Biology subjects

Anderson, C.

Publications and source records attributed to Anderson, C..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Transcriptomic analysis of repeat expansion-ataxias uncovers distinct non-neuronal cell type-specific signatures of disease across the human brain

Hereditary ataxias are a heterogeneous group of neurogenetic conditions characterised by the clinical syndrome of progressive loss of coordination from neurodegeneration of the cerebellum. A commonality across the most prevalent ataxias is the underlying disease mechanism secondary to expansions of short tandem DNA repeats. There is currently an incomplete understanding of the pathogenic mechanisms of these repeat expansion disorders, a core feature of which revolves around RNA-dysregulation. In this study, we used both bulk and single nuclear RNA-sequencing to study post-mortem brain tissue of human donors with a range of repeat-expansion ataxias to reveal further mechanistic insights. We compared post-mortem paired cerebellar and frontal cortex tissue bulk RNA-sequencing data from 23 ataxia patients and 22 sex-, age-matched controls from two brain banks (spinocerebellar ataxia (SCA)1, SCA2, SCA6, SCA7, SCA17, Friedreichs ataxia (FRDA), and 7 cases with unknown molecular diagnoses). We analysed bulk RNA-sequencing data for transcript usage, differential and cell-type-specific expression to transcriptomically profile these diseases. We also generated single nuclear RNA-sequencing data of the cerebellum from donors with SCA1, SCA2, SCA6 and FRDA to decipher changes in cell type proportions in the disease state. Using this approach, we found that: (i) despite the commonalities in the genetics of ataxia, there were components of their transcriptional signatures which were distinct; (ii) there were extensive transcriptional changes evident not only in the cerebellum but also the frontal cortex in ataxia cases; (iii) activation of immune and inflammatory pathways, as well as involvement of non-neuronal cell types was a feature of all ataxias to a lesser or greater extent. This study provides a novel resource to understand the mechanisms of disease in ataxia. Furthermore, taken together, these results highlight immune pathways and the role of non-neuronal cell types as early and potentially important therapeutic targets. These findings provide a map of transcriptomic changes in ataxia to further understanding of the underlying pathogenesis.

neuroscience↗

bioRxiv2024

Inflammation-associated monocytes express ACOD1 to curtail inflammatory behaviour in IBD and experimental colitis

Monocytes are essential for replenishing homeostatic macrophages in the intestine. However, they also accumulate in significant numbers when intestinal homeostasis is disrupted in diseases, such as inflammatory bowel disease (IBD). The molecular pathways governing monocyte behaviour across these different contexts remain poorly understood. Here, we profile the monocyte / macrophage compartment in human IBD using single-cell RNA sequencing and identify a discrete population of monocytes that accumulate in IBD, which we term inflammation associated monocytes (IAMs). These can be identified by the expression of CD319, CD274 and CCRL2, and demonstrate increased expression of IBD susceptibility genes. By performing cross-species analysis, we show an analogous population of IAMs accumulate during chemically induced colitis in mice. Using transgenic fate mapping approaches, we show these cells likely derive from a discrete precursor in the bone marrow (BM) and are locally imprinted to produce heightened IL-1{beta} and TNF in mouse and humans. Importantly, we show that co-incident with a hyper-inflammatory phenotype, these same cells uniquely and specifically express aconitate decarboxylase (ACOD1) in response to local Toll-like receptor (TLR) and interferon (IFN) receptor signalling, to limit unrestricted cytokine production. Thus, the intestinal environment after injury instructs both inflammation and recovery specifically within a transitioning population of monocytes that are absent in health.

immunology↗

bioRxiv2024

Chemoresistance of TP53 mutant AML requires the mevalonate byproduct, GGPP, for regulation of ROS and induction of a mitochondria stress response

