Biology subjects

Santiago, A.

Publications and source records attributed to Santiago, A..

17 recordsLinked to original sources

bioRxiv2026

SlMYB21 and SlMYB24 cooperatively regulate petal coloration and movement in Solanum lycopersicum

In seed plants, reproductive success depends on the precise coordination of floral organ development. Here, we identify and characterize the Solanum lycopersicum transcription factor (TF) SlMYB24 as a member of the R2R3-MYB subgroup 19. While Slmyb24 mutants exhibited no obvious phenotypic alterations, the previously characterized Slmyb21 mutant displayed defects in floral development that were further exacerbated in the Slmyb21 Slmyb24 double mutant, resulting in a severe phenotype characterized by female sterility and whitish petals that failed to open. Petals of Slmyb21 Slmyb24 exhibited reduced xanthophyll content and elevated abscisic acid (ABA) levels, accompanied by reduced water content and decreased levels of primary sugars. Integration of transcriptome (RNA-sequencing) and cistrome (DNA affinity purification sequencing, DAP-seq) data identified genes involved in carotenoid and ABA biosynthesis and water transport as candidate regulatory targets of SlMYB21 and SlMYB24. These TFs activated the promoters of PHYTOENE SYNTHASE2 (PSY2), LYCOPENE {beta}-CYCLASE (LCY-B) and the petal-expressed aquaporin TONOPLAST INTRINSIC PROTEIN1.1 (TIP1.1), whereas they repressed 9-cis-EPOXYCAROTENOID DIOXYGENASE1 (NCED1) promoter activity. In addition, SlMYB21 bound to the SlMYB24 promoter and activated its expression. Promoter studies and electrophoretic mobility shift assays revealed that SlMYB21 and SlMYB24 bind the AC-rich DNA-binding motif GTTAGGT, which is to be found in the respective promoters and is consistent with the extensive overlap in their binding profiles. Together, these results reveal that the functions of SlMYB21 and SlMYB24 extend beyond fertility to coordinate petal pigmentation and opening.

plant biology↗

bioRxiv2026

MYB28 and MYB29 transcription factors regulate iron homeostasis and iron-mobilizing coumarin biosynthesis in Arabidopsis thaliana

Iron (Fe) deficiency is a major constraint for plant growth and triggers extensive physiological and transcriptional reprogramming to maintain Fe homeostasis. Here, we identify the glucosinolate-associated transcription factors MYB28 and MYB29 as previously unrecognized regulators of Arabidopsis thaliana adaptation to Fe deficiency. Across various growth systems, loss of MYB28 increased sensitivity to Fe deficiency, whereas the myb28myb29 double mutant displayed stronger chlorosis, reduced root growth and impaired biomass accumulation, indicating cooperative but unequal functions of these transcription factors. Despite their enhanced Fe-deficiency phenotype, double mutant plants accumulated higher Fe levels in roots and exhibited stronger induction of canonical Fe-deficiency responses, suggesting impaired Fe utilization or distribution rather than defective Fe uptake. RNA-seq revealed extensive transcriptional reprogramming under Fe deficiency, with pronounced deregulation of genes involved in Fe homeostasis, redox processes and growth, particularly in the double mutant. Among these, SCOPOLETIN 8-HYDROXYLASE (S8H) emerged as a major target gene of MYB28. The expression of S8H was almost abolished in myb28 and myb28myb29 mutants, whereas expression of other coumarin biosynthetic genes remained largely unaffected. Promoter activation assays demonstrated that MYB28 activates the S8H promoter, and metabolic analyses showed accumulation of scopolin together with reduced fraxin levels in the mutants, consistent with impaired S8H activity. Collectively, our results identify MYB28 as a key regulator linking specialized metabolism to Fe homeostasis through control of coumarin biosynthesis, thereby expanding the biological functions of MYB28 and MYB29 transcription factors.

plant biology↗

bioRxiv2026

Hydroxylated monoterpenes mimic bacterial attack to trigger jasmonate-dependent self-amplifying immunity in tomato

