-and-amino-acid-bioavailability-in-young-broiler-chickens
#5
P C A Moquet, S A Salami, L Onrust, W H Hendriks, R P Kwakkel
The hypothesis was tested that butyrate presence in the digesta of distinct gastrointestinal tract (GIT) segments of broilers leads to differential effects on digesta retention time, gut morphology, and proteolytic enzymatic activities, ultimately resulting in differences in protein digestibility. A total of 320 male day-old Ross 308 broilers were randomly assigned to 5 dietary treatments: 1) control (no butyrate), 2) unprotected butyrate (main activity in the crop and gastric regions), 3) tributyrin (main activity in the small intestine), 4) fat-coated butyrate (activity in the whole GIT) and 5) unprotected butyrate combined with tributyrin, each replicated 8 times...
October 25, 2017: Poultry Science
https://www.readbyqxmd.com/read/29050441/the-physiological-response-of-broiler-chickens-to-the-dietary-supplementation-of-the-bacteriocin-nisin-and-ionophore-coccidiostats
#6
B Kieronczyk, M Sassek, E Pruszynska-Oszmalek, P Kolodziejski, M Rawski, S Swiatkiewicz, D Józefiak
The aim of this study was to investigate the effect of dietary supplementation with nisin alone or in combination with salinomycin or monensin on broiler chickens in terms of growth performance, selected blood parameters, digestive enzyme activity, apparent nutrient digestibility, and tibiotarsus mineralization, as well as selected gastrointestinal tract (GIT) organ weights, intestinal length, and central immune organ weights. Two independent experiments, each including 400 one-day-old female Ross 308 chicks differing in ionophore coccidiostats, i...
September 1, 2017: Poultry Science
https://www.readbyqxmd.com/read/29046389/the-antibody-repertoire-of-colorectal-cancer
#7
Seong Won Cha, Stefano Bonissone, Seungjin Na, Pavel A Pevzner, Vineet Bafna
Immunotherapy is becoming increasingly important in the fight against cancers, utilizing and manipulating the body's immune response to treat tumors. Understanding the immune repertoire - the collection of immunological proteins - of treated and untreated cells is possible at the genomic, but technically difficult at the protein level. Standard protein databases do not include the highly divergent sequences of somatic rearranged immunoglobulin genes, and may lead to missed identifications in a mass spectrometry search...
October 18, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29038125/modulators-of-enterococcus-faecalis-cell-envelope-integrity-and-antimicrobial-resistance-influence-stable-colonization-of-the-mammalian-gastrointestinal-tract
#8
Ismael L Banla, Sushma Kommineni, Michael Hayward, Marinelle Rodrigues, Kelli L Palmer, Nita H Salzman, Christopher J Kristich
The Gram-positive bacterium Enterococcus faecalis is both a colonizer of the gastrointestinal tract (GIT) and an agent of serious nosocomial infections. Although typically required for pathogenesis, GIT colonization by E. faecalis is poorly understood. E. faecalis tolerates high concentrations of GIT antimicrobials like cholate and lysozyme, leading us to hypothesize that resistance to intestinal antimicrobials is essential for long-term GIT colonization. Analyses of E. faecalis mutants exhibiting defects in antimicrobial resistance revealed that IreK, a determinant of envelope integrity and antimicrobial resistance, is required for long-term GIT colonization...
October 16, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/29029643/an-integrated-methodology-for-assessing-the-impact-of-food-matrix-and-gastrointestinal-effects-on-the-biokinetics-and-cellular-toxicity-of-ingested-engineered-nanomaterials
#9
Glen M DeLoid, Yanli Wang, Klara Kapronezai, Laura Rubio Lorente, Roujie Zhang, Georgios Pyrgiotakis, Nagarjun V Konduru, Maria Ericsson, Jason C White, Roberto De La Torre-Roche, Hang Xiao, David Julian McClements, Philip Demokritou
BACKGROUND: Engineered nanomaterials (ENMs) are increasingly added to foods to improve their quality, sensory appeal, safety and shelf-life. Human exposure to these ingested ENMs (iENMS) is inevitable, yet little is known of their hazards. To assess potential hazards, efficient in vitro methodologies are needed to evaluate particle biokinetics and toxicity. These methodologies must account for interactions and transformations of iENMs in foods (food matrix effect) and in the gastrointestinal tract (GIT) that are likely to determine nano-biointeractions...
October 13, 2017: Particle and Fibre Toxicology
https://www.readbyqxmd.com/read/28959642/vinblastine-an-anticancer-drug-causes-constipation-and-oxidative-stress-as-well-as-others-disruptions-in-intestinal-tract-in-rat
#10
Kaïs Rtibi, Dhekra Grami, Slimen Selmi, Mohamed Amri, Hichem Sebai, Lamjed Marzouki
The purpose of this study is to examine the gastrointestinal disorders after injection of vinblastine (2 mg kg(-1) b.w. i.v.) in rats. Animals were divided into two equal groups: Group 1 was considered as a control group (NaCl, 0.9%). Group 2 was treated with intravenous injection of vinblastine for 7 days. Loperamide (2 mg kg(-1)) was injected in a saline solution subcutaneously to induce constipation in another group of rats during the same period. Fecal parameters of the different groups have been determined...
