Spatial pattern formation induced by Gaussian white noise

The ability of Gaussian noise to induce ordered states in dynamical systems is here presented in an overview of the main stochastic mechanisms able to generate spatial patterns. These mechanisms involve: (i) a deterministic local dynamics term, accounting for the local rate of variation of the field variable, (ii) a noise component (additive or multiplicative) accounting for the unavoidable environmental disturbances, and (iii) a linear spatial coupling component, which provides spatial coherence and takes into account diffusion mechanisms. We investigate these dynamics using analytical tools, such as mean-field theory, linear stability analysis and structure function analysis, and use numerical simulations to confirm these analytical results.     

On detecting interactions between species in population dynamics

If we are to progress out of our current state of uncertainty about the role of interspecific competition in community structure, it is essential that we can distinguish competition from other types of population interaction, and from lack of interaction, in particular case studies. To make such distinctions, it is necessary to quantify the effect of species on each other. One way to do this is to calculate interaction coefficients, and another (only readily applicable in experimental systems) is to plot graphs of N against time and to contrast monocultures with mixed cultures. We show (1) that these methods often appear to give contradictory results, and (2) that the problems are most pronounced when one species has a low equilibrium population size in mixed culture. To resolve the question of whether an interspecific interaction is taking place (and if so, what kind of interaction), it is necessary to apply tests of significance which overcome the problems of serial correlation inherent in all long-term population experiments. We illustrate the use of such tests in the analysis of the results from an experimental Drosophiia system. In the past, this kind of test has generally not been applied, and this raises the question of whether some of the 'classic cases of competition' in the experimental literature were really competition at all.     

Molecular dynamics simulation of interactions in glycolytic enzymes

Two glycolytic enzymes, phosphoglycerate mutase (PGM) and enolase from Saccharomyces cerevisiae, have been chosen to detect complex formation and possible channeling, using molecular dynamics simulation. The enzymes were separated by 10 angstroms distance and placed in a water-filled box of size 173 x 173 x 173 angstroms. Three different orientations have been investigated. The two initial 3-phosphoglycerate substrate molecules near the active centers of the initial structure of PGM have been replaced with final product (2-phosphoglycerate) molecules, and 150 mM NaCl together with three Mg2+ ions have been added to the system to observe post-catalytic activity under near-physiological conditions. Analysis of interaction energies and conformation changes for 3 nsec simulation indicates that PGM and enolase do show binding affinity between their near active regions, which is necessary for channeling to occur. Interaction of the C-terminal residues Ala239 and Val240 of PGM (which partially "cap" the 2-phosphoglycerate) with enolase also favors the existence of channeling.     

Application of wavelet-based tools to study the dynamics of biological processes

The article makes use of three different examples (sensory information processing in the rat trigeminal complex, intracellular interaction in snail neurons and multimodal dynamics in nephron autoregulation) to demonstrate how modern approaches to time-series analysis based on the wavelet-transform can provide information about the underlying complex biological processes.     

Understanding protein-protein interactions by genetic suppression

Protein-protein interactions influence many cellular processes and it is increasingly being felt that even a weak and remote interplay between two subunits of a protein or between two proteins in a complex may govern the fate of a particular biochemical pathway. In a bacterial system where the complete genome sequence is available, it is an arduous task to assign function to a large number of proteins. It is possible that many of them are peripherally associated with a cellular event and it is very difficult to probe such interaction. However, mutations in the genes that encode such proteins (primary mutations) are useful in these studies. Isolation of a suppressor or a second-site mutation that restores the phenotype abolished by the primary mutation could be an elegant yet simple way to follow a set of interacting proteins. Such a reversion site need not necessarily be geometrically close to the primary mutation site.     

