Biology subjects

Joseph, L.

Publications and source records attributed to Joseph, L..

17 recordsLinked to original sources

bioRxiv2026

Oxytocin and Vasopressin Immunoreactivity Differs Across Auditory Brainstem Nuclei in Rodents with Distinct Social Systems

Oxytocin (OT) and vasopressin (AVP) are neuropeptide hormones involved in regulating animal social behavior and a broad spectrum of physiological processes. Although their distributions are well documented in neuroendocrine regions of the forebrain and midbrain, their expression in the hindbrain remains poorly understood. Here, we used immunohistochemistry to quantify OT and AVP immunoreactive puncta within three auditory brainstem nuclei, the lateral superior olive (LSO), the medial superior olive (MSO), and the medial nucleus of the trapezoid body (MNTB) in six wild-caught rodent species differing in sociality. We also quantified the volume of these nuclei and examined variation in total brain volume across species and sociality. OT and AVP puncta count differed among species and social groups. Group-living species exhibited higher OT and AVP puncta counts than monogamous and solitary species in the LSO and MNTB. In the MSO, OT puncta counts did not differ among social groups, whereas AVP puncta counts were higher in group-living than in monogamous and solitary species. Total brain volume and the volumes of the MNTB and MSO differed among species, but not across social groups, whereas LSO volume did not differ among species or sociality. These findings revealed sociality-related variation in OT and AVP immunoreactive puncta within auditory brainstem circuits and suggest that neuropeptide signaling within early auditory brainstem pathways may contribute to the neural integration of social and auditory information.

neuroscience↗

bioRxiv2026

Sociality Drives Sex Differences in Auditory Brainstem Processing Across Rodent Species

Although social behavior has been predicted to correlate with increased complexity in vocal signals, its relationship with auditory sensitivity between the sexes remains poorly understood. Here, we used phylogenetic comparative analyses to examine sex-specific differences in auditory processing across rodent species representing different social lifestyle strategies. We detected significant sex differences in click and frequency evoked auditory brainstem response (ABR) thresholds across sociality, with social female rodents exhibiting lower thresholds than solitary males. Males generally exhibited higher ABR wave I and IV amplitude ratios than females, whereas interpeak latencies were similar between the sexes across social groups. Females exhibited significantly higher binaural interaction component (BIC) relative amplitudes and faster BIC normalized latencies than males across tested interaural time differences (ITDs). Together, these findings demonstrate that sociality plays an important role in shaping differences in auditory physiology between male and female rodents and highlights the potential influence of social behavior on the evolution of mammalian auditory systems.

physiology↗

bioRxiv2026

Gestational inhalation of nanoparticles disrupts placental zone structure and induces vascular placentation in rats

Airborne contaminants represent a significant environmental health concern for vulnerable populations, including pregnant individuals. In particular, maternal inhalation of particulate matter (PM) during pregnancy has been linked to adverse outcomes such as fetal growth restriction (FGR). Increasing evidence identifies placental dysfunction as a mechanism for this condition. Placental efficiency, defined as the ratio of fetal mass to placental mass, is frequently altered in FGR. Many aspects contribute to placental efficiency including surface area available for nutrient and waste exchange and placental vascularization. In this study, we hypothesized that maternal inhalation of ultrafine PM during pregnancy would reduce the size and/or number of placental structures that are necessary for nutrient transport. Engineered titanium dioxide nanoparticles (nano-TiO2) were used as a proxy for ultrafine PM and pregnant Sprague Dawley rats were exposed via whole-body inhalation to nano-TiO2 aerosols (9.23 {+/-} 0.39 mg/m3) from gestational day (GD) 5 to 19. On GD 20, placentas were collected and processed for histological evaluation. While gestational inhalation of nano-TiO2 did not affect placental weight or efficiency, it reduced decidua and labyrinth zone size. Exposed placentas exhibited compensatory adaptations characterized by increased blood space number and maternal blood space expansion. Together, these findings indicate that inhalation of nanoparticles disrupts placental structure while simultaneously eliciting adaptive vascular responses that may preserve nutrient exchange capacity. By characterizing the effects of PM exposure on placental morphology and structure, this study highlights the placenta as a vulnerable target of inhaled pollutants and provides mechanistic insight into pathways contributing to PM-induced FGR.

pharmacology and toxicology↗

bioRxiv2025

Differences in Auditory Brainstem Responses between Laboratory-reared and Wild-caught Prairie Voles (Microtus ochrogaster)

