Being a molecular biologist and marine ecologist, I have been employing modern tools of multi-disciplinary science, especially molecular biology techniques, to study fish population genetics, adaptive gene evolution, phytoplankton community structure and phytoplankton-mediated processes such as predator-prey interactions at the base of the marine food web both within laboratory cultures and at sea. Collaborating with Dr. Hans Dam’s research group, I have extended my work to elucidate the molecular nature of phytoplankton toxin adaptation in marine grazers. We focus on the adaptation of copepods to paralytic shellfish poisoning toxins (Na+ channel blockers STX, TTX). We have discovered a novel mutation in the sodium channel of the marine copepod Acartia hudsonica. This discovery opens a way for us to study the adaptation of copepods to toxic dinoflagellate Alexandrium fundyense and has profound implications for the fate of toxic phytoplankton blooms and for understanding adaptive responses of grazers.
I have also been collaborating with various other research groups at the University of Connecticut, such as Dr. Robert B. Whitlatch to develop genetic markers to study the genetic conspecificity of the worldwide populations of the putatively invasive ascidian Didemnum vexillum and determine its native region, Dr. Robert Mason to develop a mer-lux bioreporter to study the mechanisms of bacteria in the uptaking of inorganic mercury (HgII) and methylmercury (CH3HgII); Dr. George McManus to develop molecular markers for detecting ciliate diet algae; and Dr. Charles Yarish to detect the distribution of an invasive macro alga in the Northeast coast, and the macro algae as potential vectors for toxic micro algae. I have coworked with groups of the other research institutes, e.g., Dr. Wayne Litaker at NOAA to detect the geographic distribution and genetic variation of dinoflagellate Karlodinium veneficum in the US east coast, Dr. Dr. Allen Place at the Center of Marine Biotechnology, University of Maryland Biotechnology Institute to measure the genetic deviation and toxin production from various strains of K. veneficum which were potentially linked with fish-killing events. Furthermore, I have being coworking with Dr. Guangxing Liu at Ocean University of China to study marine copepod diet. Using state-of-the-art next generation sequencing techniques, we have uncovered that copepods collected from the field ate various kinds of organisms such as jellyfish larvae, eelgrass spores and many other phytoplankters, which have never being reported before.
Investigate a novel way of light harvesting by marine phytoplankton: proton-pump rhodopsin in dinoflagellates. – NSF
Identification of Phytoplankton Collected from Long Island Sound 2013. – CTDEP
Costs and Advantages of a novel sodium channel mutation in copepods. – NSF
Proof of concept on using spliced leader to study dinoflagellate gene expression in the ocean. – NSF
Peer-Reviewed Journal Articles (*: corresponding author)
- Huan Zhang*, Yunyun Zhuang, John Gill, and Senjie Lin. 2013. Proof that dinoflagellate spliced leader (DinoSL) is a useful hook for fishing dinoflagellate transcripts from mixed microbial samples: Symbiodinium kawagutii as a case study. Protist (accepted).
- Yunyun Zhuang, Huan Zhang, Senjie Lin. 2013. Polyadenylation of 18S rRNA in algae. J. Phycology (accepted).
- Rita C. Kuo, Huan Zhang*, Yunyun Zhuang, Linda Hannick, Senjie Lin. 2012. Transcriptomic study reveals widespread spliced leader trans-splicing, high gene numbers and potential complex carbon fixation mechanisms in the euglenoid alga Eutreptiella. PLoS ONE (in press).
- Zhiling Guo, Sheng Liu, Simin Hu, Tao Li, Yousong Huang, Guangxing Liu, Huan Zhang*, Senjie Lin. 2012. Prevalent Ciliate Epibiosis on Copepods: High Genetic Diversity and Wide Biogeography Detected by Small Subunit Ribosomal RNA Gene. PLoS ONE 7(9): e44847. doi:10.1371/journal.pone.0044847).
- Udonna Ndu, Robert Mason, Huan Zhang, Senjie Lin, and Pieter Visscher. 2012. The Effect of Inorganic and Organic Ligands on the Bioavailability of Methylmercury as Determined by a mer-lux Bioreporter. Appl. Environ. Microbiol. 78(20):7276. DOI: 10.1128/AEM. 00362-12.
