Marena Trinidad

2 months ago | elifesciences.org | Santi Mestre-Fos |Lucas Ferguson |Marena Trinidad |Nicholas T. Ingolia

Ribosome profiling computational analysis Request a detailed protocol Ribosome profiling and Total RNA cDNA libraries were sequenced on an Illumina NovaSeq 150PE platform.

Dec 4, 2024 | nature.com | Yekaterina Shulgina |Marena Trinidad |Conner Langeberg |Hunter Nisonoff |Seyone Chithrananda |Petr Skopintsev | +7 more

AbstractStructured RNA lies at the heart of many central biological processes, from gene expression to catalysis. RNA structure prediction is not yet possible due to a lack of high-quality reference data associated with organismal phenotypes that could inform RNA function. We present GARNET (Gtdb Acquired RNa with Environmental Temperatures), a new database for RNA structural and functional analysis anchored to the Genome Taxonomy Database (GTDB).

Oct 2, 2024 | biorxiv.org | Honglue Shi |KEVIN WASKO |Marena Trinidad |Noor Al-Sayyad

AbstractRNA-guided CRISPR-Cas enzymes initiate programmable genome editing by recognizing a 20-base-pair DNA sequence adjacent to a short protospacer-adjacent motif (PAM). To uncover the molecular determinants of high-efficiency editing, we conducted biochemical, biophysical and cell-based assays on S. pyogenes Cas9 (SpyCas9) variants with wide-ranging genome editing efficiencies that differ in PAM binding specificity.

Aug 31, 2024 | biorxiv.org | Santi Mestre-Fos |Lucas Ferguson |Marena Trinidad |Nicholas T. Ingolia

AbstractStem cell differentiation involves a global increase in protein synthesis to meet the demands of specialized cell types. However, the molecular mechanisms underlying this translational burst and the involvement of initiation factors remains largely unknown. Here, we investigate the role of eukaryotic initiation factor 3 (eIF3) in early differentiation of human pluripotent stem cell (hPSC)-derived neural progenitor cells (NPCs).

May 22, 2024 | cell.com | Dina Silva |Marena Trinidad |Alicia Ljungdahl

SummaryHeterozygous variants in SLC6A1, encoding the GAT-1 GABA transporter, are associated with seizures, developmental delay, and autism. The majority of affected individuals carry missense variants, many of which are recurrent germline de novo mutations, raising the possibility of gain-of-function or dominant-negative effects. To understand the functional consequences, we performed an in vitro GABA uptake assay for 213 unique variants, including 24 control variants.