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Biology subjects

Schmidt, R.

Publications and source records attributed to Schmidt, R..

At least 19 recordsLinked to original sources

Localization accuracy in single-molecule fluorescence microscopy

The two prevalent methods to determine the position of individual fluorophores in the focal plane of a microscope rely either on the centroid of the fluorescence pattern produced by the fluorophore on a camera or on targeting the fluorophore's coordinate with a spatially controlled illumination minimum, as realized in MINFLUX. In both methods, (sub)nanometer localization precisions have been reached, but little is known about their accuracy, i.e., the deviation of the obtained coordinate from its ground truth. Here we report a theoretical and experimental comparison of the accuracy provided by these two strategies. We quantify substantial systematic errors in camera-based localization due to the interplay of two difficult-to-control parameters: the orientation of the fluorophore in space and its axial deviation from the focal plane (defocus). For example, within an axial range of {+/-}120 nm around the focus, the median distance between two fluorophores on a nanobody measured by camera-based localization varies by 26.5 nm. Under the same conditions, a commercial MINFLUX system yields a median variation in distance of 1.4 nm, indicating an improvement in accuracy by an order of magnitude. The accuracy of MINFLUX localization can be further improved to (sub-)[a]ngstrom levels by reducing the average distance between the coordinates targeted by the illumination minimum and the fluorophore. As it delivers unrivaled precision and accuracy for mapping fluorophores and their distances, we consider coordinate-targeted localization essential for studying labeled cells at the sub-10 nm level and for exploring structural and conformational changes of labeled biomolecules.

biophysics↗

Thermoplastic polyurethane as a base material for soft, high-density neural interfaces

Polymers used as substrate and encapsulation for implantable devices are typically deposited layer-by-layer, leaving polymer-polymer interfaces that adhere poorly and become a critical failure point. Thermoplastic polyurethane (TPU) elastomers combine four properties not found together in any other candidate: decades of clinical use in long-term implants and availability in medical grade, a stiffness well below that of polyimide and parylene C, compatibility with microfabrication, and thermoplastic self-fusion, which removes the polymer-polymer interface entirely. This work introduces TPU as a base material for soft, high-density neural interfaces and demonstrates one route to realizing them. Gold is patterned on a sacrificial copper sheet by maskless lithography and transferred into TPU by vacuum lamination, giving conformally coated tracks down to 15 um at 30 um pitch within a single, merged polymer body. An additional electroplating step produces a nanostructured pinecone gold surface that increases the electrochemically active area of the electrodes, approximately doubling the charge injection capacity. Daisy-chain silicon chips were also embedded within the soft polymer body. The films transmit up to 88% at 470 nm, a wavelength commonly used for optogenetics. TPU showed no cytotoxicity towards differentiated SH-SY5Y cells and only a mild tissue response after 9.5 months of subcutaneous implantation in rats.

bioengineering↗

A genome-wide CRISPR activation map of surface protein expression in human CD4 T cells

Surface proteins define T cell identity and function, but the abundance of each protein is not determined by transcription alone. Existing genome-wide CRISPR screens in primary human T cells either profile the transcriptome or isolate cells based on a single functional or protein phenotype. Here we present SCITO-Perturb-seq, a novel platform that couples combinatorial-indexed single-cell cytometry sequencing with pooled CRISPR activation (CRISPRa) to map the causal regulation of 201 surface proteins across 3.6 million human CD4 T cells. We find that 16% of activated genes significantly alter the expression of at least one surface protein. By applying semi-nonnegative matrix factorization to the perturbation effect matrix, we identified five modules corresponding to known CD4 T cell states. Notably, these modules group surface proteins by their shared response to perturbation, revealing coordinated regulation of proteins that are not co-expressed in unperturbed cells. SCITO-Perturb-seq represents the first genome-wide CRISPRa screen paired with direct, high-dimensional surface protein profiling, providing a comprehensive regulatory map of the CD4 T cell surface proteome.

