Biology subjects

Lange, M.

Publications and source records attributed to Lange, M..

At least 19 recordsLinked to original sources

bioRxiv2026

A Standardized Methodology for FAIRness Assessment and Multi-Dimensional Scoring in Agrosystem Research Data Infrastructures

The NFDI-consortium FAIRagro has established a systematic framework for evaluating the FAIRness of Research Data Infrastructures (RDI) within the German agrosystem research landscape. While FAIR principles are widely accepted, their practical implementation by RDIs remains challenging. By operationalizing the FAIR principles into a reproducible multi-dimensional scoring methodology, this initiative addresses the critical need for a transparent and citable benchmark of RDIs that moves beyond simple compliance. This paper details the underlying assessment criteria, comprising 20 aggregated core metrics, the iterative community-driven validation process, and the integration of these metrics into the FAIRagro Search Hub. This framework evaluates RDIs, like repositories or databases, instead of sampling hosted data sets, across the four distinct categories of FAIR independently, yielding granular, pillar-specific ratings. Unlike aggregate scoring models, which can inadvertently mask technical deficiencies by averaging performance across categories, this multi-dimensional approach ensures that a repositorys distinct strengths and bottlenecks remain fully visible. Our findings demonstrate that standardized scoring not only clarifies data accessibility for users but also highlights specific operational gaps, allowing repository providers to identify precisely where the service implementation can be enhanced. By establishing this data-driven service in the agronomy domain, we provide a scalable template for the broader NFDI and EOSC ecosystems to foster a culture of excellence in research data stewardship.

bioinformatics↗

bioRxiv2026

MYC pathway reprogramming through a TIP60 coactivator switch in neuroendocrine lineage transition in prostate cancer

Prostate adenocarcinomas (PRAD) can acquire resistance to androgen receptor signaling inhibitors through lineage transition to a cell state known as neuroendocrine prostate cancer (NEPC). Using a panel of isogenic PRAD and NEPC mouse tumoroids, we show that NEPC cells acquire new transcription factor (TF) dependencies that function in a previously undefined network. Through selective perturbation of each TF, we identify ASCL1 as a key regulator of NE lineage fate whereas MYCL functions downstream to drive NEPC growth/survival by recruitment of the TIP60/KAT5 acetyltransferase. Interestingly, while dependencies on specific TF family paralogs can vary across NEPC models, all show markedly enhanced dependency on TIP60. Moreover, the H2A.Z-acetyltransferase activity of the TIP60 complex (TIP60-C) is required for NEPC as well as the acetyl-reader BRD8, which is newly incorporated as a TIP60-C subunit with the NEPC transition. Targeted degradation studies in isogenic tumoroids reveal increased dependence on MYCL in NEPC relative to its paralog MYC in PRAD. In addition to a paralog switch (MYC to MYCL), the MYC pathway-addicted NE state is accompanied by a chaperone switch (from TIP60-C to SRCAP) for H2A.Z histone exchange and a coactivator switch (to TIP60) for MYC target gene expression. The NE-specific coupling of MYCL with TIP60 reveals a previously unappreciated opportunity to target MYC-driven NE diseases through pharmacological inhibition of TIP60.

cancer biology↗

bioRxiv2025

Extracellular matrix regulates lineage plasticity in prostate cancer through YAP/TEAD

