Relating Lateralization of Eye Use to Body Motion in the Avoidance Behavior of the Chameleon (Chamaeleo chameleon)

Lateralization is mostly analyzed for single traits, but seldom for two or more traits while performing a given task (e.g. object manipulation). We examined lateralization in eye use and in body motion that co-occur during avoidance behaviour of the common chameleon, Chamaeleo chameleon. A chameleon facing a moving threat smoothly repositions its body on the side of its perch distal to the threat, to minimize its visual exposure. We previously demonstrated that during the response (i) eye use and body motion were, each, lateralized at the tested group level (N = 26), (ii) in body motion, we observed two similar-sized sub-groups, one exhibiting a greater reduction in body exposure to threat approaching from the left and one – to threat approaching from the right (left- and right-biased subgroups), (iii) the left-biased sub-group exhibited weak lateralization of body exposure under binocular threat viewing and none under monocular viewing while the right-biased sub-group exhibited strong lateralization under both monocular and binocular threat viewing. In avoidance, how is eye use related to body motion at the entire group and at the sub-group levels? We demonstrate that (i) in the left-biased sub-group, eye use is not lateralized, (ii) in the right-biased sub-group, eye use is lateralized under binocular, but not monocular viewing of the threat, (iii) the dominance of the right-biased sub-group determines the lateralization of the entire group tested. We conclude that in chameleons, patterns of lateralization of visual function and body motion are inter-related at a subtle level. Presently, the patterns cannot be compared with humans'' or related to the unique visual system of chameleons, with highly independent eye movements, complete optic nerve decussation and relatively few inter-hemispheric commissures. We present a model to explain the possible inter-hemispheric differences in dominance in chameleons'' visual control of body motion during avoidance.     

Discordant and chameleon sequences: their distribution and implications for amyloidogenicity

Identification of ambiguous encoding in protein secondary structure is paramount to develop an understanding of key protein segments underlying amyloid diseases. We investigate two types of structurally ambivalent peptides, which were hypothesized in the literature as indicators of amyloidogenic proteins: discordant α-helices and chameleon sequences. Chameleon sequences are peptides discovered experimentally in different secondary-structure types. Discordant α-helices are α-helical stretches with strong β-strand propensity or prediction. To assess the distribution of these features in known protein structures, and their potential role in amyloidogenesis, we analyzed the occurrence of discordant α-helices and chameleon sequences in nonredundant sets of protein domains (n = 4263) and amyloidogenic proteins extracted from the literature (n = 77). Discordant α-helices were identified if discordance was observed between known secondary structures and secondary-structure predictions from the GOR-IV and PSIPRED algorithms. Chameleon sequences were extracted by searching for identical sequence words in α-helices and β-strands. We defined frustrated chameleons and very frustrated chameleons based on varying degrees of total β propensity ≥α propensity. To our knowledge, this is the first study to discern statistical relationships between discordance, chameleons, and amyloidogenicity. We observed varying enrichment levels for some categories of discordant and chameleon sequences in amyloidogenic sequences. Chameleon sequences are also significantly enriched in proteins that have discordant helices, indicating a clear link between both phenomena. We identified the first set of discordant-chameleonic protein segments we predict may be involved in amyloidosis. We present a detailed analysis of discordant and chameleons segments in the family of one of the amyloidogenic proteins, the Prion Protein.     

Conformational contagion in a protein: structural properties of a chameleon sequence

Certain sequences, known as chameleon sequences, take both alpha- and beta-conformations in natural proteins. We demonstrate that a wild chameleon sequence fused to the C-terminal alpha-helix or beta-sheet in foreign stable proteins from hyperthermophiles forms the same conformation as the host secondary structure. However, no secondary structural formation is observed when the sequence is attached to the outside of the secondary structure. These results indicate that this sequence inherently possesses an ability to make either alpha- or beta-conformation, depending on the sequentially neighboring secondary structure if little other nonlocal interaction occurs. Thus, chameleon sequences take on a satellite state through contagion by the power of a secondary structure. We propose this "conformational contagion" as a new nonlocal determinant factor in protein structure and misfolding related to protein conformational diseases.     