Prairie voles (Microtus ochrogaster) are a semi-fossorial rodent that are an emerging model in social neuroscience. Comparing laboratory-reared and wild-caught individuals is essential for understanding how environmental history shapes neural and sensory traits and for assessing the ecological validity of laboratory findings. Despite this, relatively few studies have taken this approach. We used auditory brainstem responses (ABRs) to compare ABR thresholds and ABR wave characteristics between laboratory-reared and wild-caught prairie voles. ABR recordings show that, similar to other semi-fossorial rodents, M. ochrogaster exhibit a hearing range of 1 - 46 kHz with peak sensitivity around 8 to 32 kHz. However, wild-caught prairie voles displayed significantly lower ABR thresholds at 1, 4, 8, 16, and 24 kHz compared to laboratory-reared prairie voles. There were significant differences in interpeak latency between both tested groups, with laboratory-reared prairie voles showing faster interpeak latency responses than wild-caught voles. However, there were no differences in amplitude ratios between groups. Laboratory-reared prairie voles showed faster normalized latencies and higher relative amplitude of the binaural interaction component (BIC) of the ABR than wild-caught voles. There were no significant differences in ABR thresholds, interpeak latency, amplitude ratio, normalized latency, and relative amplitude between the sexes. These differences in auditory processing support the importance of integrating both wild and captive populations to advance comparative auditory research. SUMMARY STATEMENTWild and laboratory-reared prairie voles show distinct auditory processing, highlighting how environment history shapes hearing and underscoring the need for comparative studies.

neuroscience↗

bioRxiv2025

Proteasome mutations associated with CANDLE syndrome cause altered neuronal development by dysregulating polyamine synthesis

Genetic mutations affecting proteasome function can result in multi-organ diseases, such as Chronic atypical neutrophilic dermatosis with lipodystrophy and elevated temperature (CANDLE) syndrome. Neurological symptoms associated with CANDLE suggest that proteasomal mutations may impact neuronal development and/or function. We generated cerebral organoids (COs) from CANDLE patient induced pluripotent stem cells (iPSCs), which exhibited impaired neuronal development when compared to COs from healthy control iPSCs. Impaired neuronal maturation in CANDLE COs was correlated with increased polyamines, which were also elevated in CANDLE patient CSF. The proteasome-regulated Ornithine decarboxylase (ODC), a rate limiting enzyme for polyamines, was elevated in CANDLE neurons. Inhibition of ODC reversed polyamine overproduction and repaired neuronal maturation in CANDLE COs, suggesting a potential therapeutic avenue for intervention. These findings demonstrate that dysfunction of the proteasome affects neuronal development through overproduction of polyamines via dysregulation of ODC and offer insight into potential therapeutic strategies for CNS-related proteasomal dysfunction.

neuroscience↗

bioRxiv2025

Programmed DNA elimination drives rapid genomic innovation in two thirds of all bird species

Bird genomes are among the most stable in terms of synteny and gene content across vertebrates. However, germline-restricted chromosomes (GRCs) represent a striking exception where programmed DNA elimination confines large-scale genomic changes to the germline. GRCs are known to occur in songbirds (oscines), but have been studied only in a few species of Passerides such as the zebra finch, the key model for passerine genomics. Their presence and evolutionary dynamics in most major passerine lineages remain largely unexplored, with suboscines entirely unexamined by cytogenetic or genomic methods. Here, we present the most comprehensive comparative analysis of GRCs to date, spanning 44 million years of passerine evolution. By generating the first germline reference genomes of an oscine and a suboscine, 22 novel germline draft genomes spanning nearly all major passerine lineages and a germline draft genome of a parrot outgroup, we show that the GRC is likely present in 6,700 passerine species. Our results reveal that the GRC evolves rapidly and distinctly from the standard A chromosomes (autosomes and sex chromosomes), yet retains functionally important, selectively maintained genes. We observed gene and repeat turnover occuring orders of magnitude faster than on the A chromosomes. Some GRC genes, such as cpeb1 and pim1, are widespread from an ancient duplication. In contrast, other GRC genes, like mfsd2b and bmp15, have been independently duplicated onto the GRC multiple times, suggesting adaptive constraints. The discovery of zglp1 on the zebra finch GRC, initially copied from chromosome 30 and subsequently lost from it, indicates functional replacement, where the GRC permits gene loss from the standard genome. As the GRC harbors the only zglp1 copy in most of the [~]4000 Passerides species, GRC loss would compromise essential germline functions. Our findings establish the GRC as a genomic innovator driving rapid germline evolution. This fact highlights its evolutionary significance for passerine diversification and suggests that programmed DNA elimination may be an overlooked yet phylogenetically widespread mechanism in many understudied animal lineages.

