Biology subjects

Alvarado, D.

Publications and source records attributed to Alvarado, D..

6 recordsLinked to original sources

bioRxiv2026

Over-the-counter fiber supplementation associates with metabolic and microbial shifts in rectal mucosa

Fiber supplements are the first line of treatment for all patients with benign anorectal disease. In addition, fiber has been found to support gut microbiota and reduce inflammation; however, their integrated effect on the colonic mucosal environment is incompletely defined. We evaluated how mixed-fiber formulations may collectively shape the rectal mucosal environment through coordinated effects on microbiota composition, short-chain fatty acid (SCFA) handling, and host transcription. We evaluated multi-compartment responses to a 28-day mixed-fiber intervention in 37 participants with benign anorectal disease (~15 g/day; 7.5g psyllium husk, 8g wheat dextrin) and assessed the microbiota (16S rRNA), the metabolome (GC-MS and LC-MS), and transcriptome (subset n=10) before (PRE) and after (POST) supplementation. Changes in KEGG pathways were tested with gene set enrichment analysis (GSEA). Associations were tested by Spearman correlation, and microbiota-based prediction of SCFA responses by random-forest regression. Microbiota diversity was stable after the fiber intervention, however, 10 mucosal ASVs were differentially abundant including Parabacteroides and Lachnospiraceae NK4A136 group while SCFAs, propionate and isobutyrate, both decreased in rectal tissue and butyrate decreased in serum. To understand these shifts in the metabolome, we proceeded with the transcriptome where we identified 130 differentially expressed genes and enrichment of metabolic and SCFA-related pathways. Random forest regression captured a modest signal for serum butyrate. Taken together, short-term mixed-fiber supplementation produced selective rectal mucosal taxonomic shifts and enriched mucosal metabolic and SCFA-metabolism program despite reduced SCFA pools, suggesting that even brief over-the-counter fiber supplementation may reshape the mucosal metabolic environment.

microbiology↗

bioRxiv2025

Plasticity Associated with Adoption of Social Roles in Clown Anemonefish

Central questions of animal behavior are how do individual phenotypes shape and how are individual phenotypes shaped by dominance hierarchies. Using clownfish (Amphiprion percula) as a model system, we investigated how individuals strategically modify their phenotype during hierarchy formation. We tested the overarching hypothesis that interactions among size- and age-matched rivals will lead to the emergence of social roles (dominant, subordinate, solitary), accompanied by divergence in four aspects of individual phenotypes: growth, feeding behavior, agonistic behaviors (aggression, submission), and gene expression. To test this, we created 30 replicates of juvenile clownfish, each comprising a size-matched pair housed together, and a solitary size-matched individual housed separately. Our results show that an individuals social context shapes its growth trajectory through coordinated changes in feeding behavior, agonistic behaviors, and gene expression. Individuals emerging as dominant within pairs grew twice as much compared to those emerging as subordinates, while subordinate and solitary individuals showed comparable growth. Initially, paired individuals consumed more food per capita than solitary individuals, but this difference declined as size hierarchies became established. Agonistic behaviors also decreased over time among paired individuals as size differences emerged. Transcriptomic analyses revealed upregulation of conserved vertebrate growth pathways and ossification related genes, and downregulation of satiety-associated genes, in dominant individuals compared to subordinates and solitaries. Here we identify associations between changes in gene expression, growth, and feeding behavior regulation that reinforce social role differentiation during dominance hierarchy formation in clownfish. Our findings lay the foundation for a broader framework to explore the mechanisms underpinning strategic growth in social vertebrates.

ecology↗

bioRxiv2024

Small molecule targeting of FBXO21 mediated p85αubiquitylation in acute myeloid leukemia

PI3K inhibitors that target the catalytic sub-unit p110 are used in cancer therapy to inhibit overactive PI3K signaling pathway. However, their clinical use is limited by severe adverse effects and development of resistance, highlighting the need for further research on regulation of the PI3K pathway. We have identified that FBXO21 ubiquitinates regulatory PI3K subunit p85, and silencing of FBXO21 inhibits canonical PI3K signaling. To target FBXO21, we developed a small molecule designed to interfere with substrate:ligase interaction. Our novel small molecule effectively blocks p85 ubiquitination leading to decreased PI3K pathway activation and cell death in acute myeloid leukemia (AML). Moreover, our studies demonstrate selectivity for AML cells over healthy counterparts, and elimination of AML in vivo, emphasizing FBXO21s potential as a promising therapeutic target for AML. Targeting substrate:ligase interactions provide new avenues for drug discovery that may enhance the efficacy of current therapies and benefits for improving patient outcomes. STATEMENT OF SIGNIFICANCEOur studies highlight the potential of the ubiquitin E3 ligase FBXO21 as an alternative therapeutic target for the PI3K signaling pathway, not only in AML but in cancers with aberrant PI3K signaling.

cancer biology↗

bioRxiv2024

Flanking Domains Modulate α-Synuclein Monomer Structure: A Molecular Dynamics Domain Deletion Study

