Biology subjects

Green, D. R.

Publications and source records attributed to Green, D. R..

13 recordsLinked to original sources

bioRxiv2026

MakeMyFigure: An Interactive Platform for Reproducible Quantitative Data Visualization, Analysis, and Scientific Figure Construction

Reproducible data analysis and visualization are essential for reliable biological and biomedical research, yet creating high-quality, publication-ready figures often requires moving data and results between multiple analysis, visualization, and graphics tools. This fragmented, multi-layered process can make it difficult to trace how individual figure panels were generated, preserve the underlying analytical decisions, and reproduce them later. Here, we introduce MakeMyFigure, a free and open-source platform for data visualization, analysis, and creation of multi-panel scientific figures. MakeMyFigure integrates data processing, statistical analysis, visualization, and figure assembly within a single workflow. It supports a range of quantitative data formats and structures, including feature-by-sample matrices and precomputed statistical results, and provides data-aware visualization recommendations to help users select appropriate plots from a library of 38 visualization types. These capabilities allow researchers to move directly from experimental measurements to commonly used statistical analyses and graphical representations without requiring programming expertise. Eighteen statistical procedures are implemented, and their results are drawn directly onto the plot families that support statistical annotation, keeping analytical results linked to the panels they generate. Importantly, MakeMyFigure uses machine-readable JSON specifications to record the identity and checksum of the source data, the processing steps, visualization settings, and statistical parameters used to generate each figure panel. It can also save a figure as a portable package, freezing the specifications together with the data. This allows figures to be regenerated from their recorded specifications and source data, or from the package alone on another computer, rather than relying on manually reconstructed workflows. Using published datasets from several biological fields, independent statistical validation in R, and a comparison with 15 representative analysis, visualization, and figure-generation tools, we show that MakeMyFigure combines accessible, code-free figure creation with panel-level computational reproducibility. Overall, MakeMyFigure provides a unified approach for creating, documenting, and reproducing scientific figures. Source code and documentation are available at https://github.com/surPoudel/make-my-figure, https://github.com/surPoudel/make-my-figure/releases/tag/v1.1.0.

bioinformatics↗

bioRxiv2026

A Single-Cell Framework for Classifying Human Th17 Pathogenicity Links Acylcarnitine Metabolism to Non-Pathogenic Inflammation in Type 2 Diabetes

Based on in vitro and animal studies, Th17 cells are classified as pathogenic (pTh17) or non-pathogenic (nTh17), but the inability to identify these subsets in primary human samples limits translation. We developed a single-cell ELISA to enrich human Th17s, enabling transcriptomic and flow-cytometric classification. nTh17 cells predominated in Type 2 diabetes and exhibited signatures of acylcarnitine synthesis, while knockdown of CPT1A demonstrated that acylcarnitine metabolism regulates Th17 pathogenicity.

immunology↗

bioRxiv2026

Cytokines driven by caspase-1 and RIPK3 are antagonistic

Pyroptosis, apoptosis, and necroptosis are thought to provide redundant protection against intracellular pathogens. We found that mice lacking inflammasomes, caspase-8, and MLKL were highly susceptible to infection by an environmental cytosol-invasive bacterium. Surprisingly, deletion of Ripk3 completely restored resistance despite the continued absence of all three cell death pathways. The infection outcome was determined instead by the production of antagonistic cytokines arising from these pathways. Deletion of Casp8 and Mlkl initiated an effector-triggered immunity-like response, in which RIPK3 induced type I interferons causing catastrophic susceptibility by impeding neutrophil responses. Opposing this, caspase-1-dependent IL-1{beta} production counteracted these type I interferons and restored resistance. Thus, susceptibility arose not from failure of regulated cell death, but from the activation of RIPK3-driven type I interferons unopposed by caspase-1-driven IL-1{beta}. Therefore, antagonistic cytokines embedded within cell death pathway signaling, distinct from cell death itself, can dictate the immune response to intracellular infection.

immunology↗

bioRxiv2025

Suppression of non-canonical autophagy induces endothelial and cardiac dysfunction

