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Dr. Miriam Hampel
Instituto de Ciencias Marinas de Andalucía (ICMAN)
Miriam Hampel is a Post-doc (JAE-Doc) at the Department of Ecology & Coastal Management of the Institute for Marine Sciences of Andalusia (ICMAN-CSIC) in Puerto Real, Spain, where she also did her PhD in 2003. After five years of post doctoral fellowships at the National Institute for Agriculture and Fisheries Research (IPIMAR) funded by the Fundação para a Ciência e a Tecnologia in Portugal and the Institute of Aquaculture of the University in Stirling in Scotland, funded by the European Commission, she returned to the ICMAN with a post-doc contract (JAE-Doc) of the CSIC in 2009. She has a long experience in the field of (eco-) toxicology evaluating physiological, enzymatic and molecular endpoints, including bivalves, crustaceans, copepods, snails, pelagic and benthonic fish.
Phone: +34 956 832612 ext 283
e-mail: [email protected]
PERSONAL CONTRIBUTION TO THE PROJECT
WPs 1&2&3: Effects of exposure to pharmaceutical compounds in different copepod species. WP3 leader.
WPs 7: Development of biomarkers of exposure to metal contamination in the amphipod Melita plumulosa.
WP 8: Gene expression profiling in Danio rerio and Poecilia vivipara exposed to hospital effluent mixtures.
WP 9: Interspecies variation in gene expression of two different oyster species after exposure to Linear Alkyl Benzenes (LAB).
WP10: Evaluation of molecular and enzymatic responses to metal and anti-fouling agents in marine microalgae. WP10 leader.
WP11&12: Information gathering and dissemination. WP leader.
RELATED PUBLICATIONS
·Hutchinson TH, Pounds NA, Hampel M, Williams TD (1999) Life-cycle studies with marine copepods (Tisbe battagliai) exposed to 20-hydroxyecdysone and diethylstilbestrol. Environmental Toxicology and Chemistry, V18 (12).
·Hutchinson TH, Pounds NA, Hampel M, Williams TD (1999) Impact of natural and synthetic steroids on the survival, development and reproduction of marine copepods Tisbe battagliai. Science of the total Environment, V 233, pp 167-179.
·Blasco J, Saenz V, Puppo J, Hampel M (1999) Metal Contamination and Pollution of Estuaries and Coastal Areas. UNESCO (Intergovernmental Oceanographic Commission: Technical Series) Baltic Floating University Research Bulletin. (Eds. N. Plink and A. Del Valls)
·Hampel M, Moreno-Garrido I, Sobrino C, Lubián LM, Blasco J (2001) Acute Toxicity of LAS Homologues in Marine Microalgae. Esterase Activity and Inhibition Growth as Endpoints of Toxicity. Ecotoxicology and Environmental Safety. 48, 287-292.
·Moreno-Garrido I, Hampel M, Lubián LM, Blasco J (2001) Marine microalgae toxicity test for linear alkylbenzene sulfonate (LAS) and alkylphenol ethoxylate (APEO). Fresenius’ Journal of Analytical Chemistry, 371 (4), 474-478.
·Hampel M, Blasco J (2002) Toxicity of linear alkylbenzene sulphonate (LAS) and one long-chain degradation intermediate, sulphophenyl carboxilic acid (SPC C11) on early life-stages of seabream (Sparus aurata). Ecotoxicology and Environmental Safety 51, 53-59.
·Moreno-Garrido I, Hampel M, Lubián LM, Blasco J (2003) Sediment toxicity tests using benthic marine microalgae Cylindrotheca closterium (Ehremberg) Lewin & Reimann (Bacillariophyceae). Ecotoxicology and Environmental Safety 54, 290-295.
·Moreno-Garrido I, Hampel M, Lubián LM, Blasco J (2003) Marine benthic microalgae Cylindrotheca closterium (Ehremberg) Lewin & Reimann (Bacillariophyceae) as a tool for measuring toxicity of Linear Alkylbenzene Sulphonate (LAS) in sediment. Bull. Environ. Contam. Tox., V 70, 242-247.
·Hampel M, Ortiz-Delgado JB, Moreno-Garrido I, Sarasquete C, Blasco J (2004) Sublethal Effects of Linear Alkylbenzene Sulphonate on Larvae of the Sea-bream (Sparus aurata): histological approach. Histology and Histopathology, 19: 1061-1073.
·Hampel M, González-Mazo, E., Vale C., Blasco, J. (2007) Derivation of predicted no effect concentrations (PNEC) for marine environmental risk assessment: application of different approaches to the model contaminant Linear Alkylbenzene Sulfonate (LAS) in a site specific environment. Environment International, 33: 486-491.
·Hampel M, Ortiz-Delgado JB, Sarasquete C, Blasco J (2008) Lethal and Sublethal Effects of sediment sorbed Linear Alkylbenzene Sulphonate on Juveniles of the Senegal Sole (Solea senegalensis): indicator of sublethal effects of exposure. Histology and Histopathology 23, 87-100.
·Hampel M, Canário J, Branco V, Vale C, Blasco J (2009) Environmental levels of linear alkylbenzene suphonates (LAS) in sediments from the Tagus estuary, Portugal. Environmental Monitoring and Assessment 149(1-4), 151-161. (DOI 10.1007/s10661-008-0190-0).
·Hampel M, Moreno-Garrido I, González-Mazo E, Blasco J (2009) Suitability of the marine prosobranch snail Hydrobia ulvae for sediment toxicity assessment: a case study with the anionic surfactant Linear Alkylbenzene Sulfonate (LAS). Ecotoxicology and Environmental Safety 72(4), 1303-1308. (Doi.: 10.1016/j.ecoenv.2008.09.005).
·Diz FR, Araújo CVM, Moreno-Garrido I, Hampel M, Blasco J. (2009). Application of toxicity tests to determinate lethal and sublethal effects on the harpacticoid copepod Tisbe battagliai. Ecotoxicology and Environmental Safety 72(7), 1881-1886 (Doi.: 10.1016/j.ecoenv.2009.03.004).
·Hampel M, Alonso E, Aparicio I, Bron JE, Santos JL, Taggart JB, Leaver MJ (2010) Potential physiological effects of pharmaceutical compounds in Atlantic salmon (Salmo salar), implied by transcriptomic analysis. Environmental Science and Pollution Research, 17 (4), 917. DOI: 10.1007/s11356-009-0282-6 (Impact factor: 2.87)
·Hampel M, Mauffret A, Pazdro K, Blasco J (2011). Anionic surfactant linear alkylbenzene sulphonates (LAS) in sediments from the Gulf of Gdansk (southern Baltic Sea, Poland) and its environmental implications. Environmental Monitoring and Assessment, 184(10), 6013-6023. DOI: 10.1007/s10661-011-2399-6
·García-Negrete CA, Blasco J, Volland M, Rojas TC, Hampel M, Lapresta-Fernández A, Jimenez de Haro MC, Fernández A (2012) Evolution in seawater and bivalve uptake of Au-citrate nanoparticles at environmentally relevant concentrations. Environmental Pollution 174, 134-141.
·Nieto E, Blasco J, González-Ortegón E, Drake P, Hampel M (2013) Is Atyaephyra desmarestii a useful candidate for lethal and sub-lethal toxicity tests with pharmaceutical compounds? Journal of Hazardous Materials (in press) http://dx.doi.org/10.1016/j.jhazmat.2013.08.035
·Hampel M, Alonso E, Aparicio I, Santos JL, Leaver MJ (2013) Hepatic proteome analysis of Atlantic salmon (Salmo salar) after exposeure to environmental concentrations of human pharmaceuticals. Molecular and Cellular Proteomics (accepted).
·Hampel M, Alonso E, Aparicio I, Bron JE, Santos JL, Taggart JB, Leaver MJ (2013) Environmental levels of the antidepressant drug Carbamazepine induce differential transcriptome expression in the brain of Atlantic salmon, Salmo salar. Aquatic Toxicology, Special Issue on Antidepressants (accepted).
