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1. Integrative analysis reveals associations between oral microbiota dysbiosis and host genetic and epigenetic aberrations in oral cavity squamous cell carcinoma

Author

Cai, Liuyang, Zhu, Hengyan, Mou, Qianqian, Wong, Po Yee, Lan, Linlin, Ng, Cherrie W. K., Lei, Pu, Cheung, Man Kit, Wang, Daijuanru, Wong, Eddy W. Y., Lau, Eric H. L., Yeung, Zenon W. C., Lai, Ronald, Meehan, Katie, Fung, Sherwood, Chan, Kwan Chee A., Lui, Vivian W. Y., Cheng, Alfred S. L., Yu, Jun, Chan, Paul K. S., Chan, Jason Y. K., and Chen, Zigui

Published
2024
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2. Population genomics provides insights into the genetic basis of adaptive evolution in the mushroom-forming fungus Lentinula edodes

Author

Zhang, Jingcheng, Shen, Nan, Li, Chuang, Xiang, Xingjie, Liu, Gaolei, Gui, Ying, Patev, Sean, Hibbett, David S, Barry, Kerrie, Andreopoulos, William, Lipzen, Anna, Riley, Robert, He, Guifen, Yan, Mi, Grigoriev, Igor V, Kwan, Hoi Shan, Cheung, Man Kit, Bian, Yinbing, and Xiao, Yang

Subjects
Biological Sciences, Evolutionary Biology, Genetics, Biotechnology, Human Genome, Agaricales, Genome, Genome-Wide Association Study, Metagenomics, Shiitake Mushrooms, Shiitake, Population genomics, Adaptation, Genetic divergence, GWAS, Phenotypic differentiation
Abstract

IntroductionMushroom-forming fungi comprise diverse species that develop complex multicellular structures. In cultivated species, both ecological adaptation and artificial selection have driven genome evolution. However, little is known about the connections among genotype, phenotype and adaptation in mushroom-forming fungi.ObjectivesThis study aimed to (1) uncover the population structure and demographic history of Lentinula edodes, (2) dissect the genetic basis of adaptive evolution in L. edodes, and (3) determine if genes related to fruiting body development are involved in adaptive evolution.MethodsWe analyzed genomes and fruiting body-related traits (FBRTs) in 133 L. edodes strains and conducted RNA-seq analysis of fruiting body development in the YS69 strain. Combined methods of genomic scan for divergence, genome-wide association studies (GWAS), and RNA-seq were used to dissect the genetic basis of adaptive evolution.ResultsWe detected three distinct subgroups of L. edodes via single nucleotide polymorphisms, which showed robust phenotypic and temperature response differentiation and correlation with geographical distribution. Demographic history inference suggests that the subgroups diverged 36,871 generations ago. Moreover, L. edodes cultivars in China may have originated from the vicinity of Northeast China. A total of 942 genes were found to be related to genetic divergence by genomic scan, and 719 genes were identified to be candidates underlying FBRTs by GWAS. Integrating results of genomic scan and GWAS, 80 genes were detected to be related to phenotypic differentiation. A total of 364 genes related to fruiting body development were involved in genetic divergence and phenotypic differentiation.ConclusionAdaptation to the local environment, especially temperature, triggered genetic divergence and phenotypic differentiation of L. edodes. A general model for genetic divergence and phenotypic differentiation during adaptive evolution in L. edodes, which involves in signal perception and transduction, transcriptional regulation, and fruiting body morphogenesis, was also integrated here.

Published
2022

4. Development of the early-life gut microbiome and associations with eczema in a prospective Chinese cohort

Author

Cheung, Man Kit, primary, Leung, Ting Fan, additional, Tam, Wing Hung, additional, Leung, Agnes S. Y., additional, Chan, Oi Man, additional, Ng, Rita W. Y., additional, Yau, Jennifer W. K., additional, Yuen, Lai-yuk, additional, Tong, Sylvia L. Y., additional, Ho, Wendy C. S., additional, Yeung, Apple C. M., additional, Chen, Zigui, additional, and Chan, Paul K. S., additional

Published
2023
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5. Extent of Oral–Gut Transmission of Bacterial and Fungal Microbiota in Healthy Chinese Adults

Author

Cheung, Man Kit, primary, Tong, Sylvia L. Y., additional, Wong, Martin C. S., additional, Chan, Jason Y. K., additional, Ip, Margaret, additional, Hui, Mamie, additional, Lai, Christopher K. C., additional, Ng, Rita W. Y., additional, Ho, Wendy C. S., additional, Yeung, Apple C. M., additional, Chan, Paul K. S., additional, and Chen, Zigui, additional

Published
2023
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6. Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients

Author

Lai, Christopher K. C., primary, Cheung, Man Kit, additional, Lui, Grace C. Y., additional, Ling, Lowell, additional, Chan, Jason Y. K., additional, Ng, Rita W. Y., additional, Chan, Hiu Ching, additional, Yeung, Apple C. M., additional, Ho, Wendy C. S., additional, Boon, Siaw Shi, additional, Chan, Paul K. S., additional, and Chen, Zigui, additional

Published
2022
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15. Education for the future

Author

Pietrzak, Barbara, Ward, Adrian, Cheung, Man Kit, Schwendimann, Beat A., Mollaoglu, Gurkan, Duong, Michael Tran, Ulltveit-Moe, Nils, Allareddy, Veerasathpurush, Dutton-Regester, Ken, Zhang, Jian, Scult, Matthew A., Naz, Saima, Singh, Poonam C., Yan, Hong Young, Isaacson, Kyle, Dennis, Allison F., Al-Humaidan, Eyad Ibrahim, Beardsley, Felicia Rounds, Lo, Cody, Sood, Prashant, Jones, Tyler, Nieuwenhuis, Rense, Ali, Basant A., Yu, Kun Hsing, Arthur, Patrick Kobina, Kumar, Brijesh, Chen, Alexander, Buschke, Falko, Cingl, Lubomír, Zaidi, Syed Shan e.Ali, O’Mullane, Anthony Peter, Coetzee, Vinet, Konstantinides, Nikos, Pietrzak, Barbara, Ward, Adrian, Cheung, Man Kit, Schwendimann, Beat A., Mollaoglu, Gurkan, Duong, Michael Tran, Ulltveit-Moe, Nils, Allareddy, Veerasathpurush, Dutton-Regester, Ken, Zhang, Jian, Scult, Matthew A., Naz, Saima, Singh, Poonam C., Yan, Hong Young, Isaacson, Kyle, Dennis, Allison F., Al-Humaidan, Eyad Ibrahim, Beardsley, Felicia Rounds, Lo, Cody, Sood, Prashant, Jones, Tyler, Nieuwenhuis, Rense, Ali, Basant A., Yu, Kun Hsing, Arthur, Patrick Kobina, Kumar, Brijesh, Chen, Alexander, Buschke, Falko, Cingl, Lubomír, Zaidi, Syed Shan e.Ali, O’Mullane, Anthony Peter, Coetzee, Vinet, and Konstantinides, Nikos

Abstract

We asked young scientists: Are our schools and universities adequately prepared to educate young people for future challenges? What is the most pressing issue in your field, and what one improvement could your country make to its current education system to prepare students to face it? The responses expressed concerns about the current state of education in countries around the world. Many students lack access to the information they need, and those with access are often constrained by curriculum that emphasizes rote learning and isolated subjects. Our respondents suggested a variety of improvements to prepare the next generation for success.

Published
2018

30. Spatial and seasonal variabilities of picoeukaryote communities in a subtropical eutrophic coastal ecosystem based on analysis of 18S rDNA sequences.

Author

Cheung, Man Kit., Chinese University of Hong Kong Graduate School. Division of Biology., Cheung, Man Kit., and Chinese University of Hong Kong Graduate School. Division of Biology.

