Information flow in interaction networks II: channels, path lengths, and potentials

In our previous publication, a framework for information flow in interaction networks based on random walks with damping was formulated with two fundamental modes: emitting and absorbing. While many other network analysis methods based on random walks or equivalent notions have been developed before and after our earlier work, one can show that they can all be mapped to one of the two modes. In addition to these two fundamental modes, a major strength of our earlier formalism was its accommodation of context-specific directed information flow that yielded plausible and meaningful biological interpretation of protein functions and pathways. However, the directed flow from origins to destinations was induced via a potential function that was heuristic. Here, with a theoretically sound approach called the channel mode, we extend our earlier work for directed information flow. This is achieved by constructing a potential function facilitating a purely probabilistic interpretation of the channel mode. For each network node, the channel mode combines the solutions of emitting and absorbing modes in the same context, producing what we call a channel tensor. The entries of the channel tensor at each node can be interpreted as the amount of flow passing through that node from an origin to a destination. Similarly to our earlier model, the channel mode encompasses damping as a free parameter that controls the locality of information flow. Through examples involving the yeast pheromone response pathway, we illustrate the versatility and stability of our new framework.     

Nest Mosquito Trap quantifies contact rates between nesting birds and mosquitoes

Accurate estimates of host-vector contact rates are required for precise determination of arbovirus transmission intensity. We designed and tested a novel mosquito collection device, the Nest Mosquito Trap (NMT), to collect mosquitoes as they attempt to feed on unrestrained nesting birds in artificial nest boxes. In the laboratory, the NMT collected nearly one-third of the mosquitoes introduced to the nest boxes. We then used these laboratory data to estimate our capture efficiency of field-collected bird-seeking mosquitoes collected over 66 trap nights. We estimated that 7.5 mosquitoes per trap night attempted to feed on nesting birds in artificial nest boxes. Presence of the NMT did not have a negative effect on avian nest success when compared to occupied nest boxes that were not sampled with the trap. Future studies using the NMT may elucidate the role of nestlings in arbovirus transmission and further refine estimates of nesting bird and vector contact rates.     

Cardiovascular effects and molecular targets of resveratrol

Resveratrol (3,5,4'-trihydroxy-trans-stilbene) is a polyphenol phytoalexin present in a variety of plant species and has been implicated to explain the health benefits of red wine. A wide range of health beneficial effects have been demonstrated for resveratrol in animal studies. In this review, we summarize the cardiovascular effects of resveratrol with emphasis on the molecular targets of the compound. In this regard, resveratrol stimulates endothelial production of nitric oxide, reduces oxidative stress, inhibits vascular inflammation and prevents platelet aggregation. In animal models of cardiovascular disease, resveratrol protects the heart from ischemia-reperfusion injury, reduces blood pressure and cardiac hypertrophy in hypertensive animals, and slows the progression of atherosclerosis. A number of direct and indirect target molecules mediating the aforementioned cardiovascular effects of resveratrol have been identified. These include, among others, the estrogen receptor α, the adenosine receptors, the cyclooxygenase 1, the histone/protein deacetylase sirtuin 1, the AMP-activated protein kinase, the Akt kinase, the nuclear factor-E2-related factor-2, and NF-κB. Molecular mechanisms involved in the signal cascades are discussed.     

Interaction of the α2A domain of integrin with small collagen fragments

We here present a detailed study of the ligand-receptor interactions between single and triple-helical strands of collagen and the α2A domain of integrin (α2A), providing valuable new insights into the mechanisms and dynamics of collagen-integrin binding at a sub-molecular level. The occurrence of single and triple-helical strands of the collagen fragments was scrutinized with atom force microscopy (AFM) techniques. Strong interactions of the triple-stranded fragments comparable to those of collagen can only be detected for the 42mer triple-helical collagen-like peptide under study (which contains 42 amino acid residues per strand) by solid phase assays as well as by surface plasmon resonance (SPR) measurements. However, changes in NMR signals during titration and characteristic saturation transfer difference (STD) NMR signals are also detectable when α2A is added to a solution of the 21mer single-stranded collagen fragment. Molecular dynamics (MD) simulations employing different sets of force field parameters were applied to study the interaction between triple-helical or single-stranded collagen fragments with α2A. It is remarkable that even single-stranded collagen fragments can form various complexes with α2A showing significant differences in the complex stability with identical ligands. The results of MD simulations are in agreement with the signal alterations in our NMR experiments, which are indicative of the formation of weak complexes between single-stranded collagen and α2A in solution. These results provide useful information concerning possible interactions of α2A with small collagen fragments that are of relevance to the design of novel therapeutic A-domain inhibitors.     