·Hampel M, Milan M, Blasco J, Ferraresso S, Bargelloni L (2013) Transcriptome expression fingerprinting after exposure to human pharmaceuticals in the brain of the seabream, Sparus aurata. Aquatic Toxicology (submitted).
Phone: +34 956 832612 ext 283
e-mail: [email protected]
PERSONAL CONTRIBUTION TO THE PROJECT
WPs 1&2&3: Effects of exposure to pharmaceutical compounds in different copepod species. WP3 leader.
WPs 7: Development of biomarkers of exposure to metal contamination in the amphipod Melita plumulosa.
WP 8: Gene expression profiling in Danio rerio and Poecilia vivipara exposed to hospital effluent mixtures.
WP 9: Interspecies variation in gene expression of two different oyster species after exposure to Linear Alkyl Benzenes (LAB).
WP10: Evaluation of molecular and enzymatic responses to metal and anti-fouling agents in marine microalgae. WP10 leader.
WP11&12: Information gathering and dissemination. WP leader.
RELATED PUBLICATIONS
·Hutchinson TH, Pounds NA, Hampel M, Williams TD (1999) Life-cycle studies with marine copepods (Tisbe battagliai) exposed to 20-hydroxyecdysone and diethylstilbestrol. Environmental Toxicology and Chemistry, V18 (12).
·Hutchinson TH, Pounds NA, Hampel M, Williams TD (1999) Impact of natural and synthetic steroids on the survival, development and reproduction of marine copepods Tisbe battagliai. Science of the total Environment, V 233, pp 167-179.
·Blasco J, Saenz V, Puppo J, Hampel M (1999) Metal Contamination and Pollution of Estuaries and Coastal Areas. UNESCO (Intergovernmental Oceanographic Commission: Technical Series) Baltic Floating University Research Bulletin. (Eds. N. Plink and A. Del Valls)
·Hampel M, Moreno-Garrido I, Sobrino C, Lubián LM, Blasco J (2001) Acute Toxicity of LAS Homologues in Marine Microalgae. Esterase Activity and Inhibition Growth as Endpoints of Toxicity. Ecotoxicology and Environmental Safety. 48, 287-292.
·Moreno-Garrido I, Hampel M, Lubián LM, Blasco J (2001) Marine microalgae toxicity test for linear alkylbenzene sulfonate (LAS) and alkylphenol ethoxylate (APEO). Fresenius’ Journal of Analytical Chemistry, 371 (4), 474-478.
·Hampel M, Blasco J (2002) Toxicity of linear alkylbenzene sulphonate (LAS) and one long-chain degradation intermediate, sulphophenyl carboxilic acid (SPC C11) on early life-stages of seabream (Sparus aurata). Ecotoxicology and Environmental Safety 51, 53-59.
·Moreno-Garrido I, Hampel M, Lubián LM, Blasco J (2003) Sediment toxicity tests using benthic marine microalgae Cylindrotheca closterium (Ehremberg) Lewin & Reimann (Bacillariophyceae). Ecotoxicology and Environmental Safety 54, 290-295.
·Moreno-Garrido I, Hampel M, Lubián LM, Blasco J (2003) Marine benthic microalgae Cylindrotheca closterium (Ehremberg) Lewin & Reimann (Bacillariophyceae) as a tool for measuring toxicity of Linear Alkylbenzene Sulphonate (LAS) in sediment. Bull. Environ. Contam. Tox., V 70, 242-247.
·Hampel M, Ortiz-Delgado JB, Moreno-Garrido I, Sarasquete C, Blasco J (2004) Sublethal Effects of Linear Alkylbenzene Sulphonate on Larvae of the Sea-bream (Sparus aurata): histological approach. Histology and Histopathology, 19: 1061-1073.
·Hampel M, González-Mazo, E., Vale C., Blasco, J. (2007) Derivation of predicted no effect concentrations (PNEC) for marine environmental risk assessment: application of different approaches to the model contaminant Linear Alkylbenzene Sulfonate (LAS) in a site specific environment. Environment International, 33: 486-491.
·Hampel M, Ortiz-Delgado JB, Sarasquete C, Blasco J (2008) Lethal and Sublethal Effects of sediment sorbed Linear Alkylbenzene Sulphonate on Juveniles of the Senegal Sole (Solea senegalensis): indicator of sublethal effects of exposure. Histology and Histopathology 23, 87-100.
·Hampel M, Canário J, Branco V, Vale C, Blasco J (2009) Environmental levels of linear alkylbenzene suphonates (LAS) in sediments from the Tagus estuary, Portugal. Environmental Monitoring and Assessment 149(1-4), 151-161. (DOI 10.1007/s10661-008-0190-0).
·Hampel M, Moreno-Garrido I, González-Mazo E, Blasco J (2009) Suitability of the marine prosobranch snail Hydrobia ulvae for sediment toxicity assessment: a case study with the anionic surfactant Linear Alkylbenzene Sulfonate (LAS). Ecotoxicology and Environmental Safety 72(4), 1303-1308. (Doi.: 10.1016/j.ecoenv.2008.09.005).
·Diz FR, Araújo CVM, Moreno-Garrido I, Hampel M, Blasco J. (2009). Application of toxicity tests to determinate lethal and sublethal effects on the harpacticoid copepod Tisbe battagliai. Ecotoxicology and Environmental Safety 72(7), 1881-1886 (Doi.: 10.1016/j.ecoenv.2009.03.004).
·Hampel M, Alonso E, Aparicio I, Bron JE, Santos JL, Taggart JB, Leaver MJ (2010) Potential physiological effects of pharmaceutical compounds in Atlantic salmon (Salmo salar), implied by transcriptomic analysis. Environmental Science and Pollution Research, 17 (4), 917. DOI: 10.1007/s11356-009-0282-6 (Impact factor: 2.87)
·Hampel M, Mauffret A, Pazdro K, Blasco J (2011). Anionic surfactant linear alkylbenzene sulphonates (LAS) in sediments from the Gulf of Gdansk (southern Baltic Sea, Poland) and its environmental implications. Environmental Monitoring and Assessment, 184(10), 6013-6023. DOI: 10.1007/s10661-011-2399-6
·García-Negrete CA, Blasco J, Volland M, Rojas TC, Hampel M, Lapresta-Fernández A, Jimenez de Haro MC, Fernández A (2012) Evolution in seawater and bivalve uptake of Au-citrate nanoparticles at environmentally relevant concentrations. Environmental Pollution 174, 134-141.
·Nieto E, Blasco J, González-Ortegón E, Drake P, Hampel M (2013) Is Atyaephyra desmarestii a useful candidate for lethal and sub-lethal toxicity tests with pharmaceutical compounds? Journal of Hazardous Materials (in press) http://dx.doi.org/10.1016/j.jhazmat.2013.08.035
·Hampel M, Alonso E, Aparicio I, Santos JL, Leaver MJ (2013) Hepatic proteome analysis of Atlantic salmon (Salmo salar) after exposeure to environmental concentrations of human pharmaceuticals. Molecular and Cellular Proteomics (accepted).
·Hampel M, Alonso E, Aparicio I, Bron JE, Santos JL, Taggart JB, Leaver MJ (2013) Environmental levels of the antidepressant drug Carbamazepine induce differential transcriptome expression in the brain of Atlantic salmon, Salmo salar. Aquatic Toxicology, Special Issue on Antidepressants (accepted).
·Hampel M, Milan M, Blasco J, Ferraresso S, Bargelloni L (2013) Transcriptome expression fingerprinting after exposure to human pharmaceuticals in the brain of the seabream, Sparus aurata. Aquatic Toxicology (submitted).
Dr. Françoise DENIS
Muséum National d’Histoire Naturelle (MNHN) – Station de Concarneau
She did her phD in the Universityof Brest in 1995 and after one year of contract in the Institut Pasteur in Paris, she was recruited as an assistant Professor in the University of Maine in Le Mans in 1996. She is a researcher in the UMR 7208 CNRS-MNHN-UPMC-IRD in BOREA Laboratory “Biologie des ORganismes et des Ecosystèmes Aquatiques” and is established in the marine station of Concarneau along the Atlantic coast. Her research area concerns Molecular Biology and Evolutionary Genetics. She studies the molecular processes of genetic differentiation of marine organisms. Her models are Protostomiens organisms.
