Biology subjects

Porter, J.

Publications and source records attributed to Porter, J..

14 recordsLinked to original sources

bioRxiv2026

Wolbachia-induced Cytoplasmic Incompatibility drives epigenetic and maternally-influenced post-embryonic defects

A common form of Wolbachia-induced manipulation of host reproduction is Cytoplasmic Incompatibility (CI). In CI, Wolbachia modification of sperm results in pronounced defects in paternal chromosome condensation, replication, and segregation during the first mitotic division. Recent studies in D. simulans demonstrate that CI also induces independent and distinct later developmental defects resulting in high rates of mitotic errors during the mid-blastula transition and larval lethality. Here we show that in D. melanogaster, embryos derived from CI crosses experienced significant mitotic defects during gastrulation and increased larval lethality, both of which were eliminated in the progeny of Rescue crosses (both sexes infected). Examination of CI using females from 13 genetically distinct wild-type lines of the Drosophila Genetic Reference Panel (DGRP) revealed significant variation in the strength of the CI-induced lethality. Early embryonic pre-hatching and late larval lethal phases were uncorrelated, suggesting distinct factors influence the extent of the two lethal phases. Additionally, 3rd instar larvae and adults derived from D. melanogaster CI crosses exhibited locomotor defects that were also eliminated in Rescue crosses. These studies support a model in which Wolbachia effects on the sperm chromatin produce delayed developmental and locomotor defects, suggesting the involvement of epigenetic mechanisms. Support for this idea comes from our finding that levels of the heritable chromatin mark H3K27me1 are significantly elevated in CI-derived embryos. We conclude that the full measure of CI strength should take into account pre- and post-hatching lethality as well as locomotor defects. Together our findings suggest that the strength of these CI-induced phenotypes is governed at least in part by epigenetics and the maternal genetic background. AUTHOR SUMMARYSince the discovery of the antiviral properties of the bacteria Wolbachia, numerous strategies using this insect endosymbiont have been developed to combat vector-borne disease. While the success of these strategies relies on the rapid spread of Wolbachia through a naturally uninfected insect population, the molecular mechanisms by which Wolbachia promote their spread remain poorly defined. Current research on the primary mechanism behind Wolbachia spread, cytoplasmic incompatibility (CI), focuses on understanding the dramatic decrease in egg hatch rates that occurs when uninfected females mate with infected males. Here, we demonstrate that CI also induces substantial post-hatching larva and adult locomotor defects and lethality. In accord with these developmentally delayed defects, we show Wolbachia dramatically alter an epigenetic chromatin mark. Finally, we show that host maternal factors contribute to CI strength. Taken together, these results demonstrate that CI induces a much more expansive and developmentally delayed suite of phenotypes than previously reported.

microbiology↗

bioRxiv2025

The origins and adaptive consequences of polyploidy in a dominant prairie grass

Polyploidy is ubiquitous across North American prairies, which provide essential ecosystem services and rich soil for agriculture. Yet the mechanism driving polyploid abundance is unclear. Multiple hypotheses have been proposed including polyploid abundance is proportional to the opportunity for whole genome duplication (WGD), and WGD alters phenotypes that may increase fitness. We tested these two hypotheses together in the mixed-ploidy species Andropogon gerardi, a dominant grass species in endangered North American tallgrass prairies. Leveraging a novel, phased allopolyploid reference genome, we found the A. gerardi hexaploid arose after the C4 grassland expansion in the early Pleistocene, when glacial cycles likely increased secondary contact between the diploid progenitors. We sequenced A. gerardi from 25 popula-tions and examined cytotype performance and morphology in a controlled environment to investigate the consequences of the contemporary mixed-ploidy populations. We found the 9x A. gerardi cytotype is a neopolyploid and a result of recurrent WGD events. Further, we demonstrate the 9x neopolyploids have greater growth and a decreased stomatal pore index, which is adaptive in xeric climates where the 9x cy-totype is most common. Together, our results support both hypotheses for polyploid abundance in North America: WGD is a product of opportunity and can have immediate fitness consequences. Although the changes to fitness may provide an advantage to 9x A. gerardi, the establishment of 9x may lower overall population fitness due to the lower reproductive viability of 9x individuals. Significance statementPolyploid species are abundant in North American prairies and make up many of the dominant species in the ecosystem. This prominence could be a result of whole genome duplication conferring an advantage that increases the frequency of polyploids or could simply indicate that the opportunity for whole genome duplication is higher in this ecosystem, or both. Through examining three polyploidization events in A. gerardi, the dominant species in endangered tallgrass North American prairies, we found whole genome duplication is both surprisingly common and confers traits that are beneficial in some environments.