Analysis of chameleon sequences and their implications in biological processes

Chameleon sequences have been implicated in amyloid related diseases. Here we report an analysis of two types of chameleon sequences, chameleon-HS (Helix vs. Strand) and chameleon-HE (Helix vs. Sheet), based on known structures in Protein Data Bank. Our survey shows that the longest chameleon-HS is eight residues while the longest chameleon-HE is seven residues. We have done a detailed analysis on the local and global environment that might contribute to the unique conformation of a chameleon sequence. We found that the existence of chameleon sequences does not present a problem for secondary structure prediction programs, including the first generation prediction programs, such as Chou-Fasman algorithm, and the third generation prediction programs that utilize evolution information. We have also investigated the possible implication of chameleon sequences in structural conservation and functional diversity of alternatively spliced protein isoforms.     

Free-energy landscape of a chameleon sequence in explicit water and its inherent alpha/beta bifacial property

A sequence in yeast MATalpha2/MCM1/DNA complex that folds into alpha-helix or beta-hairpin depending on the surroundings has been known as "chameleon" sequence. We obtained the free-energy landscape of this sequence by using a generalized-ensemble method, multicanonical molecular dynamics simulation, to sample the conformational space. The system was expressed with an all-atom model in explicit water, and the initial conformation for the simulation was a random one. The free-energy landscape demonstrated that this sequence inherently has an ability to form either alpha or beta structure: The conformational distribution in the landscape consisted of two alpha-helical clusters with different packing patterns of hydrophobic residues, and four beta-hairpin clusters with different strand-strand interaction patterns. Narrow pathways connecting the clusters were found, and analysis on the pathways showed that a compact structure formed at the N-terminal root of the chameleon sequence controls the cluster-cluster transitions. The free-energy landscape indicates that a small conditional change induces alpha-beta transitions. Additional unfolding simulations done with replacing amino acids showed that the chameleon sequence has an advantage to form an alpha-helix. Current study may be useful to understand the mechanism of diseases resulting from abnormal chain folding, such as amyloid disease.     

Can prey exhibit threat-sensitive generalization of predator recognition? Extending the Predator Recognition Continuum Hypothesis

Despite the importance of predator recognition in mediating predator-prey interactions, we know little about the specific characteristics that prey use to distinguish predators from non-predators. Recent experiments indicate that some prey who do not innately recognize specific predators as threats have the ability to display antipredator responses upon their first encounter with those predators if they are similar to predators that the prey has recently learned to recognize. The purpose of our present experiment is to test whether this generalization of predator recognition is dependent on the level of risk associated with the known predator. We conditioned fathead minnows to chemically recognize brown trout either as a high or low threat and then tested the minnows for their responses to brown trout, rainbow trout (closely related predator) or yellow perch (distantly related predator). When the brown trout represents a high-risk predator, minnows show an antipredator response to the odour of brown trout and rainbow trout but not to yellow perch. However, when the brown trout represents a low-risk predator, minnows display antipredator responses to brown trout, but not to the rainbow trout or yellow perch. We discuss these results in the context of the Predator Recognition Continuum Hypothesis.     

Analysis of protein chameleon sequence characteristics

Conversion of local structural state of a protein from an α-helix to a β-strand is usually associated with a major change in the tertiary structure. Similar changes were observed during the self assembly of amyloidogenic proteins to form fibrils, which are implicated in severe diseases conditions, e.g., Alzheimer disease. Studies have emphasized that certain protein sequence fragments known as chameleon sequences do not have a strong preference for either helical or the extended conformations. Surprisingly, the information on the local sequence neighborhood can be used to predict their secondary at a high accuracy level. Here we report a large scale-analysis of chameleon sequences to estimate their propensities to be associated with different local structural states such as α -helices, β-strands and coils. With the help of the propensity information derived from the amino acid composition, we underline their complexity, as more than one quarter of them prefers coil state over to the regular secondary structures. About half of them show preference for both α-helix and β-sheet conformations and either of these two states is favored by the rest.     