Hydroxylated monoterpenes (HMTPs) are emitted during resistant tomato-Pseudomonas syringae interactions and confer antibacterial resistance, yet their integration into immune signalling remains poorly understood. Here we show that HMTPs act as endogenous mimics of pathogen attack that engage canonical defence pathways in tomato. Using -terpineol as a representative HMTP, we demonstrate that this volatile activates MPK kinase-, calcium- and reactive oxygen species (ROS)-dependent signalling, promotes jasmonate and salicylic acid accumulation, and induces pathogen-like stomatal immunity independently of abscisic acid. Functional analyses revealed that HMTPs biosynthesis depends on ROS and jasmonate signalling, and HMTPs further promote their own accumulation, establishing a self-reinforcing feed-forward mechanism. Moreover, in vitro oxidative conditions drive chemical remodelling and selective interconversion among HMTPs, contributing to volatile diversification and favouring the accumulation of highly bioactive hydroxylated forms. Consistently, deuterium-labelled linalool is incorporated into plant metabolism and converted into deuterated -terpineol in planta, providing direct evidence for volatile interconversion. Together, our findings establish HMTPs as dynamic amplifiers of tomato antibacterial immunity and key actors in pathogen-associated signalling.

plant biology↗

bioRxiv2026

RAStoERK: a reference interaction atlas for insights into signaling and disease

The RAS/RAF/MEK/ERK pathway has been extensively studied for its roles in physiology and disease, yet a systems-level view of its interplay with the broader cellular context is lacking, limiting insight into paralog-specific roles, mutation-driven rewiring, and cross-pathway integration. To address this, we simultaneously mapped the interactomes of all pathway components and their activating and inactivating mutations, identifying 2,500 high-confidence interactors, 88% of which previously unreported, and generating a high-confidence, comprehensive reference map of the pathway in resting and activated states. The pathway behaves like a "molecular organism" that connects to other signaling complexes, operates from distinct subcellular sites, and integrates into networks relevant to physiology and disease. Dataset exploration uncovered paralog- and mutation-specific interaction signatures and pathway-level crosstalk, including previously unknown connections to mRNA metabolism and WNT signaling. The interactomes available at RAStoERK.univie.ac.at provide a foundational community resource for unbiased discovery, targeted mechanistic studies, and potential therapeutic exploration. HighlightsO_LIHigh-resolution interactome map of the RAS to ERK pathway in resting and active states C_LIO_LIState-dependent pathway-level interactions with signaling and functional modules C_LIO_LIMutation-driven interactome rewiring and integration into pathophysiological networks C_LIO_LIA resource to discover pathway crosstalk, disease links, and actionable interventions C_LI

molecular biology↗

bioRxiv2025

AEGIS: an annotation extraction and genomic integration resource

The GTF/GFF3 formats are the standard for storing and exchanging genome annotations. However, their flexibility often results in inconsistent and poorly formatted files across different sources, creating a major bottleneck for downstream bioinformatics analyses. Here, we present Annotation Extraction and Genomic Integration Suite (AEGIS), a comprehensive and user-friendly command-line toolkit designed to parse, validate and standardise genome annotation files. AEGIS robustly corrects common structural and formatting errors, ensuring interoperability with downstream tools. Beyond standardisation, the suite provides advanced modules for analysis, such as flexible sequence extraction (e.g. genes, CDS, proteins) with isoform handling, customisable promoter region definitions and targeted DNA motif searches. A key feature of AEGIS is its integrated workflow for comparative genomics, which combines multiple lines of evidence (i.e., sequence homology, synteny and coordinate-based lift-overs) to enable a robust gene ID correspondence and orthology assessment. We demonstrate the utility of AEGIS by comparing two major Arabidopsis thaliana annotations (TAIR10 vs. Araport11), successfully identifying and quantifying complex structural changes such as gene splits and fusions. AEGIS provides a unified solution for annotation quality control, feature extraction and comparative genomic analysis, simplifying complex workflows and enhancing reliability in bioinformatic research. The software is open-source, implemented in Python and is available on GitHub, PyPI, and as a Docker container to ensure accessibility and reproducibility.

bioinformatics↗

bioRxiv2025

Developing the Grapevine Hydric Stress Atlas: A Meta-Analysis Resource for Exploring transcriptome Responses to Drought

