代谢物组学方法及其在植物学研究中的应用

代谢物是生物体受遗传控制和环境影响的最终表达产物,以全体代谢物(代谢物组)为研究对象的代谢物组学是继基因组学和蛋白质组学后必然出现的又一门"组学"技术。该文综述了代谢物组的检测、数据的处理和分析等以及这些技术在植物目标分析、基因功能、代谢途径和代谢工程、整合植物学、信号转导等研究中的应用和前景。     

Theoretical approaches to protein aggregation

The process of protein misfolding and aggregation has been associated with an increasing number of pathological conditions that include Alzheimer's and Parkinson's diseases, and type II diabetes. In addition, the discovery that proteins unrelated to any known disorder can be converted into aggregates of morphologies similar to those found in diseased tissue has lead to the recognition that this type of assemblies represents a generic state of polypeptide chains. Therefore, despite the enormous complexity of the in vivo mechanisms that have evolved in living organisms to prevent and control the formation of protein aggregates, the process of aggregation itself appears ultimately to be caused by intrinsic properties of polypeptide chains, in particular by the tendency of the backbone to form hydrogen bonds, and be modulated by the presence of specific patterns of hydrophobic and charged residues. Theoreticians have just recently started to respond to the challenge of identifying the determinants of the aggregation process. In this review, we provide an account of the theoretical results obtained so far.     

Theoretical approaches to D-amino acid oxidase

Several substrates and roles have been proposed for D-amino acid oxidase (E.C. 1.4.3.3.); however, there is no proof that they possess the required characteristics to account for the ubiquity, large amounts and great activity of the enzyme as found in diverse cells and tissues. Based on the similar stereoposition of identically charged atoms and lateral side chain (R) with respect to the alpha-hydrogen atoms in beta-sheet conformation and in D-amino acids, it is proposed that its substrates may include several membrane-related proteins, partially in beta-sheet conformation, whose alpha-hydrogen atoms would be the real object of D-amino acid oxidase catalysis. A monooxygenase-like enzymatic activity of D-amino acid oxidase with these novel substrates is considered, for which the final products are hypothesized to be protein alpha-carbon hydroxyls resulting from the incorporation of one atom of oxygen into the substrate, the other being reduced to water. Alternatively, it is also proposed that D-amino acid oxidase (and possibly other monooxygenase enzymes) would have a hydroperoxide-synthetase activity. In this case, protein alpha-carbon hydroperoxide and not water, but another reduced molecule, would be the final products. The new enzymatic performances of D-amino acid oxidase and the possible role of its potential final products in redox and other biochemical processes are discussed.     

New approaches to phylogenetic tree search and their application to large numbers of protein alignments

Phylogenetic tree estimation plays a critical role in a wide variety of molecular studies, including molecular systematics, phylogenetics, and comparative genomics. Finding the optimal tree relating a set of sequences using score-based (optimality criterion) methods, such as maximum likelihood and maximum parsimony, may require all possible trees to be considered, which is not feasible even for modest numbers of sequences. In practice, trees are estimated using heuristics that represent a trade-off between topological accuracy and speed. I present a series of novel algorithms suitable for score-based phylogenetic tree reconstruction that demonstrably improve the accuracy of tree estimates while maintaining high computational speeds. The heuristics function by allowing the efficient exploration of large numbers of trees through novel hill-climbing and resampling strategies. These heuristics, and other computational approximations, are implemented for maximum likelihood estimation of trees in the program Leaphy, and its performance is compared to other popular phylogenetic programs. Trees are estimated from 4059 different protein alignments using a selection of phylogenetic programs and the likelihoods of the tree estimates are compared. Trees estimated using Leaphy are found to have equal to or better likelihoods than trees estimated using other phylogenetic programs in 4004 (98.6%) families and provide a unique best tree that no other program found in 1102 (27.1%) families. The improvement is particularly marked for larger families (80 to 100 sequences), where Leaphy finds a unique best tree in 81.7% of families.     

Theoretical and experimental approaches to understand morphogen gradients

Morphogen gradients, which specify different fates for cells in a direct concentration‐dependent manner, are a highly influential framework in which pattern formation processes in developmental biology can be characterized. A common analysis approach is combining experimental and theoretical strategies, thereby fostering relevant data on the dynamics and transduction of gradients. The mechanisms of morphogen transport and conversion from graded information to binary responses are some of the topics on which these combined strategies have shed light. Herein, we review these data, emphasizing, on the one hand, how theoretical approaches have been helpful and, on the other hand, how these have been combined with experimental strategies. In addition, we discuss those cases in which gradient formation and gradient interpretation at the molecular and/or cellular level may influence each other within a mutual feedback loop. To understand this interplay and the features it yields, it becomes essential to take system‐level approaches that combine experimental and theoretical strategies.     

