Biology subjects

Taylor, A.

Publications and source records attributed to Taylor, A..

At least 55 records · Page 3Linked to original sources

bioRxiv2023

Near infrared conjugated polymer nanoparticles (CPN) for tracking cells using fluorescence and optoacoustic imaging

Tracking the biodistribution of cell therapies is crucial for understanding their safety and efficacy. Optical imaging techniques are particularly useful for tracking cells due to their clinical translatability and potential for intra-operative use to validate cell delivery. However, there is a lack of appropriate optical probes for cell tracking. The only FDA-approved material for clinical use is indocyanine green (ICG). ICG can be used for both fluorescence and photoacoustic imaging, but is prone to photodegradation, and at higher concentrations, undergoes quenching and can adversely affect cell health. We have developed novel near-infrared imaging probes comprising conjugated polymer nanoparticles (CPNs) that can be fine-tuned to absorb and emit light at specific wavelengths. To compare the performance of the CPNs with ICG for in vivo cell tracking, labelled mesenchymal stromal cells (MSCs) were injected subcutaneously in mice and detected using fluorescence imaging (FI) and a form of photoacoustic imaging called multispectral optoacoustic tomography (MSOT). MSCs labelled with either ICG or CPN 770 could be detected with FI, but only CPN 770-labelled MSCs could be detected with MSOT. These results show that CPNs show great promise for tracking cells in vivo using optical imaging techniques, and for some applications, out-perform ICG.

bioengineering↗

bioRxiv2022

Phylogenetic endemism of the world's seed plants

Assessing phylogenetic endemism, i.e., the distribution of geographically restricted and evolutionarily unique species, is key to understanding biogeographic patterns and processes and critical for global conservation planning. Here, we quantified the geographic distribution and drivers of phylogenetic endemism for ~320,000 seed plants worldwide and identified centers and drivers of evolutionarily young (neoendemism) and evolutionarily old endemism (paleoendemism). Tropical and subtropical islands of the Southern Hemisphere as well as tropical mountainous regions displayed the worlds highest phylogenetic endemism. Tropical moist forests (e.g. Amazonia) and continental islands in south-east Asia emerged as centers of paleoendemism, while both high neo- and paleoendemism were found on ancient continental fragment islands (e.g. Madagascar) and in Mediterranean-climate regions. Global variation in phylogenetic endemism was best explained by a combination of past and present environmental factors (80.3% - 88.1% of variance explained). Geographic isolation and environmental heterogeneity emerged as primary drivers promoting high phylogenetic endemism. Also, warm and wet climates with long-term climatic stability showed a significant positive effect. However, environmental effects on phylogenetic endemism varied with geographic isolation, reflecting the unique evolutionary and biogeographic dynamics on oceanic islands. Long-term climatic stability promoted the persistence of paleoendemics, while isolation promoted higher neoendemism leading to oceanic islands and tropical mountainous regions being centers of both neo- and paleoendemism. Our study provides new insights into the evolutionary underpinnings of biogeographic patterns in seed plants, and by identifying areas of high evolutionary and biogeographic uniqueness, it may serve as a key resource for setting global conservation priorities.

ecology↗

bioRxiv2022

A targeted genetic modifier screen in Drosophila uncovers vulnerabilities in a genetically complex model of colon cancer

Kinases are key regulators of cellular signal transduction pathways. Many diseases including cancer are associated with global alterations in protein phosphorylation networks, as a result, kinases are frequent targets of drug discovery efforts. However, target identification and assessment, a critical step in targeted drug discovery which involves identifying essential genetic mediators of disease phenotypes, can be challenging in complex, heterogeneous diseases like cancer where multiple concurrent genomic alterations are common. Drosophila is a particularly useful genetic model system to identify novel regulators of biological processes through unbiased genetic screens. Here, we report two classic genetic modifier screens focusing on the Drosophila kinome to identify kinase regulators in two different backgrounds: KRAS TP53 PTEN APC, a multigenic cancer model that targets four genes recurrently mutated in human colon tumors and KRAS alone, a simpler model that targets one of the most frequently altered pathways in cancer. These screens identified hits that are shared by both models as well as those unique to each one, emphasizing the importance of capturing the genetic complexity of human tumor genome landscapes in experimental models. Our follow-up analysis of two hits from the KRAS only screen suggest that classical genetic modifier screens in heterozygous mutant backgrounds that result in a modest, non-lethal reduction in candidate gene activity in the context of a whole animal --a key goal of systemic drug treatment-- may be a particularly useful approach to identify most rate limiting genetic vulnerabilities in disease models as ideal candidate drug targets.

