Quantifying temporal variability in population abundances

Understanding variability of population abundances is of central concern to theoretical and applied evolutionary ecology, yet quantifying the conceptually simple idea has been substantially problematic. Standard statistical measures of variability are particularly biassed by rare events, zero counts and other 'non-Gaussian' behaviour, which are often inappropriately weighted or excluded from analysis. I conjecture that these problems are primarily a function of calculating variation as deviation from an average abundance, while the average may not be static, nor actually reflect abundance at any point in the time series. Here I describe a simple metric (population variability PV) that quantifies variability as the average percent difference between all combinations of observed abundances. Zero counts can be included if desired. Similar to standard metrics, variability is measured on a proportional scale, facilitating comparative applications. Standard metrics are based on Gaussian distributions, are over-sensitive to rare events and heavy tailed behaviour, and can inappropriately indicate 'more time-more variation' effects (reddened spectrum). Here I demonstrate that, while PV behaves similarly for 'normal' time series, it is independent of deviation from mean abundance for heavy tailed distributions, its robustness to non-Gaussian behaviour resolves artificial reddened spectrum issues, and variability calculated using PV from short time series is substantially more accurate at estimating known long term variability than standard metrics. PV therefore provides common ground for evaluating the variability of populations undergoing different dynamics, and with different statistical distributions of abundance, and can be easily generalized to a variety of contexts and disciplines.     

Phase variation of Opa proteins of <Emphasis Type="BoldItalic">Neisseria meningitidis</Emphasis> and the effects of bacterial transformation

Opa proteins are major proteins involved in meningococcal colonization of the nasopharynx and immune interactions. Opa proteins undergo phase variation (PV) due to the presence of the 5′-CTCTT-3′ coding repeat (CR) sequence. The dynamics of PV of meningococcal Opa proteins is unknown. Opa PV, including the effect of transformation on PV, was assessed using a panel of Opa-deficient strains of Neisseria meningitidis. Analysis of Opa expression from UK disease-causing isolates was undertaken. Different opa genes demonstrated variable rates of PV, between 6.4 ×10^–4 and 6.9 ×10^–3 per cell per generation. opa genes with a longer CR tract had a higher rate of PV (r ²=0.77, p=0.1212). Bacterial transformation resulted in a 180-fold increase in PV rate. The majority of opa genes in UK disease isolates (315/463, 68.0%) were in the ‘on’ phase, suggesting the importance of Opa proteins during invasive disease. These data provide valuable information for the first time regarding meningococcal Opa PV. The presence of Opa PV in meningococcal populations and high expression of Opa among invasive strains likely indicates the importance of this protein in bacterial colonization in the human nasopharynx. These findings have potential implications for development of vaccines derived from meningococcal outer membranes.     

Distributions of measurement errors for single-axis magnetic field meters during measurements near appliances

Comparisons are made between the average magnetic flux density as it would be measured with a single-axis coil probe and the flux density at the center of the probe, assuming that the probe is oriented to measure the maximum field at that point. Probability distributions of the differences between the two quantities are calculated assuming a dipole magnetic field and are found to be asymmetric. The distributions are used to estimate the uncertainty for maximum magnetic field measurements at distances that are large compared with the dimensions of the field source. Bioelectromagnetics 18:273–276, 1997. © 1997 Wiley-Liss, Inc.

1 This article is a US Government work and, as such, is in the public domain in the United States of America.

     

Normalization of Ventilation Data from 4D-CT to Facilitate Comparison between Datasets Acquired at Different Times

Purpose

The 4D-CT data used for comparing a patient’s ventilation distributions before and after lung radiotherapy are acquired at different times. As a result, an additional variable – the tidal volume (TV) – can alter the results. Therefore, in this paper we propose to normalize the ventilation to the same TV to eliminate that uncertainty.

