Biology subjects

Roberts, S.

Publications and source records attributed to Roberts, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Mitochondrial perturbation adapts the proteome from early to advanced immune responses

Dysregulated immunity, a hallmark of many human diseases, co-occurs with mitochondrial dysfunction and is commonly associated with misprimed primary immune signaling. While transcriptionally well-characterized, the impact of mitochondria on the host response at the protein level is less clear. Using in vitro and in vivo approaches including proteotranscriptomics, our data suggest that OXPHOS promotes expression of early, cell autonomous immune proteins whereas mitochondrial perturbation favors mediators of cell extrinsic responses like inflammation. This response is independent of immune cues, time-dependent, conserved, and occurs across tissues in mouse models of mitochondrial dysfunction. These data illustrate unappreciated roles for mitochondrial state in adapting host responses at the protein level, which have implications for complex disease etiology and the ancestral origins for eukaryotic immune sensing.

immunology↗

bioRxiv2026

Monoclonal nephritic factors reveal insights into C3 convertase dynamics and dysregulation

C3- and C5-nephritic factors are potent but poorly understood autoantibodies that dysregulate complement convertases. To date, their underlying mechanisms of action, epitopes, and sequences remain unknown. To address this knowledge gap, we immune profiled B cells from a nephritic factor-positive C3 glomerulopathy patient and identified the first monoclonal C3- and C5-nephritic factors. We present the structure of a C3-nephritic factor bound to a C3 convertase with the convertase protease domain unexpectedly rotated and inhibited. This rotation advances our understanding of complement convertase progression and decay, explains disease-associated convertase variants, and reveals the molecular mechanism by which nephritic factors can either activate or inhibit convertase activity. We also detail heterogeneity within and between C3- and C5-nephritic factors in terms of convertase binding, stabilizing capacity, regulator inhibition, fluid-phase activation, and disease contribution. These findings improve stratification of patients with C3 glomerulopathy, redefine basic C3 convertase dynamics, and provide insights into antibody-mediated modulation of the complement system.

immunology↗

bioRxiv2026

BEEhaviourLab: A high-throughput platform for sublethal stressor screening in insects

Behavioural responses often provide the earliest detectable signs of physiological stress yet quantifying them at scale remains challenging. Acoustic behaviours such as buzzing are central to insect locomotion and communication but are rarely measured systematically, and their potential as sensitive indicators of environmental stress remains largely unexplored. Here, we test whether changes in insect acoustic behaviour can reveal sublethal effects of pesticide exposure. Using a newly developed automated behavioural platform (BEEhaviourLab), we recorded synchronised video and audio from insects, enabling simultaneous, high-throughput quantification of locomotor activity and buzzing behaviour across multiple individuals and species without the need for tagging. We applied this system to characterise the effects of the veterinary antiparasitic moxidectin on the bumble bee Bombus terrestris. Acute contact exposure produced dose-dependent reductions in locomotion and buzzing behaviour at concentrations below lethal thresholds. Acoustic measures detected behavioural disruption with sensitivity comparable to video-based activity metrics, demonstrating that buzzing behaviour provides a sensitive and previously unused indicator of neurotoxic stress. More broadly, scalable multimodal behavioural phenotyping enables subtle behavioural disruption to be detected across large experiments, opening new opportunities to incorporate acoustic endpoints into studies of animal behaviour, environmental stress, and ecological risk assessment.

animal behavior and cognition↗

bioRxiv2026

Short-term mechanisms, long-term consequences: molecular effects of ocean acidification on juvenile snow crab

