Peripheral encoding of behaviorally relevant acoustic signals in a vocal fish: single tones

The midshipman fish, Porichthys notatus, generates acoustic signals for intraspecific communication. Nesting males produce long-duration “hums” which attract gravid females and can be effectively mimicked by pure tones. In this study we examine the encoding of tonal signals by the midshipman peripheral auditory system. Single-unit recordings were made from afferents innervating the sacculus while presenting sounds via an underwater loudspeaker. Units were characterized by iso-intensity spike rate and vector strength of synchronization curves, as well as by peri-stimulus time histograms. Additionally, response-intensity curves and responses to long-duration (up to 10 s) stimuli were obtained. As has been seen in other teleosts, afferents had highly variable activity profiles. Excitatory frequencies ranged from 60 to over 300 Hz with most units responding best around 70 or 140 Hz. Thresholds at 90 Hz ranged from 95 to 145 dB re 1 μPa. Strong synchronization provided a robust temporal code of frequency, comparable to that described for goldfish. Spike rate showed varying degrees of adaptation but high rates were generally maintained even for 10-s stimuli. The midshipman peripheral auditory system is well suited to encoding conspecific communication signals, but nonetheless shares many response patterns with the auditory system of other teleosts. Accepted: 10 February 1999     

Chemotaxis and random motility in unsteady chemoattractant fields: a computational study

We discuss a generic computational model which captures the effects of transient chemoattractant concentration on the chemotactic motility of individual cells. The model solves the appropriate unsteady chemoattractant transport equation using finite differences, while simultaneously executing biased random walks representing individual cells. The simulations were implemented for a 2D homogeneous domain, and two case studies were considered. In the first case study, we consider a single-point source at the origin of the domain which produces chemoattractant, while other cells execute biased random walks toward this point source. We observe that for continuous chemoattractant production, chemoattractant diffusivity has no effect on cell motility, as measured by the mean of time to reach the source. However, in the case of pulsed random production with a specific average duty cycle, the mean time-to-contact is generally minimal with respect to chemoattractant diffusivity over a moderate range of diffusivities. In the second case study, two mobile cells which simultaneously secrete chemoattractant are initially placed a certain distance apart and are then allowed to execute biased random walks. Our model shows that a pulsed random protocol for chemoattractant production facilitates the two cells "finding" one another compared to continuous production. From this case study we also learn that there exists a range of moderate chemoattractant diffusivities for which the mean time-to-contact is minimal when cells both produce/detect chemoattractant and chemotactically migrate. Using these case studies, we discuss how transience in chemoattractant concentration becomes important in characterizing the effectiveness of chemotaxis.     

Your attention please: increasing ambient noise levels elicits a change in communication behaviour in humpback whales (Megaptera novaeangliae)

High background noise is an important obstacle in successful signal detection and perception of an intended acoustic signal. To overcome this problem, many animals modify their acoustic signal by increasing the repetition rate, duration, amplitude or frequency range of the signal. An alternative method to ensure successful signal reception, yet to be tested in animals, involves the use of two different types of signal, where one signal type may enhance the other in periods of high background noise. Humpback whale communication signals comprise two different types: vocal signals, and surface-generated signals such as ‘breaching’ or ‘pectoral slapping’. We found that humpback whales gradually switched from primarily vocal to primarily surface-generated communication in increasing wind speeds and background noise levels, though kept both signal types in their repertoire. Vocal signals have the advantage of having higher information content but may have the disadvantage of loosing this information in a noisy environment. Surface-generated sounds have energy distributed over a greater frequency range and may be less likely to become confused in periods of high wind-generated noise but have less information content when compared with vocal sounds. Therefore, surface-generated sounds may improve detection or enhance the perception of vocal signals in a noisy environment.     

Parameter estimation in a model for multidimensional recording of neuronal data: a Gibbsian approximation approach

This article proposes improved numerical procedures for estimating parameters in a spatiotemporal lattice model introduced for the analysis of cortical activities monitored from arrays of diodes. The numerical algorithms are based on approximations inspired by statistical physics. Both Gibbsian and mean-field approximations are used; they allow for computing local conditional probabilities inside the lattice. The statistical procedures rely on the computation of pseudomaximum-likelihood estimators. The estimators are evaluated on the basis of Monte Carlo simulations. These simulations show that mean-field approximations are useful for reducing the variance of estimators when the data are recorded from arrays of 144 diodes (which are in accordance with standard practice). In light of these improved methods, we give new interpretations for a data set obtained from optical recording of a Guinea pig's auditory cortex in response to pure tone stimulations.     

