Biology subjects

Lyons, A.

Publications and source records attributed to Lyons, A..

9 recordsLinked to original sources

bioRxiv2026

The 3D Ultrastructure of C. elegans Gut Granules

We identify an endoderm-restricted organelle in published volume electron microscopy datasets of C. elegans embryos. The organelle consists of a tubular ring surrounding a membrane-bound compartment harboring a prominent dense particle and exhibits a basal polarity and size concordant with canonical gut granules. This finding offers ultrastructural detail to recent evidence that gut granules are bi-lobed organelles with two distinct compartments.

cell biology↗

bioRxiv2026

Systematic discovery of a topical bacterial consortium that targets Staphylococcus aureus to treat atopic dermatitis

Atopic dermatitis (AD) flares are frequently accompanied by Staphylococcus aureus overgrowth and activation of quorum sensing-regulated virulence pathways that amplify inflammation and barrier dysfunction. Because commensal members of the skin microbiome can inhibit S. aureus colonization and virulence, we hypothesized that a consortium sourced from healthy human skin could therapeutically target S. aureus and ameliorate AD. We curated 180 skin-derived bacterial strains and used kChip, an ultrahigh-throughput coculture platform, to profile S. aureus physiological response to over four million combinations consisting of two, three, or seven cocultured strains. This screening identified Ensemble No.2 (ENS-002), a three-strain consortium that strongly suppressed S. aureus growth and virulence in follow-up microtiter assays and a Reconstructed Human Epidermis S. aureus Activity (RHESA) model. ENS-002 is now undergoing development as a topical live biotherapeutic product (LBP) treatment for AD.

microbiology↗

bioRxiv2025

Deciphering the mechanism of protein aggregation and effects of inhibitors using single-molecule mass photometry

Aggregation of misfolded proteins is a prominent feature of many diseases and hence an attractive drug target. However, the small oligomers that are critical early species in the aggregation cascade are difficult to monitor directly owing to their heterogeneity and transience, complicating efforts to define aggregation mechanisms and target oligomers therapeutically. Here, we observe changes in oligomer populations directly using single-molecule mass photometry (SMMP). Studying the pathogenic P301L mutant of tau protein linked to frontotemporal dementia, we globally fit the growth/decay kinetics for every oligomer population observed by SMMP to microscopic models of aggregation. A simple extension to the best-fit model also accounts for amyloid fibril kinetics, as monitored by Thioflavin T fluorescence, providing the first quantitative model of aggregation kinetics across all stages of the cascade based on direct observation. Crucially, we find that models fitting amyloid kinetics alone fail to capture oligomer behavior, implying that--contrary to standard practice--amyloid kinetics cannot be relied on to deduce aggregation mechanisms. Furthermore, there is no single rate-limiting nucleation step preceding rapid growth, as generally assumed, suggesting that standard models of aggregation are overly simplistic. Repeating the analysis in the presence of aggregation inhibitors allows identification of the discrete steps in the cascade affected by the inhibitors. This work presents a powerful new approach for defining protein aggregation mechanisms and the mechanism of action of inhibitors, with applications to understanding many diseases and developing novel therapeutics.

biophysics↗

bioRxiv2025

Tumbleweed: an artificial motor protein that walks along a DNA track

Summary ParagraphMolecular motors are fundamental to life1-6 because of their ability to convert chemical energy into mechanical work, an ability that is conferred by the chemical and structural complexity of their constituent proteins. Scientists have long sought to create artificial protein motors that may reveal insights into how biological motors function. While artificial molecular motors based on small molecules7 and DNA8,9 have been developed, creating an artificial motor protein has remained an elusive goal in synthetic biology10. Here we demonstrate the realization of an artificial protein motor called Tumbleweed (TW) that walks directionally along a DNA track under external control. TW consists of three legs, each with a ligand-gated DNA-binding domain that enables selective interaction with specific sites along a DNA track11. Using single-molecule fluorescence assays and a programmable microfluidic device, we show that TW steps directionally along a designed DNA track in response to a defined sequence of ligand inputs. We built our TW molecular walker using a modular approach, combining existing proteins with known properties to achieve emergent motor function, similar to how Nature evolves new proteins. Our design strategy thus offers a a platform for engineering advanced and dynamic protein functionality. Our demonstration of TW walking represents a step toward developing fully autonomous protein motors and opens new avenues for uncovering and leveraging the principles by which biological motors transduce chemical energy into motion.