Methods

Absolute ventilation (AV) data were generated for 6 stereotactic body radiation therapy (SBRT) cases before and after treatment, using the direct geometric algorithm and diffeomorphic morphons deformable image registration (DIR). Each pair of AV distributions was converted to TV-normalized, percentile ventilation (PV) and low-dose well-ventilated-normalized ventilation (LDWV) distributions. The ventilation change was calculated in various dose regions based on the treatment plans using the DIR-registered before and after treatment data sets. The ventilation change based on TV-normalized ventilation was compared with the AV as well as the data normalized by PV and LDWV.

Results

AV change may be misleading when the TV differs before and after treatment, which was found to be up to 6.7%. All three normalization methods produced a similar trend in ventilation change: the higher the dose to a region of lung, the greater the degradation in ventilation. In low dose regions (<5 Gy), ventilation appears relatively improved after treatment due to the relative nature of the normalized ventilation. However, the LDWV may not be reliable when the ventilation in the low-dose regions varies. PV exhibited a similar ventilation change trend compared to the TV-normalized in all cases. However, by definition, the ventilation distribution in the PV is significantly different from the original distribution.

Conclusion

Normalizing ventilation distributions by the TV is a simple and reliable method for evaluation of ventilation changes.     

Optimizing biocontrol using phenological day degree models: the European earwig in pipfruit orchards

• 1 Phenological day degree models are often used as warning systems for the emergence of arthropod pests in agricultural crops or the occurrence of natural enemies of the pest species. In the present study, we report on a case study of the European earwig Forficula auricularia L., which is an important natural enemy in pipfruit orchards, and describe how such a day degree model can be used to avoid negative effects of crucial orchard management, such as spray applications and soil tillage. A precise timing of these interventions in relation to the phenology of natural enemies will enhance biocontrol.
• 2 Earwig population dynamics are characterized by single‐ and double‐brood populations, each with specific biological characteristics.
• 3 A day degree model capable of predicting the phenology of local earwig populations of both population types was developed. The model was checked for accuracy by comparing the first field observation dates of various life stages with predicted values using temperature data from the nearest weather station. In addition, variation in development time was assessed using field data.
• 4 The model was able to make predictions on a global scale. Although single‐ and double‐brood populations differ in phenology, the predictions of first appearance dates were similar. Variation in development time showed that single‐brood populations were more synchronized.
• 5 Our phenological model provides an accurate tool for predicting and simulating earwig population dynamics, as well as for enhancing the biocontrol of pests in pipfruit orchards.

     

Beyond Word Frequency: Bursts,Lulls, and Scaling in the Temporal Distributions of Words

Background

Zipf''s discovery that word frequency distributions obey a power law established parallels between biological and physical processes, and language, laying the groundwork for a complex systems perspective on human communication. More recent research has also identified scaling regularities in the dynamics underlying the successive occurrences of events, suggesting the possibility of similar findings for language as well.

Methodology/Principal Findings

By considering frequent words in USENET discussion groups and in disparate databases where the language has different levels of formality, here we show that the distributions of distances between successive occurrences of the same word display bursty deviations from a Poisson process and are well characterized by a stretched exponential (Weibull) scaling. The extent of this deviation depends strongly on semantic type – a measure of the logicality of each word – and less strongly on frequency. We develop a generative model of this behavior that fully determines the dynamics of word usage.

Conclusions/Significance

Recurrence patterns of words are well described by a stretched exponential distribution of recurrence times, an empirical scaling that cannot be anticipated from Zipf''s law. Because the use of words provides a uniquely precise and powerful lens on human thought and activity, our findings also have implications for other overt manifestations of collective human dynamics.     

Multivariate statistical analysis of net diatom species distributions in the Southwestern Atlantic and Indian Ocean

Summary Vertical net haul diatom assemblages from near South Georgia, and from between Africa and Antarctica, were examined and compared. Variation among South Georgia stations was examined by principal component, cluster and canonical discriminant analyses. Diatom distributions provide evidence for at least two distinct water masses. The region north of the island is characterized by neritic, temperate diatoms and by an assemblage with low species diversity. The region south of the island is characterized by oceanic, antarctic species and relatively high species diversity. The regions are most distinct to the west of the island, intergrading east of the island. Within the north-south division, five station groupings were detected on the basis of distribution of dominant net diatoms. By comparing classical species ecological categorizations to results of principal component analysis, a neritic-oceanic factor was identified from net diatom distributions. This factor was common to both areas in spite of the fact that Biscoe and Agulhas collections were from different seasons.     