BackgroundWhile roles for canonical autophagy in the pathophysiology of cardiovascular disease have been established, we have limited understanding of the non-canonical functions of autophagy proteins in this context. LC3-asssociated endocytosis (LANDO) is a novel non-canonical function of autophagy proteins, in which LC3 (microtubule-associated protein light chain 3) is conjugated to early endosome membranes using a portion of the canonical autophagy machinery, and functions in the endocytic recycling of several plasma membrane proteins. Here we ask whether perturbation of LANDO can promote cardiovascular pathogenesis. MethodsCardiac and endothelial functions were assessed by echocardiography and flow-mediated dilatation in mice lacking Rubicon (Rubcn-/-) or the WD domain of ATG16L1 (Atg16l1{Delta}WDki), two known effectors of LANDO. Mice with conditional depletion of Rubicon in the endothelial, myeloid and cardiomyocyte compartments were used as well. Three-dimensional murine cardiac vasculature leakiness was investigated by light sheet fluorescence microcopy. Endothelial activation induced by shear stress was characterized in vitro in primary endothelial cells isolated from murine lungs and human aortic endothelial cells. Associations between genetically predicted expression of candidate genes involved in LANDO and human cardiovascular parameters were studied in the Young Finns Study and the UK Biobank. ResultsCompared to littermate controls, young Rubcn-/- and Atg16l1{Delta}WDki mice showed a decrease in cardiac and endothelial functions, as did mice with endothelium-specific deficiency. VEGFR2 recycling to the plasma membrane and nitric oxide pathway during shear stress were disrupted in LANDO-deficient primary murine and human endothelial cells. Proteomic analysis in primary human aortic endothelial cells revealed an upregulation of intracellular hemoglobin subunit alpha (Hb-) upon shear stress, which was blunted when RUBCN was ablated. Genetic expression studies uncovered several candidate genes related to LANDO that correlated with cardiovascular parameters. These included the retromer complex subunit VPS29, disruption of which decreased Hb- expression levels in human endothelial cells. ConclusionsOur data support a pivotal role of non-canonical functions of autophagy proteins in recycling VEGFR2 upon shear stress activation in endothelial cells together with Hb- expression that may contribute to the etiology of cardiovascular diseases.

physiology↗

bioRxiv2024

Rapid metabolic regulation of a novel arginine methylation of KCa3.1 attenuates T cell exhaustion.

T cell receptor (TCR) engagement initiates the activation process, and this signaling event is regulated in multifaceted ways. Nutrient availability in the immediate niche is one such mode of regulation1-3. Here, we investigated how the availability of an essential amino acid methionine (Met) and TCR signaling might interplay in the earliest events of T cell activation to affect subsequent T cell fate and function. We found that limiting Met during only the initial 30 minutes of CD8+ T cell activation increased Ca2+ influx, Ca2+-mediated NFAT1 (Nfatc2) activation, NFAT1 promoter occupancy, and T cell exhaustion. We identified changes in the protein arginine methylome during the initial 30 min of TCR engagement and discovered a novel arginine methylation of a Ca2+-activated potassium transporter, KCa3.1, which regulates Ca2+-mediated NFAT1 signaling to ensure optimal activation. Ablation of arginine methylation in KCa3.1 led to increased NFAT1 activation, rendering T cells dysfunctional in murine tumour and infection models. Furthermore, acute Met supplementation at early stages reduced nuclear NFAT1 in tumour-infiltrating T cells and augmented their anti-tumour activity. Our findings identify a metabolic event occurring early after T cell activation that influences the subsequent fate of the cell.

immunology↗

bioRxiv2023

Phosphatidylserine clustering by membrane receptors triggers LC3-associated phagocytosis.

LC3-associated phagocytosis (LAP) represents a non-canonical function of autophagy proteins in which ATG8 family proteins (LC3 and GABARAP proteins) are lipidated onto single-membrane phagosomes as particles are engulfed by phagocytic cells1-4. LAP plays roles in innate immunity5, inflammation and anti-cancer6 responses and is initiated upon phagocytosis of particles that stimulate Toll-like receptors (TLR), Fc-receptors, and upon engulfment of dying cells6. However, how this molecular route is initiated remains elusive. Here we report that receptors that engage LAP enrich phosphatidylserine (PS) in the phagosome membrane via membrane-proximal domains that are necessary and sufficient for LAP to proceed. Subsequently, PS recruits the Rubicon-containing PI3-kinase complex to initiate the enzymatic cascade leading to LAP. Manipulation of plasma membrane PS content, PS-binding by Rubicon, or the PS-clustering domains of receptors prevents LAP and phagosome maturation. We found that pharmacologic inhibition of PS clustering promotes the ability of dendritic cells to induce anti-cancer responses to engulfed tumor cells. Therefore, the initiation of LAP represents a novel mechanism of PS-mediated signal transduction upon ligation of surface receptors.