Phone: +33 298 504 286
e-mail: [email protected]
PERSONAL CONTRIBUTION TO THE PROJECT
WP 6. The use of two bivalves, Ruditapes decussaues and Cerastoderma glaucum, in pollution biomonitoring: Effect of metals and endocrine disruptors on the stress response and reproduction. Characterization and expression analysis of some biomarkers such as superoxide dismutase, metallothionein, etc.
RELATED PUBLICATIONS
In press. Marchand J.,Denis F. & Laroche J. « Evolutionary Toxicology and Transcriptomic Approaches ». In « Ecological Biomarkers: Indicators of Ecotoxicological Effects », Amiard-Triquet C. & Amiard J-C. Edition Taylor & Francis.
Ladhar-Chaabouni R, Hamza-Chaffai A, Hardivillier Y, Chenais B., Denis F. 2010 A pilot study of genetic differentiation between two phenotypes of a Mediterranean population of the bivalbe Cerastoderma glaucum and genetic discrimination with other Cerastoderma glaucum and Cerastoderma edule populations outside the Mediterranean. Marine Ecology an evolutionary perspective (2) : 355-363
Denis F., Ravallec R., Pavillon, J.-P., Van Wormhoudt A. 2009 Genetic differentiation of atlantic populations of the intertidal copepod Tigriopus brevicornis.
Scientia Marina, 73 (3): 579-587. (IF : 1,075)
Ladhar-Chaabouni R., Mokdad-Gargouri R., Denis F., Hamza-Chaffai A. 2009 Cloning and characterization of cDNA probes for the analysis of metallothionein gene expression in the Mediterranean bivalves: Ruditapes decussates et Cerastoderma glaucum. Molecular Biology Reports, 36 (5): 1007-1014. (IF: 0,712)
Marchand J., Denis F. & Laroche J. 2008. Modifications de la variabilité génétique et de l’expression de gènes. Dans « Les Biomarqueurs dans l’évaluation de l’état écologique des milieux aquatiques », Amiard-Triquet C. & Amiard J-C. Edition TEC & DOC Lavoisier, 375 pages.
Phone: +33 298 504 286
e-mail: [email protected]
PERSONAL CONTRIBUTION TO THE PROJECT
WP 6. The use of two bivalves, Ruditapes decussaues and Cerastoderma glaucum, in pollution biomonitoring: Effect of metals and endocrine disruptors on the stress response and reproduction. Characterization and expression analysis of some biomarkers such as superoxide dismutase, metallothionein, etc.
RELATED PUBLICATIONS
In press. Marchand J.,Denis F. & Laroche J. « Evolutionary Toxicology and Transcriptomic Approaches ». In « Ecological Biomarkers: Indicators of Ecotoxicological Effects », Amiard-Triquet C. & Amiard J-C. Edition Taylor & Francis.
Ladhar-Chaabouni R, Hamza-Chaffai A, Hardivillier Y, Chenais B., Denis F. 2010 A pilot study of genetic differentiation between two phenotypes of a Mediterranean population of the bivalbe Cerastoderma glaucum and genetic discrimination with other Cerastoderma glaucum and Cerastoderma edule populations outside the Mediterranean. Marine Ecology an evolutionary perspective (2) : 355-363
Denis F., Ravallec R., Pavillon, J.-P., Van Wormhoudt A. 2009 Genetic differentiation of atlantic populations of the intertidal copepod Tigriopus brevicornis.
Scientia Marina, 73 (3): 579-587. (IF : 1,075)
Ladhar-Chaabouni R., Mokdad-Gargouri R., Denis F., Hamza-Chaffai A. 2009 Cloning and characterization of cDNA probes for the analysis of metallothionein gene expression in the Mediterranean bivalves: Ruditapes decussates et Cerastoderma glaucum. Molecular Biology Reports, 36 (5): 1007-1014. (IF: 0,712)
Marchand J., Denis F. & Laroche J. 2008. Modifications de la variabilité génétique et de l’expression de gènes. Dans « Les Biomarqueurs dans l’évaluation de l’état écologique des milieux aquatiques », Amiard-Triquet C. & Amiard J-C. Edition TEC & DOC Lavoisier, 375 pages.
Prof. Maria Bebianno
University of Algarve (UALG)
Dr Maria Bebianno is a full professor at the University of Algarve with more than 25 years of experience in marine contamination and ecotoxicology. She has published >125 papers and participated in several national and international projects. She has supervised more than 15 PhDs some of which co-supervised by colleagues from other EU countries, Brazil and Tunisia, as well as, several Pos-docs some of them from other EU countries. She has developed collaborative with teams from several universities and research centres of the EU (Spain, France, UK, and Finland) and non-EU countries (Brazil Cape Verde and China). Her research work is being developed at the Centre of Marine and Environmental Research (CIMA) of the University of Algarve where she leads the Ecotoxicology and Environmental Chemistry Group. Dr. Maria Bebianno research focused on the effects of organic and inorganic “old” and emerging contaminants on aquatic organisms. More recently the team enrolled in proteomic research applied to Ecotoxicology.
Phone: 351 289 800923
e-mail. [email protected]
Contribution to the Project
WPs4 & 5 Protein expression profiles in mussels exposed to pharmaceuticals and to nanoparticles
WP6 The use bivalves in pollution biomonitoring. Effect of metals and endocrine disruptors on the stress response and reproduction.
WPs 11 & 12 Information, gathering and dissemination
Publications
Gomes T., Pinheiro, Cancio I., Pereira C.G., Cardoso C., Bebianno M.J. The effects of copper nanoparticles exposure in the mussel Mytilus galloprovincialis. Environmental Science and Technology (in press).
Company, R., Antúnez, O., Bebianno, M. J., Cajaraville, M. P., Torreblanca, A. (2011). 2-D difference gel electrophoresis approach to assess protein expression profiles in Bathymodiolus azoricus from Mid-Atlantic Ridge hydrothermal vents, Journal of Proteomics, (in press) ( doi:10.1016/j.jprot.2011.07.012).
Gonzalez-Rey, Maria; Bebianno, M. J.,. (2011). Non-steroidal anti-inflammatory drug (NSAID) ibuprofen distresses antioxidant defense system in mussel Mytilus galloprovincialis gills. Aquatic Toxicology 105, 264-269. (doi:10.1016/j.aquatox.2011.06.015 ).
Serafim A., Lopes B., Company R., Cravo A., Gomes T., Sousa V., Bebianno M.J. (2011). A multi-biomarker approach in cross-transplanted mussels Mytilus galloprovincialis. Ecotoxicology (DOI 10.1007/s10646-011-0737-7)
Maria V. L., Bebianno, M. J. 2011. Antioxidant and Lipid Peroxidation Responses in Mytilus galloprovincialis exposed to mixtures of Benzo(a)pyrene and Copper , Comparative Biochemistry and Physiology, Part C, 154, 56-63 ( doi:10.1016/j.cbpc.2011.02.004)
Company, R., Serafim, A., Lopes, B., Cravo, A, Kalman, J , Riba, I., Del Valls, A., Blasco, J., Delgado, J., Sarmiento, A.M., Nieto, J.M., Shepherd, T.J., Nowell, G.& Bebianno, M.J. (2011). Source and impact of lead contamination on δ-aminolevulinic acid dehydratase activity in several marine bivalve species along the Gulf of Cadiz. Aquatic Toxicology 10, 146-154. (doi:10.1016/j.aquatox.2010.09.012).
Chora, S., McDonagh, B., Sheehan, D., Starita-Geribaldi, M., Roméo, M., Bebianno, M. J. (2010). Ubiquitination and carbonylation of proteins in the clam Ruditapes decussatus, exposed to nonylphenol using redox proteomics. Chemosphere 81, 1212-1217. (doi:10.1016/j.chemosphere.2010.09.03).
Chora S., Starita-Geribaldi, M., Guigonis, J-M., Samson, M., Roméo M. & Bebianno M. J. (2009). Effect of Cd in the clam Ruditapes decussatus assessed by proteomics. Aquatic Toxicology 94, 300-308 (DOI: 10.1016/j.aquatox.2009.07.014).
