Influence of denatured and intermediate states of folding on protein aggregation

We simulate the aggregation thermodynamics and kinetics of proteins L and G, each of which self-assembles to the same alpha/beta [corrected] topology through distinct folding mechanisms. We find that the aggregation kinetics of both proteins at an experimentally relevant concentration exhibit both fast and slow aggregation pathways, although a greater proportion of protein G aggregation events are slow relative to those of found for protein L. These kinetic differences are correlated with the amount and distribution of intrachain contacts formed in the denatured state ensemble (DSE), or an intermediate state ensemble (ISE) if it exists, as well as the folding timescales of the two proteins. Protein G aggregates more slowly than protein L due to its rapidly formed folding intermediate, which exhibits native intrachain contacts spread across the protein, suggesting that certain early folding intermediates may be selected for by evolution due to their protective role against unwanted aggregation. Protein L shows only localized native structure in the DSE with timescales of folding that are commensurate with the aggregation timescale, leaving it vulnerable to domain swapping or nonnative interactions with other chains that increase the aggregation rate. Folding experiments that characterize the structural signatures of the DSE, ISE, or the transition state ensemble (TSE) under nonaggregating conditions should be able to predict regions where interchain contacts will be made in the aggregate, and to predict slower aggregation rates for proteins with contacts that are dispersed across the fold. Since proteins L and G can both form amyloid fibrils, this work also provides mechanistic and structural insight into the formation of prefibrillar species.     

Bioinformatics approaches and resources for single nucleotide polymorphism functional analysis

Since the initial sequencing of the human genome, many projects are underway to understand the effects of genetic variation between individuals. Predicting and understanding the downstream effects of genetic variation using computational methods are becoming increasingly important for single nucleotide polymorphism (SNP) selection in genetics studies and understanding the molecular basis of disease. According to the NIH, there are now more than four million validated SNPs in the human genome. The volume of known genetic variations lends itself well to an informatics approach. Bioinformaticians have become very good at functional inference methods derived from functional and structural genomics. This review will present a broad overview of the tools and resources available to collect and understand functional variation from the perspective of structure, expression, evolution and phenotype. Additionally, public resources available for SNP identification and characterisation are summarised.     

Prediction of methylated CpGs in DNA sequences using a support vector machine

DNA methylation plays a key role in the regulation of gene expression. The most common type of DNA modification consists of the methylation of cytosine in the CpG dinucleotide. At the present time, there is no method available for the prediction of DNA methylation sites. Therefore, in this study we have developed a support vector machine (SVM)-based method for the prediction of cytosine methylation in CpG dinucleotides. Initially a SVM module was developed from human data for the prediction of human-specific methylation sites. This module achieved a MCC and AUC of 0.501 and 0.814, respectively, when evaluated using a 5-fold cross-validation. The performance of this SVM-based module was better than the classifiers built using alternative machine learning and statistical algorithms including artificial neural networks, Bayesian statistics, and decision trees. Additional SVM modules were also developed based on mammalian- and vertebrate-specific methylation patterns. The SVM module based on human methylation patterns was used for genome-wide analysis of methylation sites. This analysis demonstrated that the percentage of methylated CpGs is higher in UTRs as compared to exonic and intronic regions of human genes. This method is available on line for public use under the name of Methylator at http://bio.dfci.harvard.edu/Methylator/.     

Ectomycorrhizal fungi have larger fruit bodies than saprotrophic fungi

Currently we have only a limited understanding of the evolutionary and ecological significance of reproductive traits of fungi. We compared data on fruit body size, spore size and shape between saprotrophic and mutualistic (ectomycorrhizal) fungi in Northern and Central Europe. Lifestyle and reproductive traits showed strong phylogenetic signals. A phylogenetically informed analysis demonstrated that saprotrophs produce on average smaller fruit bodies than mutualistic species. The two guilds, however, do not differ in spore size. Overall this suggests that fruit bodies of ectomycorrhizal fungi produce on average more spores than saprotrophic fungi. We argue that this difference is related to resource availability: ectomycorrhizal fungi receive carbon from their hosts and, therefore, evolution favours large fruit bodies, whereas the fruit body size of saprotrophic fungi might have responded to resource availability and the distribution and size of resource patches.     

小水电代燃料工程对森林生态服务功能的影响

根据国家林业局发布的《森林生态系统服务功能评估规范》(LY/T 1721—2008),从涵养水源、保育土壤、固碳释氧和积累营养物质功能4个方面进行评价,研究小水电代燃料工程的实施对贵州省麻江县项目区森林生态服务功能的物质量及其价值的影响.结果表明: 小水电代燃料工程对森林生态系统服务功能物质量的增加有显著作用.马尾松和柏木人工林在项目区内涵养水源功能的物质量达20662.04 m³·hm^-2·a^-1,比项目区外增加20.5%,保育土壤量为119.1 t·hm^-2·a^-1,比项目区外增加29.7%,固碳释氧量为220.49 t·hm^-2·a^-1,比项目区外增加40.2%,林木营养积累量达3.49 t·hm^-2·a^-1,比项目区外增加48.5%.小水电代燃料工程对项目区森林生态系统服务功能价值增加额度表现为:固碳释氧功能(7.14 万元·hm^-2·a^-1)>涵养水源功能(6.01万元·hm^-2·a^-1)>林木营养积累功能(1.38万元·hm^-2·a^-1)>保育土壤功能(0.81万元·hm^-2·a^-1).小水电代燃料工程对提高森林生态服务功能价值和实现林区的可持续发展具有重要作用.     