Climate change poses a significant threat to agriculture, particularly in regions where increased drought periods, abnormal heat, and intensified pest pressure threaten crop productivity. Viticulture, as one of the most economically important crops, is highly vulnerable to these challenges. Understanding the molecular mechanisms underlying drought responses in grapevines is essential for developing innovative molecular breeding strategies aimed at enhancing drought tolerance, improving cultivar resilience, and promoting agricultural sustainability. In this context, transcriptomic meta-analyses have proven valuable for uncovering global regulatory trends, gene co-expression networks and conserved biological responses across diverse conditions. As part of this study, 1107 public transcriptomic datasets from Illumina (631 runs) and ABI SOLID (476 runs) platforms were searched, reclassified and reanalyzed in the latest T2T genome assembly, in order to construct condition, cultivar and tissue-specific gene expression atlases associated with drought stress in grapevine. To facilitate exploration of this data, a web-based application, the Hydric Stress Atlas App (https://plantaeviz.tomsbiolab.com/vitviz/hydric_atlas/), was developed, as part of the Vitis module within the PlantaeViz platform. Together with this tool, we generated a whole-genome co-expression network using the same datasets (https://plantaeviz.tomsbiolab.com/vitviz/networks/non_agg_gcns/T2T/hydric_stress_TI/). This water stress condition-dependent GCN allows to explore and visualize gene co-expression relationships related to stress and identify network hubs holding novel drought stress regulators. We manually curated experimental metadata, and enabled the classification of transcriptomic data by cultivar, tissue, and drought tolerance. Finally, candidate genes associated with drought tolerance were identified via network topology analysis. These genes can be further used as molecular markers, or characterized via gene editing or cisgenesis, providing insights into their molecular roles in drought tolerance. This resource contributes to a deeper understanding of grapevine drought responses, offering a pathway for sustainable viticulture and innovative biotechnological solutions to address climate-related challenges.

plant biology↗

bioRxiv2025

Organ-level Gene Regulatory Network models enable the identification of central transcription factors in Solanum lycopersicum

Tomato (Solanum lycopersicum) is a globally important crop, yet the gene regulatory networks (GRNs) controlling gene expression remain poorly understood. In this study, we constructed GRNs for roots, leaves, flowers, fruits, and seeds by inferring transcription factor (TF)-target interactions from over 10,000 RNA-seq libraries using the GENIE3 algorithm. We refined these networks with gene co-expression data and computational predictions of TF binding sequences in open chromatin sites. Our networks confirmed key TFs, including TOMATO AGAMOUS LIKE 1 and RIPENING INHIBITOR in fruit ripening, as well as ABF3 and ABF5 in abscisic acid response in leaves. Additionally, we identified novel candidate regulators, including AUXIN RESPONSE FACTOR 2A and ETHYLENE RESPONSE FACTOR.E2 in fruit ripening and G-BOX BINDING FACTOR 3 (SlGBF3) in ABA-related and drought pathways. To further validate the GRNs, we used DNA Affinity Purification Sequencing (DAP-seq) for SlGBF3, confirming the accuracy of our GRNs. This study provides a valuable resource for dissecting transcriptional regulation in tomato, with potential applications in crop improvement. The GRNs are publicly accessible through a user-friendly web platform at https://plantaeviz.tomsbiolab.com/tomviz. HighlightWe developed organ-level gene regulatory networks for tomato using 10,000+ RNA-seq libraries, validated predictions and identified new regulators of fruit ripening and ABA response. These networks are available at https://plantaeviz.tomsbiolab.com/tomviz.

systems biology↗

bioRxiv2025

A Grapevine MYC2-MYB24 Regulatory Module Activates Terpenoid Biosynthesis Upon Methyl Jasmonate Elicitation

Terpenes contribute to the characteristic flavor and aroma of grapes and their derived products while serving protective roles in plants against radiation, oxidative stress, and biotic challenges. The phytohormone methyl jasmonate (MeJA) mediates many of these processes and enhances terpene content in grape berries, but its underlying regulatory mechanism remains unclear. To address this, we treated Vitis vinifera cv. Gamay Freaux berry cell suspensions with MeJA (100 M) and cyclodextrins (50 mM), generating transcriptomic data. Upregulated genes (URGs) were enriched in jasmonic acid biosynthesis and signaling pathways, and transcription factors (TF) that represent novel candidates modulating MeJA responses. Inspection of these TFs in terms of their co-expressed genes allowed us to focus on MYC2, the sole bHLH IIIe subgroup member in grapevine. Using DAP-seq, we identified MYC2-bound genes and integrated them with MeJA-URGs and MYC2 co-expressed genes (CEGs) to produce a high-confidence target list. These targets were bound via a conserved G-box motif and included jasmonate-related genes (e.g., LOX and JAZ) and TFs such as MYB24, previously found to interact with MYC2 to activate terpenoid biosynthesis genes. Consistently, MeJA treatment induced 15 terpene synthase genes (TPS), eleven of which were bound by MYB24, MYC2, or both. Terpenoid compounds associated with these induced TPSs accumulated both intra- and extracellularly following treatment with MeJA and cyclodextrins, but not with abscisic acid (ABA). Our findings suggest that MYC2 regulates the jasmonate pathway and cooperates with MYB24 to mediate MeJA-induced terpene biosynthesis, shedding light on mechanisms that may extend to flower and fruit development, where this MYB-bHLH complex is also expressed.

