An avoidance learning submodel for a general predation model

Summary This paper attempts to determine the effect on the number of prey eaten by predators of the addition of the component avoidance learning by prey to a computer model of the predation process developed by Holling. Generality was retained by concentrating upon a basic aspect of the prey's behaviour, its distance of reaction to an approaching predator. The zebra danio (Brachydanio rerio), a small freshwater fish, was used as an analogue of a general vertebrate prey. The predator used was the largemouth bass (Micropterus salmoides).Previous work (Dill, 1973b) showed that prey reactive distance increased with increasing experience with the predator. In the present study, this increased prey reactive distance is shown to increase predator pursuit time and hypothesized to decrease predator pursuit success. These relationships were expressed mathematically and built into Holling's (1965, 1966) model of the predation process, along with an equation describing the way in which reactive distance increases following an unsuccessful attack. Other changes necessitated in the model by the addition of the avoidance learning component included: a) Modifications of the calculation of search time to remove a previously implicit time spent unsuccessfully pursuing prey, and to correct the density of prey to account for those whose reactive distances exceed that of the predator and are therefore not susceptible to discovery; b) Addition of a new subroutine (CHASE) to calculate pursuit time, unsuccessful pursuit time, pursuit success, and strike success; c) Changes in subroutine ADCOM to assign prey to different classes (with different reactive distances) according to the number of times they have been unsuccessfully attacked; and d) Addition of a stochastic element via random numbers to determine the class to which an attacked prey belongs, the time to refuge, and the predator's strike success.Simulation was used to explore the consequences of these additions. The capability of learning substantially increased the prey's probability of surviving subsequent attack. Addition of an avoidance learning component caused declines in the predator's functional responses to both prey and predator density. The new component was also suggested to decrease the predator's numerical response to prey density and to increase the probability of stability in a predator-prey interaction.From a thesis submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy, University of British Columbia.     

Sneaky egg-eating in Telmatherina sarasinorum, an endemic fish from Sulawesi

Observations of a novel behavioural tactic employed by egg-eating male Telmatherina sarasinorum are described. Four T. sarasinorum males were observed actively courting females of closely related Telmatherina antoniae , enticing the female to spawn, and then eating the eggs. The possible evolutionary implications of sneaky egg-eating behaviour are discussed.     

Designing polymers that mimic biomolecules.

A new field is emerging. Chemists are beginning to synthesize polymers with properties that are similar to those of proteins and RNA. Recent studies have identified oligomer backbones that form stable secondary structures. It is now possible to assemble specific sequences of diverse monomer sets into chain lengths that are nearly sufficient for tertiary structure formation. Such molecules will teach us how natural biopolymers fold; they will also enable us to design synthetic heteropolymers with novel structures and desirable functions.     

NMR-assisted protein structure prediction with MELDxMD

We describe the performance of MELD-accelerated molecular dynamics (MELDxMD) in determining protein structures in the NMR-data-assisted category in CASP13. Seeded from web server predictions, MELDxMD was found best in the NMR category, over 17 targets, outperforming the next-best groups by a factor of ~4 in z-score. MELDxMD gives ensembles, not single structures; succeeds on a 326-mer, near the current upper limit for NMR structures; and predicts structures that match experimental residual dipolar couplings even though the only NMR-derived data used in the simulations was NOE-based ambiguous atom–atom contacts and backbone dihedrals. MELD can use noisy and ambiguous experimental information to reduce the MD search space. We believe MELDxMD is a promising method for determining protein structures from NMR data.     

Quantitative Proteome Analysis of Temporally Resolved Phagosomes Following Uptake Via Key Phagocytic Receptors

