Biology subjects

Ramirez, I.

Publications and source records attributed to Ramirez, I..

6 recordsLinked to original sources

bioRxiv2026

Multi-step femtosecond laser-fabricated membranes for regulated migration of biomolecules and cells

Organ-on-chip (OoC) systems enable the recapitulation of key structural and functional characteristics of human tissues within controlled micro-engineered environments. In mechanically active tissues such as musculoskeletal, cardiac, and vascular systems, the incorporation of dynamic physical forces is essential for replicating the biomechanical cues governing cellular morphology and functional responses in-vivo. Without such stimuli, OoC models may fail to capture physiologically relevant tissue behaviors. Porous and semi-permeable membranes are critical components of OoCs, facilitating selective transport of nutrients, gases, and signaling molecules between cellular compartments to support biologically accurate barrier replication. Hence, fabrication strategies that permit precise modulation of membrane permeability are desirable to accommodate for the varying needs in pore size and porosity across organ systems. This study presents a two-stage fabrication process for stretchable, microporous polydimethylsiloxane (PDMS) membranes using femtosecond (fs-) pulse laser drilling. The laser-ablated pores exhibit a characteristic conical morphology, with diameters tapering from the laser entry to exit point. By modulating laser power and number of pulses, 6-15 m exit-end pore diameters were achieved in 50 m thick PDMS films. The membranes demonstrated strong mechanical resilience, with a 5-12% reduction in Youngs modulus after 500 cycles of strain loading. Furthermore, membranes fabricated at lower laser powers exhibited superior retention of elasticity, highlighting the influence of processing parameters on mechanical behavior. Cytocompatibility and permeability assessments confirmed that the membranes supported sustained cell viability and proliferation over at least three days. In size-restricted membrane pore geometries, cellular migration was constrained without any inhibition of biomolecular transport. This selective permeability is critical in multilayer OoC architectures, where a balance between biomolecular diffusion and cellular compartmentalization is necessary to preserve distinct tissue interfaces and functional organization. This work presents fs-laser micro-drilling as a robust and tunable fabrication strategy for producing mechanically resilient, selectively permeable PDMS membranes for physiologically relevant OoC applications.

bioengineering↗

bioRxiv2025

DUSP12 promotes cell cycle progression and protects cells from cell death by regulating ZPR9

Protein phosphatases are critical for regulating cell signaling, cell cycle, and cell fate decisions, and their dysregulation leads to an array of human diseases like cancer. The dual specificity phosphatases (DUSPs) have emerged as important factors driving tumorigenesis and cancer therapy resistance. DUSP12 is a poorly characterized atypical DUSP widely conserved throughout evolution. Although no direct substrate has been firmly established, DUSP12 that has been implicated in protecting cells from stress, regulating ribosomal biogenesis, and modulating cellular DNA content. In this study, we used affinity- and proximity-based biochemical purification approaches coupled to mass spectrometry to identify the zinc finger protein ZPR9 as a novel DUSP12 interactor, which was validated by in-cell and in-vitro IP assays. Interestingly, ZPR9 binds to the unique zinc-binding domain of DUSP12, which previous reports indicated was important for many of DUSP12s functions within the cell. Prior studies had implicated ZPR9 as a modulator of apoptosis, but it remained unclear if and how ZPR9 participated in the cell cycle and, more so, how it promoted cell death. Using mass spectrometry analyses, we found that overexpression of DUSP12 promoted de-phosphorylation of ZPR9 at Ser143. Overexpression of ZPR9, but not Ser143 phosphomimetic and phosphorylation-deficient mutants, led to an increase in pre-metaphase mitotic defects while knockdown of DUSP12 also showed mitotic defects in metaphase. Furthermore, knockdown of DUSP12 promoted, while knockdown of ZPR9 suppressed, stress-induced apoptosis. Our results support a model where DUSP12 protects cells from stress-induced apoptosis by promoting de-phosphorylation of ZPR9.

cell biology↗

bioRxiv2025

Human REXO4 is Required for Cell Cycle Progression

Human REXO4 is a poorly characterized exonuclease that is overexpressed in human cancers. To better understand the function of REXO4 and its relationship to cellular proliferation, we have undertaken multidisciplinary approaches to characterize its cell cycle phase-dependent subcellular localization and the cis determinants required for this localization, its importance to cell cycle progression and cell viability, its protein-protein association network, and its activity. We show that the localization of REXO4 to the nucleolus in interphase depends on an N-terminal nucleolar localization sequence and that its localization to the perichromosomal layer of mitotic chromosomes is dependent on Ki67. Depletion of REXO4 led to a G1/S cell cycle arrest, and reduced cell viability. REXO4 associated with ribosome components and other proteins involved in rRNA metabolism. We propose a model where REXO4 is important for proper rRNA processing, which is required for ribosome biogenesis, cell cycle progression, and proliferation. SIGNIFICANCE STATEMENTO_LIREXO4 is a putative RNA exonuclease with limited characterization. The authors used in silico, cell, and molecular biology approaches to characterize its localization, associations, regulation, and function. C_LIO_LIThey found that during interphase, REXO4 localizes to the nucleolus through an N-terminal nucleolar localization sequence. Whereas during mitosis, REXO4 localized to the perichromosomal layer in a Ki67-dependent manner. REXO4 was required for proper cell cycle progression, and viability. C_LIO_LIThese results indicated that REXO4 is important for regulating cell proliferation. C_LI