plant biology↗

bioRxiv2024

The Plantae Visualization Platform: a comprehensive web-based tool for the integration, visualization, and analysis of omic data across plant and related species

The increasing availability of omics data from non-model plant species has created a pressing need for centralized, user-friendly platforms that maximize the utility of these datasets in a FAIR manner. Here, we introduce PlantaeViz, a web-based tool designed for the integration, visualization, and analysis of multi-omics data across a wide range of plant species. PlantaeViz offers advanced functionalities, including gene catalogues built from curated literature, transcriptomic meta-analyses presented as gene expression atlases, gene co-expression and regulatory networks with on-the-fly ontology analyses, cistrome visualization and metabolomics-transcriptomics integration, among other tools, providing a robust framework for hypothesis generation and biological interpretation. Gene Cards applications, tailored to each plant species, provide both community-curated and automatically generated functional annotation information. One of the platforms core features is its big data approach: over 58,000 publicly available SRA transcriptomic samples have been processed and visualized to date. Significant efforts have been made in orthology assessment using multiple layers of evidence, as well as in the automatic classification and standardization of omics metadata through regular expressions and data mining. As a result, around 90% of transcriptomic runs have been successfully classified according to sample tissue. These data have been used to construct gene networks via computationally intensive methods based on diverse algorithms. We present a study case to illustrate the platforms integration and exploratory capabilities. PlantaeViz bridges genomics and functional knowledge between model and non-model plant species and aims to expand its species catalogue of species in the future, democratizing access to large-scale plant omics data. Further developments will include the incorporation of additional data types, and the implementation of new tools to further support plant research across diverse biological contexts.

bioinformatics↗

bioRxiv2024

Biosynthesis of oxyresveratrol in mulberry (Morus alba L.) is mediated by a group of p-coumaroyl-CoA 2'-hydroxylases acting upstream of stilbene synthases

Mulberry (Morus alba L.) is considered a millenary medicinal plant and a food source for silkworms. Different M. alba extracts offer a variety of biological and pharmacological properties that are in part attributed to stilbenoids, a small group of phenylpropanoids that include resveratrol and oxyresveratrol. These are naturally present in non-renewable parts of mulberry trees, impeding their efficient extraction. As a way to bypass this spatiotemporal restriction, we generated cell suspensions from mulberry twigs and demonstrated that the combined use of methyl jasmonate and methyl- or hydroxypropyl-{beta}-cyclodextrins elicited a high production of resveratrol and oxyresveratrol, both intra and extracellularly. To identify oxyresveratrol-producing enzymes (unknown to date), we first improved the structural and functional annotation of the mulberry genome by integrating short and long-read sequencing data. We further combined this data with transcriptome, metabolite and proteome time-series evidence to identify a complete set of elicited phenylpropanoid- and stilbenoid-related genes. These included 22 stilbene synthase (STS) genes and a group of six p-coumaroyl-CoA 2-hydroxylases (C2Hs) that were highly co-expressed with resveratrol and oxyresveratrol accumulation. We transiently transformed Nicotiana benthamiana plants and grapevine (Vitis vinifera L.) cell suspensions to functionally validate the role of C2Hs as the first committed step of oxyresveratrol synthesis, providing an alternative substrate for STSs by hydroxylating p-coumaroyl-coA into 24-dihydroxycinnamoyl-CoA. We offer tools for genomic and transcriptomic exploration in the context of jasmonate elicitation aiding in the characterization of novel stilbenoid-modifying and regulatory genes in the Morus genus.

molecular biology↗

bioRxiv2023

Aggregated gene co-expression networks for predicting transcription factor regulatory landscapes in a non-model plant species