- Lauren Stefaniak, Huan Zhang, Adriaan Gittenberger, Kirsty Smith, Kent Holsinger, Senjie Lin1 and Robert B. Whitlatch. 2012. Determining the native region of the putatively invasive ascidian Didemnum vexillum Kott, 2002. Journal of Experimental Marine Biology and Ecology 422–423: 64–71.
- Xin Lin, Huan Zhang, Yudong Cui, Senjie Lin. High sequence variability, diverse subcellular localizations, and ecological implications of alkaline phosphatase in dinoflagellates and other eukaryotic phytoplankton. Frontiers in Aquatic Microbiology 3, Article 235 (2012). doi:10.3389/fmicb.2012.00235.
- Xin Lin, Huan Zhang*, Bangqin Huang and Senjie Lin. 2012b. Alkaline phosphatase gene sequence characteristics and transcriptional regulation by phosphate limitation in Karenia brevis (Dinophyceae). Harmful Algae 17, 14-24. 10.1016/j.hal.2012.02.005.
- Christina L. Haska, Charles Yarish, George Kraemer, Noreen Blaschik, Robert Whitlatch, Huan Zhang and Senjie Lin. 2012. Bait worm packaging as a potential vector of invasive species. Biological Invasions. 14, 481-493.
- Lilibeth N. Miranda, Yunyun Zhuang, Huan Zhang* and Senjie Lin. 2012. Phylogenetic analysis guided by intragenomic SSU rDNA polymorphism refines classification of “Alexandrium tamarense” species complex. Harmful Algae 16, 35–48. doi:10.1016/j.hal.2012.01.002.
- Xin Lin, Huan Zhang, Bangqin Huang and Senjie Lin. 2011. Alkaline phosphatase gene sequence and transcriptional regulation by phosphate limitation in Amphidinium carterae (dinophyceae). J. Phycol. 47, 1110–1120
- Huan Zhang*, David A. Campbell, Nancy R. Sturm, Christopher F. Dungan and Senjie Lin. Spliced leader RNAs, mitochondrial gene frameshifts and multi-protein phylogeny expand support for the genus perkinsus as a unique group of alveolates. PLoS One 6(5):e19933. doi:10.1371/journal.pone.0019933
- Huan Zhang*, Christopher F. Dungan and Senjie Lin. 2011. Introns, Alternative Splicing, Spliced Leader trans-Splicing and Differential Expression of pcna and cyclin in Perkinsus marinus. Protist 162, 154-167. doi:10.1016/j.protis.2010.03.003).
- Senjie Lin, Huan Zhang, Yunyun Zhuang, Bao Tran, and John Gill. 2010. Spliced leader–based metatranscriptomic analyses lead to recognition of hidden genomic features in dinoflagellates. PNAS USA 107, 20033–20038 doi/10.1073/pnas.1007246107.
- Lin, S. and Zhang, H. 2010. Dinoflagellate meta-transcriptomics enabled by spliced leader. In C. K. Ho (ed.) Proceedings of 13th International Conference on Harmful Algae. Pp 166-170.
- Yubo Hou, Huan Zhang, Lilibeth Miranda and Senjie Lin. 2010. Serious overestimation in quantitative PCR by circular (supercoiled) plasmid standard: microalgal pcna as the model gene. PLoS ONE 5(3): e9545. doi:10.1371/journal.pone.0009545.
- Huan Zhang, David A. Campbell, Nancy R. Sturm, and Senjie Lin. 2009. Dinoflagellates spliced leader RNA genes display a variety of sequences and genomic arrangements. Biol. Evol. 26, 1757–1771.
- Senjie Lin, Huan Zhang, Yubo Hou, Yunyun Zhuang, and Lilibeth Miranda. High-Level Diversity of Dinoflagellates in the Natural Environment, Revealed by assessment of Mitochondrial cox1 and cob Genes for Dinoflagellate DNA Barcoding. Appl. Environ. Microbiol. 75, 1279–1290.
