Biology subjects

Flores, K.

Publications and source records attributed to Flores, K..

10 recordsLinked to original sources

bioRxiv2026

A generalized resource-allocation growth law reveals mechanisms of differential responses to intermittent androgen deprivation therapy in prostate cancer

Resource-limited growth frameworks often developed independently. Here, we derived a growth law by assuming a cell balancing internal competing resource demands and generalizing the growth signal through a shape parameter h, the trade-off exponent. In Liebig's single-limiting-resource regime, it recovers Droop's cell quota at h=1 and approaches Prater's growth efficiency as h grows large. h determines how sharply growth declines when allocation departs from optimal, thereby shaping populations evolution. Cyclic environmental stress tests such growth laws. Hence, we built a model from this growth law and applied it to prostate cancer growth in patients undergoing cyclic intermittent androgen deprivation therapy. We showed the model recapitulated longitudinal prostate specific antigen (PSA) and serum androgen measurements from 71 prostate cancer patients using a nonlinear mixed-effects framework (pooled and median individual R^2 {approx} 0.9 for PSA and {approx} 0.8 for serum androgen). h is well-constrained by the data and separates treatment outcomes (success vs. failure, p = 0.003). The results predict that failing cases have cancer that can adapt to a wide range of growth conditions with minimal cost. A simplified model recapitulated PSA dynamics from 32 prostate cancer patients on cyclic adaptive therapy (R^2 {approx} 0.8). Estimates of h for castration resistant cancer in adaptive cohort were similar to failure cases in the intermittent cohort. We found no statistical differences in estimated parameters between the adaptive vs. standard of care arms, suggesting that adaptive schedule may drive the differential outcome. The results support this growth law, providing a foundation for resource-limited growth across biological systems.

ecology↗

bioRxiv2026

Bacteroidales Secreted Antimicrobial Protein-1 receptor recognition is coupled to protease-activation to form bactericidal pores.

Bacteroidales secreted antimicrobial proteins (BSAPs) are diffusible MACPF-domain toxins that mediate intra-species antagonism in the gut microbiota. Here we define the mechanism of action of BSAP-1 from Bacteroides fragilis, showing how target specificity encoded within the N- and C-terminal domains is coordinated with pore-forming activity of the MACPF. We show that specificity of the toxin for its receptor is mediated by an extended interface comprised of the BSAP-1 C-terminal domain and residues on the receptor that differ from the orthologous protein of BSAP-1 producing strains. On the surface of susceptible cells, BSAP-1 undergoes proteolytic cleavage of an N-terminal regulatory domain, triggering its assembly into oligomeric pores. Cryo-electron microscopy of membrane-inserted BSAP-1 reveals a 13-subunit transmembrane {beta}-barrel pore formed through canonical MACPF rearrangements. Comparative modelling supports a conserved oligomerization mechanism across the BSAP family despite diversification of receptor-binding domains that target either proteins or glycan receptors. Together, these findings establish BSAP-1 as a receptor-targeted, protease-activated antibacterial MACPF toxin and provide a framework for understanding how gut Bacteroidales spatially restrict toxin activation to shape strain-level competition.

microbiology↗

bioRxiv2026

Looking beyond stereotyped neuron structures reveals links between beading and morphological rearrangements in aging phenotypes.

1Understanding how neuronal morphology changes during aging and acute stress is essential for elucidating mechanisms of neurodegeneration. The highly branched PVD neuron of Caenorhabditis elegans provides a powerful model for studying dendritic remodeling and degeneration-associated phenotypes such as dendritic beading. However, the complexity of this arbor presents substantial challenges for automated segmentation and quantitative analysis. In this study, we adapted a convolutional neural network (CNN)-guided region growing framework for automated dendrite tracing, coupled with two topology-based algorithms for categorizing dendritic segments by branching degree. The segmentation algorithm achieved high accuracy relative to manual tracing, with a median Dice coefficient of 0.82, while reducing analysis time by approximately tenfold. Automated dendrite categorization demonstrated strong agreement with manual annotations across branching orders, though position-based mapping performance declined with age due to progressive morphological distortion. Leveraging this platform, we investigated mechanistic differences in dendritic beading patterns observed during aging and cold shock. Consistent with prior work, aging was associated with decreased inter-bead spacing, whereas cold shock produced increased bead dispersion with stress severity. Structural analysis revealed that these trends were not driven by dendritic pruning or reduced arbor complexity. Instead, while a traditional anatomically unflexible paradigm falsely implicated lower-degree dendrites as highly vulnerable, our branching-informed framework revealed that age-dependent beading is fundamentally dictated by a segments history of successive branching events. Conversely, acute cold shock triggered systemic beading that expanded across all dendritic orders in a severity-dependent manner. Together, these findings demonstrate that chronic aging and acute stress engage distinct degenerative pathways (compartment-specific lineage vulnerability versus global architectural collapse) rather than gross morphological loss, as well as highlighting the need for paradigms that enable reliable analysis of changing morphologies.

bioinformatics↗

bioRxiv2024

Bacteroides expand the functional versatility of a universal transcription factor and transcribed DNA to program capsule diversity

