Biology subjects

Daniels, M.

Publications and source records attributed to Daniels, M..

10 recordsLinked to original sources

bioRxiv2024

Single-cell trait diversity explains niche and fitness differences in aquatic microbial communities

Two fundamental questions in ecology are how biodiversity is maintained and how it affects ecosystem functioning. Until now, it has been difficult to study the above mechanisms in natural microbial communities, yet they are important drivers of biogeochemical ecosystem functions. Here, we use a new approach to define and measure biodiversity in complex lake microbial communities (Lake Cadagno, Switzerland) based on the cell-to-cell variation in multiple functionally relevant phenotypic traits. We use stable isotope probing coupled to correlative imaging using confocal laser scanning microscopy (CLSM) and nanometer-scale secondary ion mass spectrometry (NanoSIMS) to obtain morphological (size), physiological (pigments) and metabolic (carbon and nitrogen isotope uptake and sulfur content) traits for a large number of individual cells along the environmental gradient found across lake depth. We show that cell-to-cell trait variation is significantly correlated with cell densities as a proxy for ecosystem functioning, whereas genetic diversity measured at the level of 16S and 18S is not. Our single-cell analysis provides evidence for a simultaneous increase in niche partitioning (measured as increased evenness in pigment composition) and decrease in fitness differences (measured as decreased variability in sulfur content) due to light limitation and competition for nutrients in deep layers of the lake. This leads to a negative relationship between niche and fitness differences. Our results suggest that niche and fitness differences in natural microbial communities can be understood at the level of single-cell traits, providing a mechanistic understanding of the relationship between microbial diversity and ecosystem functioning.

microbiology↗

bioRxiv2023

Interspecies interactions determine growth dynamics of biopolymer degrading populations in microbial communities.

Microbial communities perform essential ecosystem functions such as the remineralization of organic carbon that exists as biopolymers. The first step in mineralization is performed by biopolymer degraders, which harbor enzymes that can break down polymers into constituent oligo- or monomeric forms. The released nutrients not only allow degraders to grow, but also promote growth of cells that either consume the breakdown products, i.e., exploiters, or consume metabolites released by the degraders, i.e., scavengers. It is currently not clear how such remineralizing communities assemble at the microscale - how interactions between the different guilds influence their growth and spatial distribution, and hence the development and dynamics of the community. Here we address this knowledge gap by studying marine microbial communities that grow on the abundant marine biopolymer alginate. We used batch growth assays and microfluidics coupled to time-lapse microscopy to quantitatively investigate growth and spatial distribution of single cells. We found that the presence of exploiters or scavengers alters the spatial distribution of degrader cells. In general, exploiters and scavengers - which we collectively refer to as consumer cells - slowed down the growth of degrader cells. In addition, coexistence with consumers altered the production of the extracellular enzymes that breakdown polymers by degrader cells. Our findings reveal that ecological interactions by non-degrading community members have a profound impact on the functions of microbial communities that remineralize carbon biopolymers in nature. ImportanceBiopolymers are the most abundant source of carbon on the planet and their breakdown by microbial degraders releases metabolic products that allow cross-feeding cells to grow and fuel the assembly of microbial communities. While it is known that the growth of degraders can facilitate growth of downstream cross-feeders in microbial communities, it has remained generally unclear if and how cross-feeders influence growth of degraders. Bridging this knowledge gap is important because degraders primarily drive the remineralization of carbon, a central process in the carbon cycle. We found that the presence cross-feeders can influence the growth of degraders by altering their spatial distribution as well as extracellular breakdown enzyme activity. Our study sheds light on the role of microbial interactions in shaping the rate of carbon remineralization in nature.

microbiology↗

bioRxiv2023

Human primary plaque cell cultures to study mechanisms of atherosclerosis

Plaque smooth muscle cells are critical players in the initiation and advancement of atherosclerotic disease. They produce extracellular matrix (ECM) components, which play a role in lesion progression and stabilization. Despite clear phenotypic differences between plaque smooth muscle cells and vascular smooth muscle cells (VSMCs), VSMCs are still widely used as a model system in atherosclerotic research. Here we present a conditioned outgrowth method to isolate plaque smooth muscle cells. We obtained plaque cells from 27 donors (24 carotid and 3 femoral endarterectomies). We show that these cells keep their proliferative capacity for eight passages, are transcriptionally stable, retain donor-specific gene expression programs, and express extracellular matrix proteins (FN1, COL1A1, DCN) and smooth muscle cell markers (ACTA2, MYH11, CNN1). Single-cell transcriptomics of plaque tissue and cultured cells reveals that cultured plaque cells closely resemble the myofibroblast fraction of plaque smooth muscle cells. Chromatin immunoprecipitation sequencing (ChIP-seq) shows the presence of histone H3 lysine 4 dimethylation (H3K4me2) at the MYH11 promoter, pointing to their smooth muscle cell origin. Finally, we demonstrated that plaque cells can be efficiently transduced (>97%) and are capable to take up oxidized LDL (oxLDL) and undergo calcification. In conclusion, we present a method to isolate and culture primary human plaque cells that retain plaque myofibroblast-like cells phenotypical and functional capabilities - making them a suitable in vitro model for studying selected mechanisms of atherosclerosis.

cell biology↗

bioRxiv2023

Female gene networks are expressed in myofibroblast-like smooth muscle cells in vulnerable atherosclerotic plaques.

