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Davis, A.

Publications and source records attributed to Davis, A..

At least 37 records · Page 2Linked to original sources

Induction of a Muller glial-specific protective pathway safeguards the retina from diabetes induced damage

Diabetes can lead to cell-type-specific responses in the retina, including vascular lesions, glial dysfunction and neurodegeneration, all of which contribute to retinopathy. However, the molecular mechanisms underlying these cell type-specific responses, and the cell types that are sensitive to diabetes have not been fully elucidated. Employing single cell transcriptomic analyses, we profiled the transcriptional changes induced by diabetes in different retinal cell types in diabetic rat models as the disease progressed. Rod photoreceptors, a subtype of amacrine interneurons, and Muller glial cells exhibited rapid responses to diabetes at the transcript levels. Genes associated with ion regulation were upregulated in all three cell types, suggesting a common response to diabetes. Furthermore, focused studies revealed that while Muller glial cells initially increased the expression of genes playing protective roles, they cannot sustain this beneficial effect as the disease progressed. We explored one of the candidate protective genes, Zinc finger protein 36 homolog (Zfp36), and observed that depleting Zfp36 in rat Muller glial cells in vivo using AAV-based tools exacerbated early diabetes-induced phenotypes, including gliosis, neurodegeneration, and vascular defects. Notably, the over-expression of Zfp36 slowed the development of phenotypes associated with diabetic retinopathy. In summary, this work unveiled retinal cell types that are sensitive to diabetes and demonstrated that Muller glial cells can mount protective responses through Zfp36. The failure to maintain Zfp36 levels contributes to the development of diabetic retinopathy.

neuroscience↗

The reparative immunologic consequences of stem cell transplantation as a cellular therapy for refractory Crohn's disease

BackgroundTreatment strategies for Crohns disease (CD) suppress diverse inflammatory pathways but many patients remain refractory to treatment. Autologous hematopoietic stem cell transplantation (SCT) has emerged as a therapy for medically refractory CD. SCT was developed to rescue cancer patients from myelosuppressive chemotherapy but its use for CD and other immune diseases necessitates reimagining SCT as a cellular therapy that restores appropriately responsive immune cell populations from hematopoietic progenitors in the stem cell autograft (i.e. immune "reset"). Here we present a paradigm to understand SCT as a cellular therapy for immune diseases and reveal how SCT re-establishes cellular immunity utilizing high-dimensional cellular phenotyping and functional studies of the stem cell grafts. MethodsImmunophenotyping using CyTOF, single cell RNA sequencing (scRNA-seq) and T cell receptor (TCR) sequencing was performed on peripheral blood and intestinal tissue samples from refractory CD patients who underwent SCT. The stem cell graft from these patients was analyzed using flow cytometry and functionally interrogated using a murine model for engraftment. ResultsOur study revealed a remodeling of intestinal macrophages capable of supporting mucosal healing that was independently validated using multimodal studies of immune reconstitution events including CyTOF and scRNA-seq. Functional interrogation of hematopoietic stem cells (HSCs) using a xenograft model demonstrated that HSCs shape the timing of immune reconstitution, the selected reconstitution of specific cell lineages and potentially the clinical efficacy of SCT. ConclusionsThese studies indicate that SCT serves as a myeloid-directed cellular therapy re-establishing homeostatic intestinal macrophages that support intestinal healing and suggest refractory CD evolves from impairment of restorative functions in myeloid cells. Furthermore, we report heterogeneity among HSCs from CD patients which may drive SCT outcomes and suggests an unrecognized impact of CD pathophysiology on HSC in the marrow niche.

immunology↗

Infraslow dynamic patterns in human cortical networks track a spectrum of external to internal attention

