土壤-植物-大气连续体水热、CO2通量估算模型研究进展

土壤-植物-大气连续体(SPAC)水热、CO2通量的准确估算对理解陆地和大气的物质和能量交换过程有着重要意义.重点阐述了基于过程的土壤-植物-大气连续体水热、CO2通量模型,综述了统计模型、综合模型及基于遥感的模型的发展过程.其中水热通量统计模型包括基于温度和湿度以及基于温度和辐射的方法;CO2通量统计模型包括基于气候因子或蒸散因子以及基于光能利用率的方法.水热通量过程模型包括大叶、双源、多源和多层的水热传输物理模型;CO2通量过程模型包括叶片尺度及由大叶、双叶和多层方法扩展到冠层尺度的生理生态模型以及光合-蒸腾耦合模型.综合模型包括生物物理模型、生物化学模型和生物地理模型.统计模型形式简单,资料易得,对大范围的水热通量模拟具有指导意义;过程模型准确的揭示了水热和CO2通量传输的物理和生理过程,是大尺度综合模型的基础.未来生态系统水热、CO2通量估算模型将集成各种技术手段进行多尺度网络观测和大尺度机理模拟.     

8-Nitroxanthine,a product of myeloperoxidase,peroxynitrite, and activated human neutrophils,enhances generation of superoxide by xanthine oxidase

In biology, chiral recognition usually implies the ability of a protein, such as an enzyme or a drug receptor, to distinguish between the two enantiomeric forms of a chiral substrate or drug. Both diastereoisomerism and specific contacts between enzyme/receptor and substrate/drug are necessary. The minimum requirement is for four contact points including four nonplanar atoms (or groups of atoms) in both probe and target. The molecular models described by Easson and Stedman and by Ogston require three binding sites in a plane. A modified model with three binding sites in three dimensions is described. Under certain circumstances this model allows binding of both enantiomeric forms of a substrate or a drug. Enantiomer superposition of two enantiomers at an active site occurs in some specific cases (e.g., phenylalanine ammonia-lyase, isocitrate dehydrogenase) and is likely in others. The nature of enantiomer binding to racemase enzymes is discussed.     

APPLICATION OF LAVSOE,AN EUTROPHICATION MODEL,TO BLOEMHOF DAM

SUMMARY

In 1985 the Department of Water Affairs introduced an effluent phosphate standard of 1 mg l^?1 (as P) in seven potentially sensitive catchments. Although this is an uniform standard, permits can be granted for effluents to exceed the standard in cases where it can be shown that the impact of the effluent on the water environment will be negligible. This policy requires the ability to predict the trophic response of waterbodies to different P loads. Two types of models were evaluated for this purpose; i.e., simple mass balance models and complex ecological models. This paper reports the results of a study undertaken to evaluate one of the complex ecological models.

The LAVSOE model, an eutrophication model for shallow lakes which was developed in Denmark, was evaluated as a management tool for the control of eutrophication at Bloemhof Dam.

To ensure that the basic underlying principles of LAVSOE were well understood and the assumptions not violated, the evaluation of LAVSOE followed the same procedure as model development; i.e., model construction check, a priori sensitivity analysis, calibration and verification.

The aim of the model construction check was to assure that the model did what it was designed to do after it was transferred onto the Water Affairs mainframe. During this phase two additional features were added to LAVSOE to accommodate South African conditions.

The aim of the a priori sensitivity analysis was to rank the parameters in order of sensitivity.

The model was calibrated by means of a trial-and-error procedure because it was simple and had heuristic value. LAVSOE could not be calibrated successfully for simulating the observed nutrient dynamics and phytoplankton growth In Bloemhof Dam.

In this paper, the main structure and the major processes of the LAVSOE model are introduced. The results of the sensitivity analysis and the reason for the unsuccessful calibration of LAVSOE on Bloemhof Dam are discussed. Modifications to LAVSOE to make it more applicable to turbid systems is proposed.     

Dynamics of epileptic seizures: Evolution, spreading, and suppression

Dynamical properties of epileptic seizures are investigated using a recent compact continuum model for electric activity of the brain. Large amplitude limit cycles resembling electroencephalograms during epilepsy emerge when the system loses linear stability. Seizures that are confined to an onset area, or spread synchronously to other areas via spatial coupling, are studied and argued to be associated with clinical partial and secondarily generalized seizures, respectively. Suppression of such seizures is also demonstrated, which implies potential for future clinical applications.     

