Biology subjects

Shaw, K.

Publications and source records attributed to Shaw, K..

12 recordsLinked to original sources

bioRxiv2025

Extensive photophysiological variation in wild barley is linked to environmental origin

O_LIIntraspecific variation between crop wild relatives (CWRs) represents a source of untapped genetic diversity for crop improvement. At the same time, improving photosynthesis in crops has the potential to enhance yield. Thus, exploring variation for photophysiology within CWRs is an important, yet underexplored, research area. C_LIO_LIWe describe a common garden experiment where 320 wild barley accessions were grown across two seasons. A photophysiology phenotyping pipeline was employed to quantify >30 traits within this diversity panel. Population genetics, genome-wide association analyses (GWAS) and deep phenotyping were performed to address local adaptation hypotheses. C_LIO_LIHeritable variation was detected across this photophysiological spectrum, with genotype-by-environment (GxE) interactions being prevalent. Evidence for local adaptation was observed in the form of subpopulation differences, signals of selection, and allele frequency variation associated to markers identified via GWAS. Phenotyping of representative accessions across distinct water availabilities highlighted a role for stomatal conductance (gs) in adaptation to dry environments. C_LIO_LIWe identified substantial variation in key photosynthesis-associated traits in a CWR closely related to barley, an economically important crop species. Our results demonstrate that this variation is partially due to local adaptation, where plasticity in gs appears important for maintaining photosynthesis and biomass accumulation in water restricted conditions. C_LI

plant biology↗

bioRxiv2024

Characterizing vascular function in mouse models of Alzheimer's disease, atherosclerosis, and mixed Alzheimer's and atherosclerosis

SignificanceAlzheimers disease does not occur in isolation and there are many comorbidities associated with the disease - especially diseases of the vasculature. Atherosclerosis is a known risk factor for the subsequent development of Alzheimers disease, therefore understanding how both diseases interact will provide a greater understanding of co-morbid disease progression and aid the development of potential new treatments. AimThe current study characterizes hemodynamic responses and cognitive performance in APP/PS1 Alzheimers mice, atherosclerosis mice, and a mixed disease group (APP/PS1 & atherosclerosis) between the ages of 9 and 12 months. ApproachWhisker-evoked hemodynamic responses and recognition memory were assessed in awake mice, immunohistochemistry to assess amyloid pathology, and histology to characterize atherosclerotic plaque load. ResultsWe observed hemodynamic deficits in atherosclerosis mice (vs Alzheimers, mixed disease or wild-type mice), with reduced short-duration stimulus-evoked hemodynamic responses occurring when there was no concurrent locomotion during the stimulation period. Mixed Alzheimers and atherosclerosis models did not show differences in amyloid beta coverage in the cortex or hippocampus or atherosclerotic plaque burden in the aortic arch vs relevant Alzheimers or atherosclerosis controls. Consistent with the subtle vascular deficits and no pathology differences, we also observed no difference in performance on the novel object recognition task across groups. ConclusionsThese results emphasize the importance of experimental design for characterizing vascular function across disease groups, as locomotion and stimulus duration impacted the ability to detect differences between groups. Whilst atherosclerosis did reduce hemodynamic responses, these were recovered in the presence of co-occurring Alzheimers disease which may provide targets for future studies to explore the potentially contrasting vasodilatory mechanisms these diseases impact.

neuroscience↗

bioRxiv2024

Voluntary locomotion induces an early and remote hemodynamic decrease in the large cerebral veins