Acute myeloid leukemia (AML) with mutations in the tumor suppressor gene, TP53 (TP53mut AML), is fatal with a median survival of only 6 months. RNA sequencing on purified AML patient samples show TP53mut AML has higher expression of mevalonate pathway genes. We retrospectively identified a survival benefit in TP53mut AML patients who received chemotherapy concurrently with a statin, which inhibits the mevalonate pathway. Mechanistically, TP53mut AML resistance to standard AML chemotherapy, cytarabine (AraC), correlates with increased mevalonate pathway activity and a mitochondria stress response with increased mitochondria mass and oxidative phosphorylation. Pretreatment with a statin reverses these effects and chemosensitizes TP53mut AML cell lines and primary samples in vitro and in vivo. Mitochondria-dependent chemoresistance requires the geranylgeranyl pyrophosphate (GGPP) branch of the mevalonate pathway and novel GGPP-dependent synthesis of glutathione to manage AraC-induced reactive oxygen species (ROS). Overall, we show that the mevalonate pathway is a novel therapeutic target in TP53mut AML. SignificanceChemotherapy-persisting TP53mut AML cells induce a mitochondria stress response that requires mevalonate byproduct, GGPP, through its novel role in glutathione synthesis and regulation of mitochondria metabolism. We provide insight into prior failures of the statin family of mevalonate pathway inhibitors in AML. We identify clinical settings and strategies to successfully target the mevalonate pathway, particularly to address the unmet need of TP53mut AML.

cancer biology↗

bioRxiv2024

Associating EEG Functional Networks and the Effect of Sleep Deprivation as Measured Using Psychomotor Vigilance Tests

People are routinely forced to undertake cognitive challenges under the effect of sleep deprivation, due to professional and social obligations forcing them to ignore their circadian clock. However, low intra-individual and high inter-individual differences in behavioural outcomes are known to occur when people are sleep deprived, leading to the conclusion that trait-like differences to sleep deprivation could explain the differing levels of resilience. Within this study we consider if trait-like resilience to sleep deprivation, measured using psychomotor vigilance tests over a 40h constant routine protocol, could be associated with graph metrics (mean node strength, clustering coefficient, characteristic path length and stability) calculated from EEG functional networks acquired when participants are well rested (baseline). Furthermore, we investigated how stability (the consistency of a participants functional network over time measured using 2-D correlation) changed over the constant routine. We showed evidence of strong significant correlations between high mean node strength, low characteristic path length and high stability at baseline with a general resilience to extended sleep deprivation, although the same features lead to vulnerability during the period of natural sleep onset, highlighting non-uniform correlations over time. We also show significant differences in the levels of stability between resilient and vulnerable groups.

neuroscience↗

bioRxiv2024

Terrestrial 3D Laser Scanning for Ecosystem and Fire Effects Monitoring

Long-term terrestrial ecosystem monitoring is a critical component of documenting outcomes of land management actions, assessing progress towards management objectives, and guiding realistic long-term ecological goals, all through repeated observation and measurement. Traditional monitoring methods have evolved for specific applications in forestry, ecology, and fire and fuels management. While successful monitoring programs have clear goals, trained expertise, and rigorous sampling protocols, new advances in technology and data management can help overcome the most common pitfalls in data quality and repeatability. This paper presents Terrestrial Laser Scanning (TLS), a specific form of LiDAR (Light Detection and Ranging), as an emerging sampling method that can complement and enhance existing monitoring methods. TLS captures in high resolution the 3D structure of a terrestrial ecosystem (forest, grassland, etc.), and is increasingly efficient and affordable (<$30,000). Integrating TLS into ecosystem monitoring can standardize data collection, improve efficiency, and reduce bias and error. Streamlined data processing pipelines can rigorously analyze TLS data and incorporate constant improvements to inform management decisions and planning. The approach described in this paper utilizes portable, push-button TLS equipment that, when calibrated with initial transect sampling, captures detailed forestry, fuels, and ecological features in less than 5 minutes per plot. We also introduce an interagency automated processing pipeline and dashboard viewer for instant, user-friendly analysis, and data retrieval of hundreds of metrics. Forest metrics and inventories produced with these methods offer effective decision-support data for managers to quantify landscape-scale conditions and respond with efficient action. This protocol further supports interagency compatibility for efficient natural resource monitoring across jurisdictional boundaries with uniform data, language, methods, and data analysis. With continued improvement of scanner capabilities and affordability, these data will shape the future of terrestrial ecosystem monitoring as an important means to address the increasingly fast pace of ecological change facing natural resource managers.

