Fitting piecewise linear regression functions to biological responses

An iterative approach was achieved for fitting piecewise linear functions to nonrectilinear responses of biological variables. This algorithm is used to estimate the parameters of the two (or more) regression functions and the separation point(s) (thresholds, sensitivities) by statistical approximation. Although it is often unknown whether the response of a biological variable is adequately described by one rectilinear regression function or by piecewise linear regression function(s) with separation point(s), an F test is proposed to determine whether one regression line is the optimal fitted function. A FORTRAN-77 program has been developed for estimating the optimal parameters and the coordinates of the separation point(s). A few sets of data illustrating this kind of problem in the analysis of thermoregulation, osmoregulation, and the neuronal responses are discussed.     

Catch bonds: physical models and biological functions

Force can shorten the lifetimes of receptor-ligand bonds by accelerating their dissociation. Perhaps paradoxical at first glance, bond lifetimes can also be prolonged by force. This counterintuitive behavior was named catch bonds, which is in contrast to the ordinary slip bonds that describe the intuitive behavior of lifetimes being shortened by force. Fifteen years after their theoretical proposal, catch bonds have finally been observed. In this article we review recently published data that have demonstrated catch bonds in the selectin system and suggested catch bonds in other systems, the theoretical models for their explanations, and their function as a mechanism for flow-enhanced adhesion.     

Glowworms: a review of Arachnocampa spp. and kin.

The term 'glowworm' is used in connection with the flightless females of lampyrid fireflies and to describe the luminescent larvae of certain fungus gnats that belong to the subfamilies Arachnocampinae, Keroplatinae and Macrocerinae of the dipteran family Keroplatidae. This review focuses on the luminescent larval fungus gnats. The weakly luminescent species of the Holarctic feed mainly on fungal spores, but some, such as Orfelia fultoni, have turned to a carnivorous diet. Larval Australian and New Zealand Arachnocampa spp. produce brighter in vivo (but not necessarily in vitro) lights, live in cool, damp and dark places and are exclusively predatory. They lure their prey (usually small flying insects) with the help of their blue-green light emissions towards snares consisting of vertical silk threads coated with sticky mucus droplets. Fungus gnats with similar 'fishing lines' are found in the Neotropics, but they are not luminescent. The larval stage is longest in the life cycle of Arachnocampa, lasting up to a year, depending on climatic conditions such as temperature and humidity as well as food supply. In A. luminosa, but not the Australian A. flava, female pupae and even female imagines are luminescent. However, it remains to be demonstrated whether it is the light of the female, a pheromone or both that attract the males. Light organs and the chemical reactions to produce light differ between the holarctic and the Australian/New Zealand species. Prey is attracted only by the glowworm's light; odours of the fishing lines or the glowworms themselves are not involved. Recognition of the prey by the glowworm involves mechano- and chemoreception. The eyes of both larval and adult glowworms are large and functional over a spectral range covering UV to green wavelengths. Adults are poor fliers, live only for a few days, have degenerate mouth parts and do not feed. Maintenance of glowworms in captivity is possible and the impact of tourism on glowworms in natural settings can be minimized through appropriate precautions.     

Teleost polarization vision: how it might work and what it might be good for

In this review, we will discuss the recent literature on fish polarization vision and we will present a model on how the retina processes polarization signals. The model is based on a general retinal-processing scheme and will be compared with the available electrophysiological data on polarization processing in the retina. The results of this model will help illustrate the functional significance of polarization vision for both feeding behaviour and navigation. First, we examine the linkage between structure and function in polarization vision in general.     

