The significance of ectomycorrhizal fungi for sulfur nutrition of trees

Sulfur nutrition of plants is largely determined by sulfate uptake of the roots, the allocation of sulfate to the sites of sulfate reduction and assimilation, the reduction of sulfate to sulfide and its assimilation into reduced sulfur-containing amino acids and peptides, and the allocation of reduced sulfur to growing tissues that are unable to fulfill their own demand for reduced sulfur in growth and development. Association of the roots of pedunculate oak (Quercus robur L.) and beech (Fagus sylvatica L.) trees with ectomycorrhizal fungi seems to interact with these processes of sulfur nutrition in different ways, but the result of these interactions is dependent on both the plant and the fungal partners. Mycorrhizal colonisation of the roots can alter the response of sulfate uptake to sulfate availability in the soil and enhances xylem loading and, hence, xylem transport of sulfate to the leaves. As a consequence, sulfate reduction in the leaves may increase. Simultaneously, sulfate reduction in the roots seems to be stimulated by ectomycorrhizal association. Increased sulfate reduction in the leaves of mycorrhizal trees can result in enhanced phloem transport of reduced sulfur from the leaves to the roots. Different from herbaceous plants, enhanced phloem allocation of reduced sulfur does not negatively affect sulfate uptake by the roots of trees. These interactions between mycorrhizal association and the processes involved in sulfur nutrition are required to provide sufficient amounts of reduced sulfur for increased protein synthesis that is used for the enhanced growth of trees frequently observed in response to ectomycorrhizal association. This revised version was published online in June 2006 with corrections to the Cover Date.     

From 'omes to biology

Technologies that have emerged from the genome project have dramatically increased our ability to generate data on the way in which organisms respond to their environments, how they execute their programmes of development and growth, and how these are altered in the development of disease states. However, our ability to analyse these large datasets has not kept pace with our ability to generate them and consequently new strategies must be developed to address the issues associated with their analysis. One approach that we have employed quite successfully is to look at data from microarrays (or proteomics or metabolomics experiments) not as independent datasets, but rather as elements of a much larger body of biological information across various scales that must be integrated with, and interpreted within, the context of such ancillary data. Here we outline the general approach and provide three examples from published studies of the way in which we have applied this strategy.     

From 'omes to biology

Technologies that have emerged from the genome project have dramatically increased our ability to generate data on the way in which organisms respond to their environments, how they execute their programmes of development and growth, and how these are altered in the development of disease states. However, our ability to analyse these large datasets has not kept pace with our ability to generate them and consequently new strategies must be developed to address the issues associated with their analysis. One approach that we have employed quite successfully is to look at data from microarrays (or proteomics or metabolomics experiments) not as independent datasets, but rather as elements of a much larger body of biological information across various scales that must be integrated with, and interpreted within, the context of such ancillary data. Here we outline the general approach and provide three examples from published studies of the way in which we have applied this strategy.     

Future Strategies on Glioma Research: From Big Data to the Clinic

<正>Glioma,as the most common and aggressive malignant central nervous system(CNS)tumor with generally poor prognosis,has been attracting much attention in the last decade[1].Temozolomide was firstly available in the United States in1999 as a chemotherapy drug for treating brain cancers and remains as the first-line treatment for glioma.The World     

从一般系统论到后基因组时代的系统生物学

论述了贝塔朗菲的一般系统论的思想起源、主要内容,基于一般系统论的系统生物学的产生、研究思路和方法,阐述了生物学由还原论的研究方法过渡到系统论的研究方法,以及系统生物学未来的发展进行了评价。     

From computational modelling of the intrinsic apoptosis pathway to a systems-based analysis of chemotherapy resistance: achievements,perspectives and challenges in systems medicine

Our understanding of the mitochondrial or intrinsic apoptosis pathway and its role in chemotherapy resistance has increased significantly in recent years by a combination of experimental studies and mathematical modelling. This combined approach enhanced the quantitative and kinetic understanding of apoptosis signal transduction, but also provided new insights that systems-emanating functions (i.e., functions that cannot be attributed to individual network components but that are instead established by multi-component interplay) are crucial determinants of cell fate decisions. Among these features are molecular thresholds, cooperative protein functions, feedback loops and functional redundancies that provide systems robustness, and signalling topologies that allow ultrasensitivity or switch-like responses. The successful development of kinetic systems models that recapitulate biological signal transduction observed in living cells have now led to the first translational studies, which have exploited and validated such models in a clinical context. Bottom-up strategies that use pathway models in combination with higher-level modelling at the tissue, organ and whole body-level therefore carry great potential to eventually deliver a new generation of systems-based diagnostic tools that may contribute to the development of personalised and predictive medicine approaches. Here we review major achievements in the systems biology of intrinsic apoptosis signalling, discuss challenges for further model development, perspectives for higher-level integration of apoptosis models and finally discuss requirements for the development of systems medical solutions in the coming years.     