genomics↗

bioRxiv2025

Efficient Inference of Macrophylogenies: Insights from the Avian Tree of Life

The exponential growth of molecular sequence data over the past decade has enabled the construction of numerous clade-specific phylogenies encompassing hundreds or thousands of taxa. These independent studies often include overlapping data, presenting a unique opportunity to build macrophylogenies (phylogenies sampling > 1,000 taxa) for entire classes across the Tree of Life. However, the inference of large trees remains constrained by logistical, computational, and methodological challenges. The Avian Tree of Life provides an ideal model for evaluating strategies to robustly infer macrophylogenies from intersecting datasets derived from smaller studies. In this study, we leveraged a comprehensive resource of sequence capture datasets to evaluate the phylogenetic accuracy and computational costs of four methodological approaches: (1) supermatrix approaches using concatenation, including the "fast" maximum likelihood (ML) methods, (2) filtering datasets to reduce heterogeneity, (3) supertree estimation based on published phylogenomic trees, and (4) a "divide-and-conquer" strategy, wherein smaller ML trees were estimated and subsequently combined using a supertree approach. Additionally, we examined the impact of these methods on divergence time estimation using a dataset that includes newly vetted fossil calibrations for the Avian Tree of Life. Our findings highlight that recently developed fast tree search approaches offer a reasonable compromise between computational efficiency and phylogenetic accuracy, facilitating inference of macrophylogenies.

evolutionary biology↗

bioRxiv2025

An improved catalogue for whole-genome sequencing prediction of bedaquiline resistance in M. tuberculosis using a reproduciblealgorithmic approach.

Bedaquiline (BDQ) has only been approved for use for a little over a decade yet is a key drug for treating multi-drug resistant tuberculosis, however rising levels of resistance threaten to reduce its effectiveness. Catalogues of mutations associated with resistance to bedaquiline are key to detecting resistance genetically for either diagnosis or surveillance. At present building catalogues requires considerable expert knowledge, often requires the use of complex grading rules, and is an irreproducible process. We developed an automated method, catomatic, that associates genetic variants with resistance (or susceptibility) using a two-tailed binomial test with a stated background rate and applied it to a dataset of 11,867 Mycobacterium tuberculosis samples with whole genome and bedaquline susceptibility testing data. Using this framework we investigated how to best classify variants and the phenotypic significance of minor alleles. The genes mmpS5 and mmpL5 are not directly associated with bedaquline resistance, and our catalogue of Rv0678, atpE, and pepQ variants attains a cross-validated sensitivity and specificity of 79.4 {+/-} 1.8 % and 98.5 {+/-} 0.3%, respectively, for 94 {+/-} 0.4% of samples. Identifying samples with subpopulations containing Rv0678 variants improves sensitivity, and detection thresholds in bioinformatic pipelines should therefore be lowered. By using a more permissive and deterministic algorithm trained on a sufficient number of resistant samples we have reproducibly constructed an AMR catalogue for BDQ resistance-associated variants that is comprehensive and accurate. Impact StatementBedaquiline has recently received global endorsement for tuberculosis treatment, yet the genetic determinants of antimicrobial resistance remain incompletely understood. Existing gold-standard methods for building mutation catalogs lack public accessibility and reproducibility. We introduce catomatic, a reproducible and publicly available method that employs simpler statistics to increase sensitivity to resistance-associated variants. This approach has enabled investigations into mechanisms of resistance, the significance of genetic subpopulations, and key data attributes that influence the ease of classifying effects and the accuracy of BDQ resistance phenotype prediction in clinical samples. We strongly emphasise the utility in using reproducible statistics and sustainably developed software in genetics-focussed microbiology.

microbiology↗

bioRxiv2024

Sex Differences in Auditory Brainstem Responses in the Hispid Pocket Mouse (Chaetodipus hispidus)

The hispid pocket mouse (C. hispidus) is a solitary semi-fossorial rodent that has been the subject of various ecological and genetic studies. However, no previous studies have characterized its hearing ability, which is important for its survival and fitness. We collected auditory brainstem responses (ABRs) from C. hispidus and measured craniofacial and pinna morphological features to assess hearing ability and test differences in hearing thresholds, monaural and binaural ABR amplitudes and latencies between the sexes. ABR recordings revealed that similar to other small mammals, C. hispidus displayed the lowest threshold to sounds between 8-16 kHz, indicating best hearing across those frequencies. We found significant differences in auditory thresholds of the ABRs between the sexes, with females showing lower frequency hearing compared to males. However, no significant differences were detected in monaural and binaural ABR amplitudes and latencies between the sexes. We also found no significant differences in craniofacial and pinna dimensions between the sexes. These findings shed novel insights into the auditory systems across species and highlighted for the first time sex differences in auditory thresholds for this rodent species.

