有机卤呼吸微生物菌群营养交互的作用机制

有机卤呼吸细菌(organohalide-respiringbacteria,OHRB)是污染场地土壤与地下水中厌氧降解及生物修复有机卤代污染物的主力军。微生物种群间的资源竞争、生长抑制、代谢交叉喂养(crossfeeding,即营养的动态交换,包括碳源、氮源、氨基酸、维生素、核苷酸、电子供体、电子受体和其他生长因子等)、水平基因转移及其他交互作用机制是群落结构稳定平衡的基础,有利于促进有机卤代污染物消减效率的最大化。本文围绕OHRB种群及与其他微生物种群间的互作机制(如交叉喂养机制、竞争机制及抑制机制等)进行了概述,并对未来互作机制的研究进行了探讨与展望,旨在为有机卤代物污染场地生物修复效率的提高提供科学理论和技术参考依据。     

Selective association of phospholipids as a clue for the passive flip-flop diffusion through bilayer lipid membranes

We showed that the investigation of the selective association of phospholipids might contribute to the insight of the flip-flop diffusion processes. The process of selective association was studied quantitatively by testing the association probabilities for both parallel and anti-parallel orientations of the polar headgroups. The model of double chain binary mixture confirms a high capacity of phospholipids for self-association in parallel configuration of the electric dipole moments whether the cross-sectional area of the polar headgroups are in an usual range of 25–55 Ų. It is demonstrated that the aggregation of a class of phospholipids from a binary mixture is strongly dependent on the dipole-dipole interaction between the same phospholipids and is modulated by the magnitude of the electric dipole moment of the other phospholipids from that binary mixture. There are a great number of mechanisms involved in the transbilayer movement of phospholipids. We referred here only to the passive transport of lipids from one monolayer to the other. The flip-flop mechanisms raised in this paper are the breakdown of bilayer due to the increase of the packing density and the inversion of the coupled phospholipids from the opposite monolayers of the same bilayer. Thus, the pair formation promoting a drop in occupied volume decreases the packing pressure in the respective monolayer and consequently triggers a flip-flop into the other direction since the packing pressure in the other monolayer has not dropped. According to the present model for the binary mixtures of double-chain lipids, the rate of the flip-flop diffusion decreased by increasing the number of the methylene groups added to the acyl chain. This dependence may be perturbed whether the phospholipids possesses a very high cross-section area of the polar headgroups (a > 55 Ų). We think that the selective association of phospholipids is neither exclusively, nor only involved in promoting the transbilayer diffusion of phospholipids. Most probably, the selective association determines some phospholipid domains that attract certain particular proteins so that it can modulate the protein activity.     

Study on the evaluation system of urban low carbon communities in Guangdong province

In recent years, China has been gradually consolidating the establishment of Low Carbon Communities (LCC) to minimize the emission of CO₂ and other greenhouse gasses. Guangdong Province, as one of the low-carbon pilot provinces, has also paid great attention to the building of LCC. However, currently Guangdong province, or even China as a whole, has no official evaluation system in place which can be employed to evaluate the degree of low carbon of urban LCC. This paper aimed to establish a system for evaluating the urban LCC of Guangdong Province based on their actual situations. The system divided the evaluation into six categories, applied the SMART criteria to select suitable indices, and set the reference values for two zones, i.e., the Pearl River Delta zone (PRD) and the non-PRD zone. Monte Carlo and AHP were combined for the calculation of index weights, thus ensuring that the weight judgment matrixes could all pass the consistency check. In addition, this paper also laid down detailed evaluation regulations to improve the operability of this system and guarantee its wide application and better generalization. Finally, one typical urban community was selected to test the operability of this system, and the One-At-a-Time (OAT) method was used to analyze the sensitivity of each index and explore the degree of influence of these indices on evaluation results. The results showed that three indicators corresponding to green building percentage, new energy vehicles percentage and low carbon public transportation had the highest sensitivity. After field test evaluation, the evaluation system was found to have strong operability, and a high accessibility to indicator data. This system cannot only be used as a tool by the Provincial People's Government of Guangdong to evaluate the construction progress and degree of low carbon in LCC, but can also provide a reference point and experience for the Chinese government to draw upon in establishing the evaluation system of LCC at a national level.     