Meristems, metamers and modules and the development of shoot and root systems

BARLOW, P. W., 1989. Meristems, metamers and modules in the development of shoot and root systems . Root and shoot systems are hierarchical organizations whose levels are represented, in part, by cells and meristems. Meristems produce modules which in turn construct the architectural model. The latter is species specific and its structure depends on the geometrical interrelationships between the modular elements. The place of the metamer within this hierarchical scheme is discussed. Metamers derive directly from meristem activity and are externally recognizable as reiterated sub-units of the module. Another sub-unit of module construction, the cellular complex, or merophyte, is also a product of meristem activity, but, in contrast to the metamer, it is an internal, rather than an external, anatomical feature. Being cellular, it increases the ‘span’ of the cell level rather than constituting a level in its own right. Although the physical boundaries of metamer and merophyte can overlap, or even coincide, the two units belong to different conceptual schemes of module structure: the metamer is defined from a ‘classical’ morphological viewpoint, whereas the merophyte derives from a cellular conception of plant structure. Both the merophyte and the metamer have a role in clarifying the understanding of plant development since both provide insights into the functioning of the meristems from which they are derived and the structure of the module to which they contribute. For example, modules which lack an obvious metameric construction can usefully be analysed in terms of their merophytic organization. This is particularly true of roots of lower plants. Here, the merophytes reflect the presence and activity of a specialized meristematic apical cell. On the other hand, modules of higher plants, which lack such apical cells, also lack clearly defined merophytes, but their shoots have obvious metamers which reflect the activity of the meristem as a whole. It should be possible to represent the development of modules from cells, via their intermediate sub-structures of meristems and metamers, by means of formal languages of automata theory. One of these, a graphical algorithm (Petri net), is applied in this developmental context.     

Glucuronidation and sulfation of 7-hydroxycoumarin in liver matrices from human, dog, monkey, rat, and mouse

Summary Uridine 5′-diphospho-N-acetylgalactosamine glycosyltransferases (UGTs) and sulfotransferases (SULTs) are 2 phase II enzymes that are actively involved in detoxification processes as well as in drug metabolism. Compared with cytochrome P450 enzymes, the role of UGTs and SULTs in drug metabolism has received little attention. Liver microsomes, S9 fractions, and cryopreserved hepatocytes from human, dog, cynomolgus monkey, mouse, and rat were used as matrices in the study. Single compound, 7-hydroxycoumarin (7-HC), along with necessary cofactors was dosed into the matrices and incubated at 37° C; formation of two metabolites, 7-HC-glucuronide and 7-HC-sulfate, was determined with liquid chromatography with tandem mass spectrometry. Within the same species, the UGTs activities in microsomes and S9 fractions were comparable. In addition, UGTs activities in cryopreserved hepatocytes were lower than in the other matrices. Also, the SULTs activities were much higher in S9 fractions than in cryopreserved hepatocytes and microsomes. Species differences on UGTs and SULTs activities were also observed. The results indicated that S9 fractions, microsomes, and cryopreserved hepatocytes might be useful for UGTs metabolism study, whereas S9 fractions appear to be the most appropriate matrix for both UGTs and SULTs metabolism. Species differences with respect to phase II metabolism also need to be taken into consideration when selecting an in vitro system to evaluate various aspects of drug metabolism.     

Models and estimators linking individual-based and sample-based rarefaction,extrapolation and comparison of assemblages