东灵山地区落叶阔叶林长期动态的模拟

用林窗模型研究了暖温带辽东栎林的长期动态变化。用森林经营历史和实际调查数据求得模型的参数。经过与实际数据检验证明所得模型能合理地预测辽东栎林的物种组成动态变化。通过对辽东栎交生裸地的模拟,可以得到：辽东栎种群在森林动态变化过程中呈现波动的形式,波动的周期为１１０ａ左右,叶面积指数的动态变化过程与林分的竞争状况有密切的关系,生产力的变化有着明显的无规律性,变化极水稳定,在３０ａ进有一个变化的高峰期,     

WEBnm@ v2.0: Web server and services for comparing protein flexibility

Background

Normal mode analysis (NMA) using elastic network models is a reliable and cost-effective computational method to characterise protein flexibility and by extension, their dynamics. Further insight into the dynamics–function relationship can be gained by comparing protein motions between protein homologs and functional classifications. This can be achieved by comparing normal modes obtained from sets of evolutionary related proteins.

Results

We have developed an automated tool for comparative NMA of a set of pre-aligned protein structures. The user can submit a sequence alignment in the FASTA format and the corresponding coordinate files in the Protein Data Bank (PDB) format. The computed normalised squared atomic fluctuations and atomic deformation energies of the submitted structures can be easily compared on graphs provided by the web user interface. The web server provides pairwise comparison of the dynamics of all proteins included in the submitted set using two measures: the Root Mean Squared Inner Product and the Bhattacharyya Coefficient. The Comparative Analysis has been implemented on our web server for NMA, WEBnm@, which also provides recently upgraded functionality for NMA of single protein structures. This includes new visualisations of protein motion, visualisation of inter-residue correlations and the analysis of conformational change using the overlap analysis. In addition, programmatic access to WEBnm@ is now available through a SOAP-based web service. Webnm@ is available at http://apps.cbu.uib.no/webnma.

Conclusion

WEBnm@ v2.0 is an online tool offering unique capability for comparative NMA on multiple protein structures. Along with a convenient web interface, powerful computing resources, and several methods for mode analyses, WEBnm@ facilitates the assessment of protein flexibility within protein families and superfamilies. These analyses can give a good view of how the structures move and how the flexibility is conserved over the different structures.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0427-6) contains supplementary material, which is available to authorized users.     

The relationship between the concepts of genetic diversity and differentiation

Summary Diversity as a measure of individual variation within a population is widely agreed to reflect the number of different types in the population, taking into account their frequencies. In contrast, differentiation measures variation between two or more populations, demes or subpopulations. As such, it is based on the relative frequencies of types within these subpopulations and, ideally, measures the average distance of subpopulations from their respective lumped remainders. This concept of subpopulation differentiation can be applied consistently to a single population by regarding each individual as a deme (subpopulation) of its own, and it results in a measure of population differentiation _T which depends on the relative frequencies of the types and the population size. _T corresponds to several indices of variation frequently applied in population genetics and ecology, and it verifies these indices as measures of differentiation rather than diversity. For any particular frequency distribution of types, the diversity is then shown to be the size of a hypothetical population in which each type is represented exactly once, i. e. for which _T =1. Hence, the diversity of a population is its differentiation effective number of types. This uniquely specifies the link between the two concepts. Moreover, again corresponds to known measures of diversity applied in population genetics and ecology. While population differentiation can always be estimated from samples, the diversity of a population, particularly if it is large, may not be. In such cases, it is recommended that population differentiation is estimated and the corresponding sample diversity merely computed. Finally, a solution to the problem of measuring multi-locus diversities is provided.     

