| 著作名稱： | Biological Protective Effects Against Vibrio Infections in Grouper Larvae Using the Strombidium sp. NTOU1, a Marine Ciliate Amenable for Scaled-Up Culture and With an Excellent Bacteriovorous Ability |
| 年度： | 2020 |
| 類別： |
期刊論文
Front. Mar. Sci.
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| 摘要： | |
| 關鍵字： | |
| 著作名稱： | Reactive oxygen species mediate Terbufos-induced apoptosis in mouse testicular cell lines via the modulation of cell cycle and pro-apoptotic proteins. |
| 年度： | 2015 |
| 類別： |
期刊論文
Environ. Taxicol.
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| 摘要： | |
| 關鍵字： | |
| 著作名稱： | Craige B, Tsao C-C, Diener D, Hou Y, Lechtreck K-F, Rosenbaum LR, and Witman GB. CEP290 tethers flagellar transition zone microtubules to the membrane and regulates flagellar protein content |
| 年度： | 2010 |
| 類別： |
期刊論文
J. Cell Biol.
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| 摘要： | |
| 關鍵字： | |
| 著作名稱： | Huang, K. and Tsao, CC. Importin-β2: a key to two gates? |
| 年度： | 2010 |
| 類別： |
期刊論文
Protein Cell
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| 摘要： | |
| 關鍵字： | |
| 著作名稱： | Different effects of Tetrahymena IFT172 domains on anterograde and retrograde intraflagellar transport |
| 年度： | 2008 |
| 類別： |
期刊論文
Mol. Biol. Cell.
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| 摘要： | |
| 關鍵字： | |
| 著作名稱： | Tetrahymena IFT122A is not essential for cilia assembly but plays a role in returning IFT proteins from the ciliary tip to the cell body |
| 年度： | 2008 |
| 類別： |
期刊論文
J. Cell Sci.
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| 摘要： | |
| 關鍵字： | |
| 著作名稱： | The actin gene ACT1 is required for phagocytosis, motility and cell separation of Tetrahymena thermophila |
| 年度： | 2006 |
| 類別： |
期刊論文
Eukaryot. Cell
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| 摘要： | |
| 關鍵字： | |
| 著作名稱： | Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote |
| 年度： | 2006 |
| 類別： |
期刊論文
PLoS Biol.
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| 摘要： | |
| 關鍵字： | |
| 著作名稱： | Mutational analyses reveal a novel function of the nucleotide-binding domain of gamma-tubulin in the regulation of basal body biogenesis |
| 年度： | 2005 |
| 類別： |
期刊論文
J. Cell Biol.
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| 摘要： | |
| 關鍵字： | |
| 著作名稱： | Deep Learning-Based Automatic Duckweed Counting Using StarDist and Its Application on Measuring Growth Inhibition Potential of Rare Earth Elements as Contaminants of Emerging Concerns |
| 年度： | 2023 |
| 類別： |
期刊論文
Toxics
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| 摘要： | In recent years, there have been efforts to utilize surface water as a power source, material, and food. However, these efforts are impeded due to the vast amounts of contaminants and emerging contaminants introduced by anthropogenic activities. Herbicides such as Glyphosate and Glufosinate are commonly known to contaminate surface water through agricultural industries. In contrast, some emerging contaminants, such as rare earth elements, have started to enter the surface water from the production and waste of electronic products. Duckweeds are angiosperms from the Lemnaceae family and have been used for toxicity tests in aquatic environments, mainly those from the genus Lemna, and have been approved by OECD. In this study, we used duckweed from the genus Wolffia, which is smaller and considered a good indicator of metal pollutants in the aquatic environment. The growth rate of duckweed is the most common endpoint in observing pollutant toxicity. In order to observe and mark the fronds automatically, we used StarDist, a machine learning-based tool. StarDist is available as a plugin in ImageJ, simplifying and assisting the counting process. Python also helps arrange, manage, and calculate the inhibition percentage after duckweeds are exposed to contaminants. The toxicity test results showed Dysprosium to be the most toxic, with an IC50 value of 14.6 ppm, and Samarium as the least toxic, with an IC50 value of 279.4 ppm. In summary, we can provide a workflow for automatic frond counting using StarDist integrated with ImageJ and Python to simplify the detection, counting, data management, and calculation process. |
| 關鍵字： | StarDist; deep learning; cell counting; image segmentation; rare earth element |
| 著作名稱： | Performance Comparison of Five Methods for Tetrahymena Number Counting on the ImageJ Platform: Assessing the Built-in Tool and Machine-Learning-Based Extension |
| 年度： | 2022 |
| 類別： |
期刊論文
International Journal of Molecular Sciences
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| 摘要： | Previous methods to measure protozoan numbers mostly rely on manual counting, which suffers from high variation and poor efficiency. Although advanced counting devices are available, the specialized and usually expensive machinery precludes their prevalent utilization in the regular laboratory routine. In this study, we established the ImageJ-based workflow to quantify ciliate numbers in a high-throughput manner. We conducted Tetrahymena number measurement using five different methods: particle analyzer method (PAM), find maxima method (FMM), trainable WEKA segmentation method (TWS), watershed segmentation method (WSM) and StarDist method (SDM), and compared their results with the data obtained from the manual counting. Among the five methods tested, all of them could yield decent results, but the deep-learning-based SDM displayed the best performance for Tetrahymena cell counting. The optimized methods reported in this paper provide scientists with a convenient tool to perform cell counting for Tetrahymena ecotoxicity assessment. |
| 關鍵字： | ImageJ; macro language; segmentation; Tetrahymena |