ecology↗

bioRxiv2023

Constraints on Lanthanide Separation by Selective Biosorption

Rare Earth Elements (REE) are essential ingredients of sustainable energy technologies1-5, but separation of lanthanides is considered one of the hardest problems in chemistry today6. Biosorption, where molecules adsorb to the surface of biological materials, offers a sustainable alternative to environmentally harmful solvent extractions currently used for REE separations. The REE-biosorption capabilities of some microorganisms already allow for REE separations that under specialized conditions are competitive with solvent extractions7. Our recent work has discovered the genetic basis for REE biosorption selectivity8. However, it is unclear if the small changes to selectivity produced by changes to single genetic loci could allow biosorption to leapfrog existing REE separation technologies. In this article we present three models of lanthanide separation by biosorption and desorption. The first model shows that if a biosorbing microbe behaves as it if has a single type of binding site with small preference for one lanthanide, then the small changes in selectivity produced by changes to a single genetic locus could reduce the length of a separation process by {approx} 25%. Large multi-locus gene edits could reduce a separation process length by almost 90%. On the other hand, if the microbe contains multiple sites each with a distinct preference for an individual lanthanide, then separations become challenging and larger genetic edits would be needed to enable high purity. However, even if these large genetic edits are not possible, high purity separations could still be possible by combining multiple microbes, each with small increases in selectivity, with the first designed to enrich for the target lanthanide, while subsequent microbes are designed to remove contaminants.

synthetic biology↗

bioRxiv2023

Gene expression QTL mapping in stimulated iPSC-derived macrophages provides insights into common complex diseases.

Many disease-associated variants are thought to be regulatory but are not present in existing catalogues of expression quantitative trait loci (eQTL). We hypothesise that these variants may regulate expression in specific biological contexts, such as stimulated immune cells. Here, we used human iPSC-derived macrophages to map eQTLs across 24 cellular conditions. We found that 76% of eQTLs detected in at least one stimulated condition were also found in naive cells. The percentage of response eQTLs (reQTLs) varied widely across conditions (3.7% - 28.4%), with reQTLs specific to a single condition being rare (1.11%). Despite their relative rarity, reQTLs were overrepresented among disease-colocalizing eQTLs. We nominated an additional 21.7% of disease effector genes at GWAS loci via colocalization of reQTLs, with 38.6% of these not found in the Genotype-Tissue Expression (GTEx) catalogue. Our study highlights the diversity of genetic effects on expression and demonstrates how condition-specific regulatory variation can enhance our understanding of common disease risk alleles.

genomics↗

bioRxiv2023

Newly born mesenchymal cells disperse through a rapid mechanosensitive migration

Embryonic mesenchymal cells are dispersed within an extracellular matrix but can coalesce to form condensates with key developmental roles. Cells within condensates undergo fate and morphological changes, and induce cell fate changes in nearby epithelia to produce structures including hair follicles, feathers or intestinal villi. Here, by imaging of mouse and chicken embryonic skin, we find that mesenchymal cells undergo much of their dispersal in early interphase, in a stereotyped process of displacement driven by three hours of rapid and persistent migration, followed by a long period of low motility. The cell division plane and the elevated migration speed and persistence of newly born mesenchymal cells are mechanosensitive, aligning with tension in the tissue. This early G1 migratory behaviour disperses mesenchymal cells and allows the daughters of recent divisions to travel long distances to enter dermal condensates, demonstrating an unanticipated effect of a cell cycle sub-phase on core mesenchymal behaviour. HighlightsO_LIAfter mesenchymal cell division the speed and persistence of daughter cell migration is elevated for 180 minutes C_LIO_LIMesenchymal cell division and migration are directed by tissue tension C_LIO_LINewly born mesenchymal cells are uniquely responsive to tissue strain C_LIO_LINewly born mesenchymal cells are preferentially recruited to dermal condensates C_LIO_LIIncreased dispersal of newly born cells enables long distance travel to dermal condensates C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/525849v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@c69b4dorg.highwire.dtl.DTLVardef@fe0295org.highwire.dtl.DTLVardef@5b9f61org.highwire.dtl.DTLVardef@13ca1aa_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2022

Circadian distribution of epileptiform discharges in epilepsy: candidate mechanisms of variability