On the use of split moving window analysis for boundary detection in ordered dataseries from benthic communities

The capacity of Split Moving Window (SMW) boundary analysis was tested to detect the depth of the transition of a littoral to a profundal invertebrate community in two datasets that were ordered along a depth gradient. The littoral community was dominated byPolypedilum nubeculosum agg.,Potamopyrgus jenkinsi andGlyptotendipes cf.pallens. The species richness of the profundal community was much lower. Its fauna was dominated byChironomus cf.plumosus andChaoborus flavicans. The transition could be detected with small window sizes. The discontinuities are located at the same depth as the oxygen stratification. We conclude that SMW can be used to study artificial transects. Noisy datasets should be transformed to reduce the variation. The scale dependence of SMW is an advantage. Information about the nature of a discontinuity (transition, trend or local discontinuity) can be obtained by increasing the window size. The location of discontinuities that are detected at the edge of a series, with large windows, should be interpreted carefully due to the existence of a blind zone.     

Approximate Confidence Bounds for Ripley's Statistic for Random Points in a Square

Confidence envelopes for Ripley's L function for N random points in the unit square were obtained by simulation. The 90, 95 and 99th percentiles of 1000 simulations are given in tabular form for N in the range 10 to 350. Results for a number of choices of the maximum interpoint distance are reported.     

Optimising sampling methods for small mammal communities in Neotropical rainforests

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The roles of stochasticity and biotic interactions in the spatial patterning of plant species in alpine communities

Questions

Plant community composition can be influenced by multiple biotic, abiotic, and stochastic factors acting on the local species pool to determine their establishment success and abundance and subsequently the diversity of the community. We asked if the influences of biotic interactions on the composition of plant species in communities, as indicated by patterns of plant species spatial associations (independent, positive or negative), vary across a productivity gradient within a single ecosystem type. Do dominant species of communities show spatial patterning suggestive of competitive interactions with interspecific neighbors? Do species that span multiple community types exhibit the same heterospecific interactions with neighbours in each community?

Location

Three alpine communities in the southern Rocky Mountains.

Methods

We measured the occurrence of species in a 1‐cm spatial grid within 2 m × 2 m plots to determine the spatial patterns of species pairs in the three communities. A null model of independent species spatial arrangements was used to determine whether species pairs were positively, negatively or independently associated, and how these patterns differed among the communities across the gradient of resource supply and environmental stress.

Results

Positive associations, indicative of facilitation between species, were most common in the most resource‐poor and least productive community. However negative associations, suggestive of competitive interactions among species, were not more common in the two more resource‐rich, productive communities. The dominant species of these communities did exhibit higher negative than positive associations with neighbours relative to positive patterning. Independent interspecific patterning was equally common relative to positive and negative patterns in all communities. Species that previously were shown to either facilitate other species or compete with neighbours exhibited spatial patterning consistent with the earlier experimental work.

Conclusions

A large number of species exhibit a lack of net biotic interactions, and stochastic factors appear to be as important as competition and facilitation in shaping the structure of the three alpine plant communities we studied.

     

Phenotypic plasticity as a clue for invasion success of the submerged aquatic plant Elodea nuttallii

• Two closely related alien submerged aquatic plants were introduced into Europe. The new invader (Elodea nuttallii) gradually displaced E. canadensis even at sites where the latter was well established. The aim of the study was to evaluate the combined effects of environmental factors on several phenotypic characteristics of the two Elodea species, and to relate these phenotypic characteristics to the invasion success of E. nuttallii over E. canadensis.
• In a factorial design, Elodea plants were grown in aquaria containing five different nitrogen concentrations and incubated at five different light intensities. We used six functional traits (apical shoot RGR), total shoot RGR, relative elongation, root length, lateral spread, branching degree) to measure the environmental response of the species. We calculated plasticity indices to express the phenotypic differences between species.
• Light and nitrogen jointly triggered the development of phenotypic characteristics that make E. nuttallii a more successful invader in eutrophic waters than E. canadensis. The stronger invader showed a wider range of phenotypic plasticity. The apical elongation was the main difference between the two species, with E. nuttallii being more than two times longer than E. canadensis. E. canadensis formed dense side shoots even under high shade and low nitrogen levels, whereas E. nuttallii required higher light and nitrogen levels.
• We found that under more eutrophic conditions, E. nuttallii reach the water surface sooner than E. canadensis and through intensive branching outcompetes all other plants including E. canadensis. Our findings support the theory that more successful invaders have wider phenotypic plasticity.

