Biology subjects

Louie, M.

Publications and source records attributed to Louie, M..

3 recordsLinked to original sources

bioRxiv2026

Outpacing E. coli: Development of Vibrio natriegens as a Next-Generation Cloning Host

Despite transformative advances in DNA synthesis, sequencing, and automation that have accelerated recombinant DNA workflows, molecular cloning hosts have scarcely evolved past the Escherichia coli strains adopted out of convenience in the 1970s. We present NBx CyClone - an engineered strain of Vibrio natriegens - as a next-generation host for molecular cloning. This non-pathogenic marine bacterium combines broad plasmid and genetic tool compatibility, a versatile metabolism, and the fastest known doubling time of any free-living organism. By shortening growth-dependent steps, this host offers a practical route to faster, more efficient recombinant DNA workflows across research and industry.

synthetic biology↗

bioRxiv2024

Dendritome Mapping Unveils Spatial Organization of Striatal D1/D2-Neuron Morphology

Morphology is a cardinal feature of a neuron and mediates its functions, but profiling neuronal morphologies at scale remains a formidable challenge. Here we describe a generalizable pipeline for large-scale brainwide profiling of dendritic morphology of genetically-defined single neurons in the mouse brain. We generated a dataset of 3,762 3D-reconstructed and reference-atlas mapped striatal D1- and D2-medium spiny neurons (MSNs). Integrative morphometric analyses reveal distinct impacts of D1/D2 and anatomical locations on MSN morphology. To analyze striatal regional features of MSN dendrites without prior anatomical constraints, we assigned MSNs to a lattice of cubic boxes in the reference brain atlas, and summarized morphometric representation ("eigen-morph") for each box and clustered boxes with shared morphometry. This analysis reveals 6 modules with characteristic dendritic features and spanning contiguous striatal territories, each receiving distinct corticostriatal inputs. Finally, we found aging confers robust and concordant dendritic length and branching defects in D1/D2-MSNs, while Huntingtons disease (HD) mice exhibit MSN-subtype and striatal regional specific pathology. Together, our study demonstrates a systems-biology approach to profile dendritic morphology of genetically-defined single-neurons; and defines novel striatal D1/D2-MSN morphological territories and aging- or HD-associated pathologies.

neuroscience↗

bioRxiv2019

Laocoön: a tool for high-throughput automated cell counting

STRUCTURED ABSTRACTO_ST_ABSMotivationC_ST_ABSThere are current programs and plugins that automatically count the number of cells in a given image. However, many of these processes are not entirely automatic, as they require user input to specify a region of interest and are also frequently inaccurate. ResultsThis project presents laocoon, a Python package specifically designed to automatically and efficiently count the number of fluorescently-labelled cells in images. This package not only allows for reliable cell counting, but returns the proportion of cells in each cell cycle relative to all the cells in the DAPI channel, which is currently used for research purposes, but could ultimately be utilized for clinical purposes. Availability and ImplementationThis package, its corresponding execution instructions, and further information about the underlying algorithms, are currently available in the GitHub repository https://github.com/edukait/laocoon under the MIT license and can be run on the command terminal of any operating system. Alternatively, laocoon is available in the Python Package Index (PyPi), so the user can use the pip command to immediately download the package. Contactkaitlin.y.lim@gmail.com

bioinformatics↗