Barrel structures in proteins: automatic identification and classification including a sequence analysis of TIM barrels.

Automated methods for identifying and characterizing regular beta-barrels from coordinate data have been developed to analyze and classify various kinds of barrel structures based on geometric parameters such as the barrel strand number (n) and shear number (S). In total, we find 1,316 barrels in the January 1998 release of Protein Data Bank. Of 1,316 barrels, 1,277 barrels had an even shear number, corresponding to 50 nonhomologous families. The (beta alpha)8 triose phosphate isomerase (TIM) barrel (n = 8, S = 8) fold has the largest number of apparently nonhomologous entries, 16, although the trypsin like antiparallel (n = 6, S = 8) barrels (representing only three families) are the most common with 527 barrels. Of all the protein families that exhibit barrel structures, 68% are found to be various kinds of enzymes, the remainder being binding proteins and transport membrane proteins. In addition, the layers of side chains, which form the cores of barrels with S = n and S = 2n, are also analyzed. More sophisticated methods were developed for detecting TIM barrels specifically, including consideration of the amino acid propensities for the side chains that form the layers. We found that the residues on the outside of the eight stranded parallel beta-barrel, buried by the alpha-helices, are much more hydrophobic than the residues inside the barrel.     

Mirrors as enrichment for captive chimpanzees (Pan troglodytes).

At many facilities, limitations of the physical environment have reduced the opportunity for captive chimpanzees to live in large, naturalistic social groups. Convex mirrors used to increase visual access of neighboring groups may improve the social environment. This was tested in a study of 28 chimpanzees (Pan troglodytes) group-housed in conventional indoor/outdoor runs. A total of 47.8 hours of behavioral observations were conducted and comparisons made across three conditions: no mirror present, a mirror present with visual access to neighboring conspecifics, or a mirror present with visual access to the neighbors' empty run. When the mirror gave subjects visual access to neighboring animals, facial expressions, sexual, and agonistic behaviors increased, whereas affiliative behavior decreased compared with when no mirror was present. When the mirror gave subjects visual access to a neighbors' empty run, facial expressions and sexual behavior increased compared with when no mirror was present. When the mirror gave subjects visual access to a neighbor's empty run, agonism decreased compared with when a mirror gave subjects visual access to neighboring animals. When subjects had visual access to neighbors, they used the mirror 30% of the total data points; while they had visual access to the neighbors' empty run, they looked during 24% of the total data points. Juveniles' use of the mirror increased over time while adults' use remained stable. Adult males used the mirror less than did the other subjects. These findings indicate that a mirror allowing visual access to neighboring conspecifics has potential as an enrichment device that affects social behavior.     

The effect of destroying the whisker follicles in mice on the sensory nerve, the thalamocortical radiation and cortical barrel development.

Electrolytic destruction of whisker follicles in mice on the day of birth has been found to cause degeneration in the sensory nerve fibres supplying the follicles. The severity of the degeneration has been assessed in animals between 2 and 20 days old by counting the total number of myelinated fibres in the maxillary nerves on both normal and lesioned sides. The degeneration is apparent after 2 days and by 20 days the nerve on the lesioned side contains only 38% of the normal fibre content. This degeneration has also been shown to involve the trigeminal root, central to the ganglion. In addition, the lesioning procedure modifies the terminations of thalamocortical fibres in the barrel region of the sensory cortex. These terminations are normally in clusters, each corresponding to a barrel, but, after lesioning the follicles, the terminals appear to be evenly distributed in layer IV and cortical barrel structures no longer develop. In postnatal mice, electrolytic destruction of whisker follicles had less effect upon maxillary nerve fibres and cortical barrels. The number of myelinated axons surviving until day 20 increased progressively with later lesioning to reach nearly 80% of the control level when lesions were made on day 10. Cortical barrels became secure earlier than the maxillary nerve, for a normal number of cortical barrels was present at day 12 when follicles were destroyed on day 4. The implications of these results for the formation of cortical barrels is discussed.     