Geret F., Gomes T., Marty P. & Bebianno M. J. (2010). Differential protein expression in Corbicula fluminea exposed to a mixture of pharmaceutical products. Comparative Biochemistry and Physiology - Part A: Molecular & Integrative Physiology
157, S46-S47.
Bebianno, M.J. &. Barreira L. A. (2009). Polycyclic aromatic hydrocarbons concentrations and biomarker responses in the clam Ruditapes decussatus transplanted in the Ria Formosa lagoon. Ecotoxicology and Environmental Safety 72, 1849-1860 (doi:10.1016/j.ecoenv.2009.03.016)
Cravo A., Lopes B., Serafim A., Company R., Barreira L., Gomes T.& Bebianno M. J.. (2009). A multibiomarker approach in Mytilus galloprovincialis to assess environmental quality. Journal of Environmental Monitoring 11, 1673-1686 (doi: 10.1039/b909846a).
Gomes T., Gonzalez-Rey M. & Bebianno M. J., 2009 Incidence of intersex in male clams Scrobicularia plana in the Guadiana Estuary (Portugal). Ecotoxicology 18, 1104-1109.
Maria, V. L., Santos, M. A. & Bebianno, M. J. (2009). Biomarkers of damage and protection in Mytilus galloprovincialis cross transplanted in Ria Formosa Lagoon (Portugal). Ecotoxicology, 18, 1018-1028 (DOI 10.1007/s10646-009-0361).
Serafim, A.& Bebianno M. J. (2009). Metallothionein role in the kinetic model of copper accumulation and elimination in the clam Ruditapes decussatus. Environmental Research 109(4): 390-399.
Chora S., McDonagh B., Sheehan D., Starita-Geribaldi M., Roméo M. and Bebianno M. J. (2008) Ubiquitination and carbonylation as markers of oxidative-stress in Ruditapes decussatus Marine Environmental Research 66, 95-97.
Bebianno, M.J., Lopes, B., Guerra, L., Hoarau, P., Ferreira, AM. (2007). Glutathione-S-transferases and cytochrome P450 activities in Mytilus galloprovincialis from the South coast of Portugal: effect of abiotic factors Environment International 33, 550-558.
Serafim, A.& M.J. Bebianno (2007).Involvement of MT in. Zn accumulation and elimination strategies in Ruditapes decussates. Archives of Environmental Contamination and Toxicology 52, 189–199.
Serafim, A.& M.J. Bebianno (2007).Kinetic model of cadmium accumulation and elimination and metallothionein response in Ruditapes decussatus. Environmental Toxicology and Chemistry, 26 (5), 960–969.
Coelho M. R., Langston W. J. & M. J. Bebianno (2006). Effect of TBT on Ruditapes decussatus juveniles. Chemosphere 63, 1499-1505.
Hoarau, P., Damiens, G., Roméo, M., Gnassia-Barelli, M., Bebianno, M.J. (2006). Cloning and expression of a GST-pi gene in Mytilus galloprovincialis. An attempt to use the GST-pi transcript as a biomarker of pollution. Comparative Biochemistry and Physiology C 143, 196-203. Bebianno, M. J., Hoarau P., Geret F.. Serafim, M.A, Gnassia-Barelli M., Roméo M., 2004.Biomarkers in Ruditapes sp.. Biomarkers 9, 305-330.
Geret F., A. Serafim & M. J. Bebianno, 2004. Does zinc produce reactive oxygen species in Ruditapes decussatus? Ecotoxicology and Environmental Safety57, 399-409.
Geret F., H. Manduzio, R. Company, F. Leboulenger, M. J. Bebianno & J.M. Danger, 2004. Molecular cloning of superoxide dismutase (Cu/Zn-SOD) from aquatic molluscs. Marine Environmental Research 58, 619-623. Smaoui-Damak, W., Hamza-Chaffai, A., Bebianno, M.J. & Amiard, J.C., 2004. Variation of metallothionein in gills of the clam Ruditapes decussatus from the gulf of Gabés (Tunísia). Comparative Biochemistry and Physiology C 139, 181-188.
Geret F., A. Serafim & M. J. Bebianno, 2003 Variation of antioxidant enzyme activities, metallothioneins and lipid peroxidation levels in Ruditapes decussatus. Ecotoxicoloy 12(5): 417-426.
Simes D. C., M. J. Bebianno & J. J. G. Moura, 2003. Isolation and characterisation of metallothionein from the clam Ruditapes decussatus. Aquatic Toxicology 63, 307-318.
Phone: 351 289 800923
e-mail. [email protected]
Contribution to the Project
WPs4 & 5 Protein expression profiles in mussels exposed to pharmaceuticals and to nanoparticles
WP6 The use bivalves in pollution biomonitoring. Effect of metals and endocrine disruptors on the stress response and reproduction.
WPs 11 & 12 Information, gathering and dissemination
Publications
Gomes T., Pinheiro, Cancio I., Pereira C.G., Cardoso C., Bebianno M.J. The effects of copper nanoparticles exposure in the mussel Mytilus galloprovincialis. Environmental Science and Technology (in press).
Company, R., Antúnez, O., Bebianno, M. J., Cajaraville, M. P., Torreblanca, A. (2011). 2-D difference gel electrophoresis approach to assess protein expression profiles in Bathymodiolus azoricus from Mid-Atlantic Ridge hydrothermal vents, Journal of Proteomics, (in press) ( doi:10.1016/j.jprot.2011.07.012).
Gonzalez-Rey, Maria; Bebianno, M. J.,. (2011). Non-steroidal anti-inflammatory drug (NSAID) ibuprofen distresses antioxidant defense system in mussel Mytilus galloprovincialis gills. Aquatic Toxicology 105, 264-269. (doi:10.1016/j.aquatox.2011.06.015 ).
Serafim A., Lopes B., Company R., Cravo A., Gomes T., Sousa V., Bebianno M.J. (2011). A multi-biomarker approach in cross-transplanted mussels Mytilus galloprovincialis. Ecotoxicology (DOI 10.1007/s10646-011-0737-7)
Maria V. L., Bebianno, M. J. 2011. Antioxidant and Lipid Peroxidation Responses in Mytilus galloprovincialis exposed to mixtures of Benzo(a)pyrene and Copper , Comparative Biochemistry and Physiology, Part C, 154, 56-63 ( doi:10.1016/j.cbpc.2011.02.004)
Company, R., Serafim, A., Lopes, B., Cravo, A, Kalman, J , Riba, I., Del Valls, A., Blasco, J., Delgado, J., Sarmiento, A.M., Nieto, J.M., Shepherd, T.J., Nowell, G.& Bebianno, M.J. (2011). Source and impact of lead contamination on δ-aminolevulinic acid dehydratase activity in several marine bivalve species along the Gulf of Cadiz. Aquatic Toxicology 10, 146-154. (doi:10.1016/j.aquatox.2010.09.012).
Chora, S., McDonagh, B., Sheehan, D., Starita-Geribaldi, M., Roméo, M., Bebianno, M. J. (2010). Ubiquitination and carbonylation of proteins in the clam Ruditapes decussatus, exposed to nonylphenol using redox proteomics. Chemosphere 81, 1212-1217. (doi:10.1016/j.chemosphere.2010.09.03).
Chora S., Starita-Geribaldi, M., Guigonis, J-M., Samson, M., Roméo M. & Bebianno M. J. (2009). Effect of Cd in the clam Ruditapes decussatus assessed by proteomics. Aquatic Toxicology 94, 300-308 (DOI: 10.1016/j.aquatox.2009.07.014).
Geret F., Gomes T., Marty P. & Bebianno M. J. (2010). Differential protein expression in Corbicula fluminea exposed to a mixture of pharmaceutical products. Comparative Biochemistry and Physiology - Part A: Molecular & Integrative Physiology
157, S46-S47.