Early efforts to understand the human cerebral cortex focused on localization of function, assigning functional roles to specific brain regions. More recent evidence depicts the cortex as a dynamic system, organized into flexible networks with patterns of spatiotemporal activity corresponding to attentional demands. In functional MRI (fMRI), dynamic analysis of such spatiotemporal patterns is highly promising for providing non-invasive biomarkers of neurodegenerative diseases and neural disorders. However, there is no established neurotypical spectrum to interpret the burgeoning literature of dynamic functional connectivity from fMRI across attentional states. In the present study, we apply dynamic analysis of network-scale spatiotemporal patterns in a range of fMRI datasets across numerous tasks including a left-right moving dot task, visual working memory tasks, congruence tasks, multiple resting state datasets, mindfulness meditators, and subjects watching TV. We find that cortical networks show shifts in dynamic functional connectivity across a spectrum that tracks the level of external to internal attention demanded by these tasks. Dynamics of networks often grouped into a single task positive network show divergent responses along this axis of attention, consistent with evidence that definitions of a single task positive network are misleading. Additionally, somatosensory and visual networks exhibit strong phase shifting along this spectrum of attention. Results were robust on a group and individual level, further establishing network dynamics as a potential individual biomarker. To our knowledge, this represents the first study of its kind to generate a spectrum of dynamic network relationships across such an axis of attention. Significance StatementThis study provides significant insight into how cortical dynamics shift along a spectrum of external vs internal attention. Association and sensory networks show shifts in their relationship with the default mode network (DMN) along this spectrum. Notably, the constituent networks of the task positive network (TPN), such as the DAN, frontoparietal network (FPN), and ventral attention network (VAN) show divergent responses along this spectrum, indicating that definitions of a single "task positive" network are misleading. This is one of the first studies of large-scale spatiotemporal dynamics across such a breadth of tasks. These results provide a neurotypical reference spanning an axis of attention to interpret the growing functional dynamics literature and to help characterize functional dynamics as a potential biomarker.

neuroscience↗

Predicting the Purity of Multispecific Antibodies From Sequence Using Machine Learning: Methods and Applications

Multispecific antibodies are prominent therapeutic agents, but many molecular formats and drug candidates that show promise during molecular discovery stages cannot be scaled up and developed into drugs due to inadequate developability. During the discovery stages, the selection of molecule format(s), molecule design, purity, and initial physiochemical stability testing criteria largely rely on scientists experience. Machine learning, however, can identify hidden trends in large datasets, aiding in the selection of drug candidates with improved developability. In this study, we present a machine learning approach to predict antibody purity, measured by the percentage of monomer after protein A purification. Using the amino acid sequences of variable regions, molecular formats, germlines and germline pairings, and calculated physiochemical properties as inputs, machine learning models were trained to predict the percentage of monomer for a given multispecific antibody (Figure 1). The dataset employed in this study consists of [~]500 multi-specific antibodies generated during BIs internal drug discovery programs. Our results indicate that machine learning, when applied to sequence, germline, and format data, can effectively predict antibody percentage of monomer. Incorporating this approach into high-throughput multispecific antibody screening processes can save time and resources by reducing the need to test a large subset of potentially unstable antibodies. While this study focused on percentage of monomer as a test case, similar approaches can be employed to predict other antibody properties, such as melting temperature (Tm), hydrophobicity (aHIC), and solution stability properties (AC-SINS). O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=47 SRC="FIGDIR/small/570217v1_fig1.gif" ALT="Figure 1"> View larger version (11K): org.highwire.dtl.DTLVardef@f23246org.highwire.dtl.DTLVardef@c2b81aorg.highwire.dtl.DTLVardef@1c4e59dorg.highwire.dtl.DTLVardef@1bed683_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1C_FLOATNO Overview of ML model for predicting multispecific antibody purity from sequence, germline and format information. C_FIG

molecular biology↗

SenPred: A single-cell RNA sequencing-based machine learning pipeline to classify senescent cells for the detection of an in vivo senescent cell burden

Senescence classification is an acknowledged challenge within the field, as markers are cell-type and context dependent. Currently, multiple morphological and immunofluorescence markers are required for senescent cell identification. However, emerging scRNA-seq datasets have enabled increased understanding of the heterogeneity of senescence. Here we present SenPred, a machine-learning pipeline which can identify senescence based on single-cell transcriptomics. Using scRNA-seq of both 2D and 3D deeply senescent fibroblasts, the model predicts intra-experimental and inter-experimental fibroblast senescence to a high degree of accuracy (>99% true positives). We position this as a proof-of-concept study, with the goal of building a holistic model to detect multiple senescent subtypes. Importantly, utilising scRNA-seq datasets from deeply senescent fibroblasts grown in 3D refines our ML model leading to improved detection of senescent cells in vivo. This has allowed for detection of an in vivo senescent cell burden, which could have broader implications for the treatment of age-related morbidities.