Behavioural responses of the yellow emitting annelid Tomopteris helgolandica to photic stimuli

In contrast to most mesopelagic bioluminescent organisms specialised in the emission and reception of blue light, the planktonic annelid Tomopteris helgolandica produces yellow light. This unusual feature has long been suggested to serve for intraspecific communication. Yet, this virtually admitted hypothesis has never been tested. In this behavioural study of spectral colour sensitivity, we first present an illustrated repertoire of the postures and action patterns described by captive specimens. Then video tracking and motion analysis are used to quantify the behavioural responses of singled out worms to photic stimuli imitating intraspecific (yellow) or interspecific (blue) bioluminescent signals. We show the ability of T. helgolandica to react and to contrast its responses to bioluminescent‐like blue and yellow light signals. In particular, the attractive effect of yellow light and the variation of angular velocity observed according to the pattern of yellow stimuli (flashes versus glows) support the intraspecific communication hypothesis. However, given the behavioural patterns of T. helgolandica, including mechanically induced light emission, the possibility that bioluminescence may be part of escape/defence responses to predation, should remain an open question.     

Biological networks: from physical principles to biological insights

A report on the Fourth Georgia Tech and UGA International Conference on Bioinformatics 'Biological Networks: From Genomics to Epidemiology', Atlanta, USA, 13-16 November 2003.     

Behavioural response of winged aphids to visual contrasts in the field

To test the behavioural response of winged aphid spring migrants to visual contrasts, we conducted a field trial in which water traps (painted in seven different shades of green and yellow) were set up on uncovered soil and on coloured boards (also painted in seven different colours including black, brown and various shades of green). In total, 56 trap–background combinations were tested. Out of the 4904 aphid individuals caught, 64.5% belonged to Aphis ssp. Using spectral measurements of both traps and backgrounds, as well as information on insect spectral sensitivity, an empirical colour choice model was built based on photoreceptor adaptation to the background, and colour opponency of the green and blue photoreceptor. Specifically, the visual input variable C* represents the difference between green–blue colour opponency values of the trap and the background. When C* > 0, the number of aphids linearly increased with C*. The model explained 64% of the behavioural response of the aphids. Applied to intercropping scenarios of sugar beet, the behavioural model showed a higher visual attractivity of a monocrop sugar beet than intercropped sugar beet. Implications for the use of mulches and for increasing plant diversity in cropping systems are discussed.     

Synaptopodin family of natively unfolded, actin binding proteins: physical properties and potential biological functions

The synaptopodin family of proteins consists of at least 3 members: synaptopodin, the synaptopodin 2 proteins, and the synaptopodin 2-like proteins. Each family member has at least 3 isoforms that are produced by alternative splicing. Synaptopodin family members are basic proteins that are rich in proline and have little regular 2° or 3° structure at physiological temperature, pH and ionic strength. Like other natively unfolded proteins, synaptopodin family members have multiple binding partners including actin and other actin-binding proteins. Several members of the synaptopodin family have been shown to stimulate actin polymerization and to bundle actin filaments either on their own or in collaboration with other proteins. Synaptopodin 2 has been shown to accelerate nucleation of actin filament formation and to induce actin bundling. The actin polymerization activity is inhibited by Ca²⁺-calmodulin. Synaptopodin 2 proteins are localized in Z-bands of striated and heart muscle and dense bodies of smooth muscle cells. Depending on the developmental status and stress, at least one member of the synaptopodin family can occupy nuclei of some cells. Members of the synaptopodin 2 subfamily have been implicated in cancers.     

Using digital images to reconstruct three‐dimensional biological forms: a new tool for morphological studies

We examined two image‐based methods, photogrammetry and stereo vision, used for reconstructing the three‐dimensional form of biological organisms under field conditions. We also developed and tested a third ‘hybrid’ method, which combines the other two techniques. We tested these three methodologies using two different cameras to obtain digital images of museum and field sampled specimens of giant tortoises. Both the precision and repeatability of the methods were assessed statistically on the same specimens by comparing geodesic and Euclidean measurements made on the digital models with linear measurements obtained with caliper and flexible tape. We found no substantial difference between the three methods in measuring the Euclidean distance between landmarks, but spatially denser models (stereo vision and ‘hybrid’) were more accurate for geodesic distances. The use of different digital cameras did not influence the results. Image‐based methods require only inexpensive instruments and appropriate software, and allow reconstruction of the three‐dimensional forms (including their curved surfaces) of organisms sampled in the field. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 425–436.     

