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https://www.readbyqxmd.com/read/30556015/classification-of-hiv-1-protease-inhibitors-by-machine-learning-methods
#1
Yang Li, Yujia Tian, Zijian Qin, Aixia Yan
HIV-1 protease plays an important role in the processing of virus infection. Protease is an effective therapeutic target for the treatment of HIV-1. Our data set is based on a selection of 4855 HIV-1 protease inhibitors (PIs) from ChEMBL. A series of 15 classification models for predicting the active inhibitors were built by machine learning methods, including k -nearest neighors (K-NN), decision tree (DT), random forest (RF), support vector machine (SVM), and deep neural network (DNN). The molecular structures were characterized by (1) fingerprint descriptors including MACCS fingerprints and PubChem fingerprints and (2) physicochemical descriptors calculated by CORINA Symphony...
November 30, 2018: ACS Omega
https://www.readbyqxmd.com/read/30555854/gene-expression-studies-for-the-development-of-particle-therapy
#2
Sally A Amundson
Proton therapy for cancer is now in widespread use, and facilities for carbon ion therapy are showing great promise, but a more complete understanding of the mechanisms underlying particle radiation therapy is still needed in order to optimize treatment. Studies of gene expression, especially those using whole genome techniques, can provide insight into many of the questions still remaining, from the molecular mechanisms involved to predicting patient outcome. This review will summarize gene expression studies of response to proton and carbon ion beams, as well as high-energy protons and high-z high-energy particles with relevance to particle therapy...
2018: International Journal of Particle Therapy
https://www.readbyqxmd.com/read/30554147/mapping-oat-crown-rust-resistance-gene-pc45-confirms-association-with-pckm
#3
Aida Z Kebede, Jayelle R Friesen-Enns, Belaghihalli N Gnanesh, Jim G Menzies, Jennifer W Mitchell Fetch, James Chong, Aaron D Beattie, Edyta Paczos-Grzęda, Curt A McCartney
Molecular mapping of crown rust resistance genes is important to effectively utilize these genes and improve breeding efficiency through marker-assisted selection. Pc45 is a major race-specific crown rust resistance gene initially identified in the wild hexaploid oat Avena sterilis in the early 1970s. This gene was transferred to cultivated oat ( Avena sativa ) and has been used as a differential for identification of crown rust races since 1974. Previous research identified an association between virulence to Pc45 and PcKM , a crown rust resistance gene in the varieties 'Kame' and 'Morton'...
December 15, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/30552854/a-community-outbreak-of-legionnaires-disease-in-geneva-switzerland-june-to-september-2017
#4
Marie-Céline Zanella, Sabine Yerly, Abdessalam CherkaouiI, Gesuele Renzi, Aline Mamin, Laura Lourenço Cordes, Elisabeth Delaporte, Zofia Baranczuk-Turska, Olivia Keiser, Jacques Schrenzel, Stephan Harbarth, Valeria Gaia, Laurent Kaiser
PURPOSE: Eight confirmed cases of Legionnaires’ disease were identified at the Geneva University Hospitals between 28 July 2017 and 02 August 2017, leading to a detailed outbreak investigation. METHODS: Legionnaires’ disease cases were defined according to Swiss and European (ELDSNet) consensus guidelines. An outbreak investigation task force was put in place. Patients were interviewed, when feasible, with a standard questionnaire. A Legionella pneumophila urinary antigen test was performed in all cases...
November 19, 2018: Swiss Medical Weekly
https://www.readbyqxmd.com/read/30548659/clinical-and-molecular-characteristics-of-bladder-urothelial-carcinoma-subtypes
#5
Ying Li, Kai Yang, Ke Li, He Liu, Siqi Zhao, Mingli Jiao, Xinru Fu
Bladder urothelial carcinoma (BLCA) is a common malignancy with high heterogeneity. A reasonable molecular subtyping can facilitate biological study and personalized therapy of BLCA. In this study, unsupervised consensus clustering was used to acquire the molecular subtypes of BLCA based on messenger RNA (mRNA) and microRNA (miRNA) data. Gene signature markers and canonical signaling pathways were compared between different subtypes. The Database for Annotation, Visualization and Integrated Discovery (DAVID) was used for the functional annotation of overexpressed genes in different subtypes for Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways...
