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https://www.readbyqxmd.com/read/29757353/development-and-evaluation-of-a-deep-learning-model-for-protein-ligand-binding-affinity-prediction
#1
Marta M Stepniewska-Dziubinska, Piotr Zielenkiewicz, Pawel Siedlecki
Motivation: Structure based ligand discovery is one of the most successful approaches for augmenting the drug discovery process. Currently, there is a notable shift towards machine learning (ML) methodologies to aid such procedures. Deep learning has recently gained considerable attention as it allows the model to "learn" to extract features that are relevant for the task at hand. Results: We have developed a novel deep neural network estimating the binding affinity of ligand-receptor complexes...
May 10, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29752607/farseer-nmr-automatic-treatment-analysis-and-plotting-of-large-multi-variable-nmr-data
#2
João M C Teixeira, Simon P Skinner, Miguel Arbesú, Alexander L Breeze, Miquel Pons
We present Farseer-NMR ( https://git.io/vAueU ), a software package to treat, evaluate and combine NMR spectroscopic data from sets of protein-derived peaklists covering a range of experimental conditions. The combined advances in NMR and molecular biology enable the study of complex biomolecular systems such as flexible proteins or large multibody complexes, which display a strong and functionally relevant response to their environmental conditions, e.g. the presence of ligands, site-directed mutations, post translational modifications, molecular crowders or the chemical composition of the solution...
May 11, 2018: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/29700911/alarmins-as-biomarkers-of-gastrointestinal-surgical-injury-a-pilot-study
#3
Jan Maca, Michal Holub, Filip Bursa, Peter Ihnat, Petr Reimer, Zdenek Svagera, Michal Burda, Pavel Sevcik
The dysregulation of inflammatory response to surgical injury affects outcomes. Alarmins, the earliest bioactive substances from damaged cells, play a crucial role in initiating the inflammation. We analyzed serum levels of alarmins (S100A8, S100A12, high mobility group box, and heat shock protein 70) after major abdominal surgery (MAS) in surgical (S) (n = 82) and nonsurgical (NS) groups (n = 35). The main objective was determining a role of selected alarmins in host response to MAS. The secondary objectives were (i) evaluation of the relationship among alarmins and selected biomarkers (C-reactive protein, interleukin-6), (ii) influence of the place of gastrointestinal resection, and (iii) role of alarmins in MAS for cancer...
February 2018: APMIS: Acta Pathologica, Microbiologica, et Immunologica Scandinavica
https://www.readbyqxmd.com/read/29692760/the-road-to-infection-host-microbe-interactions-defining-the-pathogenicity-of-streptococcus-bovis-streptococcus-equinus-complex-members
#4
REVIEW
Christoph Jans, Annemarie Boleij
The Streptococcus bovis/Streptococcus equinus complex (SBSEC) comprises several species inhabiting the animal and human gastrointestinal tract (GIT). They match the pathobiont description, are potential zoonotic agents and technological organisms in fermented foods. SBSEC members are associated with multiple diseases in humans and animals including ruminal acidosis, infective endocarditis (IE) and colorectal cancer (CRC). Therefore, this review aims to re-evaluate adhesion and colonization abilities of SBSEC members of animal, human and food origin paired with genomic and functional host-microbe interaction data on their road from colonization to infection...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29683102/solid-lipid-particles-as-drug-carriers-effects-of-particle-preparation-methods-and-lipid-excipients-on-particle-characteristics
#5
Cintia Kieffer Gamboa, Ranoda Samir, Chengyu Wu, Huiling Mu
BACKGROUND: Oral delivery of biopharmaceuticals is limited by the absorption barriers in the gastrointestinal tract (GIT) such as low permeability across the biological membranes and the enzymatic degradation by proteases. In this study, lipid based drug delivery systems were proposed to overcome these obstacles. OBJECTIVE: The aim of this study was to evaluate the effect of particle preparation methods and excipients on the characteristics of solid lipid microparticles (SLM) and solid lipid nanoparticles (SLN)...
