Regeneration failure and the potential importance of human disturbance in a subtropical forest

Abstract. A lack of regeneration of shade‐intolerant canopy species has been reported in several subtropical South African forests. The subtropical forest of Hluhluwe‐Umfolozi Park, KwaZulu‐Natal, was examined in order to determine the extent of regeneration, the forest grain, dynamics and conservation value. Field sampling took the form of recording DBH for all woody species in 29 0.04‐ha circular plots, walking 5‐m wide transects in mature and marginal forest to record size classes of important species and analysis of 20 gaps. A community analysis was performed using the multivariate program TWINSPAN. Size‐class distributions indicate a lack of regeneration and suggest a prevalence of shade‐intolerant species in the canopy. The composition of the canopy and subcanopy are distinct from one another and the forest is coarse‐grained. Conservation of the present species composition could be aided by encouraging patch‐scale disturbance. It is hypothesized that swidden agriculture may have favoured the formation of the present forest canopy structure.     

New plant promoter and enhancer testing vectors

We describe here a set of binary vectors suitable forAgrobacterium-mediated gene transfer and specially designed for studying plant promoters. These vectors are based on the use of thegus reporter gene, contain multiple unique restriction sites upstream of thegus gene, and minimal promoters for testing the effect of enhancers or activator elements. In addition, an intron-containinggus (uidA) gene was introduced into one of these vectors in order to examine reporter gene activity in tissues whereAgrobacterium contamination may be a problem or in transient expression assays.     

Hidden Markov Models and Animal Behaviour

This paper proposes the use of hidden Markov time series models for the analysis of the behaviour sequences of one or more animals under observation. These models have advantages over the Markov chain models commonly used for behaviour sequences, as they can allow for time-trend or expansion to several subjects without sacrificing parsimony. Furthermore, they provide an alternative to higher-order Markov chain models if a first-order Markov chain is unsatisfactory as a model. To illustrate the use of such models, we fit multivariate and univariate hidden Markov models allowing for time-trend to data from an experiment investigating the effects of feeding on the locomotory behaviour of locusts (Locusta migratoria).     

Binding of small molecules to cavity forming mutants of a de novo designed protein

A central goal of protein design is to devise novel proteins for applications in biotechnology and medicine. Many applications, including those focused on sensing and catalysis will require proteins that recognize and bind to small molecules. Here, we show that stably folded α-helical proteins isolated from a binary patterned library of designed sequences can be mutated to produce binding sites capable of binding a range of small aromatic compounds. Specifically, we mutated two phenylalanine side chains to alanine in the known structure of de novo protein S-824 to create buried cavities in the core of this four-helix bundle. The parental protein and the Phe→Ala variants were exposed to mixtures of compounds, and selective binding was assessed by saturation transfer difference NMR. The affinities of benzene and a number of its derivatives were determined by pulse field gradient spin echo NMR, and several of the compounds were shown to bind the mutated protein with micromolar dissociation constants. These studies suggest that stably folded de novo proteins from binary patterned libraries are well-suited as scaffolds for the design of binding sites.     

SC-BPSO:肝癌分类中一种融合过滤器的二进制粒子群算法特征的选择方法

癌症的早期诊断能够显著提高癌症患者的存活率,在肝细胞癌患者中这种情况更加明显。机器学习是癌症分类中的有效工具。如何在复杂和高维的癌症数据集中,选择出低维度、高分类精度的特征子集是癌症分类的难题。本文提出了一种二阶段的特征选择方法SC-BPSO:通过组合Spearman相关系数和卡方独立检验作为过滤器的评价函数,设计了一种新型的过滤器方法——SC过滤器,再组合SC过滤器方法和基于二进制粒子群算法(BPSO)的包裹器方法,从而实现两阶段的特征选择。并应用在高维数据的癌症分类问题中,区分正常样本和肝细胞癌样本。首先,对来自美国国家生物信息中心(NCBI)和欧洲生物信息研究所(EBI)的130个肝组织microRNA序列数据(64肝细胞癌,66正常肝组织)进行预处理,使用MiRME算法从原始序列文件中提取microRNA的表达量、编辑水平和编辑后表达量3类特征。然后,调整SC-BPSO算法在肝细胞癌分类场景中的参数,选择出关键特征子集。最后,建立分类模型,预测结果,并与信息增益过滤器、信息增益率过滤器、BPSO包裹器特征选择算法选出的特征子集,使用相同参数的随机森林、支持向量机、决策树、KNN四种分类器分类,对比分类结果。使用SC-BPSO算法选择出的特征子集,分类准确率高达98.4%。研究结果表明,与另外3个特征选择算法相比,SC-BPSO算法能有效地找到尺寸较小和精度更高的特征子集。这对于少量样本高维数据的癌症分类问题可能具有重要意义。     

Toward high-content screening of mitochondrial morphology and membrane potential in living cells

Mitochondria are double membrane organelles involved in various key cellular processes. Governed by dedicated protein machinery, mitochondria move and continuously fuse and divide. These “mitochondrial dynamics” are bi-directionally linked to mitochondrial and cell functional state in space and time. Due to the action of the electron transport chain (ETC), the mitochondrial inner membrane displays a inside-negative membrane potential (Δψ). The latter is considered a functional readout of mitochondrial “health” and required to sustain normal mitochondrial ATP production and mitochondrial fusion. During the last decade, live-cell microscopy strategies were developed for simultaneous quantification of Δψ and mitochondrial morphology. This revealed that ETC dysfunction, changes in Δψ and aberrations in mitochondrial structure often occur in parallel, suggesting they are linked potential targets for therapeutic intervention. Here we discuss how combining high-content and high-throughput strategies can be used for analysis of genetic and/or drug-induced effects at the level of individual organelles, cells and cell populations.This article is part of a Directed Issue entitled: Energy Metabolism Disorders and Therapies.     

Metabolic differentiations of dwarf elder by NMR-based metabolomics

Sambucus plants have prominent place in folk medicine of the people from Europe and the Middle East. Sambucus ebulus (both above and under ground parts) preparations showed anti-neoplastic, antimicrobial (incl. antiviral) and anti-inflammatory properties. Elderberries accumulate sugars and fibers, vitamins and minerals, besides abundant secondary metabolites, as flavonoids, anthocyanins, phytosterols, triterpenes and iridoid glycosides, among others. Sambucus plants, however, also accumulate cyanogenic glycosides, whose presence is undesirable. Despite many applications so far the knowledge of the metabolites, accumulated in Sambucus species, is still limited and based mainly on determination of the major compounds. Here we report the application of ¹H NMR metabolic fingerprinting in combination with principal component and hierarchical clustering analyses to reveal the metabolic differences of Sambucus mature and immature fruits, and plant leaves. Moreover, we show that immature fruits and leaves of S. ebulus have similar metabolome, which apparently undergoes significant changes during the fruit ripening stage. Sambunigrin was not detectable in any sample. To the best of our knowledge this is the first report on the systematic analysis of S. ebulus metabolome.