Biology subjects

Stern, A.

Publications and source records attributed to Stern, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Temporal dynamics of RNA phage infection reveal bacterial recovery despite ongoing viral replication

Bacterial defenses against DNA phages are well documented, yet responses to RNA phages remain largely unexplored. Here, we characterize the population dynamics and host responses of Escherichia coli infected by the lytic RNA phage MS2 across multiple timescales, using bulk and single-cell transcriptomics, fluorescence microscopy, whole-genome sequencing, and genetic perturbations. Despite rapid viral takeover and extensive cell death, the bacterial population subsequently rebounds, revealing an unusual state in which host proliferation persists under intense phage pressure. Early in infection, heterogeneous subpopulations are evident, including one with low or undetectable viral transcript levels, low expression of the F-plasmid genes encoding the F-pilus (the MS2 receptor), and a distinct metabolic state. Strikingly, the rebounding population carries MS2 RNA in the great majority of cells, with evidence for active viral replication and continued cell division despite high viral loads. This rebound coincides with strong induction of biofilm-associated genes, including the pga operon, which synthesizes the biofilm-matrix exopolysaccharide PNAG. Deletion of pgaA causes earlier population decline and reduced population survival, indicating that pga-dependent matrix production delays viral lysis. Over longer timescales, phage-exposed populations show heterogeneous F-plasmid prevalence and plasmid-wide expression, consistent with dynamic cycling between plasmid-bearing and plasmid-free states: MS2 selects against F-plasmid-bearing cells, whereas conjugation may restore plasmid carriage. We propose that the biofilm-associated matrix delays viral lysis relative to continued cell division, long enough for rare F-plasmid-free daughter cells to arise and expand. Our results suggest that bacterial survival is determined by a dynamic race between viral lysis and host-cell division.

microbiology↗

bioRxiv2026

Inferring viral proteins that act as public goods during coinfection

Interactions among individuals in structured populations can alter fitness effects of mutations and reshape evolutionary processes. In many systems, including bacteria, yeast, and viruses, such interactions often result in public goods: gene products that are costly to produce yet exploitable by others. During viral coinfection of the same cell, gene products from one genome may complement deleterious mutations in another, allowing defective genomes to persist. Yet it remains difficult to infer which proteins are shareable from population sequencing data, because mutation, selection, drift, and complementation are intertwined. Here, we developed a quantitative framework to infer protein-specific public goods in the RNA bacteriophage MS2, which encodes only four proteins. We analyzed experimental evolution data generated under two multiplicity-of-infection (MOI) regimes: low MOI, where coinfection is rare, and high MOI, where coinfection is common. We first compared empirical mutation patterns between regimes and then applied a Wright-Fisher model combined with simulation-based Bayesian inference using neural posterior estimation. In a two-stage strategy, gene-specific fitness effects were inferred from low-MOI data and subsequently used to estimate protein sharing under high-MOI conditions. Across two statistical inference frameworks, lysis emerged as the strongest public-good candidate, replicase and coat showed an intermediate signal, and maturation showed the weakest evidence for sharing. Together, our results show that viral proteins differ markedly in their propensity to act as public goods. More broadly, they illustrate how coinfection can generate density-dependent selection, a general feature of social evolution that may shape evolutionary dynamics.

evolutionary biology↗

bioRxiv2026

Liquid crystalline mesophase spacing as a quantitative predictor of release kinetics for co-loaded hydrophilic and hydrophobic payloads