cell biology↗

Intraspecific trait variation modulates the temperature effect on elemental quotas and stoichiometry in marine Synechococcus

Diverse phytoplankton modulate the coupling between the ocean carbon and nutrient cycles through life-history traits such as cell size, elemental quotas, and ratios. Biodiversity is mostly considered at broad functional levels, but major phytoplankton lineages are themselves highly diverse. As an example, Synechococcus is found in nearly all ocean regions and contain extensive intraspecific variation. Here, we grew four closely related Synechococcus isolates in semi-continuous cultures across a range of temperatures (16-25{degrees}C) to quantify for the relative role of intraspecific trait variation vs. environmental change. We report differences in cell size (p<0.01) as a function of strain and clade (p<0.01). The carbon (QC), nitrogen (QN), and phosphorus (QP) cell quotas all increased with cell size. Furthermore, cell size has an inverse relationship to growth rate. Within our experimental design, temperature alone had a weak physiological effect on cell quota and elemental ratios. Instead, we find systemic intraspecific variance of C:N:P, with cell size and N:P having an inverse relationship. Our results suggest a key role for intraspecific life history traits in determining elemental quotas and stoichiometry. Thus, the extensive biodiversity harbored within many lineages may modulate the impact of environmental change on ocean biogeochemical cycles.

ecology↗

Histone chaperone HIRA, Promyelocytic Leukemia (PML) protein and p62/SQSTM1 coordinate to regulate inflammation during cell senescence and aging.

Cellular senescence, a stress-induced stable proliferation arrest associated with an inflammatory Senescence-Associated Secretory Phenotype (SASP), is a cause of aging. In senescent cells, Cytoplasmic Chromatin Fragments (CCFs) activate SASP via the anti-viral cGAS/STING pathway. PML protein organizes PML nuclear bodies (NBs), also involved in senescence and anti-viral immunity. The HIRA histone H3.3 chaperone localizes to PML NBs in senescent cells. Here, we show that HIRA and PML are essential for SASP expression, tightly linked to HIRAs localization to PML NBs. Inactivation of HIRA does not directly block expression of NF-{kappa}B target genes. Instead, an H3.3-independent HIRA function activates SASP through a CCF-cGAS-STING-TBK1-NF-{kappa}B pathway. HIRA physically interacts with p62/SQSTM1, an autophagy regulator and negative SASP regulator. HIRA and p62 co-localize in PML NBs, linked to their antagonistic regulation of SASP, with PML NBs controlling their spatial configuration. These results outline a role for HIRA and PML in regulation of SASP.

cell biology↗

Resolving clonal substructure from single cell genomic data using CopyKit

High-throughput methods for single cell copy number sequencing have enabled the profiling of thousands of cells in parallel, yet there remains a significant bottleneck for data analysis. Here we present CopyKit, a comprehensive set of computational methods for the pre-processing and analysis of single cell copy number data to resolve clonal substructure and reconstruct genetic lineages in tumors. We performed single cell DNA sequencing of 2977 cells from multiple spatial regions in two liver metastasis and 7365 cells from three primary tumors with matched metastatic tissues. In the liver metastases, CopyKit resolved clonal substructure in different spatial regions, which revealed both clonal intermixing and spatial segregation in the tumor mass. In the matched metastatic colorectal and breast cancers, CopyKit resolved metastatic lineages and identified subclones and genomic events that were associated with metastases. These applications show that CopyKit is comprehensive tool for resolving copy number substructure in tumors.

genomics↗

Multiple metals influence distinct properties of the Arabidopsis circadian clock

Circadian rhythms coordinate endogenous events with external signals, and are essential to biological function. When environmental contaminants affect these rhythms, the organism may experience fitness consequences such as reduced growth or increased susceptibility to pathogens. In their natural environment plants may be exposed to a wide range of industrial and agricultural pollutants. Here, we investigate how the addition of various metal salts to the environment can impact plant-circadian rhythms, via the promoter:luciferase system. The consequences of these environmental changes were found to be varied and complex. Therefore, in addition to Fourier-based analyses, we apply novel wavelet-based spectral hypothesis testing and clustering methodologies to organize and understand the data. We are able to classify broad sets of responses to environmental contaminants, including pollutants which increase, or decrease, the period, or which induce a lack of precision or disrupt any meaningful periodicity. The methods are general, and may be applied to discover common responses and hidden structures within a wide range of biological time series data.