双歧杆菌脂磷壁酸与5-氟尿嘧啶联用的抗肿瘤研究

目的探讨双歧杆菌脂磷壁酸与5-氟尿嘧啶（5-Fu）联用对H22荷瘤小鼠的抗肿瘤作用及免疫功能的影响。方法双歧杆菌脂磷壁酸单独或联合5-Fu处理H22荷瘤Balb／c小鼠,定期测量肿瘤大小,观察小鼠一般状况;计算抑瘤率、血红细胞数和白细胞数,取脾和胸腺计算脏器指数;HE染色分析肿瘤组织变化;MTT法检测小鼠脾T淋巴细胞增殖转化功能以及ELISA法检测小鼠脾淋巴细胞分泌IFN-γ含量。结果双歧杆菌脂磷壁酸及5-Fu单独应用均可抑制肿瘤生长,但单独5-Fu处理组小鼠一般状况差,毒性反应重;双歧杆菌脂磷壁酸与5-Fu联合应用,与单独5-Fu处理组比较,不仅抑瘤率明显提高（P〈0．01）,且荷瘤小鼠一般状况改善,白细胞数升高,脏器指数增加,小鼠脾T淋巴细胞增殖能力强,脾淋巴细胞分泌IFN-γ,水平提高;光镜观察HE染色瘤体组织,双歧杆菌脂磷壁酸处理组可见大量炎症细胞浸润。结论双歧杆菌脂磷壁酸联合5-FU能增强化疗的抑瘤作用,并能扭转化疗引起的免疫低下现象,起到增效减毒作用。     

黑河流域中游地区净初级生产力的人类占用

基于Miami模型,对黑河流域中游净初级生产力的人类占用（HANPP）及其与生态系统多样性的关系进行了研究,并对HANPP与生态足迹（EF）指标在可持续发展评估方面的价值进行了比较.结果表明：HANPP的提高将降低生态系统多样性,研究区现状年的平均HANPP率为38.61%,肃州区和甘州区的HANPP已超过生态系统潜在生产能力的极限;结合气候变化和社会经济发展状况进行分析,未来40年黑河流域中游生态系统将面临更大压力.与生态足迹（EF）相比,HANPP更适于从生态系统功能变化角度评估区域发展的可持续性.     

Effects of biodiversity,stand factors and functional identity on biomass and productivity during the restoration of subtropical forests in Central China

恢复梯度上华中亚热带森林生物多样性、林分因子及功能特性对生物量、生产力的影响 草地群落上进行的控制实验大都发现生物多样性对生态系统功能有显著促进作用。然而,在天然林中,多样性与林分因子、群落功能特性的相对作用大小仍存在争议。本文在森林恢复梯度上,研究这3类因素对生物量和生产力的相对影响。我们在湖北神农架设置了处于不同恢复阶段的24块(600 m²)亚热 带森林样地,计算了林分生物量和生产力。选择5个关键的植物功能性状,并计算了群落的功能多样性(功能丰富度、功能均匀度和功能离散度)和性状的加权平均值(CWM)。使用一般线性模型(GLMs)、变异分离等方法探究林分因子(密度、林龄、群落最大树高等)、功能特性、物种和功能多样性对生物量和生产力的相对重要性。研究结果表明,随着森林恢复,林分生物量和生产力显著增加,群落物种丰富度显著增加,而功能离散度显著降低。变异分离结果表明,多样性对生物量和生产力的单独效应不显著,但可能通过与林分因子和功能特性的协同效应来影响生物量和生产力。总体而言,我们发现林分因子对亚热带森林生物量和生产力的影响最大,功能特性显著影响生产力,但不影响生物量。这些结果说明,在森林经营中,调整林分结构和群落物种特性是提高森林碳储量和固碳潜力的有效途径。     

Protective effects of irisin on hypoxia-reoxygenation injury in hyperglycemia-treated cardiomyocytes: Role of AMPK pathway and mitochondrial protection

Recent evidence has verified the cardioprotective actions of irisin in different diseases models. However, the beneficial action of irisin on hypoxia-reoxygenation (HR) injury under high glucose stress has not been described. Herein our research investigated the influence of irisin on HR-triggered cardiomyocyte death under high glucose stress. HR model was established in vitro under high glucose treatment. The results illuminated that HR injury augmented apoptotic ratio of cardiomyocyte under high glucose stress; this effect could be abolished by irisin via modulating mitochondrial function. Irisin treatment attenuated cellular redox stress, improved cellular ATP biogenetics, sustained mitochondria potential, and impaired mitochondrion-related cell death. At the molecular levels, irisin treatment activated the 5′-adenosine monophosphate-activated protein kinase (AMPK) pathway and the latter protected cardiomyocyte and mitochondria against HR injury under high glucose stress. Altogether, our results indicated a novel role of irisin in HR-treated cardiomyocyte under high glucose stress. Irisin-activated AMPK pathway and the latter sustained cardiomyocyte viability and mitochondrial function.     

Structural characterization of proteins using residue environments

A primary challenge for structural genomics is the automated functional characterization of protein structures. We have developed a sequence-independent method called S-BLEST (Structure-Based Local Environment Search Tool) for the annotation of previously uncharacterized protein structures. S-BLEST encodes the local environment of an amino acid as a vector of structural property values. It has been applied to all amino acids in a nonredundant database of protein structures to generate a searchable structural resource. Given a query amino acid from an experimentally determined or modeled structure, S-BLEST quickly identifies similar amino acid environments using a K-nearest neighbor search. In addition, the method gives an estimation of the statistical significance of each result. We validated S-BLEST on X-ray crystal structures from the ASTRAL 40 nonredundant dataset. We then applied it to 86 crystallographically determined proteins in the protein data bank (PDB) with unknown function and with no significant sequence neighbors in the PDB. S-BLEST was able to associate 20 proteins with at least one local structural neighbor and identify the amino acid environments that are most similar between those neighbors.