鸡传染性法氏囊病病毒Gt株VP5基因缺失株感染性克隆的构建

传染性法氏囊病病毒 (IBDV)是双链,双节段RNA病毒,其基因组由A、B两个节段组成,编码结构蛋白VP1-VP4和非结构蛋白VP5。【目的】利用反向遗传操作构建拯救VP5基因缺失重组IBDV。【方法】利用体外定点突变技术,缺失IBDV Gt株VP5基因,通过多重PCR在基因组两端分别引入锤头状核酶序列(HamRz)和丁肝病毒核酶序列(HdvRz)。将带有核酶序列的IBDV基因组插入载体pCAGG的b肌动蛋白启动子下游,构建了IBDV感染性克隆pCAGGmGtA △VP5HRT,将该感染性克隆与pCAGGmGtBHRT共转染DFⅠ细胞。【结果】RT-PCR和间接免疫荧光均显示获得重组病毒,将其命名为rmGtA △VP5。IBDV VP5基因缺失感染性克隆的成功构建为从分子水平上深入研究vp5基因功能奠定了基础。     

新疆天山一号冰川地区十种藓类植物叶尖的微形态观察

在光学显微镜和扫描电镜下,对新疆天山一号冰川地区生长的10种藓类植物的叶尖（毛尖）的形态、齿（刺毛）、疣、角质层纹饰等微结构进行观察,其中电镜观察结果均为首次报道。结果表明：10种藓类植物叶尖的顶尖细胞和边缘细胞大部分都是透明的,并且细胞壁厚,细胞腔大;而叶尖边缘内卷、粗糙,细胞壁厚,干时细胞壁上下或侧面凹陷,其上有较多的小孔,这些都是明显耐旱特征,有利于水分的吸收及抵御长期寒冷、反射太阳辐射对其伤害,叶尖的类型对苔藓植物科、属级的分类意义不大,但其微形态如叶尖细胞及边缘细胞的形状、数目、细胞壁的凹陷程度以及其上角质层纹饰、乳突的微形态在同属的不同种之间存在明显差异,对于属下种间的鉴定具有一定的分类学价值。     

基于RS和GIS的阿尔泰山南麓城镇建设用地扩张与适宜性评价

近10年来,阿勒泰地区六县一市的建设用地迅速扩张,在该地区多地出现了新城。为研究阿勒泰地区城市建设用地的扩张特征、建设用地扩张与人口发展之间的协调性关系以及评价建设用地分布的适宜性,采用建设用地扩张的速度指数、强度指数、扩张系数和适宜性评价模型等方法得出了以下结论：(1)在1993-2013年期间,阿勒泰地区各县市建设用地扩展呈现从缓慢扩展到快速扩展的特点,且城市用地的增加主要依靠于城区建设用地向外部扩张;(2)在1993-2013年期间, 整个区域建设用地变化和人口增长之间出现不协调的关系,导致多地形成“空城”现象;(3)全区中适宜建设区域和不适宜建设区域分别占93.51%和6.49%,且有0.85%的城镇建设用地尚处在不适宜建设区域。其结果能为阿勒泰地区建设用地的合理发展和未来规划提供参考依据和决策支持。     

The plant cell wall

<正>Research on the many aspects of the plant cell wall has experienced rejuvenation during the past few years.This is perhaps mainly due to the commercial interest in the chemical components of the cell wall that have potential for industrial use:Cellulose for fi bers and together with hemicelluloses for bioethanol,lignin for plastics or biofuel,pectins as gel agents,let alone woody cell wall material for construction or pulp     

Advances in cellular technology in the hematology field: What have we learned so far?

Despite the advances in the hematology field, blood transfusion-related iatrogenesis is still a major issue to be considered during such procedures due to blood antigenic incompatibility. This places pluripotent stem cells as a possible ally in the production of more suitable blood products. The present review article aims to provide a comprehensive summary of the state-of-theart concerning the differentiation of both embryonic stem cells and induced pluripotent stem cells to hematopoietic cell lines. Here, we review the most recently published protocols to achieve the production of blood cells for future application in hemotherapy, cancer therapy and basic research.