plant biology↗

The retromer complex regulates C. elegans development and mammalian ciliogenesis

The mammalian retromer is comprised of subunits VPS26, VPS29 and VPS35, and a more loosely-associated sorting nexin (SNX) heterodimer. Despite known roles for the retromer in multiple trafficking events in yeast and mammalian cells, its role in development is poorly understood, and its potential function in primary ciliogenesis remains unknown. Using CRISPR-Cas9 editing, we demonstrated that vps-26 homozygous knockout C. elegans have reduced brood sizes and impaired vulval development, as well as decreased body length which has been linked to defects in primary ciliogenesis. Since many endocytic proteins are implicated in the generation of primary cilia, we addressed whether the retromer regulates ciliogenesis in mammalian cells. We observed VPS35 localized to the primary cilium, and depletion of VPS26, VPS35 or SNX1/SNX5 led to decreased ciliogenesis. Retromer also coimmunoprecipitated with the capping protein, CP110, and was required for its removal from the mother centriole. Herein, we characterize new roles for the retromer in C. elegans development and in the regulation of ciliogenesis in mammalian cells, and suggest a novel role for the retromer in CP110 removal from the mother centriole.

cell biology↗

A SARS-CoV-2 targeted siRNA-nanoparticle therapy for COVID-19

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in humans. Despite several emerging vaccines, there remains no verifiable therapeutic targeted specifically to the virus. Here we present a highly effective siRNA therapeutic against SARS-CoV-2 infection using a novel lipid nanoparticle delivery system. Multiple small-interfering RNAs (siRNAs) targeting highly conserved regions of the SARS-CoV-2 virus were screened and three candidate siRNAs emerged that effectively inhibit virus by greater than 90% either alone or in combination with one another. We simultaneously developed and screened two novel lipid nanoparticle formulations for the delivery of these candidate siRNA therapeutics to the lungs, an organ that incurs immense damage during SARS-CoV-2 infection. Encapsulation of siRNAs in these LNPs followed by in vivo injection demonstrated robust repression of virus in the lungs and a pronounced survival advantage to the treated mice. Our LNP-siRNA approaches are scalable and can be administered upon the first sign of SARS-CoV-2 infection in humans. We suggest that an siRNA-LNP therapeutic approach could prove highly useful in treating COVID-19 disease as an adjunctive therapy to current vaccine strategies.

synthetic biology↗

Respiratory bacteria stabilize and promote airborne transmission of influenza A virus

Influenza A virus (IAV) is a major pathogen of the human respiratory tract where the virus co-exists and interacts with bacterial populations comprising the respiratory microbiome. Synergies between IAV and respiratory bacterial pathogens promote enhanced inflammation and disease burden that exacerbate morbidity and mortality. We demonstrate that direct interactions between IAV and encapsulated bacteria commonly found in the respiratory tract promote environmental stability and infectivity of IAV. Antibiotic-mediated depletion of the respiratory bacterial flora abrogated IAV transmission in ferret models, indicating that these viral-bacterial interactions are operative for airborne transmission of IAV. Restoring IAV airborne transmission in antibiotic treated ferrets by co-infection with Streptococcus pneumoniae confirmed a role for specific members of the bacterial respiratory community in promoting IAV transmission. These results implicate a role for the bacterial respiratory flora in promoting airborne transmission of IAV.

microbiology↗

Evaluation of the functional role of the maize Glossy2 and Glossy2-like genes in cuticular lipid deposition