Liquid crystalline mesophases exhibit structurally programmable internal architectures that enable co-loading of chemically orthogonal molecules within a single composite material. Realizing the potential of these materials for drug delivery requires a quantitative understanding of how tuning the composition affects internal mesophase architecture and consequently performance metrics such as payload release. Here, Flash NanoPrecipitation with hydrophobic ion pairing is used to prepare nanocarriers containing liquid crystalline mesophases co-encapsulating two compounds from widely different chemical classes: hydrophilic polymyxin B (logP -6) with one of four hydrophobic co-core materials (logP 7-11), achieving >75% encapsulation efficiency and up to 32% and 50% mass loadings for polymyxin and co-core. Synchrotron SAXS is used to quantify characteristic mesophase repeat spacing, which is found to be tunable as a function of composition. A strong correlation between d-spacing and polymyxin release rate is presented. Co-core chemistry and weight fraction jointly govern mesophase architecture, and repeat distance emerges as a structural metric linking these to the hydrophilic payload release kinetics. Mucus diffusivity and antibacterial efficacy are assessed as independent performance metrics, and results corroborate the release behavior. These findings establish a quantitative framework connecting material composition, mesophase architecture, and functional performance that can be applied toward rational co-formulation design. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=86 SRC="FIGDIR/small/734853v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@a0c38eorg.highwire.dtl.DTLVardef@86d33eorg.highwire.dtl.DTLVardef@196c83dorg.highwire.dtl.DTLVardef@3423c3_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOToC Graphic TextC_FLOATNO Flash NanoPrecipitation yields liquid crystalline nanocarriers co-encapsulating with high efficiency payloads with widely distinct physicochemical properties. Synchrotron SAXS establishes characteristic repeat spacing as a quantitative structural metric directly governing hydrophilic release kinetics, providing a rational design framework linking mesophase architecture to functional performance across a range of payload structures. C_FIG

bioengineering↗

bioRxiv2026

The effect of chronic, latent Toxoplasma gondii infection on human behavior: Testing the parasite manipulation hypothesis in humans

Parasitism is one of the key, structural, interspecific interactions in ecology. One remarkable parasitic strategy that has been documented in multiple systems is the behavioral manipulation of hosts to increase parasite fitness. While not yet documented in humans, we propose that a ubiquitous zoonotic parasite - Toxoplasma gondii - may change human behavior to favor the parasite by increasing the fitness of the parasites definitive host - cats. Specifically, we assess the possibility that human behavioral changes resulting from chronic, latent T. gondii infection lead to measurable changes in attitudes, actions and dopaminergic responses towards cats that function to increase domestic cat fitness. We assessed the potential role of humans in the T. gondii lifecycle by identifying and testing behavioral changes in humans that benefit the parasite; specifically, human affection for cats. We assessed T. gondii infection status in 68 participants using T. gondii serum antibody testing, and assessed their attitudes towards cats in three ways: i) surveys, ii) participant behavior in the presence of domestic cats, and iii) participant oxytocin levels before and after interactions with cats to assess dopaminergic changes. Only 2 of 68 participants were positive for T. gondii antibodies, limiting statistical power. However, our results indicated that T. gondii-positive participants both reported a greater affection for cats in surveys, and spent more time engaged with cats during behavioral trials than T. gondii-negative participants (87% of study time engaging with cats vs 75%). Oxytocin results were inconclusive.

evolutionary biology↗

bioRxiv2025

Metabolomic fingerprints of PAH exposure - identifying toxicological biomarkers in dynamically cultured 3D cell spheroids

Environmental exposure to polycyclic aromatic hydrocarbons (PAHs) causes metabolic dysfunction, but reliable biomarkers are still needed to assess human health effects. This study used 21-day matured human HepG2 spheroids, a metabolically competent three-dimensional (3D) liver model, to assess metabolic responses to graded, non-cytotoxic concentrations of benzo[a]pyrene (BaP) and benzo[b]fluoranthene (BBF) after 24- and 96-h exposure. Untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomics, combined with multivariate and network analyses, identified compound- and time-specific metabolic signatures. At 24 hours, no metabolites showed significant changes. In contrast, at 96 hours, both PAHs consistently altered seven robust metabolites linked to polyamine metabolism, membrane dynamics, mitochondrial energy, and DNA-repair pathways. Network analysis showed BBF caused broader and more connected changes than BaP, indicating distinct toxicodynamics. These findings underscore the importance of extended exposure in revealing metabolic disruption and support a set of candidate biomarkers for future low-dose studies and improved risk assessment of airborne toxicants.

