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https://www.readbyqxmd.com/read/28214450/in-silico-structural-and-functional-analysis-of-mesorhizobium-acc-deaminase
#1
Krishnendu Pramanik, Tithi Soren, Soumik Mitra, Tushar Kanti Maiti
Nodulation is one of the very important processes of legume plants as it is the initiating event of fixing nitrogen. Although ethylene has essential role in normal plant metabolism but it has also negative impact on plants particularly in nodule formation in legume plants. It is also produced due to a variety of biotic or abiotic stresses. 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase is a rhizobial enzyme which cleaves ACC (immediate precursor of ethylene) into α-ketobutyrate and ammonia. As a result, the level of ethylene from the plant cells is decreased and the negative impact of ethylene on nodule formation is reduced...
February 11, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28213543/functional-characterization-of-a-28-kb-catabolic-island-from-pseudomonas-sp-m1-involved-in-biotransformation-of-%C3%AE-myrcene-and-related-plant-derived-volatiles
#2
Pedro Soares-Castro, Pedro Montenegro-Silva, Hermann J Heipieper, Pedro M Santos
Pseudomonas sp. M1 is able to mineralize highly hydrophobic and recalcitrant compounds such as benzene, phenol and their methylated/halogenated derivatives, as well as the backbone of several monoterpenes. The ability to use such spectrum of compounds as sole carbon source is, most probably, associated with a genetic background evolved under different environmental constraints. The outstanding performance of M1 strain regarding β-myrcene catabolism was elucidated in this work, with focus on the biocatalytical potential of β-myrcene-associated core-code, comprised in a 28-kb genomic island (GI), predicted to be organized in 8 transcriptional units...
February 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28213207/epimetabolites-discovering-metabolism-beyond-building-and-burning
#3
REVIEW
Megan R Showalter, Tomas Cajka, Oliver Fiehn
Enzymatic transformations of primary, canonical metabolites generate active biomolecules that regulate important cellular and physiological processes. Roles include regulation of histone demethylation in epigenetics, inflammation in tissue injury, insulin sensitivity, cancer cell invasion, stem cell pluripotency status, inhibition of nitric oxide signaling and others. Such modified compounds, defined as epimetabolites, have functions distinct from classic hormones as well as removed from generic anabolism and catabolism...
February 14, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28212671/an-adaptive-variant-of-trib2-rs1057001-is-associated-with-higher-expression-levels-of-thermogenic-genes-in-human-subcutaneous-and-visceral-adipose-tissues
#4
Kazuhiro Nakayama, Sadahiko Iwamoto
BACKGROUND: An obesity-related single-nucleotide polymorphism (SNP) of the Tribbles pseudokinase 2 gene (TRIB2) was shown to have underwent adaptive evolution in the last glacial period, suggesting a selective advantage of this SNP in human populations in cold environments. In order to verify this hypothesis, the effect of the TRIB2 SNP on the expression of genes involved in adaptive thermogenesis was tested using messenger RNAs prepared from adipose tissues of Japanese adults. METHODS: Complementary DNA was prepared from subcutaneous adipose tissues (SAT) and visceral adipose tissues (VAT) obtained from 48 Japanese adults...
February 17, 2017: Journal of Physiological Anthropology
https://www.readbyqxmd.com/read/28208616/immunoinformatics-features-linked-to-leishmania-vaccine-development-data-integration-of-experimental-and-in-silico-studies
#5
Rory C F Brito, Frederico G Guimarães, João P L Velloso, Rodrigo Corrêa-Oliveira, Jeronimo C Ruiz, Alexandre B Reis, Daniela M Resende
Leishmaniasis is a wide-spectrum disease caused by parasites from Leishmania genus. There is no human vaccine available and it is considered by many studies as apotential effective tool for disease control. To discover novel antigens, computational programs have been used in reverse vaccinology strategies. In this work, we developed a validation antigen approach that integrates prediction of B and T cell epitopes, analysis of Protein-Protein Interaction (PPI) networks and metabolic pathways. We selected twenty candidate proteins from Leishmania tested in murine model, with experimental outcome published in the literature...