Understanding how marine species tolerate acidified conditions is critical for predicting biological responses to ocean change. A recent one-year experiment (Long 2026) found that juvenile snow crab (Chionoecetes opilio) maintain growth and molting under acidification (pH 7.8, 7.5), and survival begins to decline only after [~]250 days under severe acidification (pH 7.5). In this companion study, we characterized whole-transcriptome responses after 8 hours and 88 days of exposure to identify molecular mechanisms underlying short-term tolerance and chronic effects of ocean acidification. The immediate transcriptional response involved strong activation of genes associated with mitochondrial metabolism and biogenesis, protein homeostasis, cuticle maintenance, and immune modulation, processes shared between moderate and severe treatments but of greater magnitude under severe acidification. After 88 days, expression patterns diverged, revealing sustained upregulation of stress- and damage-mitigation pathways in the severe treatment (pH 7.5) compared to the moderate treatment (pH 7.8). These findings indicate that crabs in severe acidification are likely to experience chronic OA stress that precedes outward physiological effects, and provides a mechanistic basis for delayed mortality. We further highlight potential early indicators of chronic acidification stress in snow crab, among which a gene likely coding for carbonic anhydrase 7 (CA7, GWK47_031192) appears to be the most promising biomarker. Summary StatementJuvenile snow crabs tolerate ocean acidification through flexible gene expression, but prolonged exposure reveals hidden cellular stress that helps explain delayed mortality.

molecular biology↗

bioRxiv2026

Understanding and addressing under-sampling in plant-pollinator networks using stacked models for missing link prediction

Pollinator diversity and pollination are under threat from anthropogenic disturbances. Plant-pollinator networks are useful tools to study the consequences of these disturbances, but their links are often under-sampled, potentially biasing conclusions. We introduce a computational method that can be used to predict which unobserved links in a plant-pollinator network dataset are missing. This method extends a state-of-the-art machine learning approach to missing link prediction based on stacked generalization, which has been promising in other contexts, to the setting of bipartite plant-pollinator networks with species traits treated as node attributes. This approach predicts missing links using an ensemble of predictors based on both observed network topology and species traits. We demonstrate this approach on synthetic and empirical plant-pollinator networks. We take advantage of a unique empirical plant-pollinator dataset which samples from three sites using (a) records of observed visits of pollinators to plant species and (b) pollen analysis with detailed species trait annotations for both plant and pollinator nodes. Visit-based sampling under-samples the links in these networks, whereas pollen-based sampling identifies additional links, allowing us to investigate missing link prediction from realistic patterns of field under-sampling. We show that full plant-pollinator networks can be partially reconstructed from the under-sampled networks using our approach. Further, we show that this method can be used to identify which features are the most important for predicting missing links, which allows for investigation into mechanisms driving plant-pollinator link formation and observation. This method is broadly applicable to under-sampled plant-pollinator networks.

ecology↗

bioRxiv2026

Epigenetic Intelligence: How Organisms Track Their Environment Through Molecular Memory

The regulation of gene expression by epigenetic markers is a growing area of focus for researchers who seek to explain rapid phenotypic acclimatization to environmental change. Yet even as empirical datasets accumulate exponentially, the mechanistic underpinnings of epigenetic changes and their role in connecting environmental variation with the regulation of gene function remain unclear. Here, we use a stochastic model of epigenetic change to generate three testable predictions: (1) that organisms require environmental feedback to track their environments through epigenetic responses, (2) that this tracking requires coordination between the addition and removal of epigenetic markers, and (3) that epigenetically driven tracking is only effective under specific subsets of environmental variability. Despite the intuitiveness of these postulates, few to no experimental studies directly test them. We review correlational evidence consistent with the models predictions, describe hypothetical mechanisms by which epigenetic strategies could evolve, and clearly identify knowledge gaps and urgent experimental needs in the field. Overall, the field of environmental epigenetics is poised for major advances, which can be enhanced through the continued synthesis of mathematical frameworks and empirical data.

genetics↗

bioRxiv2025

Development of an organotypic brain slice culture model using tissues collected from geriatric mice

