Revisiting the structural basis and energetic landscape of susceptibility difference between HLA isotypes to allergic rhinitis

The human leukocyte antigen class II (HLA II) molecules are implicated in the immunopathogenesis of allergic rhinitis (AR). The HLA II contains three allelic isotypes HLA-DR, -DQ, and -QP that exhibit considerably different susceptibility to AR. Here, we investigated the structural basis and energetic landscape of the susceptibility difference between the three HLA II isotypes to AR by combining computational analysis and experimental assay. Multiple sequence alignment revealed a low conservation among the three subtypes with sequence identity of ∼10% between them, suggesting that the peptide repertoires presented by HLA-DR, -DP and -DQ are not overlapped to each other, and they may be involved in different immune functions and dysfunctions. Structural analysis imparted that the antigenic peptides are rooted on the peptide-binding groove of HLA molecules and hold in a PPII-like helical conformation. Subsequently, the interaction behavior of 17 AR allergen-derived peptides with HLA-DR, −DP and −DQ was investigated using a statistics-based quantitative structure-activity relationship (QSAR) predictor. It was found a significant difference between the binding capabilities of these antigenic peptides to HLA-DR and to HLA-DP/-DQ; the former showed a generally higher affinity than the latter with p-value of 0.02 obtained from 2-tailed Student’s t-test. The computational findings were then confirmed by HLA II–peptide stability assay, which demonstrated that the AR allergen-derived peptides have a high in vitro selectivity for HLA-DR over HLA-DP/-DQ. Thus, the HLA-DR isotype, rather than HLA-DP and −DQ, is expected to associate with the pathological process of AR.     

Dynamics analysis of a delayed viral infection model with immune impairment

In this paper, the dynamical behavior of a delayed viral infection model with immune impairment is studied. It is shown that if the basic reproductive number of the virus is less than one, then the uninfected equilibrium is globally asymptotically stable for both ODE and DDE model. And the effect of time delay on stabilities of the equilibria of the DDE model has been studied. By theoretical analysis and numerical simulations, we show that the immune impairment rate has no effect on the stability of the ODE model, while it has a dramatic effect on the infected equilibrium of the DDE model.     

Tiling solutions for optimal biological sensing

Biological systems, from cells to organisms, must respond to the ever-changing environment in order to survive and function. This is not a simple task given the often random nature of the signals they receive, as well as the intrinsically stochastic, many-body and often self-organized nature of the processes that control their sensing and response and limited resources. Despite a wide range of scales and functions that can be observed in the living world, some common principles that govern the behavior of biological systems emerge. Here I review two examples of very different biological problems: information transmission in gene regulatory networks and diversity of adaptive immune receptor repertoires that protect us from pathogens. I discuss the trade-offs that physical laws impose on these systems and show that the optimal designs of both immune repertoires and gene regulatory networks display similar discrete tiling structures. These solutions rely on locally non-overlapping placements of the responding elements (genes and receptors) that, overall, cover space nearly uniformly.     

Co-administration of Interleukin-2 Enhances Cellular and Humoral Immune Responses to HIV Vaccine DNA Prime／MVA Boost Regime

Interleukine-2 (IL-2) is a growth factor for antigen-stimulated T lymphocytes and is responsible for T-cell clonal expansion after antigen recognition. It has been demonstrated that DNA vaccine-elicited immune responses in mice could be augmented substantially by using either an IL-2 protein or a plasmid expressing IL-2. Twenty mice, divided into four experimental groups, were immunized with: (1) sham plasmid; (2) HIV-1 DNA vaccine alone; (3) HIV-1 DNA vaccine and IL-2 protein; or (4) HIV-1 DNA vaccine and IL-2 plasmid, separately. All the groups were immunized 3 times at a 2-week interval. Fourteen days after the last DNA vaccine injection, recombinant MVA was injected into all the mice except those in group 1. ELISA and ELISPOT were employed to investigate the effect of IL-2 on DNA vaccine immune responses. The obtained results strongly indicate that the efficacy of HIV vaccine can be enhanced by co-administration of a plasmid encoding IL-2.     