2017: Toxicology Reports
https://www.readbyqxmd.com/read/28946277/the-matrix-of-fruit-vegetables-modulates-the-gastrointestinal-bioaccessibility-of-polyphenols-and-their-impact-on-dietary-protein-digestibility
#11
Claire Dufour, Michèle Loonis, Mylène Delosière, Caroline Buffière, Noureddine Hafnaoui, Véronique Santé-Lhoutellier, Didier Rémond
Fruit and vegetables (F&V) polyphenols have numerous positive health effects, ascribed either to their antioxidant activity within the gastrointestinal tract (GIT) or to bioactivity of their absorbed metabolites. The effect of the F&V matrix on the gastrointestinal bioaccessibility of polyphenols was investigated along with its possible interaction with protein digestion. Minipigs were fed a complete meal with either cubed F&V (apple, plum, artichoke) added, or the corresponding phenolic extract (PE). Gastric and ileal chymes were kinetically collected over the postprandial period...
February 1, 2018: Food Chemistry
https://www.readbyqxmd.com/read/28930195/bioaccessibility-and-cellular-uptake-of-%C3%AE-carotene-encapsulated-in-model-o-w-emulsions-influence-of-initial-droplet-size-and-emulsifiers
#12
Wei Lu, Alan L Kelly, Song Miao
The effects of the initial emulsion structure (droplet size and emulsifier) on the properties of β-carotene-loaded emulsions and the bioavailability of β-carotene after passing through simulated gastrointestinal tract (GIT) digestion were investigated. Exposure to GIT significantly changed the droplet size, surface charge and composition of all emulsions, and these changes were dependent on their initial droplet size and the emulsifiers used. Whey protein isolate (WPI)-stabilized emulsion showed the highest β-carotene bioaccessibility, while sodium caseinate (SCN)-stabilized emulsion showed the highest cellular uptake of β-carotene...
September 20, 2017: Nanomaterials
https://www.readbyqxmd.com/read/28929046/application-of-three-dimensional-printing-for-colon-targeted-drug-delivery-systems
#13
REVIEW
Nitin B Charbe, Paul A McCarron, Majella E Lane, Murtaza M Tambuwala
Orally administered solid dosage forms currently dominate over all other dosage forms and routes of administrations. However, human gastrointestinal tract (GIT) poses a number of obstacles to delivery of the drugs to the site of interest and absorption in the GIT. Pharmaceutical scientists worldwide have been interested in colon drug delivery for several decades, not only for the delivery of the drugs for the treatment of colonic diseases such as ulcerative colitis and colon cancer but also for delivery of therapeutic proteins and peptides for systemic absorption...
April 2017: International Journal of Pharmaceutical Investigation
https://www.readbyqxmd.com/read/28888462/control-of-protein-digestion-under-simulated-gastrointestinal-conditions-using-biopolymer-microgels
#14
Zipei Zhang, Ruojie Zhang, David Julian McClements
Controlling the rate and extent of protein digestion within different regions of the human gastrointestinal tract (GIT) is important for regulating hormonal responses (such as hunger, satiety, and satiation) and immune responses (such as allergenicity). In this study, hydrogel beads (biopolymer microgels) were fabricated by injecting a solution of anionic alginate molecules into a solution of cationic calcium ions using a vibrating extrusion device. A model food protein (whey protein isolate, WPI) was mixed with the alginate solution prior to bead formation...
October 2017: Food Research International
https://www.readbyqxmd.com/read/28873701/encapsulation-of-omega-3-fatty-acids-in-nanoemulsions-and-microgels-impact-of-delivery-system-type-and-protein-addition-on-gastrointestinal-fate
#15
Fang Chen, Guang-Qin Fan, Zipei Zhang, Ruojie Zhang, Ze-Yuan Deng, David Julian McClements
Carefully designed delivery systems are required to encapsulate and protect omega-3 fatty acids in commercial food and beverage products, but then release them at the required site-of-action within the human gastrointestinal tract (GIT). Previously, we showed that the oxidative stability of flaxseed oil (a plant-based source of omega-3 fatty acids) encapsulated in nanoemulsion droplets or calcium alginate microgels (hydrogel beads) was improved using caseinate as a natural antioxidant. In this study, the impact of caseinate on the digestion of flaxseed oil encapsulated in these delivery systems was investigated using a simulated GIT...