     

Comparing the performances of Diggle's tests of spatial randomness for small samples with and without edge-effect correction: application to ecological data

Diggle's tests of spatial randomness based on empirical distributions of interpoint distances can be performed with and without edge-effect correction. We present here numerical results illustrating that tests without the edge-effect correction proposed by Diggle (1979, Biometrics 35, 87-101) have a higher power for small sample sizes than those with correction. Ignoring the correction enables detection of departure from spatial randomness with smaller samples (down to 10 points vs. 30 points for the tests with correction). These results are confirmed by an example with ecological data consisting of maps of two species of trees in a West African savanna. Tree numbers per species per map were often less than 20. For one of the species, for which maps strongly suggest an aggregated pattern, tests without edge-effect correction enabled rejection of the null hypothesis on three plots out of five vs. on only one for the tests with correction.     

Strong postcranial size dimorphism in Australopithecus afarensis: results from two new resampling methods for multivariate data sets with missing data

There is considerable debate over the level of size dimorphism and inferred social behavior of Australopithecus afarensis. Most previous studies have analyzed size variation in single variables or multiple variables drawn from single elements. These approaches suffer from small sample sizes, underscoring the need for new techniques that incorporate measurements from multiple unassociated elements, reducing the influence of random sampling on size variation in fossil samples. One such technique, the template method, has recently been proposed but is limited to samples with a template specimen and is sensitive to a number of assumptions. Here we present two new resampling methods that do not require a template specimen, allow measurements from multiple unassociated elements to be included in a single analysis, and allow for significance tests between comparative and fossil multivariate data sets with missing data. Using these new methods, multivariate postcranial size dimorphism is measured using eight measurements of the femur, tibia, humerus, and radius in samples of A. afarensis, modern humans, chimpanzees, gorillas, and orangutans. Postcranial dimorphism in A. afarensis is similar to that of gorillas and orangutans, and significantly greater than in modern humans and chimpanzees. Because studies in living primates have examined the association of behavior with dimorphism in body mass and craniodental measurements, not postcrania, relationships between postcranial dimorphism and social behavior must be established to make robust behavioral inferences for A. afarensis. However, the results of this and past studies strongly suggest behavioral and mating strategies differed between A. afarensis and modern humans.     

Stability of microbial communities in goat milk during a lactation year: molecular approaches

The microbial communities in milks from one herd were evaluated during 1-year of lactation, using molecular methods to evaluate their stability and the effect of breeding conditions on their composition. The diversity of microbial communities was measured using two approaches: molecular identification by 16S and 18S rDNA sequencing of isolates from counting media (two milks), and direct identification using 16S rDNA from clone libraries (six milks). The stability of these communities was evaluated by counting on selective media and by Single Strand Conformation Polymorphism (SSCP) analysis of variable region V3 of the 16S rRNA gene and variable region V4 of the 18S rRNA gene. One hundred and eighteen milk samples taken throughout the year were analyzed. Wide diversity among bacteria and yeasts in the milk was revealed. In addition to species commonly encountered in milk, such as Lactococcus lactis, Lactococcus garvieae, Enterococcus faecalis, Lactobacillus casei, Leuconostoc mesenteroides, Staphylococcus epidermidis, Staphylococcus simulans, Staphylococcus caprae, Staphylococcus equorum, Micrococcus sp., Kocuria sp., Pantoea agglomerans and Pseudomonas putida, sequences were affiliated to other species only described in cheeses, such as Corynebacterium variabile, Arthrobacter sp., Brachybacterium paraconglomeratum, Clostridium sp. and Rothia sp. Several halophilic species atypical in milk were found, belonging to Jeotgalicoccus psychrophilus, Salinicoccus sp., Dietza maris, Exiguobacterium, Ornithinicoccus sp. and Hahella chejuensis. The yeast community was composed of Debaryomyces hansenii, Kluyveromyces lactis, Trichosporon beigelii, Rhodotorula glutinis, Rhodotorula minuta, Candida pararugosa, Candida intermedia, Candida inconspicua, Cryptococcus curvatus and Cryptococcus magnus. The analyses of microbial counts and microbial SSCP profiles both distinguished four groups of milks corresponding to four periods defined by season and feeding regime. The microbial community was stable within each period. Milks from winter were characterized by Lactococcus and Pseudomonas, those from summer by P. agglomerans and Klebsiella and those from autumn by Chryseobacterium indologenes, Acinetobacter baumanii, Staphylococcus, Corynebacteria and yeasts. However, the composition of the community can vary according to factors other than feeding. This study opens new investigation fields in the field of raw milk microbial ecology.     