Gene co-expression networks (GCNs) have not been extensively studied in non-model plants. However, the rapid accumulation of transcriptome datasets in these species represents an opportunity to explore underutilized network aggregation approaches that highlight robust co-expression interactions and improve functional connectivity. We applied and evaluated two different aggregation methods on public grapevine RNA- Seq datasets belonging to three different tissue conditions (leaf, berry and all organs). Our results show that co-occurrence-based aggregation generally yielded the best-performing networks. We applied GCNs to study several TF gene families, showing its capacity of detecting both already-described and novel regulatory relationships between R2R3-MYBs, bHLH/MYC and multiple secondary metabolism pathway reactions. Specifically, TF gene-and pathway-centered network analyses successfully ascertained the previously established role of VviMYBPA1 in controlling the accumulation of proanthocyanidins while providing insights into its novel role as a regulator of p-coumaroyl-CoA biosynthesis as well as the shikimate and aromatic amino-acid pathways. This network was validated using DNA Affinity Purification Sequencing data, demonstrating that co-expression networks of transcriptional activators can serve as a proxy of gene regulatory networks. This study presents an open repository to reproduce networks and a GCN application within the Vitviz platform, a user-friendly tool for exploring co-expression relationships.

plant biology↗

bioRxiv2022

Redox regulation of yeast Hsp70 modulates protein quality control while directly triggering an Hsf1-dependent cytoprotective response

Neurodegenerative disease affects millions of Americans every year, through diagnoses such as Alzheimers, Parkinsons, and Huntingtons diseases. One factor linked to formation of these aggregates is damage sustained to proteins by oxidative stress. Cellular protein homeostasis (proteostasis) relies on the ubiquitous Hsp70 chaperone family. Hsp70 activity has been previously shown to be modulated by modification of two key cysteines in the ATPase domain by oxidizing or thiol-modifying compounds. To investigate the biological consequences of cysteine modification on the Hsp70 Ssa1 in budding yeast, we generated cysteine null (cysteine to serine) and oxidomimetic (cysteine to aspartic acid) mutant variants of both C264 and C303 and demonstrate reduced ATP binding, hydrolysis and protein folding properties in both the oxidomimetic as well as hydrogen peroxide-treated Ssa1. In contrast, cysteine nullification rendered Ssa1 insensitive to oxidative inhibition. The oxidomimetic ssa1-2CD (C264D, C303D) allele was unable to function as the sole Ssa1 isoform in yeast cells and also exhibited dominant negative effects on cell growth and viability. Ssa1 binds to and represses Hsf1, the major transcription factor controlling the heat shock response, and the oxidomimetic Ssa1 failed to stably interact with Hsf1, resulting in constitutive activation of the heat shock response. Consistent with the in vitro findings, ssa1-2CD cells were compromised for de novo folding, post-stress protein refolding and in regulated degradation of a model terminally misfolded protein. Together these findings pinpoint Hsp70 as a key link between oxidative stress and proteostasis, information critical to understanding cytoprotective systems that prevent and manage cellular insults underlying complex disease states.

cell biology↗

bioRxiv2022

Ionic remodelling following myocardial infarction explains phenotypic variability in ECG and arrhythmic substrate but not in ejection fraction

AimsSudden death after myocardial infarction (MI) is associated with electrophysiological heterogeneities and ionic remodelling, which are reflected as variable phenotypes. Low ejection fraction (EF) is used in risk stratification, but its mechanistic links with the post-MI pro-arrhythmic heterogeneities are unknown. We aim to provide a mechanistic explanation of clinical phenotypes in acute and chronic MI, from ionic remodeling to ECG and EF, using human electromechanical modelling and simulation to augment experimental and clinical investigations. Methods and ResultsA human ventricular electromechanical modelling and simulation framework is constructed and validated with rich experimental and clinical datasets. Abnormalities caused by scar and border zone ionic remodeling are introduced in varying degrees as reported in experimental data obtained in acute and chronic infarction. Simulations enabled reproducing and explaining clinical phenotypes post-MI, from ionic remodelling to ECGs and pressure-volume loops. In acute MI, T-wave inversion and Brugada phenocopy were explained by up to 57 ms of local APD prolongation and activation failure due to the inhibition of potassium, sodium and calcium channels in the border zone. In chronic MI, upright tall T-waves highlight large repolarisation dispersion caused by uneven potassium channel expression in border and remote zones, which promoted ectopic propagation at fast pacing. Post-MI ionic remodelling reduced EF by up to 10% through inhibition of calcium transient amplitude due to weaker calcium currents or SERCA activity, but the EF at resting heart rate was not sensitive to the extent of repolarisation heterogeneity and the risk of repolarisation abnormalities at fast pacing. ConclusionsMulti-scale modelling and simulation coherently integrates experimental and clinical data at subcellular, tissue, and organ scales to unravel electromechanical disease mechanisms in MI. In acute post-MI, ionic remodelling and its effect on refractoriness and propagation failure in the BZ have a strong impact on phenotypic ECG variability, whereas in chronic post-MI, the repolarisation dispersion across the BZ is crucial. T-wave and QT abnormalities are better indicators of repolarisation heterogeneities than EF in post-MI.