Abstract

Cheung, Man Kit., Thesis (M.Phil.)--Chinese University of Hong Kong, 2007., Includes bibliographical references (leaves 81-93)., s in English and Chinese., (English) --- p.I, (Chinese) --- p.III, Acknowledgements --- p.V, Table of contents --- p.VI, List of figures --- p.IX, List of tables --- p.XI, List of Appendices --- p.XII, Chapter Chapter 1. --- General introduction --- p.1, Chapter 1.1. --- Picoeukaryotes --- p.1, Chapter 1.2. --- Conventional characterization techniques --- p.1, Chapter 1.3. --- Cloning and sequencing approach --- p.3, Chapter 1.3.1. --- Applications in prokaryotic plankton --- p.3, Chapter 1.3.2. --- Applications in eukaryotic picoplankton --- p.3, Chapter 1.4. --- Variations in diversity with environmental factors --- p.5, Chapter 1.5. --- Study site --- p.6, Chapter 1.6. --- Objectives --- p.8, Chapter Chapter 2. --- Materials and methods --- p.9, Chapter 2.1. --- Study site --- p.9, Chapter 2.2. --- Sample collection --- p.9, Chapter 2.3. --- DNA extraction and 18S rRNA gene amplification --- p.11, Chapter 2.4. --- Clone library construction and screening --- p.12, Chapter 2.5. --- Sequencing and phylogenetic analysis --- p.13, Chapter 2.6. --- Statistical analyses --- p.14, Chapter Chapter 3. --- Results --- p.15, Chapter 3.1. --- Hydrological parameters of study site --- p.15, Chapter 3.2. --- Clone libraries --- p.15, Chapter 3.3. --- Higher-level taxonomic distribution --- p.21, Chapter 3.4. --- Phylogenetic affiliations of OTUs --- p.22, Chapter 3.4.1 --- Alveolates --- p.35, Chapter 3.4.2 --- Stramenopiles --- p.36, Chapter 3.4.3 --- Rhizaria --- p.36, Chapter 3.4.4 --- Other lineages --- p.37, Chapter 3.4.5 --- Novel higher-level groups --- p.38, Chapter 3.5. --- Diversity estimates of picoeukaryotes --- p.39, Chapter Chapter 4. --- Discussion --- p.42, Chapter 4.1. --- Picoeukaryotic diversity --- p.42, Chapter 4.1.1 --- Overall diversity --- p.42, Chapter 4.1.2 --- Diversity of individual taxonomic groups --- p.44, Chapter 4.1.2.1 --- Most represented lineages --- p.44, Chapter 4.1.2.2 --- Other photosynthetic lineages --- p.52, Chapter 4.1.2.3 --- Other non-photosynthetic lineages --- p.55, Chapter 4.1.2.4 --- Novel higher-level lineages --- p.56, Chapter 4.2. --- Spatial and seasonal variations of picoeukaryotes --- p.58, Chapter 4.2.1 --- Spatial variations --- p.59, Chapter 4.2.1.1 --- Compositional variations --- p.60, Chapter 4.2.1.2 --- Variations in diversity --- p.61, Chapter 4.2.2 --- Seasonal variations --- p.65, Chapter 4.2.2.1 --- Compositional variations --- p.65, Chapter 4.2.2.2 --- Variations in diversity --- p.66, Chapter 4.3. --- Methodological aspects --- p.67, Chapter 4.3.1 --- Sample collection --- p.67, Chapter 4.3.2 --- PCR amplification --- p.68, Chapter 4.3.3 --- Cloning and RFLP screening --- p.69, Chapter 4.3.4 --- Statistical estimates --- p.71, Chapter 4.3.5 --- Future directions --- p.71, Chapter Chapter 5. --- General conclusion --- p.73, References --- p.81, http://library.cuhk.edu.hk/record=b5893282, Use of this resource is governed by the terms and conditions of the Creative Commons “Attribution-NonCommercial-NoDerivatives 4.0 International” License (http://creativecommons.org/licenses/by-nc-nd/4.0/)

Published
2007

36. A Novel Lentinula edodes Laccase and Its Comparative Enzymology Suggest Guaiacol-Based Laccase Engineering for Bioremediation.

Author

Wong, Kin-Sing, Cheung, Man-Kit, Au, Chun-Hang, and Kwan, Hoi-Shan

Subjects
*LACCASE, *COMPARATIVE studies, *ENZYMOLOGY, *GUAIACOL, *BIOREMEDIATION, *ENZYMES, *XENOBIOTICS
Abstract

Laccases are versatile biocatalysts for the bioremediation of various xenobiotics, including dyes and polyaromatic hydrocarbons. However, current sources of new enzymes, simple heterologous expression hosts and enzymatic information (such as the appropriateness of common screening substrates on laccase engineering) remain scarce to support efficient engineering of laccase for better “green” applications. To address the issue, this study began with cloning the laccase family of Lentinula edodes. Three laccases perfectio sensu stricto (Lcc4A, Lcc5, and Lcc7) were then expressed from Pichia pastoris, characterized and compared with the previously reported Lcc1A and Lcc1B in terms of kinetics, stability, and degradation of dyes and polyaromatic hydrocarbons. Lcc7 represented a novel laccase, and it exhibited both the highest catalytic efficiency (assayed with 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) [ABTS]) and thermostability. However, its performance on “green” applications surprisingly did not match the activity on the common screening substrates, namely, ABTS and 2,6-dimethoxyphenol. On the other hand, correlation analyses revealed that guaiacol is much better associated with the decolorization of multiple structurally different dyes than are the two common screening substrates. Comparison of the oxidation chemistry of guaiacol and phenolic dyes, such as azo dyes, further showed that they both involve generation of phenoxyl radicals in laccase-catalyzed oxidation. In summary, this study concluded a robust expression platform of L. edodes laccases, novel laccases, and an indicative screening substrate, guaiacol, which are all essential fundamentals for appropriately driving the engineering of laccases towards more efficient “green” applications. [ABSTRACT FROM AUTHOR]

Published
2013
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37. Optical diffraction studies on activated skeletal muscle fibres.

Author

Cheung, Man Kit., Chinese University of Hong Kong Graduate School. Division of Physics., Cheung, Man Kit., and Chinese University of Hong Kong Graduate School. Division of Physics.

Abstract

by Cheung Man Kit., Errata slip inserted, Bibliography: leaves 83-84, Thesis (M.Ph.)--Chinese University of Hong Kong, 1985, http://library.cuhk.edu.hk/record=b5885583, Use of this resource is governed by the terms and conditions of the Creative Commons “Attribution-NonCommercial-NoDerivatives 4.0 International” License (http://creativecommons.org/licenses/by-nc-nd/4.0/)

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