Biology subjects

Bailey, E.

Publications and source records attributed to Bailey, E..

10 recordsLinked to original sources

bioRxiv2026

Non-invasive genomic sampling uncovers novel connectivities and origins of confiscated gorillas

BackgroundGorillas are a group of African great apes with two species and four subspecies that are currently critically endangered or endangered. Previous studies that analysed the genetics of wild gorillas from non-invasive samples, such as faeces or hair, analysed short mitochondrial or nuclear markers, which may not reflect the wider nuclear genome. Recent technical advances in target capture hybridisation, enrich the endogenous DNA content of non-invasive samples, allowing contiguous genomic regions to be sequenced. ResultsHere, we generated georeferenced genetic data from faecal and hair samples of 280 wild gorillas, sampled from three of the four gorilla subspecies, across large parts of their present-day distributions. With this expanded representation of gorilla genetic diversity in the wild, we detected three population clusters in western lowland gorillas, with the Sangha River and its affluents acting as significant barriers to gene flow. We reconstructed patterns of past population connectivity between western lowland gorillas in the north-eastern distribution range and Cross River gorillas, which may have been facilitated by a migration corridor also used by the Central and Nigeria-Cameroon chimpanzee subspecies. Finally, we predicted the geographic origins of wild-born gorillas, achieving a mean prediction error of 65 km, with a population-level resolution for mountain gorillas and some populations of western lowland gorillas. ConclusionOur work characterises fine-scale population structure in western lowland gorillas, which will be informative for future conservation strategies. This proof of concept in predicting geographic locations of wild gorillas, will be useful for future applications to geolocalise trafficked or rescued gorillas.

evolutionary biology↗

bioRxiv2025

Genetic control of the leaf ionome in pearl millet and correlation with root and agromorphological traits

Pearl millet (Pennisetum glaucum) thrives in arid and nutrient-poor environments, establishing its role as a crucial cereal crop for food security in sub-Saharan Africa. Despite its remarkable adaptability, its yields remain below genetic potential, primarily due to limited water and nutrient availability. In this study, we conducted ionomic profiling and genome-wide association studies (GWAS) in field conditions across two growing seasons to unravel the genetic basis of nutrient acquisition in pearl millet. Soil ion content analyses revealed significant differences in nutrient distribution between field sites, while certain ions, such as phosphorus (P) and zinc (Zn), consistently displayed stratified accumulation patterns across years, suggesting stable depth-dependent trends. Evaluation of a genetically diverse panel of inbred lines revealed substantial variation in leaf ion concentrations, with high heritability estimates. Correlations between leaf ion content and root anatomical or agromorphological traits highlighted the intricate interplay between genetic and environmental factors shaping leaf ion accumulation. These analyses also uncovered potential trade-offs in nutrient acquisition strategies. GWAS identified genomic regions associated with leaf ion concentrations, and the integration of genetic and gene expression data facilitated the identification of candidate genes implicated in ion transport and homeostasis. Our findings provide valuable insights into the genetic regulation of nutrient acquisition in pearl millet, offering potential targets for breeding nutrient-efficient and climate-resilient varieties. This study underscores the importance of integrating genetic, physiological, and root architectural traits to enhance agricultural productivity and sustainability in resource-constrained environments.

plant biology↗

bioRxiv2024

YAP engages RIF1 to dampen replication stress in squamous cell carcinoma.

Squamous cell carcinoma cells experience high levels of replication stress due to oncogene-induced cell cycle deregulation. How such cells sustain rapid proliferation despite replication stress is still not fully understood. Here, we discovered, using rapid immunoprecipitation mass spectrometry of endogenous protein (RIME) analysis, that the squamous cell carcinoma oncoprotein YAP engages with RIF1, a key regulator of DNA replication and DNA damage repair under replication stress. RIF1 is highly expressed in human squamous cell carcinoma cell lines and tissues and upregulated during tumour progression. Depletion of RIF1 in squamous cell carcinoma cells exacerbates their endogenous replication stress. Mechanistically, we show that YAP interacts with RIF1 specifically at broken replication forks, and that YAP depletion impairs DNA damage repair under replication stress. Our results thus demonstrate that YAPs oncogenic functions in squamous cancers involve both transcriptional and non-transcriptional mechanisms, the latter through interaction with RIF1 to dampen replication stress.

cancer biology↗

bioRxiv2024

Somatosensory high frequency oscillations across the human central nervous system

