Validation of presence-only models for conservation planning and the application to whales in a multiple-use marine park.

Identification of species' Biologically Important Areas (BIAs) is fundamental to conservation planning and species distribution models (SDMs) are a powerful tool commonly used to do this. Presence-only data are increasingly being used to develop SDMs to aid the conservation decision-making process. The application of presence-only SDMs for marine species' is particularly attractive due to often logistical and economic costs of obtaining systematic species' distribution data. However, robust model validation is important for conservation management applications that require accurate and reliable species' occurrence data (e.g., spatially explicit risk assessments). This is commonly done using a random subset of the data and less commonly with fully independent test data. Here, we apply a spatial block cross-validation (CV) approach to validate a MaxEnt presence-only model using independent presence/absence survey data for a highly mobile, marine species (humpback whale, Megaptera novaengliae) in the Great Barrier Reef (GBR). A MaxEnt model was developed using opportunistic whale sightings (2003-2007) and then used to identify areas differing in habitat suitability (low, medium, high) to conduct a systematic, line-transect, aerial survey (2012) and derive a density surface model. A spatial block CV buffering strategy was used to validate the MaxEnt model, using the opportunistic sightings as training data and independent aerial survey sightings data as test data. Moderate performance measures indicate MaxEnt was reliable in identifying the distribution patterns of a mobile whale species on their breeding ground, indicated by areas of high density aligned to areas of high habitat suitability. Furthermore, we demonstrate that MaxEnt models can be useful and cost-effective for designing a sampling scheme to undertake systematic surveys that significantly reduces sampling effort. In this study, higher quality information on whale reproductive class (calf vs. non-calf groups) was obtained that the presence-only data lacked, while sampling only 18% of the GBR World Heritage Area. The validation approach using fully independent data provides greater confidence in the MaxEnt model, which indicates significant overlap with the main breeding ground of humpback whales and the inner shipping route. This is important when evaluating presence-only models within certain conservation management applications, such as spatial risk assessments.

Directed evolution and biophysical characterization of a full-length, soluble, human caveolin-1 variant.

Protein engineering by directed evolution can alter proteins' structures, properties, and functions. However, membrane proteins, despite their importance to living organisms, remain relatively unexplored as targets for protein engineering and directed evolution. This gap in capabilities likely results from the tendency of membrane proteins to aggregate and fail to overexpress in bacteria cells. For example, the membrane protein caveolin-1 has been implicated in many cell signaling pathways and diseases, yet the full-length protein is too aggregation-prone for detailed mutagenesis, directed evolution, and biophysical characterization. Using a phage-displayed library of full-length caveolin-1 variants, directed evolution with alternating subtractive and functional selections isolated a full-length, soluble variant, termed cavsol, for expression in E. coli. Cavsol folds correctly and binds to its known protein ligands HIV gp41, the catalytic domain of cAMP-dependent protein kinase A, and the polymerase I and transcript release factor. As expected, cavsol does not bind off-target proteins. Cellular studies show that cavsol retains the parent protein's ability to localize at the cellular membrane. Unlike truncated versions of caveolin, cavsol forms large, oligomeric complexes consisting of approximately >50 monomeric units without requiring additional cellular components. Cavsol's secondary structure is a mixture of α-helices and ß-strands. Isothermal titration calorimetry experiments reveal that cavsol binds to gp41 and PKA with low micromolar binding affinity (KD). In addition to the insights into caveolin structure and function, the approach applied here could be generalized to other membrane proteins.

Echolocation click source parameters of Australian snubfin dolphins (Orcaella heinsohni).

The Australian snubfin dolphin (Orcaella heinsohni) is endemic to Australian waters, yet little is known about its abundance and habitat use. To investigate the feasibility of Passive Acoustic Monitoring for snubfin dolphins, biosonar clicks were recorded in Cygnet Bay, Australia, using a four-element hydrophone array. Clicks had a mean source level of 200 ± 5 dB re 1 µPa pp, transmission directivity index of 24 dB, mean centroid frequency of 98 ± 9 kHz, and a root-mean-square bandwidth of 31 ± 3 kHz. Such properties lend themselves to passive acoustic monitoring, but are comparable to similarly-sized delphinids, thus requiring additional cues to discriminate between snubfins and sympatric species.

Preliminary estimates of the abundance and fidelity of dolphins associating with a demersal trawl fishery.

The incidental capture of wildlife in fishing gear presents a global conservation challenge. As a baseline to inform assessments of the impact of bycatch on bottlenose dolphins (Tursiops truncatus) interacting with an Australian trawl fishery, we conducted an aerial survey to estimate dolphin abundance across the fishery. Concurrently, we carried out boat-based dolphin photo-identification to assess short-term fidelity to foraging around trawlers, and used photographic and genetic data to infer longer-term fidelity to the fishery. We estimated abundance at ≈ 2,300 dolphins (95% CI = 1,247-4,214) over the ≈ 25,880-km2 fishery. Mark-recapture estimates yielded 226 (SE = 38.5) dolphins associating with one trawler and some individuals photographed up to seven times over 12 capture periods. Moreover, photographic and genetic re-sampling over three years confirmed that some individuals show long-term fidelity to trawler-associated foraging. Our study presents the first abundance estimate for any Australian pelagic dolphin community and documents individuals associating with trawlers over days, months and years. Without trend data or correction factors for dolphin availability, the impact of bycatch on this dolphin population's conservation status remains unknown. These results should be taken into account by management agencies assessing the impact of fisheries-related mortality on this protected species.