bioengineering↗

bioRxiv2021

The grape MYB24 mediates the coordination of light-induced terpene and flavonol accumulation in response to berry anthocyanin sunscreen depletion

The presence of naturally-occurring color mutants in plants has permitted the identification of many regulatory genes implicated in the synthesis of discrete metabolic compounds, mostly anthocyanins and carotenoids. Conversely, transcription factors that coordinate more than one specialized metabolic pathway seem challenging to screen from a forward genetics perspective. We explored the relationship between different branches of the phenylpropanoid and isoprenoid pathways while examining an infrequent berry skin color variegation in grapevine. Red and white berry skin sections were compared at the genetic, transcriptomic and metabolomic levels showing that, as in most cultivated white grape varieties, the uncolored skin section convened the non-functional alleles of the anthocyanin regulators MYBA1 and MYBA2, explaining the lack of pigments. In contrast, light-responsive flavonols and monoterpenes increased in anthocyanin-depleted areas. We disclosed an enrichment of the flavonol, terpene and carotenoid pathways among up-regulated genes from white-skin sections, accompanied by increased expressions of flavonol regulators and the still uncharacterized MYB24 gene. We used DAP-seq to examine the in vitro binding of affinity-purified MYB24 protein to genomic DNA and demonstrated its binding in the promoter regions of terpene (22) and carotenoid (6) genes, in addition to more than 30 photosynthesis and light-response genes, including the flavonol-regulator HY5 homologue (HYH). We confirmed the activation of TPS35 and HYH promoter:luciferase reporters in the presence of MYB24 and the grape bHLH MYC2, all of which correlate in their higher expression in white skin variegated sections. The integration of several datasets allowed to define a list of high confidence targets, suggesting MYB24 as a modulator of light responses including the synthesis of flavonoids (flavonols) and isoprenoids (terpenes, and putatively carotenoids). The correspondence between MYB24 and monoterpenes in all conditions surveyed implies that this regulatory network is broadly triggered towards berry ripening, and that the absence of anthocyanin sunscreens accelerates its activation most likely in a dose-dependent manner due to increased radiation exposure.

plant biology↗

bioRxiv2021

Initiation of organ maturation and fruit ripening in grapevine is controlled by the CARPO-NAC transcription factor

Grapevine is a woody temperate perennial plant and one of the most important fruit crops with global relevance in both the fresh fruit and winemaking industries. Unfortunately, global warming is affecting viticulture by altering developmental transitions and fruit maturation processes. In this context, uncovering the molecular mechanisms controlling the onset and progression of ripening could prove essential to maintain high-quality grapes and wines. Through a deep inspection of previously published transcriptomic data we identified the NAC family member VviCARPO (Controlled Adjustment of Ripening and maturation of Plant Organs) as a key regulator of grapevine maturation whose induction precedes the expression of well-known ripening associated genes. We explored VviCARPO binding landscapes through DAP-seq and overlapped its bound genes with transcriptomics datasets from stable and transient VviCARPO overexpressing grapevine plants to define a set of high-confidence targets. Among these, we identified key molecular ripening markers. Physiological, metabolic and promoter activation analyses showed that VviCARPO induces chlorophyll degradation and anthocyanin accumulation through the up-regulation of VviSGR1 and VviMYBA1, respectively, with the latter being up-regulated through a VviCARPO-VviNAC03 regulatory complex. Despite showing a closer phylogenetic relationship to senescent-related AtNAP homologues, VviCARPO complemented the nor mutant phenotype in tomato, suggesting it may have acquired a dual role as an orchestrator of both ripening- and senescence-related processes. Our data supports CARPO as a master regulator of the grapevine vegetative-to-mature phase organ transition and therefore an essential target for insuring fruit quality and environmental resilience. SIGNIFICANT STATEMENTCARPO is a grape NAC transcription factor central to fruit ripening and tissue senescence. This regulator influences multiple biological pathways common to both processes including cell wall metabolism, chlorophyll degradation, pigment production and hormone synthesis/signaling through regulation of their key genes. As various external stresses and changing climatic conditions influence vegetative growth and berry ripening, CARPO could prove a useful genetic and breeding target towards maintaining necessary crop performance and fruit-quality characteristics.

