Biology subjects

Brandt, J.

Publications and source records attributed to Brandt, J..

9 recordsLinked to original sources

bioRxiv2026

MillionTrees: A global benchmark for tree detection across geography, sensor, and annotation geometry

Airborne tree monitoring using remotely sensed data, combined with the growth of computer vision models for object detection and segmentation, can facilitate broad scale assessment of tree health, ecology and ecosystem function. However, datasets for airborne tree detection have been largely limited to a single geography, resolution, or annotation approach, making it difficult to develop general models and benchmark their utility for broad applications. We compile existing and newly published annotation datasets to create a comprehensive dataset for training and evaluating airborne tree detection in RGB imagery. The MillionTrees dataset has over a million individual trees from a broad range of forest types, tree species, and geographic locations. In addition, it has six million weakly supervised annotations from a range of sources including airborne LiDAR and photogrammetry, arborist surveys, and simulated landscapes. An evaluation standard is provided to facilitate rapid model development. We benchmark several existing tree detection algorithms and demonstrate that while current open-source models do not generalize across the diverse datasets in the benchmark, training on MillionTrees improves both within-domain and out-of-domain performance. Held-out validation datasets using ground truth derived from terrestrial LiDAR paired with overhead RGB show that overfitting to test data is common and hyperparameter tuning is an underappreciated challenge towards a global zero shot tree detection method. We discuss the limitations of the currently available data for airborne RGB tree detection, how to create more robust evaluation data and the need for better understanding of the uncertainty and utility of tree detection from airborne remote sensing.

ecology↗

bioRxiv2026

Benchmarking Molecular Methods of Protein Engineering and Surveying Protein Search Space to Bolster Artificial Intelligence-Based Designs

Proteins are complex macromolecules that drive functionality in cells across all life on Earth. Protein engineering and AI-based designs facilitate exploration of the vast search space. Herein, we explore and compare mutagenic methodologies in combination with fast and efficient phenotypic evaluation of a pink fluorophore (Magenta) to map protein search space and inform AI-based designer algorithms. We binned mutated variants as neutral, deleterious, or catastrophic based on the observed phenotype and fitness measurement (relative fluorescent units, RFUs). Importantly, we found that for a given fluorophore, about 80% of random mutations were deleterious for the artificially selected phenotype resulting in decreased fitness, 20% were neutral mutations, and 0.8% enhanced the artificially selected phenotype. Using error prone PCR (epPCR), we were able to identify four candidates in the first round and one candidate in the second round of epPCR for enhanced fluorescence and in toto enhanced RFUs by 35% after two rounds of epPCR. We compared these rates of true positive enhanced RFU generated sequences against a state of the art evolutionary algorithm approach and found that biological computation beats it in its current state. We conclude with suggestions for key improvements to enhance algorithm performance in the future. Taken together, we demonstrated that iterative rounds of variant prediction improved our algorithm, and our study can serve as a reference point for future AI driven modeling studies in red fluorescent protein engineering.

bioinformatics↗

bioRxiv2025

Cultivar- and field site-specific protein and metabolite patterns of faba bean (Vicia faba L.) seeds

Sustainable agriculture is an important component of current and future food production, particularly in the face of the rising human world population. In this context, faba bean (Vicia faba L.) is highly valuable due to its capability to enrich soils with nitrogen and because its seeds have a high nutritional value. In this study, we compared the seed chemistry of 11 faba bean cultivars grown at 13 field sites in Germany. Nitrogen and sulfur contents were determined with the Dumas method and protein contents were calculated based on the obtained nitrogen data. SDS-PAGE was used to analyze proteins, while metabolic fingerprinting was applied to screen (semi-)polar metabolites, mainly comprising specialized metabolites. The protein content differed predominantly between cultivars, but also between field sites. The sulfur content strongly depended on the field site. The patterns of proteins and metabolites were largely cultivar-specific. Additionally, the number of metabolic features varied somewhat between field sites. Our study suggests that breeding led to comprehensive changes in the seed chemistry of V. faba bean, going far beyond protein content and certain metabolites targeted in breeding. The rather high consistency when comparing field sites indicates that breeding has led to more or less stable cultivars. Future studies should place more emphasis on far-reaching effects of breeding on the seed proteome and metabolome of faba bean, as various proteins and metabolites in concert determine the nutritional quality of seeds of this important crop species.

plant biology↗

bioRxiv2024

A Metagenomic Analysis of the Fecal Microbiota of the Critically Endangered Eastern Bongo