A Novel Rule Induction Algorithm

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基于免疫模板聚类的模糊中波红外图像目标提取

借鉴生物先天性免疫与适应性免疫的协调作用机制,综合考虑中波红外图像的光谱成像机理和频域模板统计特征,提出一种免疫模板聚类目标提取算法。借鉴先天性免疫对抗原表面分子模式的识别作用,以最大类间方差,将模糊中波红外图像初分割为目标像素集、背景像素集和模糊像素集;借鉴先天性免疫的特征提呈作用,提取中波红外图像模糊像素的频域模板特征,将图像的像素灰度特征空间映射为频域模板特征空间;基于提呈得到的模板特征,对模糊像素集进行适应性免疫聚类,将模糊像素划分为目标像素或背景像素。用手部痕迹的模糊中波红外图像进行实验,并与经典边缘检测模板法和传统区域模板法进行了效果比较和定量评价,结果表明免疫模板聚类算法的目标提取率、与参考标准的重合度、绝对误差率均优于现有模板方法,能够有效实现模糊中波红外图像的目标提取。     

Exploiting the diversity of time scales in the immune system: A B-cell antibody model

Using the continuous shape space formalism, we develop an immune system model involving both B lymphocytes and antibody molecules. The binding and cross-linking of receptors on B cells stimulates the cells to divide and, with a lag, to secrete antibody. Using the method of multiple scales, we show how to correctly formulate long-time-scale equations for the population dynamics of B cells, the total antibody concentration, and rate of antibody secretion. We compare our model with previous phenomenological formulations.     

Agent-Based Network Modeling Study of Immune Responses in Progression of Ulcerative Colitis

Ulcerative colitis, an inflammatory bowel disease, is a chronic inflammatory disorder that results in ulcers of the colon and rectum without known etiology.Ulcerative colitis causes a huge public health care burden particularly in developed countries.Many studies suggest that ulcerative colitis results from an abnormal immune response against components of commensal microbiota in genetically susceptible individuals.However, understanding of the disease mechanisms at cellular and molecular levels remains largely elusive.In this paper, a network model is developed based on our previous study and computer simulations are performed using an agent-based network modeling to elucidate the dynamics of immune response in ulcerative colitis progression.Our modeling study identifies several important positive feedback loops as a driving force for ulcerative colitis initiation and progression.The results demonstrate that although immune response in ulcerative colitis patients is dominated by anti-inflammatory/regulatory cells such as alternatively activated macrophages and type Ⅱ natural killer T cells, proinflammatory cells including classically activated macrophages, T helper 1 and T helper 17 cells, and their secreted cytokines tumor necrosis factor-α, interleukin-12, interleukin-23, interleukin-17 and interferon-γ remain at certain levels (lower than those in Crohn's disease, another inflammatory bowel disease).Long-term exposure to these proinflammatory components, causes mucosal tissue damage persistently, leading to ulcerative colitis.Our simulation results are qualitatively in agreement with clinical and laboratory measurements, offering novel insight into the disease mechanisms.     

基于免疫算法的组合预测方法

利用免疫算法搜索全局最优解能力,提出了一种其于免疫算法的组合预测权系数确定的新方法,并给出了具体算法.仿真实验结果表明了免疫算法在组合预测方面具有很好的可行性和有效性.     

Fluorescent Probe ABM for Screening Gastrointestinal Patient’s Immune State

The fluorescent probe-aminoderivative of benzanthrone, ABM (developed at Riga Technical University, Riga, Latvia) was used to characterize the membranes of lymphocytes of cancer patients: 46 patients with gastrointestinal diseases, 13 patients having different primary localizations with massive metastases and intoxication. Patients were divided into three groups: (1) with decreased fluorescence intensity, (2) normal fluorescence intensity, (3) increased fluorescence intensity. The lymphocytes distribution among subsets differed between groups, in correspondence to the level of florescence intensity. Surgical treatment affected the main immunological parameters and elevated the functional activity of lymphocytes. In the advanced tumors group, fluorescence intensity correlates with the survival rate. Results suggest that determination of lymphocytes functional activity by ABM can aid evaluation of the immune status in cancer patients.