Vertebrate osmoregulation: a student laboratory exercise using teleost fish

Here, we describe a laboratory experiment as part of an upper-level vertebrate physiology course for biology majors to investigate the physiological response of vertebrates to osmoregulatory challenges. The experiment involves measuring plasma osmolality and Na+-K+-ATPase activity in gill tissue of teleost fish acclimated to water of differing salinity. We describe results obtained using the widely available goldfish (Carassius auratus) and a common baitfish, the Gulf killifish (Fundulus grandis). The procedures described are generally applicable to other fish species, and they provide an alternative to the experimental use of humans or other mammalian species to investigate osmoregulation mechanisms. In addition to reenforcing the conceptual material covered in lecture, this laboratory exercise trains students in a wide range of laboratory and analytical skills, such as calculating and performing dilutions, pipetting, tissue sampling and homogenizing, preparing standard curves, conducting enzymatic assays, and analyzing and interpreting results. Typical student results are presented and discussed, as are common experimental and conceptual mistakes made by students.     

Epitope-focused immunogen design based on the ebolavirus glycoprotein HR2-MPER region

The three human pathogenic ebolaviruses: Zaire (EBOV), Bundibugyo (BDBV), and Sudan (SUDV) virus, cause severe disease with high fatality rates. Epitopes of ebolavirus glycoprotein (GP) recognized by antibodies with binding breadth for all three ebolaviruses are of major interest for rational vaccine design. In particular, the heptad repeat 2 –membrane-proximal external region (HR2-MPER) epitope is relatively conserved between EBOV, BDBV, and SUDV GP and targeted by human broadly-neutralizing antibodies. To study whether this epitope can serve as an immunogen for the elicitation of broadly-reactive antibody responses, protein design in Rosetta was employed to transplant the HR2-MPER epitope identified from a co-crystal structure with the known broadly-reactive monoclonal antibody (mAb) BDBV223 onto smaller scaffold proteins. From computational analysis, selected immunogen designs were produced as recombinant proteins and functionally validated, leading to the identification of a sterile alpha motif (SAM) domain displaying the BDBV-HR2-MPER epitope near its C terminus as a promising candidate. The immunogen was fused to one component of a self-assembling, two-component nanoparticle and tested for immunogenicity in rabbits. Robust titers of cross-reactive serum antibodies to BDBV and EBOV GPs and moderate titers to SUDV GP were induced following immunization. To confirm the structural composition of the immunogens, solution NMR studies were conducted and revealed structural flexibility in the C-terminal residues of the epitope. Overall, our study represents the first report on an epitope-focused immunogen design based on the structurally challenging BDBV-HR2-MPER epitope.     

Separation of Single-stranded DNA,Double-stranded DNA and RNA from an Environmental Viral Community Using Hydroxyapatite Chromatography

Viruses, particularly bacteriophages (phages), are the most numerous biological entities on Earth^1,2. Viruses modulate host cell abundance and diversity, contribute to the cycling of nutrients, alter host cell phenotype, and influence the evolution of both host cell and viral communities through the lateral transfer of genes ³. Numerous studies have highlighted the staggering genetic diversity of viruses and their functional potential in a variety of natural environments. Metagenomic techniques have been used to study the taxonomic diversity and functional potential of complex viral assemblages whose members contain single-stranded DNA (ssDNA), double-stranded DNA (dsDNA) and RNA genotypes ^4-9. Current library construction protocols used to study environmental DNA-containing or RNA-containing viruses require an initial nuclease treatment in order to remove nontargeted templates ¹⁰. However, a comprehensive understanding of the collective gene complement of the virus community and virus diversity requires knowledge of all members regardless of genome composition. Fractionation of purified nucleic acid subtypes provides an effective mechanism by which to study viral assemblages without sacrificing a subset of the community’s genetic signature. Hydroxyapatite, a crystalline form of calcium phosphate, has been employed in the separation of nucleic acids, as well as proteins and microbes, since the 1960s¹¹. By exploiting the charge interaction between the positively-charged Ca²⁺ ions of the hydroxyapatite and the negatively charged phosphate backbone of the nucleic acid subtypes, it is possible to preferentially elute each nucleic acid subtype independent of the others. We recently employed this strategy to independently fractionate the genomes of ssDNA, dsDNA and RNA-containing viruses in preparation of DNA sequencing ¹². Here, we present a method for the fractionation and recovery of ssDNA, dsDNA and RNA viral nucleic acids from mixed viral assemblages using hydroxyapatite chromotography.Download video file.^{(86M, mov)}     

The interaction of amyloid Aβ(1-40) with lipid bilayers and ganglioside as studied by P solid-state NMR