Ex vivo organ slice cultures are attractive models to address specific biomedical research questions because they retain complex and dynamic three dimensional architecture. In addition, they require only a few animals as tissue donors thus greatly decreasing the number needed for live animal studies. The model has been most successful using tissues from very young mice, but has generally not been considered for aging research because of the challenge of maintaining viability of tissues collected from older mice. The brain is a high impact organ in aging and age-related disease research, so it was of interest to investigate the viability and related molecular and cellular characteristics of brain slice cultures (BSCs) derived from old mice. Coronal sections of 200 m thickness were collected from the middle third of the brain of 21 month old C57BL/6JN mice, cultured in a standard media concoction for seven days, exposed to chemical stressors glucose, hydrogen peroxide, lipopolysaccharide, or sodium hypochlorite for 24 to 48 hours, and then rinsed and cultured for another seven days. Results in non-treated BSCs showed cellular viability of greater than 80 percent with specific aging pathways relatively unaffected. Chemical stressors selectively targeted pathways of aging including DNA damage, autophagy, and inflammation. These preliminary observations suggest that BSCs derived from geriatric mice have potential for research into brain aging and age-related neurodegenerative conditions, and could serve as a prototype for developing organ slice cultures for other organs collected from old mice.

cell biology↗

bioRxiv2025

MetaBeeAI: an AI pipeline for full-text systematic reviews in biology

The volume and complexity of scientific literature are expanding rapidly, making it increasingly difficult to extract and synthesise information across studies. This challenge is particularly acute in the biological sciences, where evidence spans multiple levels of organisation and heterogeneous experimental designs. Large Language Model (LLM) pipelines offer a scalable route to evidence synthesis, but many existing approaches lack transparency, modularity, and effective mechanisms for human oversight. We present MetaBeeAI, an open-source, modular pipeline that integrates established LLM techniques into a coherent, auditable workflow for structured data extraction in biology. MetaBeeAI combines modular prompting, multi-pass extraction, and expert-in-the-loop validation within an interface that presents model outputs alongside source text, enabling inspection, correction, and iterative refinement. The pipeline produces machine-readable records of prompts, configurations, and expert annotations, supporting reproducibility and continuous improvement. We apply MetaBeeAI to 924 research papers on bees and pesticides, extracting structured information on species, compounds, exposure designs, and experimental context. Evaluation demonstrates improved consistency, convergence with expert judgement, and robustness across heterogeneous biological studies, highlighting the value of expert-guided refinement. MetaBeeAI provides a transparent and extensible framework for scalable evidence synthesis, supporting reliable integration of LLMs into biological research workflows.

ecology↗

bioRxiv2025

From Blue to Pink: Resazurin as a High-Throughput Proxy for Metabolic Rate in Oysters

Metabolic rate assays are critical tools for assessing organismal stress and resilience, yet their widespread application in aquaculture and ecological monitoring is limited. Improving these assays is essential for hatchery managers, farmers, and scientists seeking to identify resilient stocks and monitor stress in shellfish populations. Resazurin, a redox-sensitive dye commonly used in cell viability assays, offers a promising, high-throughput assay for metabolic rate assessment, but its application at the whole-organism level remains under explored. This study evaluates the efficacy of a resazurin-based metabolic assay in oysters (Crassostrea gigas and Crassostrea virginica) through four experimental approaches: (1) adaptation of the resazurin assay to measure oyster metabolism, (2) examination of temperature effects on oyster metabolism, (3) characterization of acute thermal stress responses, (4) examination of genetic variability in metabolism, and (5) correlations between metabolism and predicted performance in a selective breeding case study. Our findings confirm that resazurin fluorescence is correlated with oxygen consumption, validating its use as a measure of metabolism. Thermal performance assays reveal expected metabolic responses to temperature, including identification of optima and tipping points where metabolic stimulation shifts to depression under temperature stress. Acute thermal stress experiments demonstrate that oysters exhibiting greater metabolic depression are more likely to survive, supporting metabolism as a predictor of mortality. Further, genetic variation in stress responses is detected as family-level variation in metabolism. Metabolism of 50 families (C. virginica) selectively bred for performance in varying environments was measured and significantly correlated with predicted performance. By establishing resazurin as an additional reliable and scalable method for metabolic assessment, this study lays the groundwork for its broader adoption in aquaculture and conservation. Implementing this approach may provide a tool to enhance stock selection, improve hatchery management practices, and support adaptive strategies in the face of climate variability and increased environmental stress in coastal oceans.

