Biology subjects

Thomson, A. R.

Publications and source records attributed to Thomson, A. R..

4 recordsLinked to original sources

bioRxiv2026

iPSC-Derived Chondroprogenitors as a Promising Cell Source for Cartilage Engineering: A Comparison with MSCs in Unmodified and Peptide-Functionalized Alginate Hydrogels

Articular cartilage degeneration is a hallmark of degenerative joint diseases, yet its limited regenerative capacity poses significant challenges for tissue engineering. While mesenchymal stem cells (MSCs) are the most commonly employed cell type in cartilage tissue engineering, they exhibit donor variability, restricted expansion capacity, and tendencies toward fibrocartilage formation and hypertrophic differentiation. Human induced pluripotent stem cell-derived chondroprogenitors (iCPs) represent a promising alternative, offering scalable production of developmentally relevant cells with intrinsic chondrogenic commitment. However, their performance within three-dimensional biomaterial scaffolds remains largely unexplored. Here, we compared chondrogenic differentiation of iCPs and MSCs within alginate hydrogels of varying stiffness (0.37 - 4.55 kPa) exhibiting physiologically relevant stress relaxation properties. Intermediate stiffness (2% alginate, ~2.17 kPa) optimally supported chondrogenesis for both cell types. While MSCs differentiated as single cells, iCPs spontaneously self-organized into cartilaginous aggregates without requiring a separate pellet pre-culture step, showing significantly higher hyaline indices and reduced COL10 expression, despite initial low viability in hydrogels. To further enhance chondrogenesis, we functionalized 2% alginate gels with RGD and HAVDI peptides mimicking integrin- and cadherin-mediated signaling. HAVDI/RGD functionalization significantly enhanced hyaline cartilage marker expression in both cell types, with iCPs exhibiting superior matrix composition characterized by elevated aggrecan and SOX9 expression and reduced COL10 and MMP13 compared to MSCs. These findings establish iCPs as a promising cell source for cartilage tissue engineering and disease modeling, particularly within biomaterials integrating mechanical and bioactive cues that recapitulate the native cartilage microenvironment.

cell biology↗

bioRxiv2025

Characterising the association between posterior parietal metabolite levels and cortical macrostructure in a cohort spanning childhood to adulthood.

Postnatal brain development is characterised by dynamic macrostructural changes, including cortical thinning and cortical flattening during childhood and adolescence. These macro-structural changes are parallel with developmental changes in brain neurochemistry, probed in the human brain using Magnetic Resonance Spectroscopy (MRS). This includes neurotransmitters such glutamate and gamma-aminobutyric acid (GABA), as well as building blocks of neuronal and associated tissue such as N-acetyl aspartate (NAA), and those involved in metabolism such as creatine (Cr). While previous research has linked MRS-measured neuro-metabolite levels to bulk tissue composition (e.g., gray matter, white matter, and cerebrospinal fluid), the relationship between neurochemistry and more granular macrostructural metrics, such as cortical thickness, area, volume, and local gyrification, remains unexplored. This study investigates the association between MRS-measured neuro-metabolite levels in the posterior parietal cortex (PPC) and PPC-voxel cortical macrostructural metrics in a developmental cohort of 86 individuals aged 5-35 years. We also examine whether PPC metabolite concentrations associate with whole-brain structural metrics to determine whether associations are region-specific or more broadly generalisable. Our findings reveal significant positive associations between PPC cortical thickness, volume, local gyrification index (LGI) and Glx (glutamate + glutamine) levels, likely because differences in cortical microstructure, including dendritic arbour complexity, contributes to variation in both cortical macrostructure and Glx activity across development. Additionally, PPC Glx:GABA+ ratio negatively associated with subcortical gray matter volume, while PPC total NAA positively associated with cerebral white matter volume, suggesting a link between regional neurochemistry and broader brain structure. These results highlight the importance of accounting for macrostructural and broader brain structural characteristics when interpreting the neuroanatomical correlates of MRS-measured metabolites, beyond controlling for bulk tissue composition. This approach is particularly crucial when comparing neuro-metabolite levels across groups with known structural differences, such as developmental cohorts or individuals with neurodevelopmental conditions. Key pointsO_LIPosterior parietal cortex (PPC) Glx levels are positively associated with PPC cortical thickness and local gyrification index, likely because differences in cortical microstructure, including dendritic arbour complexity, contributes to both cortical macrostructure and neuro-metabolic traits across development. C_LIO_LIThe PPC Glx:GABA+ ratio is negatively associated with subcortical gray matter volume, while PPC total NAA is positively associated with cerebral white matter volume, suggesting a link between regional neurochemistry and broader brain structure. C_LIO_LIThese findings emphasise the importance of considering more detailed macrostructural characteristics, as well as bulk tissue composition (white matter, gray matter, cerebral spinal fluid), when interpreting MRS-measured metabolite differences. C_LI

neuroscience↗

bioRxiv2021

How coiled-coil assemblies accommodate multiple aromatic residues

Rational protein design requires understanding the contribution of each amino acid to a targeted protein fold. For a subset of protein structures, namely the ;-helical coiled coils (CCs), knowledge is sufficiently advanced to allow the rational de novo design of many structures, including entirely new protein folds. However, current CC design rules center on using aliphatic hydrophobic residues predominantly to drive the folding and assembly of amphipathic helices. The consequences of using aromatic residues--which would be useful for introducing structural probes, and binding and catalytic functionalities--into these interfaces is not understood. There are specific examples of designed CCs containing such aromatic residues, e.g., phenylalanine-rich sequences, and the use of polar aromatic residues to make buried hydrogen-bond networks. However, it is not known generally if sequences rich in tyrosine can form CCs, or what CC assemblies these would lead to. Here we explore tyrosine-rich sequences in a general CC-forming background and resolve new CC structures. In one of these, an antiparallel tetramer, the tyrosine residues are solvent accessible and pack at the interface between the core and the surface. In the other more-complex structure, the residues are buried and form an extended hydrogen-bond network.

biochemistry↗

bioRxiv2018

Navigating the structural landscape of de novo α-helical bundles

The association of amphipathic helices in water leads to -helical-bundle protein structures. However, the driving force for this--the hydrophobic effect--is not specific and does not define the number or the orientation of helices in the associated state. Rather, this is achieved through deeper sequence-to-structure relationships, which are increasingly being discerned. For example, for one structurally extreme but nevertheless ubiquitous class of bundle--the -helical coiled coils--relationships have been established that discriminate between all-parallel dimers, trimers and tetramers. Association states above this are known, as are antiparallel and mixed arrangements of the helices. However, these alternative states are less-well understood. Here, we describe a synthetic-peptide system that switches between parallel hexamers and various up-down-up-down tetramers in response to single-amino-acid changes and solution conditions. The main accessible states of each peptide variant are characterized fully in solution and, in most cases, to high-resolution X-ray crystal structures. Analysis and inspection of these structures helps rationalize the different states formed. This navigation of the structural landscape of -helical coiled coils above the dimers and trimers that dominate in nature has allowed us to design rationally a well-defined and hyperstable antiparallel coiled-coil tetramer (apCC-Tet). This robust de novo protein provides another scaffold for further structural and functional designs in protein engineering and synthetic biology.

biochemistry↗