Improved understanding of gene expression regulation using systems biology

This article reviews the current state of systems biology approaches, including the experimental tools used to generate ‘omic’ data and computational frameworks to interpret this data. Through illustrative examples, systems biology approaches to understand gene expression and gene expression regulation are discussed. Some of the challenges facing this field and the future opportunities in the systems biology era are highlighted.     

Improved understanding of gene expression regulation using systems biology

This article reviews the current state of systems biology approaches, including the experimental tools used to generate 'omic' data and computational frameworks to interpret this data. Through illustrative examples, systems biology approaches to understand gene expression and gene expression regulation are discussed. Some of the challenges facing this field and the future opportunities in the systems biology era are highlighted.     

Recent advances in exploring physiology and biodiversity of ectomycorrhizas highlight the functioning of these symbioses in ecosystems

Ectomycorrhizas, the dominating mycorrhizal symbiosis in boreal, temperate and some tropical forests, are formed by 5000-6000 species of the asco- and basidiomycetes. This high diversity of fungal partners allows optimal foraging and mobilisation of various nitrogen and phosphorus forms from organic soil layers. In this review, two approaches to study the functioning of this multitude of symbiotic associations are presented. On selected culture models, physiological and molecular investigations have shown that the supply of hexoses has a key function in controlling the plant-fungus interaction via partner-specific regulation of gene expression. Environmental factors which affect fungal carbon supply, such as increased nitrogen availability, also affect mycorrhiza formation. Based on such laboratory results, the adaptative capability of ectomycorrhizas to changing field conditions is discussed. The second approach consists of analysing the distribution of mycorrhizas in ecosystem compartments and to relate distribution patterns to variations of ecological factors. Recent advances in identification of fungal partners in ectomycorrhizas by analysing the internal transcribed spacer of ribosomal DNA are presented, which can help to resolve sampling problems in field studies. The limits of the laboratory and the field approaches are discussed. Despite some problems, this combined approach is the most promising. Direct investigation of gene expression, which has been introduced for soil bacteria, will be difficult in the case of mycorrhizal fungi which constitute organisms with functionally varying structures.     

Transmembrane calcium transport and the activation of cardiac contraction

It has been known for a century that extracellular Ca2+ ions are needed for triggering contraction in the heart. However, the two possible mechanisms of Ca2+ entry into the cardiac cells have only been discovered and investigated recently: these are the voltage-gated Ca2+ channels and the Na+-Ca2+ exchange. This paper reviews the field of the control of cardiac contractility by the sarcolemma and describes various techniques used to study the Ca2+ transport and the corresponding two components of contraction: phasic and tonic tension. The most controversial issue of the past 5 years, attracting the attention of many investigators, is whether or not the Na+-Ca2+ exchange in the heart is electrogenic and voltage-dependent and thus contributes to the beat-to-beat regulation of free intracellular [Ca2+]. This paper concentrates on this controversy and gives an up-to-date view of the major steps in the development of our present concept of this transport and of some of the recent experimental approaches. The contribution of an electrogenic, voltage-dependent Na+-Ca2+ exchange to the regulation of contraction, as well as to cardia electrical activity, is discussed, and the alterations of both of these cardiac functions due to Na+ accumulation intracellularly (owing to various interventions) are described.     

Combination of PAGE and LA-ICP-MS as an analytical workflow in metallomics: state of the art, new quantification strategies, advantages and limitations

Metallomics (more specifically, metalloproteomics) is an emerging field that encompasses the role, uptake, transport and storage of trace metals, which are essential to preserve the functions of proteins within a biological system. The current strategies for metal-binding and metalloprotein analysis based on the combination of polyacrylamide gel electrophoresis (PAGE) and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) are discussed in this review. The advantages, limitations and the most recently developed and applied quantification approaches for this methodology are also described.     

植物萜类代谢工程

植物萜类化合物不仅在植物生命活动中起重要作用,而且具有重要商业价值。随着近年来萜类代谢途径和调控机理研究的深入,代谢工程已成为提高萜类产量最有潜力的途径之一。对萜类代谢工程领域具代表性的研究结果进行了全面回顾,然后讨论了萜类代谢工程的研究方法和策略,其中重点探讨了功能基因组学方法在萜类代谢途径及调控机理研究方面的应用。     

Yeast sphingolipids: metabolism and biology

Sphingolipids have recently emerged as important bioactive molecules in addition to being critical structural components of cellular membranes. These molecules have been implicated in regulating cell growth, differentiation, angiogenesis, apoptosis, and senescene. To study sphingolipid mediated biology, it is necessary to investigate sphingolipid metabolism and its regulation. The yeast Saccharomyces cerevisiae has allowed such studies to take place as the sphingolipid metabolic and regulatory pathways appear conserved across species. Using yeast genetic approaches most enzymes of sphingolipid metabolism have been identified and cloned which has led to identification of their mammalian homologues. Many of the yeast enzymes are targets of fungal toxins thus underscoring the importance of this pathway in yeast cell regulation. This review focuses on the yeast sphingolipid metabolic pathway and its role in regulation of yeast biology. Implication of the insights gained from yeast to mammalian cell regulation are discussed.     

