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https://www.readbyqxmd.com/read/29076577/prediction-of-protein-disorder-based-on-iupred
#1
Zsuzsanna Dosztányi
Many proteins contain intrinsically disordered regions (IDRs), functional polypeptide segments that in isolation adopt a highly flexible conformational ensemble instead of a single, well-defined structure. Disorder prediction methods, which can discriminate ordered and disordered regions from the amino acid sequence, have contributed significantly to our current understanding of the distinct properties of IDPs by enabling the characterization of individual examples as well as large-scale analyses of these protein regions...
October 27, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/29036655/mfib-a-repository-of-protein-complexes-with-mutual-folding-induced-by-binding
#2
Erzsébet Fichó, István Reményi, István Simon, Bálint Mészáros
Motivation: It is commonplace that intrinsically disordered proteins (IDPs) are involved in crucial interactions in the living cell. However, the study of protein complexes formed exclusively by IDPs is hindered by the lack of data and such analyses remain sporadic. Systematic studies benefited other types of protein-protein interactions paving a way from basic science to therapeutics; yet these efforts require reliable datasets that are currently lacking for synergistically folding complexes of IDPs...
November 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28817585/selecting-targets-for-the-diagnosis-of-schistosoma-mansoni-infection-an-integrative-approach-using-multi-omic-and-immunoinformatics-data
#3
Gardenia B F Carvalho, Daniela M Resende, Liliane M V Siqueira, Marcelo D Lopes, Débora O Lopes, Paulo Marcos Z Coelho, Andréa Teixeira-Carvalho, Jeronimo C Ruiz, Cristina T Fonseca
In order to effectively control and monitor schistosomiasis, new diagnostic methods are essential. Taking advantage of computational approaches provided by immunoinformatics and considering the availability of Schistosoma mansoni predicted proteome information, candidate antigens of schistosomiasis were selected and used in immunodiagnosis tests based on Enzime-linked Immunosorbent Assay (ELISA). The computational selection strategy was based on signal peptide prediction; low similarity to human proteins; B- and T-cell epitope prediction; location and expression in different parasite life stages within definitive host...
2017: PloS One
https://www.readbyqxmd.com/read/28327786/polymorphisms-in-genes-tlr1-2-and-4-are-associated-with-differential-cytokine-and-chemokine-serum-production-in-patients-with-leprosy
#4
Nadja de Lima Santana, Jamile Leão Rêgo, Joyce Moura Oliveira, Lucas Frederico de Almeida, Marcos Braz, Lídia Maria Medeiros Machado, Paulo Roberto Lima Machado, Léa Cristina Castellucci
BACKGROUND: Leprosy or hansen's disease is a spectral disease whose clinical forms mostly depends on host's immune and genetic factors. Different Toll-like receptors (TLR) variants have been described associated with leprosy, but with some lack of replication across different populations. OBJECTIVES: To evaluate the role of polymorphisms in genes TLR1, TLR2 and TLR4 and susceptibility to leprosy in a genetic case control study; to verify the association between genotypes of these markers and the immunological profile in the serum of patients with leprosy...
April 2017: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/27924015/tstmp-target-selection-for-structural-genomics-of-human-transmembrane-proteins
#5
Julia Varga, László Dobson, István Reményi, Gábor E Tusnády
The TSTMP database is designed to help the target selection of human transmembrane proteins for structural genomics projects and structure modeling studies. Currently, there are only 60 known 3D structures among the polytopic human transmembrane proteins and about a further 600 could be modeled using existing structures. Although there are a great number of human transmembrane protein structures left to be determined, surprisingly only a small fraction of these proteins have 'selected' (or above) status according to the current version the TargetDB/TargetTrack database...
January 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27800449/molecular-typing-of-staphylococcus-aureus-isolate-responsible-for-staphylococcal-poisoning-incident-in-homemade-food
#6
Guerrino Macori, Alberto Bellio, Daniela Manila Bianchi, Silvia Gallina, Daniela Adriano, Fabio Zuccon, Francesco Chiesa, Pier Luigi Acutis, Francesco Casalinuovo, Lucia Decastelli
In October 2012, two persons fell ill with symptoms consistent with staphylococcal food poisoning after eating home-canned tuna fish and tomatoes. Laboratory investigation detected the enterotoxins in the home-canned tuna and molecular analysis of the isolated Staphylococcus aureus confirmed it carried toxin genes. Qualitative enzyme-linked immunosorbent assay and enzime linked fluorescent assay methods and quantitative assay identified the enterotoxins in the food leftovers, specifically staphylococcal enterotoxins type A (SEA) and D (SED), respectively 0...
