MapGene2Chrom基于Perl和SVG语言绘制基因物理图谱

遗传图谱表现形式简洁明了,为分析遗传规律、克隆基因提供了便利。Gbrowse、MapViewer等工具虽然能够协助研究人员绘制相似形式的物理图谱,但有很大的局限性:(1)数据需提前布置好;(2)输出结果无法灵活修改。鉴于此,文章基于Perl和SVG语言,开发了一款生物辅助作图软件MapGene2Chrom的本地版与网页版,该软件能够依据输入数据快速绘制相应的物理图谱。该软件输入数据格式简单,输出结果易于修改,图片格式为SVG矢量图,具有很好的移植性,以期为研究人员绘制物理图谱提供便利。     

Inhibition of bleomycin‐induced pulmonary fibrosis by bone marrow‐derived mesenchymal stem cells might be mediated by decreasing MMP9, TIMP‐1, INF‐γ and TGF‐β

The study was aimed to investigate the mechanism and administration timing of bone marrow‐derived mesenchymal stem cells (BMSCs) in bleomycin (BLM)‐induced pulmonary fibrosis mice. Thirty‐six mice were divided into six groups: control group (saline), model group (intratracheal administration of BLM), day 1, day 3 and day 6 BMSCs treatment groups and hormone group (hydrocortisone after BLM treatment). BMSCs treatment groups received BMSCs at day 1, 3 or 6 following BLM treatment, respectively. Haematoxylin and eosin and Masson staining were conducted to measure lung injury and fibrosis, respectively. Matrix metalloproteinase (MMP9), tissue inhibitor of metalloproteinase‐1 (TIMP‐1), γ‐interferon (INF‐γ) and transforming growth factor β1 (TGF‐β) were detected in both lung tissue and serum. Histologically, the model group had pronounced lung injury, increased inflammatory cells and collagenous fibres and up‐regulated MMP9, TIMP‐1, INF‐γ and TGF‐β compared with control group. The histological appearance of lung inflammation and fibrosis and elevation of these parameters were inhibited in BMSCs treatment groups, among which, day 3 and day 6 treatment groups had less inflammatory cells and collagenous fibres than day 1 treatment group. BMSCs might suppress lung fibrosis and inflammation through down‐regulating MMP9, TIMP‐1, INF‐γ and TGF‐β. Delayed BMSCs treatment might exhibit a better therapeutic effect. Copyright © 2015 John Wiley & Sons, Ltd. Highlights are as follows:

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Glass transition investigations on highly crosslinked epoxy resins by molecular dynamics simulations

Molecular dynamics simulations at the atomistic level were performed to investigate the glass transition of a highly crosslinked thermoset epoxy resin system composed of diglycidyl ether bisphenol A and isophorone diamine. The crosslinked model was first constructed using a cyclic dynamic method, and extended by investigating the effect of conversion degree on the static properties of local structure, internal energy and volume shrinkage. Based on this model, a systematic investigation on volume, energy and dynamic properties against temperature was made, which determined the glass transition temperature (T_g). The T_gs obtained from various volumetric and energy properties agree well with the differential scanning calorimetry experimental data available, yet a dynamic T_g obtained from the diffusion coefficient is relatively higher. Moreover, the investigation on epoxy segmental dynamics confirmed that the glass transition of the highly crosslinked epoxy resin has a strong dependence on the backbone bond torsional kinetics.     

A linear model for characterization of synchronization frequencies of neural networks

The synchronization frequency of neural networks and its dynamics have important roles in deciphering the working mechanisms of the brain. It has been widely recognized that the properties of functional network synchronization and its dynamics are jointly determined by network topology, network connection strength, i.e., the connection strength of different edges in the network, and external input signals, among other factors. However, mathematical and computational characterization of the relationships between network synchronization frequency and these three important factors are still lacking. This paper presents a novel computational simulation framework to quantitatively characterize the relationships between neural network synchronization frequency and network attributes and input signals. Specifically, we constructed a series of neural networks including simulated small-world networks, real functional working memory network derived from functional magnetic resonance imaging, and real large-scale structural brain networks derived from diffusion tensor imaging, and performed synchronization simulations on these networks via the Izhikevich neuron spiking model. Our experiments demonstrate that both of the network synchronization strength and synchronization frequency change according to the combination of input signal frequency and network self-synchronization frequency. In particular, our extensive experiments show that the network synchronization frequency can be represented via a linear combination of the network self-synchronization frequency and the input signal frequency. This finding could be attributed to an intrinsically-preserved principle in different types of neural systems, offering novel insights into the working mechanism of neural systems.     

T lymphocytes and aortic aneurysms

Aortic aneurysms are common and life threatening problems with high rates of death. The initiation and progression of aneurysms are characterized by extensive extracellular matrix degradation and immune cells invasion within arterial wall. During the pathogenesis of all aneurysms, inflammation and immune cells play a significant role. Although T cells are abundant in aneurysm tissue, their functions in initiation and propagation of aneurysms remain unclear. This review summarizes the current state of knowledge of T lymphocytes on this disease and focuses on potential mechanisms of specific T cell responses.     

Distribution and characteristics of telocytes as nurse cells in the architectural organization of engineered heart tissues

Interstitial Cajal-like cells are a distinct type of interstitial cell with a wide distribution in mammalian organs and tissues,and have been given the name"telocytes".Recent studies have demonstrated the potential roles of telocytes in heart development,renewal,and repair.However,further research on the functions of telocytes is limited by the complicated in vivo environment.This study was designed to construct engineered heart tissue(EHT)as a three-dimensional model in vitro to better understand the role of telocytes in the architectural organization of the myocardium.EHTs were constructed by seeding neonatal cardiomyocytes in collagen/Matrigel scaffolds followed by culture under persistent static stretch.Telocytes in EHTs were identified by histology,toluidine blue staining,immunofluorescence,and transmission electron microscopy.The results from histology and toluidine blue staining demonstrated widespread putative telocytes with compact toluidine blue-stained nuclei,which were located around cardiomyocytes.Prolongations from the cell bodies showed a characteristic dichotomous branching pattern and formed networks in EHTs.Immunofluorescence revealed positive staining of telocytes for CD34 and vimentin with typical moniliform prolongations.A series of electron microscopy images further showed that typical telocytes embraced the cardiomyocytes with their long prolongations and exhibited a marked appearance of nursing cardiomyocytes during the construction of EHTs.This finding highlights the great importance of telocytes in the architectural organization of EHTs.It also suggests that EHT is an appropriate physical and pathological model system in vitro to study the roles of telocytes during heart development and regeneration.