Biology subjects

Hilbert, L.

Publications and source records attributed to Hilbert, L..

16 recordsLinked to original sources

bioRxiv2026

Bayesian optimisation and graph-based rheology enable sequence-dependent modelling of DNA materials

Bridging molecular and emergent properties is essential for designing soft matter. Synthetic DNA materials are attractive in this context because their sequence design space supports a wide range of material properties. Targeted design of DNA materials is hindered by scale differences and manual exploration of vast design spaces. We address this challenge with a computational workflow that links sequence-level design to rheological material properties. Concretely, we use machine learning to parametrise scalable, DNA-sequence-aware simulations, which we then evaluate using graph-based rheology. In our example, we study materials composed of self-interacting, multivalent DNA nanostars assembled from single strands. Structure and flexibility of nanostars are quantified with nucleotide-level oxDNA simulations, enabling Bayesian optimisation of a more coarse-grained bead-spring model. The bead-spring model allows efficient simulation of network formation between nanostars, governed by hybridisation free energies, which are computed with oxDNA and NUPACK. Nanostar valency and network connectivity are translated into rheological material properties with a graph-based method that we extend to include hydrodynamic interactions, yielding good agreement with experimental reference data. We generalise our findings by analysing theoretical graph representations of DNA materials and show how machine learning can optimise sequence affinities to produce desired rheological responses. Our work illustrates how machine learning can bridge scales and automate coarse-graining to facilitate targeted design of DNA materials through sequence-property relationships. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/728076v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@20b8c6org.highwire.dtl.DTLVardef@42f843org.highwire.dtl.DTLVardef@b90119org.highwire.dtl.DTLVardef@1f72d66_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2026

Diverse megamammals exploited by humans, chronology and palaeoecology at Taima-Taima, Late Pleistocene, South America

The arrival of humans to the Americas at the end of the Pleistocene has been one of the foundations of the hypothesis that hunter-gatherer groups had a direct role in the extinction of megafauna. However, empirical evidence of the exploitation of megafauna by humans and associated chronological context are still scarce, especially in South America. Using evidence of modifications on osteological remains, we provide a reassessment of the megafauna that was exploited at the classic Taima-Taima site (Venezuela), with an updated chronology and paleoenvironmental inferences. Our results show that, at least, five species of extinct megaherbivores were probably exploited at the site, expanding the previous records, restricted to the proboscidean Notiomastodon platensis and the giant armadillo Glyptotherium cf. G. cylindricum. The new data of the other exploited taxa include the terrestrial sloth Glossotherium, the macrauchenid cf. Xenorhinotherium bahiense and a toxodontid; both killing and slaughtering activities were likely practised at the site. Seven new enamel radiocarbon dates show an age of 15.3-17.8 cal kyr BP for the fossiliferous strata, although this is likely to be a minimum age given the materials propensity for modern carbon uptake. The study of phytoliths and starch grains from the dental calculus of N. platensis identified five plant taxa from the phytoliths: arboreal dicotyledons, Poaceae, Marantaceae, Asteraceae and Arecaceae. Ecometrics studies of dental diversity reveal how no other single site on the continent preserves such a diversity of grazing and browsing megaherbivores exploited by humans.

paleontology↗

bioRxiv2023

Transcriptional clusters follow a conserved condensation-dispersal sequence during stem cell differentiation

