Biology subjects

Hernandez, A. I.

Publications and source records attributed to Hernandez, A. I..

4 recordsLinked to original sources

bioRxiv2026

Phased Chromosome-level Genome and Organellar Assemblies of Castilleja foliolosa Provide Vital Resource for Orobanchaceae Genomics

Castilleja (Orobanchaceae) is a diverse, facultatively hemiparasitic plant genus characterized by a complex evolutionary history of reticulate evolution and significant taxonomic ambiguity. High-quality genomic resources have historically been limited, hindering robust macro-evolutionary and macro-ecological inquiries. Here, we present the first high-quality, phased, chromosome-level reference genome for the diploid species Castilleja foliolosa. Utilizing a hybrid assembly strategy, we integrated long-read PacBio HiFi sequencing with Omni-C proximity ligation data to generate a highly contiguous nuclear assembly, complemented by reconstructed mitochondrial and chloroplastic genomes. The primary nuclear haplotype spans approximately 510 Mbp, containing 39,417 predicted genes and a substantial repetitive landscape covering ~66% of the genome. Our organellar assemblies reveal notable structural complexity: the chloroplast maintains heteroplasmy via two primary structural haplotypes, while the 611 kbp mitogenome adopts a circular master topology existing in two isomeric forms. Comparative genomic analyses demonstrate a largely conserved chromosomal architecture relative to the closely related Pedicularis cranolopha, punctuated by the presence of lineage-specific genes. Functional enrichment of Castilleja-specific orthogroups identifies a consistent association with telomere maintenance, DNA integration, and zinc ion binding, likely stemming from the substantial repeat content. This reference genome provides a robust framework for dissecting the genomic drivers of taxonomic diversification and adaptation within the Orobanchaceae family. This resource significantly enhances our capacity to untangle reticulate evolutionary patterns, offering a definitive foundation for future comparative studies of genome evolution in the Orobanchaceae lineage of parasitic plants.

plant biology↗

bioRxiv2025

Transcriptomic Signatures of Hippocampal Subregions and Neuronal Nuclei in Active Place Avoidance Memory Maintenance

The gene expression changes associated with memory acquisition, consolidation and reconsolidation, all active epochs in memory formation, have been well characterized in the rodent hippocampus. Less is known, however, of the changes in gene expression supporting the maintenance of memory, particularly when it remains undisturbed or offline days after the memory experience. In this study, we used a combination of spatial transcriptomic and single nuclear RNA sequencing (snRNA-seq) to measure the gene expression changes in the dorsal hippocampus during an early phase of offline memory maintenance, 3 days after the post-training retention test of an active place avoidance memory. Through spatial transcriptomics we identified spatially regionalized differential gene expression and biological process enrichment, with CA1, CA3, and DG exhibiting differential expression of genes involved in post-synaptic function, synaptic vesicle transport, and neuronal differentiation, respectively. Notably, through snRNA-seq, differentially expressed genes detected in clusters of hippocampal neurons from the trained animal were largely defined by their down regulation of genes involved in ATP synthesis and cytoplasmic translation. With both techniques we also examined the gene expression changes in a putative subset of memory-associated neurons through the detection of eYFP mRNA in the Arc-Cre/flox-eYFP double transgenic mouse line. Amongst this population of cells, we detected a limited number of differentially expressed genes unique to each subregional population and associated with synaptic plasticity and post-synaptic signaling. Our results suggest that two overarching transcriptomic patters contribute to the functional changes in hippocampal cells during offline memory maintenance: a regional distribution of pathways linked to synaptic functions, and a reduction of metabolic activity across hippocampal sub-regions and memory-associated neuronal ensembles.

neuroscience↗

bioRxiv2025

Rescue of hippocampal synaptic plasticity and memory performance by Fingolimod (FTY720) in APP/PS1 model of Alzheimer's disease is accompanied by correction in metabolism of sphingolipids, polyamines, and phospholipid saturation composition

Previously, our metabolomic, transcriptomic, and genomic studies characterized the ceramide/sphingomyelin pathway as a therapeutic target in Alzheimers disease, and we demonstrated that FTY720, a sphingosine-1-phospahate receptor modulator approved for treatment of multiple sclerosis, recovers synaptic plasticity and memory in APP/PS1 mice. To further investigate how FTY720 rescues the pathology, we performed metabolomic analysis in brain, plasma, and liver of trained APP/PS1 and wild-type mice. APP/PS1 mice showed area-specific brain disturbances in polyamines, phospholipids, and sphingolipids. Most changes were completely or partially normalized in FTY720-treated subjects, indicating rebalancing the "sphingolipid rheostat", reactivating phosphatidylethanolamine synthesis via mitochondrial phosphatidylserine decarboxylase pathway, and normalizing polyamine levels that support mitochondrial activity. Synaptic plasticity and memory were rescued, with spermidine synthesis in temporal cortex best corresponding to hippocampal CA3-CA1 plasticity normalization. FTY720 effects, also reflected in other pathways, are consistent with promotion of mitochondrial function, synaptic plasticity, and anti-inflammatory environment, while reducing pro-apoptotic and pro-inflammatory signals.

neuroscience↗

bioRxiv2024

Spatially Resolved Transcriptomic Signatures of Hippocampal Subregions and Arc-Expressing Ensembles in Active Place Avoidance Memory

The rodent hippocampus is a spatially organized neuronal network that supports the formation of spatial and episodic memories. We conducted bulk RNA sequencing and spatial transcriptomics experiments to measure gene expression changes in the dorsal hippocampus following the recall of active place avoidance (APA) memory. Through bulk RNA sequencing, we examined the gene expression changes following memory recall across the functionally distinct subregions of the dorsal hippocampus. We found that recall induced differentially expressed genes (DEGs) in the CA1 and CA3 hippocampal subregions were enriched with genes involved in synaptic transmission and synaptic plasticity, while DEGs in the dentate gyrus (DG) were enriched with genes involved in energy balance and ribosomal function. Through spatial transcriptomics, we examined gene expression changes following memory recall across an array of spots encompassing putative memory-associated neuronal ensembles marked by the expression of the IEGs Arc, Egr1, and c-Jun. Within samples from both trained and untrained mice, the subpopulations of spatial transcriptomic spots marked by these IEGs were transcriptomically and spatially distinct from one another. DEGs detected between Arc+ and Arc-spots exclusively in the trained mouse were enriched in several memory-related gene ontology terms, including "regulation of synaptic plasticity" and "memory." Our results suggest that APA memory recall is supported by regionalized transcriptomic profiles separating the CA1 and CA3 from the DG, transcriptionally and spatially distinct IEG expressing spatial transcriptomic spots, and biological processes related to synaptic plasticity as a defining the difference between Arc+ and Arc-spatial transcriptomic spots.

neuroscience↗