Amyloid β-peptide (Aβ) is a major component of plaques in Alzheimer's disease, and formation of senile plaques has been suggested to originate from regions of neuronal membrane rich in gangliosides. We analyzed the mode of interaction of Aβ with lipid bilayers by multinuclear NMR using ³¹P nuclei. We found that Aβ (1-40) strongly perturbed the bilayer structure of dimyristoylphosphatidylcholine (DMPC), to form a non-lamellar phase (most likely micellar). The ganglioside GM1 potentiated the effect of Aβ (1-40), as viewed from ³¹P NMR. The difference of the isotropic peak intensity between DMPC/Aβ and DMPC/GM1/Aβ suggests a specific interaction between Aβ and GM1. We show that in the DMPC/GM1/Aβ system there are three lipid phases, namely a lamellar phase, a hexagonal phase and non-oriented lipids. The latter two phases are induced by the presence of the Aβ peptide, and facilitated by GM1.     

Syntheses of daidzein-7-yl β- -glucopyranosiduronic acid and daidzein-4′,7-yl di-β- -glucopyranosiduronic acid

Syntheses of the title compounds — commonly known as ‘daidzein 7-glucuronide’ and ‘daidzein 4′,7-diglucuronide’ — are described. Selective 7-deacetylation of 4′,7-di-O-acetyldaidzein is employed.     

The Macroecology of Airborne Pollen in Australian and New Zealand Urban Areas

The composition and relative abundance of airborne pollen in urban areas of Australia and New Zealand are strongly influenced by geographical location, climate and land use. There is mounting evidence that the diversity and quality of airborne pollen is substantially modified by climate change and land-use yet there are insufficient data to project the future nature of these changes. Our study highlights the need for long-term aerobiological monitoring in Australian and New Zealand urban areas in a systematic, standardised, and sustained way, and provides a framework for targeting the most clinically significant taxa in terms of abundance, allergenic effects and public health burden.     

Humid tropical rain forest has expanded into eucalypt forest and savanna over the last 50 years

Tropical rain forest expansion and savanna woody vegetation thickening appear to be a global trend, but there remains uncertainty about whether there is a common set of global drivers. Using geographic information techniques, we analyzed aerial photography of five areas in the humid tropics of northeastern Queensland, Australia, taken in the 1950s and 2008, to determine if changes in rain forest extent match those reported for the Australian monsoon tropics using similar techniques. Mapping of the 1950s aerial photography showed that of the combined study area (64,430 ha), 63% was classified as eucalypt forests/woodland and 37% as rain forest. Our mapping revealed that although most boundaries remained stable, there was a net increase of 732 ha of the original rain forest area over the study period, and negligible conversion of rain forest to eucalypt forest/woodland. Statistical modeling, controlling for spatial autocorrelation, indicated distance from preexisting rain forest as the strongest determinant of rain forest expansion. Margin extension had a mean rate across the five sites of 0.6 m per decade. Expansion was greater in tall open forest types but also occurred in shorter, more flammable woodland vegetation types. No correlations were detected with other local variables (aspect, elevation, geology, topography, drainage). Using a geographically weighted mean rate of rain forest margin extension across the whole region, we predict that over 25% of tall open forest (a forest type of high conservation significance) would still remain after 2000 years of rain forest expansion. This slow replacement is due to the convoluted nature of the rain forest boundary and the irregular shape of the tall open forest patches. Our analyses point to the increased concentration of atmospheric CO(2) as the most likely global driver of indiscriminate rain forest expansion occurring in northeastern Australia, by increasing tree growth and thereby overriding the effects of fire disturbance.     

Effect of an environmental school-based obesity prevention program on changes in body fat and body weight: a randomized trial

This study tested the efficacy of two school-based programs for prevention of body weight/fat gain in comparison to a control group, in all participants and in overweight children. The Louisiana (LA) Health study utilized a longitudinal, cluster randomized three-arm controlled design, with 28 months of follow-up. Children (N = 2,060; mean age = 10.5 years, SD = 1.2) from rural communities in grades 4-6 participated in the study. Seventeen school clusters (mean = 123 children/cluster) were randomly assigned to one of three prevention arms: (i) primary prevention (PP), an environmental modification (EM) program, (ii) primary + secondary prevention (PP+SP), the environmental program with an added classroom and internet education component, or (iii) control (C). Primary outcomes were changes in percent body fat and BMI z scores. Secondary outcomes were changes in behaviors related to energy balance. Comparisons of PP, PP+SP, and C on changes in body fat and BMI z scores found no differences. PP and PP+SP study arms were combined to create an EM arm. Relative to C, EM decreased body fat for boys (-1.7 ± 0.38% vs. -0.14 ± 0.69%) and attenuated fat gain for girls (2.9 ± 0.22% vs. 3.93 ± 0.37%), but standardized effect sizes were relatively small (<0.30). In conclusion, this school-based EM programs had modest beneficial effects on changes in percent body fat. Addition of a classroom/internet program to the environmental program did not enhance weight/fat gain prevention, but did impact physical activity and social support in overweight children.