Fractional Chemotaxis Diffusion Equations

We introduce mesoscopic and macroscopic model equations of chemotaxis with anomalous subdiffusion for modelling chemically directed transport of biological organisms in changing chemical environments with diffusion hindered by traps or macro-molecular crowding. The mesoscopic models are formulated using Continuous Time Random Walk master equations and the macroscopic models are formulated with fractional order differential equations. Different models are proposed depending on the timing of the chemotactic forcing. Generalizations of the models to include linear reaction dynamics are also derived. Finally a Monte Carlo method for simulating anomalous subdiffusion with chemotaxis is introduced and simulation results are compared with numerical solutions of the model equations. The model equations developed here could be used to replace Keller-Segel type equations in biological systems with transport hindered by traps, macro-molecular crowding or other obstacles.Comment: 25page

Anomalous thermodynamics at the micro-scale

Particle motion at the micro-scale is an incessant tug-of-war between thermal fluctuations and applied forces on one side, and the strong resistance exerted by fluid viscosity on the other. Friction is so strong that completely neglecting inertia - the overdamped approximation - gives an excellent effective description of the actual particle mechanics. In sharp contrast with this result, here we show that the overdamped approximation dramatically fails when thermodynamic quantities such as the entropy production in the environment is considered, in presence of temperature gradients. In the limit of vanishingly small, yet finite inertia, we find that the entropy production is dominated by a contribution that is anomalous, i.e. has no counterpart in the overdamped approximation. This phenomenon, that we call entropic anomaly, is due to a symmetry-breaking that occurs when moving to the small, finite inertia limit. Strong production of anomalous entropy is traced back to intense sweeps down the temperature gradient.Comment: 4 pages, 1 figure, supplementary information uploaded as a separate pdf file (see other formats link

Human cancers over express genes that are specific to a variety of normal human tissues

We have analyzed gene expression data from 3 different kinds of samples: normal human tissues, human cancer cell lines and leukemic cells from lymphoid and myeloid leukemia pediatric patients. We have searched for genes that are over expressed in human cancer and also show specific patterns of tissue-dependent expression in normal tissues. Using the expression data of the normal tissues we identified 4346 genes with a high variability of expression, and clustered these genes according to their relative expression level. Of 91 stable clusters obtained, 24 clusters included genes preferentially expressed either only in hematopoietic tissues or in hematopoietic and 1-2 other tissues; 28 clusters included genes preferentially expressed in various non-hematopoietic tissues such as neuronal, testis, liver, kidney, muscle, lung, pancreas and placenta. Analysis of the expression levels of these 2 groups of genes in the human cancer cell lines and leukemias, identified genes that were highly expressed in cancer cells but not in their normal counterparts, and were thus over expressed in the cancers. The different cancer cell lines and leukemias varied in the number and identity of these over expressed genes. The results indicate that many genes that are over expressed in human cancer cells are specific to a variety of normal tissues, including normal tissues other than those from which the cancer originated. It is suggested that this general property of cancer cells plays a major role in determining the behavior of the cancers, including their metastatic potential.Comment: To appear in PNA

Hydrodynamic object recognition using pressure sensing

Hydrodynamic sensing is instrumental to fish and some amphibians. It also represents, for underwater vehicles, an alternative way of sensing the fluid environment when visual and acoustic sensing are limited. To assess the effectiveness of hydrodynamic sensing and gain insight into its capabilities and limitations, we investigated the forward and inverse problem of detection and identification, using the hydrodynamic pressure in the neighbourhood, of a stationary obstacle described using a general shape representation. Based on conformal mapping and a general normalization procedure, our obstacle representation accounts for all specific features of progressive perceptual hydrodynamic imaging reported experimentally. Size, location and shape are encoded separately. The shape representation rests upon an asymptotic series which embodies the progressive character of hydrodynamic imaging through pressure sensing. A dynamic filtering method is used to invert noisy nonlinear pressure signals for the shape parameters. The results highlight the dependence of the sensitivity of hydrodynamic sensing not only on the relative distance to the disturbance but also its bearing