SignificanceBehavior regulates dural and cerebral vessels, with spontaneous locomotion inducing dural vessel constriction and increasing stimulus-evoked cerebral hemodynamic responses. It is vital to investigate the function of different vascular network components, surrounding and within the brain, to better understand the role of the neurovascular unit in health and neurodegeneration. AimWe characterized locomotion-induced hemodynamic responses across vascular compartments of the whisker barrel cortex: artery, vein, parenchyma, draining and meningeal vein. ApproachUsing 2D-OIS, hemodynamic responses during locomotion were recorded in 9-12-month-old awake mice: wild-type, Alzheimers disease (AD), atherosclerosis or mixed (atherosclerosis/AD) models. Within somatosensory cortex, responses were taken from pial vessels inside the whisker barrel region ([WBR]: "whisker artery" and "whisker vein"), a large vein from the sagittal sinus adjacent to the WBR (draining vein), and meningeal vessels from the dura mater (which do not penetrate cortical tissue). ResultsWe demonstrate that locomotion evokes an initial decrease in total hemoglobin (HbT) within the draining vein before the increase in HbT within WBR vessels. The locomotion event size influences the magnitude of the HbT increase in the pial vessels of the WBR, but not of the early HbT decrease within the draining veins. Following locomotion onset, an early HbT decrease was also observed in the overlying meningeal vessels, which unlike within the cortex did not go on to exceed baseline HbT levels during the remainder of the locomotion response. We show that locomotion-induced hemodynamic responses are altered in disease in the draining vein and whisker artery, suggesting this could be an important neurodegeneration biomarker. ConclusionThis initial reduction in HbT within the draining and meningeal veins potentially serves as a space saving mechanism, allowing for large increases in cortical HbT associated with locomotion. Given this mechanism is impacted by disease it may provide an important target for vascular-based therapeutic interventions.

neuroscience↗

bioRxiv2024

Signaling pathway evaluation of leading ATRi, PARPi and CDK7i cancer compounds targeting the DNA Damage Response using Causal Inference

IntroductionThere are many cancer drugs in development which target the DNA damage response (DDR), following early successes of drugs such as olaparib. However, various challenges to the success of these inhibitors exist, including the emergence of resistance, the identification of appropriate biomarkers to identify patients who will respond to treatment, as well as the identification of combination therapies that improve efficacy without a concomitant increase in toxicity. While the identification of biomarkers of resistance could aid in overcoming these challenges, current methods mostly generate lists of potential genes, proteins that display changes in cancer patients, without exposing the underlying, and often critical, mechanisms of resistance. MethodsWe have developed the Adaptable Large-Scale Causal Analysis (ALaSCA) software platform, which applies Pearlian Causal Inference (PCI) techniques to specifically transcriptomic, proteomic and phenotypic multi-omics data. ALaSCA quantifies the causal contributions of different biological pathways to an outcome such as responsiveness to treatment. The strength of applying PCI to biological pathways lies in quantifying the causal contributions of targets, through their related pathways, to drug sensitivity - as opposed to merely enriching or grouping lists of genes into pathways. We applied ALaSCA to transcriptomic data for several different compounds related to three known inhibitor types that target DDR proteins: an ATR, a CDK7, and several PARP inhibitors. Our aim was to use causal methods to evaluate biological signaling pathways to identify resistance mechanisms that can be used for patient stratification and development of combination therapies in breast, ovarian and non-small cell lung cancer (NSCLC). Key findingsWe observed that niraparib seems to have a different resistance mechanism than other PARPi inhibitors in breast and NSCLC, which is driven by CDK1 as opposed to base excision or nucleotide excision repair. Additionally, CDK7 appears to be a significant driver of PARP inhibitor resistance, especially for niraparib, through predominantly the G2/M cell cycle phase and to a lesser extent nucleotide excision repair in breast and ovarian cancer, but not in NSCLC. Lastly, we identified that genes from the homologous recombination pathway drive resistance to AZD6738, an ATR inhibitor, in breast cancer, and that AZD6738 and irinotecan have differing resistance mechanisms in ovarian cancer, indicating the potential of combining these treatments. Next stepsOur findings demonstrate the potential of ALaSCA to generate interesting insights for treatments when applied to public data and well-known inhibitors. Partnership with industry drug discovery groups using proprietary data to rerun the above evaluations will further refine and confirm these findings.

bioinformatics↗

bioRxiv2023

The genetic basis of dynamic non-photochemical quenching and photosystem II efficiency in fluctuating light reveals novel molecular targets for maize (Zea mays) improvement