Sexual differences in auditory sensitivity: mismatch of hearing threshold and call frequency in a tettigoniid (orthoptera,tettigoniidae: Zaprochilinae)

Summary Sexual dimorphism of the ear of an undescribed species of zaprochiline tettigoniid is described. The internal trachea, dedicated to hearing in other tettigoniids, is unmodified in the male but fully developed in the female. The external auditory spiracle is also lost in the male. In contrast, there is no difference between the sexes in the number of sensilla within the hearing organ. The male is 10 dB less sensitive than the female. The characteristic frequency of the hearing organ at 35 kHz does not match the carrier frequency of the male's call at 51 kHz. As a result of this mismatch the female is remarkably insensitive to the male's call (threshold at 75 dB SPL), and the male is even less sensitive (thresholds80 dB SPL). In nature this provides a maximum hearing range of the male of less than 50 cm.     

Understanding cyclical thrombocytopenia: a mathematical modeling approach

Cyclical thrombocytopenia (CT) is a rare hematological disease characterized by periodic oscillations in the platelet count. Although first reported in 1936, the pathogenesis and an effective therapy remain to be identified. Since besides fluctuations in platelet levels the patients hematological profile have been consistently normal, a destabilization of a peripheral control mechanism might play an important role in the genesis of this disorder. In this paper, we investigate through computer simulations the mechanisms underlying the platelet oscillations observed in CT. First, we collected the data published in the last 40 years and quantified the significance of the platelet fluctuations using Lomb-Scargle periodograms. Our analysis reveals that the incidence of the statistically significant periodic data is equally distributed in men and women. The mathematical model proposed in this paper captures the essential features of hematopoiesis and successfully duplicates the characteristics of CT. With the same parameter changes, the model is able to fit the platelet counts and to qualitatively reproduce the TPO oscillations (when data is available). Our results indicate that a variation in the megakaryocyte maturity, a slower relative growth rate of megakaryocytes, as well as an increased random destruction of platelets are the critical elements generating the platelet oscillations in CT.     

Comprehensive mutagenesis of HIV-1 protease: a computational geometry approach

A computational geometry technique based on Delaunay tessellation of protein structure, represented by C(alpha) atoms, is used to study effects of single residue mutations on sequence-structure compatibility in HIV-1 protease. Profiles of residue scores derived from the four-body statistical potential are constructed for all 1881 mutants of the HIV-1 protease monomer and compared with the profile of the wild-type protein. The profiles for an isolated monomer of HIV-1 protease and the identical monomer in a dimeric state with an inhibitor are analyzed to elucidate changes to structural stability. Protease residues shown to undergo the greatest impact are those forming the dimer interface and flap region, as well as those known to be involved in inhibitor binding.     

Gating and conduction of nano-channel forming proteins: a computational approach

Monitoring conformational changes in ion channels is essential to understand their gating mechanism. Here, we explore the structural dynamics of four outer membrane proteins with different structures and functions in the slowest nonzero modes of vibration. Normal mode analysis was performed on the modified elastic network model of channel in the membrane. According to our results, when membrane proteins were analyzed in the dominant mode, the composed pores, TolC and α-hemolysin showed large motions at the intramembrane β-barrel region while, in other porins, OmpA and OmpF, largest motions observed in the region of external flexible loops. A criterion based on equipartition theorem was used to measure the possible amplitude of vibration in channel forming proteins. The current approach complements theoretical and experimental techniques including HOLE, Molecular Dynamics (MD), and voltage clamp used to address the channel’s structure and dynamics and provides the means to conduct a theoretical simultaneous study of the structure and function of the channel.

