Biology subjects

Daly, J.

Publications and source records attributed to Daly, J..

11 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↗

bioRxiv2025

Quantifying vector diversion effects in zoonotic systems: A modelling framework for arbovirus transmission between reservoir and dead-end hosts

Vector-borne disease transmission involves complex interactions between vectors, reservoir hosts and dead-end hosts. We present a mathematical model for the vectorial capacity that incorporates multiple host types and their interactions, focusing specifically on West Nile virus transmission by Culex pipiens mosquitoes. Our model integrates climate-dependent parameters affecting vector biology with vector control interventions to predict transmission potential under various scenarios. We demonstrate how vector control interventions targeting one host type can significantly impact transmission dynamics across all host populations. By examining the effects of different vector control tool modes of action (repellency, preprandial killing, disarming and postprandial killing), we develop target product profiles that minimise unintended consequences of vector control. Notably, we identify the optimal intervention characteristics needed to prevent repellency on dead-end hosts from inadvertently increasing transmission among reservoir hosts. This research provides valuable insights for public health officials designing targeted vector control strategies and offers a flexible modelling framework that can be adapted to other vector-borne diseases with complex host dynamics. Author summaryMosquitoes that spread diseases like West Nile virus dont just bite one type of animal--they feed on birds, humans, and other mammals. This creates a complex web of disease transmission that current prevention strategies often overlook. We developed a mathematical model to understand what happens when mosquito control methods target different types of hosts in this network. Our research reveals a surprising and concerning finding: when people use repellents to protect themselves from mosquitoes, those mosquitoes dont simply disappear--they redirect to birds instead. Since birds are the main animals that can spread West Nile virus to other mosquitoes, this redirection can actually increase disease transmission in the bird population by up to 23%. More infected birds ultimately means more infected mosquitoes and higher risk for humans. However, we also identified a solution. We found that if repellent products could kill just 2% of the mosquitoes they encounter before those mosquitoes find alternative hosts, this would eliminate the harmful redirection effect. Our work provides specific guidelines for developing better mosquito control products and helps public health officials understand the broader consequences of different intervention strategies. This framework can be applied to other mosquito-borne diseases beyond West Nile virus.

ecology↗

bioRxiv2025

CRISPR activation screens map the genomic landscape of cancer glycome remodeling

Many cancer types upregulate expression of sialic acid-containing glycans. These oligosaccharides subsequently engage inhibitory Siglec receptors on immune cells, allowing cancer cells to evade immune surveillance. The genetic mechanisms by which this glycome remodeling occurs remain poorly defined. Understanding the ways that cancer cells change their cell surface glycosylation is critical for identification of biomarkers and targets for glycan-directed immunotherapy. In this study, we performed multiple gain-of-function CRISPR activation (CRISPRa) screens to broadly define genetic pathways that regulate expression of Siglec-binding glycans. We show that Siglec ligand expression is largely controlled through genetic competition between genes that catalyze 2-3 sialylation and GlcNAcylation of galactose residues. Perturbation of enzyme expression at this key biosynthetic node provides multiple "paths" by which cancers can acquire elevated expression of Siglec ligands. We further show that cancer glycome remodeling is aided by overexpression of novel "professional ligands" that facilitate Siglec-glycan binding. Notably, we also find that expression of the CD24 gene is genetically dispensable for cell-surface binding of the inhibitory receptor Siglec-10. Finally, by integrating our functional genetic model with clinical tumor genomic data, we identify the sulfotransferase enzyme GAL3ST4 as a potential novel driver of immune evasion in glioma cells. Taken together, this study provides a first-in-class genomic atlas to aid understanding of cancer-associated glycosylation and identifies immediately actionable targets for cancer immunotherapy.

genomics↗

bioRxiv2024

Cryopreservation of the collector urchin embryo, Tripneustes gratilla

The collector urchin, Tripneustes gratilla, is an ecologically important member of the grazing community of Hawaiis coral reefs. Beyond its ability to maintain balance between native seaweeds and corals, T. gratilla has also been used as a food source and a biocontrol agent against alien invasive algae species. Due to overexploitation, habitat degradation, and other stressors, their populations face local extirpation. However, artificial reproductive techniques, such as cryopreservation, could provide more consistent seedstock throughout the year to supplement aquaculture efforts. Although the sperm and larvae of temperate urchins have been successfully cryopreserved, tropical urchins living on coral reefs have not. Here, we investigated the urchin embryos tolerance to various cryoprotectants and cooling rates to develop a cryopreservation protocol for T. gratilla. We found that using 1M Me2SO with a cooling rate of 9.7{degrees}C/min on gastrula stage embryos produced the best results with survival rates of up to 85.5% and up to 50.8% maturation to the 4-arm echinopluteus stage, assessed three days after thawing. Continued research could see cryopreservation added to the repertoire of artificial reproductive techniques for T. gratilla, thereby assisting in the preservation of this ecologically important urchin, all while augmenting aquaculture efforts that contribute to coral reef restoration.