Measurement of the Pressure-volume Curve in Mouse Lungs

In recent decades the mouse has become the primary animal model of a variety of lung diseases. In models of emphysema or fibrosis, the essential phenotypic changes are best assessed by measurement of the changes in lung elasticity. To best understand specific mechanisms underlying such pathologies in mice, it is essential to make functional measurements that can reflect the developing pathology. Although there are many ways to measure elasticity, the classical method is that of the total lung pressure-volume (PV) curve done over the whole range of lung volumes. This measurement has been made on adult lungs from nearly all mammalian species dating back almost 100 years, and such PV curves also played a major role in the discovery and understanding of the function of pulmonary surfactant in fetal lung development. Unfortunately, such total PV curves have not been widely reported in the mouse, despite the fact that they can provide useful information on the macroscopic effects of structural changes in the lung. Although partial PV curves measuring just the changes in lung volume are sometimes reported, without a measure of absolute volume, the nonlinear nature of the total PV curve makes these partial ones very difficult to interpret. In the present study, we describe a standardized way to measure the total PV curve. We have then tested the ability of these curves to detect changes in mouse lung structure in two common lung pathologies, emphysema and fibrosis. Results showed significant changes in several variables consistent with expected structural changes with these pathologies. This measurement of the lung PV curve in mice thus provides a straightforward means to monitor the progression of the pathophysiologic changes over time and the potential effect of therapeutic procedures.     

Geographic variation in density-dependent dynamics impacts the synchronizing effect of dispersal and regional stochasticity

Explanations for the ubiquitous presence of spatially synchronous population dynamics have assumed that density-dependent processes governing the dynamics of local populations are identical among disjunct populations, and low levels of dispersal or small amounts of regionalized stochasticity (Moran effect) can act to synchronize populations. In this study we used historical spatially referenced data on gypsy moth (Lymantria dispar) outbreaks to document that density-dependent processes can vary substantially across geographical landscapes. This variation may be due in part to geographical variation in habitat (e.g., variation in forest composition). We then used a second-order log-linear stochastic model to explore how inter-population variation in density-dependent processes affects synchronization via either synchronous stochastic forcing or dispersal. We found that geographical variation in direct density-dependence (first order) greatly diminishes synchrony caused by stochasticity but only slightly decreases synchronization via dispersal. Variation in delayed density-dependence (second order) diluted synchrony caused by regional stochasticity to a lesser extent than first-order variation, but it did not have any influence on synchrony caused by dispersal. In general, synchronization caused by dispersal was primarily dependent upon the instability of populations and only weakly, if at all, affected by similarities in density-dependence among populations. We conclude that studies of synchrony should carefully consider both the nature of the synchronizing agents and the pattern of local density-dependent processes, including how these vary geographically.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

A new null hypothesis for measuring the degree of plant community organization

An attempt is made to derive a measure for the degree of plant community organization, which would not be based on species co-occurrence and co-abundance. The use of the independent random distribution hypothesis (IRDH) is suggested for this purpose. The hypothesis is expected to be valid, if no deterministic phytosociological-structure-generating mechanism is present. If structural variability is used as a statistic for testing the hypothesis, deviances from the conditions of IRDH (species distributions are independent from each other, environmental gradients are lacking) will be attributable either to species interactions (smaller structural variability than expected), or to environmental heterogeneity (greater structural variability than expected). Structural variability is evaluated as the variance of species diversity, the indexN=exp(H') is used for measuring diversity. The precise measure of the degree of community organizationW is computed as the shift between two empirical distributions:D ^* (VN) or Bootstrap distribution of variance of diversity in the community, andD ^o (VN) or the random community variability distribution, which is evaluated after simulating the IRDH conditions.A satisfactory interpretation can be given to the results of evaluatingW for 11 data sets of 10 relevés each.Abbreviation IRDH Independent random distribution hypothesis     

Receptor-Dependent and -Independent Axonal Retrograde Transport of Poliovirus in Motor Neurons