Treatment-related neuroendocrine prostate cancer (NEPC) is an increasingly frequent mechanism of resistance to androgen receptor pathway inhibitor (ARPI) therapy in prostate adenocarcinoma (PRAD). This lineage transition is dependent on upregulation of the NE-specifying transcription factor ASCL1, typically in a genetic background of RB1 and TP53 loss. Here we identify extracellular matrix-integrin-YAP1/TEAD signaling as a critical brake on NEPC lineage transition. Deletion of Itgb1, the shared B1 subunit required for collagen and laminin-mediated integrin activation, is sufficient to induce ASCL1 and NE lineage gene expression, by activating LATS1/2 kinases with subsequent inactivation of YAP1/TEAD signaling. Conversely, restoration of YAP1/TEAD signaling by pharmacological LATS1/2 inhibition, or by expression of constitutively active YAP1/TAZ mutants, prevents or reverts NEPC lineage transition. NOTCH and AR cooperate with YAP/TEAD to repress ASCL1, such that combined inhibition leads to complete reprograming of PRAD into NEPC in vitro, providing a dynamic platform to dissect the molecular events responsible for lineage transition over time. We find that lineage transition is accompanied by a redistribution of FOXA1 and TEAD cistromes from PRAD to NEPC-specific enhancers and requires the pioneering activity of FOXA1. Thus, extracellular matrix/integrin signaling in the PRAD tumor microenvironment restrains NE lineage plasticity, highlighting a potential path for pharmacological inhibitors in modulating treatment-induced lineage change.

cancer biology↗

bioRxiv2025

Microbial and organic matter composition jointly drive phosphorus cycling genes and phosphorus availability in Amazonian soils

Soil phosphorus (P) is a limiting factor for vegetation growth in the Amazon rainforest, where plants depend on microorganisms for organic matter cycling and nutrient uptake. However, forest-to-agriculture conversion changes plant-microbe-soil interactions, affecting P cycling, which may additionally changed by land-use intensity. This study examined the 30-year effects of converting a primary forest into two contrasting systems: a low-intensity agroforest and a high-intensity citrus plantation. We investigated how microbial and water-extractable organic matter (WEOM) composition interacted with soil physicochemical attributes and P fractions (labile, moderately labile, non-labile, and residual). Agroforest soils retained physicochemical and enzymatic attributes similar to the primary forest, while soils of the citrus plantation showed increased P in all fractions due to fertilization and reduced soil organic matter content, mainly in deeper layers. Microbial and WEOM composition patterns reflected land-use, with agroforest representing an intermediate state between primary forest and citrus plantation. Proteobacteria and nutrient-rich WEOM were more abundant in the agroforest, whereas Ascomycota and nutrient-poor WEOM predominated the citrus plantation. Genes related to "P acquisition" were more abundant in agroforest soils, while genes related to "P-compound synthesis" were more abundant in citrus plantation. Labile P was negatively correlated with genes related to microbial metabolism, suggesting that reduced P availability may induce a boost in microbial activity for internal P-cycling. These findings demonstrate that forest-to-agriculture conversion strongly affects microbial functions, with responses aligning with land-use intensity and WEOM resource availability. Nonetheless, microbes adapt by shifting strategies: prioritizing mineralization and solubilization or favoring biosynthesis depending on P availability.

microbiology↗

bioRxiv2025

Antitachycardia Pacing is More Effective When Delivered to the Left Bundle Branch Area Compared to the Right Ventricle in a Pre-clinical Model of Ischemic Ventricular Tachycardia

BackgroundAnti-tachycardia pacing (ATP) delivered from implantable cardioverter defibrillators (ICDs) provides critically timed pacing pulses to terminate ventricular tachycardia (VT). Physiological pacing through left bundle branch area (LBBA) pacing has emerged as a clinically relevant alternative to induce synchronous activation of the ventricles. The main objective of this study was to compare the efficacy and safety of ATP delivered to an LBBA lead and a conventional RV lead. MethodsUsing a preclinical animal model (n=7), pacing leads were implanted in the RV apex and LBBA and connected to ICDs. The left anterior descending artery was occluded for two hours to cause an ischemia-reperfusion injury (IRI). Four days following IRI, VT episodes were induced using programmed electrical stimulation (PES), and burst ATP therapy was delivered to the RV or LBBA leads for each VT episode. ResultsVT was induced 80 times, with a mean VT cycle length (VT CL) of 180.0{+/-}30.0 ms. ATP delivered to the LBBA terminated VT more often than RV ATP (70.2% vs 47.3%, P = 0.04), and there was no significant difference in negative outcomes of VT acceleration or VF induction. Activation sequences from the basket catheter were determined for the pre-therapy VT and captured ATP beats, and correlation coefficients were computed to the activation sequences during ATP delivery. The number of ATP pulses required for the activation sequences to correlate with the captured ATP pattern rather than the pre-therapy VT pattern was lower for LBBA ATP compared to RV ATP (4.1 vs. 5.1 beats, P = 0.04). Successful LBBA ATP demonstrated earlier and more frequent Purkinje activations preceding myocardial activation than successful RV ATP. ConclusionImproved performance of LBBA ATP compared to RV ATP provides further incentive for the wide use of LBBA leads in patients who need cardiac electrotherapy.