Social interaction analysis in captive orcas (Orcinus orca)

The management of socially complex species in captivity is challenging. Research on their social behavior improves our understanding of interactions in captive animals and captive‐group management. We conducted a detailed analysis of social relationships shown by the orcas kept at Loro Parque zoo and their tendency to reconcile after aggressive episodes. Affiliative interactions were the most frequent social activities compared to agonistic or sexual interactions. Within affiliative behaviors, we documented the pattern “gentle tongue bite”, where an animal touches the other's tongue with his teeth but does not bite it. Affiliative interactions between a specific pair of orcas occurred significantly more often than expected by chance, and together with low levels of agonistic interactions, indicated particular affinity between some individuals. The most frequently observed low‐level agonistic relationship was that of the two older males (Tekoa–Keto); however, they also showed frequent sexual and affiliative interactions. Sexual‐like behaviors (pursuit, mount, and penis between males) were found in both sexes. Finally, the observed corrected conciliatory tendency (31.57%) was within the range described for other primate and cetacean species. This study provides a systematic way to assess social interactions as well as conflict management strategies in cetaceans housed in zoos and zoo‐like facilities and may help to improve animal welfare and management of animals in controlled environments.     

The effects of enriching laboratory cages using various physical structures on multiple measures of welfare in singly-housed rats

The single housing of laboratory rats may be recommended in some situations such as hypothesis-driven or test-specific studies, during electroencephalogram recording of phases of sleep and after surgical procedures. However, as single housing of laboratory rats has been shown to be stressful, modification of the housing environment is needed to improve the welfare of these animals. This experiment was carried out to investigate the long-term effects of environmental enrichment on some behavioural, physiological, pathological and psychological measures of welfare. With two batches of animals, 24 rats were housed singly in either enriched cages (EC) (n = 12 cages) or unenriched cages (UC) (n = 12 cages). Behaviour was sampled every week and so was body weight and weight gain over a six-week observation period. Behaviours of the rats in the elevated plus-maze were recorded on the seventh week, whereas organ weights were recorded postmortem. The results revealed that long-term single housing of rats in super-enriched cages increased levels of indicators of good welfare including sleep, exploration, movement and feeding behaviour, body weights, weight gains and the relative weights of the thymus gland and spleen, and decreased levels of indicators of poor welfare such as stationary behaviour and the relative weight of adrenal glands. Thus, enrichment of conventional cages of newly weaned singly-housed laboratory rats with multiple physical structures appeared to improve their ability to control the environment and to promote their species-specific behaviour; changes that can ultimately result in good welfare.     

Activation of a wide-spread network of inhibitory neurons in barrel cortex

Abstract The one-to-one correspondence of whiskers to barrels in layer IV of rodent somatosensory cortex can be demonstrated by a precise match between columns of heavy 2-deoxyglucose (2DG) label in layer IV barrels and other layers which correspond to stimulated whiskers. While there is specificity of peripheral-to-central mapping, the extent to which integration and/or modulation are generated by circuitry within or interactions between the barrel-defined whisker columns is not clear. Following stimulation of selected whiskers, large cells at the layer IV-V boundary throughout the barrel field are heavily labeled by 2-deoxyglucose (2DG) at high resolution. Many of these cells are outside the barrel columns of the stimulated whiskers. Further, the number of cells labeled is not directly related to the number of activated barrel columns. These neurons are not labeled in animals anesthetized before 2DG injection and are not as heavily labeled in barrel fields of somnolent animals. Most of the heavily labeled neurons immunolabel for glutamate decarboxylase (GAD) and are presumed to be inhibitory, while a smaller number of labeled neurons, presumed to be excitatory, immunolabel for glutamate (Glu). Similar populations of large, heavily 2DG-labeled neurons are found in other cortical areas. These relatively few neurons are exceptionally active and may modulate integrative functions of cerebral cortex.     

