Potential of Airborne LiDAR Derived Vegetation Structure for the Prediction of Animal Species Richness at Mount Kilimanjaro

The monitoring of species and functional diversity is of increasing relevance for the development of strategies for the conservation and management of biodiversity. Therefore, reliable estimates of the performance of monitoring techniques across taxa become important. Using a unique dataset, this study investigates the potential of airborne LiDAR-derived variables characterizing vegetation structure as predictors for animal species richness at the southern slopes of Mount Kilimanjaro. To disentangle the structural LiDAR information from co-factors related to elevational vegetation zones, LiDAR-based models were compared to the predictive power of elevation models. 17 taxa and 4 feeding guilds were modeled and the standardized study design allowed for a comparison across the assemblages. Results show that most taxa (14) and feeding guilds (3) can be predicted best by elevation with normalized RMSE values but only for three of those taxa and two of those feeding guilds the difference to other models is significant. Generally, modeling performances between different models vary only slightly for each assemblage. For the remaining, structural information at most showed little additional contribution to the performance. In summary, LiDAR observations can be used for animal species prediction. However, the effort and cost of aerial surveys are not always in proportion with the prediction quality, especially when the species distribution follows zonal patterns, and elevation information yields similar results

Displaying functional molecules on plant virus-based nanoparticles

Plant virus nanoparticles (VNPs) have many unique advantages, including their ability to self-assemble with precise symmetry and polyvalency, their monodispersity and stability under a range of conditions, their inherent safety (biocompatibility and non-infectivity in mammals), and the rapid, simple and scalable production that can be achieved by molecular farming in plants. The structures of many plant viruses have been solved at atomic or near-atomic resolution and the genome sequences are well characterized, so plant VNPs can easily be modified to introduce new functions. However, selection for smaller genomes often causes the loss of transgenes during infection. This can be addressed by using the ribosomal skip (overcoat) strategy or chemical conjugation, although this reduces the density of peptides on the particle surface. This thesis describes new plant virus display systems for applications such as bone tissue engineering, bioimaging and plant biomass degradation. The first chapter describes Potato virus X (PVX) engineered to present mineralization-inducing peptides (MIPs) equivalent to non-collagenous proteins of the extracellular matrix. The mineralization of recombinant PVX particles was achieved using saturated hydroxyapatite solution and simulated body fluid, which closely mimic the mineral phase of human bone. These studies lay the foundations for the further exploitation of biomimetic VNPs in bone regeneration. The second chapter describes iLOV-displaying PVX and Tobacco mosaic virus (TMV) nanoparticles for bioimaging, which currently requires overcoating or chemical conjugation. Surprisingly, PVX particles with direct iLOV-coat protein (CP) fusions were infectious but this was not the case for TMV. The PVX particles may be useful for molecular imaging under low oxygen conditions, such as tumor metastasis, or for the analysis of particle behavior in hydrogels when combined with MIPs. A new strategy for protein display on TMV is also described, using a ribosomal skip sequence. Although not directly comparable, an eight-fold increase in the abundance of the displayed iLOV target protein was achieved compared to a malaria epitope fusion proteins created by using a read-through motif (Turpen et al., 1995), which may be advantageous in particular for vaccine production. The third chapter explores PVX and TMV as biocatalysts, using the protein-based attachment of endoglucanases as a case study. SpyTag/SpyCatcher technology allowed the rapid formation of a stable isopeptide bond between the enzyme and scaffold. The catalytic efficiency of flexible recombinant PVX particles was higher than that of rigid TMV particles, indicating that the morphology of the template influences catalytic activity. The results presented in this thesis provide new insights into PVX and TMV display systems and will be beneficial for many application areas by overcoming the limitations of genetic fusions, such as size constraints and the need for post-translational modifications

Raw abundances of epigaeic arthropods on Mount Kilimanjaro

There are several data sets originating from the same pitfall trap samples. The other data set I just submitted contains mean abundances per plot. This data set now contains raw data at trap level (several traps per plot). I am planning to upload more data sets on specific taxa (spiders, springtails, beetles), and my colleagues should upload some more data sets on snails, millipedes and more springtails containing (but not limited to) specimen caught in the same pitfall trap samples. Abstract We sampled arthropod assemblages in disturbed and undisturbed vegetation types along an elevational gradient of 860–4550 m asl on the southern slopes of Mt. Kilimanjaro, Tanzania. On each site, ten pitfall traps were evenly spaced along two 50 m transects, with a distance of 10 m between individual traps and 20 m between transects. Pitfall traps were filled with 100–200 ml of a mixture of ethylene glycol and water (1:1 vol/vol) with a drop of liquid soap to break surface tension. Traps were exposed for 7 days each during two to five sampling events in both the dry and wet seasons between May 2011 and October 2012. As the number of individuals collected in ten traps was very high, we had to confine the sorting and subsequent analysis to sub-sets of at least three traps per sampling site and sampling event. Unfortunately, we had to find out later that the ethylen glycol procured locally was actually a mixture of ethylen glycol and 2-ethoxyethanol, which is a strong oxidizing chemical. Therefore, any sequencing of specimen caught in pitfall traps was impossible

