Biology subjects

Gonzalez, J. C.

Publications and source records attributed to Gonzalez, J. C..

8 recordsLinked to original sources

bioRxiv2026

N-terminal Trimming Supports Proteostasis Under Secretory Protein Mislocalization Stress

Secretory proteins that fail to enter the endoplasmic reticulum (ER) are mislocalized to the cytosol, where they threaten cellular proteostasis. How cells manage these mislocalized proteins remains poorly understood. Here, we show that inefficient Sec61 translocon activity induces a transcriptional stress response, which is enhanced by blocking NRF-1-dependent adaptation of proteasomal capacity. To maintain proteasomal capacity, thermodynamically stable mislocalized proteins persist in the cytosol of HepG2 and HEK293T cells, while mislocalized proteins that are inherently more aggregation-prone are preferentially ubiquitinated and degraded. This triaging process is accomplished through N-terminal trimming of the signal sequence of thermodynamically stable proteins, which simultaneously reduces their aggregation and prevents proteasomal degradation. These findings reveal a stability-dependent cytosolic triaging mechanism that matches substrate burden to proteasome capacity when ER import is challenged.

cell biology↗

bioRxiv2025

Genomic Analysis Reveals Recent Population Decline and Exceptionally Low Genome-Wide Heterozygosity of the Critically Endangered Philippine Eagle, Pithecophaga jefferyi (Aves: Accipitridae)

The Philippine Eagle (Pithecophaga jefferyi), is one of the rarest eagles in the world and is the national bird of the Philippines. It is listed by the International Union for Conservation of Nature (IUCN) as a critically endangered raptor and has been the subject of an intensive captive breeding program which started more than 30 years ago to ensure the survival and conservation of the species. To infer the genetic diversity and demographic history of the Philippine Eagle, we sequenced and analyzed the genomes of 35 individuals under the captive breeding program of the Philippine Eagle Foundation. Phylogenetic analysis of the draft reference sequence generated in this study placed P. jefferyi within the subfamily Circaetinae of Accipitridae. Demographic history reconstruction from genome-wide variants revealed two historical bottlenecks, as well as an ongoing population decline which was found to predate documented deforestation in the Philippines. This observation suggests that unobserved natural or anthropogenic factors might have severely affected the Philippine Eagle population long before habitat fragmentation. Genome-wide heterozygosity estimates placed the Philippine Eagle as having one of the lowest genome-wide heterozygosity levels measured among raptors. This highlights the precarious genetic state of the Philippine Eagle, as critically low heterozygosity raises risks of inbreeding depression, reduced reproductive success, and increased vulnerability to diseases, climate change, and habitat loss. The genomic resources generated in this study can therefore guide conservation strategies such as breeding program design, genetic monitoring, and other efforts to diversify existing populations to ensure both demographic stability and genetic resilience of the Philippine Eagle. Subject AreasPhilippine Eagle, Genomics, Genome-wide heterozygosity, Demographic History, Conservation, Biodiversity, Bioinformatics

genomics↗

bioRxiv2025

A phylogeny aware analysis of gene function for the biodiversity genomics era

In the biodiversity genomics era, vast gene catalogs have rapidly accumulated, but how gene functions map onto major evolutionary transitions remains vague. We integrated phylogenomics with functional annotations to trace the emergence of [~]4.5 million genes and their associated functions in 508 representative species across the tree of life. Using this top-down, function-centric approach, we mapped the evolutionary history of well-annotated biological functions, revealing key insights and widespread parallelism. For instance, the largest bursts of gene and function gains aligned with key evolutionary transitions, including the origins of eukaryotes, animals, land plants, and vertebrates. Independent transitions to multicellularity and terrestrial life showed convergent enrichment of semantically similar functions (involving entirely different gene families), and the presence of orthologous genes often belonging to ancient gene families. For example, terrestrialization nodes in slime molds, plants, and animals coincided with gains in stress-tolerance and developmental genes, whereas multicellularity in animals, fungi, plants, and slime molds consistently involved expansions in cell-adhesion and communication functions. Thus, our framework enables scalable interpretation of new genomes in an evolutionary context and offers a roadmap for exploring the genomic basis of biodiversity.

evolutionary biology↗

bioRxiv2025

Stainless Steel-Synthesized Gold Nanoparticles: Insights into Blood-Brain Barrier Permeability and Microglial Interaction.