systems biology↗

bioRxiv2024

Diverse patterns of intra-host genetic diversity in chronically infected SARS-CoV-2 patients

In rare individuals with a severely immunocompromised system, chronic infections of SARS-CoV-2 may develop, where the virus replicates in the body for months. Sequencing of some chronic infections has uncovered dramatic adaptive evolution and fixation of mutations reminiscent of lineage-defining mutations of variants of concern (VOCs). This has led to the prevailing hypothesis that VOCs emerged from chronic infections. To examine the mutation dynamics and intra-host genomic diversity of SARS-CoV-2 during chronic infections, we focused on a cohort of nine immunocompromised individuals with chronic infections and performed longitudinal sequencing of viral genomes. We show that sequencing errors may cause erroneous inference of high genetic diversity, and to overcome this we used duplicate sequencing across patients and time-points, allowing us to distinguish errors from low frequency mutations. We further find recurrent low frequency mutations that we flag as most likely sequencing errors. This stringent approach allowed us to reliably infer low frequency mutations and their dynamics across time. We inferred a synonymous divergence rate of the virus of [~]2x10-6 mutations/base/day, consistent with the SARS-CoV-2 mutation rate estimated in tissue culture. The rate of non-synonymous divergence varied widely among the different patients. We highlight two patients with opposing patterns: in one patient the rate of divergence was zero, yet this patient harbored multiple presumably defective viruses at low frequencies throughout the infection. Another patient exhibited dramatic adaptive evolution, including clonal competition. Overall, our results suggest that the emergence of highly divergent variants from chronic infections is likely a very rare event and this emphasizes the need to better understand the conditions that allow such emergence events.

evolutionary biology↗

bioRxiv2024

Scalable Extraction of Airway Mucins from Porcine Trachea

Mucins are a major component of the innate defense system in the airways and their biological functions are important to consider in pulmonary disease research. However, the available mucus models for basic research relevant to the lung can be difficult to acquire in sufficient quantity to conduct such studies. Here, we present a new strategy to isolate airway mucins from pig trachea at the milligram to gram scale for use in pulmonary disease research. Using this protocol, we were able to isolate mucins with minimal DNA contamination consisting of [~]70% by weight protein. Compared to porcine gastric mucins extracted with the same procedure, the porcine tracheal extract possessed significantly greater O-linked glycoprotein (mucin) content. Particle tracking microrheology was used to evaluate the biophysical properties of porcine trachea mucins. We found porcine tracheal mucins formed a much tighter mesh network and possessed a significantly greater microviscosity compared to lab extracted porcine gastric mucins. In comparison to mucus harvested from human airway tissue cultures, we found porcine tracheal mucins also possessed a greater microviscosity suggesting these mucins can form into a gel-like material at physiological total solids concentrations. These studies establish an accessible means to isolate airway mucins from porcine trachea at large scale for use in pulmonary disease research.

biochemistry↗

bioRxiv2024

Navigating a fine balance: point-mutant cheater viruses disrupt the viral replication cycle

Cheater viruses, alternatively denoted as defective interfering viruses, cannot replicate on their own yet replicate faster than the wild type (WT) when the two viruses coinfect the same cell. Cheaters must possess dual genetic features: a defect, which leads to their inability to infect cells on their own, and a selective advantage over WT during co-infection. Previously, we have discovered two point-mutant cheaters of the MS2 bacteriophage. Here, we set out to discover the possible repertoire of cheater MS2 viruses by performing experimental evolution at a very high multiplicity of infection (MOI). Our results revealed a third point-mutant cheater that arose in eight biological replicas. Each of the three cheaters disrupts the fine balance necessary for phage replication, in different ways that create a defect + advantage. We found that over time, the point mutant cheaters accumulate additional "helper" mutations, which alter other stages of the viral replication cycle, complementing the disruptions created by the original cheater. Intriguingly, cheater and helper mutations almost always reside in very close proximity on the genome. This region encodes for multiple functions: overlapping reading frames as well as overlapping RNA structures critical for transitioning from one stage to another in the viral replication cycle. This region of overlap explains the dual functions of cheaters, as one mutation can have pleiotropic effects. Overall, these findings underscore how viruses, whose dense genomes often have overlapping functions, can easily evolve point-mutant cheaters, and how cheaters can evolve to alter the intricate balance of the viral replication cycle.