bioengineering↗

bioRxiv2025

Accounting for spatial interactions in the upscaling of ecosystem services

O_LIMaps of ecosystem service (ES) supply are frequently used to guide spatial planning, policy making, and ecosystem management. However, these are typically based upon coarse land-cover proxies. This approach lacks a strong mechanistic basis, and neglects spatial biodiversity dynamics and interactions among landscape properties that can modify ES provision. C_LIO_LIWe present an analytical framework for ES upscaling that incorporates spatial interactions between landscape properties to determine ES supply. The resulting models can be viewed as a spatially informed ES production function. The approach comprises seven steps that include several elements absent from most existing approaches, notably a procedure for identifying geodata variables that represent the true mechanistic drivers, the inclusion of spatial interactions in the upscaling model, and modification following expert feedback on the selected model. C_LIO_LIWe demonstrate the approach using two example ES from German grasslands: biodiversity conservation and water supply. We show that the inclusion of spatial interactions in the upscaling model improved model predictions from 15% to 33% depending on the ES evaluated. In addition, inclusion of spatial interactions led to reduced error associated with the upscaled estimates. C_LIO_LIBy overcoming several shortcomings of existing, upscaling approaches we generate resulting maps of ES supply that can more reliably inform spatial planning Further, the underlying models allow for simulation of changes in the drivers of ES supply and estimation of respective outcomes. These advantages have the potential to better link detailed local-scale ecological understanding and land management with large-scale ES supply mapping, and thus better inform decision making and spatial planning. C_LI

ecology↗

bioRxiv2025

FSP1-mediated lipid droplet quality control prevents neutral lipid peroxidation and ferroptosis

Lipid droplets (LDs) are organelles that store and supply lipids based on cellular needs. While mechanisms preventing oxidative damage to membrane phospholipids are established, the vulnerability of LD neutral lipids to peroxidation and protective mechanisms are unknown. Here, we identify LD-localized Ferroptosis Suppressor Protein 1 (FSP1) as a critical regulator that prevents neutral lipid peroxidation by recycling coenzyme Q10 (CoQ10) to its lipophilic antioxidant form. Lipidomics reveal that FSP1 loss leads to the accumulation of oxidized triacylglycerols and cholesteryl esters, and biochemical reconstitution of FSP1 with CoQ10 and NADH suppresses triacylglycerol peroxidation in vitro. Notably, polyunsaturated fatty acid (PUFA)-rich triacylglycerols enhance cancer cell sensitivity to FSP1 loss and inducing PUFA-rich LDs triggers triacylglycerol peroxidation and LD-initiated ferroptosis when FSP1 activity is impaired. These findings uncover the first LD lipid quality control pathway, wherein LD-localized FSP1 maintains neutral lipid integrity to prevent the buildup of oxidized lipids and induction of ferroptosis.

