Applying distance sampling to fin whale calls recorded by single seismic instruments in the northeast Atlantic

Automated methods were developed to detect fin whale calls recorded by an array of ocean bottom seismometers (OBSs) deployed off the Portuguese coast between 2007 and 2008. Using recordings collected on a single day in January 2008, a standard seismological method for estimating earthquake location from single instruments, the three-component analysis, was used to estimate the relative azimuth, incidence angle, and horizontal range between each OBS and detected calls. A validation study using airgun shots, performed prior to the call analysis, indicated that the accuracy of the three-component analysis was satisfactory for this preliminary study. Point transect sampling using cue counts, a form of distance sampling, was then used to estimate the average probability of detecting a call via the array during the chosen day. This is a key step to estimating density or abundance of animals using passive acoustic data. The average probability of detection was estimated to be 0.313 (standard error: 0.033). However, fin whale density could not be estimated due to a lack of an appropriate estimate of cue (i.e., vocalization) rate. This study demonstrates the potential for using a sparse array of widely spaced, independently operating acoustic sensors, such as OBSs, for estimating cetacean density.

Estimating resource acquisition and at-sea body condition of a marine predator

1. Body condition plays a fundamental role in many ecological and evolutionary processes at a variety of scales and across a broad range of animal taxa. An understanding of how body condition changes at fine spatial and temporal scales as a result of interaction with the environment provides necessary information about how animals acquire resources. 2. However, comparatively little is known about intra- and interindividual variation of condition in marine systems. Where condition has been studied, changes typically are recorded at relatively coarse time-scales. By quantifying how fine-scale interaction with the environment influences condition, we can broaden our understanding of how animals acquire resources and allocate them to body stores. 3. Here we used a hierarchical Bayesian state-space model to estimate the body condition as measured by the size of an animal's lipid store in two closely related species of marine predator that occupy different hemispheres: northern elephant seals (Mirounga angustirostris) and southern elephant seals (Mirounga leonina). The observation model linked drift dives to lipid stores. The process model quantified daily changes in lipid stores as a function of the physiological condition of the seal (lipid:lean tissue ratio, departure lipid and departure mass), its foraging location, two measures of behaviour and environmental covariates. 4. We found that physiological condition significantly impacted lipid gain at two time-scales - daily and at departure from the colony - that foraging location was significantly associated with lipid gain in both species of elephant seals and that long-term behavioural phase was associated with positive lipid gain in northern and southern elephant seals. In northern elephant seals, the occurrence of short-term behavioural states assumed to represent foraging were correlated with lipid gain. Lipid gain was a function of covariates in both species. Southern elephant seals performed fewer drift dives than northern elephant seals and gained lipids at a lower rate. 5. We have demonstrated a new way to obtain time series of body condition estimates for a marine predator at fine spatial and temporal scales. This modelling approach accounts for uncertainty at many levels and has the potential to integrate physiological and movement ecology of top predators. The observation model we used was specific to elephant seals, but the process model can readily be applied to other species, providing an opportunity to understand how animals respond to their environment at a fine spatial scale.

Heterogeneous properties of central lateral and parafascicular thalamic synapses in the striatum

To understand the principles of operation of the striatum it is critical to elucidate the properties of the main excitatory inputs from cortex and thalamus, as well as their ability to activate the main neurons of the striatum, the medium spiny neurons (MSNs). As the thalamostriatal projection is heterogeneous, we set out to isolate and study the thalamic afferent inputs to MSNs using small localized injections of adeno-associated virus carrying fusion genes for channelrhodopsin-2 and YFP, in either the rostral or caudal regions of the intralaminar thalamic nuclei (i.e. the central lateral or parafascicular nucleus). This enabled optical activation of specific thalamic afferents combined with whole-cell, patch-clamp recordings of MSNs and electrical stimulation of cortical afferents, in adult mice. We found that thalamostriatal synapses differ significantly in their peak amplitude responses, short-term dynamics and expression of ionotropic glutamate receptor subtypes. Our results suggest that central lateral synapses are most efficient in driving MSNs to depolarization, particularly those of the direct pathway, as they exhibit large amplitude responses, short-term facilitation and predominantly express postsynaptic AMPA receptors. In contrast, parafascicular synapses exhibit small amplitude responses, short-term depression and predominantly express postsynaptic NMDA receptors, suggesting a modulatory role, e.g. facilitating Ca(2+)-dependent processes. Indeed, pairing parafascicular, but not central lateral, presynaptic stimulation with action potentials in MSNs, leads to NMDA receptor- and Ca(2+)-dependent long-term depression at these synapses. We conclude that the main excitatory thalamostriatal afferents differ in many of their characteristics and suggest that they each contribute differentially to striatal information processing.

