Biology subjects

Holmes, H.

Publications and source records attributed to Holmes, H..

6 recordsLinked to original sources

bioRxiv2026

Gag proteolysis drives HIV-1 envelope conformational closure through the gp41 cytoplasmic tail

HIV-1 must present a fusion-competent envelope glycoprotein (Env) to enter host cells while concealing the very conformation targeted by broadly neutralising antibodies (bnAbs). How the virus resolves this conflict has remained unclear. Using a minimally invasive nanobody-labelling strategy targeting Env's V4 loop, we combine single-virus FRET, fluorescence lifetime cross-correlation spectroscopy, and DNA-PAINT super-resolution microscopy to resolve Env conformation on individual, intact virions from the primary isolate JR-FL. We show that immature virions predominantly display an open Env conformation, while Gag maturation drives acquisition of the tightly closed, fusion-competent State 1 that harbours the principal bnAb epitope. Truncating the Env cytoplasmic tail abolishes this regulation, identifying the gp41 tail as the conduit linking Gag lattice maturation to Env's conformational fate. We further show that bnAb b12 preferentially binds open Env on immature virions, supporting a decoy mechanism that shields mature virions from immune recognition, with direct implications for HIV-1 vaccine design.

biophysics↗

bioRxiv2026

Development and characterization of a miniaturized focused ultrasound extraction (FUSE) system to enable rapid, point-of-care genetic testing

Point-of-care (POC) molecular detection has enabled rapid and accessible testing at or near the site of need, facilitating timely decision-making in clinical, field, and industrial settings. Despite these advancements, molecular detection platforms remain limited in their ability to prepare DNA from complex tissue matrices, restricting their applicability to a narrow range of sample types. To address sample preparation inefficiencies, focused ultrasound extraction (FUSE) has been developed for the rapid release of DNA from robust tissue matrices. FUSE disintegrates target tissue and releases DNA by delivering high pressure ultrasound pulses that generate a cavitation bubble cloud. In prior work, FUSE was performed using large, laboratory-based equipment. Here, a miniaturized FUSE device was designed and tested to enable POC DNA sample preparation. Design constraints were defined based on prior FUSE experiments, and based on these metrics, a 750 kHz cylindrical transducer was fabricated. The pressure output was measured, and high-speed optical imaging demonstrated that the transducer generated sustained cavitation within the defined focal region. The feasibility of DNA extraction from piscine and timber tissues was evaluated, and results show that the device can release DNA with quality suitable for PCR-based detection from both tissue types. These results demonstrate the potential of this device to rapidly extract DNA from complex samples and expand the applicability of molecular detection platforms.

bioengineering↗

bioRxiv2025

Alpha-BET: Functional labeling of envelope glycoproteins with single domain antibodies for in-virus single molecule imaging

We present Alpha-BET, a structure-guided strategy leveraging AlphaFold to identify optimal ALFA-tag insertion sites for minimally disruptive labeling of viral glycoproteins with high-affinity nanobodies. Applied to HIV-1 Env, SARS-CoV-2 S, and NiV G, Alpha-BET preserves structural integrity and function. For HIV-1 Env, we demonstrate super-resolution DNA-PAINT MINFLUX 3D imaging enabled by tag insertion, showcasing its power for visualizing native trimers in single virions and potential for broader applications in virus research.

biophysics↗

bioRxiv2024

Decentralizing genetic testing for biodiversity monitoring and biosurveillance with the Nucleic Acid Barcode Identification Tool (NABIT) and Molecular Development Kit (MDK).