Tracking the dynamics of pathogen interactions: modeling ecological and immune-mediated processes in a two-pathogen single-host system

Traditionally, epidemiological studies have focused on understanding the dynamics of a single pathogen, assuming no interactions with other pathogens. Recently, a large body of work has begun to explore the effects of immune-mediated interactions, arising from cross-immunity and antibody-dependent enhancement, between related pathogen strains. In addition, ecological processes such as a temporary period of convalescence and pathogen-induced mortality have led to the concept of ecological interference between unrelated diseases. There remains, however, the need for a systematic study of both immunological and ecological processes within a single framework. In this paper, we develop a general two-pathogen single-host model of pathogen interactions that simultaneously incorporates these mechanisms. We are then able to mechanistically explore how immunoecological processes mediate interactions between diseases for a pool of susceptible individuals. We show that the precise nature of the interaction can induce either competitive or cooperative associations between pathogens. Understanding the dynamic implications of multi-pathogen associations has potentially important public health consequences. Such a framework may be especially helpful in disentangling the effects of partially cross-immunizing infections that affect populations with a pre-disposition towards immunosuppression such as children and the elderly.     

Unraveling the dynamics of protein interactions with quantitative mass spectrometry

Knowledge of structure and dynamics of proteins and protein complexes is important to unveil the molecular basis and mechanisms involved in most biological processes. Protein complex dynamics can be defined as the changes in the composition of a protein complex during a cellular process. Protein dynamics can be defined as conformational changes in a protein during enzyme activation, for example, when a protein binds to a ligand or when a protein binds to another protein. Mass spectrometry (MS) combined with affinity purification has become the analytical tool of choice for mapping protein–protein interaction networks and the recent developments in the quantitative proteomics field has made it possible to identify dynamically interacting proteins. Furthermore, hydrogen/deuterium exchange MS is emerging as a powerful technique to study structure and conformational dynamics of proteins or protein assemblies in solution. Methods have been developed and applied for the identification of transient and/or weak dynamic interaction partners and for the analysis of conformational dynamics of proteins or protein complexes. This review is an overview of existing and recent developments in studying the overall dynamics of in vivo protein interaction networks and protein complexes using MS-based methods.     

非线性鸣声对雄性凹耳蛙应答的影响

为了解非线性鸣声对凹耳蛙(Odorrana tormota)应答音的影响以及非线性鸣声是否能够增强鸣声的不可预测性,本研究通过回放非线性鸣声和线性鸣声来刺激陌生雄性凹耳蛙,并记录应答次数及统计分析应答音相关参数。结果表明,回放非线性鸣声时会引起陌生蛙(n=22)更多次数的应答,但两种刺激引起的首次应答时间没有显著差异。对应答音相关参数分析表明,线性鸣声引起的应答音在总时长上比非线性鸣声引起的应答音更长且具有显著差异,而其他声音参数(包括平均基频、最大基频、最小基频、主频)均没有显著差异。推测当陌生雄蛙听到同类鸣叫时,出于保护领地和资源的本能反应,陌生蛙都会第一时间作出反应,因此在两类声音的应答反应时间上并没有区别。而在应答次数上,非线性鸣声引起了凹耳蛙更多次数的应答,可能是由于鸣声中的非线性现象使得声音更加复杂,包含更多信息,容易提高声音接收者对这类声音的关注度。本研究结果表明,凹耳蛙鸣声中包含的非线性现象能够增强其声音的不可预测性,引起陌生蛙产生更多的应答次数。     

Mucin-lectin interactions assessed by flow cytometry

The O-glycosylated domains of mucins and mucin-type glycoproteins contain 50-80% of carbohydrate and possess expanded conformations. Herein, we describe a flow cytometry (FCM) method for determining the carbohydrate-binding specificities of lectins to mucin. Biotinylated mucin was immobilized on streptavidin-coated beads, and the binding specificities of the major mucin sugar chains, as determined by GC-MS and MALDI-ToF, were monitored using fluorescein-labeled lectins. The specificities of lectins toward specific biotinylated glycans were determined as controls. The advantage of flexibility, multiparametric data acquisition, speed, sensitivity, and high-throughput capability makes flow cytometry a valuable tool to study diverse interactions between glycans and proteins.     

Vegetation dynamics in Brittany heathlands after fire

The vegetation dynamics of heathlands in Brittany have been followed for three years in areas subject to fire in August 1976. The pre-fire vegetation had been analysed and mapped before its destruction. The structure of the community and the processes taking place in it (in terms of biomass, primary productivity, phenology, mineral nutrition and food value) had been examined. The redevelopment of the canopy was studied by the point-contact method along permanent line transects. This semi-quantitative study permits calculation of the relative frequency of each species and, from this, its cover. The growth form of each species and the stratification of the community are also indicated by this method. Permanent plots were also used to record changes in the vegetation, by means of a census of individuals and records of the development and growth strategy of each species. The plots were located in homogeneous areas, or on bare soil around seed parents in order to examine seed dispersal and seedling establishment. These two methods yielded detailed information on the nature of the secondary successions following fire in the heathlands of Brittany.