cell biology↗

bioRxiv2024

Leucine Aminopeptidase LyLAP enables lysosomal degradation of membrane proteins

Proteolysis of hydrophobic helices is required for complete breakdown of every transmembrane protein trafficked to the lysosome and sustains high rates of endocytosis. However, the lysosomal mechanisms for degrading hydrophobic domains remain unknown. Combining lysosomal proteomics with functional genomic data mining, we identify Lysosomal Leucine Aminopeptidase (LyLAP; formerly Phospholipase B Domain-Containing 1) as the hydrolase most tightly associated with elevated endocytic activity. Untargeted metabolomics and biochemical reconstitution demonstrate that LyLAP is not a phospholipase, but a processive monoaminopeptidase with strong preference for N-terminal leucine - an activity necessary and sufficient for breakdown of hydrophobic transmembrane domains. LyLAP is upregulated in pancreatic ductal adenocarcinoma (PDA), which relies on macropinocytosis for nutrient uptake, and its ablation led to buildup of undigested hydrophobic peptides, which compromised lysosomal membrane integrity and inhibited PDA cell growth. Thus, LyLAP enables lysosomal degradation of membrane proteins, and may represent a vulnerability in highly endocytic cancer cells. One sentence summaryLyLAP degrades transmembrane proteins to sustain high endocytosis and lysosomal membrane stability in pancreatic cancer.

biochemistry↗

bioRxiv2024

RegVelo: gene-regulatory-informed dynamics of single cells

RNA velocity has emerged as a popular approach for modeling cellular change along the phenotypic landscape but routinely omits regulatory interactions between genes. Conversely, methods that infer gene regulatory networks (GRNs) do not consider the dynamically changing nature of biological systems. To integrate these two currently disconnected fields, we present RegVelo, an end-to-end dynamic, interpretable, and actionable deep learning model that learns a joint model of splicing kinetics and gene regulatory relationships and allows us to perform in silico perturbation predictions. When applied to datasets of the cell cycle, human hematopoiesis, and murine pancreatic endocrinogenesis, RegVelo demonstrates superior predictive power for interactions and perturbation simulations, for example, compared to methods that focus solely on dynamics or GRN inference. To leverage RegVelos full potential, we studied the dynamics of zebrafish neural crest development and underlying regulatory mechanisms using our Smart-seq3 dataset and shared gene expression and chromatin accessibility measurements. Using RegVelos in silico perturbation predictions, validated by CRISPR/Cas9-mediated knockout and single-cell Perturb-seq, we establish transcription factor tfec as an early driver and elf1 as a novel regulator of pigment cell fate and propose a gene-regulatory circuit involving tfec and elf1 interactions via the toggle-switch model.

developmental biology↗

bioRxiv2024

Endothelial Rho kinase controls blood vessel integrity and angiogenesis

BackgroundThe Rho kinases 1 and 2 (ROCK1/2) are serine-threonine specific protein kinases that control actin cytoskeleton dynamics. They are expressed in all cells throughout the body, including cardiomyocytes, smooth muscle cells and endothelial cells, and intimately involved in cardiovascular health and disease. Pharmacological ROCK inhibition is beneficial in mouse models of hypertension, atherosclerosis, and neointimal thickening that display overactivated ROCK. However, the consequences of endothelial ROCK signaling deficiency in vivo remain unknown. To address this issue, we analyzed endothelial cell (EC) specific ROCK1 and 2 deletions. MethodsWe generated Cdh5-CreERT2 driven, tamoxifen inducible loss of function alleles of ROCK1 and ROCK2 and analyzed mouse survival and vascular defects through cellular, biochemical, and molecular biology approaches. ResultsWe observed that postnatal or adult loss of endothelial ROCK1 and 2 was lethal within a week. Mice succumbed to multi-organ hemorrhage that occurred because of loss of vascular integrity. ECs displayed deficient cytoskeletal actin polymerization that prevented focal adhesion formation and disrupted junctional integrity. Retinal sprouting angiogenesis was also perturbed, as sprouting vessels exhibited lack of polymerized actin and defective lumen formation. In a three-dimensional endothelial sprouting assay, combined knockdown of ROCK1/2 or knockdown or ROCK2 but not ROCK1 led to reduced sprouting, lumenization and cell polarization defects caused by defective actin and altered VE-cadherin dynamics. The isoform specific role of endothelial ROCK2 correlated with ROCK2 substrate specificity for FAK and LIMK. By analyzing single and three allele mutants we show that one intact allele of ROCK2 is sufficient to maintain vascular integrity in vivo. ConclusionEndothelial ROCK1 and 2 maintain junctional integrity and ensure proper angiogenesis and lumen formation. The presence of one allele of ROCK2 is sufficient to maintain vascular growth and integrity. These data indicate the need of careful consideration for the use of ROCK inhibitors in disease settings.