A plausible molecular interpretation of the polar coordinate model with a centripetal degeneracy of distinctive field values

I have attempted to interpret, in molecular terms, the polar coordinate model for epimorphic regulation, revised to accommodate the rigorouslyheld constraints of the polar coordinate system (Sibatani, 1981). If the angular coordinate of the field value is represented by a physical variable in the form of a proportion function, R, to be defined as the intensity ratio of two morphogen curves, then R can stay unchanged along any radius mapped on the actual space, while the intensity of the two morphogens together approaches zero towards the field centre, satisfying the requirement of the centripetal degeneracy of the distinctive angular field values. Implications of this idea are discussed in theoretical and molecular terms as well as in respect of interpretations of some experimental data.     

以供能比评价主食产品中马铃薯原料添加程度的指标构建研究

通过初步构建马铃薯供能比评价指标,比较以马铃薯供能比评价不同马铃薯原料添加程度的适用性,分析发现,马铃薯供能比与马铃薯质量占比之间差异最大可超过35%,二者间回归系数为0.958 4~0.999 9。以马铃薯供能比作为评价指标可较好地反映不同马铃薯原料对马铃薯主食产品的能量贡献程度,而不受其原料形态的影响。建议在马铃薯主食产品的生产、加工和市场监管等马铃薯主食产业各环节中,引入马铃薯供能比评价指标,用以对马铃薯主食产品中马铃薯原料添加程度的评价参考。     

Inducible RNAi system and its application in novel therapeutics

RNA interference (RNAi) was discovered as a cellular defense mechanism more than decade ago. It has been exploited as a powerful tool for genetic manipulation. Characterized with specifically silencing target gene expression, it has great potential application for disease treatment. Currently, there are human clinical trials in progress or planned. Despite the excitement regarding this prominent technology, there are many obstacles and concerns that prevent RNAi from being widely used in the therapeutic field. Among them, the non-spatial and non-temporal control is the most difficult challenge, as well as off-target effects and triggering type I immune responses. Inducible RNAi technology can effectively regulate target genes by inducer-mediated small hairpin RNA expression. Combination with inducible regulation systems this makes RNAi technology more sophisticated and may provide a wider application field. This review discusses approaches of inducible RNAi systems, the potential problem areas and solutions and their therapeutic applications. Given the limitations discussed herein being resolved, we believe that inducible RNAi will be a major therapeutic modality within the next several years.     

Trends in research on shallow water food webs

Making sense of the spider–web networks of interactions between species in food webs has been a major pre-occupation of ecologists over the last 60 years. This review describes the early attempts to reduce this complexity through the grouping of individual taxa into functional categories (such as trophic levels), through adopting the energy flow or systems approach as epitomised by the International Biological Programme, and most recently by the derivation of web statistics by food web theorists. The strengths and weaknesses of these approaches are discussed in relation to empirical field experiments for unravelling the processes responsible for organising communities and an assessment made of the representation of these approaches in the marine biological literature.     

茉莉素介导的长春花生物碱次生代谢转录调控机制

萜类吲哚生物碱（terpeniod indole alkaloids, TIAs）是植物中产生的一类具有药理活性的次生代谢产物.药用植物长春花（Catharanthus roseus）因含有长春碱和长春新碱等重要的抗肿瘤萜类吲哚生物碱而成为研究TIAs次生代谢的主要模式植物.应用正、反向遗传学和各种代谢组学技术对长春花TIAs次生代谢途径及其调控进行了较深入的研究,相继鉴定了参与TIAs代谢途径调控的CrORCAs、CrMYCs、CrZCTs和CrWRKYs等转录因子,特别是发现茉莉素（jasmonates, JAs）介导TIAs生物合成的转录调控网络. 本文以长春花TIAs生物合成途径为模式,重点论述其代谢途径中的关键酶、参与调节的转录因子,尤其是茉莉素介导的调控网络及机制,解析植物中这些天然抗癌生物碱合成积累水平低的制约因素和组织细胞特异性,讨论基于这些新知识的长春花抗肿瘤TIAs代谢工程策略和工厂化绿色生产前景.     

Mass spectrometry-based proteomics strategies for protease cleavage site identification

Protease-catalyzed hydrolysis of peptide bonds is one of the most pivotal post-translational modifications fulfilling manifold functions in the regulation of cellular processes. Therefore, dysregulation of proteolytic reactions plays a central role in many pathophysiological events. For this reason, understanding the molecular mechanisms in proteolytic reactions, in particular the knowledge of proteases involved in complex processes, expression levels and activity of protease and knowledge of the targeted substrates are an indispensable prerequisite for targeted drug development. The present review focuses on mass spectrometry-based proteomic methods for the analysis of protease cleavage sites, including the identification of the hydrolyzed bonds as well as of the surrounding sequence. Peptide- and protein-centric approaches and bioinformatic tools for experimental data interpretation will be presented and the major advantages and drawbacks of the different approaches will be addressed. The recent applications of these approaches for the analysis of biological function of different protease classes and potential future directions will be discussed.     

Life Is the Existence, Interaction (Functioning), and Reproduction of Unique, Highly Organized Nucleotide and Amino Acid Consequences

The most recent achievements in molecular endocrinology concerning mechanisms of molecular regulation of gene expression are discussed. The author's concept is presented about probable trends in the field of study of the programs of individual development of living organism, coded in the genome.