genetics↗

bioRxiv2022

Multicentre comparison of biological and functional properties of mesenchymal stromal cells from different sources cultivated using a harmonised manufacturing workflow

BackgroundMesenchymal stromal cells (MSCs), commonly sourced from adipose tissue, bone marrow and umbilical cord, have been widely used in many medical conditions due to their therapeutic potential. Yet, the still limited understanding of the underlying mechanisms of action hampers clinical translation. Clinical potency can vary considerably depending on tissue source, donor attributes, but importantly, also culture conditions. Lack of standard procedures hinders inter-study comparability and delays the progression of the field. The aim of this study was A-to assess the impact on MSC characteristics when different laboratories performed analysis on the same MSC material using harmonised culture conditions and B-to understand source-specific differences. MethodsThree independent institutions performed a head-to-head comparison of human-derived adipose (A-), bone marrow (BM-), and umbilical cord (UC-) MSCs using harmonised culture conditions. In each centre, cells from one specific tissue source were isolated and later distributed across the network to assess their biological properties, including cell expansion, immune phenotype, and tri-lineage differentiation (part A). To assess tissue specific function, angiogenic and immunomodulatory properties and the in vivo biodistribution were compared in one expert lab (part B). ResultsBy implementing a harmonised manufacturing workflow, we obtained largely reproducible results across three independent laboratories in part A of our study. Unique growth patterns and differentiation potential were observed for each tissue source, with similar trends observed between centres. Immune phenotyping verified expression of typical MSC surface markers and absence of contaminating surface markers. Depending on the established protocols in the different laboratories, quantitative data varied slightly. Functional experiments in part B concluded that conditioned media from BM-MSCs significantly enhanced tubulogenesis and endothelial migration in vitro. In contrast, immunomodulatory studies reported superior immunosuppressive abilities for A-MSCs. Biodistribution studies in healthy mice showed lung entrapment after administration of all three types of MSCs, with a significantly faster clearance of BM-MSCs. ConclusionThese results show the heterogeneous behaviour and regenerative properties of MSCs as a reflection of intrinsic tissue-origin properties while providing evidence that the use of standardised culture procedures can reduce but not eliminate inter-lab and operator differences. HighlightsIn this study, we have: - Provided a harmonised manufacturing workflow that has demonstrated reproducible results across three independent laboratories when expanding MSCs. - Defined a multi-assay matrix capable of identifying functional differences in terms of angiogenesis, wound healing abilities and immunosuppressive properties. - Demonstrated similar in vivo biodistribution properties regardless of cell origin.

cell biology↗

bioRxiv2022

Computed tomography lacks sensitivity to image gold labelled mesenchymal stromal cells in vivo as evidenced by multispectral optoacoustic tomography.

Elucidating the mechanisms of action and long-term safety of cell therapies is necessary for their clinical translation. Non-invasive imaging technologies such as bioluminescence imaging (BLI), computed tomography (CT) and multispectral optoacoustic tomography (MSOT) have been proposed as tools for longitudinal cell monitoring but their performances have not been compared. Here, we evaluate combinations of these modalities to track the in vivo distribution of gold-labelled mesenchymal stromal cells (MSCs). We found that injected MSCs labelled with gold nanoparticles and expressing the reporter gene firefly luciferase could be detected with BLI and MSOT but not CT. We conclude that the MSCs did not carry enough contrast agent to be tracked by CT, demonstrating that CT tracking of gold-labelled cells is not a practical approach as high amounts of gold, which might impair cell viability, are necessary.

cell biology↗

bioRxiv2022

Simplified fecal community transplant restores Clostridioides difficile colonization resistance to antibiotic perturbed murine communities