Bebianno, M.J. &. Barreira L. A. (2009). Polycyclic aromatic hydrocarbons concentrations and biomarker responses in the clam Ruditapes decussatus transplanted in the Ria Formosa lagoon. Ecotoxicology and Environmental Safety 72, 1849-1860 (doi:10.1016/j.ecoenv.2009.03.016)
Cravo A., Lopes B., Serafim A., Company R., Barreira L., Gomes T.& Bebianno M. J.. (2009). A multibiomarker approach in Mytilus galloprovincialis to assess environmental quality. Journal of Environmental Monitoring 11, 1673-1686 (doi: 10.1039/b909846a).
Gomes T., Gonzalez-Rey M. & Bebianno M. J., 2009 Incidence of intersex in male clams Scrobicularia plana in the Guadiana Estuary (Portugal). Ecotoxicology 18, 1104-1109.
Maria, V. L., Santos, M. A. & Bebianno, M. J. (2009). Biomarkers of damage and protection in Mytilus galloprovincialis cross transplanted in Ria Formosa Lagoon (Portugal). Ecotoxicology, 18, 1018-1028 (DOI 10.1007/s10646-009-0361).
Serafim, A.& Bebianno M. J. (2009). Metallothionein role in the kinetic model of copper accumulation and elimination in the clam Ruditapes decussatus. Environmental Research 109(4): 390-399.
Chora S., McDonagh B., Sheehan D., Starita-Geribaldi M., Roméo M. and Bebianno M. J. (2008) Ubiquitination and carbonylation as markers of oxidative-stress in Ruditapes decussatus Marine Environmental Research 66, 95-97.
Bebianno, M.J., Lopes, B., Guerra, L., Hoarau, P., Ferreira, AM. (2007). Glutathione-S-transferases and cytochrome P450 activities in Mytilus galloprovincialis from the South coast of Portugal: effect of abiotic factors Environment International 33, 550-558.
Serafim, A.& M.J. Bebianno (2007).Involvement of MT in. Zn accumulation and elimination strategies in Ruditapes decussates. Archives of Environmental Contamination and Toxicology 52, 189–199.
Serafim, A.& M.J. Bebianno (2007).Kinetic model of cadmium accumulation and elimination and metallothionein response in Ruditapes decussatus. Environmental Toxicology and Chemistry, 26 (5), 960–969.
Coelho M. R., Langston W. J. & M. J. Bebianno (2006). Effect of TBT on Ruditapes decussatus juveniles. Chemosphere 63, 1499-1505.
Hoarau, P., Damiens, G., Roméo, M., Gnassia-Barelli, M., Bebianno, M.J. (2006). Cloning and expression of a GST-pi gene in Mytilus galloprovincialis. An attempt to use the GST-pi transcript as a biomarker of pollution. Comparative Biochemistry and Physiology C 143, 196-203. Bebianno, M. J., Hoarau P., Geret F.. Serafim, M.A, Gnassia-Barelli M., Roméo M., 2004.Biomarkers in Ruditapes sp.. Biomarkers 9, 305-330.
Geret F., A. Serafim & M. J. Bebianno, 2004. Does zinc produce reactive oxygen species in Ruditapes decussatus? Ecotoxicology and Environmental Safety57, 399-409.
Geret F., H. Manduzio, R. Company, F. Leboulenger, M. J. Bebianno & J.M. Danger, 2004. Molecular cloning of superoxide dismutase (Cu/Zn-SOD) from aquatic molluscs. Marine Environmental Research 58, 619-623. Smaoui-Damak, W., Hamza-Chaffai, A., Bebianno, M.J. & Amiard, J.C., 2004. Variation of metallothionein in gills of the clam Ruditapes decussatus from the gulf of Gabés (Tunísia). Comparative Biochemistry and Physiology C 139, 181-188.
Geret F., A. Serafim & M. J. Bebianno, 2003 Variation of antioxidant enzyme activities, metallothioneins and lipid peroxidation levels in Ruditapes decussatus. Ecotoxicoloy 12(5): 417-426.
Simes D. C., M. J. Bebianno & J. J. G. Moura, 2003. Isolation and characterisation of metallothionein from the clam Ruditapes decussatus. Aquatic Toxicology 63, 307-318.
Dr. Benoît Chenais
Université Le Mans (UM)
Benoît Chénais is Professor of genetics and cell biochemistry at the University of Maine – Le Mans since 2005. His main research topics include:
1) characterization and expression of stress response genes in marine invertebrates, and
2) characterization and functional studies of DNA transposable elements.
Previously visiting scientist at Lady Davis Institute for Medical Research, McGill University, Montréal, Canada (2002-2003) and assistant professor at University of Reims, France, at the School of Pharmacy (1994-2004), he has a greatly diversified experience in biochemical and molecular biology researches (see also http://perso.univ-lemans.fr/~bchenais/B_Chenais_e.html). Co-author of more than 30 publications, and editor of Open Journal of Genetics (http://www.scirp.org/journal/ojgen/ ).
Phone: +33 243 833 251
e-mail: [email protected]
PERSONAL CONTRIBUTION TO THE PROJECT
WP 6. The use of two bivalves, Ruditapes decussates and Cerastoderma glaucum, in pollution biomonitoring: Effect of metals and endocrine disruptors on the stress response and reproduction. Characterization and expression analysis of some biomarkers such as superoxide dismutase, metallothionein, etc. WP6 leader.
RELATED PUBLICATIONS
Ladhar-Chaabouni R, Hamza-Chaffai A, Hardivillier Y, Chénais B, Denis F.
Pilot study for genetic differentiation between two phenotypes of the Mediterranean population of C. glaucum and genetic discrimination between this population and others of C. glaucum and C. edule outside the Mediterranean.
Marine Ecology Evol. Persp. 2010, 31, 355-363.
Marchand J, Leignel V, Moreau B, Chénais B.
Characterization and sequence analysis of manganese 1 superoxide dismutases from Brachyura (Crustacea: Decapoda): particular emphasis for hydrothermal Bythograeidae versus littoral crabs.
Comp. Biochem. Physiol. Part B, 2009, 153, 191-199.
Leignel V, Marchand J, Moreau B, Chénais B.
Metallothionein genes from hydrothermal crabs (Bythograeidae, Decapoda): Characterization, sequence analysis and comparison with coastal crabs.
Comp. Biochem. Physiol., part C, 2008, 148, 6-13.
Leignel V, Cibois M, Moreau B, Chénais B.
Identification of new subgroup of HSP70 in Bythograeidae (hydrothermal crabs) and Xanthidae.
Gene, 396, 84-92, 2007.
1) characterization and expression of stress response genes in marine invertebrates, and
2) characterization and functional studies of DNA transposable elements.
Previously visiting scientist at Lady Davis Institute for Medical Research, McGill University, Montréal, Canada (2002-2003) and assistant professor at University of Reims, France, at the School of Pharmacy (1994-2004), he has a greatly diversified experience in biochemical and molecular biology researches (see also http://perso.univ-lemans.fr/~bchenais/B_Chenais_e.html). Co-author of more than 30 publications, and editor of Open Journal of Genetics (http://www.scirp.org/journal/ojgen/ ).
Phone: +33 243 833 251
e-mail: [email protected]
PERSONAL CONTRIBUTION TO THE PROJECT
WP 6. The use of two bivalves, Ruditapes decussates and Cerastoderma glaucum, in pollution biomonitoring: Effect of metals and endocrine disruptors on the stress response and reproduction. Characterization and expression analysis of some biomarkers such as superoxide dismutase, metallothionein, etc. WP6 leader.
RELATED PUBLICATIONS
Ladhar-Chaabouni R, Hamza-Chaffai A, Hardivillier Y, Chénais B, Denis F.
Pilot study for genetic differentiation between two phenotypes of the Mediterranean population of C. glaucum and genetic discrimination between this population and others of C. glaucum and C. edule outside the Mediterranean.
Marine Ecology Evol. Persp. 2010, 31, 355-363.
Marchand J, Leignel V, Moreau B, Chénais B.
Characterization and sequence analysis of manganese 1 superoxide dismutases from Brachyura (Crustacea: Decapoda): particular emphasis for hydrothermal Bythograeidae versus littoral crabs.
Comp. Biochem. Physiol. Part B, 2009, 153, 191-199.
