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At least 433 records · Page 24Linked to original sources

bioRxiv2024

Human Astrocytes Synchronize Neural Organoid Networks

Biological neural networks exhibit synchronized activity within and across interconnected regions of the central nervous system. Understanding how these coordinated networks are established and maintained may reveal therapeutic targets for neurodegeneration and neuromodulation. Here, we tested the influence of astrocytes upon synchronous network activity using human pluripotent stem cell-derived bioengineered neural organoids. This study revealed that astrocytes significantly increase activity within individual organoids and across long distances among numerous rapidly merged organoids via influencing synapses and bioenergetics. Treatment of amyloid protein inhibited synchronous activity during neurodegeneration, yet this can be rescued by propagating activity from neighboring networks. Altogether, this study identifies critical contributions of human astrocytes to biological neural networks and delivers a rapid, reproducible, and scalable model to investigate long-range functional communication of the nervous system in healthy and disease states.

neuroscience↗

bioRxiv2024

FoldMark: Protecting Protein Generative Models with Watermarking

Proteins are the principal architects of life, fueling advances in bioengineering, drug discovery, and synthetic biology. The integration of generative AI with computational protein science has revolutionized protein design while also posing dual-use risks, such as enabling the creation of pandemic-capable proteins that require strong biosecurity safeguards. Here, we introduce FoldMark, a first-of-its-kind watermarking strategy leveraging distributional and evolutionary principles tailored for protein generative models, balancing watermark capacity and structural quality. FoldMark achieves over 95% watermark bit accuracy at 32 bits with minimal impact on structural quality (>0.9 scTM scores) for leading models including AlphaFold3, ESMFold, RFDiffusion, and RFDiffusionAA. For user tracing, FoldMark can successfully trace up to 1 million users. To validate FoldMark in wet lab, we applied it to structure-based design of EGFP and CRISPR-Cas13, showing wildtype-level function (98% fluorescence, 95% editing efficiency) and >90% watermark detection, demonstrating its practical utility for safeguarding AI-driven protein research.

bioinformatics↗

bioRxiv2024

Making Neurobots and Chimerical Ctenophores

Making living machines using biological materials (cells, tissues, and organs) is one of the challenges in developmental biology and modern biomedicine. Constraints in regeneration potential and immune self-defense mechanisms limit the progress in the field. Here, we present unanticipated features related to self-recognition and ancestral neuro-immune architectures of new emerging reference species - ctenophores or comb jellies. These are descendants of the earliest survival metazoan lineage with unique tissues, organs and independent origins of major animal traits such as neurons, muscles, mesoderm, and through-gut. Thus, ctenophores convergently evolved complex organization, compared to bilaterians. Nevertheless, their neural and immune systems are likely functionally coupled, enabling designs and experimental construction of hybrid neural systems and even entire animals. This report illustrates impressive opportunities to build both chimeric animals and neurobots using ctenophores as models for bioengineering. The obtained neurobots and chimeric animals from three ctenophore species (Bolinopsis, Mnemiopsis, and Pleurobrachia) were able to be autonomous and survive for days. In sum, the unification of biodiversity, cell biology, and neuroscience opens unprecedented opportunities for experimental synthetic biology.

developmental biology↗

bioRxiv2024

Detecting Special Genes in Marine Symbionts: A Phylogeny-Deviation Approach Identifies Recombination-Enhancing Variants

Different microbes possess special traits that enable adaptation to their specific niches, often through specialized genes. Identifying such species-special genes provides insights into microbial physiology and offers new tools for bioengineering. However, beyond the search for orphan genes, there are few methods for detecting genes that are homologous to those in other species yet contain unusual functional regions. In investigating the extreme recombination frequency of the marine symbiont bacterium Ca. E. kahalalidifaciens, we developed a computational approach to identify vairants that substantially deviate from phylogenetic expectations. This unbiased strategy successfully identified multiple Holliday junctions-related genes in Ca. E. kahalalidifaciens as candidates responsible for its exceptional recombination capacity. Heterologous expression of these gene variants in Escherichia coli significantly enhanced recombination efficiency. These high-efficient variants offer insights into improving tools for genetic manipulations, and our gene-identification approach can be applied broadly for microbial genome mining.