Fecal communities transplanted into individuals can eliminate recurrent Clostridioides difficile infection (CDI) with high efficacy. However, this treatment is only used once CDI becomes resistant to antibiotics or has recurred multiple times. We sought to investigate whether a fecal community transplant (FCT) pre-treatment could be used to prevent CDI altogether. We treated male C57BL/6 mice with either clindamycin, cefoperazone, or streptomycin, and then inoculated them with the microbial community from untreated mice before challenging with C. difficile. We measured colonization and sequenced the V4 region of the 16S rRNA gene to understand the dynamics of the murine fecal community in response to the FCT and C. difficile challenge. Clindamycin-treated mice became colonized with C. difficile but cleared it naturally and did not benefit from the FCT. Cefoperazone-treated mice became colonized by C. difficile, but the FCT enabled clearance of C. difficile. In streptomycin-treated mice, the FCT was able to prevent C. difficile from colonizing. Then we diluted the FCT and repeated the experiments. Cefoperazone-treated mice no longer cleared C. difficile. However, streptomycin-treated mice colonized with 1:102 dilutions resisted C. difficile colonization. Streptomycin-treated mice that received a FCT diluted 1:103, C. difficile colonized but later was cleared. In streptomycin-treated mice, inhibition of C. difficile was associated with increased relative abundance of a group of bacteria related to Porphyromonadaceae and Lachnospiraceae. These data demonstrate that C. difficile colonization resistance can be restored to a susceptible community with a FCT as long as it complements the missing populations. ImportanceAntibiotic use, ubiquitous with the healthcare environment, is a major risk factor for Clostridioides difficile infection (CDI), the most common nosocomial infection. When C. difficile becomes resistant to antibiotics, a fecal microbiota transplant from a healthy individual can effectively restore the gut bacterial community and eliminate the infection. While this relationship between the gut bacteria and CDI is well established, there are no therapies to treat a perturbed gut community to prevent CDI. This study explored the potential of restoring colonization resistance to antibiotic-induced susceptible gut communities. We described the effect gut bacteria community variation has on the effectiveness of a fecal community transplant for inhibiting CDI. These data demonstrated that communities susceptible to CDI can be supplemented with fecal communities but the effectiveness depended on the structure of the community following the perturbation. Thus, a simplified bacterial community may be able to recover colonization resistance to patients treated with antibiotics.

microbiology↗

bioRxiv2022

Climate and ant richness explain the global distribution of ant-plant mutualisms

Biotic interactions are known to play an important role in shaping species geographic distributions and diversity patterns. However, the role of mutualistic interactions in shaping global diversity patterns remains poorly quantified, particularly with respect to interactions with invertebrates. Moreover, it is unclear how the nature of different mutualisms interacts with abiotic drivers and affects diversity patterns of mutualistic organisms. Here, we present a global-scale biogeographic analysis of three different ant-plant mutualisms, differentiating between plants bearing domatia, extrafloral nectaries (EFNs), and elaiosomes, based on comprehensive geographic distributions of [~]15,000 flowering plants and [~]13,000 ant species. Domatia and extrafloral nectaries involve indirect plant defenses provided by ants, while elaiosomes attract ants to disperse seeds. Our results show distinct biogeographic patterns of different ant-plant mutualisms, with domatium- and EFN-bearing plant richness decreasing sharply from the equator towards the poles, while elaiosome-bearing plants prevail at mid-latitudes. Contemporary climate, especially mean annual temperature and precipitation, emerge as the most important predictor of ant-associated plant diversity. In hot and moist regions, typically the tropics, domatium- and EFN-bearing plant richness increases with related ant guild richness, while in warm regions plants with elaiosomes are strongly linked to interacting ants. Our results suggest that ant richness in combination with climate drives the spatial variation of plants bearing domatia, extrafloral nectaries, and elaiosomes, highlighting the importance of mutualistic interactions for understanding plant biogeography and its response to global change.

ecology↗

bioRxiv2022

Actin nano-architecture of phagocytic podosomes

Podosomes are actin-enriched adhesion structures important for multiple cellular processes, including migration, bone remodeling, and phagocytosis. Here, we characterized the structure and organization of phagocytic podosomes using interferometric photoactivated localization microscopy (iPALM), a super-resolution microscopy technique capable of 15-20 nm resolution, together with structured illumination microscopy (SIM) and localization-based superresolution microscopy. Phagocytic podosomes were observed during frustrated phagocytosis, a model in which cells attempt to engulf micro-patterned IgG antibodies. For circular patterns, this resulted in regular arrays of podosomes with well-defined geometry. Using persistent homology, we developed a pipeline for semi-automatic identification and measurement of podosome features. These studies revealed an "hourglass" shape of the podosome actin core, a protruding "knob" at the bottom of the core, and two actin networks extending from the core. Additionally, the distributions of paxillin, talin, myosin II, -actinin, cortactin, and microtubules relative to actin were characterized.