December 12, 2018: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/30548157/sox2-regulates-p63-and-stem-progenitor-cell-state-in-the-corneal-epithelium
#6
Swarnabh Bhattacharya, Laura Serror, Eshkar Nir, Dalbir Dhiraj, Anna Altshuler, Maroun Khreish, Beatrice Tiosano, Peleg Hasson, Lia Panman, Chen Luxenburg, Daniel Aberdam, Ruby Shalom-Feuerstein
Mutations in key transcription factors SOX2 and P63 were linked with developmental defects and post-natal abnormalities such as corneal opacification, neovascularization and blindness. The latter phenotypes suggest that SOX2 and P63 may be involved in corneal epithelial regeneration. While P63 has been shown to be a key regulator of limbal stem cells (LSCs), the expression pattern and function of SOX2 in the adult cornea remained unclear. Here we show that SOX2 regulates P63 to control corneal epithelial stem/progenitor cell function...
December 10, 2018: Stem Cells
https://www.readbyqxmd.com/read/30547399/a-multiattribute-gaussian-graphical-model-for-inferring-multiscale-regulatory-networks-an-application-in-breast-cancer
#7
Julien Chiquet, Guillem Rigaill, Martina Sundqvist
This chapter addresses the problem of reconstructing regulatory networks in molecular biology by integrating multiple sources of data. We consider data sets measured from diverse technologies all related to the same set of variables and individuals. This situation is becoming more and more common in molecular biology, for instance, when both proteomic and transcriptomic data related to the same set of "genes" are available on a given cohort of patients.To infer a consensus network that integrates both proteomic and transcriptomic data, we introduce a multivariate extension of Gaussian graphical models (GGM), which we refer to as multiattribute GGM...
2019: Methods in Molecular Biology
https://www.readbyqxmd.com/read/30544005/in-silico-identification-and-evaluation-of-potential-interaction-of-azadirachta-indica-phytochemicals-with-plasmodium-falciparum-heat-shock-protein-90
#8
Michael Oluwatoyin Daniyan, Oluwatoyin Tolulope Ojo
Plasmodium falciparum heat shock protein 90 (PfHsp90) has been investigated as a potential target of antimalarial drug action using naturally occurring compounds. In this study, we performed in silico screening of 236 phytochemicals of Azadirachta indica, a plant known to possess antimalarial activity, and identified fourteen (14) potential non-carcinogenic, non-mutagenic, non-teratogenic and non-genotoxic phytochemicals. These phytochemicals were docked into the ATP-binding site of PfHsp90 using Autodock vina, and docked poses were rescored using PLANTS ChemPlp, X-Score version 1...
December 4, 2018: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/30543470/endemicity-of-the-high-risk-clone-klebsiella-pneumoniae-st340-coproducing-qnrb-ctx-m-15-and-kpc-2-in-a-brazilian-hospital
#9
Fernanda Modesto Tolentino, Maria Fernanda Campagnari Bueno, Gabriela Rodrigues Franscisco, Diego Diniz de Paula Barcelos, Suzana Margareth Lobo, Francieli Maira Moreira Batista Tomaz, Natal Santos da Silva, Leonardo Neves de Andrade, Tiago Casella, Ana Lucia da Costa Darini, Milena Polotto, Doroti de Oliveira Garcia, Mara Correa Lelles Nogueira
The dissemination of multiresistant Klebsiella pneumoniae carbapenemase (KPC)-2-producing Klebsiella pneumoniae isolates belonging to international high-risk clones poses a major health care threat. In this study, 48 nonduplicated, carbapenem-resistant K. pneumoniae isolated from 2011 to 2014 in a tertiary hospital were investigated. The blaKPC-2 gene was the only determinant for carbapenem resistance. The blaCTX-M-15 gene was the main determinant for the production of extended-spectrum beta-lactamase (ESBL), whereas aph(3')-Ia and qnrB were the most common genes associated with resistance to aminoglycosides and quinolones, respectively...
December 13, 2018: Microbial Drug Resistance: MDR: Mechanisms, Epidemiology, and Disease
https://www.readbyqxmd.com/read/30542317/silent-free-fall-at-disease-onset-a-perspective-on-therapeutics-for-progressive-multiple-sclerosis
#10
REVIEW
Patrizia LoPresti
Central nervous system (CNS) degeneration occurs during multiple sclerosis (MS) following several years of reversible autoimmune demyelination. Progressive CNS degeneration appears later during the course of relapsing-remitting MS (RRMS), although it starts insidiously at disease onset. We propose that there is an early subclinical phase also for primary-progressive (PP) MS. Consensus exists that many different cell types are involved during disease onset. Furthermore, the response to the initial damage, which is specific for each individual, would result in distinct pathological pathways that add complexity to the disease and the mechanisms underlying progressive CNS degeneration...
