Analysis of conformational motions and related key residue interactions responsible for a specific function of proteins with elastic network model

Protein collective motions play a critical role in many biochemical processes. How to predict the functional motions and the related key residue interactions in proteins is important for our understanding in the mechanism of the biochemical processes. Normal mode analysis (NMA) of the elastic network model (ENM) is one of the effective approaches to investigate the structure-encoded motions in proteins. However, the motion modes revealed by the conventional NMA approach do not necessarily correspond to a specific function of protein. In the present work, a new analysis method was proposed to identify the motion modes responsible for a specific function of proteins and then predict the key residue interactions involved in the functional motions by using a perturbation approach. In our method, an internal coordinate that accounts for the specific function was introduced, and the Cartesian coordinate space was transformed into the internal/Cartesian space by using linear approximation, where the introduced internal coordinate serves as one of the axes of the coordinate space. NMA of ENM in this internal/Cartesian space was performed and the function-relevant motion modes were identified according to their contributions to the specific function of proteins. Then the key residue interactions important for the functional motions of the protein were predicted as the interactions whose perturbation largely influences the fluctuation along the internal coordinate. Using our proposed methods, the maltose transporter (MalFGK₂) from E. Coli was studied. The functional motions and the key residue interactions that are related to the channel-gating function of this protein were successfully identified.     

禽流感H5N1亚型病毒感染ICR小鼠的动物模型

目的 建立H5N1禽流感病毒感染ICR小鼠的疾病动物模型.方法 将100 μL H5N1 禽流感病毒原液(EID50为105.37/0.2 mL) 鼻腔接种ICR小鼠,设生理盐水组、正常尿囊液组对照,接毒后14 d内每隔12 h观察一次,主要观测指标有临床体征、体重和体温变化、死亡率、病理变化、病毒分离和血清抗体检测 (ELISA方法).结果 被感染的ICR小鼠的病程可以划分为潜伏期 (第0～1天)、急性感染期 (第2～7天)、恢复期 (第8～14天),急性感染期表现出活动明显减少,弓背,反应性差,扎堆;接毒后第1天开始体温和体重下降,第6天体温和体重停止下降;接毒组ICR小鼠累计的死亡率为60%;急性感染期ICR小鼠的肺部病变最严重,表现为间质性肺炎,肺间质充血、水肿和淋巴细胞浸润,毛细血管扩张,上皮细胞变性、坏死、脱落,并有充血和单核细胞浸润;接毒后第1天至第8天可在小鼠的肺、脑、气管和心、肝、脾、肾分离到病毒;接毒后第6天从ICR小鼠血清中检测到抗体.结论 本实验室建立的H5N1禽流感病毒感染ICR小鼠的模型在临床表现、体重变化、死亡率、病理变化、病毒复制指标能达到禽流感病毒疾病模型的造模要求,符合人类禽流感感染疾病的基本特征.     

Administration of signalling molecules dictates stem cell homing for in situ regeneration

Ex vivo‐expanded stem cells have long been a cornerstone of biotherapeutics and have attracted increasing attention for treating intractable diseases and improving tissue regeneration. However, using exogenous cellular materials to develop restorative treatments for large numbers of patients has become a major concern for both economic and safety reasons. Advances in cell biological research over the past two decades have expanded the potential for using endogenous stem cells during wound healing processes, and in particular, recent insight into stem cell movement and homing has prompted regenerative research and therapy based on recruiting endogenous cells. Inspired by the natural healing process, artificial administration of specific chemokines as signals systemically or at the injury site, typically using biomaterials as vehicles, is a state‐of‐the‐art strategy that potentiates stem cell homing and recreates an anti‐inflammatory and immunomodulatory microenvironment to enhance in situ tissue regeneration. However, pharmacologically coaxing endogenous stem cells to act as therapeutics in the field of biomedicine remains in the early stages; its efficacy is limited by the lack of innovative methodologies for chemokine presentation and release. This review describes how to direct the homing of endogenous stem cells via the administration of specific signals, with a particular emphasis on targeted signalling molecules that regulate this homing process, to enhance in situ tissue regeneration. We also provide an outlook on and critical considerations for future investigations to enhance stem cell recruitment and harness the reparative potential of these recruited cells as a clinically relevant cell therapy.     

Identifying a Kinase Network Regulating FGF14:Nav1.6 Complex Assembly Using Split-Luciferase Complementation

Kinases play fundamental roles in the brain. Through complex signaling pathways, kinases regulate the strength of protein:protein interactions (PPI) influencing cell cycle, signal transduction, and electrical activity of neurons. Changes induced by kinases on neuronal excitability, synaptic plasticity and brain connectivity are linked to complex brain disorders, but the molecular mechanisms underlying these cellular events remain for the most part elusive. To further our understanding of brain disease, new methods for rapidly surveying kinase pathways in the cellular context are needed. The bioluminescence-based luciferase complementation assay (LCA) is a powerful, versatile toolkit for the exploration of PPI. LCA relies on the complementation of two firefly luciferase protein fragments that are functionally reconstituted into the full luciferase enzyme by two interacting binding partners. Here, we applied LCA in live cells to assay 12 kinase pathways as regulators of the PPI complex formed by the voltage-gated sodium channel, Nav1.6, a transmembrane ion channel that elicits the action potential in neurons and mediates synaptic transmission, and its multivalent accessory protein, the fibroblast growth factor 14 (FGF14). Through extensive dose-dependent validations of structurally-diverse kinase inhibitors and hierarchical clustering, we identified the PI3K/Akt pathway, the cell-cycle regulator Wee1 kinase, and protein kinase C (PKC) as prospective regulatory nodes of neuronal excitability through modulation of the FGF14:Nav1.6 complex. Ingenuity Pathway Analysis shows convergence of these pathways on glycogen synthase kinase 3 (GSK3) and functional assays demonstrate that inhibition of GSK3 impairs excitability of hippocampal neurons. This combined approach provides a versatile toolkit for rapidly surveying PPI signaling, allowing the discovery of new modular pathways centered on GSK3 that might be the basis for functional alterations between the normal and diseased brain.     