cell biology↗

bioRxiv2022

Machine learning improves global models of plant diversity

Despite the paramount role of plant diversity for ecosystem functioning, biogeochemical cycles, and human welfare, knowledge of its global distribution is incomplete, hampering basic research and biodiversity conservation. Here, we used machine learning (random forests, extreme gradient boosting, neural networks) and conventional statistical methods (generalised linear models, generalised additive models) to model species richness and phylogenetic richness of vascular plants worldwide based on 830 regional plant inventories including c. 300,000 species and predictors of past and present environmental conditions. Machine learning showed an outstanding performance, explaining up to 80.9% of species richness and 83.3% of phylogenetic richness. Current climate and environmental heterogeneity emerged as the primary drivers, while past environmental conditions left only small but detectable imprints on plant diversity. Finally, we combined predictions from multiple modelling techniques (ensemble predictions) to reveal global patterns and centres of plant diversity at multiple resolutions down to 7,774 km2. Our predictive maps provide the most accurate estimates of global plant diversity available to date at grain sizes relevant for conservation and macroecology.

ecology↗

bioRxiv2022

Investigating the temporal pattern of neuroimaging-based brain age estimation as a biomarker for Alzheimer's Disease related neurodegeneration

Neuroimaging-based brain-age estimation via machine learning has emerged as an important new approach for studying brain aging. The difference between ones estimated brain age and chronological age, the brain age gap (BAG), has been proposed as an Alzheimers Disease (AD) biomarker. However, most past studies on the BAG have been cross-sectional. Identifying how an individuals BAG temporal pattern changes over time would enable improved prediction of clinical outcome based on neurophysiological changes and better understanding of AD progression. To fill this gap, our study conducted predictive modeling using large neuroimaging data with up to 8 years of follow-up to examine the temporal patterns of the BAGs trajectory and how it varies by subject-level characteristics and disease status. To the best of our knowledge, this is the first effort to take a longitudinal approach to investigate the pattern and rate of change in BAG over time in individuals who progress from mild cognitive impairment (MCI) to clinical AD. Combining multimodal imaging data in a support vector regression model to estimate brain age yielded improved performance than single modality. Multilevel modeling results showed the BAG followed a linear increasing trajectory with a significantly faster rate in individuals with MCI who progressed to AD compared to cognitively normal or MCI individuals who did not progress. The dynamic changes in the BAG during AD progression were further moderated by gender and APO{varepsilon}4 carriership. Findings demonstrate the BAG as a potential biomarker for understanding individual specific temporal patterns related to AD progression.

neuroscience↗

bioRxiv2022

Identification of genetic loci in lettuce mediating quantitative resistance to fungal pathogens

Lactuca sativa L. (lettuce) is an important leafy vegetable crop grown and consumed globally. Chemicals are routinely used to control major pathogens, including the causal agents of grey mould (Botrytis cinerea) and lettuce drop (Sclerotinia sclerotiorum). With increasing prevalence of pathogen resistance to fungicides and environmental concerns, there is an urgent need to identify sources of genetic resistance to B. cinerea and S. sclerotiorum in lettuce. We demonstrated genetic variation for quantitative resistance to B. cinerea and S. sclerotiorum in a set of 97 diverse lettuce and wild relative accessions, and between the parents of lettuce mapping populations. Transcriptome profiling across multiple lettuce accessions enabled us to identify genes with expression correlated with resistance, predicting the importance of post-transcriptional gene regulation in the lettuce defence response. We identified five genetic loci influencing quantitative resistance in a F10 mapping population derived from a Lactuca serriola (wild relative) x lettuce cross, which each explained 5-10% of the variation. Differential gene expression analysis between the parent lines, and integration of data on correlation of gene expression and resistance in the diversity set, highlighted potential causal genes underlying the quantitative trait loci. Key MessageWe demonstrate genetic variation for quantitative resistance against important fungal pathogens in lettuce and its wild relatives, map loci conferring resistance and predict key molecular mechanisms using transcriptome profiling.