2018: Frontiers in Neurology
https://www.readbyqxmd.com/read/30534123/structural-immunology-of-complement-receptors-3-and-4
#11
REVIEW
Thomas Vorup-Jensen, Rasmus Kjeldsen Jensen
Complement receptors (CR) 3 and 4 belong to the family of beta-2 (CD18) integrins. CR3 and CR4 are often co-expressed in the myeloid subsets of leukocytes, but they are also found in NK cells and activated T and B lymphocytes. The heterodimeric ectodomain undergoes considerable conformational change in order to switch the receptor from a structurally bent, ligand-binding in-active state into an extended, ligand-binding active state. CR3 binds the C3d fragment of C3 in a way permitting CR2 also to bind concomitantly...
2018: Frontiers in Immunology
https://www.readbyqxmd.com/read/30533595/culture-negative-periprosthetic-joint-infection-an-update-on-what-to-expect
#12
Timothy L Tan, Michael M Kheir, Noam Shohat, Dean D Tan, Matthew Kheir, Chilung Chen, Javad Parvizi
Background: Culture-negative periprosthetic joint infection (PJI) is a challenging condition to treat. The most appropriate management of culture-negative PJI is not known, and there is immense variability in the treatment outcome of this condition. The purpose of this study was to elucidate the characteristics, outcomes, and risk factors for failure of treatment of culture-negative PJI. Methods: A retrospective review of 219 patients (138 hips and 81 knees) who had undergone surgery for the treatment of culture-negative PJI was performed utilizing a prospectively collected institutional PJI database...
September 25, 2018: JB & JS open access
https://www.readbyqxmd.com/read/30527445/enzymatic-phosphorylation-of-ser-in-a-type-i-collagen-peptide
#13
Yimin Qiu, Erik Poppleton, Arya Mekkat, Hongtao Yu, Sourav Banerjee, Sandra E Wiley, Jack E Dixon, David L Kaplan, Yu-Shan Lin, Barbara Brodsky
Phosphoproteomics studies have reported phosphorylation at multiple sites within collagen, raising the possibility that these post-translational modifications regulate the physical or biological properties of collagen. In this study, molecular dynamics simulations and experimental studies were carried out on model peptides to establish foundational principles of phosphorylation of Ser residues in collagen. A (Gly-Xaa-Yaa)11 peptide was designed to include a Ser-containing sequence from type I collagen that was reported to be phosphorylated...
November 16, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/30526476/consensus-map-integration-and-qtl-meta-analysis-narrowed-a-locus-for-yield-traits-to-0-7-cm-and-refined-a-region-for-late-leaf-spot-resistance-traits-to-0-38-cm-on-linkage-group-a05-in-peanut-arachis-hypogaea-l
#14
Qing Lu, Hao Liu, Yanbin Hong, Haifen Li, Haiyan Liu, Xingyu Li, Shijie Wen, Guiyuan Zhou, Shaoxiong Li, Xiaoping Chen, Xuanqiang Liang
BACKGROUND: Many large-effect quantitative trait loci (QTLs) for yield and disease resistance related traits have been identified in different mapping populations of peanut (Arachis hypogaea L.) under multiple environments. However, only a limited number of QTLs have been used in marker-assisted selection (MAS) because of unfavorable epistatic interactions between QTLs in different genetic backgrounds. Thus, it is essential to identify consensus QTLs across different environments and genetic backgrounds for use in MAS...
December 7, 2018: BMC Genomics
https://www.readbyqxmd.com/read/30522624/concomitant-methicillin-resistant-staphylococcus-aureus-infection-in-tubercular-sacroiliitis-masquerading-as-anti-tubercular-drug-resistance-role-for-molecular-diagnosis
#15
Narendran Pushpasekaran, Deepak Gupta, Abhishek Kashyap, Sumit Arora, Ajay Kumar Gupta
A 23-year-old female on anti-tubercular therapy for tuberculous sacroiliitis presented with right sided gluteal and thigh abscess. Suspecting treatment failure, surgical evacuation of purulent material was done. The bacteriological isolation showed positivity for methicillin-resistant Staphylococcus aureus. Although the microbiological and histopathology examination of the specimen were negative for tubercular isolates, the cartridge based -nucleic acid amplification tests revealed positive genes for Mycobacterium tuberculosis and additional primers showed sensitivity for rifampicin and isoniazid...
October 2018: Indian Journal of Tuberculosis
https://www.readbyqxmd.com/read/30514738/kabuki-syndrome-international-consensus-diagnostic-criteria
#16
Margaret P Adam, Siddharth Banka, Hans T Bjornsson, Olaf Bodamer, Albert E Chudley, Jaqueline Harris, Hiroshi Kawame, Brendan C Lanpher, Andrew W Lindsley, Giuseppe Merla, Noriko Miyake, Nobuhiko Okamoto, Constanze T Stumpel, Norio Niikawa
BACKGROUND: Kabuki syndrome (KS) is a clinically recognisable syndrome in which 70% of patients have a pathogenic variant in KMT2D or KDM6A . Understanding the function of these genes opens the door to targeted therapies. The purpose of this report is to propose diagnostic criteria for KS, particularly when molecular genetic testing is equivocal. METHODS: An international group of experts created consensus diagnostic criteria for KS. Systematic PubMed searches returned 70 peer-reviewed publications in which at least one individual with molecularly confirmed KS was reported...
