Sydney Burge

We present a tour de force of atomistic molecular dynamics simulations involving the coordinated effort of 14 research groups of the Ascona B-DNA Consortium (ABC). This initiative provides a complete characterization of the 2080 DNA hexamers embedded in 190 carefully selected 20-mer duplexes, each simulated in replicate for at least 10 microseconds in explicit solvent. This community effort delivers unprecedented, validated FAIR data to support coarse-grained and AI models of DNA at cellular scale.

In mid-April, the University of Florida Emerging Pathogens Institute hosted its annual Research Day, featuring a special guest this year, Pepper the cat-chat bot, inspired by a real housecat.

The Asian citrus psyllid, Diaphorina citri, transmits the putative causal agent of citrus greening disease, ‘Candidatus Liberibacter asiaticus’. The transmission occurs in a propagative, circulative manner. Specific protein–protein interactions are required for the accomplishment of the transmission process. We employed the far-Western technique, also known as protein overlay assay, and mass spectrometry to identify D. citri proteins that specifically recognize membrane proteins of ‘Ca. L. asiaticus’. Whole-body protein extracts of D. citri were separated by electrophoresis and blotted onto polyvinylidene difluoride membranes.

Entamoeba histolytica is a protozoan parasite that causes amebic colitis, a leading cause of severe diarrheal disease worldwide, and amebic liver abscess, the most common extraintestinal manifestation of infection. Although most infections are asymptomatic, severe and fulminant disease is associated with high mortality, particularly among individuals exposed to corticosteroids or other forms of immunosuppression. The increasing use of molecular diagnostic tools has improved understanding of the epidemiology of E. histolytica and enabled distinction from morphologically identical but nonpathogenic Entamoeba species; however, these diagnostics remain underutilized in many endemic settings due to cost and infrastructure limitations.

Plasmodium vivax malaria is an increasing global health threat and the second leading cause of malaria globally. An efficacious vaccine aimed at preventing disease and transmission would greatly facilitate malaria elimination. The P. vivax circumsporozoite protein (PvCSP) is considered a leading pre-erythrocytic stage vaccine target. While P. falciparum malaria vaccines currently in clinical use have CSP as the critical component, their limited efficacy and the need for multiple doses continue to pose challenges for malaria vaccines. This study evaluated a novel customized size-tuned nanoparticle production and conjugation protocol co-displaying PvCSP with a TLR agonist as a vaccine platform to induce sporozoite-neutralizing antibodies to prevent sporozoite infection of hepatocytes.

Mutations in the MAPT gene encoding tau protein can be causative for frontotemporal lobar degeneration, FTLD-tau. Preclinical mouse models expressing these disease-causing MAPT alleles have successfully modeled biochemical and neuropathological phenomena similar to those seen in human FTLD-tau. Here, we have generated and characterized mice that constitutively overexpress P301L human tau under the CaMKII promoter. Overall, this new cTauP301L model recapitulates disease-associated pathology and memory deficits, with limited disruption of the murine genome and a lack of longevity-restricting motor phenotypes. The cTauP301L mouse is a robust, new alternative to existing mouse models of tauopathy.

Proteomics provides key insights into systems regulating cell behavior and can elucidate key epigenetic states influencing biological functions in health and disease. Integrating different modalities of proteomics allows for a comprehensive understanding of how systems change in response to a stimulus. A current limitation is that these data are often captured individually with a limited scope of how systems regulating biological processes interact. Using the MPOInt pipeline and its associated R package and pre-existing clinical data, we identify several pathways that may be targets in driving the growth of aggressive cancers, including treatment-resistant estrogen receptor-positive breast cancer. Overall, MPOInt adds clinical context to data that is traditionally difficult to interpret and generates a unique network centered around epigenetic factors for each collection of data.

Studies have shown that use of immunomodulators during the acute phase of SARS-CoV-2 infection may decrease development of post-acute sequelae of SARS-CoV-2 (PASC) or long COVID; however, such studies have not been conducted in children. The objective of the study was to evaluate the effectiveness of steroid use during the acute phase of SARS-CoV-2 infection in preventing long COVID in children. We conducted a retrospective cohort study using target trial emulation methodology to compare children and youth who did and did not receive dexamethasone, prednisone, prednisolone or methylprednisolone within 12 days of SARS-CoV-2 infection.

Cytomegalovirus (CMV) is among the most common infectious complications following allogeneic hematopoietic cell transplantation (allo-HCT). The CMV T-cell immunity panel (CMV-TCIP, Viracor) assesses CMV cell-mediated immunity (CMV-CMI); however, its utility among pediatric allo-HCT recipients remains unknown. A retrospective analysis (January 2020–January 2024) among pediatric (≤ 18 years) allo-HCT recipients with CMV DNAemia and at least one CMV-TCIP test was performed.

Methods for unknown metabolite characterization rely heavily on one or more of the following: spectroscopic approaches; tandem mass spectrometry (MS/MS); ion mobility or liquid chromatography; and/or guided intervention through reverse metabolomics, derivatization, etc. The limitations of these methodologies vary widely. Additionally, tandem mass spectrometry is often insufficient for unambiguous identification, and guided interventions can be limited in scope. A complementary approach to high-resolution mass spectrometry that is high-throughput, is robust, and provides nondiscrete data that can rationally inform metabolite structure is desirable. Here, we present an optimized method utilizing sodium bicarbonate for hydrogen–deuterium exchange (HDX) to label slowly exchanging and labile sites over time, after which back-exchange of all labile sites leaves only slowly exchanging sites labeled for subsequent MS analysis.