An animated interactive 3D complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:3     

Responses of mink to auditory stimuli: Prerequisites for applying the ‘cognitive bias’ approach

The aim of the study was to determine and validate prerequisites for applying a cognitive (judgement) bias approach to assessing welfare in farmed mink (Neovison vison). We investigated discrimination ability and associative learning ability using auditory cues. The mink (n = 15 females) were divided into two groups (High, n = 8; Low, n = 7, representing the frequency of the tone they were habituated to, 18 and 2 kHz respectively) and were tested using a habituation–dishabituation procedure in experiment 1. In experiment 2 one auditory stimulus was followed by an inter-trial-interval (safe/neutral situation), whereas another auditory stimulus was followed by an aversive stimulus (air blow) before the inter-trial-interval (danger situation). We observed behaviour including latencies to show a response during both experiments. The High mink showed significant habituation in experiment 1 but the Low mink only showed habituation in experiment 2. Regardless of the frequency used (2 and 18 kHz), cues predicting the danger situation initially elicited slower responses compared to those predicting the safe situation but quickly became faster. Using auditory cues as discrimination stimuli for female farmed mink in a judgement bias approach would thus appear to be feasible. However several specific issues are to be considered in order to successfully adapt a cognitive bias approach to mink, and these are discussed.     

Central auditory neurophysiology of a sound-producing fish: the mesencephalon of Pollimyrus isidori (Mormyridae)

This paper describes the auditory neurophysiology of the mesencephalon of P. isidori, a soundproducing mormyrid fish. Mormyrids have a specialized pressure-sensitive auditory periphery, and anatomical studies indicate that acoustic information is relayed to the mesencephalic nucleus MD. Fish were stimulated with tone bursts and clicks, and responses of MD neurons were recorded extracellularly. Auditory neurons had best frequencies (BF) and best sensitivities (BS) that fell within the range of frequencies and levels of the natural communication sounds of these fish. BSs were in the range of 0 to — 35 dB (re. 1.0 dyne/cm²). Many of the neurons were tuned (Q_{10 dB}: 2–6), and had BFs in the range of 100–300 Hz where the animal's sounds have their peak energy. A range of different physiological cell types were encountered, including phasic, sustained, and complex neurons. Some of the sustained neurons showed strong phase-locking to tones. Many neurons exhibited non-monotonic rate-level functions. Frequencies flanking the BF often caused a reduction in spontaneous activity suggesting inhibition. Many neurons showed excellent representation of click-trains, and some showed a temporal representation of inter-click-intervals with errors less than 1 ms.Abbreviations BF best frequency - BS best sensitivity - ELa anterior exterolateral toral nucleus - ELp posterior exterolateral toral nucleus - EOCD electric organ command discharge - FFT fast Fourier transform - HRP horseradish peroxidase - ICI inter-clickinterval - MD mediodorsal toral nucleus (=auditory nucleus) - OR onset response rate - PSTH peri-stimulus-time-histogram - R synchronization coefficient - RA response area - SS steady state response rate     

Aerodynamic performance of a hovering hawkmoth with flexible wings: a computational approach

Insect wings are deformable structures that change shape passively and dynamically owing to inertial and aerodynamic forces during flight. It is still unclear how the three-dimensional and passive change of wing kinematics owing to inherent wing flexibility contributes to unsteady aerodynamics and energetics in insect flapping flight. Here, we perform a systematic fluid-structure interaction based analysis on the aerodynamic performance of a hovering hawkmoth, Manduca, with an integrated computational model of a hovering insect with rigid and flexible wings. Aerodynamic performance of flapping wings with passive deformation or prescribed deformation is evaluated in terms of aerodynamic force, power and efficiency. Our results reveal that wing flexibility can increase downwash in wake and hence aerodynamic force: first, a dynamic wing bending is observed, which delays the breakdown of leading edge vortex near the wing tip, responsible for augmenting the aerodynamic force-production; second, a combination of the dynamic change of wing bending and twist favourably modifies the wing kinematics in the distal area, which leads to the aerodynamic force enhancement immediately before stroke reversal. Moreover, an increase in hovering efficiency of the flexible wing is achieved as a result of the wing twist. An extensive study of wing stiffness effect on aerodynamic performance is further conducted through a tuning of Young's modulus and thickness, indicating that insect wing structures may be optimized not only in terms of aerodynamic performance but also dependent on many factors, such as the wing strength, the circulation capability of wing veins and the control of wing movements.     