The Eastern Bongo (Tragelaphus eurycerus isaaci) is a critically endangered mammal. In zoos, this animal has been known to have a sensitive gastrointestinal tract. Using a metagenomic approach the purpose of this study was to determine the microbiota of two adult (n=2) Eastern Bongos living in a zoo in South Dakota, as well as a juvenile (n=6) over a six-week period to see the microbial succession, and to learn if there were pathogenic microorganisms present which are capable of causing gastrointestinal disease. The dominant phylum in seven samples was Bacillota with Pseudomonadota dominant in only one of the juvenile samples. Functional classifications showed Protein Synthesis was the most predominant (11.36-35.71%). Almost equally predominant were Energy and Precursor Metabolites Generation (7.00-13.27%) and Stress Response, Defense and Virulence (8.44-12.90%). Finally, we also determined the resistomes which will contribute to the One Health approach.

microbiology↗

bioRxiv2022

In flagranti - Functional morphology of copulatory organs of odontopygid millipedes (Diplopoda: Juliformia: Spirostreptida)

The copulatory organs of many animal groups exhibit a high degree of morphological complexity and diversity that is thought to have evolved on the basis of different selective mechanisms including lock- and-key mechanism, pleiotropy, sperm competition, internal courtship and female choice. Identifying the effects of these different selective mechanisms on copulatory organs one of the central topics of the study of sexual selection. To tackle this challenge, knowledge of the functions of all parts of the copulatory organs is indispensable. Here we study the functional morphology of the gonopods (male copulatory organs) and vulvae (female copulatory organs) in the odontopygid millipede Spinotarsus (Diplopoda, Spirostreptida, Odontopygidae). While the vulvae of female odontopygids are rather simple, male gonopods are complex, walking leg-derived copulatory organs that exhibit many movable sub-parts. Using CT-based 3D reconstruction, confocal laser scanning microscopy and mating observations we revise the functional morphology of odontopygid gonopods, propose biological roles and evaluate the possible involvement of different selective mechanisms underlying their evolution.

zoology↗

bioRxiv2022

A distinct subset of oligodendrocyte lineage cells interact with the developing dorsal root entry during its genesis

Oligodendrocytes are the myelinating cell of the CNS and are critical for the functionality of the nervous system. In the packed CNS, we know distinct profiles of oligodendrocytes are present. Here, we used intravital imaging in zebrafish to identify a distinct oligodendrocyte lineage cell (OLC) that resides on the dorsal root ganglia sensory neurons in the spinal cord. Our profiling of OLC cellular dynamics revealed a distinct cell cluster that interacts with peripheral sensory neurons at the dorsal root entry zone (DREZ). With pharmacological, physical and genetic manipulations, we show that the entry of dorsal root ganglia pioneer axons across the DREZ is important to produce sensory located oligodendrocyte lineage cells. These oligodendrocyte lineage cells on peripherally derived sensory neurons display distinct processes that are stable and do not express mbp. Upon their removal, sensory behavior related to the DRG neurons is abolished. Together, these data support the hypothesis that peripheral neurons at the DREZ can also impact oligodendrocyte development.

neuroscience↗

bioRxiv2021

Reassembling a cannon in the DNA defense arsenal: genetics of StySA, a BREX phage exclusion system in Salmonella lab strains

Understanding mechanisms that shape horizontal exchange in prokaryotes is a key problem in biology. A major limit on DNA entry is imposed by restriction-modification (RM) processes that depend on the pattern of DNA modification at host-specified sites. In classical RM, endonucleolytic DNA cleavage follows detection of unprotected sites on entering DNA. Recent investigation has uncovered BREX systems, RM-like activities that employ host protection by DNA modification but replication arrest without evident nuclease action on unmodified phage DNA. We show that the historical stySA RM locus of Salmonella enterica sv Typhimurium is a BREX homolog. The stySA29 allele of the hybrid strain LB5000 carries a mutated version of the ancestral LT2 BREX system. Surprisingly, both a restriction and a methylation defect are observed for this lineage despite lack of mutations in brxX, the modification gene homolog. Instead, flanking genes pglZ and brxC each carry multiple mutations () in C-terminal domains. To avoid plasmid artifacts and potential stoichiometric interference, we chose to investigate this system in situ, replacing the mutated pglZ and brxC genes with wild type (WT). PglZ-WT supports methylation in the presence of either BrxC or BrxC-WT but not in the presence of a deletion/insertion allele, {Delta}brxC::cat. Restriction of phage L requires both BrxC-WT and PglZ-WT, implicating the BrxC C-terminus specifically in restriction activity. Disruption of four other CDS with cat cassettes still permitted modification, suggesting that BrxC, PglZ and BrxX are principal components of the modification activity. BrxL is required for restriction only. A partial disruption of brxL disrupts transcription globally.

