Biology subjects

Carpenter, D.

Publications and source records attributed to Carpenter, D..

6 recordsLinked to original sources

bioRxiv2026

Hepatocyte UBE4A protects against MASLD/MASH by maintaining ER homeostasis via UBXN4 interaction

Molecular understanding of the regulation of endoplasmic reticulum (ER) functions in healthy and MASLD livers is limited. Here, we elucidate that Ube4A, a cytosolic E3 ubiquitin ligase, protects against MASLD development by maintaining ER homeostasis during nutritional stress. Hepatocyte-Ube4A deletion (HUKO) augments Gubra-Amylin-diet (GAN-D)-induced steatosis, inflammation, insulin resistance, ER stress and markers of steatohepatitis of the liver in both sexes of mice. Proteomic studies reveal that in addition to altered metabolic and fibrogenic pathways, levels of many ER proteins are also changed in HUKO livers. Impaired ER functions sensitize HUKO livers to nutrition- or chemical (tunicamycin)-induced ER stress. Moreover, HUKO primary hepatocytes exhibit increased ER stress. Furthermore, Ube4A maintains ER homeostasis by facilitating ER-associated protein degradation (ERAD). The lipogenic protein SCD1 is identified as one of the ERAD targets of Ube4A. SCD1 stability and triglyceride accumulation are amplified in HUKO primary hepatocytes. The liver Ube4A-interactome studies identified the ERAD mediator UBXN4 as a major Ube4A interacting protein. Alphafold3-based molecular modelling and interaction site mapping analyses pinpointed the Ube4A binding residues for UBXN4. ER-localized Ube4A-UBXN4 complex facilitates ERAD (e.g., SCD1) and UBXN4-binding deficient Ube4A mutants fail to enhance this process. Finally, Ube4A and UBXN4 are downregulated in the livers of human MASLD and MASH patients and this complex is diminished in GAN-D-fed mouse livers. In conclusion, Ube4A preserves ER homeostasis by maintaining ERAD via its interaction with UBXN4, which maintains liver health. Enhancing levels and/or preserving interaction of these proteins may offer new therapeutic strategies for MASLD treatment.

physiology↗

bioRxiv2026

Challenges in establishing epidemiological cut-off values for the Burkholderia cepacia complex

The Burkholderia cepacia complex (BCC) is comprised of 24 species of Gram-negative bacteria that cause opportunistic infections. While antimicrobial susceptibility testing (AST) has historically been used to guide treatment for BCC infections, recent work highlighting problems with AST for these organisms led the Clinical and Laboratory Sciences Institute (CLSI) to remove disk diffusion (DD) and minimal inhibitory concentration (MIC) breakpoints for BCC from its M100 standards document. Epidemiological cut-off values (ECVs) may be helpful to clinicians in the absence of breakpoints, as they may be used to determine whether an isolate has a wild-type or non-wild-type phenotype. Here we present an analysis of BCC ECVs for ceftazidime (CAZ), levofloxacin (LVX), meropenem (MEM), minocycline (MIN), and trimethoprim-sulfamethoxazole (TMP-SMX). ECVs were calculated using MIC data from 3 previous studies and 3 independent laboratories for 1,896 BCC isolates. ECVs were 16 g/ml for CAZ, 8 g/ml for LVX, 16 g/ml for MEM, and 8 g/ml for MIN. The ECV for TMP-SMX varied depending on the analysis from 2 g/ml, 8 g/ml, and 16 g/ml and therefore could not be reliably established. Challenges with establishing ECVs for BCC include limitations with the pooled MIC dataset, broad MIC distributions, and high ECVs that are above the obsolete susceptible MIC breakpoints. These challenges limit the clinical utility of ECVs for these organisms and supported removal of ECVs from the CLSI M100 standards document. IMPORTANCEThe Burkholderia cepacia complex is a group of bacterial species that cause difficult-to-treat opportunistic infections. Recently, clinical breakpoints, which are used to determine whether organisms are susceptible to certain antimicrobials, were removed from Clinical and Laboratory Standards Institute (CLSI) standards for these organisms due to problems with antimicrobial susceptibility testing performance. Clinicians are now faced with the challenge of how to treat these complex infections without clinical breakpoints. Here we determine epidemiological cut-off values (ECVs) for relevant antimicrobials for the B. cepacia complex. While we established ECVs for four antimicrobials, we encountered significant challenges in our analyses, including limitations with data for these organisms and high ECVs that are not clinically useful. These challenges limit the practical use of these ECVs in helping guide clinicians on treatment and supported the eventual removal of ECVs from the CLSI M100 standards document.

