A mathematical model for the phase of sexual reproduction in monogonont rotifers

Recently, the optimal sex allocation in monogonont rotifers is studied in [1], and, as a closely related question, the relative frequencies of the relevant types of mictic females. The authors focus on the evolution of the age at which young mictic females lose their fertilization susceptibility and they address the threshold age of fertilization that maximizes resting egg production. Assuming that a stationary population is achieved, with stable age distribution, they obtain their results, without knowing the stationary population. Our aim is to study this problem in the framework of the theory of nonlinear age-dependent population dynamics developed by G. F. Webb in [13], which is more appropriate from the mathematical point of view and permits to us to obtain analytically the stationary population and consequently it is analytically shown that a threshold age of fertilization equal to the age of maturation is not an ESS, despite the fact that then the production of resting eggs is maximum, which has been obtained by simulation in [1]. Received: 30 June 1998 / Revised version: 17 May 1999 / Published on line: 5 May 2000     

Continental gateways and the dynamics of mammalian faunas

Continental gateways occur where mountainous topography interacts with changing climate and sea level to open or close dispersal corridors. The interaction of permeable or impermeable montane barriers with changing or stable climate yields four biogeographic states, each associated with changes in diversification rates and ecological structure of faunas. For example, permeable montane barriers and climatic stability result in low rates of immigration and extinction, elevated endemic speciation, and stable ecological structure. Three examples from the mammalian fossil record test these scenarios. (1) In Miocene faunas of Pakistan, immigration rates peaked and faunal proportions changed during an interval of cooling and open corridors. (2) In Miocene faunas of Spain, elevated extinction and origination rates and changing trophic structure occurred during regional aridification with open corridors. (3) In Quaternary faunas of South Africa, ungulates experienced range reductions and elevated extinction during the transition from glacial to interglacial climates as corridors closed.     

采用CFD数值模拟技术优化发酵罐内桨叶组合

使用CFD模拟软件Fluent对实验室用7L通气搅拌发酵罐内不同桨叶组合的搅拌效果进行气液两相流模拟.首先对发酵罐自带桨叶组合进行模拟,针对模拟结果提出两种改进桨型组合,对比分析3种组合的速度矢量图、速度分布柱形图和速度云图,以此优化出一种搅拌效果较好的桨型组合.结果表明:发酵罐内的流场可受通气的影响而发生改变,通气发酵过程的模拟采用多相流模型更为准确;底层桨离底距离的不同可导致发酵罐内流场的不同,以六直叶圆盘涡轮桨为底桨时,离底距离应不小于T/3;液相死区的大小是由桨叶组合、桨叶安装位置以及气液两相的相互作用共同导致的,不能单纯靠提高转速改善;在800 r/min下,搅拌效果组合3为最佳.     

Siwalik synopsis: A long stratigraphic sequence for the Later Cenozoic of South Asia

The Tertiary sediments of northern Pakistan are an exceptional record of terrestrial sedimentation and represent most of Neogene time. Foremost is the Siwalik Group of the Potwar Plateau, for which multiple, superposed fossil levels span ∼18–6 Ma. Well-developed magnetostratigraphic control provides secure dating so that Siwalik fossil horizons may be interpolated into a time scale with resolution to 100,000 years. We describe the geographic setting of the Potwar, give an overview of the temporal distribution of faunas, and discuss changes in paleohabitat and paleoecology with coinciding faunal change, as seen from the Siwalik viewpoint. The long Siwalik biostratigraphy of many successive assemblages with its resolved time scale may be compared directly with other well-dated sequences. Immigrant arrival and timing of faunal change may be traced. The basins of the Iberian Peninsula show somewhat different timing of introduction of hipparionine horses, and faunal turnover in the Siwaliks clearly precedes the Vallesian crisis in Spain. In contrast to the increasingly seasonal precipitation of the late Miocene Potwar, the paleohabitat of coeval North China appears to have been moist and equable, with high diversity faunas. Continued development and comparison of resolved Neogene records allow increasing resolution of the patterns of faunal change on regional to global levels.     