Spatiotemporal organization of transcription is essential for organism development. Most eukaryotic genes are transcribed by RNA polymerase II (Pol II). In stem cells, Pol II forms prominent clusters, which gradually disappear during differentiation, such that only smaller clusters remain. Here, we ask whether the formation and loss of large Pol II clusters is a stereotypical process explicable by changes in the Pol II transcriptional state during differentiation. We assess clusters by super-resolution microscopy in differentiating mouse embryonic stem cells, sperm precursor formation in fruit flies, and germ layer induction in zebrafish. In all cases, Pol II clusters first become larger and rounder, then unfold, and finally disperse into small clusters. These shape changes are accompanied by initial increase in recruited Pol II, subsequent transition into transcript elongation, and finally reduction of active enhancers. We reproduce these observations using a biophysical surface condensation model, where enhancers support Pol II cluster formation, and transcriptional activity unfolds clusters. Our work indicates that changes in enhancer marks and transcriptional activity during differentiation define a stereotyped trajectory through a generally applicable space of cluster shapes. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=189 HEIGHT=200 SRC="FIGDIR/small/547621v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1fb769borg.highwire.dtl.DTLVardef@27f6a0org.highwire.dtl.DTLVardef@1b0ab7corg.highwire.dtl.DTLVardef@1ca932d_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2023

Amphiphiles formed from synthetic DNA-nanomotifs mimic the dispersal of transcriptional clusters in the cell nucleus

Stem cells exhibit prominent clusters controlling the transcription of genes into RNA. These clusters form by a phase-separation mechanism, and their size and shape are controlled via an amphiphilic effect of transcribed genes. Here, we construct amphiphile-nanomotifs purely from DNA, and achieve similar size and shape control for phase-separated droplets formed from fully synthetic, self-interacting DNA-nanomotifs. Low amphiphile concentrations induce rounding of droplets, followed by splitting and, ultimately, full dispersal at higher concentrations. Super-resolution microscopy data obtained from zebrafish embryo stem cells reveal a comparable transition for transcriptional clusters with increasing transcription levels. Brownian dynamics and lattice simulations further confirm that addition of amphiphilic particles is sufficient to explain the observed changes in shape and size. Our work reproduces key aspects of the complex organization of transcription in biological cells using relatively simple, DNA sequence-programmable nanostructures, opening novel ways to control mesoscopic organization of synthetic nanomaterials. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/525851v2_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1a8cc4borg.highwire.dtl.DTLVardef@fc6651org.highwire.dtl.DTLVardef@a17c74org.highwire.dtl.DTLVardef@1f1cf14_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2022

Synchronization of oscillatory growth prepares fungal hyphae for fusion

Communication is crucial for organismic interactions, from bacteria, to fungi, to humans. Humans may use the visual sense to monitor the environment before starting acoustic interactions. In comparison, fungi lack a visual system, instead, hyphae use a cell-to-cell dialogue based on secreted signaling molecules to orchestrate cell fusion and establish hyphal networks. Hyphae alternate roles as signal-sender and signal-receiver, as can be visualized via the putative signaling protein, Soft, which is recruited in an oscillatory manner to the respective cytoplasmic membrane of interacting hyphae. Here, we show that signal oscillations already occur in single hyphae of Arthrobotrys flagrans in the absence of a potential fusion partner. They occurred in the same phase as growth oscillations. Once two fusion partners came into each others vicinity, their oscillation frequencies slowed down (entrainment phase) and transit into anti-phasic synchronization of the two cells oscillations with frequencies of 130 +/-20 sec. Single-cell oscillations, transient entrainment, and anti-phasic oscillations were reproduced by a mathematical model where nearby hyphae can absorb and secrete a limited molecular signaling component into a shared extra-cellular space. We show that intracellular Ca2+ concentrations oscillate in two approaching hyphae, and depletion of Ca2+ in the surrounding affected vesicle-driven extension of the hyphal tip, abolished single-cell molecular oscillations and the anti-phasic synchronization of two hyphae. Our results suggest that single hyphae engage in a "monologue" that may be used for exploration of the environment and can dynamically shift their extra-cellular signaling systems into a "dialogue" to initiate hyphal fusion. Significance statementCommunication at the cellular level often relies on chemical signal exchange. One prominent example is the fusion of fungal hyphae to form complex hyphal networks. As opposed to mating-type dependent cell fusion, cell-fusion events described here occur in genetically identical cells. Relying only on one chemical signaling channel raises the question of how communication is initiated. We discovered that individual hyphae constantly perform signal oscillations, comparable to a cellular "monologue" until they meet another hypha with which they then coordinate signal oscillations in a cell-to-cell dialogue. We also show that signal oscillations are mechanistically interlinked with calcium-dependent growth oscillations. Although the signaling molecule(s) has not been identified yet, it is highly likely linked to the hyphal growth machinery.

