Biology subjects

Walsh, T.

Publications and source records attributed to Walsh, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Molecular Glue-like Degraders of TEM β-Lactamases by Periplasmic Protease DegP

Antimicrobial resistance is one of the most serious challenges to global health, yet the development of new molecules with novel mechanisms of action to combat resistance is lacking. Here, we report the discovery of molecular glue-like compounds that recruit TEM-family {beta}-lactamases to the bacterial protease DegP for degradation. {beta}-lactamase inhibitor tazobactam was found to accelerate degradation of TEM {beta}-lactamases by DegP, which was further enhanced by linkerless incorporation of dipeptide motifs enriched among DegP substrates. The resulting molecular glue-like degraders showed improved synergy with {beta}-lactam piperacillin against resistant E. coli compared to tazobactam, as well as good pharmacokinetic properties for oral dosing. Collectively, this work establishes periplasmic targeted protein degradation as a promising new mechanism for combating {beta}-lactamase resistance.

molecular biology↗

bioRxiv2025

The collision of two genomes threatens global food security

Human activity alters selection pressures and redistributes biodiversity, creating opportunities for hybridization when dilerent species come into secondary contact. It is now well-established that ancient hybridization plays an important role in adaptive radiation 1, but its role in recent anthropogenic adaptation remains unclear. We investigated this in a study of hybridizing native and invasive Helicoverpa moths in Brazil, which are among the most economically damaging crop pests globally. Native H. zea has recently evolved Bt resistance and is better adapted to maize as a host plant, while invasive H. armigera is resistant to pyrethroid pesticides and is better adapted to soybean. Using a decade-long time series of 975 genomes from both species, we demonstrate rapid, bidirectional adaptive introgression of structural variants that cause resistance to two distinct pesticides. In one direction, a pyrethroid resistance gene from H. armigera (CYP337B3) is now almost fixed in native H. zea. In the other direction, ~30% of recently-sampled invasive H. armigera carry a H. zea-derived trypsin repeat cluster. Using controlled crosses, we show that this trypsin repeat cluster confers resistance to Bt (Cry1Ac) soy in the H. armigera genomic background. Thus, hybridization has combined H. armigera adaptation to soy with H. zea Cry1Ac resistance to facilitate exploitation of Brazilian Bt soy monoculture -- a vast anthropogenic habitat exceeding the area of Germany. Our results show that the combinatorial mechanisms that produce biodiversity can also drive rapid anthropogenic adaptation on ecological timescales, with consequences for global food security.

evolutionary biology↗

bioRxiv2025

Extreme mobility creates contrasting patterns of panmixia, isolation-by-distance and hybridization in four flying-fox species (Pteropus)

Speciation results from shifts between genetic connectivity and isolation of populations. Flying-foxes (Pteropus) are a compelling model to study the interplay of these evolutionary processes due to their rapid radiation in the island-rich region of the Indo-Australian Archipelago. Here, we investigate the population genetics of the highly mobile flying-foxes Pteropus alecto, P. conspicillatus, P. poliocephalus, and P. scapulatus across large parts of their overlapping ranges in Australia, Indonesia, and New Guinea. Using reduced-representation sequencing, we examined the extent to which panmixia, isolation-by-distance, and hybridization are prevalent in these populations. Phylogenetic and demographic modeling approaches indicate that isolation-by-distance, despite ongoing gene flow, occurs in P. alecto and P. conspicillatus populations while P. poliocephalus and P. scapulatus are panmictic across Australia. We further find that hybridization and asymmetric gene flow from P. conspicillatus to P. alecto plays a role in shaping the historic and contemporary populations of these recently diverged species, which exhibit gene flow along a geographic ring connecting Indonesia to Australia and New Guinea. Together, our findings indicate that long-range population connectivity and limited restrictions on gene flow have shaped the evolution and diversification of flying-foxes.