Aggregates of misfolded -synuclein proteins (asyn) are key markers of Parkinsons disease. Asyn proteins have three domains: an N-terminal domain, a hydrophobic NAC core implicated in aggregation, and a proline-rich C-terminal domain. Proteins with truncated C-terminal domains are known to be prone to aggregation and suggest that understanding domain-domain interactions in asyn monomers could help elucidate the role of the flanking domains in modulating protein structure. To this end, we used Gaussian accelerated molecular dynamics (GAMD) to simulate wild-type (WT), N-terminal truncated ({Delta}N), C-terminal truncated ({Delta}C), and isolated NAC domain asyn protein variants (isoNAC). Using clustering and contact analysis, we found that removal of the N-terminal domain led to increased contacts between NAC and C-terminal domains and the formation of interdomain {Delta}-sheets. Removal of either flanking domain also resulted in increased compactness of every domain. We also found that the contacts between flanking domains in the WT protein result in an electrostatic potential (ESP) that may lead to favorable interactions with anionic lipid membranes. Removal of the C-terminal domain disrupts the ESP in a way that could result in over-stabilized protein-membrane interactions. These results suggests that cooperation between the flanking domains may modulate the proteins structure in a way that helps maintain elongation and creates an ESP that may aid favorable interactions with the membrane.

biophysics↗

bioRxiv2022

Tissue-specific modifier alleles determine Mertk loss-of-function traits

Knockout (KO) mouse models play critical roles in elucidating biological processes behind disease-associated or disease-resistant traits. As a consequence of gene KO, mice display certain phenotypes. Based on insight into the molecular role of said gene in a biological process, it is inferred that the particular biological process causally underlies the trait. This approach has been crucial towards understanding the basis of pathological and/or advantageous traits associated with Mertk KO. MERTK is a receptor tyrosine kinase with a critical role in phagocytosis of apoptotic cells or cellular debris. Therefore, early-onset, severe retinal degeneration was described to be a direct consequence of failed phagocytosis of photoreceptor outer segments by retinal pigment epithelia. Similarly, enhanced anti-tumor immunity was inferred to result from the failure of macrophages to dispose cancer cell corpses, resulting in a pro-inflammatory tumor microenvironment. Here we report that the loss of Mertk alone is not sufficient for retinal degeneration. This trait only manifests when the function of the paralog Tyro3 is concomitantly lost. Additionally, the dramatic resistance against two syngeneic mouse tumor models observed in Mertk KO cannot, at least entirely, be ascribed to the loss of Mertk. The widely used Mertk KO carries multiple coincidental changes in its genome that affect the expression of a number of genes, including Tyro3. Nonetheless, neither Tyro3, nor macrophage phagocytosis by alternate genetic redundancy, accounts for the absence of anti-tumor immunity in two independent Mertk KOs. Collectively, our results indicate that context-dependent epistasis of independent modifier alleles determine Mertk KO traits.

immunology↗

bioRxiv2020

Goblet cell LRRC26 regulates BK channel activation and protects against colitis in mice

Goblet cells (GCs) are specialized cells of the intestinal epithelium contributing critically to mucosal homeostasis. One of the functions of GCs is to produce and secrete MUC2, the mucin that forms the scaffold of the intestinal mucus layer coating the epithelium and separates the luminal pathogens and commensal microbiota from the host tissues. Although a variety of ion channels and transporters are thought to impact on MUC2 secretion, the specific cellular mechanisms that regulate GC function remain incompletely understood. Previously, we demonstrated that leucine-rich-repeat-containing protein 26 (LRRC26), a known regulatory subunit of the Ca2+-and voltage-activated K+ channel (BK channel), localizes specifically to secretory cells within the intestinal tract. Here, utilizing a mouse model in which MUC2 is fluorescently tagged allowing visualization of single GCs in intact colonic crypts, we show that murine colonic GCs have functional LRRC26-associated BK channels. In the absence of LRRC26, BK channels are present in GCs, but are not activated at physiological conditions. In contrast, all tested MUC2-negative cells completely lacked BK channels. Moreover, LRRC26-associated BK channels underlie the BK channel contribution to the resting transepithelial current across mouse distal colonic mucosa. Genetic ablation of either LRRC26 or BK-pore forming -subunit in mice results in a dramatically enhanced susceptibility to colitis induced by dextran sodium sulfate (DSS). These results demonstrate that normal potassium flux through LRRC26-associated BK channels in GCs has protective effects against colitis in mice. SignificanceA primary function of goblet cells (GCs) of the intestinal epithelium is to generate a protective mucus layer lining the intestinal lumen. GC dysfunction is linked to Inflammatory Bowel Disease (IBD). GC mucus secretion is thought to be dependent on contributions of an ensemble of anion and cation fluxes, although understanding remains limited. Here, it is shown in mouse colon that the Ca2+- and voltage-dependent BK-type K+ channel, specifically in association with the LRRC26 regulatory subunit, plays a critical role in normal GC function, protecting mice against chemically-induced colitis. The results demonstrate that normal K+ fluxes mediated by LRRC26-containing BK channels are required for normal GC function, potentially providing insights into the potential role of BK channels in IBD.

physiology↗