Biology subjects

Holt, J.

Publications and source records attributed to Holt, J..

11 recordsLinked to original sources

bioRxiv2026

Testing Thirty Years of Hypotheses: Ancient Trout-Salmon Introgression and Limited Pre-Colonial Gene Flow Between Rainbow and Cutthroat Trout Shaped Pacific Salmonid Evolution

Introgression is the transfer of genetic material between species or populations through hybridization and backcrossing. While often deleterious or neutral in nature, introgression can also have beneficial consequences for the recipient lineage. Oncorhynchus is a genus of ray-finned fish (family Salmonidae) composed of nine species of Pacific trout and eight species of Pacific salmon, in which deep introgression has long been proposed to explain patterns of gene-tree-species-tree discordance, and in which hybridization is extensively observed between introduced and endemic species. In this study, we identified well-supported introgression between the ancestral lineage of Pacific trout and the ancestor of Chinook and coho salmon, a long-posited but previously untested hypothesis. While other salmon lineages (pink, chum, sockeye, and masu salmon) have been sympatric with trout for extended periods, providing an opportunity for hybridization to occur, we found no evidence of introgression between trout and these other salmon lineages. Our findings suggest mito-nuclear incompatibilities serve as a possible barrier to gene flow between the clade comprised of pink, chum, and sockeye salmon and all other lineages in Oncorhynchus. Within Pacific trout, we detected no historical introgression between cutthroat and rainbow trout lineages, suggesting that the extensive hybridization observed between them today reflects recent, primarily human-mediated contact rather than long-term gene flow. These findings show that ancestral introgression has shaped the evolutionary history of Oncorhynchus and should be accounted for in future comparative phylogenetic studies of the genus.

evolutionary biology↗

bioRxiv2025

Dissection of ergosterol metabolism reveals a pathway optimized for membrane phase separation

Sterols are among the most abundant lipids in eukaryotic cells, yet are synthesized through notoriously long metabolic pathways. It has been proposed that the molecular evolution of such pathways must have required each step to increase the capacity of its product to condense and order phospholipids. Here we carry out a systematic analysis of the ergosterol pathway that leverages the yeast vacuoles capacity to phase-separate as a predictive biophysical readout for each intermediate. In the post-synthetic steps specific to ergosterol biosynthesis, we find that successive modifications act to oscillate ordering capacity, settling on a level that supports phase separation while retaining fluidity of the resulting domains. Simulations carried out with each intermediate showed how conformers in the sterols alkyl tail are capable of modulating long-range ordering of phospholipids, which could underlie changes in phase behavior. Our results indicate that the complexity of sterol metabolism could have resulted from the need to balance lipid interactions required for membrane organization.

biophysics↗

bioRxiv2024

RGS10 Attenuates Systemic Immune Dysregulation Induced by Chronic Inflammatory Stress

Regulator of G-protein signaling 10 (RGS10), a key homeostatic regulator of immune cells, has been implicated in multiple diseases associated with aging and chronic inflammation including Parkinsons Disease (PD). Interestingly, subjects with idiopathic PD display reduced levels of RGS10 in subsets of peripheral immune cells. Additionally, individuals with PD have been shown to have increased activated peripheral immune cells in cerebral spinal fluid (CSF) compared to age-matched healthy controls. However, it is unknown whether CSF-resident peripheral immune cells in individuals with PD also exhibit decreased levels of RGS10. Therefore, we performed an analysis of RGS10 levels in the proteomic database of the CSF from the Michael J. Fox Foundation Parkinsons Progression Markers Initiative (PPMI) study. We found that RGS10 levels are decreased in the CSF of individuals with PD compared to healthy controls and prodromal individuals. Moreover, we find that RGS10 levels decrease with age but not PD progression and that males have less RGS10 than females in PD. Importantly, studies have established an association between chronic systemic inflammation (CSI) and neurodegenerative diseases, such as PD, and known sources of CSI have been identified as risk factors for developing PD; however, the role of peripheral immune cell dysregulation in this process has been underexplored. As RGS10 levels are decreased in the CSF and circulating peripheral immune cells of individuals with PD, we hypothesized that RGS10 regulates peripheral immune cell responses to CSI prior to the onset of neurodegeneration. To test this, we induced CSI for 6 weeks in C57BL6/J mice and RGS10 KO mice to assess circulating and CNS-associated peripheral immune cell responses. We found that RGS10 deficiency synergizes with CSI to induce a bias for inflammatory and cytotoxic cell populations, a reduction in antigen presentation in peripheral blood immune cells, as well as in and around the brain that is most notable in males. These results highlight RGS10 as an important regulator of the systemic immune response to CSI and implicate RGS10 as a potential contributor to the development of immune dysregulation in PD.

immunology↗

bioRxiv2024

Locus coeruleus injury modulates ventral midbrain neuroinflammation during DSS-induced colitis

Parkinsons disease (PD) is characterized by a decades-long prodrome, consisting of a collection of non-motor symptoms that emerges prior to the motor manifestation of the disease. Of these non-motor symptoms, gastrointestinal dysfunction and deficits attributed to central norepinephrine (NE) loss, including mood changes and sleep disturbances, are frequent in the PD population and emerge early in the disease. Evidence is mounting that injury and inflammation in the gut and locus coeruleus (LC), respectively, underlie these symptoms, and the injury of these systems is central to the progression of PD. In this study, we generate a novel two-hit mouse model that captures both features, using dextran sulfate sodium (DSS) to induce gut inflammation and N-(2-chloroethyl)-N-ethyl-2-bromobenzylamine (DSP-4) to lesion the LC. We first confirmed the specificity of DSP-4 for central NE using neurochemical methods and fluorescence light-sheet microscopy of cleared tissue, and established that DSS-induced outcomes in the periphery, including weight loss, gross indices of gut injury and systemic inflammation, the loss of tight junction proteins in the colonic epithelium, and markers of colonic inflammation, were unaffected with DSP-4 pre-administration. We then measured alterations in neuroimmune gene expression in the ventral midbrain in response to DSS treatment alone as well as the extent to which prior LC injury modified this response. In this two-hit model we observed that DSS-induced colitis activates the expression of key cytokines and chemokines in the ventral midbrain only in the presence of LC injury and the typical DSS-associated neuroimmune is blunted by pre-LC lesioning with DSP-4. In all, this study supports the growing appreciation for the LC as neuroprotective against inflammation-induced brain injury and draws attention to the potential for NEergic interventions to exert disease-modifying effects under conditions where peripheral inflammation may compromise ventral midbrain dopaminergic neurons and increase the risk for development of PD.

neuroscience↗

bioRxiv2024

Determining susceptibility loci in triple negative breast cancer using a novel pre-clinical model

Breast cancer (BC) is the most common cancer and the second cause of death in US women. Our lack of understanding of how genetic variants affect molecular mechanisms that mediate BC aggression poses a substantial obstacle to advancements in cancer diagnosis and therapy. To examine genetic variants on BC traits, a novel murine model was created with robust phenotypic and genomic variation. The FVB C3(1)-T-antigen ("C3Tag") mouse develops spontaneous tumors in the mammary glands of female mice with a mean latency of 4-5 months of age. This genetically engineered mouse model (GEMM) is well established to resemble human basal-like TNBC. TNBC is an aggressive subtype with few clinical approaches and poor patient outcomes. Thus, to model human heterogeneity in BC outcomes, we systematically crossed the C3Tag GEMM into the BXD recombinant inbred family - the largest and best characterized genetic reference population. The new model is termed "BXD-BC" and F1 hybrids of the cross have isogenic genomes that are reproducible. BXD-BCs are a potent tool to determine the impact of genetic modifiers on BC tumor traits. We hypothesized that examination of BXD-BC GEMMs will enable the identification of susceptibility loci, candidate genes, and molecular networks that underlie variation of multiple BC phenotypes. Using N=29 BXD-BC strains, we demonstrated significant heritable variations in the severity of TNBC characteristics such as tumor latency, multiplicity, and survival. Interestingly, 2 BXD-BC strains never developed tumors out to 1 year of age. Thus, BXD-BC strains demonstrate variance in cancer susceptibility and progression compared to the parent C3Tag GEMM, indicating the presence of genetic modifiers. Through an unbiased systematic quantification of breast cancer severity across BXD-BC hybrids, we identified several significant quantitative trait loci (QTL) and candidate genes for specific tumor traits. In combination with public human GWAS datasets, we defined syntenic regions, candidate genes, and underlying networks through cross-species systems genetics analyses to demonstrate the translational validity of conserved, biologically relevant, and targetable candidates. Our findings suggest conserved candidates predicting TNBC patient survival. In sum, the BXD-BC resource is an innovative, reliable, and robust preclinical model that reflects robust genetic heterogeneity. Using cutting edge systems genetics, we have identified genetic modifiers of BC phenotypic variation that could be targeted to advance therapeutic limitations or as biomarkers of risk or response to therapy.

genetics↗

bioRxiv2023

Predicting the Purity of Multispecific Antibodies From Sequence Using Machine Learning: Methods and Applications

Multispecific antibodies are prominent therapeutic agents, but many molecular formats and drug candidates that show promise during molecular discovery stages cannot be scaled up and developed into drugs due to inadequate developability. During the discovery stages, the selection of molecule format(s), molecule design, purity, and initial physiochemical stability testing criteria largely rely on scientists experience. Machine learning, however, can identify hidden trends in large datasets, aiding in the selection of drug candidates with improved developability. In this study, we present a machine learning approach to predict antibody purity, measured by the percentage of monomer after protein A purification. Using the amino acid sequences of variable regions, molecular formats, germlines and germline pairings, and calculated physiochemical properties as inputs, machine learning models were trained to predict the percentage of monomer for a given multispecific antibody (Figure 1). The dataset employed in this study consists of [~]500 multi-specific antibodies generated during BIs internal drug discovery programs. Our results indicate that machine learning, when applied to sequence, germline, and format data, can effectively predict antibody percentage of monomer. Incorporating this approach into high-throughput multispecific antibody screening processes can save time and resources by reducing the need to test a large subset of potentially unstable antibodies. While this study focused on percentage of monomer as a test case, similar approaches can be employed to predict other antibody properties, such as melting temperature (Tm), hydrophobicity (aHIC), and solution stability properties (AC-SINS). O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=47 SRC="FIGDIR/small/570217v1_fig1.gif" ALT="Figure 1"> View larger version (11K): org.highwire.dtl.DTLVardef@f23246org.highwire.dtl.DTLVardef@c2b81aorg.highwire.dtl.DTLVardef@1c4e59dorg.highwire.dtl.DTLVardef@1bed683_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1C_FLOATNO Overview of ML model for predicting multispecific antibody purity from sequence, germline and format information. C_FIG

molecular biology↗

bioRxiv2023

Dispersal of a dominant competitor can drive multispecies coexistence in biofilms

Despite competition for both space and nutrients, bacterial species often coexist within structured, surface-attached communities termed biofilms. While these communities play important, widespread roles in ecosystems and are agents of human infection, understanding how multiple bacterial species assemble to form these communities and what physical processes underpin the composition of multispecies biofilms remains an active area of research. Using a model three-species community composed of P. aeruginosa, E. coli, and E. faecalis, we show with cellular scale resolution that biased dispersal of the dominant community member, P. aeruginosa, prevents competitive exclusion from occurring, leading to coexistence of the three species. A P. aeruginosa bqsS deletion mutant no longer undergoes periodic mass dispersal, leading to local competitive exclusion of E. coli. Introducing periodic, asymmetric dispersal behavior into minimal models parameterized by only maximal growth rate and local density supports the intuition that biased dispersal of an otherwise dominant competitor can permit coexistence generally. Colonization experiments show that WT P. aeruginosa is superior at colonizing new areas in comparison to{Delta} bqsS P. aeruginosa, but at the cost of decreased local competitive ability against E. coli and E. faecalis. Overall, our experiments document how one species modulation of a competition-dispersal-colonization trade-off can go on to influence the stability of multispecies coexistence in spatially structured ecosystems.

microbiology↗

bioRxiv2022

Widespread convergent evolution of alpha-neurotoxin resistance in African mammals

Convergent evolution is central to the study of adaptation and has been used to understand both the limits of evolution and the diverse patterns and processes which result in adaptive change. Resistance to snake venom -neurotoxins (NTXs) is a case of widespread convergence having evolved several times in snakes, lizards, and mammals. Despite extreme toxicity of NTXs, substitutions in its target, the nicotinic acetylcholine receptor (nAChR), prevent NTX binding and render species resistant. Recently, the published meerkat (Herpestidae) genome revealed that meerkats have the same substitutions in nAChR as the venom resistant Egyptian mongoose (Herpestidae), suggesting that venom-resistant nAChRs may be ancestral to Herpestids. Like the mongoose, many other species of feliform carnivores prey on venomous snakes, though their venom resistance has never been explored. To evaluate the prevalence and ancestry of NTX resistance in mammals, we generate a dataset of mammalian nAChR utilizing museum specimens and public datasets. We find five instances of convergent evolution within feliform carnivores, and an additional eight instances across all mammals sampled. Tests of selection show that these substitutions are evolving under positive selection. Repeated convergence suggests that this adaptation played an important role in the evolution of mammalian physiology and potentially venom evolution.

evolutionary biology↗

bioRxiv2021

Directed Evolution of AAV Targeting Primate Retina by Intravitreal Injection Identifies R100, a Variant Demonstrating Robust Gene Delivery and Therapeutic Efficacy in Non-Human Primates

Targeted AAV vectors are needed for safe and efficient delivery to and transduction of specific tissue target(s) in patients. Effective intravitreal delivery for retina gene therapy is not feasible with wildtype AAV. We employed directed evolution in nonhuman primates (NHP) to discover an AAV variant (R100) for intravitreal treatment of multiple target cells in the primate retina. R100 demonstrated superior transduction of human retinal cells compared to wildtype AAV. Furthermore, three R100-based gene therapeutics demonstrated safety, delivery, and durable pan-retinal expression of intracellular or secreted transgenes throughout the NHP retina following intravitreal administration. Finally, efficacy of R100-mediated delivery of therapeutic transgenes was demonstrated in patient-derived retinal cells (monogenic diseases) and in an NHP model of pathogenic retinal angiogenesis.

bioengineering↗

bioRxiv2019

Potential impacts of insect-induced harvests in the mixed forests of New England

Forest insects and pathogens (FIPs) have significant impacts on U.S. forests, each year affecting an area nearly three times the area of wildfires and timber harvesting combined. We surveyed family forest owners (FFOs) in the northeastern U.S. and 84% of respondents indicated they would harvest in at least one of the presented FIP infestation scenarios. This harvest response represents a potentially significant shift in the timing, extent, and species selection of harvesting in the Northeast. Here we used the landowner survey, regional forest inventory data, and characteristics of the emerald ash borer (EAB, Agrilus planipennis) invasion to examine the potential for a rapidly spreading FIP to alter harvest regimes and affect regional forest conditions. Twenty-five percent of the FFO parcels in the Connecticut River Watershed in New England are likely to be harvested in response to EAB within 10 years. This prediction represents an increase in harvest frequencies, from 2.9%/yr (historically) to 3.7%/yr, on FFO woodlands. At typical harvest intensities, this would result in 13% of the total aboveground biomass removed through these harvests, with 81% of that biomass from species other than ash, creating a forest disturbance that is over twice the magnitude of the disturbance from EAB alone.

ecology↗

bioRxiv2019

Compounding the disturbance: Family forest owner reactions to invasive forest insects

Invasive forest insect and pathogens (FIP) are having significant, direct, adverse impacts. Interactions between FIPs and forest owners have the potential to create ecosystem impacts that compound direct impacts. We assessed family forest owners responses to numerous contingent behavior, FIP-outbreak scenarios in the northeastern U.S. based on FIP outbreak attributes. Sixty-two percent of scenario responses (n=2,752) reflected a harvest intent as a result of FIPs; 84% of respondents (n=688) would consider harvesting in at least one of the four hypothetical scenarios presented to them. Harvest intention increased with greater FIP-related tree mortality and decreased with delayed total tree mortality. Owners with larger holdings, who had previously harvested forest products, and live on their forestland had greater intentions to harvest in response to FIPs. Results suggest that FIPs could transform the regional harvest regime with socio-ecological impacts that are distinct from those caused by FIPs or harvesting alone.

ecology↗