neuroscience↗

bioRxiv2024

Hearing in Two Closely Related Peromyscus Species (Peromyscus maniculatus and P. leucopus)

The genus Peromyscus has been extensively used as a model for ecological, behavioral, and evolutionary studies. We used auditory brainstem responses (ABRs), craniofacial morphology, and pinna measurements to compare characteristics that could impact the threshold, amplitude, and latency of ABRs in two wild-caught species, P. leucopus and P. maniculatus. We observed significant differences in craniofacial and pinna attributes between species, with P. leucopus exhibiting larger features and bigger overall size compared to P. maniculatus. ABR recordings showed similar hearing thresholds with peak sensitivity between 8 to 46 kHz for both species. We found that amplitude of ABR wave I and IV increased significantly with increasing intensity, while no main effect of species was detected. Latency of wave I and IV significantly decreased with increasing intensity in both species. Finally, we observed longer latencies of the binaural interaction component (BIC) at longer interaural time differences (ITDs) in P. leucopus, while no differences were observed across relative BIC amplitude between species. These results provide additional ABR related data that expands the use of both Peromyscus species as future models for auditory research.

neuroscience↗

bioRxiv2022

Repeated evolution of bedaquiline resistance in Mycobacterium tuberculosis is driven by truncation of mmpR5

The antibiotic Bedaquiline (BDQ) is a key component of new WHO regimens for drug resistant tuberculosis (TB) but predicting BDQ resistance (BDQ-R) from genotypes remains challenging. We analysed a collection (n=505) of Mycobacterium tuberculosis from two high prevalence areas in South Africa (Cape Town and Johannesburg, 2019-2020), and found 53 independent acquisitions of 31 different mutations within the mmpR5 regulatory gene, with a particular enrichment of truncated MmpR5 in BDQ-R isolates by either frameshift or introduction of an insertion element. Truncations occurred across three M. tuberculosis lineages, impacting 66% of BDQ-R isolates. Extending our analysis to 1,961 isolates with minimum inhibitory concentrations (MICs) revealed that mmpR5-disrupted isolates had a median BDQ MIC of 0.25 mg/L, compared to the wild-type median of 0.06 mg/L. By matching mmpR5-disrupted isolates with phylogenetically close control isolates without the disruption, we were able to estimate the impact on MIC of individual mutations. In conclusion, as the MIC increase borders the ECOFF threshold for BDQ-R, we recommend the continued use of MICs and detection of MmpR5 truncations to identify modest shifts in BDQ-R.

microbiology↗

bioRxiv2022

Candida khanbhai sp. nov., a new clinically relevant yeast within the Candida haemulonii species complex

Invasive fungal infections caused by non-albicans Candida species are increasingly reported. Recent advances in diagnostic and molecular tools enabled better identification and detection of these emerging pathogenic yeasts. Several of these emerging species belong to the Candida haemulonii species complex, which attracted much attention due to the rapid global emergence of its multi-drug resistant member Candida auris. Here, we describe a new clinically relevant yeast isolated from geographically distinct regions, representing the proposed novel species Candida khanbhai, member of the C. haemulonii species complex. Moreover, several members of the C. haemulonii species complex were observed to be invalidly described, including Candida auris and Candida vulturna. Hence, the opportunity was taken to correct this here, formally validating the names of various yeast species.

microbiology↗

bioRxiv2022

Sustained plumage divergence despite weak genomic differentiation and broad sympatry in sister species of Australian woodswallows (Artamus spp.)

Plumage divergence can function as a strong premating barrier when species come into secondary contact. When it fails to do so, the results are often genome homogenization and phenotypic hybrids at the zone of contact. This is not the case in the largely sympatric masked woodswallow and white-browed woodswallow species (Passeriformes: Artamidae: Artamus spp) complex in Australia where phenotypic integrity is sustained despite no discernible mitochondrial structure in earlier work. This lack of structure may suggest recent divergence, ongoing gene flow or both, and phenotypic hybrids are reported albeit rarely. Here, we further assessed the population structure and differentiation across the species nuclear genomes using ddRAD-seq. As found in the mitochondrial genome, no structure or divergence within or between the two species was detected in the nuclear genome. This coarse sampling of the genome nonetheless revealed peaks of differentiation around the genes SOX5 and Axin1. Both are involved in the Wnt//-catenin signaling pathway, which regulates feather development. Reconstruction of demographic history and estimation of parameters supports a scenario of secondary contact. Our study informs how divergent plumage morphs may arise and be sustained despite whole-genome homogenization and reveals new candidate genes potentially involved in plumage divergence.

