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Bioinformatics & pathogenicity prediction

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https://www.readbyqxmd.com/read/27931036/clinical-exome-sequencing-reveals-mkrn3-pathogenic-variants-in-familial-and-nonfamilial-idiopathic-central-precocious-puberty
#1
Nelmar Valentina Ortiz-Cabrera, Rosa Riveiro-Álvarez, Miguel Ángel López-Martínez, Pilar Pérez-Segura, Isabel Aragón-Gómez, María José Trujillo-Tiebas, Leandro Soriano-Guillén
BACKGROUND/AIMS: Idiopathic central precocious puberty (ICPP) is the premature activation of the hypothalamic-pituitary-gonadal axis in the absence of organic disease. Up to now, just gain-of-function mutations of KISS1/KISS1R and loss-of-function mutations of the maternally imprinted gene MKRN3 are the known genetic causes of ICPP. Our intention is to evaluate variants present in genes related to the pubertal onset pathway that could act as disease-causing or predisposing variants. METHODS: We studied the clinical exome of 20 patients diagnosed with ICPP using the Illumina platform...
December 9, 2016: Hormone Research in Pædiatrics
https://www.readbyqxmd.com/read/27922074/resistance-gene-identification-from-larimichthys-crocea-with-machine-learning-techniques
#2
Yinyin Cai, Zhijun Liao, Ying Ju, Juan Liu, Yong Mao, Xiangrong Liu
The research on resistance genes (R-gene) plays a vital role in bioinformatics as it has the capability of coping with adverse changes in the external environment, which can form the corresponding resistance protein by transcription and translation. It is meaningful to identify and predict R-gene of Larimichthys crocea (L.Crocea). It is friendly for breeding and the marine environment as well. Large amounts of L.Crocea's immune mechanisms have been explored by biological methods. However, much about them is still unclear...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27914961/expanding-the-clinical-and-genetic-spectrum-of-g6pd-deficiency-the-occurrence-of-bcgitis-and-novel-missense-mutation
#3
Taj Ali Khan, Humaira Mazhar, Mehboob Nawaz, Kalsoom Kalsoom, Muhammad Ishfaq, Huma Asif, Hazir Rahman, Muhammad Qasim, Farkhanda Naz, Mubashir Hussain, Baharullah Khattak, Waheed Ullah, Otavio Cabral-Marques, Jawad Butt, Asif Iqbal
Glucose-6-phosphate dehydrogenase (G6PD) is a key enzyme in the pentose phosphate pathway that ensures sufficient production of coenzyme nicotinamide adenine dinucleotide phosphate (NADPH) by catalyzing the reduction of NADP+ to NADPH. Noteworthy, the latter mediates the production of reactive oxygen species (ROS) by phagocytic cells such as neutrophils and monocytes. Therefore, patients with severe forms of G6PD deficiency may present impaired NADPH oxidase activity and become susceptible to recurrent infections...
November 30, 2016: Microbial Pathogenesis
https://www.readbyqxmd.com/read/27904804/mining-snps-in-extracellular-vesicular-transcriptome-of-trypanosoma-cruzi-a-step-closer-to-early-diagnosis-of-neglected-chagas-disease
#4
Pallavi Gaur, Anoop Chaturvedi
One of the newest and strongest members of intercellular communicators, the Extracellular vesicles (EVs) and their enclosed RNAs; Extracellular RNAs (exRNAs) have been acknowledged as putative biomarkers and therapeutic targets for various diseases. Although a very deep insight has not been possible into the physiology of these vesicles, they are believed to be involved in cell-to-cell communication and host-pathogen interactions. EVs might be significantly helpful in discovering biomarkers for possible target identification as well as prognostics, diagnostics and developing vaccines...
2016: PeerJ
https://www.readbyqxmd.com/read/27899486/functional-investigations-of-hnf1a-identify-rare-variants-as-risk-factors-for-type-2-diabetes-in-the-general-population
#5
Laeya Abdoli Najmi, Ingvild Aukrust, Jason Flannick, Janne Molnes, Noel Burtt, Anders Molven, Leif Groop, David Altshuler, Stefan Johansson, Lise Bjørkhaug, Pål Rasmus Njølstad
Variants in HNF1A encoding hepatocyte nuclear factor-1A are associated with maturity-onset diabetes of the young (MODY3) and type 2 diabetes. We investigated whether functional classification of HNF1A rare coding variants can inform models of diabetes risk prediction in the general population by analyzing the effect of 27 HNF1A variants identified in well-phenotyped populations (n = 4115). Bioinformatics tools classified 11 variants as likely pathogenic and showed no association with diabetes risk (combined MAF = 0...