Leignel V, Marchand J, Moreau B, Chénais B.
Metallothionein genes from hydrothermal crabs (Bythograeidae, Decapoda): Characterization, sequence analysis and comparison with coastal crabs.
Comp. Biochem. Physiol., part C, 2008, 148, 6-13.
Leignel V, Cibois M, Moreau B, Chénais B.
Identification of new subgroup of HSP70 in Bythograeidae (hydrothermal crabs) and Xanthidae.
Gene, 396, 84-92, 2007.
Dr. Justine Marchand
Université Le Mans (UM)
After a phD of the University of Brest obtained in 2006 and two years of contract in Brest and Le Mans, she has been recruited as an assistant Professor in the University of Maine in Le Mans in 2007 in the EA 2160 “Sea, Molecules, Health”Laboratory (Mer, Molecules, Santé). Her research area concerns Molecular Biology and Evolutionary Genetics. She explores the molecular processes of acclimation and adaptation of marine organisms living in particular environmental conditions (metals, endocrine disruptors, pesticides), through the characterization of stress response genes and their expression patterns by QPCR on models such as mollusks, crustaceans, fishes and microalgae.
Phone: +33 243 833 250
e-mail: [email protected]
PERSONAL CONTRIBUTION TO THE PROJECT
WP 6. The use of two bivalves, Ruditapes decussaues and Cerastoderma glaucum, in pollution biomonitoring: Effect of metals and endocrine disruptors on the stress response and reproduction. Characterization and expression analysis of some biomarkers such as superoxide dismutase, metallothionein, etc.
RELATED PUBLICATIONS
In press. Marchand J., Denis F. & Laroche J. « Evolutionary Toxicology and Transcriptomic Approaches ». In « Ecological Biomarkers: Indicators of Ecotoxicological Effects », Amiard-Triquet C. & Amiard J-C. Edition Taylor & Francis.
2010. Marchand J., Evrard E., Quiniou L., Laroche J. Genetic polymorphism and its potential relation to environmental stress in five populations of the European flounder Platichthys flesus, along the French Atlantic Coast. Marine Environmental Research, 70: 201-209.
2010.Evrard E., Marchand J., Théront M., Pichavant K., Durand G., Quiniou L., Laroche J. Impacts of mixtures of herbicides on molecular and physiological responses of the European flounderPlatichthys flesus. Comparative Biochemistry and Physiology Part C, 152 (3): 321-331.
2009. Leignel V., Marchand J.« Biomarkers overview and environmental applications » (Chapter 18). In “Impact, Monitoring and Management of Environmental Pollution ». Ahmed El Nemr editor, NOVA publisher.
2009. Marchand J., Leignel V., Moreau B., Chénais B. Characterization and sequence analysis of manganese superoxide dismutases from Brachyura (Crustacea: Decapoda) : Hydrothermal Bythograeidae versus littoral crabs. Comparative Biochemistry and Physiology Part B, 153: 191-199.
2008. Marchand J., Denis F.& Laroche J. « Modifications de la variabilité génétique et de l’expression de gènes ». Dans « Les Biomarqueurs dans l’évaluation de l’état écologique des milieux aquatiques », Amiard-Triquet C. & Amiard J-C. Edition TEC & DOC Lavoisier, 375 pages.
2008. Leignel V, Marchand J, Moreau B, Chénais B. Metallothionein genes from hydrothermal crabs (Bythograeidae, Decapoda): Characterization, sequence analysis and comparison with coastal crabs. Comparative Biochemistry and Physiology Part C, 148: 6-13.
2006. Marchand J., Tanguy, A., Charrier, G., Quiniou, L., Moraga, D. & Laroche, J. Molecular identification and expression study of differentially regulated
genes in the European flounder Platichthys flesus in response to pesticides exposure. Marine Biotechnology, 8 (3): 275-294.
2004. Marchand J., Quiniou, L., Riso, R., Thébaut, M.T. & Laroche, J. Physiological cost of tolerance to toxicants in the European flounder Platichthys flesus, along the French Atlantic Coast. Aquatic Toxicology, 70: 327-343.
2003. Marchand J., Tanguy, A., Quiniou, L., Laroche, J. & Moraga, D. Genetic and physiological responses of flounder (Platichthys flesus) populations to contamination in different estuaries from the Atlantic Coast. Marine Ecology Progress Series, 260: 273-284.
Phone: +33 243 833 250
e-mail: [email protected]
PERSONAL CONTRIBUTION TO THE PROJECT
WP 6. The use of two bivalves, Ruditapes decussaues and Cerastoderma glaucum, in pollution biomonitoring: Effect of metals and endocrine disruptors on the stress response and reproduction. Characterization and expression analysis of some biomarkers such as superoxide dismutase, metallothionein, etc.
RELATED PUBLICATIONS
In press. Marchand J., Denis F. & Laroche J. « Evolutionary Toxicology and Transcriptomic Approaches ». In « Ecological Biomarkers: Indicators of Ecotoxicological Effects », Amiard-Triquet C. & Amiard J-C. Edition Taylor & Francis.
2010. Marchand J., Evrard E., Quiniou L., Laroche J. Genetic polymorphism and its potential relation to environmental stress in five populations of the European flounder Platichthys flesus, along the French Atlantic Coast. Marine Environmental Research, 70: 201-209.
2010.Evrard E., Marchand J., Théront M., Pichavant K., Durand G., Quiniou L., Laroche J. Impacts of mixtures of herbicides on molecular and physiological responses of the European flounderPlatichthys flesus. Comparative Biochemistry and Physiology Part C, 152 (3): 321-331.
2009. Leignel V., Marchand J.« Biomarkers overview and environmental applications » (Chapter 18). In “Impact, Monitoring and Management of Environmental Pollution ». Ahmed El Nemr editor, NOVA publisher.
2009. Marchand J., Leignel V., Moreau B., Chénais B. Characterization and sequence analysis of manganese superoxide dismutases from Brachyura (Crustacea: Decapoda) : Hydrothermal Bythograeidae versus littoral crabs. Comparative Biochemistry and Physiology Part B, 153: 191-199.
2008. Marchand J., Denis F.& Laroche J. « Modifications de la variabilité génétique et de l’expression de gènes ». Dans « Les Biomarqueurs dans l’évaluation de l’état écologique des milieux aquatiques », Amiard-Triquet C. & Amiard J-C. Edition TEC & DOC Lavoisier, 375 pages.
2008. Leignel V, Marchand J, Moreau B, Chénais B. Metallothionein genes from hydrothermal crabs (Bythograeidae, Decapoda): Characterization, sequence analysis and comparison with coastal crabs. Comparative Biochemistry and Physiology Part C, 148: 6-13.
2006. Marchand J., Tanguy, A., Charrier, G., Quiniou, L., Moraga, D. & Laroche, J. Molecular identification and expression study of differentially regulated
genes in the European flounder Platichthys flesus in response to pesticides exposure. Marine Biotechnology, 8 (3): 275-294.
2004. Marchand J., Quiniou, L., Riso, R., Thébaut, M.T. & Laroche, J. Physiological cost of tolerance to toxicants in the European flounder Platichthys flesus, along the French Atlantic Coast. Aquatic Toxicology, 70: 327-343.
2003. Marchand J., Tanguy, A., Quiniou, L., Laroche, J. & Moraga, D. Genetic and physiological responses of flounder (Platichthys flesus) populations to contamination in different estuaries from the Atlantic Coast. Marine Ecology Progress Series, 260: 273-284.
Dr Amparo Torreblanca
Universidad de Valencia (UVEG)
Dr Amparo Torreblanca is a full professor at the University of Valencia, PhD in Biology 1989, post-doc researcher in Dep. of Biochemistry, The Hospital for Sick Children, Toronto, Canada in the field of protein-metal interaction(1989-1990). Since 1993 she has been working at the University of Valencia. She is specialized in Environmental Physiology and leads the research group “Ecophysiology of aquatic animals and biomarkers of global change”. The group focuses on the effects of environmetal contamination on aquatic animals, with the search for physiological and biochemical biomarkers of pollution. The group has optimized the separation of proteins trough Differential in Gel Electrophoresis (DIGE) in heart, enterocytes and liver of sea bream and has characterized the ecophysiology of populations of the zebra mussel (Dreissena polymorpha) through their protein profiles. She has taken part in international postgraduated courses and is the Coordinator of a Doctorate Programme in Environmental Contamination, Toxicology and Health at the University of Valencia.