Women presenting with coronary artery disease (CAD) more often present with fibrous atherosclerotic plaques, which are currently understudied. Phenotypically modulated smooth muscle cells (SMCs) contribute to atherosclerosis in women. How these phenotypically modulated SMCs shape female versus male plaques is unknown. Here, we show sex-stratified gene regulatory networks (GRNs) from human carotid atherosclerotic tissue. Prioritization of these networks identified two main SMC GRNs in late-stage atherosclerosis. Single-cell RNA-sequencing mapped these GRNs to two SMC phenotypes: a phenotypically modulated myofibroblast-like SMC network and a contractile SMC network. The myofibroblast-like GRN was mostly expressed in plaques that were vulnerable in females. Finally, mice orthologs of the female myofibroblast-like genes showed retained expression in advanced plaques from female mice but were downregulated in male mice during atherosclerosis progression. Female atherosclerosis is driven by GRNs that promote a fibrous vulnerable plaque rich in myofibroblast-like SMCs.

bioinformatics↗

bioRxiv2022

Small molecule inhibition of multiple RNA binding proteins underlies Musashi-2 independent phenotypes

RNA binding proteins (RBPs) are key regulators of gene expression. Small molecules targeting these RBP-RNA interactions are a rapidly emerging class of therapeutics for treating a variety of diseases. Ro-08-2750 (Ro) is a small molecule inhibitor identified as a competitive inhibitor of Musashi(MSI)-RNA interactions. Here we show Ro potently inhibits adrenocortical steroidogenesis and viability independent of MSI2 in multiple cell lines. We identified Ro-interacting proteins using an unbiased proteome-wide approach and discovered it is broadly targeting RBPs. To confirm this finding, we leveraged the large-scale ENCODE data and found a subset of RBPs whose depletion phenocopies Ro inhibition. We conclude that Ro is a promiscuous inhibitor of multiple RBPs, many containing RRM1 domains. Moreover, we provide a general framework for validating the specificity and identifying targets of RBP inhibitors in a cellular context.

molecular biology↗

bioRxiv2022

Effects of interspecies interactions on marine community ecosystem function

Microbial communities perform key ecosystem processes collectively. One such process is the degradation of carbohydrate polymers, which are the dominant pool of organic carbon in natural environments. Carbohydrate polymers are often degraded in a stepwise manner. Individual steps are performed by different microbial species, which form trophic cascades with carbon polymers at the bottom and fully oxidised carbon at the top. It is widely believed that these trophic cascades are hierarchically organised, where organisms at each level rely on organisms at the levels below. However, whether and how the higher-level organisms can also affect processes at the lower levels is not well understood. Here we studied how carbohydrate polymer degradation mediated by secreted enzymes is affected by species at higher trophic levels, i.e., species that cannot produce the enzymes for polymer degradation but can grow in presence of the polymer degraders. We used growth and enzyme assays in combination with transcriptomics to study how chitin degradation by a number of Vibrio strains is affected by the presence of different cross-feeders that consume metabolic by-products. We found that interactions between the degraders and cross-feeders influence the rate of chitin degradation by the community. Furthermore, we show that this is a result of changes in chitinase expression by degraders. Overall, our results demonstrate that interactions between species can influence key ecosystem functions performed by individuals within microbial communities. These results challenge the perspective that trophic cascades based on metabolically coupled microbial communities are unidirectional and provide mechanistic insights into these downstream interactions.

microbiology↗

bioRxiv2022

Intercellular collectivity is governed by enzyme secretion strategies in marine polysaccharide degrading bacteria