A Case Study of Orangutan and Siamang Behavior Within a Mixed-Species Zoo Exhibit

This empirical case study assessed the behavior and welfare of 2 orangutans (Pongo abelii) and 2 siamangs (Symphalangus syndactylus) within a mixed-species zoo exhibit. The study used instantaneous scan-sampling to record behavior, location, and interspecies proximity over 174 hr and all-occurrences data for any interactions between species. Results revealed frequent affiliative interactions between the female orangutan and siamang pair and an absence of agonistic or aggressive encounters. All individuals used the majority of the exhibit without segregation by species. Both orangutans spent most of their time on the ground (above 70% of all scans), and low levels of foraging were identified (1–4% of scans for all individuals). Overall, the findings support the notion that mixed-species exhibits may be enriching to the species involved through increased stimulation and opportunities for interaction. A poststudy incident also highlights the need for careful and continual monitoring of mixed-species exhibits over time.     

Importance of cooperation and affiliation in the evolution of primate sociality

The idea that competition and aggression are central to an understanding of the origins of group‐living and sociality among human and nonhuman primates is the dominant theory in primatology today. Using this paradigm, researchers have focused their attention on competitive and aggressive behaviors, and have tended to overlook the importance of cooperative and affiliative behaviors. However, cooperative and affiliative behaviors are considerably more common than agonistic behaviors in all primate species. The current paradigm often fails to explain the context, function, and social tactics underlying affiliative and agonistic behavior. Here, we present data on a basic question of primate sociality: how much time do diurnal, group‐living primates spend in social behavior, and how much of this time is affiliative and agonistic? These data are derived from a survey of 81 studies, including 28 genera and 60 species. We find that group‐living prosimians, New World monkeys, Old World monkeys, and apes usually devote less than 10% of their activity budget to active social interactions. Further, rates of agonistic behaviors are extremely low, normally less than 1% of the activity budget. If the cost to the actors of affiliative behavior is low even if the rewards are low or extremely variable, we should expect affiliation and cooperation to be frequent. This is especially true under conditions in which individuals benefit from the collective environment of living in stable social groups. Am J Phys Anthropol 128:84–97, 2005. © 2005 Wiley‐Liss, Inc.     

Evaluation of the preference to and behavioral effects of an enriched environment on male rhesus monkeys.

Two environments were provided to laboratory rhesus monkeys to determine if the animals spent more time (for the purposes of this study, defined as the cage side preference) in an enriched cage side than an unenriched cage side. The side (right or left) of a double-wide cage in which the animal spent the most time (as determined by Chi square analysis) was initially determined during baseline observations. The "nonpreferred" side was then enriched during the experimental phase of the study. The enrichment consisted of a perch, a Tug-A-Toy suspended inside the cage, a Kong toy suspended on the outside of the cage, and a grooming board mounted on the outside of the cage. No statistically significant changes in use of the enrichments were detected over time. Fifty percent of the animals switched cage side preference to the enriched side during the study. All subjects showed reduced behavioral pathology during exposure to the enriched environment with a return of behavioral pathology when the enrichments were removed.     

Clusters in social behaviour of female domestic cats (Felis silvestris catus) living in confinement

Associations between different agonistic and affiliative behavioural patterns of female domestic cats (Felis silvestris catus) were studied. In three groups of intact cats living in confinement frequencies of fourteen agonistic and affiliative behavioural patterns were recorded. The technique of factor analysis (Principal Components Analysis followed by varimax rotation on a dyads X behavioural patterns matrix) was used to detect clusters in these behavioural patterns. Five factors (or types of interindividual relationships) were extracted per group. They accounted collectively for at least 77% of the total variance present in the data. Although differences existed between groups with respect to behavioural patterns included in each factor, four clusters of behaviours could be discriminated: (I) social rubbing, lordosis and rolling in front of partner (sexual behaviour), (II) allogrooming, social sniffing, nosing, sniffing rear and treading (inspection-affiliative behaviour), (III) offensive behaviour and staring, and (IV) defensive behaviour and staring. The role of these clusters in group living is discussed.     