genetics↗

bioRxiv2021

Colorectal cancer progression is potently reduced by a glucose-free, high-protein diet: comparison to anti-EGFR therapy

Background & AimsTo enable rapid proliferation, colorectal tumor cells up-regulate epidermal growth factor receptor (EGFR) signaling and perform high level of aerobic glycolysis, resulting in substantial lactate release into the tumor microenvironment and impaired anti-tumor immune responses. We hypothesized that an optimized nutritional intervention designed to reduce aerobic glycolysis of tumor cells may boost EGFR-directed antibody (Ab)-based therapy of pre-existing colitis-driven colorectal carcinoma (CRC). MethodsCRC development was induced by azoxymethane (AOM) and dextran sodium sulfate (DSS) administration to C57BL/6 mice. AOM/DSS treated mice were fed a glucose-free, high-protein diet (GFHPD) or an isoenergetic control diet (CD) in the presence or absence of i.p. injection of PBS, an irrelevant control mIgG2a or an anti-EGFR mIgG2a. Ex vivo, health status, tumor load, metabolism, colonic epithelial cell differentiation and immune cell infiltration were studied. Functional validation was performed in murine and human CRC cell lines MC-38 or HT29-MTX. ResultsAOM/DSS treated mice on GFHPD displayed reduced systemic glycolysis, resulting in improved tumoral energy homeostasis and diminished tumor load. Comparable but not additive to an anti-EGFR-Ab therapy, GFHPD was accompanied by enhanced tumoral differentiation and decreased colonic PD-L1 and splenic PD-1 immune checkpoint expression, presumably promoting intestinal barrier function and improved anti-tumor immune responses. In vitro, glucose-free, high-amino acid culture conditions reduced proliferation but improved differentiation of CRC cells in combination with down-regulation of PD-L1 expression. ConclusionWe here found GFHPD to metabolically reprogram colorectal tumors towards balanced OXPHOS, thereby improving anti-tumor T-cell responses and reducing CRC progression with a similar efficacy as EGFR-directed antibody therapy. SynopsisConsumption of glucose-free, high protein diet (GFHPD), comparable to EGFR-directed antibody-based therapy, efficaciously dampens colorectal tumor burden but does not have additive effects in combination with anti-EGFR therapy. GFHPD boosts amino acid metabolism, resulting in improved tumor differentiation and anti-tumor immune responses. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/448354v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@e0c8fforg.highwire.dtl.DTLVardef@1abee36org.highwire.dtl.DTLVardef@a41e22org.highwire.dtl.DTLVardef@b678ab_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2019

The signal and the noise - characteristics of antisense RNA in complex microbial communities

High-throughput sequencing has allowed unprecedented insight into the composition and function of complex microbial communities. With the onset of metatranscriptomics, it is now possible to interrogate the transcriptome of multiple organisms simultaneously to get an overview of the gene expression of the entire community. Studies have successfully used metatranscriptomics to identify and describe relationships between gene expression levels and community characteristics. However, metatranscriptomic datasets contain a rich suite of additional information which is just beginning to be explored. In this minireview we discuss the different computational strategies for handling antisense expression in metatranscriptomic samples and highlight their potentially detrimental effects on downstream analysis and interpretation. We also surveyed the antisense transcriptome of multiple genomes and metagenome-assembled genomes (MAGs) from five different datasets and found high variability in the level of antisense transcription for individual species which were consistent across samples. Importantly, we tested the hypothesis that antisense transcription is primarily the product of transcriptional noise and found mixed support, suggesting that the total observed antisense RNA in complex communities arises from a compounded effect of both random, biological and technical factors. Antisense transcription can provide a rich set of information, from technical details about data quality to novel insight into the biology of complex microbial communities.\n\nKey pointsO_LISeveral fundamentally different approaches are used to handle antisense RNA\nC_LIO_LIPrevalence of antisense RNA is highly variable between communities, genomes, and genes.\nC_LIO_LIAntisense RNA is likely an opaque mixture of technical, biological and random effects\nC_LI

microbiology↗