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Stein, F.

Publications and source records attributed to Stein, F..

At least 19 recordsLinked to original sources

The C-terminus of the KREH1 helicase is important for RNA binding and association with mitochondrial RNA editing complexes in T. brucei

Mitochondrial pre-mRNA editing in kinetoplastids, a clade that includes human-infective parasitic protists such as Trypanosoma and Leishmania, is required to produce translatable, functional gene products from otherwise nonfunctional mitochondrial precursor transcripts of essential respiratory chain complex subunits. RNA editing is a template-guided process in which cognate guide RNAs (gRNAs) anneal to specific sites at the pre-mRNA and direct the complementary insertion and/or deletion of uridines. Large multi-modular complexes - like the RNA-Editing Substrate-binding Complex (RESC) and the RNA-Editing Catalytic Complexes (RECC) - organize and catalyze RNA editing, respectively. Within these assemblies, Kinetoplast RNA Editing Helicases (KREHs) play an important role in ribonucleoprotein complex remodeling, particularly in pan-editing, when transcripts are extensively modified throughout their length by multiple gRNAs. However, the mechanisms by which KREH RNA helicases facilitate pan-editing, and their specific roles in this process, remain unclear. Here, we define the molecular properties of the Trypanosoma brucei DEAD-box RNA editing helicase KREH1. Cellular co-proteome analyses reveal that KREH1 interacts with subunits of the RESC complex and biochemical experiments show that KREH1 is an RNA-dependent ATPase that unwinds double-stranded RNA substrates. We show that the flexible C-terminus of KREH1 is important for RNA binding and, consequently, for enzymatic activity in vitro and interactions with the RESC complex in vivo. Overall, our experiments refine the role of KREH1 in the pan-editing process and establish its utility as a molecular tool for investigating higher-order RNA editing complexes in the cellular context.

molecular biology↗

Intrinsic flexibility of Type VII secretion central pore is required for substrate translocation

Mycobacteria have up to five distinct type VII secretion pathways that play diverse roles in the cell ranging from iron uptake to virulence. To date, high-resolution structures of a hexameric ring-like pore complex have only been determined for closely related mycobacterial ESX-5 systems. The most significant difference between them is the arrangement and flexibility of the inner transmembrane helices of the EccC5 subunit within the central pore, leading to either a closed or to a semi-open conformation of the pore. In this work, we probed the functional roles of several central pore-forming residues in mediating secretion and demonstrate their crucial role in ESX-5 substrate translocation efficiency. Structural characterization of an ESX-5 variant with a conserved proline (P73A) surprisingly revealed rigidification of the pore-forming helices. In summary, our data demonstrate that maintaining the conformational flexibility of the central ESX-5 pore is essential for substrate secretion. Our findings reveal how the rigid structural ESX-5 scaffold with separate sections - facing the periplasm, the inner mycobacterial cell wall membrane and facing the cytosol - provides a complex framework for a high level of pore dynamics, restricted to the inner EccC5 subunit pore-forming helices. Their proper integration is required to generate a functional secretion system. The high level of conservation of several pore-forming residues across different type VII secretion systems indicates our findings to be general valid for these systems. SIGNIFICANCE STATEMENTA key virulence signature of the deadliest pathogenic mycobacteria is the presence of a number of highly specialized the type-VII secretion systems, which translocate distinct infection-promoting proteins through a central pore. Recent high-resolution structures of one of these systems (ESX-5) have revealed closed or partially closed pore states. This raises the question of how pore opening is mediated to allow substrate transport. Here, we demonstrate that this system is highly sensitive to even subtle changes within the central pore. Loss of conformational pore flexibility impairs secretion. A comprehensive understanding on the structure and associated dynamics of the central pore of type-VII secretion systems is essential to further unraveling mycobacterial virulence and developing future strategies for combatting it.

microbiology↗

Secure Attachment despite Childhood Maltreatment: Behavioral and Neural Correlates of Interpersonal Resilience

