Biology subjects

Gray, C.

Publications and source records attributed to Gray, C..

At least 19 recordsLinked to original sources

bioRxiv2026

The role of a G-quadruplex structure in mediating the interactions of miR-1249-3p with the 3-UTR of the HNRNPK mRNA

Heterogenous nuclear riboprotein K (hnRNP K) is an important regulator of multiple signaling pathways involved in DNA repair and function whose expression has been found to be mis-regulated in many cancers and neurological diseases. The expression regulation of hnRNP K is not fully understood however it has been shown that the microRNA miR-1249-3p targets its mRNA 3-untranslated region (UTR), regulating its translation. In this study we identified a guanosine-rich sequence in the HNRNPK 3-UTR within the miR-1249-3p binding site that has the potential to form a G-quadruplex (GQ) structure. By using various biophysical methods, we show that this sequence forms a parallel GQ structure which modulates the binding of miR-1249-3p to HNRNPK 3-UTR in vitro. Additionally, using luciferase reporter assays, we determined that this GQ structure affects the hnRNP K protein expression, suggesting modulation of the binding interaction of miR-1249-3p to the 3-UTR of HNRNPK. This HNRNPK mRNA GQ-miR binding axis is an unexplored mechanism of regulation, offering a novel therapeutic target for diseases caused by abnormal hnRNP K expression.

biochemistry↗

bioRxiv2026

High frame rate in vivo two-photon microscopy to quantify murine cerebrospinal fluid flow heterogeneity

Cerebrospinal fluid (CSF) flows through perivascular spaces (PVSs) surrounding brain vasculature, and impaired flow has been linked to neurodegenerative diseases such as Alzheimer's. However, the mechanisms driving CSF flow and its oscillatory dynamics remain poorly understood. Using high frame rate two-photon imaging (up to 113 Hz), we show that CSF flow is spatially heterogeneous and highly pulsatile, quantified using a regional CSF pulsatility index (PI). Reduced-order simulations with realistic domain length and Windkessel boundary conditions show that arterial pulsations generate peak CSF velocities but contribute negligibly to net transport. PI varies non-monotonically in space and substantially with downstream hydraulic resistance and compliance, indicating that CSF pulsatility is an emergent property of the hydraulic network rather than simply a consequence of local arterial wall motion. Measurements and simulations of the phase between arterial wall motion and CSF velocity further constrain proposed CSF driving mechanisms. Finally, we perform mouse-specific simulations to estimate average and peak wall shear stresses which support the potential role of pulsatile CSF flow in perivascular mechanotransduction. Together, these results establish CSF pulsatility as a measurable signature of network-scale CSF dynamics.

neuroscience↗

bioRxiv2026

Differential chromatin looping regulated by two GA-binding transcription factors creates an X-specific chromatin environment for dosage compensation

The mechanisms by which differential occupancy of transcription factors (TFs) at similar binding sites leads to context-specific targeting of large transcription complexes remain poorly understood. X chromosome upregulation (XCU), the most highly conserved step in dosage compensation and best studied in Drosophila, serves as a model for understanding how differential occupancy of similar TFs functions context-specifically. Sequence variation within GA-repeat motifs that accumulated on the X chromosome over evolutionary time promotes the binding of a specific GA-binding TF (CLAMP) that recruits the dosage compensation complex (DCC) while outcompeting another similar TF (GAF). However, the mechanism by which CLAMP-GAF competition drives specific targeting of the DCC to the X chromosome remains unknown. Because DCC binding sites cluster in 3D space, we combined Micro-C and Hi-ChIP to determine that CLAMP and GAF directly mediate largely mutually exclusive 3D genomic contacts. Specifically, we show that CLAMP but not GAF drives local short-range interactions that directly link high affinity DCC binding sites with active, dosage-compensated housekeeping genes. In contrast, GAF mediates interactions between transcriptionally silent insulator regions on the X chromosome spanning a wider range of genomic distances. Together, these findings demonstrate that CLAMP outcompetes GAF at active regions on the X chromosome, but not autosomes, to create an X-chromosome specific chromatin environment for dosage compensation. Overall, we provide new insight into how differential TF binding at similar binding sites drives context-specific targeting of transcription complexes.