April 20, 2018: Pharmaceutical Nanotechnology
https://www.readbyqxmd.com/read/29664968/water-system-is-a-controlling-variable-modulating-bacterial-diversity-of-gastrointestinal-tract-and-performance-in-rainbow-trout
#6
Omolola C Betiku, Carl J Yeoman, T Gibson Gaylord, Benjamin Americus, Sarah Olivo, Glenn C Duff, Wendy M Sealey
A two-phase feeding study evaluating performance of rainbow trout and comparing luminal and mucosal gastrointestinal tract (GIT) bacterial community compositions when fed two alternative protein diets in two rearing systems was conducted. Alternative protein diets (animal protein and plant protein diets) balanced with crystalline amino acids: lysine, methionine and threonine or unbalanced, were fed to rainbow trout in two separate water systems (recirculating (RR) and flow-through (FF)) for a period of 16 weeks...
2018: PloS One
https://www.readbyqxmd.com/read/29651876/novel-hits-for-acetylcholinesterase-inhibition-derived-by-docking-based-screening-on-zinc-database
#7
Irini Doytchinova, Mariyana Atanasova, Iva Valkova, Georgi Stavrakov, Irena Philipova, Zvetanka Zhivkova, Dimitrina Zheleva-Dimitrova, Spiro Konstantinov, Ivan Dimitrov
The inhibition of the enzyme acetylcholinesterase (AChE) increases the levels of the neurotransmitter acetylcholine and symptomatically improves the affected cognitive function. In the present study, we searched for novel AChE inhibitors by docking-based virtual screening of the standard lead-like set of ZINC database containing more than 6 million small molecules using GOLD software. The top 10 best-scored hits were tested in vitro for AChE affinity, neurotoxicity, GIT and BBB permeability. The main pharmacokinetic parameters like volume of distribution, free fraction in plasma, total clearance, and half-life were predicted by previously derived models...
December 2018: Journal of Enzyme Inhibition and Medicinal Chemistry
https://www.readbyqxmd.com/read/29622825/gastrointestinal-food-allergy-in-ghanaian-children-a-case-series
#8
Taiba J Afaa, Adwoa Ka Afrane, Victor Etwire
Background: Food allergy is an adverse health effect arising from a specific immune response that occurs reproducibly on exposure to a given food. Food allergies are classified into three types: Ig(immunoglobulin)E mediated, mixed IgE and cell mediated and cell-mediated non IgE mediated. Gastrointestinal (GIT) food allergy has classically encompassed a number of different clinical entities: food protein-induced enterocolitis syndrome (FPIES), food protein-induced proctocolitis (FPIP), food protein-induced enteropathy and eosinophilic gastrointestinal disorders (EGID)...
September 2017: Ghana Medical Journal
https://www.readbyqxmd.com/read/29600388/alpha-synuclein-is-present-in-dental-calculus-but-not-altered-in-parkinson-s-disease-patients-in-comparison-to-controls
#9
Sabrina Schmid, Eva Goldberg-Bockhorn, Silke Schwarz, Nicole Rotter, Jan Kassubek, Kelly Del Tredici, Elmar Pinkhardt, Markus Otto, Albert C Ludolph, Patrick Oeckl
INTRODUCTION: In autopsy cases staged for sporadic Parkinson's disease (PD), the neuropathology is characterized by a preclinical phase that targets the enteric nervous system of the gastrointestinal tract (GIT). Therefore, the ENS might be a source of potential (presymptomatic) PD biomarkers. METHODS: In this clinically based study, we examined the alpha-synuclein (αSyn) concentration in an easily accessible protein storage medium of the GIT, dental calculus, in 21/50 patients with PD and 28/50 age- and gender-matched controls using ELISA...
March 29, 2018: Journal of Neurology
https://www.readbyqxmd.com/read/29596640/multiple-factors-confounding-phylogenetic-detection-of-selection-on-codon-usage
#10
Simon Laurin-Lemay, Hervé Philippe, Nicolas Rodrigue
Detecting selection on codon usage (CU) is a difficult task, since CU can be shaped by both the mutational process and selective constraints operating at the DNA, RNA and protein levels. Yang and Nielsen (2008) developed a test (which we call CUYN) for detecting selection on CU using two competing mutation-selection models of codon substitution. The null model assumes that CU is determined by the mutation bias alone, whereas the alternative model assumes that both mutation bias and/or selection act on CU. In applications on mammalian-scale alignments, the CUYN test detects selection on CU for numerous genes...