bioinformatics↗

bioRxiv2024

Lignocellulose Degradation in Bacteria and Fungi for Biomass Conversion

Lignocellulose biomass is one of the most abundant resources for sustainable biofuels. However, scaling up the biomass-to-biofuels conversion process for widespread usage is still pending. Bottlenecks during the process of enzymatic hydrolysis are the high cost of enzymes and the labor-intensive need for substrate-dependent enzyme mixtures. Current research efforts are therefore targeted at searching for or engineering lignocellulolytic enzymes of high efficiency. One way is to engineer multi-enzyme complexes that mimic the bacterial cellulosomal system, known to increase degradation efficiency up to 50-fold when compared to freely-secreted enzymes. However, these designer cellulosomes are instable and less efficient than wild type cellulosomes. Fungi cellulosomes discovered in recent years have significant differences from bacterial counterparts and hold great potential for industrial applications, both as designer cellulosomes and as additions to the enzymatic repertoire. Up to date, they are only found in a few anaerobic fungi. In this review, we extensively compared the degradation mechanisms in bacteria and fungi, and highlighted the essential gaps in applying these mechanisms in industrial applications. To better understand cellulosomes in microorganisms, we examined their sequences in 66,252 bacterial species and 823 fungal species and identified several bacterial species that are potentially cellulosome-producing. These findings act as a valuable resource in the biomass community for further proteomic and genetic sequence analysis. We also collated the current strategies of bioengineering lignocellulose degradation to suggest concepts that could be favorable for industrial usage.

microbiology↗

bioRxiv2024

Defining and Controlling Axial Nephron Patterning in Human Kidney Organoids with Synthetic Wnt-Secreting Organizers

Current human pluripotent stem cell-derived kidney organoids contain nephron-like structures that lack organotypic patterning. It is thought that during human development, nephrons form their proximal-distal axial polarity in response to collecting duct-derived signals that are absent in kidney organoids. To delineate how nephron polarities establish, we profiled human kidney development by spatial transcriptomic approaches. Our analyses describe a new axial polarity in the nephron and demonstrate that the nephron proximal-distal polarity develops adjacent to a transcriptional boundary in the collecting duct where non-canonical WNT11 is downregulated and canonical WNT9B ligand is upregulated. The nephron region closest to this boundary in turn activates a series of canonical WNT target genes inferring positional nephron identities. To establish whether a canonical WNT source can improve organoid patterning to an in vivo-like state, we bioengineered self-organizing WNT-secreting synthetic organizers. Organizer-coupled kidney organoids respond to WNT ligands by forming expression gradients and developing distal cell identities. Tuning the WNT dose produced nephrons with continuous patterning along the proximal-distal axis. Strikingly, polarized iPSC-derived nephrons directed their distal tubules towards the WNT-source, indicating axial patterning and morphogenetic programs are tuned by WNTs from the synthetic organizers. Our data present a strategy to control organ patterning, build an artificial kidney, and highlights the power of synthetic organizer systems for advancing organoid models.

synthetic biology↗

bioRxiv2024

Octadecanoids as emerging lipid mediators in cnidarian-dinoflagellate symbiosis

Oxylipin signaling has been suggested as a potential mechanism for the inter-partner recognition and homeostasis regulation of cnidarian-dinoflagellate symbiosis, which maintains the ecological viability of coral reefs. Here we assessed the effects of symbiosis and symbiont identity on a model cnidarian, the sea anemone Exaiptasia diaphana, using mass spectrometry to quantify octadecanoid oxylipins (i.e., 18-carbon-derived oxygenated fatty acids). A total of 84 octadecanoids were reported, and distinct stereospecificity was observed for the synthesis of R- and S-enantiomers for symbiont-free anemones and free-living cultured dinoflagellate symbionts, respectively. Symbiont-derived 13(S)-hydroxy-octadecatetraenoic acid (13(S)- HOTE) linked to a 13S-lipoxygnase was translocated to the host anemone with a 32-fold increase, suggesting it as a biomarker of symbiosis and as a potential agonist of host receptors that regulate inflammatory transcription. Only symbiosis with the native symbiont Breviolum minutum decreased the abundance of pro-inflammatory 9(R)-hydroxy-octadecadienoic acid (9(R)-HODE) in the host. In contrast, symbiosis with the non-native symbiont Durusdinium trenchii was marked by higher abundance of autoxidation-derived octadecanoids, corroborating previous evidence for cellular stress in this association. The putative octadecanoid signaling pathways reported here suggest foundational knowledge gaps that can support the bioengineering and selective breeding of more optimal host-symbiont pairings to enhance resilience and survival of coral reefs.