O_LIThe escalating threats to biodiversity, public health, and food security posed by emerging infectious diseases and illegal wildlife trafficking requires novel approaches to biosurveillance. This paper introduces two innovations developed to address these multifaceted challenges: the Nucleic Acid Barcode Identification Tool (NABIT) and the Molecular Development Kit (MDK). C_LIO_LIThe NABIT is a handheld, battery-powered device that enables genetic tests to be performed at the point of contact by non-technical users, creating a critical bridge between centralized laboratories and the field by reducing barriers to accessible and routine genetic testing. Verification testing and validation results for the NABIT and the lyophilized assays used with it demonstrate key performance parameters, including sample preparation, detection sensitivity, and stability of field-ready assays after 17 months without refrigeration. C_LIO_LIThe MDK complements the NABIT by providing a framework for third-party development and deployment of field-ready genetic assays. Similar to software development kits (SDKs), the MDK offers documentation, software tools, and NABIT hardware to accelerate the development of new assays, enabling early detection strategies and minimizing future losses. Crucially, the MDK empowers scientists worldwide to contribute to a new ecosystem for wildlife genetics and biosurveillance by developing their own field-ready tests for the NABIT. C_LIO_LIIn summary, the NABIT and MDK present the potential for a paradigm shift in biosurveillance, ecosystem monitoring, and biodiversity conservation, enabling decentralized genetic testing, early disease detection, and rapid response to protect sensitive ecosystems, public health, and food security. C_LI

bioengineering↗

bioRxiv2022

Identification of a Female-produced Sex Attractant Pheromone of the Winter Firefly, Photinus corrusca

Firefly flashes are well-known visual signals used by these insects to find, identify, and choose mates. However, many firefly species have lost the ability to produce light as adults. These "unlighted" species generally lack developed adult light organs, are diurnal rather than nocturnal, and are believed to use volatile pheromones acting over a distance to locate mates. While cuticular hydrocarbons, which may function in mate recognition at close range, have been examined for a handful of the over 2000 extant firefly species, no volatile pheromone has ever been identified. In this study, using coupled gas chromatography - electroantennographic detection, we detected a single female-emitted compound that elicited antennal responses from wild-caught male winter fireflies, Photinus corrusca. The compound was identified as (1S)-exo-3-hydroxycamphor (hydroxycamphor). In field trials at two sites across the species eastern North American range, large numbers of male P. corrusca were attracted to synthesized hydroxycamphor, verifying its function as a volatile sex attractant pheromone. Males spent more time in contact with lures treated with synthesized hydroxycamphor than those treated with solvent only in laboratory two-choice assays. Further, using single sensillum recordings, we characterized a pheromone-sensitive odorant receptor neuron in a specific olfactory sensillum on male P. corrusca antennae and demonstrated its sensitivity to hydroxycamphor. Thus, this study has identified the first volatile pheromone and its corresponding sensory neuron for any firefly species, and provides a tool for monitoring P. corrusca populations for conservation, and further inquiry into the chemical and cellular bases for sexual communication among fireflies.

ecology↗

bioRxiv2022

DNA Release from Complex Plant Tissue Using Focused Ultrasound Extraction (FUSE)

Sample preparation in genomics is a critical step that is often overlooked in molecular workflows and impacts the success of downstream genetic applications. This study explores the use of a recently developed focused ultrasound extraction (FUSE) technique to enable the rapid release of DNA from plant tissues for genetic analysis. FUSE generates a dense acoustic cavitation bubble cloud that pulverizes targeted tissue into acellular debris. This technique was applied to leaf samples of American chestnut (Castanea dentata), tulip poplar (Liriodendron tulipifera), red maple (Acer rubrum), and chestnut oak (Quercus montana). We observed that FUSE can extract high quantities of DNA in 9-15 minutes, compared to the 30 minutes required for conventional DNA extraction. FUSE extracted DNA quantities of 24.33 {+/-} 6.51 ng/mg and 35.32 {+/-} 9.21 ng/mg from American chestnut and red maple, respectively, while conventional methods yielded 6.22 {+/-} 0.87 ng/mg and 11.51 {+/-} 1.95 ng/mg, respectively. The quality of the DNA released by FUSE allowed for successful amplification and next-generation sequencing. These results indicate that FUSE can improve DNA extraction efficiency for leaf tissues. Continued development of this technology aims to adapt to field-deployable systems to increase the cataloging of genetic biodiversity, particularly in low-resource biodiversity hotspots.

genetics↗