biophysics↗

bioRxiv2022

Quantifying oligomer populations in real time during protein aggregation using single-molecule mass photometry

Protein aggregation is a hallmark of many neurodegenerative diseases. The early stages of the aggregation cascade are crucial because small oligomers are thought to be key neurotoxic species, but they are difficult to study because they feature heterogeneous mixtures of transient states. We show how the populations of different oligomers can be tracked as they evolve over time during aggregation by using single-molecule mass photometry to measure individually the masses of the oligomers present in solution. Applying the approach to tau protein, whose aggregates are linked to diseases including Alzheimers and frontotemporal dementia, we found that tau existed in an equilibrium between monomers, dimers, and trimers before aggregation was triggered. Once aggregation commenced, the monomer population dropped continuously, paired first with a rise in the population of the smallest oligomers and then a steep drop as the protein was incorporated into larger oligomers and fibrils. Fitting these populations to kinetic models allowed different models of aggregation to be tested, identifying the most likely mechanism and quantifying the microscopic rates for each step in the mechanism. This work demonstrates a powerful new approach for characterizing previously inaccessible regimes in protein aggregation and building quantitative mechanistic models.

biophysics↗

bioRxiv2020

Structural dynamics of the SARS-CoV-2 frameshift-stimulatory pseudoknot reveal topologically distinct conformers

The RNA pseudoknot that stimulates -1 programmed ribosomal frameshifting in SARS coronavirus-2 (SARS-CoV-2) is a possible drug target. To understand how this 3-stemmed pseudoknot responds to the mechanical tension applied by ribosomes during translation, which is thought to play a key role during frame-shifting, we probed its structural dynamics under tension using optical tweezers. Unfolding curves revealed that the frameshift signal formed multiple different structures: at least two distinct pseudoknotted conformers with different unfolding forces and energy barriers, as well as alternative stem-loop structures. Refolding curves showed that stem 1 formed first in the pseudoknotted conformers, followed by stem 3 and then stem 2. By extending the handle holding the RNA to occlude the 5' end of stem 1, the proportion of the different pseudoknot conformers could be altered systematically, consistent with structures observed in cryo-EM images and computational simulations that had distinct topologies: the 5' end of the RNA threaded through the 3-helix junction to form a ring-knot, or unthreaded as in more standard H-type pseudoknots. These results resolve the folding mechanism of the frameshift signal in SARS-CoV-2 and highlight the dynamic conformational heterogeneity of this RNA, with important implications for structure-based drug-discovery efforts.

biophysics↗

bioRxiv2020

Sequence-dependent mechanics of collagen reflect its structural and functional organization