Poliovirus (PV), when injected intramuscularly into the calf, is incorporated into the sciatic nerve and causes an initial paralysis of the inoculated limb in transgenic (Tg) mice carrying the human PV receptor (hPVR/CD155) gene. We have previously demonstrated that a fast retrograde axonal transport process is required for PV dissemination through the sciatic nerves of hPVR-Tg mice and that intramuscularly inoculated PV causes paralytic disease in an hPVR-dependent manner. Here we showed that hPVR-independent axonal transport of PV was observed in hPVR-Tg and non-Tg mice, indicating that several different pathways for PV axonal transport exist in these mice. Using primary motor neurons (MNs) isolated from these mice or rats, we demonstrated that the axonal transport of PV requires several kinetically different motor machineries and that fast transport relies on a system involving cytoplasmic dynein. Unexpectedly, the hPVR-independent axonal transport of PV was not observed in cultured MNs. Thus, PV transport machineries in cultured MNs and in vivo differ in their hPVR requirements. These results suggest that the axonal trafficking of PV is carried out by several distinct pathways and that MNs in culture and in the sciatic nerve in situ are intrinsically different in the uptake and axonal transport of PV.In humans, paralytic poliomyelitis results from the invasion of the central nervous system by circulating poliovirus (PV), probably via the blood-brain barrier. This conclusion is supported by the finding that circulating PV after intravenous inoculation in mice appears to cross the blood-brain barrier at a high rate in a human PV receptor (hPVR/CD155)-independent manner (44). After the virus enters the central nervous system, it replicates in neurons, especially in motor neurons (MNs), inducing the cell death that causes paralytic poliomyelitis. Along with this route of dissemination, a neuron-specific pathway has been reported in humans (31), monkeys (18), and PV-sensitive transgenic (Tg) mice carrying the hPVR gene (34, 37). This neuron-specific pathway appears to be important in causing “provocation poliomyelitis,” which is triggered by injuries after PV ingestion (11). Using differentiated PC12 cells and a PV-sensitive Tg mouse line, we have shown that intramuscularly inoculated PV is taken up by endocytosis at synapses.hPVR is a member of the immunoglobulin (Ig) superfamily, with three linked extracellular Ig-like domains, followed by a membrane-spanning domain and a cytoplasmic domain. Two membrane-bound forms (α and δ) and two secreted forms (β and γ) of hPVR derived by alternative splicing are likely to be expressed in human cells (23). Membrane-bound hPVRs are considered to play important roles in the early steps of infection, such as the binding of the virus to the cell surface, its entry into the cell, and the uncoating of the virus. The N-terminal Ig-like domain harbors the sites for PV binding, and anti-hPVR monoclonal antibodies (MAbs) directed against this region block PV infection (9, 24, 39).hPVR has the ability to alter the conformation of PV from the 160S intact infectious particle to a 135S particle from which the viral capsid protein VP4 is missing (2, 29). PV-related materials recovered from the sciatic nerves of PV-sensitive Tg mice after intramuscular inoculation with PV were mainly composed of intact 160S virions. The amount of 160S particles recovered was greatly reduced by coinjection with MAb p286, which specifically recognizes hPVR (34). Thus, most of the intramuscularly inoculated PV is incorporated into the sciatic nerves of PV-sensitive Tg mice as intact particles in an hPVR-dependent manner. This surprising finding might be due to either of two alternative, yet not mutually exclusive, possibilities: (i) a small number of PVRs bound per virion does not result in a conformational change in the viral capsid with a loss of VP4, but it is sufficient to induce endocytosis of the virus on the cell surface, or (ii) a cellular inhibitor(s) of PV uncoating may exist in the endocytic pathway responsible for PV uptake and transport in Tg mice (34).This mouse strain also allowed us to demonstrate that PV inoculated into the calf was incorporated into the sciatic nerve and retrogradely transported through the axons as intact virion particles. Furthermore, PV dissemination via the neural pathway has been found to rely on a fast retrograde axonal transport system and was inhibited by MAb p286 (34). Moreover, the efficient direct interaction of the hPVR cytoplasmic domain with Tctex-1, a light chain of cytoplasmic dynein (21), has been suggested to play an important role in retrograde transport, together with microtubule integrity (33). Cytoplasmic dynein, a minus-end-directed microtubule-based motor complex (13, 14, 17, 43), is implicated in the transport of early and late endosomes, lysosomes, synaptic vesicles, and endoplasmic reticulum along microtubules (1, 8, 13, 14, 17, 43). Notwithstanding the recent progress in the understanding of PV trafficking, the molecular determinants of the axonal transport of PV in MNs have not yet been elucidated.Despite the importance of axonal retrograde transport in health and disease, the direct visualization of retrograde transport and its quantitative analysis have been hampered by the lack of a reliable assay for living MNs. Such an assay was established in MNs by using a nontoxic fluorescent fragment of tetanus toxin (TeNT H_C), which binds to MNs and is retrogradely transported (28). Here, we applied this assay to the visualization of PV in living MNs.We employed hPVR-Tg and non-Tg mice, together with cultured MNs isolated from these mice, to clarify the mechanisms of axonal retrograde transport of PV. Experiments involving cultured MNs showed that the entry and axonal transport of PV are strictly hPVR dependent. However, hPVR-independent axonal transport of PV can be observed in non-Tg as well as in hPVR-Tg mice, suggesting that multiple axonal transport routes for PV are present in vivo.     