genomics↗

Tunable Expression of an AAV Payload Using ADAR-mediated RNA Editing

A challenge of "once-and-done" adeno associated virus (AAV)-based gene therapy is the inability to modulate the level of therapeutic protein expression post-administration. Herein, we demonstrate the utility of an adenosine deaminase acting on RNA (ADAR) - mediated gene switch to control AAV-delivered gene expression. Using a premature termination codon (PTC) in the human Factor IX (hFIX) transgene, we established an ON switch, where expression of hFIX is contingent on rescuing the PTC mutation via RNA editing. In vitro and in vivo studies demonstrated silencing of the hFIX transgene by the PTC mutation and induction of protein expression by administration of an ADAR-recruiting trigger RNA. Mice transduced with a hepatotropic AAV capsid encoding an ApoE-hAAT hFIX-PTC transgene expression cassette showed a dose-dependent response between the levels of LNP-delivered trigger RNA and the amount of plasma hFIX expression achieved. We observed predictable and reproducible levels of hFIX expression upon multiple rounds of RNA editing and demonstrated that this system can achieve clinically relevant levels of hFIX. This work suggests that ADAR-mediated RNA editing may be a valuable tool for tunable expression of therapeutic transgenes in applied gene therapies.

synthetic biology↗

TAOK3 inhibition constrains invasion, potentiates paclitaxel, and reprograms the tumor microenvironment toward anti-tumor immunity in cervical cancer

TAOK3 is a lesser-studied MAPK family serine/threonine kinase our group has shown to be targeted by HPV integration, suggesting a potential role in driving invasive cervical cancer (ICC). Here, we profiled TAOK3 expression in patient tumors, metastases, and cervical cancer models and localized TAOK3 within a tumor epithelial subpopulation by integrating two single-cell RNA-seq datasets. Functional consequences of TAOK3 loss were assessed with siRNA and CRISPRi in cell lines and 3D spheroids. In vivo effects were evaluated in intracervical xenografts with species-specific RNA-seq to resolve tumor versus microenvironmental responses. TAOK3 mRNA/protein were elevated in primary and metastatic ICC and primarily localized to a keratin-positive epithelial subset (T3epi) enriched for cadherin/S100 binding, vesicle/endocytic pathways, and leading-edge programs. TAOK3 silencing reprogrammed transcriptomes and proteomes toward reduced WNT/cell-cycle and motility signaling, altered endocytosis and cytoskeleton organization, and reshaped phospho-networks linked to chromatin remodeling and ERBB2-ERBB3/cytoskeletal kinase activity. Functionally, TAOK3 inhibition prolonged G2/M, suppressed invasion, and enhanced sensitivity to low dose paclitaxel. Prolonged inactivation induced methuosis-like cell death with extracellular ATP release. In xenografts, TAOK3 knockdown reduced tumor burden, downregulated KRT14--a leader cell marker--within the human tumor compartment, and enriched microenvironmental pathways for immune activation, with a specific decrease in CD206+ M2 macrophages. TAOK3 delineates an invasion-competent epithelial state in ICC and coordinates cell-cycle control, cytoskeleton-membrane dynamics, and tumor-immune crosstalk. Genetic or pharmacologic TAOK3 inhibition constrains tumor growth, potentiates paclitaxel, and remodels the microenvironment toward anti-tumor immunity, supporting TAOK3 as a potential therapeutic target and biomarker in ICC. Statement of SignificanceTAOK3 marks an invasion-competent epithelial subpopulation in cervical cancer. TAOK3 inhibition slows tumor growth, enhances chemoresponse, and reduces M2 macrophages, revealing TAOK3 as a potential therapeutic target and biomarker for patient stratification.

cancer biology↗

GCK-4 regulates apical actin organization and lumen formation in the C. elegans intestine

Epithelial tubes are an essential component of many organ systems. The formation of their lumens depends on the close coordination of epithelial polarity, the apical actin cytoskeleton, and apical junctions, yet the mechanisms that organize the apical cytoskeleton and junctions downstream of polarity remain poorly understood. Here, we identify the Ste20 family kinase GCK-4, the single C. elegans ortholog of the mammalian kinases LOK and SLK, as a critical regulator of intestinal lumen formation. GCK-4 localizes to the apical membrane during early lumen formation and to microvillar tips as these structures develop. Its loss results in a lethal cystic lumen phenotype, without disrupting the establishment of epithelial polarity, and in occasional failure to maintain attachment between the pharynx and intestine. Lumens in gck-4 mutant animals show irregular junction patterning, severely impaired apical accumulation of both actin and the membrane-actin linker Ezrin/Radixin/Moesin protein ERM-1, and microvilli atrophy. In Drosophila and mammalian cells, the GCK-4 orthologs are thought to organize the apical actin network largely through phosphorylation of ERM proteins. In contrast, ERM-1 phosphorylation is only partially reduced in gck-4 mutants and is not abolished, indicating that GCK-4 acts through additional targets and is not the principal ERM-1 kinase in the intestine. Together, these findings identify GCK-4 as a key regulator of apical actin and junction organization during lumen formation, and demonstrate that Ste20 kinases can control apical cytoskeletal architecture at least partially independently of ERM phosphorylation.