evolutionary biology↗

bioRxiv2021

recount3: summaries and queries for large-scale RNA-seq expression and splicing

We present recount3, a resource consisting of over 750,000 publicly available human and mouse RNA sequencing (RNA-seq) samples uniformly processed by our new Monorail analysis pipeline. To facilitate access to the data, we provide the recount3 and snapcount R/Bioconductor packages as well as complementary web resources. Using these tools, data can be downloaded as study-level summaries or queried for specific exon-exon junctions, genes, samples, or other features. Monorail can be used to process local and/or private data, allowing results to be directly compared to any study in recount3. Taken together, our tools help biologists maximize the utility of publicly available RNA-seq data, especially to improve their understanding of newly collected data. recount3 is available from http://rna.recount.bio.

genomics↗

bioRxiv2019

Genome of an iconic Australian bird: Chromosome-scale assembly and linkage map of the superb fairy-wren (Malurus cyaneus)

The superb fairy-wren, Malurus cyaneus, is one of the most iconic Australian passerine species. This species belongs to an endemic Australasian clade, Meliphagides, which diversified early in the evolution of the oscine passerines. Today, the oscine passerines comprise almost half of all avian species diversity. Despite the rapid increase of available bird genome assemblies, this part of the avian tree has not yet been represented by a high-quality reference. To rectify that, we present the first chromosome-scale genome assembly of a Meliphagides representative: the superb fairy-wren. We combined Illumina shotgun and mate-pair sequences, PacBio long-reads, and a genetic linkage map from an intensively sampled pedigree of a wild population to generate this genome assembly. Of the final assembled 1.07Gb genome, 894Mb (84.8%) was anchored onto 25 chromosomes resulting in a final scaffold N50 of 68.11 Mb. This high-quality bird genome assembly is also one of only a handful which is also accompanied by a genetic map and recombination landscape. In comparison to other pedigree-based bird genetic maps, we find that the zebrafinch (Taeniopygia) genetic map more closely resembles the fairy-wren map rather than the map from the more closely-related Ficedula flycatcher. Lastly, we also provide a predictive gene and repeat annotation of the genome assembly. This new high quality, annotated genome assembly will be an invaluable resource not only to the superb fairy-wren species and relatives but also broadly across the avian tree by providing a new reference point for comparative genomic analyses.

genomics↗

bioRxiv2017

Current geography masks dynamic history of gene flow during speciation in northern Australian birds

During early stages of speciation, genome divergence is greatly influenced by gene flow. As populations diverge, geography can allow or restrict gene flow in the form of barriers. Current geography, e.g. whether sister species are allopatric or parapatric, is often used to predict the potential for gene flow during the divergence process. We test the validity of this assumption in eight meliphagoid bird species codistributed across four regions. These regions are separated by known biogeographic barriers within and between northern Australia and Papua New Guinea. We find that bird populations across the same barrier have a range of divergence levels and probability of gene flow regardless of range connectivity. Geographic distance and maximum range connectivity over time can better predict divergence and probability of gene flow than whether populations are currently allopatric or parapatric. We also find support for a nonlinear decrease of the probability of gene flow during the divergence process. This implies that although gene flow influences divergence early in speciation, other factors associated with higher divergence restrict gene flow later in speciation. Current geography may then mislead inferences regarding potential for gene flow during speciation under a complex and dynamic history of geographic and reproductive isolation.

evolutionary biology↗

bioRxiv2016

De-novo emergence and template switching of SINE retroposons during the early evolution of passerine birds

Passeriformes (\"perching birds\" or passerines) make up more than half of all extant bird species. Here, we resolve their deep phylogenetic relationships using presence/absence patterns of short interspersed elements (SINEs), a group of retroposons which is abundant in mammalian genomes but considered largely inactive in avian genomes. The resultant retroposon-based phylogeny provides a powerful and independent corroboration of previous indications derived from sequence-based analyses. Notably, SINE activity began in the common ancestor of Eupasseres (passerines excl. the New Zealand wrens Acanthisittidae) and ceased before the rapid diversification of oscine passerines (songbirds). Furthermore, we find evidence for very recent SINE activity within suboscine passerines, following the emergence of a SINE via acquisition of a different tRNA head as we suggest through template switching. We propose that the early evolution of passerines was unusual among birds in that it was accompanied by activity of SINEs. Their genomic and transcriptomic impact warrants further study in the light of the massive diversification of passerines.

evolutionary biology↗