Pygmy Sperm Whale (Kogin breiJiceps) stranding record in Tasmania, Australia, and diet of a single specimen

This study describes the stranding record of the Pygmy Sperm Whale, Kogia breviceps, in Tasmanian waters, and the diet of a single individual. The Pygmy Sperm Whale is one of the most commonly stranded cetaceans in some parts of Australia, although it occurs infrequently in the Tasmanian stranding record, with only seven known stranding events. Dietary items were investigated from a single juvenile male Pygmy Sperm Whale stranded in southeast Tasmania. The recoverable diet consisted of approximately three kilograms of reconstructed cephalopod prey mass from at least 11 cephalopod species within nine families. Using reconstructed biomass, the most important family was Histioteuthidae (Histioteuthis atlantica and H. miranda: 29% of reconstructed biomass), followed by Ommastrephidae (unknown sp.: 27% of reconstructed biomass), Enoploteuthidae (Enoploteuthis sp): 25% of reconstructed biomass), Cranchiidae (Cranchia scabra and Teuthowenia pellucida), Chiroteuthidae (Chiroteuthis veranyi), Brachioteuthidae (Brachioteuthis linkovskyi), Neoteuthidae (Nototeuthis dimegacotyle), Pyroteuthidae (Pyroteuthis margaritifera) and Sepiolidae (Heteroteuthis sp.). Collection and analysis of biological material from Pygmy Sperm Whale strandings around Australia should be a high priority to better understand the ecology of this poorly known species

Long-term species, sexual and individual variations in foraging strategies of fur seals revealed by stable isotopes in whiskers

Background: Individual variations in the use of the species niche are an important component of diversity in trophic interactions. A challenge in testing consistency of individual foraging strategy is the repeated collection of information on the same individuals. Methodology/Principal Findings: The foraging strategies of sympatric fur seals (Arctocephalus gazella and A. tropicalis) were examined using the stable isotope signature of serially sampled whiskers. Most whiskers exhibited synchronous delta C-13 and delta N-15 oscillations that correspond to the seal annual movements over the long term (up to 8 years). delta C-13 and delta N-15 values were spread over large ranges, with differences between species, sexes and individuals. The main segregating mechanism operates at the spatial scale. Most seals favored foraging in subantarctic waters (where the Crozet Islands are located) where they fed on myctophids. However, A. gazella dispersed in the Antarctic Zone and A. tropicalis more in the subtropics. Gender differences in annual time budget shape the seal movements. Males that do not perform any parental care exhibited large isotopic oscillations reflecting broad annual migrations, while isotopic values of females confined to a limited foraging range during lactation exhibited smaller changes. Limited inter-individual isotopic variations occurred in female seals and in male A. tropicalis. In contrast, male A. gazella showed large inter-individual variations, with some males migrating repeatedly to high-Antarctic waters where they fed on krill, thus meaning that individual specialization occurred over years. Conclusions/Significance: Whisker isotopic signature yields unique long-term information on individual behaviour that integrates the spatial, trophic and temporal dimensions of the ecological niche. The method allows depicting the entire realized niche of the species, including some of its less well-known components such as age-, sex-, individual- and migration-related changes. It highlights intrapopulation heterogeneity in foraging strategies that could have important implications for likely demographic responses to environmental variability

Syndecan-1 regulates the biological activities of interleukin-34

IL-34 is a challenging cytokine sharing functional similarities with M-CSF through M-CSFR activation. It also plays a singular role that has recently been explained in the brain, through a binding to the receptor protein tyrosine phosphatase RPTPβ/ζ. The aim of this paper was to look for alternative binding of IL-34 on other cell types. Myeloid cells (HL-60, U-937, THP-1) were used as cells intrinsically expressing M-CSFR, and M-CSFR was expressed in TF-1 and HEK293 cells. IL-34 binding was studied by Scatchard and binding inhibition assays, using 125I-radiolabelled cytokines, and surface plasmon resonance. M-CSFR activation was analysed by Western blot after glycosaminoglycans abrasion, syndecan-1 overexpression or repression and addition of a blocking anti-syndecan antibody. M-CSF and IL-34 induced different patterns of M-CSFR phosphorylations, suggesting the existence of alternative binding for IL-34. Binding experiments and chondroitinase treatment confirmed low affinity binding to chondroitin sulphate chains on cells lacking both M-CSFR and RPTPβ/ζ. Amongst the proteoglycans with chondroitin sulphate chains, syndecan-1 was able to modulate the IL-34-induced M-CSFR signalling pathways. Interestingly, IL-34 induced the migration of syndecan-1 expressing cells. Indeed, IL-34 significantly increased the migration of THP-1 and M2a macrophages that was inhibited by addition of a blocking anti-syndecan-1 antibody. This paper provides evidence of alternative binding of IL-34 to chondroitin sulphates and syndecan-1 at the cell surface that modulates M-CSFR activation. In addition, IL-34-induced myeloid cell migration is a syndecan-1 dependent mechanism

Genome wide prediction of protein function via a generic knowledge discovery approach based on evidence integration

