Journey to the centre of the cell: Virtual reality immersion into scientific data

Visualization of scientific data is crucial not only for scientific discovery but also to communicate science and medicine to both experts and a general audience. Until recently, we have been limited to visualizing the three‐dimensional (3D) world of biology in 2 dimensions. Renderings of 3D cells are still traditionally displayed using two‐dimensional (2D) media, such as on a computer screen or paper. However, the advent of consumer grade virtual reality (VR) headsets such as Oculus Rift and HTC Vive means it is now possible to visualize and interact with scientific data in a 3D virtual world. In addition, new microscopic methods provide an unprecedented opportunity to obtain new 3D data sets. In this perspective article, we highlight how we have used cutting edge imaging techniques to build a 3D virtual model of a cell from serial block‐face scanning electron microscope (SBEM) imaging data. This model allows scientists, students and members of the public to explore and interact with a “real” cell. Early testing of this immersive environment indicates a significant improvement in students’ understanding of cellular processes and points to a new future of learning and public engagement. In addition, we speculate that VR can become a new tool for researchers studying cellular architecture and processes by populating VR models with molecular data.      

High abundance of non-mycorrhizal plant species in severely phosphorus-impoverished Brazilian <Emphasis Type="Italic">campos rupestres</Emphasis>

Background and aims

We sought to describe the species and functional composition of Brazilian campos rupestres plant communities on severely nutrient-impoverished white sands, to test hypotheses relating plant communities and physiological adaptations to infertile soils. Based on recently-published information on a south-western Australian dune chronosequence, we hypothesised that campos rupestres plant communities would similarly contain a relatively large proportion of non-mycorrhizal species, because of the phosphorus-(P) impoverished nature of the soils. We also sought to test the hypothesis that many of these non-mycorrhizal species have high leaf manganese (Mn) concentrations as a consequence of carboxylate exudation to mobilise soil P.

Methods

We conducted flora surveys and quantified mycorrhizal status and foliar Mn concentrations in field sites with strongly-weathered sandy soils. Rhizosphere carboxylates were collected from glasshouse-grown plants to assess a potential correlation of carboxylates and leaf Mn concentrations.

Results

Soils were depleted of all major plant nutrients. Non-mycorrhizal plants were abundant in most field sites (mean relative cover = 48%). Vellozia species were dominant aboveground; belowground, roots were colonised more by dark septate endophytic fungi than by mycorrhizal fungi. From the field sites, foliar Mn concentrations in non-mycorrhizal species increased with decreasing soil P concentrations, but only when soil Mn concentrations were above a minimum threshold (exchangeable [Mn] above detection limit). Across all species, however, there was no relationship of foliar Mn concentrations with soil P concentrations.

Conclusions

Our hypothesis that white-sand campos rupestres communities contain a relatively large proportion of non-mycorrhizal plants was supported. Comparison with similar ecosystems in south-western Australia suggests that plant communities on severely P-impoverished sandy soils, despite differing evolutionary histories and little overlap in plant families, follow convergent evolutionary paths towards increasing abundance of non-mycorrhizal species.

     

Expression of a polyphemusin variant in transgenic tobacco confers resistance against plant pathogenic bacteria,fungi and a virus

Antimicrobial cationic peptides provide a promising means of engineering plant resistance to a range of plant pathogens, including viruses. PV5 is a synthetic structural variant of polyphemusin, a cationic peptide derived from the horseshoe crab-Limulus polyphemus. PV5 has been shown to be benign toward eukaryotic membranes but with enhanced antimicrobial activity against animal pathogens. In this work, the cytotoxicity of PV5 toward tobacco protoplasts and leaf discs was assessed using TTC (2,3,5-triphenyltetrazolium chloride) and Evans blue colorimetric assays. PV5 showed no measurable cytotoxic effects even at levels as high as 60 μg. As a possible approach to enhancing plant resistance, a gene encoding PV5 was fused to the signal sequence encoding the C-terminus portion of the BiP protein from Pseudotsuga menziesii, under the control of 2 × 35S CaMV promoter. When introduced into Nicotiana tabacum var Xanthi gene integration and expression was confirmed by both Southern and northern analyses. When transgenic plants were subsequently challenged with bacterial and fungal phytopathogens enhanced resistance was observed. Moreover, transgenic plants also displayed antiviral properties against Tobacco Mosaic Virus making PV5 an excellent candidate for conferring unusually broad spectrum resistance to plants and the first anti-plant virus antimicrobial peptide.     

