Biology subjects

Unger, A.

Publications and source records attributed to Unger, A..

11 recordsLinked to original sources

bioRxiv2026

A rapid, automation-friendly, cell-free and purification-free pipeline for binding and kinetic characterisation of de novo designed binders with high quality standardised per-design data

De novo protein binders can now be generated far faster than they can be tested. Current validation routes - display selection, cell-free two-hybrid assays, or surface-based biophysics - require cell culture, colony picking, protein purification, target labeling or sensor immobilisation, take 2 to 8 weeks, and require additional methods for affinity and kinetics characterisation. Here we report an end-to-end, cell- and purification-free pipeline that goes from gene to binding affinity and kinetics in three days without genetically modified organisms, cell culture, purification, labelling or immobilisation. An automated, metric-driven loop of RFdiffusion, ProteinMPNN and AlphaFold2 initial-guess generates and filters designs, which are ranked by Boltz-2 ipSAE, assembled by Golden Gate cloning from linear DNA, expressed in a cell-free protein synthesis lysate as fluorescent protein fusions, and screened directly in the unpurified product by flow-induced dispersion analysis (FIDA). Against human growth hormone, 11 of 30 designs (37%) bound, and the four strongest had equilibrium dissociation constants of 0.93-9.98 nM with on- and off-rates resolved from the same cell-free material. Each sample run measures expression level, hydrodynamic radius, oligomeric and aggregation state alongside the binding readout, producing the standardised, per-design datasets that model training requires.

molecular biology↗

bioRxiv2026

From Field Photosynthesis to Genetic Architecture: Insights from the First Dedicated Photosynthesis Hackathon

Photosynthesis is among the most consequential yet genetically complex traits in crop plants, and translating its natural variation into actionable genomic targets remains a central challenge for breeding climate-resilient varieties. To start addressing this, researchers are generating increasingly large, multi-environment field photosynthesis datasets. Yet, these data have been structurally under-analysed since their inception. Here we report the outcomes of the first dedicated hackathon focused on computational mining of such field data held in Accra, Ghana, in March 2026. Bringing together data scientists, plant physiologists, geneticists, and breeders from Europe and Africa, these interdisciplinary teams used photosynthetic data collected with hand-held fluorometers to genome-wide marker data across four crop species: cowpea (Vigna unguiculata), barley (Hordeum vulgare), common bean (Phaseolus vulgaris), and potato (Solanum tuberosum). Despite using different species and methods, independent teams identified the same three key findings. First, mechanism-informed feature engineering and dynamic modelling recover genetic signals that are not detected or discarded in standard analysis pipelines, resulting in traits with improved heritability and meaningful associations with yield. Secondly, machine learning methods proved effective at uncovering genetic associations, with temporally resolved features substantially outperforming single time-point measurements. Third, raw chlorophyll fluorescence and absorbance traces consistently contained more information and predictive power than the extracted parameters currently used. A defining feature of this event was having experimentalists and data scientists working together, enabling AI approaches to be grounded in domain knowledge and biological mechanisms rather than relying on data alone.

plant biology↗

bioRxiv2026

Bacterial Spores as a Scalable, Modular Platform forthe Production of Amyloids for Materials

We present a proof-of-concept platform in which amyloids are displayed on the surface of engineered Bacillus subtilis spores for bioengineered materials. Amyloids possess high tensile strength, elasticity, and tunable assembly, but their use is limited by inaccessible native sources and low-yield or toxic heterologous expression. Here, spores were engineered to display the native amyloid TasA and Humboldt squid suckerins 9 and 10 as fusions to the spore coat protein CotY. Amyloid production and fibril formation were confirmed by Western blot and X-34 staining, and quantitative analysis indicated mg/L-level yields. Atomic force microscopy revealed altered stiffness and surface ultrastructure, and incorporation of amyloid-displaying spores into resin-based 3D printing modified tensile strength. These findings highlight spore-based amyloid display as a scalable, modular platform for materials applications, leveraging established industrial spore production.

bioengineering↗

bioRxiv2025

skNAC is a Key Driver of Cardiomyocyte Integrity Against Pathological Cardiac Hypertrophy and Heart Failure

