Biology subjects

Heymann, M.

Publications and source records attributed to Heymann, M..

7 recordsLinked to original sources

bioRxiv2026

A generative AI framework for disease-specific lung microtissue bioengineering

Generative Lung Architecture Modeling (GLAM) is an integrated bioengineering framework that couples high-resolution three-dimensional tissue imaging with generative artificial intelligence to de novo design and 3D-bioprint anatomically detailed lung microtissue models. Native extracellular 3D matrix architectures of pulmonary parenchyma were extracted from healthy, fibrotic, and emphysematous in vivo mouse disease models and processed through a computational pipeline containing pre-trained image segmentation and 3D mesh generation. The resulting datasets were used to train a U-Net generative diffusion model with attention layers capable of synthesizing healthy and diseased lung tissue architectures. Microtissue cubes of about 200 - 300 {micro}m edge length of native and synthetic datasets were fabricated through high-resolution two-photon stereolithography with gelatin-methacryloyl biomaterial ink and successfully seeded with cells, demonstrating biological compatibility. In closing the loop between biological imaging, generative modeling, and high-resolution biofabrication, this integrated framework establishes generative AI as a functional design layer for tissue engineering. The resulting lung microtissues retained architectural features of the native and original tissues, making them an application-ready platform for customizable and scalable fabrication of biological tissue surrogates for preclinical modeling, drug testing, and precision regenerative bioengineering.

bioengineering↗

bioRxiv2026

Reconstituting organotypic 2D microtissue co-cultures via sequential stenciling

In mammalian organisms, native tissue function depends on precise spatial organization down to the cellular level. Reconstituting tissue architectures in 2D in vitro platforms can provide a means to study direct and indirect cell-cell interactions in a variety of tissue contexts while remaining compatible with high-throughput assays and high-resolution live imaging. We combine cost-effective stereolithography leveraging 3D printing with replica molding to stencil spatially defined, multicellular culture systems with sub-millimeter resolution onto planar substrates. The system is designed for ease of use, requires no complex fabrication setups and scales readily to 96-well plates. Sequential stencil application and removal under a biosafety cabinet enables controlled positioning of multiple cell types and supported the maturation of tissue assemblies. We demonstrate the utility of this stencil-based patterning strategy in three applications. First, we employ a combination of two circular stencils to recreate a structural feature characteristic for the tumor microenvironment of solid tumors: the encapsulation of colorectal cancer cells by cancer-associated fibroblasts. Resulting cell patternings reproduce native tissue dynamics of the densely packed tumor tissues, in which cancer-associated fibroblast cells actively compress the cancer cells and confer targeted therapy resistance. Second, we probe the synthetic, diffusible morphogen system synNotch in patterned cell patches, where GFP-releasing cells generate a ligand-dependent gradient. Third, we recapitulate the characteristic crypt-villus architecture of the mammalian intestine by patterning intestinal organoids within a stencil-restricted crypt region and allowing differentiating cells to collectively migrate along a designed villus axis. The presented strategy allows for rebuilding multicellular tissue architectures in vitro with biologically relevant spatial precision for high-throughput drug screenings and dissection of tissue-specific cellular interactions.

bioengineering↗

bioRxiv2022

Engineering Principles and Algorithmic Design Synthesis for Ultracompact Bio-Hybrid Perfusion Chip

Bioinspired 3D microfluidic systems that combine vascularization with extracellular matrix architectures of organotypic geometry, composition and biophysical traits can help advance our understanding of microorgan physiology. Here, two-photon stereolithography is adopted to fabricate freestanding perfusable 3D cell scaffolds with micrometer resolution from gelatin methacryloyl hydrogel derived from extracellular matrix protein. As a proof of concept, we introduce an ultracompact bio-hybrid chip layout to demonstrate perfusion and cell seeding of double-digit m proteinaceous channels. This perfusion chip consists of a standardized microfluidic interface fabricated from standard resin and a GM10 bioink channel printed atop of this interface. In addition, we demonstrate that algorithmic design synthesis can recapitulate intact alveoli and capillary networks with tunable design parameters to implement vascularized alveolar tissue models. This approach will allow for a systematic investigation of cell-cell and tissue dynamics in response to defined structural, mechanical and bio-molecular cues and is ultimately scalable to fabricate organ-on-a-chip systems.