Epilepsy is a serious neurological disorder characterised by a tendency to have recurrent, spontaneous, seizures. Classically, seizures are assumed to occur at random. However, recent research has uncovered underlying rhythms both in seizures and in key signatures of epilepsy - so-called interictal epileptiform activity - with timescales that vary from hours and days through to months. Understanding the physiological mechanisms that determine these rhythmic patterns of epileptiform discharges remains an open question. Many people with epilepsy identify precipitants of their seizures, the most common of which include stress, sleep deprivation and fatigue. To quantify the impact of these physiological factors, we analysed 24-hour EEG recordings from a cohort of 107 people with idiopathic generalized epilepsy. We found two subgroups with distinct distributions of epileptiform discharges: one with highest incidence during sleep and the other during day-time. We interrogated these data using a mathematical model that describes the transitions between background and epileptiform activity in large-scale brain networks. This model was extended to include a time-dependent forcing term, where the excitability of nodes within the network could be modulated by other factors. We calibrated this forcing term using independently-collected human cortisol (the primary stress-responsive hormone characterised by circadian and ultradian patterns of secretion) data and sleep-staged EEG from healthy human participants. We found that either the dynamics of cortisol or sleep stage transition, or a combination of both, could explain most of the observed distributions of epileptiform discharges. Our findings provide conceptual evidence for the existence of underlying physiological drivers of rhythms of epileptiform discharges. These findings should motivate future research to explore these mechanisms in carefully designed experiments using animal models or people with epilepsy. Author summary65 million people have epilepsy worldwide. Many of these people report specific triggers that make their seizures (the primary symptom of epilepsy) more likely. Here, we use a mathematical model to understand the relationship between possible triggers and rhythms in epileptiform activity observed across the day. The mathematical model describes the activity of connected brain regions, and how the excitability of these regions can change in response to different stimuli. Based on data collected from people with idiopathic generalized epilepsy, we identify transitions between sleep stages and variation in concentration of the stress-hormone cortisol as candidate factors that influence how likely it is for epileptiform activity to occur. By including those factors into the model, we show they can explain most of the daily variability. More broadly, our approach provides a framework for better understanding what factors drive the occurrence of epileptiform activity and offers the potential to suggest experiments that can validate model predictions.

neuroscience↗

bioRxiv2022

Activating and repressing gene expression between chromosomes during stochastic fate specification

DNA elements act across long genomic distances to regulate gene expression in processes including enhancer-promoter interactions and imprinting. During the gene-regulatory phenomenon of transvection in Drosophila, DNA elements on one allele of a gene act between chromosomes to increase or decrease expression of another allele of the gene. Despite the discovery of transvection over 60 years ago, little is known about its biological role. Furthermore, how different cis regulatory DNA elements contribute to the activation or repression of transvection at distinct times during development is unclear. Here, we studied the stochastic expression of spineless (ss) in developing photoreceptors in the fly eye to understand gene activation and repression between chromosomes. We identified a biological role for transvection in regulating expression of naturally occurring ss alleles. We characterized CRISPR-engineered deletions of sequences across the ss locus and identified DNA elements required for activating and repressing transvection. We found that different enhancers participated in transvection at different times during development to promote gene expression and specify cell fates. Bringing a silencer element on a heterologous chromosome into proximity with the ss locus "reconstituted" the gene, leading to repression. Our studies show that transvection regulates gene expression via distinct DNA elements at specific timepoints in development, with implications for genome organization and architecture.

developmental biology↗

bioRxiv2022

Validated Preclinical Murine Model for Therapeutic Testing against Multidrug Resistant Pseudomonas aeruginosa

The rise in infections caused by antibiotic resistant bacteria is outpacing the development of new antibiotics. The ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) are a group of clinically important bacteria that have developed resistance to multiple antibiotics and are commonly referred to as multidrug resistant (MDR). The medical and research communities have recognized that without new antimicrobials, infections by MDR bacteria will soon become a leading cause of morbidity and mortality. Therefore, there is an ever growing need to expedite the development of novel antimicrobials to combat these infections. Toward this end, we set out to refine an existing murine model of pulmonary Pseudomonas aeruginosa infection to generate a robust preclinical tool that can be used to rapidly and accurately predict novel antimicrobial efficacy. This refinement was achieved by characterizing the virulence of a panel of genetically diverse MDR P. aeruginosa strains in this model, both by LD50 analysis and natural history studies. Further, we defined two antibiotic regimens (aztreonam and amikacin) that can be used a comparators during the future evaluation of novel antimicrobials, and validated that the model can effectively differentiate between successful and unsuccessful treatment as predicted by in vitro inhibitory data. This validated model represents an important tool in our arsenal to develop new therapies to combat MDR P. aeruginosa, with the ability to provide rapid preclinical evaluation of novel antimicrobials that can also serve to support data from clinical studies during the investigational drug development process.

microbiology↗

bioRxiv2022

Aotus nancymaae model predicts human immune response to the placental malaria vaccine candidate VAR2CSA