April 19, 2016: Italian Journal of Food Safety
https://www.readbyqxmd.com/read/27661787/salvage-therapy-or-simplification-of-salvage-regimens-with-dolutegravir-plus-ritonavir-boosted-darunavir-dual-therapy-in-highly-cart-experienced-subjects-an-italian-cohort
#7
Amedeo F Capetti, Gaetana Sterrantino, Maria V Cossu, Giovanni Cenderello, Anna M Cattelan, Giuseppe V De Socio, Stefano Rusconi, Niccolò Riccardi, Gian M Baldin, Serena Cima, Fosca P Niero, Giuliano Rizzardini, Lolita Sasset
BACKGROUND: Dolutegravir plus darunavir provide a high genetic barrier to HIV-1 resistance and are suitable for simple salvage regimens. METHODS: All HIV-1-infected subjects treated with dolutegravir plus boosted darunavir dual therapy between March 2011 and September 2015 were included in an observational cohort. Data were collected at baseline and at weeks 4, 12, 24 and 48. RESULTS: We enrolled 113 subjects. After week 24, one was lost at follow-up, one dropped out for grade 2 elevation of liver enzymes, one died from illicit drug abuse and one from cancer-related sepsis...
2017: Antiviral Therapy
https://www.readbyqxmd.com/read/27263433/-the-effect-of-the-i-d-polymorphism-of-the-angiotensin-converting-enzyme-gene-on-the-cardiovascular-risk-and-graft-survival-of-kidney-transplant-patients
#8
Roland Fedor, Dávid Ágoston Kovács, Lajos Lőcsey, Miklós Fagyas, László Asztalos, Attila Tóth
INTRODUCTION: Renal transplantation provides longer life expectancy in patients with renal failure. Nonetheless, this improved life expectancy is still shorter than that for the general population. The main couse of death in renal transplant patients is cardiovascular disease, and chronic allograft nephropathy is the most significant cause of graft loss. Genetic polymorphisms of the renin angiotensin system have been implicated in both chronic allograft nephropathy and fatal cardiovascular diseases...
June 12, 2016: Orvosi Hetilap
https://www.readbyqxmd.com/read/27153630/topdom-database-of-conservatively-located-domains-and-motifs-in-proteins
#9
Julia Varga, László Dobson, Gábor E Tusnády
UNLABELLED: The TOPDOM database-originally created as a collection of domains and motifs located consistently on the same side of the membranes in α-helical transmembrane proteins-has been updated and extended by taking into consideration consistently localized domains and motifs in globular proteins, too. By taking advantage of the recently developed CCTOP algorithm to determine the type of a protein and predict topology in case of transmembrane proteins, and by applying a thorough search for domains and motifs as well as utilizing the most up-to-date version of all source databases, we managed to reach a 6-fold increase in the size of the whole database and a 2-fold increase in the number of transmembrane proteins...
September 1, 2016: Bioinformatics
https://www.readbyqxmd.com/read/26984204/renin-angiotensin-aldosterone-system-blockade-in-chronic-kidney-disease-current-strategies-and-a-look-ahead
#10
REVIEW
Francesca Viazzi, Barbara Bonino, Francesca Cappadona, Roberto Pontremoli
The Renin-Angiotensin-Aldosterone System (RAAS) is profoundly involved in the pathogenesis of renal and cardiovascular organ damage, and has been the preferred therapeutic target for renal protection for over 30 years. Monotherapy with either an Angiotensin Converting Enzime Inhibitor (ACE-I) or an Angiotensin Receptor Blocker (ARB), together with optimal blood pressure control, remains the mainstay treatment for retarding the progression toward end-stage renal disease. Combining ACE-Is and ARBs, or either one with an Aldosterone Receptor Antagonist (ARA), has been shown to provide greater albuminuria reduction, and to possibly improve renal outcome, but at an increased risk of potentially severe side effects...