Macrophages operate at the forefront of innate immunity and their discrimination of foreign versus “self” particles is critical for a number of responses including efficient pathogen killing, antigen presentation, and cytokine induction. In order to efficiently destroy the particles and detect potential threats, macrophages express an array of receptors to sense and phagocytose prey particles. In this study, we accurately quantified a proteomic time-course of isolated phagosomes from murine bone marrow-derived macrophages induced by particles conjugated to seven different ligands representing pathogen-associated molecular patterns, immune opsonins or apoptotic cell markers. We identified a clear functional differentiation over the three timepoints and detected subtle differences between certain ligand-phagosomes, indicating that triggering of receptors through a single ligand type has mild, but distinct, effects on phagosome proteome and function. Moreover, our data shows that uptake of phosphatidylserine-coated beads induces an active repression of NF-κB immune responses upon Toll-like receptor (TLR)-activation by recruitment of anti-inflammatory regulators to the phagosome. This data shows for the first time a systematic time-course analysis of bone marrow-derived macrophages phagosomes and how phagosome fate is regulated by the receptors triggered for phagocytosis.Macrophages exist in many different tissue subsets, are extremely plastic in response to cytokines and pathogen-associated molecular patterns and perform a wide range of biological functions (1, 2). One of the most important functions of macrophages is phagocytosis, defined as the active uptake of large particles (>0.5 μm) by cells (3). Phagocytosis is an important cellular mechanism for almost all eukaryotes, highly conserved in evolution (4), and, in mammals, is a key part of the innate immune response to invading microorganisms. Moreover, during homeostasis and development, macrophages phagocytose apoptotic cells and cell debris to recycle cellular building blocks (5, 6). Phagocytosis is induced through the binding of particles as diverse as microbes, apoptotic cells, or even inert beads to cell surface receptors. After internalization, newly formed phagosomes engage in a maturation process that involves fusion with various organelles, including endosomes and ultimately lysosomes (7, 8). This leads to the formation of phagolysosomes that degrade the foreign matter. Antigens from the particle are presented via MHC class I and II molecules, bridging innate and adaptive immunity.In order to effectively phagocytose the diverse types of particulates they can encounter, macrophages express a vast array of receptors to sense and respond to the different ligands; however, only a small subset are solely sufficient to trigger phagocytosis (9). The classic phagocytic receptors are the Fc receptor, which internalizes immunoglobulin-bound particles (10), and the complement receptors, which binds to complement-opsonized particles (11). Other well characterized ligands for phagocytic receptors include mannan, a polysaccharide common in bacterial membranes and fungal cell walls (12), that activates mannose receptors (13, 14); lipopolysaccharide (LPS)¹, a glycolipid that constitutes the major portion of the outermost membrane of Gram-negative bacteria, that triggers CD14 as well as scavenger receptors and toll-like receptors (15–20); and phosphatidylserine (PS), a lipid normally restricted to the inner leaflet of eukaryotic plasma membranes, but exposed in the outer leaflet during apoptosis. PS provides an “eat me” signal for macrophage clearance (21, 22) and triggers a range of receptors including TIM-4, BAI1, and Stabilin-2 (23–27). Similarly, calreticulin, an endoplasmic reticulum protein that is also transported to the plasma membrane serves as a apoptotic signal has been proposed as a phagocytic ligand triggering the phagocytic receptor low-density lipoprotein receptor-related protein (LRP) (28–30).Although it is established that phagosome function is affected by various activation states, including rate of maturation, degradative capacity, and antigen cross-presentation capabilities (31–33), controversy exists around whether phagosome activity can be controlled directly, without prior activation, by receptor engagement at the phagosome level during biogenesis (34–38). Here, we dissect the role that individual ligands play in controlling downstream phagosome maturation using a reductionist strategy of ligating single ligands to microparticles and analyzing resulting phagosomes by quantitative proteomics and fluorescent phagosome functional assays.     

A new stereophotographic technique for analyzing the three-dimensional structure of fish schools

Synopsis A technique using two downward-directed 35 mm cameras has been modified to measure the three-dimensional structure of fish schools. The resulting stereo pairs of photographs are analyzed, producing the 3-coordinate location of each fish's nose, after correction for lens distortion and refraction. Separation angles (bearing and elevation) and distance can then be determined for any pair of fish in the school. The technique's high level of accuracy is demonstrated for an underwater calibration field. It is then applied to the measurement of the 3-D structure of schools of coho salmon (Oncorhymchus kisutch) swimming in a hatchery trough. Although the fish were not organized in a rigid crystal lattice, the analysis provided some evidence of structure.     

Effects of varying salinities on Lepeophtheirus salmonis survival on juvenile pink and chum salmon

Survival of the sea louse Lepeophtheirus salmonis on juvenile Pacific salmon Oncorhynchus gorbuscha and Oncorhynchus keta was examined with respect to salinity (0, 7, 14, 21 and 28). Rapid mortality was observed in fresh water (0) but motile stage sea lice tolerated higher salinities (7, 14, 21 and 28) for up to 7 days. These findings suggest that salinities juvenile Pacific salmon typically encounter during early marine residence have little affect on motile sea louse survival.