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Bioinformatics & pathogenicity prediction

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https://www.readbyqxmd.com/read/29785196/a-computational-approach-using-bioinformatics-to-screening-drug-targets-for-leishmania-infantum-species
#1
Miguel Angel Chávez-Fumagalli, Mônica Santos Schneider, Daniela Pagliara Lage, Grasiele de Sousa Vieira Tavares, Débora Vasconcelos Costa Mendonça, Thaís Teodoro de Oliveira Santos, Rodrigo Maia Pádua, Ricardo Andrez Machado-de-Ávila, João Paulo Viana Leite, Eduardo Antonio Ferraz Coelho
Background: The development of new therapeutic strategies to treat patients for leishmaniasis has become a priority. The antileishmanial activity of the strychnobiflavone flavonoid was recently demonstrated against Leishmania amazonensis and Leishmania infantum amastigotes and promastigotes. The biological effect of this molecule was identified due to its capacity to interfere in the parasite mitochondrial membrane; however, the underlying molecular mechanism remains unclear. Methods and Results: In this study, a computational approach using bioinformatics was performed to screen biological targets of strychnobiflavone in L...
2018: Evidence-based Complementary and Alternative Medicine: ECAM
https://www.readbyqxmd.com/read/29784887/identification-of-the-thioredoxin-partner-of-vkor-in-mycobacterial-disulfide-bond-formation
#2
Na Ke, Cristina Landeta, Xiaoyun Wang, Dana Boyd, Markus Eser, Jon Beckwith
Disulfide bonds influence stability and activity of many proteins. In Escherichia coli the DsbA and DsbB enzymes promote disulfide bond formation. Other bacteria, including the Actinobacteria, use instead of DsbB the enzyme VKOR (Vitamin K Epoxide Reductase), which is found either fused to or encoded in the same operon as a dsbA -like protein. Mycobacterium tuberculosis and other gram-positive Actinobacteria secrete to the cell envelope many proteins with even numbers of cysteines. These organisms have predicted oxidoreductases and VKOR orthologs...
May 21, 2018: Journal of Bacteriology
https://www.readbyqxmd.com/read/29775997/improved-acmg-compliant-in-silico-prediction-of-pathogenicity-for-missense-substitutions-encoded-by-tp53-variants
#3
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/29774014/oral-microbiota-community-dynamics-associated-with-oral-squamous-cell-carcinoma-staging
#4
Chia-Yu Yang, Yuan-Ming Yeh, Hai-Ying Yu, Chia-Yin Chin, Chia-Wei Hsu, Hsuan Liu, Po-Jung Huang, Song-Nian Hu, Chun-Ta Liao, Kai-Ping Chang, Yu-Liang Chang
Oral squamous cell carcinoma (OSCC) is a highly aggressive cancer and the fourth leading malignancy among males in Taiwan. Some pathogenic bacteria are associated with periodontitis and oral cancer. However, the comprehensive profile of the oral microbiome during the cancer's progression from the early stage to the late stage is still unclear. We profiled the oral microbiota and identified bacteria biomarkers associated with OSCC. The microbiota of an oral rinse from 51 healthy individuals and 197 OSCC patients at different stages were investigated using 16S rRNA V3V4 amplicon sequencing, followed by bioinformatics and statistical analyses...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29772263/comparative-analysis-of-microrna-expression-in-dog-lungs-infected-with-the-h3n2-and-h5n1-canine-influenza-viruses
#5
Yun Zheng, Xinliang Fu, Lifang Wang, Wenyan Zhang, Pei Zhou, Xin Zhang, Weijie Zeng, Jidang Chen, Zongxi Cao, Kun Jia, Shoujun Li
MicroRNAs, a class of noncoding RNAs 18 to 23 nucleotides (nt) in length, play critical roles in a wide variety of biological processes. The objective of this study was to examine differences in microRNA expression profiles derived from the lungs of beagle dogs infected with the avian-origin H3N2 canine influenza virus (CIV) or the highly pathogenic avian influenza (HPAI) H5N1 virus (canine-origin isolation strain). After dogs were infected with H3N2 or H5N1, microRNA expression in the lungs was assessed using a deep-sequencing approach...