     

Lipid dynamics and protein-lipid interactions in rat colonic epithelial cell basolateral membranes

Lipid dynamics and lipid-protein interactions were examined in basolateral membranes prepared from rat proximal and distal colonic epithelial cells. The results demonstrate that: (1) these membranes have a high lipid fluidity, as assessed by steady-state fluorescence polarization studies using seven fluorescent probes; (2) lipid compositional differences exist between these membranes but their fluidity is similar; (3) fluorescence polarizations studies, using diphenylhexatriene (DPH), detect a thermotropic transition at 22–23°C in each membrane; (4) several membrane protein activities, including adenylate cyclase and sodium-potassium dependent adenosine triphosphatase ($\text{(}\text{Na}{}^{\mathrm{+}}\text{+}\text{K}{}^{\mathrm{+}}\text{)-}\text{ATPase}$) appear to be functionally dependent on the physical state of the proximal basolateral membrane's lipid.     

Lipid bilayer polypeptide interactions studied by molecular dynamics simulation

A model membrane with a polypeptide alpha-helix inserted has been simulated by molecular dynamics at a temperature well above the gel/liquid crystalline phase transition temperature. Order parameters of the lipids and other equilibrium and dynamic quantities have been calculated. Three systems, polyglycine constrained into an alphahelical configuration, glycophorin with similarly conformationally constrained backbone and finally glycophorin free to change its backbone conformation, have been studied. In all cases there was an ordering of the chains close to the helix. This effect was, however, much smaller for glycophorin with its rather bulky side chains than for polyglycine. The dynamics of the lipids were affected by the neighbouring helix, not drastically however. Lateral diffusion and reorientational time correlations of lipids close to the helix were slower than for the bulk ones, but not more than two or three times. Thus, we did not find any evidence of bound or frozen boundary lipids.     

Amphipathic-Lipid-Packing-Sensor interactions with lipids assessed by atomistic molecular dynamics

The Amphipathic-Lipid-Packing-Sensor (ALPS) motif targets the protein ArfGAP1 to curved membranes during vesicle formation in the Golgi apparatus. ALPS specifically recognizes lipid packing defects due to the positive curvature of budding vesicles. In this work we assessed the microscopic interactions between ALPS and two phospholipid membranes at different degrees of lipid packing by explicit molecular dynamics (MD). Simulations were performed within loosely packed membranes composed of a mixture of dioleoylphosphatidylcholine (DOPC)/dioleoylglycerol (DOG) at a molar ratio 85:15. Some other simulations were performed in pure DOPC for which lipid packing is tighter. We show that the presence of DOG causes packing defects at the phosphate level and thereby modifies some properties of the bilayer. This leads to a higher hydration of the lipid headgroups. When embedded in a membrane with such defects, ALPS displays a higher degree of conformational flexibility than in a more packed membrane. We propose that lipid packing sensing by ALPS may have an entropic origin and that its flexibility is a key feature.     

Time-dependent platelet-vessel wall interactions induced by intestinal ischemia-reperfusion

Platelets roll and adhere in venules exposed to ischemia-reperfusion (I/R). This platelet-endothelial adhesion may influence leukocyte trafficking because platelet depletion decreases I/R-induced leukocyte emigration. The objectives of this study were 1) to assess the time course of platelet adhesion in the small bowel after I/R and 2) to determine the roles of endothelial and/or platelet P-selectin and P-selectin glycoprotein ligand-1 (PSGL-1) in this adhesion. The adhesion of fluorescently labeled platelets was monitored by intravital microscopy in postcapillary venules exposed to 45 min of ischemia and up to 8 h of reperfusion. Peak platelet adhesion was observed at 4 h of reperfusion. To assess the contributions of platelet and endothelial cell P-selectin, platelets from P-selectin-deficient and wild-type mice were infused into wild-type and P-selectin-deficient mice, respectively. Platelets deficient in P-selectin exhibited low levels of adhesion comparable to that in sham-treated animals. In the absence of endothelial P-selectin, platelet adhesion was reduced by 65%. Treatment with a blocking antibody against PSGL-1 reduced adhesion by 57%. These results indicate that I/R induces a time-dependent platelet-endothelial adhesion response in postcapillary venules via a mechanism that involves PSGL-1 and both platelet and endothelial P-selectin, with platelet P-selectin playing a greater role.     

