Biology subjects

Schmitt, V.

Publications and source records attributed to Schmitt, V..

3 recordsLinked to original sources

bioRxiv2026

Proteogenomics of Blumeria hordei supports RNA and protein coding innovative potential derived from transposable elements

Some filamentous plant-pathogenic fungi have comparably large genome sizes within the fungal kingdom due to the proliferation of transposable elements (TEs). Blumeria hordei (Bh), the causal agent of the powdery mildew disease on barley, is a filamentous obligate biotrophic fungus. Compared to other ascomycetes, it contains a low number of genes but a high genomic TE content of approximately 75%. Yet, a comprehensive understanding of the contribution of TEs to the RNA and protein landscape of Bh is lacking. Here, we use Bh as a model to study transcripts and proteins derived from genes and individual TEs. Therefore, we created two high-quality genome assemblies of the German Bh isolate TUM1 and the Australian Bh isolate AUS1. We applied deep proteomics with mass spectrometry, long-read and short-read sequencing on both DNA and RNA. Based on these multi-omic resources, we completed nearly gapless genome assemblies, new gene and TE annotations, and effector predictions. Using long-read RNA sequencing, we detected extensive co-transcription of TEs and genes as TE-gene chimeric transcripts. We identified previously unpredicted splice variants or genes, partially supported by proteomics. The intergenic and TE genomic space of Bh TUM1 gives rise to thousands of transcripts and several novel TE-derived proteins that lack from previous TE protein predictions. Together, this supports an existing potential for expression of novel transcripts and proteins from highly abundant TEs in the Bh genome.

plant biology↗

bioRxiv2020

Bacterial protein domains with a novel Ig-like fold bind human CEACAM receptors

Streptococcus agalactiae, also known as group B Streptococcus (GBS), is the major cause of neonatal sepsis in humans. A critical step to infection is adhesion of bacteria at mucosal surfaces. Though several GBS adhesins have been identified, the host receptor targets of these adhesins remain unknown. We report here that surface-expressed {beta} protein from GBS binds to human CEACAM1 and CEACAM5 receptors. A crystal structure of the complex showed that the IgSF domain in {beta} represents a novel Ig-fold subtype called IgI3, in which unique features allow binding to CEACAM1. Bioinformatic assessments revealed that this newly identified IgI3 fold is not exclusively present in GBS. Instead, the IgI3 fold is predicted to be present in adhesins from other clinically important human pathogens. We confirmed the interaction between CEACAM1 and the predicted IgI3-containing adhesin in two different streptococcal pathogens. Overall, our results indicate that the IgI3 fold could provide a broadly applied mechanism for bacteria to target CEACAMs.

microbiology↗

bioRxiv2018

Implementing new portable touchscreen-setups to enhance cognitive research and enrich zoo-housed animals

AbstractsTo understand the evolutionary development of cognition, comparing the cognitive capacities of different animal species is essential. However, getting access to various species with sufficient sample sizes can be very challenging. Zoos, housing large ranges of animal taxa, would offer ideal research environments, but zoo-based studies on cognition are still rare. The use of touchscreen-computers to explore the cognitive abilities of nonhuman animals has shown to be highly applicable, and simultaneously offers new enrichment possibilities for captive animals. To facilitate zoo-based research, I here illustrate the assembly and usage of newly developed touchscreen-computer-systems (Zoo-based Animal-Computer-Interaction System, ZACI), which can be used in various zoo environments and, importantly, with different taxa (e.g. primates, birds). The developed setups are portable, can be attached to various mesh sizes, and do not need any external power supply while being used. To evaluate the usability of the ZACI, they have been tested with experimentally naive subjects of three great ape species (orang-utans, chimpanzees, gorillas) housed at Zoo Heidelberg, Germany, demonstrating to be easy to handle, animal-proof, and of great interest to the animals. Animals could be tested within their social group, as each subject had access to its own device during testing. To support the implementation of touchscreen-setups at other facilities, I also illustrate the training procedure and present first data on the apes performance in a simple object discrimination task. Portable touchscreen-setups offer the great possibility to enhance collaboration between zoos and researchers, allow a standardisation of methods, and improve data collection.

animal behavior and cognition↗