Maize (Zea mays L.) is a major global crop species which uses C4 photosynthesis. Although C4 is typically considered to be more efficient than C3 photosynthesis, especially under warmer and drier conditions, there is substantial evidence that its efficiency can still be further improved, which may benefit crop performance. Improving photosynthetic efficiency via targeted manipulation of non-photochemical quenching has focused on a limited set of genes that are known to be important determinants of the NPQ response in C3 plants. The C4 pathway may alter NPQ responses but only relatively few studies have explored genetic variation in NPQ kinetics in species that perform C4 photosynthesis. In addition, studies of NPQ responses in field-grown plants of either C3 or C4 species are especially limited. Here we apply high-definition phenotyping of NPQ responses and photosynthetic efficiency and quantitative trait locus (QTL) mapping using a field-grown maize Multi-parent Advanced Generation Inter-Cross (MAGIC) population, which combines the allelic diversity of eight contrasting inbred lines. We find substantial and consistent variation for dynamic NPQ and PSII efficiency for two subsequent field seasons. Further exploration of candidate genes within three major QTL regions identified a strong impact of allelic variation in expression of the minor PSII antenna protein CP24 (LHCB6) on a major QTL for NPQ and efficiency of PSII photochemistry on chromosome 10.

plant biology↗

bioRxiv2023

Ras-dependent activation of BMAL2 regulates hypoxic metabolism in pancreatic cancer

KRAS is the archetypal oncogenic driver of pancreatic cancer. To identify new modulators of KRAS activity in human pancreatic ductal adenocarcinoma (PDAC), we performed regulatory network analysis on a large collection of expression profiles from laser capture microdissected samples of PDAC and benign controls. We discovered that BMAL2, a member of the PAS family of transcription factors, promotes tumor initiation, progression, and post-resection survival, and is highly correlated with KRAS activity. Functional analysis of BMAL2 target genes suggested a role in regulating the hypoxia response, a hallmark of PDAC. Knockout of BMAL2 in multiple human PDAC cell lines reduced cancer cell viability, invasion, and glycolysis, leading to broad dysregulation of cellular metabolism, particularly under hypoxic conditions. We find that BMAL2 directly regulates hypoxia-responsive target genes and is necessary for the stabilization of HIF1A under low oxygen conditions, while simultaneously destabilizing HIF2A. Notably, in vivo xenograft studies demonstrated that BMAL2 loss significantly impairs tumor growth and reduces tumor volume, underscoring its functional importance in tumor progression. We conclude that BMAL2 is a master transcriptional regulator of hypoxia responses in PDAC that works downstream of KRAS signaling, possibly serving as a long-sought molecular switch that distinguishes HIF1A- and HIF2A-dependent modes of hypoxic metabolism. Statement of SignificanceWe annotate the landscape of KRAS-associated transcriptional drivers of pancreatic cancer initiation, progression, and overall survival, leading to the identification of BMAL2 as a novel regulator of hypoxic metabolism. BMAL2 helps execute the oncogenic transcriptional programs of KRAS and serves as a long-sought switch between HIF1A- and HIF2A-dependent modes of hypoxic metabolism.