developmental biology↗

bioRxiv2024

Zebrahub-Multiome: Uncovering Gene Regulatory Network Dynamics During Zebrafish Embryogenesis

During embryonic development, gene regulatory networks (GRNs) drive molecular differentiation of cell types. However, the temporal dynamics of these networks remain poorly understood. Here, we present Zebrahub-Multiome, a single-cell multiomic atlas that captures chromatin accessibility and gene expression from 94,562 cells across six stages of zebrafish embryogenesis (10-24 hours post-fertilization), capturing key developmental stages from the end of gastrulation to the onset of organogenesis. By measuring regulatory element activity alongside transcriptional output from the same cells, we identify 640,000 cis-regulatory elements organized into 402 hierarchically structured modules corresponding to specific developmental pathways. Early embryonic stages employ broadly shared regulatory programs that progressively fragment into lineage-specific modules. Timeresolved gene regulatory network inference reveals that transcription factors undergo functional transitions - from multilineage regulators to specialized, lineage-committed factors. These quantitative measurements reveal the regulatory network rewiring that drives cell fate specification. Our interactive web portal (zebrahub.org/epigenomics) enables exploration of gene dynamics, regulatory networks, and perturbation predictions, providing a quantitative framework for understanding vertebrate developmental regulation.

developmental biology↗

bioRxiv2024

Ultrack: pushing the limits of cell tracking across biological scales

Tracking live cells across 2D, 3D, and multi-channel time-lapse recordings is crucial for understanding tissue-scale biological processes. Despite advancements in imaging technology, achieving accurate cell tracking remains challenging, particularly in complex and crowded tissues where cell segmentation is often ambiguous. We present Ultrack, a versatile and scalable cell-tracking method that tackles this challenge by considering candidate segmentations derived from multiple algorithms and parameter sets. Ultrack employs temporal consistency to select optimal segments, ensuring robust performance even under segmentation uncertainty. We validate our method on diverse datasets, including terabyte-scale developmental time-lapses of zebrafish, fruit fly, and nematode embryos, as well as multi-color and label-free cellular imaging. We show that Ultrack achieves state-of-the-art performance on the Cell Tracking Challenge and demonstrates superior accuracy in tracking densely packed embryonic cells over extended periods. Moreover, we propose an approach to tracking validation via dual-channel sparse labeling that enables high-fidelity ground truth generation, pushing the boundaries of long-term cell tracking assessment. Our method is freely available as a Python package with Fiji and napari plugins and can be deployed in a high-performance computing environment, facilitating widespread adoption by the research community.

developmental biology↗

bioRxiv2024

Challenges and Progress in RNA Velocity: Comparative Analysis Across Multiple Biological Contexts

Single-cell RNA sequencing is revolutionizing our understanding of cell state dynamics, allowing researchers to observe the progression of individual cells transcriptomic profiles over time. Among the computational techniques used to predict future cellular states, RNA velocity has emerged as a predominant tool for modeling transcriptional dynamics. RNA velocity leverages the mRNA maturation process to generate velocity vectors that predict the likely future state of a cell, offering insights into cellular differentiation, aging, and disease progression. Although this technique has shown promise across biological fields, the performance accuracy varies depending on the RNA velocity method and dataset. We established a comparative pipeline and analyzed the performance of five RNA velocity methods on three datasets based on local consistency, method agreement, identification of driver genes, and robustness to sequencing depth. This benchmark provides a resource for scientists to understand the strengths and limitations of different RNA velocity methods.