An investigation into utilising gestational body mass index as a screening tool for adverse birth outcomes and maternal morbidities in a group of pregnant women in Khayelitsha

OBJECTIVE

The aim of this study was to investigate the ability of the gestational body mass index (BMI) method to screen for adverse birth outcomes and maternal morbidities.

DESIGN

This was a substudy of a randomised controlled trial, the Philani Mentor Mothers' study.

SETTING AND SUBJECTS

The Philani Mentor Mothers' study took place in a peri-urban settlement, Khayelitsha, between 2009 and 2010. Pregnant women living in the area in 2009-2010 were recruited for the study.

OUTCOME MEASURES

Maternal anthropometry (height and weight) and gestational weeks were obtained at baseline to calculate the gestational BMI, which is maternal BMI adjusted for gestational age. Participants were classified into four gestational BMI categories: underweight, normal, overweight and obese. Birth outcomes and maternal morbidities were obtained from clinic cards after the births.

RESULTS

Pregnant women were recruited into the study (n = 1 058). Significant differences were found between the different gestational BMI categories and the following birth outcomes: maternal (p-value = 0.019), infant hospital stay (p-value = 0.03), infants staying for over 24 hours in hospital (p-value = 0.001), delivery mode (p-value = 0.001), birthweight (p-value = 0.006), birth length (p-value = 0.007), birth head circumference (p-value = 0.007) and pregnancy-induced hypertension (p-value = 0.001).

CONCLUSION

To the best of our knowledge, this is the first study that has used the gestational BMI method in a peri-urban South African pregnant population. Based on the findings that this method is able to identify unfavourable birth outcomes, it is recommended that it is implemented as a pilot study in selected rural, peri-urban and urban primary health clinics, and that its ease and effectiveness as a screening tool is evaluated. Appropriate medical and nutritional advice can then be given to pregnant women to improve both their own and their infants' birth-related outcomes and maternal morbidities.

(Meta)population dynamics of infectious diseases

The metapopulation concept provides a very powerful tool for analysing the persistence of spatially-disaggregated populations, in terms of a balance between local extinction and colonization. Exactly the same approach has been developed by epidemiologists, in order to understand patterns of diseases persistence. There is great scope for further cross-fertilization between areas. Recent work on the spatitemporal dynamics of measles illustrates that the large datasets and rich modelling literature on many infectious diseases offer great potential for developing and testing ideas about metapopulations.

NMR quantitation: influence of RF inhomogeneity

The NMR peak integral is ideally linearly dependent on the sine of excitation angle (θ), which has provided unsurpassed flexibility in quantitative NMR by allowing the use of a signal of any concentration as the internal concentration reference. Controlling the excitation angle is particularly critical for solvent proton concentration referencing to minimize the negative impact of radiation damping, and to reduce the risk of receiver gain compression. In practice, due to the influence of RF inhomogeneity for any given probe, the observed peak integral is not exactly proportional to sin θ. To evaluate the impact quantitatively, we introduce a RF inhomogeneity factor I(θ) as a function of the nominal pulse excitation angle and propose a simple calibration procedure. Alternatively, I(θ) can be calculated from the probe's RF profile, which can be readily obtained as a gradient image of an aqueous sample. Our results show that without consideration of I(θ), even for a probe with good RF homogeneity, up to 5% error can be introduced due to different excitation pulse angles used for the analyte and the reference. Hence, a simple calibration of I(θ) can eliminate such errors and allow an accurate description of the observed NMR signal's dependence on the excitation angle in quantitative analysis.

Geographic variation of the major histocompatibility complex in Eastern Atlantic grey seals (Halichoerus grypus)

Pathogen-driven balancing selection maintains high genetic diversity in many vertebrates, particularly in the major histocompatibility complex (MHC) immune system gene family, which is often associated with disease susceptibility. In large natural populations where subpopulations face different pathogen pressures, the MHC should show greater genetic differentiation within a species than neutral markers. We examined genetic diversity at the MHC-DQB locus and nine putatively neutral microsatellite markers in grey seals (Halichoerus grypus) from eight United Kingdom (UK) colonies, the Faeroe Islands and Sable Island, Canada. Five DQB alleles were identified in grey seals, which varied in prevalence across the grey seal range. Among the seal colonies, significant differences in DQB allele and haplotype frequencies and in average DQB heterozygosity were observed. Additionally, the DQB gene exhibited greater differentiation among colonies compared with neutral markers, yet a weaker pattern of isolation by distance (IBD). After correcting for the underlying IBD pattern, subpopulations breeding in similar habitats were more similar to one another in DQB allele frequencies than populations breeding in different habitats, but the same did not hold true for microsatellites, suggesting that habitat-specific pathogen pressure influences MHC evolution. Overall, the data are consistent with selection at MHC-DQB loci in grey seals with both varying selective pressures and geographic population structure appearing to influence the DQB genetic composition of breeding colonies.

