Biology subjects

Wheeler, B.

Publications and source records attributed to Wheeler, B..

5 recordsLinked to original sources

bioRxiv2025

AA-ending codon-based computational analyses uncover novel cytoplasmic effectors in the Magnaporthe oryzae secretome

Phytopathogens secrete diverse, sequence-unrelated effector proteins outside (apoplastic) or into (cytoplasmic) plant cells to suppress host defenses and cause devastating diseases. Effectors rapidly evolve to avoid counter-detection by the host, and fungal cytoplasmic effectors lack recognizable host cell-targeting motifs, impeding cataloguing of the full suite of host-deployed effectors encoded in pathogen genomes. In the devastating rice blast fungus Magnaporthe oryzae, cytoplasmic and apoplastic effectors are secreted by different routes, but candidates must be confirmed by fluorescent labelling, consequently few are known. AA-ending codon usage rates are the fraction of AA-ending codons as a percentage of the total number of AA- and synonymous AG-ending codons in an mRNA. In M. oryzae, high AA % rates of the corresponding mRNAs distinguished seven experimentally confirmed cytoplasmic effectors from four experimentally confirmed apoplastic effectors, but whether AA % rates can identify new effectors is unknown. Here, using computational analyses and live-cell imaging confirmation, we successfully predicted, based on AA % rates, two new cytoplasmic effectors and two apoplastic effectors in the M. oryzae secretome. Our findings support the notion that cytoplasmic effector mRNAs are globally enriched for AA-ending codons, aiding effector discovery and the search for novel sources of durable crop resistance.

plant biology↗

bioRxiv2025

Systematic development of degradable polyester biomaterials via ring-opening copolymerization of succinic anhydride and epoxides

Degradable polyester materials are widely utilized in medicine as resorbable sutures, implantable devices, and drug delivery. These applications require precise and tunable degradation control; predictable number-average molecular weight ([M]n), narrow polydispersity (PDI), and diverse material properties define polyester utility, which are not easily achieved through well-established synthesis approaches. Ring-opening copolymerization (ROCOP) provides reproducible[M] n control, narrow PDI, and expands monomer diversity. In this work, poly(cyclohexene succinate) (PCS) and poly(propylene succinate) (PPS) were synthesized through a central composite design of experiments approach, systematically varying anhydride:epoxide ratio, monomer:catalyst ratio, reaction temperature, and reaction time. Reduced synthesis factor-response models explained significant variation for all characterized properties relevant to degradation control. PCS and PPS readily degraded under base-catalyzed hydrolysis conditions with significantly higher mass loss in PPS materials compared to PCS, highlighting the monomer selection influence in degradation behaviour. These findings highlight the potential for ROCOP to generate degradable biomaterials with reproducible material properties in application-specific biomedical use.

bioengineering↗

bioRxiv2025

Development of itaconate polymer microparticles for intracellular regulation of pro-inflammatory macrophage activation

Itaconate (IA) is an endogenous metabolite and a potent regulator of the innate immune system. Its use in immunomodulatory therapies has faced limitations due to inherent challenges in achieving controlled delivery and requirements for high extracellular concentrations to achieve internalization of the highly polar small molecule to achieve its intracellular therapeutic activity. Microparticle (MP)-based delivery strategies are a promising approach for intracellular delivery of small molecule metabolites through macrophage phagocytosis and subsequent intracellular polymer degradation-based delivery. Toward the goal of intracellular delivery of IA, degradable polyester polymer-(poly(itaconate-co-dodecanediol)) based IA polymer microparticles (IA-MPs) were generated using an emulsion method, forming micron-scale ([~] 1.5 {micro}m) degradable microspheres. IA-MPs were characterized with respect to their material properties and IA release kinetics to inform particle fabrication. Treatment of murine bone marrow-derived macrophages with an optimized particle concentration of 0.1 mg/million cells enabled phagocytosis-mediated internalization and low levels of cytotoxicity. Flow cytometry demonstrated IA-MP-specific regulation of IA-sensitive inflammatory targets. Metabolic analyses demonstrated that IA-MP internalization inhibited oxidative metabolism and induced glycolytic reliance, consistent with the established mechanism of IA-associated inhibition of succinate dehydrogenase. This development of IA-based polymer microparticles provides a basis for additional innovative metabolite-based microparticle drug delivery systems for the treatment of inflammatory disease.

bioengineering↗

bioRxiv2020

Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first six months of the COVID-19 pandemic

Three-dimensional structures of SARS-CoV-2 and other coronaviral proteins archived in the Protein Data Bank were used to analyze viral proteome evolution during the first six months of the COVID-19 pandemic. Analyses of spatial locations, chemical properties, and structural and energetic impacts of the observed amino acid changes in >48,000 viral proteome sequences showed how each one of the 29 viral study proteins have undergone amino acid changes. Structural models computed for every unique sequence variant revealed that most substitutions map to protein surfaces and boundary layers with a minority affecting hydrophobic cores. Conservative changes were observed more frequently in cores versus boundary layers/surfaces. Active sites and protein-protein interfaces showed modest numbers of substitutions. Energetics calculations showed that the impact of substitutions on the thermodynamic stability of the proteome follows a universal bi-Gaussian distribution. Detailed results are presented for six drug discovery targets and four structural proteins comprising the virion, highlighting substitutions with the potential to impact protein structure, enzyme activity, and functional interfaces. Characterizing the evolution of the virus in three dimensions provides testable insights into viral protein function and should aid in structure-based drug discovery efforts as well as the prospective identification of amino acid substitutions with potential for drug resistance.

molecular biology↗

bioRxiv2020

The Atlas of the In Vivo HIV CD4 T Cell Reservoir

ABSTRACTThe latent reservoir is a main barrier for curing HIV. But because latently-infected cells cannot be phenotyped directly, the features of the in vivo reservoir have remained elusive. Here, we describe a method that leverages high-dimensional phenotyping using CyTOF to trace latently-infected cells reactivated ex vivo to their original pre-activation states. Our results suggest that contrary to common assumptions, the reservoir is not randomly distributed among cell subsets, and is remarkably conserved between individuals. However, reservoir composition differs between tissues and blood, as do cells successfully reactivated by different latency reversing agents. Most importantly, by selecting 8-10 of our 39 original CyTOF markers, we were able to isolate highly purified populations of unstimulated in vivo latent cells, thereby validating the PP-SLIDE approach for reservoir characterization. These purified populations were highly enriched for replication-competent and intact provirus, transcribed HIV, and displayed clonal expansion. The ability to isolate unstimulated latent cells from infected individuals enables previously impossible studies of HIV persistence.Competing Interest StatementThe authors have declared no competing interest.View Full Text

immunology↗