Proteomic analysis of pathogenesis-related proteins (PRs) induced by compatible and incompatible interactions of pepper mild mottle virus (PMMoV) in Capsicum chinense L3 plants

Resistance conferred by the L³ gene is active against most ofthe tobamoviruses, including the Spanish strain (PMMoV-S), aP_1,2 pathotype, but not against certain strains of pepper mildmottle virus (PMMoV), termed P_1,2,3 pathotype, such as the Italianstrain (PMMoV-I). Both viruses are nearly identical at theirnucleotide sequence level (98%) and were used to challenge Capsicumchinense PI159236 plants harbouring the L³ gene in order tocarry out a comparative proteomic analysis of PR proteins inducedin this host in response to infection by either PMMoV-S or PMMoV-I.PMMoV-S induces a hypersensitive reaction (HR) in C. chinensePI159236 plant leaves with the formation of necrotic local lesionsand restriction of the virus at the primary infection sites.In this paper, C. chinense PR protein isoforms belonging tothe PR-1, β-1,3-glucanases (PR-2), chitinases (PR-3), osmotin-likeprotein (PR-5), peroxidases (PR-9), germin-like protein (PR-16),and PRp27 (PR-17) have been identified. Three of these PR proteinisoforms were specifically induced during PMMoV-S-activationof C. chinense L³ gene-mediated resistance: an acidic β-1,3-glucanaseisoform (PR-2) (M_r 44.6; pI 5.1), an osmotin-like protein (PR-5)(M_r 26.8; pI 7.5), and a basic PR-1 protein isoform (M_r 18;pI 9.4–10.0). In addition, evidence is presented for adifferential accumulation of C. chinense PR proteins and mRNAsin the compatible (PMMoV-I)–C. chinense and incompatible(PMMoV-S)–C. chinense interactions for proteins belongingto all PR proteins detected. Except for an acidic chitinase(PR-3) (M_r 30.2; pI 5.0), an earlier and higher accumulationof PR proteins and mRNAs was detected in plants associated withHR induction. Furthermore, the accumulation rates of PR proteinsand mRNA did not correlate with maximal accumulation levelsof viral RNA, thus indicating that PR protein expression mayreflect the physiological status of the plant. Key words: Capsicum chinense, compatible interaction, incompatible interaction, HR-induction, PMMoV, PR proteins Received 5 December 2007; Revised 21 January 2008 Accepted 22 January 2008     

Understanding the interactions of different substrates with wild-type and mutant acylaminoacyl peptidase using molecular dynamics simulations

Acylaminoacylpeptidase (AAP) belongs to peptidase protein family, which can degrade amyloid β-peptide forms in the brains of patients, and hence leads to Alzheimer’s disease. And so, AAP is considered to be a novel target in the design of drugs against Alzheimer’s disease. In this investigation, six molecular dynamics simulations were used to find that the interaction between the wild-type and R526V AAP with two different substrates (p-nitrophenylcaprylate and Ac-Leu-p-nitroanilide). Our results were as follows: firstly, Ac-Leu-p-nitroanilide bound to R526V AAP to form a more disordered loop (residues 552–562) in the α/β-hydrolase fold like of AAP, which caused an open and inactive AAP domain form, secondly, binding p-nitrophenylcaprylate and Ac-Leu-p-nitroanilide to AAP can decrease the flexibility of residues 225–250, 260–270, and 425–450, in which the ordered secondary structures may contain the suitable geometrical structure and so it is useful to serine attack. Our theoretical results showed that the binding of the two substrates can induce specific conformational changes responsible for the diverse AAP catalytic specificity. These theoretical substrate-induced structural diversities can help explain the abilities of AAPs to recognize and hydrolyze extremely different substrates.