Human gut Bacteroides species encode numerous (eight or more) tightly regulated capsular polysaccharides (CPS). Specialized paralogs of the universal transcription elongation factor NusG, called UpxY (Y), and an anti-Y UpxZ (Z) are encoded by the first two genes of each CPS operon. The Y-Z regulators combine with promoter inversions to limit CPS transcription to a single operon in most cells. Y enhances transcript elongation whereas Z inhibits noncognate Ys. How Y distinguishes among cognate CPS operons and how Z inhibits only noncognate Ys are unknown. Using in-vivo nascent-RNA sequencing and promoter-less in vitro transcription (PIVoT), we establish that Y recognizes a paused RNA polymerase via sequences in both the exposed non-template DNA and the upstream duplex DNA. Y association is aided by novel pause-then-escape nascent RNA hairpins. Z binds non-cognate Ys to directly inhibit Y association. This Y-Z hierarchical regulatory program allows Bacteroides to create CPS subpopulations for optimal fitness.

microbiology↗

bioRxiv2024

Phosphorothioate DNA modification by BREX Type 4 systems in the human gut microbiome

Among dozens of microbial DNA modifications regulating gene expression and host defense, phosphorothioation (PT) is the only known backbone modification, with sulfur inserted at a non-bridging oxygen by dnd and ssp gene families. Here we explored the distribution of PT genes in 13,663 human gut microbiome genomes, finding that 6.3% possessed dnd or ssp genes predominantly in Bacillota, Bacteroidota, and Pseudomonadota. This analysis uncovered several putative new PT synthesis systems, including Type 4 Bacteriophage Exclusion (BREX) brx genes, which were genetically validated in Bacteroides salyersiae. Mass spectrometric analysis of DNA from 226 gut microbiome isolates possessing dnd, ssp, and brx genes revealed 8 PT dinucleotide settings confirmed in 6 consensus sequences by PT-specific DNA sequencing. Genomic analysis showed PT enrichment in rRNA genes and depletion at gene boundaries. These results illustrate the power of the microbiome for discovering prokaryotic epigenetics and the widespread distribution of oxidation-sensitive PTs in gut microbes. One-sentence SummaryApplication of informatic, mass spectrometric, and sequencing-based mapping tools to human gut bacteria revealed new phosphorothioate epigenetic systems widespread in the gut microbiome.

microbiology↗

bioRxiv2024

A pervasive large conjugative plasmid mediates multispecies biofilm formation in the intestinal microbiota increasing resilience to perturbations

Although horizontal gene transfer is pervasive in the intestinal microbiota, we understand only superficially the roles of most exchanged genes and how the mobile repertoire affects community dynamics. Similarly, little is known about the mechanisms underlying the ability of a community to recover after a perturbation. Here, we identified and functionally characterized a large conjugative plasmid that is one of the most frequently transferred elements among Bacteroidales species and is ubiquitous in diverse human populations. This plasmid encodes both an extracellular polysaccharide and fimbriae, which promote the formation of multispecies biofilms in the mammalian gut. We use a hybridization-based approach to visualize biofilms in clarified whole colon tissue with unprecedented 3D spatial resolution. These biofilms increase bacterial survival to common stressors encountered in the gut, increasing strain resiliency, and providing a rationale for the plasmids recent spread and high worldwide prevalence.

microbiology↗

bioRxiv2023

Adaptation to volumetric compression drives hepatoblastoma cells to an apoptosis-resistant and invasive phenotype

Liver cancer involves tumor cells rapidly growing within a packed tissue environment. Patient tumor tissues reveal densely packed and deformed cells, especially at tumor boundaries, indicative of physical crowding and compression. It is not well understood how these physical signals modulate tumor evolution and therapeutic susceptibility. Here we investigate the impact of volumetric compression on liver cancer (HepG2) behavior. We find that conditioning cells under a highly compressed state leads to major transcriptional reprogramming, notably the loss of hepatic markers, the epithelial-to-mesenchymal transition (EMT)-like changes, and altered calcium signaling-related gene expression, over the course of several days. Biophysically, compressed cells exhibit increased Rac1-mediated cell spreading and cell-extracellular matrix interactions, cytoskeletal reorganization, increased YAP and {beta}-catenin nuclear translocation, and dysfunction in cytoplasmic and mitochondrial calcium signaling. Furthermore, compressed cells are resistant to chemotherapeutics and desensitized to apoptosis signaling. Apoptosis sensitivity can be rescued by stimulated calcium signaling. Our study demonstrates that volumetric compression is a key microenvironmental factor that drives tumor evolution in multiple pathological directions and highlights potential countermeasures to re-sensitize therapy-resistant cells. Significance statementCompression can arise as cancer cells grow and navigate within the dense solid tumor microenvironment. It is unclear how compression mediates critical programs that drive tumor progression and therapeutic complications. Here, we take an integrative approach in investigating the impact of compression on liver cancer. We identify and characterize compressed subdomains within patient tumor tissues. Furthermore, using in vitro systems, we induce volumetric compression (primarily via osmotic pressure but also via mechanical force) on liver cancer cells and demonstrate significant molecular and biophysical changes in cell states, including in function, cytoskeletal signaling, proliferation, invasion, and chemoresistance. Importantly, our results show that compressed cells have impaired calcium signaling and acquire resistance to apoptosis, which can be countered via calcium mobilization.

