水域生态学中生物稳定同位素样品采集、处理与保存

稳定同位素分析技术由于能够刻画复杂的食物网结构并追踪食物网中的能量流而成为水域生态学研究中的重要手段。但是当水生生物样品采集、处理和保存过程中存在不确定性时, 营养关系分析中的同位素结果可能会产生误导性解释。文章采用数据模拟分析和文献总结的方法, 研究了水域生态系统中样品采集、处理和保存对于稳定同位素的影响, 概括性地建议了水域生态系统中适合应用稳定同位素分析技术开展生态学研究的样品采集、处理和保存的注意事项。但今后仍需进一步评估样品采集、处理和保存对稳定同位素比值的影响效果, 确定化学动力学在水生生物样品采集、处理和保存中的作用, 以进一步完善水生生物样品的采集、处理和保存稳定同位素生态学研究规范。     

Tables of dose conversion coefficients for estimating internal and external radiation exposures to terrestrial and aquatic biota

Dose conversion coefficients (DCCs) for assessment of internal and external radiation exposures to terrestrial and aquatic biota are compiled for 75 radionuclides, for 14 terrestrial and 22 aquatic reference organisms. DCC values for internal exposure are calculated based on a homogeneous distribution of the radionuclides in both types of organisms. DCC values for external exposure of aquatic organisms are calculated for complete immersion in water. For external exposure of terrestrial organisms the soil is considered as a planar and homogenously contaminated volume source with a surface roughness of 3 mm and a thickness of 10 cm, respectively. For in-soil-organisms, DCC values for external exposure are given assuming that these organisms live in the middle of a uniformly contaminated 50 cm-thick soil layer. The tables can be used for assessment of exposures of animals and plants living in various habitats. The list of considered organisms covers the Reference Animals and Plants as adopted by the ICRP.     

Protein targeting into plastids: a key to understanding the symbiogenetic acquisitions of plastids

Recent progress in molecular phylogenetics has proven that photosynthetic eukaryotes acquired plastids via primary and secondary endosymbiosis and has given us information about the origin of each plastid. How a photosynthetic endosymbiont became a plastid in each group is, however, poorly understood, especially for the organisms with secondary plastids. Investigating how a nuclear-encoded plastid protein is targeted into a plastid in each photosynthetic group is one of the most important keys to understanding the evolutionary process of symbiogenetic plastid acquisition and its diversity. For organisms which originated through primary endosymbiosis, protein targeting into plastids has been well studied at the molecular level. For organisms which originated through secondary endosymbiosis, molecular-level studies have just started on the plastid-targeted protein-precursor sequences and the targeting pathways of the precursors. However, little information is available about how the proteins get across the inner two or three envelope membranes in organisms with secondary plastids. A good in vitro protein-import system for isolated plastids and a cell transformation system must be established for each group of photosynthetic eukaryotes in order to understand the mechanisms, the evolutionary processes and the diversity of symbiogenetic plastid acquisitions in photosynthetic eukaryotes.     

Theoretical aspects of enzyme induction and inhibition leading to the reversal of resistance to biocides

The well-known phenomena of enzyme induction and inhibition have been applied in the enunciation of two mechanisms which could be used in the reversal of resistance which organisms develop towards biocides (drugs and pesticides) in many cases. For those biocides active per se which are metabolized by inducible enzymes to non-toxic metabolites, resistant organisms would be those possessing high levels of drug-metabolizing enzymes (Mechanism 1). For those biocides inactive per se but requiring metabolic activation for activity, resistant organisms would be those possessing low levels of drug metabolizing enzymes (Mechanism 2). In mechanism 1, the addition of enzyme inhibitors to the biocide would be effective in reversing resistance. In mechanism 2 the addition of an enzyme inducer to the biocide would increase the susceptibility of the resistant organisms. An ectoparasite insecticide 2-chloro-1-(2,4 dichlorophenyl) vinyl diethylphosphate (chlorfenvinphos or supona) is used as an example for mechanism 1. The malarial drugs primaquine and chloroquine are used as examples of mechanism 2.     