physiology↗

bioRxiv2025

Oral L-arginine cures arginase 1-dependent chronic cutaneous leishmaniasis by redirecting the T helper cell response

Leishmania (L.) mexicana-induced cutaneous leishmaniasis (CL) is a neglected tropical disease characterized by localized chronic ulcers (LCL) and, in rare cases, by disseminated skin lesions (DCL). The therapeutic options for CL are currently limited, and the immune dysregulation leading to chronicity of disease is poorly understood. Here, we identified interleukin (IL)-10-dependent upregulation of arginase 1 (ARG1) in cutaneous CX3CR1+ myeloid cells as central immunometabolic determinant of chronic CL in L. mexicana-infected C57BL/6 wild-type (WT) mice. Deletion of Arg1 in myeloid cells (Arg1{Delta}Cx3cr1) enabled parasite control and clinical healing. Single-cell RNA sequencing revealed that ARG1, together with interferon-{gamma} produced by T-helper 1 (Th1) cells, caused pathologic differentiation of Ly6Chigh monocytes into inflammatory macrophages (iMACs) that simultaneously expressed ARG1, nitric oxide synthase type 2 (NOS2) and the chemokines CXCL9/10. These Arg1+Nos2+Cxcl9/10+iMACs induced a lasting depletion of L-arginine in the skin, served as parasite niche, and maintained a self-perpetuating cycle of host cell recruitment. In Arg1{Delta}Cx3cr1 mice, the ARG1+NOS2+ host cell niche for the parasite was diminished. Prophylactic or therapeutic oral L-arginine supplementation restored tissue arginine levels, reduced parasite burden, and prevented or resolved chronic disease. L-arginine-treated mice showed enhanced T cell expansion and Th1 differentiation, remained free of clinical relapses, and were resistant to reinfection. As skin lesion biopsies from L. mexicana-infected LCL and DCL patients demonstrated a similar pattern of Th1/Th2 cytokine, Arg1 and Nos2 mRNA expression as seen in mice, we suggest metabolic reprogramming by oral L-arginine as a promising and easy-to-apply host-directed therapy for human L. mexicana CL. ONE SENTENCE SUMMARYArginase 1-mediated arginine depletion accounts for chronic cutaneous leishmaniasis, which can be prevented and even cured by oral L-arginine therapy.

immunology↗

bioRxiv2025

Uncovering Host-Parasite Dynamics: Gene Expression Shifts in Hematodinium-infected Chionoecetes bairdi in Response to Temperature ChangeChanges in gene expression under differing temperature regimes of infected Chionoecetes bairdi and the parasitic dinoflagellate Hematodinium sp.

Parasites can have profound effects on their hosts, and those effects can be altered by changing environmental conditions. The dinoflagellate Hematodinium sp. is a common and deadly parasite of the crab Chionoecetes bairdi, a species vulnerable to rising ocean temperatures. To examine the impact of parasitism under various temperature conditions, infected crabs (n = 9) were held under three temperature regimes (4{degrees}C, 7.5{degrees}C, and 10{degrees}C) for 17 days. RNAseq was performed on samples from three timepoints, and the relationships of temperature and time to gene expression were examined. Transcriptomes for C. bairdi and Alveolata symbiotes were created, and genes linked to immune function were identified within both host and parasite. Within the host, 1721 contigs were differentially expressed in response to a temperature increase, with 86% of these increased in expression. In total, 3013 contigs linked to temperature response were identified. Additionally, numerous changes in biological processes were observed in Hematodinium over the course of the experiment, including development and microtubule-based processes and ribosomal assembly. Through understanding the impact of changes in temperature on gene expression within both Hematodinium and infected C. bairdi, we provide a more complete picture of the response of these species to rising ocean temperatures.

molecular biology↗

bioRxiv2025

Stress attenuation by the adrenergic-specific lncRNA NESPR prevents cell death in neuroblastoma cells