Aims In ecology and conservation biology, the number of species counted in a biodiversity study is a key metric but is usually a biased underestimate of total species richness because many rare species are not detected. Moreover, comparing species richness among sites or samples is a statistical challenge because the observed number of species is sensitive to the number of individuals counted or the area sampled. For individual-based data, we treat a single, empirical sample of species abundances from an investigator-defined species assemblage or community as a reference point for two estimation objectives under two sampling models: estimating the expected number of species (and its unconditional variance) in a random sample of (i) a smaller number of individuals (multinomial model) or a smaller area sampled (Poisson model) and (ii) a larger number of individuals or a larger area sampled. For sample-based incidence (presence–absence) data, under a Bernoulli product model, we treat a single set of species incidence frequencies as the reference point to estimate richness for smaller and larger numbers of sampling units.Methods The first objective is a problem in interpolation that we address with classical rarefaction (multinomial model) and Coleman rarefaction (Poisson model) for individual-based data and with sample-based rarefaction (Bernoulli product model) for incidence frequencies. The second is a problem in extrapolation that we address with sampling-theoretic predictors for the number of species in a larger sample (multinomial model), a larger area (Poisson model) or a larger number of sampling units (Bernoulli product model), based on an estimate of asymptotic species richness. Although published methods exist for many of these objectives, we bring them together here with some new estimators under a unified statistical and notational framework. This novel integration of mathematically distinct approaches allowed us to link interpolated (rarefaction) curves and extrapolated curves to plot a unified species accumulation curve for empirical examples. We provide new, unconditional variance estimators for classical, individual-based rarefaction and for Coleman rarefaction, long missing from the toolkit of biodiversity measurement. We illustrate these methods with datasets for tropical beetles, tropical trees and tropical ants.Important findings Surprisingly, for all datasets we examined, the interpolation (rarefaction) curve and the extrapolation curve meet smoothly at the reference sample, yielding a single curve. Moreover, curves representing 95% confidence intervals for interpolated and extrapolated richness estimates also meet smoothly, allowing rigorous statistical comparison of samples not only for rarefaction but also for extrapolated richness values. The confidence intervals widen as the extrapolation moves further beyond the reference sample, but the method gives reasonable results for extrapolations up to about double or triple the original abundance or area of the reference sample. We found that the multinomial and Poisson models produced indistinguishable results, in units of estimated species, for all estimators and datasets. For sample-based abundance data, which allows the comparison of all three models, the Bernoulli product model generally yields lower richness estimates for rarefied data than either the multinomial or the Poisson models because of the ubiquity of non-random spatial distributions in nature.     

Loss of translational entropy in binding,folding, and catalysis

There is a loss of translational entropy associated with the formation of a complex between two molecules in solution. Estimation of this contribution is essential for understanding binding, protein-protein association, and catalysis. Based on the cell model of liquids, it is possible to estimate the loss of translational entropy in all these cases. The resulting formulas are straightforward, and the calculations are easy to perform. Comparison of the results with experimental data suggests that the proposed method provides estimates that are much more accurate than those obtained with existing methods. Proteins 28:144–149, 1997. © 1997 Wiley-Liss Inc.     

Dimensions,energetics, and denaturant effects of the protein unstructured state

Determining the energetics of the unfolded state of a protein is essential for understanding the folding mechanics of ordered proteins and the structure–function relation of intrinsically disordered proteins. Here, we adopt a coil‐globule transition theory to develop a general scheme to extract interaction and free energy information from single‐molecule fluorescence resonance energy transfer spectroscopy. By combining protein stability data, we have determined the free energy difference between the native state and the maximally collapsed denatured state in a number of systems, providing insight on the specific/nonspecific interactions in protein folding. Both the transfer and binding models of the denaturant effects are demonstrated to account for the revealed linear dependence of inter‐residue interactions on the denaturant concentration, and are thus compatible under the coil‐globule transition theory to further determine the dimension and free energy of the conformational ensemble of the unfolded state. The scaling behaviors and the effective θ‐state are also discussed.     

Structure,development and function of the branchial sieve of the common bream,Abramis brama,white bream,Blicca bjoerkna and roach,Rutilus rutilus

