Biology subjects

Carlson, R.

Publications and source records attributed to Carlson, R..

10 recordsLinked to original sources

bioRxiv2026

Does specific membrane surface area constrain Escherichia coli energy spillage and therefore aerobic and anaerobic growth rates?

The physical dimensions of bacterial cells are finite, tightly regulated, and constrain phenotype based on cell surface area to volume ratios. Additionally, bacterial membranes have limited capacity to host proteins, constraining enzymatic potential per area. We combine these biophysical properties into an aggregate parameter termed specific membrane surface area (sMSA, nm2 gcdw-1) which is readily integrated into systems biology analyses including constraint-based stoichiometric models. sMSA-based analyses have remarkable agency to predict and interpret bacterial phenotypes including maximum growth rate, respiration efficiency, and potential for maintenance energy generation. The presented Escherichia coli research 1) quantitatively recreates the membrane proteome from central metabolism as a function of growth rate, 2) demonstrates that the maximum growth rate of both aerobic and anaerobic E. coli cultures abides by similar cell biology constraints including a Pareto tradeoff between simultaneous synthesis of biomass macromolecules and generation of maintenance energy, 3) quantifies the areal capacity of E. coli membranes to dissipate Gibbs energy during enthalpic and entropic dominated metabolisms, and 4) presents evidence that sMSA theory could permit isogenic populations to host multiple concurrent phenotypes with equivalent fitness metrics.The results support our sMSA theory, based on cell geometry and membrane enzyme capacity, as a substantial driver of metabolism in both oxic and anoxic environments.

systems biology↗

bioRxiv2026

Expanded stoichiometric model of chondrocyte metabolism: response to cyclical shear and compressive loading

Cartilage deterioration is a hallmark osteoarthritis, and there is substantial interest in developing strategies for cartilage repair. Cyclical mechanical stimulation has been known for decades to drive synthesis of cartilage matrix proteins. Matrix synthesis requires activation of central metabolism for producing precursors to non-essential amino acids required for protein translation. However, there are gaps in knowledge regarding how mechanical stimuli affect chondrocyte central metabolism. Here, we find that cyclical shear and compression drive differences in chondrocyte central metabolism in a sex-dependent manner. Based on established biochemistry, we developed and tested a stoichiometric model containing 139 metabolites and 172 reactions from central metabolism that includes production of key cartilage matrix proteins. We then used experimental metabolomics data from shear and compressive stimulation of osteoarthritic chondrocytes to constrain this model and ran multiple simulations examining the potential for producing matrix proteins and ATP. Our results show that both shear and compression can stimulate osteoarthritic chondrocyte metabolism in a manner consistent with production of cartilage matrix proteins, with notable differences between male and female chondrocytes. Additionally, and importantly, our simulation results suggest that nitrogen availability is a key limitation to chondrocyte synthesis of matrix proteins. These results are a starting point for using central metabolism of chondrocytes to optimize synthesis of matrix proteins for cartilage repair. For example, increasing glutamine levels in the presence of cyclical compression has potential to increase production of both types II and VI collagen. These strategies have potential for improving cartilage tissue engineering and repair.

bioengineering↗

bioRxiv2026

Injury Causes Altered Metabolism including O2 Consumption in Bovine and Human Chondrocytes

Traumatic joint injuries both disrupt chondrocyte metabolism and increase the risk for post-traumatic osteoarthritis. Yet the relationships between trauma, altered metabolism, and cartilage degradation remains unclear. This study compares the metabolic responses of bovine (normal) and osteoarthritic (OA) chondrocytes to physiological and injurious mechanical stimuli under normoxic (20% O2) and hypoxic (5% O2) conditions. Using primary chondrocytes encapsulated in agarose, physiological and injurious mechanical stimulation, targeted metabolomic profiling of central carbon metabolites, and O2 saturation measurements, we find that healthy bovine chondrocytes exhibit robust, time-dependent adaptation to mechanical stimuli, whereas OA chondrocytes display a blunted response, particularly under injury conditions. Injurious mechanical stimuli led to altered O2 consumption and glutamine accumulation, suggesting disrupted respiration and reduced protein synthesis hypothesized to be a result of altered mitochondrial metabolism in OA cells. These findings underscore the role of mechanical cues in chondrocyte metabolism and inform future studies aimed at identifying metabolic targets relevant to post-traumatic osteoarthritis progression.