November 29, 2016: Diabetes
https://www.readbyqxmd.com/read/27898768/transcriptome-and-small-rnaome-dynamics-during-a-resistant-and-susceptible-interaction-between-cucumber-and-downy-mildew
#6
Alyssa Burkhardt, Brad Day
Cucumber ( L.) downy mildew, caused by the obligate oomycete pathogen (Berk. and Curt.) Rostov., is the primary factor limiting cucumber production. Although sources of resistance have been identified, such as plant introduction line PI 197088, the genes and processes involved in mediating resistance are still unknown. In the current study, we conducted a comprehensive transcriptome and small RNAome analysis of a resistant (PI 197088) and susceptible ('Vlaspik') cucumber during a time course of infection using Illumina sequencing...
March 2016: Plant Genome
https://www.readbyqxmd.com/read/27895760/prioritization-of-non-coding-disease-causing-variants-and-long-non-coding-rnas-in-liver-cancer
#7
Hua Li, Zekun He, Yang Gu, Lin Fang, Xin Lv
There are multiple bioinformatics tools available for the detection of coding driver mutations in cancers. However, the prioritization of pathogenic non-coding variants remains a challenging and demanding task. The present study was performed to discriminate non-coding disease-causing mutations and prioritize potential cancer-implicated long non-coding RNAs (lncRNAs) in liver cancer using a logistic regression model. A logistic regression model was constructed by combining 19,153 disease-associated ClinVar and human gene mutation database pathogenic variants as the response variable and non-coding features as the predictor variable...
November 2016: Oncology Letters
https://www.readbyqxmd.com/read/27890593/evaluation-of-the-crystal-structure-of-a-fimbrillin-fima-from-porphyromonas-gingivalis-as-a-therapeutic-target-for-photo-activated-disinfection-with-toluidine-blue-o
#8
Maryam Pourhajibagher, Abbas Bahador
BACKGROUND: Porphyromonas gingivalis is one of the etiological agents in the initiation of combined periodontal-endodontic (perio-endo) lesions. Successful treatment of perio-endo lesions with photo-activated disinfection (PAD) as a novel therapeutic approach depends on the selection of an appropriate target site, specific photosensitizer (PS), and wavelength of light. Since the fimbrillin (FimA) is the most important pathogenic agent in P. gingivalis it was evaluated as a target site against PAD with toluidine blue O (TBO) as a PS...
November 23, 2016: Photodiagnosis and Photodynamic Therapy
https://www.readbyqxmd.com/read/27887025/design-and-expression-of-a-chimeric-vaccine-candidate-for-avian-necrotic-enteritis
#9
Amin Rostami, Fatemeh Goshadrou, Reza Pilehchian Langroudi, S Zahra Bathaie, Ali Riazi, Jafar Amani, Gholamreza Ahmadian
Necrotic enteritis is an economically important disease of poultry mainly caused by Clostridium perfringens The bacteria release multiple toxins of which NetB, alpha toxin and TpeL have been reported to play important roles in pathogenicity and/or severity of the disease. In this study, the sequence of clostridial toxins NetB, alpha toxin and TpeL were analyzed using bioinformatics tools to determine protein domains with high immunogenicity factor. Several chimeric trivalent proteins consisting of the immunogenic regions of the three toxins were designed and evaluated...
November 24, 2016: Protein Engineering, Design & Selection: PEDS
https://www.readbyqxmd.com/read/27872839/insight-into-the-exoproteome-of-the-tissue-derived-trypomastigote-form-of-trypanosoma-cruzi
#10
Rayner M L Queiroz, Carlos A O Ricart, Mara O Machado, Izabela M D Bastos, Jaime M de Santana, Marcelo V de Sousa, Peter Roepstorff, Sébastien Charneau
The protozoan parasite Trypanosoma cruzi causes Chagas disease, one of the major neglected infectious diseases. It has the potential to infect any nucleated mammalian cell. The secreted/excreted protein repertoire released by T. cruzi trypomastigotes is crucial in host-pathogen interactions. In this study, mammalian tissue culture-derived trypomastigotes (Y strain) were used to characterize the exoproteome of the infective bloodstream life form. Proteins released into the serum-free culture medium after 3 h of incubation were harvested and digested with trypsin...
