Biology subjects

Bernal, M.

Publications and source records attributed to Bernal, M..

7 recordsLinked to original sources

bioRxiv2026

SYNBRIDGE: A VERSATILE FRAMEWORK FOR BIDIRECTIONAL INTERCONVERSION BETWEEN BIOBRICKS AND GOLDEN GATE ASSEMBLY STANDARDS

Component reusability and interoperability are fundamental to synthetic biology. While BioBricks laid the groundwork for part domestication, Golden Gate-based assembly standards, in particular Modular Cloning (MoClo), revolutionized multipart assembly. Despite widespread adoption, standardized conversion between these two popular frameworks remains challenging due to sequence incompatibilities. While de novo synthesis remains constrained by cost and sequence complexity, conventional PCR-based conversion suffers from off-target binding driven by sequence redundancy in multigene devices, unscalable primer optimization costs, and amplicon size constraints. To address interconversion from an engineering perspective, we present SynBridge: a closed-loop idempotent workflow for bidirectional BioBrick-MoClo conversion built around two core operations, Bri2Mo and Mo2Bri. As a proof of concept, we validated SynBridge by constructing a composite genetic system integrating a BioBrick module for LuxR-mediated RFP expression with a MoClo-assembled device for thermoregulated GFP expression. Quantitative cloning efficiency and functional characterization confirmed a robust and reproducible workflow that operates without requiring ad-hoc solutions. SynBridge provides a versatile engineering tool that ensures backward compatibility, maximizes part reusability, and establishes a standardized interchangeability framework suitable for automated procedures.

synthetic biology↗

bioRxiv2026

Strategies for the modulation of mitochondrial metabolism and activity in the treatment of neurodegenerative diseases: A systematic review and meta-analysis.

Neurodegenerative diseases (NDDs) are currently raising their prevalences and new preclinical low-cost investigations of drug design are urging. NDDs encompass a wide range of disorders, including Alzheimers, Parkinsons, ALS and others, many of which share mitochondrial dysfunction as a common pathological feature. As such, targeting mitochondrial metabolism has emerged as a promising therapeutic strategy. However, while rodent models are widely used in NDD research, they are costly and time-consuming, raising the need to consider other alternatives to accelerate the search for novel therapies. In this line, zebrafish (Danio rerio) have gained outstanding popularity as a valuable option. This systematic review aims to provide an extensive overview about the current strategies that use zebrafish assays to investigate modulations of mitochondrial function as new therapies against NDDs. The review was performed following an electronic search of different databases (PubMed, Embase, Scopus and Web of Science) after the PRISMA procedure. Articles published in the English language were identified and screened based on the keywords used: mitochondrial metabolism, therapy, neurodegenerative diseases and zebrafish. Following 176 entries, exclusion criteria reduced the record to 34 final studies. Overall, we found that these studies investigate 37 compounds: 24 natural, 6 semisynthetic, 5 synthetic and 2 compounds of not-determined origin; to ameliorate 9 prevalent diseases: ARSACS, Alzheimers, Parkinsons, Huntingtons diseases, Leigh and Wolfram syndromes, Amyotrophic lateral sclerosis, Limb - girdle muscular dystrophy 2G and hyperglycemia-associated amnesia. Additionally, a meta-analysis of these compounds and their gene interactions provides insights into their mechanisms of action and advances our understanding of NDDs, and furnishes us with a powerful tool to predictive potential new drugs or to repurpose existing ones. To conclude, this systematic review suggests that zebrafish have become an effective model for screening potential drugs for NDDs with symptomatology difficult to replicate in rodent models. Moreover, the use of computational tools is also emphasized as a promising strategy to guide therapeutic discovery more efficiently, reducing both time and costs, in developing treatments for NDDs. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=102 SRC="FIGDIR/small/710294v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@18893a1org.highwire.dtl.DTLVardef@1943a12org.highwire.dtl.DTLVardef@709146org.highwire.dtl.DTLVardef@51a488_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

Dynamic Tracking and Single-Cell Analysis of Starvation-Induced Autophagic Responses in Breast Cancer Cells