August 2016: Internal and Emergency Medicine
https://www.readbyqxmd.com/read/26907316/prevalence-of-heart-failure-and-adherence-to-process-indicators-which-socio-demographic-determinants-are-involved
#11
Alessandra Buja, Giuliana Solinas, Modesta Visca, Bruno Federico, Rosa Gini, Vincenzo Baldo, Paolo Francesconi, Gino Sartor, Mariadonata Bellentani, Gianfranco Damiani
Interest in chronic conditions reflects their role as the first cause of death and disability in developed countries; improving the management of these conditions is a priority for health care services. The aim of this study was to establish which sociodemographic factors influence adherence to standards of care for chronic heart failure (CHF). A generalized multilevel structural equation model was developed and applied to a sample of patients with CHF obtained from administrative data flows in six Italian regions to ascertain any associations between adherence to standards of care for CHF and sociodemographic variables...
February 2016: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/26020669/-effect-of-pravastatine-plus-ezetimibe-on-carotid-intima-media-thickness-in-patients-with-lupus-erythematosus
#12
Olga Lidia Vera-Lastra, Arturo Olvera-Acevedo, Claudia Hernández, Gabriela Medina, Ana Laura Carrillo-González, Ulises Ángeles-Garay, Ana Lilia Peralta-Amaro, Luis Jara
BACKGROUND: Patients with systemic lupus erythematosus (SLE) have accelerated atherosclerosis that can be assessed by the carotid intima media thickness (CIMT) measurement. A prompt hypolipidemic treatment should be a part of the integral management. The aim of this study is to determine the effect of therapy with pravastatin plus ezetimibe on the CIMT in SLE patients. METHODS: Longitudinal, prospective, quasi-experimental trial. Out of 60 SLE patients in whom a carotid ultrasound was performed, we chose 22 with a CIMT>0...
2015: Revista Médica del Instituto Mexicano del Seguro Social
https://www.readbyqxmd.com/read/26018427/the-human-transmembrane-proteome
#13
László Dobson, István Reményi, Gábor E Tusnády
BACKGROUND: Transmembrane proteins have important roles in cells, as they are involved in energy production, signal transduction, cell-cell interaction, cell-cell communication and more. In human cells, they are frequently targets for pharmaceuticals; therefore, knowledge about their properties and structure is crucial. Topology of transmembrane proteins provide a low resolution structural information, which can be a starting point for either laboratory experiments or modelling their 3D structures...
2015: Biology Direct
https://www.readbyqxmd.com/read/25957909/cox-2-rs20417-polymorphism-is-associated-with-stroke-and-white-matter-disease
#14
Jamary Oliveira-Filho, Ana C P Ornellas, Cathy R Zhang, Luciana M B Oliveira, Théo Araújo-Santos, Valeria M Borges, Laís M G B Ventura, Francisco J F B Reis, Roque Aras, André M Fernandes, Jonathan Rosand, Steven M Greenberg, Karen L Furie, Natalia S Rost
BACKGROUND: To investigate the effect of COX-2 polymorphism and its product, prostaglandin E2 (PGE2), on stroke risk in an endemic area for Chagas disease. In a separate cohort, to investigate the effect of COX-2 polymorphisms on the total burden of cerebral white matter disease. METHODS: Cases were outpatients with ischemic stroke; controls were stroke-free subjects from 2 outpatient clinics (heart failure and caregivers of a movement disorders clinic). We extracted DNA from total blood to investigate the rs20417 COX-2 polymorphism...
August 2015: Journal of Stroke and Cerebrovascular Diseases: the Official Journal of National Stroke Association
https://www.readbyqxmd.com/read/25943549/cctop-a-consensus-constrained-topology-prediction-web-server
#15
László Dobson, István Reményi, Gábor E Tusnády
The Consensus Constrained TOPology prediction (CCTOP; http://cctop.enzim.ttk.mta.hu) server is a web-based application providing transmembrane topology prediction. In addition to utilizing 10 different state-of-the-art topology prediction methods, the CCTOP server incorporates topology information from existing experimental and computational sources available in the PDBTM, TOPDB and TOPDOM databases using the probabilistic framework of hidden Markov model. The server provides the option to precede the topology prediction with signal peptide prediction and transmembrane-globular protein discrimination...
