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https://www.readbyqxmd.com/read/29775997/improved-acmg-compliant-in-silico-prediction-of-pathogenicity-for-missense-substitutions-encoded-by-tp53-variants
#1
Cristina Fortuno, Paul A James, Erin L Young, Bing Feng, Magali Olivier, Tina Pesaran, Sean V Tavtigian, Amanda B Spurdle
Clinical interpretation of germline missense variants represents a major challenge, including those in the TP53 Li-Fraumeni syndrome gene. Bioinformatic prediction is a key part of variant classification strategies. We aimed to optimize the performance of the Align-GVGD tool used for p53 missense variant prediction, and compare its performance to other bioinformatic tools (SIFT, PolyPhen-2) and ensemble methods (REVEL, BayesDel). Reference sets of assumed pathogenic and assumed benign variants were defined using functional and/or clinical data...
May 18, 2018: Human Mutation
https://www.readbyqxmd.com/read/29775968/in-silico-structure-prediction-and-inhibition-mechanism-studies-of-athda14-as-revealed-by-homology-modeling-docking-molecular-dynamics-simulation
#2
Ming-Lang Zhao, Wang Wang, Hu Nie, Sha-Sha Cao, Lin-Fang Du
Histone deacetylases (HDACs) play a significant role in the epigenetic mechanism by catalyzing deacetylation of lysine on histone in both animals and plants. HDACs involved in growth, development and response to stresses in plants. Arabidopsis thaliana histone deacetylase 14 (AtHDA14) is found to localize in the mitochondria and chloroplasts, and it involved in photosynthesis and melatonin biosynthesis. However, its mechanism of action was still unknowns so far. Therefore, in this study, we constructed AtHDA14 protein model using homology modeling method, validated using PROCHECK and presented using Ramachandran plots...
May 6, 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29775704/alkaline-active-cyanide-dihydratase-of-flavobacterium-indicum-mtcc-6936-growth-optimization-purification-characterization-and-in-silico-analysis
#3
Virender Kumar, Vijay Kumar, Tek Chand Bhalla
The present work explores a rare cyanide dihydratase of Flavobacterium indicum MTCC 6936 for its potential of cyanide degradation. The enzyme is purified to 12 fold with a yield of 76%. SDS and native-PAGE analysis revealed that enzyme was monomer of 40 kDa size. The enzyme works well in mesophilic range at wide array of pH. The thermostability profile of cyanide dihydratase revealed that the enzyme is quite stable at 30 °C and 35 °C with half-life of 6 h 30 min and 5 h respectively. Km and Vmax for cyanide dihydratase of F...
May 15, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29775626/microrna-21-up-regulates-metalloprotease-by-down-regulating-timp3-during-cumulus-cell-oocyte-complex-in-vitro-maturation
#4
Bo Pan, Julang Li
Cumulus cells and the remodeling of their extracellular matrix around oocytes are essential for oocyte maturation and ovulation in the ovary. An important extracellular metalloprotease, ADAMTS1, and its partner VERSICAN, mediate essential cumulus-oocyte-complex (COC) structural remodeling. However, how the expression of these proteinases is regulated during oocyte maturation is unclear. Here we report that both ADAMTS1 and VERSICAN significantly increased in porcine cumulus cells during COC in vitro maturation (IVM)...
May 15, 2018: Molecular and Cellular Endocrinology
https://www.readbyqxmd.com/read/29775277/cid-9998128-compound-is-a-potential-multi-target-drug-for-alzheimer-s-disease
#5
Nguyen Quoc Thai, Zuzana Bednarikova, Miroslav Gancar, Huynh Quang Linh, Chin-Kun Hu, Mai Suan Li, Zuzana Gazova
We have probed capability of small CID 9998128 compound as a potential multi-target drug for the Alzheimer's disease (AD) using in silico and in vitro experiments. By all-atom simulation and MM-PBSA method we have demonstrated that this compound strongly binds to both amyloid beta 42 (Aβ42 ) fibrils and β-secretase and the van der Waals interaction is dominating over the electrostatic interaction in binding affinity. A detailed analysis at the atomic level revealed that indazole in CID 99998128 structure made a major contribution to instability of all studied complexes...