evolutionary biology↗

bioRxiv2024

Focal persistence and phylodynamics of Heartland virus in Georgia

Heartland virus (HRTV) is an emerging tick-bone virus associated with severe illness in the U.S. There are large gaps in knowledge of HRTV diversity, evolution, and transmission due to a paucity of HRTV-positive samples and genome sequences. We identified a focal site of HRTV- positive Amblyomma americanum ticks in central Georgia and developed a novel multiplex- amplicon sequencing assay to generate full HRTV genome sequences. By screening over 21,000 field-collected ticks from 2021-2023, we identified six positive pools. Five were collected from the site in central Georgia where our group first detected HRTV-positive ticks in 2019, and one from a site in western Georgia approximately 175 km away. The HRTV genome sequences from Georgia were highly related, even across this distance and over five years. Reference HRTV genome sequences from across the U.S. were also geographically clustered. Time-scaled phylogenetic analysis suggested recent spread of HRTV in the U.S., with all available sequences sharing a common ancestor within the last 300 years, and sequences from Georgia sharing a common ancestor within the last 40 years. Our observed spatial clustering of HRTV and the high degree of genetic conservation in our persistent focus suggest the importance of small spatial dynamics in HRTV transmission ecology. Author SummaryHeartland virus (HRTV) was first discovered in humans in 2009 and has since caused over 60 cases of severe and fatal disease in the United States. HRTV is transmitted by the lone star tick, Amblyomma americanum, across the Southeast, East coast, and Midwest. Little information is known about how this virus circulates and changes across time and space due to a lack of genetic data. Here, we created a new procedure to generate more genetic sequence data for HRTV and collected over 21,000 ticks to screen for HRTV across three years in Georgia. We generated 6 new HRTV sequences and compared them to existing sequences from our group in Georgia, and across the country, finding evidence of regional clustering of HRTV and highly related HRTV across time in Georgia. Our analyses additionally found that this virus was likely introduced to the U.S. in the last 300 years. Our study provides new context and information in understanding the landscape and transmission of HRTV in the U.S.

genomics↗

bioRxiv2024

Resolving the chromatin impact of mosaic variants with targeted Fiber-seq

Accurately quantifying the functional consequences of non-coding mosaic variants requires the pairing of DNA sequence with both accessible and closed chromatin architectures along individual DNA molecules--a pairing that cannot be achieved using traditional fragmentation-based chromatin assays. We demonstrate that targeted single-molecule chromatin fiber sequencing (Fiber-seq) achieves this, permitting single-molecule, long-read genomic and epigenomic profiling across targeted >100 kilobase loci with [~]10-fold enrichment over untargeted sequencing. Targeted Fiber-seq reveals that pathogenic expansions of the DMPK CTG repeat that underlie Myotonic Dystrophy 1 are characterized by somatic instability and disruption of multiple nearby regulatory elements, both of which are repeat length-dependent. Furthermore, we reveal that therapeutic adenine base editing of the segmentally duplicated {gamma}-globin (HBG1/HBG2) promoters in primary human hematopoietic cells induced towards an erythroblast lineage increases the accessibility of the HBG1 promoter as well as neighboring regulatory elements. Overall, we find that these non-protein coding mosaic variants can have complex impacts on chromatin architectures, including extending beyond the regulatory element harboring the variant.

genomics↗

bioRxiv2024

Chromosome structural rearrangements in invasive haplodiploid ambrosia beetles revealed by the genomes of Euwallacea fornicatus and Euwallacea similis (Coleoptera, Curculionidae, Scolytinae)

Bark and ambrosia beetles are among the most ecologically and economically damaging introduced plant pests worldwide, with life history traits including polyphagy, haplodiploidy, inbreeding polygyny and symbiosis with fungi contributing to their dispersal and impact. Species vary in host tree ecologies, with many attacking stressed or recently dead trees, such as the globally distributed E. similis (Ferrari). Other species, like the Polyphagous Shot Hole Borer (PSHB) Euwallacea fornicatus (Eichhoff), can attack over 680 host plants and is causing considerable economic damage in several countries worldwide. Despite their notoriety, publicly accessible genomic resources for Euwallacea Hopkins species are scarce, hampering better understanding of their invasive capabilities as well as modern control measures, surveillance and management. Using a combination of long and short read sequencing platforms we assembled and annotated high quality (BUSCO > 98% complete) chromosome level genomes for these species. Comparative macro-synteny analysis showed an increased number of chromosomes in the haplodiploid inbreeding species of Euwallacea compared to diploid outbred species, due to fission events. This suggests that life history traits can impact chromosome structure. Further, the genome of E. fornicatus had a higher relative proportion of repetitive elements, up to 17% more, than E. similis. Additionally, metagenomic assembly pipelines identified microbiota associated with both species including Fusarium fungal symbionts and a novel Wolbachia strain. These novel genomes of haplodiploid inbreeding species will contribute to the understanding of how life history traits are related to their evolution and will contribute to the management of these invasive pests. SignificanceScolytinae are significant forestry pests around the world and commonly translocated due to human trade of wood and plant products. Life history traits including inbreeding and haplodiploidy are attributed to their successful establishment in novel environments. Euwallacea fornicatus is widely distributed and attacks a wide variety of live host trees. This study reports the genome of this species and for, E. similis, which colonises dead host trees. The genome assemblies presented herein are highly complete and scaffolded to pseudo-chromosomal level. Comparative analyses of these genomes and of other Scolytinae highlight significant chromosomal rearrangements between haplodiploid inbreeding Euwallacea and diploid outbreeding scolytinae species. Higher relative proportions of transposable elements were identified E. fornicatus, which may promote the species ability to attack live host trees. These genomes are the first for haplodiploid beetles and will contribute to the understanding of evolution of life history traits and the management of invasive insects.