May 14, 2018: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29770047/emerging-infectious-diseases-prediction-and-detection
#6
N H Ogden, P AbdelMalik, Jrc Pulliam
Emerging infectious diseases (EIDs), including West Nile virus, severe acute respiratory syndrome (SARS) and Lyme disease, have had a direct effect within Canada, while many more EIDs such as Zika, chikungunya and Ebola are a threat to Canadians while travelling. Over 75% of EIDs affecting humans are, or were originally, zoonoses (infectious diseases transmitted from animals to humans). There are two main ways by which infectious diseases can emerge: by changes in their geographical ranges and by adaptive emergence, a genetic change in a microorganism that results in it becoming capable of invading a new niche, often by jumping to a new host species such as humans...
October 5, 2017: Canada Communicable Disease Report, Relevé des Maladies Transmissibles Au Canada
https://www.readbyqxmd.com/read/29769048/functional-insights-from-proteome-wide-structural-modeling-of-treponema-pallidum-subspecies-pallidum-the-causative-agent-of-syphilis
#7
Simon Houston, Karen Vivien Lithgow, Kara Krista Osbak, Chris Richard Kenyon, Caroline E Cameron
BACKGROUND: Syphilis continues to be a major global health threat with 11 million new infections each year, and a global burden of 36 million cases. The causative agent of syphilis, Treponema pallidum subspecies pallidum, is a highly virulent bacterium, however the molecular mechanisms underlying T. pallidum pathogenesis remain to be definitively identified. This is due to the fact that T. pallidum is currently uncultivatable, inherently fragile and thus difficult to work with, and phylogenetically distinct with no conventional virulence factor homologs found in other pathogens...
May 16, 2018: BMC Structural Biology
https://www.readbyqxmd.com/read/29755439/dicer-like-proteins-regulate-sexual-development-via-the-biogenesis-of-perithecium-specific-micrornas-in-a-plant-pathogenic-fungus-fusarium-graminearum
#8
Wenping Zeng, Jie Wang, Ying Wang, Jing Lin, Yanping Fu, Jiatao Xie, Daohong Jiang, Tao Chen, Huiquan Liu, Jiasen Cheng
Ascospores act as the primary inoculum of Fusarium graminearum , which causes the destructive disease Fusarium head blight (FHB), or scab. MicroRNAs (miRNAs) have been reported in the F. graminearum vegetative stage, and Fgdcl2 is involved in microRNA-like RNA (milRNA) biogenesis but has no major impact on vegetative growth, abiotic stress or pathogenesis. In the present study, we found that ascospore discharge was decreased in the Fgdcl1 deletion mutant, and completely blocked in the double-deletion mutant of Fgdcl1 and Fgdcl2 ...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29750426/the-upregulation-of-tmprss4-partly-ascribed-to-the-downregulation-of-mir%C3%A2-125a%C3%A2-5p-promotes-the-growth-of-human-lung-adenocarcinoma-via-the-nf%C3%A2-%C3%AE%C2%BAb-signaling-pathway
#9
Xiaoxi Fan, Yicheng Liang, Yang Liu, Yunpeng Bai, Chunlu Yang, Shun Xu
In this study, with the aid of microarray technology, transmembrane protease serine 4 (TMPRSS4), a novel member of the serine protease family, was found to be upregulated in the majority of lung adenocarcinoma (LUAD) tissues compared to normal lung tissues. Of note, the clinical significance of TMPRSS4 in LUAD has not yet been reported, at least to the best of our knowledge. Through immunohistochemistry assays, we found that TMPRSS4 was overexpressed in LUAD tissues and that the TMPRSS4 expression level was also proportionally associated with the AJCC clinical stage, T stage and pathological grade...
May 7, 2018: International Journal of Oncology
https://www.readbyqxmd.com/read/29727465/biphasic-zinc-compartmentalisation-in-a-human-fungal-pathogen
#10
Aaron C Crawford, Laura E Lehtovirta-Morley, Omran Alamir, Maria J Niemiec, Bader Alawfi, Mohammad Alsarraf, Volha Skrahina, Anna C B P Costa, Andrew Anderson, Sujan Yellagunda, Elizabeth R Ballou, Bernhard Hube, Constantin F Urban, Duncan Wilson
Nutritional immunity describes the host-driven manipulation of essential micronutrients, including iron, zinc and manganese. To withstand nutritional immunity and proliferate within their hosts, pathogenic microbes must express efficient micronutrient uptake and homeostatic systems. Here we have elucidated the pathway of cellular zinc assimilation in the major human fungal pathogen Candida albicans. Bioinformatics analysis identified nine putative zinc transporters: four cytoplasmic-import Zip proteins (Zrt1, Zrt2, Zrt3 and orf19...
