Biology subjects

Newman, C.

Publications and source records attributed to Newman, C..

16 recordsLinked to original sources

bioRxiv2025

Depletion of microenvironmental syndecan-2 impairs hematopoietic stem cell self-renewal and cytokine responses

Syndecan-2 is a heparan sulfate proteoglycan highly enriched on murine bone marrow hematopoietic stem cells (HSCs) compared to terminally differentiated hematopoietic cells. Syndecan-2 binds growth factors via its heparan sulfate glycosaminoglycan chains to coordinate cell signaling. Knockdown of syndecan-2 reduces HSC self-renewal ability and promotes cell cycling via Cdkn1c. In this study, we analyzed the function of syndecan-2 expressed by bone marrow niche cells in hematopoiesis and HSC self-renewal. We determined that syndecan-2 is highly expressed by bone marrow mesenchymal stromal cells and moderately expressed by endothelial cells. To test the function of niche-expressed syndecan-2 in hematopoiesis, we generated transgenic mice depleted of Sdc2 in Lepr-targeted mesenchymal stromal cells (Sdc2{Delta}MSC mice) or Cdh5-targeted endothelial cells (Sdc2{Delta}EC mice). Loss of syndecan-2 from endothelial or mesenchymal stromal cells did not change bone marrow HSC frequencies or numbers. However, depletion of syndecan-2 from Lepr-targeted mesenchymal stromal cells, but not Cdh5-targeted endothelial cells, diminishes HSC self-renewal ability analyzed by competitive transplants into lethally irradiated mice. Ex vivo studies further show that HSCs co-cultured with HS-5 stromal cells depleted of SDC2 exhaust more rapidly than HSCs cultured with control HS-5 cells. Single-cell RNA sequencing analyses reveal that the depletion of Sdc2 from mesenchymal stromal cells significantly remodels the HSC transcriptome by enriching for pathways associated with excessive growth factor signaling. Together, our findings suggest that HSC self-renewal is supported by cell-extrinsic mechanisms enacted by syndecan-2 from the MSC niche, highlighting the importance of the niche proteoglycome in HSC functions. KEY POINTSO_LIThe heparan sulfate proteoglycan syndecan-2 expressed by mesenchymal stromal cells but not endothelial cells regulates HSC self-renewal C_LIO_LIDepletion of syndecan-2 from Lepr-targeted mesenchymal stromal cells remodels the hematopoietic stem cell transcriptional landscape C_LI

cell biology↗

bioRxiv2025

Inhibition of farnesyltransferase activity diminishes hematopoietic stem cell ex vivo expansion ability

ABSTRACT/SUMMARYThe rationale underlying this work is that elucidating the contribution of farnesyltransferase activity to hematopoietic stem cell expansion ex vivo will provide knowledge needed to better support hematopoietic stem cell expansion techniques for clinical applications that rely on this approach, like hematopoietic cell transplants and gene therapy. We discovered that pharmacological inhibition of farnesyltransferase activity with lonafarnib substantially diminished the ex vivo expansion potential of human and mouse hematopoietic stem cells, highlighting that hematopoietic stem cells rely on isoprenoids for their ex vivo maintenance.

cell biology↗

bioRxiv2025

LIPT1 loss confers replication stress and PARP inhibitor sensitivity through PrimPol-mediated ssDNA gaps

Replication stress (RS) and altered metabolism are two hallmarks of cancer, yet how metabolic perturbations contribute to RS remains poorly understood. Lipotransferase 1 (LIPT1) catalyzes the covalent attachment of lipoic acid to mitochondrial 2-ketoacid dehydrogenases, sustaining flux through the tricarboxylic acid (TCA) cycle. Loss of LIPT1 causes accumulation of 2-hydroxyglutarate (2-HG), which is known to inhibit -ketoglutarate (-KG)-dependent histone demethylases and promotes heterochromatin formation. Here, we show that 2-HG-driven heterochromatin impedes replication fork progression, causing fork stalling and RS in LIPT1-deficient cancer cells. To bypass stalled forks, PrimPol-mediated repriming resumes DNA synthesis but leaves behind single-stranded DNA (ssDNA), which requires poly (ADP-ribose) polymerase 1 (PARP1) for repair. Furthermore, nascent DNA at reprimed forks undergoes MRE11-dependent degradation, further destabilizing replication fork integrity. Consequently, LIPT1 deficiency promotes replication and genome instability, and therapeutic vulnerability to PARP inhibitor. Together, these findings reveal a mechanistic link between mitochondrial lipoylation and replication fork stability, uncovering a metabolic basis for genome instability in cancer.

cell biology↗

bioRxiv2024

Food for thought: Rosy-faced lovebirds (Agapornis roseicollis) are capable of associative symbol learning and inference-based quantity discrimination

Cognitive capacity for quantity discrimination is highly adaptive in various ecological contexts and subject to convergent evolution across diverse animal species, yet the underlying mechanism involved is not fully understood. Discrimination accuracy generally increases with the ratio between two quantities; however, this ability is expected to differ across ratio ranges. To test this we presented a novel symbol system to 28 rosy-faced lovebirds (Agapornis roseicollis), associating additive tally marks with symbols representing a one-to-one correspondence with different food quantities. Trained lovebirds could spontaneously infer the relative food quantities represented by other symbols. Lovebirds proved capable of (1) associating symbols (i.e., object-file symbolism); with (2) "more-less" quantity inference, by deducing food quantities based on their knowledge of this symbol-quantity association; and (3) enhancing their performance in relation to disparity ratio (conforming to Webers law) and absolute difference. Furthermore (4), the influence of food ratio and absolute difference varied with different ratio ranges. Within a small ratio range ([≤] 3) discrimination performance improved with increments of ratio or absolute difference, whereas within a higher ratio range (> 3), the effect of these factors diminished. We conclude that rosy-faced lovebirds are capable of advanced numeracy and quantity discrimination, similar to larger parrot species.

animal behavior and cognition↗

bioRxiv2024

Multiple transcription factors regulate the expression of genes for error prone DNA polymerases in Acinetobacter baumannii

Acinetobacter baumannii is an opportunistic pathogen causing several infections that are increasingly diSicult to treat due to its ability to rapidly gain antibiotic resistances. These resistances can arise due to mutations during the DNA damage response (DDR), through the activity of error-prone DNA polymerases, such as DNA polymerase V (DNA Pol V). Currently, the DDR in A. baumannii is not well understood and the regulation of genes encoding multiple copies of DNA Pol V is not fully characterized. Through genome wide mutagenesis, we have identified a novel TetR-like family regulator of genes that encode DNA Pol V, which we have named Error-prone polymerase regulator, EppR. We have found that EppR represses the expression of the genes encoding DNA Pol V and itself through direct binding to a conserved EppR motif in their promoters. Lastly, we show that EppR also regulates UmuDAb, previously identified as a regulator of genes encoding DNA Pol V. These two gene products are functionally required to ensure regulation of expression of genes encoding DNA Pol Vs and umuDAb. With these results, we propose a co-repressor model for the regulation of genes encoding DNA Pol V and umuDAb. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=155 SRC="FIGDIR/small/615892v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@502a49org.highwire.dtl.DTLVardef@10844bcorg.highwire.dtl.DTLVardef@1d8be41org.highwire.dtl.DTLVardef@b2a68e_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

microbiology↗

bioRxiv2024

A workflow for practical training in ecological genomics using Oxford Nanopore long-read sequencing

Long-read single molecule sequencing technologies continue to grow in popularity for genome assembly and provide an effective way to resolve large and complex genomic variants. However, uptake of these technologies for teaching and training is hampered by the complexity of high molecular weight DNA extraction protocols, the time required for library preparation and the costs for sequencing, as well as challenges with downstream data analyses. Here, we present a full long-read workflow optimised for teaching, that covers each stage from DNA extraction, to library preparation and sequencing, to data QC and genome assembly and characterisation, that can be completed in under two weeks. We use a specific case study of plant identification, where students identify an anonymous plant sample by sequencing and assembling the genome and comparing it to other samples and to reference databases. In testing, long-read genome skimming of nine wild-collected plant species extracted with a modified kit-based approach produced an average of 8Gb of Oxford Nanopore data, enabling the complete assembly of plastid genomes, and partial assembly of nuclear genomes. In the classroom, all students were able to complete the protocols, and to correctly identify their plant samples based on BOLD searches of barcoding loci extracted from the plastid genome, coupled with phylogenetic analyses of whole plastid genomes. We supply all the learning material and raw data allowing this to be adapted to a range of teaching settings.

genomics↗

bioRxiv2024

Pre-implantation genome-wide methylation enables environmental adaptation in a social meso-carnivore

Many wild populations are increasingly stressed by rapid climatic change. While behavioural plasticity can enable limited tactical adaptive responses, standing genetic variation limits the species capacity to respond to climate change velocity. Epigenetic modification may provide a more rapid and plastic adaptive mechanism, but has been little studied in wild-living animals. Here we investigated CpG methylation during the pre-natal and early-life development of 95 European badger cubs between 2003 and 2011). During 10-months of delayed pre-implantation variability in precipitation between previous years February and April was the top determinant of methylation patterns among neonates, followed by mean temperature and temperature variability. Among the 4,641 significant weather-associated CpG sites, most occurred in the 47S rDNA region. Methylation of 47S rDNA was also associated with early-life weight, implying a mechanism that relays environmental stress to phenotypic stress. We also detected evidence for predictive adaptive response. Among the 1,641 CpG sites associated with early-life weight, pathways were associated with early-life growth, immune regulation, and to the development of aggression for competitive access to weather-limited food resources were over-represented. We conclude that a species epigenetics can have an important role in adaptive plasticity to environmental changes with important implications for biodiversity conservation and management.

genomics↗

bioRxiv2024

Investigating the use of odour and colour foraging cues by rosy-faced lovebirds (Agapornis roseicollis) using deep-learning based behavioural analysis

Olfaction and vision can play important roles in optimizing foraging decisions of birds, enabling them to maximize their net rate of energy intake while searching for, handling, and consuming food. Parrots have been used extensively in avian cognition research, and some species use olfactory cues to find food. Here we pioneered machine learning analysis and pose-estimation with convolutional neural networks (CNNs) to elucidate the relative importance of visual and olfactory cues for informing foraging decisions in the rosy-faced lovebird (Agapornis roseicollis) as a non-typical model species. In a binary choice experiment, we used markerless body pose tracking to analyse bird response behaviours. Rosy-faced lovebirds quickly learnt to discriminate the feeder provisioned with food by forming an association with visual (red/green papers) but not olfactory (banana/almond odour) cues. When visual cues indicated the provisioned and empty feeders, feeder choice was more successful, choice latency shorter, and interest in the empty feeder significantly lower. This demonstrates that visual cues alone are sufficient to inform lovebird foraging decisions without needing to use olfactory cues, suggesting that selection has not driven olfactory-based foraging in lovebird evolution.

animal behavior and cognition↗

bioRxiv2021

No part gets left behind: Tiled nanopore sequencing of whole ASFV genomes stitched together using Lilo

African Swine Fever virus (ASFV) is the causative agent of a deadly, panzootic disease, infecting wild and domesticated suid populations. Contained for a long time to the African continent, an outbreak of a particularly infectious variant in Georgia in 2007 initiated the spread of the virus around the globe, severely impacting pork production and local economies. The virus is highly contagious and has a mortality of up to 100% in domestic pigs. It is critical to track the spread of the virus, detect variants associated with pathology, and implement biosecurity measures in the most effective way to limit its spread. Due to its size and other limitations, the 170-190kbp large DNA virus has not been well sequenced with fewer than 200 genome sequences available in public repositories. Here we present an efficient, low-cost method of sequencing ASFV at scale. The method uses tiled PCR amplification of the virus to achieve greater coverage, multiplexability and accuracy on a portable sequencer than achievable using shotgun sequencing. We also present Lilo, a pipeline for assembling tiled amplicon data from viral or microbial genomes without relying on polishing against a reference, allowing for structural variation and hypervariable region assembly other methods fail on. The resulting ASFV genomes are near complete, lacking only parts of the highly repetitive 3- and 5telomeric regions, and have a high level of accuracy. Our results will allow sequencing of ASFV at optimal efficiency and high throughput to monitor and act on the spread of the virus.

bioinformatics↗

bioRxiv2021

Direct lysis RT-qPCR of SARS-CoV-2 in cell culture supernatant allows for fast and accurate quantification of virus, opening a vast array of applications

An enormous global effort is being made to study SARS-CoV-2 and develop safe and effective treatments. Studying the entire virus replication cycle of SARS-CoV-2 is essential to identify host factors and treatments to combat the infection. However, quantification of released virus often requires lengthy procedures, such as endpoint dilution assays or reinfection with engineered reporter viruses. Quantification of viral RNA in cell supernatant is faster and can be performed on clinical isolates. However, viral RNA purification is expensive in time and resources and often unsuitable for high-throughput screening. Here, we show a direct lysis RT-qPCR method allowing sensitive, accurate, fast, and cheap quantification of SARS-CoV-2 in culture supernatant. During lysis, the virus is completely inactivated, allowing further processing in low containment areas. This protocol facilitates a wide array of high- and low-throughput applications from basic quantification to studying the biology of SARS-CoV-2 and to identify novel antiviral treatments in vitro.

microbiology↗

bioRxiv2021

Patterns of Mustelid gammaherpesvirus 1 (MusGHV-1) genital reactivation linked to stressors in adult European badgers (Meles meles)

Herpesvirus infections are common and mostly asymptomatic in vertebrates, but can result in impaired reproduction. It is therefore important to understand infection patterns and associated risk factors, particularly the effects of different stressors. Here we use Mustelid gammaherpesvirus 1 (MusGHV-1) infection in European badgers (Meles meles) as a host-pathogen wildlife model to study the effects of a variety of demographic, social, physiological and environmental stressors on viral reactivation in the genital tract. We collected 251 genital swabs from 151 free-ranging individuals across 3 trapping seasons (spring, summer and autumn). We screened for MusGHV-1 using PCR and explored possible links between genital MusGHV-1 reactivation and stressors, and their interactions, using logistic regression. In adults, reactivation was more likely in males, especially those in poorer body condition during summer. In females, reactivation was more likely when living in social groups comprising a higher percentage of cubs, but counter to our predictions, recent lactation appeared not influential. In relation to age, reactivation was more common in individuals over 8 years old than among prime age adults, and among juveniles (<2 years old), especially females and individuals in better body condition, likely due to early puberty. Environmentally, reactivation was more prevalent in summer when food abundance is typically low. Our results evidence age effects on MusGHV-1 reactivation; in juveniles MusGHV-1 shedding in the genital tract is likely related to primary infection, while in adults, genital MusGHV-1 reactivation from latency was associated with aging, social and/ or environmental stress. ImportanceThe immuno-suppressive effects of elevated stress levels facilitate disease development, and can ultimately cause host extinction at the population level, especially where diseases are transmitted sexually. The impacts of stress on host-pathogen dynamics through disease, however, are still poorly understood outside the laboratory or captive environments. Our study provides rare evidence from a free-ranging wild mammal population that the infection dynamics of a common and sexually transmittable gammaherpesvirus are linked to demographic, social, physiological and environmental stress. We propose that the effects of stressors on STIs and viral reactivation are an important factor to be taken into account in conservation efforts when working with vulnerable wildlife populations.

microbiology↗

bioRxiv2020

Negative density-dependent parasitism in a group-living carnivore

Animals living at high population densities commonly experience greater exposure to disease, leading to increased parasite burdens. However, social animals can benefit immunologically and hygienically from cooperation, and individuals may alter their socio-spatial behaviour in response to infection, both of which could counteract density-related increases in exposure. Consequently, the costs and benefits of sociality for disease are often uncertain. Here, we use a long-term study of a wild European badger population (Meles meles) to investigate how within-population variation in host density determines infection with multiple parasites. Four out of five parasite taxa exhibited consistent spatial hotspots of infection, which peaked among badgers living in areas of low local population density. Combined movement, survival, spatial, and social network analyses revealed that parasite avoidance was the likely cause of this negative density dependence, with possible roles for localised mortality, encounter-dilution effects, and micronutrient-enhanced immunity. These findings demonstrate that animals can organise their societies in space to minimise parasite infection, with important implications for badger behavioural ecology and for the control of badger-associated diseases.

ecology↗

bioRxiv2019

Interactions of a bacterial RND transporter with a transmembrane small protein in a lipid environment

The small protein AcrZ in Escherichia coli interacts with the transmembrane portion of the multidrug efflux pump AcrB and increases the resistance of the bacterium to a subset of the antibiotic substrates of that transporter. It is not clear how the physical association of the two proteins selectively changes activity of the pump for defined substrates. Here, we report cryo-EM structures of AcrB and the AcrBZ complex in lipid environments, and comparisons suggest that conformational changes occur in the drug binding pocket as a result of AcrZ binding. Simulations indicate that cardiolipin preferentially interacts with the AcrBZ complex, due to increased contact surface, and we observe that the drug sensitivity of bacteria lacking AcrZ is exacerbated when combined with cardiolipin deficiency. Taken together, the data suggest that AcrZ and lipid cooperate to allosterically modulate the activity of AcrB. This mode of regulation by a small protein and lipid may occur for other membrane proteins.

microbiology↗

bioRxiv2018

Heterochrony of puberty in the European Badger (Meles meles) can be explained by growth rate and group-size: Evidence for two endocrinological phenotypes

Puberty is a key stage in mammalian ontogeny, involving endocrinological, physiological and behavioural changes, moderated by intrinsic and extrinsic factors. Thus, not all individuals within one population achieve sexual maturity simultaneously. Here, using the European badger (Meles meles) as a model, we describe male testosterone and female oestrone profiles (using Enzyme-immunoassays) from first capture (3 months, post-weaning) until 28 months (attaining sexual maturity and final body size), along with metrics of somatic growth, scent gland development and maturation of external reproductive organs as well as intra-specific competition. In both sexes, endocrinological puberty commenced at ca. 11 months. Thereafter, cub hormone levels followed adult seasonal hormone patterns but at lower levels, with the majority of cubs reaching sexual maturity during their second mating season (22-28 months). Interestingly, there was evidence for two endocrinological phenotypes among male cubs (less evident in females), with early developers reaching sexual maturity at 11 months (first mating season) and late developers reaching sexual maturity at 22-26 months (second mating season). Early developers also attained a greater proportion of their ultimate adult size by 11 months, exhibiting faster growth rates than late developers (despite having similar adult size). Male cubs born into larger social groups tended to follow the late developer phenotype. Our results support the hypothesis that a minimum body size is required to reach sexual maturity, which may be achieved at different ages, even within a single population, where early maturity can confer individual fitness advantages and enhance population growth rate.

zoology↗

bioRxiv2018

Subclinical infection of macaques and baboons with a baboon simartevirus

Simarteviruses (Arteriviridae: Simartevirus) are commonly found at high titers in the blood of African monkeys but do not cause overt disease in these hosts. In contrast, simarteviruses cause severe disease in Asian macaques upon accidental or experimental transmission. Here, we sought to better understand the host-dependent drivers of simartevirus pathogenesis by infecting olive baboons (n=4) and rhesus macaques (n=4) with the simartevirus Southwest baboon virus 1 (SWBV-1). Surprisingly, none of the animals in our study showed signs of disease following SWBV-1 inoculation. Three animals (two rhesus monkeys and one olive baboon) became infected and sustained high levels of SWBV-1 viremia for the duration of the study. The course of SWBV-1 infection was highly predictable: plasma viremia peaked between 1x107 and 1x108 vRNA copies/ml at 3-10 days post-inoculation, which was followed by a relative nadir and then establishment of a stable set-point between 1x106 and 1x107 vRNA copies/ml for the remainder of the study (56 days). We characterized cellular and antibody responses to SWBV-1 infection in these animals, demonstrating that macaques and baboons mount similar responses to SWBV-1 infection, yet these responses are ineffective at clearing SWBV-1 infection. SWBV-1 sequencing revealed the accumulation of non-synonymous mutations in a region of the genome that corresponds to an immunodominant epitope in the simartevirus major envelope glycoprotein GP5, which likely contribute to viral persistence by enabling escape from host antibodies.\n\nOne Sentence SummarySimartevirus infection has multiple disease manifestations following cross-species transmission.\n\nAccessible Summary/ImportanceSimarteviruses are known to infect African monkeys, such as olive baboons, without causing overt disease. In contrast, accidental infection of Asian monkeys, such as rhesus monkeys, has resulted in severe and often fatal disease. We used a simartevirus found circulating among captive olive baboons (Southwest baboon virus 1; SWBV-1) to experimentally infect both olive baboons and rhesus monkeys to model infection with the same virus in both natural and non-natural hosts. Surprisingly, neither baboons nor macaques displayed any laboratory abnormalities or signs of disease over the course of infection, despite robust SWBV-1 replication. In the accompanying study by Cornish et al., a similar experimental approach was undertaken: African patas monkeys and rhesus monkeys were infected with the simartevirus simian hemorrhagic fever virus (SHFV). In contrast to our study, SHFV caused disease in both of these hosts, albeit with much more severe disease developing in the macaques. Interestingly, we observed similar levels of immune cell activation in simartevirus-infected animals across both studies, suggesting that finer nuances of the host response, and perhaps properties of each individual simartevirus, may influences pathogenicity of these viruses in primates. Taken together, our collective findings highlight the wide clinical spectrum of simartevirus infection, ranging from highly-lethal hemorrhagic disease to persistent infection without any overt signs of disease, even in non-natural primate hosts.

microbiology↗

bioRxiv2017

Infection via mosquito bite alters Zika virus replication kinetics in rhesus macaques

For more than three decades it has been recognized that small amounts of vector saliva can significantly alter the infectivity of vector-borne pathogens and subsequent in vivo dynamics. Mouse and nonhuman primate models now serve as useful platforms to study Zika virus (ZIKV) pathogenesis, candidate therapies, and vaccines, but they rely on needle inoculation of virus: the effects of mosquito-borne infection on disease outcome have not been explored in these models. To model vector-borne transmission of ZIKV in nonhuman primates, we infected Aedes aegypti mosquitoes with ZIKV and allowed them to feed on four ZIKV-naive rhesus macaques. We compared ZIKV replication kinetics and tissue distribution between animals that were subcutaneously inoculated with 104 plaque-forming units of ZIKV and those that were exposed via mosquito bite. Here, we show that infection via mosquito bite delays ZIKV replication to peak viral loads in rhesus macaques. Importantly, in mosquito-infected animals ZIKV tissue distribution was limited to hemolymphatic tissues, female reproductive tract tissues, kidney, and liver, potentially emulating key features of human ZIKV infections, most of which are characterized by mild or asymptomatic disease. This newly developed system will be valuable for studying ZIKV disease because it more closely mimics human infection by mosquito bite than needle-based inoculations.

microbiology↗