Plant epidermal cells express unique molecular machinery that juxtapose the assembly of intracellular lipid components and the unique extracellular cuticular lipids that are unidirectionally secreted to plant surfaces. In maize (Zea mays L.), mutations at the glossy2 (gl2) locus affect the deposition of extracellular cuticular lipids. Sequence-based genome scanning identified a novel gl2 homolog in the maize genome, Gl2-like. Sequence homology identifies that both the Gl2-like and Gl2 genes are members of the BAHD superfamily of acyltransferases, with close sequence homology to the Arabidopsis CER2 gene. Transgenic experiments demonstrate that Gl2-like and Gl2 functionally complement the Arabidopsis cer2 mutation, with differential impacts on the cuticular lipids and the lipidome of the plant, particularly affecting the longer alkyl chain acyl lipids, particularly at the 32-carbon chain length. Site-directed mutagenesis of the putative BAHD catalytic HXXXDX-motif indicates that Gl2-like requires this catalytic capability to fully complement the cer2 function, but Gl2 can accomplish this without the need for this catalytic motif. These findings demonstrate that both Gl2 and Gl2-like overlap in their cuticular lipid function, however the two genes have evolutionary diverged to acquire non-overlapping functions. One-sentence summaryTransgenesis dissection of the functional roles of the maize Glossy2 and Glossy2-Like genes in cuticular lipid deposition.

biochemistry↗

Classification and characterisation of livestock production systems in northern Tanzania

Livestock keepers in sub-Saharan Africa face a growing range of pressures, including climate change, land loss, restrictive policies, and population increase. Widespread adaptation in response to such pressures can lead to the emergence of new, non-traditional typologies of livestock production. We sought to characterise livestock production systems in northern Tanzania, a region undergoing rapid social, economic, and environmental change. Questionnaire and spatial data were collected from 404 livestock-keeping households in 21 villages in Arusha and Manyara Regions in 2016. Multiple factor analysis and hierarchical cluster analysis were used to classify households into livestock production systems based on household-level characteristics. Indicators of vulnerability, including household-level reports of hunger, illness, livestock loss, land loss and crop losses were compared between production systems. Three distinct clusters emerged through this process. The ethnic, environmental and livestock management characteristics of households in each cluster broadly mapped onto traditional definitions of pastoral, agro-pastoral and smallholder livestock production in the region, suggesting that this quantitative classification system is complementary to more qualitative classification methods. Our findings also suggest that traditional systems of livestock production continue to persist in northern Tanzania. Nonetheless, we found indicators of substantial change within livestock production systems, most notably the adoption of crop agriculture in the majority of pastoral households. Smallholder households were less likely than either pastoral or agro-pastoral households to report hunger, illness, and livestock, land or crop losses. Livelihoods that rely solely on livestock are relatively rare in northern Tanzania, which represents an important shift in production in the region, particularly among pastoralists. Policy initiatives to improve household and community well-being should recognise the continuing distinctiveness of traditional livestock production systems in the region.

systems biology↗

Cell type- and stage-specific expression of Otx2 is coordinated by a cohort of transcription factors and multiple cis-regulatory modules in the retina

Transcription factors (TFs) are often used repeatedly during development and homeostasis to control distinct processes in the same and/or different cellular contexts. Considering the limited number of TFs in the genome and the tremendous number of events that need to be regulated, re-use of TFs is an advantageous strategy. However, the mechanisms that control the activation of TFs in different cell types and at different stages of development remain unclear. The neural retina serves as a model of the development of a complex tissue. We used this system to analyze how expression of the homeobox TF, Orthodenticle homeobox 2 (Otx2), is regulated in a cell type- and stage-specific manner during retinogenesis. We identified seven Otx2 cis-regulatory modules (CRMs), among which the O5, O7 and O9 CRMs mark three distinct cellular contexts of Otx2 expression. These include mature bipolar interneurons, photoreceptors, and retinal progenitor/precursor cells. We discovered that Otx2, Crx and Sox2, which are well-known TFs regulating retinal development, bind to and activate the O5, O7 or O9 CRMs respectively. The chromatin status of these three CRMs was found to be distinct in vivo in different retinal cell types and at different stages, as revealed by ATAC-seq and DNase-seq analyses. We conclude that retinal cells utilize a cohort of TFs with different expression patterns, and multiple CRMs with different chromatin configurations, to precisely regulate the expression of Otx2 in a cell type- and stage-specific manner in the retina.

developmental biology↗

Optimal spatial prioritization of control resources for elimination of invasive species under demographic uncertainty

