Biology subjects

Weinstock, M.

Publications and source records attributed to Weinstock, M..

7 recordsLinked to original sources

bioRxiv2025

Miniscope Processing Suite (MPS): An Intuitive, No-Code, Scalable Pipeline for Long Duration Calcium Imaging

Miniscope calcium imaging provides a unique window into the activity of neurons during behavior while enabling spatial localization of individual cells across time. Despite its potential to revolutionize in vivo imaging alongside the rise of optogenetic tools, miniscopes remain underutilized. This gap may stem from the lack of an easy-to-use preprocessing software tailored to miniscope data. To address this need, we developed the first no-code end-to-end scalable pipeline for preprocessing large miniscope recordings: the Miniscope Processing Suite (MPS). MPS is the first implementation of Constrained Non-negative Matrix Factorization (CNMF) with Nonnegative Double Singular Value Decomposition (NNDSVD) initialization, multi-lasso segmentation, and parallelized temporal and spatial updates, enabling analysis of recordings exceeding three hours on a standard hardware. We tested a large dataset consisting of 28 operant behavior sessions (77 hrs, 7.26 TB of video data) on a single workstation. MPS completed the analysis in 55.6 hrs, (averaging 0.72 minute of processing time per minute of recording), which is 10-20X faster than traditional pipelines. Packaged as an easy downloadable plug-and-play software with a graphical user interface and requiring no coding or Git experience, MPS lowers the barrier to miniscope analysis while improving on current methodologies.

neuroscience↗

bioRxiv2025

Temporal shifts in microRNAs signify the inflammatory state of primary murine microglial cells

The primary function of microglia is to maintain brain homeostasis. However, in several neurodegenerative diseases, such as Alzheimers disease, the pathophysiological hallmarks that drive disease progression involve neurotoxicity and alterations in neuroinflammation. In this study, we exposed murine neonatal primary microglial cultures to external signals that mimic the in vivo stimuli caused by pathogens, injury, or toxic agents. In the presence of benzoyl ATP (bzATP) and lipopolysaccharide (LPS), we observed a coordinated increase in the expression of interleukins and chemokines. We focused on the dynamics of the differentially expressed microRNAs (miRNAs) that are statistically significant (DEMs) and tracked their post-activation dynamics. Monitoring miRNAs 3 and 8 hours (h) post-activation revealed robust changes in 33 and 57 DEMs, most of which were upregulated. The DEMs exhibiting the strongest temporal regulation included miR-155, miR-132, miR-3473e, miR-222, and miR-146b. Additionally, a strong downregulation of miR-3963 was attributed to the exposure to bzATP. Through their regulation of TNF and NF{kappa}B signaling pathways, the identified DEMs reflect the cellular response to inflammatory signals. We incubated the activated cells with ladostigil, a neuroprotective compound that has been shown to reduce oxidative stress, inflammation, and cognitive decline. While there was no significant effect 3 h post-activation, at 8 h, a few miRNAs implicated in inflammation suppression such as miR-27a, miR-27b, and miR-23b were upregulated in a ladostigil-dependent manner. We conclude that the miRNA expression profile provides a sensitive indicator of the regulatory mechanisms underlying inflammation-related responses in microglia. We propose that primary microglia subjected to controlled activation paradigms can serve as a robust model for inflammatory states in the brain to monitor the aging brain along the progression of neurodegenerative diseases.

cell biology↗

bioRxiv2023

Developmental remodeling repurposes larval neurons for sexual behaviors in adult Drosophila

Most larval neurons in Drosophila are repurposed during metamorphosis for functions in adult life, but their contribution to the neural circuits for sexually dimorphic behaviors is unknown. Here, we identify two interneurons in the nerve cord of adult Drosophila females that control ovipositor extrusion, a courtship rejection behavior performed by mated females. We show that these two neurons are present in the nerve cord of larvae as mature, sexually monomorphic interneurons. During pupal development, they acquire the expression of the sexual differentiation gene, doublesex, undergo doublesex-dependent programmed cell death in males, and are remodeled in females for functions in female mating behavior. Our results demonstrate that the neural circuits for courtship in Drosophila are built in part using neurons that are sexually reprogrammed from former sex-shared activities in larval life.

neuroscience↗

bioRxiv2023

Deep learning-based codon optimization with large-scale synonymous variant datasets enables generalized tunable protein expression