2016: Frontiers in Chemistry
https://www.readbyqxmd.com/read/27866247/identification-of-potential-peripheral-blood-diagnostic-biomarkers-for-patients-with-juvenile-idiopathic-arthritis-by-bioinformatics-analysis
#11
Zhi-Qiang Tu, Hai-Yan Xue, Wei Chen, Lan-Fang Cao, Wei-Qi Zhang
Juvenile idiopathic arthritis (JIA) is common childhood rheumatic disease harming children health. However, there is still lack of effective biomarkers for diagnosis JIA at early onset. We aim to construct a classification model to predict JIA disease. The peripheral blood gene expression profile data of JIA were downloaded from GEO database. We compared and analyzed differentially expressed genes (DEGs) between different JIA samples through Pearson's correlation coefficient method and unsupervised clustering analysis...
November 19, 2016: Rheumatology International
https://www.readbyqxmd.com/read/27863272/genome-wide-analysis-of-aberrant-gene-expression-and-methylation-profiles-reveals-susceptibility-genes-and-underlying-mechanism-of-cervical-cancer
#12
Hongmei Lin, Yifei Ma, Yongqing Wei, Hui Shang
BACKGROUND: This study aimed to explore the molecular mechanism of cervical cancer (CC) by integrated bioinformatic analyses of gene expression and methylation profiles. METHODS: The gene expression and methylation microarrays in CC samples and normal controls were respectively downloaded from the GEO database. After screening the differentially expressed genes (DEGs) with Limma package and the CC-related methylation sites with CpGassoc package in R language, DEGs with CC-related methylation sites were identified from the intersection of the above two groups of results with 50kb upstream and downstream of a gene as the gene region...
October 26, 2016: European Journal of Obstetrics, Gynecology, and Reproductive Biology
https://www.readbyqxmd.com/read/27834932/functional-studies-and-in-silico-analyses-to-evaluate-non-coding-variants-in-inherited-cardiomyopathies
#13
Giulia Frisso, Nicola Detta, Pamela Coppola, Cristina Mazzaccara, Maria Rosaria Pricolo, Antonio D'Onofrio, Giuseppe Limongelli, Raffaele Calabrò, Francesco Salvatore
Point mutations are the most common cause of inherited diseases. Bioinformatics tools can help to predict the pathogenicity of mutations found during genetic screening, but they may work less well in determining the effect of point mutations in non-coding regions. In silico analysis of intronic variants can reveal their impact on the splicing process, but the consequence of a given substitution is generally not predictable. The aim of this study was to functionally test five intronic variants (MYBPC3-c.506-2A>C, MYBPC3-c...
November 10, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27832917/immune-response-characterization-and-vaccine-potential-of-a-recombinant-chimera-comprising-b-cell-epitope-of-aeromonas-hydrophila-outer-membrane-protein-c-and-ltb
#14
Mahima Sharma, Aparna Dixit
Aeromonas hydrophila is one of the most virulent fish pathogens, causing colossal economic losses to the aquaculture industry annually. The absence of a safe and effective vaccine makes it very difficult to control this infection. Outer membrane proteins have been widely illustrated to confer protective immunity against a broad spectrum of gram negative bacteria. In the current study, we have analyzed the ability of B-cell epitopes of A. hydrophila's outer membrane protein C (OmpC) to confer protection against bacterial virulence...
December 7, 2016: Vaccine
https://www.readbyqxmd.com/read/27830184/novel-hspb1-mutation-causes-both-motor-neuronopathy-and-distal-myopathy
#15
D J Lewis-Smith, J Duff, A Pyle, H Griffin, T Polvikoski, D Birchall, R Horvath, P F Chinnery
OBJECTIVE: To identify the cause of isolated distal weakness in a family with both neuropathic and myopathic features on EMG and muscle histology. METHODS: Case study with exome sequencing in 2 affected individuals, bioinformatic prioritization of genetic variants, and segregation analysis of the likely causal mutation. Functional studies included Western blot analysis of the candidate protein before and after heat shock treatment of primary skin fibroblasts. RESULTS: A novel HSPB1 variant (c...
