Publications (2011 - )

Books

Rivera-Monroy, V., Lee S.Y., Kristensen, E., Twilley, R. (eds) 2107. Mangrove Ecosystems: A Global Biogeographic Perspective - Structure, Function and Services. ISBN 9783319622040

(Springer USA. Eleven chapters, 449 pages)

Lee S.Y.  2012. (member of editorial board) The Living Species in China’s Seas. Volumes 1 & 2. China Ocean Press. ISBN 9787502782320

Lee S.Y.  2012. (member of editorial board) An Illustrated Guide to Species in China’s Seas, Volumes 1 - 8.Ocean Press, China.

Special issue of international journal

Friess, D., Lee, S.Y., Primavera, J.H., (ed.) 2016. Turning the Tide on Mangrove Loss. Marine Pollution Bulletin. Volume 109, issue 2, pp.673-782. Elsevier.

Book chapters

Primavera J.H., Friess, D.A., Van Lavieren, H., Lee S.Y. 2018. Chapter 1. The mangrove Ecosystem. Pp.1- 34 In Sheppard C. (ed) World Seas: an Environmental Evaluation. Second edition. Volume 3: Ecological Issues and Environmental Impacts. Academic Press. ISBN 9780128050521

Rivera-Monroy, V., Lee S.Y., Kristensen, E., Twilley, R.R. 2017. Chapter 1 Introduction. Pp. 1-16. In Rivera-Monroy, V., Lee S.Y., Kristensen, E., Twilley, R.R. (eds) Mangrove Ecosystem Structure and Function: a biogeographic perspective. Springer, New York. ISBN 9783319622040

Lee S.Y., Rivera-Monroy, V., Kristensen, E., Twilley, R.R. 2017. Epilogue. Pp. 383-386. In Rivera-Monroy, V., Lee S.Y., Kristensen, E., Twilley, R.R. (eds) Mangrove Ecosystem Structure and Function: a biogeographic perspective. Springer, New York. ISBN 9783319622040

Lee S.Y., Jones, G., Diele, K., Nordhaus, I., 2017. Biodiversity. Pp. 55-86. In Rivera-Monroy, V., Lee S.Y., Kristensen, E., Twilley, R.R. (eds) Mangrove Ecosystem Structure and Function: a biogeographic perspective. Springer, New York. ISBN 9783319622040

Primavera, J.H., Lee S.Y. 2015. The Magical Mangroves of KII. Pp.322-330 In: Hegan, A. (Ed.). (2015). No More Endings: Saving Species One Story at a Time. Melbourne, Florida: Motivational Press.

Lee S.Y. 2015. Chapter 9, Ecology of Brachyura. Pp.469-543. In Castro, P., Davie, P., Guinot, D., Schram, F., J.C. von Vaupel Klein (Eds) Treatise in Zoology. The Crustacea. Brill, Leiden, the Netherlands. ISBN 9789004188730

Hutchison, J., Philipp, D.P., Claussen, J.E., Aburto-Oropeza, O., Carrasquilla-Henao, M., Castellanos- Galindo, G.A., Costa, M.T., Daneshgar, P.D., Hartmann, H.J., Juanes, F., Khan, M.E., Knowles, L., Knudsen, E., Lee S.Y., Murchie, K.J., Tiedemann, J.,     zu Ermgassen, P., Spalding, M. 2015. Building an expert judgment-based model of mangrove fisheries. Pp. 17-42 In: Mangrove as Fish Habitat. (eds) Murchie, K.J., Daneshgar, P.P. American Fisheries Society. ISBN-13: 9781934874424

Refereed journal papers

Pitt K.A., Lee S.Y., Connolly R.M., Bui, THH, Doriean N. 2018. Sources and fates of organic matter in constructed versus natural coastal waterways. Marine Pollution Bulletin 135:505-513

Adame, M.F., Rozainah M.Z., Fry B., Chong V.C., Then Y.H.A., Brown C.J., Lee S.Y. 2018. Loss and recovery of carbon and nitrogen after mangrove clearing. Ocean and Coastal Management 161:117- 126

Natin P., Lee S.Y. 2018. Estuarine caridean shrimp (Palaemon debilis Dana, 1852) (Decapoda: Caridea) can differentiate olfactory cues from different mangrove species for microhabitat selection. Journal of Experimental Marine Biology and Ecology 501:99-108

Henderson C.J., Stevens T.F., Gilby B., Lee S.Y. 2018. Spatial conservation of large mobile elasmobranchs requires an understanding of spatio-temporal seascape utilisation. ICES Journal of Marine Science 75: 553-561.