Lipid classes and fatty acid patterns are altered in the brain of γ-synuclein null mutant mice

The well-documented link between α-synuclein and the pathology of common human neurodegenerative diseases has increased attention to the synuclein protein family. The involvement of α-synuclein in lipid metabolism in both normal and diseased nervous system has been shown by many research groups. However, the possible involvement of γ-synuclein, a closely-related member of the synuclein family, in these processes has hardly been addressed. In this study, the effect of γ-synuclein deficiency on the lipid composition and fatty acid patterns of individual lipids from two brain regions has been studied using a mouse model. The level of phosphatidylserine (PtdSer) was increased in the midbrain whereas no changes in the relative proportions of membrane polar lipids were observed in the cortex of γ-synuclein-deficient compared to wild-type (WT) mice. In addition, higher levels of docosahexaenoic acid were found in PtdSer and phosphatidylethanolamine (PtdEtn) from the cerebral cortex of γ-synuclein null mutant mice. These findings show that γ-synuclein deficiency leads to alterations in the lipid profile in brain tissues and suggest that this protein, like α-synuclein, might affect neuronal function via modulation of lipid metabolism.

The functional response of a generalist predator

BACKGROUND

Predators can have profound impacts on the dynamics of their prey that depend on how predator consumption is affected by prey density (the predator's functional response). Consumption by a generalist predator is expected to depend on the densities of all its major prey species (its multispecies functional response, or MSFR), but most studies of generalists have focussed on their functional response to only one prey species.

METHODOLOGY AND PRINCIPAL FINDINGS

Using Bayesian methods, we fit an MSFR to field data from an avian predator (the hen harrier Circus cyaneus) feeding on three different prey species. We use a simple graphical approach to show that ignoring the effects of alternative prey can give a misleading impression of the predator's effect on the prey of interest. For example, in our system, a "predator pit" for one prey species only occurs when the availability of other prey species is low.

CONCLUSIONS AND SIGNIFICANCE

The Bayesian approach is effective in fitting the MSFR model to field data. It allows flexibility in modelling over-dispersion, incorporates additional biological information into the parameter priors, and generates estimates of uncertainty in the model's predictions. These features of robustness and data efficiency make our approach ideal for the study of long-lived predators, for which data may be sparse and management/conservation priorities pressing.

Comparison of the 1988 and 2002 phocine distemper epizootics in British harbour seal Phoca vitulina populations

In 1988 and 2002 dramatic and well-documented phocine distemper epizootics occurred in Europe. While their progression and impact were remarkably similar and consistent over much of Europe, mortality in the UK varied greatly between and within the 2 epizootics. We use antibody levels in blood samples to show that 51% (Bayesian 95% CI: 41 to 61%) of the individuals alive in 5 UK harbour seal populations at the end of the 1988 epizootic had been exposed to the virus, and that the equivalent figure after the 2002 outbreak was 22% (95% CI: 16 to 30%). Antibody prevalence was significantly higher in females than males after the 2002 epizootic. Combining these estimates with information on reductions in the numbers of animals observed hauled out during surveys of the Wash, Moray Firth, and Orkney populations and a simple epidemiological model, suggests that the differences between the 2 epizootics were primarily due to a 27% (95% CI: 8 to 43%) fall in R0, the basic reproductive rate of the virus. The large geographic variation in population effects observed within the UK during each epizootic appears to have been mainly due to differences in case mortality, with R0 being remarkably similar in all the populations investigated.

R: A quantitative measure of NMR signal receiving efficiency

Recognizing that the sensitivity of NMR is influenced by factors such as conductance and dielectric constant of the sample, we propose the receiving efficiency R to characterize how efficiently the NMR signal can be observed from a unit transverse magnetization in a sample under optimal probe tuning and matching conditions. Conveniently, the relative receiving efficiency can be defined as the ratio of the NMR signal induced by a unit transverse magnetization in a sample of interest and a reference solution. Based on the reciprocal relationship between excitation and observation in NMR, the relative receiving efficiency can be correlated with the 90 degrees pulse length (tau(90)). In the special case of perfect probe tuning (impedance matched to 50 Omega), R is inversely proportional to tau(90). Application of the NMR receiving efficiency in quantitative analysis potentially enables a single external concentration reference for almost any sample, eliminating the need to know its exact chemical composition or detailed electromagnetic properties.