Nemo: a computational tool for analyzing nematode locomotion

The nematode Caenorhabditis elegans responds to an impressive range of chemical, mechanical and thermal stimuli and is extensively used to investigate the molecular mechanisms that mediate chemosensation, mechanotransduction and thermosensation. The main behavioral output of these responses is manifested as alterations in animal locomotion. Monitoring and examination of such alterations requires tools to capture and quantify features of nematode movement. In this paper, we introduce Nemo (nematode movement), a computationally efficient and robust two-dimensional object tracking algorithm for automated detection and analysis of C. elegans locomotion. This algorithm enables precise measurement and feature extraction of nematode movement components. In addition, we develop a Graphical User Interface designed to facilitate processing and interpretation of movement data. While, in this study, we focus on the simple sinusoidal locomotion of C. elegans, our approach can be readily adapted to handle complicated locomotory behaviour patterns by including additional movement characteristics and parameters subject to quantification. Our software tool offers the capacity to extract, analyze and measure nematode locomotion features by processing simple video files. By allowing precise and quantitative assessment of behavioral traits, this tool will assist the genetic dissection and elucidation of the molecular mechanisms underlying specific behavioral responses.Comment: 12 pages, 2 figures. accepted by BMC Neuroscience 2007, 8:8

Asexual and sexual replication in sporulating organisms

This paper develops models describing asexual and sexual replication in sporulating organisms. Replication via sporulation is the replication strategy for all multicellular life, and may even be observed in unicellular life (such as with budding yeast). We consider diploid populations replicating via one of two possible sporulation mechanisms: (1) Asexual sporulation, whereby adult organisms produce single-celled diploid spores that grow into adults themselves. (2) Sexual sporulation, whereby adult organisms produce single-celled diploid spores that divide into haploid gametes. The haploid gametes enter a haploid "pool", where they may recombine with other haploids to form a diploid spore that then grows into an adult. We consider a haploid fusion rate given by second-order reaction kinetics. We work with a simplified model where the diploid genome consists of only two chromosomes, each of which may be rendered defective with a single point mutation of the wild-type. We find that the asexual strategy is favored when the rate of spore production is high compared to the characteristic growth rate from a spore to a reproducing adult. Conversely, the sexual strategy is favored when the rate of spore production is low compared to the characteristic growth rate from a spore to a reproducing adult. As the characteristic growth time increases, or as the population density increases, the critical ratio of spore production rate to organism growth rate at which the asexual strategy overtakes the sexual one is pushed to higher values. Therefore, the results of this model suggest that, for complex multicellular organisms, sexual replication is favored at high population densities, and low growth and sporulation rates.Comment: 8 pages, 5 figures, to be submitted to Journal of Theoretical Biology, figures not included in this submissio

Rational design of biosafe crop resistance to a range of nematodes using RNA interference

Double stranded RNA (dsRNA) molecules targeting two genes have been identified that suppress economically important parasitic nematode species of banana. Proteasomal Alpha Subunit 4 (pas-4) and Actin-4 (act-4) were identified from a survey of sequence databases and cloned sequences for genes conserved across four pests of banana, Radopholus similis, Pratylenchus coffeae, Meloidogyne incognita and Helicotylenchus multicinctus. These four species were targeted with dsRNAs containing exact 21 nucleotide matches to the conserved regions. Potential off-target effects were limited by comparison to Caenorhabditis, Drosophila, rat, rice and Arabidopsis genomes. In vitro act-4 dsRNA treatment of R. similis suppressed target gene expression by 2.3 fold, nematode locomotion by 66 ± 4% and nematode multiplication on carrot discs by 49 ± 5%. The best transgenic carrot hairy root lines expressing act-4 or pas-4 dsRNA reduced transcript message abundance of target genes in R. similis by 7.9 fold and 4 fold and nematode multiplication by 94 ± 2% and 69 ± 3%, respectively. The same act-4 and pas-4 lines reduced P. coffeae target transcripts by 1.7 and 2 fold and multiplication by 50 ± 6% and 73 ± 8%. Multiplication of M. incognita on the pas-4 lines was reduced by 97 ± 1% and 99 ± 1% while target transcript abundance was suppressed 4.9 and 5.6 fold. There was no detectable RNAi effect on non-target nematodes exposed to dsRNAs targeting parasitic nematodes. This work defines a framework for development of a range of non-protein defences to provide broad resistance to pests and pathogens of crops

