Publications

Motivated by the question of how biological systems maintain homeostasis in changing environments, Shinar and Feinberg introduced in 2010 the concept of absolute concentration robustness (ACR). A biochemical system exhibits ACR in some species if the steady-state value of that species does not depend on initial conditions. Thus, a system with ACR can maintain a constant level of one species even as the initial condition changes. Despite a great deal of interest in ACR in recent years, the following basic question remains open: How can we determine quickly whether a given biochemical system has ACR? Although various approaches to this problem have been proposed, we show that they are incomplete. Accordingly, we present new methods for deciding ACR, which harness computational algebra. We illustrate our results on several biochemical signaling networks.

Tight junctions play an essential role in sealing tissues, by forming belts of adhesion strands around cellular perimeters. Recent work has shown that the condensation of ZO1 scaffold proteins is required for tight junction assembly. However, the mechanisms by which junctional condensates initiate at cell-cell contacts and elongate around cell perimeters remain unknown. Combining biochemical reconstitutions and live-cell imaging of MDCKII tissue, we found that tight junction belt formation is driven by adhesion receptor-mediated ZO1 surface condensation coupled to local actin polymerization. Adhesion receptor oligomerization provides the signal for surface binding and local condensation of ZO1 at the cell membrane. Condensation produces a molecular scaffold that selectively enriches junctional proteins. Finally, ZO1 condensates directly facilitate local actin polymerization and filament bundling, driving the elongation into a continuous tight junction belt. More broadly, our work identifies how cells couple surface condensation with cytoskeleton organization to assemble and structure adhesion complexes.

Common genetic variants in a conserved cis-regulatory element (CRE) at histone deacetylase (HDAC)9 are a major risk factor for cardiovascular disease, including stroke and coronary artery disease. Given the consistency of this association and its proinflammatory properties, we examined the mechanisms whereby HDAC9 regulates vascular inflammation. HDAC9 bound and mediated deacetylation of NLRP3 in the NACHT and LRR domains leading to inflammasome activation and lytic cell death. Targeted deletion of the critical CRE in mice increased Hdac9 expression in myeloid cells to exacerbate inflammasome-dependent chronic inflammation. In human carotid endarterectomy samples, increased HDAC9 expression was associated with atheroprogression and clinical plaque instability. Incorporation of TMP195, a class IIa HDAC inhibitor, into lipoprotein-based nanoparticles to target HDAC9 at the site of myeloid-driven vascular inflammation stabilized atherosclerotic plaques, implying a lower risk of plaque rupture and cardiovascular events. Our findings link HDAC9 to atherogenic inflammation and provide a paradigm for anti-inflammatory therapeutics for atherosclerosis.

The glycocalyx, a highly heterogeneous glycoprotein layer of cilia regulates adhesion and force transduction and is involved in signaling. The high-resolution molecular architecture of this layer is currently not understood. The structure of the ciliary coat is described in the green alga Chlamydomonas reinhardtii by cryo-electron tomography and proteomic approaches and the high-resolution cryoEM structure of the main component, FMG1B is solved. FMG1B is described as a mucin orthologue which lacks the major O-glycosylation of mammalian mucins but is N-glycosylated. FMG1A, a previously undescribed isoform of FMG1B is expressed in C. reinhardtii. By microflow-based adhesion assays, increased surface adhesion in the glycocalyx deficient double-mutant fmg1b-fmg1a is observed. It is found this mutant is capable of surface-gliding, with neither isoform required for extracellular force transduction by intraflagellar transport. The results find FMG1 to form a protective layer with adhesion-regulative instead of adhesion-conferring properties and an example of an undescribed class of mucins.