cell biology↗

bioRxiv2022

A DNA segregation module for synthetic cells

The bottom-up construction of an artificial cell requires the realization of synthetic cell division. Significant progress has been made towards reliable compartment division, yet mechanisms to segregate the DNA-encoded informational content are still in their infancy. Herein, droplets of DNA Y-motifs are formed by liquid-liquid phase separation (LLPS). Entropy-driven DNA droplet segregation is obtained by cleaving the linking component between two populations of DNA Y-motifs. In addition to enzymatic cleavage, photolabile sites are introduced for spatio-temporally controlled DNA segregation in bulk as well as in cell-sized water-in-oil droplets and giant unilamellar lipid vesicles (GUVs). Notably, the segregation process is slower in confinement than in bulk. The ionic strength of the solution and the nucleobase sequences are employed to regulate the segregation dynamics. The experimental results are corroborated in a lattice-based theoretical model which mimics the interactions between the DNA Y-motif populations. Altogether, engineered DNA droplets, reconstituted in GUVs, could represent a strategy towards an entropy-driven DNA segregation module within bottom-up assembled synthetic cells. Table of Contents O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY An entropy-driven DNA segregation module for bottom-up assembled synthetic cells is realized. It is based on DNA droplets that are engineered to segregate upon enzymatic or photocleavage inside giant unilamellar lipid vesicles (GUVs). The segregation kinetics is altered by the confinement, as confirmed by lattice-based numerical simulations. DNA segregation is further controlled by temperature, ionic strengths and nucleobase sequence. C_FIG_DISPLAY

biophysics↗

bioRxiv2022

Noise facilitates entrainment of a population of uncoupled limit cycle oscillators

Many biological oscillators share two properties: they are subject to stochastic fluctuations (noise) and they must reliably adjust their period to changing environmental conditions (entrainment). While noise seems to distort the ability of single oscillators to entrain, in populations of oscillators noise allows entrainment for a wider range of input amplitudes and periods. Here, we investigate, how this effect depends on the noise intensity and the number of oscillators in the population. We have found that, if a population consists of a sufficient number of oscillators, increasing noise intensity leads to faster entrainment after a phase change of the input signal (jet lag) and increases sensitivity to low-amplitude input signals. SIGNIFICANCELive is characterized by rhythms, such as daily changes in activity or the heartbeat. These rhythms are reflected in molecular oscillations generated at the level of individual cells. These oscillations are inherently noisy, but still cells reliably synchronize to external signals and provide reliable timing for other biological processes. Here, we show how noise can be beneficial to cell populations in terms of synchronization to external signals. Specifically, noise can increase the sensitivity to weak external signals and speed up adjustment to jet-lag-like perturbations.