Intraspecific variation in gill morphology of juvenile Nile perch, Lates niloticus, in Lake Nabugabo, Uganda

Several studies have demonstrated intraspecific variation in fish gill size that relates to variation in dissolved oxygen (DO) availability across habitats. In Lake Nabugabo, East Africa, ecological change over the past 12 years has coincided with a shift in the distribution of introduced Nile perch such that a larger proportion of the population now inhabits waters in or near wetland ecotones where DO is lower than in open waters of the lake. In this study, we compared gill size of juvenile Nile perch between wetland and exposed (open-water) habitats of Lake Nabugabo in 2007, as well as between Nile perch collected in 1996 and 2007. For Nile perch of Lake Nabugabo [<20 cm total length (TL)], there was a significant habitat effect on some gill traits. In general, fish from wetland habitats were characterized by a longer total gill filament length and average gill filament length than conspecifics from exposed habitats. Nile perch collected from wetland areas in 2007 had significantly larger gills (total gill filament length) than Nile perch collected in 1996, but there was no difference detected between Nile perch collected from exposed sites in 2007 and conspecifics collected in 1996.     

Long-wavelength absorbing and fluorescent chameleon labels for proteins, peptides, and amines

Long-wavelength absorbing labels that change their color and fluorescence upon conjugation to proteins and other biomolecules provide two critical advantages over the wealth of conventional amine-reactive labels. At first, the progress of the labeling reaction can be monitored continuously either visually or by spectrometry without prior purification. Then, the labeled biomolecule can be investigated with red or near-infrared light, which minimizes background interference in biological samples. These unique characteristics are met by a group of long-wavelength absorbing cyanine dyes carrying a reactive chloro substituent for nucleophilic substitution with primary amines, which is accompanied by a color change from green to blue. In addition to this so-called chameleon effect, the dyes display an increase in fluorescence during the labeling reaction. Despite their structural similarity, the reactivity of the dyes differs strongly. The fastest labeling kinetics is observed with dye S 0378 as its five-membered ring affords a stabilizing effect on the intermediate carbocation during an S(N)1-type of nucleophilic substitution. The reaction mechanism of the amine-reactive cyanine dyes provides a blueprint for the design of future long-wavelength absorbing chameleon dyes.     

Anti‐predator response of naïve and experienced common bully to chemical alarm cues

Histological analysis of the skin of common bully Gobiomorphus cotidianus , a New Zealand native eleotrid fish, revealed the presence of club cells in the epidermis. Epidermal club cells are frequently associated with the production of alarm substance (Schreckstoff). The behavioural responses of perch‐naïve and perch‐experienced common bullies to either conspecific skin extract or chemical cues from an introduced predator, perch Perca fluviatilis , were then examined. Both perch‐naïve and perch‐experienced common bullies exhibited a behavioural response when exposed to conspecific skin extract, indicating the probable presence of an alarm substance. In contrast, only perch‐experienced common bullies recognized and exhibited a subsequent behavioural response to the odour of perch. This study is the first to document the presence of epidermal club cells and a behavioural response to a conspecific chemical alarm signal for fishes in the Eleotridae. The results indicate that common bully can learn to recognize perch odour as a threat, and that this ability may be a result of previous predator labelling involving a conspecific alarm substance.     

Experimental Evidence of Threat-Sensitive Collective Avoidance Responses in a Large Wild-Caught Herring School

Aggregation is commonly thought to improve animals'' security. Within aquatic ecosystems, group-living prey can learn about immediate threats using cues perceived directly from predators, or from collective behaviours, for example, by reacting to the escape behaviours of companions. Combining cues from different modalities may improve the accuracy of prey antipredatory decisions. In this study, we explored the sensory modalities that mediate collective antipredatory responses of herring (Clupea harengus) when in a large school (approximately 60 000 individuals). By conducting a simulated predator encounter experiment in a semi-controlled environment (a sea cage), we tested the hypothesis that the collective responses of herring are threat-sensitive. We investigated whether cues from potential threats obtained visually or from the perception of water displacement, used independently or in an additive way, affected the strength of the collective avoidance reactions. We modified the sensory nature of the simulated threat by exposing the herring to 4 predator models differing in shape and transparency. The collective vertical avoidance response was observed and quantified using active acoustics. The combination of sensory cues elicited the strongest avoidance reactions, suggesting that collective antipredator responses in herring are mediated by the sensory modalities involved during threat detection in an additive fashion. Thus, this study provides evidence for magnitude-graded threat responses in a large school of wild-caught herring which is consistent with the “threat-sensitive hypothesis”.     