biochemistry↗

bioRxiv2024

Biochemical dissection of a fungal highly reducing polyketide synthase condensing region reveals basis for acyl group selection.

Fungal highly reducing polyketide synthases (hrPKSs) are remarkable multidomain enzymes that catalyse the biosynthesis of a diverse range of structurally complex compounds. During biosynthesis, the ketosynthase (KS) and acyltransferase (AT) domains of the condensing region are visited by the acyl carrier protein (ACP) domain during every cycle, catalysing chain priming and elongation reactions. Despite their significance, our comprehension of how these steps contribute to biosynthetic fidelity remains poorly understood. Herein, we report the full in vitro reconstitution of each catalytic step carried out by a hrPKS condensing region. Application of intact protein mass spectrometry shows that the AT domain operates selective acyl transfer to the ACP domain, ensuring loading of the correct starter / extender units, which is governed by a substrate recycling mechanism and kinetic parameters towards each substrate. The KS domain is shown to select for the correct starter unit for transacylation and subsequent chain elongation, yet harbours flexibility towards the extender unit supplied. This work provides the first comprehensive interrogation of a fungal hrPKS condensing region, which both affirms and expands our understanding of how these systems function, and provides a framework for future bioengineering efforts.

biochemistry↗

bioRxiv2024

Bovine Formative Embryonic Stem Cell Plasticity in Embryonic and Extraembryonic Differentiation

Bovine embryonic stem cells (bESCs) can greatly enhance understanding of bovine embryonic development and applications for disease-resistance, biomedical and zoonotic pre-clinical models. However, formative bESCs with distinct morphology and complete differentiation capacity are still unreported. We document here the generation of bESCs which are pluripotent both in vitro and in vivo, and efficiently converted into neural progenitor cells (NPCs) and primordial germ cell-like cells (PGCLCs) by direct differentiation. These cells exhibited distinct metabolic features from human and mouse ESCs and early embryos. Formative bESCs contributed to a wide range of cell types within embryonic and extraembryonic tissues after aggregating with mouse and bovine embryos. The establishment of bovine formative ESCs with dual developmental plasticity represents a milestone for agricultural biotechnology and decoding the underlying mechanism of bona fide bovine pluripotency. Summary statementGenerating bovine ESCs would greatly enhance understanding of bovine embryonic development and bioengineering of cattle for disease-resistance, biomedical and zoonotic pre-clinical models.

developmental biology↗

bioRxiv2025

Competing signaling pathways controls electrotaxis

Understanding how cells migrate following exogenous cues is one of the most fundamental questions for biology, medicine, and bioengineering. Growing evidence shows that electrotaxis, the directed cell migration toward electric potential gradients, represents a precise and programmable method to control cell migration. Most data suggest that the polarization of membrane components and the following downstream signaling are central to electrotaxis. Unfortunately, how these multiple mechanisms coordinate with the motile machinery of the cell to respond to an electric field is still poorly understood. Here, we develop a mechanistic model that explains and recapitulate electrotaxis across different cell types. Using the zebrafish proteome, we identify membrane proteins directly related to migration signaling pathways that polarize anodally and cathodally. Further, we show that simultaneous and asymmetric distribution of charged membrane receptors towards the anode and the cathode establishes multiple cooperative and competing stimuli for downstream signaling pathways. The resulting polarization of signals controls the actomyosin network dynamics, directing the anodal and cathodal migration of the cell. Our theoretical framework rationalizes the physical processes that determine electrotaxis across cell types and provides a physical framework to test multiple electrotactic pathways. These results together show us how to control cell migration to, e.g., enhance, cancel, or switch directed cell migration, which opens up new avenues not only to promote tissue regeneration or arrest tumor progression but also to design better biomimetic-engineered tissue constructs.

biophysics↗

bioRxiv2025

Microgravity Accelerates Skeletal Muscle Degeneration: Functional and Transcriptomic Insights from a Muscle Lab-on-Chip Model Onboard the ISS.