Synopsis The filter feeding organ of cyprinid fishes is the branchial sieve, which consists of a mesh formed by gill rakers and tiny channels on the gill arches. In order to establish its possible role during growth we measured the following morphological gill raker parameters over a range of sizes in three cyprinid fishes, bream, white bream and roach: inter raker distance, bony raker length, raker width, cushion length and channel width. At any given standard length common bream has the largest inter raker distance, roach the lowest and white bream is intermediate. In the comb model of filter feeding the inter raker distance is considered to be a direct measure of the mesh size and retention ability (= minimal size of prey that can be retained) of a filter. For the three species under study there is a conflict between the comb model and experimental data on particle retention. Lammens et al. (1987) found that common bream has a large retention ability whereas roach and white bream have a much smaller one. A new model, the channel model (Hoogenboezem et al. 1991) has been developed for common bream; in this model the lateral gill rakers can regulate the mesh size of the medial channels on the other side of the gill slit. The present data indicate that this model is not appropriate for white bream and roach. At any given standard length white bream and roach only reach 70% of the raker length of common bream, which means that in this model the gill slits should to be very narrow during filter feeding. The gill rakers consist of a bony raker and a fleshy cushion. The bony rakers have a rather long needle-like part outside the cushion in bream, but not in white bream and roach which have blunt gill rakers. Blunt gill rakers are not suited to reduce the diameter of the medial channels. The comb model seems more appropriate for white bream and roach, but doubts about the validity of this simple model remain. The sum of the areas of the medial channels is an approximation of the area through which water flows in the filter. This channel area therefore gives an impression of the capacity or flow rate of the filter. With this capacity estimation and an estimation of energy consumption we calculated an energy ratio of filter feeding. The energy ratio decreases with increasing standard length with an exponent close to the expected exponent of -0.40. The energy ratio is highest in bream, intermediate in white bream and lowest in roach.     

Subcellular topology of rat liver methionyl-, leucyl-, and arginyl-tRNA synthetases

We have investigated the distribution of methionyl-, leucyl-, and arginyl- tRNA synthetases in primary liver fractions obtained by differential centrifugation of homogenates in isotonic sucrose: 78-93% of synthetase activities are recovered in the cytosolic fraction. Microsomes contain only 4.8%, 19.4%, and 6.4% of the methionyl-, leucyl-, and arginyl-tRNA synthetases activities, respectively. This proportion increases up to 11.3%, 26.1%, and 20.7%, respectively, when the homogenization medium is supplemented with 5 mM Mg2+ and 25 mM K+. The presence of protease inhibitors in the homogenization medium does not increase the proportion of synthetases recovered in microsomes. After subfractionation of microsomes by isopycnic centrifugation, the distributions of the 3 synthetases display a second peak overlapping that of at a density of 1.12. In addition, methionyl- and leucyl- tRNA synthetases display a second peak overlapping that of RNA. This suggests that a small proportion of these synthetases (0.7% and 5.71% of total activities, respectively) bind to the d domain of the ER. The Golgi complex, the plasma membranes, and the peroxisomes lack aminoacyl-tRNA synthetase activity. The 3 synthetases are readily detached from membranes when intact microsomes are washed with 250 mM sucrose alone or containing 5 mM PPi, or 320 mM KCl. The binding of methionyl-tRNA synthetases to microsomes was measured in vitro, at 4 degrees C, with a sample of the cytosolic fraction as a source of synthetase. Microsomes stripped of their bound polysomes display a binding capacity that is not significantly different from that of unstripped microsomes. Even in the presence of cations, the amount of synthetase bound to the membranes remained low by comparison with the cytosolic content.     

Automatic real-time calibration,assessment, and maintenance of generic Raman models for online monitoring of cell culture processes

Raman spectroscopy is a multipurpose analytical technology that has found great utility in real-time monitoring and control of critical performance parameters of cell culture processes. As a process analytical technology (PAT) tool, the performance of Raman spectroscopy relies on chemometric models that correlate Raman signals to the parameters of interest. The current calibration techniques yield highly specific models that are reliable only on the operating conditions they are calibrated in. Furthermore, once models are calibrated, it is typical for the model performance to degrade over time due to various recipe changes, raw material variability, and process drifts. Maintaining the performance of industrial Raman models is further complicated due to the lack of a systematic approach to assessing the performance of Raman models. In this article, we propose a real-time just-in-time learning (RT-JITL) framework for automatic calibration, assessment, and maintenance of industrial Raman models. Unlike traditional models, RT-JITL calibrates generic models that can be reliably deployed in cell culture experiments involving different modalities, cell lines, media compositions, and operating conditions. RT-JITL is a first fully integrated and fully autonomous platform offering a self-learning approach for calibrating and maintaining industrial Raman models. The efficacy of RT-JITL is demonstrated on experimental studies involving real-time predictions of various cell culture performance parameters, such as metabolite concentrations, viability, and viable cell density. RT-JITL framework introduces a paradigm shift in the way industrial Raman models are calibrated, assessed, and maintained, which to the best of authors' knowledge, have not been done before.     

