Biology subjects

Cartagena, P.

Publications and source records attributed to Cartagena, P..

3 recordsLinked to original sources

bioRxiv2025

UC Irvine Brain Initiative Cell Atlas Network (BICAN) Brain Procurement Program for the Center for Multiomic Human Brain Cell Atlas Project

High-quality neurotypical postmortem human brain tissue is essential but difficult to obtain for constructing comprehensive human brain cell atlases. Here we describe the establishment of UC Irvines Brain Procurement Program, a coordinated initiative to collect and process neurotypical donor brains for multiomic mapping studies within the NIH BRAIN Initiative Cell Atlas Network (BICAN) consortium. Through partnerships with the Orange County Coroners Office, the UC Irvine Willed Body Program, UCI Medical Center, and the Childrens Hospital of Orange County, we have developed standardized workflows encompassing donor identification, postmortem brain recovery and processing, region-of-interest dissection, neurotypical donor selection, and data management. Our experience demonstrates the feasibility of a community-based, multi-institutional procurement framework while highlighting challenges in recruiting neurotypical donors and ensuring demographic representation reflective of Southern California. We further identify opportunities to strengthen outreach and donation pathways. This program provides a scalable model for advancing population-reflective, high-quality human brain cell atlas efforts. HighlightsO_LIEstablish a multi-site pipeline for procuring high-quality neurotypical human brains. C_LIO_LIDemonstrate feasibility of donor collection across childhood to adulthood. C_LIO_LIIdentify barriers and propose strategies to improve broad donor recruitment. C_LI

neuroscience↗

bioRxiv2023

Extensive profiling of transcription factors in postmortem brains defines genomic occupancy in disease-relevant cell types and links TF activities to neuropsychiatric disorders

Transcription factors (TFs) orchestrate gene expression programs crucial for cell physiology, but our knowledge of their function in the brain is limited. Using bulk tissues and sorted nuclei from multiple human post-mortem brain regions, we generated a multi-omic resource (1121 total experiments) that includes binding maps for more than 100 TFs. We demonstrate improved measurements of TF activity, including motif recognition and gene expression modeling, upon identification and removal of regions of high TF occupancy. Further, we find that predictive TF binding models demonstrate a bias for these high occupancy sites. Neuronal TFs SATB2 and TBR1 bind unique regions depleted for such sites and promote neuronal gene expression. Several TFs, including TBR1 and PKNOX1, are enriched for risk variants associated with neuropsychiatric disorders, predominantly in neurons. These data are a powerful resource for future studies seeking to understand the role of TFs in epigenetic regulation in the human brain.

genomics↗

bioRxiv2021

Whole Chloroplast Genomes reveals the uniqueness of Bolivian native cacao (Theobroma cacao) from the northern part of Bolivia

We report the complete chloroplast sequences of two varieties of Theobroma cacao collected in the Bolivian Amazonia using Next-Generation Sequencing. Comparisons made between these two chloroplast genomes and the Belizean reference plastid genome identified 19 and 22 nucleotide variants. The phylogenetic analysis reported three main T. cacao clades belonging to the Forastero, Criollo and Trinitario groups. The Bolivian Native Cacao varieties were located inside the Trinitario group forming their unique branch. The Bolivian Native Cacao branch reveals a possible new subpopulation different from the well-characterized T. cacao subpopulations. The phylogenetic trees showed that the relationships among the T. cacao varieties were consistent with their geographical locations placing the Cacao Center of Origin in Western Amazon. The data presented here will contribute to the usage of ultrabarcoding to distinguish different T. cacao varieties and to identify native cacaos from introduced cacaos. Thus helping in the conservation of local native varieties of T. cacao.

plant biology↗