- Senjie Lin, Gustaf Sandh, Huan Zhang, Jiujun Cheng, Keri Perkins, Edward J. Carpenter and Birgitta Bergman. Two flavodoxin genes in Trichodesmium (Oscillatoriales, Cyanophyceae): Remarkable sequence divergence and possible functional diversification. J. Exp. Mar. Biol. Ecol. 371, 93–101.
- Lauren Stefaniak, Gretchen Lambert, Adriaan Gittenberger, Huan Zhang, Senjie Lin and Robert B. Whitlatch. Genetic conspecificity of the worldwide populations of Didemnum vexillum Kott, 2002. Aquatic Invasions 4, 29-44. DOI 10.3391/ai.2009.4.1.3.
- Huan Zhang and Senjie Lin. Retrieval of Missing Spliced Leader in Dinoflagellates. PLoS ONE 4(1): e4129. doi:10.1371/journal.pone.0004129.
- Shozo Yokoyama, Takashi Tada, Huan Zhang, and Lyle Britt. Elucidation of phenotypic adaptations: molecular analyses of dim-light vision proteins in vertebrates PNAS USA, 105, 13480-13485.
- Huan Zhang, Wayne Litaker, Mark W. Vandersea, Patricia Tester and Senjie Lin. Geographic distribution of Karlodinium veneficum in the US east coast as detected by ITS- ferredoxin Real-Time PCR assay. J. Plankton Res. 30:905-922.
- Huan Zhang and Senjie Lin. 2008. Status of mRNA editing and SL RNA trans-splicing groups Oxyrrhis, Noctiluca, Heterocapsa, and Amphidinium as basal lineages of dinoflagellates Phycol. 44:703-711.
- Akihiro Okamura, Huan Zhang, Naomi Mikawa, Aya Kotake, Yoshiaki, Yamada, Tomoko, Utoh, Noriyuki Horie, Satoru Tanaka, Hideo P. Oka and Katsumi Tsukamoto. Decline in non-native freshwater eels in Japan: ecology and future perspectives. Environmental Biology of Fishes 81:347-358.
- Huan Zhang, Debashish Bhattacharya, Lucie Maranda and Senjie Lin. 2008. Mitochondrial cob and cox1 and their mRNA editing in Dinophysis acuminata from Narragansett Bay, with special reference to the phylogenetic position of Dinophysis. Environ. Microbiol. 74:1546–1554.
- Senjie Lin, Huan Zhang and Michael W. Gray. 2008. RNA editing in dinoflagellates and its implications for the evolutionary history of the editing machinery. In: Harold C. Smith (ed.), RNA and DNA Editing (Molecular Mechanisms and Their Integration into Biological Systems), John Wiley & Sons, Inc., Hoboken, New Jersey 280-309.
- Huan Zhang, Debashish Bhattacharya and Senjie Lin. 2007. A three-gene dinoflagellate phylogeny suggests reconciliation of Exuviaella with Prorocentrum and a basal position for Amphidinium and J. Mol. Evol. 65:463–474.
- Huan Zhang, Yubo Hou, Lilibeth Miranda, David A. Campbell, Nancy R. Sturm, Terry Gaasterland, and Senjie Lin. 2007. Spliced leader RNA trans-splicing in dinoflagellates. PNAS USA, 104, 4618-4623.
- Senjie Lin, Huan Zhang, Yubo Hou, Lilibeth Miranda, and Bhattacharya Debashish. Development of a dinoflagellate-oriented PCR primer set leads to the detection of picoplanktonic dinoflagellates from long island sound. Appl. Environ. Microbiol.. 78, 5626–5630.
- Senjie Lin, Huan Zhang and Angela Dubois. Low abundance distribution of Pfiesteria piscicida in Pacific and Western Atlantic as detected by mtDNA-18S rDNA real-time polymerase chain reaction. J. Plankton Res., 28, 667-681.
- Senjie Lin, Huan Zhang and Nianzhi Jiao. 2006. Potential utility of mitochondrial cytochrome b and its mRNA editing in resolving closely related dinoflagellates: a case study of Prorocentrum (Dinophyceae). Phycol. 42, 646–654 (2006)
- Huan Zhang, Yubo Hou and Senjie Lin. Isolation and characterization of PCNA from the dinoflagellate Pfiesteria piscicida. J. Eukaryot. Microbiol.,53, 142–150.
