EFFICIENCY DYNAMICS ON SCALE-FREE NETWORKS WITH COMMUNITIES

The simple efficiency model is developed on scale-free networks with communities to study the effect of the communities in complex networks on efficiency dynamics. For some parameters, we found that the state of system will transit from a stagnant phase to a growing phase as the strength of community decreases.

The inhibitory effect of intestinal bacterial metabolite of ginsenosides on CYP3A activity

The intestinal bacterial metabolites of ginsenosides are responsible for the main pharmacological activities of ginseng. The purpose of this study was to find whether these metabolites influence hepatic metabolic enzymes and to predict the potential for ginseng-prescription drug interactions. Utilizing the probe reaction of CYP3A activity, testosterone 6beta-hydroxylation, the effects of derivatives of 20(S)-protopanaxadiol and 20(S)-protopanaxatriol families on CYP3A activity in rat liver microsomes were assayed. Our results showed that ginsenosides from the 20(S)-protopanaxadiol and 20(S)-protopanaxatriol family including Rb-1, Rb-2, Rc, Compound-K, Re, and Rg(1), had no inhibitory effect, whereas Rg(2), 20(S)-panaxatriol and 20(S)-protopanaxatriol exhibited competitive inhibitory activity against CVP3A activity in these microsomes with the inhibition constants (K) of 86.4+/-0.8mum, 1.7+/-0.1mum, and 3.2+/-0.2 mum, respectively. This finding demonstrates that differences in their chemical structure might influence the effects of ginsenosides on CYP3A activity and that ginseng-derived products might have potential for significant ginseng-drug interactions.

Thermokinetic investigation of effect of temperature on optimum NaCl concentration for petroleum bacterial growth

The power-time curves of growth of three strains of petroleum bacteria at different NaCl concentrations at 40.0 and 50.0 degreesC have been determined by using a 2277 Thermometric Thermal Activity Analyser. An equation of a power-time curve, ln[alphaP(K)/P(t) - 1] = ln[(alphaK - N-0)/N-0] - alphakt, was established based on the generalized logistic equation, where P(t) is the thermal power at time t, K the carrying capacity, P-K = P0K, P-0 the thermal power of one cell, N-0 the bacterial population at time zero, alpha = (k - D)/k. The method of four observed points with the same time interval was used to calculate the value of P-K. The growth rate constant k and the death rate constant D were calculated. The NaCl concentration of optimum growth rate of petroleum bacteria at 40.0 and 50.0 degreesC, respectively, have been obtained according to the curves k - D versus NaCl concentration, which are 0.26, 0.54 and 0.57 mol l(-1) for B-1, B-2 and B-3, respectively, at 50.0 degreesC, 0.26, 0.55 and 0.56 mol l(-1) for B-1, B-2 and B-3, respectively, at 40.0 degreesC. The results indicated that the effect of temperature on NaCl concentration of optimum growth rate was small. (C) 2002 Elsevier Science B.V. All rights reserved.

Rapid world wide depletion of predatory fish communities

Serious concerns have been raised about the ecological effects of industrialized fishing1, 2, 3, spurring a United Nations resolution on restoring fisheries and marine ecosystems to healthy levels4. However, a prerequisite for restoration is a general understanding of the composition and abundance of unexploited fish communities, relative to contemporary ones. We constructed trajectories of community biomass and composition of large predatory fishes in four continental shelf and nine oceanic systems, using all available data from the beginning of exploitation. Industrialized fisheries typically reduced community biomass by 80% within 15 years of exploitation. Compensatory increases in fast-growing species were observed, but often reversed within a decade. Using a meta-analytic approach, we estimate that large predatory fish biomass today is only about 10% of pre-industrial levels. We conclude that declines of large predators in coastal regions5 have extended throughout the global ocean, with potentially serious consequences for ecosystems5, 6, 7. Our analysis suggests that management based on recent data alone may be misleading, and provides minimum estimates for unexploited communities, which could serve as the ‘missing baseline’8 needed for future restoration efforts.