Optimal patch use and metapopulation dynamics

Summary We compared the metapopulation dynamics of predator—prey systems with (1) adaptive global dispersal, (2) adaptive local dispersal, (3) fixed global dispersal and (4) fixed local dispersal by predators. Adaptive dispersal was modelled using the marginal value theorem, such that predators departed patches when the instantaneous rate of prey capture was less than the long-term rate of prey capture averaged over all patches, scaled to the movement time between patches. Adaptive dispersal tended to stabilize metapopulation dynamics in a similar manner to conventional fixed dispersal models, but the temporal dynamics of adaptive dispersal models were more unpredictable than the smooth oscillations of fixed dispersal models. Moreover, fixed and adaptive dispersal models responded differently to spatial variation in patch productivity and the degree of compartmentalization of the system. For both adaptive dispersal and fixed dispersal models, localized (stepping-stone) dispersal was more strongly stabilizing than global (island) dispersal. Variation among predators in the probability of dispersal in relation to local prey density had a strong stabilizing influence on both within-patch and metapopulation dynamics. These results suggest that adaptive space use strategies by predators could have important implications for the dynamics of spatially heterogeneous trophic systems.     

Extending the range of amide proton relaxation dispersion experiments in proteins using a constant-time relaxation-compensated CPMG approach

Relaxation compensated constant-time Carr–Purcell–Meiboom–Gill relaxation dispersion experiments for amide protons are presented that detect s-ms time-scale dynamics of protein backbone amide sites. Because of their ten-fold larger magnetogyric ratio, much shorter 180° pulses can be applied to ¹H than to ¹⁵N spins; therefore, off-resonance effects are reduced and a wider range of effective rf fields can often be used in the case of ¹H experiments. Applications to [¹H-¹⁵N]-ubiquitin and [¹H-¹⁵N]-perdeuterated HIV-1 protease are discussed. In the case of ubiquitin, we present a pulse sequence that reduces artifacts that arise from homonuclear ³J(H_N-H) coupling. In the case of the protease, we show that relaxation dispersion of both ¹H and ¹⁵N spins provides a more comprehensive picture of slow backbone dynamics than does the relaxation dispersion of either spin alone. We also compare the relative merits of ¹H versus ¹⁵N transverse relaxation measurements and note the benefits of using a perdeuterated protein to measure the relaxation dispersion of both spin types.     

Somaclonal Variation in the Gliadin Patterns of Grains of Regenerated Wheat Plants

Maddock, S. E., Risiott, R., Parmar, S., Jones, M. G. K. andShewry, P. R. 1985. Somaclonal variation in the gliadin patternsof grains of regenerated wheat plants.—J. exp. Bot. 36:1976–1984. The banding patterns of the gliadin storageproteins of the grains of 590 regenerated plants from six wheatcultivars were examined by polyacrylamide gel electrophoresisusing lactate buffer. Variation additional to that present incontrol material was observed at a low frequency (1%). Two variantlines showed extensive changes in banding patterns which wereaccompanied by morphological variation of the plants. More limitedvariation in the form of an extra –gliadin band was observedin a third line. Differences in the seed gliadins were not foundin four lines which had shown stable phenotypic changes in heightin field trials. Key words: Wheat, somaclonal variation, gliadins, tissue culture, seed proteins     