May 18, 2018: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/29775159/bioinformatics-functional-analysis-of-let-7a-mir-34a-and-mir-199a-b-reveals-novel-insights-into-immune-system-pathways-and-cancer-hallmarks-for-hepatocellular-carcinoma
#6
Bangly Soliman, Ahmed Salem, Mohamed Ghazy, Nourhan Abu-Shahba, Mahmoud El Hefnawi
Let-7a, miR-34a, and miR-199 a/b have gained a great attention as master regulators for cellular processes. In particular, these three micro-RNAs act as potential onco-suppressors for hepatocellular carcinoma. Bioinformatics can reveal the functionality of these micro-RNAs through target prediction and functional annotation analysis. In the current study, in silico analysis using innovative servers (miRror Suite, DAVID, miRGator V3.0, GeneTrail) has demonstrated the combinatorial and the individual target genes of these micro-RNAs and further explored their roles in hepatocellular carcinoma progression...
May 2018: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/29774036/the-pattern-and-distribution-of-induced-mutations-in-j-curcas-using-reduced-representation-sequencing
#7
Fatemeh Maghuly, Stephan Pabinger, Julie Krainer, Margit Laimer
Mutagenesis in combination with Genotyping by Sequencing (GBS) is a powerful tool for introducing variation, studying gene function and identifying causal mutations underlying phenotypes of interest in crop plant genomes. About 400 million paired-end reads were obtained from 82 ethylmethane sulfonate (EMS) induced mutants and 14 wild-type accessions of Jatropha curcas for the detection of Single Nucleotide Polymorphisms (SNPs) and Insertion/Deletions (InDels) by two different approaches (nGBS and ddGBS) on an Illumina HiSeq 2000 sequencer...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29773067/in-silico-molecular-docking-and-adme-studies-of-1-3-4-thiadiazole-derivatives-in-relation-to-in-vitro-pon1-activity
#8
Belgin Sever, Kaan Kucukoglu, Hayrunnisa Nadaroglu, Mehlika Dilek Altintop
BACKGROUND: Paraoxonase 1 (PON1) is a paraoxonase, arylesterase and lactonase associated with protection of lipoproteins and cell membranes against oxidative modification. OBJECTIVE: Based on antioxidative properties of PON1 and widely usage of 1,3,4-thiadiazole derivatives in pharmaceutical, agricultural, and materials chemistry, herein we aimed to evaluate PON1 activator potentials of 1,3,4-thiadiazole based compounds. METHOD: 2-[[5-(2,4-Difluoro/dichlorophenylamino)-1,3,4-thiadiazol-2-yl]thio] acetophenone derivatives (1-18), previously synthesized by our research group, were in vitro evaluated for their activator effects on PON1 which was purified using ammonium sulfate precipitation (60-80%) and DEAE-Sephadex anion exchange chromatography...
May 17, 2018: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/29772285/new-prediction-methods-for-solubility-parameters-based-on-molecular-sigma-profiles-using-pharmaceutical-materials
#9
Andreas Niederquell, Nicole Wyttenbach, Martin Kuentz
Solubility parameters have been applied extensively in the chemical and pharmaceutical sciences. Particularly attractive is calculation of solubility parameters based on chemical structure and recently, new in silico methods have been proposed. Thus, screening charge densities of molecular surfaces (i.e. so-called σ-profiles) are used by the conductor-like screening model for real solvents (COSMO-RS) and can be employed in a quantitative structure property relationship (QSPR) to predict solubility parameters...
May 14, 2018: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/29769627/clinical-and-functional-characterization-of-the-cdh1-germline-variant-c-1679c-g-in-three-unrelated-families-with-hereditary-diffuse-gastric-cancer
#10
Laura Pena-Couso, José Perea, Soraia Melo, Fátima Mercadillo, Joana Figueiredo, João Miguel Sanches, Antonio Sánchez-Ruiz, Luis Robles, Raquel Seruca, Miguel Urioste
Germline changes in the CDH1 tumor suppressor gene predispose to diffuse gastric cancer and lobular breast cancer. In carriers of deleterious germline CDH1 variants, prophylactic gastrectomy is recommended. In case of germline missense variants, it is mandatory to assess the functional impact on E-cadherin, the protein encoded by CDH1, and to predict their clinical significance. Herein, we have identified a recurrent germline missense variant, c.1679C>G, segregating with gastric cancer in three unrelated Spanish families...