Ouyang, X., Lee S.Y., Connolly, R.M. 2018. Partitioning of sources of CO2 efflux in establishing mangrove ecosystems using experimental isotope labelling of seedlings. Limnology and Oceanography 63: 731- 340. DOI: 10.1002/lno.10663

Ouyang, X., Lee S.Y., Connolly, R.M., Kainz, M. 2018. Spatially explicit valuation of wetlands for cyclone mitigation in Australia and China. Scientific Reports 8:3035. DOI:10.1038/s41598-018-21217-z, 9pp.

Peng, Y.S., Zhang, M., Lee S.Y. 2017. Food availability and reduced predation risk drive the distributional patterns of two pulmonate gastropods in a mangrove-saltmarsh transitional habitat. Marine Environmental Research 130:21-29

Henderson, C.J., Gilby, B., Lee S.Y., Stevens, T.F. 2017. Contrasting effects of habitat complexity and connectivity on biodiversity in seagrass meadows. Marine Biology 164:117 DOI 10.1007/s00227-017-3149-2

Kamal, S., Warnken, J., Bakhtiyari, M., Lee S.Y.* 2017. Sediment distribution in shallow estuaries at fine scale: in situ evidence of 3D structural complexity effects by mangrove pneumatophores. Hydrobiologia 803:121-132. DOI: 10.1007/s10750-017-3178-3

Kristensen, E., Lee S.Y., Mangion, P., Quintana, C.O., Valdemarsen, T. 2017. Trophic fractionation of stable isotopes and food source partitioning by leaf-eating crabs in mangrove environments. Limnology and Oceanography 62:2097-2112. DOI: 10.1002/lno.10553

Henderson, C.J., Olds, A., Lee S.Y., Gilby, B.L., Maxwell, P.S., Connolly, R.M. and Stevens, T.F. 2017. Marine reserves and seascape context shape fish assemblages in seagrass. Marine Ecology Progress Series 566:135-144.

Ouyang, X., Lee S.Y., Connolly, R.M. 2017. Global patterns of root decomposition rates and the fate of root carbon production in mangroves and saltmarsh. Earth Sciences Reviews 166:53-63.

Lee S.Y.*, Khim, J.-S. 2017. Hard science is essential to restoring soft-sediment intertidal habitats in East Asia. Chemosphere 168:765-776

Abudullah, M.M., Lee S.Y. 2017. Structure of mangrove meiofaunal assemblages driven by local sediment conditions in subtropical southeast Australia. Estuarine Coastal and Shelf Science http://dx.doi.org/10.1016/j.ecss.2016.10.039

Spencer D.M., Brown I.W., Lee S.Y., Lemckert C.J. 2017. Physical oceanographic processes affecting spanner crab (Ranina ranina) catchability – a review. Fisheries Research 186:248-257.

Ouyang, X., Lee S.Y., Connolly, R.M. 2017. Structural equation modelling unravels factors regulating sediment carbon stock and CO2 flux in a subtropical mangrove. Science of the Total Environment 578:513-522

Kwon, B.-O., Lee Y., Park, J., Ryu, J., Hong, J., Son, H., Lee S.Y., Nam, J., Koh, C-H., Khim, J.S. 2016. Temporal dynamics and spatial heterogeneity of microalgal biomass in the intertidal flats of the Saemangeum area, Korea. J Sea Research 116:1-11.

Werry, J.M., Sumpton, W., Otway, N., Lee S.Y.*, Mayer, D. 2016. Rainfall: a key driver for movement of bull shark, Carcharhinus leucas, into beach areas. Global Ecology and Conservation. (In revision)

Friess, D., Lee S.Y., Primavera, J.H. 2016. Turning the tide on mangrove loss. Marine Pollution Bulletin 109:673-675.

Henderson, C.J., Stevens, T., Lee S.Y. 2016. Assessing the suitability of a non-lethal biopsy punch for sampling fish muscle tissue.     Fish Physiology and Biochemistry 42:1521-1526

Peng, Y., Zheng, M., Zheng Z., Wu, G., Chen, Y., Xu, H., Tian, G., Peng, S., Chen, G., Lee S.Y. 2016. Virtual increase or latent loss? A reassessment of mangrove populations and their conservation in Guangdong, southern China. Marine Pollution Bulletin 109:691-699.

Harada, Y., Lee S.Y.* 2016. Opportunistic leaf foraging behavior in the mangrove sesarmid crab (Neosarmatium trispinosum) maximizes nutrient intake in a low-quality food environment. Estuarine, Coastal and Shelf Science 174:41-48.