Chronic pressure overload induces cardiac hypertrophy and heart failure through coordinated alterations in proteome homeostasis, metabolism and sarcomere organisation. The muscle-specific -isoform of the nascent polypeptide-associated complex (skNAC) is essential for sarcomere assembly during development, but its role in adult hearts remains largely unknown. Here, we show that skNAC expression is reduced in hypertrophic cardiomyocytes, mouse models of pressure overload, and human hypertrophic hearts, in association with disease severity. Cardiomyocyte-specific skNAC deletion results in basal hypertrophy, systolic dysfunction, and premature death, and exacerbates pressure overload-induced heart failure. At the molecular level, skNAC associates with ribosomes and is required for sarcomere organisation maintenance, while its loss induces autophagy and ultrastructural defects. Integrated transcriptomic and proteomic analyses reveal early downregulation of metabolic gene expression despite increased abundance of corresponding proteins, indicating compensatory metabolic responses. Gain-of-function studies confirm a protective role against hypertrophy. Together, these data establish skNAC as a key regulator of cardiac proteome homeostasis and metabolic adaptation during pathological remodelling.

physiology↗

bioRxiv2025

Peroxisome protein import deficiency causes heart failure in mouse and human

Peroxisomes are ubiquitous cellular organelles with potentially vital roles in lipid and reactive oxygen metabolism. The metabolic demands of the heart are substantial; however, the contribution of peroxisomes to cardiac development, health, and their role in heart failure (HF) remain largely unexplored. We developed and examined a mouse and an engineered human myocardium (EHM) model with a deficiency in cardiac peroxisome biogenesis to investigate the role of peroxisomes in cardiac function and pathology. In the EHM, loss of peroxisome protein import and subsequent peroxisomal metabolic impairment trigger mitochondrial damage and compromise cellular respiration and energy production. Peroxisome dysfunction results in incoherent electrical conduction, defective Ca2+-handling, and ultimately presentation of a HF phenotype with pathological force generation. These phenotypes are mirrored in an orthogonal murine model system with defective cardiac peroxisome biogenesis. Preload-dependent deficits in force generation due to insufficient energy supply are eventually fatal. Thus, peroxisomes play an important role in sustaining normal heart operations. Vice versa, peroxisome maintenance is compromised in pressure overload-induced HF, establishing peroxisomes as potential modulators of pathology and targets of therapy.

cell biology↗

bioRxiv2025

Titin cleavage impairs cardiac mechanical connectivity to drive diastolic failure and fibrosis

Titin, the largest human protein, serves as the elastic backbone of sarcomeres in muscle cells and imparts passive stiffness to cardiomyocytes. While proteolytic cleavage of elastic titin has been linked to cardiovascular disease, the isolated effects of titin stiffness loss in the living heart remain poorly understood. Here, we developed a knock-in mouse model allowing for the selective cleavage of cardiac titin springs in vivo. Using a time-resolved approach combining MRI, echocardiography, immunofluorescence, and molecular profiling, we demonstrate that titin cleavage does not dilate the heart but induces concentric remodeling, impaired diastolic function, and low-output heart failure. Mechanistically, compromised titin-based restoring forces trigger internal mechanical imbalance and dysconnectivity, which activate fibroblasts and promote extracellular matrix remodeling, revealing titins essential role in maintaining cardiac mechanical homeostasis.

physiology↗

bioRxiv2023

Inhibition of mammalian mtDNA transcription paradoxically activates liver fatty acid oxidation to reverse diet-induced hepatosteatosis and obesity

The oxidative phosphorylation (OXPHOS) system in mammalian mitochondria plays a key role in harvesting energy from ingested nutrients1, 2. Mitochondrial metabolism is very dynamic and can be reprogrammed to support both catabolic and anabolic reactions, depending on physiological demands or disease states3, 4. Rewiring of mitochondrial metabolism is intricately linked to metabolic diseases5, 6 and is also necessary to promote tumour growth7-11. Here, we demonstrate that per oral treatment with an inhibitor of mitochondrial transcription (IMT)11 shifts whole animal metabolism towards fatty acid oxidation, which, in turn, leads to rapid normalization of body weight, reversal of hepatosteatosis and restoration of glucose tolerance in mice on high-fat diet. Paradoxically, the IMT treatment causes a severe reduction of OXPHOS capacity concomitant with a marked upregulation of fatty acid oxidation in the liver, as determined by proteomics and non-targeted metabolomics analyses. The IMT treatment leads to a marked reduction of complex I, the main dehydrogenase that feeds electrons into the ubiquinone (Q) pool, whereas the levels of electron transfer flavoprotein dehydrogenase (ETF-DH) and other dehydrogenases connected to the Q pool are increased. This rewiring of metabolism caused by reduced mtDNA expression in the liver provides a novel principle for drug treatment of obesity and obesity-related pathology.

