Biology subjects

Larson, L.

Publications and source records attributed to Larson, L..

7 recordsLinked to original sources

bioRxiv2025

BOTany Methods: Accessible Automation for Plant Synthetic Biology

Most members of the synthetic biology community, particularly plant scientists, lack access to liquid handling robots to scale up experiments, enhance reproducibility, and accelerate the Design, Build, Test, Learn cycle. Biofoundries enable high throughput data acquisition to train AI models and to develop new bioproducts, but they are capital-intensive to set up and not widely distributed. Entry-level, 3D-printed robots offer more affordable alternatives, but suffer from a shortage of validated protocols that can be modified without prior coding experience. To enhance access to biological automation, we developed a collection of modular BOTany Methods using Opentrons OT-2 robots to streamline the most common methods for molecular biology research and education. Our comprehensive workflow offers automation for a variety of procedures, ranging from simple but repetitive tasks (such as primer dilution and PCR setup) to more complex operations, including Plant Modular Cloning (MoClo), bacterial transformation, and plasmid extraction. Our BOTany Methods enable undergraduate students and other early career researchers to run designer experiments using table-based inputs, without editing the custom Python scripts. This pipeline enables end-to-end molecular cloning with minimal user intervention, enhancing throughput and traceability for synthetic biology applications. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/671538v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@1b98282org.highwire.dtl.DTLVardef@2727bdorg.highwire.dtl.DTLVardef@a2157borg.highwire.dtl.DTLVardef@1305107_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2024

Patterned Electrical Brain Stimulation by a Wireless Network of Implantable Microdevices

Transmitting meaningful information into brain circuits by electronic means is a challenge facing brain-computer interfaces. A key goal is to find an approach to inject spatially structured local current stimuli across swaths of sensory areas of the cortex. Here, we introduce a fully wireless approach to multipoint patterned electrical microstimulation by a spatially distributed epicortically implanted network of silicon microchips to target specific areas of the cortex. Each sub-millimeter-sized microchip harvests energy from an external radio-frequency source and converts this into biphasic current injected focally into tissue by a pair of integrated microwires. The amplitude, period, and repetition rate of injected current from each chip are controlled across the implant network by implementing a pre-scheduled, collision-free bitmap wireless communication protocol featuring sub-millisecond latency. As an in vivo demonstration, a network of 30 wireless stimulators was chronically implanted into motor and sensory areas of the cortex in a freely moving rat for three months. We explored the effects of patterned intracortical electrical stimulation on trained animal behavior at average RF powers well below safety limits.

neuroscience↗

bioRxiv2023

Determination of Optimal Nutrient Levels in Baru Seedlings (Dipterix alata Vog.) Using the Mathematical Chance Method

This work aimed to determine the optimal ranges by the Mathematical Chance (ChM) method in baru seedlings. To determine optimal ranges by ChM, the nutritional information from an experiment conducted in a protected environment from October 13, 2011, to February 11, 2012, in Selviria-MS and for seedling production, used a nursery with 50% light reduction polypropylene mesh and 15 x 21.5 cm plastic bags, which have a capacity of 1.8 L, which were filled with different substrate combinations. The ranges found for macronutrients with the ChM method were, in g kg-1, from 19.06 to 28.14; 1.52 to 3.38; 17.9 to 24.0; 1.76 to 3.54; 0.74 to 1.50; 1.26 to 2.26 for N, P, K, Ca, Mg and S, respectively. The ranges found for micronutrients with the ChM method were, in mg kg 1, from 21.79 to 33.59; 1.0 to 21.40; 75 to 104.4; 14.0 to 82.8; 18.0 to 24.4 for B, Cu, Fe, Mn, and Zn, respectively.

plant biology↗

bioRxiv2021

Acquisition of the L452R mutation in the ACE2-binding interface of Spike protein triggers recent massive expansion of SARS-Cov-2 variants