Effects of resources and mortality on the growth and reproduction of Nile perch in Lake Victoria

1. A collapse of Nile perch stocks of Lake Victoria could affect up to 30 million people. Furthermore, changes in Nile perch population size‐structure and stocks make the threat of collapse imminent. However, whether eutrophication or fishing will be the bane of Nile perch is still debated. 2. Here, we attempt to unravel how changes in food resources, a side effect of eutrophication, and fishing mortality determine fish population growth and size structures. We parameterised a physiologically structured model to Nile perch, analysed the influence of ontogenetic diet shifts and relative resource abundances on existence boundaries of Nile perch and described the populations on either side of these boundaries. 3. Our results showed that ignoring ontogenetic diet shifts can lead to over‐estimating the maximum sustainable mortality of a fish population. Size distributions can be indicators of processes driving population dynamics. However, the vulnerability of stocks to fishing mortality is dependent on its environment and is not always reflected in size distributions. 4. We suggest that the ecosystem, instead of populations, should be used to monitor long‐term effects of human impact.     

Certain heptapeptide and large sequences representing an entire helix, strand or coil conformation in proteins are associated as chameleon sequences

Helices, strands and coils in proteins of known three-dimensional structure, corresponding to heptapeptide and large sequences (‘probe’ peptides), were scanned against peptide sequences of variable length, comprising seven or more residues that correspond to a different conformation (‘target’ peptides) in protein crystal structures available from the Protein Data Bank (PDB). Where the ‘probe’ and ‘target’ peptide sequences exactly match, they correspond to ‘chameleon’ sequences in protein structures. We observed ∼548 heptapeptide and large chameleon sequences that included peptides in the coil conformation from 53,794 PDB files that were analyzed. However, after excluding several chameleon peptides based on the quality of protein structure data, redundancy and peptides associated with cloning artifacts, such as, histidine-tags, we observed only ten chameleon peptides in structurally different proteins and the maximum length comprised seven amino acid residues. Our analysis suggests that the quality of protein structure data is important for identifying possibly, the ‘true chameleons’ in PDB. Majority of the chameleon sequences correspond to an entire strand in one protein that is observed as part of helix sequence in another protein. The heptapeptide chameleons are characterized with a high propensity of alanine, leucine and valine amino acid residues. The total hydropathy values range between −11.2 and 22.9, the difference in solvent accessibility between 2.0 Å² and 373 Å² units and the difference in total number of residue neighbor contacts between 0 and 7 residues. Our work identifies for the first time heptapeptide and large sequences that correspond to a single complete helix, strand or coil, which adopt entirely different secondary structures in another protein.     

Predator odor recognition and antipredatory response in fish: does the prey know the predator diel rhythm?

We studied in a laboratory experiment using stream tanks if two percid prey fish, the perch (Perca fluviatilis) and the ruffe (Gymnocephalus cernuus), can recognize and respond to increased predation risk using odors of two piscivores, the pike (Esox lucius) and the burbot (Lota lota). Burbot is night-active most of the year but pike hunts predominantly visually whenever there is enough light. Perch is a common day-active prey of pike and dark-active ruffe that of burbot. We predicted that besides recognizing the predator odors, the prey species would respond more strongly to odors of the predator which share the same activity pattern. Both perch and ruffe clearly responded to both predator fish odors. They decreased movements and erected the spiny dorsal fins. Fin erection showed clearly the black warning ornamentation in the fin and thus erected fin may function besides as mechanical defense also as warning ornament for an approaching predator. No rapid escape movements were generally observed. Both perch and ruffe responded more strongly to pike odor than to burbot. There were no clear differences in response between day and night. In conclusion, we were able to verify clear predator odor recognition by both prey fish. Both perch and ruffe responded to both predator odors and it seemed that pike forms a stronger threat for both prey species. Despite of diel activity differences both perch and ruffe used the same antipredatory strategies, but the day-active perch seemed to have a more flexible antipredatory behavior by responding more strongly to burbot threat during the night when burbot is active.     

