Biology subjects

Ng, S. L.

Publications and source records attributed to Ng, S. L..

7 recordsLinked to original sources

bioRxiv2025

Cell-substrate friction controls biofilm development

Bacteria often live in biofilms, surface-attached communities that can form on nearly any surface, from coarse sands to smooth glass. It is often hypothesized that cell-substrate friction can impact biofilm growth and development on these disparate surfaces. However, the experimental difficulty in measuring the friction between a biofilm and its surface has limited our understanding of how friction forces impact emergent colony-level behaviors and morphologies. Here, we demonstrate that increasing cell-substrate friction increases the biofilm contact angle, which, in turn, decreases the horizontal biofilm range expansion rate. We first used individual-based simulations to isolate the impact of friction. In this simple model, we found that increasing friction increases biofilm contact angle, and, in turn, that the contact angle emerges from a simple dynamic force balance between cell-substrate friction, cell-cell steric forces, and cell-cell adhesion, reminiscent of Youngs equation for sessile liquid drops. We developed an approach to directly measure the friction between bacterial colonies and agar surfaces, and found that the friction between the substrate and the biofilm is higher on substrates made with higher agar weight percentage. Additionally, we observed that biofilm contact angles increase with friction, following a Young-equation-like balance. Finally, we found that contact angle increases with agar percentage for a wide range of bacteria, suggesting that the biophysical impact of friction may play a role for a wide array of microbes.

biophysics↗

bioRxiv2025

Macrophage-like vascular smooth muscle cells dominate early atherosclerosis and are inhibited by targeting iron regulation

Vascular smooth muscle cells (VSMCs) contribute dynamically to atherosclerosis at all stages but the molecular drivers of their phenotypic switching, especially during early plaque development, and how they contribute to plaque progression remain unclear. We performed spatial transcriptomics on 12 human aortic tissues with and without atherosclerotic plaque. Macrophage-like SMCs were the predominant cell-type in the atheroma, displaying high iron storage and dysregulation, confirmed by spatial elemental mapping with nuclear microscopy. The combination of soluble iron and oxidized LDL promoted foamy macrophage-like VSMC cell state transition, while chelation inhibited this switching. In vivo, iron dysregulation induced neointimal thickening and macrophage-like switching in wire-injured Ldlr-/- mice, which was significantly reversed by ferrostatin-1, a ferroptosis inhibitor. These data show how targeting iron regulation modifies the macrophage-like VSMC cell state, and inhibits disease progression in atherogenesis.

genomics↗

bioRxiv2022

Trade-offs constrain adaptive pathways to T6 survival

Many microbial communities are characterized by intense competition for nutrients and space. One way for an organism to gain control of these resources is by eliminating nearby competitors. The Type VI Secretion System (T6) is a nano-harpoon used by many bacteria to inject toxins into neighboring cells. While much is understood about mechanisms of T6-mediated toxicity, little is known about the ways that competitors can defend themselves against this attack, especially in the absence of their own T6. Here we use directed evolution to examine the evolution of T6 resistance, subjecting eight replicate populations of Escherichia coli to T6 attack by Vibrio cholerae. Over ~500 generations of competition, the E. coli evolved to survive T6 attack an average of 27-fold better than their ancestor. Whole genome sequencing reveals extensive parallel evolution. In fact, we found only two pathways to increased T6 survival: apaH was mutated in six of the eight replicate populations, while the other two populations each had mutations in both yejM and yjeP. Synthetic reconstruction of individual and combined mutations demonstrate that yejM and yjeP are synergistic, with yejM requiring the mutation in yejP to provide a benefit. However, the mutations we identified are pleiotropic, reducing cellular growth rates, and increasing susceptibility to antibiotics and elevated pH. These trade-offs underlie the effectiveness of T6 as a bacterial weapon, and help us understand how the T6 shapes the evolution of bacterial interactions. SignificanceBacteria are the most abundant organisms on Earth and often live in dense, diverse communities, where they interact with each other. One of the most common interactions is antagonism. While most research has focused on diffusible toxins (e.g., antibiotics), bacteria have also evolved a contact-dependent nano-harpoon, the Type VI Secretion System (T6), to kill neighboring cells and compete for resources. While the co-evolutionary dynamics of antibiotic exposure is well understood, no prior work has examined how targets of T6 evolve resistance. Here, we use experimental evolution to observe how an Escherichia coli target evolves resistance to T6 when it is repeatedly competing with a Vibrio cholerae killer. After 30 rounds of competition, we identified mutations in three genes that improve E. coli survival, but found that these mutations come at a cost to other key fitness components. Our findings provide new insight into how contact-dependent antagonistic interaction drives evolution in a polymicrobial community.

evolutionary biology↗

bioRxiv2022

Vertical growth dynamics of biofilms

During the biofilm life cycle, bacteria attach to a surface then reproduce, forming crowded, growing communities. Many theoretical models of biofilm growth dynamics have been proposed; however, difficulties in measuring biofilm height accurately across relevant time and length scales have prevented testing these models or their biophysical underpinnings empirically. Using white light interferometry, we measure the heights of microbial colonies with nanometer precision from inoculation to their final equilibrium height, producing a novel and detailed empirical characterization of vertical growth dynamics. We show that models relying on logistic growth or nutrient depletion fail to capture biofilm height dynamics on short and long time scales. Our empirical results support a simple model inspired by the fact that biofilms only interact with the environment through their interfaces. This interface model captures the growth dynamics from short to long time scales (10 minutes to 14 days) of diverse microorganisms, including prokaryotes like gram-negative and gram-positive bacteria and eukaryotes like aerobic and anaerobic yeast. This model provides heuristic value, highlighting the biophysical constraints that limit vertical growth as well as establishing a quantitative model for biofilm development.