Placental malaria vaccines (PMV) are being developed to prevent severe sequelae of placental malaria (PM) in pregnant women and their offspring. The leading candidate vaccine antigen VAR2CSA mediates parasite binding to placental receptor chondroitin sulfate A (CSA). Despite promising results in small animal studies, recent human trials of the first two PMV candidates (PAMVAC and PRIMVAC) generated limited cross-reactivity and cross-inhibitory activity to heterologous parasites. Here, we immunized Aotus nancymaae monkeys with three PMV candidates (PAMVAC, PRIMVAC and ID1-ID2a_M1010) adjuvanted with Alhydrogel(R), and exploited the model to investigate boosting of functional vaccine responses during PM episodes as well as with nanoparticle antigens. PMV candidates induced high levels of antigen-specific IgG with significant cross-reactivity across PMV antigens by ELISA. Conversely, PMV antibodies recognized native VAR2CSA and blocked CSA-adhesion of only homologous parasites and not heterologous parasites. PM episodes did not significantly boost VAR2CSA antibody levels or serum functional activity; nanoparticle and monomer antigens alike boosted serum reactivity but not functional activities. Overall, PMV candidates induced functional antibodies with limited heterologous activity in Aotus monkeys, similar to responses reported in humans. The Aotus model appears suitable for preclinical down-selection of PMV candidates and assessment of antibody boosting by PM episodes. Research in Context Evidence before this studyThe Plasmodium falciparum erythrocyte membrane protein VAR2CSA is the leading vaccine candidate antigen to protect pregnant women against placental malaria (PM), which causes serious adverse pregnancy outcomes particularly in first-time mothers living in malaria-endemic areas. Two VAR2CSA-based vaccines (PAMVAC and PRIMVAC) induced strong heterologous functional antibodies in small animals, but induced antibodies with limited cross-inhibitory functional activity in human clinical trials. These observations highlighted the need to establish new animal models that could better recapitulate human pathogenesis and immunity. In ongoing development of a nonhuman primate model for PM, we established an Aotus nancymaae model susceptible to P. falciparum infection during pregnancy that reproduces all the immunoparasitological and histological features of human PM. In this study, we explore the new Aotus model as a platform for evaluating PM vaccine (PMV) immunogenicity and for boosting of vaccine responses during PM episodes. Added value of this studyIn this manuscript, we demonstrate that PMV (including PAMVAC and PRIMVAC) are immunogenic in Aotus monkeys, inducing antibodies with mainly homologous and little heterologous functional activity, as seen in humans but contrary to preclinical reports on these vaccines in small animals. Implications of all the available evidenceOur findings suggest Aotus is a suitable model to assess immunogenicity of VAR2CSA-derived vaccines, in contrast to small animal models. PMV data from human trials and Aotus monkeys suggest that improvements to current VAR2CSA immunogens and/or adjuvants are needed to enhance protective antibody responses, as are studies that evaluate the potential for natural infection to boost vaccine antibody in pregnancy. Therefore, the Aotus PM model may be useful to assess second-generation PMVs seeking to increase strain-transcending activity and to prioritize these for further clinical development.

immunology↗

bioRxiv2021

Temporally dynamic antagonism between transcription and chromatin compaction controls stochastic photoreceptor specification

Stochastic mechanisms diversify cell fates during development. How cells randomly choose between two or more fates remains poorly understood. In the Drosophila eye, the random mosaic of two R7 photoreceptor subtypes is determined by expression of the transcription factor Spineless (Ss). Here, we investigated how cis-regulatory elements and trans factors regulate nascent transcriptional activity and chromatin compaction at the ss gene locus during R7 development. We find that the ss locus is in a compact state in undifferentiated cells. An early enhancer drives ss transcription in all R7 precursors to open the ss locus. In differentiating cells, transcription ceases and the ss locus stochastically remains open or compacts. In SsON R7s, ss is open and competent for activation by a late enhancer, whereas in SsOFF R7s, ss is compact and repression prevents expression. Our results suggest that a temporally dynamic antagonism, in which transcription drives decompaction and then compaction represses transcription, controls stochastic cell fate specification.

developmental biology↗

bioRxiv2021

Transfer rate of enveloped and non-enveloped viruses between fingerpads and surfaces

