末端限制性片段长度多态性技术分析硝化细菌微生物多样性

利用T_RFLP(末端限制性片段长度多态性)技术,分析硝化细菌富集反应器中的微生物群落结构,并对硝化细菌的丰度进行半定量研究。结果表明,培养48h后,硝化细菌富集效果最佳,多样性指数与初始培养相比下降了62.80%,富集出的硝化细菌主要为亚硝酸盐氧化菌(Nitrobacter)。同时对投加该硝化细菌前后的对虾养殖水体进行微生物多样性的动态研究,并推测了虾塘水中可能稳定存在的几种主要细菌种类,其中投加富集硝化细菌前后均存在的细菌种类包括短芽孢杆菌Brevibacillus brevis、微杆菌Microbacterium lactium、固氮弧菌Azoarcus indigens或者霍氏鲍特菌Bordetella holmesii。     

Using reaction mechanism to measure enzyme similarity

The concept of reaction similarity has been well studied in terms of the overall transformation associated with a reaction, but not in terms of mechanism. We present the first method to give a quantitative measure of the similarity of reactions based upon their explicit mechanisms. Two approaches are presented to measure the similarity between individual steps of mechanisms: a fingerprint-based approach that incorporates relevant information on each mechanistic step; and an approach based only on bond formation, cleavage and changes in order. The overall similarity for two reaction mechanisms is then calculated using the Needleman-Wunsch alignment algorithm. An analysis of MACiE, a database of enzyme mechanisms, using our measure of similarity identifies some examples of convergent evolution of chemical mechanisms. In many cases, mechanism similarity is not reflected by similarity according to the EC system of enzyme classification. In particular, little mechanistic information is conveyed by the class level of the EC system.     

Long‐term datasets: From descriptive to predictive data using ecoinformatics

This Special Feature includes contributions on data‐processing of large ecological datasets under the heading ecoinformatics. Herewith the latter term is now al so established in the Journal of Vegetation Science. Ecoinfomatics is introduced as a rapid growing field within community ecology which is generating exciting new developments in ecology and in particular vegetation ecology. In our field, ecoinformatics deals with the understanding of patterns of species distributions at local and regional scales, and on the assemblages of species in relation to their properties, the local environment and their distribution in the region. Community ecology using ecoinformatics is related to bioinformatics, community ecology, biogeography and macroecology. We make clear how ecoinformatics in vegetation science and particularly the IAVS Working Group on Ecoinformatics has developed from the work of the old Working Group for Data Processing which was active during the 1970s and 1980s. Recent developments, including the creation of TURBOVEG and Syn Bio Sys in Europa and VEGBANK in the USA, form a direct link with these pioneer activities, both scientifically and personally. The contributions collected in this Special Feature present examples of seco‐infeveral types of the use of databases and the application of programmes and models. The main types are the study of long‐term vegetation dynamics in different cases of primary and secondary succession and the understanding of successional developments in terms of species traits. Among the future developments of great significance we mention the use of a variety of different large datasets for the study of the distribution and ecology and conservation of rare and threatened species.     

Fragment molecular orbital calculations for biomolecules

Exploring biomolecule behavior, such as proteins and nucleic acids, using quantum mechanical theory can identify many life science phenomena from first principles. Fragment molecular orbital (FMO) calculations of whole single particles of biomolecules can determine the electronic state of the interior and surface of molecules and explore molecular recognition mechanisms based on intermolecular and intramolecular interactions. In this review, we summarized the current state of FMO calculations in drug discovery, virology, and structural biology, as well as recent developments from data science.     

Anthropology and the Mining Arena in New Caledonia: Issues and Positionalities

In the last 25 years, the mining sector has become an important field of investigation and controversy for anthropologists. As an object, the ‘mine’ itself poses specific problems that make it particularly fertile ground for the exploration of inextricably linked theoretical, methodological, ethical, and political issues. In this paper, I explore the issue of the positionality of anthropologists within the mining arena. The analysis of positionality is taken beyond an individual perspective focusing on ethics, engagement and responsibility, to additionally include discussions of networking, alliance-building and institutionalising processes. I shall begin by dealing with the problems posed by the anthropology of mining and the various perspectives that respond to it. In the second section, I narrow the focus to the case of New Caledonia. In the third section, I present the context and challenges associated with the discussed cases. I portray the cases in question and, in particular, the new arena represented by the National Centre for Technological Research (CNRT) ‘Nickel and its Environment’, an agency established in 2008 to fund research on nickel in New Caledonia. The analysis in terms of a ‘hybrid’ forum of this arena will be complemented by the consideration of the social demand for the anthropology of mining. In the concluding section, the paper outlines options for further research while stressing the need for a balanced, ‘symmetrical’ approach of the multiple actors’ agendas constitutive of the mining arena.     

Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence,full structure,and active site microenvironment similarity

The development of accurate protein function annotation methods has emerged as a major unsolved biological problem. Protein similarity networks, one approach to function annotation via annotation transfer, group proteins into similarity-based clusters. An underlying assumption is that the edge metric used to identify such clusters correlates with functional information. In this contribution, this assumption is evaluated by observing topologies in similarity networks using three different edge metrics: sequence (BLAST), structure (TM-Align), and active site similarity (active site profiling, implemented in DASP). Network topologies for four well-studied protein superfamilies (enolase, peroxiredoxin (Prx), glutathione transferase (GST), and crotonase) were compared with curated functional hierarchies and structure. As expected, network topology differs, depending on edge metric; comparison of topologies provides valuable information on structure/function relationships. Subnetworks based on active site similarity correlate with known functional hierarchies at a single edge threshold more often than sequence- or structure-based networks. Sequence- and structure-based networks are useful for identifying sequence and domain similarities and differences; therefore, it is important to consider the clustering goal before deciding appropriate edge metric. Further, conserved active site residues identified in enolase and GST active site subnetworks correspond with published functionally important residues. Extension of this analysis yields predictions of functionally determinant residues for GST subgroups. These results support the hypothesis that active site similarity-based networks reveal clusters that share functional details and lay the foundation for capturing functionally relevant hierarchies using an approach that is both automatable and can deliver greater precision in function annotation than current similarity-based methods.     

Characterizing coal and mineral mines as a regional source of stress to stream fish assemblages

Mining impacts on stream systems have historically been studied over small spatial scales, yet investigations over large areas may be useful for characterizing mining as a regional source of stress to stream fishes. The associations between co-occurring stream fish assemblages and densities of various “classes” of mining occurring in the same catchments were tested using threshold analysis. Threshold analysis identifies the point at which fish assemblages change substantially from best available habitat conditions with increasing disturbance. As this occurred over large regions, species comprising fish assemblages were represented by various functional traits as well as other measures of interest to management (characterizing reproductive ecology and life history, habitat preferences, trophic ecology, assemblage diversity and evenness, tolerance to anthropogenic disturbance and state-recognized game species). We used two threshold detection methods: change-point analysis with indicator analysis and piecewise linear regression. We accepted only those thresholds that were highly statistically significant (p ≤ 0.01) for both techniques and overlapped within ≤5% error. We found consistent, wedge-shaped declines in multiple fish metrics with increasing levels of mining in catchments, suggesting mines are a regional source of disturbance. Threshold responses were consistent across the three ecoregions occurring at low mine densities. For 47.2% of the significant thresholds, a density of only ≤0.01 mines/km² caused a threshold response. In fact, at least 25% of streams in each of our three study ecoregions have mine densities in their catchments with the potential to affect fish assemblages. Compared to other anthropogenic impacts assessed over large areas (agriculture, impervious surface or urban land use), mining had a more pronounced and consistent impact on fish assemblages.     

Identification and engineering of the cytochalasin gene cluster from Aspergillus clavatus NRRL 1

Cytochalasins are a group of fungal secondary metabolites with diverse structures and bioactivities, including cytochalasin E produced by Aspergillus clavatus, which is a potent anti-angiogenic agent. Here, we report the identification and characterization of the cytochalasin gene cluster from A. clavatus NRRL 1. As a producer of cytochalasin E and K, the genome of A. clavatus was analyzed and the ∼30 kb ccs gene cluster was identified based on the presence of a polyketide synthase–nonribosomal peptide synthetases (PKS–NRPS) and a putative Baeyer–Villiger monooxygenase (BVMO). Deletion of the central PKS–NRPS gene, ccsA, abolished the production of cytochalasin E and K, confirming the association between the natural products and the gene cluster. Based on bioinformatic analysis, a putative biosynthetic pathway is proposed. Furthermore, overexpression of the pathway specific regulator ccsR elevated the titer of cytochalasin E from 25 mg/L to 175 mg/L. Our results not only shed light on the biosynthesis of cytochalasins, but also provided genetic tools for increasing and engineering the production.     

Shift in chicken intestinal gene association networks after infection with Salmonella

A primary infection of Salmonella enteritidis causes a spatial-temporal dependent change in the gene expression patterns in the intestine of chickens (Gallus gallus). This is the result of a dynamic intestinal response to adapt to the altered environment and to optimize its ‘health’ and functionality under the new circumstances. By inferring gene association networks (GANs), the complexities of and changes in biological networks can be uncovered. Within such GANs highly interacting (hub) genes can be identified, which are supposed to be high-level regulators connected to multiple processes. By exploring the intestinal expression of genes differing between control and Salmonella infected chicken in a time-dependent manner differences in GANs were found. In control chickens more developmental processes were observed, whereas in infected chickens relatively more processes were associated to ‘defense/pathogen response’. Moreover the conserved protein domains of the identified hub genes in controls were nuclear-associated, whereas hub genes in infected chickens were involved in ‘cellular communication’. The shift in topology and functionality of the intestinal GANs in control and Salmonella infected animals and the identification of GAN-specific hubs is a first step to understand the complexity of biological networks and processes regulating intestinal health and functionality under normal and disturbed conditions.