A new Late Pleistocene non-anthropogenic vertebrate assemblage from the northern Iberian Peninsula: Artazu VII (Arrasate,Basque Country)

Late Pleistocene palaeontological sites without human intervention are limited in the Cantabrian region, and even more so those with a good state of preservation and rich biodiversity. A new vertebrate fossiliferous locality discovered at Kobate Quarry (Arrasate, northern Iberian Peninsula) is presented in this article. This site, in which remains of 40 different vertebrate taxa were accumulated, acted as a natural trap. The preliminary vertebrate faunal list includes five amphibian taxa, four reptiles, seven species of birds and 24 mammalian taxa. While small mammals are represented by 13 small mammal taxa (seven in the Order Rodentia, five in the Order Eulipotyphla, and one in the Order Chiroptera), the large mammal fauna comprises eleven species, including ungulates and carnivores. The palaeoecology inferred from this faunal assemblage suggests the existence of large forested areas with some grassland and a watercourse nearby, within a notably warm and humid climate. These palaeoenvironmental conditions, combined with AMS and AAR results carried out in macrofaunal bone samples, suggest that the deposit from Artazu VII would be located in the first half of the Late Pleistocene, in the Marine Isotope Stage (MIS) 5c.     

Fossil record and dynamics of Late Miocene small mammal faunas of the Vienna Basin and adjacent basins,Austria

The Late Miocene small mammal assemblages of the hinterland of Lake Pannon in Austrian Basins are represented by 99 species-level taxa and 30,400 specimens. The fossil-bearing localities can be grouped into eight intervals spanning about three million years from the Early Vallesian to the Middle Turolian. Each time slice is characterised by the occurrence and/or dominance of certain species. The retreat of Lake Pannon is reflected by a distinct diversification. This pattern may be a regional signal due to increasing habitat availability but may also be taphonomically biased due to a rather poor Earliest Vallesian record. Nevertheless, the overall community structure is quite stable throughout the Vallesian and no indication of a Vallesian Crisis can be detected. Instead, a moderate turnover occurs with the onset of the Turolian, reflected by the increasing abundance of xerophilic taxa.     

Spatial heterogeneity of wind forcing: application to artificial reef functioning influenced by the circulation in the Bay of Marseilles, France

In the frame of the largest French project of artificial production reefs, initiated by the city of Marseilles in 2001, the present study aimed at describing the hydrodynamic pattern of the coastal area considered, by the use of a 3D numerical modelling. Results were local wind statistics, bottom current fields and drifting particle maps. The knowledge of the hydrodynamic connexions between particle (such as larvae) sources or targeted areas linked to the reefs, allows us to explain the success or failure of the reefs' colonizing. Moreover, the study confirms the wind spatial variability and demonstrates the error resulting from the use of an average but locally absent wind direction.     

Modelling and simulation of the architecture and development of the oil-palm (t Elaeis guineensis Jacq.) root system

The objective of this work was to model the architecture and growth dynamics of the oil-palm root system. The morphological and functional unit of the root system, called root architectural unit and its development sequence enabled us to establish the basis of a mathematical formalization of the root system architecture. The topology of the branched structures and the processes of growth, branching and mortality were described and modelled by stochastic processes (graph model, automata, laws of probability). The models obtained were then combined with geometrical parameters in an overall mathematical model: the reference axis. Simulation of this model provided 3-D numerical models. Validations of the overall model based on comparing the 3-D numerical models with observed root systems, appeared satisfactory.     

Methionyl-tRNA synthetase from E. coli: direct evidence for exchange of protomers in the dimeric enzyme by using deuteration and small-angle neutron scattering

Direct demonstration of the reversible dissociation of native dimeric methionyl-tRNA synthetase from E. coli has been obtained using small angle neutron scattering and deuterated enzyme. Structural parameters of the fully deuterated dimer are very similar to the hydrogenated one. Analysis of the variations of the intensity and of the radius of gyration of a stoichiometric mixture of the two types of dimer (hydrogenated and deuterated), as a function of D2O content in the solvent, enabled us to characterize an hybrid dimer, having both hydrogenated and deuterated protomers. By separating the contribution of each protomer to the scattering, the radius of gyration of the protomer in situ and the distance between the centers of mass of each protomer in the dimer are determined.     

Modelling and simulation of the architecture and development of the oil-palm (Elaeis guineensis Jacq.) root system

A stochastic model of oil-palm (Elaeis guineensis Jacq.) root system architecture and development has been developed. This model enabled us to create 3-D numerical models of complete root systems by simulation. The application of a postprocessor software, called RACINES, to these 3-D numerical models, provided an estimation of some parameters of plant root systems. The objective of this paper is to present oil-palm root characteristics as possible outputs of the application of this RACINES software. The outputs described in this article cover (i) spatial distribution of roots under plantation conditions, (ii) the estimation and distribution of total root biomass, per root type or per soil horizon and (iii) the location and quantification of absorbent surfaces. The computing techniques used were based on voxellization of space and creation of 3-D virtual sceneries exactly reproducing observed planting designs. By comparing the results of observations and simulations for spatial distribution (by trench wall density maps) and root biomasses (by real and virtual sampling) we were able to carry out additional numerical validations of the model.     