bioinformatics↗

bioRxiv2024

CLCC1 promotes hepatic neutral lipid flux and nuclear pore complex assembly

Imbalances in lipid storage and secretion lead to the accumulation of hepatocyte lipid droplets (LDs) (i.e., hepatic steatosis). Our understanding of the mechanisms that govern the channeling of hepatocyte neutral lipids towards cytosolic LDs or secreted lipoproteins remains incomplete. Here, we performed a series of CRISPR-Cas9 screens under different metabolic states to uncover mechanisms of hepatic neutral lipid flux. Clustering of chemical-genetic interactions identified CLIC-like chloride channel 1 (CLCC1) as a critical regulator of neutral lipid storage and secretion. Loss of CLCC1 resulted in the buildup of large LDs in hepatoma cells and knockout in mice caused liver steatosis. Remarkably, the LDs are in the lumen of the ER and exhibit properties of lipoproteins, indicating a profound shift in neutral lipid flux. Finally, remote homology searches identified a domain in CLCC1 that is homologous to yeast Brl1p and Brr6p, factors that promote the fusion of the inner and outer nuclear envelopes during nuclear pore complex assembly. Loss of CLCC1 lead to extensive nuclear membrane herniations, consistent with impaired nuclear pore complex assembly. Thus, we identify CLCC1 as the human Brl1p/Brr6p homolog and propose that CLCC1-mediated membrane remodeling promotes hepatic neutral lipid flux and nuclear pore complex assembly.

cell biology↗

bioRxiv2024

Plant species richness and the root economics space drive soil fungal communities

Trait-based approaches have been increasingly used to relate plants to soil microbial communities. However, the plant organs mediating this plant-microbe interaction - the roots - have been largely overlooked. The recent discovery of the root economics space offers a predictive framework for the structure of soil microbial communities, and specifically soil-borne fungal communities. Applying this novel approach, our study in a grassland plant diversity experiment reveals distinct root trait strategies at the level of the plant community. In addition to significant effects of plant species richness, we show that both axes of the root economics space - the collaboration and conservation gradient - are strong drivers of the composition of the different guilds of soil fungi, including saprotrophic, plant pathogenic, and mycorrhizal fungi. Our results illustrate that the root economics space and plant species richness jointly determine the effects of plants on fungal communities and their potential role in plant health and ecosystem functioning.

ecology↗

bioRxiv2024

Delay of innate immune responses following influenza B virus infection affects the development of robust antibody response in ferrets