Polysaccharide breakdown by bacteria requires the activity of enzymes that degrade polymers extracellularly. This generates a localized pool of breakdown products that are accessible to the enzyme producers themselves as well as to other organisms. Marine bacterial taxa often show marked differences in the production and secretion of degradative enzymes that break down polysaccharides. These differences can have profound effects on the pool of diffusible breakdown products and hence on the ecological dynamics. However, the consequences of differences in enzymatic secretions on cellular growth dynamics and interactions are unclear. Here we combine experiments and models to study the growth dynamics of single cells within populations of marine Vibrionaceae strains that grow on the abundant marine polymer alginate, using microfluidics coupled to quantitative single-cell analysis and mathematical modelling. We find that strains that have low extracellular secretions of alginate lyases show stronger aggregative behaviors compared to strains that secrete high levels of enzymes. One plausible reason for this observation is that low secretors require a higher cellular density to achieve maximal growth rates in comparison with high secretors. Our findings indicate that increased aggregation increases intercellular synergy amongst cells of low-secreting strains. By mathematically modelling the impact of the level of degradative enzyme secretion on the rate of oligomer loss to diffusion, we find that enzymatic capability modulates the propensity of cells within clonal populations to cooperate or compete with each other. Our experiments and models demonstrate that marine bacteria display distinct aggregative behaviors and intercellular interactions based on their enzymatic secretion capabilities when growing on polysaccharides.

microbiology↗

bioRxiv2022

Changes in interactions over ecological time scales influence single cell growth dynamics in a metabolically coupled marine microbial community

Microbial communities thrive in almost all habitats on earth. Within these communities, cells interact through the release and uptake of metabolites. These interactions can have synergistic or antagonistic effects on individual community members. The collective metabolic activity of microbial communities leads to changes in their local environment. As the environment changes over time, the nature of the interactions between cells can change. We currently lack understanding of how such dynamic feedbacks affect the growth dynamics of individual microbes and of the community as a whole. Here we study how interactions mediated by the exchange of metabolites through the environment change over time within a simple marine microbial community. We used a microfluidic-based approach that allows us to disentangle the effect cells have on their environment from how they respond to their environment. We found that the interactions between two species - a degrader of chitin and a cross-feeder that consumes metabolic by-products - changes dynamically over time as cells modify their environment. Cells initially interact positively and then start to compete at later stages of growth. Our results demonstrate that interactions between microbes are not static and depend on the state of the environment, emphasizing the importance of disentangling how modifications of the environment affects species interactions. This experimental approach can shed new light on how interspecies interactions scale up to community level processes in natural environments.

microbiology↗

bioRxiv2021

Human islet expression levels of Prostaglandin E2 synthetic enzymes, but not prostaglandin EP3 receptor, are positively correlated with markers of β-cell function and mass in non-diabetic obesity

Elevated islet production of prostaglandin E2 (PGE2), an arachidonic acid metabolite, and expression of Prostaglandin E2 Receptor subtype EP3 (EP3) are well-known contributors to the {beta}-cell dysfunction of type 2 diabetes (T2D). Yet, many of the same pathophysiological conditions exist in obesity, and little is known about how the PGE2 production and signaling pathway influences non-diabetic beta-cell function. In this work, plasma arachidonic acid and PGE2 metabolite levels were quantified in a cohort of non-diabetic and T2D human subjects to identify their relationship with glycemic control, obesity, and systemic inflammation. In order to link these findings to processes happening at the islet level, cadaveric human islets were subject to gene expression and functional assays. Interleukin-6 (IL-6) and cyclooxygenase-2 (COX-2) mRNA levels, but not those of EP3, positively correlated with donor body mass index (BMI). IL-6 expression also strongly correlated with the expression of COX-2 and other PGE2 synthetic pathway genes. Insulin secretion assays using an EP3-specific antagonist confirmed functionallyrelevant up-regulation of PGE2 production. Yet, islets from obese donors were not dysfunctional, secreting just as much insulin in basal and stimulatory conditions as those from non-obese donors as a percent of content. Islet insulin content, on the other hand, was increased with both donor BMI and islet COX-2 expression, while EP3 expression was unaffected. We conclude up-regulated islet PGE2 production may be part of the {beta}-cell adaption response to obesity and insulin resistance that only becomes dysfunctional when both ligand and receptor are highly expressed in T2D.

pharmacology and toxicology↗

bioRxiv2019

A translational kidney organoid system bolsters human relevance of clinical development candidate

A major challenge in drug discovery is gaining confidence in the human relevance of pre-clinical animal studies. While human iPSC-derived organoids offer exciting opportunities to address this, concerns about applicability and scalability remain. Here, we report a high-throughput organoid platform for assessment of kidney disease targeting compounds in a human system. We confirmed platform reproducibility by single cell RNA-Seq (scRNA-Seq) and derived a NanoString panel for efficient quality control (QC). Organoid transplantation in rats for 2 to 4 weeks promoted organoid maturation and vascularization. In functional studies, cyclosporine A (CsA) and GFB-887, a novel TRPC5 channel blocker, protected kidney organoids from injury. Pharmacodynamic studies with GFB-887 delivered orally to rats were also successfully performed in human transplanted organoids. These data show how human organoids can deliver confidence in taking development candidate compounds to the clinic, fulfilling their promise to revolutionize drug discovery.

genomics↗