Microgravity accelerates skeletal muscle degeneration, mimicking aging, yet its effects on human muscle cell function and signaling remain underexplored. Using a muscle lab-on-chip model onboard the International Space Station, we examined how microgravity and electrically stimulated contractions influence muscle biology and age-related muscle changes. Our 3D bioengineered muscle model, cultured for 21 days (12 days in microgravity), included myobundles from young, active and older, sedentary individuals, with and without electrically stimulated contraction. Real-time data collected within an autonomous Space Tango CubeLabTM showed reduced contraction magnitude in microgravity. Global transcriptomic analysis revealed increased gene expression and particularly mitochondrial-related gene expression in microgravity for the electrically stimulated younger myobundles, while the older myobundles were less responsive. Moreover, a comparative analysis using a skeletal muscle aging gene expression database revealed that certain age-induced genes showed changes in expression in myobundles from the younger cohort when exposed to microgravity, whereas these genes remained unchanged in myobundles from the older cohort. Younger, electrically stimulated myobundles in microgravity exhibited higher expression of 45 aging genes involved in key aging pathways related to inflammation and immune function, mitochondrial dysfunction, and cellular stress; and decreased expression of 41 aging genes associated with inflammation, and cell growth. This study highlights a unique age-related molecular signature in muscle cells exposed to microgravity and underscores electrical stimulation as a potential countermeasure. These insights advance understanding of skeletal muscle aging and microgravity-induced degeneration, informing strategies for mitigating age-related muscle atrophy in space and on Earth.

cell biology↗

bioRxiv2025

Metabolic modeling reveals synergistic growth benefits of engineering maize symbiosis with rhizobia and arbuscular mycorrhizal fungi

Engineering a novel N2-fixing rhizobia symbiosis in cereal crops is a strategy being pursued to improve agricultural sustainability. However, if such a symbiosis were introduced, it would have to be economically viable in the context of existing nutrient acquisition strategies, including the existing symbiosis with arbuscular mycorrhizal fungi (AMF) that the vast majority of plants already engage in. This raises the question of how the metabolic costs and benefits from these separate symbioses that have partially overlapping functions might impact nutrient status and subsequent plant growth. To address this, we developed metabolic models describing how the relative growth rate of Zea mays is impacted by the AMF Rhizophagus irregularis and a hypothetical N2-fixing symbiosis with Bradyrhizobium diazoefficiens both in isolation and in tandem. To validate the AMF component of our model, we conducted field evaluation of mutant AMF-incompatible maize hybrids and found that the empirically measured AMF-mediated growth benefit agreed well with our models predictions. Our model of the rhizobium symbiosis predicted that the lower N content of cereal crops makes the relative growth rate cost associated with acquiring nitrogen from N2-fixing rhizobia smaller than in legumes. Finally, our model also predicted positive synergies between rhizobia and AMF under nutrient-limited conditions but negative synergies under nutrient, particularly phosphorus, replete conditions. These findings indicate that these bioengineering strategies could improve cereal crop yields and may achieve greater gains in tandem, but soil nutrient status of target sites as well as the nitrogen requirements of specific varieties should be considered.

systems biology↗

bioRxiv2025

How Does Sampling Affect the AI Prediction Accuracy of Peptides' Physicochemical Properties?

