浅水湖泊生态系统稳态转换的阈值判定方法

浅水湖泊生态系统对人类干扰的反应会随着干扰力度的改变或增强而出现突然的变化,即发生稳态转换;对其机理和驱动机制的揭示将有助于对湖泊富营养化的控制及恢复.基于“多稳态”理论的稳态转换研究已广泛开展,但对浅水湖泊生态系统稳态转换的驱动机制结论各异,采用的阈值判定方法相差很大,主要有实验观测、模型模拟和统计分析3种.实验观测多关注少数特定指标,指标筛选过程复杂且工作量大;模型模拟虽能从较为全面的尺度上理解生态系统稳态变化的特征和主要机理过程,但在模型误差和不确定性的处理等问题上尚存在不足;统计分析方法基于对长时间序列数据的统计变化规律分析,用以判断或者预警稳态转换现象的发生,是目前最为常用的方法.目前稳态转换领域的研究大都是对已发生的稳态转换进行机制分析或过程反演,对未来预测与预警的问题仍然亟需加强.     

Fluctuation Induces Evolutionary Branching in a Mathematical Model of Ecosystems

Ecological systems are always subjected to various environmental fluctuations. They evolve under these fluctuations and the resulting systems are robust against them. The diversity in ecological systems is also acquired through the evolution. How do the fluctuations affect the evolutionary processes? Do the fluctuations have direct impact on the species diversity in ecological systems? In the present paper, we investigate the relation between the environmental fluctuation and the evolution of species diversity with a mathematical model of evolutionary ecology. In the model, individual organisms compete for a single restricted resource and the temporal fluctuation in the resource supply is introduced as the environmental fluctuation. The evolutionary process is represented by the mutational change of genotypes which determines their resource utilization strategies. We found that when the environmental state is switched form static to fluctuating conditions, the initial closely related population distributed around the genotype adapted for the static environment is destabilized and divided into two groups in the genotype space; i.e., the evolutionary branching is induced by the environmental fluctuation. The consequent multiple species structures is evolutionary stable at the presence of the fluctuation. We perform the evolutionary invasion analysis for the phenomena and illustrate the mechanisms of the branchings. The results indicate a novel process of increasing the species diversity via evolutionary branching, and the analysis reveals the mechanisims of the branching preocess as the response to the environmental fluctuation. The robustness of the evolutionary process is also discussed.     

Observation volumes and {gamma}-factors in two-photon fluorescence fluctuation spectroscopy

Fluorescence fluctuation spectroscopy has become an important measurement tool for investigating molecular dynamics, molecular interactions, and chemical kinetics in biological systems. Although the basic theory of fluctuation spectroscopy is well established, it is not widely recognized that saturation of the fluorescence excitation can dramatically alter the size and profile of the fluorescence observation volume from which fluorescence fluctuations are measured, even at relatively modest excitation levels. A precise model for these changes is needed for accurate analysis and interpretation of fluctuation spectroscopy data. We here introduce a combined analytical and computational approach to characterize the observation volume under saturating conditions and demonstrate how the variation in the volume is important in two-photon fluorescence correlation spectroscopy. We introduce a simple approach for analysis of fluorescence correlation spectroscopy data that can fully account for the effects of saturation, and demonstrate its success for characterizing the observed changes in both the amplitude and relaxation timescale of measured correlation curves. We also discuss how a quantitative model for the observed phenomena may be of broader importance in fluorescence fluctuation spectroscopy.     

Current fluctuations in discrete transport systems far from equilibrium. Breakdown of the fluctuation dissipation theorem

A recently developed theoretical approach to transport fluctuations around stable steady states in discrete biological transport systems is used in order to investigate general fluctuation properties at nonequilibrium. An expression for the complex frequency dependent admittance at nonequilibrium is derived by calculation of the linear current response of the transport systems to small disturbances in the applied external voltage. It is shown that the Nyquist or fluctuation dissipation theorem, by which at equilibrium the macroscopic admittance or linear response can be expressed in terms of fluctuation properties of the system, breaks down at nonequilibrium. The spectral density of current fluctuations is decomposed into one term containing the macroscopic admittance and a second term which is bilinear in current. This second term is generated by microscopic disturbances, which cannot be excited by external macroscopic perturbations. At special examples it is demonstrated that this second term is decisive for the occurrence of excess noise e.g. the 1/f(2)-Iorentzian noise generated by the opening and closing of nerve channels in biological membranes.     