molecular biology↗

bioRxiv2026

Cue-Dependent Fear Learning Drives Nucleus Accumbens Spine Plasticity

Nucleus accumbens (NAc) dopamine 2 receptor expressing medium spiny neurons (D2-MSNs) are involved in stress and aversive learning, where repeated stress increases excitatory spine density. Whether this plasticity reflects cue-specific learning or generalized stress response remains unknown. Using Pavlovian fear conditioning in Tac1-Cre/Tdtomato mice, we dissociated associative plasticity from the effects of foot shock stress. Acute fear conditioning produced distinct physiological outcomes between stress in the presence or absence of a cue. Conditioning for 7 days consolidated cue learning and increased excitatory transmission frequency via an increase in the total spine density. However, repeated exposure to foot shock did not lead to this synaptic remodeling. Our results suggest that morphological changes supporting synaptic plasticity on NAc D2-MSNs are due to cue-dependent learning, but not foot shock stress alone. We propose that NAc D2-MSNs encode learning and response to threat cues, which may heighten later stress responsivity.

neuroscience↗

bioRxiv2025

Tracking active heterotrophic microbial communities in the Guaymas Basin deep biosphere with BONCAT-FACS

The marine deep biosphere harbors microbial communities that drive organic matter transformations and biogeochemical cycles. Previous work on these communities has focused either on genomic characterization or metabolic activity measurements. However, to understand microbial ecophysiology in the deep biosphere taxonomic identity and metabolic function must be connected on both single-cell and ecosystem scales. In this work, we optimized a bioorthogonal non-canonical amino acid tagging fluorescence-activated cell sorting (BONCAT-FACS) workflow for low-biomass deep-biosphere sediments obtained during International Ocean Discovery Program Expedition 385 (IODP 385). BONCAT-FACS with 16S rRNA gene amplicon sequencing as well as metagenomics of sediment communities was applied to characterize translationally active communities in hydrothermally altered subsurface sediments of the Guaymas Basin. Our results revealed a heterotrophic microbial population throughout all sediments examined, with taxa translationally active down to our deepest sampling point, 154 meters below the seafloor. Based on 16S rRNA gene identities, the translationally active microbial community was dominated by heterotrophic members of the Gammaproteobacteria, Bacilli, Deinococci, and Alphaproteobacteria. These taxa are likely key contributors to cycling the large quantities of hydrothermally altered organic matter in Guaymas Basin sediments. To further elucidate the metabolic capacity of active taxa, we mapped 16S rRNA gene amplicons to metagenome assembled genomes (MAGs) previously obtained from IODP 385. These MAGs contained genes associated with C1 metabolism, carbohydrate degradation, and fermentation, indicating that active taxa leverage these metabolisms for energy conservation. Our results demonstrate that BONCAT-FACS provides high-throughput and single-cell insights into the metabolic activity of microbes in the low-biomass marine subsurface.

microbiology↗

bioRxiv2025

Spatial Analysis of Placentae During Congenital Cytomegalovirus Infection Reveals Distinct Cellular Profiles in Immune Cells and Trophoblasts

Withdrawal StatementThe authors have withdrawn the manuscript because the data it contained has been updated. Consequently, they request that this work should not be cited as a reference for any projects to ensure the use of the most current information. For any questions or further clarifications, readers are encouraged to contact the corresponding author directly

immunology↗

bioRxiv2024

Diminished placental Factor XIIIA1 expression associates with long term ART and preterm birth in pregnant people living with HIV.

We previously showed a link between maternal vascular malperfusion and pre-term birth (PTB) in pregnant people living with HIV (PPLH) initiating antiretroviral treatment (ART) before pregnancy, indicating poor placental vascularisation. After measuring antenatal plasma angiogenic factors to seek mechanistic insights, low levels of plasma Factor XIIIA1 (FXIIIA1) and vascular-endothelial-growth-factor (VEGF) was significantly associated with PTB at the time closest to delivery (median 34 weeks) in PPLH initiating ART before pregnancy. Knowing that FXIIIA1 is crucial for haemostasis, angiogenesis, implantation and pregnancy maintenance and that expression is found on placental macrophages (Hofbauer cells), we examined placentae at delivery from matching participants who either initiating ART before pregnancy or during gestation. Highest FXIIIA1 expression was on Hofbauer cells but was significantly lower in PTB regardless of HIV infection, but was significantly lower in PPLH in PTB from women who initiated ART before pregnancy. To test the hypothesis that antiretroviral drugs may disrupt vascularisation in the placenta, we used a human umbilical vein endothelial cell (HUVEC) matrigel angiogenesis assay. We identified that addition of pre-treated FXIIIA1-expressing MCSF-and IL-10-induced placenta-like macrophages with physiological concentrations of tenofovir, 3TC, and efavirenz resulted in significantly inhibited angiogenesis; akin to the inhibition observed with titratable concentrations of ZED1301, an inhibitor of FXIIIA1. Overall, an efavirenz-containing ART combination inhibits vasculogenesis without causing toxicity and likely does so through inhibition of a FXIIIA1-mediated-placental macrophage pathway.

immunology↗

bioRxiv2024

Fructose consumption in pregnancy and associations with maternal and offspring hepatic and whole-body adiposity: a scoping review.