TransPath: a computational method for locating ion transit pathways through membrane proteins

The finely tuned structures of membrane channel proteins allow selective passage of ions through the available aqueous pores. To understand channel function, it is crucial to locate the pores and study their physical and chemical properties. Here, we propose a new pore-searching algorithm (TransPath), which uses the Configurational Bias Monte Carlo (CBMC) method to generate transmembrane trajectories driven by both geometric and electrostatic features. The trajectories are binned into groups determined by a vector distance criterion. From each group, a representative trajectory is selected based on the Rosenbluth weight, and the geometrically optimal path is obtained by simulated annealing. Candidate ion pathways can then be determined by analysis of the radius and potential profiles. The proposed method and its implementation are illustrated using the bacterial KcsA potassium channel as an example. The procedure is then applied to the more complex structures of the bacterial E. coli chloride channel homolog and a homology model of the ClC-0 channel.     

Faunal assembly in chironomids (Diptera): generic association and spread

Faunal assembly in chironomids was analysed using published data in the fauna of three rivers in southern England and of Great Britain as a whole. Two questions, both relating to the generic composition of local faunal assemblages, were asked: (i) to what extent are faunas from different sites within a single geographical area associated in terms of the occurrence of genera ('generic association'); (ü) given the total number of species observed, is the number of different genera represented ('generic spread') more than would be expected by chance. The latter question relates to the hypothesis that if interspecific competition is a strong organizing force of local faunal assemblages, species would be more likely to occur as widely spread out among different genera, thus decreasing overlap in resource use and hence the possibility of outright competition. Null models of species occurrence were constructed through Monte Carlo simulation to evaluate quantitatively these two questions. Generic association of faunal assemblages from three localities was statistically significant, though there was some variation among different subfamilies of Chironomidae. No evidence of generic diversification (more genera occurring in the fauna than expected by chance) was found. These results and the original questions were given critical considerations in the discussion.     

Clump spacing in a desert dwarf shrub community

A Monte Carlo method based on Ripley's K function-a cumulative function related to the number of plants encountered at different distances from other plants-is used to test the null hypothesis of random distribution of shrub clumps in a desert dwarf shrub community in Namaqualand, South Africa, where Psilocaulon arenosum is the dominant shrub. The method takes into account the apparent regularity of pattern caused by the finite size (up to 2 m diameter) of the clumps. It is shown that the clump centres are significantly aggregated (compared to random expectation) at distances on the order of 1 m. Such aggregation is expected, as a simple result of regeneration near to seed sources, if the time between catastrophic droughts is short in relation to the time required for development of a non-aggregated or regular pattern determined by moisture competition. No significant regulatiry was detected at distances of 3 m or less. One subplot showed regularity above 3 m, but this pattern was not shown by the other subplot and may not be a competition effect. These results support a hypothesis of aggregation caused by regeneration pattern decaying slowly toward randomness as larger individuals compete.We thank C. J. F. ter Braak for suggesting the method of spatial analysis; 1. Noy-Meir, C. J. F. ter Braak and two unnamed reviewers for helpful comments; the Netherlands Science Research Council (ZWO) for financial support to I. C. Prentice (grant B84-218); and Prof. D. von Willert for material support to M. J. A. Werger.     

Configurational-bias sampling technique for predicting side-chain conformations in proteins

Prediction of side-chain conformations is an important component of several biological modeling applications. In this work, we have developed and tested an advanced Monte Carlo sampling strategy for predicting side-chain conformations. Our method is based on a cooperative rearrangement of atoms that belong to a group of neighboring side-chains. This rearrangement is accomplished by deleting groups of atoms from the side-chains in a particular region, and regrowing them with the generation of trial positions that depends on both a rotamer library and a molecular mechanics potential function. This method allows us to incorporate flexibility about the rotamers in the library and explore phase space in a continuous fashion about the primary rotamers. We have tested our algorithm on a set of 76 proteins using the all-atom AMBER99 force field and electrostatics that are governed by a distance-dependent dielectric function. When the tolerance for correct prediction of the dihedral angles is a <20 degrees deviation from the native state, our prediction accuracies for chi1 are 83.3% and for chi1 and chi2 are 65.4%. The accuracies of our predictions are comparable to the best results in the literature that often used Hamiltonians that have been specifically optimized for side-chain packing. We believe that the continuous exploration of phase space enables our method to overcome limitations inherent with using discrete rotamers as trials.     