Due to its natural influenza susceptibility, clinical signs, transmission, and similar sialic acid residue distribution, the ferret is the primary animal model for human influenza research. Antibodies generated following infection of ferrets with human influenza viruses are used in surveillance to detect antigenic drift and cross-reactivity with vaccine viruses and circulating strains. Inoculation of ferrets, with over 1500 human clinical influenza isolates (1998-2019) resulted in lower antibody responses (HI<1:160) to 86% (387/448) influenza B viruses (IBV) compared to 2.7% (30/1094) influenza A viruses (IAV). In this directed analysis, we show that the immune responses in ferrets inoculated with IBV (B/Victoria or B/Yamagata lineage) were delayed and reduced compared to IAV (A/H1pdm09 or A/H3N2). Analysis of innate gene expression in the ferret upper respiratory tract and peripheral blood indicated that IAV generated a strong inflammatory response, including an early activation of the interferon (IFN) response; whereas IBV elicited a delayed and reduced response. Serum levels of cytokines, chemokines, and IFNs were all much higher following IAV-infection than IBV-infection in ferrets. Pro-Inflammatory (MCP-1, MIP-1B, TNFA), IFN (IFNB, IFNG), TH1/TH2 (IP-10, IL-2), and T-effector (IL-12p40) proteins were significantly higher in sera of IAV-infected than IBV-infected ferrets over twenty-eight days following challenge. Serum levels of Type-I/II/III IFNs were detected following IAV-infection throughout the 28-day period and Type-III IFN was only detected by day 28 for IBV. An early increase in IFN-lambda levels corresponded to gene expression following IAV-infection. Reduced innate immune responses detected following IBV-infection reflected the subsequent delayed and reduced serum antibodies. Differences in serum antibody responses by IBV were not observed in antibody secreting cells in the spleen or peripheral blood. These findings help in understanding the antibody responses in humans following IBV vaccination or infection and consideration of potential addition of innate immunomodulators to overcome low responses. AUTHOR SUMMARYThe ferret is the primary animal model for human influenza research. Using a ferret model, we studied the differences in both innate and adaptive immune responses following infection with influenza A and B viruses. Antibodies generated following infection of ferrets is used for surveillance assays to detect antigenic drift and cross-reactivity with vaccine viruses and circulating influenza strains. Influenza A virus (IAV) infection of ferrets to generate these reagents resulted in a strong antibody response, but Influenza B virus (IBV) infection generated weak antibody responses. In this study using influenza-infected ferrets, we found that IAV resulted in an early activation of the interferon and pro-inflammatory response, whereas IBV showed a delay and reduction in these responses. Serum levels of interferons and other cytokines or chemokines were much higher in ferrets following IAV infection. These reduced innate responses were reflected the subsequent delayed and reduced antibody responses to IBV in the sera. These findings may help in understanding low antibody responses in humans following influenza B vaccination and infection and may warrant the use of innate immunomodulators to overcome these weak responses.

microbiology↗

bioRxiv2024

Single-cell transcriptional dynamics in a living vertebrate

The ability to quantify transcriptional dynamics in individual cells via live imaging has revolutionized our understanding of gene regulation. However, such measurements are lacking in the context of vertebrate embryos. We addressed this deficit by applying MS2-MCP mRNA labeling to the quantification of transcription in zebrafish, a model vertebrate. We developed a platform of transgenic organisms, light sheet fluorescence microscopy, and optimized image analysis that enables visualization and quantification of MS2 reporters. With these tools, we obtained single-cell, real-time measurements of transcriptional dynamics of the segmentation clock. Our measurements challenge the traditional view of smooth clock oscillations and instead suggest a model of discrete transcriptional bursts that are organized in space and time. Together, these results highlight how measuring single-cell transcriptional activity in the context of vertebrate organisms can reveal unexpected features of gene regulation and how this data can fuel the dialogue between theory and experiment.

developmental biology↗

bioRxiv2023

Differentiation SELEX approach identifies RNA aptamers with different specificities for HIV-1 capsid assembly forms

The HIV-1 capsid protein (CA) assumes distinct assembly forms during replication, each presenting unique, solvent-accessible surfaces that facilitate multifaceted functions and host factor interactions. However, contributions of individual CA assemblies remain unclear, as the evaluation of CA in cells presents several technical challenges. To address this need, we sought to identify CA assembly form-specific aptamers. Aptamer subsets with different specificities emerged from within a highly converged, pre-enriched aptamer library previously selected to bind the CA hexamer lattice. Subsets were either highly specific for CA lattice or bound both CA lattice and CA hexamer. We further evaluated four representatives to reveal aptamer structural features required for binding, highlighting interesting features and challenges in aptamer structure determination. Importantly, our aptamers bind biologically relevant forms of CA and we demonstrate aptamer-mediated affinity purification of CA from cell lysates without virus or host modification. Thus, we have identified CA assembly form-specific aptamers that represent exciting new tools for the study of CA.

molecular biology↗