Information transmission in the central nervous system (CNS) relies on the propagation of action potentials (neuronal spikes), traditionally thought to be inaccessible with electroencephalography (EEG). Converging evidence from human and animal recordings however demonstrates that high frequency oscillations (HFOs) in EEG recordings represent neuronal population spiking, complementing standard low-frequency EEG recordings in cortex. Here, we developed an approach to simultaneously record HFOs to somatosensory stimulation across the entire human CNS noninvasively: from spinal over subcortical to cortical stages. Our approach provides a detailed temporal and spectral characterization of HFOs at each CNS level, delineating how they evolve across the somatosensory processing hierarchy. Critically, we show that low and high frequency electrophysiological responses represent at least partly independent processing channels across the CNS. We thus demonstrate the feasibility of studying the full spectrum of neuronal information processing across the CNS, offering a multi-level window into human neurophysiology in health and disease.

neuroscience↗

bioRxiv2024

Evaluating noise correction approaches for non-invasive electrophysiology of the human spinal cord

The spinal cord is a vital component of the central nervous system for the processing of sensorimotor information transmitted between the body and the brain. Electrospinography (ESG) is the most accessible non-invasive technique for recording spinal signals in humans, but the vast and detrimental impact of physiological noise (mostly of cardiac nature) has prevented widespread adoption. Here, we aim to address this issue by examining various denoising algorithms for cardiac artefact reduction - including principal component analysis-based techniques (PCA), independent component analysis-based approaches (ICA) and signal space projection (SSP). We observed that in situations where large numbers of spinal electrodes are used, SSP offers the best results in terms of balancing the removal of harmful noise and preserving neural information of interest. In cases where only a small number of electrodes are available, an approach based on PCA is deemed helpful. Approaches based on ICA were found to be unsuitable for cardiac artefact removal in ESG, due to a suboptimal balance of artefact removal and signal preservation. Finally, we also approached this issue from a signal-enhancement perspective and observed that in cases where extensive electrode arrays are used in the context of task-based designs, a spatial filtering technique based on canonical correlation analysis (CCA) reveals clear evoked spinal potentials even with single-trial resolution. Taken together, there are several appropriate algorithms for physiological noise removal in ESG, rendering this an accessible and easy-to-use technique for non-invasive assessments of human spinal cord function.

neuroscience↗

bioRxiv2024

Local genetic adaptation to habitat in wild chimpanzees

How populations adapt to their environment is a fundamental question in biology. Yet we know surprisingly little about this process, especially for endangered species such as non-human great apes. Chimpanzees, our closest living relatives, are particularly interesting because they inhabit diverse habitats, from rainforest to woodland-savannah. Whether genetic adaptation facilitates such habitat diversity remains unknown, despite having wide implications for evolutionary biology and conservation. Using 828 newly generated exomes from wild chimpanzees, we find evidence of fine-scale genetic adaptation to habitat. Notably, adaptation to malaria in forest chimpanzees is mediated by the same genes underlying adaptation to malaria in humans. This work demonstrates the power of non-invasive samples to reveal genetic adaptations in endangered populations and highlights the importance of adaptive genetic diversity for chimpanzees. One-Sentence SummaryChimpanzees show evidence of local genetic adaptation to habitat, particularly to pathogens, such as malaria, in forests.

evolutionary biology↗

bioRxiv2022

Low diversity and microdiversity of comammox bacteria in wastewater systems suggests wastewater-specific adaptation within the Ca. Nitrospira nitrosa cluster.

Studies have found Ca. Nitrospira nitrosa-like bacteria to be the principal or sole comammox bacteria in nitrogen removal systems for wastewater treatment. In contrast, multiple populations of strict ammonia and nitrite oxidizers co-exist in similar systems. This apparent lack of diversity is surprising and could impact the feasibility of leveraging comammox bacteria for nitrogen removal. We used full-length 16S rRNA gene sequencing and genome-resolved metagenomics to compare population-level (i.e., species) diversity of comammox bacteria with that of strict nitrifiers in full-scale wastewater treatment systems and assess whether these observations were consistent or diverged at the strain-level. Full-length 16S rRNA gene sequencing indicated that while Nitrosomonas-like bacteria exhibited higher population-level diversity, the effective microdiversity of most Nitrospira-like bacteria were comparatively higher except for one Nitrospira Lineage II population. Comammox bacterial metagenome assembled genomes (MAGs) were associated with Ca. Nitrospira nitrosa. The average amino acid identity between comammox bacterial MAGs (93% {+/-} 3) across systems was significantly higher than that of the Nitrosomonas-like ammonia oxidizers (73%{+/-}8) and the Nitrospira-like nitrite oxidizer MAGs (75%{+/-}13), suggesting that the same comammox population was detected in all systems. Comammox bacteria and some ammonia oxidizers MAGs were significantly less microdiverse than most ammonia and nitrite oxidizers. Interestingly, strain-resolved analysis also indicates that different nitrogen removal systems harbor different comammox bacterial strains within the Ca. Nitrospira nitrosa cluster. These results suggest that comammox bacteria associated with Ca. Nitrospira nitrosa have low species- and strain-level diversity in nitrogen removal systems and may thus harbor specific adaptations to the wastewater ecosystem.

microbiology↗

bioRxiv2019

Long solids retention times and attached growth phase favor prevalence of comammox bacteria in nitrogen removal systems.

The discovery of the complete ammonia oxidizing (comammox) bacteria overturns the traditional two-organism nitrification paradigm which largely underpins the design and operation of nitrogen removal during wastewater treatment. Quantifying the abundance, diversity, and activity of comammox bacteria in wastewater treatment systems is important for ensuring a clear understanding of the nitrogen biotransformations responsible for ammonia removal. To this end, we conducted a yearlong survey of 14 full-scale nitrogen removal systems including mainstream conventional and simultaneous nitrification-denitrification and side-stream partial nitrification-anammox systems with varying process configurations. Metagenomics and genome-resolved metagenomics identified comammox bacteria in mainstream conventional and simultaneous nitrification-denitrification systems, with no evidence for their presence in side-stream partial nitrification-anammox systems. Further, comammox bacterial diversity was restricted to clade A and these clade A comammox bacteria were detected in systems with long solids retention times (>10 days) and/or in the attached growth phase. Using a newly designed qPCR assay targeting the amoB gene of clade A comammox bacteria in combination with quantitation of other canonical nitrifiers, we show that long solids retention time is the key process parameter associated with the prevalence and abundance of comammox bacteria. The increase in comammox bacterial abundance was not associated with concomitant decrease in the abundance of canonical nitrifiers; however, systems with comammox bacteria showed significantly better and temporally stable ammonia removal compared to systems where they were not detected. Finally, in contrast to recent studies, we do not find any significant association of comammox bacterial prevalence and abundance with dissolved oxygen concentrations in this study.\n\nHighlightsO_LIClade A comammox bacteria were detected in wastewater nitrogen removal systems.\nC_LIO_LINew qPCR assay targeting the amoB gene of clade A comammox bacteria was developed.\nC_LIO_LIComammox bacteria are prevalent in mainstream conventional and simultaneous nitrification-denitrification systems with long solids retention times (>10 days).\nC_LIO_LIComammox bacteria were not detected in sidestream partial nitrification-anammox systems included in this study.\nC_LI\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC=\"FIGDIR/small/696351v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (28K):\norg.highwire.dtl.DTLVardef@3228c9org.highwire.dtl.DTLVardef@113dfb8org.highwire.dtl.DTLVardef@1c4adaforg.highwire.dtl.DTLVardef@166f997_HPS_FORMAT_FIGEXP M_FIG GRAPHICAL ABSTRACT\n\nC_FIG

microbiology↗

bioRxiv2018

EquCab3, an Updated Reference Genome for the Domestic Horse

EquCab2, a high-quality reference genome for the domestic horse, was released in 2007. Since then, it has served as the foundation for nearly all genomic work done in equids. Recent advances in genomic sequencing technology and computational assembly methods have allowed scientists to improve reference assemblies of large animal and plant genomes in terms of contiguity and composition. In 2014, the equine genomics research community began a project to improve the reference sequence for the horse, building upon the solid foundation of EquCab2 and incorporating new short-read data, long-read data, and proximity ligation data. The result, EquCab3, is presented here. The count of non-N bases in the incorporated chromosomes is improved from 2.33Gb in EquCab2 to 2.41Gb from EquCab3. Contiguity has also been improved nearly 40-fold with a contig N50 of 4.5Mb and scaffold contiguity enhanced to where all but one of the 32 chromosomes is comprised of a single scaffold.

genomics↗

bioRxiv2017

Development of a high-density, 2M SNP genotyping array and 670k SNP imputation array for the domestic horse

BackgroundTo date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent availability of whole genome sequences has created the opportunity to develop a next generation, high-density equine SNP array.\n\nResultsUsing whole genome sequence from 153 individuals representing 24 distinct breeds collated by the equine genomics community, we cataloged over 23 million de novo discovered genetic variants. Leveraging genotype data from individuals with both whole genome sequence, and genotypes from lower-density, legacy SNP arrays, a subset of [~]5 million high-quality, high-density array candidate SNPs were selected based on breed representation and uniform spacing across the genome. Considering probe design recommendations from a commercial vendor (Affymetrix, now Thermo Fisher Scientific) a set of [~]2 million SNPs were selected for a next-generation high-density SNP chip (MNEc2M). Genotype data were generated using the MNEc2M array from a cohort of 332 horses from 20 breeds and a lower-density array, consisting of [~]670 thousand SNPs (MNEc670k), was designed for genotype imputation.\n\nConclusionsHere, we document the steps taken to design both the MNEc2M and MNEc670k arrays, report genomic and technical properties of these genotyping platforms, and demonstrate the imputation capabilities of these tools for the domestic horse.

genomics↗