BackgroundFructose is a major component in the Western diet, and its increased intake has been linked to adverse metabolic health, including impaired hepatic function and increased adiposity. The early life period, including preconceptionally, pregnancy and the newborn period, are critical periods in determining later metabolic health. However, the impact of excess fructose intake during this time on maternal, fetal, and offspring hepatic and whole-body adiposity, are ill defined. ObjectivesTo understand the effects of maternal fructose consumption pre- and during pregnancy on maternal, fetal and offspring hepatic and whole-body adiposity. MethodsA systematic search of MEDLINE, EMBASE, and CENTRAL was performed up to August 23, 2022, to identify studies that focused on maternal fructose consumption pre- and during pregnancy on hepatic and whole-body adiposity in the mother, fetus, and offspring. Citations, abstracts, and full texts were screened in duplicate. Hepatic adiposity was defined as elevated hepatic triglycerides or overall hepatic fat accumulation. Whole-body adiposity was defined as increased adipose tissue or adipocyte hypertrophy. ResultsAfter screening 2334 citations, 33 experimental studies reporting maternal fructose consumption pre- and during pregnancy in rodents were included. Prenatal fructose exposure was associated with maternal (9 out of 12) and offspring (6 out of 10) whole-body adiposity. A high proportion of studies (13 out of 14) supported the association between fructose during pregnancy and increased maternal hepatic adiposity. Fetal hepatic adiposity and elevated expression of hepatic lipogenic proteins were noted in four studies. Offspring hepatic adiposity was supported in 14 of the 17 articles that discussed hepatic results, with five studies demonstrating more severe effects in female offspring. ConclusionsFructose consumption during pregnancy in rodent models is associated with maternal, fetal, and offspring hepatic, whole-body adiposity and underlying sex-specific effects. There are no human fructose studies and its effects in the early life period. Registration numberH8F26 on Open Science Framework

developmental biology↗

bioRxiv2024

Predicting photosynthetic structures using thermodynamics and machine learning

Oxygenic photosynthesis is responsible for nearly all biomass production on Earth, and may have been a prerequisite for establishing a complex biosphere rich in multicellular life. Life on Earth has evolved to perform photosynthesis in a wide range of light environments, but with a common basic architecture of a light-harvesting antenna system coupled to a photochemical reaction centre. Using a generalized thermodynamic model of light-harvesting, coupled with an evolutionary algorithm, we predict the type of light-harvesting structures that might evolve in light of different intensities and spectral profiles. We reproduce qualitatively the pigment composition, linear absorption profile and structural topology of the antenna systems of multiple types of oxygenic photoautotrophs, suggesting that the same physical principles underlie the development of distinct antenna structures in various light environments. Finally we apply our model to representative light environments that would exist on Earth-like exoplanets, predicting that both oxygenic and anoxygenic photosynthesis could evolve around low mass stars, though the latter would seem to work better around the coolest M-dwarfs. We see this as an interesting first step toward a general evolutionary model of basic biological processes and proof that it is meaningful to hypothesize on the nature of biology beyond Earth.

biophysics↗

bioRxiv2024

DERIVATION OF ELEPHANT INDUCED PLURIPOTENT STEM CELLS

The crisis of biodiversity loss in the anthropogenic era requires new tools for studying non-model organisms. Elephants, for example, are both an endangered species and excellent models studying complex phenotypes like size, social behavior, and longevity, but they remain severely understudied. Here we report the first derivation of elephant (Elephas maximus) induced pluripotent stem cells (emiPSCs) achieved via a two-step process of chemical-media induction and colony selection, followed by overexpression of elephant transcription factors OCT4, SOX2, KLF4, MYC {+/-} NANOG and LIN28A, and modulation of the TP53 pathway. Since the seminal discovery of reprogramming by Shinya Yamanaka, iPSCs from many species including the functionally extinct northern white rhinocerous have been reported, but emiPSCs have remained elusive. While for multiple species the reprogramming protocol was adopted with little changes compared to model organisms like mouse and human, our emiPSC protocol requires a longer timeline and inhibition of TP53 expansion genes that are hypothesized to confer unique cancer resistance in elephants. iPSCs unlock tremendous potential to explore cell fate determination, cell and tissue development, cell therapies, drug screening, disease modeling, cancer development, gametogenesis and beyond to further our understanding of this iconic megafauna. This study opens new frontiers in advanced non-model organism cellular models for genetic rescue and conservation.