plant biology↗

bioRxiv2022

PCYT2 controls muscle health and muscle aging

Muscle degeneration is the most prevalent cause for frailty and dependency in inherited diseases and ageing, affecting hundreds of millions of people. Elucidation of pathophysiological mechanisms, as well as effective treatments for muscle diseases represents an important goal in improving human health. Here, we show that phosphatidylethanolamine cytidyltransferase (PCYT2/ECT), the critical enzyme of the Kennedy branch of phosphatidylethanolamine (PE) synthesis pathway, has an essential role in muscle health. Human genetic deficiency in PCYT2 causes a severe disease with failure to thrive and progressive muscle weakness. Pcyt2 mutant zebrafish recapitulate the patient phenotypes, indicating that the role of PCYT2/PE in muscle is evolutionary conserved. Muscle specific Pcyt2 knockout mice exhibited failure to thrive, impaired muscle development, progressive muscle weakness, muscle loss, accelerated ageing, and reduced lifespan. Mechanistically, Pcyt2 deficiency affects mitochondrial bioenergetics and physicochemical properties of the myofiber membrane lipid bilayer, in particular under exercise strain. We also show that PCYT2 activity declines in the aging muscles of humans and mice. AAV-based delivery of PCYT2 rescued muscle weakness in Pcyt2 knock-out mice and, importantly, improved muscle strength in old mice, offering a novel therapeutic avenue for rare disease patients and muscle aging. Thus, PCYT2 plays a fundamental, specific, and conserved role in vertebrate muscle health, linking PCYT2 and PCYT2 synthesized PE lipids to severe muscle dystrophy, exercise intolerance and aging.

genetics↗

bioRxiv2021

Drought stress increases the expression of barley defence genes with negative consequences for infesting cereal aphids

Crops are exposed to myriad abiotic and biotic stressors with negative consequences. Two stressors that are expected to increase under climate change are drought and infestation with herbivorous insects, including important aphid species. Expanding our understanding of the impact drought has on the plant-aphid relationship will become increasingly important under future climate scenarios. Here we use a previously characterised plant-aphid system comprising a susceptible variety of barley, a wild relative of barley with partial-aphid resistance, and the bird cherry-oat aphid to examine the drought-plant-aphid relationship. We show that drought has a negative effect on plant physiology and aphid fitness and provide evidence to suggest that plant resistance influences aphid responses to drought stress, with the expression of aphid detoxification genes increasing under drought when feeding on the susceptible plant but decreasing on the partially-resistant plant. Furthermore, we show that the expression of thionin genes, plant defensive compounds that contribute aphid resistance, increase ten-fold in susceptible plants exposed to drought stress but remain at constant levels in the partially-resistant plant, suggesting they play an important role in modulating aphid populations. This study highlights the role of plant defensive processes in mediating the interactions between the environment, plants, and herbivorous insects.

plant biology↗

bioRxiv2021

Development of an in-situ printing system with human platelet lysate based bioink to treat corneal perforation

PurposeCorneal perforation is a clinical emergency. Tissue glue to seal the perforation, and supplementary topical medication represents existing standard treatment. Previously, our group developed a transparent human platelet lysate (hPL)-based biomaterial that showed good cell compatibility and accelerated corneal epithelial cells healing in-vitro. This study aims to develop a novel treatment method for corneal perforation using this biomaterial. MethodsRheometry was used to measure the hPL-based biomaterial behaviour at room and corneal surface temperatures. Its adhesiveness to porcine skin and burst pressure limit were also measured. Based on rheological behaviour, a hand-held biopen was developed to extrude it onto the cornea. An animal trial (5 New Zealand white rabbits) to compare impact of the biomaterial and cyanoacrylate glue (control group) on a 2mm perforation was conducted to evaluate safety and efficacy. ResultsThe hPL-based biomaterial showed higher adhesiveness compared to commercial fibrin glue and withstood burst pressure approximately 6.4x higher than routine intraocular pressure. Treatment rabbits had lower pain scores and faster recovery, despite generating similar scar-forming structure compared to controls. No secondary corneal ulcer was generated in rabbits treated with the bio-adhesive. ConclusionsThis study reports a novel in-situ printing system capable of delivering a hPL-based, transparent bio-adhesive and successfully treating small corneal perforations. Bio-adhesive-treated rabbits recovered faster and required no additional analgesia. Both groups showed scarred corneal tissue after healing, however no infection and inflammation was observed by 3 weeks. The delivery system was easy to use and may represent an alternative treatment for corneal perforation. HighlightsO_LIThis study presents a novel in situ printing system to treat corneal perforation C_LIO_LIThe system is comprised of a human platelet lysate-based bio-adhesive and a pen-like hand held delivery system C_LIO_LIMechanical tests showed our transparent bio-adhesive has a higher adhesiveness compared to existing treatments and burst pressure threshold approximately 6.4 times higher than normal intraocular pressure. C_LIO_LIIn vivo rabbit trial showed that compared to cyanoacrylate glue, the bio-adhesive was safer, faster healing and led to less pain in rabbits. C_LI