Increasing recombinant protein expression is of broad interest in industrial biotechnology, synthetic biology, and basic research. Codon optimization is an important step in heterologous gene expression that can have dramatic effects on protein expression level. Several codon optimization strategies have been developed to enhance expression, but these are largely based on bulk usage of highly frequent codons in the host genome, and can produce unreliable results. Here, we develop deep contextual language models that learn the codon usage rules from natural protein coding sequences across members of the Enterobacterales order. We then fine-tune these models with over 150,000 functional expression measurements of synonymous coding sequences from three proteins to predict expression in E. coli. We find that our models recapitulate natural context-specific patterns of codon usage and can accurately predict expression levels across synonymous sequences. Finally, we show that expression predictions can generalize across proteins unseen during training, allowing for in silico design of gene sequences for optimal expression. Our approach provides a novel and reliable method for tuning gene expression with many potential applications in biotechnology and biomanufacturing.

synthetic biology↗

bioRxiv2022

Antibody optimization enabled by artificial intelligence predictions of binding affinity and naturalness

Traditional antibody optimization approaches involve screening a small subset of the available sequence space, often resulting in drug candidates with suboptimal binding affinity, developability or immunogenicity. Based on two distinct antibodies, we demonstrate that deep contextual language models trained on high-throughput affinity data can quantitatively predict binding of unseen antibody sequence variants. These variants span a KD range of three orders of magnitude over a large mutational space. Our models reveal strong epistatic effects, which highlight the need for intelligent screening approaches. In addition, we introduce the modeling of "naturalness", a metric that scores antibody variants for similarity to natural immunoglobulins. We show that naturalness is associated with measures of drug developability and immunogenicity, and that it can be optimized alongside binding affinity using a genetic algorithm. This approach promises to accelerate and improve antibody engineering, and may increase the success rate in developing novel antibody and related drug candidates.

bioinformatics↗

bioRxiv2021

Profiles and Dynamics of the Transcriptome of Microglial Cells Reveal their Inflammatory Status

The primary role of microglia in the maintenance of brain homeostasis is to respond to disturbances in the microenvironment. In this study, we cultured murine neonatal microglia and activated them with lipopolysaccharide (LPS) and benzoyl ATP (bzATP) to characterize changes in the transcriptome in response to various in vivo stimuli caused by pathogens, injury, or toxins. Activation by bzATP, an agonist of purinergic receptors, induces a transient wave of transcriptional changes. However, a long-lasting transcriptional profile affecting thousands of genes occurs only following a combination of bzATP and LPS. This profile is dominated by a coordinated induction of cytokines (e.g., IL1- and IL1-{beta}), chemokines, and their direct regulators. Many of these inflammatory-related genes are up-regulated by several orders of magnitude. We identified the TNF- and NF-{kappa}B pathways as the principal hubs for signaling of interleukin and chemokine induction in this cell system. We propose that primary microglia under controlled activation paradigms can be used for testing reagents that could attenuate their activated state. Such a microglial system could serve as a model for changes occurring in the aging brain and neurodegenerative diseases. Highlight points* Primary murine microglia cultures release cytokines following activation with bzATP and LPS * The wave of changes in gene expression by bzATP is transient. * bzATP+LPS causes a transcription program dominated by the induction of interleukins and chemokines.

neuroscience↗

bioRxiv2021

Emotional states as distinct configurations of functional brain networks

The conceptualization of emotional states as patterns of interactions between large-scale brain networks has recently gained support. Yet, few studies have directly examined the brains network structure during emotional experiences. Here, we investigated the brains functional network organization during experiences of sadness, amusement, and neutral states elicited by movies, in addition to a resting-state. We tested the effects of the experienced emotion on individual variability in the brains functional connectome. Next, for each state, we defined a community structure of the brain and quantified its segregation and integration. We found that sadness, relative to amusement, was associated with higher modular integration and increased connectivity of cognitive control networks: the salience and fronto-parietal networks. Moreover, in both the functional connectome and the emotional report, the similarity between individuals was dependent on the sex. Our results suggest that the experience of emotion is linked to a reconfiguration of whole-brain distributed, not emotion-specific, functional networks and that the brains topological structure carries information about the subjective emotional experience.

neuroscience↗