A theoretical model for the association of amphiphilic transmembrane peptides in lipid bilayers

A theoretical model is proposed for the association of trans-bilayer peptides in lipid bilayers. The model is based on a lattice model for the pure lipid bilayer, which accounts accurately for the most important conformational states of the lipids and their mutual interactions and statistics. Within the lattice formulation the bilayer is formed by two independent monolayers, each represented by a triangular lattice, on which sites the lipid chains are arrayed. The peptides are represented by regular objects, with no internal flexibility, and with a projected area on the bilayer plane corresponding to a hexagon with seven lattice sites. In addition, it is assumed that each peptide surface at the interface with the lipid chains is partially hydrophilic, and therefore interacts with the surrounding lipid matrix via selective anisotropic forces. The peptides would therefore assemble in order to shield their hydrophilic residues from the hydrophobic surroundings. The model describes the self-association of peptides in lipid bilayers via lateral and rotational diffusion, anisotropic lipid-peptide interactions, and peptide-peptide interactions involving the peptide hydrophilic regions. The intent of this model study is to analyse the conditions under which the association of trans-bilayer and partially hydrophilic peptides (or their dispersion in the lipid matrix) is lipid-mediated, and to what extent it is induced by direct interactions between the hydrophilic regions of the peptides. The model properties are calculated by a Monte Carlo computer simulation technique within the canonical ensemble. The results from the model study indicate that direct interactions between the hydrophilic regions of the peptides are necessary to induce peptide association in the lipid bilayer in the fluid phase. Furthermore, peptides within each aggregate are oriented in such a way as to shield their hydrophilic regions from the hydrophobic environment. The average number of peptides present in the aggregates formed depends on the degree of mismatch between the peptide hydrophobic length and the lipid bilayer hydrophobic thickness: The lower the degree of mismatch is the higher this number is. Received: 30 December 1996 / Accepted: 9 May 1997     

Frailty modeling for spatially correlated survival data,with application to infant mortality in Minnesota

The use of survival models involving a random effect or 'frailty' term is becoming more common. Usually the random effects are assumed to represent different clusters, and clusters are assumed to be independent. In this paper, we consider random effects corresponding to clusters that are spatially arranged, such as clinical sites or geographical regions. That is, we might suspect that random effects corresponding to strata in closer proximity to each other might also be similar in magnitude. Such spatial arrangement of the strata can be modeled in several ways, but we group these ways into two general settings: geostatistical approaches, where we use the exact geographic locations (e.g. latitude and longitude) of the strata, and lattice approaches, where we use only the positions of the strata relative to each other (e.g. which counties neighbor which others). We compare our approaches in the context of a dataset on infant mortality in Minnesota counties between 1992 and 1996. Our main substantive goal here is to explain the pattern of infant mortality using important covariates (sex, race, birth weight, age of mother, etc.) while accounting for possible (spatially correlated) differences in hazard among the counties. We use the GIS ArcView to map resulting fitted hazard rates, to help search for possible lingering spatial correlation. The DIC criterion (Spiegelhalter et al., Journal of the Royal Statistical Society, Series B 2002, to appear) is used to choose among various competing models. We investigate the quality of fit of our chosen model, and compare its results when used to investigate neonatal versus post-neonatal mortality. We also compare use of our time-to-event outcome survival model with the simpler dichotomous outcome logistic model. Finally, we summarize our findings and suggest directions for future research.     

Pattern analysis in successional communities – An approach for studying shifts in ecological interactions

Abstract. Many ecological studies have addressed issues of vegetation spatial patterns in attempts to understand the processes generating them. We investigated changes in ecological processes during succession via the analysis of shrubs’ spatial patterns in a system of linear sand dunes, an arid ecosystem located in the Negev Desert in Israel during three consecutive years. We hypothesized that spatial patterns change from clustered to regular as succession progresses due to changes in the relative importance of facilitation and competition in this environment. In this ecosystem communities of early successional stages are frequently disturbed by high rates of sand movement, whereas in later successional stages sand stability is high. We mapped in the field individual shrubs on high‐resolution aerial photographs, and converted the digital images to a GIS data set. Using Ripley's K‐function we analysed spatial patterns at three levels: the single‐species level, among species and at the individual level, in three communities characterizing different successional stages. In the early successional communities we found clustered spatial patterns, in comparison with stable habitats where spatial patterns tended to be regular. We argue that these shifts in spatial patterns are indicative of the assumption that in this sand‐dune system ecological interactions change from facilitation to competition as succession progresses. Further, we argue that these interactions operate in different spatial scales at the different successional stages, and that the study of these processes should be conducted at the spatial scales specific to each community.