A Bloch equation approach to intensity dependent optical spectra of light harvesting complex II

On the basis of the recent progress in the resolution of the structure of the antenna light harvesting complex II (LHC II) of the photosystem II, we propose a microscopically motivated theory to predict excitation intensity-dependent spectra. We show that optical Bloch equations provide the means to include all 2( N ) excited states of an oligomer complex of N coupled two-level systems and analyze the effects of Pauli Blocking and exciton-exciton annihilation on pump-probe spectra. We use LHC Bloch equations for 14 Coulomb coupled two-level systems, which describe the S (0) and S (1) level of every chlorophyll molecule. All parameter introduced into the Hamiltonian are based on microscopic structure and a quantum chemical model. The derived Bloch equations describe not only linear absorption but also the intensity dependence of optical spectra in a regime where the interplay of Pauli Blocking effects as well as exciton-exciton annihilation effects are important. As an example, pump-probe spectra are discussed. The observed saturation of the spectra for high intensities can be viewed as a relaxation channel blockade on short time scales due to Pauli blocking. The theoretical investigation is useful for the interpretation of the experimental data, if the experimental conditions exceed the low intensity pump limit and effects like strong Pauli Blocking and exciton-exciton annihilation need to be considered. These effects become important when multiple excitations are generated by the pump pulse in the complex.     

The influence of external environment fluctuations on the signal formation of microbiosensors

This part of theoretical analysis describes the fluctuations of output signal of microbiosensors when the number of accessible molecular recognition elements (enzymes, receptors, antibodies, etc.) fluctuated under external environmental influences. The mean electric current, dispersion correlating function, as well as spectral density of output current fluctuation are analyzed, and it is shown that a comparison of theoretically calculated mean current and correlation function with experimental data allow a determination of the kinetic parameters of substrate binding reaction with the molecular recognition element of biosensor.     

Transition between two regimes describing internal fluctuation of DNA in a nanochannel

We measure the thermal fluctuation of the internal segments of a piece of DNA confined in a nanochannel about 50-100 nm wide. This local thermodynamic property is key to accurate measurement of distances in genomic analysis. For DNA in ~100 nm channels, we observe a critical length scale ~10 m for the mean extension of internal segments, below which the de Gennes' theory describes the fluctuations with no fitting parameters, and above which the fluctuation data falls into Odijk's deflection theory regime. By analyzing the probability distributions of the extensions of the internal segments, we infer that folded structures of length 150-250 nm, separated by ~10 m exist in the confined DNA during the transition between the two regimes. For ~50 nm channels we find that the fluctuation is significantly reduced since the Odijk regime appears earlier. This is critical for genomic analysis. We further propose a more detailed theory based on small fluctuations and incorporating the effects of confinement to explicitly calculate the statistical properties of the internal fluctuations. Our theory is applicable to polymers with heterogeneous mechanical properties confined in non-uniform channels. We show that existing theories for the end-to-end extension/fluctuation of polymers can be used to study the internal fluctuations only when the contour length of the polymer is many times larger than its persistence length. Finally, our results suggest that introducing nicks in the DNA will not change its fluctuation behavior when the nick density is below 1 nick per kbp DNA.     

Fluorescence correlation spectroscopy and quantitative cell biology

Fluorescence correlation spectroscopy (FCS) analyzes fluctuations in fluorescence within a small observation volume. Autocorrelation analysis of FCS fluctuation data can be used to measure concentrations, diffusion properties, and kinetic constants for individual fluorescent molecules. Photon count histogram analysis of fluorescence fluctuation data can be used to study oligomerization of individual fluorescent molecules. If the FCS observation volume is positioned inside a living cell, these parameters can be measured in vivo. FCS can provide the requisite quantitative data for analysis of molecular interaction networks underlying complex cell biological processes.     