December 4, 2018: Journal of Medical Genetics
https://www.readbyqxmd.com/read/30514647/porphyria-cutanea-tarda-and-hepatoerythropoietic-porphyria-identification-of-19-novel-uroporphyrinogen-iii-decarboxylase-mutations
#17
Yedidyah Weiss, Brenden Chen, Makiko Yasuda, Irina Nazarenko, Karl E Anderson, Robert J Desnick
Porphyria Cutanea Tarda (PCT) is a cutaneous porphyria that results from the hepatic inhibition of the heme biosynthetic enzyme uroporphyrinogen decarboxylase (UROD), and can occur either in the absence or presence of an inherited heterozygous UROD mutation (PCT subtypes 1 and 2, respectively). A heterozygous UROD mutation causes half-normal levels of UROD activity systemically, which is a susceptibility factor but is not sufficient alone to cause type 2 PCT. In both Types 1 and 2 PCT, the cutaneous manifestations are precipitated by additional factors that lead to generation of an inhibitor that more profoundly reduces hepatic UROD activity...
November 28, 2018: Molecular Genetics and Metabolism
https://www.readbyqxmd.com/read/30509980/probing-the-mechanism-of-inhibition-of-amyloid-%C3%AE-1-42-induced-neurotoxicity-by-the-chaperonin-groel
#18
Marielle A Wälti, Joseph Steiner, Fanjie Meng, Hoi Sung Chung, John M Louis, Rodolfo Ghirlando, Vitali Tugarinov, Avindra Nath, G Marius Clore
The human chaperonin Hsp60 is thought to play a role in the progression of Alzheimer's disease by mitigating against intracellular β-amyloid stress. Here, we show that the bacterial homolog GroEL (51% sequence identity) reduces the neurotoxic effects of amyloid-β(1-42) (Aβ42) on human neural stem cell-derived neuronal cultures. To understand the mechanism of GroEL-mediated abrogation of neurotoxicity, we studied the interaction of Aβ42 with GroEL using a variety of biophysical techniques. Aβ42 binds to GroEL as a monomer with a lifetime of ∼1 ms, as determined from global analysis of multiple relaxation-based NMR experiments...
December 3, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/30507436/consensus-on-molecular-imaging-and-theranostics-in-prostate-cancer
#19
REVIEW
Stefano Fanti, Silvia Minozzi, Gerald Antoch, Ian Banks, Alberto Briganti, Ignasi Carrio, Arturo Chiti, Noel Clarke, Matthias Eiber, Johann De Bono, Karim Fizazi, Silke Gillessen, Sam Gledhill, Uwe Haberkorn, Ken Herrmann, Rodney J Hicks, Frederic Lecouvet, Rodolfo Montironi, Piet Ost, Joe M O'Sullivan, Anwar R Padhani, Jack A Schalken, Howard I Scher, Bertrand Tombal, R Jeroen A van Moorselaar, Heindrik Van Poppel, Hebert Alberto Vargas, Jochen Walz, Wolfgang A Weber, Hans-Jürgen Wester, Wim J G Oyen
Rapid developments in imaging and treatment with radiopharmaceuticals targeting prostate cancer pose issues for the development of guidelines for their appropriate use. To tackle this problem, international experts representing medical oncologists, urologists, radiation oncologists, radiologists, and nuclear medicine specialists convened at the European Association of Nuclear Medicine Focus 1 meeting to deliver a balanced perspective on available data and clinical experience of imaging in prostate cancer, which had been supported by a systematic review of the literature and a modified Delphi process...
December 2018: Lancet Oncology
https://www.readbyqxmd.com/read/30505180/genetic-characterization-of-antibiotic-resistant-staphylococcus-aureus-from-milk-in-the-north-west-province-south-africa
#20
Muyiwa Ajoke Akindolire, Ajay Kumar, Collins Njie Ateba
Food borne diseases are a major public health concern worldwide. Staphylococcus aureus is one of the potential food borne pathogens which causes nosocomial and community acquired infections. In the present study, 74 representative strains of S. aureus isolated and characterized in previous study from different milk samples were subjected to random amplified polymorphic DNA (RAPD) polymerase chain reaction (PCR) and enterobacterial repetitive intergenic consensus (ERIC)-PCR to generate fingerprints to determine the genetic relationships of the isolated strains...
November 2018: Saudi Journal of Biological Sciences
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