evolutionary biology↗

bioRxiv2024

Synthetic mucus biomaterials synergize with antibiofilm agents to combat Pseudomonas aeruginosa biofilms

Bacterial biofilms are often highly resistant to antimicrobials causing persistent infections which when not effectively managed can significantly worsen clinical outcomes. As such, alternatives to standard antibiotic therapies have been highly sought after to address difficult-to-treat biofilm-associated infections. We hypothesized a biomaterial-based approach using the innate functions of mucins to modulate bacterial surface attachment and virulence could provide a new therapeutic strategy against biofilms. Based on our testing in Pseudomonas aeruginosa biofilms, we found synthetic mucus biomaterials can inhibit biofilm formation and significantly reduce the thickness of mature biofilms. In addition, we evaluated if synthetic mucus biomaterials could work synergistically with DNase and/or -amylase for enhanced biofilm dispersal. Combination treatment with these antibiofilm agents and synthetic mucus biomaterials resulted in up to 3 log reductions in viability of mature P. aeruginosa biofilms. Overall, this work provides a new bio-inspired, combinatorial approach to address biofilms and antibiotic-resistant bacterial infections.

bioengineering↗

bioRxiv2024

The Extracellular Matrix Limits Nanoparticle Diffusion and Cellular Uptake in a Tissue-Specific Manner

Overexpression and remodeling of the extracellular matrix (ECM) in cancer and other diseases may significantly reduce the ability of nanoparticles to reach target sites, preventing effective delivery of therapeutic cargo. Here, we evaluate how tissue-specific properties of the ECM affect nanoparticle diffusion using fluorescence video microscopy and cellular uptake via flow cytometry. In addition, we determined how PEGylation chain size and branching influence the ability of nanoparticles to overcome the ECM barrier from different tissues. We found that purified collagen, in the absence of other ECM proteins and polysaccharides, presented a greater barrier to nanoparticle diffusion as compared to decellularized ECM from the liver, lung, and small intestine submucosa. Nanoparticles with dense PEG coatings achieved up to [~]2000-fold enhancements in diffusion rate and cellular uptake up to [~]5-fold greater than non-PEGylated nanoparticles in the presence of ECM. We also found nanoparticle mobility in the ECM varied significantly between tissue types and the optimal nanoparticle PEGylation strategy to enhance ECM penetration was strongly dependent on ECM concentration. Overall, our data supports the use of low molecular weight PEG coatings which provides an optimal balance of nanoparticle penetration through ECM and uptake in target cells. However, tissue-specific enhancements in ECM penetration and cellular uptake were observed for nanoparticles bearing a branched PEG coating. These studies provide new insight into tissue specific ECM barrier functions which can facilitate the design of nanoparticles that effectively transport through target tissues, improving their therapeutic efficacy.