Neuroblastoma is a pediatric cancer of the sympathetic nervous system characterized by heterogeneous cell states that mirror normal differentiation trajectories. Each state is governed by a core regulatory transcriptional circuitry that reinforces cell identity through an autoregulatory feedforward loop. We identified the long non-coding RNA NESPR as specifically expressed in adrenergic neuroblastoma cells. NESPR expression correlates with high-risk neuroblastoma clinical parameters and poor patient survival. NESPR is located within an insulated gene neighborhood alongside PHOX2B, a master transcription factor of the adrenergic identity. NESPR depletion reduced cell proliferation and increased caspase activity in neuroblastoma cell lines, and NESPR knockout in a neuroblastoma zebrafish model led to reduced tumor penetrance. Subcellular localization revealed NESPR to be a cytosolic long non-coding RNA, suggesting a trans-regulatory function. RNA-sequencing following NESPR depletion revealed a shift from an adrenergic to a mesenchymal cell state, due to proteotoxic stress-induced molecular reprogramming. These findings suggest NESPR as a regulator of neuroblastoma cell identity with potential therapeutic opportunities in high-risk neuroblastoma cases.

genetics↗

bioRxiv2025

Non-coding RNA Repertoire in Reef-Building Corals

Non-coding RNAs (ncRNAs) play critical regulatory roles in gene expression regulation that influences diverse biological processes in response to environmental change. Yet their characterization in non-model organisms, particularly sessile, benthic ecosystem engineers such as reef-building corals that are sensitive to climate change, remains limited. This study provides the first comprehensive analysis of the ncRNA repertoire of species from three ecologically important coral genera from Moorea, French Polynesia: Acropora pulchra, Pocillopora tuahiniensis, and Porites evermanni. These species demonstrate differing symbiotic partners, life history strategies, and physiological traits, offering a broad framework for documenting ncRNA variation in corals. We identified homologs for ncRNA biogenesis and functional machinery, characterized long ncRNAs (lncRNAs), microRNAs (miRNAs), and piwiRNAs (piRNAs), and assessed their genomic context and potential targets. Our findings reveal the presence of conserved ncRNA machinery across these coral species, indicating their capability to generate and utilize ncRNAs for the regulation of gene expression. We identified only a single miRNA conserved with corals and Eumetazoans (miR-100), four miRNAs shared across all three species, previously identified in other cnidarian taxa (miR-100, miR-2023, miR-2025, miR-2036), as well as several species-specific miRNAs. Predicted gene targets of the characterized miRNAs included immune response regulation in A. pulchra and P. tuahiniensis and signal transduction pathways in P. evermanni and P. tuahiniensis. Proximity analysis indicated >71-99% of piRNAs overlapped with genes, with genomic maintenance and stability identified as the primary functional enrichment of those genes. Our characterization of lncRNAs found little sequence overlap across each species (<2%), although lncRNAs in all three species were often in proximity to immune-related genes. This study lays the groundwork for the repertoire and regulatory roles of ncRNAs in reef-building corals, thereby expanding our understanding of epigenetic regulation in environmentally sensitive marine invertebrates and its potential implications in acclimatization and adaptation to environmental change.

molecular biology↗

bioRxiv2024

Repression of CADM1 transcription by HPV type 18 is mediated by three-dimensional rearrangement of promoter-enhancer interactions