- Huan Zhang and Senjie Lin. J. Eukaryot. Microbiol., 52, 538–545.
- Huan Zhang and Senjie Lin. Development of a cob-18S dual-gene Real-Time PCR assay for Pfiesteria shumwayae and quantification of this species in the natural environment. Appl. Environ. Microbiol.71, 7053-7063.
- Senjie Lin and Huan Zhang. Isolation of mitochondrial cytochrome b gene and development of a real-time quantitative PCR assay for detecting Neoparamoeba aestuarina. Shellfish Research 24, 733-739.
- Huan Zhang, Debashish Bhattacharya and Senjie Lin. Phylogeny of Dinoflagellates Based on Mitochondrial Cytochrome b and Nuclear Small Subunit rDNA Sequence Comparisons. J. Phycol. 41, 411–420.
- Senjie Lin, Margaret R. Mulholland, Huan Zhang, Timothy N. Feinstein, Frank J. Jochem and Edward J. Carpenter. Intense grazing and prey-dependent growth of Pfiesteria piscicida (Dinophyceae). J. Phycol. 40: 1062-1073.
- Akihiro Okamura, Huan Zhang, Tomoko Utoh, et al. Artificial hybrid between Anguilla anguilla and A. japonica. J. Fish Biology 64, 1450-1454.
- George McManus, Huan Zhang and Senjie Lin. Marine planktonic ciliates that prey on macroalgae and enslave their chloroplasts. Limnology & Oceanography 49, 308-313.
- Senjie Lin, Timothy N. Feinstein, Huan Zhang and Edward J. Carpenter. 2003. Development of an immunofluorescence technique for detecting Pfiesteria piscicida. Harmful Algae 2: 223-231.
- Huan Zhang, Kunihiko Futami and Nobuaki Okamoto. 2003 Isolation of c-myc genes from goldfish and their tissue specific expression. Fish Biol. 63, 1266-1273.
- Huan Zhang and Senjie Lin. 2003. Complex gene structure of the form II Rubisco in the dinoflagellate Prorocentrum minimum (dinophyceae). Phycology 39, 1160-1171.
- Senjie Lin, Timothy N. Feinstein, Huan Zhang and Edward J. Carpenter. 2003. Development of an immunofluorescence technique for detecting Pfiesteria piscicida. Harmful Algae 2, 223-231.
- Senjie Lin and Huan Zhang. 2003. Mitogen-associated protein kinase (MAPK) in Pfiesteria piscicida. Environ. Microbiol. 69, 343-349.
- Huan Zhang, Kunihiko Futami, Yoshiaki Yamada, Noriyuki Horie, Akihiro Okamura, Tomoko Utoh, Naomi Mikawa, Hideo P. Oka Nobuaki Okamoto. Isolation of freshwater and deep-sea type opsin genes from the common Japanese conger J. Fish Biol. 61, 313-324.
- Satoru Tanaka, Huan Zhang, Yoshiaki Yamada, Akihiro Okamura, Noriyuki Horie, Tomoko Utoh, Naomi Mikawa, Hideo P. Oka and H. 2002. Inhibitory effect of sodium bicarbonate on the motility of sperm of Japanese eel. J. Fish Biol. 60, 1134-1141.
- Senjie Lin, Huan Zhang, David F. Spencer, John E. Norman and Michael W. Gray. 2002. Widespread and extensive editing of mitochondrial mRNAs in dinoflagellates. Mol. Biol. 320, 727-739.
- Satoru Tanaka, Huan Zhang, Noriyuki Horie, Yoshiaki Yamada, Akihiro Okamura, Tomoko Utoh, Naomi Mikawa, Hideo P. Oka & H. 2002. Long –term cryopreservation of sperm of Japanese eel. J. Fish Biol. 60,139-146.
- Huan Zhang and Senjie Lin. 2002. Detection and Quantification of Pfiesteria piscicida by Using the Mitochondrial Cytochrome b Appl. Environ. Microbiol. 68, 989-994.
- Noriyuki Horie, Tomoko Utoh, Yoshiaki Yamada, Akihiro Okamura, Huan Zhang, Naomi Mikawa, Atsushi Akazawa, Satoru Tanaka and Hideo P. Oka. 2002. Development of embryos and larvae in the common Japanese conger Conger myriaster. Fisheries Scis. 68, 972-983.
