Toward consistent assignment of structural domains in proteins

The assignment of protein domains from three-dimensional structure is critically important in understanding protein evolution and function, yet little quality assurance has been performed. Here, the differences in the assignment of structural domains are evaluated using six common assignment methods. Three human expert methods (AUTHORS (authors' annotation), CATH and SCOP) and three fully automated methods (DALI, DomainParser and PDP) are investigated by analysis of individual methods against the author's assignment as well as analysis based on the consensus among groups of methods (only expert, only automatic, combined). The results demonstrate that caution is recommended in using current domain assignments, and indicates where additional work is needed. Specifically, the major factors responsible for conflicting domain assignments between methods, both experts and automatic, are: (1) the definition of very small domains; (2) splitting secondary structures between domains; (3) the size and number of discontinuous domains; (4) closely packed or convoluted domain-domain interfaces; (5) structures with large and complex architectures; and (6) the level of significance placed upon structural, functional and evolutionary concepts in considering structural domain definitions. A web-based resource that focuses on the results of benchmarking and the analysis of domain assignments is available at     

A proposal for using the ensemble approach to understand genetic regulatory networks

Understanding the genetic regulatory network comprising genes, RNA, proteins and the network connections and dynamical control rules among them, is a major task of contemporary systems biology. I focus here on the use of the ensemble approach to find one or more well-defined ensembles of model networks whose statistical features match those of real cells and organisms. Such ensembles should help explain and predict features of real cells and organisms. More precisely, an ensemble of model networks is defined by constraints on the "wiring diagram" of regulatory interactions, and the "rules" governing the dynamical behavior of regulated components of the network. The ensemble consists of all networks consistent with those constraints. Here I discuss ensembles of random Boolean networks, scale free Boolean networks, "medusa" Boolean networks, continuous variable networks, and others. For each ensemble, M statistical features, such as the size distribution of avalanches in gene activity changes unleashed by transiently altering the activity of a single gene, the distribution in distances between gene activities on different cell types, and others, are measured. This creates an M-dimensional space, where each ensemble corresponds to a cluster of points or distributions. Using current and future experimental techniques, such as gene arrays, these M properties are to be measured for real cells and organisms, again yielding a cluster of points or distributions in the M-dimensional space. The procedure then finds ensembles close to those of real cells and organisms, and hill climbs to attempt to match the observed M features. Thus obtains one or more ensembles that should predict and explain many features of the regulatory networks in cells and organisms.     

阔叶丰花草——浙江茜草科一新归化种

首次记载阔叶丰花草 (Spermacoce latifolia Aubl.),一种原产南美热带地区的茜草科植物,为浙江归化植物一新记录,并通过实地调查和访问对其入侵途径进行了分析,认为可能是由于植物园引种或农作物种子贸易而无意引进浙江温州的。     

An integrative approach to species discovery in odonates: from character‐based DNA barcoding to ecology

Modern taxonomy requires an analytical approach incorporating all lines of evidence into decision‐making. Such an approach can enhance both species identification and species discovery. The character‐based DNA barcode method provides a molecular data set that can be incorporated into classical taxonomic data such that the discovery of new species can be made in an analytical framework that includes multiple sources of data. We here illustrate such a corroborative framework in a dragonfly model system that permits the discovery of two new, but visually cryptic species. In the African dragonfly genus Trithemis three distinct genetic clusters can be detected which could not be identified by using classical taxonomic characters. In order to test the hypothesis of two new species, DNA‐barcodes from different sequence markers (ND1 and COI) were combined with morphological, ecological and biogeographic data sets. Phylogenetic analyses and incorporation of all data sets into a scheme called taxonomic circle highly supports the hypothesis of two new species. Our case study suggests an analytical approach to modern taxonomy that integrates data sets from different disciplines, thereby increasing the ease and reliability of both species discovery and species assignment.     