New pulsed EPR methods and their application to characterize mitochondrial complex I

Electron Paramagnetic Resonance (EPR) spectroscopy is the method of choice to study paramagnetic cofactors that often play an important role as active centers in electron transfer processes in biological systems. However, in many cases more than one paramagnetic species is contributing to the observed EPR spectrum, making the analysis of individual contributions difficult and in some cases impossible. With time-domain techniques it is possible to exploit differences in the relaxation behavior of different paramagnetic species to distinguish between them and separate their individual spectral contribution. Here we give an overview of the use of pulsed EPR spectroscopy to study the iron-sulfur clusters of NADH:ubiquinone oxidoreductase (complex I). While FeS cluster N1 can be studied individually at a temperature of 30 K, this is not possible for FeS cluster N2 due to its severe spectral overlap with cluster N1. In this case Relaxation Filtered Hyperfine (REFINE) spectroscopy can be used to separate the overlapping spectra based on differences in their relaxation behavior.     

Complex I: a complex gateway to the powerhouse

Complex I, the main entry point for electrons to the respiratory chain, is of critical importance for cellular energy homeostasis. In this issue of Cell Metabolism, Kruse and coworkers (2008) describe the first mouse knockout for a complex I structural subunit, thus advancing our understanding of complex I in disease.     

Complex plasmas: III. Experiments on strong coupling and long-range correlations

This paper continues a series of review papers devoted to the physics of complex plasmas, in which one of the components (dust) is in a crystalline or liquid state, while the others (electron, ions, and neutral atoms) are in a gaseous state. This review is devoted to the experimental investigations of new phenomena incomplex plasmas. The experiments are explained using estimates based on the theory of elementary processes in complex plasmas, including the new phenomena considered in the previous parts of the review. The paper describes (i) the experiments on multilayer plasma crystals, including the study of their structure and phase transitions; (ii) the experiments on dust monolayer crystals; (iii) the experiments on plasma clusters formed by small number of dust grains; (iv) the experiments on dust ion-sound waves, dust acoustic waves, dust lattice waves, and dust shear waves; (v) the experiments on shock waves; (vi) the experiments on the ionization instabilities and the creation of dust voids and dust clumps; and (vii) the experiments on Mach cones excited either by fast grains or laser radiation.     

Steady-state kinetic approaches to complex biological systems

Steady-state kinetic approaches to study the biochemical systems have been extremly useful. In this paper we use this approach to explain the inhibition of electron transport in structurally bound multienzyme systems and in applying the work-energy cost transfer function to living tissues as studied by³¹P NMR spectroscopy. We show that in both systems the steady-state approach leads to equations and predictions that are in accordance with the experimental data.     

Proprioceptors and their contribution to somatosensory mapping: complex messages require complex processing

This review of other people's work concentrates on two matters. First, which of the various receptors are chiefly involved in creating the central representations or maps of the body that both underlie the conscious perception of our body image and are needed to control our motor performance. Second, how are these relatively well-charted signals used in sensorimotor mapping, with particular attention paid to various human psychophysical observations and illusions that throw light on the central integrative mechanisms involved. Detailed citation is largely restricted to developments since earlier reviews.     

Electron tomography of negatively stained complex viruses: application in their diagnosis

Pattern recognition receptors are a key component of the first line host defense against infection, recognizing specific microbial products. We hypothesize that monocyte hyporesponsiveness in human sepsis is associated with a downregulation of the pattern recognition receptors Toll-like receptor (TLR)-2 and TLR4. Protein expression of CD14, TLR2 and TLR4 on blood monocytes was examined using flow cytometry from 29 patients with sepsis and 14 healthy controls. In addition LPS stimulated TNF-α and IL-10 production was studied in a 24 hour whole blood assay. We found an increased expression of CD14, TLR2 and TLR4 in patients with sepsis compared to controls (p < 0.01). In patients with sepsis, death was associated with significant lower CD14 and TLR2 expression at admission (CD14: 25.7 +- 19.1 vs 39.1 +- 17.3 mean fluorescence intensity [MFI], p = 0.02; TLR2: 21.8 +- 9.4 vs. 30.9 +- 9.6, p = 0.01). At 72 hours the TLR2 expression on monocytes was associated with the IL-10 inducibility after LPS stimulation (r = 0.52, p = 0.02) and the CD14 expression with the IL-6, IL-10 and TNF inducibility. We conclude that septic patients are characterized by an increased expression of CD14, TLR2 and TLR4 on monocytes compared to controls. Death is associated with downregulation of TLR2 and CD14 expression on monocytes correlating with reduced cytokine inducibility. We suggest that CD14 and TLR2 are a key factor in monocyte hyporesponsibility during severe sepsis.