Peng Y., Diao J., Zheng M., Guan D., Zhang R., Chen G., Lee S.Y. 2016. Early growth adaptability of four mangrove species under the canopy of an introduced mangrove plantation: implications for restoration. Forest Ecology and Management 373:179-188

Van de Merwe, J.P., Lee S.Y., Connolly, R.M., Pitt, K., Steven, A. 2016. Assessing temporal and spatial trends in estuarine nutrient dynamics using a multi-species stable isotope approach. Ecological Indicators 67:338-345

M.M. Abdullah, Lee S.Y. 2016 Meiofauna and depositing crabs: is the interaction physical or trophic? Journal of Experimental Marine Biology and Ecology 479:69-75.

Lee S.Y.* 2016. From blue to black: anthropogenic forcing of carbon and nitrogen influx in mangrove-lined estuaries in the South China Sea. Marine Pollution Bulletin 109:682-690.

Alberts-Hubatsch, Lee S.Y., H., Nordhaus, I., Diele, K., Meynecke, J.-O., Wolff, M. 2016. Life-history, movement and habitat use of Scylla serrata – current knowledge and future challenges. Hydrobiologia 763:5-21. DOI 10.1007/s10750-015-2393-z.

Bui, H.T.H., Lee S.Y.* 2015. Potential contributions of gut microbiota to the nutrition of the detritivorous sesarmid crab Parasesarma erythodactyla. Marine Biology 162: 1969-1981 (DOI: 10.1007/s00227- 015-2723-8)

Morris, C., Lee S.Y.*, van de Merwe, J. 2015. δ¹⁵N of estuarine fishes as a quantitative indicator of urbanization. Ecological Indicators 56:41-49

Bui, H., Lee S.Y. 2015. Endogenous cellulase production in the leaf litter foraging mangrove crab, Parasesarma erythodactyla. Comparative Biochemistry and Physiology B. 179:27-36

Ouyang, X., Lee S.Y. 2014. Updated estimates of carbon accumulation rates in coastal marsh sediments. Biogeosciences 11: 5057-5071. Doi:10.5194/bg-11-5057-2014.

Alberts-Hubatsch, Lee S.Y., H., Diele, K., Mattias, W., Nordhaus, I. 2014. Microhabitat use of early benthic stage mud crabs (Scylla serrata Forskål, 1775) in eastern Australia. Journal of Crustacean Biology 34:604-610.

Spencer, D., Lemckert, C., Yu, Y., Gustafson, J., Lee S.Y., Zhang, H. 2014. Quantifying dispersion in an estuary: A Lagrangian drifter approach. Journal of Coastal Research SI70:29-34

Kamal, S., Lee S.Y.*, Warnken, J. 2014. Investigating three-dimensional meso-scale habitat complexity and its ecological implications using low-cost RGB-D sensor technology. Methods in Ecology and Evolution 5:845-853.– featured on journal web page and blog+video; ‘Editor’s pick’, short-listed for the Robert May prize in Ecology).

Lee S.Y.*, Primavera J.H., Dahdouh-Geubas F., McKee, K., Bosire J.O., Cannicci, S., Diele, K., Koedam, N., Marchand C., Mendelssohn, I., Mukherjee, N., Record, S. 2014. Ecological role and services of tropical mangrove ecosystems: a reassessment. Global Ecology and Biogeography 23:726-743.

Bui, T.H.H. and Lee S.Y.* 2014. Does ‘you are what you eat’ apply to mangrove grapsid crabs? PLoS One 9(2) : M. Doi :10.1371/journal.pone.0089074 (IF 4.489) 12pp.

Clua, E., Chauvet, C., Read, T., Werry, J., Lee S.Y. 2013. Behavioural patterns of a Tiger Shark (Galeocerdo cuvier) feeding aggregation on a whale carcass in Prony bay, New Caledonia. Marine & Freshwater Behaviour and Physiology 46:1-20.

Werry, J.M., Lee S.Y., Lemckert, C.J., Otway, N. 2012. Natural or artificial? Habitat use by the bull shark Carcharhinus leucas. PLoS One. 7(11):e49796 doi:10.1371/journal.pone.0049796. 17pp.

Lee, K.M., Lee S.Y., Connolly, R.M. 2012. Combining process indices from network analysis with structural population measures to indicate response of estuarine trophodynamics to pulse organic enrichment. Ecological Indicators 18: 652-658.