March 27, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29595967/microgel-in-microgel-biopolymer-delivery-systems-controlled-digestion-of-encapsulated-lipid-droplets-under-simulated-gastrointestinal-conditions
#11
Da Ma, Zongcai Tu, Hui Wang, Zipei Zhang, David Julian McClements
Structural design principles are increasingly being used to develop colloidal delivery systems for bioactive agents. In this study, oil droplets were encapsulated within microgel-in-microgel systems. Initially, a nanoemulsion was formed that contained small whey protein-coated oil droplets (d43 = 211 nm). These oil droplets were then loaded into either carrageenan-in-alginate (O/MC/MA) or alginate-in-carrageenan (O/MA/MC) microgels. A vibrating nozzle encapsulation unit was used to form the smaller inner microgels (d43 =170-324 m), while a hand-held syringe was used to form the larger outer microgels (d43 =2200-3400 m)...
March 29, 2018: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/29558152/bacteria-mediated-tumor-therapy-utilizing-photothermally-controlled-tnf-%C3%AE-expression-via-oral-administration
#12
Jin-Xuan Fan, Zi-Hao Li, Xin-Hua Liu, Diwei Zheng, Ying Chen, Xian-Zheng Zhang
Oral drug administration is widely adopted for diverse drugs, and enjoys the convenience of use and capbility to reach different parts of the body via the bloodstream. However, it is generally not feasible for biomacromolecular anti-tumor drugs such as protein and nucleic acids due to the the limited absorption through gastrointestinal tract (GIT) and the poor tumor targeting. Here, we report a non-invasive thermally-sensitive programmable therapetic system using bacteria E. coli MG1655 as an vehicle for tumor treatments via oral administration...
March 20, 2018: Nano Letters
https://www.readbyqxmd.com/read/29532415/in-vitro-git-tolerance-of-microencapsulated-bifidobacterium-bifidum-atcc-35914-using-polysaccharide-protein-matrix
#13
Rabia Iqbal, Tahir Zahoor, Nuzhat Huma, Amer Jamil, Gülhan Ünlü
Longevity of probiotic is the main concern for getting maximum benefits when added in food product. Bifidobacterium, a probiotic, tends to lose its viability during gastrointestinal track (GIT) transit and storage of food. Their viability can be enhanced through microencapsulation technology. In this study, Bifidobacterium bifidum (B. bifidum) ATCC 35914 was encapsulated by using two experimental plans. In the first plan, chitosan (CH) at 0.6, 0.8, and 1.0% and sodium alginate (SA) at 4, 5, and 6% were used...
March 12, 2018: Probiotics and Antimicrobial Proteins
https://www.readbyqxmd.com/read/29478671/encapsulation-protection-and-delivery-of-bioactive-proteins-and-peptides-using-nanoparticle-and-microparticle-systems-a-review
#14
REVIEW
David Julian McClements
There are many examples of bioactive proteins and peptides that would benefit from oral delivery through functional foods, supplements, or medical foods, including hormones, enzymes, antimicrobials, vaccines, and ACE inhibitors. However, many of these bioactive proteins are highly susceptible to denaturation, aggregation or hydrolysis within commercial products or inside the human gastrointestinal tract (GIT). Moreover, many bioactive proteins have poor absorption characteristics within the GIT. Colloidal systems, which contain nanoparticles or microparticles, can be designed to encapsulate, retain, protect, and deliver bioactive proteins...
March 2018: Advances in Colloid and Interface Science
https://www.readbyqxmd.com/read/29475865/bacterial-community-dynamics-across-the-gastrointestinal-tracts-of-dairy-calves-during-preweaning-development
#15
Juliana Dias, Marcos Inácio Marcondes, Shirley Motta de Souza, Barbara Cardoso da Mata E Silva, Melline Fontes Noronha, Rafael Tassinari Resende, Fernanda Samarini Machado, Hilário Cuquetto Mantovani, Kimberly A Dill-McFarland, Garret Suen
Microbial communities play critical roles in the gastrointestinal tracts (GIT) of preruminant calves by influencing performance and health. However, little is known about the establishment of microbial communities in the calf GIT or their dynamics during development. In this study, next-generation sequencing was used to assess changes in the bacterial communities of the rumen, jejunum, cecum, and colon in 26 crossbred calves at four developmental stages (7, 28, 49, and 63 days old). Alpha diversity differed among GIT regions with the lowest diversity and evenness in the jejunum, whereas no changes in alpha diversity were observed across developmental stage...
