The use of stable isotope ratios in whitebait otolith carbonate to identify the source of prey for Western Australian penguins

A methodology has been developed and used to investigate a direct link between juvenile whitebait (Hyperlophus vittatus), the key prey species sampled from the stomachs of Little Penguins (Eudyptula minor), and the specific nursery area of that prey. A unique application of existing methodology initially involved the measurement of the stable isotopes of oxygen (δ¹⁸O:δ¹⁶O) and carbon (δ¹³C:δ¹²C) in sagittal otolith carbonate, using standard mass spectrometric techniques. The results indicated that the inshore distribution of juvenile (0+ year old) whitebait between Cockburn Sound and Koombana Bay, Western Australia consisted of a number of separate assemblages. Measured differences in stable oxygen isotope ratios were attributed to variations in freshwater input to the embayments that provided the whitebait habitats. In contrast, the measured stable carbon isotope ratios probably resulted from the different isotopic compositions of the food webs in the various habitats. Secondly, a comparison of the average value of carbon and oxygen isotope signatures of pooled otoliths from samples of whitebait from a number of different nearshore coastal sites (assemblages), with that of whitebait obtained from the stomachs of penguins at their main breeding site (Penguin Island) indicated that the values from the penguins resemble most closely those of the average otolith values obtained from whitebait from only one site (Becher Point). Assuming that the whitebait sampled were representative of the whitebait in the nearshore habitats and the diets of the penguins, then these results imply that at the time of sampling the penguins were feeding on whitebait from only one site.     

Tropical pasture carbon cycling: relationships between C source/sink strength, above-ground biomass and grazing

We measured net ecosystem CO₂ exchange (NEE) in Panamá over C₄ pasture plots that varied in grazing intensity. After adjusting for variation in light, there were noticeable effects of grazing‐related variables on CO₂ exchange that were largely dependent on the developmental stage of the plant canopy. Above‐ground productivity was positively related to grazing intensity (r²=0.30). Two experimentally grazed fields had significantly lower standing crop biomass but no significant difference in CO₂ uptake (24.2 μmol/m²/s) compared with two ungrazed fields (20.3 μmol/m²/s). Grazed fields had significantly lower ecosystem respiration rates (10.3 μmol/m²/s) than did ungrazed fields (17.6 μmol/m²/s). These results suggest that, although these pastures were possible sources of CO₂ during the time intervals sampled, the size of the sources tended to be dampened by cattle grazing through reductions in ecosystem respiration. Thus, it appears that disturbance caused by cattle grazing will not always result in an increase in CO₂ release from tropical pastures to the atmosphere.     

Assessing conservation attitudes and behaviors of Congolese children neighboring the world's first bonobo (Pan paniscus) release site

Poaching and habitat destruction in the Congo Basin threaten African great apes including the bonobo (Pan paniscus), chimpanzees (Pan troglodytes), and gorillas (Gorilla spp.) with extinction. One way to combat extinction is to reintroduce rescued and rehabilitated apes and repopulate native habitats. Reintroduction programs are only successful if they are supported by local populations. Ekolo ya Bonobo, located in Equateur province of the Democratic Republic of Congo (DRC), is the world's only reintroduction site for rehabilitated bonobos. Here we assess whether children, of the Ilonga‐Pôo, living adjacent to Ekolo ya Bonobo demonstrate more pro‐ape conservation attitudes than children living in, Kinshasa, the capital city. We examined children's attitudes toward great apes because children are typically the focus of conservation education programs. We used the Great Ape Attitude Questionnaire to test the Contact Hypothesis, which posits that proximity to great ape habitat influences pro‐conservation attitudes toward great apes. Ilonga‐Pôo children who live in closer contact with wild bonobos felt greater responsibility to protect great apes compared to those in Kinshasa who live outside the natural habitat of great apes. These results suggest that among participants in the DRC, spatial proximity to a species fosters a greater sense of responsibility to protect and conserve. These results have implications for the successful implementation of great ape reintroduction programs in the Congo Basin. The data analyzed in this study were collected in 2010 and therefore provide a baseline for longitudinal study of this reintroduction site.     

Early Life Stress Interacts with the Diet Deficiency of Omega-3 Fatty Acids during the Life Course Increasing the Metabolic Vulnerability in Adult Rats

Early stress can cause metabolic disorders in adulthood. Omega-3 polyunsaturated fatty acids (n-3 PUFAs) deficiency has also been linked to the development of metabolic disorders. The aim of this study was to assess whether an early stressful event such as maternal separation interacts with the nutritional availability of n-3 PUFAs during the life course on metabolic aspects. Litters were randomized into: maternal separated (MS) and non-handled (NH). The MS group was removed from their dam for 3 hours per day and put in an incubator at 32°C on days 1° to 10° postnatal (PND). On PND 35, males were subdivided into diets that were adequate or deficient in n-3 PUFAs, and this intervention was applied during the subsequent 15 weeks. Animal''s body weight and food consumption were measured weekly, and at the end of the treatment tissues were collected. MS was associated with increased food intake (p = 0.047) and weight gain (p = 0.012), but no differences were found in the NPY hypothalamic content between the groups. MS rats had also increased deposition of abdominal fat (p<0.001) and plasma triglycerides (p = 0.018) when compared to the NH group. Interactions between early life stress and n-3 PUFAs deficiency were found in plasma insulin (p = 0.033), HOMA index (p = 0.049), leptin (p = 0.010) and liver PEPCK expression (p = 0.050), in which the metabolic vulnerability in the MS group was aggravated by the n-3 PUFAs deficient diet exposure. This was associated with specific alterations in the peripheral fatty acid profile. Variations in the neonatal environment interact with nutritional aspects during the life course, such as n-3 PUFAs diet content, and persistently alter the metabolic vulnerability in adulthood.     

