scholarly journals Identification of a novel antimicrobial peptide from amphioxus Branchiostoma japonicum by in silico and functional analyses

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Haohan Liu ◽  
Miaomiao Lei ◽  
Xiaoyuan Du ◽  
Pengfei Cui ◽  
Shicui Zhang
Keyword(s):  
Antimicrobial Peptide ◽  
In Silico ◽  
Functional Analyses

scholarly journals Antimicrobial peptide induced colloidal transformations in bacteria-mimetic vesicles: Combining in silico tools and experimental methods

2021 ◽  
Vol 596 ◽  
pp. 352-363
Author(s):  
Rafael V.M. Freire ◽  
Yeny Pillco-Valencia ◽  
Gabriel C.A. da Hora ◽  
Madeleine Ramstedt ◽  
Linda Sandblad ◽  
...  
Keyword(s):  
Antimicrobial Peptide ◽  
In Silico ◽  
Experimental Methods ◽  
In Silico Tools

scholarly journals Genomic Analysis of Glioblastoma Multiforme Reveals a Key Transcription Factor Signature Relevant to Prognosis and the Immune Processes

2021 ◽  
Vol 11 ◽  
Author(s):  
Zhen-Hang Li ◽  
Yan-Lei Guan ◽  
Guo-Bin Zhang
Keyword(s):  
Glioblastoma Multiforme ◽  
In Silico ◽  
Prognostic Value ◽  
Genomic Analysis ◽  
Predictive Biomarkers ◽  
Risk Scores ◽  
Functional Aspects ◽  
Number Variation ◽  
Inflammatory Processes ◽  
Functional Analyses

IntroductionGlioblastoma multiforme (GBM) develops through the accumulation of both genetic and expression alterations. Although many gene signatures have been developed as prognostic and predictive biomarkers, their robustness and functional aspects are less well characterized. The expression of most genes is regulated by transcription factors (TFs); therefore, we aimed to investigate a TF signature relevant to GBM prognosis.MethodsWe used bioinformatic methods and data from public databases to establish four clusters of key TF genes, among which cluster 1, comprising 24 TFs, showed significant prognostic value. Further in silico functional analyses were applied to investigate the utility of the TF signature.ResultsDifferent mutation and copy number variation patterns were observed between different risk score groups (based on the TF signature). In silico analyses suggested that the cases with relative high risk scores were involved in immune and inflammatory processes or pathways.ConclusionThe TF signature has significant prognostic value in different cohorts or subgroups of patients with GBM and could lead to the development immunotherapy for GBM.

scholarly journals In silico functional analyses and discovery of survivalassociated microRNA signatures in pediatric osteosarcoma

Oncoscience ◽  
2014 ◽  
Vol 1 (9) ◽  
pp. 599-608 ◽  
Author(s):  
Patricia C. Sanchez-Diaz ◽  
Tzu-Hung Hsiao ◽  
Yi Zou ◽  
Aaron J. Sugalski ◽  
Josefine Heim-Hall ◽  
...  
Keyword(s):  
In Silico ◽  
Functional Analyses ◽  
Pediatric Osteosarcoma

scholarly journals Whole exome sequencing identifies rare coding variants in novel human-mouse ortholog genes in African individuals diagnosed with non-syndromic hearing impairment

2020 ◽  
pp. 153537022096038
Author(s):  
Oluwafemi G Oluwole ◽  
Kevin K Esoh ◽  
Edmond Wonkam-Tingang ◽  
Noluthando Manyisa ◽  
Jean Jacques Noubiap ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Hearing Impairment ◽  
Whole Exome Sequencing ◽  
In Silico ◽  
Homozygous Variant ◽  
Whole Exome ◽  
African Populations ◽  
Mouse Orthologs ◽  
Syndromic Hearing Impairment ◽  
Functional Analyses

Physiologically, the human and murine hearing systems are very similar, justifying the extensive use of mice in experimental models for hearing impairment (HI). About 340 murine HI genes have been reported; however, whether variants in all human-mouse ortholog genes contribute to HI has been rarely investigated. In humans, nearly 120 HI genes have been identified to date, with GJB2 and GJB6 variants accounting for half of congenital HI cases, of genetic origin, in populations of European and Asian ancestries, but not in most African populations. The contribution of variants in other known genes of HI among the populations of African ancestry is poorly studied and displays the lowest pick-up rate. We used whole exome sequencing (WES) to investigate pathogenic and likely pathogenic (PLP) variants in 34 novel human-mouse orthologs HI genes, in 40 individuals from Cameroon and South Africa diagnosed with non-syndromic hearing impairment (NSHI), and compared the data to WES data of 129 ethnically matched controls. In addition, protein modeling for selected PLP gene variants, gene enrichment, and network analyses were performed. A total of 4/38 murine genes, d6wsu163e, zfp719, grp152 and minar2, had no human orthologs. WES identified three rare PLP variants in 3/34 human-mouse orthologs genes in three unrelated Cameroonian patients, namely: OCM2, c.227G>C p.(Arg76Thr) and LRGI1, c.1657G>A p.(Gly533Arg) in a heterozygous state, and a PLP variant MCPH1, c.2311C>G p.(Pro771Ala) in a homozygous state. In silico functional analyses suggest that these human-mouse ortholog genes functionally co-expressed interactions with well-established HI genes: GJB2 and GJB6. The study found one homozygous variant in MCPH1, likely to explain HI in one patient, and suggests that human-mouse ortholog variants could contribute to the understanding of the physiology of hearing in humans. Impact statement Despite, human and murine hearing system being very similar, the contribution of variants in relevant mouse-ortholog genes to hearing impairment (HI) has not been fully investigated. The contribution of variants in the known non-syndromic hearing impairment (NSHI) genes among Africans is poorly studied, suggesting that the novel gene(s) and mutations are yet to be discovered in NSHI in the African populations. Using whole exome sequencing (WES), this study identified rare candidate pathogenic and likely pathogenic (PLP) variants in 3/34 novel human-mouse ortholog genes in 3/40 individuals, with one homozygous variant, MCPH1, c.2311C>G p.(Pro771Ala), likely to explain HI in one patient. In silico functional analyses suggest that these human-mouse ortholog genes could contribute to the understanding of the physiology of hearing in humans and thus the variants identified in those genes deserve additional investigations.