The recent rise in mutational variants of SARS-CoV-2, especially with changes in the Spike protein, is of significant concern due to the potential ability for these mutations to increase viral infectivity, virulence and/or ability to escape protective antibodies. Here, we investigated genetic variations in a 414-583 amino acid region of the Spike protein, partially encompassing the ACE2 receptor-binding domain (RBD), across a subset of 570 nasopharyngeal samples isolated between April 2020 and February 2021, from Washington, California, Arizona, Colorado, Minnesota and Illinois. We found that samples isolated since November have an increased number of amino acid mutations in the region, with L452R being the dominant mutation. This mutation is associated with a recently discovered CAL.20C viral variant from clade 20C, lineage B.1.429, that since November-December 2020 is associated with multiple outbreaks and is undergoing massive expansion across California. In some samples, however, we found a distinct L452R-carrying variant of the virus that, upon detailed analysis of the GISAID database genomes, is also circulating primarily in California, but emerged even more recently. The newly identified variant derives from the clade 20A (lineage B.1.232) and is named CAL.20A. We also found that the SARS-CoV-2 strain that caused the only recorded case of infection in an ape - gorillas in the San Diego Zoo, reported in January 2021 - is CAL.20A. In contrast to CAL.20C that carries two additional to L452R mutations in the Spike protein, L452R is the only mutation found in CAL.20A. According to the phylogenetic analysis, however, emergence of CAL.20C was also specifically triggered by acquisition of the L452R mutation. Further analysis of GISAID-deposited genomes revealed that several independent L452R-carrying lineages have recently emerged across the globe, with over 90% of the isolates reported between December 2020 - February 2021. Taken together, these results indicate that the L452R mutation alone is of significant adaptive value to SARS-CoV-2 and, apparently, the positive selection for this mutation became particularly strong only recently, possibly reflecting viral adaptation to the containment measures or increasing population immunity. While the functional impact of L452R has not yet been extensively evaluated, leucine-452 is positioned in the receptor-binding motif of RBD, in the interface of direct contact with the ACE2 receptor. Its replacement with arginine is predicted to result in both a much stronger binding to the receptor and escape from neutralizing antibodies. If true, this in turn might lead to significantly increased infectivity of the L452R variants, warranting their close surveillance and in-depth functional studies.

microbiology↗

bioRxiv2020

APOBEC3B expression generates an immunogenic model of Kras mutant lung cancer

Mutations in oncogenes such as KRAS and EGFR cause a high proportion of lung cancers. Drugs targeting these proteins cause tumour regression but ultimately fail to cure these cancers, leading to intense interest in how best to combine them with other treatments, such as immunotherapies. However, preclinical systems for studying the interaction of lung tumours with the host immune system are inadequate, in part due to the low tumour mutational burden in genetically engineered mouse models. Here we set out to develop mouse models of mutant KRAS-driven lung cancer with an elevated tumour mutational burden by expressing the human DNA cytosine deaminase, APOBEC3B, to mimic the mutational signature seen in human lung cancer. This failed to substantially increase clonal tumour mutational burden and autochthonous tumours remained refractory to immunotherapy. However, by establishing clonal cell lines from these tumours we generated an immunogenic syngeneic transplantation model of KRAS mutant lung adenocarcinoma that was sensitive to immunotherapy. Unexpectedly, we found that anti-tumour immune responses were not directed against neoantigens but instead targeted derepressed endogenous retroviral antigens. The ability of KRASG12C inhibitors to cause regression of KRASG12C-expressing versions of these tumours was markedly potentiated by the adaptive immune system, providing a unique opportunity for the study of combinations of targeted and immunotherapies in immune-hot lung cancer.

cancer biology↗

bioRxiv2020

Wireless Ensembles of Sub-mm Microimplants Communicating as a Network near 1 GHz in a Neural Application

Multichannel electrophysiological sensors and stimulators, especially those used for studying the nervous system, are most commonly based on monolithic microelectrode arrays. Such architecture limits the spatial flexibility of individual electrode placement, posing constraints for scaling to a large number of nodes, particularly across non-contiguous locations. We describe the design and fabrication of sub-millimeter size electronic microchips ("Neurograins") which autonomously perform neural sensing or electrical microstimulation, with emphasis on their wireless networking and powering. An [~]1 GHz electromagnetic transcutaneous link to an external telecom hub enables bidirectional communication and control at the individual neurograin level. The link operates on a customized time division multiple access (TDMA) protocol designed to scale up to 1000 neurograins. The system is demonstrated as a cortical implant in a small animal (rat) model with anatomical limitations restricting the implant to 48 neurograins. We suggest that the neurograin approach can be generalized to overcome many scalability issues for wireless sensors and actuators as implantable microsystems.

neuroscience↗

bioRxiv2019

APOBEC3A Catalyzes Mutation and Drives Carcinogenesis In Vivo

The APOBEC3 family of antiviral DNA cytosine deaminases is implicated as the second largest source of mutation in cancer. This mutational process may be a causal driver or inconsequential passenger to the overall tumor phenotype. We show that human APOBEC3A expression in murine colon and liver tissues increases tumorigenesis. All other APOBEC3 family members including APOBEC3B did not as strongly promote liver tumor formation. DNA sequences from APOBEC3A-expressing animals display hallmark APOBEC signature mutations in TCA/T motifs. Bioinformatic comparisons of the observed APOBEC3A mutation signature in murine tumors, previously reported APOBEC3A and APOBEC3B mutation signatures in yeast, and reanalyzed APOBEC mutation signatures in human tumor data sets support cause-and-effect relationships for APOBEC3A-catalyzed deamination and mutagenesis in driving multiple human cancers.

cancer biology↗