December 2016: Neurology. Genetics
https://www.readbyqxmd.com/read/27804176/comparison-of-bioinformatics-prediction-molecular-modeling-and-functional-analyses-of-foxc1-mutations-in-patients-with-axenfeld-rieger-syndrome
#16
Morteza Seifi, Tim Footz, Sherry A M Taylor, Michael A Walter
Mutations in the forkhead box C1 gene (FOXC1) cause Axenfeld-Rieger syndrome (ARS). Here, we investigated the effect of four ARS missense variants on FOXC1 structure and function, and examined the predictive value of four in silico programs for all 31 FOXC1 missense variants identified to date. Molecular modeling of the FOXC1 forkhead domain predicts that c.402G> A (p.C135Y) alters FOXC1's structure. In contrast, c.378A> G (p.H128R) and c.481A> G (p.M161V) are not predicted to change FOXC1's structure...
November 2, 2016: Human Mutation
https://www.readbyqxmd.com/read/27787831/in-silico-prediction-of-linear-b-cell-epitopes-on-proteins
#17
Yasser El-Manzalawy, Drena Dobbs, Vasant G Honavar
Antibody-protein interactions play a critical role in the humoral immune response. B-cells secrete antibodies, which bind antigens (e.g., cell surface proteins of pathogens). The specific parts of antigens that are recognized by antibodies are called B-cell epitopes. These epitopes can be linear, corresponding to a contiguous amino acid sequence fragment of an antigen, or conformational, in which residues critical for recognition may not be contiguous in the primary sequence, but are in close proximity within the folded protein 3D structure...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27785597/exome-sequencing-identifies-a-novel-mutation-in-gja8-associated-with-inherited-cataract-in-a-chinese-family
#18
Mei Ren, Xin Guang Yang, Xiao Jie Dang, Jin An Xiao
BACKGROUND: Congenital cataract is a clinical and genetic heterogeneous group of eye disorders that causes visual impairment and childhood blindness. In this study, a Chinese family with congenital cataract is studied. METHODS: In order to identify the genetic defects which were associated with congenital cataract, a whole-exome sequencing approach is performed to screen for the potential mutation-causing disease. RESULTS: The result revealed a novel heterozygous mutation (c...
October 26, 2016: Graefe's Archive for Clinical and Experimental Ophthalmology
https://www.readbyqxmd.com/read/27778110/surface-proteome-mining-for-identification-of-potential-vaccine-candidates-against-campylobacter-jejuni-an-in-silico-approach
#19
Kusum Mehla, Jayashree Ramana
Campylobacter jejuni remains a major cause of human gastroenteritis with estimated annual incidence rate of 450 million infections worldwide. C. jejuni is a major burden to public health in both socioeconomically developing and industrialized nations. Virulence determinants involved in C. jejuni pathogenesis are multifactorial in nature and not yet fully understood. Despite the completion of the first C. jejuni genome project in 2000, there are currently no vaccines in the market against this pathogen. Traditional vaccinology approach is an arduous and time extensive task...
October 24, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/27777222/comprehensive-assessment-and-performance-improvement-of-effector-protein-predictors-for-bacterial-secretion-systems-iii-iv-and-vi
#20
Yi An, Jiawei Wang, Chen Li, André Leier, Tatiana Marquez-Lago, Jonathan Wilksch, Yang Zhang, Geoffrey I Webb, Jiangning Song, Trevor Lithgow
Bacterial effector proteins secreted by various protein secretion systems play crucial roles in host-pathogen interactions. In this context, computational tools capable of accurately predicting effector proteins of the various types of bacterial secretion systems are highly desirable. Existing computational approaches use different machine learning (ML) techniques and heterogeneous features derived from protein sequences and/or structural information. These predictors differ not only in terms of the used ML methods but also with respect to the used curated data sets, the features selection and their prediction performance...
October 24, 2016: Briefings in Bioinformatics
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