physiology↗

bioRxiv2022

Reduced mitochondrial transcription sensitizes acute myeloid leukemia cells to BCL-2 inhibition

Overcoming drug-resistance and the subsequent relapse that often occurs with monotherapy is crucial in the treatment of acute myeloid leukemia. We here demonstrate that therapy-resistant leukemia initiating cells can be targeted using a novel inhibitor of mitochondrial transcription (IMT). The compound inhibits mitochondrial RNA polymerase activity and sensitizes the resistant population to the induction of apoptosis. In vitro studies on acute myeloid leukemia cells demonstrate that IMT prevents cell proliferation, and together with a selective BCL-2 inhibitor, venetoclax, induces apoptosis and suppress oxidative phosphorylation (OXPHOS) synergistically. AML mouse models treated with IMT in combination with venetoclax show prolonged survival in venetoclax-resistant models. Our findings suggest that certain therapy-resistant leukemia cell populations display a unique dependency on mitochondrial transcription and can be targeted with IMT.

cancer biology↗

bioRxiv2021

Human engineered skeletal muscle of hypaxial origin from pluripotent stem cells with advanced function and regenerative capacity

Human pluripotent stem cell derived muscle models show great potential for translational research. Here, we describe developmentally inspired methods for derivation of skeletal muscle cells and their utility in three-dimensional skeletal muscle organoid formation as well as skeletal muscle tissue engineering. Key steps include the directed differentiation of human pluripotent stem cells to embryonic muscle progenitors of hypaxial origin followed by primary and secondary fetal myogenesis into hypaxial muscle with development of a satellite cell pool and evidence for innervation in vitro. Skeletal muscle organoids faithfully recapitulate all steps of embryonic myogenesis in 3D Tissue engineered muscle exhibits organotypic maturation and function, advanced by thyroid hormone. Regenerative competence was demonstrated in a cardiotoxin injury model with evidence of satellite cell activation as underlying mechanism. Collectively, we introduce a hypaxial muscle model with canonical properties of bona fide skeletal muscle in vivo to study muscle development, maturation, disease, and repair.

cell biology↗

bioRxiv2020

Graded titin cleavage progressively reduces tension and uncovers the source of A-band stability in contracting muscle

The giant muscle protein titin is a major contributor to passive force; however, its role in active force generation is unresolved. Here, we use a novel titin-cleavage (TC) mouse model that allows specific and rapid cutting of elastic titin to quantify how titin-based forces define myocyte ultrastructure and mechanics. We show that under mechanical strain, as titin cleavage doubles from heterozygous to homozygous TC muscles, Z-disks become increasingly out of register while passive and active forces are reduced. Interactions of elastic titin with sarcomeric actin filaments are revealed. Strikingly, when titin-cleaved muscles contract, myosin-containing A-bands become split and adjacent myosin filaments move in opposite directions while also shedding myosins. This establishes intact titin filaments as critical force-transmission networks, buffering the forces observed by myosin filaments during contraction. To perform this function, elastic titin must change stiffness or extensible length, unveiling its fundamental role as an activation-dependent spring in contracting muscle.

cell biology↗

bioRxiv2019

A HaloTag-TEV genetic cassette for mechanical phenotyping of native proteins

Single-molecule methods using recombinant proteins have generated transformative hypotheses on how mechanical forces are generated and sensed in biological tissues. However, testing these mechanical hypotheses on native molecules in their natural environment remains inaccessible to conventional genetics, biophysics and molecular biology tools. To address these limitations, here we demonstrate a genetically engineered knock-in mouse model carrying a HaloTag-TEV insertion in the protein titin, the main determinant of myocyte stiffness. Using our system, we have specifically severed the titin filament by digestion with TEV protease, and found that the response of muscle fibers to length changes requires mechanical transduction through titins intact polypeptide chain. HaloTag-based covalent tethering has enabled directed examination of the dynamics of titin under 1-100 pN forces using recently developed magnetic tweezers. At pulling forces lower than 10 pN, titin domains are readily recruited to the unfolded state, and produce 41.5 zJ mechanical work during refolding. Our results support an active role of titin in muscle contraction in coordination with actomyosin motors. Insertion of the HaloTag-TEV cassette in proteins with mechanical roles opens new grounds to explore the molecular basis of cellular force generation, mechanosensing and mechanotransduction.

biophysics↗