plant biology↗

bioRxiv2025

Increases in invertebrate abundance and shifts in assemblage composition following Rodent Eradication on Lord Howe Island

Invasive species are one of the major threatening processes impacting biodiversity on islands. In particular, introduced rodents represent one of the most serious threats to island ecosystems, affecting a wide range of native plants, vertebrates and invertebrates. While nearly ubiquitous on human-modified islands, the last four decades have seen the advent of targeted rodent eradications, which have generally resulted in positive impacts for biodiversity. Invertebrates, which are crucial to the functioning of island ecosystems, are known to be negatively impacted by rodents, but their response to rodent removal is less well understood. The largest rodent eradication on an inhabited island was undertaken in 2019 on Australias Lord Howe Island, which successfully extirpated black rats (Rattus rattus) and house mice (Mus musculus) more than a century after their introduction. To examine the impacts of rodents on invertebrates on Lord Howe Island, we collected arboreal and terrestrial species both pre- and post-eradication and identified them to Order. Total invertebrate abundance increased after the eradication of rodents, alongside substantial shifts in assemblage composition, however Ordinal diversity did not change significantly. Orders with large increases in abundance included Isopoda and Blattodea, while the abundance of Coleoptera and Polydesmida did not change. In addition, the abundance of large invertebrates, which are presumably subject to stronger rat predation, rose dramatically following rodent eradication. Our results suggest an ecological rearrangement following the relaxation of predation pressure and augment documented evidence of improved biodiversity outcomes for forest tree species, seabirds and land birds.

ecology↗

bioRxiv2025

Efficient packaging of HIV-1 genomes via recognition of its adenosine-rich content by a heterologous RNA-binding domain

The HIV-1 genome (gRNA) has an unusually biased nucleotide content and is rich in adenosines. Selective packaging of the gRNA is thought to be driven by specific binding of the nucleocapsid (NC) domain of the viral Gag protein to the packaging signal ({Psi}) in the host cell cytosol. However, deletion of regions within {Psi} reduces--but does not completely abolish--genome packaging. To probe whether another feature of the gRNA may contribute to the selective gRNA packaging process, we replaced NC with heterologous RNA-binding domains (RBDs) with distinct RNA-binding properties. Surprisingly, despite disparate RNA binding specificities, all Gag-RBD chimeras successfully recruited the gRNA to the plasma membrane, suggesting that the initial gRNA recognition in the cytosol is not rate limiting. Notwithstanding, many chimeras exhibiting G/C binding specificity were arrested at the assembly stage. Only the Gag-SRSF5 chimera, which multimerized efficiently on adenosine-rich sequences on the gRNA, assembled efficiently and packaged gRNA at near wild-type levels. Importantly, rationally designed mutations that altered the A/G-rich binding specificity of Gag-SRSF5 decreased genome encapsidation efficiency. Furthermore, many Gag chimeras displayed potent dominant negative activities, highlighting NC functions as a targetable step in virus replication. Together, our findings reveal an unexpected aspect of the HIV-1 gRNA, its biased nucleotide content, as a key driver of selective genome packaging. SIGNIFICANCEHow HIV-1 selectively packages its genome (gRNA) into virions is poorly understood. To probe this, we replaced the viral nucleocapsid (NC) protein with heterologous RNA-binding domains (RBDs) from cellular hnRNP and SR protein families. Remarkably, despite their distinct RNA-binding specificities, all Gag-RBD chimeras successfully recruited the gRNA to the plasma membrane, suggesting that the initial gRNA recognition is not rate limiting. Only the Gag-SRSF5 chimera packaged gRNA efficiently which correlated with its capacity to multimerize on adenosine-rich sequences on the gRNA. Notably, several Gag chimeras exhibited strong dominant negative effects, underscoring NC functions as a targetable step in virus replication. Together, these findings uncover that the biased nucleotide content of the HIV-1 gRNA facilitates its selective packaging into virus particles.