genomics↗

bioRxiv2023

Rapid evolution of pesticide resistance via adaptation and interspecific introgression in a major North American crop pest

Insect crop pests threaten global food security. This threat is amplified through the spread of non-native species and the evolution of pesticide resistance, which can be introduced to a population though de novo mutation or gene flow. We investigate these processes in an economically important noctuid crop pest, Helicoverpa zea, which has rapidly evolved resistance to several pesticides. Its sister species Helicoverpa armigera, first detected as an invasive species in Brazil in 2013, introduced the pyrethroid resistance gene CYP337B3 to South American H. zea via introgression. To understand whether this contributes to pesticide resistance in North America, we sequenced 237 H. zea genomes across 10 sample sites in the US. First, we report H. armigera introgression into the North American H. zea population. Two individuals sampled in Texas in 2019 carry H. armigera haplotypes in a 4Mbp region containing CYP337B3. Second, we show that the remarkable dispersal ability of H. zea results in a panmictic North American population. Third, we detect signatures of selection in non-admixed H. zea, identifying a selective sweep at a second pesticide resistance locus with a similar name: CYP333B3. We estimate that its derived allele conferred a [~]4.9% fitness advantage and show that this estimate explains independently observed rare nonsynonymous CYP333B3 mutations approaching fixation over a [~]20-year period. We also detect putative signatures of selection at a kinesin gene associated with Bt resistance. Our results show that pesticide resistance in H. zea evolved rapidly and recently via two independent mechanisms: interspecific introgression and rapid intraspecific adaptation.

evolutionary biology↗

bioRxiv2023

Induction of antiviral gene expression by cyclosporine A, but not inhibition of cyclophilin A or B, contributes to its restriction of human coronavirus 229E infection in a lung epithelial cell line

The development of antivirals with an extended spectrum of activity is an attractive possibility to protect against future emerging coronaviruses (CoVs). Cyclosporine A (CsA), a clinically approved immunosuppressive drug, has established antiviral activity against diverse unrelated viruses, including several CoVs. However, its antiviral mechanisms of action against CoV infection have remained elusive, precluding the rational design of non-immunosuppressive derivatives with improved antiviral activities. In this study, we evaluated the mechanisms of CsA against HCoV-229E infection in a human lung epithelial cell line. We demonstrate that the antiviral activity of CsA against HCoV-229E is independent of classical CsA target proteins, cyclophilin A or B, which are not required host factors for HCoV-229E in A549 cells. Instead, CsA treatment induces expression of antiviral genes in a manner dependent on interferon regulatory factor 1, but independent of classical interferon responses, which contributes to its inhibitory effect against HCoV-229E infection. Our results also point to a role for the HCoV-229E nucleoprotein in antagonizing activation of type I interferon, but we show that CsA treatment does not affect evasion of innate immune signaling pathways by HCoV-229E. Overall, our findings further the understanding of the antiviral mechanisms of CsA against CoV infection and highlight a novel immunomodulatory strategy to inhibit CoV infection that may inform future drug development efforts.

microbiology↗

bioRxiv2022

Regulatory fine-tuning and horizontal gene transfer stabilize mobile colistin resistance