bioengineering↗

bioRxiv2023

Using big sequencing data to identify chronic SARS-Coronavirus-2 infections

The evolution of SARS-Coronavirus-2 (SARS-CoV-2) has been characterized by the periodic emergence of highly divergent variants, many of which may have arisen during chronic infections of immunocompromised individuals. Here, we harness a global phylogeny of [~]11.7 million SARS-CoV-2 genomes and search for clades composed of sequences with identical metadata (location, age, and sex) spanning more than 21 days. We postulate that such clades represent repeated sampling from the same chronically infected individual. A set of 271 such chronic-like clades was inferred, and displayed signatures of an elevated rate of adaptive evolution, in line with validated chronic infections. More than 70% of adaptive mutations present in currently circulating variants are found in BA.1 chronic-like clades that predate the circulating variants by months, demonstrating the predictive nature of such clades. We find that in chronic-like clades the probability of observing adaptive mutations is approximately 10-20 higher than that in global transmission chains. We next employ language models to find mutations most predictive of chronic infections and use them to infer hundreds of additional chronic-like clades in the absence of metadata and phylogenetic information. Our proposed approach presents an innovative method for mining extensive sequencing data and providing valuable insights into future evolutionary patterns.

evolutionary biology↗

bioRxiv2023

Mutation rate, selection, and epistasis inferred from RNA virus haplotypes via neural posterior estimation

RNA viruses are particularly notorious for their high levels of genetic diversity, which is generated through the forces of mutation and natural selection. However, disentangling these two forces is a considerable challenge, and this may lead to widely divergent estimates of viral mutation rates, as well as difficulties in inferring fitness effects of mutations. Here, we develop, test, and apply an approach aimed at inferring the mutation rate and key parameters that govern natural selection, from haplotype sequences covering full length genomes of an evolving virus population. Our approach employs neural posterior estimation, a computational technique that applies simulation-based inference with neural networks to jointly infer multiple model parameters. We first tested our approach on synthetic data simulated using different mutation rates and selection parameters while accounting for sequencing errors. Reassuringly, the inferred parameter estimates were accurate and unbiased. We then applied our approach to haplotype sequencing data from a serial-passaging experiment with the MS2 bacteriophage. We estimated that the mutation rate of this phage is around 0.2 mutations per genome per replication cycle (95% highest density interval: 0.051-0.56). We validated this finding with two different approaches based on single-locus models that gave similar estimates but with much broader posterior distributions. Furthermore, we found evidence for reciprocal sign epistasis between four strongly beneficial mutations that all reside in an RNA stem-loop that controls the expression of the viral lysis protein, responsible for lysing host cells and viral egress. We surmise that there is a fine balance between over and under-expression of lysis that leads to this pattern of epistasis. To summarize, we have developed an approach for joint inference of the mutation rate and selection parameters from full haplotype data with sequencing errors, and used it to reveal features governing MS2 evolution.

evolutionary biology↗

bioRxiv2022

Genetic risk for Multiple Sclerosis originated in Pastoralist Steppe populations

Multiple sclerosis (MS) is a modern neuro-inflammatory and -degenerative disease, which is most prevalent in Northern Europe. Whilst it is known that inherited risk to MS is located within or within close proximity to immune genes, it is unknown when, where and how this genetic risk originated 1. By using the largest ancient genome dataset from the Stone Age 2, along with new Medieval and post-Medieval genomes, we show that many of the genetic risk variants for MS rose to higher frequency among pastoralists located on the Pontic Steppe, and were brought into Europe by the Yamnaya-related migration approximately 5,000 years ago. We further show that these MS-associated immunogenetic variants underwent positive selection both within the Steppe population, and later in Europe, likely driven by pathogenic challenges coinciding with dietary, lifestyle, and population density changes. This study highlights the critical importance of this period as a determinant of modern immune responses and its subsequent impact on the risk of developing MS in a changing environment.