Competition among plants: Concepts, individual-based modelling approaches, and a proposal for a future research strategy

Competition is a key process in plant populations and communities. We thus need, if we are to predict the responses of ecological systems to environmental change, a comprehensive and mechanistic understanding of plant competition. Considering competition, however, only at the population level is not sufficient because plant individuals usually are different, interact locally, and can adapt their behaviour to the current state of themselves and of their biotic and abiotic environment. Therefore, simulation models that are individual-based and spatially explicit are increasingly used for studying competition in plant systems. Many different individual-based modelling approaches exist to represent competition, but it is not clear how good they are in reflecting essential aspects of plant competition. We therefore first summarize current concepts and theories addressing plant competition. Then, we review individual-based approaches for modelling competition among plants. We distinguish between approaches that are used for more than 10 years and more recent ones. We identify three major gaps that need to be addressed more in the future: the effects of plants on their local environment, adaptive behaviour, and below-ground competition. To fill these gaps, the representation of plants and their interactions have to be more mechanistic than most existing approaches. Developing such new approaches is a challenge because they are likely to be more complex and to require more detailed knowledge and data on individual-level processes underlying competition. We thus need a more integrated research strategy for the future, where empirical and theoretical ecologists as well as computer scientists work together on formulating, implementing, parameterization, testing, comparing, and selecting the new approaches.     

Networks, epidemics and vaccination through contact tracing

We consider a (social) network whose structure can be represented by a simple random graph having a pre-specified degree distribution. A Markovian susceptible-infectious-removed (SIR) epidemic model is defined on such a social graph. We then consider two real-time vaccination models for contact tracing during the early stages of an epidemic outbreak. The first model considers vaccination of each friend of an infectious individual (once identified) independently with probability ρ. The second model is related to the first model but also sets a bound on the maximum number an infectious individual can infect before being identified. Expressions are derived for the influence on the reproduction number of these vaccination models. We give some numerical examples and simulation results based on the Poisson and heavy-tail degree distributions where it is shown that the second vaccination model has a bigger advantage compared to the first model for the heavy-tail degree distribution.     

Clades, clans, and reciprocal monophyly under neutral evolutionary models

The Yule model and the coalescent model are two neutral stochastic models for generating trees in phylogenetics and population genetics, respectively. Although these models are quite different, they lead to identical distributions concerning the probability that pre-specified groups of taxa form monophyletic groups (clades) in the tree. We extend earlier work to derive exact formulae for the probability of finding one or more groups of taxa as clades in a rooted tree, or as ‘clans’ in an unrooted tree. Our findings are relevant for calculating the statistical significance of observed monophyly and reciprocal monophyly in phylogenetics.     

Extracellular regulation of VEGF: Isoforms,proteolysis, and vascular patterning

The regulation of vascular endothelial growth factor A (VEGF) is critical to neovascularization in numerous tissues under physiological and pathological conditions. VEGF has multiple isoforms, created by alternative splicing or proteolytic cleavage, and characterized by different receptor-binding and matrix-binding properties. These isoforms are known to give rise to a spectrum of angiogenesis patterns marked by differences in branching, which has functional implications for tissues. In this review, we detail the extensive extracellular regulation of VEGF and the ability of VEGF to dictate the vascular phenotype. We explore the role of VEGF-releasing proteases and soluble carrier molecules on VEGF activity. While proteases such as MMP9 can ‘release’ matrix-bound VEGF and promote angiogenesis, for example as a key step in carcinogenesis, proteases can also suppress VEGF's angiogenic effects. We explore what dictates pro- or anti-angiogenic behavior. We also seek to understand the phenomenon of VEGF gradient formation. Strong VEGF gradients are thought to be due to decreased rates of diffusion from reversible matrix binding, however theoretical studies show that this scenario cannot give rise to lasting VEGF gradients in vivo. We propose that gradients are formed through degradation of sequestered VEGF. Finally, we review how different aspects of the VEGF signal, such as its concentration, gradient, matrix-binding, and NRP1-binding can differentially affect angiogenesis. We explore how this allows VEGF to regulate the formation of vascular networks across a spectrum of high to low branching densities, and from normal to pathological angiogenesis. A better understanding of the control of angiogenesis is necessary to improve upon limitations of current angiogenic therapies.     