microbiology↗

bioRxiv2025

Metabolic syndrome enhances SARS-CoV-2 disease severity and reduces mRNA vaccine efficacy in a mouse model

Metabolic syndrome (MetS) is a cluster of pathophysiological conditions linked to the disruption of metabolic processes associated with energy storage and consumption. Approximately one-third of adults in the United States are currently diagnosed with MetS. Patients with MetS experience higher mortality rates following SARS-CoV-2 infection and exhibit poor vaccine efficacy following influenza virus vaccination compared to metabolically healthy individuals. However, the specific impact of MetS on immune responses to SARS-CoV-2 infection and vaccination has not been widely studied. To address this gap, we utilized high-fat diet feeding to establish a murine model of MetS, in which mice exhibit the same diagnostic criteria for MetS as human patients. We then used high-fat diet-induced MetS mice and regular chow diet-fed wild-type mice to analyze immune responses to SARS-CoV-2 infection and vaccination. Following SARS-CoV-2 infection, we monitored mice for disease severity, measured levels of virally induced inflammation, and quantified viral titers in various tissues. Our results indicate that MetS mice exhibit accelerated mortality post-infection, accompanied by elevated mRNA levels of inflammatory cytokine transcripts at sites of infection. Additionally, MetS alters the degree of viral replication across various tissues. Furthermore, our vaccination studies revealed that MetS reduces the potency of vaccine-induced neutralizing antibodies against both the ancestral SARS-CoV-2 strain and the Delta variant. Overall, our findings suggest that MetS exacerbates SARS-CoV-2 disease severity and diminishes vaccine efficacy, underscoring the need for tailored strategies to protect individuals with MetS from severe outcomes following infection and vaccination. ImpactThis study represents the first detailed account of the failure to generate protective neutralizing antibody responses to SARS-CoV-2 in mice with metabolic syndrome (MetS) following vaccination. The insights gained from this research inform future vaccine design and aid in identifying individuals at greater risk of breakthrough infections. By specifically isolating the risk associated with MetS, rather than obesity alone, these findings lay the groundwork for future investigations aimed at enhancing immune responses in individuals with MetS. This work is highly relevant to a broad audience, as it addresses a critical unmet need in vaccine development and provides essential guidance for the rational design of vaccines to protect vulnerable populations affected by MetS.

immunology↗

bioRxiv2020

Sharing the burden? Earthworms and woodlice show seasonal complementarity in peak abundances in soil in an oak-beech temperate woodland.

Complementarity between functional analogues can confer resistance and resilience on ecosystems in the face of environmental change. High biodiversity can lead to increased ecosystem functionality through complementary effects. Earthworms, woodlice and millipedes can have high densities in leaf litter and soils, but little is known about their seasonal patterns. The two groups play important roles in the breakdown and incorporation of organic matter into soils. Differences in peak abundance could affect the rates of litter break down and incorporation in different seasons. We sampled earthworms, woodlice and millipedes from leaf litter soil every month for ten years in a New Forest woodland. We used non-parametric regression to explore monthly and yearly variation in the abundance of decomposer organisms and soil temperature and moisture. Earthworms have a distinct seasonal peak in density different from woodlice and millipedes. Earthworm peak density is in the winter and spring and is correlated with greatest soil moisture. Woodlice (and millipede) have their peak density is in the summer and is correlated with the highest soil temperatures. This means that earthworms, woodlice and millipedes have complementary peaks in abundance. These two groups have similar functional roles in litter decomposition and these data imply ecological complementarity in this important ecological process. This effect is likely to be widespread in lowland woodland in the UK and Europe, with only extreme temperatures and low pH limiting the distribution. Increased summer drought as a result of climate change may lead to changes in the relative abundance of these three groups and in particular local extinctions of earthworms which will in turn affect litter decomposition.