| 著作名稱： | Establishing a High-Throughput Locomotion Tracking Method for Multiple Biological Assessments in Tetrahymena |
| 年度： | 2022 |
| 類別： |
期刊論文
Cells
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| 摘要： | Protozoa are eukaryotic, unicellular microorganisms that have an important ecological role, are easy to handle, and grow rapidly, which makes them suitable for ecotoxicity assessment. Previous methods for locomotion tracking in protozoa are largely based on software with the drawback of high cost and/or low operation throughput. This study aimed to develop an automated pipeline to measure the locomotion activity of the ciliated protozoan Tetrahymena thermophila using a machine learning-based software, TRex, to conduct tracking. Behavioral endpoints, including the total distance, velocity, burst movement, angular velocity, meandering, and rotation movement, were derived from the coordinates of individual cells. To validate the utility, we measured the locomotor activity in either the knockout mutant of the dynein subunit DYH7 or under starvation. Significant reduction of locomotion and alteration of behavior was detected in either the dynein mutant or in the starvation condition. We also analyzed how Tetrahymena locomotion was affected by the exposure to copper sulfate and showed that our method indeed can be used to conduct a toxicity assessment in a high-throughput manner. Finally, we performed a principal component analysis and hierarchy clustering to demonstrate that our analysis could potentially differentiate altered behaviors affected by different factors. Taken together, this study offers a robust methodology for Tetrahymena locomotion tracking in a high-throughput manner for the first time. |
| 關鍵字： | Tetrahymena; protozoa; TRex; locomotion; toxicity; complexity reduction |
| 著作名稱： | Chlamydomonas IC140 is essential for the flagellar assembly while B9D1 affects the level of intraflagellar transport proteins and is dispensable for structural integrity of the transition zone |
| 年度： | 2016 |
| 類別： |
會議論文
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| 摘要： | We characterized a Chlamydomonas mutant without flagella obtained from insertional mutagenesis. In this Lu3 strain, the ultrastructure of its basal body and transition zone showed no defect, but the axoneme terminated abruptly distal to the transition zone. A 60-kb chromosomal region containing IC140 and B9D1 was deleted in the Lu3 mutant, and re-transformation of both genes was sufficient to restore the flagellar assembly and motility. Reintroducing IC140, encoding a subunit of the I1 flagellar inner arm dynein complex, could partially rescue the flagellar formation and motility, but the resulted b9d1 strain exhibited incomplete flagellation and flagellar length heterogeneity. Unexpectedly, the ic140 strain, derived from restoration of the transition zone protein B9d1 in the Lu3 background, failed to assemble any flagella. We found the level of intraflagellar transport (IFT) proteins markedly decreased in the strains without B9D1 but not in the ic140 strain. Our results indicated that B9D1 is not essential for the structural integrity of the transition zone, but its disruption lowered the protein level of IFT and compromised the flagellar biogenesis. We also uncovered a novel role of IC140 that it is required not only for the flagellar motility but also for the axonemal assembly through an unidentified mechanism. |
| 關鍵字： | |
| 著作名稱： | Chlamydomonas MKS1 is required for fully assembly of flagella beyond the transition zone. |
| 年度： | 2014 |
| 類別： |
會議論文
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| 摘要： | |
| 關鍵字： | |
| 著作名稱： | Preliminary characterization of a protofilamant-ribbon gene in Tetrahymena thermophila |
| 年度： | 2013 |
| 類別： |
會議論文
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| 摘要： | |
| 關鍵字： | |
| 著作名稱： | 利用原生生物四膜蟲作為評價環境汙染的一種簡易工具 |
| 年度： | 2023 |
| 類別： |
會議論文
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| 摘要： | |
| 關鍵字： | |
| 著作名稱： | 塑化劑DEP對單胞藻的 功能毒理學分析 |
| 年度： | 2022 |
| 類別： |
會議論文
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| 摘要： | |
| 關鍵字： | |
| 著作名稱： | 連結教室與研究室：從單胞藻與纖毛的生長組裝談起 |
| 年度： | 2011 |
| 類別： |
會議論文
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| 摘要： | Chlamydomonas is a unicellular diflagellated green microalga that is widely used in biochemical, cell biological, and genetic researches. It is easy to culture and inexpensive to maintain in the laboratory setting. Furthermore, with sequenced genome, Chlamydomonas is amenable to isolate mutants and identify the affected gene, which allows functional genomic analysis through insertional mutagenesis, phenotypic screen, and molecular genetic analysis. A preliminary implementation of this system in the sophomore Genetics Laboratory course at Department of Biological Sciences and Technology in National University of Tainan during fall semester of 2010 shows that using a cell-wall defect strain and a revised procedure to transform Chlamydomonas by glass beads method, undergraduate students can perform fairly well in generating insertional mutants. Among tens of thousands of transformants, a dozen of cell motility mutants were obtained throughout the course. Along with other experimental modules, such as strain culturing and handling, phenotype observation, nucleic acid preparation, polymerase chain reaction, and DNA gel electrophoresis, students can learn both basic concepts and hands-on experience in functional genomics, which lays down the foundation for further in-depth research.
（This program is supported by College of Environmental Sciences and Ecology and National University of Tainan.）
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