Effect of irrigation on quality attributes of olive oil

Two irrigation treatments were applied to olive trees of the major commercial Cretan variety cv. Koroneiki, (a) irrigation with 0.4 evaporation class "A" pan and (b) rain-feed only, in two successive crop years to assess the effect of irrigation on olive oil quality. Olive fruits were harvested at their semiblack maturity stage. Data obtained indicated that irrigation increased fruit weight and oil content, but the standard quality indices (free fatty acids, peroxide value, K(232), and K(270)) of the oil were not affected significantly. However, irrigation affected some aspects of olive oil composition. There were changes in the proportions of polyunsaturated fatty acids (PUFAs), triacylglycerol molecular species, sterols, and aliphatic alcohols. Furthermore, the concentrations of the dialdehydic form of elenolic acid linked to 3,4-DHPEA (3,4-DHPEA-EDA) and the isomer of oleuropeine aglycon (3,4-DHPEA-EA) were higher in oils from non-irrigated trees. Tocopherol and total volatiles were higher in the oil produced from the non-irrigated trees. Such oil was graded more pungent when compared to oils produced from fruits of irrigated trees, although both oils were graded satisfactory by consumers.

Olive oil qualitative parameters after orchard irrigation with saline water

The effect of irrigation with saline water on oil quality was studied in the two olive ( Olea europaea L.) cultivars Koroneiki and Mastoidis, which are the main varieties grown extensively on the island of Crete. Plants (5 years old) were grown outdoors in containers, filled with freely drained light soil. Four treatments were applied, differing in the NaCl added to the irrigation water as follows: 0 (control) 50, 100, and 150 mM NaCl. Drip irrigation was applied regularly, during the dry season (from April to October). Plants in all treatments were irrigated when the soil-water potential reached -40 kPa at a depth of 30 cm. Data showed that increased NaCl levels in irrigation water resulted in a decrease in oil content in the fruits and an increase in total phenols and their secoiridoid derivatives in olive oils from harvested fruits. Furthermore, changes also took place in the composition of fatty acids and triacylglycerol molecular species. The extent of alterations was different for the two varieties and greater in cv. Koroneiki. This fitted with agronomic evidence that cv. Koroneiki is less saline-tolerant than cv. Mastoidis.

Passive acoustic detection of deep-diving beaked whales

Beaked whales can remain submerged for an hour or more and are difficult to sight when they come to the surface to breathe. Passive acoustic detection (PAD) not only complements traditional visual-based methods for detecting these species but also can be more effective because beaked whales produce clicks regularly to echolocate on prey during deep foraging dives. The effectiveness of PAD for beaked whales depends not only on the acoustic behavior and output of the animals but also on environmental conditions and the quality of the passive sonar implemented. A primary constraint on the range at which beaked whale clicks can be detected involves their high frequencies, which attenuate rapidly, resulting in limited ranges of detection, especially in adverse environmental conditions. Given current knowledge of source parameters and in good conditions, for example, with a wind speed of 2 ms, a receiver close to the surface should be able to detect acoustically Cuvier's beaked whales with a high probability at distances up to 0.7 km, provided the listening duration exceeds the deep dive interval, about 2.5 h on average. Detection ranges beyond 4 km are unlikely and would require low ambient noise or special sound propagation conditions.

Evaluating the influence of epidemiological parameters and host ecology on the spread of phocine distemper virus through populations of harbour seals

BACKGROUND

Outbreaks of phocine distemper virus (PDV) in Europe during 1988 and 2002 were responsible for the death of around 23,000 and 30,000 harbour seals, respectively. These epidemics, particularly the one in 2002, provided an unusual opportunity to estimate epidemic parameters for a wildlife disease. There were marked regional differences in the values of some parameters both within and between epidemics.

METHODOLOGY AND PRINCIPAL FINDINGS

We used an individual-based model of seal movement that allowed us to incorporate realistic representations of space, time and animal behaviour into a traditional epidemiological modelling framework. We explored the potential influence of a range of ecological (foraging trip duration, time of epidemic onset, population size) and epidemiological (length of infectious period, contact rate between infectious and susceptible individuals, case mortality) parameters on four readily-measurable epidemic characteristics (number of dead individuals, duration of epidemic, peak mortality date and prevalence) and on the probability that an epidemic would occur in a particular region. We analysed the outputs as if they were the results of a series of virtual experiments, using Generalised Linear Modelling. All six variables had a significant effect on the probability that an epidemic would be recognised as an unusual mortality event by human observers.

CONCLUSIONS

Regional and temporal variation in contact rate was the most likely cause of the observed differences between the two epidemics. This variation could be a consequence of differences in the way individuals divide their time between land and sea at different times of the year.