evolutionary biology↗

bioRxiv2021

#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol

We seek to completely revise current models of airborne transmission of respiratory viruses by providing never-before-seen atomic-level views of the SARS-CoV-2 virus within a respiratory aerosol. Our work dramatically extends the capabilities of multiscale computational microscopy to address the significant gaps that exist in current experimental methods, which are limited in their ability to interrogate aerosols at the atomic/molecular level and thus ob-scure our understanding of airborne transmission. We demonstrate how our integrated data-driven platform provides a new way of exploring the composition, structure, and dynamics of aerosols and aerosolized viruses, while driving simulation method development along several important axes. We present a series of initial scientific discoveries for the SARS-CoV-2 Delta variant, noting that the full scientific impact of this work has yet to be realized. ACM Reference FormatAbigail Dommer1{dagger}, Lorenzo Casalino1{dagger}, Fiona Kearns1{dagger}, Mia Rosenfeld1, Nicholas Wauer1, Surl-Hee Ahn1, John Russo,2 Sofia Oliveira3, Clare Morris1, AnthonyBogetti4, AndaTrifan5,6, Alexander Brace5,7, TerraSztain1,8, Austin Clyde5,7, Heng Ma5, Chakra Chennubhotla4, Hyungro Lee9, Matteo Turilli9, Syma Khalid10, Teresa Tamayo-Mendoza11, Matthew Welborn11, Anders Christensen11, Daniel G. A. Smith11, Zhuoran Qiao12, Sai Krishna Sirumalla11, Michael OConnor11, Frederick Manby11, Anima Anandkumar12,13, David Hardy6, James Phillips6, Abraham Stern13, Josh Romero13, David Clark13, Mitchell Dorrell14, Tom Maiden14, Lei Huang15, John McCalpin15, Christo- pherWoods3, Alan Gray13, MattWilliams3, Bryan Barker16, HarindaRajapaksha16, Richard Pitts16, Tom Gibbs13, John Stone6, Daniel Zuckerman2*, Adrian Mulholland3*, Thomas MillerIII11,12*, ShantenuJha9*, Arvind Ramanathan5*, Lillian Chong4*, Rommie Amaro1*. 2021. #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy ofDeltaSARS-CoV-2 in a Respiratory Aerosol. In Supercomputing 21: International Conference for High Perfor-mance Computing, Networking, Storage, and Analysis. ACM, New York, NY, USA, 14 pages. https://doi.org/finalDOI

biophysics↗

bioRxiv2021

Development of GPC2-directed chimeric antigen receptors using mRNA for pediatric brain tumors

Pediatric brain tumors are the leading cause of cancer death in children with an urgent need for innovative therapies. Here we show that the cell surface oncoprotein glypican 2 (GPC2) is highly expressed on multiple lethal pediatric brain tumors, including medulloblastomas, embryonal tumors with multi-layered rosettes, other CNS embryonal tumors, as well as definable subsets of highly malignant gliomas. To target GPC2 on these pediatric brain tumors with adoptive cellular therapies and mitigate potential inflammatory neurotoxicity, we developed four mRNA chimeric antigen receptor (CAR) T cell constructs using the highly GPC2-specific fully human D3 single chain variable fragment. First, we validated and prioritized these CARs using in vitro cytotoxicity and T cell degranulation assays with GPC2-expressing neuroblastoma cells. Next, we expanded the testing of the two most potent GPC2-directed CAR constructs prioritized from these studies to GPC2-expressing medulloblastoma and high-grade glioma cell lines, showing significant GPC2-specific cell death in multiple models. Finally, locoregional delivery bi-weekly of two to four million GPC2-directed mRNA CAR T cells induced significant and sustained tumor regression in two orthotopic medulloblastoma models, and significantly prolonged survival in an aggressive orthotopic thalamic diffuse midline glioma model. No GPC2-directed CAR T cell related neurologic or systemic toxicity was observed. Taken together, these data show that GPC2 is a highly differentially expressed cell surface protein on multiple malignant pediatric brain tumors that can be targeted safely with local delivery of mRNA CAR T cells. One Sentence SummaryGlypican 2 is expressed on the surface of multiple pediatric brain tumors and can be successfully targeted with mRNA chimeric antigen receptor T cells.

cancer biology↗

bioRxiv2021

In vivo engineered B cells retain memory and secrete high titers of anti-HIV antibodies in mice

