Biology subjects

Glaser, J.

Publications and source records attributed to Glaser, J..

11 recordsLinked to original sources

bioRxiv2025

Hybrid Solid-Liquid Optics Enable Scalable, High-Resolution, Multi-Immersion Light-Sheet Microscopy

Modern biology increasingly depends on data-driven discovery, requiring scalable and affordable high-content 3D imaging across molecular to organ scales. Although tissue clearing, expansion microscopy, and light-sheet microscopy (LSM) enable subcellular-resolution imaging of intact specimens, their scalability remains fundamentally limited by detection optics: immersion objectives deliver high-resolution, aberration-free imaging but with short working distances, high cost, and multi-immersion incompatibility, while air objectives offer long working distances and portability at lower cost but suffer from severe aberrations and reduced photon collection when imaging immersed samples. We introduce the Hybrid Solid-Liquid Immersion Lens (HySIL) framework, which pairs an off-the-shelf solid optical component with a refractive index-matched liquid to precompensate aberrations and enhance resolution. Building on HySIL, we developed SCOPE and Super-SCOPE, objective-agnostic imaging devices achieving submicron lateral resolution (<0.75 {micro}m) across centimeter-scale samples using inexpensive air objectives with >30 mm working distances. Integration with a low-cost LSM platform yielded a compact, scalable system demonstrated for multi-immersion, multi-color, subcellular-resolution mapping of cleared or expanded mouse, salamander, and cavefish brains, human iPSC-derived organoids, and 3D histopathology of breast tissue. HySIL and SCOPE establish an accessible foundation for scalable, high-resolution volumetric imaging, advancing data-driven biological discovery.

bioengineering↗

bioRxiv2025

A brain-wide, trial- and time-dependent deterministic drive for self-initiated action decisions

Deciding when to act in the absence of external cues is essential for exploration, learning, and survival. Yet the neural mechanisms underlying such decisions remain controversial, with current views favoring either deterministic or stochastic underpinnings. We simultaneously recorded from large neuronal populations in cortical, thalamic, pallidal, and cerebellar regions as mice self-initiated voluntary actions. Action onset timing was predictable from firing patterns up to several seconds in advance with predictions correlated across regions, demonstrating a prominent deterministic drive that spans regions. Computational modeling indicated that this drive has an initial value and rate that vary trial-by-trial, and the rate increases within trials. Although the deterministic drive is sufficient to trigger action, noise within trials also contributes to setting action timing. Therefore, discrete (across-trial) and continuous (within-trial) sources of variability synergize to time self-initiated actions. This synergy is observed brain-wide, suggesting a distributed decision-making process rather than a hierarchical, modular one.

neuroscience↗

bioRxiv2024

Neural dynamics hierarchy in motor cortex and striatum across naturalistic behaviors

Mammals perform a wide range of movements actuated by diverse patterns of muscle activity. Primary motor cortex (M1) and striatum are implicated in controlling these movements, but how their activity dynamics are organized to accommodate such diversity is poorly understood. We developed a paradigm that enabled us to investigate neural dynamics across diverse motor behaviors in mice. In contrast to existing views, we found neither behavior-specific nor behavior-invariant organization in single-neuron activity, population-level covariation, and muscle activity correlation. Instead, the similarity of activity dynamics between behaviors varied differentially across behavior pairs, forming a hierarchical organization. The same hierarchical organization was shared between M1 and striatum, despite stronger muscle activity correlation in M1 and greater behavior specificity in striatum. Network modeling indicated that striatal activity is sufficient to drive hierarchical dynamics in muscle pattern-generating circuits. These hierarchical dynamics may reflect a tradeoff between behavioral specialization and generalization in motor system function.

neuroscience↗

bioRxiv2024

Comparative single-cell analyses reveal evolutionary repurposing of a conserved gene program in bat wing development

Bats are the only mammals capable of self-powered flight, an evolutionary innovation based on the transformation of forelimbs into wings. The bat wing is characterized by an extreme elongation of the second to fifth digits and a wing membrane called chiropatagium connecting them. Here we investigated the developmental and cellular origin of this structure by comparing bat and mouse limbs using omics tools and single-cell analyses. Despite the substantial morphological differences between the species, we observed an overall conservation of cell populations and gene expression patterns including interdigital apoptosis. Single-cell analyses of micro-dissected embryonic chiropatagium identified a specific fibroblast population, independent of apoptosis-associated interdigital cells, as the origin of this tissue. These distal cells express a conserved gene program including the transcription factors MEIS2 and TBX3, which are commonly known to specify and pattern the early proximal limb. Transgenic ectopic expression of MEIS2 and TBX3 in mouse distal limb cells resulted in the activation of genes expressed during wing development and phenotypic changes related to wing morphology, such as the fusion of digits. Our results elucidate fundamental molecular mechanisms of bat wing development and illustrate how drastic morphological changes can be achieved through repurposing of existing developmental programs during evolution.