Modelling Infectious Hematopoietic Necrosis Virus Dispersion from Marine Salmon Farms in the Discovery Islands,British Columbia,Canada

Finite volume ocean circulation and particle tracking models are used to simulate water-borne transmission of infectious hematopoietic necrosis virus (IHNV) among Atlantic salmon (Salmo salar) farms in the Discovery Islands region of British Columbia, Canada. Historical simulations for April and July 2010 are carried out to demonstrate the seasonal impact of river discharge, wind, ultra-violet (UV) radiation, and heat flux conditions on near-surface currents, viral dispersion and survival. Numerical particles released from infected farm fish in accordance with IHNV shedding rates estimated through laboratory experiments are dispersed by model oceanic flows. Viral particles are inactivated by ambient UV radiation levels and by the natural microbial community at rates derived through laboratory studies. Viral concentration maps showing temporal and spatial changes are produced and combined with lab-determined minimum infectious dosages to estimate the infective connectivity among farms. Results demonstrate that neighbouring naïve farms can become exposed to IHNV via water-borne transport from an IHNV diseased farm, with a higher risk in April than July, and that many events in the sequence of farm outbreaks in 2001-2002 are consistent with higher risks in our farm connectivity matrix. Applications to other diseases, transfers between farmed and wild fish, and the effect of vaccinations are also discussed.     

大型水母声学观测与评估技术研究进展

20世纪末以来,世界多个海域频繁出现大型水母暴发现象,对海洋生态系统、海洋渔业、沿海工业和滨海旅游业带来了巨大的灾难。为了研究大型水母生态习性,进而揭示其暴发机理并进行灾害的预警防治,近些年来国内外学者开展了大量的采用网具、目视、水下摄像、声学技术、航空影像等多种手段的大型水母监测调查工作,其中使用声学技术对大型水母进行资源评估和行为跟踪目前在欧美、日本、韩国等渔业发达国家已经开展了相关应用,在资源评估、运动学规律等研究中展现出较好的观测效果和应用潜力。目前我国在大型水母声学观测研究应用领域鲜有文献报道,通过介绍国际上利用声学技术对大型水母进行资源调查与评估、空间分布监测、运动规律等研究成果,为今后我国开展大型水母声学调查研究提供理论基础和科学依据。通过本文的分析,建议可以借鉴国际上采用科学鱼探仪、高分辨率成像声呐、声学信标等方法对大型水母进行监测调查和资源评估的研究成果,结合实际情况将声学技术逐步研究并应用到我国大型水母资源调查与评估、自然生态习性研究、重点水域大型水母动态监测预警中去,完善我国大型水母监测调查体系。     

Survival rates of mutant genes under artificial selection using individual and family information

We have used diffusion and branching process methods to investigate fixation rates, probabilities of survival per generation, and times to fixation of mutant genes under different selection methods incorporating individual and family information. Diffusion approximations fit well to simulated results even for large selection coefficients. Methods that give much weight to family information, such as BLUP evaluation which is widely used in animal breeding, reduce fixation rates of mutant genes because of the reduced effective population sizes. In general, it is observed that even mutants with relatively small heterozygous effects (say 0.1 phenotypic standard deviation) are practically ‘safe’ (i.e. their probability of loss from one generation to the next is smaller than, say, 10%) after just a few generations, typically less than 10. For methods of selection with larger effective size, such as within-family selection, the mutant is ‘safe’ in the population somewhat earlier but eventual fixation takes a longer time. Finally we evaluate the amount by which the use of marker assisted selection reduces the fixation probability of newly arisen mutants.     

3D Macroporous Nitrogen‐Enriched Graphitic Carbon Scaffold for Efficient Bioelectricity Generation in Microbial Fuel Cells

Microbial fuel cell (MFC) can generate electricity based on oxidation of organic compounds by exoelectogens, giving rise to a promising potential for recovering electrical energy from organic wastewater. The structure and property of anode materials have inherent impact to extracellular electron transfer (EET), an interfacial process that greatly limits bioelectricity production of MFC. Herein, a three dimensional (3D) macroporous nitrogen‐enriched graphitic carbon (NGC) scaffold is fabricated from commercially available melamine foam using facile pyrolysis method. The NGC electrode is demonstrated to promote EET ef?ciently, achieving a power density of 750 mW m^?2 based on pure cultured Shewanella oneidensis MR‐1 in acetate‐feeding MFC. The unique 3D open‐cell structure not only offers habitats for colonization of electroactive bio?lm up to a maximal density but also provides macroporous architecture for internal mass transfer without concern of bio‐blocking and bio‐fouling. Additionally, nitrogen incorporation also plays a signi?cant role in enhancing EET, where pyrrolic nitrogen is much more active than graphitic and pyridinic nitrogen as indicated by density functional theory calculation. This work provides a proof‐of‐concept demonstration of a high‐ef?ciency, cost‐effective, easily scaling‐up, and environmentally friendly anode material of bioelectrochemical systems for electricity generation, hydrogen production, and pollutant degradation.     

Heterogeneous nanomechanical properties of type I collagen in longitudinal direction

Biomechanics and Modeling in Mechanobiology - Collagen is an abundant structural biopolymer in mammal vertebrates, providing structural support as well as mechanical integrity for connective...