Biology subjects

Kusters, R.

Publications and source records attributed to Kusters, R..

6 recordsLinked to original sources

bioRxiv2026

Multi-omics Characterization of Duck Embryonic Stem Cells for Cultivated Meat

Industrializing cultivated meat requires cell lines with high proliferative capacity, genetic stability, and suspension adaptability. We present a comprehensive multi-omics framework, integrating genomics, transcriptomics, and proteomics, to characterize a commercial duck Embryonic Stem Cell (dESC) line. Our analysis demonstrates continuous proliferation in protein-free suspension media while maintaining a stable genome and a functional conserved transcriptome. Broad-scale transcriptomics confirms the absence of hazardous pathway activation, and targeted assays verify sustained pluripotency marker expression during scale-up. Compositional analysis reveals a low-fat biomass containing all nine essential amino acids with an amino acid profile comparable to conventional duck meat. Furthermore, proteomic profiling demonstrates inter-batch reproducibility and protein distributions comparable to duck breast and liver. This study provides the first detailed molecular characterization of a commercial cultivated meat cell line, establishing a reference for the stability and safety assessment of future cultivated meat cell lines.

cell biology↗

bioRxiv2026

Proteomics for cultivated meat: the importance of Analytical Standardization

Cultivated meat production requires robust and validated analytical methods for comprehensive characterization. While transcriptomics-based approaches establish the foundational profile of molecular analysis, proteomics provides additional resolution that further enhances scientific certainty in both product development and safety characterization. However, the industry adoption of proteomics is currently hindered by technical complexity and a critical lack of analytical standardization, which leads to significant workflow-dependent variations in proteome coverage. To address this gap, we investigated the influence of key workflow steps (digestion, cleanup, LC-MS conditions) on the proteome profile of cultivated duck biomass. We compared five bottom-up sample preparation protocols - two traditional in-solution options (urea and SDC-based protocols), two device-based approaches (PreOmics iST and EasyPep kits), and an innovative protocol (SPEED), and demonstrated that device-based protocols offered the highest peptide yield and proteome coverage. However, optimization allowed cost-effective in-solution methods to achieve comparable performance. Specifically, an optimal digestion time of 3 hours at 37{degrees}C and the use of polymer-based desalting columns significantly enhanced protein identification ([~]4500 - 5000 IDs). Moreover, data independent acquisition (DIA) provided deeper proteome coverage than data dependent acquisition (DDA) with higher precision ([~]6500 vs 5000 IDs). The validated Standard Operating Procedures presented here establish a standardized framework for bulk bottom-up proteomics in cultivated meat, facilitating the generation of reliable and comparable data required for robust multi-omics characterization. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/713501v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@3866f0org.highwire.dtl.DTLVardef@ee20eforg.highwire.dtl.DTLVardef@1b42c69org.highwire.dtl.DTLVardef@1cfd295_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIComplexity and non-standardization limit MS-proteomics use in cultivated meat (CM). C_LIO_LICM protein profile varies with sample prep, LC-MS, and data processing pipeline. C_LIO_LIDevice-based and optimized cost-effective protocols offer a high proteome coverage. C_LIO_LIProteomics can complement transcriptomics for a comprehensive CM characterization. C_LIO_LIProposed standardized methods ensure reliable data for future regulatory submissions. C_LI

systems biology↗

bioRxiv2025

Integrative multi-omics modelling for cultivated meat production, quality, and safety

Cell culture technology, which offers a promising solution for complementary food production, is slowly becoming a reality with the first wave of regulatory approvals in pioneering markets. However, significant challenges remain for large-scale cultivated meat commercialization, including effective scaling, cost efficiency, and product quality, but also scientific evidence to support regulatory approval and building consumer trust. In this paper, we discuss the potential of an integrative multi-omics approach to characterize and optimize cultivated meat production. By analyzing a network-based interactome model that integrates the transcriptomic, proteomic, and metabolomic layers, we achieve a system-level understanding of cellular metabolism and regulatory mechanisms. This approach can allow for precise monitoring and targeted interventions of critical quality and safety attributes associated with cellular biomass. We then describe a Target-Action-Metabolite (TAM) framework, which utilizes insights from the interactome to optimize cell culture conditions through actionable interventions. We illustrate the potential use of this framework through a case study involving Duck Embryonic Stem Cells (dESCs) for use in cell-cultured meat products, providing hypotheses for improving key metabolic pathways through targeted interventions on metabolites present in culture media. Finally, our paper highlights the potential of this interactome-based strategy to enhance bioprocess efficiency, improve product quality and ensure safety attributes, addressing regulatory challenges associated with cultivated meat production. HighlightsO_LIIntegrative multi-omics as a novel approach to support cultivated meat production. C_LIO_LIInteractome Models map molecular interactions to monitor and improve production. C_LIO_LIMulti-omics based strategy to scientifically support cell-culture safety assessment. C_LIO_LITarget-Action-Metabolites Framework to guide non-genetic interventions. C_LIO_LICase study with avian interactome model to enhance cellular metabolism. C_LI

bioinformatics↗

bioRxiv2019

Actin shells control buckling and wrinkling of biomembranes

Global changes of cell shape under mechanical or osmotic external stresses are mostly controlled by the mechanics of the cortical actin cytoskeleton underlying the cell membrane. Some aspects of this process can be recapitulated in vitro on reconstituted actin-and-membrane systems. In this paper, we investigate how the mechanical properties of a branched actin network shell, polymerized at the surface of a liposome, control membrane shape when the volume is reduced. We observe a variety of membrane shapes depending on the actin thickness. Thin shells undergo buckling, characterized by a cup-shape deformation of the membrane that coincides with the one of the actin network. Thick shells produce membrane wrinkles, but do not deform their outer layer. For intermediate micrometerthick shells, wrinkling of the membrane is observed, and the actin layer is slightly deformed. Confronting our experimental results with a theoretical description, we determine the transition between buckling and wrinkling depending on the thickness of the actin shell and the size of the liposome. We thus unveil the generic mechanism by which biomembranes are able to accommodate their shape against mechanical compression, through thickness adaptation of their cortical cytoskeleton.

biophysics↗

bioRxiv2018

A new actin depolymerase: a catch bond Myosin 1 motor

The regulation of actin dynamics is essential for various cellular processes. Former evidence suggests a correlation between the function of non-conventional myosin motors and actin dynamics. We investigate the contribution of myosin1b to actin dynamics using sliding motility assays. We observe that sliding on myosin1b immobilized or bound to a fluid bilayer enhances actin depolymerization at the barbed end, while sliding on myosin II, although 5 times faster, has no effect. This work reveals a non-conventional myosin motor as a new type of depolymerase and points to its singular interactions with the actin barbed end.

biophysics↗

bioRxiv2018

A direct proof that sole actin dynamics drive membrane deformations

Cell membrane deformations are crucial for proper cell function. Specialized protein assemblies initiate inward or outward membrane deformations that turn into, for example, filopodia or endocytic intermediates. Actin dynamics and actin-binding proteins are involved in this process, although their detailed role remains controversial. We show here that a dynamic, branched actin network is sufficient, in absence of any membrane-associated proteins, to initiate both inward and outward membrane deformation. With actin polymerization triggered at the membrane of liposomes, we produce inward filopodia-like structures at low tension, while outward endocytosis-like structures are robustly generated regardless of tension. Our results are reminiscent of endocytosis in mammalian cells, where actin polymerization forces are required when membrane tension is increased, and in yeast, where they are always required to overcome the opposing turgor pressure. By combining experimental observations with physical modeling, we propose a mechanism for actin-driven endocytosis under high tension or high pressure conditions.

biophysics↗