Biology subjects

Acree, C.

Publications and source records attributed to Acree, C..

7 recordsLinked to original sources

bioRxiv2026

Correlative MIMS-EM imaging reveals metabolic turnover from organelle to organismal scales in C. elegans during dietary restriction

Metabolism is spatially compartmentalized across scales, from distinct tissues to cells and orga-nelles. However, most approaches for studying metabolic activity obscure spatial organization and intra-compartment heterogeneity within bulk biochemical measurements. On the other hand, multi-isotope mass spectrometry coupled with scanning electron microscopy (MIMS-EM) maps the fates of labeled nutrients in situ at nanometer-scale resolution, preserving ultrastructural con-text. Here we adapt MIMS-EM for Caenorhabditis elegans, where the compact metazoan body plan uniquely enables visualization of virtually all tissue types and their resident organelles within a single cross-sectional image. Using pulse-chase labeling of dietary carbon and nitrogen, we apply this approach to understanding the metabolic program induced in early stages of dietary restriction (DR). While DR is widely proposed to enhance organismal healthspan by enhancing broadscale turnover, proteomic studies have suggested more nuanced models. MIMS-EM across intact animals reveals that DR induces non-uniform effects between tissues and car-bon/nitrogen resources, accelerating carbon turnover in the muscle and hypodermis, but not in-testine. At the organelle scale, MIMS-EM revealed heterogeneity within mitochondrial networks that was independent of diet and stable over time. Spatial analysis of isotope signatures within intestinal mitochondrial networks also indicated greater similarity between neighboring mitochon-dria than distal mitochondria, supporting models of local mitochondrial mixing. Collectively, these results reveal that DR induces compartment- and resource-specific remodeling strategies across an intact animal while establishing C. elegans MIMS-EM as a powerful platform for multi-scale, integrative models of nutrient handling.

physiology↗

bioRxiv2026

QuantEM: An optimized platform of vision transformer-based models for segmentation and analysis of electron microscopy data

Electron microscopy (EM) is essential for resolving cellular ultrastructure, yet quantitative analysis remains limited by labor-intensive segmentation and the scarcity of generalizable models. Here we present QuantEM, an open-source platform for segmentation and analysis of EM data across imaging modalities, tissues, and species. We assembled the largest curated collection of intracellular EM datasets to date, comprising over 15,000 two-dimensional images and 1,700 three-dimensional acquisitions from more than 600 datasets, including nearly 4,000 newly released acquisitions. Using this resource, we trained an EM-specific vision transformer foundation model and systematically optimized adaptation strategies for organelle segmentation. QuantEM provides pretrained models for mitochondria, endoplasmic reticulum, nuclei, and lipid droplets, integrated with interactive proofreading and downstream quantitative analyses through standalone and napari interfaces. Across diverse naive datasets, QuantEM consistently matches or exceeds existing models on zero-shot segmentation while requiring less data for finetuning. We further demonstrate its utility by revealing previously unrecognized subcellular compartmentation of hepatic glucokinase using immuno-electron microscopy.

cell biology↗

bioRxiv2025

Calorie Restriction modulates beta cell IP3R activity to regulate Ca2+ homeostasis and cell network connectivity