Antibiotic resistance tends to carry fitness costs, making it difficult to understand how resistance can be stably maintained in pathogen populations over the long-term. Here, we investigate this problem in the context of mcr-1, a fitness-costly gene that confers resistance to the last-resort antibiotic, colistin. Here we show that regulatory evolution has fine-tuned the expression of mcr-1, allowing E. coli to reduce the cost of mcr-1 while simultaneously increasing colistin resistance. Conjugative plasmids have transferred low cost/high resistance mcr-1 alleles across an incredible diversity of E. coli strains, further stabilizing mcr-1 at the species level. Crucially, regulatory mutations were associated with increased mcr-1 stability in pig farms following a ban on the use of colistin as a growth promoter that decreased colistin consumption by 90%. Our study shows how the rapid evolution and horizontal transmission of resistance genes can combine to stabilize resistance and reduce the efficiency of interventions aimed at reducing AMR by limiting antibiotic consumption.

evolutionary biology↗

bioRxiv2022

The redlegged earth mite draft genome provides new insights into pesticide resistance evolution and demography in its invasive Australian range

Genomic data provide valuable insights into pest management issues such as resistance evolution, historical patterns of pest invasions and ongoing population dynamics. We assembled the first reference genome for the redlegged earth mite, Halotydeus destructor (Tucker, 1925), to investigate adaptation to pesticide pressures and demography in its invasive Australian range using whole-genome pool-seq data from regionally distributed populations. Our reference genome comprises 132 autosomal contigs, with a total length of 48.90 Mb. We observed a large complex of ace genes, which has presumably evolved from a long history of organophosphate selection in H. destructor and may contribute toward organophosphate resistance through copy number variation, target-site mutations, and structural variants. In the putative ancestral H. destructor ace gene, we identified three target-site mutations (G119S, A201S, and F331Y) segregating in organophosphate resistant populations. Additionally, we identified two new para sodium channel gene mutations (L925I and F1020Y) that may contribute to pyrethroid resistance. Regional structuring observed in population genomic analyses indicates that gene flow in H. destructor does not homogenise populations across large geographic distances. However, our demographic analyses were equivocal on the magnitude of gene flow; the short invasion history of H. destructor makes it difficult to distinguish scenarios of complete isolation vs. ongoing migration. Nonetheless, we identified clear signatures of reduced genetic diversity and smaller inferred effective population sizes in eastern vs. western populations, which is consistent with the stepping-stone invasion pathway of this pest in Australia. These new insights will inform development of diagnostic genetic markers of resistance, further investigation into the multifaceted organophosphate resistance mechanism, and predictive modelling of resistance evolution and spread.

genomics↗

bioRxiv2022

Genome-wide SNPs reveal the social structure and invasion pathways of the invasive tropical fire ant (Solenopsis geminata)

Elucidating invasion pathways of invasive species is often challenging because invasive populations frequently have low genetic diversity caused by genetic bottlenecks during introduction events. Genome-wide sequencing such as Restriction Site-Associated DNA Sequencing (RADseq) can overcome these challenges by generating thousands of genome-wide single nucleotide polymorphic (SNP) markers. The tropical fire ant, Solenopsis geminata, is a global invader with low genetic diversity in its introduced range, making RADseq one of the best available methods to investigate its population genetics. We used double digest RADseq to generate 3,834 SNPs to compare the genetic diversity of S. geminata in its introduced range to its most likely source of introduction, determined the invasion pathways among populations at an unprecedented level of detail for this species, and determined the social structure of S. geminata workers collected in 13 locations worldwide. We found that introduced S. geminata went through a strong genetic bottleneck. We also identified multiple secondary introduction events among S. geminata populations, indicating that the bridgehead effect is an important driver in the global spread of this species. We found that all colonies in the introduced range were polygyne (i.e., with more than one queen) which may increase their invasion success and potential to cause adverse effects.

genetics↗

bioRxiv2022

Rounding up the annual ryegrass genome: high-quality reference genome of Lolium rigidum

The genome of the major agricultural weed species, annual ryegrass (Lolium rigidum) was assembled, annotated and analysed. Annual ryegrass is a major weed in wheat cropping, and has the remarkable capacity to evolve resistance to herbicides with various modes of action. The chromosome-level assembly was achieved using short- and long-read sequencing in combination with Hi-C mapping. The assembly size is 2.44Gb with N50=361.79Mb across 1,764 scaffolds where the seven longest sequences correspond to the seven chromosomes. Genome completeness assessed through BUSCO returned a 99.8% score for complete (unique and duplicated) and fragmented genes using the Viridiplantae set. We found evidence for the expansion of herbicide resistance-related gene families including detoxification genes. The reference genome assembly of L. rigidum is pivotal for the management of this highly problematic weed species which leverages genomic tools to devise new control options.

genomics↗

bioRxiv2022

Complex multiple introductions drive fall armyworm invasions into Asia and Australia

The fall armyworm (FAW) Spodoptera frugiperda is thought to have undergone a rapid west-to-east spread since 2016 when it was first identified in western Africa. Between 2018 and 2020, it was also recorded from South Asia (SA), Southeast Asia (SEA), East Asia (EA), and Pacific/Australia (PA). Population genomic analyses enabled the understanding of pathways, population sources, and gene flow in this notorious agricultural pest species. Using neutral single nucleotide polymorphic (SNP) DNA markers, we detected genome introgression that suggested most populations were overwhelmingly C- and R-strain hybrids. SNP and mitochondrial DNA markers identified multiple introductions that were most parsimoniously explained by anthropogenic-assisted spread, i.e., associated with international trade of live/fresh plants and plant products, and involved bridgehead populations in countries to enable successful pest establishment in neighbouring countries. Distinct population genomic signatures between Myanmar and China do not support the African origin spread nor the Myanmar source population to China hypotheses. Significant genetic differentiation between populations from different Australian states supported multiple pathways involving distinct SEA populations. Our study identified Asia as a biosecurity hotspot and a FAW genetic melting pot, and demonstrated the use of genome analysis to disentangle preventable human-assisted pest introductions from unpreventable natural pest spread.

evolutionary biology↗

bioRxiv2021

Restoring fertility in yeast hybrids: breeding and quantitative genetics of beneficial traits

Hybrids species can harbour a combination of beneficial traits from each parent and may exhibit hybrid vigour, more readily adapting to new harsher environments. Inter-species hybrids are also sterile and therefore an evolutionary dead-end unless fertility is restored, usually via auto-polyploidisation events. In the Saccharomyces genus, hybrids are readily found in nature and in industrial settings, where they have adapted to severe fermentative conditions. Due to their hybrid sterility, the development of new commercial yeast strains has so far been primarily conducted via selection methods rather than breeding. In this study, we overcame infertility by creating tetraploid intermediates of Saccharomyces inter-species hybrids, to allow continuous multigenerational breeding. We incorporated nuclear and mitochondrial genetic diversity within each parental species, allowing for quantitative genetic analysis of traits exhibited by the hybrids, and for nuclear-mitochondrial interactions to be assessed. Using pooled F12 generation segregants of different hybrids with extreme phenotype distributions, we identified QTLs for tolerance to high and low temperatures, high sugar concentration, high ethanol concentration, and acetic acid levels. We identified QTLs that are species specific, that are shared between species, as well as hybrid specific, where the variants do not exhibit phenotypic differences in the original parental species. Moreover, we could distinguish between mitochondria-type dependent and independent traits. This study tackles the complexity of the genetic interactions and traits in hybrid species, bringing hybrids into the realm of full genetic analysis of diploid species, and paves the road for the biotechnological exploitation of yeast biodiversity.