Upon infection, human papillomavirus (HPV) manipulates host cell gene expression to create an environment that is supportive of a productive and persistent infection. The virus-induced changes to the host cells transcriptome are thought to contribute to carcinogenesis. Here, we show by RNA-sequencing that oncogenic HPV18 episome replication in primary human foreskin keratinocytes (HFKs) drives host transcriptional changes that are consistent between multiple HFK donors. We have previously shown that HPV18 episome replication in HFKs results in post-transcriptional stabilisation of the host chromatin insulation protein CTCF. Since CTCF is an important regulator of host cell transcription via coordination of epigenetic boundaries and long-range chromosomal interactions, we hypothesised that HPV18-induced stabilisation of CTCF may contribute to host transcription reprogramming. Analysis of CTCF binding in the host cell genome by ChIP-Seq revealed that while the total number of CTCF binding sites is not altered by the virus, there are a sub-set of CTCF binding sites that are either enriched or depleted of CTCF. Many of these altered sites are clustered within regulatory elements of differentially expressed genes, including the tumour suppressor gene cell adhesion molecule 1 (CADM1), which supresses epithelial cell growth and invasion. We show that HPV18 establishment results in reduced CTCF binding at the CADM1 promoter and upstream enhancer. Loss of CTCF binding is coincident with epigenetic repression of CADM1, in the absence of CpG hypermethylation, while adjacent genes including the transcriptional regulator ZBTB16 are activated. These data indicate that the CADM1 locus is subject to topological rearrangement following HPV18 establishment. We tested this hypothesis using 4C-Seq (circular chromosome confirmation capture-sequencing) and show that HPV18 establishment causes a loss of long-range chromosomal interactions between the CADM1 transcriptional start site and the upstream transcriptional enhancer. These data show that HPV18 manipulates host cell promoter-enhancer interactions to drive transcriptional reprogramming that may contribute to HPV-induced disease progression. AUTHOR SUMMARYInfection with oncogenic HPV is the cause of numerous cancer types, which generally arise after persistent HPV infection. Upon infection, HPV alters the gene expression profile of infected cells to facilitate virus replication and persistence. Multiple mechanisms of HPV-induced host cell reprogramming have been previously suggested. Here, we show that HPV infection induces rearrangement of specific genomic loci by altering the chromatin binding of the host cell protein CTCF, an important regulator of chromatin architecture. Loss of CTCF binding to a cluster of binding sites at the CADM1 locus on chromosome 11 is coincident with epigenetic reprogramming and disruption of long-range chromatin interactions, resulting in transcriptional repression of CADM1. Our data show that repression of CADM1 is an early event in HPV-driven disease, preceding hypermethylation of the CADM1 transcriptional promoter that is frequently observed in HPV-driven cancers, demonstrating a novel mechanism of HPV-induced host cell transcriptional reprogramming.

microbiology↗

bioRxiv2024

Long-term ketogenic diet causes hyperlipidemia, liver dysfunction, and glucose intolerance from impaired insulin trafficking and secretion in mice

A ketogenic diet (KD) is a very low-carbohydrate, very high-fat diet proposed to treat obesity and type 2 diabetes. While KD grows in popularity, its effects on metabolic health are understudied. Here we show that, in male and female mice, while KD protects against weight gain and induces weight loss, over long-term, mice develop hyperlipidemia, hepatic steatosis, and severe glucose intolerance. Unlike high fat diet-fed mice, KD mice are not insulin resistant and have low levels of insulin. Hyperglycemic clamp and ex vivo GSIS revealed cell-autonomous and whole-body impairments in insulin secretion. Major ER/Golgi stress and disrupted ER-Golgi protein trafficking was indicated by transcriptomic profiling of KD islets and confirmed by electron micrographs showing a dilated Golgi network likely responsible for impaired insulin granule trafficking and secretion. Overall, our results suggest long-term KD leads to multiple aberrations of metabolic parameters that caution its systematic use as a health promoting dietary intervention.

physiology↗

bioRxiv2024

DNA methylation modulates transcriptional noise in response to elevated pCO2 in the eastern oyster (Crassostrea virginica)