INBREEDING DEPRESSION IN A SELF-COMPATIBLE,ANDRODIOECIOUS CRUSTACEAN,EULIMNADIA TEXANA

The observation that offspring produced by the mating of close relatives are often less fit than those produced by matings between unrelated individuals (i.e., inbreeding depression) has commonly been explained in terms of the increased probability of expressing deleterious recessive alleles among inbred offspring (the partial dominance model). This model predicts that inbreeding depression should be limited in regularly inbreeding populations because the deleterious alleles that cause inbreeding depression (i.e., the genetic load) should be purged by regularly exposing these alleles to natural selection. We indirectly test the partial dominance model using four highly inbred populations of an androdioecious crustacean, the clam shrimp Eulimnadia texana. These shrimp are comprised of males and hermaphrodites, the latter capable of either self-fertilizing or mating with a male (i.e., outcrossing between hermaphrodites is impossible). Hermaphrodites are further subdivided into monogenics (produced via self-fertilization) and amphigenics (produced via self-fertilization or outcrossing). Electrophoretic evidence suggests significant differences in heterozygosity among populations, but that selfing rates were not statistically different (average s = 0.67). Additional electrophoretic analyses reveal that three previously described sex-linked loci (Fum, Idh-1, and Idh-2) are all tightly linked to each other, with crossing over on the order of 1% per generation. Although selfing rates are clearly high, we present evidence that early inbreeding depression (hatching rates, juvenile survival, and age at sexual maturity) exists in all four populations. For all of these factors, inbreeding depression was inferred by the positive correlation of multilocus heterozygosity and fitness. Cumulative inbreeding depression (8) is between 0.41 and 0.47 across all populations, which appears to be too low to limit the effects of purging via identity disequilibrium. Instead, we suggest that the maintenance of inbreeding depression in these populations is due to the observed linkage group, which we suggest contains a large number of genes including many related to fitness. Segregation of such a large linkage group would explain our observations of the predominance of amphigenic hermaphrodites in our field samples and of survival differences between monogenics and amphigenics within selfed clutches. We propose that a modified form of the overdominance model for inbreeding depression operating at the level of linkage groups maintains the observed levels of inbreeding depression in these populations even in the face of high rates of selfing.     

Monitoring occurrence,extinction, and colonization probabilities for gibbon populations

All gibbon species (Family: Hylobatidae) are considered threatened with extinction and recognized on the International Union for Conservation of Nature Red List of Threatened Species. Because gibbons are one of the most threatened families of primates, monitoring their status is now critically important. Long-term monitoring programs applying occupancy approaches, in addition to assessing occurrence probability, improves understanding of other population parameters such as site extinction or colonization probabilities, which elucidate temporal and spatial changes and are therefore important for guiding conservation efforts. In this study, we used multiple season occupancy models to monitor occurrence, extinction, and colonization probabilities for northern yellow-cheeked crested gibbon Nomascus annamensis in three adjacent protected areas in the Central Annamites mountain range, Vietnam. We collected data at 30 listening posts in 2012, 2014, and 2016 using the auditory point count method. Occurrence probabilities were highest in 2012 (0.74, confidence interval [CI]: 0.56–0.87) but slightly lower in 2014 (0.66, CI: 0.51–0.79) and 2016 (0.67, CI: 0.49–0.81). Extinction probabilities during the 2012–2014 and 2014–2016 intervals were 0.26 (0.14–0.44) and 0.25 (0.12–0.44), respectively. Colonization probabilities during 2012–2014 were 0.44 (0.19–0.73) and between 2014 and 2016 was 0.51 (0.26–0.75). Although local site extinctions have occurred, high recolonization probability helped to replenish the unoccupied sites and kept the occurrence probability stable. Long-term monitoring programs which use occurrence probability alone might not fully reveal the true dynamics of gibbon populations. We strongly recommend including multiple season occupancy models to monitor occurrence, extinction, and colonization probabilities in long-term gibbon monitoring programs.