Effect of temperature and temperature fluctuation on thermophilic anaerobic digestion of cattle manure

The influence of temperature, 50 and 60 degrees C, at hydraulic retention times (HRTs) of 20 and 10 days, on the performance of anaerobic digestion of cow manure has been investigated in completely stirred tank reactors (CSTRs). Furthermore, the effect of both daily downward and daily upward temperature fluctuations has been studied. In the daily downward temperature fluctuation regime the temperatures of each reactor was reduced by 10 degrees C for 10 h while in the daily upward fluctuation regime the temperature of each reactor was increased 10 degrees C for 5 h. The results show that the methane production rate at 60 degrees C is lower than that at 50 degrees C at all experimental conditions of imposed HRT except when downward temperature fluctuations were applied at an HRT of 10 days. It also was found that the free ammonia concentration not only affects the acetate-utilising bacteria but also the hydrolysis and acidification process. The upward temperature fluctuation affects the maximum specific methanogenesis activity more severely as compared to imposed downward temperature fluctuations. The results clearly reveal the possibility of using available solar energy at daytime to heat up the reactor(s) without the need of heat storage during nights, especially at an operational temperature of 50 degrees C and at a 20 days HRT, and without the jeopardising of the overheating.     

Nonstationary fluctuation analysis and direct resolution of single channel currents at postsynaptic sites.

In order to measure unitary properties of receptor channels at the postsynaptic site, the noise within the decay phases of inhibitory postsynaptic currents (IPSCs) and of N-methyl-D-aspartate (NMDA)-dependent excitatory postsynaptic currents (EPSCs) in rat hippocampal neurons was studied by nonstationary fluctuation analysis. Least squares scaling of the mean current was used to circumvent the wide variation in amplitude of postsynaptic currents. The variance of fluctuations around the expected current was analyzed to calculate single channel conductance, and fluctuation kinetics were studied with power spectra. The single channel conductance underlying the IPSC was measured as 14 pS, whereas that underlying the EPSC was 42 pS. Openings of the EPSC channel could also be resolved directly in low-noise whole-cell recordings, allowing verification of the accuracy of the fluctuation analysis. The results are the first measurements of the properties of single postsynaptic channels activated during synaptic currents, and suggest that the technique can be widely applicable in investigations of synaptic mechanism and plasticity.     

IDI2, a second isopentenyl diphosphate isomerase in mammals

We recently described the identification of a novel isopentenyl diphosphate isomerase, IDI2 in humans and mice. Our current data indicate that, in humans, IDI2 is expressed only in skeletal muscle. Expression constructs of human IDI2 in Saccharomyces cerevisiae can complement isomerase function in an idi1-deficient yeast strain. Furthermore, IDI2 has the ability to catalyze the isomerization of [(14)C]IPP to [(14)C]DMAPP. Enzyme kinetic analysis of partially purified IDI2 demonstrate the novel isozyme has a maximal relative specific activity of 1.2 x 10(-1) +/- 0.3 micromol min(-1) mg(-1) at pH 8.0 with a K(IPP)(m) value of 22.8 microm IPP. Both isozymes, IDI1 and IDI2 are localized to the peroxisome by a PTS1-dependent pathway. Finally, our data suggest that IDI2 is regulated independently from IDI1, by a mechanism that may involve PPARalpha.     

Wavelet transform analysis of NMR structure ensembles to reveal internal fluctuations of enzymes

Internal motions and flexibility are essential for biological functions in proteins. To assess the internal fluctuations and conformational flexibility of proteins, reliable computational methods are needed. In this study, wavelet transformation was used to filter out the noise and facilitate investigating the internal positional fluctuations of enzymes within nuclear magnetic resonance (NMR) structure ensembles. Moreover, potential active sites were identified by combining with positional fluctuation score, sequence conservation, and solvent accessible surface area. Among the total 107 catalytic residues in 44 examined enzymes, 69 residues were identified correctly. Our results suggest that wavelet transform analysis of structure ensemble is applicable to extract essential fluctuation information of proteins; furthermore, analysis of positional fluctuations is helpful for the identification of catalytic residues.     

