Biology subjects

Young, D. J.

Publications and source records attributed to Young, D. J..

4 recordsLinked to original sources

bioRxiv2026

Canopy traits reveal climate-associated genetic differentiation in a California oak common garden

Background and Aims. Phenotypic variation in plant populations reflecting historical climate adaptation may affect performance under future climates. In long-lived trees, height and stem diameter are commonly used to assess growth, but these measures may not fully capture complementary structural and functional dimensions of performance, such as canopy development and vigor. We investigated whether canopy traits reveal climate-associated genetic differentiation in Quercus lobata. Methods. Using drone-based remote sensing of 1,395 12-year-old Quercus lobata trees from 601 families in a common garden, we quantified canopy volume and greenness, using the Normalized Difference Vegetation Index (NDVI). Previous analyses indicated that trees originating from warmer climates grew more in common gardens than those from cooler climates. To assess whether canopy traits showed similar patterns, we tested for family-level variation in each trait and associations with climate of origin. Key Results. Canopy volume and greenness showed significant genetic variation among families and significant associations with climate of origin. Trees from hotter climates had greater canopy volume and greenness than trees from cooler climates. Conclusions. These covarying traits provide novel evidence of climate-associated genetic differentiation in tree performance, consistent with historical climate selection. Trees originating from climates with hot summers, moderate winters, and low precipitation performed best in the garden, suggesting that they will perform better than trees adapted to cool, wet conditions under future climate change.

evolutionary biology↗

bioRxiv2025

Identification of translation events that drive nonsense-mediated mRNA decay reveals functional roles for noncoding RNAs

The nonsense-mediated mRNA decay (NMD) pathway targets mRNAs undergoing premature translation termination for degradation. Previously, RNA-seq of yeast lacking NMD revealed that most genes targeted by NMD lack obvious premature termination codons (PTCs). We developed a combined approach using RNA-seq and a novel 40S ribosome profiling strategy to identify cryptic premature termination events that could account for NMD on nearly all these transcripts, including many non-coding RNA transcript isoforms associated with annotated genes. Many NMD-targeted transcripts appear to be involved in two-promoter gene regulatory systems and share properties with long un-decoded transcript isoforms (LUTIs). In particular, we show that the DAL5 LUTI regulates expression of the DAL5 protein-coding mRNA in response to changes to environmental nitrogen. Our work expands the functional roles for LUTIs and establishes the importance of NMD in their regulation. HIGHLIGHTSO_LI40S ribosome profiling reveals a comprehensive catalog of NMD substrates in yeast. C_LIO_LIMost NMD targets have short uORFs or iORFs, resulting in premature termination. C_LIO_LIMany long undecoded transcript isoforms (LUTIs) contain NMD-triggering uORFs. C_LIO_LILUTIs, such as DAL5, play a role in metabolic regulation (i.e. nitrogen and thiamine). C_LI

molecular biology↗

bioRxiv2024

In vivo tracking of ex vivo generated 89Zr-oxine labeled plasma cells by PET in a non-human primate model

B cells are an attractive platform for engineering to produce protein-based biologics absent in genetic disorders, and potentially for the treatment of metabolic diseases and cancer. As part of pre-clinical development of B cell medicines, we demonstrate a method to collect, ex vivo expand, differentiate, radioactively label, and track adoptively transferred non-human primate (NHP) B cells. These cells underwent 10- to 15-fold expansion, initiated IgG class switching, and differentiated into antibody secreting cells. Zirconium-89-oxine labeled cells were infused into autologous donors without any preconditioning and tracked by PET/CT imaging. Within 24 hours of infusion, 20% of the initial dose homed to the bone marrow and spleen and distributed stably and equally between the two. Interestingly, approximately half of the dose homed to the liver. Image analysis of the bone marrow demonstrated inhomogeneous distribution of the cells. The subjects experienced no clinically significant side effects or laboratory abnormalities. A second infusion of B cells into one of the subjects resulted in an almost identical distribution of cells, suggesting a non-limiting engraftment niche and feasibility of repeated infusions. This work supports the NHP as a valuable model to assess the potential of B cell medicines as potential treatment for human diseases.

bioengineering↗

bioRxiv2020

Validation and Long-Term Follow Up of CD33 Off-Targets Predicted In Vitro and In Silico Using Error-Corrected Sequencing in Rhesus Macaques

ABSTRACTThe programmable nuclease technology CRISPR/Cas9 has revolutionized gene editing in the last decade. Due to the risk of off-target editing, accurate and sensitive methods for off-target characterization are crucial prior to applying CRISPR/Cas9 therapeutically. Here, we utilized a rhesus macaque model to ask whether CIRCLE-Seq (CS), an in vitro off-target prediction method, more accurately identifies off-targets compared to in silico prediction (ISP) based solely on genomic sequence comparisons. We use AmpliSeq HD error-corrected sequencing to validate off-target sites predicted by CIRCLE-Seq and ISP for guide RNAs designed against TET2 and CD33 genes. A gRNA targeting TET2 designed using modern algorithms and predicted to have low off-target risk by both ISP and CIRCLE-Seq created no detectable mutations at off-target sites in hematopoietic cells following transplantation, even when applying highly sensitive error-corrected sequencing. In contrast, a CD33 gRNA designed using less robust algorithms with over 10-fold more off-targets sites predicted by both ISP and CIRCLE-Seq, however there was poor correlation between the sites predicted by the two methods. When almost 500 sites identified by each method were searched for in hematopoietic cells following transplantation, 19 detectable mutations in off-target sites were detected via error-corrected sequencing. Of these 19 sites, 8 sites were predicted in the top 500 sites by both methods, 8 by CIRCLE-Seq only, and 3 by ISP only. Cells with off-target editing exhibited no expansion or abnormal behavior in vivo in animals followed for up to 2 years. In conclusion, neither methodology predicted all sites, and a combination of careful gRNA design, followed by screening for predicted off-target sites in target cells by multiple methods may be required for optimizing safety of clinical development.Competing Interest StatementThe authors have declared no competing interest.View Full Text

molecular biology↗