February 10, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28207381/personalized-models-of-human-atrial-electrophysiology-derived-from-endocardial-electrograms
#6
Cesare Corrado, John Whitaker, Henry Chubb, Steven Williams, Matthew Wright, Jaswinder Gill, Mark O'Neill, Steven Niederer
OBJECTIVE: Computational models represent a novel framework for understanding the mechanisms behind atrial fibrillation (AF) and offer a pathway for personalizing and optimizing treatment. The characterization of local electrophysiological properties across the atria during procedures remains a challenge. The aim of this work is to characterize the regional properties of the human atrium from multi-electrode catheter measurements. METHODS: We propose a novel method that characterizes regional electrophysiology properties by fitting parameters of an ionic model to conduction velocity and effective refractory period restitution curves obtained by a s1 s2 pacing protocol applied through a multi-electrode catheter...
May 30, 2016: IEEE Transactions on Bio-medical Engineering
https://www.readbyqxmd.com/read/28205163/hybrid-in-silico-in-vitro-approaches-for-the-identification-of-functional-cholesterol-binding-domains-in-membrane-proteins
#7
Coralie Di Scala, Jacques Fantini
In eukaryotic cells, cholesterol is an important regulator of a broad range of membrane proteins, including receptors, transporters, and ion channels. Understanding how cholesterol interacts with membrane proteins is a difficult task because structural data of these proteins complexed with cholesterol are scarce. Here, we describe a dual approach based on in silico studies of protein-cholesterol interactions, combined with physico-chemical measurements of protein insertion into cholesterol-containing monolayers...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28204975/surface-and-exoproteomes-of-gram-positive-pathogens-for-vaccine-discovery
#8
Massimiliano Biagini, Fabio Bagnoli, Nathalie Norais
Reverse vaccinology has been very successful in the discovery of vaccine candidates against many pathogenic bacteria by integrating genome and proteome mining. This great achievement was facilitated by the complementarity of the in silico prediction of antigens and the empirical data on protein localization, expression, and immunogenicity obtained through different techniques based on electrophoresis, immunoblotting and mass spectrometry. An iterative process between information provided by DNA sequence analysis and proteomic data has been established leading to precise antigen identification...
February 16, 2017: Current Topics in Microbiology and Immunology
https://www.readbyqxmd.com/read/28202748/rna-splicing-in-human-disease-and-in-the-clinic
#9
REVIEW
Diana Baralle, Emanuele Buratti
Defects at the level of the pre-mRNA splicing process represent a major cause of human disease. Approximately 15-50% of all human disease mutations have been shown to alter functioning of basic and auxiliary splicing elements. These elements are required to ensure proper processing of pre-mRNA splicing molecules, with their disruption leading to misprocessing of the pre-mRNA molecule and disease. The splicing process is a complex process, with much still to be uncovered before we are able to accurately predict whether a reported genomic sequence variant (GV) represents a splicing-associated disease mutation or a harmless polymorphism...
March 1, 2017: Clinical Science (1979-)
https://www.readbyqxmd.com/read/28202629/improving-the-in-silico-assessment-of-proarrhythmia-risk-by-combining-herg-human-ether-%C3%A3-go-go-related-gene-channel-drug-binding-kinetics-and-multichannel-pharmacology
#10
Zhihua Li, Sara Dutta, Jiansong Sheng, Phu N Tran, Wendy Wu, Kelly Chang, Thembi Mdluli, David G Strauss, Thomas Colatsky
BACKGROUND: The current proarrhythmia safety testing paradigm, although highly efficient in preventing new torsadogenic drugs from entering the market, has important limitations that can restrict the development and use of valuable new therapeutics. The CiPA (Comprehensive in vitro Proarrhythmia Assay) proposes to overcome these limitations by evaluating drug effects on multiple cardiac ion channels in vitro and using these data in a predictive in silico model of the adult human ventricular myocyte...
February 2017: Circulation. Arrhythmia and Electrophysiology
https://www.readbyqxmd.com/read/28202045/identification-of-micrornas-and-their-response-to-the-stress-of-plant-allelochemicals-in-aphis-gossypii-hemiptera-aphididae
#11
Kang-Sheng Ma, Fen Li, Ying Liu, Ping-Zhuo Liang, Xue-Wei Chen, Xi-Wu Gao
BACKGROUND: MicroRNAs (miRNAs) are a group of short non-coding RNAs involved in the inhibition of protein translation or in mRNA degradation. Although the regulatory roles of miRNAs in various biological processes have been investigated, there is as yet an absence of studies about the regulatory roles of miRNAs involved in the metabolism of plant allelochemicals in insects. RESULTS: We constructed five small RNA libraries from apterous Aphis gossypii adults that had fed on an artificial diet containing various allelochemicals...