systems biology↗

bioRxiv2022

Clustered transposon insertion via formation of chromatin loops

Transposons, which are DNA sequences that can move to new positions in the genome, make up a large fraction of eukaryotic genomes and occur in clusters. The insertion of transposons into the genome is hindered by compact folding of chromatin, supposedly preventing aberrant or even pathogenic insertion. Chromatin can, however, be decompacted as a consequence of transposon insertion, leading to increased accessibility and, in consequence, further insertions. While these observations suggest a positive feedback between chromatin unfolding and transposon insertion, how such a feedback might contribute to clustered transposon insertion remains poorly understood. In this study, we analyze polymer models of a self-interacting chromatin domain that unfolds as increasing numbers of transposons are inserted and block the self-interaction. On the one hand, we find that, if additional transposons are inserted adjacently to already inserted transposons, the unfolding of the chromatin domain changes from a sharp globule-coil transition to a more gradual extension of loops from a core that remains folded. On the other hand, we find that adjacent transposon insertion emerges either when transposases are excluded from densely packed chromatin, or when transposon insertion proceeds very quickly in relation to the thermal equilibration of polymer configurations. We thus derive from our model physical conditions for clustered transposon insertion and the resulting spatial compartmentalization of chromatin. An according role was recently suggested for LINE-1 and Alu repeats, which occur in clusters and drive the mesoscopic compartmentalization of the mammalian genome. Significance StatementA large part of the genome is composed of repetitive sequences, so-called transposons. Transposons are involved in important processes, such as early embryonic development or control over which genes are used by the cell. Transposons frequently occur in clusters, where many similar sequence motifs are grouped together. Recent studies suggest that the insertion of transposons can result in local unfolding of the genome, favoring insertion of yet more transposons. Our work simulates a simplified region of the genome and transposases, which are the molecules that insert transposons into the genome. Surprisingly, large and fast-acting transposases favor the formation of distinct loops that contain most of the inserted transposons, providing a potential explanation for the clustered insertion of transposons.

biophysics↗

bioRxiv2021

Deep-learning microscopy image reconstruction with quality control reveals second-scale rearrangements in RNA polymerase II clusters

Fluorescence microscopy, a central tool of biological research, is subject to inherent trade-offs in experiment design. For instance, image acquisition speed can only be increased in exchange for a lowered signal quality, or for an increased rate of photo-damage to the specimen. Computational denoising can recover some loss of signal, extending the trade-off margin for high-speed imaging. Recently proposed denoising on the basis of neural networks shows exceptional performance but raises concerns of errors typical of neural networks. Here, we present a work-flow that supports an empirically optimized reduction of exposure times, as well as per-image quality control to exclude images with reconstruction errors. We implement this work-flow on the basis of the denoising tool Noise2Void and assess the molecular state and three-dimensional shape of RNA Polymerase II (Pol II) clusters in live zebrafish embryos. Image acquisition speed could be tripled, achieving 2-second time resolution and 350-nanometer lateral image resolution. The obtained data reveal stereotyped events of approximately 10 seconds duration: initially, the molecular mark for initiated Pol II increases, then the mark for active Pol II increases, and finally Pol II clusters take on a stretched and unfolded shape. An independent analysis based on fixed sample images reproduces this sequence of events, and suggests that they are related to the transient association of genes with Pol II clusters. Our work-flow consists of procedures that can be implemented on commercial fluorescence microscopes without any hardware or software modification, and should therefore be transferable to many other applications.

systems biology↗

bioRxiv2021

A stochastic oscillator model simulates the entrainment of vertebrate cellular clocks by light

The circadian clock is a cellular mechanism that synchronizes various biological processes with respect to the time of the day. While much progress has been made characterizing the molecular mechanisms underlying this clock, it is less clear how external light cues influence the dynamics of the core clock mechanism and thereby entrain it with the light-dark cycle. Zebrafish-derived cell cultures possess clocks that are directly light-entrainable, thus providing an attractive laboratory model for circadian entrainment. Here, we have developed a stochastic oscillator model of the zebrafish circadian clock, which accounts for the core clock negative feedback loop, light input, and the proliferation of single-cell oscillator noise into population-level luminescence recordings. The model accurately predicts the entrainment dynamics observed in bioluminescent clock reporter assays upon exposure to a wide range of lighting conditions. Furthermore, we have applied the model to obtain refitted parameter sets for cell cultures exposed to a variety of pharmacological treatments and predict changes in single-cell oscillator parameters. Our work paves the way for model-based, large-scale screens for genetic or pharmacologically-induced modifications to the entrainment of circadian clock function. Author summaryThe circadian clock is a key, cell-autonomous timing mechanism that is encountered in most organisms. It is entrained by environmental lighting conditions and in turn temporally coordinates most aspects of physiology according to the time of day. Cell lines derived from zebrafish are attractive experimental models for studying how clocks are entrained by light since they possess clocks that respond directly to light stimuli. Here we describe a mathematical model for the behavior of the circadian clock in zebrafish cell lines during exposure to a range of lighting conditions. Using this model, we can determine how different pharmacological treatments may affect the entrainment dynamics of the clock and the degree of synchronization of individual cells circadian clocks in bioluminescent clock reporter assays. Our current model is mathematically simple and thus easy to apply and extend in future studies.