bioengineering↗

bioRxiv2025

Metabolic remodeling of microorganisms by obligate intracellular parasites alters mutualistic community composition

Bacteria carry many types of obligate intracellular parasites, including plasmids and bacteriophage. During infection, these parasites redirect intracellular resources away from bacterial processes toward parasite production. Because parasite-induced metabolic changes influence host traits such as growth rate, nutrient uptake, and waste excretion, parasitic infection should alter how microbes contribute to important community and ecosystem functions. Yet there are few empirical tests of how infection shapes metabolically-mediated interactions between host and non-host species. Here, we integrated a genome-scale metabolic modeling approach with an in vitro obligate cross-feeding system to investigate the metabolic consequences of two intracellular parasites of Escherichia coli: the conjugative plasmid F128 and the filamentous phage M13. We examined the impact of these parasites on interactions between bacteria in a multispecies community composed of E. coli, Salmonella enterica, and Methylobacterium extorquens. Modeling predicted that parasitic infection of E. coli should have consequences for host growth rate and the secretion and reuptake of carbon byproducts. These theoretical results aligned broadly with in vitro experiments, where we found that parasitic infection changed the excretion profile of E. coli, inducing the net externalization of lactate. We also found that parasite-driven changes to metabolism increased the density of cross-feeding species and changes to community composition were generalizable across community interactions and some host and parasite genotypes. Our work emphasizes that microbes infected by obligate intracellular parasites have different metabolisms than uninfected cells and demonstrates that these metabolic shifts can have significant consequences for microbial community structure and function. IMPORTANCEThe intracellular parasites of bacteria shape the structure and function of microbial communities in a variety of ways, including by killing their hosts or transferring genetic material. This study uses a combination of flux balance analysis and an in vitro system consisting of Escherichia coli, Salmonella enterica, Methylobacterium extorquens, and two intracellular parasites of E. coli, the F128 plasmid and the filamentous phage M13, to investigate how parasites change the community contributions of their hosts via metabolic remodeling. Flux balance analysis suggests that parasites change intracellular demand for different metabolic processes, leading to shifts in the identities and concentrations of compounds that infected hosts externalize into the environment. This finding is supported by experimental results, which additionally show that infection can induce the production of lactate. These findings extend our understanding of how bacteriophage and plasmids shape the structure and function of microbial communities.

ecology↗

bioRxiv2024

Cell Geometry and Membrane Protein Crowding Constrain Growth Rate, Overflow Metabolism, Respiration, and Maintenance Energy.

The rules of prokaryotic cell design remain elusive. Here, a theory is presented for interpreting growth rate, overflow metabolism, respiration efficiency, and maintenance energy flux based on cell dimensions, membrane protein crowding, and metabolism. The theory employs biophysical properties and systems analysis to successfully interpret phenotypes of Escherichia coli K-12 strains MG1655 and NCM3722. These strains are genetically similar but differ in surface area-to-volume (SA:V) ratios ([~]30%), growth rate on glucose ([~]40%), and overflow-inducing growth rates ([~]80%). Six predictions were tested and validated using experimental phenomics, proteomics, and mutant data. Analyses did not require assumptions regarding cytosolic macromolecular crowding highlighting the distinct properties of the theory. Cell geometry and membrane protein crowding are significant biophysical constraints of cell biology.

systems biology↗

bioRxiv2022

Backscattering Mueller Matrix polarimetry on whole brain specimens shows promise for minimally invasive mapping of microstructural orientation features