July 1, 2015: Nucleic Acids Research
https://www.readbyqxmd.com/read/25392424/expediting-topology-data-gathering-for-the-topdb-database
#16
László Dobson, Tamás Langó, István Reményi, Gábor E Tusnády
The Topology Data Bank of Transmembrane Proteins (TOPDB, http://topdb.enzim.ttk.mta.hu) contains experimentally determined topology data of transmembrane proteins. Recently, we have updated TOPDB from several sources and utilized a newly developed topology prediction algorithm to determine the most reliable topology using the results of experiments as constraints. In addition to collecting the experimentally determined topology data published in the last couple of years, we gathered topographies defined by the TMDET algorithm using 3D structures from the PDBTM...
January 2015: Nucleic Acids Research
https://www.readbyqxmd.com/read/23808314/-the-composition-of-lipids-and-lipid-peroxidation-in-the-pancreas-of-quails-exposed-to-nitrates-and-correction-by-the-amaranth-s-seeds
#17
S I Tsekhmistrenko, N V Ponomarenko
Researches of features of lipid composition, functioning of the system of antioxidant defense, maintenance of lipid peroxidation products in the quail's pancreas on the early postnatal ontogenesis stages are conducted for actions of nitrates and feeding with amaranth's seeds in mixed fodder. The arrival of nitrates in the organism of quails results in the decline of general lipids maintenance and nonetherified fat acids in the pancreas. Using of amaranth's seeds in mixed fodder on the background of the nitrate loading results in the increase of activity of the enzimes system of antioxidant defence, the growth of general lipid level in the quail's pancreas...
March 2013: Ukraïnsʹkyĭ Biokhimichnyĭ Z︠h︡urnal
https://www.readbyqxmd.com/read/23513484/-utility-of-chromosome-banding-with-alu-i-enzyme-for-identifying-methylated-areas-in-breast-cancer
#18
Alicia Rojas-Atencio, Leonard Yamarte, Karelis Urdaneta, Marisol Soto-Alvarez, Francisco Alvarez Nava, Jenny Cañizalez, Maribel Quintero, Raquel Atencio, Richard González
Cancer is a group of disorders characterized by uncontrolled cell growth which is produced by two successive events: increased cell proliferation (tumor or neoplasia) and the invasive capacity of these cells (metastasis). DNA methylation is an epigenetic process which has been involved as an important pathogenic factor of cancer. DNA methylation participates in the regulation of gene expression, directly, by preventing the union of transcription factors, and indirectly, by promoting the "closed" structure of the chromatine...
December 2012: Investigación Clínica
https://www.readbyqxmd.com/read/23363296/alzheimer-s-disease-and-diabetes-new-insights-and-unifying-therapies
#19
REVIEW
Arianna Vignini, Alessia Giulietti, Laura Nanetti, Francesca Raffaelli, Lucia Giusti, Laura Mazzanti, Leandro Provinciali
Several research groups have begun to associate the Alzheimer Disease (AD) to Diabetes Mellitus (DM), obesity and cardiovascular disease. This relationship is so close that some authors have defined Alzheimer Disease as Type 3 Diabetes. Numerous studies have shown that people with type 2 diabetes have twice the incidence of sporadic AD. Insulin deficiency or insulin resistance facilitates cerebral β-amyloidogenesis in murine model of AD, accompanied by a significant elevation in APP (Amyloid Precursor Protein) and BACE1 (β-site APP Cleaving Enzime 1)...
May 2013: Current Diabetes Reviews
https://www.readbyqxmd.com/read/23203988/pdbtm-protein-data-bank-of-transmembrane-proteins-after-8-years
#20
Dániel Kozma, István Simon, Gábor E Tusnády
The PDBTM database (available at http://pdbtm.enzim.hu), the first comprehensive and up-to-date transmembrane protein selection of the Protein Data Bank, was launched in 2004. The database was created and has been continuously updated by the TMDET algorithm that is able to distinguish between transmembrane and non-transmembrane proteins using their 3D atomic coordinates only. The TMDET algorithm can locate the spatial positions of transmembrane proteins in lipid bilayer as well. During the last 8 years not only the size of the PDBTM database has been steadily growing from ∼400 to 1700 entries but also new structural elements have been identified, in addition to the well-known α-helical bundle and β-barrel structures...
January 2013: Nucleic Acids Research
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