developmental biology↗

Intelliwaste: NMR of 13C-labeled Spent Media Enables Non-Invasive Metabolic Fingerprinting of Pluripotent Stem Cells and LIS1-Associated Neuropathology

Metabolic dysregulation is increasingly recognized as a key contributor to neurodevelopmental disorders. Here, we present Intelliwaste, a non-invasive, cost-effective method for profiling carbon metabolism in pluripotent stem cells and brain organoids using 13C-labeled metabolites and 1H and 13C NMR spectroscopy. This approach enables longitudinal analysis of extracellular fluxes without disrupting cell viability. We apply Intelliwaste to human embryonic stem cells (hESCs) cultured in a defined media enriched with >95% 13C1-Glucose. Under these conditions, 13C3-lactate emerged as the most abundant labeled product, with 20-50-fold lower fluxes to 13C3-alanine, 13C2-acetate, 13C3-serine, and 13C3-pyruvate, and 100-300-fold lower fluxes to 13C1-formate and multiple 13C-labeled glutamate species. These profiles allow for precise quantification of fractional metabolic isotopic labeling and glucose-derived carbon flow. To demonstrate biological utility, we first examine the effect of L-glutamine omission, which selectively reduces 13C3-alanine/13C3-lactate and 13C4-glutamate/13C3-lactate flux ratios, while the 13C3-Glutamate/13C3-Lactate and 13C2-Glutamate/13C3-Lactate flux ratios remained unchanged. These findings suggest a specific role for extracellular glutamine in modulating the activity of alanine aminotransferase and pyruvate carboxylase. We then characterized LIS1 mutant hESCs--a model of lissencephaly--and observed significantly increased flux ratios involving 13C4-, 13C3-, and 13C2-glutamate relative to 13C3-lactate, indicating enhanced glutamate production via the TCA cycle. These findings establish Intelliwaste as a powerful tool for metabolic profiling in the study of human neurodevelopment and disease. Its non-destructive nature makes it particularly well-suited for tracking metabolic changes during differentiation and in patient-derived organoid models of neurological disorders.

cell biology↗

Pre-myelinating oligodendrocyte ADGRG1 is required for axon ensheathment and CNS myelin formation

Myelin is essential for axonal health and rapid propagation of action potentials. In the central nervous system (CNS), myelination is initiated with axon ensheathment by pre-myelinating oligodendrocytes (preOLs), followed by iterative membrane wrapping and longitudinal extension along the axon. The molecular mechanisms that govern preOL development remain largely unknown. In this study, we identify the adhesion G protein-coupled receptor ADGRG1 (also called GPR56) as a key, evolutionarily conserved regulator of this process. We show that ADGRG1 is highly expressed in preOLs and that its conditional deletion in mouse preOLs leads to simplified preOL morphology and defective axon ensheathment, resulting in CNS hypomyelination. Live imaging in zebrafish demonstrated conserved function of Adgrg1 in axon ensheathment. Mechanistically, we show that ADGRG1 promotes preOL maturation by RhoA activation. Collectively, these findings reveal an ADGRG1-mediated RhoA signaling pathway that governs axon ensheathment and myelin formation.

neuroscience↗

Bayesian Nonparametric Identification of Frequency-Selective Neural Oscillatory States