biophysics↗

bioRxiv2022

Evolution of a cis-acting SNP that controls Type VI Secretion in Vibrio cholerae

Mutations in regulatory mechanisms that control gene expression contribute to phenotypic diversity and thus facilitate the adaptation of microbes and other organisms to new niches. Comparative genomics can be used to infer rewiring of regulatory architecture based on large effect mutations like loss or acquisition of transcription factors but may be insufficient to identify small changes in non-coding, intergenic DNA sequence of regulatory elements that drive phenotypic divergence. In human-derived Vibrio cholerae, the response to distinct chemical cues triggers production of multiple transcription factors that can regulate the Type VI Secretion System (T6), a broadly distributed weapon for interbacterial competition. However, to date, the signaling network remains poorly understood because no regulatory element has been identified for the major T6 locus. Here we identify a conserved cis-acting single nucleotide polymorphism (SNP) controlling T6 transcription and activity. Sequence alignment of the T6 regulatory region from diverse V. cholerae strains revealed conservation of the SNP that we rewired to interconvert V. cholerae T6 activity between chitin-inducible and constitutive states. This study supports a model of pathogen evolution through a non-coding cis-regulatory mutation and preexisting, active transcription factors that confers a different fitness advantage to tightly regulated strains inside a human host and unfettered strains adapted to environmental niches. ImportanceOrganisms sense external cues with regulatory circuits that trigger the production of transcription factors, which bind specific DNA sequences at promoters ("cis" regulatory elements) to activate target genes. Mutations of transcription factors or their regulatory elements create phenotypic diversity, allowing exploitation of new niches. Waterborne pathogen Vibrio cholerae encodes the Type VI Secretion System "nanoweapon" to kill competitor cells when activated. Despite identification of several transcription factors, no regulatory element has been identified in the promoter of the major Type VI locus, to date. Combining phenotypic, genetic, and genomic analysis of diverse V. cholerae strains, we discovered a single nucleotide polymorphism in the Type VI promoter that switches its killing activity between a constitutive state beneficial outside hosts and an inducible state for constraint in a host. Our results support a role for non-coding DNA in adaptation of this pathogen.

microbiology↗

bioRxiv2020

Accumulation of dead cells from contact killing facilitates coexistence in bacterial biofilms

Bacterial communities govern their composition using a wide variety of social interactions, some of which are antagonistic. Many antagonistic mechanisms, such as the Type VI Secretion System (T6SS), require killer cells to directly contact target cells. The T6SS is hypothesized to be a highly potent weapon, capable of facilitating the invasion and defense of bacterial populations. However, we find that the efficacy of the T6SS is severely limited by the material consequences of cell death. Through experiments with Vibrio cholerae strains that kill via the T6SS, we show that dead cell debris quickly accumulates at the interface that forms between competing strains, preventing contact and thus preventing killing. While previous experiments have shown that T6SS killing can reduce a population of target cells by as much as one-million-fold, we find that as a result of the formation of dead cell debris barriers, the impact of T6SS killing depends sensitively on the initial concentrations of killer and target cells. Therefore, while the T6SS provides defense against contacting competitors on a single cell level, it is incapable of facilitating invasion or the elimination of competitors on a community level.

microbiology↗

bioRxiv2017

Gene neighbourhood integrity disrupted by CTCF loss in vivo

The mammalian genome is coiled, compacted and compartmentalized into complex non-random three-dimensional chromatin loops in the nucleus1-3. At the core of chromatin loop formation is CCCTC-binding factor (CTCF), also described as a \"weaver of the genome\"45. Anchored by CTCF, chromatin loops are proposed to form through a loop extrusion process6, organising themselves into gene neighbourhoods2 that harbour insulated enhancer-promoter domains, restricting enhancer activities to genes within loops, and insulating genes from promiscuous interactions outside of loops2,7-9. Studies targeting CTCF binding site deletions at gene neighbourhood boundaries result in localised gene expression dysregulation8,10-12, and global CTCF depletion recently showed CTCF to be crucial for higher hierarchical chromatin organisation of topologically associating domains (TADs)13. However, the role for CTCF in maintaining sub-TAD CTCF gene neighbourhoods and how gene transcription is affected by CTCF loss remains unclear. In particular, how CTCF gene neighbourhoods govern genome-wide enhancer-promoter interactions require clarification. Here, we took an in vivo approach to assess the global dissolution of CTCF anchored structures in mouse cardiomyocyte-specific Ctcf-knockout (Ctcf-KO), and uncovered large-scale ectopic de novo Enhancer-Promoter (E-P) interactions. In vivo cardiomyocyte-specific Ctcf-KO leads to a heart failure phenotype14, but our analysis integrates genome-wide transcription dysregulation with aberrant E-P interactions in context of CTCF-loop structures, identifying how genes engage their E-P interactions, requiring CTCF looping for their maintenance. Our study points to a mammalian genome that possesses a strong propensity towards spontaneous E-P interactions in vivo, resulting in a diseased transcriptional state, manifest as organ failure. This work solidifies the role of CTCF as the central player for specifying global E-P connections.

genomics↗