Protein Folding Using a Vortex Fluidic Device.

Essentially all biochemistry and most molecular biology experiments require recombinant proteins. However, large, hydrophobic proteins typically aggregate into insoluble and misfolded species, and are directed into inclusion bodies. Current techniques to fold proteins recovered from inclusion bodies rely on denaturation followed by dialysis or rapid dilution. Such approaches can be time consuming, wasteful, and inefficient. Here, we describe rapid protein folding using a vortex fluidic device (VFD). This process uses mechanical energy introduced into thin films to rapidly and efficiently fold proteins. With the VFD in continuous flow mode, large volumes of protein solution can be processed per day with 100-fold reductions in both folding times and buffer volumes.

Affinity-Guided Design of Caveolin-1 Ligands for Deoligomerization.

Caveolin-1 is a target for academic and pharmaceutical research due to its many cellular roles and associated diseases. We report peptide WL47 (1), a small, high-affinity, selective disrupter of caveolin-1 oligomers. Developed and optimized through screening and analysis of synthetic peptide libraries, ligand 1 has 7500-fold improved affinity compared to its T20 parent ligand and an 80% decrease in sequence length. Ligand 1 will permit targeted study of caveolin-1 function.

Shear-stress-mediated refolding of proteins from aggregates and inclusion bodies.

Recombinant protein overexpression of large proteins in bacteria often results in insoluble and misfolded proteins directed to inclusion bodies. We report the application of shear stress in micrometer-wide, thin fluid films to refold boiled hen egg white lysozyme, recombinant hen egg white lysozyme, and recombinant caveolin-1. Furthermore, the approach allowed refolding of a much larger protein, cAMP-dependent protein kinase A (PKA). The reported methods require only minutes, which is more than 100 times faster than conventional overnight dialysis. This rapid refolding technique could significantly shorten times, lower costs, and reduce waste streams associated with protein expression for a wide range of industrial and research applications.

Discriminating between the vocalizations of Indo-Pacific humpback and Australian snubfin dolphins in Queensland, Australia.

Australian snubfin and Indo-Pacific humpback dolphins co-occur throughout most of their range in coastal waters of tropical Australia. Little is known of their ecology or acoustic repertoires. Vocalizations from humpback and snubfin dolphins were recorded in two locations along the Queensland coast during 2008 and 2010 to describe their vocalizations and evaluate the acoustic differences between these two species. Broad vocalization types were categorized qualitatively. Both species produced click trains burst pulses and whistles. Principal component analysis of the nine acoustic variables extracted from the whistles produced nine principal components that were input into discriminant function analyses to classify 96% of humpback dolphin whistles and about 78% of snubfin dolphin calls correctly. Results indicate clear acoustic differences between the vocal whistle repertoires of these two species. A stepwise routine identified two principal components as significantly distinguishable between whistles of each species: frequency parameters and frequency trend ratio. The capacity to identify these species using acoustic monitoring techniques has the potential to provide information on presence/absence, habitat use and relative abundance for each species.

Multivariate analysis of behavioural response experiments in humpback whales (Megaptera novaeangliae).

The behavioural response study (BRS) is an experimental design used by field biologists to determine the function and/or behavioural effects of conspecific, heterospecific or anthropogenic stimuli. When carrying out these studies in marine mammals it is difficult to make basic observations and achieve sufficient samples sizes because of the high cost and logistical difficulties. Rarely are other factors such as social context or the physical environment considered in the analysis because of these difficulties. This paper presents results of a BRS carried out in humpback whales to test the response of groups to one recording of conspecific social sounds and an artificially generated tone stimulus. Experiments were carried out in September/October 2004 and 2008 during the humpback whale southward migration along the east coast of Australia. In total, 13 'tone' experiments, 15 'social sound' experiments (using one recording of social sounds) and three silent controls were carried out over two field seasons. The results (using a mixed model statistical analysis) suggested that humpback whales responded differently to the two stimuli, measured by changes in course travelled and dive behaviour. Although the response to 'tones' was consistent, in that groups moved offshore and surfaced more often (suggesting an aversion to the stimulus), the response to 'social sounds' was highly variable and dependent upon the composition of the social group. The change in course and dive behaviour in response to 'tones' was found to be related to proximity to the source, the received signal level and signal-to-noise ratio (SNR). This study demonstrates that the behavioural responses of marine mammals to acoustic stimuli are complex. In order to tease out such multifaceted interactions, the number of replicates and factors measured must be sufficient for multivariate analysis.