microbiology↗

bioRxiv2024

TIA1 Mediates Divergent Inflammatory Responses to Tauopathy in Microglia and Macrophages

The RNA binding protein TIA1 is known to regulate stress responses. Here we show that TIA1 plays a much broader role in inflammatory cells, being required for the microglial sensome. We crossed TIA1 cKO mice (using a CX3CR1 driven cre element) to PS19 MAPT P301S tauopathy mice. The peripheral macrophages of TIA1 cKO mice exhibited a hyper-inflammatory phenotype with increased cytokine signaling, as expected. Surprisingly, the brains of these mice showed striking reductions in inflammation, including decreases in microglial inflammatory cytokines (TNF and IL-1{beta}) and sensome markers (CLEC7A, TREM2, ITGAX); these reductions were accompanied by corresponding decreases in tau pathology. Analysis of the brain TIA1 protein interactome identified brain selective TIA1 protein mediated pathways, including strong interactions with the microglial protein C1q, which directs pruning of dystrophic neurons. These results uncover a previously unknown regulatory role for TIA1 in microglial activation in the context of neurodegenerative disease and highlights the divergent regulation of two mononuclear phagocytic lineages: microglia and macrophages.

neuroscience↗

bioRxiv2024

A low-cost and versatile paramagnetic bead DNA extraction method for Mycobacterium ulcerans environmental surveillance.

In Australia, native possums are an animal reservoir for Mycobacterium ulcerans, the causative agent of Buruli ulcer, a neglected tropical skin disease that can progress to extensive ulceration with deformity and disability. Surveillance of possum excreta for shedding of M. ulcerans can be used to inform geospatial modelling to predict locations at which humans are at increased risk of disease acquisition. This discovery provides opportunities to disrupt transmission pathways. However, the significant expense of commercial kits used for DNA extraction from environmental samples in large scale surveillance studies can hinder implementation of public health measures. To address this barrier, we developed a low-cost method for extraction of nucleic acids from possum excreta, possum tissue swabs, and mycobacterial cultures, using a guanidinium thiocyanate lysis solution and paramagnetic beads for DNA clean-up. In 96-well plate format for high-throughput processing, the SPRI-bead DNA extraction method for possum excreta was 3-fold less sensitive but only 1/6 the cost of a widely used commercial kit. While a SPRI-bead microtube-based extraction method for tissue swabs sampled from possums was 4-fold more sensitive and 1/5 the cost of the corresponding commercial kit. Furthermore, when used for preparing DNA from pure mycobacterial cultures, the SPRI-bead method produced genomic DNA with quality metrics comparable to more laborious techniques. The methods described here provide an economical means to continue large-scale M. ulcerans environmental surveillance that should facilitate efforts to halt the spread of Buruli ulcer in Victoria, Australia, with potential for applicability in other endemic countries. IMPORTANCEBuruli ulcer is a neglected tropical skin disease, with an incidence that has dramatically increased in temperate southeastern Australia over the last decade. In this region of the world Buruli ulcer is a zoonosis, Australian native possums are a major wildlife reservoir of the causative agent, Mycobacterium ulcerans, and mosquitoes the vector to humans. Infected possums shed M. ulcerans in their excreta, and excreta surveys using PCR to screen for the presence of pathogen DNA are a powerful means to predict future areas of Buruli ulcer risk for humans. However, excreta surveys across large geographic areas require testing of many thousands of samples. The cost of commercial DNA extraction reagents used for preparing samples for PCR testing can become prohibitive to effective surveillance. Here, we describe a simple, low-cost method for extracting DNA from possum excreta using paramagnetic beads. The method is versatile and adaptable to a variety of other sample types including swabs collected from possum tissues and pure cultures of mycobacteria.

microbiology↗

bioRxiv2023

Mussels on the move: new records of the invasive non-native quagga mussel (Dreissena rostriformis bugensis) in Great Britain using eDNA and a new probe-based qPCR assay