Plant nutrition research: Priorities to meet human needs for food in sustainable ways

The world population is expanding rapidly and will likely be 10 billion by the year 2050. Limited availability of additional arable land and water resources, and the declining trend in crop yields globally make food security a major challenge in the 21st century. According to the projections, food production on presently used land must be doubled in the next two decades to meet food demand of the growing world population. To achieve the required massive increase in food production, large enhancements in application of fertilizers and improvements of soil fertility are indispensable approaches. Presently, in many developing countries, poor soil fertility, low levels of available mineral nutrients in soil, improper nutrient management, along with the lack of plant genotypes having high tolerance to nutrient deficiencies or toxicities are major constraints contributing to food insecurity, malnutrition (i.e., micronutrient deficiencies) and ecosystem degradation. Plant nutrition research provides invaluable information highly useful in elimination of these constraints, and thus, sustaining food security and well-being of humans without harming the environment. The fact that at least 60% of cultivated soils have growth-limiting problems with mineral-nutrient deficiencies and toxicities, and about 50% of the world population suffers from micronutrient deficiencies make plant nutrition research a major promising area in meeting the global demand for sufficient food production with enhanced nutritional value in this millennium. Integration of plant nutrition research with plant genetics and molecular biology is indispensable in developing plant genotypes with high genetic ability to adapt to nutrient deficient and toxic soil conditions and to allocate more micronutrients into edible plant products such as cereal grains.     

From components to regulatory motifs in signalling networks.

The developments in biochemistry and molecular biology over the past 30 years have produced an impressive parts list of cellular components. It has become increasingly clear that we need to understand how components come together to form systems. One area where this approach has been growing is cell signalling research. Here, instead of focusing on individual or small groups of signalling proteins, researchers are now using a more holistic perspective. This approach attempts to view how many components are working together in concert to process information and to orchestrate cellular phenotypic changes. Additionally, the advancements in experimental techniques to measure and visualize many cellular components at once gradually grow in diversity and accuracy. The multivariate data, produced by experiments, introduce new and exciting challenges for computational biologists, who develop models of cellular systems made up of interacting cellular components. The integration of high-throughput experimental results and information from legacy literature is expected to produce computational models that would rapidly enhance our understanding of the detail workings of mammalian cells.     

From blastocyst to gastrula: gene regulatory networks of embryonic stem cells and early mouse embryogenesis

To date, many regulatory genes and signalling events coordinating mammalian development from blastocyst to gastrulation stages have been identified by mutational analyses and reverse-genetic approaches, typically on a gene-by-gene basis. More recent studies have applied bioinformatic approaches to generate regulatory network models of gene interactions on a genome-wide scale. Such models have provided insights into the gene networks regulating pluripotency in embryonic and epiblast stem cells, as well as cell-lineage determination in vivo. Here, we review how regulatory networks constructed for different stem cell types relate to corresponding networks in vivo and provide insights into understanding the molecular regulation of the blastocyst–gastrula transition.     

Plant metabolomics: from holistic hope, to hype, to hot topic

In a short time, plant metabolomics has gone from being just an ambitious concept to being a rapidly growing, valuable technology applied in the stride to gain a more global picture of the molecular organization of multicellular organisms. The combination of improved analytical capabilities with newly designed, dedicated statistical, bioinformatics and data mining strategies, is beginning to broaden the horizons of our understanding of how plants are organized and how metabolism is both controlled but highly flexible. Metabolomics is predicted to play a significant, if not indispensable role in bridging the phenotype-genotype gap and thus in assisting us in our desire for full genome sequence annotation as part of the quest to link gene to function. Plants are a fabulously rich source of diverse functional biochemicals and metabolomics is also already proving valuable in an applied context. By creating unique opportunities for us to interrogate plant systems and characterize their biochemical composition, metabolomics will greatly assist in identifying and defining much of the still unexploited biodiversity available today.     

重庆特有濒危植物缙云黄芩的繁育系统研究

缙云黄芩（Scutellaria tsinyunensis）为重庆市缙云山特有分布种,目前已经处于濒危状态。本文在定点观测的基础上,运用过氧化氢检测法、花粉-胚珠比（P/O）和套袋实验等方法对缙云黄芩的开花特征和繁育系统进行了分析。结果表明：缙云黄芩花展示和花设计具有适合蜂类等传粉昆虫的传粉综合征,熊蜂(Bombus)和食芽蝇为主要的访花者,P/O为7 618±390,繁育系统为专性异交,传粉套袋实验也证实其必需传粉者异花传粉且可能自交不亲和;其雌雄蕊紧靠的花部结构及花粉活力和柱头可授性低、昆虫的访花频率较低等内外因素致使其自然坐果率较低(20.08%)且结实少(5.6个/株)。由于缙云黄芩小坚果萌发率较低,其有性生殖能力较低,居群扩大困难,应尽快采用人工栽培助其复壮等保护措施。     

From Gene to Protein: Determination of Melanin Synthesis

Melanin production in mammals is regulated at a variety of levels (tissue, cellular, and subcellular), and many gene loci are involved in the determination of color patterns directed by the melanocyte. Many of the genes involved in these complex processes have now been cloned, and even the simplest mutation can lead to dramatic changes in the phenotype of the individual. Many, if not all, of the pigment related genes have pleiotropic effects on the development and differentiation of the organism, and perhaps because of this, the melanocyte is evolving as an important model for the study of gene regulation and action at the functional level. In view of the importance of pigmentation as a photoprotective barrier and as a cosmetic factor affecting appearance and social acceptance, the importance of these studies seems destined to increase significantly in the future.     