A Multiplex Label-Free Approach to Avian Influenza Surveillance and Serology

Influenza serology has traditionally relied on techniques such as hemagglutination inhibition, microneutralization, and ELISA. These assays are complex, challenging to implement in a format allowing detection of several types of antibody-analyte interactions at once (multiplex), and troublesome to implement in the field. As an alternative, we have developed a hemagglutinin microarray on the Arrayed Imaging Reflectometry (AIR) platform. AIR provides sensitive, rapid, and label-free multiplex detection of targets in complex analyte samples such as serum. In preliminary work, we demonstrated the application of this array to the testing of human samples from a vaccine trial. Here, we report the application of an expanded label-free hemagglutinin microarray to the analysis of avian serum samples. Samples from influenza virus challenge experiments in mallards yielded strong, selective detection of antibodies to the challenge antigen in most cases. Samples acquired in the field from mallards were also analyzed, and compared with viral hemagglutinin inhibition and microneutralization assays. We find that the AIR hemagglutinin microarray can provide a simple and robust alternative to standard methods, offering substantially greater information density from a simple workflow.     

Behavioral and electrophysiological analysis of general anesthesia in 3 background strains of Drosophila melanogaster

General anesthetics achieve behavioral unresponsiveness via a mechanism that is incompletely understood. The study of genetic model systems such as the fruit fly Drosophila melanogaster is crucial to advancing our understanding of how anesthetic drugs render animals unresponsive. Previous studies have shown that wild-type control strains differ significantly in their sensitivity to general anesthetics, which potentially introduces confounding factors for comparing genetic mutations placed on these wild-type backgrounds. Here, we examined a variety of behavioral and electrophysiological endpoints in Drosophila, in both adult and larval animals. We characterized these endpoints in 3 commonly used fly strains: wild-type Canton Special (CS), and 2 commonly used white-eyed strains, isoCJ1 and w¹¹¹⁸. We found that CS and isoCJ1 show remarkably similar sensitivity to isoflurane across a variety of behavioral and electrophysiological endpoints. In contrast, w¹¹¹⁸ is resistant to isoflurane compared to the other 2 strains at both the adult and larval stages. This resistance is however not reflected at the level of neurotransmitter release at the larval neuromuscular junction (NMJ). This suggests that the w¹¹¹⁸ strain harbors another mutation that produces isoflurane resistance, by acting on an arousal pathway that is most likely preserved between larval and adult brains. This mutation probably also affects sleep, as marked differences between isoCJ1 and w¹¹¹⁸ have also recently been found for behavioral responsiveness and sleep intensity measures.     

Effects of nutrients and warming on Planktothrix dynamics and diversity: a palaeolimnological view based on sedimentary DNA and RNA

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Pan‐African phylogeography of a model organism,the African clawed frog ‘Xenopus laevis’

The African clawed frog Xenopus laevis has a large native distribution over much of sub‐Saharan Africa and is a model organism for research, a proposed disease vector, and an invasive species. Despite its prominent role in research and abundance in nature, surprisingly little is known about the phylogeography and evolutionary history of this group. Here, we report an analysis of molecular variation of this clade based on 17 loci (one mitochondrial, 16 nuclear) in up to 159 individuals sampled throughout its native distribution. Phylogenetic relationships among mitochondrial DNA haplotypes were incongruent with those among alleles of the putatively female‐specific sex‐determining gene DM‐W, in contrast to the expectation of strict matrilineal inheritance of both loci. Population structure and evolutionarily diverged lineages were evidenced by analyses of molecular variation in these data. These results further contextualize the chronology, and evolutionary relationships within this group, support the recognition of X. laevis sensu stricto, X. petersii, X. victorianus and herein revalidated X. poweri as separate species. We also propose that portions of the currently recognized distributions of X. laevis (north of the Congo Basin) and X. petersii (south of the Congo Basin) be reassigned to X. poweri.     