cancer biology↗

bioRxiv2022

Parasite transmission in size-structured populations

Host heterogeneity can impact parasite transmission, but determining underlying traits and incorporating them into transmission models remains challenging. Body size is easily measured and influences numerous ecological interactions, including transmission. In the snail-schistosome system, larger snails have a higher exposure to parasites but lower susceptibility to infection per parasite. We quantified the impact of size-based heterogeneity on population-level transmission by conducting transmission trials in differently size-structured snail populations and competing size-dependent transmission models. Populations with greater proportions of large snails had lower prevalence, and small snails were shielded from infection by co-occurring large conspecifics. Using the winning size-explicit model, we then estimated that schistosome transmission varies dramatically across time due to seasonal changes in snail population size structure. Thus, incorporating traits such as body size, which are impacted by and directly affect host ecology, into transmission models could yield insights for natural dynamics and disease mitigation in many systems. Open Research StatementAll experimental data and novel code used for data analysis are currently available on Figshare via this private link: https://figshare.com/s/7d70b88220b912e7eec5. Data will be made public on Figshare upon acceptance. Data set utilized for Figure 4 are from the following source: Rumi, A., D. Gutierrez Gregoric, and A. Roche. 2009. Tendencias Del Crecimiento Individual en Poblaciones Naturales de Biomphalaria spp. (Gastropoda, Planorbidae) en la Cuenca del Plata, Argentina. Comunicaciones de la Sociedad Malacologica del Uruguay. URL: https://www.redalyc.org/articulo.oa?id=52414008002 O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/519457v2_fig4.gif" ALT="Figure 4"> View larger version (22K): org.highwire.dtl.DTLVardef@18be9forg.highwire.dtl.DTLVardef@8ad57eorg.highwire.dtl.DTLVardef@c674b6org.highwire.dtl.DTLVardef@11876df_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 4.C_FLOATNO Predicted infection success of a single schistosome parasite given exposure of a snail in a natural population with varying body size structure over time. A) Distribution of body sizes from a population of Biomphalaria tenagophilia in del Plata Basin, Argentina from 2000-2001(Rumi et al. 2009). Number of snails sampled at each timepoint represented as n=. B) Points are the mean {+/-} 95% confidence interval of the predicted infection success of a single schistosome introduced into this snail population from simulated transmission trials using the fully size-dependent model. Grey line is the predicted successful infection from a transmission model that ignores size-based exposure and susceptibility. Substantial changes in snail population size structure cause month-to-month estimates of schistosome success to diverge substantially from predictions that ignore size dependence. In particular, the size-null prediction tends to overestimate schistosome success except at the times in which the population is heavily dominated by small snails. C_FIG

ecology↗

bioRxiv2022

Spread of new mutations through space

The terms population size and population density are often used interchangeably, when in fact they are quite different. When viewed in a spatial landscape, density is defined as the number of individuals within a square unit of distance, while population size is simply the total count of a population. In discrete population genetics models, the effective population size is known to influence the interaction between selection and random drift with selection playing a larger role in large populations while random drift has more influence in smaller populations. Using a spatially explicit simulation software we investigate how population density affects the flow of new mutations through a geographical space. Using population density, selectional advantage, and dispersal distributions, a model is developed to predict the speed at which the new allele will travel, obtaining more accurate results than current diffusion approximations provide. We note that the rate at which a neutral mutation spreads begins to decay over time while the rate of spread of an advantageous allele remains constant. We also show that new advantageous mutations spread faster in dense populations.

evolutionary biology↗

bioRxiv2021

The effects of locomotion on sensory-evoked haemodynamic responses in the cortex of awake mice

Investigating neurovascular coupling in awake rodents is becoming ever more popular due, in part, to our increasing knowledge of the profound impacts that anaesthesia can have upon brain physiology. Although awake imaging brings with it many advantages, we still do not fully understand how voluntary locomotion during imaging affects sensory-evoked haemodynamic responses. In this study we investigated how evoked haemodynamic responses can be affected by the amount and timing of locomotion. Using an awake imaging set up, we used 2D-Optical Imaging Spectroscopy (2D-OIS) to measure changes in cerebral haemodynamics within the sensory cortex of the brain during either 2s whisker stimulation or spontaneous (no whisker stimulation) experiments, whilst animals could walk on a spherical treadmill. We show that locomotion alters haemodynamic responses. The amount and timing of locomotion relative to whisker stimulation is important, and can significantly impact sensory-evoked haemodynamic responses. If locomotion occurred before or during whisker stimulation, the amplitude of the stimulus-evoked haemodynamic response was significantly altered. Therefore, monitoring of locomotion during awake imaging is necessary to ensure that conclusions based on comparisons of evoked haemodynamic responses (e.g., between control and disease groups) are not confounded by the effects of locomotion.

neuroscience↗

bioRxiv2021

APOE4 genotype increases neuronal calcium signals and decreases pial arteriole responsivity and vasomotion in visual cortex of awake mice

