Biology subjects

Ko, C.-C.

Publications and source records attributed to Ko, C.-C..

4 recordsLinked to original sources

bioRxiv2025

Genome editing of phylogenetically distinct bacteria using portable retron-mediated recombineering

Advanced genome editing technologies have enabled rapid and flexible rewriting of the Escherichia coli genome, benefiting fundamental biology and biomanufacturing. Unfortunately, some of the most useful technologies to advance genome editing in E. coli have not yet been ported into other bacterial species. For instance, the addition of bacterial retrons to the genome editing toolbox has increased the efficiency of recombineering in E. coli by enabling sustained, abundant production of ssDNA recombineering donors by reverse transcription that install flexible, precise edits in the prokaryotic chromosome. To extend the utility of this technology beyond E. coli, we surveyed the portability and versatility of retron-mediated recombineering across three different bacterial phyla (Proteobacteria, Bacillota and Actinomycetota) and a total of 15 different species. We found that retron recombineering is functional in all species tested, reaching editing efficiencies above 20% in six of them, above 40% in three of them, and above 90% in two of them. We also tested the extension of the recombitron architecture optimizations and strain backgrounds in a subset of hosts to additionally increase editing rates. The broad recombitron survey carried out in this study forms the basis for widespread use of retron-derived technologies through the whole Bacteria domain.

bioengineering↗

bioRxiv2024

METCAM/MUC18 plays a tumor promoter role in the development of nasopharyngeal carcinoma type III

Our previous studies by testing the effects of huMETCAM/MUC18 over-expression on the tumorigenesis of the NPC-TW01 cell line supports the notion that huMETCAM/MUC18 plays a tumor suppressor role in the development of nasopharyngeal carcinoma (NPC) type I. However, it is not clear if this notion also holds true for another NPC cell line, NPC-TW04, which was established from NPC type III. For this purpose, we further investigated the effects of huMETCAM/MUC18 over-expression in the NPC-TW04 cell line on their in vitro cellular behaviors and in vivo tumorigenesis in athymic nude mice. First, the G418-resistant clones were obtained after transfection of the huMETCAM/MUC18 cDNA into the NPC-TW04 cell line. Then, one NPC-TW04 clone, which expressed a high level of huMETCAM/MUC18, and one empty vector (control) clone were used for testing effects of huMETCAM/MUC18 over-expression on their in vitro behaviors (intrinsic growth rate, motility, and invasiveness, and growth on three-dimensional basement membrane) and in vivo tumorigenesis (via subcutaneous injection) in the athymic nude mice. Time course of tumor proliferation and final tumor volumes/weights were determined. Tumor sections were used for histology and immunohistochemistry (IHC) analyses. Tumor lysates were used to determine levels of huMETCAM/MUC18 and various downstream key effectors. We found that over-expression of huMETCAM/MUC18 increased in vitro motility and invasiveness, induced the invasive growth in the 3D basement membrane culture assay, and increased in vivo tumorigenicity of NPC-TW04 cell line. The expression levels of downstream effectors, such as an anti-apoptosis index, proliferation index, an index of metabolic switch to aerobic glycolysis, angiogenesis indexes and survival pathway index, were increased, whereas the pro-apoptosis index decreased in the tumors. Thus, contrary to the role of huMETCAM/MUC18 in the NPC-TW01 cells, huMETCAM/MUC18 over-expression in the NPC-TW04 cells increased epithelial-to-mesenchymal transition and also in vitro invasive growth and in vivo tumorigenesis, suggesting that it plays a tumor promoter role in the development of NPC type III by reducing apoptosis and increasing anti-apoptosis, angiogenesis, proliferation and metabolic switch to aerobic glycolysis.

cancer biology↗

bioRxiv2020

Genome analysis of Salmonella enterica serovar Typhimurium bacteriophage L, indicator for StySA (StyLT2III) restriction-modification system action

Bacteriophage L, a P22-like phage of Salmonella enterica sv Typhimurium LT2, was important for definition of mosaic organization of the lambdoid phage family and for characterization of restriction-modification systems of Salmonella. We report the complete genome sequences of bacteriophage L cI-40 13-am43 and L cII-101; the deduced sequence of wildtype L is 40,633 bp long with a 47.5% GC content. We compare this sequence with those of P22 and ST64T, and predict 71 Coding Sequences, 2 tRNA genes and 14 intergenic rho-independent transcription terminators. The overall genome organization of L agrees with earlier genetic and physical evidence; for example, no secondary immunity region (ImmI: ant, arc) or genes for superinfection exclusion (sieA and sieB) are present. Proteomic analysis confirmed identification of virion proteins, along with low levels of assembly intermediates and host cell envelope proteins. The genome of L is 99.9% identical at the nucleotide level to that reported for phage ST64T, despite isolation on different continents ~35 years apart. DNA modification by the epigenetic regulator Dam is generally incomplete. Dam modification is also selectively missing in one location, corresponding to the P22 phase-variation-sensitive promoter region of the serotype-converting gtrABC operon. The number of sites for SenLTIII (StySA) action may account for stronger restriction of L (13 sites) than of P22 (3 sites).

genetics↗

bioRxiv2020

A new species of subgenus Typhlodromus (Anthoseius) De Leon (Acari: Phytoseiidae), and phytoseiid mites intercepted in samples imported from 12 different countries to Taiwan

Global trade has increased the invasion risk of exotic organisms and damaged agricultural and natural ecosystems. The Bureau of Animal and Plant Health Inspection and Quarantine (BAPHIQ) handles quarantine services of animal- and plant-associated pests and diseases in Taiwan. The predatory mite family Phytoseiidae (Acari: Mesostigmata) is a well-known group due to the potential use of certain species as biocontrol agents for small phytophagous pests. Some species are available in commercial markets and frequently used in biological control in many agricultural systems especially in greenhouse crops. However, exotic biological control agents may interfere with native or naturalized populations of predatory mites and they may threaten indigenous populations via intraguild predation. The present study aims to provide the phytoseiid mite species found in plant quarantine from 2006-2013. Twenty-five species belonging two subfamilies and eight genera were found in samples imported to Tawan from twelve countries, including one new species Typhlodromus (Anthoseius) ueckermanni sp. nov. from South Africa. The checklist provides distribution, remarks, and also an identification key for all species.

zoology↗