zoology↗

bioRxiv2023

Comparative analysis of myoglobin in Cetaceans and humans reveals novel regulatory elements and evolutionary flexibility

Cetacea and other diving mammals have undergone numerous adaptations to their aquatic environment, among them high levels of the oxygen-carrying intracellular hemoprotein myoglobin in skeletal muscles, especially those responsible for swimming. Hypotheses regarding the mechanisms leading to these high myoglobin levels often invoke exercise, hypoxia, and other physiological pathways that impact gene regulation, and increase myoglobin gene expression. Here we explore an alternative hypothesis: that Cetacean myoglobin genes have evolved high levels of transcription driven by the intrinsic developmental mechanisms that drive muscle cell differentiation. We have used luciferase assays in differentiated C2C12 cells to test this hypothesis. Contrary to our hypothesis, we find that the myoglobin gene from the minke whale, Balaenoptera acutorostrata, has a low level of expression, less than 10% that of humans. This low expression level is broadly shared among Cetaceans, and Artiodactylans. Previous work on regulation of the human gene has identified a core muscle-specific enhancer comprised of two regions, the "AT element" and a C-rich sequence 5 of the AT element termed the "CCAC-box". Comparative analysis of the minke whale gene supports the importance of the AT element, but the minke whale CCAC-box ortholog has little effect. Instead, critical positive input has been identified in a G-rich region 3 of the AT element. Also, a conserved E-box in exon 1 positively affects expression, despite having been assigned a repressive role in the human gene. Last, a novel region 5 of the core enhancer has been identified, which we hypothesize may function as a boundary element. These results illustrate regulatory flexibility during evolution. They also support the hypothesis that the induction of transcription by physiological signaling pathways, and evolved protein stability are important in leading to the high myoglobin protein levels found in Cetaceans.

molecular biology↗

bioRxiv2023

The first proof of concept demonstration of nanowarming in coral tissue

Climate change is causing ocean acidification and warming, resulting in mass bleaching and death of corals globally. Cryopreservation and biobanking to secure the genetics of threatened populations is currently limited to coral sperm and larvae, which are only available during brief annual spawning events and are impacted by ocean warming, so there is an urgent need for methods to enable biobanking activities year-round. Here, we used vitrification and nanowarming to successfully recover adult coral tissues in a novel sample type, the single-polyp microfragment (SPMF). Fluorescence and confocal microscopy showed clearly defined tissues and green fluorescent protein fluorescence around the polyp mouth post-warming in 43.3% of SPMFs at 24 hours post-warming, and 30.0% at one month. These advances provide a basis for continued research and development of a field-ready protocol for cryopreservation of adult coral tissues, to permit biobanking of threatened coral species throughout the year and support reef restoration efforts.

ecology↗

bioRxiv2023

Cryopreservation and revival of Hawaiian stony corals via isochoric vitrification

Corals are under siege by both local and global threats, creating a wordwide reef crisis. Cryopreservation is an important intervention measure and a vital component of the modern coral conservation toolkit, but preservation techniques are currently limited to sensitive reproductive materials that can only be obtained a few nights per year during spawning. Here, we report the first successful cryopreservation and revival of cm-scale coral fragments via mL-scale isochoric vitrification. We demonstrate coral viability at 24h post-thaw using a calibrated oxygen-uptake respirometry technique, and further show that the method can be applied in a passive, electronics-free configuration. Finally, we detail a complete prototype coral cryopreservation pipeline, which provides a platform for essential next steps in modulating postthaw stress and initiating long-term growth. These findings pave the way towards an approach that can be rapidly deployed around the world to secure the biological genetic diversity of our vanishing coral reefs.

biophysics↗

bioRxiv2023

Metrics of Coral Microfragment Viability

Coral reefs are being degraded at unprecedented rates and decisive intervention actions are urgently needed to help them. One such intervention in aid of reefs is coral cryopreservation. Although the cryopreservation of coral sperm and larvae has been achieved, preservation of coral fragments including both its tissue and skeleton, has not. The goal of this paper was to understand and assess the physiological stressors that might underlie coral fragment cryopreservation and the long-term consequences of these physiological exposures to continued growth. Therefore, we assessed small fragments ([~]0.5 x0.5 mm2) from the Hawaiian coral, Porites compressa, examining: 1) the sensitivity of the fragments and their algal symbionts to chilling temperatures; 2) the sensitivity of the coral to complex cryoprotectants; 3) methods to safely remove the algal symbionts from the coral fragment for cryopreservation, given the two symbiotic partners may require different cryopreservation protocols; 4) continued growth over time of coral fragments once returned to running seawater after treatment exposures; and, 5) assessment of health and viability of microfragments after treatments examining the distribution of green fluorescent protein and fluorescent symbionts. Technological advances in cryo-technology promise to support successful coral fragment cryopreservation soon, and its success could help secure much of the genetic and biodiversity of reefs in the next decade.

cell biology↗

bioRxiv2022

Tank Fouling Community Enhances Coral Microfragment Growth

Anthropogenic stressors threaten reefs worldwide and natural in situ coral reproduction may be inadequate to meet this challenge. Land-based culture can provide increased coral growth, especially with microfragments. We tested whether culture methods using different algal fouling communities could improve the growth and health metrics of microfragments of the Hawaiian coral, Porites compressa. Culture method fouling communities were: 1) similar to a reef environment (Mini Reef); 2) clean tanks managed to promote crustose coralline algae (Clean Start); and, 3) tanks curated beforehand with poorly-competing algae (Green Film) assessed in winter and summer months. The Green Film method during the winter produced the fastest microfragment mean growth at 28 days until the first row of new polyps developed and the highest tank metric scores. Time efficient, standardized methods for land-based culture designed to maximize growth and production of coral fragments will contribute considerably to the success of large scale restoration efforts.

zoology↗

bioRxiv2022

Securing algal endosymbiont communities for reef-building corals

Photosynthetic dinoflagellates that live in symbiosis with corals (family Symbiodiniaceae) are fundamental for the survival of coral reef ecosystems. During coral bleaching events, it is assumed that these symbionts remain available in the water column, in sediments, or are seeded from unbleached coral colonies. Yet, this hypothesis has not been verified and it remains unclear whether some diversity of Symbiodiniaceae may be lost in the process. Culture methods have been developed for some Symbiodiniaceae, but for the vast majority of these photosynthetic symbionts, known culture methods are not successful at maintaining them for extensive periods. For these unculturable symbionts, cryopreservation, which places cells and tissues in suspended animation for days to decades, offers the best hope for saving the biodiversity of these crucial coral partners. Some cryopreservation processes use slow freezing, but if the cells are sensitive to low temperatures, as is the case for Symbiodiniaceae, then rapid freezing, called vitrification, is needed. We here, tested two published vitrification protocols that had been designed for algal symbionts extracted from Hawaiian corals, but we were unable to recover living symbionts after vitrification and warming. Therefore, we report a successful optimisation of the former vitrification protocols, which we tested on algal symbionts freshly extracted from three Hawaiian coral species, the development of ultra-rapid laser-warming cryopreservation techniques for symbionts, and banking procedures for algal symbionts. We also present some successful uptake of cryopreserved algal symbionts by coral larvae, although at a low rate. It is unclear why the former vitrification protocols failed but we propose that it may have been related to thermal stress and bleaching events that occurred on several occasions throughout the Hawaiian Islands. Maintenance of biodiversity is essential for sustaining functional, productive ecosystems with the adaptability to effectively recover from disturbances. By successfully cryopreserving and banking coral symbionts, we provide a critically needed component for securing Symbiodiniaceae biodiversity into the future.

zoology↗

bioRxiv2020

Nascent mutant Huntingtin exon 1 chains do not stall on ribosomes during translation but aggregates do recruit machinery involved in ribosome quality control

Mutations that cause Huntingtons Disease involve a polyglutamine (polyQ) sequence expansion beyond 35 repeats in exon 1 of Huntingtin. Intracellular inclusion bodies of mutant Huntingtin protein are a key feature of Huntingtons disease brain pathology. We previously showed that in cell culture the formation of inclusions involved the assembly of disordered structures of mHtt exon 1 fragments (Httex1) and they were enriched with translational machinery when first formed. We hypothesized that nascent mutant Httex1 chains co-aggregate during translation by phase separation into liquid-like disordered aggregates and then convert to more rigid, amyloid structures. Here we further examined the mechanisms of inclusion assembly in a human epithelial kidney (AD293) cell culture model and examined whether ribosome quality control machinery previously implicated in stalled ribosomes were involved. We found mHttex1 did not appear to stall translation of its own nascent chain and there was no recruitment of RNA into inclusions. However, proteins involved in translation or ribosome quality control were co-recruited into the inclusions (Ltn1 and Rack1) compared to a protein not anticipated to be involved (NACAD). Furthermore, we observed co-aggregation with other proteins previously identified in inclusions, including Upf-1 and chaperone-like proteins Sgta and Hspb1, which also suppressed aggregation at high co-expression levels. The newly formed inclusions contained immobile mHttex1 molecules which points to the disordered aggregates being mechanically rigid prior to amyloid formation.

cell biology↗