Extracellular matrix mechanics influence diverse cellular functions, yet surprisingly little is known about the mechanical properties of their constituent collagen proteins. In particular, network-forming collagen IV, an integral component of basement membranes, has been far less studied than fibril-forming collagens. A key feature of collagen IV is the presence of interruptions in the triple-helix-defining (Gly-X-Y) sequence along its collagenous domain. Here, we used atomic force microscopy (AFM) to determine the impact of sequence heterogeneity on the local flexibility of collagen IV and of the fibril-forming collagen III. Our extracted flexibility profile of collagen IV reveals that it possesses highly heterogeneous mechanics, ranging from semi-flexible regions as found for fibril-forming collagens to a lengthy region of high flexibility towards its N terminus. A simple model in which flexibility is dictated only by the presence of interruptions fit the extracted profile reasonably well, providing insight into the alignment of chains and demonstrating that interruptions - particularly when coinciding in multiple chains - significantly enhance local flexibility. To a lesser extent, sequence variations within the triple helix lead to variable flexibility, as seen along the continuously triple-helical collagen III. We found this fibril-forming collagen to possess a high-flexibility region around its matrix-metalloprotease (MMP) binding site, suggesting a unique mechanical fingerprint of this region that is key for matrix remodeling. Surprisingly, proline content did not correlate with local flexibility in either collagen type. We also found that physiologically relevant changes in pH and chloride concentration did not alter the flexibility of collagen IV, indicating such environmental changes are unlikely to control its compaction during secretion. Although extracellular chloride ions play a role in triggering collagen IV network formation, they do not appear to modulate the structure of its collagenous domain. Significance StatementCollagens are the predominant proteins in vertebrates, forming diverse hierarchical structures to support cells and form connective tissues. Despite their mechanical importance, surprisingly little is established about the molecular encoding of mechanics. Here, we image single collagen proteins and find that they exhibit variable flexibility along their backbones. By comparing collagens with continuous and discontinuous triple-helix-forming sequences, we find that the type of helix interruption correlates with local flexibility, providing the first steps towards a much-needed map between sequence, structure, and mechanics in these large proteins. Our results inform our understanding of collagens ability to adopt compact conformations during cellular secretion and suggest a physical mechanism by which higher-order structure may be regulated by the distinct molecular properties of different collagens.

biophysics↗

bioRxiv2019

Global Genetic Cartography of Urban Metagenomes andAnti-Microbial Resistance

We have created a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities across 3 years. This is the first systematic, worldwide study cataloging the urban microbial ecosystem. We identify taxonomically-defined microorganisms collected across three years. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics AMR markers, and novel genetic elements, including 10,928 viral, 1302 bacteria, and 2 archaea novel species. We identify 4,424 species of urban microorganisms and a consistent "core" of 31 species found in nearly all samples that is largely distinct from any human commensal microbiome. Profiles of AMR genes show geographic variation in type and density. Together, these results constitute a high-resolution, global metagenomic atlas, which enables the discovery of new genetic components, highlights potential forensic applications, and provides an essential first draft of the global AMR burden of the worlds cities.

microbiology↗

bioRxiv2018

Conformational flexibility of collagen molecules: composition and environmental effects

The predominant structural protein in vertebrates is collagen, which plays a key role in extracellular matrix and connective tissue mechanics. Despite its prevalence and physical importance in biology, the mechanical properties of molecular collagen are far from established. The flexibility of its triple helix is unresolved, with descriptions from different experimental techniques ranging from flexible to semirigid. Furthermore, it is unknown how collagen type (homo-vs. heterotrimeric) and source (tissue-derived vs. recombinant) influence flexibility. Using SmarTrace, a chain tracing algorithm we devised, we performed statistical analysis of collagen conformations collected with atomic force microscopy (AFM) to determine the proteins mechanical properties. Our results show that types I, II and III collagens - the key fibrillar varieties - exhibit molecular flexibilities that are very similar. However, collagen conformations are strongly modulated by salt, transitioning from compact to extended as KCl concentration increases, in both neutral and acidic pH. While analysis with a standard worm-like chain model suggests that the persistence length of collagen can attain almost any value within the literature range, closer inspection reveals that this modulation of collagens conformational behaviour is not due to changes in flexibility, but rather arises from the induction of curvature (either intrinsic or induced by interactions with the mica surface). By modifying standard polymer theory to include innate curvature, we show that collagen behaves as an equilibrated curved worm-like chain (cWLC) in two dimensions. Analysis within the cWLC model shows that collagens curvature depends strongly on pH and salt, while its persistence length does not. Thus, we find that triple-helical collagen is well described as semiflexible, irrespective of source, type, pH and salt environment. These results demonstrate that collagen is more flexible than its conventional description as a rigid rod, which may have implications for its cellular processing and secretion.

biophysics↗