evolutionary biology↗

bioRxiv2024

Enhancer adoption by an LTR retrotransposongenerates viral-like particles causingdevelopmental limb phenotypes

Mammalian genomes are scattered with transposable elements (TEs). TEs are epigenetically silenced to prevent harmful effects caused by either global activation leading to genome instability or insertional mutation disturbing gene transcription. However, whether the activation of a single element can contribute to pathological phenotypes without directly affecting gene expression is largely unknown. Here, we show that tissue-specific expression of a TE in the embryo leads to the production of viral-like particles (VLPs) which can affect organ formation. Failure to silence an LTR retrotransposon inserted upstream of the Fgf8 gene results in its co-expression with Fgf8 in the developing embryo. While local gene regulation is unaffected, the LTR retrotransposon participates in chromatin folding at the locus and adopts the expression of the regulatory domain it is located in. This drives the production of VLPs in the Fgf8-expressing cells of the developing limb, triggering apoptotic cell death at the time of digit outgrowth and resulting in a limb malformation resembling human ectrodactyly. This phenotype can be rescued by knock-out or knock-in of the retrotransposon causing mutations preventing its full retroviral cycle. Insertion of the same element at other developmental loci faithfully recapitulates expression according to the neighboring regulatory activity. Our findings provide a mechanism by which TE insertion is incorporated into the local genomic regulatory landscape and show how VLP production in post-implantation embryos can interfere with organ formation.

developmental biology↗

bioRxiv2022

Combinatorial effects on gene expression at the Lbx1/Fgf8 locus resolve Split-Hand/Foot Malformation type 3

Split-Hand/Foot Malformation type 3 (SHFM3) is a congenital limb malformation associated with tandem duplications at the LBX1/FGF8 locus. Yet, the disease patho-mechanism remains unsolved. Here we investigated the functional consequences of SHFM3-associated rearrangements on chromatin conformation and gene expression in vivo in transgenic mice. We show that the Lbx1/Fgf8 locus consists of two separate, but interacting, regulatory domains. Re-engineering of a SHFM3-associated duplication and a newly reported inversion in mice resulted in restructuring of the chromatin architecture. This led to an ectopic activation of the Lbx1 and Btrc genes in the apical ectodermal ridge (AER) in an Fgf8-like pattern. Artificial repositioning of the AER-specific enhancers of Fgf8 was sufficient to induce misexpression of Lbx1 and Btrc. We provide evidence that the SHFM3 phenotype is the result of a combinatorial effect on gene misexpression and dosage in the developing limb. Our results reveal new insights into the molecular mechanism underlying SHFM3 and provide novel conceptual framework for how genomic rearrangements can cause gene misexpression and disease.

genetics↗

bioRxiv2021

Language Models for the Prediction of SARS-CoV-2 Inhibitors

The COVID-19 pandemic highlights the need for computational tools to automate and accelerate drug design for novel protein targets. We leverage deep learning language models to generate and score drug candidates based on predicted protein binding affinity. We pre-trained a deep learning language model (BERT) on [~]9.6 billion molecules and achieved peak performance of 603 petaflops in mixed precision. Our work reduces pre-training time from days to hours, compared to previous efforts with this architecture, while also increasing the dataset size by nearly an order of magnitude. For scoring, we fine-tuned the language model using an assembled set of thousands of protein targets with binding affinity data and searched for inhibitors of specific protein targets, SARS-CoV-2 Mpro and PLpro. We utilized a genetic algorithm approach for finding optimal candidates using the generation and scoring capabilities of the language model. Our generalizable models accelerate the identification of inhibitors for emerging therapeutic targets.

bioinformatics↗

bioRxiv2021

Temporal Progression: A case study in Porcine Survivability through Hemostatic Nanoparticles