plant biology↗

bioRxiv2021

Design and execution of a Verification, Validation, and Uncertainty Quantification plan for a numerical model of left ventricular flow after LVAD implantation

Backgroundleft ventricular assist devices (LVADs) are implantable pumps that act as a life support therapy for patients with severe heart failure. Despite improving the survival rate, LVAD therapy can carry major complications. Particularly, the flow distortion introduced by the LVAD in the left ventricle (LV) may induce thrombus formation. While previous works have used numerical models to study the impact of multiple variables in the intra-LV stagnation regions, a comprehensive validation analysis has never been executed. The main goal of this work is to present a model of the LV-LVAD system and to design and follow a verification, validation and uncertainty quantification (VVUQ) plan based on the ASME V&V40 and V&V20 standards to ensure credible predictions. MethodsThe experiment used to validate the simulation is the SDSU cardiac simulator, a bench mock-up of the cardiovascular system that allows mimicking multiple operation conditions for the heart-LVAD system. The numerical model is based on Alya, the BSCs in-house platform for numerical modelling. Alya solves the Navier-Stokes equation with an Arbitrarian Lagrangian-Eulerian (ALE) formulation in a deformable ventricle and includes pressure-driven valves, a 0D Windkessel model for the arterial output and a LVAD boundary condition modeled through a dynamic pressure-flow performance curve. The designed VVUQ plan involves: (a) a risk analysis and the associated credibility goals; (b) a verification stage to ensure correctness in the numerical solution procedure; (c) a sensitivity analysis to quantify the impact of the inputs on the four quantities of interest (QoIs) (average aortic root flow [Formula], maximum aortic root flow [Formula], average LVAD flow [Formula], and maximum LVAD flow [Formula]); (d) an uncertainty quantification using six validation experiments that include extreme operating conditions. ResultsNumerical code verification tests ensured correctness of the solution procedure and numerical calculation verification showed small numerical errors. The total Sobol indices obtained during the sensitivity analysis demonstrated that the ejection fraction, the heart rate, and the pump performance curve coefficients are the most impactful inputs for the analysed QoIs. The Minkowski norm is used as validation metric for the uncertainty quantification. It shows that the midpoint cases have more accurate results when compared to the extreme cases. The total computational cost of the simulations was above 100 [core-years] executed in around three weeks time span in Marenostrum IV supercomputer. ConclusionsThis work details a novel numerical model for the LV-LVAD system, that is supported by the design and execution of a VVUQ plan created following recognised international standards. We present a methodology demonstrating that stringent VVUQ according to ASME standards is feasible but computationally expensive.

bioengineering↗

bioRxiv2018

AAK1 inhibits WNT signaling by promoting clathrin-mediated endocytosis of LRP6

{beta}-catenin-dependent WNT signal transduction governs normal development and adult tissue homeostasis. Inappropriate pathway activity mediates a vast array of human diseases, including bone density disorders, neurodegeneration and cancer. Although several WNT-directed therapeutics are in clinical trials, new targets, compounds and strategies are needed. We performed a gain-of-function screen of the human kinome to identify new druggable regulators of {beta}-catenin-dependent transcription. We found that over-expression of the AP2 Associated Kinase 1 (AAK1) strongly inhibited WNT signaling. Reciprocally, silencing of AAK1 expression or pharmacological inhibition of AAK1 kinase activity using a new, selective and potent small molecule inhibitor activated WNT signaling. This small molecule is a cell active dual AAK1/BMP2K inhibitor that represents the best available tool to study AAK1-dependent signaling pathways. We report that AAK1 and the WNT co-receptor LRP6 physically co-complex and that AAK1 promotes clathrin-mediated endocytosis of LRP6. Collectively, our data support a WNT-induced negative feedback loop mediated by AAK1-driven, clathrin-mediated endocytosis of LRP6.\n\nSummary StatementA gain-of-function screen of the human kinome revealed AAK1 as a negative regulator of WNT signaling. We show that AAK1 promotes clathrin-mediated endocytosis of LRP6, resulting in downregulation of WNT signaling. We use a new selective and potent AAK1/BMP2K small molecule probe to validate our findings.

cell biology↗