Young mice possessing the e4 allele of the Apolipoprotein (APOE) gene (a risk factor for Alzheimers disease (AD)) have previously been shown to have dramatic decreases in vascular function, suggesting APOE4 may confer its risk via the vasculature. However, in human carriers, vascular and cognitive function decrease later in life. Mouse data may be confounded by an increased impact of anaesthesia and surgery in APOE4 animals, and has also focused on sensory cortices, ignoring medial lobe structures more sensitive to AD. To clarify how APOE4 expression alters neurovascular function, we studied the visual cortex and hippocampus of awake APOE3 and APOE4 targeted replacement mice, using 2-photon microscopy of neurons and blood vessels. We found milder vascular deficits than studies using anaesthetised preparations: functional hyperaemia was unaffected in APOE4 mice and neuronal or vascular function did not decrease with age. Instead, vascular responsiveness was lower at all ages, arteriole vasomotion was reduced and neuronal calcium signals during visual stimulation were increased. This suggests that, independently, APOE4 expression is not catastrophic but alters neurovascular physiology towards a state more sensitive to insults such as surgery or beta amyloid accumulation. Understanding how APOE4 expression interacts with these insults will be critical for understanding the emergence of AD in APOE4 carriers.

neuroscience↗

bioRxiv2021

Choice of method of place cell classification determines the population of cells identified.

Place cells, spatially responsive hippocampal cells, provide the neural substrate supporting navigation and spatial memory. Historically most studies of these neurons have used electrophysiological recordings from implanted electrodes but optical methods, measuring intracellular calcium, are becoming increasingly common. Several methods have been proposed as a means to identify place cells based on their calcium activity but there is no common standard and it is unclear how reliable different approaches are. Here we tested three methods that have previously been applied to two-photon hippocampal imaging or electrophysiological data, using both model datasets and real imaging data. These methods use different parameters to identify place cells, including the peak activity in the place field, compared to other locations (the Peak method); the stability of cells activity over repeated traversals of an environment (Stability method); and a combination of these parameters with the size of the place field (Combination method). The three methods performed differently from each other on both model and real data. The Peak method showed high sensitivity and specificity for detecting model place cells and was the most robust to variations in place field width, reliability and field location. In real datasets, vastly different numbers of place cells were identified using the three methods, with little overlap between the populations identified as place cells. Therefore, choice of place cell detection method dramatically affects the number and properties of identified cells. We recommend the Peak method be used in future studies to identify place cell populations, unless there is an explicit theoretical reason for detecting cells with more narrowly defined properties. Author SummaryPlace cells are hippocampal cells that have spatially constrained receptive fields, the place field. These cells have been widely studied in the context of navigation, more recently using virtual reality environments in combination with optical methods of recording neuronal activity. However, there is a lack of consensus regarding how to identify place cells in these data. In this study we tested the sensitivity and specificity of three methods of identifying place cells. By comparing these methods and quantifying the populations of place cells they identify, we aimed to increase our understanding of exactly the populations that are currently being studied under the name "place cells". Although the appropriate method may depend on the experimental design, we generally recommend a single method going forward, which will increase consensus within the field about what should be included in a place cell population, and allow us to better compare results between studies.

neuroscience↗

bioRxiv2019

Hippocampus has lower oxygenation and weaker control of brain blood flow than cortex, due to microvascular differences

The hippocampus is essential for spatial and episodic memory but is damaged early in Alzheimers disease and is very sensitive to hypoxia. Understanding how it regulates its oxygen supply is therefore key for designing interventions to preserve its function. However, studies of neurovascular function in the hippocampus in vivo have been limited by its relative inaccessibility. Here we compared hippocampal and visual cortical neurovascular function in awake mice, using two photon imaging of individual neurons and vessels and measures of regional blood flow and haemoglobin oxygenation. We show that blood flow, blood oxygenation and neurovascular coupling were decreased in the hippocampus compared to neocortex, because of differences in both the vascular network and pericyte and endothelial cell function. Modelling oxygen diffusion indicates that these features of the hippocampal vasculature could explain its sensitivity to damage during neurological conditions, including Alzheimers disease, where the brains energy supply is decreased.

neuroscience↗