BDNF and trkB mRNA Expression in Neurons of the Neonatal Mouse Barrel Field Cortex: Normal Development and Plasticity after Cauterizing Facial Vibrissae

Development of the central somatosensory system is profoundly modulated by the sensory periphery. Cauterization of facial whiskers alters the segregation pattern of barrels in rodents only during a few days just after birth (critical period). Although a molecular basis of the segregation of barrel neurons and the critical period for the anatomical plasticity observed in layer IV barrel neuron is not clear yet, the accumulating evidence suggests that neurotrophins modulate synaptic connections including central nervous system. In this study, we showed by in situ hybridization that mouse barrel side neurons express brain-derived neurotrophic factor (BDNF) mRNA and both catalytic and non-catalytic forms of trkB mRNA. Cautery of row C vibrissae on the right side of the face within 24 h after birth (post natal day 0, PND0) reduced the expression of BDNF and trkB mRNA from the division region between the contralateral row C barrels at PND7. The vibrissae in row A, C, and E were cauterized at PND0 followed by quantitative RT-PCR for BDNF and trkB mRNA with total RNA isolated from the barrel region at PND7. The result showed that BDNF, but not trkB, mRNA was increased several-fold in the contralateral barrel region. These data suggest that the expression of BDNF mRNA is differentially regulated between injured barrels and actively innervated barrels. The differential expression of the mRNA encoding neurotrophins and their receptors may be important in regulating the injury-dependent re-segregation of barrels.     

Infrared dichroism of twisted beta-sheet barrels. The structure of E. coli outer membrane proteins

The infrared dichroic ratios of the amide bands from oriented beta-barrels yield an experimental value for the mean orientation, beta, of the beta-strands, relative to the barrel axis. For a barrel of n strands, this then gives the shear number, S, that characterizes the stagger of the beta-sheet. Combining values of beta and n specifies the barrel geometry by using the optimized model of Murzin, Lesk & Chothia for regular barrels. Application to published infrared data on the Escherichia coli outer membrane protein, OmpA yields S=9-10 (n=8), a barrel radius of 0.81(+/-0.01) nm, and an internal free volume of 0.031 nm(3) per residue, where the average twist of the beta-sheets is theta approximately 28 degrees, and their coiling angle is epsilon approximately 1 degrees. Hydrophobic matching of the 2.6 nm transmembrane stretch partly determines the shear number of the OmpA beta-barrel.     

Philosophy of environmental enrichment: Past,present, and future

The brief tenure of environmental enrichment has been influenced both directly and indirectly by the field of psychology, from the work of B.F. Skinner to that of Hal Markowitz. Research on enrichment supports the supposition that an enriched environment does indeed contribute to a captive animal’s well‐being. Critical elements of effective environmental enrichment are 1) assessing the animal’s natural history, individual history, and exhibit constraints and 2) providing species‐appropriate opportunities, i.e., the animal should have some choices within its environment. This paper presents a historic perspective of environmental enrichment, proposes a broader, more holistic approach to the enrichment of animals in captive environments, and describes a framework or process that will ensure a consistent and self‐sustaining enrichment program. Zoo Biol 20:211–226, 2001. © 2001 Wiley‐Liss, Inc.     

FLUORESCENCE CONCENTRATION IMMUNOASSAY FOR RAPID DETECTION OF CAMPYLOBACTER SPP. IN CHICKEN RINSE WATER

A total of 215 freshly processed post-chill whole chicken carcasses were assessed for Campylobacter spp. contamination by a fluorescence concentration immunoassay (FCIA) procedure. Whole chicken carcasses were sampled with low volume water rinses from which 5 ml portions were enriched with brucella enrichment broth with or without oxyrase supplement in a test tube enrichment system. After a 24h stationary incubation at 42C, each sample was assayed using a FCIA procedure for the presence or absence of campylobacters. The FCIA procedure indicated Campylobacter spp. contamination in 84% of carcasses using oxyrase supplemented enrichment, while only 47% of the chicken carcasses were positive from nonsupplemented enrichment. The corresponding incidence rates detected by culture method were 92% and 87% for oxyrase supplemented and unsupplemented samples, respectively. The FCIA procedure can be completed in less than 1 h with 48 samples including a positive and a negative control assayed on one plate. In summary, the test tube oxyrase-supplemented stationary enrichment system followed by the use of the FCIA procedure was found to be an effective, rapid method for the detection of Campylobacter spp. in chicken rinse water.     

Impact of environmental enrichment in mice. 1: effect of housing conditions on body weight,organ weights and haematology in different strains

Currently, environmental enrichment is a very common means of improving animal well-being, especially for laboratory animals. Although environmental enrichment seems to be a possible way for improving the well-being of animals, the consideration of housing laboratory animals should not only focus solely on animal well-being, manpower and economics but also on the precision and accuracy of the experimental results. The purpose of the present study was to evaluate the effects of enriched cages (nest box, nesting material, climbing bar) on body weight, haematological data and final organ weights. BALB/c, C57BL/6 and A/J mice, originated from Harlan Winkelmann, were used for the experiments - 16 animals of each strain. Animals at 3 weeks of age were marked and separated randomly to enriched or non-enriched cages, in groups of four, half for each housing condition. Both cages were type III Makrolon cages, only the enriched cages contained a nest box, a wood bar for climbing and nesting material. Animals were kept in a clean animal room under specific pathogen free (SPF) conditions. Body weights were recorded every week. Blood samples were collected at 14 weeks of age (white blood cells (WBC), red blood cells (RBC), haemoglobin (HGB), and haematocrit (HCT) were analysed). At 15 weeks of age, the animals were euthanized by CO(2) in their home cages, and final body weight and organ weights (heart, liver, kidney, adrenal, spleen and uterus) were recorded immediately. Although nearly all the test variables were not affected by environmental enrichment in their mean values, the enriched group showed higher coefficients of variation in many variables, and strain differences of both housing conditions were not consistent. The influences of enrichment were shown to be strain- and test-dependent. Such effects may lead to an increase in the number of animals which is necessary or may change the experimental results, especially when a study, using enriched housing conditions, focuses on strain differences. Since the same enrichment design can result in different influences, a positive or a negative or no adverse effect, due to the strain and the variables studied, researchers need to collect more information before enrichment designs are introduced into experimental plans.     

Social interactions among captive brushtail possums (Trichosurus vulpecula)

A biological control strategy relying on a self-disseminating agent may provide the only affordable long-term technique for reducing brushtail possum (Trichosurus vulpecula) numbers throughout New Zealand. The objective of this study was to determine the frequency and patterns of social interactions in single and mixed-sex groups of possums, in order to identify interactions that may assist in the dissemination of biocontrol agents. Thirty-two sexually mature wild-caught possums (16 female, 16 male) were housed in captive groups (of four) in enclosures during the breeding and non-breeding seasons. Groups consisted of either all females, females and males or all males. Four types of social interactions were defined: threats, fights, affiliative and sexual interactions. Interactions only occurred between two animals at one time and were most frequent in the non-breeding season. Within all female groups, possums readily engaged in interactions that had either an agonistic or affiliative nature. Mixed-sex groups interacted less frequently than females, but also engaged in both agonistic and affiliative interactions. In contrast, possums in all male groups rarely interacted, with only a few fights and no affiliative interactions observed. Some mixed-sex dyads appeared to 'associate' during the breeding period. Young were produced by three females that regularly associated with a male and one female that showed little associative behaviour. Given the different interaction patterns observed in each group type, biological control agents that rely on specific interaction patterns for dissemination, are likely to spread at different rates among different possum groups and in different seasons.     

Effects of social and spatial density changes inCercopithecus aethiops sabaeus

Findings from two experiments usingCercopithecus aethiops sabaeus (the St. Kitts vervet) are reported. In the first experiment, group number was systematically altered in two groups of animals similar in age and sex but dissimilar in terms of their prior histories. These changes resulted in significant increases in selected affiliative behaviors, decreases in nonsocial behaviors, and no changes in agonistic behaviors. In the second experiment the living space of a well established group of animals was decreased. This change also resulted in a significant increase in the frequency of affiliative behaviors but in no change in agonistic behaviors. Results of the experiments are discussed. This research was in part supported by FY-1976 (Veterans Administration) and The H. F. Guggenheim Foundation through a grant to the Behavioral Sciences Foundation.     

The effect of vibrissa deprivation pattern on the form of plasticity induced in rat barrel cortex

Plasticity was induced in the barrel cortex of adolescent rats by depriving every second vibrissa on the contralateral vibrissa pad.This produced a chessboard pattern of barrels in the cortex where each barrel receiving its principal input from a spared vibrissa was surrounded by barrels for which the principal vibrissa had been deprived and conversely, each barrel receiving its principal input from a deprived vibrissa was surrounded by barrels for which the principal vibrissa had been spared. After 7 days' deprivation, responses to the regrown vibrissae were depressed in layers II/III (49% of control levels) and IV (60%). Depression was far greater than that seen with "all vibrissa" deprivation, suggesting that activity in the spared vibrissae accentuated the depression of the deprived vibrissae. Depression was not due to subcortical changes as thalamic Ventral Posterior Medial (VPM) responses to deprived vibrissa were unchanged. The short latency responses in layer IV (5-7 ms) were unaffected by deprivation, but the number of cells responding at intermediate latencies (8-13 ms) was markedly reduced (to 66% of control). Potentiation of the spared vibrissa response was substantial in the near side of the neighbouring barrel (2.2-fold increase in layers II/III, 2.9-fold in layer IV) but had not spread to the far side after 7 days' deprivation. Sparing multiple vibrissae may increase the rate of potentiation since 7 days is insufficient time for potentiation in single vibrissa spared animals. Potentiation was not due to subcortical changes as thalamic VPm responses to the spared vibrissa were normal. However, in the spared barrel the response latency decreased by 1-2 ms. Only the cells responding at short latency exhibited potentiated responses (39% increase) suggesting that some thalamocortical plasticity is still possible at P28-35. These results show that chessboard pattern deprivation is capable of inducing substantial plasticity over a wide area of barrel cortex. All the major forms of plasticity seen with other vibrissa deprivation patterns were present, although no other single deprivation pattern studied so far causes the complete repertoire seen with chessboard deprivation.     

Behavioral and cardiophysiological responses of common marmosets (Callithrix jacchus) to social and environmental changes

Under captive conditions common marmosets (Callithrix jacchus) show socially monogamous propensities. Male and female form a social bond as characterized by signs of behavioral arousal during separation of the pairmates, high levels of affiliative interactions between pairmates and agonistic responses towards strange conspecifics. In the present study behavioral and cardiophysiological responses of mated individuals of common marmosets were recorded while the animals were in an unfamiliar environment (1) alone, (2) with the pairmate, or (3) with an opposite-sexed stranger. Pairmates of 6 established pairs were tested in 3 replicates yielding a total of 36 trials per experiment. A trial was divided into three 10-min segments (baseline; unfamiliar environment; reunion). Behavioral responses were videotaped with a remote controlled camera system installed within the cage. Systolic (SBP) and diastolic blood pressure (DBP), and heart rate (HR) as well as locomotor activity (ACT) were recorded telemtrically through peritoneally implanted transmitters. The individuals’ responses measured while in an unfamiliar environment was only reduced by the pairmate, but not by an opposite-sexed stranger. No affiliative behaviors occurred between strange conspecifics, whereas aggressive and sexual behaviors were observed. During reunion with the pairmate individuals recovered physiologically. The present study shows that an individualized pair bond exists between pairmates of common marmosets. Further, it becomes evident that establishing a social bond with the pairmate is important for maintaining physiological homeostasis.