Biology subjects

Ramirez, B.

Publications and source records attributed to Ramirez, B..

4 recordsLinked to original sources

bioRxiv2025

The pos-1 3' untranslated region governs germline specification and proliferation to ensure reproductive robustness

During fertilization, haploid gametes combine to form a zygote. The male (sperm) and female (oocyte) gametes contribute a similar amount of DNA, but the oocyte contributes nearly all the cytoplasm. Oocytes are loaded with maternal mRNAs thought to be essential for embryonic patterning after fertilization. A conserved suite of RNA-binding proteins (RBPs) regulates the spatiotemporal translation and stability of maternal mRNAs. POS-1 is a CCCH-type tandem zinc finger RBP expressed in fertilized Caenorhabditis elegans zygotes from maternally supplied mRNA. POS-1 accumulates in the posterior of the embryo where it promotes posterior cell fate. Here, we show that the pos-1 3' untranslated region (UTR) is essential for POS-1 patterning and contributes to maximal reproductive fecundity. We engineered a pos-1 mutant where most of the endogenous pos-1 3'UTR was removed using CRISPR genome editing. Our results show that the 3'UTR represses POS-1 expression in the maternal germline but increases POS-1 protein levels in embryos after fertilization. In a wild-type background, POS-1 repression via the 3'UTR has little impact on fertility. In a sensitized background, the deletion mutant has a complex pleiotropic phenotype where most adult homozygous progeny lack either one or both gonad arms. Most phenotypes become more penetrant at elevated temperature. Together, our results support an emerging model where the 3'UTRs of maternal transcripts, rather than being essential, contribute to reproductive robustness during stress.

developmental biology↗

bioRxiv2025

Electronic Cigarette Aerosol Exposure Induces Airway Remodeling in 3D Human Tracheobronchial Epithelial Tissues: From Goblet Cell Hyperplasia to Squamous Metaplasia

Electronic cigarette (EC) aerosols are increasingly recognized for their disruptive effects on airway physiology, yet the temporal progression of epithelial remodeling remains poorly characterized. While squamous metaplasia, mucin hypersecretion, and ciliary dysfunction are hallmark features of smoking-related airway disease, analogous data for EC exposure are limited. To address this gap, we employed a 3D human tracheobronchial epithelial tissue (hTET) model derived from airway basal stem cells and exposed it daily to NJOY ACE "Classic Tobacco" aerosols (1 or 5 puffs) or clean air for 1, 2, or 3 weeks. Remodeling was assessed via immunolabeling and Western blot analysis. MUC5AC expression revealed a transient hypersecretory response, peaking at week 2 and declining by week 3. Multiparametric analysis demonstrated progressive squamous remodeling: early ciliary loss and involucrin upregulation emerged by week 1, with severity increasing in a puff-dependent manner. By week 2, tissues exhibited marked ciliary depletion, altered epithelial thickness, horizontal nuclear reorientation, and elevated involucrin. At week 3, both exposure groups developed a squamous metaplasia phenotype, characterized by involucrin-positive squamous cells replacing ciliated cells. Quantitative analysis confirmed sustained involucrin elevation, with the 1-puff group reaching levels comparable to the 5-puff group by week 3. These findings delineate a sequential pathological trajectory initiated by EC aerosols, progressing from transient goblet cell activation to squamous metaplasia. This human-relevant model underscores the potential for repeated low-level EC exposure to induce airway epithelial remodeling and pathology.

pharmacology and toxicology↗

bioRxiv2025

An interactive dashboard for global reports of the Ralstonia solanacearum species complex

The Ralstonia solanacearum species complex (RSSC) is a globally distributed group of gram-negative, soil-borne bacteria that cause wilt diseases on a broad range of hosts. Due to these pathogens impact on economically important plant species, there is a need for consolidated and visualized information on RSSC pathogen isolation data. We developed an interactive dashboard designed to allow users to explore and analyze the genetic diversity of the RSSC. The dashboard visualizes data in the form of maps, charts, and tables with a variety of user-interactive filters for taxonomic, geographic, and host of isolation specifications. This Ralstonia Wilt Dashboard will aid in communicating knowledge to researchers, regulatory scientists, and other stakeholders to improve disease control and regulation. This report highlights the deployment of the Ralstonia Wilt Dashboard and provides four case studies that address focused scientific questions (https://ralstoniadashboard.shinyapps.io/RalstoniaWiltDashboard/).

microbiology↗

bioRxiv2024

A robust and inducible precise genome editing via an all-in-one prime editor in human pluripotent stem cells

Prime editing (PE) allows for precise genome editing in human pluripotent stem cells (hPSCs), such as introducing single nucleotide modifications, small deletions, or insertions at a specific genomic locus, a strategy that shows great promise for creating "Disease in a dish" models. To improve the effectiveness of prime editing in hPSCs, we systematically compared and combined the "inhibition of mismatch repair pathway and p53" on top of the "PEmax" to generate an all-in-one "PE-Plus" prime editor. We show that PE-Plus conducts the most efficient editing among the current PE tools in hPSCs. We further established an inducible prime editing platform in hPSCs by incorporating the all-in-one PE vector into a safe-harbor locus and demonstrated temporal control of precise editing in both hPSCs and differentiated cells. By evaluating disease-associated mutations, we show that this platform allows efficient creation of both monoallelic and biallelic disease-relevant mutations in hPSCs. In addition, this platform enables the efficient introduction of single or multiple edits in one step, demonstrating potential for multiplex editing. Therefore, our method presents an efficient and controllable multiplex prime editing tool in hPSCs and their differentiated progeny.

cell biology↗