Effects of chameleon dispense-to-plunge speed on particle concentration,complex formation,and final resolution: A case study using the Neisseria gonorrhoeae ribonucleotide reductase inactive complex

Ribonucleotide reductase (RNR) is an essential enzyme that converts ribonucleotides to deoxyribonucleotides and is a promising antibiotic target, but few RNRs have been structurally characterized. We present the use of the chameleon, a commercially-available piezoelectric cryogenic electron microscopy plunger, to address complex denaturation in the Neisseria gonorrhoeae class Ia RNR. Here, we characterize the extent of denaturation of the ring-shaped complex following grid preparation using a traditional plunger and using a chameleon with varying dispense-to-plunge times. We also characterize how dispense-to-plunge time influences the amount of protein sample required for grid preparation and preferred orientation of the sample. We demonstrate that the fastest dispense-to-plunge time of 54 ms is sufficient for generation of a data set that produces a high quality structure, and that a traditional plunging technique or slow chameleon dispense-to-plunge times generate data sets limited in resolution by complex denaturation. The 4.3 Å resolution structure of Neisseria gonorrhoeae class Ia RNR in the inactive α4β4 oligomeric state solved using the chameleon with a fast dispense-to-plunge time yields molecular information regarding similarities and differences to the well studied Escherichia coli class Ia RNR α4β4 ring.     

Competition in Umbra-Perca fish assemblages: experimental and field evidence

Summary One potentially important effect of interspecific competition in freshwater fish communities is to increase predation intensity from gape-limited piscivores by lowering growth rates of prey species. We investigated the operation and consequences of competition between central mudminnows (Umbra limi) and yearling yellow perch (Perca flavescens) in a system where size-limited predation on mudminnows by larger perch is a principle structuring mechanism. During laboratory experiments in which mudminnows foraged for patchily-presented food in the presence and absence of yearling perch, the food intake of mudminnows decreased at both the population and individual-fish levels when perch were present. Mudminnows were neither less active nor did they occupy lower-quality food patches in the presence of perch; exploitation competition, rather than interference or predator avoidance, appeared responsible for reduced feeding success. To assess effects of competition in the field, we examined size distributions and condition factors of yearling mudminnows and perch in small Wisconsin lakes having mudminnow-only and mudminnow-perch assemblages. Yearling mudminnows were smaller and in poorer condition in an assemblage composed (by mass) of 45% yearling perch than in two mudminnow-only assemblages. Conversely, yearling perch were larger and in better condition when the mudminnow-perch assemblage contained only 45% perch then when it contained 92% perch. Our experimental and field results indicated that an asymmetrical competitive relationship could contribute directly to the interspecific population dominance of perch over mudminnows in Umbra-Perca assemblages through reduced food intake, growth, and condition of mudminnows, and indirectly through increased vulnerability of mudminnows to size-limited predation.     

The solution structure of a chimeric LEKTI domain reveals a chameleon sequence

The conversion of an alpha-helical to a beta-strand conformation and the presence of chameleon sequences are fascinating from the perspective that such structural features are implicated in the induction of amyloid-related fatal diseases. In this study, we have determined the solution structure of a chimeric domain (Dom1PI) from the multidomain Kazal-type serine proteinase inhibitor LEKTI using multidimensional NMR spectroscopy. This chimeric protein was constructed to investigate the reasons for differences in the folds of the homologous LEKTI domains 1 and 6 [Lauber, T., et al. (2003) J. Mol. Biol. 328, 205-219]. In Dom1PI, two adjacent phenylalanine residues (F28 and F29) of domain 1 were substituted with proline and isoleucine, respectively, as found in the corresponding P4' and P5' positions of domain 6. The three-dimensional structure of Dom1PI is significantly different from the structure of domain 1 and closely resembles the structure of domain 6, despite the sequence being identical to that of domain 1 except for the two substituted phenylalanine residues and being only 31% identical to the sequence of domain 6. The mutation converted a short 3(10)-helix into an extended loop conformation and parts of the long COOH-terminal alpha-helix of domain 1 into a beta-hairpin structure. The latter conformational change occurs in a sequence stretch distinct from the region containing the substituted residues. Therefore, this switch from an alpha-helical structure to a beta-hairpin structure indicates a chameleon sequence of seven residues. We conclude that the secondary structure of Dom1PI is determined not only by the local protein sequence but also by nonlocal interactions.     