Gold nanoparticles (AuNPs) are emerging as promising tools in biomedical research due to their unique physicochemical properties. However, their interactions with resident immune cells of the central nervous system (CNS) and the blood-brain barrier (BBB) remain poorly understood. This work attempts to fill this gap by evaluating the interaction of green synthetic nanoparticles -prepared using stainless steel as a sustainable reducing agent-with microglia cells, as well as their ability to permeate and potentially affect BBB properties. Using in vitro BBB models, we demonstrate that stainless steel-synthesized AuNPs (ss-AuNPs) effectively cross the barrier without compromising its integrity. In microglial cells, ss-AuNPs exhibited dose-dependent cytotoxic effects, with higher concentrations reducing cell viability while inducing minimal inflammatory responses. Similarly, in primary microglial cultures, ss-AuNPs at higher doses stimulated interleukin-6 (IL-6) release, although no significant pro-inflammatory activation was observed at lower doses. These results highlight the potential of green-synthesized AuNPs for CNS-targeted applications while underscoring the importance of dose optimization for safety.

immunology↗

bioRxiv2025

Distinct alpha-synuclein strains derived from Parkinson's disease patient tissues trigger differential inclusion pathology in a novel biosensor cell model

Background-Synuclein (Syn) can misfold and aggregate to form fibrillar {beta}-sheet-rich aggregates ("strains") that are phosphorylated (p-Syn) and deposited into intracellular inclusions in the brain, the pathological hallmark of synucleinopathies including Parkinsons disease (PD), dementia with Lewy bodies (DLB), and multiple system atrophy (MSA). Previously, we reported that seed amplification assays such as real-time quaking-induced conversion (RT-QuIC) amplifies and detects Syn strains from the patient skin. However, whether skin-derived Syn strains induce disease-specific pathological features in a biological system is unknown. MethodsWe generated a U251 human glioblastoma cell line expressing fluorescently tagged Syn carrying the PD-linked A53T mutation and Forster resonance energy transfer (FRET)-based U251 biosensor cells. Using fluorescence microscopy coupled with in situ detergent extraction, FRET-Flow cytometry and high-content confocal imaging, we examined the pathological burden and morphology of p-Syn inclusions seeded by RT-QuIC-amplified patient skin and brain Syn strains in Syn-expressing U251 cells, FRET-based Syn biosensor cells and Syn biosensor cell-derived neurons. ResultsU251 cells allow robust and rapid in situ detection of detergent-insoluble intracellular Syn inclusions triggered by exogenous Syn seeds. In U251 FRET-based biosensor cells, PD skin-amplified strains induce a greater pathological burden and distinct p-Syn inclusion morphology from PD brain-amplified and DLB skin-amplified strains. Inclusion morphology of DLB and MSA skin- and brain-amplified strains are comparable. Furthermore, skin-amplified Syn strains induce neuronal inclusions and cause degeneration of induced neurons reprogrammed from the U251 biosensor cells. Finally, biosensor cell-propagated PD skin Syn strains induce higher seeding activity measured by RT-QuIC than PD brain and DLB skin Syn strains, linking intracellular pathological burden to in vitro seeding activity. ConclusionsWe report the detection of distinct PD strains derived from patient skin and brain tissues that trigger unique pathological phenotypes in U251 Syn biosensor cells and cause degeneration of reprogrammed neurons from the same cell lineage. Moreover, DLB and MSA skin Syn strains mimic pathological features of their brain Syn strains in these biosensor cells. Therefore, the U251 Syn biosensor cell model is a robust tool to potentially discriminate PD and DLB synucleinopathies and to study Syn tissue- and strain-specific etiology and pathogenesis. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/646513v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@acf0a5org.highwire.dtl.DTLVardef@1eb0d17org.highwire.dtl.DTLVardef@a89c75org.highwire.dtl.DTLVardef@1b7eca4_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2022

Circadian regulation of dentate gyrus excitability mediated by G-protein signaling