Biolistic transformation of arbuscular mycorrhizal fungi

Gene transfer systems have proved effective for the transformation of a range of organisms for both fundamental and applied studies. Biolistic transformation is a powerful method for the gene transfer into various organisms and tissues that have proved recalcitrant to more conventional means. For fungi, the biolistic approach is particularly effective where protoplasts are difficult to obtain and/or the organisms are difficult to culture. This is particularly applicable to arbuscular mycorrhizal (AM) fungi, being as they are obligate symbionts that can only be propagated in association with intact plants or root explants. Furthermore, these fungi are aseptate and protoplasts cannot be released. Recent advancements in gene transformation systems have enabled the use of biolistic technology to introduce foreign DNA linked to molecular markers into these fungi. In this review we discuss the development of transformation strategies for AM fungi by biolistics and highlight the areas of this technology which require further development for the stable transformation of these elusive organisms.     

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.     

Statistical measures for defining an individual's degree of independence within state-dependent dynamic games

Background  

For organisms living or interacting in groups, the decision-making processes of an individual may be based upon aspects of both its own state and the states of other organisms around it. Much research has sought to determine how group decisions are made, and whether some individuals are more likely to influence these decisions than others. State-dependent modelling techniques are a powerful tool for exploring group decision-making processes, but analyses conducted so far have lacked methods for identifying how dependent an individual's actions are on the rest of the group.     

Saccharomyces cerevisiae as a model organism: a comparative study

Background

Model organisms are used for research because they provide a framework on which to develop and optimize methods that facilitate and standardize analysis. Such organisms should be representative of the living beings for which they are to serve as proxy. However, in practice, a model organism is often selected ad hoc, and without considering its representativeness, because a systematic and rational method to include this consideration in the selection process is still lacking.

Methodology/Principal Findings

In this work we propose such a method and apply it in a pilot study of strengths and limitations of Saccharomyces cerevisiae as a model organism. The method relies on the functional classification of proteins into different biological pathways and processes and on full proteome comparisons between the putative model organism and other organisms for which we would like to extrapolate results. Here we compare S. cerevisiae to 704 other organisms from various phyla. For each organism, our results identify the pathways and processes for which S. cerevisiae is predicted to be a good model to extrapolate from. We find that animals in general and Homo sapiens in particular are some of the non-fungal organisms for which S. cerevisiae is likely to be a good model in which to study a significant fraction of common biological processes. We validate our approach by correctly predicting which organisms are phenotypically more distant from S. cerevisiae with respect to several different biological processes.

Conclusions/Significance

The method we propose could be used to choose appropriate substitute model organisms for the study of biological processes in other species that are harder to study. For example, one could identify appropriate models to study either pathologies in humans or specific biological processes in species with a long development time, such as plants.     

Dispersion and natural-enemy action

Animal dispersion was defined by Wynne-Edwards (1962) as 'the placement of individuals and groups of individuals within the habitats they occupy, and the processes by which this is brought about'. This paper deals with a limited aspect of this theme, namely with the influence of the dispersion of host or enemy individuals on their mutual interaction. Obviously, there can only be a relation between feeding organisms and food, between killer and victim, if they coincide in space and in time. Thus, what first seemed to be a limited topic evolves as one of the basic chapters of relations among organisms, that of coincidence (cf. Thalenhorst, 1951). It seems to be impossible to deal with space coincidence here without mentioning time coincidence, too. Recognizing the tremendous amount of information available on this subject, I should like to give some examples only, first on enemy action without man's interference and secondly on human action which either favours or disrupts space coincidence of both groups of organisms. For the sake of brevity, the term host will be frequently used for host and prey together and examples will mostly refer to insects.     

Using neural networks for prediction of the subcellular location of proteins.

Neural networks have been trained to predict the subcellular location of proteins in prokaryotic or eukaryotic cells from their amino acid composition. For three possible subcellular locations in prokaryotic organisms a prediction accuracy of 81% can be achieved. Assigning a reliability index, 33% of the predictions can be made with an accuracy of 91%. For eukaryotic proteins (excluding plant sequences) an overall prediction accuracy of 66% for four locations was achieved, with 33% of the sequences being predicted with an accuracy of 82% or better. With the subcellular location restricting a protein's possible function, this method should be a useful tool for the systematic analysis of genome data and is available via a server on the world wide web.     