This paper focuses on the analysis of time series representation of blood loss and cytokines in animals experiencing trauma to understand the temporal progression of factors affecting survivability of the animal. Trauma related grave injuries cause exsanguination and lead to death. 50% of deaths especially in the armed forces are due to trauma injuries. Restricting blood loss usually requires the presence of first responders, which is not feasible in certain cases. Hemostatic nanoparticles have been developed to tackle these kinds of situations to help achieve efficient blood coagulation. Hemostatic nanoparticles were administered into trauma induced porcine animals (pigs) to observe impact on the cytokine and blood loss experienced by them. In this paper we present temporal models to study the impact of the hemostatic nanoparticles and provide snapshots about the trend in cytokines and blood loss in the porcine data to study their progression over time. We utilized Piecewise Aggregate Approximation, Similarity based Merging and clustering to evaluate the impact of the different hemostatic nanoparticles administered. In some cases the fluctuations in the cytokines may be too small. So in addition we highlight situations where temporal modelling that produces a smoothed time series may not be useful as it may remove out the noise and miss the overall fluctuations resulting from the nanoparticles. Our results indicate certain nanoparticles stand out and lead to novel hypothesis formation.

bioengineering↗

bioRxiv2021

Computational Design Map for Heterogeneous Experimental Studies

This paper focuses on the discovery of a computational design map of disparate heterogeneous outcomes from bioinformatics experiments in pig (porcine) studies to help identify key variables impacting the experiment outcomes. Specifically we aim to connect discoveries from disparate laboratory experimentation in the area of trauma, blood loss and blood clotting using data science methods in a collaborative ensemble setting. Trauma related grave injuries cause exsanguination and death, constituting up to 50% of deaths especially in the armed forces. Restricting blood loss in such scenarios usually requires the presence of first responders, which is not feasible in certain cases. Moreover, a traumatic event may lead to a cytokine storm, reflected in the cytokine variables. Hemostatic nanoparticles have been developed to tackle these kinds of situations of trauma and blood loss. This paper highlights a collaborative effort of using data science methods in evaluating the outcomes from a lab study to further understand the efficacy of the nanoparticles. An intravenous administration of hemostatic nanoparticles was executed in pigs that had to undergo hemorrhagic shock and blood loss and other immune response variables, cytokine response variables are measured. Thus, through various hemostatic nanoparticles used in the intervention, multiple data outcomes are produced and it becomes critical to understand which nanoparticles are critical and what variables are key to study further variations in the lab. We propose a collaborative data mining framework which combines the results from multiple data mining methods to discover impactful features. We used frequent patterns observed in the data from these experiments. We further validate the connections between these frequent rules by comparing the results with decision trees and feature ranking. Both the frequent patterns and the decision trees help us identify the critical variables that stand out in the lab studies and need further validation and follow up in future studies. The outcomes from the data mining methods help produce a computational design map of the experimental results. Our preliminary results from such a computational design map provided insights in determining which features can help in designing the most effective hemostatic nanoparticles.

bioengineering↗

bioRxiv2021

The imprinted Zdbf2 gene finely tunes control of feeding and growth in neonates

Genomic imprinting refers to the mono-allelic and parent-specific expression of a subset of genes. While long recognized for their role in embryonic development, imprinted genes have recently emerged as important modulators of postnatal physiology, notably through hypothalamus-driven functions. Here, using mouse models of loss, gain and parental inversion of expression, we report that the paternally expressed Zdbf2 gene controls neonatal growth in mice, in a dose-sensitive but parent-of-origin-independent manner. We further found that Zdbf2-KO neonates failed to fully activate hypothalamic circuits that stimulate appetite, and suffered milk deprivation and diminished circulating Insulin Growth Factor 1 (IGF-1). Consequently, only half of Zdbf2-KO pups survived the first days after birth and those surviving were smaller. This study demonstrates that precise imprinted gene dosage is essential for vital physiological functions at the transition from intra- to extra-uterine life, here the adaptation to oral feeding and optimized body weight gain.

molecular biology↗

bioRxiv2018

Supercharging enables organized assembly of synthetic biomolecules

There are few methods for the assembly of defined protein oligomers and higher order structures that could serve as novel biomaterials. Using fluorescent proteins as a model system, we have engineered novel oligomerization states by combining oppositely supercharged variants. A well-defined, highly symmetrical 16-mer (two stacked, circular octamers) can be formed from alternating charged proteins; higher order structures then form in a hierarchical fashion from this discrete protomer. During SUpercharged PRotein Assembly (SuPrA), electrostatic attraction between oppositely charged variants drives interaction, while shape and patchy physicochemical interactions lead to spatial organization along specific interfaces, ultimately resulting in protein assemblies never before seen in nature.

bioengineering↗