Nutrient stress induces dynamic and heterogeneous cellular responses that are often reduced to population averages or endpoint measurements. AURORA is a longitudinal single-cell phenotyping framework integrating high-content time-lapse imaging, trajectory-aware quality control, multi-compartment morphology, reference phenotypic states, and cross-cell-line aggregation of state-occupancy behaviors. AURORA is applied to MCF-7, MDA-MB-231, A-549, and HT-1080 cancer cells during 4 h exposure to Earle's balanced salt solution (EBSS). Population-level Total Autophagy shows sustained EBSS-associated elevation in MCF-7, A-549, and HT-1080, but a stronger early response followed by attenuation in MDA-MB-231. Longitudinal analysis shows that these averages arise from cell-line- and time-dependent changes in single-cell distributions rather than uniform displacement. Feature-level analysis further identifies distinct combinations of nuclear, whole-cell, and autophagosome-associated organization, compactness, and shape in each model. Projection of EBSS-treated cells into Complete-defined phenotypic landscapes reveals line-specific redistribution among reference states. Despite this specificity, dominant state-occupancy signatures converge into six recurrent higher-order programs, linking different cellular routes to partially shared remodeling architectures. Because DAPGreen is not paired with a flux inhibitor or ratiometric reporter, these findings describe an autophagy-associated imaging phenotype rather than autophagic flux. AURORA therefore distinguishes population-average change from heterogeneous single-cell adaptation during dynamic stress responses.

cancer biology↗

bioRxiv2024

Hydroxyurea induces ER stress and cytoplasmic protein aggregation

The endoplasmic reticulum (ER) lumen provides the proper redox environment for disulfide bond formation, which is required for the appropriate folding of proteins that enter the secretory pathway and constitute membranes. Defective protein folding in the ER activates proteostatic mechanisms that are now beginning to be elucidated. Here, we show that hydroxyurea (HU) causes ER stress and triggers a transient perinuclear ER expansion, which leads to the clustering of nuclear pore complexes. This striking phenotype is mimicked by diamide (DIA), a specific thiol stress inductor, and prevented or rapidly reverted by dithiothreitol, a dithiol-reducing agent, suggesting that ER expansion is caused by disulfide stress. ER expansion induced by HU or DIA depends on glutathione (GSH), is Ire1-independent, and is associated with a unique transcriptome program that differs from the canonical unfolding protein response (UPR). The ER luminal expansion accumulates Hsp70 Bip1 chaperone, and it evolves parallel with the appearance of cytoplasmic protein aggregates containing heat stress proteins (HSPs), indicating that both HU and DIA are impinging on protein folding. Thus, our data reveal that HU induces disulfide stress that impinges on protein folding in the cytoplasm and ER.

cell biology↗

bioRxiv2021

The anti-angiogenic compound dimethyl fumarate inhibits the serine synthesis pathway and increases glycolysis in endothelial cells

A pathological and persistent angiogenesis is observed in several diseases like retinopathies, diabetes, psoriasis and cancer. Dimethyl fumarate, an ester from the Krebs cycle intermediate fumarate, is approved as a drug for the treatment of psoriasis and multiple sclerosis, and its anti-angiogenic activity has been reported in vitro and in vivo. However, it is not known whether dimethyl fumarate is able to modulate endothelial cell metabolism, considered an essential feature for the angiogenic switch. By means of different experimental approximations, including proteomics, isotope tracing and metabolomics experimental approaches, in this work we studied the possible role of dimethyl fumarate in endothelial cell energetic metabolism. We demonstrate for the first time that dimethyl fumarate promotes glycolysis and diminishes cell respiration, which could be a consequence of a down-regulation of serine and glycine synthesis through inhibition of PHGDH activity in endothelial cells. This new target can open a new field of study regarding the mechanism of action of dimethyl fumarate.

biochemistry↗

bioRxiv2020

Arabidopsis thaliana Zn2+-efflux ATPases HMA2 and HMA4 are required for resistance to the necrotrophic fungus Plectosphaerella cucumerina BMM