BACKGROUND: The automation of many common molecular biology techniques has resulted in the accumulation of vast quantities of experimental data. One of the major challenges now facing researchers is how to process this data to yield useful information about a biological system (e.g. knowledge of genes and their products, and the biological roles of proteins, their molecular functions, localizations and interaction networks). We present a technique called Global Mapping of Unknown Proteins (GMUP) which uses the Gene Ontology Index to relate diverse sources of experimental data by creation of an abstraction layer of evidence data. This abstraction layer is used as input to a neural network which, once trained, can be used to predict function from the evidence data of unannotated proteins. The method allows us to include almost any experimental data set related to protein function, which incorporates the Gene Ontology, to our evidence data in order to seek relationships between the different sets. RESULTS: We have demonstrated the capabilities of this method in two ways. We first collected various experimental datasets associated with yeast (Saccharomyces cerevisiae) and applied the technique to a set of previously annotated open reading frames (ORFs). These ORFs were divided into training and test sets and were used to examine the accuracy of the predictions made by our method. Then we applied GMUP to previously un-annotated ORFs and made 1980, 836 and 1969 predictions corresponding to the GO Biological Process, Molecular Function and Cellular Component sub-categories respectively. We found that GMUP was particularly successful at predicting ORFs with functions associated with the ribonucleoprotein complex, protein metabolism and transportation. CONCLUSION: This study presents a global and generic gene knowledge discovery approach based on evidence integration of various genome-scale data. It can be used to provide insight as to how certain biological processes are implemented by interaction and coordination of proteins, which may serve as a guide for future analysis. New data can be readily incorporated as it becomes available to provide more reliable predictions or further insights into processes and interactions

SEGMA: an automatic SEGMentation Approach for human brain MRI using sliding window and random forests

Quantitative volumes from brain magnetic resonance imaging (MRI) acquired across the life course may be useful for investigating long term effects of risk and resilience factors for brain development and healthy aging, and for understanding early life determinants of adult brain structure. Therefore, there is an increasing need for automated segmentation tools that can be applied to images acquired at different life stages. We developed an automatic segmentation method for human brain MRI, where a sliding window approach and a multi-class random forest classifier were applied to high-dimensional feature vectors for accurate segmentation. The method performed well on brain MRI data acquired from 179 individuals, analyzed in three age groups: newborns (38–42 weeks gestational age), children and adolescents (4–17 years) and adults (35–71 years). As the method can learn from partially labeled datasets, it can be used to segment large-scale datasets efficiently. It could also be applied to different populations and imaging modalities across the life course

Are acoustical parameters of begging call elements of thin-billed prions related to chick condition?

Chicks of burrowing petrels use begging calls to advertise their hunger levels when parents arrived at the nest. In a previous study, adult thin-billed prions Pachyptila belcheri responded to higher begging call rates of their single chick by regurgitating larger meals. We tested whether acoustic parameters of begging call elements may also be involved in signalling. To describe variation in begging, we determined begging session parameters, namely the duration, number of calls and the mean and maximum rate of calling. We then digitised calls and carried out a semi-automatic extraction of six acoustic parameters of call elements, including mean and maximum acoustic frequency, the length of call elements and the location of the maximum frequency and amplitude within calls. Chicks showed strong individual differences in all parameters. While the session parameters were correlated with body condition and with the meal size the chick received, none of the acoustic parameters were related to body condition and provisioning. A cross-fostering experiment showed the same pattern, as only session parameters changed related to an experimentally altered body condition, while acoustical cues appear to play no role in signalling hunger levels. We suggest that this may be explained by the absence of sibling competition in these birds. As parents do not need to decide which chick to feed, immediate information on condition at the time of adult arrival may not be required

Effects of Hydrographic Variability on the Spatial, Seasonal and Diel Diving Patterns of Southern Elephant Seals in the Eastern Weddell Sea

Weddell Sea hydrography and circulation is driven by influx of Circumpolar Deep Water (CDW) from the Antarctic Circumpolar Current (ACC) at its eastern margin. Entrainment and upwelling of this high-nutrient, oxygen-depleted water mass within the Weddell Gyre also supports the mesopelagic ecosystem within the gyre and the rich benthic community along the Antarctic shelf. We used Conductivity-Temperature-Depth Satellite Relay Data Loggers (CTD-SRDLs) to examine the importance of hydrographic variability, ice cover and season on the movements and diving behavior of southern elephant seals in the eastern Weddell Sea region during their overwinter feeding trips from Bouvetøya. We developed a model describing diving depth as a function of local time of day to account for diel variation in diving behavior. Seals feeding in pelagic ice-free waters during the summer months displayed clear diel variation, with daytime dives reaching 500-1500 m and night-time targeting of the subsurface temperature and salinity maxima characteristic of CDW around 150–300 meters. This pattern was especially clear in the Weddell Cold and Warm Regimes within the gyre, occurred in the ACC, but was absent at the Dronning Maud Land shelf region where seals fed benthically. Diel variation was almost absent in pelagic feeding areas covered by winter sea ice, where seals targeted deep layers around 500–700 meters. Thus, elephant seals appear to switch between feeding strategies when moving between oceanic regimes or in response to seasonal environmental conditions. While they are on the shelf, they exploit the locally-rich benthic ecosystem, while diel patterns in pelagic waters in summer are probably a response to strong vertical migration patterns within the copepod-based pelagic food web. Behavioral flexibility that permits such switching between different feeding strategies may have important consequences regarding the potential for southern elephant seals to adapt to variability or systematic changes in their environment resulting from climate change