systems biology↗

bioRxiv2021

RNA polymerase II clusters form in line with liquid phase wetting of chromatin

It is essential for cells to control which genes are transcribed into RNA. In eukaryotes, two major control points are recruitment of RNA polymerase II (Pol II) into a paused state and subsequent pause release to begin transcript elongation. Pol II associates with macromolecular clusters during recruitment, but it remains unclear how Pol II recruitment and pause release might affect these clusters. Here, we show that clusters exhibit morphologies that are in line with wetting of chromatin by a liquid phase enriched in recruited Pol II. Applying instantaneous structured illumination microscopy and stimulated emission double depletion microscopy to pluripotent zebrafish embryos, we find recruited Pol II associated with large clusters, and elongating Pol II with dispersed clusters. A lattice kinetic Monte Carlo model representing recruited Pol II as a liquid phase reproduced the observed cluster morphologies. In this model, chromatin is a copolymer chain containing regions that attract or repel recruited Pol II, supporting droplet formation by wetting or droplet dispersal, respectively.

biophysics↗

bioRxiv2020

The domain-within-domain packing of euchromatin can be described as multiplicative cascades

The genome is packed into the cell nucleus in the form of chromatin. Biochemical approaches have revealed that chromatin is packed within domains, which group into larger domains, and so forth. Such domain-within-domain packing, also called hierarchical packing, is equally visible in super-resolution microscopy images of large-scale chromatin organization. While previous work has suggested that chromatin is partitioned into distinct domains via microphase separation, it is unclear how these domains organize into a hierarchical packing. A particular challenge is to find an image analysis approach that fully incorporates such hierarchical packing, so that hypothetical governing mechanisms of euchromatin packing can be compared against the results of such an analysis. Here, we obtain 3D STED super-resolution images from pluripotent zebrafish embryos labeled with improved DNA fluorescence stains, and demonstrate how the hierarchical packing of euchromatin in these images can be described as multiplicative cascades. Multiplicative cascades are an established theoretical concept to describe the placement of ever-smaller structures within bigger structures. Importantly, these cascades can generate artificial image data by applying a single rule again and again, and can be fully specified using only four parameters. Here, we show how the typical patterns of euchromatin organization are reflected in the values of these four parameters. In particular, we can pinpoint the values required to mimic a microphase-separated configuration of euchromatin. We suspect that the concept of multiplicative cascades can also be applied to images of other types of chromatin. In particular, cascade parameters could serve as test quantities to assess whether microphase separation or other theoretical models accurately reproduce the hierarchical packing of chromatin. SIGNIFICANCEDNA is stored inside the cell nucleus in the form of chromatin. Chromatin exhibits a striking three-dimensional organization, where small domains group into larger domains, which again group into larger domains, and so forth. While this hierarchical domain-within-domain organization is obvious from microscopy images, it is still not entirely clear how it is established, or how it should be properly characterized. Here, we demonstrate that multiplicative cascades - a concept from theoretical physics used to characterize for example cloud patterns, galaxy locations, or soil patterns - are also ideally suited to describe the domain-within-domain organization of chromatin. This description is rather simple, using only four numbers, and can thus facilitate testing of competing theories for the domain-within-domain organization of chromatin.

biophysics↗

bioRxiv2019

Quantitative measurements of chromatin modification dynamics during zygotic genome activation

