Journal of applied bioinformatics & computational biology最新文献

英文中文

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

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.

免疫信息学已经显著下降到发现针对不同微生物的强抗体竞争对手。在动量研究中，混合使用多种T细胞(CD4+和CD8+)和B细胞表位期望装置来发现含有大量抗埃博拉核蛋白(NP)表位的肽，并通过预测、对接和大众包含装置检查肽向人类白细胞抗原(HLA)原子的引入。此外，ELISA测定了从健全志愿者血液中分离出来的肽激活边缘血单个核细胞中的IFN-γ。经过预期检验，获得了6种含有不同T和B细胞表位的肽，并排除了有产生免疫系统和不良易感反应风险的肽。所有肽对扎伊尔埃博拉病毒感染均显示100%的保护作用。预测装置、Auto dock Vina和CABS-dock结果证实了预期肽与各种HLA等位基因结合的能力。人群纳入调查预计在四个大陆(非洲、美洲、亚洲和欧洲)，预期的不敏感反应中有较高的纳入率(约85%)。与未受刺激的细胞相比，肽激活细胞显示IFN-γ释放水平升高。因此，被识别的NP肽可以被认为是对抗埃博拉病毒的潜在工程抗体竞争对手。

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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

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.

阿尔茨海默病(AD)是一种终身进行性神经退行性疾病，与大脑中淀粉样蛋白前体蛋白(APP)加工产生的β淀粉样肽(a β)积累有关。尽管人们对阿尔茨海默病进行了几十年的研究，但仍没有药物用于干预其病理过程。我们在早老素1突变体和淀粉样前体蛋白(APP)家族性AD基因转基因动物模型中进行的研究表明，β2AR基因敲除(β2AR- ko)对老年AD动物有益。一项持续20年的流行病学研究一致表明，单纯使用β受体阻滞剂作为抗高血压药物与老年AD患者的脑损伤和脑萎缩减少有关。为了了解老年β2AR-KO AD小鼠具有更好学习记忆能力的原因，我们研究了β2AR-KO在双转基因AD小鼠中的基因组效应。在分析中，β 2ar - ko的主要基因组意义被指向影响蛋白质加工和递呈，包括膜结构和MHC I类和II类蛋白复合物，以及蛋白质降解的溶酶体和水解酶活性，这对淀粉样β肽的积累至关重要，淀粉样β肽是AD的标志。

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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

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.

目的:测试和评估一种有效的迭代图像处理策略，以提高临床前PET图像的质量。一种新的基于迭代分辨率子集的方法来降低噪声和提高分辨率(RSEMD)已经在阿尔茨海默病(AD)斑块沉积的小鼠大脑PET成像研究中得到了证明。材料与方法:应用RSEMD方法对转基因AD小鼠模型进行无创检测β -淀粉样蛋白斑块的影像学研究。数据采集采用西门子Inveon®微型PET/CT设备。通过组织学染色计数斑块沉积程度来确定对照和AD小鼠脑内示踪剂的定量摄取。采用临床前成像软件inviCRO®对恢复PET图像与小鼠脑图谱进行拟合，获得不同脑区时间活动曲线(TAC)。结果:在所有的AD研究中，与传统的OSEM方法重建的图像相比，后处理后的图像具有更高的分辨率和更低的噪声。一般来说，信噪比在大约10次迭代时达到平台，与次优PET脑图像相比，改进因子约为2。结论:基于分辨率子集的RSEMD方法快速收敛、迭代反卷积图像处理算法已被用于定量研究阿尔茨海默病病理随时间的变化。RSEMD方法可以应用于次优的临床PET脑图像，将图像质量提高到诊断可接受的水平，对于促进早期诊断AD进展至关重要。

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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

OBJECTIVEBioluminescent 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.METHODSIn 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.RESULTSWe 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.CONCLUSIONThe 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.

目的生物发光成像是一种有价值的无创技术，可用于研究活体动物的肿瘤动力学和特异性生物分子事件，以更好地了解人类疾病对动物模型的影响。本研究的目的是开发和测试从数据采集到获得3D图像的生物发光图像处理自动化方法背后的策略。方法为了优化该流程，开发了一种基于多模态图像处理环境的半自动化图像处理方法。为了确定生物发光源的位置和强度，我们使用CCD相机在成像物体表面检测到的光通量。对于模体标定测试和目标表面重建，我们采用了MLEM算法。对于内部生物发光源，我们使用扩散近似来平衡介质边界上的内部和外部强度，然后确定光子通量的初始阶近似，然后应用一种新的迭代反卷积方法来获得最终重建结果。结果我们发现重建技术成功地使用了深度依赖的光传输方法和半自动图像处理，提供了一个真实的肺肿瘤三维模型。我们的图像处理软件可以优化和减少体积成像和定量评估的时间。结论从光幻象和肺小鼠肿瘤图像中获得的数据证明了图像重建算法和半自动化方法在生物发光图像处理过程中的实用性。我们建议，开发的图像处理方法可以应用于临床前影像学研究:肿瘤生长特征，识别转移，并潜在地确定癌症治疗的有效性。

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