bioengineering↗

bioRxiv2021

An osmotic laxative renders mice susceptible to prolonged Clostridioides difficile colonization and hinders clearance

Antibiotics are a major risk factor for Clostridioides difficile infections (CDIs) because of their impact on the microbiota. However, non-antibiotic medications such as the ubiquitous osmotic laxative polyethylene glycol (PEG) 3350 also alter the microbiota. Clinicians also hypothesize that PEG helps clear C. difficile. But whether PEG impacts CDI susceptibility and clearance is unclear. To examine how PEG impacts susceptibility, we treated C57Bl/6 mice with 5-day and 1-day doses of 15% PEG in the drinking water and then challenged the mice with C. difficile 630. We used clindamycin-treated mice as a control because they consistently clear C. difficile within 10 days post-challenge. PEG treatment alone was sufficient to render mice susceptible and 5-day PEG-treated mice remained colonized for up to 30 days post-challenge. In contrast, 1-day PEG treated mice were transiently colonized, clearing C. difficile within 7 days post-challenge. To examine how PEG treatment impacts clearance, we administered a 1-day PEG treatment to clindamycin-treated, C. difficile-challenged mice. Administering PEG to mice after C. difficile challenge prolonged colonization up to 30 days post-challenge. When we trained a random forest model with community data from 5 days post-challenge, we were able to predict which mice would exhibit prolonged colonization (AUROC = 0.90). Examining the dynamics of these bacterial populations during the post-challenge period revealed patterns in the relative abundances of Bacteroides, Enterobacteriaceae, Porphyromonadaceae, Lachnospiraceae, and Akkermansia that were associated with prolonged C. difficile colonization in PEG-treated mice. Thus, the osmotic laxative, PEG, rendered mice susceptible to C. difficile colonization and hindered clearance. ImportanceDiarrheal samples from patients taking laxatives are typically rejected for Clostridiodes difficile testing. However, there are similarities between the bacterial communities from people with diarrhea or C. difficile infections (CDI) including lower diversity compared to communities from healthy patients. This observation led us to hypothesize that diarrhea may be an indicator of C. difficile susceptibility. We explored how osmotic laxatives disrupt the microbiotas colonization resistance to C. difficile by administering a laxative to mice either before or after C. difficile challenge. Our findings suggest that osmotic laxatives disrupt colonization resistance to C. difficile, and prevent clearance among mice already colonized with C. difficile. Considering that most hospitals recommend not performing C. difficile testing on patients taking laxatives and laxatives are prescribed prior to administering fecal microbiota transplants via colonoscopy to patients with recurrent CDIs, further studies are needed to evaluate if laxatives impact microbiota colonization resistance in humans.

microbiology↗

bioRxiv2021

Norepinephrine activates β1-adrenergic receptors localized to the inner nuclear membrane in cortical astrocytes