May 16, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29767246/dnajc3-mutation-in-thai-familial-type-2-diabetes-mellitus
#11
Sirikul Kulanuwat, Watip Tangjittipokin, Prapaporn Jungtrakoon, Chutima Chanprasert, Jatuporn Sujjitjoon, Ninareeman Binnima, Pa-Thai Yenchitsomanus, Nattachet Plengvidhya
Type 2 diabetes mellitus (T2D) is a heterogeneous disease, with certain cases presenting an autosomal dominant type. The rare coding variants of disease‑causing genes in T2D remain mostly unclear. The present study aimed to identify the disease‑causing gene conducting whole exome sequencing in a Thai T2D family with an autosomal dominant transmission of T2D with no evidence of mutations in known maturity‑onset diabetes of the young (MODY) genes. Candidate variants were selected according to certain criteria of mutation prediction programs, followed by segregation analysis with diabetes in the family...
May 14, 2018: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29766501/impact-of-gastrointestinal-disease-states-on-oral-drug-absorption-implications-for-formulation-design-a-pearrl-review
#12
REVIEW
Angela Effinger, Caitriona M O'Driscoll, Mark McAllister, Nikoletta Fotaki
OBJECTIVES: Drug product performance in patients with gastrointestinal (GI) diseases can be altered compared to healthy subjects due to pathophysiological changes. In this review, relevant differences in patients with inflammatory bowel diseases, coeliac disease, irritable bowel syndrome and short bowel syndrome are discussed and possible in vitro and in silico tools to predict drug product performance in this patient population are assessed. KEY FINDINGS: Drug product performance was altered in patients with GI diseases compared to healthy subjects, as assessed in a limited number of studies for some drugs...
May 16, 2018: Journal of Pharmacy and Pharmacology
https://www.readbyqxmd.com/read/29765811/comparative-genome-analysis-of-bacillus-velezensis-reveals-a-potential-for-degrading-lignocellulosic-biomass
#13
Long Chen, Wei Gu, Hai-Yan Xu, Gui-Lian Yang, Xiao-Feng Shan, Guang Chen, Yuan-Huan Kang, Chun-Feng Wang, Ai-Dong Qian
Genomes of 24 sequenced Bacillus velezensis strains were characterized to identity shared and unique genes of lignocellulolytic enzymes and predict potential to degrade lignocellulose. All 24 strains had genes that encoded lignocellulolytic enzymes, with potential to degrade cellulose and hemicelluloses. Several lignocellulosic genes related to cellulose degradation were universally present, including one GH5 (endo-1,4-β-glucanase), one GH30 (glucan endo-1,6-β-glucosidase), two GH4 (6-phospho-β-glucosidase, 6-phospho-α-glucosidase), one GH1 (6-phospho-β-galactosidase), one GH16 (β-glucanase) and three GH32 (two sucrose-6-phosphate hydrolase and levanase)...
May 2018: 3 Biotech
https://www.readbyqxmd.com/read/29765654/membrane-assisted-extraction-of-monoterpenes-from-in-silico-solvent-screening-towards-biotechnological-process-application
#14
L Janoschek, L Grozdev, S Berensmeier
This work focuses on the process development of membrane-assisted solvent extraction of hydrophobic compounds such as monoterpenes. Beginning with the choice of suitable solvents, quantum chemical calculations with the simulation tool COSMO-RS were carried out to predict the partition coefficient (log P ) of (S)-(+)-carvone and terpinen-4-ol in various solvent-water systems and validated afterwards with experimental data. COSMO-RS results show good prediction accuracy for non-polar solvents such as n-hexane, ethyl acetate and n-heptane even in the presence of salts and glycerol in an aqueous medium...
April 2018: Royal Society Open Science
https://www.readbyqxmd.com/read/29764719/potential-use-of-bitter-melon-momordica-charantia-derived-compounds-as-antidiabetics-in-silico-and-in-vivo-studies
#15
Olusola Olalekan Elekofehinti, Esther Opeyemi Ariyo, Moses Orimoloye Akinjiyan, Olanrewaju Sam Olayeriju, Akeem Olalekan Lawal, Isaac Gbadura Adanlawo, Joao Batista Teixeira Rocha
Momordica charantia (bitter lemon) belongs to the cucurbitaceae family which has been extensively used in traditional medicines for the cure of various ailments such as cancer and diabetes. The underlying mechanism of M. charantia to maintain glycemic control was investigated. GLP-1 and DPP-4 gene modulation by M. charantia (5-20% inclusion in rats diet) was investigated in vivo by RT-PCR and possible compounds responsible for diabetic action predicted through in silico approach. Phytochemicalss previously characterized from M...