October 2017: Food Research International
https://www.readbyqxmd.com/read/28854862/pediococcus-acidolactici-and-pediococcus-pentosaceus-isolated-from-a-rainbow-trout-ecosystem-have-probiotic-and-abf1-adsorbing-degrading-abilities-in-vitro
#16
Maria Pia Martinez, Maria Laura Gonzalez Pereyra, Gabriela Alejandra Pena, Valeria Poloni, Guillermina Fernandez Juri, Lilia Reneé Cavaglieri
Probiotics are being used in biological control of bacterial pathogens, as an alternative to antibiotics, to improve health and production parameters in fish farming. Fish farming production is severely affected by aflatoxins (AFs), which are a significant problem in aquaculture systems. Aflatoxins exert substantial impact on production, causing disease with high mortality and a gradual decline of reared fish stock quality. Some aspects of aflatoxicosis in fish, particularly its effects on the gastrointestinal tract, have not been well documented...
September 11, 2017: Food Additives & Contaminants. Part A, Chemistry, Analysis, Control, Exposure & Risk Assessment
https://www.readbyqxmd.com/read/28740169/analysis-of-newly-detected-tetracycline-resistance-genes-and-their-flanking-sequences-in-human-intestinal-bifidobacteria
#17
Na Wang, Xiaomin Hang, Min Zhang, Xianglong Liu, Hong Yang
Due to tetracycline abuse, the safe bifidobacteria in the human gastrointestinal intestinal tract (GIT) may serve as a reservoir of tetracycline resistance genes. In the present investigation of 92 bifidobacterial strains originating from the human GIT, tetracycline resistance in 29 strains was mediated by the tet(W), tet(O) or tet(S) gene, and this is the first report of tet(O)- and tet(S)-mediated tetracycline resistance in bifidobacteria. Antibiotic resistance genes harbored by bifidobacteria are transferred from other bacteria...
July 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28732078/impact-of-diabetes-mellitus-on-indeterminate-results-of-the-quantiferon-tb-gold-in-tube-test-a-propensity-score-matching-analysis
#18
Hong-Joon Shin, Tae-Ok Kim, Hyung-Joo Oh, Ha-Young Park, Jin-Sun Chang, Seong Ahn, Yu-Il Kim, Sung-Chul Lim, Yong-Soo Kwon
BACKGROUND: The sensitivity of interferon-gamma release assays (IGRAs) in the detection of Mycobacterium tuberculosis infection could be affected by conditions of immune dysregulation. For this reason, diabetes mellitus (DM) may increase the frequency of indeterminate results of IGRAs. However, there have been inconsistent reports of role of DM on indeterminate IGRA results. METHODS: We retrospectively reviewed all patients who underwent QuantiFERON-TB Gold In-Tube testing (QFT-GIT) at Chonnam National University Hospital...
2017: PloS One
https://www.readbyqxmd.com/read/28609116/the-underexposed-role-of-food-matrices-in-probiotic-products-reviewing-the-relationship-between-carrier-matrices-and-product-parameters
#19
Joost Flach, Mark van der Waal, Maurits van den Nieuwboer, Eric Claassen, Olaf Larsen
Probiotic microorganisms are increasingly incorporated into food matrices in order to confer proposed health benefits on the consumer. It is important that the health benefits, sensory properties, shelf-life and probiotic gastrointestinal tract (GIT) survival of these products are carefully balanced as they determine functionality and drive consumer acceptance. The strain-specific effects of probiotic species are imperative in this process but carrier matrices may play a pivotal role as well. This study therefore recapitulates the wealth of knowledge on carrier matrices and their interaction with probiotic strains...
June 13, 2017: Critical Reviews in Food Science and Nutrition
https://www.readbyqxmd.com/read/28588563/insight-into-potential-probiotic-markers-predicted-in-lactobacillus-pentosus-mp-10-genome-sequence
#20
Hikmate Abriouel, Beatriz Pérez Montoro, Carlos S Casimiro-Soriguer, Antonio J Pérez Pulido, Charles W Knapp, Natacha Caballero Gómez, Sonia Castillo-Gutiérrez, María D Estudillo-Martínez, Antonio Gálvez, Nabil Benomar
Lactobacillus pentosus MP-10 is a potential probiotic lactic acid bacterium originally isolated from naturally fermented Aloreña green table olives. The entire genome sequence was annotated to in silico analyze the molecular mechanisms involved in the adaptation of L. pentosus MP-10 to the human gastrointestinal tract (GIT), such as carbohydrate metabolism (related with prebiotic utilization) and the proteins involved in bacteria-host interactions. We predicted an arsenal of genes coding for carbohydrate-modifying enzymes to modify oligo- and polysaccharides, such as glycoside hydrolases, glycoside transferases, and isomerases, and other enzymes involved in complex carbohydrate metabolism especially starch, raffinose, and levan...
2017: Frontiers in Microbiology
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