Factors affecting the lytic susceptibility of some marine and terrestrial bacteria

Eighteen gram-negative marine bacteria and two terrestrial species, Escherichia coli and Pseudomonas aeruginosa, were examined for their sensitivity to lysis in distilled water after exposure to a salt solution containing a sea water concentration of Mg2+ (0.05 M) or to 0.5 M NaCl. A spectrum of lytic susceptibility was observed among the marine bacteria ranging from those organisms which lysed in distilled water after exposure to the Mg2+-containing solution, through organisms which could be sensitized to lysis by washing with the NaCl solution, to organisms which failed to lyse in distilled water even after having been washed with a solution of 0.5 M NaCl. Pseudomonas aeruginosa and E. coli fell within this spectrum, the former being capable of being induced to lyse in distilled water by washing with 0.5 M NaCl, while the latter failed to lyse in distilled water after this treatment. It was thus concluded that no overall distinction could be made between marine and terrestrial bacteria on the basis of the sensitivity of the two groups of organisms to lysis in freshwater. Quite large decreases in optical density and increases in the release of ultraviolet-absorbing material took place when cells preexposed to the Mg2+-containing solution or to 0.5 M NaCl were subsequently suspended in distilled water even though in some cases no loss of cell numbers could be detected. In most cases two to three times as much K+ as Na+ and 1/10 to 1/100 as much Mg2+ was required to prevent these changes. For three of the marine bacteria and P. aeruginosa grown in a terrestrial type medium little difference in the requirements for Na+ and K+ to prevent the optical density changes was noted. For P. aeruginosa grown in a marine type medium, cells required more K+ than Na+ to prevent these changes.     

Direct Determination of Activities for Microorganisms of Chesapeake Bay Populations

We used three methods in determination of the metabolically active individual microorganisms for Chesapeake Bay surface and near-bottom populations over a period of a year. Synthetically active bacteria were recognized as enlarged cells in samples amended with nalidixic acid and yeast extract and incubated for 6 h. Microorganisms with active electron transport systems were identified by the reduction of a tetrazolium salt electron acceptor. Microorganisms active in uptake of amino acids, thymidine, and acetate were determined by microautoradiography. In conjunction with enumeration of active organisms, a total direct count was made for each sample preparation by epifluorescence microscopy. For the majority of samples, numbers of amino acid uptake-active organisms were greater than numbers of organisms determined to be active by other direct measurements. Within a sample, the numbers of uptake-active organisms (amino acids or thymidine) and electron transport system-active organisms were significantly different for 68% of the samples. Numbers of synthetically active bacteria were generally less than numbers determined by the other direct activity measurements. The distribution of total counts in the 11 samplings showed a seasonal pattern, with significant dependence on in situ water temperature, increasing from March to September and then decreasing through February. Synthetically active bacteria and amino acid uptake-active organisms showed a significant dependence on in situ temperature, independent of the function of temperature on total counts. Numbers of active organisms determined by at least one of the methods used exceeded 25% of the total population of all samplings, and from June through September, >85% of the total population was found to be active by at least one direct activity measurement. Thus, active rather than dormant organisms compose a major portion of the microbial population in this region of Chesapeake Bay.     

Discovering lactic acid bacteria by genomics

This review summarizes a collection of lactic acid bacteria that are now undergoing genomic sequencing and analysis. Summaries are presented on twenty different species, with each overview discussing the organisms fundamental and practical significance, nvironmental habitat, and its role in fermentation, bioprocessing, or probiotics. For those projects where genome sequence data were available by March 2002, summaries include a listing of key statistics and interesting genomic features. These efforts will revolutionize our molecular view of Gram–positive bacteria, as up to 15 genomes from the low GC content lactic acid bacteria are expected to be available in the public domain by the end of 2003. Our collective view of the lactic acid bacteria will be fundamentally changed as we rediscover the relationships and capabilities of these organisms through genomics.     