Fomites can represent a reservoir for pathogens, which may be subsequently transferred from surfaces to skin. In this study we aim to understand how different factors (including virus type, surface type, time since last handwash, and direction of transfer) affect virus transfer rates, defined as the fraction of virus transferred, between fingerpads and fomites. To determine this, 360 transfer events were performed with 20 volunteers using Phi6 (a surrogate for enveloped viruses) and MS2 (a surrogate for non-enveloped viruses), and three clean surfaces (stainless steel, painted wood, and plastic). Considering all transfer events (all surfaces and both transfer directions combined), the mean transfer rates of Phi6 and MS2 were 0.17 and 0.26, respectively. Transfer of MS2 was significantly higher than Phi6 (P<0.05). Surface type was a significant factor that affected the transfer rate of Phi6: Phi6 is more easily transferred to and from stainless steel and plastic than to and from painted wood. Direction of transfer was a significant factor affecting MS2 transfer rates: MS2 is more easily transferred from surfaces to fingerpads than from fingerpads to surfaces. Data from these virus transfer events, and subsequent transfer rate distributions, provide information which can be used to refine quantitative microbial risk assessments. This study is the first to provide a large-scale data set of transfer events with a surrogate for enveloped viruses, which extends the reach of the study to the role of fomites in the transmission of human enveloped viruses like influenza and SARS-CoV-2. ImportanceThis study created the first large-scale data set for the transfer of enveloped viruses between skin and surfaces. The data set produced by this study provides information on modelling the distribution of enveloped and non-enveloped virus transfer rates, which can aid in the implementation of risk assessment models in the future. Additionally, enveloped and non enveloped viruses were applied to experimental surfaces in an equivalent matrix to avoid matrix effects, so results between different viral species can be directly compared without confounding effects of different matrices. Our results indicating how virus type, surface type, time since last handwash, and direction of transfer affect virus transfer rates can be used in decision-making processes to lower the risk of viral infection from transmission through fomites.

microbiology↗

bioRxiv2020

The histidine phosphotransfer AHP4 plays a negative role in Arabidopsis plant response to drought

Cytokinin plays an important role in plant stress responses via a multistep signaling pathway, involving the histidine phosphotransfer proteins (HPs). In Arabidopsis thaliana, the AHP2, AHP3 and AHP5 proteins are known to impact drought responses; however, the role of AHP4 in drought adaptation remains undetermined. In the present study, using a loss-of-function approach we showed that AHP4 possesses a negative regulatory role in Arabidopsiss response to drought. This is evidenced by both higher survival rates of ahp4 than wild-type (WT) plants under drought conditions, and the down-regulated AHP4 expression in WT during periods of dehydration. Comparative transcriptome analysis of ahp4 and WT plants revealed AHP4-mediated expression of several dehydration- and/or abscisic acid (ABA)-responsive genes involved in regulation of various physiological and biochemical processes important for plant drought acclimation. In comparison with WT, ahp4 plants showed increased wax crystal accumulation in stems, thicker cuticles in leaves, greater sensitivity to exogenous ABA at germination, narrow stomatal apertures, heightened leaf temperatures during dehydration, and longer root length under osmotic stress. Additionally, ahp4 plants showed greater photosynthetic efficiency, lower levels of reactive oxygen species (ROS), reduced electrolyte leakage and lipid peroxidation, and increased anthocyanin contents under drought, when compared with WT. These differences displayed in ahp4 plants are likely due to up-regulation of genes that encode enzymes involved in ROS-scavenging and non-enzymatic antioxidant metabolism. The role of AHP4 in negative regulation of multiple protective mechanisms associated with drought tolerance could make editing of AHP4 a promising approach for the production of drought-tolerant crop plants. Significance statementLoss-of-function analysis of the cytokinin signaling member AHP4 revealed its function in Arabidopsis adaptation to drought as a negative regulator, affecting various physiological and biochemical processes by modulating the expression of a large set of genes potentially in a crosstalk with ABA. AHP4 and its homologs are promising candidates for gene editing to develop drought-tolerant crop cultivars.

plant biology↗

bioRxiv2020

CX3CR1 Engagement by Respiratory Syncytial Virus Leads to Induction of Nucleolin and Dysregulation of Cilia-related Genes