cell biology↗

bioRxiv2024

Exposure to HIV alters the composition of maternal microchimeric T cells in infants

Infants exposed to HIV but uninfected (iHEU) display altered cellular immunity and are at increased risk of infection through poorly understood mechanisms. We previously reported that iHEU have lower levels of maternal microchimerism (MMc), maternal cells transferred to the offspring in utero/during breastfeeding. We evaluated MMc levels in T cell subsets in iHEU and HIV unexposed infants (iHU) to determine whether a selective deficiency in MMc may contribute to altered cellular immunity. Across all infants, MMc levels were highest in CD8+ T cells; however, the level of MMc in the CD8 T cell subset was significantly lower in iHEU compared to iHU.

immunology↗

bioRxiv2024

Quantifying the IUCN Red List: Using historical assessments to calculate future extinction risk

The IUCN Red List of Threatened Species assigns species to discrete categories based on a common set of criteria to capture relative extinction risk. Some quantitative analyses require a continuous probability of extinction not provided by discrete categories. Furthermore, the criteria may not translate to extinction risk in a universal way across species, because some species attributes are not incorporated into the criteria. Here we calculate extinction risk using Markov Models parameterised with historical IUCN Red List assessment data, and we provide quantitative extinction risk for use in downstream analyses. We find that taxonomy, body size, and habitat specialism interact with extinction risk in ways not fully captured by the existing categories. For example, an Endangered habitat specialist appears equally at risk compared to a Critically Endangered habitat generalist. We hope our findings will support more accurate quantitative biodiversity analyses of species extinctions and declines using Red List data.

ecology↗

bioRxiv2023

Nucleus Accumbens Local Circuit for Cue-Dependent Aversive Learning

Response to threatening environmental stimuli requires detection and encoding of important environmental features that dictate threat. Aversive events are highly salient which promotes associative learning about stimuli that signal this threat. The nucleus accumbens is uniquely positioned to process this salient, aversive information and promote motivated output, through plasticity on the major projection neurons in the brain area. We uncovered a nucleus accumbens core local circuit whereby excitatory plasticity facilitates learning and recall of discrete aversive cues. We demonstrate that putative nucleus accumbens substance P release and long-term excitatory plasticity on dopamine 2 receptor expressing projection neurons is required for cue-dependent fear learning. Additionally, we found fear learning and recall were dependent on distinct projection-neuron subtypes. Our work demonstrates a critical role for Nucleus Accumbens substance P in cue-dependent aversive learning.

neuroscience↗

bioRxiv2022

Recovering birds and mammals across Europe continue to be negatively impacted by threats but benefit from conservation measures

Even during ongoing global biodiversity losses and extinctions, numerous species have shown recoveries in terms of increased abundance and/or range extent. Understanding the mechanisms that contribute to, or limit, these recoveries is critical not just to ensure they continue, but to promote similar recoveries across broader ecosystems. Here, we explore the changes in abundance and range extent of selected 47 recovering species (24 mammals and 23 birds) in Europe using official data reported by EU Member States and supplemented using the Living Planet Index database. We investigate how the diversity of ongoing threats and conservation measures contribute to the likelihood and extent of recoveries. For birds, long-term recoveries were less likely among species impacted by a greater diversity of threats, although this may be mitigated by the diversity of conservation measures in place. Similarly, for mammals, populations with reported threats recovered less quickly while those with management actions in place recovered more quickly. To achieve the aims of the UN Decade on Restoration, we need to ensure, even for recovering species, that threats continue to be reduced and that conservation management actions are ongoing and effective.

ecology↗

bioRxiv2022

Non-rapid eye movement sleep determines resilience to social stress

Resilience, the ability to overcome stressful conditions, is found in most mammals and varies significantly among individuals. A lack of resilience can lead to the development of neuropsychiatric and sleep disorders, often within the same individual. Despite extensive research into the brain mechanisms causing maladaptive behavioral-responses to stress, it is not clear why some individuals exhibit resilience. To examine if sleep has a determinative role in maladaptive behavioral-response to social stress, we investigated individual variations in resilience using a social-defeat model for male mice. Our results reveal a direct, causal relationship between sleep amount and resilience--demonstrating that sleep increases after social-defeat stress only occur in resilient mice. Further, we found that within the prefrontal cortex, a regulator of maladaptive responses to stress, pre-existing differences in sleep regulation predict resilience. Overall, these results demonstrate that increased NREM sleep, mediated cortically, is an active response to social-defeat stress that is both necessary and sufficient for promoting resilience. They also show that differences in resilience are strongly correlated with inter-individual variability in sleep regulation.