Mean abundances of epigeic arthropods on Mount Kilimanjaro

On each site, ten pitfall traps were evenly spaced along two 50 m transects, with a distance of 10 m between individual traps and 20 m between transects. Pitfall traps were filled with 100–200 ml of a mixture of ethylene glycol and water (1:1 vol/vol) with a drop of liquid soap to break surface tension. Traps were exposed for 7 days each during two to five sampling events in both the dry and wet seasons between May 2011 and October 2012. As the number of individuals collected in ten traps was very high, we had to confine the sorting and subsequent analysis to sub-sets of at least three traps per sampling site and sampling event. The number of sampling events and considered samples is given in Table S2 (Röder et al. 2017). To address imbalances in the data set, we first calculated the mean abundances per trap per sampling event for each sampling site. We then calculated mean abundance per sampling site from the mean abundances per sampling event such that the number of replicates for statistical testing summed up to a total of N = 59 sampling sites. Unfortunately, we had to find out later that the ethylen glycol procured locally was actually a mixture of ethylen glycol and 2-ethoxyethanol, which is a strong oxidizing chemical. Therefore, any sequencing of specimen caught in pitfall traps was impossible

Adoption of the 2A Ribosomal Skip Principle to Tobacco Mosaic Virus for Peptide Display

Plant viruses are suitable as building blocks for nanomaterials and nanoparticles because they are easy to modify and can be expressed and purified using plants or heterologous expression systems. Plant virus nanoparticles have been utilized for epitope presentation in vaccines, for drug delivery, as nanospheres and nanowires, and for biomedical imaging applications. Fluorescent protein fusions have been instrumental for the tagging of plant virus particles. The monomeric non-oxygen-dependent fluorescent protein iLOV can be used as an alternative to green fluorescent protein. In this study, the iLOV sequence was genetically fused either directly or via a glycine-serine linker to the C-terminus of the Tobacco mosaic virus (TMV) coat protein (CP) and also carried an N-terminal Foot-and-mouth disease virus (FMDV) 2A sequence. Nicotiana benthamiana plants were inoculated with recombinant viral vectors and a systemic infection was achieved. The presence of iLOV fusion proteins and hybrid particles was confirmed by western blot analysis and transmission electron microscopy. Our data suggest that TMV-based vectors are suitable for the production of proteins at least as large as iLOV when combined with the FMDV 2A sequence. This approach allowed the simultaneous production of foreign proteins fused to the CP as well as free CP subunits

Small, Smaller, Nano: New Applications for Potato Virus X in Nanotechnology

Nanotechnology is an expanding interdisciplinary field concerning the development and application of nanostructured materials derived from inorganic compounds or organic polymers and peptides. Among these latter materials, proteinaceous plant virus nanoparticles have emerged as a key platform for the introduction of tailored functionalities by genetic engineering and conjugation chemistry. Tobacco mosaic virus and Cowpea mosaic virus have already been developed for bioimaging, vaccination and electronics applications, but the flexible and filamentous Potato virus X (PVX) has received comparatively little attention. The filamentous structure of PVX particles allows them to carry large payloads, which are advantageous for applications such as biomedical imaging in which multi-functional scaffolds with a high aspect ratio are required. In this context, PVX achieves superior tumor homing and retention properties compared to spherical nanoparticles. Because PVX is a protein-based nanoparticle, its unique functional properties are combined with enhanced biocompatibility, making it much more suitable for biomedical applications than synthetic nanomaterials. Moreover, PVX nanoparticles have very low toxicity in vivo, and superior pharmacokinetic profiles. This review focuses on the production of PVX nanoparticles engineered using chemical and/or biological techniques, and describes current and future opportunities and challenges for the application of PVX nanoparticles in medicine, diagnostics, materials science, and biocatalysis

Systemic Infection of Nicotiana benthamiana with Potato virus X Nanoparticles Presenting a Fluorescent iLOV Polypeptide Fused Directly to the Coat Protein

Plant virus-based nanoparticles can be produced in plants on a large scale and are easily modified to introduce new functions, making them suitable for applications such as vaccination and drug delivery, tissue engineering, and in vivo imaging. The latter is often achieved using green fluorescent protein and its derivatives, but the monovalent fluorescent protein iLOV is smaller and more robust. Here, we fused the iLOV polypeptide to the N-terminus of the Potato virus X (PVX) coat protein, directly or via the Foot-and-mouth disease virus 2A sequence, for expression in Nicotiana benthamiana. Direct fusion of the iLOV polypeptide did not prevent the assembly or systemic spread of the virus and we verified the presence of fusion proteins and iLOV hybrid virus particles in leaf extracts. Compared to wild-type PVX virions, the PVX particles displaying the iLOV peptide showed an atypical, intertwined morphology. Our results confirm that a direct fusion of the iLOV fluorescent protein to filamentous PVX nanoparticles offers a promising tool for imaging applications