May 4, 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29700415/comparative-systems-analysis-of-the-secretome-of-the-opportunistic-pathogen-aspergillus-fumigatus-and-other-aspergillus-species
#11
R P Vivek-Ananth, Karthikeyan Mohanraj, Muralidharan Vandanashree, Anupam Jhingran, James P Craig, Areejit Samal
Aspergillus fumigatus and multiple other Aspergillus species cause a wide range of lung infections, collectively termed aspergillosis. Aspergilli are ubiquitous in environment with healthy immune systems routinely eliminating inhaled conidia, however, Aspergilli can become an opportunistic pathogen in immune-compromised patients. The aspergillosis mortality rate and emergence of drug-resistance reveals an urgent need to identify novel targets. Secreted and cell membrane proteins play a critical role in fungal-host interactions and pathogenesis...
April 26, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29698425/complexity-of-type-specific-56-kda-antigen-cd4-t-cell-epitopes-of-orientia-tsutsugamushi-strains-causing-scrub-typhus-in-india
#12
Arunachalam Ramaiah, Munegowda C Koralur, Gregory A Dasch
Orientia tsutsugamushi (Ots) is an obligate, intracellular, mite-transmitted human pathogen which causes scrub typhus. Understanding the diversity of Ots antigens is essential for designing specific diagnostic assays and efficient vaccines. The protective immunodominant type-specific 56 kDa antigen (TSA) of Ots varies locally and across its geographic distribution. TSA contains four hypervariable domains. We bioinformatically analyzed 345 partial sequences of TSA available from India, most of which contain only the three variable domains (VDI-III) and three spacer conserved domains (SVDI, SVDII/III, SVDIII)...
2018: PloS One
https://www.readbyqxmd.com/read/29695702/-prediction-of-bacterial-and-archaeal-allergenicity-with-allpred-program
#13
A O Bragin, V S Sokolov, P S Demenkov, T V Ivanisenko, E Yu Bragina, Yu G Matushkin, V A Ivanisenko
Nowadays, allergic disorders have become one of the most important social problems in the world. This can be related to the advent of new allergenic agents in the environment, as well as an increasing density of human contact with known allergens, including various proteins. Thus, the development of computer programs designed for the prediction of allergenic properties of proteins becomes one of the urgent tasks of mo dern bioinformatics. Previously we developed a web accessible Allpred Program (http://www-bionet...
March 2018: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/29692759/report-of-a-novel-shox-missense-variant-in-a-boy-with-short-stature-and-his-mother-with-leri-weill-dyschondrosteosis
#14
Laura Lucchetti, Paolo Prontera, Amedea Mencarelli, Ester Sallicandro, Annalisa Mencarelli, Marta Cofini, Alberto Leonardi, Gabriela Stangoni, Laura Penta, Susanna Esposito
Heterozygous mutations in the SHOX gene or in the upstream and downstream enhancer elements are associated with 2-22% of cases of idiopathic short stature (OMIM #300582) and with 60% of cases of Leri-Weill dyschondrosteosis (OMIM #127300) with which female subjects are generally more severely affected. Approximately 80-90% of SHOX pathogenic variants are deletions or duplications, and the remaining 10-20% are point mutations that primarily give rise to missense variants. The clinical interpretation of novel variants, particularly missense variants, can be challenging and can remain of uncertain significance...
2018: Frontiers in Endocrinology
https://www.readbyqxmd.com/read/29690800/characterization-of-a-rare-variant-c-2635-2a-g-of-the-msh2-gene-in-a-family-with-lynch-syndrome
#15
Filomena Cariola, Vittoria Disciglio, Anna M Valentini, Claudio Lotesoriere, Candida Fasano, Giovanna Forte, Luciana Russo, Antonio Di Carlo, Floranna Guglielmi, Andrea Manghisi, Ivan Lolli, Maria L Caruso, Cristiano Simone
INTRODUCTION: Lynch syndrome is caused by germline mutations in one of the mismatch repair genes ( MLH1, MSH2, MSH6, and PMS2) or in the EPCAM gene. Lynch syndrome is defined on the basis of clinical, pathological, and genetic findings. Accordingly, the identification of predisposing genes allows for accurate risk assessment and tailored screening protocols. CASE DESCRIPTION: Here, we report a family case with three family members manifesting the Lynch syndrome phenotype, all of which harbor the rare variant c...