Profiling of Complex Microbial Populations by Denaturing Gradient Gel Electrophoresis Analysis of Polymerase Chain Reaction-Amplified Genes Coding for 16S rRNA

We describe a new molecular approach to analyzing the genetic diversity of complex microbial populations. This technique is based on the separation of polymerase chain reaction-amplified fragments of genes coding for 16S rRNA, all the same length, by denaturing gradient gel electrophoresis (DGGE). DGGE analysis of different microbial communities demonstrated the presence of up to 10 distinguishable bands in the separation pattern, which were most likely derived from as many different species constituting these populations, and thereby generated a DGGE profile of the populations. We showed that it is possible to identify constituents which represent only 1% of the total population. With an oligonucleotide probe specific for the V3 region of 16S rRNA of sulfate-reducing bacteria, particular DNA fragments from some of the microbial populations could be identified by hybridization analysis. Analysis of the genomic DNA from a bacterial biofilm grown under aerobic conditions suggests that sulfate-reducing bacteria, despite their anaerobicity, were present in this environment. The results we obtained demonstrate that this technique will contribute to our understanding of the genetic diversity of uncharacterized microbial populations.

Introduction to Molecular Analysis of Ectomycorrhizal Communities

A number of methods are available for those researchers considering the addition of molecular analyses of ectomycorrhizal (EcM) fungi to their research projects and weighing the various approaches they might take. Analyzing natural EcM fungal communities has traditionally been a highly skilled, time-consuming process relying heavily on exacting morphological characterization of EcM root tips. Increasingly powerful molecular methods for analyzing EcM communities make this area of research available to a much wider range of researchers. Ecologists can gain from the body of work characterizing EcM while avoiding the requirement for exceptional expertise by carefully combining elements of traditional methods with the more recent molecular approaches. A cursory morphological analysis can yield a traditional quantification of EcM fungi based on tip numbers, a unit with functional and historical significance. Ectomycorrhizal root DNA extracts may then be analyzed with molecular methods widely used for characterizing microbiota. These range from methods applicable only to the simple mixes resulting from careful morphotyping, to community-oriented methods that identify many types in mixed samples as well as provide an estimate of their relative abundances. Extramatrical hyphae in bulk soil can also be more effectively studied, extending characterization of EcM fungal communities beyond the rhizoplane. The trend toward techniques permitting larger sample sets without prohibitive labor and time requirements will also permit us to more frequently address the issues of spatial and temporal variability and better characterize the roles of EcM fungi at multiple scales.

Stable Isotope Probing:Linking Functional Activity to Specific Members of Microbial Communities

Linking organisms or groups of organisms to specific functions within natural environments is a fundamental challenge in microbial ecology. Advances in technology for manipulating and analyzing nucleic acids have made it possible to characterize the members of microbial communities without the intervention of laboratory culturing. Results from such studies have shown that the vast majority of soil organisms have never been cultured, highlighting the risks of culture-based approaches in community analysis. The development of culture-independent techniques for following the flow of substrates through microbial communities therefore represents an important advance. These techniques, collectively known as stable isotope probing (SIP), involve introducing a stable isotope-labeled substrate into a microbial community and following the fate of the substrate by extracting diagnostic molecular species such as fatty acids and nucleic acids from the community and determining which specific molecules have incorporated the isotope. The molecules in which the isotope label appears provide identifying information about the organism that incorporated the substrate. Stable isotope probing allows direct observations of substrate assimilation in minimally disturbed communities, and thus represents an exciting new tool for linking microbial identity and function. The use of lipids or nucleic acids as the diagnostic molecule brings different strengths and weaknesses to the experimental approach, and necessitates the use of significantly different instrumentation and analytical techniques. This short review provides an overview of the lipid and nucleic acid approaches, discusses their strengths and weaknesses, gives examples of applications in various settings, and looks at prospects for the future of SIP technology.