Identifying neural oscillations is essential for linking fast brain dynamics to underlying cognitive processes. However, this is challenging because oscillatory events can be brief, embedded in 1/f-like background activity, and may comprise an unknown number of spectrally distinct states. Conventional approaches often apply narrowband band-pass filters to one or a few predefined frequency bands and then use amplitude thresholding to identify oscillatory events, but detection outcomes can be highly sensitive to these choices. Although recent unsupervised alternatives based on hidden Markov models (HMMs) address these limitations, they still require the number of states to be specified in advance and can underfit or overfit when this number is misspecified. We propose a Bayesian nonparametric method that identifies distinct oscillatory states while inferring an appropriate number of states directly from the data. This method combines time-delay embedding (TDE) with the Dirichlet-process Gaussian mixture model (DP-GMM). TDE augments the signal with time-shifted copies, enabling the DP-GMM to capture frequency-specific local autocovariance structures, while the Dirichlet-process prior adapts model complexity by pruning inactive components. We benchmarked the approach against a filter-based thresholding method and the time-delay embedded HMM using single-channel synthetic data designed to mimic neural time series (e.g., EEG, MEG, and local field potentials), with multiple frequency components masked by 1/f-like noise. In this setting, the proposed model reliably recovered multiple distinct frequency components under noisy conditions while also inferring the number of oscillatory states. Applied to a resting-state motor-cortex MEG dataset, the model identified multiple frequency-selective, short-lived oscillatory states alongside distinct aperiodic states with different spectral profiles. These states exhibited substantial inter-individual heterogeneity in peak frequency, occurrence rate, and power. Overall, this provides an unsupervised framework for discovering frequency-selective oscillatory states without predefining frequency bands or fixing the number of states.

neuroscience↗

Site-specific genome engineering of primary human natural killer cells for programmable anti-tumor function

Natural killer (NK) cells are emerging as a promising platform for engineered adoptive cell therapies. However, gene editing in NK cells remains challenging, and more effective strategies are needed. Here, we established a robust, feeder-free, and modular workflow for genome engineering in primary human NK cells, combining CRISPR/Cas9 with AAV6-mediated transgene delivery. Efficient site-specific transgene integration was achieved at various loci and can be coupled with concurrent disruption of the target locus in a single editing step. Furthermore, transgene expression was tunable according to the integration site and promoter. We applied this strategy to target a chimeric antigen receptor (CAR) transgene to a panel of inhibitory NK receptor loci, establishing a synergistic approach to enhance anti-tumor activity and facilitate the reliable comparison of CAR variants without expression bias. We identified TIGIT as an ideal locus that supports strong CAR expression and anti-tumor function. This genome engineering framework, which leverages multiple, complementary and precisely controlled genetic edits, can support the rational design of future NK-cell therapies tailored to overcome cell-intrinsic limitations and tumor-specific barriers.

immunology↗

Cross-kingdom degradomics identifies natural plant small RNAs with disease protecting activity

RNA interference (RNAi) is a highly specific process regulating genes transcriptionally or post-transcriptionally via silencing. small regulatory RNAs (sRNAs) provide the specificity of post-transcriptional silencing by binding to complementary mRNAs leading to their degradation or translational repression. sRNAs are promising non-chemical control agents against plant pests and diseases. Their application requires, however, a deep understanding of the determinants of functional specificity and efficiency. In nature, interacting plants and pathogens follow the manipulative strategy of cross-kingdom RNAi (ckRNAi) based on the targeted transfer of sRNAs. In this study, we employed a genome-wide approach to explore the diversity of natural ck-sRNAs exchanged in the pathogenic interaction of Brachypodium distachyon with the fungal pathogen Fusarium graminearum. By deep-sequencing of the cross-kingdom sRNAome, transcriptome and degradome 258 ckRNAi-mediating sRNAs were discovered. In a simulation-based approach, specific sequence characteristics allowed categorizing sRNAs into functionality classes. Subsequent genome annotation analyses revealed the organization of plant ck-sRNAs in long non-coding RNAs. Moreover, comparative sequence analyses revealed an evolution of ck-sRNAs towards invariant mRNA target regions. Functional analyses with sRNA candidates confirmed an antipathogenic activity at exceptionally low application doses. It indicates natural sRNA as untapped resource and potential blueprint for the development of highly specific and effective plant-derived bioprotectants.

plant biology↗

LGL-1 and the RhoGAP protein PAC-1 redundantly control polarization of the C. elegans embryonic epidermal epithelium