February 16, 2017: BMC Molecular Biology
https://www.readbyqxmd.com/read/28197629/rab27a-rab27b-and-vps36-are-downregulated-in-advanced-prostate-cancer-and-show-functional-relevance-in-prostate-cancer-cells
#12
Thomas Stefan Worst, Yannic Meyer, Maria Gottschalt, Cleo-Aron Weis, Jost von Hardenberg, Christine Frank, Annette Steidler, Maurice Stephan Michel, Philipp Erben
Paracrine and long-range signaling via extracellular vesicles, such as exosomes and microvesicles, is deemed crucial for tumorigenesis, invasion and spread of solid tumors. The ESCRT machinery (endosomal sorting complexes required for transport) and Rab-proteins act as key players in vesicular trafficking and secretion. Yet, their role in prostate cancer (PCa) is unknown. Therefore, this study aimed to elucidate the relevance of these components in PCa. In silico reanalysis of genes with known involvement in vesicular trafficking and secretion in an existing microarray dataset revealed low expression of RAB27A, RAB27B and VPS36 to be predictive for reduced BCR-free survival in patients with localized PCa (p=0...
February 10, 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/28196344/identification-characterization-and-in-silico-admet-prediction-of-roflumilast-degradation-products
#13
Mariana S Pinheiro, Gil M Viana, Bárbara de A Abrahim Vieira, Alessandra Mendonça Teles de Souza, Carlos Rangel Rodrigues, Rita de Cássia E E Marins, Lúcio M Cabral, Valéria P de Sousa
The present study reports the degradation behavior of roflumilast (RFL), a new drug developed for the treatment of chronic obstructive pulmonary disease. The degradation of RFL was tested under various stress conditions as per the guidelines of the International Conference on Harmonization. The degradation products (DPs) of RFL were identified, characterized and in silico predictions were made of their pharmacokinetic properties, absorption, distribution, metabolism, excretion and toxicity (ADMET). RFL was subjected to various stress conditions including photodegradation, alkaline and acidic hydrolysis, oxidative and metallic degradation...
February 6, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28195732/in-vivo-predictive-dissolution-ipd-and-biopharmaceutical-modeling-and-simulation-future-use-of-modern-approaches-and-methodologies-in-a-regulatory-context
#14
H Lennernas, A Lindahl, A Van Peer, C Ollier, T Flanagan, R Lionberger, A Nordmark, S Yamashita, L Yu, G L Amidon, V Fischer, E Sjögren, P Zane, M McAllister, B Abrahamsson
The overall objective of OrBiTo, a project within Innovative Medicines Initiative (IMI), is to streamline and optimize the development of orally administered drug products through the creation and efficient application of biopharmaceutics tools. This toolkit will include both experimental and computational models developed on improved understanding of the highly dynamic gastrointestinal (GI) physiology relevant to the GI absorption of drug products in both fasted and fed states. A part of the annual OrBiTo-meeting in 2015 was dedicated to the presentation of the most recent progress in the development of the regulatory use of PBPK in silico modeling, in vivo predictive dissolution (IPD) tests and their application to biowaivers...
February 14, 2017: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/28195550/novel-germline-mutation-leu512met-in-the-thyrotropin-receptor-gene-tshr-leading-to-sporadic-non-autoimmune-hyperthyroidism
#15
Stephanie A Roberts, Jennifer E Moon, Andrew Dauber, Jessica R Smith
BACKGROUND: Primary nonautoimmune hyperthyroidism is a rare cause of neonatal hyperthyroidism. This results from an activating mutation in the thyrotropin-receptor (TSHR). It can be inherited in an autosomal dominant manner or occur sporadically as a de novo mutation. Affected individuals display a wide phenotype from severe neonatal to mild subclinical hyperthyroidism. We describe a 6-month-old boy with a de novo mutation in the TSHR gene who presented with accelerated growth, enlarging head circumference, tremor and thyrotoxicosis...