Invasive non-native species (INNS) pose a worldwide environmental threat, negatively impacting invaded ecosystems on an ecological and economical scale. In recent decades, quagga mussels (Dreissena rostriformis bugensis) have successfully invaded several countries in Western Europe from the Ponto-Caspian region, being recorded for the first time in Great Britain (GB) in 2014, in Wraysbury, near London. In recent years, environmental DNA (eDNA) analysis has proven to be a sensitive and effective method for early detection and monitoring of a number of INNS. Previously, a dye-based quantitative PCR (qPCR) assay was developed for the detection of quagga mussels from eDNA samples. Here, a target-specific probe was designed to further increase the specificity of this assay and used to obtain an updated distribution of this species in GB. Twenty-four sites were sampled, including sites with established populations near London and sites spread across the East Midlands and East Anglia regions. Positive detections were obtained for 11 of the 24 sites, and these were widely spread, as far as Nottingham (East Midlands) and Norfolk (East Anglia). Detection rates were 100% at the three sites with known established populations, while rates were lower (3-50% of positive replicates) in the eight newly-identified sites, consistent with an early stage of invasion. Of particular concern was the detection of quagga mussels in major waterways and in popular recreational sites, highlighting urgent measures are needed to control pathways and spread. Our study demonstrates that quagga mussels are considerably more widespread in GB than previously thought and provides a much-needed step towards operational use of eDNA for monitoring quagga mussels.

ecology↗

bioRxiv2023

Mycobacterium ulcerans not detected by PCR on human skin in Buruli ulcer endemic areas of south eastern Australia

IntroductionMycobacterium ulcerans (MU) causes Buruli ulcer (BU), a geographically restricted infection that can result in skin loss, contracture, and permanent scarring. Lesion-location maps compiled from more than 640 cases in south eastern Australia suggest biting insects are likely involved in transmission, but it is unclear whether MU is brought by insects to their target or if MU is already on the skin and inoculation is an opportunistic event that need not be insect dependent. MethodsWe validated a PCR swab detection assay and defined its dynamic range using laboratory cultured M. ulcerans and fresh pigskin. We invited volunteers in Buruli-endemic and non-endemic areas to sample their skin surfaces with self-collected skin swabs tested by IS2404 quantitative PCR. ResultsPigskin validation experiments established a limit-of-detection of 0.06 CFU/cm2 at a qPCR cycle threshold (Ct) of 35. Fifty-seven volunteers returned their self-collected kits of 4 swabs (bilateral ankles, calves, wrists, forearms), 10 from control areas and 47 from endemic areas. Collection was timed to coincide with the known peak-transmission period of Buruli. All swabs from human volunteers tested negative (Ct [≥]35). ConclusionsM. ulcerans was not detected on the skin of humans from highly BU endemic areas. Author SummaryBuruli ulcer (BU) incidence is increasing in temperate south eastern Australia. We have yet to develop public health programs to assist people avoid BU partly because the precise mode of transmission is contentious. Recent research has shown that environmental contamination with M. ulcerans (the cause of BU) is widespread in endemic areas as a result of faecal shedding from infected possums that live close to humans, although direct human-possum contact is rare. We investigated the possibility that the skin of humans in endemic areas could become transiently contaminated with M. ulcerans while outdoors. If this were the case then BU prevention programs could be developed around skin protection and regular washing/showering. To study this possibility, we developed a sensitive skin swab PCR-assay that we tested using a pigskin laboratory model so we could be confident in our results. We asked volunteers to collect their own skin swabs after spending at least 4 hours outside during the known period of peak Buruli transmission. Fifty seven volunteers returned swab sets for testing. Our results were negative. We did not find evidence that humans in our endemic zone have M. ulcerans contamination on their skin.

microbiology↗

bioRxiv2021

Longitudinal in vivo changes in radial peripapillary capillaries and optic nerve head structure in non-human primates with early experimental glaucoma