Accurate AI prediction of peptide physicochemical properties is essential for advancing peptide-based biomedicine, biotechnology, and bioengineering. However, the performance of predictive AI models is significantly affected by the representativeness of the training data, which depends on the sample size and sampling methods employed. This study addresses the challenge of determining the optimal sample size and sampling methods to enhance the predictive accuracy and generalization capacity of AI models for estimating the aggregation propensity, hydrophilicity, and isoelectric point of tetrapeptides. Four sampling methods were evaluated: Latin Hypercube Sampling (LHS), Uniform Design Sampling (UDS), Simple Random Sampling (SRS), and Probability-Proportional-to-Size Sampling (PPS), across sample sizes ranging from 100 to 20,000. A sample size of approximately 12,000 (7.5% of the total tetrapeptide dataset) marks a key threshold for stable and consistent model performance. This study provides valuable insights into the interplay between sample size, sampling strategies, and model performance, offering a foundational framework for optimizing data collection and AI model training for the prediction of peptides physicochemical properties, especially for prediction in the complete sequence space of longer peptides with more than four amino acids.

bioinformatics↗

bioRxiv2025

Optimisation of Ramonda serbica LEA protein production in Escherichia coli and its secondary structure analysis

Desiccation, an extreme form of dehydration, reduces the cellular water content to below 5 % and poses a major challenge for most plants. Ramonda serbica, a tertiary relict and homoiochlorophyllous resurrection plant, is an exceptional model for investigating vegetative desiccation tolerance. Late Embryogenesis Abundant (LEA) proteins are strongly involved in this adaptive trait, but their exact molecular function is still unclear. In this study, we report the first successful recombinant production of the desiccation-induced LEA protein, RsLEAP30, from a dicotyledonous resurrection plant species using an Escherichia coli expression system. By employing immobilised metal affinity and size-exclusion chromatography, we achieved to purify RsLEAP30 to purity over 95 %, providing a robust and scalable method for producing other LEA proteins. Structural characterisation by circular dichroism spectroscopy, combined with in silico modelling, revealed that RsLEAP30 is predominantly disordered but contains -helical regions. We suggest that this structural duality underpins the protective role of RsLEAP30 in chloroplasts, likely via interactions with thylakoids and desiccation-sensitive proteins within photosynthesis-associated proteins. This function may be crucial for the rapid recovery of photosynthetic components upon rehydration. Our study provides new insights into the structure-function relationship of LEA proteins in resurrection plants and establishes a foundation for future investigations. Understanding the protective mechanisms of RsLEAP30 will pave the way for bioengineering strategies aimed at improving the drought tolerance of crops.

biochemistry↗

bioRxiv2025

Epigenome and interactome profiling uncovers principles of distal regulation in the barley genome

Regulation of transcription initiation is the ground level of modulating gene expression during plant development. This process relies on interactions between transcription factors and cis- regulatory elements (CREs), which become promising targets for crop bioengineering. To annotate CREs in the barley genome and understand mechanisms of distal regulation, we profiled several epigenetic features across three stages of barley embryo and leaves, and performed HiChIP to identify activating and repressive genomic interactions. Using machine learning, we integrated the data into seven chromatin states, predicting [~]77,000 CRE candidates, collectively representing 1.43% of the barley genome. Identified genomic interactions, often spanning multiple genes, linked thousands of CREs with their targets and revealed notably frequent promoter-promoter contacts. Using the LEA gene family as an example, we discuss possible roles of these interactions in transcription regulation. On the Vrn3 gene, we demonstrate the potential of our datasets to predict CREs for other developmental stages.

genomics↗

bioRxiv2025

Engineering Cortical Networks: An Open Platform for Controlled Human Circuit Formation and Synaptic Analysis In vitro