cell biology↗

bioRxiv2023

Oxygen isotopes in orangutan teeth reveal recent and ancient climate variation

Studies of climate variation commonly rely on chemical and isotopic changes recorded in sequentially-produced growth layers, such as in corals, shells and tree rings, as well as in accretionary deposits--ice and sediment cores, and speleothems. Oxygen isotopic compositions ({delta}18O) of tooth enamel are a direct method of reconstructing environmental variation experienced by an individual animal. Here we utilize long-forming orangutan dentitions (Pongo spp.) to probe recent and ancient rainfall trends on a weekly basis over [~] 3-11 years per individual. We first demonstrate the lack of any consistent isotopic enrichment effect during exclusive nursing, supporting the use of primate first molar teeth as environmental proxies. Comparisons of {delta}18O values (n = 2016) in twelve molars from six modern Bornean and Sumatran orangutans reveal a high degree of overlap, with more consistent annual and bimodal rainfall patterns in the Sumatran individuals. Comparisons with fossil orangutan {delta}18O values (n = 955 measurements from six molars) reveal similarities between modern and late Pleistocene fossil Sumatran individuals, but differences between modern and late Pleistocene/early Holocene Bornean orangutans. These suggest drier and more open environments with reduced monsoon intensity during this earlier period in northern Borneo, consistent with other Niah Caves studies and long-term speleothem {delta}18O records in the broader region. This approach can be extended to test hypotheses about the paleoenvironments that early humans encountered in southeast Asia.

paleontology↗

bioRxiv2022

Death induced by survival gene elimination (DISE) contributes to neurotoxicity in Alzheimer's disease

Alzheimers disease (AD) is characterized by progressive neurodegeneration, but the specific events that cause cell death remain poorly understood. Death Induced by Survival gene Elimination (DISE) is a cell death mechanism mediated by short (s) RNAs acting through the RNA induced silencing complex (RISC). DISE is thus a form of RNA interference, in which G-rich 6mer seed sequences in the sRNAs (position 2-7) target hundreds of C-rich 6mer seed matches in genes essential for cell survival, resulting in the activation of cell death pathways. Here, using Argonaute precipitation and RNAseq (Ago-RP-Seq), we analyze RISC-bound sRNAs to quantify 6mer seed toxicity in several model systems. In mouse AD models and aging brain, in induced pluripotent stem cell-derived neurons from AD patients, and in cells exposed to A{beta}42 oligomers, RISC-bound sRNAs show a shift to more toxic 6mer seeds compared to controls. In contrast, in brains of "SuperAgers", humans over age 80 who have superior memory performance, RISC-bound sRNAs are shifted to more nontoxic 6mer seeds. Cells depleted of nontoxic sRNAs are sensitized to A{beta}42-induced cell death, and reintroducing nontoxic RNAs is protective. Altogether, the correlation between DISE and A{beta}42 toxicity suggests that increasing the levels of nontoxic miRNAs in the brain or blocking the activity of toxic RISC-bound sRNAs could ameliorate neurodegeneration.

neuroscience↗

bioRxiv2022

A molecular mechanism for membrane chaperoning by a late embryogenesis abundant protein

Environmental stress can result in substantial damage to proteins, membranes, and genetic material, impacting organismal survival1-3. Stress tolerance can be conferred by intrinsically disordered proteins (IDPs)4 that lack stable tertiary structure. IDPs from the large family of late embryogenesis abundant (LEA) proteins confer a fitness advantage when heterologously expressed5,6. Such protection suggests a general molecular function leading to stress tolerance, although the mechanisms remain unclear. Here, we report that a tardigrade LEA protein that confers stress tolerance in yeast acts as a molecular chaperone for the mitochondrial membrane. This protein, named HeLEA1, localizes to the mitochondrial matrix, and harbors conserved LEA sequence motifs that undergo dynamic disorder-to-helical transition upon binding to negatively charged membranes. Yeast expressing HeLEA1 show increased mitochondrial membrane fluidity, increased membrane potential, and enhanced tolerance to hyperosmotic stress under non-fermentative growth without significantly altering mitochondrial lipid composition or triggering a generic stress response. We demonstrate that membrane binding ameliorates excess surface tension, possibly by stabilizing lipid packing defects. Evolutionary analysis suggests that HeLEA1 homologs localize to different membrane-bound organelles and share similar sequence and biophysical features. We suggest that membrane chaperoning by LEA proteins represents a general biophysical solution that can operate across the domains of life.

biophysics↗

bioRxiv2022

Anti-apoptotic BH3-only proteins inhibit Bak

Bcl-2 family proteins regulate induction of intrinsic apoptosis through initiating mitochondrial outer membrane permeabilization (MOMP). Activation of the MOMP effectors Bax and Bak is controlled by interplay levels of anti-apoptotic Bcl-2 proteins (e.g. Mcl-1) and pro-apoptotic BH3-only proteins (e.g. BIM). Using a genome-wide CRISPR-dCas9 transactivation screen we identified two Bcl-2 family proteins, BNIP5 and Bcl-G, as inhibitors of Bak, but not Bax induced apoptosis. BNIP5 was able to block Bak activation in different cell types and in response to various cytotoxic therapies. The BH3 domain of BNIP5 was both necessary and sufficient to block Bak activation. Mechanistically, the BH3 domains of BNIP5 and Bcl-G act as a selective Bak activators, while not inhibiting anti-apoptotic proteins. This led to increased binding of activated Bak to Mcl-1, which prevented apoptosis engagement, identifying BNIP5 and Bcl-G as anti-apoptotic BH3-only proteins.