Phone: +34 963543378
e-mail: [email protected]
Contribution to the Project
WP 3 Protein expression profiles in copepods.
WP 8 Expression analysis in fish.
WP 9 Interspecies variation in gene expression in oysters.
WPs 11 & 12 Information, gathering and dissemination.
RELATED PUBLICATIONS:
Torreblanca A, Del Ramo J, Sarkar B. Cadmium effect on zinc metabolism in human trophoblast cells: involvement of cadmium-induced metallothionein, Toxicology, A 72, 2, 167-174. 1992
Del Ramo, J;. Martínez, M; Pastor, A; Torreblanca, A y Diaz-Mayans, J. Effect of cadmium preexposure in cadmium accumulation by brine shrimp Artemia. Involvement of low molecular weight cadmium binding ligands. Marine Environmental Research 35: 29-33. 1993.
Torreblanca, A; Del Ramo, J y Díaz Mayans, J. Effect of subletal exposure to mercury in the biochemical composition of hepatopancreas in Procambarus clarkii during the recovery after starvation. Marine Environmental Research 35: 73-77. 1993.
Rubio, MR; Tineo, P; Diaz, J y Torreblanca, A.Effects of cadmium exposure on the ultrastructure of hepatopancreatic cells of Thais haemastoma. Marine Environmental Research 35: 47-51. 1993.
Martinez, M; Torreblanca, A; Del Ramo, J; Pastor, A y Díaz-Mayans, J. Cadmium induced metallothionein in hepatopancreas of Procambarus clarkii: Quantification by a silver-saturation method. Comp. Biochem. Physiol. C. 105: 263-267. 1993.
Martínez M.; Torreblanca A.; Del Ramo J. y Díaz-Mayans J. Effects of sublethal exposure to lead on levels of energetic compounds in Procambarus clarkii (Girard, 1852). Bull. Environ. Contam. Toxicol. 52 (5) 729-733. 1994.
Del Ramo, J; Torreblanca, A.; Martínez, M., Pastor, A. y Díaz-Mayans, J. Quantification of cadmium induced metallothionein in crustaceans by the silver-saturation method. Mar Environ Res. 39: 121-125. 1995.
Torreblanca,A; del Ramo,J; Martínez, M.; Pastor A; J. Díaz-Mayans. Effects of 20-hydroxyecdysone administration on zinc and copper levels in Procambarus clarkii. Comp. Biochem. Physiol. 113C (2): 201-204. 1996.
Martínez M.; Del Ramo, J.; Torreblanca, A.; Pastor, A.; y Díaz-Mayans J. Cadmium toxicity, accumulation, and metallothionein induction in Echinogammarus echinosetosus. Journal of Environmental Science and Health. (Part A). A31:1605-1617. 1996.
Sarabia R.; Torreblanca, A; J. del Ramo; J. Díaz Mayans. Effects of low mercury concentration exposure on hatching, growth and survival in the Artemiastrain La Mata parthenogenetic diploid. Comp. Biochem. Physiol 120(A): 93-97. 1998
Martínez M.; Del Ramo J.; Torreblanca A.; Díaz-Mayans J. Effect of cadmium exposure on zinc levels in Artemia. Aquaculture 172: 315-325. 1999.
Porte, C.; Sole, M.; Borghi, V.; Martinez, M.; Chamorro, J.; Torreblanca, A.; Ortiz, M.; Orbea, A.; Soto, M.; Cajaraville, MP. Chemical,
biochemical and cellular responses in the digestive gland of the mussel Mytilus galloprovincialisfrom the spanish mediterranean coast.Biomarkers6(5):
335-350. 2001. DOI: 10.1080/13547500110044771
Sarabia R.; Del Ramo J, Varó I, Díaz Mayans, J.; Torreblanca, A. Comparing the acute response to cadmium toxicity of nauplii from different populations of Artemia. Environmental Toxicology and Chemistry 21(2): 437-444. 2002.
Sarabia, R., Del Ramo, J., Díaz-Mayans, J., Torreblanca, A. Developmental and reproductive effects of low cadmium concentration on Artemia
parthenogenetica. Journal of Environmental Science and Health A38(6) 1065-1071. 2003.
Lavado, R.; Ureña, R.; Martín, R.; Torreblanca, A.; del Ramo, J.; Raldúa, D.; Porte, C. The combined use of chemical and biochemical markers to
assess water quality along the Ebro River . Environmental Pollution 139(2): 330-9. 2006. DOI: 10.1016/j.envpol.2005.05.003
Sarabia, R.; Varó, I.; Amat, F; Pastor, A.; del Ramo, J; Díaz-Mayans, J. and Torreblanca, A. Comparative toxicokinetics of cadmium in Artemia.
Arch Environ Contam Toxicol 50(1): 111-20. 2006. DOI: 10.1007/s00244-005-7026-5
Ureña, R, Peri, S, del Ramo,J, Torreblanca, A. Metal and metallothionein content in tissues from wild and farmed Anguilla anguilla at commercial
size.Environ Int, 2007. 33(4): p. 532-9. DOI: 10.1016/j.envint.2006.10.007
Varó, I.; Nunes, B.; Amat, F.; Torreblanca, A.; Guillerminho, L; Navarro, J.C. Effect of sublethal concentrations of copper sulphate on seabream Sparus aurata fingerlings. Aquat. Linving Resour. 2007. vol 20: 265-270.DOI: 10.1051/alr:2007039
Sarabia, R.; Del Ramo, J.; Varó, I.; Díaz-Mayans, J; Torreblanca, A. Sublethal zinc exposure has a detrimental effect on reproductive performance but not on the cyst hatching success of Artemia parthenogenetica. Sci. Total Environ Sci. Total Environ., 389: 48-52. 2008. DOI: 10.1016/j.scitotenv.2008.03.002
Ureña, R.; Bebianno M. J.; del Ramo, J.; Torreblanca, A (2008) Metallothionein in the freshwater gastropod Melanopsis dufouri chronically exposed to cadmium. Ecotoxicology and environmental safety Ecotoxicology and Environmental Safety, 73 (5) 779-787. 2010. DOI: 10.1016/j.ecoenv.2010.02.010
Varo, I.; Rigos, G.; Navarro, J.C.; Del Ramo, J.J.; Calduch-Giner, J.; Hernandez, A.; Pertusa, J.; Torreblanca, A.Effect of ivermectin on the liver of gilthead sea bream Sparus aurata: a proteomic approach. Chemosphere.80 570 -577 2010. DOI: 10.1016/j.chemosphere.2010.04.030
Company, R.; Antúnez, O.; João Bebianno, M.; Cajaraville, M.P.; Torreblanca, A. 2-D Difference gel electrophoresis approach to assess protein expression profiles in Bathymodiolus azoricus from mid-atlantic ridge hydrothermal vents. Journal of Proteomics. Volume 74 (12) 2011, 2909-2919. DOI:
10.1016/j.jprot.2011.07.012
Guinot, D.; Ureña, R. Pastor, A.; Varó, I; del Ramo, J.; Torreblanca, A. Long-term effect of temperature on bioaccumulation of dietary metals and metallothionein induction in Sparus aurata Chemosphere,87, (11) 2012, 1215-1221. DOI:10.1016/j.chemosphere.2012.01.020
Cotou, E; Henrya, M; Zerib, C; Rigos, G; Torreblanca, A; Catsikib; V.A. Short-term exposure of the European sea bass Dicentrarchus labrax to copper-based antifouling treated nets: copper bioavailability and biomarkers responses. Chemophere (in press) http://dx.doi.org/10.1016/j.chemosphere.2012.05.075,
Phone: +34 963543378
e-mail: [email protected]
Contribution to the Project
WP 3 Protein expression profiles in copepods.