April 1, 2018: International Journal of Biological Markers
https://www.readbyqxmd.com/read/29664915/accurate-prediction-of-functional-structural-and-stability-changes-in-pitx2-mutations-using-in-silico-bioinformatics-algorithms
#16
Morteza Seifi, Michael A Walter
Mutations in PITX2 have been implicated in several genetic disorders, particularly Axenfeld-Rieger syndrome. In order to determine the most reliable bioinformatics tools to assess the likely pathogenicity of PITX2 variants, the results of bioinformatics predictions were compared to the impact of variants on PITX2 structure and function. The MutPred, Provean, and PMUT bioinformatic tools were found to have the highest performance in predicting the pathogenicity effects of all 18 characterized missense variants in PITX2, all with sensitivity and specificity >93%...
2018: PloS One
https://www.readbyqxmd.com/read/29653233/three-novel-variants-p-glu178lys-p-val245met-p-ser250phe-of-the-phenylalanine-hydroxylase-pah-gene-impair-protein-expression-and-function-in-vitro
#17
Yanan Zong, Ning Liu, Shanshan Ma, Ying Bai, Fangxia Guan, Xiangdong Kong
Phenylketonuria (PKU) is the most common inherited metabolic disease, an autosomal recessive disorder affecting >10,000 newborns each year globally. It can be caused by over 1000 different naturally occurring mutations in the phenylalanine hydroxylase (PAH) gene. We analyzed three novel naturally occurring PAH gene variants: p.Glu178Lys (c.532G>A), p.Val245Met (c.733G>A) and p.Ser250Phe (c.749C>T). The mutant effect on the PAH enzyme structure and function was predicted by bioinformatics software...
April 10, 2018: Gene
https://www.readbyqxmd.com/read/29652992/-phenotypic-and-mutational-analysis-of-a-pedigree-affected-with-hereditary-coagulation-factor-%C3%A2-deficiency
#18
Mengcha Tian, Hong Xia, Zhishan Zhang, Yanhui Jin, Kankan Su, Mingshan Wang
OBJECTIVE: To explore the molecular pathogenesis for a pedigree affected with coagulation factor Ⅴ (FⅤ) deficiency. METHODS: Prothrombin time (PT), activated partial thromboplastin time (APTT), fibrinogen (FIB), coagulation factor Ⅱ activity (FⅡ: C), FⅤ activity (FⅤ: C), coagulation factor Ⅶ activity (FⅦ: C), and coagulation factor Ⅹ activity (FⅩ: C) were determined with a STAGO automatic coagulometer. FⅤ antigen (FⅤ: Ag) was detected with enzyme linked immunosorbent assay (ELISA)...
April 10, 2018: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/29650461/towards-designing-a-synthetic-antituberculosis-vaccine-the-rv3587c-peptide-inhibits-mycobacterial-entry-to-host-cells
#19
Mary Lilian Carabali-Isajar, Marisol Ocampo, Deisy Carolina Rodriguez, Magnolia Vanegas, Hernando Curtidor, Manuel Alfonso Patarroyo, Manuel Elkin Patarroyo
Mycobacterium tuberculosis is considered one of the most successful pathogens in the history of mankind, having caused 1.7 million deaths in 2016. The amount of resistant and extensively resistant strains has increased; BCG has been the only vaccine to be produced in more than 100 years though it is still unable to prevent the disease's most disseminated form in adults; pulmonary tuberculosis. The search is thus still on-going for candidate antigens for an antituberculosis vaccine. This paper reports the use of a logical and rational methodology for finding such antigens, this time as peptides derived from the Rv3587c membrane protein...
April 4, 2018: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/29648582/inference-of-the-human-polyadenylation-code
#20
Michael K K Leung, Andrew Delong, Brendan J Frey
Motivation: Processing of transcripts at the 3'-end involves cleavage at a polyadenylation site followed by the addition of a poly(A)-tail. By selecting which site is cleaved, the process of alternative polyadenylation enables genes to produce transcript isoforms with different 3'-ends. To facilitate the identification and treatment of disease-causing mutations that affect polyadenylation and to understand the sequence determinants underlying this regulatory process, a computational model that can accurately predict polyadenylation patterns from genomic features is desirable...
April 10, 2018: Bioinformatics
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