bioengineering↗

bioRxiv2020

Microfluidic determination of liquid-liquid phase separation binodals

Liquid-liquid phase separation plays important roles in the compartmentalization of cells. Developing an understanding of how phase separation is encoded in biomacromolecules requires quantitative mapping of their phase behavior. Given that such experiments require large quantities of the biomolecule of interest, these efforts have been lagging behind the recent breadth of biological insights. Herein, we present a microfluidic phase chip that enables the measurement of saturation concentrations over at least three orders of magnitude for a broad spectrum of biomolecules and solution conditions. The phase chip consists of five units, each made of twenty individual sample chambers to allow the measurement of five sample conditions simultaneously. The analytes are slowly concentrated via evaporation of water, which is replaced by oil, until the sample undergoes phase separation into a dilute and dense phase. We show that the phase chip lowers the required sample quantity by 98% while offering six-fold better statistics in comparison to standard manual experiments that involve centrifugal separation of dilute and dense phase. We further show that the saturation concentrations measured in chip are in agreement with previously reported data for a variety of biomolecules. Concomitantly, time-dependent changes of the dense phase morphology and potential off-pathway processes, including aggregation, can be monitored microscopically. In summary, the phase chip is suited to exploring sequence-to-binodal relationships by enabling the determination of a large number of saturation concentrations at low protein cost.

biophysics↗

bioRxiv2019

A low-cost fluorescence reader for in vitro transcription and nucleic acid detection with Cas13a

Point-of-care testing (POCT) in low-resource settings requires tools that can operate independent of typical laboratory infrastructure. Due to its favorable signal-to-background ratio, a wide variety of biomedical tests utilize fluorescence as a readout. However, fluorescence techniques often require expensive or complex instrumentation and can be difficult to adapt for POCT. To address this issue, we developed a pocket-sized fluorescence detector costing less than $15 that is easy to manufacture and can operate in low-resource settings. It is built from standard electronic components, including an LED and a light dependent resistor, filter foils and 3D printed parts, and reliably detected less than 10 nM fluorescein concentrations (with a lower limit of detection of {approx}6.8 nM), which is sufficient to follow typical biochemical reactions used in POCT applications. All assays are conducted on filter paper, which allows for a flat detector architecture to improve signal collection. We validate the device by quantifying in vitro RNA transcription and also demonstrate sequence-specific detection of target RNAs in the nanomolar range using a Cas13a-based fluorescence assay. Cas13a is a RNA-guided, RNA-targeting CRISPR effector with promiscuous RNase activity upon recognition of its RNA target. Cas13a sensing is highly specific and adaptable and in combination with our detector represents a promising approach for nucleic acid POCT. Furthermore, our open-source device architecture could be a valuable educational tool that integrates hardware, software and biochemistry concepts.

bioengineering↗

bioRxiv2019

Bidirectional FtsZ filament treadmilling promotes membrane constriction via torsional stress

FtsZ is a key component in bacterial cell division, being the primary protein of the presumably contractile Z ring. In vivo and in vitro, it shows two distinctive features that could so far however not be mechanistically linked: self-organization into directionally treadmilling vortices on solid supported membranes, and shape deformation of flexible liposomes. In cells, circumferential treadmilling of FtsZ was shown to recruit septum-building enzymes, but an active force production remains elusive. To gain mechanistic understanding of FtsZ dependent membrane deformations and constriction, we designed an in vitro assay based on soft lipid tubes pulled from FtsZ decorated giant lipid vesicles (GUVs) by optical tweezers. FtsZ actively transformed these tubes into spring-like structures, where GTPase activity promoted spring compression. Operating the optical tweezers in lateral vibration mode and assigning spring constants to FtsZ coated tubes, we found that FtsZ rings indeed exerts 0.14 - 1.09 pN forces upon GTP hydrolysis, through torsional stress induced by bidirectional treadmilling. These directional forces could further be demonstrated to induce membrane budding with constricting necks on both, giant vesicles and E.coli cells devoid of their cell walls.

biophysics↗

bioRxiv2017

Authentic Enzyme Intermediates Captured "on-the-fly" by Mix-and-Inject Serial Crystallography

Ever since the first atomic structure of an enzyme was solved, the discovery of the mechanism and dynamics of reactions catalyzed by biomolecules has been the key goal for the understanding of the molecular processes that drive life on earth. Despite a large number of successful methods for trapping reaction intermediates, the direct observation of an ongoing reaction has been possible only in rare and exceptional cases. Here, we demonstrate a general method for capturing enzyme catalysis in-action by mix-and-inject serial crystallography. Specifically, we follow the catalytic reaction of the Mycobacterium tuberculosis -lactamase with the 3rd generation antibiotic ceftriaxone by time-resolved serial femtosecond crystallography. The results reveal, in near atomic detail, antibiotic cleavage and inactivation on the millisecond to second time scales including the crossover from transition state kinetics to steady-state kinetics.\n\nSynopsisAn enzymatically catalyzed reaction is initiated by diffusion based mixing of substrate and followed at runtime by time-resolved serial crystallography using a free electron laser.

biophysics↗