A new pipoid frog (Anura,Pipimorpha) from the Paleogene of Patagonia. Paleobiogeographical implications

The aim of the present contribution is to describe a new genus and species of Pipoidea from the Huitrera Formation (Eocene) from Patagonia, Argentina. The new genus shows a unique combination of characters indicating that it is a valid taxon different from other pipimorphs, including the coeval Llankibatrachus truebae. The phylogenetic analysis resulted in the nesting of the new taxon within a previously unrecognized endemic clade of South American aglossans. This new clade turns out to be the sister-group of crown-group Pipidae. This phylogenetic proposal reinforces the hypothesis sustaining the dispersal of pipids between Africa and South America through an island chain or a continental bridge across the Atlantic Ocean by Early Tertiary times.     

A degree-day simulation model for the population dynamics of the rice bug, Leptocorisa acuta (Thunb.)

The rice bug, Leptocorisa acuta (Thunb.) is a major pest of the rice crop in India. A computer simulation model of the bug's population dynamics was formulated using the information generated on the thermal requirements of development stages. It is a mechanistic model which follows the state variable–rate variable approach. The model works based on the accumulation of heat units over stage-specific thresholds of development. Validation using light trap catches has shown that the model has satisfactory predictive value. Simulated population dynamics over the years were compared and the influence of global warming on bug population dynamics was predicted. The model can forecast the pest population in the field and help in timely adoption of management practices.     

Effect of gold nanoparticle on stability of the DNA molecule: A study of molecular dynamics simulation

An understanding of the mechanism of DNA interactions with gold nanoparticles is useful in today medicine applications. We have performed a molecular dynamics simulation on a B-DNA duplex (CCTCAGGCCTCC) in the vicinity of a gold nanoparticle with a truncated octahedron structure composed of 201 gold atoms (diameter ～1.8 nm) to investigate gold nanoparticle (GNP) effects on the stability of DNA. During simulation, the nanoparticle is closed to DNA and phosphate groups direct the particles into the major grooves of the DNA molecule. Because of peeling and untwisting states that are occur at end of DNA, the nucleotide base lies flat on the surface of GNP. The configuration entropy is estimated using the covariance matrix of atom-positional fluctuations for different bases. The results show that when a gold nanoparticle has interaction with DNA, entropy increases. The results of conformational energy and the hydrogen bond numbers for DNA indicated that DNA becomes unstable in the vicinity of a gold nanoparticle. The radial distribution function was calculated for water hydrogen–phosphate oxygen pairs. Almost for all nucleotide, the presence of a nanoparticle around DNA caused water molecules to be released from the DNA duplex and cations were close to the DNA.     

A simple model for the dynamics of a host-parasite-hyperparasite interaction

Hyperparasites can play a crucial role in the control of a host-parasite interaction if they are successfully established in the community. We investigated the specific traits of the hyperparasite and those of the release event which allow a successful regulation of primary parasite populations. This study has been motivated by the case study of chestnut-Cryphonectria parasitica-Cryphonectria Hypovirus interaction. We use a model of SIR/SIS type which assumes a limited diffusion of the parasite. Our model emphasizes the thresholds for invasion linked to the ecological specificities of both the pathogen and the hyperparasite (transmission rates and virulence) and to the initial conditions of the system (population sizes of the different categories). The predictions are consistent with data on the observed spread of the virus. "Mild" strains of the hyperparasite, characterized by a high vertical transmission rate and low virulence, are more prone to establish than "severe" strains. It also demonstrates that the horizontal transmission of the virus, which is controlled by a vegetative incompatibility system in the fungus, is not the unique constraint for the virus establishment. This study may contribute to theoretical and practical aspects of the biological control of plant diseases with a hyperparasite and to the ecology of biological invasions.     