As a potential single-shot HIV therapy, transplanted engineered B cells allow robust secretion of broadly neutralizing antibodies (bNAbs). However, ex vivo engineering of autologous B cells is expensive and requires specialized facilities, while allogeneic B cell therapy necessitates MHC compatibility. Here, we develop in vivo B cell engineering, by injecting two adeno associated viral vectors, one coding for saCas9 and another coding for a bNAb. Following immunizations, we demonstrate memory retention and bNAb secretion at neutralizing titers. We observed minimal CRISPR/Cas9 off-target cleavage, using unbiased CHANGE-Seq analysis, while on-target cleavage at undesired tissues is reduced by expressing saCas9 from a B cell specific promoter. In vivo B cell engineering is thus a safe, potent and scalable method for expressing desired antibodies against HIV and beyond. One sentence summaryB cells can be engineered in vivo to robustly secrete anti-HIV bNAbs in a safe, durable and scalable manner.

immunology↗

bioRxiv2020

AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics

We develop a generalizable AI-driven workflow that leverages heterogeneous HPC resources to explore the time-dependent dynamics of molecular systems. We use this workflow to investigate the mechanisms of infectivity of the SARS-CoV-2 spike protein, the main viral infection machinery. Our workflow enables more efficient investigation of spike dynamics in a variety of complex environments, including within a complete SARS-CoV-2 viral envelope simulation, which contains 305 million atoms and shows strong scaling on ORNL Summit using NAMD. We present several novel scientific discoveries, including the elucidation of the spikes full glycan shield, the role of spike glycans in modulating the infectivity of the virus, and the characterization of the flexible interactions between the spike and the human ACE2 receptor. We also demonstrate how AI can accelerate conformational sampling across different systems and pave the way for the future application of such methods to additional studies in SARS-CoV-2 and other molecular systems. ACM Reference FormatLorenzo Casalino1{dagger}, Abigail Dommer1{dagger}, Zied Gaieb1{dagger}, Emilia P. Barros1, Terra Sztain1, Surl-Hee Ahn1, Anda Trifan2,3, Alexander Brace2, Anthony Bogetti4, Heng Ma2, Hyungro Lee5, Matteo Turilli5, Syma Khalid6, Lillian Chong4, Carlos Simmerling7, David J. Hardy3, Julio D. C. Maia3, James C. Phillips3, Thorsten Kurth8, Abraham Stern8, Lei Huang9, John McCalpin9, Mahidhar Tatineni10, Tom Gibbs8, John E. Stone3, Shantenu Jha5, Arvind Ramanathan2*, Rommie E. Amaro1*. 2020. AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics. In Supercomputing 20: International Conference for High Performance Computing, Networking, Storage, and Analysis. ACM, New York, NY, USA, 14 pages. https://doi.org/finalDOI

biophysics↗

bioRxiv2020

Globally defining the effects of mutations in a picornavirus capsid

The capsids of non-enveloped viruses are highly multimeric and multifunctional protein assemblies that protect the viral genome between infection cycles, dictate host and cell tropism, and mediate evasion of humoral immune responses. As such, capsids play key roles in viral biology and pathogenesis. Despite their importance, a comprehensive understanding of how mutations affect viral fitness across different structural and functional attributes of the capsid is lacking. To address this limitation, we globally define the effects of mutations in the capsid of a human picornavirus, generating a comprehensive dataset encompassing >90% of all possible single amino acid mutations. Moreover, we use this information to identify structural and sequence determinants that accurately predict mutational fitness effects, refine evolutionary analyses, and define the sequence specificity of key capsid encoded motifs. Finally, capitalizing on the sequence requirements identified in our dataset for capsid encoded protease cleavage sites, we implement and validate a bioinformatic approach for identifying novel host proteins targeted by viral proteases. Our findings present the most comprehensive investigation of mutational fitness effects in a picornavirus capsid to date and illuminate important aspects of viral biology, evolution, and host interactions.

microbiology↗