ecology↗

bioRxiv2020

Primary human colonic mucosal barrier crosstalk with super oxygen-sensitive Faecalibacterium prausnitzii in continuous culture

The gut microbiome plays an important role in human health and disease. Gnotobiotic animal and in vitro cell-based models provide some informative insights into mechanistic crosstalk. However, there is no existing system for a chronic co-culture of a human colonic mucosal barrier with super oxygen-sensitive commensal microbes, hindering the study of human-microbe interactions in a controlled manner. Here, we investigated the effects of an abundant super oxygen-sensitive commensal anaerobe, Faecalibacterium prausnitzii, on a primary human mucosal barrier using a Gut-MIcrobiome (GuMI) physiome platform that we designed and fabricated. Chronic continuous co-culture of F. prausnitzii for two days with colon epithelia, enabled by continuous flow of completely anoxic apical media and aerobic basal media, resulted in a strictly anaerobic apical environment fostering growth of and butyrate production by F. prausnitzii, while maintaining a stable colon epithelial barrier. We identified elevated differentiation and hypoxia-responsive genes and pathways in the platform compared with conventional aerobic static culture of the colon epithelia, attributable to a combination of anaerobic environment and continuous medium replenishment. Furthermore, we demonstrated anti-inflammatory effects of F. prausnitzii through HDAC and the TLR-NFKB axis. Finally, we identified that butyrate largely contributes to the anti-inflammatory effects by downregulating TLR3 and TLR4. Our results are consistent with some clinical observations regarding F. prausnitzii, thus motivating further studies employing this platform with more complex engineered colon tissues for understanding the interaction between the human colonic mucosal barrier and microbiota, pathogens, or engineered bacteria.Competing Interest StatementA provisional patent was filed.View Full Text

bioengineering↗

bioRxiv2018

The malaria-protective human glycophorin structural variant DUP4 shows somatic mosaicism and association with hemoglobin levels

Glycophorin A and glycophorin B are red blood cell surface proteins that are both receptors for the parasite Plasmodium falciparum, which is the principal cause of malaria in sub-Saharan Africa. DUP4 is a complex structural genomic variant that carries extra copies of a glycophorin A - glycophorin B fusion gene, and has a dramatic effect on malaria risk by reducing the risk of severe malaria by up to 40%. Using fiber-FISH and Illumina sequencing, we validate the structural arrangement of the glycophorin locus in the DUP4 variant, and reveal somatic variation in copy number of the glycophorin A-glycophorin B fusion gene. By developing a simple, specific, PCR-based assay for DUP4 we show the DUP4 variant reaches a frequency of 13% in a village in south-eastern Tanzania. We genotype a substantial proportion of that village and demonstrate an association of DUP4 genotype with hemoglobin levels, a phenotype related to malaria, using a family-based association test. Taken together, we show that DUP4 is a complex structural variant that may be susceptible to somatic variation, and show that it is associated with a malarial-related phenotype in a non-hospitalized population.\n\nSignificance statementPrevious work has identified a human complex genomic structural variant called DUP4, which includes two novel glycophorin A-glycophorin B fusion genes, is associated with a profound protection against severe malaria. In this study, we present data showing the molecular basis of this complex variant. We also show evidence of somatic variation in the copy number of the fusion genes. We develop a simple robust assay for this variant and demonstrate that DUP4 is at an appreciable population frequency in Tanzania and that it is associated with higher hemoglobin levels in a malaria-endemic village. We suggest that DUP4 is therefore protective against malarial anemia.

genetics↗