Populations of invasive species often spread heterogeneously across a landscape, consisting of local populations that cluster in space but are connected by dispersal. A fundamental dilemma for invasive species control is how to optimally allocate limited fiscal resources across local populations. Theoretical work based on perfect knowledge of demographic connectivity suggests that targeting local populations from which migrants originate (sources) can be optimal. However, demographic processes such as abundance and dispersal can be highly uncertain, and the relationship between local population density and damage costs (damage function) is rarely known. We used a metapopulation model to understand how observational uncertainty in abundance and connectivity, and imperfect knowledge of the damage function, affect return on investment (ROI) for optimal control strategies. Budget, observational uncertainty, and the damage function had strong effects on the optimal resource allocation strategy. Uncertainty in dispersal probability was the least important determinant of ROI. The damage function determined which resource prioritization strategy was optimal when connectivity was symmetric but not when it was asymmetric. When connectivity was asymmetric, prioritizing source populations had a higher ROI than allocating effort equally across local populations, regardless of the damage function, but uncertainty in connectivity structure and abundance reduced ROI of the optimal prioritization strategy by 57% on average depending on the control budget. With low budgets (monthly removal rate of 6.7% of population), there was little advantage to prioritizing resources, especially when connectivity was high or symmetric, and observational uncertainty had only minor effects on ROI. Allotting funding for improved monitoring appeared to be most important when budgets were moderate (monthly removal of 13-20% of the population). Our result showed that multiple sources of observational uncertainty should be considered concurrently for optimizing ROI. Accurate estimates of connectivity direction and abundance were more important than accurate estimates of dispersal rates. Developing cost-effective surveillance methods to reduce observational uncertainties, and quantitative frameworks for determining how resources should be spatially apportioned to multiple monitoring and control activities are important and challenging future directions for optimizing ROI for invasive species control programs.

ecology↗

Photoperiod sensing of the circadian clock is controlled by ELF3 and GI

ELF3 and GI are two important components of the Arabidopsis circadian clock. They are not only essential for the oscillator function but are also pivotal in mediating light inputs to the oscillator. Lack of either results in a defective oscillator causing severely compromised output pathways, such as photoperiodic flowering and hypocotyl elongation. Although single loss of function mutants of ELF3 and GI have been well-studied, their genetic interaction remains unclear. We generated an elf3 gi double mutant to study their genetic relationship in clock-controlled growth and phase transition phenotypes. We found that ELF3 and GI repress growth differentially during the night and the day, respectively. Circadian clock assays revealed that ELF3 and GI are essential Zeitnehmers that enable the oscillator to synchronize the endogenous cellular mechanisms to external environmental signals. In their absence, the circadian oscillator fails to synchronize to the light-dark cycles even under diurnal conditions. Consequently, clock-mediated photoperiod-responsive growth and development is completely lost in plants lacking both genes, suggesting that ELF3 and GI together convey photoperiod sensing to the central oscillator. Since ELF3 and GI are conserved across flowering plants and represent important breeding and domestication targets, our data highlight the possibility of developing photoperiod-insensitive crops by adjusting the allelic combination of these two key genes.\n\nOne sentence summaryELF3 and GI are essential for circadian clock mediated photoperiod sensing.

plant biology↗

Genetic Determinants of Telomere Length in African American Youth

Telomere length (TL) is associated with numerous disease states and is affected by genetic and environmental factors. However, TL has been mostly studied in adult populations of European or Asian ancestry. These studies have identified 34 TL-associated genetic variants recently used as genetic proxies for TL. The generalizability of these associations to pediatric populations and racially diverse populations, specifically of African ancestry, remains unclear. Furthermore, six novel variants associated with TL in a population of European children have been identified but not validated. We measured TL from whole blood samples of 492 healthy African American youth (children and adolescents between 8 and 20 years old) and performed the first genome-wide association study of TL in this population. We were unable to replicate neither the 34 reported genetic associations found in adults nor the six genetic associations found in European children. However, we discovered a novel genome-wide significant association between TL and rs1483898 on chromosome 14. Our results underscore the importance of examining these genetic associations with TL in diverse pediatric populations such as African Americans.

genetics↗