Novel families of toxin-like peptides in insects and mammals: a computational approach

Most animal toxins are short proteins that appear in venom and vary in sequence, structure and function. A common characteristic of many such toxins is their apparent structural stability. Sporadic instances of endogenous toxin-like proteins that function in non-venom context have been reported. We have utilized machine learning methodology, based on sequence-derived features and guided by the notion of structural stability, in order to conduct a large-scale search for toxin and toxin-like proteins. Application of the method to insect and mammalian sequences revealed novel families of toxin-like proteins. One of these proteins shows significant similarity to ion channel inhibitors that are expressed in cone snail and assassin bug venom, and is surprisingly expressed in the bee brain. A toxicity assay in which the protein was injected to fish induced a strong yet reversible paralytic effect. We suggest that the protein may function as an endogenous modulator of voltage-gated Ca(2+) channels. Additionally, we have identified a novel mammalian cluster of toxin-like proteins that are expressed in the testis. We suggest that these proteins might be involved in regulation of nicotinic acetylcholine receptors that affect the acrosome reaction and sperm motility. Finally, we highlight a possible evolutionary link between venom toxins and antibacterial proteins. We expect our methodology to enhance the discovery of additional novel protein families.     

A novel yeast two-hybrid approach to identify CDPK substrates: characterization of the interaction between AtCPK11 and AtDi19, a nuclear zinc finger protein

Calcium-dependent protein kinases (CDPKs) are sensor-transducer proteins capable of decoding calcium signals in diverse phosphorylation-dependent calcium signaling networks in plants and some protists. Using a novel yeast two-hybrid (YTH) approach with constitutively active and/or catalytically inactive forms of AtCPK11 as bait, we identified AtDi19 as an AtCPK11-interacting protein. AtDi19 is a member of a small family of stress-induced genes. The interaction was confirmed using pull-down assays with in vitro translated AtCPK11 and GST-AtDi19 and localization studies in Arabidopsis protoplasts cotransfected with AtCPK11:GFP and AtDi19:DsRed2 protein fusions. We further showed that the interaction of AtDi19 is specific to both AtCPK4 and AtCPK11, whereas other closely related CPKs from Arabidopsis interacted weakly (e.g., AtCPK12) or did not interact (e.g., AtCPK26, AtCPK5 and AtCPK1) with AtDi19. Deletion analyses showed that a region containing two predicted nuclear localization signals (NLS) and a nuclear export signal (NES) of AtDi19 is essential for interaction with AtCPK11. We further demonstrated that AtDi19 is phosphorylated by AtCPK11 in a Ca(2+)-dependent manner at Thr105 and Ser107 within the AtDi19 bipartite NLS using in vitro kinase assays. Our data suggest that disruption of the autoinhibitor domain leading to the formation of a constitutively active CDPK may stabilize kinase-substrate interactions without affecting specificity.     

Modeling the structure of agitoxin in complex with the Shaker K+ channel: a computational approach based on experimental distance restraints extracted from thermodynamic mutant cycles

Computational methods are used to determine the three-dimensional structure of the Agitoxin (AgTx2)-Shaker complex. In a first stage, a large number of models of the complex are generated using high temperature molecular dynamics, accounting for side chain flexibility with distance restraints deduced from thermodynamic analysis of double mutant cycles. Four plausible binding mode candidates are found using this procedure. In a second stage, the quality and validity of the resulting complexes is assessed by examining the stability of the binding modes during molecular dynamics simulations with explicit water molecules and by calculating the binding free energies of mutant proteins using a continuum solvent representation and comparing with experimental data. The docking protocol and the continuum solvent model are validated using the Barstar-Barnase and the lysozyme-antibody D1.2 complexes, for which there are high-resolution structures as well as double mutant data. This combination of computational methods permits the identification of two possible structural models of AgTx2 in complex with the Shaker K+ channel, additional structural analysis providing further evidence in favor of a single model. In this final complex, the toxin is bound to the extracellular entrance of the channel along the pore axis via a combination of hydrophobic, hydrogen bonding, and electrostatic interactions. The magnitude of the buried solvent accessible area corresponding to the protein-protein contact is on the order of 1000 A with roughly similar contributions from each of the four subunits. Some side chains of the toxin adopt different conformation than in the experimental solution structure, indicating the importance of an induced-fit upon the formation of the complex. In particular, the side chain of Lys-27, a residue highly conserved among scorpion toxins, points deep into the pore with its positively charge amino group positioned at the outer binding site for K+. Specific site-directed mutagenesis experiments are suggested to verify and confirm the structure of the toxin-channel complex.     