Non-stationary fluctuation analysis of the Na current in myelinated nerve fibers of Xenopus laevis: experiments and stochastic simulations

Na current fluctuations under voltage-clamp conditions during pulse steps in the potential range from -65 to -30 mV were measured in myelinated nerve fibers of Xenopus laevis. The covariance functions for four consecutive 1 ms intervals were calculated. The time courses of the covariance functions were well fitted with monoexponential functions with time constants between 0.5 and 3 ms, larger at the end of the pulse and larger at more positive potentials. To analyze the underlying channel kinetics we simulated current fluctuations at a step to -35 mV of eight published Na channel models and calculated corresponding covariance functions. None of the models did explain the experimental fluctuation results. We therefore developed a new Na channel model that satisfactorily described the results. Features that distinguished this model from the other tested ones were a slower deactivation rate, and an inactivation transition directly from a closed state.     

Na channel kinetics: developing models from non-stationary current fluctuations by analytic methods

In a previous study, we analyzed Na current fluctuations in myelinated axons from Xenopus laevis under voltage clamp conditions. The statistical properties were analyzed in terms of covariance functions for consecutive time intervals of varying duration during the pulse step. The underlying channel kinetics was analyzed by performing stochastic simulations of published Na channel models and calculating corresponding covariance functions. None of the models explained the fluctuation results. We therefore developed a novel minimal Na channel model that satisfactorily described the results. In the present paper, we extend the analysis and specify the possible models explaining the experimental data by using analytical methods. We derive general relations between the experimental data, including the covariance functions, and the rate constants of specific one-open-state models. A general feature of these models is that they comprise an inactivation step from the first closed state and a relatively low backward rate from the open state. This is in accordance the minimal model inferred from numerical stochastic calculations in the previous study.     

Thermal fluctuation spectroscopy of DNA thermal denaturation

We have developed the technique of thermal fluctuation spectroscopy to measure the thermal fluctuations in a system. This technique is particularly useful to study the denaturation dynamics of biomolecules like DNA. Here we present a study of the thermal fluctuations during the thermal denaturation (or melting) of double-stranded DNA. We find that the thermal denaturation of heteropolymeric DNA is accompanied by large, non-Gaussian thermal fluctuations. The thermal fluctuations show a two-peak structure as a function of temperature. Calculations of enthalpy exchanged show that the first peak comes from the denaturation of AT rich regions and the second peak from denaturation of GC rich regions. The large fluctuations are almost absent in homopolymeric DNA. We suggest that bubble formation and cooperative opening and closing dynamics of basepairs causes the additional fluctuation at the first peak and a large cooperative transition from a partially molten DNA to a completely denatured state causes the additional fluctuation at the second peak.     

T cell development in the thymus: from periodic seeding to constant output

T cell development occurs in the thymus throughout life. Recent experimental findings show that the seeding of the thymus by multi-potent stem cells from the bone marrow is periodic rather than continuous, as previously assumed. However it is well known that the output rate of cells from the thymus is relatively constant. A quantitative model is used to verify the current hypotheses regarding T cell development in the steady state mouse thymus. The results show that the thymus could be at a periodic steady state with out-of-phase thymocyte populations. Experiments to examine possible periodic fluctuations in the thymus are proposed and methods for further analysis are outlined.     

Real-time nanoscopy by using blinking enhanced quantum dots

Superresolution optical microscopy (nanoscopy) is of current interest in many biological fields. Superresolution optical fluctuation imaging, which utilizes higher-order cumulant of fluorescence temporal fluctuations, is an excellent method for nanoscopy, as it requires neither complicated optics nor illuminations. However, it does need an impractical number of images for real-time observation. Here, we achieved real-time nanoscopy by modifying superresolution optical fluctuation imaging and enhancing the fluctuation of quantum dots. Our developed quantum dots have higher blinking than commercially available ones. The fluctuation of the blinking improved the resolution when using a variance calculation for each pixel instead of a cumulant calculation. This enabled us to obtain microscopic images with 90-nm and 80-ms spatial-temporal resolution by using a conventional fluorescence microscope without any optics or devices.     

MALDI imaging mass spectrometry: molecular snapshots of biochemical systems

Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) is emerging as a powerful tool for investigating the distribution of molecules within biological systems through the direct analysis of thin tissue sections. Unique among imaging methods, MALDI-IMS can determine the distribution of hundreds of unknown compounds in a single measurement. We discuss the current state of the art of MALDI-IMS along with some recent applications and technological developments that illustrate not only its current capabilities but also the future potential of the technique to provide a better understanding of the underlying molecular mechanisms of biological processes.