Contextual flexibility in the vocal repertoire of an Amazon parrot

Background

Understanding the role of avian vocal communication in social organisation requires knowledge of the vocal repertoire used to convey information. Parrots use acoustic signals in a variety of social contexts, but no studies have evaluated cross-functional use of acoustic signals by parrots, or whether these conform to signal design rules for different behavioural contexts. We statistically characterised the vocal repertoire of 61 free-living Lilac-crowned Amazons (Amazona finschi) in nine behavioural contexts (nesting, threat, alarm, foraging, perched, take-off, flight, landing, and food soliciting). We aimed to determine whether parrots demonstrated contextual flexibility in their vocal repertoire, and whether these acoustic signals follow design rules that could maximise communication.

Results

The Lilac-crowned Amazon had a diverse vocal repertoire of 101 note-types emitted at least twice, 58 of which were emitted ≥5 times. Threat and nesting contexts had the greatest variety and proportion of exclusive note-types, although the most common note-types were emitted in all behavioural contexts but with differing proportional contribution. Behavioural context significantly explained variation in acoustic features, where threat and nesting contexts had the highest mean frequencies and broad bandwidths, and alarm signals had a high emission rate of 3.6 notes/s. Three Principal Components explained 72.03 % of the variation in temporal and spectral characteristics of notes. Permutated Discriminant Function Analysis using these Principal Components demonstrated that 28 note-types (emitted by >1 individual) could be correctly classified and significantly discriminated from a random model.

Conclusions

Acoustic features of Lilac-crowned Amazon vocalisations in specific behavioural contexts conformed to signal design rules. Lilac-crowned Amazons modified the emission rate and proportional contribution of note-types used in each context, suggesting the use of graded and combinatorial variation to encode information. We propose that evaluation of vocal repertoires based on note-types would reflect the true extent of a species’ vocal flexibility, and the potential for combinatorial structures in parrot acoustic signals.

     

Comparative physiological responses to stressors in animals.

1. The species-specific experimental response to stressors (SSERTS) analysis has been applied to a number of species under varied short and long term conditions. 2. The measure provides quantitative data relating to the physiological responses of animals when exposed to stressors and results are presented comparing these for different methods of immobilization, euthanasia, etc. at intra- and inter-species level. 3. It is suggested that the SSERTS measure is of greater value for measuring the responses of animals to stressors than is the measurement of the concentration of single blood variables.     

Bioavailability,Biodistribution, and CNS Toxicity of Clinical-Grade Parvovirus H1 after Intravenous and Intracerebral Injection in Rats