Meynecke, J.O., Grubert, M., Arthur, J.M., Boston, R. Lee S.Y. 2012. The influence of the La Niña-El Niño cycle on giant mud crab (Scylla serrata) catches in northern Australia. Estuarine, Coastal and Shelf Science 100:93-101

Werry, J.M., Lee S.Y., Otway, N., Hu, Y., Sumpton, W. 2011. A multi-faceted approach for quantifying the estuarine-nearshore transition in the life cycle of the bull shark, Carcharhinus leucas. Marine and Freshwater Research 62: 1421-1431.

Noriega, R., Werry, J.M., Sumpton, W., Mayer, D., Lee S.Y. 2011. Trends in annual CPUE and evidence of sex and size segregation of Sphyrna lewini: management implications in coastal waters of northeastern Australia. Fisheries Research 110: 472-477.

Meynecke, J.-O., Lee S.Y.    2011. Climate-coastal fisheries relationships and their spatial variation in Queensland, Australia. Fisheries Research 110: 365-376.

Lee, K.M., Lee S.Y., Connolly, R.M. 2011. Short-term response of estuarine sandflat trophodynamics to pulse anthropogenic physical disturbance – support for the Intermediate Disturbance Hypothesis. Estuarine, Coastal and Shelf Science 92:639-648.

Lee, K.M., Lee S.Y., Connolly, R.M. 2011. Combining stable isotope enrichment, compartmental modelling and ecological network analysis for quantitative measurement of food web dynamics. Methods in Ecology and Evolution 2: 56-65.

* corresponding author; underlined names are research students with me as principal supervisor

July 2018

ENGLISH

中大基因工程隊伍設計「甲型流感病毒現場快速測試」

在國際遺傳工程機器設計競賽奪得金獎

香港中文大學（中大）理學院生命科學學院及工程學院十五位本科生組成的基因工程隊伍，憑著設計一款嶄新的甲型流感病毒快速測試方法，早前在美國波士頓舉行的國際遺傳工程機器設計(International Genetically Engineered Machine，簡稱iGEM)世界賽中榮獲金獎，乃中大第五度在這比賽中奪金，成績驕人，參賽作品極具應用潛力，或有助醫學界對抗日益嚴重的禽流感病毒威脅。

中大隊伍今年參賽項目的主題為「巧換博士:甲型流感病毒現場快速測試」(Dr. Switch: A Rapid On-Site Method for Subtyping Influenza A virus) 。現時，大部分病毒樣本測試均在實驗室進行，運輸過程加上測試時間，往往需時一天或更久，即使有其他方法進行快速測試，但只能檢測病毒的類型 (即甲、乙或丙型)，未能分辨其亞種(即H1N1、H5N1或H7N9等)，可能錯失控制疫情的黃金時間。基因工程隊於是研發一套甲型流感病毒快速測試系統，能夠利用病毒的核糖核酸(Ribonucleic acid，簡稱RNA)分辨其種類，而且測試能夠在動物農莊、口岸或家禽市場等地點，即場進行測試，數小時內便有結果。

這個測試的運作原理來自指尖轉換(Toehold Switches)的設計。指尖轉換是一款人造生物感測器，理論上能轉換任何核酸分子的結構，而流感病毒正是核酸病毒的一種。當核酸分子轉換結構後，便會引發基因表達的出現，從而提供明確、能夠目測的訊息，例如測試劑轉變顏色，表示被檢測分子存在。科學家成功利用這個原理檢測寨卡病毒。

中大基因工程隊是首支隊伍開發了一個平台(http://2017.igem.org/Team:Hong_Kong-CUHK) ，用作設計指尖轉換用的核酸序列，供科學界免費使用。中大這個項目和英國牛津大學及瑞士洛桑理工學院同被提名為最佳診斷設計獎，最後該奬項由牛津大學奪得。

基因工程隊在設計病毒測試方法時，特意訪問了不同持份者，包括醫學專家、政府和雞販，希望測試方法更迎合使用者的需要。例如，他們原先估計雞販有興趣自行為雞隻做病毒檢測，減少禽流感擴散造成的大量金錢損失。不過，他們訪問一家有自家農場的本地餐廳負責人後，發現雞販的想法與他們估計的相反。雞販認為檢測應交由中立組織或政府進行，自行檢測禽流感的誘因不大。學生其後亦有聯絡相關政府部門，例如衛生署、漁農自然護理署等，這些訪問都讓學生進一步了解流感檢測的具體流程和用家實際需要，對研究有直接幫助。