neuroscience↗

bioRxiv2021

Trivial Excitation Energy Transfer to Carotenoids is an Unlikely Mechanism for Non-Photochemical Quenching in LHCII

Higher plants defend themselves from bursts of intense light via the mechanism of Non-Photochemical Quenching (NPQ). It involves the Photosystem II (PSII) antenna protein (LHCII) adopting a conformation that favours excitation quenching. In recent years several structural models have suggested that quenching proceeds via energy transfer to the optically forbidden and short-lived S1 states of a carotenoid. It was proposed that this pathway was controlled by subtle changes in the relative orientation of a small number of pigments. However, quantum chemical calculations of S1 properties are not trivial and therefore its energy, oscillator strength and lifetime are treated as rather loose parameters. Moreover, the models were based either on a single LHCII crystal structure or Molecular Dynamics (MD trajectories) about a single minimum. Here we try and address these limitations by parameterizing the vibronic structure and relaxation dynamics of lutein in terms of observable quantities, namely linear absorption (LA) transient absorption (TA) and two-photon excitation (TPE) spectra. We also analyze a number of minima taken from an exhaustive meta-dynamical search of the LHCII potential energy surface. We show that trivial, Coulomb-mediated energy transfer to S1 is an unlikely quenching mechanism. Pigment movements are insufficient to switch the system between quenched and unquenched states. Modulation of S1 energy level as a quenching switch is similarly unlikely. Moreover, the quenching predicted by previous models is likely an artefact of quantum chemical over-estimation of S1 oscillator strength and the real mechanism likely involves non-trivial inter-molecular states.

biophysics↗

bioRxiv2021

Factors influencing maternal microchimerism throughout infancy and its impact on infant T cell immunity

Determinants of the acquisition and maintenance of maternal microchimerism (MMc) during infancy and the impact of MMc on infant immune responses are unknown. We examined factors which influence MMc detection and level across infancy and the effect of MMc on T cell responses to BCG vaccination in a cohort of HIV exposed, uninfected and HIV unexposed infants in South Africa. MMc was measured in whole blood from 58 infants using a panel of quantitative PCR assays at day one and 7, 15, and 36 weeks of life. Infants received BCG at birth, and selected whole blood samples from infancy were stimulated in vitro with BCG and assessed for polyfunctional CD4+ T cell responses. MMc was present in most infants across infancy with levels ranging from 0-1,193/100,000 genomic equivalents and was positively impacted by absence of maternal HIV, maternal-infant HLA compatibility, infant female sex, and exclusive breastfeeding. Initiation of maternal antiretroviral therapy prior to pregnancy partially restored MMc level in HIV exposed, uninfected infants. Birth MMc was associated with an improved polyfunctional CD4+ T cell response to BCG. These data emphasize that both maternal and infant factors influence the level of MMc, which may subsequently impact infant T cell responses. O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

immunology↗

bioRxiv2020

A novel female-specific circadian clock mechanism regulating metabolism

Circadian clocks enable organisms to predict and align their behaviors and physiologies to constant daily day-night environmental cycle. Because the ubiquitin ligase Siah2 has been identified as a potential regulator of circadian clock function in cultured cells, we have used Siah2-deficient mice to examine its function in vivo. Our experiments demonstrate a striking and unexpected sexually dimorphic effect of Siah2 deficiency on the regulation of rhythmically expressed genes. The absence of Siah2 in females, but not in males, altered the expression of core circadian clock genes and drastically remodeled the rhythmic hepatic transcriptome. Siah2 loss, only in females, increased the expression of 100s of genes selectively at mid-day, resulting in a >50% increase in the number of rhythmically expressed genes, and shifted the expression of 100s of other genes from a mid-night peak, to a mid-day peak. The combined result is a near inversion of overall rhythmicity in gene expression selectively in Siah2-deficient females. This dramatic reorganization created a substantial misalignment between rhythmic liver functions and feeding/behavioral rhythms, and consequently disrupted daily patterns of lipid/lipoprotein metabolism and metabolic responses to high-fat diet. Collectively, our results suggest that Siah2 is part of a female-specific circadian mechanism important for maintaining metabolic homeostasis and may play a key role in establishing sexual dimorphisms in metabolism, and broadly reveal that circadian clocks may drive rhythms using novel sex-specific transcriptional pathways.

physiology↗