The autonomous parvovirus H1 (H1PV) is transmitted in rodent populations. The natural host is the rat, in which H1PV infection is pathogenic only in fetuses and newborns. H1PV infection of human cancer cells leads to strong oncolytic effects in preclinical models. In preparation for a clinical trial of H1PV injection in patients with malignant brain tumors, H1PV had to be prepared to Good Manufacturing Practice standards, including extensive toxicology testing in rats. Because the trial involves direct intracerebral injection of H1PV into the tumor and around the resection cavity, possible toxicity to CNS tissue had to be investigated. In addition, quantitative blood levels and the tissue distribution of H1PV after single intracerebral or intravenous injection were measured. Direct injection of H1PV into rat brain at 3 dose levels (maximum, 7.96 × 107 pfu) did not cause any macroscopic or histologic pathology. Furthermore, H1PV infection of the brain did not alter central or autonomous nervous system function. H1PV DNA was detected in almost all organs at 6 h, 48 h, and 14 d after intravenous and intracerebral injection, with the highest levels in liver and spleen. H1PV concentrations in most organs were similar after intravenous and intracerebral injection, indicating high permeability of the blood–brain barrier for this small virus. The current results demonstrate wide organ distribution of H1PV after intravenous or intracerebral injection, confirm that H1PV is nonpathogenic in adult rats even after direct injection into the brain, and form the basis for the ongoing ParvOryx01 clinical trial.Abbreviations: H1PV, parvovirus H1; GMP, good manufacturing practice; LLOQ, lowest limit of quantification; VG, viral genomesParvovirus H1 (H1PV) is a small single-stranded nonenveloped DNA virus of 5.1 kb that belongs to the family Parvoviridae. The natural host is the rat but, similar to other related parvoviruses, H1PV can infect and replicate in cells of various other species, including humans.²⁴ However, a systematic screening of species susceptible to H1PV infection has not yet been performed.²⁴ In its natural host, H1PV is pathogenic only in newborns and is embryo- and fetotoxic. The detrimental effects on progeny depend on the age at infection: whereas rats inoculated with H1PV during the ovular preimplantation period do not reveal any reproductive impairment, infection of dams in the middle of the gestational period typically results in fetal death. When infected during late gestation or within the first few days after birth, the progeny frequently develop the so-called ‘osteolytic syndrome,’ characterized by dwarfism and various mongoloid-like features.^{10,11,17,18,23}Because H1PV is readily transmitted in rodent populations in the absence of natural immunity, laboratory animals are routinely tested for the presence of antiH1PV antibodies. Antibodies to H1PV were found in 10.4% of rats caught from feral populations.⁸ To our knowledge, there is currently no detailed information about the bioavailability and tissue distribution of H1PV after natural or experimental infection in vivo, although the route of virus excretion is known to follow fecal and oronasal routes.¹⁸In addition to being a naturally occurring virus in the rodent population, H1PV has oncosuppressive properties, inhibiting the formation of spontaneous as well as chemically or virally induced tumors in laboratory animals.^6,25,26 More recent investigations demonstrated the direct oncolytic potential of the virus in a number of cancers.^1,2,7,22 H1PV infection of tumor cell cultures, including human tumor cells, and of experimental tumors in vivo led to efficient cell killing and tumor regression.¹⁴ The parvoviral cytotoxicity is attributed, at least in part, to the viral regulatory nonstructural protein NS1, and the smaller nonstructural protein NS2 may modulate NS1 cytotoxicity. One promising tumor entity in which H1PV showed strong oncolytic effects is malignant brain tumors (specifically, glioblastoma).¹³ The encouraging rates of complete remissions after intratumoral or intravenous H1PV injection of rats bearing large intracranial gliomas provided the rationale for a clinical trial in patients with recurrent glioblastoma.¹²For clinical use, an H1 virus stock conforming with the standards of Good Manufacturing Practice (GMP) had to be available. To comply with GMP requirements, the purity, infectivity, and stability of the virus preparation had to be demonstrated by the manufacturer. Furthermore, prior to injection in patients, this GMP virus preparation had to undergo extensive nonclinical safety testing. To support the clinical phase I protocol, which includes intravenous infusions as well as direct injection of H1PV into brain tumors, both routes of administration were included in the test protocol. Due to the permissiveness for H1PV infection and replication, rats were defined as the appropriate and sufficient species in which to investigate the potential toxicity profile of H1PV. This species selection was approved by the regulatory authority (Paul-Ehrlich Institut, Langen, Germany).This report focuses on (1) the tissue availability and biodistribution of H1PV after single intravenous and intracranial injection and (2) the potential CNS toxicity of H1PV after direct injection into the rat brain. The results from these studies, along with those of additional studies after single- and repeated-dose administration (reported elsewhere),¹⁵ were mandatory for the regulatory approval of the clinical trial (ParvOryx01) that started in October 2011. In addition to providing safety information of direct clinical relevance, the data offer insights into the biology of H1PV in its natural host (rats), including organ distribution, relative organ concentration, penetration of the blood–brain barrier, viral shedding, and infection-associated behavioral changes. Because the data were generated with purified virus under highly controlled test conditions, the results add valuable information to the understanding of H1PV infection in its natural host. In addition, making these results available may help to reduce the number of future animal experiments in this or related areas of research.