Honeybee navigation: critically examining the role of the polarization compass

Although it is widely accepted that honeybees use the polarized-light pattern of the sky as a compass for navigation, there is little direct evidence that this information is actually sensed during flight. Here, we ask whether flying bees can obtain compass cues derived purely from polarized light, and communicate this information to their nest-mates through the ‘waggle dance’. Bees, from an observation hive with vertically oriented honeycombs, were trained to fly to a food source at the end of a tunnel, which provided overhead illumination that was polarized either parallel to the axis of the tunnel, or perpendicular to it. When the illumination was transversely polarized, bees danced in a predominantly vertical direction with waggles occurring equally frequently in the upward or the downward direction. They were thus using the polarized-light information to signal the two possible directions in which they could have flown in natural outdoor flight: either directly towards the sun, or directly away from it. When the illumination was axially polarized, the bees danced in a predominantly horizontal direction with waggles directed either to the left or the right, indicating that they could have flown in an azimuthal direction that was 90° to the right or to the left of the sun, respectively. When the first half of the tunnel provided axial illumination and the second half transverse illumination, bees danced along all of the four principal diagonal directions, which represent four equally likely locations of the food source based on the polarized-light information that they had acquired during their journey. We conclude that flying bees are capable of obtaining and signalling compass information that is derived purely from polarized light. Furthermore, they deal with the directional ambiguity that is inherent in polarized light by signalling all of the possible locations of the food source in their dances, thus maximizing the chances of recruitment to it.     

Platyrrhine color signals: New horizons to pursue

Like catarrhines, some platyrrhines show exposed and reddish skin, raising the possibility that reddish signals have evolved convergently. This variation in skin exposure and color combined with sex‐linked polymorphic color vision in platyrrhines presents a unique, and yet underexplored, opportunity to investigate the relative importance of chromatic versus achromatic signals, the influence of color perception on signal evolution, and to understand primate communication broadly. By coding the facial skin exposure and color of 96 platyrrhines, 28 catarrhines, 7 strepsirrhines, 1 tarsiiform, and 13 nonprimates, and by simulating the ancestral character states for these traits, we provide the first analysis of the distribution and evolution of facial skin exposure and color in platyrrhini. We highlight ways in which studying the presence and use of color signals by platyrrhines and other primates will enhance our understanding of the evolution of color signals, and the forces shaping color vision.     

Physical properties of lipid bilayer membranes: relevance to membrane biological functions

Over the last 25 years one of us (WKS) has been investigating physical properties of lipid bilayer membranes. In 1991 a group led by WKS was organized into the Laboratory of Structure and Dynamics of Biological Membranes, the effective member of which is AW. Using mainly the electron paramagnetic resonance (EPR) spin-labeling method, we obtained unexpected results, which are significant for the better understanding of the functioning of biological membranes. We have developed a new pulse EPR spin-labeling method for the detection of membrane domains and evaluation of lipid exchange rates. This review will be focused on our main results which can be summarized as follows: (1) Unsaturation of alkyl chains greatly reduces the ordering and rigidifying effects of cholesterol although the unsaturation alone gives only minor fluidizing effects, as observed by order and reorientational motion, and rather significant rigidifying effects, as observed by translational motion of probe molecules; (2) Fluid-phase model membranes and cell plasma membranes are not barriers to oxygen and nitric oxide transport; (3) Polar carotenoids can regulate membrane fluidity in a way similar to cholesterol; (4) Formation of effective hydrophobic barriers to the permeation of small polar molecules across membranes requires alkyl chain unsaturation and/or the presence of cholesterol; (5) Fluid-phase micro-immiscibility takes place in cis-unsaturated phosphatidylcholine-cholesterol membranes and induces the formation of cholesterol-rich domains; (6) In membranes containing high concentrations of transmembrane proteins a new lipid domain is formed, with lipids trapped within aggregates of proteins, in which the lipid dynamics is diminished to the level of gel-phase.     