Histone posttranslational modifications (PTMs) are key gene expression regulators, but their rapid dynamics during development remain difficult to capture. We describe an approach that images fluorescent antibody fragments to quantify PTM enrichment and active transcription at defined loci during zygotic genome activation in living zebrafish embryos. The technique reveals a drastic increase in histone H3 Lys27 acetylation (H3K27ac) before genome activation both at a specific locus and globally.

cell biology↗

bioRxiv2019

Spreading of molecular mechanical perturbations on linear filaments

Global changes in the state of spatially distributed systems can often be traced back to events resulting from local interactions. Whether the results of local interactions grow into global changes, however, depends (i) on the system geometry and (ii) the spatial spreading of the outcomes of local interactions. Here, we investigate how different spreading behaviors of local events determine their global impact in one-dimensional systems of different size. In particular, we combine in vitro experiments where groups of myosin motors propel actin filaments, single-molecule resolution simulations of these in vitro experiments, and an abstracted spin chain model. All three approaches lead to the same two conclusions. First, local events that become long-term stable only after they have spread to full system size have more impact in smaller systems. Second, local events that are relatively stable upon initial occurrence and then spread to full system size have more impact in larger systems. Our work provides highly specific predictions for future experiments that resolve actin-myosin-crosslinker interactions along actin filaments. Also, the conclusions from our work should generally apply to local-to-global spreading in finite, one-dimensional geometries.\n\nSignificance StatementWe address the fundamental question of how results of local interactions spread in one-dimensional systems of different size. To this end, we reconstituted the molecular contractile machinery of muscle, which is organized around linear actin filaments of different length and drives their forward sliding. In addition, we use detailed simulations that follow the mechanically interacting molecules individually. Lastly, we used a more abstract theoretical physics model, which transfers our results to all systems with one-dimensional geometry and local interactions. All three approaches give the same results: local interactions that persist only once they cover the whole system affect smaller systems more strongly; local interactions that are relatively stable even before spreading affect larger systems more strongly.

biophysics↗

bioRxiv2017

Transcription establishes microenvironments that organize euchromatin

Chromatin is organized into heterochromatin, which is transcriptionally inactive, and euchromatin, which can switch between transcriptionally active and inactive states. This switch in euchromatin activity is accompanied by changes in its spatial distribution. How euchromatin rearrangements are established is unknown. Here we use super-resolution and live-cell microscopy to show that transcriptionally inactive euchromatin moves away from transcriptionally active euchromatin. This movement is driven by the formation of RNA-enriched microenvironments that exclude inactive euchromatin. Using theory, we show that the segregation into RNA-enriched microenvironments and euchromatin domains can be considered an active microemulsion. The tethering of transcripts to chromatin via RNA polymerase II forms effective amphiphiles that intersperse the two segregated phases. Taken together with previous experiments, our data suggest that chromatin is organized in the following way: heterochromatin segregates from euchromatin by phase separation, while transcription organizes euchromatin similar to an active microemulsion.

cell biology↗

bioRxiv2017

Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos

SUMMARYUpon fertilization, the genome of animal embryos remains transcriptionally inactive until the maternal-to-zygotic transition. At this time, the embryo takes control of its development and transcription begins. How the onset of zygotic transcription is regulated remains unclear. Here, we show that a dynamic competition for DNA binding between nucleosome-forming histones and transcription factors regulates zebrafish genome activation. Taking a quantitative approach, we found that the concentration of non-DNA bound core histones sets the time for the onset of transcription. The reduction in nuclear histone concentration that coincides with genome activation does not affect nucleosome density on DNA, but allows transcription factors to compete successfully for DNA binding. In agreement with this, transcription factor binding is sensitive to histone levels and the concentration of transcription factors also affects the time of transcription. Our results demonstrate that the relative levels of histones and transcription factors regulate the onset of transcription in the embryo.

developmental biology↗