Differential dynamics of the serotonin1A receptor in membrane bilayers of varying cholesterol content revealed by all atom molecular dynamics simulation

Abstract

The serotonin_1A receptor belongs to the superfamily of G protein-coupled receptors (GPCRs) and is a potential drug target in neuropsychiatric disorders. The receptor has been shown to require membrane cholesterol for its organization, dynamics and function. Although recent work suggests a close interaction of cholesterol with the receptor, the structural integrity of the serotonin_1A receptor in the presence of cholesterol has not been explored. In this work, we have carried out all atom molecular dynamics simulations, totaling to 3?μs, to analyze the effect of cholesterol on the structure and dynamics of the serotonin_1A receptor. Our results show that the presence of physiologically relevant concentration of membrane cholesterol alters conformational dynamics of the serotonin_1A receptor and, on an average lowers conformational fluctuations. Our results show that, in general, transmembrane helix VII is most affected by the absence of membrane cholesterol. These results are in overall agreement with experimental data showing enhancement of GPCR stability in the presence of membrane cholesterol. Our results constitute a molecular level understanding of GPCR-cholesterol interaction, and represent an important step in our overall understanding of GPCR function in health and disease.     

A molecular dynamics simulation of the flavin mononucleotide–RNA aptamer complex

We report on an unrestrained molecular dynamics simulation of the flavin mononucleotide (FMN)–RNA aptamer. The simulated average structure maintains both cross‐strand and intermolecular FMN–RNA nuclear Overhauser effects from the nmr experiments and has all qualitative features of the nmr structure including the G10–U12–A25 base triple and the A13–G24, A8–G28, and G9–G27 mismatches. However, the relative orientation of the hairpin loop to the remaining part of the molecule differs from the nmr structure. The simulation predicts that the flexible phosphoglycerol part of FMN moves toward G27 and forms hydrogen bonds. There are structurally long‐lived water molecules in the FMN binding pocket forming hydrogen bonds within FMN and between FMN and RNA. In addition, long‐lived water is found bridging primarily RNA backbone atoms. A general feature of the environment of long‐lived “structural” water is at least two and in most cases three or four potential acceptor atoms. The 2′‐OH group of RNA usually acts as an acceptor in interactions with the solvent. There are almost no intrastrand O2′H(n)⋮O4′(n + 1) hydrogen bonds within the RNA backbone. In the standard case the preferred orientation of the 2′‐OH hydrogen atoms is approximately toward O3′ of the same nucleotide. However, a relatively large number of conformations with the backbone torsional angle γ in the trans orientation is found. A survey of all experimental RNA x‐ray structures shows that this backbone conformation occurs but is less frequent than found in the simulation. Experimental nmr RNA aptamer structures have a higher fraction of this conformation as compared to the x‐ray structures. The backbone conformation of nucleotide n + 1 with the torsional angle γ in the trans orientation leads to a relatively short distance between 2′‐OH(n) and O5′(n + 1), enabling hydrogen‐bond formation. In this case the preferred orientation of the 2′‐OH hydrogen atom is approximately toward O5′(n + 1). We find two relatively short and dynamically stable types of backbone–backbone next‐neighbor contacts, namely C2′(H)(n)⋮O4′(n + 1) and C5′(H)(n + 1)⋮O2′(n). These interactions may affect both backbone rigidity and thermodynamic stability of RNA helical structures. © 1999 John Wiley & Sons, Inc. Biopoly 50: 287–302, 1999     

Effects of fluorescent probe NBD-PC on the structure, dynamics and phase transition of DPPC. A molecular dynamics and differential scanning calorimetry study

We present a combined theoretical (molecular dynamics, MD) and experimental (differential scanning calorimetry, DSC) study of the effect of 7-nitrobenz-2-oxa-1,3-diazol-4-yl (NBD) acyl chain-labeled fluorescent phospholipid analogs (C6-NBD-PC and C12-NBD-PC) on 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayers. DSC measurements reveal that < 1 mol% of NBD-PC causes elimination of the pre-transition and a large loss of cooperativity of the main transition of DPPC. Labeling with C6-NBD-PC or C12-NBD-PC shifts the main transition temperature to lower or higher values, respectively. Following our recent report on the location and dynamics of these probes (BBA 1768 (2007) 467-478) in fluid phase DPPC, we present a detailed analysis of 100-ns MD simulations of systems containing either C6-NBD-PC or C12-NBD-PC, focused on their influence on several properties of the host bilayer. Whereas most monitored parameters are not severely affected for 1.6 mol% of probe, for the higher concentration studied (6.2 mol%) important differences are evident. In agreement with published reports, we observed that the average area per phospholipid molecule increases, whereas DPPC acyl chain order parameters decrease. Moreover, we predict that incorporation of NBD-PC should increase the electrostatic potential across the bilayer and, especially for C12-NBD-PC, slow lateral diffusion of DPPC molecules and rotational mobility of DPPC acyl chains.     