Calorie restriction (CR) promotes beta cell longevity by regulating cell identity, organelle and protein homeostasis, and metabolism pathways. CR beta cells have higher cAMP levels and mitochondria with an elevated potential to generate ATP. However, CR beta cells have reduced insulin secretion due to increased peripheral insulin sensitivity. How CR impacts beta cell Ca2+ homeostasis to regulate beta cell insulin release remains unknown. We investigated this question using acute pancreatic tissue slices prepared from ad-libitum (AL) or CR mice loaded with a low affinity Ca2+ indicator and recorded cytosolic Ca2+ gradients with fast confocal imaging. We exposed these slices to increasing glucose concentrations and applied our semi-automatic analysis pipeline to detect thousands of individual beta cells followed by identification of individual Ca2+ spiking events. We observed that CR beta cells have fast short-amplitude Ca2+ oscillations that correlate with largely disconnected beta cell networks across the islet. Using acetylcholine stimulation, we found that faster IP3R-driven Ca2+ oscillations linked to higher cytosolic cAMP levels protect beta cells against acute depletion of ER Ca2+ stress. Therefore, this study provides new mechanistic insight into adaptation of beta cell and of beta cell networks to CR interventions. Article highlightsO_LIBeta cells from calorie restricted (CR) mice have decreased insulin release, however the mechanisms underlying this adaptive response remain unknown. C_LIO_LICR beta cells have elevated basal cytosolic cAMP ([cAMP]cyt) compared to beta cells in control ad libitum fed (AL) mice, and they operate with faster and shorter cytosolic Ca2+ oscillations. C_LIO_LIWhile AL beta cells form interconnected activity networks, CR beta cells are largely disconnected and fire more independently of each other. C_LIO_LIIslets of CR mice can sustain prolonged activity during ER stressing conditions due to elevated IP3R activity and improved Ca2+ homeostasis. C_LI Why did we undertake this study?We have previously shown that calorie restriction (CR) promotes beta cell longevity by enhancing beta cell identity and organelle homeostasis mechanisms. This long-lived phenotype correlated with the onset of enhanced peripheral insulin sensitivity and reduced beta cell insulin release in vivo despite higher cAMP levels and increased potential for mitochondrial ATP generation. However, the mechanisms underlying the reduced cell insulin release phenotype of CR beta cells remains unknown. Therefore, we investigated the underlying Ca2+ homeostasis mechanisms regulating insulin release in AL and CR beta cells. What is the specific question(s) we wanted to answer?We were interested in determining what are the cell Ca2+ activity patterns during basal and glucose-stimulated conditions in AL and CR beta cells. In addition, we also investigated how CR beta cells respond to epinephrine inhibition and supra-stimulatory concentrations of acetylcholine (ACh), which drive acute beta cell stress by disrupting normal cAMP and ER Ca2+ signaling, respectively. Finally, we investigate whether CR beta cells formed more interconnected beta cell networks driven by changes in Ca2+ activity patterns. What did we find?We found that CR beta cells are more active with significantly higher rates of Ca2+ oscillation at basal and high glucose concentrations. In fact, CR beta cells have shorter inter-Ca2+ event intervals that are more resistant to depletion of cAMP by epinephrine application. In contrast, stimulation of IP3R activity (to force depletion of ER Ca2+ stores) by supraphysiological ACh concentrations revealed that CR beta cells were able to sustain a prolonged Ca2+ activity versus AL beta cells. Surprisingly, this enhanced beta cell activity profile reduced beta cell activity network connectivity. What are the implications of our findings?Our work demonstrates that CR beta cells have higher baseline and glucose-stimulated Ca2+ activity due to higher cAMP levels. These cells also have dominant IP3R activity that grants improved ER Ca2+ homeostasis and significantly reduces beta cell network connectivity to tone down insulin secretion. These studies provide a mechanistic understanding of how beta cells adapt to CR and to CR-associated enhanced insulin sensitivity.

cell biology↗

bioRxiv2023

Caloric restriction promotes beta cell longevity and delays aging and senescence by enhancing cell identity and homeostasis mechanisms.

Caloric restriction (CR) extends organismal lifespan and health span by improving glucose homeostasis mechanisms. How CR affects organellar structure and function of pancreatic beta cells over the lifetime of the animal remains unknown. Here, we used single nucleus transcriptomics to show that CR increases the expression of genes for beta cell identity, protein processing, and organelle homeostasis. Gene regulatory network analysis link this transcriptional phenotype to transcription factors involved in beta cell identity (Mafa) and homeostasis (Atf6). Imaging metabolomics further demonstrates that CR beta cells are more energetically competent. In fact, high-resolution light and electron microscopy indicates that CR reduces beta cell mitophagy and increases mitochondria mass, increasing mitochondrial ATP generation. Finally, we show that long-term CR delays the onset of beta cell aging and senescence to promote longevity by reducing beta cell turnover. Therefore, CR could be a feasible approach to preserve compromised beta cells during aging and diabetes.