Image analysis as a tool for quantitative phycology: a computational approach to cyanobacterial taxa identification

In the following work we discuss the application of image processing and pattern recognition to the field of quantitative phycology. We overview the area of image processing and review previously published literature pertaining to the image analysis of phycological images and, in particular, cyanobacterial image processing. We then discuss the main operations used to process images and quantify data contained within them. To demonstrate the utility of image processing to cyanobacteria classification, we present details of an image analysis system for automatically detecting and classifying several cyanobacterial taxa of Lake Biwa, Japan. Specifically, we initially target the genus Microcystis for detection and classification from among several species of Anabaena. We subsequently extend the system to classify a total of six cyanobacteria species. High-resolution microscope images containing a mix of the above species and other nontargeted objects are analyzed, and any detected objects are removed from the image for further analysis. Following image enhancement, we measure object properties and compare them to a previously compiled database of species characteristics. Classification of an object as belonging to a particular class membership (e.g., “Microcystis,”“A. smithii,”“Other,” etc.) is performed using parametric statistical methods. Leave-one-out classification results suggest a system error rate of approximately 3%. Received: September 6, 1999 / Accepted: February 6, 2000     

Understanding the impact of root morphology on overturning mechanisms: a modelling approach

BACKGROUND AND AIMS: The Finite Element Method (FEM) has been used in recent years to simulate overturning processes in trees. This study aimed at using FEM to determine the role of individual roots in tree anchorage with regard to different rooting patterns, and to estimate stress distribution in the soil and roots during overturning. METHODS: The FEM was used to carry out 2-D simulations of tree uprooting in saturated soft clay and loamy sand-like soil. The anchorage model consisted of a root system embedded in a soil block. Two root patterns were used and individual roots removed to determine their contribution to anchorage. KEY RESULTS: In clay-like soil the size of the root-soil plate formed during overturning was defined by the longest roots. Consequently, all other roots localized within this plate had no influence on anchorage strength. In sand-like soil, removing individual root elements altered anchorage resistance. This result was due to a modification of the shape and size of the root-soil plate, as well as the location of the rotation axis. The tap root and deeper roots had more influence on overturning resistance in sand-like soil compared with clay-like soil. Mechanical stresses were higher in the most superficial roots and also in leeward roots in sand-like soil. The relative difference in stresses between the upper and lower sides of lateral roots was sensitive to root insertion angle. Assuming that root eccentricity is a response to mechanical stresses, these results explain why eccentricity differs depending on root architecture. CONCLUSIONS: A simple 2-D Finite Element model was developed to better understand the mechanisms involved during tree overturning. It has been shown how root system morphology and soil mechanical properties can modify the shape of the root plate slip surface as well as the position of the rotation axis, which are major components of tree anchorage.     

Understanding the dynamics of Salmonella infections in dairy herds: a modelling approach

There is evidence of variation in the infection dynamics of different Salmonella serotypes in cattle--ranging from transient epidemics to long term persistence and recurrence. We seek to identify possible causes of these differences. In this study we present mathematical models which describe both managed population dynamics and epidemiology and use these to investigate the effects of demographic and epidemiological factors on epidemic behaviour and threshold for invasion. In particular, when the system is perturbed by higher culling or pathogen-induced mortality we incorporate mechanisms to constrain the lactating herd size to remain constant in the absence of pathogen or to lie within a fairly small interval in the presence of pathogen. A combination of numerical and analytical techniques is used to analyse the models. We find that the epidemiologically dominating management group can change from the dry/lactating cycle to the weaned group with increasing culling rate. Pseudovertical transmission is found to have little effect on the invasion criteria, while indirect transmission has significant influence. Pathogen-induced mortality, recovery, immune response and pathogen removal are found to be factors inducing damped oscillations; variation in these factors between Salmonella serotypes may be responsible for some of the observed differences in within herd dynamics. Specifically, higher pathogen-induced mortality, shorter infectious period, more persistent immune response and more rapid removal of faeces result in a lower number of infectives and smaller epidemics but a greater tendency for damped oscillations.