Respiratory syncytial virus (RSV) contains a conserved CX3C motif on the ectodomain of the G-protein. The motif has been indicated as facilitating attachment of the virus to the host initiating infection via the human CX3CR1 receptor. The natural CX3CR1 ligand, CX3CL1, has been shown to induce signaling pathways resulting in transcriptional changes in the host cells. We hypothesize that binding of RSV to CX3CR1 via CX3C leads to transcriptional changes in host epithelial cells. Using transcriptomic analysis, the effect of CX3CR1 engagement by RSV was investigated. Normal human bronchial epithelial (NHBE) cells were infected with RSV virus containing either wildtype G-protein, or a mutant virus containing a CX4C mutation in the G-protein. RNA sequencing was performed on mock and 4-days-post-infected cultures. NHBE cultures were also treated with purified recombinant wild-type A2 G-protein. Here we report that RSV infection resulted in significant changes in the levels 766 transcripts. Many nuclear associated proteins were upregulated in the WT group, including Nucleolin. Alternatively, cilia-associated genes, including CC2D2A and CFAP221 (PCDP1), were downregulated. The addition of recombinant G-protein to the culture lead to the suppression of cilia-related genes while also inducing Nucleolin. Mutation of the CX3C motif (CX4C) reversed these effects on transcription decreasing nucleolin induction and lessening the suppression of cilia-related transcripts in culture. Furthermore, immunohistochemical staining demonstrated decreases in in ciliated cells and altered morphology. Therefore, it appears that engagement of CX3CR1 leads to induction of genes necessary for RSV entry as well as dysregulation of genes associated with cilia function. ImportanceRespiratory Syncytial Virus (RSV) has an enormous impact on infants and the elderly including increased fatality rates and potential for causing lifelong lung problems. Humans become infected with RSV through the inhalation of viral particles exhaled from an infected individual. These virus particles contain specific proteins that the virus uses to attach to human ciliated lung epithelial cells, initiating infection. Two viral proteins, G-protein and F-protein, have been shown to bind to human CX3CR1and Nucleolin, respectively. Here we show that the G-protein induces Nucleolin and suppresses gene transcripts specific to ciliated cells. Furthermore, we show that mutation of the CX3C-motif on the G-protein, CX4C, reverses these transcriptional changes.

microbiology↗

bioRxiv2020

Pooling nasopharyngeal swab specimens to increase testing capacity for SARS-CoV-2

The recent emergence of SARS-CoV-2 has lead to a global pandemic of unprecedented proportions. Current diagnosis of COVID-19 relies on the detection of SARS-CoV-2 RNA by RT-PCR in upper and lower respiratory specimens. While sensitive and specific, these RT-PCR assays require considerable supplies and reagents, which are often limited during global pandemics and surge testing. Here, we show that a nasopharyngeal swab pooling strategy can detect a single positive sample in pools of up to 10 samples without sacrificing RT-PCR sensitivity and specificity. We also report that this pooling strategy can be applied to rapid, moderate complexity assays, such as the BioFire COVID-19 test. Implementing a pooling strategy can significantly increase laboratory testing capacity while simultaneously reducing turnaround times for rapid identification and isolation of positive COVID-19 cases in high risk populations.

microbiology↗

bioRxiv2020

Controls on and consequences of specific leaf area variation with permafrost depth in a boreal forest

Specific leaf area (SLA, leaf area per unit dry mass) is a key canopy structural characteristic, a measure of photosynthetic capacity, and an important input into many terrestrial process models. Although many studies have examined SLA variation, relatively few data exist from high latitude, climate-sensitive permafrost regions. We measured SLA and soil and topographic properties across a boreal forest permafrost transition, in which forest composition changed as permafrost deepened from 54 to >150 cm over 75 m hillslope transects in Caribou-Poker Creeks Research Watershed, Alaska. We characterized both linear and threshold relationships between topographic and edaphic variables and SLA and developed a conceptual model of these relationships. We found that the depth of the soil active layer above permafrost was significantly and positively correlated with SLA for both coniferous and deciduous boreal tree species. Intraspecific SLA variation was associated with a fivefold increase in net primary production, suggesting that changes in active layer depth due to permafrost thaw could strongly influence ecosystem productivity. While this is an exploratory study to begin understanding SLA variation in a non-contiguous permafrost system, our results indicate the need for more extensive evaluation across larger spatial domains. These empirical relationships and associated uncertainty can be incorporated into ecosystem models that use dynamic traits, improving our ability to predict ecosystem-level carbon cycling responses to ongoing climate change.

ecology↗