May 1, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29461224/-microecological-changes-in-the-intestine-and-its-effect-on-the-condition-of-hard-tissues-of-teeth-in-adolescence
#16
T Shishniashvili, T Suladze, M Makhviladze, M Pkhaladze
On the background of microecological changes in the gastrointestinal tract, mineral and protein metabolism is disrupted, biochemical changes occur in the phosphorus-calcium metabolism in the bones of the skeleton and hard tissues of the teeth. The aim of the research was to study the activity of the caries process, characterized by progressive decalcification, under conditions of microecological changes in the intestine and its effect on the processes of endogenous calcium assimilation in adolescence. Within the frames of the research 68 adolescents aged 11 to 17 years with various degrees of pathology of the gastrointestinal tract were examined...
January 2018: Georgian Medical News
https://www.readbyqxmd.com/read/29458538/the-double-adjuvants-ltb-and-cpg-significantly-enhanced-the-immuno-protective-effects-of-recombinant-git-derived-from-staphylococcus-aureus-and-streptococcus-in-mice
#17
Jinzhu Ma, Liquan Yu, Baifen Song, Yongzhong Yu, Shaoduo Zhang, Yuhua Wei, Zhijun Wu, Di Yao, Wei Yu, Zhanbo Zhu, Yudong Cui
PURPOSE: In this study, we prepared GapC1-150-IsdB126-361-TRAP (GIT) proteins plus heat-labile enterotoxin B (LTB) as an intra-molecular adjuvant, together with CpG to further enhance its immunogenicity. METHODOLOGY: Initially, the target genes were acquired and inserted into pET-32a (+) vectors to express LTB-GIT protein. LTB-GIT expression was confirmed by Western blotting and its immunocompetence was estimated through ELISA. Further, we immunized BALB/c mice with the LTB-GIT plus CpG adjuvant...
March 2018: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/29457292/antibodies-against-h3-and-h4-histones-from-the-sera-of-hiv-infected-patients-catalyze-site-specific-degradation-of-these-histones
#18
Svetlana V Baranova, Pavel S Dmitrenok, Anastasiya D Zubkova, Nikita V Ivanisenko, Elena S Odintsova, Valentina N Buneva, Georgy A Nevinsky
Histones and their posttranslational modified forms play pivotal roles in chromatin functioning and gene transcription. Also, histones are harmful when they enter the intercellular space; their administration to animals results in systemic inflammatory and toxic responses. Autoantibodies having enzymatic activities (abzymes) are the specific feature of several autoimmune and viral diseases. Electrophoretically homogeneous IgGs containing no canonical proteases were purified from sera of HIV-infected patients by using several affinity chromatographies...
February 19, 2018: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/29405577/impacts-of-dietary-pleurotus-eryngii-polysaccharide-on-nutrient-digestion-metabolism-and-immune-response-of-the-small-intestine-and-colon-an-itraq-based-proteomic-analysis
#19
Gaoxing Ma, Benard Muinde Kimatu, Liyan Zhao, Wenjian Yang, Fei Pei, Qiuhui Hu
Pleurotus eryngii polysaccharides have been shown to exert significant biological activities to the host. However, few studies have been conducted on its effects on gastrointestinal tract (GIT) health alteration. In the present study, small intestinal and colonic proteome alterations generated by dietary supplementation with a novel homogeneous P. eryngii polysaccharide (PEP) in C57BL/6 mice, based on the isobaric tag for relative and absolute quantification (iTRAQ) proteomics, are investigated. Compared to the control group, PEP supplementation result in a total of 113 and 194 significant differential proteins (DPs) in the small intestine and colon, respectively...
April 2018: Proteomics
https://www.readbyqxmd.com/read/29362395/chitin-digestibility-is-dependent-on-feeding-behaviors-which-determine-acidic-chitinase-mrna-levels-in-mammalian-and-poultry-stomachs
#20
Eri Tabata, Akinori Kashimura, Azusa Kikuchi, Hiromasa Masuda, Ryo Miyahara, Yusuke Hiruma, Satoshi Wakita, Misa Ohno, Masayoshi Sakaguchi, Yasusato Sugahara, Vaclav Matoska, Peter O Bauer, Fumitaka Oyama
Chitin, a polymer of N-acetyl-D-glucosamine (GlcNAc), functions as a major structural component in chitin-containing organism including crustaceans, insects and fungi. Recently, we reported that acidic chitinase (Chia) is highly expressed in mouse, chicken and pig stomach tissues and that it can digest chitin in the respective gastrointestinal tracts (GIT). In this study, we focus on major livestock and domestic animals and show that the levels of Chia mRNA in their stomach tissues are governed by the feeding behavior...
January 23, 2018: Scientific Reports
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