In Vivo Neutralization of α-Cobratoxin with High-Affinity Llama Single-Domain Antibodies (VHHs) and a VHH-Fc Antibody

Small recombinant antibody fragments (e.g. scFvs and V_HHs), which are highly tissue permeable, are being investigated for antivenom production as conventional antivenoms consisting of IgG or F(ab’)₂ antibody fragments do not effectively neutralize venom toxins located in deep tissues. However, antivenoms composed entirely of small antibody fragments may have poor therapeutic efficacy due to their short serum half-lives. To increase serum persistence and maintain tissue penetration, we prepared low and high molecular mass antivenom antibodies. Four llama V_HHs were isolated from an immune V_HH-displayed phage library and were shown to have high affinity, in the low nM range, for α-cobratoxin (α–Cbtx), the most lethal component of Naja kaouthia venom. Subsequently, our highest affinity V_HH (C2) was fused to a human Fc fragment to create a V_HH2-Fc antibody that would offer prolonged serum persistence. After in planta (Nicotiana benthamiana) expression and purification, we show that our V_HH2-Fc antibody retained high affinity binding to α–Cbtx. Mouse α–Cbtx challenge studies showed that our highest affinity V_HHs (C2 and C20) and the V_HH2-Fc antibody effectively neutralized lethality induced by α–Cbtx at an antibody:toxin molar ratio as low as ca. 0.75×:1. Further research towards the development of an antivenom therapeutic involving these anti-α-Cbtx V_HHs and V_HH2-Fc antibody molecules should involve testing them as a combination, to determine whether they maintain tissue penetration capability and low immunogenicity, and whether they exhibit improved serum persistence and therapeutic efficacy.     

Optimization of Whole-Body Zebrafish Sectioning Methods for Mass Spectrometry Imaging

Mass spectrometry imaging (MSI) methods and protocols have become widely adapted to a variety of tissues and species. However, the MSI literature contains minimal information on whole-body cryosection preparation for the zebrafish (ZF; Danio rerio), a model organism routinely used in developmental, toxicity, and carcinogenicity studies. The optimal medium for embedding and cryosectioning a whole organism or soft-tissue specimen for histological examination is a synthetic polymer mixture that is incompatible with MSI as a result of ion suppression. We describe the optimal methods and results for embedding and cryosectioning whole-body ZF for MALDI-MSI. We evaluated 13 distinct embedding media formulations and found a supportive hydrogel with the consistency of cartilage to be the optimal embedding medium. The hydrogel medium does not interfere with MSI data collection, aids in tissue stability, is readily available for purchase, and is easy to prepare and handle during cryosectioning. Additionally, we decreased the matrix cluster interference commonly caused by α-cyano-4-hydroxycinnamic acid by adding ammonium phosphate to the solvent spray solution. The optimized methods developed in our laboratory produced high-quality cryosections, as well as high-quality mass spectral images of sectioned ZF.     

The intD mobile genetic element from Dichelobacter nodosus, the causative agent of ovine footrot, is associated with the benign phenotype

The Gram-negative anaerobic pathogen Dichelobacter nodosus is the principal causative agent of footrot in sheep. The intA, intB and intC elements are mobile genetic elements which integrate into two tRNA genes downstream from csrA (formerly glpA) and pnpA in the D. nodosus chromosome. CsrA homologues act as global repressors of virulence in several bacterial pathogens, as does polynucleotide phosphorylase, the product of pnpA. We have proposed a model in which virulence in D. nodosus is controlled in part by the integration of genetic elements downstream from csrA and pnpA, altering the expression of these putative global regulators of virulence. We describe here a novel integrated genetic element, the intD element, which is 32 kb in size and contains an integrase gene, intD, several genes related to genes on other integrated elements of D. nodosus, a type IV secretion system and a putative mobilisation region, suggesting that the intD element has a role in the transfer of other genetic elements. Most of the D. nodosus strains examined which contained the intD gene were benign, with intD integrated next to pnpA, supporting our previous observation that virulent strains of D. nodosus have the intA element next to pnpA.     

Resolution effects in reconstructing ancestral genomes

Background

The reconstruction of ancestral genomes must deal with the problem of resolution, necessarily involving a trade-off between trying to identify genomic details and being overwhelmed by noise at higher resolutions.

Results

We use the median reconstruction at the synteny block level, of the ancestral genome of the order Gentianales, based on coffee, Rhazya stricta and grape, to exemplify the effects of resolution (granularity) on comparative genomic analyses.

Conclusions

We show how decreased resolution blurs the differences between evolving genomes, with respect to rate, mutational process and other characteristics.