Understanding microscale physiology and microstructural cellular features of the brain is key to understanding the mechanisms of neurodegenerative diseases and injury, as well as the prominent changes that neurons and glia in the brain undergo in development and aging which reflect functional state. Non-invasive imaging modalities sensitive to the microscale - especially diffusion magnetic resonance imaging (dMRI) - are extremely promising for three-dimensional mapping of cellular microstructure of brain tissues and brain connectivity via tractography; however, there is a need for robust validation techniques to verify and improve the biological accuracy of fiber orientation information derived from these techniques. Recent advances in dMRI acquisition and modeling have moved toward probing of the more complex grey matter architecture, challenging current validation techniques, which are largely based on ex vivo staining and microscopy focusing on white matter. Polarized light imaging (PLI) has been shown to be a successful technique for high resolution, direct, microstructural imaging and has been applied to dMRI validation with clear advantages over conventional staining and microscopy techniques. Conventionally, PLI is applied to thin, sectioned samples in transmission mode, but unlike histologic staining, PLI can be extended to operate with high sensitivity in reflectance mode and even extended to 3D imaging to bridge the gap toward in vivo validation of dMRI measurements of orientation features in both gray and white matter of the brain. In this report we investigate the use of backscattering Mueller Matrix polarimetry to characterize the microstructural content of intact Ferret brain specimens. The experimental results show that backscattering polarimetry can probe white matter fiber coherence and fiber orientation in whole brain specimens, and show promise for probing grey matter microstructure. Ultimately, these preliminary results motivate further study to fully understand how backscattering polarimetry can best be used for validation of in vivo microstructural imaging of the brain.

bioengineering↗

bioRxiv2020

Pseudomonas aeruginosa reverse diauxie is an optimized, resource utilization strategy

Pseudomonas aeruginosa is a globally-distributed bacterium often found in medical infections. The opportunistic pathogen uses a different, carbon catabolite repression (CCR) strategy than many, model microorganisms. It does not utilize a classic diauxie phenotype, nor does it follow common systems biology assumptions including preferential consumption of glucose with an overflow metabolism. Despite these contradictions, P. aeruginosa is competitive in many, disparate environments underscoring knowledge gaps in microbial ecology and systems biology. Physiological, omics, and in silico analyses were used to quantify the P. aeruginosa CCR strategy known as reverse diauxie. An ecological basis of reverse diauxie was identified using a genome-scale, metabolic model interrogated with in vitro omics data. Reverse diauxie preference for lower energy, nonfermentable carbon sources, such as acetate or succinate over glucose, was predicted using a multidimensional strategy which minimized resource investment into central metabolism while completely oxidizing substrates. Application of a common, in silico optimization criterion, which maximizes growth rate, did not predict the reverse diauxie phenotypes. This study quantifies P. aeruginosa metabolic strategies foundational to its wide distribution and virulence.

systems biology↗

bioRxiv2020

Spectrum of genes for inherited hearing loss in the Israeli Jewish population, including the novel human deafness gene ATOH1

Mutations in more than 150 genes are responsible for inherited hearing loss, with thousands of different, severe causal alleles that vary among populations. The Israeli Jewish population includes communities of diverse geographic origins, revealing a wide range of deafness-associated variants and enabling clinical characterization of the associated phenotypes. Our goal was to identify the genetic causes of inherited hearing loss in this population, and to determine relationships among genotype, phenotype, and ethnicity. Genomic DNA samples from informative relatives of 88 multiplex families, all of self-identified Jewish ancestry, with either non-syndromic or syndromic hearing loss, were sequenced for known and candidate deafness genes using the HEar-Seq gene panel. The genetic causes of hearing loss were identified for 60% of the families. One gene was encountered for the first time in human hearing loss: ATOH1 (Atonal), a basic helix-loop-helix transcription factor responsible for autosomal dominant progressive hearing loss in a five-generation family. Our results demonstrate that genomic sequencing with a gene panel dedicated to hearing loss is effective for genetic diagnoses in a diverse population. Comprehensive sequencing enables well-informed genetic counseling and clinical management by medical geneticists, otolaryngologists, audiologists, and speech therapists and can be integrated into newborn screening for deafness.

