Biology subjects

Kraft, J.

Publications and source records attributed to Kraft, J..

5 recordsLinked to original sources

bioRxiv2026

Sugar metabolism drives shoot branching by repressing BRC1 through miR319-targeted TCP4 in Rosa.

The coupling between sugar availability and shoot branching is well established, yet the underlying molecular mechanisms remain largely unknown. Here, using genome-wide profiling, we characterized the sugar signalling pathways by identifying 10 miRNAs repressed by glycolysis, the tricarboxylic acid (TCA) cycle, and/or the oxidative pentose phosphate pathway (OPPP) in rose buds. Focusing on RhmiR319, a miRNA repressed under active sugar metabolism, we demonstrate that disruption of both glycolysis/the TCA cycle and the OPPP induces the RhmiR319 accumulation, leading to the concomitant repression of its targets, RhTCP4a and RhTCP4b. We additionally reveal that the miR319/TCP4 module regulates shoot branching in Arabidopsis, as miR319 overexpression impairs shoot branching, whereas TCP4 promotes it. Altered branching patterns in Rose and Arabidopsis were associated with the expression of the branching integrator BRC1. Finally, we provide molecular evidence supporting that RhTCP4a/b directly binds to the RhBRC1 promoter and represses its transcription. Together, these results establish the miR319-TCP4-BRC1 regulatory module as a key component in the regulation of shoot branching in response to sugar status. We propose that the miR319-TCP4-BRC1 module is conserved between annual and perennial species and may integrate multiple hormonal and metabolic signals to shape shoot branching in plants.

plant biology↗

bioRxiv2026

Systematic Validation of AlphaFold-Predicted Interactomes with LUCIA

Mapping protein-protein interactions (PPIs) at structural resolution is essential for understanding cellular machinery. While tools like AlphaFold enable proteome-wide structural predictions, the field lacks high-throughput experimental methods to verify these predictions at scale and establish empirical thresholds for confidence metrics, such as the widely used interface predicted Template Modeling (ipTM) score. We developed LUCIA (LUminescent Cell-free Interaction Assay), a rapid biochemical screening platform bypassing traditional cloning and protein expression to validate direct binary interactions within days. Applying this to herpesviruses, clinically relevant human pathogens with large proteomes, we generated an exhaustive computational interactome of 23,215 AlphaFold-predicted dimer models across three species (HSV-1, HCMV, and KSHV), accessible via our HerpesPPIs database. Using the HSV-1 interactome as a benchmark, testing 83 high-confidence predicted dimers with LUCIA yielded 23 novel, experimentally validated interactions. By calibrating AlphaFold metrics against this direct binding data, we demonstrated that an ipTM score [≥] 0.80 identifies bona fide interactions with a positive predictive value of 77%. To demonstrate the functional power of this pipeline, we characterized a previously unknown interaction between HSV-1 UL42 and UL8, linking the viral DNA polymerase and helicase-primase complexes. Structure-guided mutations at the predicted and LUCIA-verified UL42-UL8 interface strongly reduced binding in vitro and completely abolished viral replication in cell culture. Combining the scalable LUCIA platform with computational predictions enables researchers to rapidly translate atomic-level models into validated biological mechanisms without the need to solve experimental structures.

microbiology↗

bioRxiv2026

Co-expression-based models improve eQTL predictions and highlightnovel transcriptome-wide genes associated with schizophrenia

Non-coding genetic variants statistically associated with complex heritability phenotypes are thought to act primarily through transcriptome regulatory mechanisms. Predictions of gene expression in tissue like the human brain traditionally rely primarily on cis-eQTLs. Here, we introduce INGENE and MODULE, trans-eQTLs models designed to enhance the prediction of gene expression by capturing the collective impact of candidate trans-eQTLs acting within co-expression networks. Exploiting RNA-seq data in six post-mortem brain regions (amygdala, caudate nucleus, dorsal/subgenual anterior cingulate cortex, dorsolateral prefrontal cortex, and hippocampus), we validate our models on two testing datasets, demonstrating increased gene predictability compared to both an original cis-based model and to EpiXcan, the leading benchmark in cis-model performance. Integration of cis- and trans-predictions significantly improves gene-level expression imputation (MLE = 0.05) for 18,744 genes across the six brain regions considered. Applying cis and trans models to PGC wave 3 genotypes identifies 766 SCZ-associated genes across brain regions (pFDR < .01), emphasizing the complementary nature of cis and trans predictions in trait association discovery. Of these genes, 641 represent novel transcriptome-wide associations with schizophrenia, highlighting the role of trans-heritability and genetic interactions underlying risk for this disorder, in addition to further supporting 125 previous candidates.

genomics↗

bioRxiv2019

Detection and quantification of house mouse Eimeria at the species level - challenges and solutions for the assessment of Coccidia in wildlife

Detection and quantification of coccidia in studies of wildlife can be challenging. Therefore, the prevalence of coccidia is often not assessed at the parasite species level in non-livestock animals. Parasite species-specific prevalences are especially important when studying evolutionary questions in wild populations. We tested whether increased host population density increases the prevalence of individual Eimeria species at the farm level, as predicted by epidemiological theory. We studied free-living commensal populations of the house mouse (Mus musculus) in Germany and established a strategy to detect and quantify Eimeria infections. We show that a novel diagnostic primer targeting the apicoplast genome (Ap5) and coprological assessment after flotation provide complementary detection results increasing sensitivity. Genotyping PCRs confirm detection in a subset of samples and cross-validation of different PCR markers does not indicate a bias towards a particular parasite species in genotyping. We were able to detect double infections and to determine the preferred niche of each parasite species along the distal-proximal axis of the intestine. Parasite genotyping from tissue samples provides an additional indication for the absence of species bias in genotyping amplifications. Three Eimeria species were found infecting house mice at different prevalences: Eimeria ferrisi (16.7%; 95% CI 13.2 - 20.7), E. falciformis (4.2%; 95% CI 2.6 - 6.8) and E. vermiformis (1.9%; 95% CI 0.9 - 3.8). We also find that mice in dense populations are more likely to be infected with E. falciformis and E. ferrisi.\n\nWe provide methods for the assessment of prevalences of coccidia at the species level in rodent systems. We show and discuss how such data can help to test hypotheses in ecology, evolution and epidemiology on a species level.

microbiology↗

bioRxiv2019

Integrating case studies into graduate teaching assistant training to improve instruction in biology laboratory courses

Todays biology laboratory courses are primarily instructed by graduate teaching assistants (GTAs) working toward their own graduate degrees in a science field. Even though GTAs are the driving instructional force in biology laboratories, they receive little to no training in pedagogical principles and applications. Here, we present the GTAs self-reported unmet training needs with respect to teaching biology laboratory courses. To address these needs, we developed three training cases along with instructions for implementation in online and in-person GTA trainings. We piloted our training materials for GTA training in person at Iowa State University and in a Center for the Integration of Research, Teaching, and Learning three-part online workshop. Upon completion of these training sessions, GTAs reported an increase in both their confidence and knowledge of student-centered instructional approaches. Furthermore, examination of the online workshop participants lesson plans demonstrated that GTAs were able to implement effective teaching practices in their own lesson plans. For brief training sessions, these are positive outcomes suggesting these cases are effective tools that could be incorporated into a variety of GTA training programs to improve instruction in biology laboratory courses.

scientific communication and education↗