The elemental stoichiometry of aquatic and terrestrial ecosystems and its relationships with organismic lifestyle and ecosystem structure and function: a review and perspectives

C, N and P are three of the most important elements used to build living beings, and their uptake from the environment is consequently essential for all organisms. We have reviewed the available studies on water, soils and organism elemental content ratios (stoichiometry) with the aim of identifying the general links between stoichiometry and the structure and function of organisms and ecosystems, in both aquatic and terrestrial contexts. Oceans have variable C:N:P ratios in coastal areas and a narrow range approximating the Redfield ratio in deep water and inner oceanic areas. Terrestrial ecosystems have a general trend towards an increase in soil and plant N:P ratios from cool and temperate to tropical ecosystems, but with great variation within each climatic area. The C:N:P content ratio (from now on C:N:P ratio) is more constrained in organisms than in the water and soil environments they inhabit. The capacity to adjust this ratio involves several mechanisms, from leaf re-absorption in plants to the control of excretion in animals. Several differences in C:N:P ratios are observed when comparing different taxa and ecosystems. For freshwater ecosystems, the growth rate hypothesis (GRH), which has consistent experimental support, states that low N:P supply determines trophic web structures by favoring organisms with a high growth rate. For terrestrial organisms, however, evidence not yet conclusive on the relevance of the GRH. Recent studies suggest that the N:P ratio could play a role, even in the evolution of the genomes of organisms. Further research is warranted to study the stoichiometry of different trophic levels under different C:N:P environment ratios in long-term ecosystem-scale studies. Other nutrients such as K or Fe should also be taken into account. Further assessment of the GRH requires more studies on the effects of C:N:P ratios on anabolic (growth), catabolic (respiration), storage and/or defensive allocation. Combining elemental stoichiometry with metabolomics and/or genomics should improve our understanding of the coupling of different levels of biological organization, from elemental composition to the structure and evolution of ecosystems, via cellular metabolism and nutrient cycling.     

Biocontrol agents of Botrytis cinerea tested in climate chambers by making artificial infection on tomato leafs

To reduce the use of chemical agents, that are causing damage to the environment, in the fight against Botrytis cinerea, different BCA's were tested for their possibility to control Botrytis cinerea in a biological way. In order to investigate the effectiveness of the different micro organisms and Elot-Vis, experiments were carried out in climate chambers with 5 weeks old tomato plants. Leafs on the plant were inoculated with drops of a suspension that contained spores of Botrytis cinerea. The possible antagonists that were tested in these experiments were Trichoderma harzianum (Trichodex), T. asperellum (Biofungus), T. hamatum (T382), Bacillus subtilis (Serenade and Phytovit) and Pseudomonas aeruginosa (7NSK2 and KMPCH). For all these different micro organisms the direct and the indirect influence on Botrytis cinerea was investigated. In tests where the direct influence of the antagonists was examined, the spores of the moulds or the bacteria were suspended together with spores of Botrytis cinerea and subsequently drops of this suspension were pippeted on the leafs. After a while by ideal circumstances for Botrytis cinerea the infections on the inoculated leafs were counted. For the indirect influence of the antagonists, also leafs of 5 weeks old tomato plants were inoculated with a suspension of Botrytis cinerea spores. The roots of the tomato plants that were used for testing the indirect influence were treated during there growth with a suspension of the antagonist to see if induced systemic resistance pathway (ISR) was activated. For testing the effectiveness of Elot-Vis, tomato plants were sprayed a few times with a solution of this product during their growth. Results of the climate chamber test of the plants that were treated with Elot-Vis, showed a reduction of Botrytis cinerea infections on the inoculated leafs. Biological control agents seem to be not always very effective against Botrytis cinerea. The biological control agents that are containing micro organisms are also depending on the circumstances of the environment for an optimal development. These conditions are not always that optimal to compete with Botrytis cinerea or other micro organisms that are present on the plant.     