O_LIZinc is an essential nutrient at low concentrations, but toxic at slightly higher ones. This could be used by plants to fight pathogens colonization. C_LIO_LIElemental distribution in Arabidopsis thaliana leaves inoculated with the necrotrophic fungus Plectosphaerella cucumerina BMM (PcBMM) was determined and compared to mock-inoculated ones. Infection assays were carried out in wild type and long-distance zinc trafficking double mutant hma2hma4, defective in root-to-shoot zinc partitioning. Expression levels of genes involved in zinc homeostasis or in defence phytohormone-mediated pathways were determined. C_LIO_LIZinc and manganese levels increased at the infection site. Zinc accumulation was absent in hma2hma4. HMA2 and HMA4 transcription levels were upregulated upon PcBMM inoculation. Consistent with a role of these genes in plant immunity, hma2hma4 mutants were more susceptible to PcBMM infection, phenotype rescued upon zinc supplementation. Transcript levels of genes involved in the salicylic acid, ethylene and jasmonate pathways were constitutively upregulated in hma2hma4 plants. C_LIO_LIThese data are consistent with a role of zinc in plant immunity not only of hyperaccumulator plants, but also of plants containing ordinary levels of zinc. This new layer of immunity seems to run in parallel to the already characterized defence pathways, and its removal has a direct effect on pathogen resistance. C_LI

plant biology↗

bioRxiv2019

Do Arabidopsis Squamosa promoter binding Protein-Like genes act together in plant acclimation to copper or zinc deficiency?

The genome of Arabidopsis thaliana encodes approximately 260 copper (Cu)-dependent proteins, which include enzymes in central pathways of photosynthesis, respiration and responses to environmental stress. Under Cu-deficient growth conditions, Squamosa promoter binding Protein-Like 7 (SPL7) activates the transcription of genes encoding Cu acquisition systems and mediates a metabolic reorganization to economize on Cu. The transcription factor SPL7 groups among comparably large proteins in the SPL family, which additionally comprises a second group of small SPL proteins targeted by miRNA156 with roles in plant development. SPL7 shares extended regions of sequence homology with SPL1 and SPL12. Therefore, we investigated the possibility of a functional overlap between these three members of the group of large SPL family proteins. We compared the spl1 spl12 double mutant and the spl1 spl7 spl12 triple mutant with the wild type and the spl7 single mutant under normal and Cu-deficient growth conditions. Biomass production, chlorophyll content and tissue elemental composition at the seedling stage, as well as plant and flower morphology during reproductive stages, confirmed the involvement of SPL7, but provided no indication for important roles of SPL1 or SPL12, in the acclimation of Arabidopsis to Cu deficiency. Furthermore, we analyzed the effects of zinc (Zn) deficiency on the same set of mutants. Different from what is known in the green alga Chlamydomonas reinhardtii, Arabidopsis did not activate Cu deficiency responses under Zn deficiency, and there was no Cu overaccumulation in either shoot or root tissues of Zn-deficient wild-type plants. Known Zn deficiency responses were unaltered in spl7, spl1 spl12 and spll spl7 spl12 mutants. We observed that CuZnSOD activity is strongly downregulated in Zn-deficient A. thaliana, in association with an about 94% reduction in the abundance of the CDS2 transcript, a known target of miR398. However, different from the known Cu deficiency responses of Arabidopsis, this Zn deficiency response was independent of SPL7and not associated with an upregulation of MIR398b primary transcript levels. Our data suggest that there is no conservation in A. thaliana of the crosstalk between Zn and Cu homeostasis mediated by the single SPL family protein CRR1 in Chlamydomonas. In the future, resolving how the specificity of SPL protein activation and recognition of target gene promoters is achieved will advance our understanding of the specific functions of different SPL family proteins in either Cu deficiency response regulation or growth and development of land plants.\n\n\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@fadf53org.highwire.dtl.DTLVardef@5bcffborg.highwire.dtl.DTLVardef@1b38ee7org.highwire.dtl.DTLVardef@16aeff3org.highwire.dtl.DTLVardef@1af5e1f_HPS_FORMAT_FIGEXP M_TBL C_TBL

plant biology↗