Biology subjects

Sorensen, R.

Publications and source records attributed to Sorensen, R..

4 recordsLinked to original sources

bioRxiv2026

Cue-guided performance is disrupted during pedunculotegmental-induced motor arrest

Optogenetic stimulation of the rostral pedunculotegmental nucleus (PTg) induces global motor arrest, but it remains unclear whether this is merely a suppression of motor activity or a broader disruption of brain processes required to guide action. We developed a visuospatial cue task for rats, to test if sensory information presented during PTg-induced arrest can guide later responses. Here, we show that optogenetic stimulation during cue presentation reduces accuracy to chance level. By moving stimulation to only before or only after the cue, we found that performance was only affected when stimulation and cue presentation overlapped, that rats recover cue-guided behavior almost immediately at the end of stimulation, and that stimulation does not appear to abolish responses based on cue information acquired before arrest. These findings indicate that stimulation of the rostral PTg does not only pause motor output but transiently disrupts the ability to process and use cue information effectively.

neuroscience↗

bioRxiv2024

Protein Carrier AAV

AAV is widely used for efficient delivery of DNA payloads. The extent to which the AAV capsid can be used to deliver a protein payload is unexplored. Here, we report engineered AAV capsids that directly package proteins - Protein Carrier AAV (pcAAV). Nanobodies inserted into the interior of the capsid mediate packaging of a cognate protein, including Green Fluorescent Protein (GFP), Streptococcus pyogenes Cas9, Cre recombinase, and the engineered peroxidase APEX2. We show that protein packaging efficiency is affected by the nanobody insertion position, the capsid protein isoform into which the nanobody is inserted, and the subcellular localization of the packaged protein during recombinant AAV capsid production; each of these factors can be rationally engineered to optimize protein packaging efficiency. We demonstrate that proteins packaged within pcAAV retain their enzymatic activity and that pcAAV can bind and enter the cell to deliver the protein payload. Establishing pcAAV as a protein delivery platform may expand the utility of AAV as a therapeutic and research tool.

synthetic biology↗

bioRxiv2020

Trimmed Constrained Mixed Effects Models: Formulations and Algorithms.

Mixed effects (ME) models inform a vast array of problems in the physical and social sciences, and are pervasive in meta-analysis. We consider ME models where the random effects component is linear. We then develop an efficient approach for a broad problem class that allows nonlinear measurements, priors, and constraints, and finds robust estimates in all of these cases using trimming in the associated marginal likelihood. The software accompanying this paper is disseminated as an open-source Python package called LimeTr. LimeTr is able to recover results more accurately in the presence of outliers compared to available packages for both standard longitudinal analysis and meta-analysis, and is also more computationally efficient than competing robust alternatives. Supplementary materials that reproduce the simulations, as well as run LimeTr and third party code are available online. We also present analyses of global health data, where we use advanced functionality of LimeTr, including constraints to impose monotonicity and concavity for dose-response relationships. Nonlinear observation models allow new analyses in place of classic approximations, such as log-linear models. Robust extensions in all analyses ensure that spurious data points do not drive our understanding of either mean relationships or between-study heterogeneity.

bioinformatics↗

bioRxiv2019

Genetic analysis of seed and pod traits in a set of Recombinant Inbred Lines (RILs) in peanut (Arachis hypogaea L.)

Although seed and pod traits are important for peanut breeding, little is known about the inheritance of these traits. A recombinant inbred line (RIL) population of 156 lines from a cross of Tifrunner x NC 3033 was genotyped with the Axiom_Arachis1 SNP array and SSRs to generate a genetic map composed of 1524 markers in 29 linkage groups (LG). The genetic positions of markers were compared with their physical positions on the peanut genome to confirm the validity of the linkage map and explorethe distribution of recombination and potential chromosomal rearrangements. These traits were phenotyped over three consecutive years for the purpose of developing trait-associated markers for breeding. Forty-nine QTL were identified in 14 LG for seed size index, kernel percentage, seed weight, pod weight, single-kernel, double-kernel, pod area and pod density. Twenty QTL demonstrated phenotypic variance explained (PVE) greater than 10% and eight more than 20%. Of note, seven of the eight major QTL for pod area, pod weight and seed weight (PVE >20% variance) were attributed to NC 3033 and located in a single linkage group, LG B06_1. In contrast, the most consistent QTL for kernel percentage were located on A07/B07 and derived from Tifrunner.

plant biology↗