基因工程隊的指導教授之一、中大生命科學學院副教授陳廷峰教授表示：「這班來自不同學系的本科生參與科學研究的熱誠，令人讚賞。他們在短短一年多內，由訂立主題開始，過程中經歷多次失敗，甚至缺乏研究經費，最終取得驕人成果，展現的團隊精神，匯聚分子生物學和工程學系的知識，至為難得。希望他們保持這份熱誠，繼續參與科研，貢獻社會。」

iGEM比賽簡介

今年共有331隊來自世界各地的隊伍參賽，只有108隊奪得金獎。

iGEM比賽為國際合成生物學界每年一度的盛事。iGEM由麻省理工學院於2004年創立，旨在促進學生在合成生物學的學習、交流與合作，以培養合成生物學人才。比賽隊伍須利用基本且可交替的生物部件，設計及建立有效的生物系統。參賽作品水平超卓，有效推動解決醫學、食品營養、能源及環境等方面難題的硏究。

2017年12月4日

>>Photo Album

>>Press release:

http://www.cpr.cuhk.edu.hk/en/press_detail.php?id=2667

>>Media:

https://news.mingpao.com/pns/dailynews/web_tc/article/20171207/s00011/1512583853159

http://s.nextmedia.com/realtime/a.php?i=20171207&s=6996647&a=57549850

4 Dec  2017 Chinese (繁)

A genetic engineering team of 15 undergraduate students of life science and biomedical engineering at The Chinese University of Hong Kong (CUHK), has been awarded a Gold medal at the international Genetically Engineered Machine (iGEM) 2017 Giant Jamboree held in Boston, USA, for developing a novel rapid test for an influenza subtype. The winning project has extensive potential applications and may help fight the growing threat of a bird flu epidemic. This is the fifth time that a CUHK team has won gold in the annual premier synthetic biology competition.

The winning project designed by the CUHK team was named “Dr. Switch: A Rapid On-Site Method for Subtyping Influenza A virus”. Presently, diagnostic testing for viruses is only available in the laboratory and it often takes a day or more for the result to come back, due to lengthy transportation and testing time. There is a rapid test which is quicker, but the result is preliminary (Only type A, B or C) which cannot show the subtype of the virus (H1N1, H5N1 or H7N9, etc.). The CUHK iGEM team has developed a rapid test system that can distinguish the subtype of the Influenza A virus. The test can be done on-site in animal farms, at borders or in markets, and the results will come within hours, which will improve anti-epidemic efficiency.

This novel test is based on the Toehold Switch mechanism that, in theory, could detect any RNA target sequence, including the Influenza A virus. A Toehold switch, acting as a biosensor, will undergo conformational change and gene expression, which will produce a visible signal like colour change, in the presence of a specific RNA target – known as a trigger. It was recently used for the detection of Zika.

The CUHK iGEM team is the first group to have developed a web-based tool (http://2017.igem.org/Team:Hong_Kong-CUHK) to help researchers designing Toehold Switch, and applied this method to detect influenza viral subtypes that could work in hours. Their project was nominated for the Best Diagnostic Project, together with the University of Oxford and the Ecole Polytech Fed de Lausanne (EPFL). The prize went to Oxford in the end.

Students have interviewed various stakeholders, including medical experts, government organisations and most importantly, poultry workers. They hoped the test can cater more to the needs of users. For example, the students at first estimated that poultry workers would be interested in conducting virus tests for their own poultry, which could reduce the financial losses caused by the spread of bird flu. However, when they visited a poultry farm owner, they received an answer different from what they expected. The owner’s view was that the test should be conducted by the government or an independent inspection body. Students then consulted government organisations such as the Department of Health, and the Agriculture, Fisheries and Conservation Department. All these visits allowed students to further understand the procedures for influenza testing.

Prof. Chan Ting Fung, one of the instructors of the team and associate professor of the School of Life Science at CUHK, remarked, “The enthusiasm of the undergraduate students for scientific research is admirable. They have spent just over a year, selected their topic of research, failed many times, but finally they achieved a remarkable result. They also showed team spirit and demonstrated the importance of combining molecular biology and engineering knowledge. I hope they will continue to uphold their enthusiasm, participate in scientific research and contribute to society.”

About iGEM Competition

There were 331 teams from around the world participating in this year’s world giant jamboree, and of them only 108 teams achieved gold.

iGEM is an annual premier synthetic biology competition worldwide for high school, undergraduate and postgraduate students.  It was established by the Massachusetts Institute of Technology (MIT) in 2004 to foster students’ learning in synthetic biology, promote collaboration among students and nurture biology talents.  Participating teams are required to specify, design, build and test simple biological systems made from standard, interchangeable biological parts.  The accomplishments of these student teams often lead to important advances or provide solutions to tackle problems in medicine, food and nutrition, energy and the environment.

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>>Press release: