Biology subjects

Hoffman, E. A.

Publications and source records attributed to Hoffman, E. A..

9 recordsLinked to original sources

bioRxiv2026

Long-term population decline and recombination heterogeneity shape genomic diversity in the American alligator

The loss of genetic diversity caused by population bottlenecks can significantly impact the ability of a species to adapt to disease, natural disasters, and changing environments. Over the last 175, years, American alligator (A. mississippiensis) populations underwent a decline due to habitat destruction and exploitation followed by a rebound resulting from dedicated conservation efforts. Despite a current census population of millions, microsatellite data indicates a significant paucity of genetic variation within alligators. Using whole genome sequences from 19 individuals sampled from the species geographic range, we quantified nucleotide diversity, heterozygosity, inbreeding, demographic history, and fine-scale recombination rates. We find that American alligator genomes exhibit low nucleotide diversity and elevated homozygosity relative to many vertebrates, but these patterns are dominated by numerous short runs of homozygosity (ROHs), rather than long tracts indicative of recent inbreeding. Demographic history reconstruction based on site-frequency-spectrum analyses support a prolonged decline in effective population size beginning in the last glacial period, indicating that this reduced genetic diversity largely predates intensive human exploitation. Additionally, we uncover a highly structured recombination landscape, with recombination consistently elevated at distal chromosomal regions and suppressed across large central segments. This heterogeneity is associated with genomic spatial variation in nucleotide diversity, suggesting that the recombination landscape contributes to the persistence of homozygosity following population expansion. Together, our results highlight that demographic recovery does not necessarily equate to genetic recovery and show how long-term population history and genomic architecture continue to shape diversity in a "recovered" species.

genomics↗

bioRxiv2026

Mapping frog genomic diversity on a continental scale

Genetic variation is a key component of population resilience and thus an essential tool for wildlife management. For most species, however, we lack information about their current range-wide genomic diversity and how historical and contemporary factors have shaped those patterns. To address these gaps, we built new georeferenced genomic datasets for 2,481 individuals from 46 frog species to develop a genomic diversity atlas representing 43% of species native to the United States and Canada. We identified geographic "hotspots" of high genomic diversity and "coldspots" of low genomic diversity across species and analyzed potential explanations for these patterns. Our results show that several species have their lowest diversity at northern latitudes, at range edges, or within fragmented populations, suggesting areas in need of careful monitoring. More than half (56.8%) of species exhibited a latitudinal gradient in genomic diversity, but we found little evidence for an association between genomic diversity and human disturbance. Furthermore, discordant latitudinal patterns among species suggest that a combination of factors, including range center-edge dynamics and range fragmentation, interact to produce variable diversity patterns. Our study provides a general framework for mapping range-wide genomic diversity of multiple species to support genetically informed biodiversity conservation.

evolutionary biology↗

bioRxiv2025

Unlocking new understanding of Plasmodium sporozoite biology with expansion microscopy

Transmission of malaria relies on the formation of sporozoites in the mosquito midgut and their subsequent invasion of the salivary gland. Despite their importance, our understanding of the cell biology of sporozoite formation and salivary gland invasion is limited. Here, we apply a technique called Mosquito Tissue Ultrastructure Expansion Microscopy (MoTissU-ExM), which physically expands infected mosquito tissues while preserving both host and parasite ultrastructure. Using MoTissU-ExM we are able to observe a range of parasite structures and organelles including features previously seen only by electron microscopy as well as structure not observed before. We leverage MoTissU-ExM to investigate a number of cell biology events during sporozoite formation and salivary gland invasion. In particular we focus on the rhoptries, a secretory organelle important for host cell invasion. We establish a timeline for sporozoite rhoptry biogenesis, show that two rhoptries are used up during salivary gland invasion, and provide the first evidence that rhoptry pairs are specialized for different invasion events. Building on this new knowledge, we characterize the rhoptry protein RON11 and identify it as the first protein involved in sporozoite rhoptry biogenesis. Disruption of RON11 led to the production of sporozoites that specifically fail to invade the salivary gland epithelial cell, thereby blocking transmission of these parasites.