Precise Regulation of Gene Expression Dynamics Favors Complex Promoter Architectures

Promoters process signals through recruitment of transcription factors and RNA polymerase, and dynamic changes in promoter activity constitute a major noise source in gene expression. However, it is barely understood how complex promoter architectures determine key features of promoter dynamics. Here, we employ prototypical promoters of yeast ribosomal protein genes as well as simplified versions thereof to analyze the relations among promoter design, complexity, and function. These promoters combine the action of a general regulatory factor with that of specific transcription factors, a common motif of many eukaryotic promoters. By comprehensively analyzing stationary and dynamic promoter properties, this model-based approach enables us to pinpoint the structural characteristics underlying the observed behavior. Functional tradeoffs impose constraints on the promoter architecture of ribosomal protein genes. We find that a stable scaffold in the natural design results in low transcriptional noise and strong co-regulation of target genes in the presence of gene silencing. This configuration also exhibits superior shut-off properties, and it can serve as a tunable switch in living cells. Model validation with independent experimental data suggests that the models are sufficiently realistic. When combined, our results offer a mechanistic explanation for why specific factors are associated with low protein noise in vivo. Many of these findings hold for a broad range of model parameters and likely apply to other eukaryotic promoters of similar structure

Enzymatic capacities of metabolic fuel use in cuttlefish (Sepia officinalis) and responses to food deprivation: insight into the metabolic organization and starvation survival strategy of cephalopods

Food limitation is a common challenge for animals. Cephalopods are sensitive to starvation because of high metabolic rates and growth rates related to their "live fast, die young" life history. We investigated how enzymatic capacities of key metabolic pathways are modulated during starvation in the common cuttlefish (Sepia officinalis) to gain insight into the metabolic organization of cephalopods and their strategies for coping with food limitation. In particular, lipids have traditionally been considered unimportant fuels in cephalopods, yet, puzzlingly, many species (including cuttlefish) mobilize the lipid stores in their digestive gland during starvation. Using a comprehensive multi-tissue assay of enzymatic capacities for energy metabolism, we show that, during long-term starvation (12 days), glycolytic capacity for glucose use is decreased in cuttlefish tissues, while capacities for use of lipid-based fuels (fatty acids and ketone bodies) and amino acid fuels are retained or increased. Specifically, the capacity to use the ketone body acetoacetate as fuel is widespread across tissues and gill has a previously unrecognized capacity for fatty acid catabolism, albeit at low rates. The capacity for de novo glucose synthesis (gluconeogenesis), important for glucose homeostasis, likely is restricted to the digestive gland, contrary to previous reports of widespread gluconeogenesis among cephalopod tissues. Short-term starvation (3-5 days) had few effects on enzymatic capacities. Similar to vertebrates, lipid-based fuels, putatively mobilized from fat stores in the digestive gland, appear to be important energy sources for cephalopods, especially during starvation when glycolytic capacity is decreased perhaps to conserve available glucose

Wild Skylarks Seasonally Modulate Energy Budgets but Maintain Energetically Costly Inflammatory Immune Responses throughout the Annual Cycle

A central hypothesis of ecological immunology is that immune defences are traded off against competing physiological and behavioural processes. During energetically demanding periods, birds are predicted to switch from expensive inflammatory responses to less costly immune responses. Acute phase responses (APRs) are a particularly costly form of immune defence, and, hence, seasonal modulations in APRs are expected. Yet, hypotheses about APR modulation remain untested in free-living organisms throughout a complete annual cycle. We studied seasonal modulations in the APRs and in the energy budgets of skylarks Alauda arvensis, a partial migrant bird from temperate zones that experiences substantial ecological changes during its annual cycle. We characterized throughout the annual cycle changes in their energy budgets by measuring basal metabolic rate (BMR) and body mass. We quantified APRs by measuring the effects of a lipopolysaccharide injection on metabolic rate, body mass, body temperature, and concentrations of glucose and ketone. Body mass and BMR were lowest during breeding, highest during winter and intermediate during spring migration, moult and autumn migration. Despite this variation in energy budgets, the magnitude of the APR, as measured by all variables, was similar in all annual cycle stages. Thus, while we find evidence that some annual cycle stages are relatively more energetically constrained, we find no support for the hypothesis that during these annual cycle stages birds compromise an immune defence that is itself energetically costly. We suggest that the ability to mount an APR may be so essential to survival in every annual cycle stage that skylarks do not trade off this costly form of defence with other annual cycle demands