cell biology↗

bioRxiv2020

Polyamine Metabolism Regulates the T Cell Epigenome Through Hypusination

We report here a central role for polyamines in T cell differentiation and function. Deficiency in ornithine decarboxylase (ODC), a critical enzyme for polyamine synthesis, resulted in a profound failure of CD4+ T cells to adopt correct subset specification, underscored by ectopic expression of multiple cytokines and lineage-defining transcription factors across TH1, TH2, TH17, and Treg polarizing conditions, and enhanced colitogenic potential. T cells deficient in deoxyhypusine synthase (DHPS) or deoxyhypusine hydroxylase (DOHH), which sequentially utilize polyamines to generate hypusine, phenocopied Odc-deficient T cells, and mice in which T cells lacked Dhps or Dohh developed colitis. Polyamine-hypusine pathway enzyme deficiency caused widespread chromatin and transcriptional dysregulation accompanied by alterations in histone methylation, histone acetylation, and TCA cycle metabolites. Epigenetic modulation by 2-hydroxyglutarate, or histone acetyltransferase inhibition, restored CD4+ T cell subset specification. Thus, polyamine synthesis via hypusine is critical for maintaining the epigenome to focus TH cell subset fidelity.

immunology↗

bioRxiv2020

Dynamic metabolic reprogramming in dendritic cells: an early response to influenza infection that is essential for effector function

Infection with the influenza virus triggers an innate immune response aimed at initiating the adaptive response to halt viral replication and spread. However, the metabolic response fueling the molecular mechanisms underlying changes in innate immune cell homeostasis remain undefined. Thus, we compared the metabolic response of dendritic cells to that of those infected with active and inactive influenza A virus or treated with toll like receptor agonists. While influenza infects dendritic cells, it does not productively replicate in these cells, and therefore metabolic changes upon infection may represent an adaptive response on the part of the host cells. Using quantitative mass spectrometry along with pulse chase substrate utilization assays and metabolic flux measurements, we found global metabolic changes 17 hours post infection, including significant changes in carbon commitment via glycolysis and glutaminolysis, as well as ATP production via TCA cycle and oxidative phosphorylation. Influenza infection of dendritic cells led to a metabolic phenotype, distinct from that induced by TLR agonists, with significant resilience in terms of metabolic plasticity. We identified Myc as one transcription factor modulating this response. Restriction of either Myc activity or mitochondrial substrates resulted in significant changes in the innate immune functions of dendritic cells, including reduced motility and T cell activation. Transcriptome analysis of inflammatory dendritic cells isolated following influenza infection showed similar metabolic reprogramming occurs in vivo. Thus, early in the infection process dendritic cells respond with global metabolic restructuring that is present in lung DC 9 days following infection and impacts their effector function, suggesting that metabolic switching in dendritic cells plays a vital role in initiating the immune response to influenza infection. Author SummaryIn response to influenza infection we found that dendritic cells, cells that are critical in mounting an effective immune response, undergo a profound metabolic shift. They alter the concentration and location of hundreds of proteins, including c-MYC, mediating a shift to a highly glycolytic phenotype that is also flexible in terms of fueling respiration. Dendritic cells initiate the immune response to influenza and activate the adaptive response allowing viral clearance and manifesting immune memory for protection against subsequent infections. We found that limiting access to specific metabolic pathways or substrates diminished key immune functions. Previously we described an immediate, fixed, hypermetabolic state in infected respiratory epithelial cells. We now show the metabolic responses of epithelial and dendritic cells are distinct. Here, we also demonstrate that dendritic cells tailor their metabolic response to the pathogen or TLR stimulus. This metabolic reprogramming occurs rapidly in vitro and it is sustained in inflammatory dendritic cells in vivo for at least 9 days following influenza infection. Thus, drugs targeting metabolism are likely to have cell- and pathogen-specific activities in the context of infection. These studies open the possibility of modulating the immune response to viral infection via customizing metabolic therapy to enhance or diminish the function of specific cells.

immunology↗

bioRxiv2019

Colour preferences of Spotted Wing Drosophila, Drosophila suzukii, under field conditions in various crops

The authors have withdrawn this manuscript because of conflicting authorship views of an unnamed person claiming authorship. Therefore, the authors do not wish this work to be cited as reference for the project.\n\nHowever, the original results of the withdrawn preprint remain valid. If you have any questions, please contact the corresponding author (Johannes.fahrentrapp@zhaw.ch).

ecology↗