February 14, 2017: Journal of Pediatric Endocrinology & Metabolism: JPEM
https://www.readbyqxmd.com/read/28194627/fragment-based-in-silico-modeling-of-multi-target-inhibitors-against-breast-cancer-related-proteins
#16
Alejandro Speck-Planche, M Natália D S Cordeiro
Breast cancer is the most frequent cancer reported in women, being responsible for hundreds of thousands of deaths. Chemotherapy has proven to be effective against this malignant neoplasm depending on different biological factors such as the histopathology, grade, and stage, among others. However, breast cancer cells have become resistant to current chemotherapeutic regimens, urging the discovery of new anti-breast cancer drugs. Computational approaches have the potential to offer promising alternatives to accelerate the search for potent and versatile anti-breast cancer agents...
February 13, 2017: Molecular Diversity
https://www.readbyqxmd.com/read/28193166/vacsol-a-high-throughput-in-silico-pipeline-to-predict-potential-therapeutic-targets-in-prokaryotic-pathogens-using-subtractive-reverse-vaccinology
#17
Muhammad Rizwan, Anam Naz, Jamil Ahmad, Kanwal Naz, Ayesha Obaid, Tamsila Parveen, Muhammad Ahsan, Amjad Ali
BACKGROUND: With advances in reverse vaccinology approaches, a progressive improvement has been observed in the prediction of putative vaccine candidates. Reverse vaccinology has changed the way of discovery and provides a mean to propose target identification in reduced time and labour. In this regard, high throughput genomic sequencing technologies and supporting bioinformatics tools have greatly facilitated the prompt analysis of pathogens, where various predicted candidates have been found effective against certain infections and diseases...
February 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28192183/measuring-kinetics-and-potency-of-herg-block-for-cipa
#18
Monique J Windley, Najah Abi-Gerges, Bernard Fermini, Jules C Hancox, Jamie I Vandenberg, Adam P Hill
INTRODUCTION: The Comprehensive in vitro Proarrhythmic Assay (CiPA) aims to update current cardiac safety testing to better evaluate arrhythmic risk. A central theme of CiPA is the use of in silico approaches to risk prediction incorporating models of drug binding to hERG. To parameterize these models, accurate in vitro measurement of potency and kinetics of block is required. The Ion Channel Working Group was tasked with: i) selecting a protocol that could measure kinetics of block and was easily implementable on automated platforms for future rollout in industry and ii) acquiring a reference dataset using the standardized protocol...
February 10, 2017: Journal of Pharmacological and Toxicological Methods
https://www.readbyqxmd.com/read/28191571/a-computer-based-prediction-platform-for-the-reaction-of-ozone-with-organic-compounds-in-aqueous-solution-kinetics-and-mechanisms
#19
Minju Lee, Lorenz C Blum, Emanuel Schmid, Kathrin Fenner, Urs von Gunten
Ozonation of secondary wastewater effluents can reduce the discharge of micropollutants by transforming their chemical structures. Therefore, a better understanding of the formation of transformation products during ozonation is important. In this study, a computer-based prediction platform for the kinetics and mechanisms of the reactions of ozone with organic compounds was developed to enable in silico predictions of transformation products. With the developed prediction platform, reaction kinetics expressed as second-order rate constants for the reactions of ozone with selected organic compounds (kO3, M(-1) s(-1)) can be predicted based on an adapted kO3 prediction model from a previous study (Lee et al...
February 13, 2017: Environmental Science. Processes & Impacts
https://www.readbyqxmd.com/read/28187756/a-novel-mttt-mutation-m-15933g%C3%A2-%C3%A2-a-revealed-in-analysis-of-mitochondrial-dna-in-patients-with-suspected-mitochondrial-disease
#20
Heidi K Soini, Antti Väisänen, Mikko Kärppä, Reetta Hinttala, Laura Kytövuori, Jukka S Moilanen, Johanna Uusimaa, Kari Majamaa
BACKGROUND: Mitochondrial diseases present with variable multi-organ symptoms. Common disease-causing mutations in mitochondrial DNA (mtDNA) are regularly screened in diagnostic work-up, but novel mutations may remain unnoticed. METHODS: Patients (N = 66) with a clinical suspicion of mitochondrial disease were screened for their mtDNA coding region using conformation sensitive gel electrophoresis and sequencing. Long-PCR was used to detect deletions followed by POLG1 sequencing in patients with multiple deletions...
February 10, 2017: BMC Medical Genetics
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