May 12, 2018: Pathophysiology: the Official Journal of the International Society for Pathophysiology
https://www.readbyqxmd.com/read/29764441/case-report-identification-of-an-hnf1b-p-arg527gln-mutation-in-a-maltese-patient-with-atypical-early-onset-diabetes-and-diabetic-nephropathy
#16
Nikolai Paul Pace, Johann Craus, Alex Felice, Josanne Vassallo
BACKGROUND: The diagnosis of atypical non-autoimmune forms of diabetes mellitus, such as maturity onset diabetes of the young (MODY) presents several challenges, in view of the extensive clinical and genetic heterogeneity of the disease. In this report we describe a case of atypical non autoimmune diabetes associated with a damaging HNF1β mutation. This is distinguished by a number of uncharacteristic clinical features, including early-onset obesity, the absence of renal cysts and diabetic nephropathy...
May 15, 2018: BMC Endocrine Disorders
https://www.readbyqxmd.com/read/29763937/bacteriophage-cocktail-for-biocontrol-of-escherichia-coli-o157-h7-stability-and-potential-allergenicity-study
#17
Karina Ramirez, Carmina Cazarez-Montoya, Hector Samuel Lopez-Moreno, Nohelia Castro-Del Campo
Escherichia coli O157:H7 has become a global public health and a food safety problem. Despite the implementation of control strategies that guarantee the safety in various products, outbreaks persist and new alternatives are necessary to reduce this pathogen along the food chain. Recently, our group isolated and characterised lytic bacteriophages against E. coli O157:H7 with potential to be used as biocontrol agents in food. To this end, phages need certain requirements to allow their manufacture and application...
2018: PloS One
https://www.readbyqxmd.com/read/29763903/central-precocious-puberty-caused-by-a-heterozygous-deletion-in-the-mkrn3-promoter-region
#18
Delanie Macedo, Monica M França, Luciana Montenegro, Marina Cunha-Silva, Danielle S Bessa, Ana Paula Abreu, Ursula B Kaiser, Berenice B Mendonca, Alexander A L Jorge, Vinicius N Brito, Ana C Latronico
<br>Context: Loss-of-function mutations in the coding region of MKRN3, a maternally imprinted gene at chromosome 15q11.2, are a common cause of familial central precocious puberty (CPP). Whether MKRN3 alterations in regulatory regions can cause CPP has not been explored to date. We aimed to investigate potential pathogenic variants in the promoter region of MKRN3 in patients with idiopathic CPP. Patients/ Methods: A cohort of 110 patients with idiopathic CPP was studied. Family history of precocious sexual development was present in 25%...
May 15, 2018: Neuroendocrinology
https://www.readbyqxmd.com/read/29763804/chalcones-and-bis-chalcones-as-potential-%C3%AE-amylase-inhibitors-synthesis-in-vitro-screening-and-molecular-modelling-studies
#19
Adebayo Tajudeen Bale, Khalid Mohammed Khan, Uzma Salar, Sridevi Chigurupati, Tolulope Fasina, Farman Ali, Kanwal, Abdul Wadood, Muhammad Taha, Sitanshu Sekhar Nanda, Mehreen Ghufran, Shahnaz Perveen
Despite of a diverse range of biological activities associated with chalcones and bis-chalcones, they are still neglected by the medicinal chemist for their possible α-amylase inhibitory activity. So, the current study is based on the evaluation of this class for the identification of new leads as α-amylase inhibitors. For that purpose, a library of substituted chalcones 1-13 and bis-chalcones 14-18 were synthesized and characterized by spectroscopic techniques EI-MS and 1 H NMR. CHN analysis was carried out and found in agreement with the calculated values...
May 7, 2018: Bioorganic Chemistry
https://www.readbyqxmd.com/read/29763729/in-silico-identification-of-molecular-mimics-involved-in-the-pathogenesis-of-clostridium-botulinum-atcc-3502-strain
#20
Tulika Bhardwaj, Shafiul Haque, Pallavi Somvanshi
Bacterial pathogens invade and disrupt the host defense system by means of protein sequences structurally similar at global and local level both. The sharing of homologous sequences between the host and the pathogenic bacteria mediates the infection and defines the concept of molecular mimicry. In this study, various computational approaches were employed to elucidate the pathogenicity of Clostridium at genome-wide level. Genome-wide study revealed that the pathogen mimics the host (Homo sapiens) and unraveled the complex pathogenic pathway of causing infections...
May 12, 2018: Microbial Pathogenesis
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