Ontogenetic and spatial variability in trophic biomarkers of juvenile saffron cod (<Emphasis Type="Italic">Eleginus gracilis</Emphasis>) from the Beaufort,Chukchi and Bering Seas

Climate models indicate the Arctic will undergo dramatic environmental change with forecasted increases in temperature and river runoff. Saffron cod (Eleginus gracilis) is abundant in nearshore waters and appears in the diet of many Arctic sea birds and marine mammals; however, little is known about its early ecology and consequently how they might be affected by environmental changes. We aimed to characterize the mechanisms of spatial and ontogenetic variation in trophic biomarkers (lipid classes, fatty acids and bulk C and N stable isotopes) of saffron cod from the Western Arctic, Chukchi and Bering Seas. Size-standardized analyses showed a significant difference in lipid condition metrics and trophic biomarkers as a function of survey location. Both ontogeny and sampling location played an important role in determining lipid stores with elevated levels in both small offshore juveniles (<55 mm) and larger inshore juveniles (>75 mm). Higher lipid storage in Arctic juveniles was associated with elevated levels of diatom fatty acid markers, but not with nearshore carbon input. Increased lipids were found in age-1 juveniles from Prudhoe Bay in the Western Beaufort that were feeding at a lower trophic level than similarly sized age-0 juveniles from surface trawls in the Bering Sea. The use of otolith annuli revealed two discrete patterns of growth that help explain the trade-offs between energy storage and rapid growth that diverge between the Arctic and Bering Sea. Laboratory temperature-growth experiments confirmed that saffron cod have a eurythermal growth response and are able to store excess lipids at temperatures as high as 20 °C.     

Shifts in symbiotic associations in plants capable of forming multiple root symbioses across a long‐term soil chronosequence

Changes in soil nutrient availability during long‐term ecosystem development influence the relative abundances of plant species with different nutrient‐acquisition strategies. These changes in strategies are observed at the community level, but whether they also occur within individual species remains unknown. Plant species forming multiple root symbioses with arbuscular mycorrhizal (AM) fungi, ectomycorrhizal (ECM) fungi, and nitrogen‐(N) fixing microorganisms provide valuable model systems to examine edaphic controls on symbioses related to nutrient acquisition, while simultaneously controlling for plant host identity. We grew two co‐occurring species, Acacia rostellifera (N₂‐fixing and dual AM and ECM symbioses) and Melaleuca systena (AM and ECM dual symbioses), in three soils of contrasting ages (c. 0.1, 1, and 120 ka) collected along a long‐term dune chronosequence in southwestern Australia. The soils differ in the type and strength of nutrient limitation, with primary productivity being limited by N (0.1 ka), co‐limited by N and phosphorus (P) (1 ka), and by P (120 ka). We hypothesized that (i) within‐species root colonization shifts from AM to ECM with increasing soil age, and that (ii) nodulation declines with increasing soil age, reflecting the shift from N to P limitation along the chronosequence. In both species, we observed a shift from AM to ECM root colonization with increasing soil age. In addition, nodulation in A. rostellifera declined with increasing soil age, consistent with a shift from N to P limitation. Shifts from AM to ECM root colonization reflect strengthening P limitation and an increasing proportion of total soil P in organic forms in older soils. This might occur because ECM fungi can access organic P via extracellular phosphatases, while AM fungi do not use organic P. Our results show that plants can shift their resource allocation to different root symbionts depending on nutrient availability during ecosystem development.