Journal of applied bioinformatics & computational biology最新文献

Production of a prodigious drug with anticancer and immunosuppressive properties 生产一种具有抗癌和免疫抑制特性的神奇药物

Journal of applied bioinformatics & computational biology Pub Date : 2019-01-01 DOI: 10.4172/2329-9533-c1-009

P. Girish

引用次数: 0

In silico identified immunogenic Ebola nucleoprotein peptides elicit immune response 在硅鉴定免疫原性埃博拉核蛋白肽引发免疫反应

Journal of applied bioinformatics & computational biology Pub Date : 2019-01-01 DOI: 10.4172/2329-9533-c1-008

Sahil Jain, M. Baranwal

{"title":"In silico identified immunogenic Ebola nucleoprotein peptides elicit immune response","authors":"Sahil Jain, M. Baranwal","doi":"10.4172/2329-9533-c1-008","DOIUrl":"https://doi.org/10.4172/2329-9533-c1-008","url":null,"abstract":"Immunoinformatics has dropped significantly to discovering strong antibody competitors against different microorganisms. In the momentum study, a blend of various T (CD4+ and CD8+) and B cell epitope expectation devices was applied to discover peptides containing numerous epitopes against Ebola nucleoprotein (NP) and the introduction of peptides to human leukocyte antigen (HLA) atoms was examined by forecast, docking and populace inclusion apparatuses. Further, ELISA was done to gauge IFN-γ in peptide animated fringe blood mononuclear cells disengaged from the blood of sound volunteers. Six peptides containing various T and B cell epitopes were acquired after expectation examines and dispensing with the peptides at risk to create immune system and unfavorably susceptible reaction. All peptides showed 100% conservancy in Zaire Ebola infection. Forecast devices, Auto dock Vina and CABS-dock results affirmed the capacity of anticipated peptides to tie with assorted HLA alleles. Populace inclusion investigation anticipated high inclusion (> 85%) for anticipated insusceptible reaction in four landmasses (Africa, America, Asia and Europe). Peptide animated cells showed upgraded IFN-γ emission when contrasted with unstimulated cells. Thusly, the recognized NP peptides can be considered as potential engineered antibody competitors against Ebola virus.","PeriodicalId":91303,"journal":{"name":"Journal of applied bioinformatics & computational biology","volume":"14 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70289524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

MD simulations of estrogen receptors (ER) and docking analysis of DPN analogues reveal insights about subtype-receptor selectivity 雌激素受体(ER)的MD模拟和DPN类似物的对接分析揭示了亚型受体选择性的见解

Journal of applied bioinformatics & computational biology Pub Date : 2019-01-01 DOI: 10.4172/2329-9533-c1-007

Marlet Martinez

引用次数: 0

Profiling of Differential Expression of Genes in Mice Carrying Both Mutant Presenilin 1 and Amyloid Precursor Protein Transgenes with or without Knockout of B₂ Adrenergic Receptor Gene. B2肾上腺素能受体基因敲除小鼠早老素1突变体和淀粉样前体蛋白突变体基因差异表达谱

Journal of applied bioinformatics & computational biology Pub Date : 2018-01-01 Epub Date: 2018-09-18 DOI: 10.4172/2329-9533.1000155

Yuan Zhou, Lintao Chen, Xi Zhou, Yechun Pei, Shuangshuang Wei, Anum Mehmood, Yang K Xiang, Dayong Wang

{"title":"Profiling of Differential Expression of Genes in Mice Carrying Both Mutant Presenilin 1 and Amyloid Precursor Protein Transgenes with or without Knockout of B2 Adrenergic Receptor Gene.","authors":"Yuan Zhou, Lintao Chen, Xi Zhou, Yechun Pei, Shuangshuang Wei, Anum Mehmood, Yang K Xiang, Dayong Wang","doi":"10.4172/2329-9533.1000155","DOIUrl":"https://doi.org/10.4172/2329-9533.1000155","url":null,"abstract":"Alzheimer's disease (AD) is a lifelong progressive neurodegenerativa disease related with accumulation of amyloid β peptide (Aβ) produced by processing of amyloid precursor protein (APP) in the brain. In spite of several-decades effort on AD, there is still no medicine used to intervene with its pathological processes. Our previous studies made in transgenic animal models harboring familial AD genes of mutant presenilin 1 and amyloid precursor protein (APP) showed that β2AR gene knock-out (β2AR-KO) is beneficial in senile AD animals. Consistently, an epidemiological study lasted for two decades showed that the sole usage of β blockers as antihypertensive medicines is associated with fewer brain lesions and less brain shrinkage seen in senile AD patients. In order to understand why senile β2AR-KO AD mice had better learning and memory, genomic effects of β2AR-KO in the double transgenic AD mice were investigated. In the analysis, major genomic significance of β2AR-KO was directed to influence protein-processing and presentation involving membrane structure and MHC class I and II protein complex, and lysosome and hydrolase activity for protein degradation, which are critical for accumulation of amyloid β peptide, the hallmark of AD.","PeriodicalId":91303,"journal":{"name":"Journal of applied bioinformatics & computational biology","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6497178/pdf/nihms-1003171.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37216506","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Iterative Image Processing for Early Diagnostic of Beta-Amyloid Plaque Deposition in Pre-Clinical Alzheimer's Disease Studies. 迭代图像处理用于阿尔茨海默病临床前研究中β -淀粉样斑块沉积的早期诊断。