PurposeThere is conflicting evidence as to whether a loss of radial peripapillary capillaries (RPCs) precedes neuronal loss in glaucoma. We examined the time-course of in vivo changes in RPCs, optic nerve head (ONH) structure, and retinal nerve fiber layer thickness (RNFLT) in experimental glaucoma (EG). MethodsSpectral domain optical coherence tomography images were acquired before and approximately every 2 weeks after inducing unilateral EG in 9 rhesus monkeys to quantify mean anterior lamina cribrosa surface depth (ALCSD), minimum rim width (MRW), and RNFLT. Perfused RPC density was measured from adaptive optics scanning laser ophthalmoscope images acquired on the temporal half of the ONH. The time of first significant change was quantified as when values fell and remained outside of the 95% confidence interval established from control eyes. ResultsMean ALCSD and/or MRW were the first parameters to change in 8 EG eyes. RPC density changed first in the 9th. At their first points of change, mean ALCSD posteriorly deformed by 100.2 {+/-} 101.2 m, MRW thinned by 82.3 {+/-} 65.9 m, RNFLT decreased by 25 {+/-} 14 m, and RPC density decreased by 4.5 {+/-} 2.1%. RPC density decreased before RNFL thinning in 5 EG eyes. RNFLT decreased before RPC density decreased in 2 EG eyes, while 2 EG eyes had simultaneous changes. ConclusionsIn most EG eyes, RPC density decreased before (or simultaneous with) a change in RNFLT, suggesting that vascular factors may play a role in axonal loss in some eyes in early glaucoma.

bioengineering↗

bioRxiv2020

Validation of a Single-step, Single-tube Reverse Transcription-Loop-Mediated Isothermal Amplification Assay for Rapid Detection of SARS-CoV-2 RNA

2.IntroductionThe SARS-CoV-2 pandemic of 2020 has resulted in unparalleled requirements for RNA extraction kits and enzymes required for virus detection, leading to global shortages. This has necessitated the exploration of alternative diagnostic options to alleviate supply chain issues. AimTo establish and validate a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the detection of SARS-CoV-2 from nasopharyngeal swabs. MethodologyWe used a commercial RT-LAMP mastermix from OptiGene Ltd in combination with a primer set designed to detect the CDC N1 region of the SARS-CoV-2 nucleocapsid (N) gene. A single-tube, single-step fluorescence assay was implemented whereby as little as 1 L of universal transport medium (UTM) directly from a nasopharyngeal swab could be used as template, bypassing the requirement for RNA purification. Amplification and detection could be conducted in any thermocycler capable of holding 65{degrees}C for 30 minutes and measure fluorescence in the FAM channel at one-minute intervals. ResultsAssay evaluation by assessment of 157 clinical specimens previously screened by E-gene RT-qPCR revealed assay sensitivity and specificity of 87% and 100%, respectively. Results were fast, with an average time-to-positive (Tp) for 93 clinical samples of 14 minutes (SD {+/-}7 minutes). Using dilutions of SARS-CoV-2 virus spiked into UTM, we also evaluated assay performance against FDA guidelines for implementation of emergency-use diagnostics and established a limit-of-detection of 54 Tissue Culture Infectious Dose 50 per ml (TCID50 mL-1), with satisfactory assay sensitivity and specificity. A comparison of 20 clinical specimens between four laboratories showed excellent interlaboratory concordance; performing equally well on three different, commonly used thermocyclers, pointing to the robustness of the assay. ConclusionWith a simplified workflow, N1-STOP-LAMP is a powerful, scalable option for specific and rapid detection of SARS-CoV-2 and an additional resource in the diagnostic armamentarium against COVID-19. 3. Data summaryThe authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

microbiology↗

bioRxiv2018

Enspara: Modeling molecular ensembles with scalable data structures and parallel computing

Markov state models (MSMs) are quantitative models of protein dynamics that are useful for uncovering the structural fluctuations that proteins undergo, as well as the mechanisms of these conformational changes. Given the enormity of conformational space, there has been ongoing interest in identifying a small number of states that capture the essential features of a protein. Generally, this is achieved by making assumptions about the properties of relevant features--for example, that the most important features are those that change slowly. An alternative strategy is to keep as many degrees of freedom as possible and subsequently learn from the model which of the features are most important. In these larger models, however, traditional approaches quickly become computationally intractable. In this paper, we present enspara, a library for working with MSMs that provides several novel algorithms and specialized data structures that dramatically improve the scalability of traditional MSM methods. This includes ragged arrays for minimizing memory requirements, MPI-parallelized implementations of compute-intensive operations, and a flexible framework for model estimation.