The Effect of Proton Temperature Anisotropy on the Solar Minimum Corona and Wind

A semi-empirical, axisymmetric model of the solar minimum corona is developed by solving the equations for conservation of mass and momentum with prescribed anisotropic temperature distributions. In the high-latitude regions, the proton temperature anisotropy is strong and the associated mirror force plays an important role in driving the fast solar wind; the critical point where the outflow velocity equals the parallel sound speed is reached already at 1.5 Rsun from Sun center. The slow wind arises from a region with open field lines and weak anisotropy surrounding the equatorial streamer belt. The model parameters were chosen to reproduce the observed latitudinal extent of the equatorial streamer in the corona and at large distance from the Sun. We find that the magnetic cusp of the closed-field streamer core lies at about 1.95 Rsun. The transition from fast to slow wind is due to a decrease in temperature anisotropy combined with the non-monotonic behavior of the non-radial expansion factor in flow tubes that pass near the streamer cusp. In the slow wind, the plasma beta is of order unity and the critical point lies at about 5 Rsun, well beyond the magnetic cusp. The predicted outflow velocities are consistent with OVI Doppler dimming measurements from UVCS/SOHO. We also find good agreement with polarized brightness (pB) measurements from LASCO/SOHO and HI Ly-alpha images from UVCS/SOHO.Comment: 36 pages, 13 figures. AAS LaTeX Macros v5.0. To appear in The Astrophysical Journal, Vol. 598, No. 2, Issue December 1, 200

Low-frequency components in harbor porpoise (Phocoena phocoena) clicks : communication signal, by-products, or artifacts?

Author Posting. © Acoustical Society of America, 2008. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 124 (2008): 4059-4068, doi:10.1121/1.2945154.Underwater sound signals for biosonar and communication normally have different source properties to serve the purposes of generating efficient acoustic backscatter from small objects or conveying information to conspecifics. Harbor porpoises (Phocoena phocoena) are nonwhistling toothed whales that produce directional, narrowband, high-frequency (HF) echolocation clicks. This study tests the hypothesis that their 130 kHz HF clicks also contain a low-frequency (LF) component more suited for communication. Clicks from three captive porpoises were analyzed to quantify the LF and HF source properties. The LF component is 59 (S.E.M=1.45 dB) dB lower than the HF component recorded on axis, and even at extreme off-axis angles of up to 135°, the HF component is 9 dB higher than the LF component. Consequently, the active space of the HF component will always be larger than that of the LF component. It is concluded that the LF component is a by-product of the sound generator rather than a dedicated pulse produced to serve communication purposes. It is demonstrated that distortion and clipping in analog tape recorders can explain some of the prominent LF components reported in earlier studies, emphasizing the risk of erroneous classification of sound types based on recording artifacts.This work was supported by the Carlsberg Foundation and Oticon, and via a Steno Scholarship from the Danish Natural Science Research Council to PTM

Cell morphology governs directional control in swimming bacteria

The ability to rapidly detect and track nutrient gradients is key to the ecological success of motile bacteria in aquatic systems. Consequently, bacteria have evolved a number of chemotactic strategies that consist of sequences of straight runs and reorientations. Theoretically, both phases are affected by fluid drag and Brownian motion, which are themselves governed by cell geometry. Here, we experimentally explore the effect of cell length on control of swimming direction. We subjected Escherichia coli to an antibiotic to obtain motile cells of different lengths, and characterized their swimming patterns in a homogeneous medium. As cells elongated, angles between runs became smaller, forcing a change from a run-and-tumble to a run-and-stop/reverse pattern. Our results show that changes in the motility pattern of microorganisms can be induced by simple morphological variation, and raise the possibility that changes in swimming pattern may be triggered by both morphological plasticity and selection on morphology