cell biology↗

bioRxiv2023

Dietary road salt and monarch butterflies: minimal effects on larval growth, immunity, wing coloration, and migration to Mexico

The spectacular migration of the monarch butterfly is under threat from the loss of habitat and the decline of their milkweed host plants. In the northern part of their range, roadsides could potentially produce millions of monarchs annually due to high densities of milkweed, however roadside milkweed can accumulate chemicals from roads, such as sodium from road salt. Controlled lab studies have shown mixed effects of sodium on monarch development: small increases can be beneficial as sodium is an important micronutrient in brain and muscle development, but large increases can sometimes decrease survival. It is unclear how dietary sodium affects performance in ecologically relevant conditions, and the migration itself. In this experiment, we raised monarchs outdoors, in migration-inducing conditions, on milkweed sprayed with three levels of sodium chloride. We released 2500 tagged monarchs and held an additional 250 for further lab assays. While our recovery rates to the wintering grounds were low (N = 7 individuals), individuals from all three sodium chloride treatments made it to Mexico. Butterflies reared on control milkweed and low salt concentrated sodium in their tissues, while those on high salt diets excreted sodium, suggesting levels were above a physiological optimum. There were no effects of treatment on wing coloration, survival, body size, immunity, or parasite prevalence. Taken together, our results suggest that monarchs are robust to levels of sodium in milkweeds found along roadsides, which is promising with respect to monarch conservation efforts that promote roadside habitat. Significance StatementMonarch butterflies are a flagship species for pollinator conservation, and were recently being listed as endangered by the IUCN. Roadside habitat is a target for monarch breeding habitat as they often have high densities of milkweed, the monarch hostplant. However, roadsides can also have high levels of pollutants, such as salt from deicing treatments. We reared monarch caterpillars on sodium treated milkweeds, measuring a suite of performance measures, and releasing nearly 2500 tagged monarchs for migration. We found little effect of salt on migration to Mexico, survival, body size, development time, parasite prevalence, immunity, or coloration. Monarchs appear robust to levels of sodium found in milkweed along roadsides, supporting the possibility of roadsides as habitat.

ecology↗

bioRxiv2020

DUSP7 Regulates the Activity of ERK2 to PromoteProper Chromosome Alignment During Cell Division

Human cell division is a highly regulated process that relies on the accurate capture and movement of chromosomes to the metaphase plate. Errors in the fidelity of chromosome congression and alignment can lead to improper chromosome segregation, which is correlated with aneuploidy and tumorigenesis. Here we show that the dual specificity phosphatase DUSP7 is important for regulating chromosome alignment. DUSP7 bound to ERK2 and regulated the abundance of active phospho-ERK2 through its phosphatase activity. Overexpression of DUSP7, but not catalytic dead mutants, led to a marked decrease in phopho-ERK2 and mitotic chromosome misalignment, while knockdown of DUSP7 also led to defective chromosome congression that resulted in a prolonged mitosis. Consistently, chemical inhibition of the MEK kinase that phosphorylates ERK2 or ERK2 itself led to chromosome alignment defects. Our results support a model where MEK phosphorylation and DUSP7 dephosphorylation regulate the levels of active phospho-ERK2 to promote proper cell division.

cell biology↗

bioRxiv2020

The myosin regulatory light chain Myl5 localizes to mitotic spindle poles and is required for proper cell division

Myosins are ATP-dependent actin-based molecular motors critical for diverse cellular processes like intracellular trafficking, cell motility and cell invasion. During cell division, myosin MYO10 is important for proper mitotic spindle assembly, the anchoring of the spindle to the cortex, and positioning of the spindle to the cell mid-plane, while myosin MYO2 functions in actomyosin ring contraction to promote cytokinesis. However, myosins are regulated by myosin regulatory light chains (RLCs), and whether RLCs are important for cell division has remained unexplored. Here, we have determined that the previously uncharacterized myosin RLC Myl5 associates with the mitotic spindle and is required for cell division. Myl5 localized to the mitotic spindle poles and spindle microtubules during early mitosis, an area overlapping with MYO10 localization. Depletion of Myl5 led to defects in chromosome congression and to a slower progression through mitosis. We propose that Myl5 is a novel myosin RLC that is important for cell division.

cell biology↗