Biology subjects

Dodge, A.

Publications and source records attributed to Dodge, A..

4 recordsLinked to original sources

bioRxiv2026

A robust mutation spectrum analysis framework for high-depth error-corrected sequencing data

Comparing mutational spectra across experimental groups requires inference at the level of the biological replicate. Error-corrected sequencing (ECS) generates hundreds to thousands of mutations per replicate, yet classical pooled G2 tests treat individual mutations as independent observations and ignore replicate-level variability, inflating statistical significance (pseudo-replication). We present a replicate-aware Ridge-Penalized Dirichlet-Multinomial (RP-DMM) framework that models biological replicates directly and accounts for overdispersion. An L2 (ridge) penalty, with strength chosen by leave-one-out cross-validation, stabilizes spectrum estimates by shrinking weakly supported mutation categories toward a common baseline, and inference uses a parametric bootstrap. We also provide a complementary non-parametric rank-permutation test for sparse datasets. In simulations, the pooled G2 test became increasingly anti-conservative as mutation depth increased, with false-positive rates approaching 100% under the null hypothesis. RP-DMM maintained Type I error near the nominal 5% level and had substantially greater power than the rank-permutation test. Regularization was most consequential for high-dimensional spectra. False positive rates approached the nominal 5% level once the lower-mutation group contained approximately 300-500 mutations, depending on the number of biological replicates. A practical target of approximately 400 mutations in the lower-mutation group provided robust Type I error control across all scenarios examined; below this, the rank-permutation test performed robustly and is preferred. In Duplex Sequencing data from benzo[a]pyrene-exposed mice, RP-DMM distinguished exposure-associated mutational signatures from comparisons with higher mutation counts but null effect size, whereas the pooled G2 test declared all comparisons significant. The cross-validated penalty decreased as mutation depth increased, indicating that regularization strength should be tuned to the data. The framework is implemented in the MutSeqR R package.

bioinformatics↗

bioRxiv2024

Clearing truncated tau protein restores neuronal function and prevents microglia activation in tauopathy mice

Tau protein truncated at aspartate 421 (Asp421) is a characteristic feature of Alzheimers disease (AD) and other tauopathies. It is likely to have a role in their pathogenesis by promoting tau aggregation. Here, using two tauopathy mouse models, we show that a monoclonal antibody against Asp421, 5G2, led to a) a 59-74% clearance of insoluble tau protein in the brains of JNPL3 tauopathy mice following a thirteen-week treatment period, b) a 46% decrease of tau levels in brain interstitial fluid immediately following a single dose of 5G2 as examined by brain microdialysis in awake JNPL3 mice, c) improved neuronal function and d) reduced microglial activation as determined by two-photon imaging in awake PS19 tauopathy mice, where we also found tau accumulation earlier than signs of microglial activation. For mechanistic insight using culture models, 5G2 prevented toxicity of AD brain-derived pathological tau protein, cleared intracellular tau, and prevented microgliosis. We also knocked down the intracellular Fc receptor and ubiquitin E3 ligase, TRIM21, and found a reduction in cellular retention of tau antibodies, which appeared to reduce the acute efficacy (24 h) of tau antibodies but not their longer-term efficacy (5 days). Overall, these findings strongly support the feasibility of targeting Asp421 truncated tau protein to treat tauopathies, indicate that tau-associated abnormalities of neuronal activity precede microglial activation and that antibody-mediated tau clearance via the TRIM21 pathway is mostly transient.

neuroscience↗

bioRxiv2024

Halofilins as Emerging Bactofilin Families of Archaeal Cell Shape Plasticity Orchestrators

Bactofilins are rigid, non-polar bacterial cytoskeletal filaments that link cellular processes to specific curvatures of the cytoplasmic membrane. Although homologs of bactofilins have been identified in archaea and eukaryotes, functional studies have remained confined to bacterial systems. Here, we characterize representatives of two new families of archaeal bactofilins from the pleomorphic archaeon Haloferax volcanii, halofilin A (HalA) and halofilin B (HalB). HalA and HalB polymerize in vitro, assembling into straight bundles. HalA polymers are highly dynamic and accumulate at positive membrane curvatures in vivo, whereas HalB forms more static foci that localize in areas of local negative curvatures on the outer cell surface. Gene deletions and live-cell imaging show that halofilins are critical in maintaining morphological integrity during shape transition from disk (sessile) to rod (motile). Morphological defects in {Delta}halA result in accumulation of highly positive curvatures in rods but not in disks. Conversely, disk-shaped cells are exclusively affected by halB deletion, resulting in flatter cells. Furthermore, while {Delta}halA and {Delta}halB cells imprecisely determine the future division plane, defects arise predominantly during the disk-to-rod shape remodeling. In fact, the deletion of halA in the haloarchaeon Halobacterium salinarum, whose cells are consistently rod-shaped, impacted morphogenesis but not cell division. Increased levels of halofilins enforced drastic deformations in cells devoid of S-layer, suggesting that HalB polymers are more stable at defective S-layer lattice regions. Our results set halofilins apart from their bacterial correlate, where they provide mechanical scaffolding instead of directing envelope synthesis.

microbiology↗

bioRxiv2018

Stimulus-responsive self-assembly of enzymatic fractal structures by computational design

Fractal topologies, which are statistically self-similar over multiple length scales, are pervasive in nature. The recurrence of patterns at increasing length scales in fractal-shaped branched objects, e.g., trees, lungs, and sponges, results in high effective surface areas, and provides key functional advantages, e.g., for molecular trapping and exchange. Mimicking these topologies in designed protein-based assemblies will provide access to novel classes of functional biomaterials for wide ranging applications. Here, we describe a modular, multi-scale computational design method for the reversible self-assembly of proteins into tunable supramolecular fractal-like topologies in response to phosphorylation. Computationally-guided atomic-resolution modeling of fusions of symmetric, oligomeric proteins with Src homology 2 (SH2) binding domain and its phosphorylatable ligand peptide was used to design iterative branching leading to fractal-like assembly formation by enzymes of the atrazine degradation pathway. Structural characterization using various microscopy techniques and Cryo-electron tomography revealed a variety of dendritic, hyperbranched, and sponge-like topologies which are self-similar over three decades ([~]10nm-10m) of length scale, in agreement with models from multi-scale computational simulations. We demonstrate control over mesoscale topology (by linker design), formation dynamics, and functional enhancements due to dynamic multi-component assemblies constructed with three atrazine degradation pathway enzymes. The described design method should enable the construction of a variety of novel, spatiotemporally responsive catalytic biomaterials featuring fractal topologies.

biophysics↗