Organisms evolve mechanisms that regulate the properties of biogenic crystals to support a wide range of functions, from vision and camouflage to communication and thermal regulation. Yet, the mechanism underlying the formation of diverse intracellular crystals remains enigmatic. Here we unravel the biochemical control over crystal morphogenesis in zebrafish iridophores. We show that the chemical composition of the crystals determines their shape, particularly through the ratio between the nucleobases guanine and hypoxanthine. We reveal that these variations in composition are genetically controlled through tissue-specific expression of specialized paralogs, which exhibit remarkable substrate selectivity. This orchestrated combination grants the organism with the capacity to generate a broad spectrum of crystal morphologies. Overall, our findings suggest a mechanism for the morphological and functional diversity of biogenic crystals and may, thus, inspire the development of genetically designed biomaterials and medical therapeutics.

Differential equation models are crucial to scientific processes across many disciplines, and the values of model parameters are important for analyzing the behaviour of solutions. Identifying these values is known as a parameter estimation, a type of inverse problem, which has applications in areas that include industry, finance and biomedicine. A parameter is called globally identifiable if its value can be uniquely determined from the input and output functions. Checking the global identifiability of model parameters is a useful tool when exploring the well-posedness of a given model. This problem has been intensively studied for ordinary differential equation models, where theory, several efficient algorithms and software packages have been developed. A comprehensive theory for PDEs has hitherto not been developed due to the complexity of initial and boundary conditions. Here, we provide theory and algorithms, based on differential algebra, for testing identifiability of polynomial PDE models. We showcase this approach on PDE models arising in the sciences.

Motile cilia and flagella produce regular bending waves that enable single-cell navigation due to non-planar waveforms with characteristic torsion. However, it is not known how torsion, a geometric property of the three-dimensional waveform, relates to mechanical twist deformations of the axoneme, the conserved cytoskeletal core of cilia and flagella. Here we show that axoneme twisting and torsion are coupled and that twist waves propagate along the beating axoneme of Chlamydomonas reinhardtii algae. We resolve the three-dimensional shapes of the axonemal waveform with nanometre precision at millisecond timescales using defocused dark-field microscopy and beat-cycle averaging, observing regular hetero-chiral torsion waves propagating base to tip. To investigate whether the observed torsion results from axonemal twist, we attach gold nanoparticles to axonemes and measure their cross-section rotation during beating. We find that, locally, the axonemal cross-section co-rotates with the bending plane, evidencing twist-torsion coupling. Our results demonstrate the link between shape and mechanical deformation in beating axonemes and can inform models of the dynamics of motor proteins inside the axoneme responsible for shaping the beat of motile cilia.

Liver regeneration is supported by hepatocytes and, in certain conditions, biliary epithelial cells (BECs). BECs are facultative liver stem cells that form organoids in culture and engraft in damaged livers. However, BEC heterogeneity in the homeostatic liver remains to be fully elucidated. Here, we exploit systemic lentiviral vector (LV) administration to achieve efficient and lifelong gene transfer to BECs in mice. We find that LV-marked BECs retain organoid formation potential and predominantly respond to liver damage; however, they are less clonogenic and display a hepatocyte-primed transcriptome compared to untransduced BECs. We thus identify a BEC subset committed to hepatocyte lineage in the absence of liver damage, characterized by a transcriptional network orchestrated by hepatocyte nuclear factor 4α. We also report in vivo targeting of such BECs in non-human primates. This work highlights intrinsic BEC heterogeneity and that in vivo LV gene transfer to the liver may persist following BEC-mediated repair of hepatic damage.

Inferring historical population sizes is key to identifying drivers of ecological and evolutionary change and crucial to predicting the future of species on our rapidly changing planet. The pairwise sequentially Markovian coalescent (PSMC) method provided a revolutionary framework to reconstruct species' demographic histories over millions of years based on the genome sequence of a single individual. Here, we detected and solved a common artifact in PSMC and related methods: recent population peaks followed by population collapses. Combining real and simulated genomes, we show that these peaks do not represent true population dynamics. Instead, ill-set default parameters cause false peaks in our own and published data, which can be avoided by adjusting parameter settings. Furthermore, we show that certain changes in population structure can cause similar patterns. Newer methods, like Beta-PSMC, perform better but do not always avoid this artifact. Our results suggest testing multiple parameters that split the first time window before interpreting recent population peaks followed by collapses and call for the development of robust methods.