Neuronal circuits are complex networks formed by specific neuron connections across brain regions. Understanding their development is key to studying circuit-related dysfunctions in brain diseases. Human-induced pluripotent stem cell (iPSC) models aid in this research but lack precise architecture, limiting insights into neuronal interactions and activity-dependent processes. Microfluidic technologies offer structural control but are restricted by closed systems that hinder 3D integration, scalability, and cell retrieval. To address these limitations, we developed an open cortical network platform integrating iPSC-derived cortical neurons with bioengineering techniques. Using a polydimethylsiloxane (PDMS)-based microgroove topography and a cell plating guide, we created neuronal nodes for controlled circuit assembly. This design enables large-scale functional cortical circuits without physical barriers, allowing optogenetic control of neural activity and flexible network modifications, including cellular composition, neurite directionality, and synapse formation. The open design facilitates neuronal material accessibility, supporting multi-level analyses such as proteomics. This platform serves as a powerful tool for investigating neuronal network development and function, offering new opportunities to study both normal and pathological states, including molecular changes linked to connectivity loss in brain diseases.

neuroscience↗

bioRxiv2025

Illuminating Glucomannan Synthases to Explore Cell Wall Synthesis Bottlenecks

Hemicelluloses are important dietary fibers and a key component of lignocellulosic biomass. Despite numerous observations for fluorescently tagged cellulose synthases, the subcellular journeys and biochemical activities of intracellular cellulose synthase-like enzymes such as {beta}-mannan synthases (ManS) remain largely unexplored. This study identifies C-terminal fluorescent protein tags that maintain ManS activity in the yeast to accelerate the Design, Build, Test, Learn cycles for polysaccharide biosynthesis. Using the Amorphophallus konjac ManS as a case study, we demonstrate that the enzyme co-localizes with a known yeast marker for the Golgi apparatus despite the toxic effects of plant glucomannan accumulation in Pichia pastoris. The ManS first transmembrane domain was found to be critical for the punctate localization of the enzyme, its overall expression level and its function. Additionally, we explored how fluorescently tagged ManS is influenced by genetic or chemical perturbations of native yeast cell wall components, such as reducing protein mannosylation and severely disrupting {beta}-1,3-glucans. Finally, we identified alternative feeding strategies and episomal vectors for Pichia, which were extended to Saccharomyces cerevisiae, to accelerate hemicellulose research. We propose that expanding the Plant MoClo-compatible plasmid repertoire is essential to swiftly prototype carbohydrate-active enzymes in yeast before proceeding with more time-intensive analyses in plants. Requiring only hours or days instead of weeks or months for plant transformation/regeneration, our yeast prototyping strategies can de-risk the bioengineering of carbohydrate-active enzymes.

synthetic biology↗

bioRxiv2025

Dissecting the effects of single amino acid substitutions in SARS-CoV2 Mpro

Successfully predicting the effects of amino acid substitutions on protein function and stability remains challenging. Recent efforts to improve computational models have included training and validation on high-throughput experimental datasets, such as those generated by deep mutational scanning (DMS) approaches. However, DMS signals typically conflate a substitutions effects on protein function with those on in vivo protein abundance; this limits the resolution of mechanistic insights that can be gleaned from DMS data. Distinguishing functional changes from abundance-related effects is particularly important for substitutions that exhibit intermediate outcomes (e.g., partial loss-of-function), which are difficult to predict. Here, we explored changes in in vivo abundance for substitutions at representative positions in the SARS-CoV-2 Main Protease (Mpro). For this study, we used previously published DMS results to identify "rheostat" positions, which are defined by having substitutions that sample a broad range of intermediate outcomes. We generated 10 substitutions at each of six positions and separately measured effects on function and abundance. Results revealed an [~]45-fold range of change for abundance, demonstrating that it can make significant contributions to DMS outcomes. Moreover, the six tested positions showed diverse substitution sensitivities for function and abundance. Some positions influenced only one parameter. Others exhibited rheostatic effects on both parameters, which to our knowledge, provides the first example of such behavior. Since effects on function and abundance may arise through different biophysical bases, these results underscore the need for datasets that independently measure these parameters in order to build predictors with enhanced mechanistic insights. ABSTRACT for broader audienceChanging one amino acid in a protein can affect its function, its abundance, or both. Understanding these separate effects will help scientists predict how protein changes alter biology, which is important for understanding pathogen evolution, improving personalized medicine, and bioengineering. This work reports a study to experimentally separate these effects for the main protease of SARS-CoV-2 and suggests strategies for building better prediction models for emerging variants of this key viral protein.

biochemistry↗