cancer biology↗

bioRxiv2023

A ubiquitous mobile genetic element disarms a bacterial antagonist of the gut microbiota

DNA transfer is ubiquitous in the gut microbiota, especially among species of Bacteroidales. In silico analyses have revealed hundreds of mobile genetic elements shared between these species, yet little is known about the phenotypes they encode, their effects on fitness, or pleiotropic consequences for the recipients genome. Here, we show that acquisition of a ubiquitous integrative and conjugative element encoding an antagonistic system shuts down the native contact-dependent antagonistic system of Bacteroides fragilis. Despite inactivating the native antagonism system, mobile element acquisition increases fitness of the B. fragilis transconjugant over its progenitor by arming it with a new weapon. This DNA transfer causes the strain to change allegiances so that it no longer targets ecosystem members containing the same element yet is armed for communal defense.

microbiology↗

bioRxiv2022

Parameter estimation and identifiability analysis for a bivalent analyte model of monoclonal antibody-antigen binding

1Discovery research for therapeutic antibodies and vaccine development requires an in-depth understanding of antibody-antigen interactions. Label-free techniques such as Surface Plasmon Resonance (SPR) enable the characterization of biomolecular interactions through kinetics measurements, typically by binding antigens in solution to monoclonal antibodies immobilized on a SPR chip. 1:1 Langmuir binding model is commonly used to fit the kinetics data and derive rate constants. However, in certain contexts it is necessary to immobilize the antigen to the chip and flow the antibodies in solution. One such scenario is the screening of monoclonal antibodies (mAbs) for breadth against a range of antigens, where a bivalent analyte binding model is required to adequately describe the kinetics data unless antigen immobilizaion density is optimized to eliminate avidity effects. A bivalent analyte model is offered in several existing software packages intended for standard throughput SPR instruments, but lacking for high throughput SPR instruments. Existing methods also do not explore multiple local minima and parameter identifiability, issues common in non-linear optimization. Here, we have developed a method for analyzing bivalent analyte binding kinetics directly applicable to high throughput SPR data collected in a non-regenerative fashion, and have included a grid search on initial parameter values and a profile likelihood method to determine parameter identifiability. We fit the data of a broadly neutralizing HIV-1 mAb binding to HIV-1 envelope glycoprotein gp120 to a system of ordinary differential equations modeling bivalent binding. Our identifiability analysis discovered a non-identifiable parameter when data is collected under the standard experimental design for monitoring the association and dissociation phases. We used simulations to determine an improved experimental design, which when executed, resulted in the reliable estimation of all rate constants. These methods will be valuable tools in analyzing the binding of mAbs to an array of antigens to expedite therapeutic antibody discovery research. 2 Author summaryWhile commercial software programs for the analysis of bivalent analyte binding kinetics are available for low-throughput instruments, they cannot be easily applied to data generated by high-throughput instruments, particularly when the chip surface is not regenerated between titration cycles. Further, existing software does not address common issues in fitting non-linear systems of ordinary differential equations (ODEs) such as optimizations getting trapped in local minima or parameters that are not identifiable. In this work, we introduce a pipeline for analysis of bivalent analyte binding kinetics that 1) allows for the use of high-throughput, non-regenerative experimental designs, 2) optimizes using several sets of initial parameter values to ensure that the algorithm is able to reach the lowest minimum error and 3) applies a profile likelihood method to explore parameter identifiability. In our experimental application of the method, we found that one of the kinetics parameters (kd2) cannot be reliably estimated with the standard length of the dissociation phase. Using simulation and identifiability analysis we determined the optimal length of dissociation so that the parameter can be reliably estimated, saving time and reagents. These methodologies offer robust determination of the kinetics parameters for high-throughput bivalent analyte SPR experiments.

biophysics↗

bioRxiv2021

The Core Human Fecal Metabolome

Summary ParagraphAmong the biomolecules at the center of human health and molecular biology is a system of molecules that defines the human phenotype known as the metabolome. Through an untargeted metabolomic analysis of fecal samples from human individuals from Africa and the Americas--the birthplace and the last continental expansion of our species, respectively--we present the characterization of the core human fecal metabolome. The majority of detected metabolite features were ubiquitous across populations, despite any geographic, dietary, or behavioral differences. Such shared metabolite features included hyocholic acid and cholesterol. However, any characterization of the core human fecal metabolome is insufficient without exploring the influence of industrialization. Here, we show chemical differences along an industrialization gradient, where the degree of industrialization correlates with metabolomic changes. We identified differential metabolite features like leucyl-leucine dipeptides and urobilin as major metabolic correlates of these behavioral shifts. Our results indicate that industrialization significantly influences the human fecal metabolome, but diverse human lifestyles and behavior still maintain a core human fecal metabolome. This study represents the first characterization of the core human fecal metabolome through untargeted analyses of populations along an industrialization gradient.

biochemistry↗