Journal of applied bioinformatics & computational biology Pub Date : 2017-08-01 Epub Date: 2017-05-31 DOI: 10.4172/2329-9533.1000134

Nikolai V Slavine, Padmakar V Kulkarni, Roderick W McColl

{"title":"Iterative Image Processing for Early Diagnostic of Beta-Amyloid Plaque Deposition in Pre-Clinical Alzheimer's Disease Studies.","authors":"Nikolai V Slavine, Padmakar V Kulkarni, Roderick W McColl","doi":"10.4172/2329-9533.1000134","DOIUrl":"https://doi.org/10.4172/2329-9533.1000134","url":null,"abstract":"Purpose: To test and evaluate an efficient iterative image processing strategy to improve the quality of sub-optimal pre-clinical PET images. A novel iterative resolution subsets-based method to reduce noise and enhance resolution (RSEMD) has been demonstrated on examples of PET imaging studies of Alzheimer's disease (AD) plaques deposition in mice brains.Materials and methods: The RSEMD method was applied to imaging studies of non-invasive detection of beta-amyloid plaque in transgenic mouse models of AD. Data acquisition utilized a Siemens Inveon® micro PET/CT device. Quantitative uptake of the tracer in control and AD mice brains was determined by counting the extent of plaque deposition by histological staining. The pre-clinical imaging software inviCRO® was used for fitting the recovery PET images to the mouse brain atlas and obtaining the time activity curves (TAC) from different brain areas.Results: In all of the AD studies the post-processed images proved to have higher resolution and lower noise as compared with images reconstructed by conventional OSEM method. In general, the values of SNR reached a plateau at around 10 iterations with an improvement factor of about 2 over sub-optimal PET brain images.Conclusions: A rapidly converging, iterative deconvolution image processing algorithm with a resolution subsets-based approach RSEMD has been used for quantitative studies of changes in Alzheimer's pathology over time. The RSEMD method can be applied to sub-optimal clinical PET brain images to improve image quality to diagnostically acceptable levels and will be crucial in order to facilitate diagnosis of AD progression at the earliest stages.","PeriodicalId":91303,"journal":{"name":"Journal of applied bioinformatics & computational biology","volume":"6 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5602576/pdf/nihms888928.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35425098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Semi-automated Image Processing for Preclinical Bioluminescent Imaging. 用于临床前生物发光成像的半自动图像处理。

Journal of applied bioinformatics & computational biology Pub Date : 2015-12-22 DOI: 10.4172/2329-9533.1000114

N. Slavine, R. Mccoll

{"title":"Semi-automated Image Processing for Preclinical Bioluminescent Imaging.","authors":"N. Slavine, R. Mccoll","doi":"10.4172/2329-9533.1000114","DOIUrl":"https://doi.org/10.4172/2329-9533.1000114","url":null,"abstract":"OBJECTIVE\u0000Bioluminescent imaging is a valuable noninvasive technique for investigating tumor dynamics and specific biological molecular events in living animals to better understand the effects of human disease in animal models. The purpose of this study was to develop and test a strategy behind automated methods for bioluminescence image processing from the data acquisition to obtaining 3D images.\u0000\u0000\u0000METHODS\u0000In order to optimize this procedure a semi-automated image processing approach with multi-modality image handling environment was developed. To identify a bioluminescent source location and strength we used the light flux detected on the surface of the imaged object by CCD cameras. For phantom calibration tests and object surface reconstruction we used MLEM algorithm. For internal bioluminescent sources we used the diffusion approximation with balancing the internal and external intensities on the boundary of the media and then determined an initial order approximation for the photon fluence we subsequently applied a novel iterative deconvolution method to obtain the final reconstruction result.\u0000\u0000\u0000RESULTS\u0000We find that the reconstruction techniques successfully used the depth-dependent light transport approach and semi-automated image processing to provide a realistic 3D model of the lung tumor. Our image processing software can optimize and decrease the time of the volumetric imaging and quantitative assessment.\u0000\u0000\u0000CONCLUSION\u0000The data obtained from light phantom and lung mouse tumor images demonstrate the utility of the image reconstruction algorithms and semi-automated approach for bioluminescent image processing procedure. We suggest that the developed image processing approach can be applied to preclinical imaging studies: characteristics of tumor growth, identify metastases, and potentially determine the effectiveness of cancer treatment.","PeriodicalId":91303,"journal":{"name":"Journal of applied bioinformatics & computational biology","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2015-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"70289437","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6