Human Basal Tear Peptidome Characterization by CID, HCD, and ETD Followed by in Silico and in Vitro Analyses for Antimicrobial Peptide Identification

2015 ◽  
Vol 14 (6) ◽  
pp. 2649-2658 ◽  
Author(s):  
Mikel Azkargorta ◽  
Javier Soria ◽  
Claudia Ojeda ◽  
Fanny Guzmán ◽  
Arantxa Acera ◽  
...  
Keyword(s):  
Antimicrobial Peptide ◽  
In Silico ◽  
Peptide Identification

scholarly journals In silico and functional analyses of immunomodulatory peptides encrypted in the human gut metaproteome

2020 ◽  
Vol 70 ◽  
pp. 103969
Author(s):  
Noelia Cambeiro-Pérez ◽  
Claudio Hidalgo-Cantabrana ◽  
Marco Antonio Moro-García ◽  
Aitor Blanco-Míguez ◽  
Florentino Fdez-Riverola ◽  
...  
Keyword(s):  
In Silico ◽  
Human Gut ◽  
Immunomodulatory Peptides ◽  
Functional Analyses

Discovering New In Silico Tools for Antimicrobial Peptide Prediction

2012 ◽  
Vol 13 (9) ◽  
pp. 1148-1157 ◽  
Author(s):  
Marc Torrent ◽  
M. Victoria Nogues ◽  
Ester Boix
Keyword(s):  
Antimicrobial Peptide ◽  
In Silico ◽  
Peptide Prediction ◽  
In Silico Tools

scholarly journals Utilizing the Potential of Antimicrobial Peptide LL-37 for Combating SARS-COV- 2 Viral Load in Saliva: an In Silico Analysis

2021 ◽  
Author(s):  
Nireeksha Nireeksha ◽  
Pavan Gollapalli ◽  
Sudhir Rama Varma ◽  
Mithra N. Hegde ◽  
N. Suchetha Kumari
Keyword(s):  
Viral Load ◽  
Antimicrobial Peptide ◽  
In Silico ◽  
English Language ◽  
Ex Vivo ◽  
Experimental Studies ◽  
In Silico Analysis ◽  
Docking Studies ◽  
Viral Membrane

AbstractLimiting the spread of virus during the recent pandemic outbreak was a major challenge. Viral loads in saliva, nasopharyngeal and oropharyngeal swabs were the major cause for droplet transmission and aerosols. Saliva being the major contributor for the presence of viral load is the major key factor; various mouthwashes and their combination were analyzed and utilized in health care centers to hamper the spread of virus and decrease viral load. The compositions of these mouthwashes to an extent affected the viral load and thereby transmission, but there is always a scope for other protocols which may provide better results. Here we evaluated the potential of antimicrobial peptide LL-37 in decreasing the viral load of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through an in silico work and evidence from other studies. This narrative review highlighted a brief nonsystematic methodology to include the selected articles for discussion. Accessible electronic databases (Medline, Scopus, Web of Science, SciELO, and PubMed) were used to find studies that reported the salivary viral load of SARS-CoV-2 published between December 2019 and June 2021. The following keywords were utilized for brief searching of the databases: “saliva,” “viral load,” and “SARS-CoV-2.” Articles in English language, in vitro cell-line studies, ex vivo studies, and clinical trials explaining the viral load of SARS-CoV-2 in saliva and strategies to decrease viral load were included in this review. The search was complemented by manual searching of the reference lists of included articles and performing a citation search for any additional reviews. The antiviral potential of cationic host defense peptide LL-37 was evaluated using computational approaches providing in silico evidence. The analysis of docking studies and the display of positive interfacial hydrophobicity of LL-37 resulting in disruption of COVID-19 viral membrane elucidate the fact that LL-37 could be effective against all variants of SARS-CoV-2. Further experimental studies would be needed to confirm the binding of the receptor-binding domain with LL-37. The possibility of using it in many forms further to decrease the viral load by disrupting the viral membrane is seen.

scholarly journals In-silico based identification and functional analyses of miRNAs and their targets in Cowpea (Vigna unguiculata L.)

AIMS Genetics ◽  
2017 ◽  
Vol 4 (2) ◽  
pp. 138-165 ◽  
Author(s):  
Zareen Gul ◽  
◽  
Muhammad Younas Khan Barozai ◽  
Muhammad Din
Keyword(s):  
Vigna Unguiculata ◽  
In Silico ◽  
Functional Analyses
Sign in / Sign up

Export Citation Format

Share Document