genetics↗

bioRxiv2020

PARP1 and MGMT interaction-based sensitivity to DNA damage in Ewing sarcoma

The Ewing family of sarcomas comprises the fourth most common highly aggressive bone tumor. Four of five Ewing sarcoma chemotherapeutics induce DNA damage, as does radiation therapy. At relapse, two additional DNA-damaging agents are routinely used to re-induce remission, indicating that Ewing sarcoma is intrinsically sensitive to DNA damage. However, current treatment regimens are relatively ineffective, specifically for relapsed or metastatic disease. Several preclinical studies, including our study in the Pediatric Preclinical Testing Program (PPTP), provide evidence for the synthetic lethal combination of PARP1 inhibitor talazoparib with a DNA-methylating agent, temozolomide, for Ewing sarcoma. Nevertheless, in both preclinical studies and clinical trials, doses of temozolomide were significantly reduced because of toxicity of the drug combination. Temozolomide-induced DNA lesions are repaired via poly(ADP) ribose polymerase I (PARP1)-dependent base excision repair and by O6-methylguanine-DNA methyltransferase (MGMT) in a single-step adduct removal. Here, we provide evidence that the two DNA repair pathways act in an epistatic manner in lesion removal. Further, we demonstrate that PARP1 and MGMT physically interact, and that this association is stimulated upon DNA damage. Protein co-immunoprecipitation and microscale thermophoresis analyses revealed that PARP1/MGMT complex formation is DNA and PARylation-independent. Collectively, our results show that: 1) DNA damage response pathways mediated by PARP1 and MGMT work epistatically to eliminate temozolomide-induced DNA adducts; 2) PARP1 and MGMT physically interact; and 3) PARP1/MGMT interaction is increased in response to DNA damage. We discuss how our findings may affect therapeutic advancement for Ewing sarcoma and potentially other cancer types.

biochemistry↗

bioRxiv2017

Scaling up DNA data storage and randomaccess retrieval

Current storage technologies can no longer keep pace with exponentially growing amounts of data. 1 Synthetic DNA offers an attractive alternative due to its potential information density of ~ 1018 B/mm3, 107 times denser than magnetic tape, and potential durability of thousands of years.2 Recent advances in DNA data storage have highlighted technical challenges, in particular, coding and random access, but have stored only modest amounts of data in synthetic DNA. 3,4,5 This paper demonstrates an end-to-end approach toward the viability of DNA data storage with large-scale random access. We encoded and stored 35 distinct files, totaling 200MB of data, in more than 13 million DNA oligonucleotides (about 2 billion nucleotides in total) and fully recovered the data with no bit errors, representing an advance of almost an order of magnitude compared to prior work. 6 Our data curation focused on technologically advanced data types and historical relevance, including the Universal Declaration of Human Rights in over 100 languages,7 a high-definition music video of the band OK Go,8 and a CropTrust database of the seeds stored in the Svalbard Global Seed Vault.9 We developed a random access methodology based on selective amplification, for which we designed and validated a large library of primers, and successfully retrieved arbitrarily chosen items from a subset of our pool containing 10.3 million DNA sequences. Moreover, we developed a novel coding scheme that dramatically reduces the physical redundancy (sequencing read coverage) required for error-free decoding to a median of 5x, while maintaining levels of logical redundancy comparable to the best prior codes. We further stress-tested our coding approach by successfully decoding a file using the more error-prone nanopore-based sequencing. We provide a detailed analysis of errors in the process of writing, storing, and reading data from synthetic DNA at a large scale, which helps characterize DNA as a storage medium and justify our coding approach. Thus, we have demonstrated a significant improvement in data volume, random access, and encoding/decoding schemes that contribute to a whole-system vision for DNA data storage.

bioengineering↗