A combination of bioactive and nonbioactive alkyl-peptides form a more stable nanofiber structure for differentiating neural stem cells: a molecular dynamics simulation survey

Self-assembling alkyl-peptides are important molecules due to their ability to construct nano-level structures such as nanofibers to be utilized as tissue engineering scaffolds. The bioactive epitope of FAQRVPP which acts as neural stem cells (NSCs) outgrowth inducing factor is used in nanofiber structures. Based on previous experimental studies the density and distribution pattern of the epitopes on the surface of the nanofibers plays an important role in the differentiation function efficiency. We decided to survey and compare the stability of two pre-constructed fiber structures in the forms of all-functionalized nanofiber (containing only bioactive alkyl-peptides) and distributed functionalized nanofiber (a combination of nonbioactive and bioactive alkyl-peptides with ratio 2:1). Our findings reveal that the all-functionalized fiber shows an unstable structure and is split into intermediate micelle-like structures to reduce compactness and steric hindrance of functional epitopes whereas the distributed functionalized fiber shows an integrated stable nanofiber with a more amount of beta sheets that are well-organized and oriented around the hydrophobic core. The hydrogen bonds and energy profiles of the structures indicate the role of hydrophobic interactions during the alkyl-chain core formation and the important role of electrostatic interactions and hydrogen bond network in the stability of the final structures. Finally, it seems that the possibility of the presence of intermediate structure is increased in the all-functionalized nanofiber environment, and it can reduce functional efficiency of the scaffolds. These findings can help to design more efficient nanofiber structures with different goals in scaffolds for tissue engineering. Abbreviations MD Molecular Dynamics

NSCs Neural Stem Cells

PME Particle mesh Ewald

RDF Radial Distribution Function

RG Radius of gyration

RASA Relative Accessible Surface Area

RMSD Root Mean Square Deviations

SASA Solvent Accessible Surface Area.

Communicated by Ramaswamy H. Sarma     

A model for the upstream motion of elvers in the Adour River

The aim of this paper is contributing to the study of the exploitation of the European eel (Anguilla anguilla) in the basin of the French river 'Adour'. This exploitation constitutes the basis of the economy of local professional fishermen, who have recently noticed a diminution of the hunting of elvers. In order to design a sustainable exploitation strategy, we must know as much as possible about eel life cycle. For that purpose, we build a model to describe a phase of eels evolution, their migration upstream the river. Our model is based on the biological details of eels behaviour and constitutes a virtual laboratory, useful to test different hypotheses about eels migration.     

A simulation study of mutations in the genetic regulatory hierarchy for butterfly eyespot focus determination

The color patterns on the wings of butterflies have been an important model system in evolutionary developmental biology. A recent computational model tested genetic regulatory hierarchies hypothesized to underlie the formation of butterfly eyespot foci [Evans, T.M., Marcus, J.M., 2006. A simulation study of the genetic regulatory hierarchy for butterfly eyespot focus determination. Evol. Dev. 8, 273-283]. The computational model demonstrated that one proposed hierarchy was incapable of reproducing the known patterns of gene expression associated with eyespot focus determination in wild-type butterflies, but that two slightly modified alternative hierarchies were capable of reproducing all of the known gene expressions patterns. Here we extend the computational models previously implemented in Delphi 2.0 to two mutants derived from the squinting bush brown butterfly (Bicyclus anynana). These two mutants, comet and Cyclops, have aberrantly shaped eyespot foci that are produced by different mechanisms. The comet mutation appears to produce a modified interaction between the wing margin and the eyespot focus that results in a series of comet-shaped eyespot foci. The Cyclops mutation causes the failure of wing vein formation between two adjacent wing-cells and the fusion of two adjacent eyespot foci to form a single large elongated focus in their place. The computational approach to modeling pattern formation in these mutants allows us to make predictions about patterns of gene expression, which are largely unstudied in butterfly mutants. It also suggests a critical experiment that will allow us to distinguish between two hypothesized genetic regulatory hierarchies that may underlie all butterfly eyespot foci.