IL-20: biological functions and clinical implications

Summary IL-20 belongs to the IL-10 family and plays a role in skin inflammation and the development of hematopoietic cells. Little is known about its other biological functions and clinical implications, however. Updated information about IL-20, such as its identification, expression, receptors, signaling, biological activities, and potential clinical implications, is illustrated in this review based on our research and on data available in the literature. Our studies of IL-20 show that it is a pleiotropic cytokine with potent inflammatory, angiogenic, and chemoattractive characteristics. Inflammation and angiogenesis are essential for the pathogenesis of rheumatoid arthritis and atherosclerosis. Based on in vitro data and clinical samples, we demonstrated that IL-20 is involved in the diseases of rheumatoid arthritis and atherosclerosis. In addition, we found in our studies that IL-20 signaled through different molecules in several cells. The present review presents the clinical implications of IL-20 in rheumatoid arthritis and atherosclerosis. It may provide new therapeutic options in the future.This work was supported by a grant from Chi-Mei Medical Center, Tainan, Taiwan.     

Cephalopod dynamic camouflage: bridging the continuum between background matching and disruptive coloration

Individual cuttlefish, octopus and squid have the versatile capability to use body patterns for background matching and disruptive coloration. We define—qualitatively and quantitatively—the chief characteristics of the three major body pattern types used for camouflage by cephalopods: uniform and mottle patterns for background matching, and disruptive patterns that primarily enhance disruptiveness but aid background matching as well. There is great variation within each of the three body pattern types, but by defining their chief characteristics we lay the groundwork to test camouflage concepts by correlating background statistics with those of the body pattern. We describe at least three ways in which background matching can be achieved in cephalopods. Disruptive patterns in cuttlefish possess all four of the basic components of ‘disruptiveness’, supporting Cott''s hypotheses, and we provide field examples of disruptive coloration in which the body pattern contrast exceeds that of the immediate surrounds. Based upon laboratory testing as well as thousands of images of camouflaged cephalopods in the field (a sample is provided on a web archive), we note that size, contrast and edges of background objects are key visual cues that guide cephalopod camouflage patterning. Mottle and disruptive patterns are frequently mixed, suggesting that background matching and disruptive mechanisms are often used in the same pattern.     

Antibody-hapten interactions: circular and linear polarization of the fluorescence of dansyl bound to anti-dansyl antibodies

The fluorescence spectra of several dansyl derivatives (dansylamide, ?-N-dansyl-l-lysine, dansyl-l-alanine, and α-N-dansyl-l-alanine amide) bound to anti-dansyl antibodics (induced by an α-N-dansyl-poly d,l-alanine-poly l-lysine conjugate) are shifted by about 60 nm to the blue, and the quantum yields are markedly enhanced, compared to their respective fluorescence properties in water. The light emitted by the bound haptens is partly circularly polarized, reflecting the asymmetry induced in the bound chromophores by the antibody combining site. In contradistinction, the fluorescence spectrum of 1-dansyl-2-alanine diaminoethane bound to anti-alanine antibodies is similar to that of the free fluorophore in water and lacks circular polarization. These results imply that in this case the fluorophore of the hapten protrudes out of the site into the aqueous solvent. No circular dichroism is observed in the 300 to 400 nm region for the dansyl-anti-dansyl complex. Thus a change in the mode of interaction between the chromophore and its binding site takes place upon electronic excitation. The heterogeneity of the antibody binding sites is expressed by the dependence of the circular polarization of fluorescence on excitation wavelength. Differences in the circular polarization of luminescence were also observed when the residues attached to the dansyl group have been varied. This may reflect differences in the alignment of the fluorophore within the binding sites for the different dansyl derivatives.The linear polarization of dansylamide dissolved in glycerol is not constant across the emission band, indicating that the transition dipole moments related to the various vibronic states do not have the same spatial directions. Vibronic mixing of the emitting excited state with higher electronic states is thus indicated. Dansyl-l-alanine bound to anti-dansyl antibodies exhibitsan even more pronounced variation of the linear polarization across the emission band. In this case, the dependence of the linear polarization of the emitted light on excitation wavelength is anomalous, which is again a reflection of the heterogeneity of the population of the antibody molecules. The implications of these results to the studies of the fluorescence polarization of dansyl-protein complexes are discussed.