genetics↗

bioRxiv2020

Genomic balancing selection is key to the invasive success of the fall armyworm

A successful biological invasion involves survival in a newly occupied environment. If a population bottleneck occurs during an invasion, the resulting depletion of genetic variants could cause increased inbreeding depression and decreased adaptive potential, which may result in a fitness reduction. How invasive populations survive in the newly occupied environment despite reduced heterozygosity and how, in many cases, they maintain moderate levels of heterozygosity are still contentious issues1. The Fall armyworm (FAW; Lepidoptera: Spodoptera frugiperda), a polyphagous pest, is native to the Western hemisphere. Its invasion in the Old World was first reported from West Africa in early 2016, and in less than four years, it swept sub-Saharan Africa and Asia, finally reaching Australia. We used population genomics approaches to investigate the factors that may explain the invasive success of the FAW. Here we show that genomic balancing selection played a key role in invasive success by restoring heterozygosity before the global invasion. We observe a drastic loss of mitochondrial polymorphism in invasive populations, whereas nuclear heterozygosity exhibits a mild reduction. The population from Benin in West Africa has the lowest length of linkage disequilibrium amongst all invasive and native populations despite its reduced population size. This result indicates that balancing selection increased heterozygosity by facilitating the admixture of invasive populations from distinct origins and that, once heterozygosity was sufficiently high, FAW started spreading globally in the Old World. As comparable heterozygosity levels between invasive and native populations are commonly observed1, we postulate that the restoration of heterozygosity through balancing selection could be widespread among successful cases of biological invasions.

evolutionary biology↗

bioRxiv2020

Spectrum of genes for inherited hearing loss in the Israeli Jewish population, including the novel human deafness gene ATOH1

Mutations in more than 150 genes are responsible for inherited hearing loss, with thousands of different, severe causal alleles that vary among populations. The Israeli Jewish population includes communities of diverse geographic origins, revealing a wide range of deafness-associated variants and enabling clinical characterization of the associated phenotypes. Our goal was to identify the genetic causes of inherited hearing loss in this population, and to determine relationships among genotype, phenotype, and ethnicity. Genomic DNA samples from informative relatives of 88 multiplex families, all of self-identified Jewish ancestry, with either non-syndromic or syndromic hearing loss, were sequenced for known and candidate deafness genes using the HEar-Seq gene panel. The genetic causes of hearing loss were identified for 60% of the families. One gene was encountered for the first time in human hearing loss: ATOH1 (Atonal), a basic helix-loop-helix transcription factor responsible for autosomal dominant progressive hearing loss in a five-generation family. Our results demonstrate that genomic sequencing with a gene panel dedicated to hearing loss is effective for genetic diagnoses in a diverse population. Comprehensive sequencing enables well-informed genetic counseling and clinical management by medical geneticists, otolaryngologists, audiologists, and speech therapists and can be integrated into newborn screening for deafness.

genetics↗

bioRxiv2020

Whole genome sequencing of global Spodoptera frugiperda populations: evidence for complex, multiple introductions across the Old World

Native to the Americas, the invasive Spodoptera frugiperda (fall armyworm; FAW) was reported in West Africa in 2016, followed by chronological order of detections across the Old World and the hypothesis of an eastward Asia expansion. We explored population genomic signatures of American and Old World FAW and identified 12 maternal mitochondrial DNA genome lineages across the invasive range, while from 870 high-quality nuclear single nucleotide polymorphic DNA markers five distinct New World population clusters were identified, broadly reflected their native geographical ranges and absence of host-plant preferences. We identified unique admixed Old World populations, and admixed and non-admixed Asian FAW individuals, all of which suggested multiple introductions underpinned the pests global spread. Directional gene flow from the East into eastern Africa was also detected, in contrast to the west-to-east spread hypothesis. Our study demonstrated population genomic approaches via international partnership to address global emerging pest threats and biosecurity challenges.

genomics↗

bioRxiv2020

A comparative 'omics approach to candidate pathogenicity factor discovery in the brain-eating amoeba Naegleria fowleri

Of the 40 described Naegleria species, only N. fowleri can establish infection in humans, killing almost invariably within two weeks. In the brain, the amoeba performs piece-meal ingestion, or trogocytosis, of brain material causing massive inflammation. Conversely, its close relative Naegleria gruberi, which is used as a laboratory model organism, is non-pathogenic. The exact pathogenicity factors distinguishing N. fowleri from its harmless relatives are unclear. We have here taken an -omics approach to understanding N. fowleri biology and infection at the system level. We provide the first analysis of genomic diversity between strains, finding little conservation in synteny but high conservation in protein complement. We also demonstrate that the N. fowleri genome encodes a similarly complete cellular repertoire to that found in N. gruberi. Our comparative genomic analysis, together with a transcriptomic analysis of low versus high pathogenicity N. fowleri cultured in a mouse infection model, allowed us to construct a model of cellular systems involved in pathogenicity and furthermore provides ~500 novel candidate pathogenicity factors in this currently rare but highly fatal pathogen.

microbiology↗