Exploring the genomes: From Arabidopsis to crops

Model systems have played a crucial role for understanding biological processes at genetic, molecular and systems levels. Arabidopsis thaliana is one of the best studied model species for higher plants. Large genomic resources and mutant collections made Arabidopsis an excellent source for functional and comparative genomics. Rice and Brachypodium have a great potential to become model systems for grasses. Given the agronomic importance of grass crops, it is an attractive strategy to apply knowledge from Arabidopsis to grasses. Despite many efforts successful reports are sparse. Knowledge transfer should generally work best between orthologous genes that share functionality and a common ancestor. In higher plants, however, recent genome projects revealed an active and rapid evolution of genome structure, which challenges the concept of one-to-one orthologous mates between two species. In this study, we estimated on the example of protein families that are involved in redox related processes, the impact of gene expansions on the success rate for a knowledge transfer from Arabidopsis to the grass species rice, sorghum and Brachypodium. The sparse synteny between dicot and monocot plants due to frequent rearrangements, translocations and gene losses strongly impairs and reduces the number of orthologs detectable by positional conservation. To address the limitations of sparse synteny and expanded gene families, we applied for the detection of orthologs in this study orthoMCL, a sequence-based approach that allows to group closely related paralogs into one orthologous gene cluster. For a total of 49 out of 170 Arabidopsis genes we could identify conserved copy numbers between the dicot model and the grass annotations whereas approximately one third (34.7%, 59 genes) of the selected Arabidopsis genes lack an assignment to any of the grass genome annotations. The remaining 62 Arabidopsis genes represent groups that are considerably biased in their copy numbers between Arabidopsis and all or most of the three grass genomes.     

Systems biology of lipid metabolism: From yeast to human

Lipid metabolism is highly relevant as it plays a central role in a number of human diseases. Due to the highly interactive structure of lipid metabolism and its regulation, it is necessary to apply a holistic approach, and systems biology is therefore well suited for integrated analysis of lipid metabolism. In this paper it is demonstrated that the yeast Saccharomyces cerevisiae serves as an excellent model organism for studying the regulation of lipid metabolism in eukaryotes as most of the regulatory structures in this part of the metabolism are conserved between yeast and mammals. Hereby yeast systems biology can assist to improve our understanding of how lipid metabolism is regulated.     

Production of Plant Made Pharmaceuticals: From Plant Host to Functional Protein

In the last two decades plants have emerged as valuable alternatives to mammalian cells for the production of pharmaceuticals and their potential as expression systems was shown by the commercial availability and acceptance of several plant made therapeuticals in clinical trials. Plants have many advantages over yeast, insect and bacterial expression systems such as the potential to properly fold the expressed proteins and the synthesis of more human-like N-glycans on the proteins. However, several constraints, such as expression yields, downstream processing and structural authenticity, currently limit the widespread use of plant expression systems. In this review, the focus is on the current limitations of plant systems for the production of pharmaceuticals and the possibilities to overcome these obstacles. A comparison is made with insect cell and yeast expression systems. Furthermore, the importance of glycosylation, in particular N-glycosylation for the biological function(s) of therapeutics in the human body will be discussed in detail and an overview of the state of art in the humanization of the N-glycosylation pathway in plants is provided.     

Cocon: From NMR Correlation Data to Molecular Constitutions

The constitutional assignment of natural products by NMR spectroscopy is usually based on 2D NMR experiments like COSY, HSQC, and HMBC. In this paper, the resulting connectivity information is used as input for the new structure generating program Cocon which both improves and dramatically accelerates the process of constitutional assignment. Cocon allows to quantify the value of connectivity information (2D NMR correlation data) for structure elucidation problems. Applying Cocon, it is systematically evaluated to which degree the NMR experiments COSY, ¹H,¹³C-HMBC and 1,1-ADEQUATE constrain the number of constitutions compatible with the data sets of two secondary metabolites from marine sponges.Electronic Supplementary Material available.     

From Atoms to Cells: Using Mesoscale Landscapes to Construct Visual Narratives

Modeling and visualization of the cellular mesoscale, bridging the nanometer scale of molecules to the micrometer scale of cells, is being studied by an integrative approach. Data from structural biology, proteomics, and microscopy are combined to simulate the molecular structure of living cells. These cellular landscapes are used as research tools for hypothesis generation and testing, and to present visual narratives of the cellular context of molecular biology for dissemination, education, and outreach.