biophysics↗

bioRxiv2018

BisPin and BFAST-Gap: Mapping Bisulfite-Treated Reads

BackgroundBisPin is a new multiprocess bisulfite-treated short DNA read mapper written in Python 2.7. It performs alignments using BFAST, leveraging its multithreading functionality and thorough hash-based indexing strategy. BisPin is feature rich and supports directional, nondirectional, PBAT, and hairpin construction strategies. BisPin approaches read mapping by converting the Cs to Ts and the Gs to As in both the reads and the reference genome. BisPin uses fast rescoring to disambiguate ambiguously aligned reads for a superior amount of uniquely mapped reads compared to other mappers. The performance of BisPin was evaluated on both real and simulated data in comparison to other read mappers.\n\nBFAST-Gap is a modified version of BFAST meant for Ion Torrent reads. It uses a parameterized logistic function to determine the weights of the gap open and extension penalties based on the homopolymer run length of the DNA read. This is because the Ion Torrent sequencing technology can overcall and undercall homopolymer runs. BisPin works with both BFAST-Gap and BFAST. BFAST-Gap is compatible with indexes built with BFAST. There are few mappers that specifically address Ion Torrent data. BFAST-Gap works with Illumina reads as well.\n\nResultsBisPin with BFAST consistently had a higher amount of uniquely mapped reads compared to other mappers on real data using a variety of construction strategies. Using a hairpin validation strategy, BisPin was superior using the maximum score, and it mapped 73% of reads correctly.\n\nBisPin with BFAST-Gap on Ion Torrent reads with a logistic gap open penalty function improved mapping accuracy with real and simulated data. On simulated bisulfite Ion Torrent data, the area under the curve was improved by approximately seven, and on one real data set, the uniquely mapped percent was improved by seven percent. BFAST-Gap performed better than TMAP on simulated regular Ion Torrent reads, and TMAP is designed for Ion Torrent reads. Other read mappers had worse performance.\n\nConclusionsBisPin and BFAST-Gap have consistently good accuracy with a variety of data. BisPin is feature-rich. This makes BisPin and BFAST-Gap useful additions to read mapping software.

bioinformatics↗

bioRxiv2018

Fast NeighborNet: Improving the Speed of the Neighbor-Net Phylogenetic Network Algorithm with Multithreading and a Relaxed Search Strategy

Fast Neighbor-Net is a command-line Java program that has fast implementations of the popular Neighbor-Net phylo-genetic split network approach. This allows more efficiency in computationally intensive tasks such as larger scale data analysis and bootstrapping. The canonical search phase iteratively finds a pair of connected components that minimizes a distance function in {Theta}(n3) time in the input taxa count. A relaxed search strategy has been implemented that has averagecase time complexity of[O] (n2 log n) but with {Theta}(n3) worst-case time complexity. This search strategy sacrifices some accuracy for speed. The original approachs implementation has been improved by using good programming practice. These improvements increased run-time performance by a constant factor of approximately 2 and reduced memory requirements by a constant factor of approximately 6. These search strategies allow multithreading to better use modern CPU hardware. PFAM data of 2000-30,000 taxa were used for testing performance. The canonical implementation with three threads improved average performance by approximately 2.1. The relaxed search has good quality, and the accuracy was tested on a mammal and a eukaryote data set. Kendall tau distance was used as a rough measure of topological similarity for the relaxed and canonical search strategies.

bioinformatics↗

bioRxiv2017

InfoTrim: A DNA Read Quality Trimmer Using Entropy

Biological DNA reads are often trimmed before mapping, genome assembly, and other tasks to improve the quality of the results. Biological sequence complexity relates to alignment quality as low complexity regions can align poorly. There are many read trimmers, but many do not use sequence complexity for trimming. Alignment of reads generated from whole genome bisulfite sequencing is especially challenging since bisulfite treated reads tend to reduce sequence complexity. InfoTrim, a new read trimmer, was created to explore these issues. It is evaluated against five other trimmers using four read mappers on real and simulated bisulfite treated DNA data. InfoTrim produces reasonable results consistent with other trimmers.

bioinformatics↗