BackgroundChildhood maltreatment is a traumatic interpersonal stressor that increases vulnerability for depression in adulthood. However, some individuals show secure attachment despite childhood maltreatment, a pattern that can be described as interpersonal resilience. The present study examined the behavioral and neural correlates of interpersonal resilience, defined as secure attachment in adults exposed to childhood maltreatment. MethodsWe analyzed structural 3T MRI data from 1,317 adults, including healthy participants and individuals with partially or fully remitted major depression. Gray matter volume was estimated from structural MRI data using voxel-based morphometry. Attachment style and childhood maltreatment were assessed using the Relationship Scales Questionnaire and the Childhood Trauma Questionnaire, respectively. A 2x2 design (childhood maltreatment by attachment style) tested main and interaction effects on behavioral outcomes and brain structure. ResultsInterpersonally resilient individuals with secure attachment and maltreatment reported significantly better mental health outcomes compared to insecurely attached adults with maltreatment. Differences included lower self-reported and rater-based depressive symptoms, lower global symptom severity, and higher global functioning. In the neuroimaging analyses, we identified a significant childhood maltreatment by attachment style interaction in the left supramarginal gyrus, with larger gray matter volume in resilient individuals compared to all other groups. This effect remained robust across multiple sensitivity analyses, controlling for medication load, antidepressant intake, diagnosis group, as well as in a complementary dimensional analysis. ConclusionsThe results identify a potential neural correlate of interpersonal resilience. Larger gray matter volume in the left supramarginal gyrus, a region previously implicated in perspective taking and self-other distinction among other functions, may be relevant to more adaptive interpersonal functioning after early adversity. Together with the robust behavioral effects, these findings are consistent with secure attachment as a protective factor that may be associated with attenuated effects of childhood maltreatment on mental health.

neuroscience↗

Identifying Novel Estrogenic Mitochondrial Targets in Hypothalamic Proopiomelanocortin Neurons by Chemoproteomics

Loss of estrogens at menopause is linked to impaired brain metabolism and increased risk of Alzheimers disease (AD). However, estrogen replacement therapies are limited due to the deleterious effects of estrogen on peripheral organs and increased risk of vascular dementia. We have developed a non-steroidal estrogenic compound, STX, which does not bind to the classical estrogen receptors and {beta}, but mimics estrogenic signaling in the central nervous system (CNS) without the peripheral reproductive actions. STX is protective against neurodegeneration in stroke and AD models, but its molecular targets are unknown. Here, we identified and validated STX neural targets using chemoproteomic, molecular biological, electrophysiological and metabolic assays of hypothalamic proopiomelanocortin (POMC) neurons. Chemoproteomic profiling identified voltage dependent anion channels (VDAC1-3) as major intracellular binding partners in mHypo43 (POMC) cells. Based on quantitative single-cell PCR, Vdac2 was identified as the dominant isoform in female hypothalamic POMC neurons. Seahorse metabolic flux analyses showed that STX potently increased glycolysis, oxidative respiration and mitochondrial ATP production in mHypo43 cells. Nanomolar concentrations of STX enhanced VDAC2 voltage-dependent gating in reconstituted lipid membranes and shifted the low-conductance states toward anion selectivity, consistent with increased ATP flux. Together, these findings reveal a mechanism for the neuroprotective effects of STX through enhancing mitochondrial bioenergetics and modulating VDAC channel properties, potentially increasing cellular energy stores. Therefore, this work identifies previously unrecognized estrogenic mitochondrial targets and provides a mechanistic basis for the neuroprotective actions of STX relevant to menopause-associated brain vulnerability.

neuroscience↗

Decoding translational control by cis-regulatory elements and RNA binding proteins in human effector T cells

T cells are central players in killing virally infected and malignant cells. To achieve this, T cells depend on dynamic, tightly regulated alterations of the proteome. To decipher the rules instructing translation in T cells, we performed transcriptome and proteome analysis of polysome fractions from human effector CD8+ T cells. Transcriptome analysis informed on ribosomal occupancy of RNAs and uncovered the rapid and RNA-specific redistribution upon T cell activation. With machine learning, we identified RNA binding motifs that predict the RNA (re)distribution among the polysome fractions. Using matched proteome analysis, we identified polysome-associated RBPs and their swift shuttling across polysome fractions upon T cell activation. Integrating sequence feature analysis with polysome RBP localization uncovered PTBP1 as a positive translation regulator, through its interactions with cis-regulatory elements in 3'UTRs of target mRNAs. In conclusion, the multi-level analysis presented here identifies rules of selective translation control which shape the T cell proteome.

immunology↗

Loss of nuclear-cytoplasmic compartmentalization is a hallmark of aging in podocytes

The nuclear envelope, with its nuclear pore complexes, establishes a selective barrier that maintains the spatial organization of the cellular proteome. Whether this barrier remains intact in long-lived postmitotic cells during aging is largely unknown. Here, we show that aging podocytes experience a progressive loss of nuclear-cytoplasmic compartmentalization. Using subcellular proteomics and quantitative imaging, we identify a global redistribution of proteins between the nucleus and cytoplasm, affecting key regulators of RNA processing, chromatin organization, and cellular metabolism. Loss of compartmentalization is accompanied by mitochondrial dysfunction, increased reactive oxygen species production, and aberrant nuclear accumulation of YAP1, linking nuclear barrier failure to metabolic and transcriptional dysregulation. These findings identify nuclear envelope dysfunction as a driver of proteome disorganization and cellular decline in aging podocytes and suggest that loss of nuclear-cytoplasmic compartmentalization represents a general mechanism contributing to dysfunction in long-lived cells.

cell biology↗

Multi-modal single-cell profiling reveals transcriptional states and commitment dynamics during sexual reproduction in the diatom Pseudo-nitzschia multistriata

Diatoms, single-celled photosynthetic eukaryotes, traditionally considered primarily influenced by resource availability, are now recognized to exhibit complex developmental processes reminiscent of those in multicellular organisms. Sexual reproduction is an obligate choice in many species, albeit with variable frequency and efficiency. In order to explore decision making mechanisms and cellular heterogeneity inherent to this specific phase of the diatom life cycle, we applied a multi-modal strategy to follow sexual reproduction events in the model diatom Pseudo-nitzschia multistriata: i) we employed image-enabled cell sorting to link sexual stages morphology with gene expression ii) we developed a single-nucleus RNA sequencing assay, and iii) conducted proteomic profiling. Combining phenotypes with single-cell profiling allowed us to identify sexual state-specific transcription programs and different states within morphologically identical parental cells, revealing a widespread commitment of the majority of the population to sexual reproduction. This implies that the bottleneck to successful sexual reproduction in this species can be placed downstream of the signalling phase between mating cells, with additional, yet unidentified, factors influencing mating success at sea.

microbiology↗

Interpretable Hierarchical RNNs for rs-fMRI: Promise and Limits of Individualized Brain Dynamics

Modeling individual brain dynamics from resting-state fMRI (rs-fMRI) remains challenging due to substantial inter-subject variability, noise, and limited data length per subject. Here, we systematically evaluate whether hierarchical shallow piecewise-linear recurrent neural networks (shPLRNNs), recently introduced as interpretable dynamical system reconstruction models, can generate individualized rs-fMRI time series while preserving subject-specific functional connectivity structure. We applied the framework to 1,423 rs-fMRI samples from healthy participants of the Marburg-Munster Affective Disorders Cohort Study (MACS). Simulated rs-fMRI data reproduced substantial empirical FC structure, with comparable reconstruction accuracy on the validation and held-out test sets. Generalization to unseen individuals was heterogeneous and strongly depended on how typical a subjects connectivity pattern was relative to the training cohort, with template similarity explaining 37% of variance in reconstruction accuracy. Learned subject-specific parameters exhibited significant test-retest stability and higher within-subject than between-subject similarity on longitudinal data from two different timepoints, supporting their interpretation as individualized dynamical markers. Associations between individual parameters and demographic or cognitive variables were statistically significant but modest in effect size, and predictive performance remained below that obtained using empirical rs-fMRI features directly. Empirical FC was used as a reference for static subject information rather than as a target to be outperformed. Together, these results suggest that hierarchical shPLRNNs can extract meaningful and partially stable individual-specific dynamical structure from rs-fMRI data. The findings delineate key trade-offs between model expressivity, generalization and subject specificity, and point to directions for future methodological refinement in individualized brain modeling. Graphical AbstractA hierarchical dynamical RNN captures substantial individual rs-fMRI functional connectivity structure using compact subject-specific parameters embedded in shared population dynamics. The resulting representations generalize to held-out subjects and show test-retest stability, but only modest associations with phenotypic variables. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=150 SRC="FIGDIR/small/713153v3_ufig1.gif" ALT="Figure 1"> View larger version (61K): org.highwire.dtl.DTLVardef@1b029edorg.highwire.dtl.DTLVardef@90bdd6org.highwire.dtl.DTLVardef@9f6b77org.highwire.dtl.DTLVardef@486c9e_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

Muscle LIM Protein is a Non-Canonical RNA-Binding Protein that Engages in RNA-Dependent Cytoskeletal Assemblies

Muscle LIM Protein (MLP) is a key component of the cardiomyocyte Z disc that is essential for sarcomere integrity and cardiac homeostasis. Accordingly, loss of MLP function results in (cardio)myopathy phenotypes in animal models and human patients. In this study, we present the first RNA-binding proteome (RBPome) of human cardiomyocytes using enhanced RNA interactome capture (eRIC). Data integration with existing RBPome datasets identified MLP as an evolutionary conserved and previously unrecognized non-canonical RNA-binding protein (RBP) in cardiomyocytes. Using complementary biochemical approaches, we confirmed direct RNA association of MLP. Moreover, RNA integrity was required for MLP interactions with cytoskeletal proteins and for the formation of higher-order MLP-containing assemblies, revealed by co-immunoprecipitation and RNA-dependent sedimentation profiling. Subcellular fractionation and imaging analyses indicated that MLPs association with cytoskeletal complexes may be weaker and more dynamic compared to core sarcomere proteins like -actinin. Domain mapping identified two glycine-rich regions within MLP as RNA contact sites, and RNA-binding-deficient MLP mutants showed impaired association with cytoskeletal complexes. Together, our findings suggest RNA binding as a regulated property of MLP and uncover an RNA-dependent layer of cytoskeletal organization in cardiomyocytes.

molecular biology↗

An ancient monoaminergic signaling system coordinates contractility in a nerveless sponge

Chemical neurotransmission was a key animal innovation, enabling multicellular coordination of physiology and locomotion. Sponges are early-diverging animals that lack neurons and muscles, yet still coordinate contraction and relaxation of their filter-feeding water canals. Here, we show that Spongilla lacustris synthesizes the monoamines tryptamine, phenethylamine, and tyramine to elicit distinct canal behaviors. We identify previously uncharacterized decarboxylases and vesicular transporters coexpressed in secretory neuroid and metabolic cells. Using phosphoproteomics and label-free 3D imaging, we show that tryptamine activates GPCR signaling and Rho GTPases, remodeling adhesion and actomyosin networks in contractile canal epithelia to drive localized constrictions and whole-body deflations. Together, these findings define an ancestral monoaminergic system linking secretory and contractile cell types that predate neurons and was later elaborated for neuromodulation of synaptic transmission.

evolutionary biology↗

An Integrated Method for Profiling Lipid-Protein Interactions Using Multifunctional Lipid Probes

Cellular lipids shape health and disease through specific protein interactions, yet lipid-protein networks remain poorly defined. Despite rapid advances in functional lipid probes, the field still lacks a practical, dedicated protocol for conducting lipid-protein interaction studies. We describe detailed methods for determining lipid interactomes from cells using multifunctionalized lipid derivatives. We provide protocols that detail 1) how to treat cells with lipid derivatives and perform photochemistry to obtain lipid-protein conjugates; 2) how to perform click chemistry with a fluorophore and observe lipid-protein conjugates by in-gel fluorescence; 3) how to perform click chemistry with azide beads and prepare lipid-protein conjugates for proteomic analysis. We provide context on important parameters for each step and include guidelines for controls, as well as suggestions for troubleshooting based on common problems encountered during the preparation of this protocol. This protocol enables mapping lipid interactomes across diverse biological systems. The entire workflow from cell treatment to complete proteomic sample preparation requires [~]15 hours over four days, depending on the type of experimental readout (in-gel fluorescence or proteomics), and the usage of pause points. Practitioners are expected to be familiar with standard biochemical techniques, such as sterile sample handling and tissue culture and gel electrophoresis. Additional skills are needed for mass spectrometric analysis, and collaboration with a proteomics core facility is recommended. The described procedures uniquely enable the identification of the protein interactors (the interactome) of select lipid species, providing for a major shift in the characterization of the biological roles of lipids in cellular systems.

biochemistry↗

TMEM9 and SEC22B interact with ClC-5 to shape renal proximal tubule function and Dent's Disease type I pathogenesis

Cl-/H+ antiporter ClC-5 is a key regulator of renal proximal tubule function, primarily by controlling endosomal acidification. Loss-of-function mutations in ClC-5 cause Dents Disease type 1 (DD1), a rare renal tubulopathy that progresses to kidney failure with varying severity. To understand the specific mechanisms linking ClC-5 loss-of-function with DD1 phenotypic heterogeneity, three ClC-5 pathogenic mutations (I524K, E527D and V523{Delta}) were investigated using renal proximal tubule epithelial cell lines. We have identified distinct intracellular retention patterns of these ClC-5 mutants, all leading to altered endolysosomal pH and disrupted secretory pathway organization. Through an interactome analysis, we have uncovered several ClC-5 partners including TMEM9, which interacted with all ClC-5 forms. TMEM9 knockdown (KD) recapitulated key DD1 characteristics, like defective endocytosis and epithelial dedifferentiation, but paradoxically enhanced endosomal acidification. The secretory pathway was also altered in cells lacking TMEM9 (e.g. enlarged endosomes, and fragmented Golgi apparatus). A similar phenotype was observed in cells depleted of SEC22B; an R-SNARE that we have found to specifically interact with wild-type ClC-5, but not the mutants. Notably, its deletion impaired ClC-5 trafficking, causing its retention at the Golgi and endosomes. Altogether, our findings highlight the relevance of TMEM9 and SEC22B in ClC-5 function, suggesting them as DD1 pathophysiology modifiers.

cell biology↗

Integrative Multi-Omics Identifies CDK1 as a Key Signaling Regulator of CD4+ T Cell Effector Function

CD4 T cell differentiation is orchestrated by coordinated signaling, transcriptional, and epigenomic programs, yet how signaling connects to chromatin and genetic variation in human T cells remains unclear. Here, we generated an integrative multi-omics map of human CD4 T cell activation and differentiation, combining phosphoproteomics, transcriptomics, and chromatin accessibility under Th0, Th1, and iTreg polarization. Within 10 minutes of activation, we observed rapid phosphorylation changes of RNA-binding proteins accompanied by degradation of effector-associated transcripts, preceding chromatin remodeling and later transcriptional activation of the same genes. Moreover, our data highlights how site-specific phosphorylation refines TF activity during T cell differentiation and activation, and identifies CDK1 as a regulator of Th1 effector function. Indeed, we found that a low dose of CKD1 inhibition impairs IFN-{gamma} expression and pro-inflammatory differentiation, while preserving regulatory features in iTregs. Single-cell multi-omic profiling upon CDK1 inhibition revealed how CDK1 activity shapes subset-specific gene regulatory networks, which are enriched for genetic variants associated with immune-traits. Specifically, CDK1-sensitive TFs, including IRF8, connect immune trait heritability to enhancer accessibility at IFNG and TNF loci. Together, these results establish CDK1 as a signaling hub that couples phosphorylation to gene regulation and genetic risk, with therapeutic relevance in autoimmune disease.

genomics↗

Febrile temperature enhances Plasmodium falciparum cytoadhesion by disrupting the endothelial glycocalyx

Fever, a universal host defense response in infection and inflammation, paradoxically contributes to neurological complications in malaria. Febrile temperatures are known to enhance parasite virulence protein expression, but direct effects on the human endothelium remain unknown. We found that a 1-hour exposure to 40 {degrees}C, representative of fever in children with cerebral malaria, increased adhesion of Plasmodium falciparum-infected red blood cells and neutrophils to 3D brain microvascular models displaying a wide wall shear stress gradient. Mechanistically, this brief hyperthermia triggered rapid endothelial glycocalyx shedding, exposing endothelial receptors for binding. This response was more pronounced in brain than in pulmonary microvessels, revealing a greater vulnerability of the cerebral vasculature to fever. Pharmacological inhibition of matrix metalloproteinase activity preserved glycocalyx integrity and abolished the temperature-induced increase in adhesion. These findings identify fever as a host-specific amplifier of malaria-associated microvascular pathology, highlighting the importance of antipyretic strategies to mitigate disease severity.

microbiology↗

A bridge-like lipid transfer protein is critical for generation of invasive stages in malaria parasites

Malaria blood stages build and maintain an intricate system of membranes during their cycle of rapid growth and schizogony (daughter-cell formation), requiring precise mechanisms of lipid synthesis and trafficking. Lipid transfer proteins (LTPs) at ER membrane contact sites (MCSs) have emerged as key for lipid distribution processes but remain largely unexplored in protozoans. Here we use the ER adaptor VAP to identify essential mechanisms of lipid transfer at ER-MCSs in P. falciparum. One PfVAP-interacting LTP was the bridge-like PfVPS13L1, which allows bulk flow of lipids between two apposed membranes. PfVPS13L1 bridges the ER with the nascent inner membrane complex (IMC), a de novo-generated organelle required for schizogony. Its loss-of-function reduced IMC growth and led to smaller anucleated progeny, impairing schizogony. Our data supports a model in which VPS13L1 is critical for the formation of apicomplexan invasive stages by mediating bulk transfer of lipids from the ER to the growing IMC.

cell biology↗

Epiproteomic control of the epitranscriptome drives cortical neurogenesis

Neurological conditions are the leading cause of ill health worldwide. Here, we show that the neurodevelopmental disorder-associated ubiquitin ligase UBE3C regulates the cellular composition of the murine cerebral cortex and human brain organoids, with its loss favoring neurogenesis and suppressing glial fate. Using genetic complementation, we demonstrate that disease-associated UBE3C mutations alter its autoubiquitination activity and disrupt cortical lamination. Proteomic profiling of UBE3C-deficient forebrains and organoids identifies Cbll1 as a UBE3C substrate, and we show that the UBE3C-Cbll1 duo drives N6-methyladenosine (m6A) mRNA methylation. Hyperactivation of m6A writers in UBE3C-deficient neural progenitors impairs cell cycle exit, a defect reversible in vivo by the METTL3 inhibitor STM2457. Our findings uncover an epiproteomic mechanism controlling m6A-mediated gene expression and define a regulatory axis linking ubiquitin signaling to epitranscriptomic control of neural fate. This work provides a mechanistic framework for understanding neurodevelopmental disorders and highlights potential therapeutic strategies.

cell biology↗

A cross-species multimodal database of gene expression in cardiac hypertrophy

Changes in gene expression determine the pathophysiological response of the heart during increased workload and biomechanical stress.1,2 Understanding the complex gene expression regulation during physiological and pathological stress provides insight into mechanisms that mediate the transition from cardiac hypertrophy to heart failure. We curated and generated a multi-omics database of cardiac hypertrophy and heart failure and exemplified its usage by evaluating the regulation of UCK2, a gene that belongs to a conserved cardiomyocyte hypertrophy gene expression signature with unknown function in heart disease. To provide the community with simple access to the database, we developed CHEERIO (Cardiac HypErtrophy gEne expRessIOn Database), a free and easy-to-use interactive web application to explore rodent and human gene expression during early, late, physiological and pathological cardiac hypertrophy, as well as heart failure at transcriptome, translatome, proteome, bulk and single-cell resolution. CHEERIO is freely available at https://voelkerslab.shinyapps.io/CHEERIO/.

physiology↗

Image-based screens identify regulators of endogenous Dvl2 biomolecular condensates

Dishevelled (Dvl) proteins are essential transducers in Wnt signaling pathways, which have been implicated in development, stem cell maintenance, and human diseases such as cancer. Several studies have shown that Dvl proteins form dynamic biomolecular condensates. However, how cellular signals and cell states influence the formation of biomolecular condensates remains poorly understood. Here, we analyzed cells with endogenous Dvl2 condensates using image-based cell sorting in combination with phosphoproteomics and identified protein enrichment for Wnt/PCP signaling and the G2/M cell cycle transition. We then performed an image-based high-throughput screen to identify small molecule kinase inhibitors that affect Dvl2 liquid-liquid phase separation. Strikingly, CK1{delta}/{varepsilon} inhibition blocked Dvl2 condensate formation. Its effect on Wnt signaling was modulated in genetic epistasis experiments with loss-of-function alleles of APC, Axin1, and MCC. Our study highlights the interplay between post-translational modifications and condensate dynamics, opening new avenues for research on their role in cellular signaling and disease intervention.

cell biology↗