Widespread fluorescence in terrestrial and marine samples investigated from India

The discovery of green fluorescent protein (GFP) from jellyfish Aequorea victoria has provoked numerous studies to unveil the myriads of biomedical applications. Consequently, several studies also revealed the prevalence of fluorescence in different marine and terrestrial organisms. However, since GFP's discovery or the Nobel prize award on GFP, the fluorescence has not been explored so far from India. The current study presents the widespread fluorescent organisms resources available in India for biomedical and toxicological applications. Fluorescence emission from different plant and animal components were examined by direct observations using UV torchlight. Investigation revealed that blue light excited fluorescence in several organisms. For the first time, this study observed GFP like fluorescence in many terretrial and marine organisms of India. Observations are indicating that fluorescent proteins have essential ecological functions that are yet to be determined. The examined plant and animal components were not bioluminescent. In comparison, the potential untouched research areas on fluorescence aspects are detailed. A thorough review of fluorescent organisms reported hitherto is also provided to spread the current knowledge on fluorescence.     

Isolation and characterization of fecal bacteria capable of 16 alpha-dehydroxylating corticoids.

For more than a decade it has been known that the fecal flora of humans and rats includes organisms capable of 16 alpha-dehydroxylating corticoids, but their identity has remained unknown. To isolate these organisms, Mueller-Hinton agar plates were seeded with fresh feces from Proteus-free rats and incubated anaerobically. On an average, 1 of every 35 colonies consisted of organisms synthesizing 16 alpha-dehydroxylase. Isolation of the individual colonies yielded two obligate anerobes, strains 144 and 146, which elaborated the enzyme. The steroid transformation could be attained by the microbial culture alone in prereduced media or in aerobic media in the presence of Escherichia coli. Although both strains were phenotypically similar to Eubacterium lentum, they differed between themselves in their enzymatic equipment.     

Radiation: microbial evolution, ecology, and relevance to mars missions

Ultraviolet (UV) radiation has been an important environmental parameter during the evolution of life on Earth, both in its role as a mutagen and as a selective agent. This was probably especially true during the time from 3.8 to 2.5 billion years ago, when atmospheric ozone levels were less than 1% of present levels. Early Mars may not have had an "ozone shield" either, and it never developed a significant one. Even though Mars is farther away from the Sun than the Earth, a substantial surficial UV flux is present on Mars today. But organisms respond to dose rate, and on Mars, like on Earth, organisms would be exposed to diurnal variations in UV flux. Here we present data on the effect of diurnal patterns of UV flux on microbial ecosystems in nature, with an emphasis on photosynthesis and DNA synthesis effects. These results indicate that diurnal patterns of metabolism occur in nature with a dip in photosynthesis and DNA synthesis in the afternoon, in part regulated by UV flux. Thus, diurnal patterns must be studied in order to understand the effect of UV radiation in nature. The results of this work are significant to the success of human missions to Mars for several reasons. For example, human missions must include photosynthetic organisms for food production and likely oxygen production. An evolutionary approach suggests which organisms might be best suited for high UV fluxes. The diurnal aspect of these studies is critical. Terraforming is a potential goal of Mars exploration, and it will require studies of the effect of Martian UV fluxes, including their diurnal changes, on terrestrial organisms. Such studies may suggest that diurnal changes in UV only require mitigation at some times of day or year.     

Bacteria as a new model system for aging studies: investigations using light microscopy

Aging-the decline in an individual's condition over time-is at the center of an active research field in medicine and biology. Some very basic questions have, however, remained unresolved, the most fundamental being: do all organisms age? Or are there organisms that would continue to live forever if not killed by external forces? For a long time it was believed that aging only affected organisms such as animals, plants, and fungi. Bacteria, in contrast, were assumed to be potentially immortal and until recently this assertion remained untested. We used phase-contrast microscopy (on an Olympus BX61) to follow individual bacterial cells over many divisions to prove that some bacteria show a distinction between an aging mother cell and a rejuvenated daughter, and that these bacteria thus age. This indicates that aging is a more fundamental property of organisms than was previously assumed. Bacteria can now be used as very simple model system for investigating why and how organisms age.