Convergence of specialised behaviour, eye movements and visual optics in the sandlance (Teleostei) and the chameleon (Reptilia)

Chameleons have a number of unusual, highly specialised visual features, including telescopic visual optics with a reduced lens power, wide separation of the eye's nodal point from the axis of rotation, a deep-pit fovea, rapid pre-calculated strikes for prey based on monocular depth judgements (including focus), and a complex pattern of partially independent alternating eye movements. The same set of features has been acquired independently by a teleost, the sandlance Limnichthyes fasciatus. Despite its underwater lifestyle, this fish displays visual behaviour and rapid strikes for prey that are remarkably similar to those of the chameleon [1]. In a direct comparison of the two species, we have revealed other, previously unsuspected, similarities, such as corneal accommodation, which was unknown in teleosts, as well as bringing together, for the first time, data collected from both species. The sandlance is the only teleost, among thousands studied, that has corneal refraction, corneal accommodation and reduced lens power, as well as sharing the other specialised optical features seen in chameleons. The independent eye movement pattern in the sandlance is also unusual and similar to that of the chameleon. The selection pressures that have produced this remarkable example of convergence may relate to common visual constraints in the life styles of these two phylogenetically disparate species.     

Morphogenesis of the prehensile autopodium in the common chameleon (Chamaeleo Chamaeleo)

This report documents the development of the autopodium of the common chameleon (Chamaeleo chamaeleo) using light microscopy, scanning electron microscopy, and transmission electron microscopy. Three main periods were distinguished during the morphogenesis of this structure. In the first period (stages 33-35 of chameleon development) the autopodium is paddle-shaped with a prominent apical ectodermal ridge (AER) along the distal margin. During this period the AER has structural features similar to other reptilian and avian vertebrates except for the scarcity or absence of gap junctions. The second period of autopodium morphogenesis (stage 36 of chameleon development) is characterized by the formation of a central cleft which divides this structure into two digital segments. In the forelimb the autopodial cleft occupies the space between digits 3 and 4. In the hindlimb the cleft occupies the space between digits 2 and 3. Mesenchymal cell death constitutes a constant feature during cleft formation. In addition to cell death during this process, we have observed that the AER flattens out in the zone of cleft formation while in the digital portions of the autopodium it takes on a polystratified appearance. In the last period of autopodial morphogenesis (stage 37 of chameleon development) digits become free by means of interdigital mesenchymal cell death.     

Selection of TAR RNA-binding chameleon peptides by using a retroviral replication system

The interaction between the arginine-rich motif (ARM) of the human immunodeficiency virus (HIV) Tat protein and TAR RNA is essential for Tat activation and viral replication. Two related lentiviruses, bovine immunodeficiency virus (BIV) and Jembrana disease virus (JDV), also require Tat ARM-TAR interactions to mediate activation, but the viruses have evolved different RNA-binding strategies. Interestingly, the JDV ARM can act as a "chameleon," adopting both the HIV and BIV TAR binding modes. To examine how RNA-protein interactions may evolve in a viral context and possibly to identify peptides that recognize HIV TAR in novel ways, we devised a retroviral system based on HIV replication to amplify and select for RNA binders. We constructed a combinatorial peptide library based on the BIV Tat ARM and identified peptides that, like the JDV Tat ARM, also function through HIV TAR, revealing unexpected sequence characteristics of an RNA-binding chameleon. The results suggest that a retroviral screening approach may help identify high-affinity TAR binders and may provide new insights into the evolution of RNA-protein interactions.