Studies in cardiomyocytes have established that adrenergic receptors, conventionally thought to initiate signaling events exclusively from the plasma membrane, can also localize to and signal from the nuclear membrane. Activation of these receptors by their endogenous cationic ligands requires transmembrane uptake mediated by organic cation transporter 3 (OCT3). We have demonstrated that OCT3 is densely localized to outer nuclear membranes in neurons and astrocytes, suggesting that nuclear adrenergic signaling is also present in the central nervous system. In this study, we examined the subcellular localization of {beta}1-adrenergic receptors, their G-protein signaling partners, and catecholamine transporters in mouse astrocytes. We identified a population of {beta}1-adrenergic receptors localized to astrocyte inner nuclear membranes. We demonstrated that key components of Gs-mediated signaling are localized to the nuclear compartment and identified OCT3 and other catecholamine transporters localized to plasma and nuclear membranes. Treatment of astrocytes with norepinephrine induced rapid increases in nuclear PKA activity which were blocked by pretreatment with inhibitors of catecholamine transport. These data indicate that nuclear {beta}1-adrenergic receptors are functionally coupled to Gs-coupled signaling mediators and that their activation by norepinephrine requires transporter-mediated uptake. These receptors represent a powerful mechanism by which norepinephrine may alter astrocyte gene expression and brain function.

cell biology↗

bioRxiv2021

Vascular epiphytes contribute disproportionately to global centres of plant diversity

AimVascular epiphytes are ubiquitous features of wet tropical forests where they contribute substantially to local and regional plant diversity. While some basic epiphyte distribution patterns are relatively well studied, little effort has been made to understand the drivers responsible for constraining their global distribution. This study quantifies the substantial contribution of epiphytes to global gradients and centres of vascular plant diversity and explores whether epiphytes vary from terrestrial plants in relation to contemporary and historical environmental variables. LocationGlobal. Time periodPresent. Major taxa studiedVascular epiphytes. MethodsWe integrated EpiList 1.0, a comprehensive list comprising > 30,000 vascular epiphyte species, and species distributions derived from the GIFT database to describe the global biogeography of epiphytes. We used generalized linear mixed effects models to assess the relationship between epiphytic and terrestrial plant diversity, and contemporary and historical environmental predictors. ResultsWe find that epiphytes substantially contribute to global centres of vascular plant diversity, accounting for up to 39% of the vascular flora in the Neotropics. Epiphytes decrease in species numbers with increasing latitude at a rate three times faster than terrestrial plants, a trend that is driven mainly by the distribution of tropical forests and precipitation. Further, large regional differences emerge that are explained by several large endemic angiosperm families (e.g., Neotropical Bromeliaceae) that are absent in other tropical regions. Main conclusionsOur results show that epiphytes are disproportionately diverse in most global centres of plant diversity and play an important role in driving the global latitudinal diversity gradient for plants. The distribution of precipitation and tropical forests emerge as major drivers of the latitudinal diversity gradient in epiphyte species richness. Finally, our findings demonstrate how epiphyte floras in different biogeographical realms are composed of different families and higher taxa revealing an important signature of historical biogeography.

ecology↗

bioRxiv2021

Middle Eastern Genetic Variation Improves Clinical Annotation of the Human Genome

Genetic variation in populations of Middle Eastern origin remains highly underrepresented in most comprehensive genomic databases. This underrepresentation hampers the functional annotation of the human genome and challenges accurate clinical variant interpretation. To highlight the importance of capturing genetic variation in the Middle East, we aggregated whole exome and genome sequencing data from 2116 individuals in the Middle East and established the Middle East Variation (MEV) database. Of the high-impact coding (missense and loss of function) variants in this database, 53% were absent from the most comprehensive Genome Aggregation Database (gnomAD), thus representing a unique Middle Eastern variation dataset which might directly impact clinical variant interpretation. We highlight 39 variants with minor allele frequency >1% in the MEV database that were previously reported as rare disease variants in ClinVar and the Human Gene Mutation Database (HGMD). Furthermore, the MEV database consisted of 281 putative homozygous loss of function (LoF) variants, or complete knockouts, of which 31.7% (89/281) were absent from gnomAD. This set represents either complete knockouts of 83 unique genes in reportedly healthy individuals, with implications regarding disease penetrance and expressivity, or might affect dispensable exons, thus refining the clinical annotation of those regions. Intriguingly, 24 of those genes have several clinically significant variants reported in ClinVar and/or HGMD. Our study shows that genetic variation in the Middle East improves functional annotation and clinical interpretation of the genome and emphasizes the need for expanding sequencing studies in the Middle East and other underrepresented populations.

genomics↗