Ocean acidification significantly affects marine calcifiers like oysters, warranting the study of molecular mechanisms like DNA methylation that contribute to adaptive plasticity in response to environmental change. However, a consensus has not been reached on the extent to which methylation modules gene expression, and in turn plasticity, in marine invertebrates. In this study, we investigated the impact of pCO2 on gene expression and DNA methylation in the eastern oyster, Crassostrea virginica. After a 30-day exposure to control (572 ppm) or elevated pCO2 (2,827 ppm), whole genome bisulfite sequencing (WGBS) and RNA-Seq data were generated from adult female gonad tissue and male sperm samples. Although differentially methylated loci (DML) were identified in females (89) and males (2,916), there were no differentially expressed genes, and only one differentially expressed transcript in females. However, gene body methylation impacted other forms of gene activity in sperm, such as the maximum number of transcripts expressed per gene and changes in the predominant transcript expressed. Elevated pCO2 exposure increased gene expression variability (transcriptional noise) in males but decreased noise in females, suggesting a sex-specific role of methylation in gene expression regulation. Functional annotation of genes with changes in transcript-level expression or containing DML revealed several enriched biological processes potentially involved in elevated pCO2 response, including apoptotic pathways and signal transduction, as well as reproductive functions. Taken together, these results suggest that DNA methylation may regulate gene expression variability to maintain homeostasis in elevated pCO2 conditions and could play a key role in environmental resilience in marine invertebrates.

physiology↗

bioRxiv2023

Phase-changing citrate macromolecule combats oxidative pancreatic islet damage, enables islet engraftment and function in the omentum

Clinical outcomes for total-pancreatectomy followed by intraportal islet autotransplantation (TP-IAT) to treat chronic pancreatitis (CP) patients are suboptimal due to the inflammatory state of the patients pancreas, oxidative tissue damage during the isolation process, and the harsh engraftment conditions in the livers vasculature, which include ischemia-reperfusion injury, and instant blood-mediated inflammatory reactions. We describe the use of the thermoresponsive, antioxidant macromolecule poly(polyethylene glycol citrate-co-N-isopropylacrylamide) (PPCN) to protect islet redox status and function in vitro and in vivo and to create a viable extrahepatic islet engraftment site in the abdomen. PPCN in aqueous media transitions from a liquid to an elastic hydrogel when exposed to body temperature via temperature-induced macromolecular self-assembly. Islets entrapped in the PPCN hydrogel and exposed to oxidative stress remain functional and support long-term euglycemia, in contrast to islets entrapped in a biologic scaffold (BS). When applied to the omentum of non-human primates (NHPs), PPCN is well-tolerated, safe, and mostly resorbed without fibrosis at 3 months post-implantation. To obtain autologous islets, a partial pancreatectomy was performed, followed by STZ administration to induce diabetes and destroy any remaining endogenous islets. Application of the autologous islets to the momentum using PPCN restored normoglycemia with minimal insulin requirements for over 100 days. These results support the use of PPCN as a scaffold for minimally invasive delivery of islets to the omentum of pancreatitis patients and highlight the importance of scaffold antioxidant properties as a new mechanism to protect islet function and maximize long-term autologous graft performance. One Sentence SummaryOmentum islet transplantation using a thermoresponsive, antioxidative polymer supports autologous islet viability and function in nonhuman primates.

bioengineering↗

bioRxiv2023

CyVerse: Cyberinfrastructure for Open Science

CyVerse, the largest publicly-funded open-source research cyberinfrastructure for life sciences, has played a crucial role in advancing data-driven research since the 2010s. As the technology landscape evolved with the emergence of cloud computing platforms, machine learning and artificial intelligence (AI) applications, CyVerse has enabled access by providing interfaces, Software as a Service (SaaS), and cloud-native Infrastructure as Code (IaC) to leverage new technologies. CyVerse services enable researchers to integrate institutional and private computational resources, custom software, perform analyses, and publish data in accordance with open science principles. Over the past 13 years, CyVerse has registered more than 110,000 verified accounts from 160 countries and was used for over 1,600 peer-reviewed publications. Since 2011, 45,000 students and researchers have been trained to use CyVerse. The platform has been replicated and deployed in two countries outside the US, with additional private deployments on commercial clouds for US government agencies and multinational corporations. In this manuscript, we present a strategic blueprint for creating and managing SaaS cyberinfrastructure and IaC as free and open-source software.

scientific communication and education↗