Biology subjects

Ramos, M. A.

Publications and source records attributed to Ramos, M. A..

5 recordsLinked to original sources

bioRxiv2026

Integrative optical genome mapping and long-read sequencing resolve constitutional complex rearrangements at nucleotide resolution

Complex rearrangements are one of the rarest types of structural variants (SVs) and can be divided into two categories: complex chromosomal rearrangements (CCRs) and complex genomic rearrangements (CGRs). CCRs include structural rearrangements that present at least three breakpoints and show exchange of genetic material between more than two chromosomes and CGRs are rearrangements that present more than one junction and/or more than one SV in cis. They are usually formed by one of the chromoanagenesis mechanisms, where a massive disruptive cellular event leads to multiple structural rearrangements. Classical cytogenomic techniques have been commonly applied for their characterization, but methodologies that involve longer DNA molecules, namely optical genome mapping (OGM) and long-read genome sequencing (lrGS), present a considerably higher SV detection resolution, revealing more details about the rearrangements, including precise breakpoint location. Here, we describe six patients with complex rearrangements investigated through a combination of different techniques: karyotyping, chromosomal microarray, and OGM were performed to characterize the rearrangements. Subsequently, lrGS was used to further resolve the alterations, refine their breakpoints' location, and sequence their junction points. Three patients presented CCRs involving three, four, and six chromosomes, while three exhibited CGRs involving one different chromosome each, providing a variety of complex SVs to show the importance of each technique and their combination in rearrangement resolution. In total, the complex rearrangements presented 127 breakpoints, 66 junction points and involved 14 of the 24 chromosomes. Higher-resolution techniques revealed additional complexity in all cases. Despite the advances provided by OGM and lrGS, conventional karyotyping remained indispensable for complete rearrangement resolution. In two patients, the findings supported a novel mechanism combining features of the different chromoanagenesis processes. Furthermore, evidence of inherited alterations was identified, and the comprehensive characterization of the rearrangements enabled more accurate genotype-phenotype correlations. Our findings indicate that an integrated approach combining karyotyping, OGM, and lrGS can completely resolve SVs, including complex rearrangements.

genomics↗

bioRxiv2025

The specificity and structure of DNA crosslinking by the gut bacterial genotoxin colibactin

Accumulating evidence has connected the chemically unstable, DNA-damaging gut bacterial natural product colibactin to colorectal cancer, including the identification of mutational signatures that are thought to arise from colibactin-DNA interstrand crosslinks (ICLs). However, we currently lack direct information regarding the structure of this lesion. Here, we combine mass spectrometry and nuclear magnetic resonance spectroscopy to elucidate the specificity and structure of the colibactin-DNA ICL. We find that colibactin alkylates within the minor groove of AT-rich DNA, explaining the origins of mutational signatures. Unexpectedly, we discover that the chemically unstable central motif of colibactin mediates the sequence specificity of crosslinking. By directly elucidating colibactins interactions with DNA, this work enhances our understanding of the structure and genotoxic mechanisms of this cancer-linked gut bacterial natural product.

biochemistry↗

bioRxiv2025

ESMStabP: A Regression Model for Protein Thermostability Prediction

Accurately predicting protein thermostability is crucial for numerous applications in biotechnology, pharmaceuticals, and food science. Experimental methods for determining protein melting temperatures are often time-consuming and costly, driving the need for efficient computational alternatives. In this paper, we introduce ESMStabP, an enhanced regression model for predicting protein thermostability. To improve model performance and generalizability, we assembled a significantly larger dataset by combining and cleaning datasets previously utilized in other thermostability models. Building on Deep-StabP, ESMStabP incorporates significant improvements, using embeddings from the ESM2 protein language model and thermophilic classifications. The predictions from ESMStabP outperform DeepStabP and other existing predictors, achieving an R2 of 0.95 and a Pearson correlation coefficient (PCC) of 0.97. Despite these improvements, challenges such as dataset availability. This work underscores the critical role of specific layer identification for model development and outlines potential directions for future advancements in protein stability predictions

bioinformatics↗

bioRxiv2023

L. pneumophila resists its self-harming metabolite HGA via secreted factors and collective peroxide scavenging

Many pathogenic bacteria, including Legionella pneumophila, infect humans from environmental reservoirs. To survive in these reservoirs, bacteria must withstand microbe-on-microbe competition. We previously discovered that L. pneumophila can compete with neighboring bacteria via an antimicrobial metabolite called homogentisic acid (HGA) (Levin, Goldspiel, and Malik 2019). Curiously, L. pneumophila strains that secrete HGA are not wholly immune to its effects: low-density bacteria are strongly inhibited by HGA whereas high-density cells are tolerant. How do these bacteria tolerate HGA and avoid self-harm during interbacterial competition? Here, we find that HGA toxicity occurs via the production of toxic hydroperoxides and multiple factors facilitate high-density tolerance. First, HGA only becomes fully toxic after >1 hour of oxidation. While this manifests as a delay in killing within well-mixed liquid cultures, in a biofilm environment, this could provide time for HGA to diffuse away before becoming toxic. Second, HGA generates quantities of hydroperoxides that can be collectively scavenged by high-density, but not low-density cells. And third, high-density cells produce one or more secreted factors that are transiently protective from HGA. In combination, we propose that the bacteria are able to deploy HGA to generate a pool of reactive oxygen species surrounding their own biofilms, while maintaining non-toxic conditions within them. Overall, these findings help to explain how broadly toxic molecules can be used as inter-bacterial weapons. They also provide insights about why some of our current decontamination methods to control L. pneumophila are ineffective, leading to recurrent disease outbreaks.

microbiology↗

bioRxiv2017

Control of Mast Cell Regulated Exocytosis by Munc13 Proteins

Mast cells (MCs) are involved in pathogen defense and inflammatory reactions. Upon stimulation, they release substances stored in their granules via regulated exocytosis. In other cell types, Munc13 proteins play essential roles in regulated exocytosis. We found that MCs express Munc13-2 and -4, and we studied their roles using global and conditional knockout (KO) mice. In a model of systemic anaphylaxis, we found no difference between WT and Munc13-2 KO mice, but global and MC-specific Munc13-4 KO mice developed less hypothermia. This protection correlated with lower plasma histamine levels and histological evidence of defective MC degranulation, and not with changes in MC development, distribution, numbers or morphology. In vitro assays revealed that the defective MC response in the absence of Munc13-4 was limited to regulated exocytosis, leaving other MC secretory effector responses intact. Single cell capacitance measurements in MCs from mouse mutants with different expression levels of Munc13-4 in their MCs showed that as levels of Munc13-4 decrease, the rate of exocytosis declines first, and the total amount of exocytosis follows. A requirement for Munc13-2 in MC exocytosis was revealed only in the absence of Munc13-4. Electrophysiology and electron microscopy studies showed that the number of multigranular compound events (granule-to-granule homotypic fusion) was severely reduced in the absence of Munc13-4. We conclude that while Munc13-2 plays a minor role, Munc13-4 is essential for regulated exocytosis in MCs, and that this MC effector response is required for a full IgE-mediated anaphylactic response.

cell biology↗