microbiology↗

bioRxiv2023

Lactoylglutathione promotes inflammatory signaling in macrophages

Chronic, systemic inflammation is a pathophysiological manifestation of metabolic disorders. Inflammatory signaling leads to elevated glycolytic flux and a metabolic shift towards aerobic glycolysis and lactate generation. This rise in lactate corresponds with increased generation of lactoylLys modifications on histones, mediating transcriptional responses to inflammatory stimuli. Lactoylation is also generated through a non-enzymatic S-to-N acyltransfer from the glyoxalase cycle intermediate, lactoylglutathione (LGSH). Here, we report a regulatory role for LGSH in inflammatory signaling. In the absence of the primary LGSH hydrolase, glyoxalase 2 (GLO2), RAW264.7 macrophages display significant elevations in LGSH, while demonstrating a potentiated inflammatory response when exposed to lipopolysaccharides, corresponding with a rise in histone lactoylation. Interestingly, our data demonstrate that lactoylation is associated with more compacted chromatin than acetylation in an unstimulated state, however, upon stimulation, regions of the genome associated with lactoylation become markedly more accessible. Lastly, we demonstrate a spontaneous S-to-S acyltransfer of lactate from LGSH to CoA, yielding lactoyl-CoA. This represents the first known mechanism for the generation of this metabolite. Collectively, these data suggest that LGSH, and not intracellular lactate, is a primary contributing factor facilitating the inflammatory response.

biochemistry↗

bioRxiv2023

Island demographics and trait associations in white-tailed deer

When a population is isolated and composed of few individuals, genetic drift is the paramount evolutionary force that results in the loss of genetic diversity. Inbreeding might also occur, resulting in genomic regions that are identical by descent, manifesting as runs of homozygosity (ROHs) and the expression of recessive traits. Likewise, the genes underlying traits of interest can be revealed by comparing fixed SNPs and divergent haplotypes between affected and unaffected individuals. Populations of white-tailed deer (Odocoileus virginianus) on islands of Saint Pierre and Miquelon (SPM, France) have high incidences of leucism and malocclusions, both considered genetic defects; on the Florida Keys islands (USA) deer exhibit smaller body sizes, a polygenic trait. Here we aimed to reconstruct island demography and identify the genes associated with these traits in a pseudo case-control design. The two island populations showed reduced levels of genomic diversity and a build-up of deleterious mutations compared to mainland deer; there was also significant genome-wide divergence in Key deer. Key deer showed higher inbreeding levels, but not longer ROHs, consistent with long-term isolation. We identified multiple trait-related genes in ROHs including LAMTOR2 which has links to pigmentation changes, and NPVF which is linked to craniofacial abnormalities. Our mixed approach of linking ROHs, fixed SNPs and haplotypes matched a high number ([~]50) of a-priori body size candidate genes in Key deer. This suite of biomarkers and candidate genes should prove useful for population monitoring, noting all three phenotypes show patterns consistent with a complex trait and non-Mendelian inheritance.

genomics↗

bioRxiv2023

Genome-scale chromatin interaction dynamic measurements for key components of the RNA Pol II general transcription machinery

BackgroundA great deal of work has revealed in structural detail the components of the machinery responsible for mRNA gene transcription initiation. These include the general transcription factors (GTFs), which assemble at promoters along with RNA Polymerase II (Pol II) to form a preinitiation complex (PIC) aided by the activities of cofactors and site-specific transcription factors (TFs). However, less well understood are the in vivo PIC assembly pathways and their kinetics, an understanding of which is vital for determining on a mechanistic level how rates of in vivo RNA synthesis are established and how cofactors and TFs impact them. ResultsWe used competition ChIP to obtain genome-scale estimates of the residence times for five GTFs: TBP, TFIIA, TFIIB, TFIIE and TFIIF in budding yeast. While many GTF-chromatin interactions were short-lived (< 1 min), there were numerous interactions with residence times in the several minutes range. Sets of genes with a shared function also shared similar patterns of GTF kinetic behavior. TFIIE, a GTF that enters the PIC late in the assembly process, had residence times correlated with RNA synthesis rates. ConclusionsThe datasets and results reported here provide kinetic information for most of the Pol II-driven genes in this organism and therefore offer a rich resource for exploring the mechanistic relationships between PIC assembly, gene regulation, and transcription. The relationships between gene function and GTF dynamics suggest that shared sets of TFs tune PIC assembly kinetics to ensure appropriate levels of expression.

biochemistry↗

bioRxiv2022

Hidden species diversity in a living fossil vertebrate

Ancient, species-poor lineages persistently occur across the Tree of Life. These evolutionarily unique lineages are likely to contain unrecognized species diversity masked by the low rates of morphological evolution that characterize living fossils [1, 2]. Halecomorphi is a major clade of ray-finned fishes that diverged from its closest relatives over 200 million years ago [3, 4] yet is represented by only one recognized living species in eastern North America, the Bowfin Amia calva Linnaeus. Here, we use double digest restriction-site associated DNA (ddRAD) sequencing and high-resolution computed tomography to illuminate recent speciation in the bowfins. Our results support the resurrection of a second living species of Bowfin with the timing of diversification dating to the Pleistocene. In turn, we expand the species diversity of an ancient lineage that is integral to studies of vertebrate genomics and development [2, 3, 5], yet is facing growing conservation threats driven by the caviar fishery [6].

evolutionary biology↗

bioRxiv2019

Fragile X Mental Retardation Protein regulates R-loop formation and prevents global chromosome fragility

Fragile X syndrome (FXS) is the most prevalent inherited intellectual disability caused by mutations in the Fragile X Mental Retardation 1 (FMR1) gene. The protein product of FMR1, FMRP, is known as a translational repressor whose nuclear function is not understood. Here we report that FMRP is a genome maintenance protein. We show that FX cells exhibit elevated level of chromosome breaks, both spontaneous and replication stress-induced. We demonstrate that FMRP is required for abating R-loop accumulation, thereby preventing chromosome breakage. Through mapping FMRP-bound chromatin loci in normal cells and correlating with FX-specific chromosome breaks, we identified novel FXS-susceptible genes. We show that FX cells have reduced expression of the uridine diphosphoglucuronosyl transferase 1 family enzymes, suggesting defective xenobiotics glucuronidation and consequential neurotoxicity in FXS.

genomics↗

bioRxiv2017

Second-generation method for analysis of chromatin binding using formaldehyde crosslinking kinetics

Formaldehyde crosslinking underpins many of the most commonly used experimental approaches in the chromatin field, especially in capturing site-specific protein-DNA interactions. Extending such assays to assess the stability and binding kinetics of protein-DNA interactions is more challenging, requiring absolute measurements with a relatively high degree of physical precision. We previously described an experimental framework called CLK, which uses time-dependent formaldehyde crosslinking data to extract chromatin binding kinetic parameters. Many aspects of formaldehyde behavior in cells are unknown or undocumented, however, and could potentially impact analyses of CLK data. Here we report biochemical results that better define the properties of formaldehyde crosslinking in budding yeast cells. These results have the potential to inform interpretations of standard chromatin assays including chromatin immunoprecipitation, and the chemical complexity we uncovered resulted in the development of an improved method for measuring binding kinetics using the CLK approach. Optimum conditions included an increased formaldehyde concentration and more robust glycine quench conditions. Notably, we find that formaldehyde crosslinking rates can vary dramatically for different protein-DNA interactions in vivo. Some interactions were crosslinked much faster than the time scale for macromolecular interaction, making them suitable for kinetic analysis. For other interactions, we find the crosslinking reaction occurred on the same time scale or slower than binding dynamics; for these it was in some cases possible to compute the in vivo equilibrium-binding constant but not on- and off-rates for binding. Selected TATA-binding protein-promoter interactions displayed dynamic behavior on the minute to several minutes time scale.

biochemistry↗