- Kunihiko Futami, Takeru Komiya, Huan Zhang and Nobuaki Okamoto. 2001. Differential expression of mas and two types of c-myc genes in a tetraploid fish, the common carp (Cyprinus carpio). Gene 269, 113-119.
- Yoshiaki Yamada, Huan Zhang, Akihiro Okamura, Satoru Tanaka, Noriyuki Horie, Naomi Mikawa, Tomoko Utoh and Hideo P. Oka. 2001. Morphological and histological changes in the swim bladder during maturation of the Japanese eel. Fish Biology 58,804-814.
- Akihiro Okamura, Huan Zhang, Yoshiaki Yamada, Satoru Tanaka, Noriyuki Horie, Naomi Mikawa, Tomoko Utoh and Hideo P. Oka. Re-examination of the spermatozoal ultrastructure of eels: observations of the external morphology of spermatozoa in three species. J. of Fish Biology 57, 161-169.
- Huan Zhang, Kunihiko Futami, Noriyuki Horie, Akihiro Okamura, TomokoUtoh, Naomi Mikawa, Yoshiaki Yamada, Satoru Tanaka and Nobuaki Okamoto. Molecular cloning of fresh water and deep-sea rod opsin genes from Japanese eel Anguilla japonica and their expressional analysis during sexual maturation. FEBS letters 469, 39-43.
- Kunihiko Futami, Takeru Komiya, Huan Zhang and Nobuaki Okamoto. Determination of heterogeneous transcription start points of two c-myc genes from the common carp (Cyprinus carpio). Gene 245, 43-47.
- Akihiro Okamura, Tomoko Utoh, Huan Zhang, Yoshiaki Yamada, Noriyuki Horie, Naomi Mikawa, Satoru Tanaka and Hideo P. Oka. Seasonal changes in maturity in the Conger Eel Conger myriaster at the Pacific coast of Atsumi Peninsula, central Japan. Nippon Suisan Gakkashi 66, 412-416 (2000) (in Japanese).
- Kunihiko Futami, Huan Zhang and Nobuaki Okamoto. Molecular evolution of two c-myc genes of a tetraploid teleosts, the common carp. Protein, Nucleic acid, Enzume 45, 2943-2948 (2000) (in Japanese).
- Huan Zhang, Naomi Mikawa, Yoshiaki Yamada, Noriyuki Horie, Akihiro Okamura, Tomoko Utoh, Satoru Tanaka and Takashi Motonobu. 1999. Detection of foreign eels in the natural waters of Japan by PCR. Fisheries Science 65, 684-686.
- Shozo Yokoyama, Huan Zhang, F. Bernhard Radlwimmer and Nathan S. Blow. 1999. Adaptive evolution of color vision of the Comoran coelacanth (Latimeria chalumnae). PNAS 96, 6279-6284.
- Huan Zhang and Takashi Motonobu. 1999. Spawning migration and Visual adaptation of Japanese eel. Kaiyo Monthly special 18, 141-145 (in Japanese).
- Shozo Yokoyama and Huan Zhang: Cloning and characterization of the pineal gland-specific opsin gene of marine lamprey (Petromyzon marinus). Gene 202, 89-93 (1997).
- Huan Zhang and Shozo Yokoyama. 1997. Molecular evolution of the rhodopsin gene of marine lamprey, Petromyzon marinus. Gene 191, 1-6.
- Huan Zhang, Nobuaki Okamoto and Yayoi Ikeda. 1995. Two c-myc genes from a tetraploid fish, the common carp (Cyprinus carpio). Gene 153, 231-236.
- Huan Zhang, Hang Zhang, Nobuaki Okamoto and Yayoi Ikeda. 1994. Cloning and sequencing of a c-myc gene from goldfish Carassius auratus. Fisheries Science 60, 707-711.
- Huan Zhang, Nobuaki Okamoto and Yayoi Ikeda. 1993. Molecular cloning of carp cellular myc (c-myc) cDNA. Gyobyo Kenkyu 28, 111-117.