Apical-basal polarity is essential for epithelial organization and function and is established by conserved cortical polarity proteins. However, the requirements for canonical polarity factors vary between tissues and organisms. For example, the basolateral protein lethal giant larvae (Lgl) is essential for epithelial polarity in Drosophila but dispensable in C. elegans. To better define the epithelial polarity program in C. elegans, we performed a genome-wide RNAi screen for synthetic lethality with lgl-1. Combined loss of LGL-1 and the RhoGAP PAC-1 caused embryonic lethality due to elongation defects and epidermal rupture. Epidermal cells showed expansion of the apical domain and aPKC, accompanied by mislocalization of junctional proteins and LET-413Scribble. These defects indicate overactivity of apical polarity determinants. Consistently, partial inactivation of aPKC or CDC-42 suppressed lethality in pac-1; lgl-1 animals. Together, our results identify PAC-1 and LGL-1 as redundant inhibitors of apical polarity in the C. elegans embryonic epidermis and provide new insights into how conserved mechanisms are adapted across species.

developmental biology↗

Exploration of novel biomarkers for neurodegenerative diseases using proteomic analysis and ligand-binding assays

Neurodegenerative diseases are a major cause of morbidity and mortality world-wide, and their public health burden continues to increase. There is an urgent need to develop reliable and sensitive biomarkers to aid the timely diagnosis, disease progression monitoring, and therapeutic development for neurodegenerative disorders. Proteomic screening strategies, including antibody microarrays, are a powerful tool for biomarker discovery, but their findings should be confirmed using quantitative assays. The current study explored the feasibility of combining an exploratory proteomic strategy and confirmatory ligand-binding assays to screen for and validate biomarker candidates for neurodegenerative disorders. It analyzed cerebrospinal fluid (CSF) and plasma samples from patients with Alzheimers disease, Parkinsons disease, and multiple sclerosis and healthy controls. The screening antibody microarray identified differentially expressed proteins between patients with neurodegenerative diseases and healthy controls. Quantitative ligand-binding assays confirmed that cluster of differentiation 14 (CD14) levels were elevated in CSF of patients with Alzheimers disease, whereas osteopontin levels were increased in CSF of patients with Parkinsons disease. The current study demonstrated the utility of combining an exploratory proteomic approach and quantitative ligandbinding assays to identify biomarker candidates for neurodegenerative disorders. To further validate and expand these findings, large-scale analyses using well characterized samples should be conducted.

neuroscience↗

Robustness in Hopfield neural networks with biased memory patterns

Biological neural networks are able to store and retrieve patterns in the presence of different types of noise. Hopfield neural networks have been inspired by biological neural networks and provide a model for auto-associative memory patterns. An important parameter in these networks is the pattern bias, i.e. the mean activity level of the network, which is closely related to the degree of sparseness in the coding scheme. Here we studied the relation between robustness against different types of biologically-motivated noise and pattern bias. To do so, we developed performance and robustness measures, which are applicable to varying degrees of sparseness of the memory representations, using analytically-optimized thresholds and corruption tolerances adjusted by mutual information. We then applied these tools in numerical simulations and found that, for different types of noise, the pattern load, i.e. the number of patterns that the network has to store, determined which pattern bias is most robust. Across different types of noise, the higher the pattern load was, the more biased was the most robust performing pattern representation. Given the variation in the sparseness level in different brain regions, our findings suggest that memory pattern encoding schemes (i.e. degree of sparseness) in different brain regions might be adapted to the expected memory load in order to best mitigate the adverse effects of disruptions.

neuroscience↗

Adhesion G protein-coupled receptor ADGRG1 promotes protective microglial response in Alzheimer's disease

Germline genetic architecture of Alzheimers disease (AD) indicates microglial mechanisms of disease susceptibility and outcomes. However, the mechanisms that enable microglia to mediate protective responses to AD pathology remain elusive. Adgrg1 is specifically expressed in yolk-sac-derived microglia. This study reveals the role of yolk-sac-derived microglia in AD pathology, highlighting the function of ADGRG1 in modulating microglial protective responses to amyloid deposition. Utilizing both constitutive and inducible microglial Adgrg1 knockout 5xFAD models, we demonstrate that Adgrg1 deficiency leads to increased amyloid deposition, exacerbated neuropathology, and accelerated cognitive impairment. Transcriptomic analyses reveal a distinct microglial state characterized by downregulated genes associated with homeostasis, phagocytosis, and lysosomal functions. Functional assays in mouse models and human embryonic stem cells-derived microglia support that microglial ADGRG1 is required for efficient A{beta} phagocytosis. Together, these results uncover a GPCR-dependent microglial response to A{beta}, pointing towards potential therapeutic strategies to alleviate disease progression by enhancing microglial functional competence.

neuroscience↗

Reduced accrual of mineral-associated organic matter after two years of enhanced rock weathering in cropland soils, though no net losses of soil organic carbon

Enhanced rock weathering (ERW), the application of crushed silicate rock to soil, can remove atmospheric carbon dioxide by converting it to (bi)carbonate ions or solid carbonate minerals. However, few field studies have empirically evaluated ERW in field settings. A critical question remains as to whether additions of crushed rock might positively or negatively affect soil organic matter (SOM) - Earths largest terrestrial organic carbon (C) pool and a massive reservoir of organic nitrogen (N). Here, in three irrigated cropland sites in California, USA, we investigated the effect of crushed meta-basalt rock additions on different pools of soil organic carbon and nitrogen (i.e., mineral-associated organic matter and particulate organic matter), active microbial biomass, and microbial community composition. After two years of crushed rock additions, mineral-associated organic matter (MAOM) stocks were lower in the upper surface soil (0-10 cm) compared to unamended controls. At the two sites where baseline pre-treatment data were available, neither total SOC nor SON decreased over the two years of study in crushed rock or unamended control plots. However, the accrual rate of MAOM-C and MAOM-N at 0-10 cm was lower in plots with crushed rock vs. unamended controls. Before ERW is deployed at large scales, our results suggest that field trials should assess the effects of crushed rock on SOM pools, especially over multi-year time scales, to accurately assess changes in net C and understand the mechanisms driving interactions between ERW and SOM cycling.

ecology↗

Altered Extracellular Matrix Structure and Elevated Stiffness in a Brain Organoid Model for Disease

The viscoelasticity of tissues impacts their shape, as well as the growth and differentiation of their cells. Nevertheless, little is known about changes in viscoelastic properties during brain malformations. Lissencephaly is a severe malformation of cortical development caused by LIS1 mutations, which results in a lack of cortical convolutions. Here, we show that human-derived brain organoids with LIS1 mutation are stiffer than control ones at multiple developmental times. This stiffening is accompanied by abnormal ECM expression and organization, as well as elevated water content, as measured by diffusion-weighted MRI. Proteolytic cleavage of ECM components by short-term treatment with the catalytic subunit of MMP9 reduced the stiffening and water diffusion levels of mutated organoids to control levels. Finally, based on the molecular and rheological properties obtained, we generated a computational microstructure mechanical model that can successfully predict mechanical changes that follow differential ECM localization and integrity in the developing brain. Overall, our study reveals that LIS1 is essential for the expression and organization of ECM proteins during brain development, and its mutation leads to a substantial viscoelastic change. To our knowledge, this is the first study to elucidate how tissue mechanics change in disease states using human brain organoids.

developmental biology↗

Between a Warm Winter and a Cold Spell: Physiological Responses to Changing Winter Climate in Amphibians

Climate change is swiftly altering environmental winter conditions, leading to significant ecological impacts such as phenological shifts in many species. As a result, animals might face physiological mismatches due to longer or earlier activity periods and are at risk of being exposed to late spring freezes. Our study points for the first time to the complex physiological challenges that amphibians face as a result of changing thermal conditions due to winter climate change. We investigated the physiological responses to a period of warmer winter days and sudden spring freeze in the common toad (Bufo bufo) by acclimating them to 4{degrees}C or 8{degrees}C for 48 h or exposing them to 4{degrees}C or -2{degrees}C for 6 h, respectively. We assessed the daily energy demands, determined body condition and cold tolerance, explored the molecular responses to freezing through hepatic tissue transcriptome analysis, and measured blood glucose levels. Toads acclimated to higher temperatures showed a higher daily energy expenditure and a reduced cold tolerance suggesting faster depletion of energy stores and the loss of winter acclimation during warmer winters. Blood sugar levels were higher in frozen toads indicating the mobilization of cryoprotective glucose with freezing which was further supported by changed patterns in proteins related to glucose metabolism. Overall, our results emphasize that increased thermal variability incurs physiological costs that may reduce energy reserves and thus affect amphibian health and survival. This might pose a serious threat to breeding adults and may have subsequent effects at the population level.

ecology↗