The central circadian regulator within the suprachiasmatic nucleus transmits time of day information by a diurnal spiking rhythm that is driven by intrinsic activity of molecular clock genes controlling membrane excitability. Most brain regions, including the hippocampus, harbor similar intrinsic circadian transcriptional machinery but whether these molecular programs generate oscillations of membrane properties is unexplored. Here, we show that intrinsic excitability of mouse dentate granule neurons exhibits a 24-hour oscillation that controls spiking probability. Diurnal changes in excitability are mediated by antiphase G-protein regulation of potassium and sodium conductances to reduce excitability during the light phase. Disruption of the circadian transcriptional machinery by conditional deletion of Bmal1 enhances excitability selectively during the light phase, increasing engram recruitment and spatial discrimination memory. These results reveal that circadian transcriptional machinery regulates intrinsic excitability, highlighting the role of cell-autonomous oscillations in hippocampal function and behavior. HighlightsDentate neurons exhibit a 24-hour oscillation of excitability with low excitability during the Light phase Reduced excitability results from G-protein regulation of passive and active properties Bmal1 deletion disrupts G-protein regulation to enhance excitability during the Light Bmal1 deletion enhances the size of memory engrams and spatial discrimination

neuroscience↗

bioRxiv2021

The S-palmitoylome and DHHC-PAT interactome of Drosophila melanogaster S2R+ cells indicate a high degree of conservation to mammalian palmitoylomes

Protein S-palmitoylation, the addition of a long-chain fatty acid to target proteins, is among the most frequent reversible protein modification in Metazoa, affecting subcellular protein localization, trafficking and protein-protein interactions. S-palmitoylated proteins are abundant in the neuronal system and are associated with neuronal diseases and cancer. Despite the importance of this post-translational modification, it has not been thoroughly studied in the model organism Drosophila melanogaster. Here we present the palmitoylome of Drosophila S2R+ cells, comprising 198 proteins, an estimated 3.5% of expressed genes in these cells. Comparison of orthologs between mammals and Drosophila suggests that S-palmitoylated proteins are more conserved between these distant phyla than non-S-palmitoylated proteins. To identify putative client proteins and interaction partners of the DHHC family of protein acyl-transferases (PATs) we established DHHC-BioID, a proximity biotinylation-based method. In S2R+ cells ectopic expression of the DHHC-PAT dHip14-BioID in combination with Snap24 or an interaction-deficient Snap24- mutant, as a negative control, resulted in biotinylation of Snap24 but not the Snap24-mutant. DHHC-BioID in S2R+ cells using 10 different DHHC-PATs as bait identified 520 putative DHHC-PAT interaction partners of which 48 were S-palmitoylated and are therefore putative DHHC-PAT client proteins. Comparison of putative client protein/DHHC-PAT combinations indicates that CG8314, CG5196, CG5880 and Patsas have a preference for transmembrane proteins, while S-palmitoylated proteins with the Hip14-interaction motif are most enriched by DHHC-BioID variants of approximated and dHip14. Finally, we show that BioID is active in larval and adult Drosophila and that dHip14-BioID rescues dHip14 mutant flies, indicating that DHHC-BioID is non-toxic. In summary we provide the first systematic analysis of a Drosophila palmitoylome. We show that DHHC-BioID is sensitive and specific enough to identify DHHC-PAT client proteins and provide DHHC-PAT assignment for ca. 25% of the S2R+ cell palmitoylome, providing a valuable resource. In addition, we establish DHHC-BioID as a useful concept for the identification of tissue-specific DHHC-PAT interactomes in Drosophila.

biochemistry↗

bioRxiv2021

Divergent early antibody responses define COVID-19 disease trajectories

A damaging inflammatory response is strongly implicated in the pathogenesis of severe COVID-19 but mechanisms contributing to this response are unclear. In two prospective cohorts, early non-neutralizing, afucosylated, anti-SARS-CoV-2 IgG predicted progression from mild, to more severe COVID-19. In contrast to the antibody structures that predicted disease progression, antibodies that were elicited by mRNA SARS-CoV-2 vaccines were low in Fc afucosylation and enriched in sialylation, both modifications that reduce the inflammatory potential of IgG. To study the biology afucosylated IgG immune complexes, we developed an in vivo model which revealed that human IgG-Fc{gamma}R interactions can regulate inflammation in the lung. Afucosylated IgG immune complexes induced inflammatory cytokine production and robust infiltration of the lung by immune cells. By contrast, vaccine elicited IgG did not promote an inflammatory lung response. Here, we show that IgG-Fc{gamma}R interactions can regulate inflammation in the lung and define distinct lung activities associated with the IgG that predict severe COVID-19 and protection against SARS-CoV-2. One Sentence SummaryDivergent early antibody responses predict COVID-19 disease trajectory and mRNA vaccine response and are functionally distinct in vivo.

immunology↗