生态系统服务供给量的确定——最小数据法在黑河流域中游的应用

确定生态系统服务供给量与付费标准是进行生态系统服务付费研究的关键问题。最小数据方法是一个推导生态系统服务供给曲线的数学模型,该模型通过分析土地利用收益的空间分布,计算出生态系统服务机会成本的空间分布,从而推导出生态系统服务供给曲线。介绍了最小数据方法,然后以黑河流域张掖市甘州区为例,以植被蒸散发量的减少表征生态系统服务,通过调查获得机会成本的空间分布,利用最小数据方法推导了水资源服务供给曲线。结果表明:随着补偿价格的提高,农业部门提供的水资源服务逐渐增加。当补偿价格从0.067元m-3(农业用水价格)提高到3元m-3(建筑用水水价),农业部门提供的水资源服务由2.08×106m3a-1增加到2.7×108m3a-1。这表明,采用生态系统服务付费政策可以有效减少农业用水量,同时这也为补偿标准的制定提供一种新的思路。     

Enzymatic hydrolysis of waste cellulose

Interstitial flow (IF) modulates both the biochemical and biophysical cues surrounding cells. It represents a very important regulating mechanism for cell/tissue function and has been commonly utilized in tissue engineering (TE). This article discusses the possible regulating mechanisms of IF on fibroblasts, the various fibroblast responses to IF, the current challenges in understanding the IF–fibroblast relationship and the application of IF for fibroblast involved TE. In particular, IF can affect fibroblast growth at both intracellular (e.g., calcium signaling, protein/proteinase secretion) and cellular (e.g., autocrine/paracrine signaling, proliferation, differentiation, alignment, adhesion, migration) levels. One major challenge for understanding IF–fibroblast interaction has been the determination of the flow and cell growth condition at microlevel especially in a three‐dimensional environment. To utilize IF and optimize the fluidic environment for TE, several influencing factors in the system including perfusate composition, flow profile, nutrient supply, signaling molecule effect, scaffold property, and fibroblast type should be considered. Biotechnol. Bioeng. 2010;107: 1–10. © 2010 Wiley Periodicals, Inc.     

Differentiation-dependent expression of hypothetical proteins in the neuroblastoma cell line N1E-115

Several protein cascades, including signaling, cytoskeletal, chaperones, metabolic, and antioxidant proteins, have been shown to be involved in the process of neuronal differentiation (ND) of neuroblastoma cell lines. No systematic approach to detect hitherto unknown and unnamed proteins or structures that have been predicted upon nucleic acid sequences in ND has been published so far. We therefore decided to screen hypothetical protein (HP) expression by protein profiling. Two-dimensional gel electrophoresis with subsequent matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF/TOF) identification was used for expression analysis of undifferentiated and dimethylsulfoxide-induced neuronally differentiated N1E-115 cells. We unambiguously identified six HPs: Q8C520, Q99LF4, Q9CXS1, Q9DAF8, Q91WT0, and Q8C5G2. A prefoldin domain in Q91WT0, a t-SNARE domain in Q9CXS1, and a bromodomain were observed in Q8C5G2. For the three remaining proteins, no putative function using Pfam, BLOCKS, PROSITE, PRINTS, InterPro, Superfamily, CoPS, and ExPASy could be assigned. While two proteins were present in both cell lines, Q9CXS1 was switched off (i.e., undetectably low) in differentiated cells only, and Q9DAF8, Q91WT0, and Q8C5G2 were switched on in differentiated cells exclusively. Herein, using a proteomic approach suitable for screening and identification of HP, we present HP structures that have been only predicted so far based upon nucleic acid sequences. The four differentially regulated HPs may play a putative role in the process of ND.     

A computational protocol to probe the role of solvation effects on the reduction potential of azurin mutants

Semiquantitative relationships between thermodynamic parameters of Cu2+ reduction experimentally measured for a series of azurin mutants and the solvation free energy of the oxidized state of the proteins were derived. Solvation free energy calculations were carried out within an ONIOM/PCM scheme specifically adapted to this protein series. The method proved to be able to capture the main determinants of the measured reduction parameters, providing satisfactory predictions of the E degrees '.     

A bioelectrochemical study of a suspension of Escherichia coli cells metabolizing glucose and lactose

The metabolism of glucose and lactose in Escherichia coli K-12 cells has been studied using a bioelectrochemical (BEC) approach. The magnitude and the duration of the response of a BEC anode were found to be functions of the composition of nutrient media and the concentration of bacterial cells. The amount of electricity that is generated enzymatically during the metabolism of a particular substrate depends on the activity of the relevant enzymes. This suggests that the BEC approach can be used for evaluating the activity of particular enzyme systems.