cell biology↗

bioRxiv2023

Mechanism of target site selection by type V-K CRISPR-associated transposases

Unlike canonical CRISPR-Cas systems that rely on RNA-guided nucleases for target cleavage, CRISPR-associated transposases (CASTs) repurpose nuclease-deficient CRISPR effectors to facilitate RNA-guided transposition of large genetic payloads. Type V-K CASTs offer several potential upsides for genome engineering, due to their compact size, easy programmability, and unidirectional integration. However, these systems are substantially less accurate than type I-F CASTs, and the molecular basis for this difference has remained elusive. Here we reveal that type V-K CASTs undergo two distinct mobilization pathways with remarkably different specificities: RNA-dependent and RNA-independent transposition. Whereas RNA-dependent transposition relies on Cas12k for accurate target selection, RNA-independent integration events are untargeted and primarily driven by the local availability of TnsC filaments. The cryo-EM structure of the untargeted complex reveals a TnsB-TnsC-TniQ transpososome that encompasses two turns of a TnsC filament and otherwise resembles major architectural aspects of the Cas12k-containing transpososome. Using single-molecule experiments and genome-wide meta-analyses, we found that AT-rich sites are preferred substrates for untargeted transposition and that the TnsB transposase also imparts local specificity, which collectively determine the precise insertion site. Knowledge of these motifs allowed us to direct untargeted transposition events to specific hotspot regions of a plasmid. Finally, by exploiting TnsBs preference for on-target integration and modulating the availability of TnsC, we suppressed RNA-independent transposition events and increased type V-K CAST specificity up to 98.1%, without compromising the efficiency of on-target integration. Collectively, our results reveal the importance of dissecting target site selection mechanisms and highlight new opportunities to leverage CAST systems for accurate, kilobase-scale genome engineering applications.

molecular biology↗

bioRxiv2021

Unbiased profiling of CRISPR RNA-guided transposition products by long-read sequencing

Bacterial transposons propagate through either non-replicative (cut-and-paste) or replicative (copy-and-paste) pathways, depending on how the mobile element is excised from its donor source. In the well-characterized E. coli transposon Tn7, a heteromeric TnsA-TnsB transposase directs cut-and-paste transposition by cleaving both strands at each transposon end during the excision step. Whether a similar pathway is involved for RNA-guided transposons, in which CRISPR-Cas systems confer DNA target specificity, has not been determined. Here, we apply long-read, population-based whole-genome sequencing (WGS) to unambiguously resolve transposition products for two evolutionarily distinct transposon types that employ either Cascade or Cas12k for RNA-guided DNA integration. Our results show that RNA-guided transposon systems lacking functional TnsA primarily undergo copy-and-paste transposition, generating cointegrate products that comprise duplicated transposon copies and insertion of the vector backbone. Finally, we report natural and engineered transposon variants encoding a TnsAB fusion protein, revealing a novel strategy for achieving RNA-guided transposition with fewer molecular components.

molecular biology↗

bioRxiv2020

CRISPR RNA-guided integrases for high-efficiency and multiplexed bacterial genome engineering

Tn7-like transposons are pervasive mobile genetic elements in bacteria that mobilize using heteromeric transposase complexes comprising distinct targeting modules. We recently described a Tn7-like transposon from Vibrio cholerae that employs a Type I-F CRISPR-Cas system for RNA-guided transposition, in which Cascade directly recruits transposition proteins to integrate donor DNA downstream of genomic target sites complementary to CRISPR RNA. However, the requirement for multiple expression vectors and low overall integration efficiencies, particularly for large genetic payloads, hindered the practical utility of the transposon. Here, we present a significantly improved INTEGRATE (insertion of transposable elements by guide RNA-assisted targeting) system for targeted, multiplexed, and marker-free DNA integration of up to 10 kilobases at ~100% efficiency. Using multi-spacer CRISPR arrays, we achieved simultaneous multiplex insertions in three genomic loci, and facile multi-loci deletions when combining orthogonal integrases and recombinases. Finally, we demonstrated robust function in other biomedically- and industrially-relevant bacteria, and developed an accessible computational algorithm for guide RNA design. This work establishes INTEGRATE as a versatile and portable tool that enables multiplex and kilobase-scale genome engineering.

molecular biology↗