WP 8 Expression analysis in fish.
WP 9 Interspecies variation in gene expression in oysters.
WPs 11 & 12 Information, gathering and dissemination.
RELATED PUBLICATIONS:
Torreblanca A, Del Ramo J, Sarkar B. Cadmium effect on zinc metabolism in human trophoblast cells: involvement of cadmium-induced metallothionein, Toxicology, A 72, 2, 167-174. 1992
Del Ramo, J;. Martínez, M; Pastor, A; Torreblanca, A y Diaz-Mayans, J. Effect of cadmium preexposure in cadmium accumulation by brine shrimp Artemia. Involvement of low molecular weight cadmium binding ligands. Marine Environmental Research 35: 29-33. 1993.
Torreblanca, A; Del Ramo, J y Díaz Mayans, J. Effect of subletal exposure to mercury in the biochemical composition of hepatopancreas in Procambarus clarkii during the recovery after starvation. Marine Environmental Research 35: 73-77. 1993.
Rubio, MR; Tineo, P; Diaz, J y Torreblanca, A.Effects of cadmium exposure on the ultrastructure of hepatopancreatic cells of Thais haemastoma. Marine Environmental Research 35: 47-51. 1993.
Martinez, M; Torreblanca, A; Del Ramo, J; Pastor, A y Díaz-Mayans, J. Cadmium induced metallothionein in hepatopancreas of Procambarus clarkii: Quantification by a silver-saturation method. Comp. Biochem. Physiol. C. 105: 263-267. 1993.
Martínez M.; Torreblanca A.; Del Ramo J. y Díaz-Mayans J. Effects of sublethal exposure to lead on levels of energetic compounds in Procambarus clarkii (Girard, 1852). Bull. Environ. Contam. Toxicol. 52 (5) 729-733. 1994.
Del Ramo, J; Torreblanca, A.; Martínez, M., Pastor, A. y Díaz-Mayans, J. Quantification of cadmium induced metallothionein in crustaceans by the silver-saturation method. Mar Environ Res. 39: 121-125. 1995.
Torreblanca,A; del Ramo,J; Martínez, M.; Pastor A; J. Díaz-Mayans. Effects of 20-hydroxyecdysone administration on zinc and copper levels in Procambarus clarkii. Comp. Biochem. Physiol. 113C (2): 201-204. 1996.
Martínez M.; Del Ramo, J.; Torreblanca, A.; Pastor, A.; y Díaz-Mayans J. Cadmium toxicity, accumulation, and metallothionein induction in Echinogammarus echinosetosus. Journal of Environmental Science and Health. (Part A). A31:1605-1617. 1996.
Sarabia R.; Torreblanca, A; J. del Ramo; J. Díaz Mayans. Effects of low mercury concentration exposure on hatching, growth and survival in the Artemiastrain La Mata parthenogenetic diploid. Comp. Biochem. Physiol 120(A): 93-97. 1998
Martínez M.; Del Ramo J.; Torreblanca A.; Díaz-Mayans J. Effect of cadmium exposure on zinc levels in Artemia. Aquaculture 172: 315-325. 1999.
Porte, C.; Sole, M.; Borghi, V.; Martinez, M.; Chamorro, J.; Torreblanca, A.; Ortiz, M.; Orbea, A.; Soto, M.; Cajaraville, MP. Chemical,
biochemical and cellular responses in the digestive gland of the mussel Mytilus galloprovincialisfrom the spanish mediterranean coast.Biomarkers6(5):
335-350. 2001. DOI: 10.1080/13547500110044771
Sarabia R.; Del Ramo J, Varó I, Díaz Mayans, J.; Torreblanca, A. Comparing the acute response to cadmium toxicity of nauplii from different populations of Artemia. Environmental Toxicology and Chemistry 21(2): 437-444. 2002.
Sarabia, R., Del Ramo, J., Díaz-Mayans, J., Torreblanca, A. Developmental and reproductive effects of low cadmium concentration on Artemia
parthenogenetica. Journal of Environmental Science and Health A38(6) 1065-1071. 2003.
Lavado, R.; Ureña, R.; Martín, R.; Torreblanca, A.; del Ramo, J.; Raldúa, D.; Porte, C. The combined use of chemical and biochemical markers to
assess water quality along the Ebro River . Environmental Pollution 139(2): 330-9. 2006. DOI: 10.1016/j.envpol.2005.05.003
Sarabia, R.; Varó, I.; Amat, F; Pastor, A.; del Ramo, J; Díaz-Mayans, J. and Torreblanca, A. Comparative toxicokinetics of cadmium in Artemia.
Arch Environ Contam Toxicol 50(1): 111-20. 2006. DOI: 10.1007/s00244-005-7026-5
Ureña, R, Peri, S, del Ramo,J, Torreblanca, A. Metal and metallothionein content in tissues from wild and farmed Anguilla anguilla at commercial
size.Environ Int, 2007. 33(4): p. 532-9. DOI: 10.1016/j.envint.2006.10.007
Varó, I.; Nunes, B.; Amat, F.; Torreblanca, A.; Guillerminho, L; Navarro, J.C. Effect of sublethal concentrations of copper sulphate on seabream Sparus aurata fingerlings. Aquat. Linving Resour. 2007. vol 20: 265-270.DOI: 10.1051/alr:2007039
Sarabia, R.; Del Ramo, J.; Varó, I.; Díaz-Mayans, J; Torreblanca, A. Sublethal zinc exposure has a detrimental effect on reproductive performance but not on the cyst hatching success of Artemia parthenogenetica. Sci. Total Environ Sci. Total Environ., 389: 48-52. 2008. DOI: 10.1016/j.scitotenv.2008.03.002
Ureña, R.; Bebianno M. J.; del Ramo, J.; Torreblanca, A (2008) Metallothionein in the freshwater gastropod Melanopsis dufouri chronically exposed to cadmium. Ecotoxicology and environmental safety Ecotoxicology and Environmental Safety, 73 (5) 779-787. 2010. DOI: 10.1016/j.ecoenv.2010.02.010
Varo, I.; Rigos, G.; Navarro, J.C.; Del Ramo, J.J.; Calduch-Giner, J.; Hernandez, A.; Pertusa, J.; Torreblanca, A.Effect of ivermectin on the liver of gilthead sea bream Sparus aurata: a proteomic approach. Chemosphere.80 570 -577 2010. DOI: 10.1016/j.chemosphere.2010.04.030
Company, R.; Antúnez, O.; João Bebianno, M.; Cajaraville, M.P.; Torreblanca, A. 2-D Difference gel electrophoresis approach to assess protein expression profiles in Bathymodiolus azoricus from mid-atlantic ridge hydrothermal vents. Journal of Proteomics. Volume 74 (12) 2011, 2909-2919. DOI:
10.1016/j.jprot.2011.07.012
Guinot, D.; Ureña, R. Pastor, A.; Varó, I; del Ramo, J.; Torreblanca, A. Long-term effect of temperature on bioaccumulation of dietary metals and metallothionein induction in Sparus aurata Chemosphere,87, (11) 2012, 1215-1221. DOI:10.1016/j.chemosphere.2012.01.020
Cotou, E; Henrya, M; Zerib, C; Rigos, G; Torreblanca, A; Catsikib; V.A. Short-term exposure of the European sea bass Dicentrarchus labrax to copper-based antifouling treated nets: copper bioavailability and biomarkers responses. Chemophere (in press) http://dx.doi.org/10.1016/j.chemosphere.2012.05.075,
Dr. Jun Yu
Beijing Institute of Genomics, Chinese Academy of Sciences (BIG)
Dr. Jun Yu is currently a professor and Associate Director of Beijing Institute of Genomics (BIG), Chinese Academy of Sciences (CAS). He has joint appointments and supervises graduate students at the Institute of Computing Technology and Zhejiang University. Dr. Yu obtained his B.S. degree in biochemistry from Jilin University in 1983 and Ph.D. degree in
biomedical sciences from New York University Medical School in 1990. He had served as a Research Assistant Professor at NYU since 1990 until he joined University of Washington Genome Center in 1993. Dr. Yu's primary research interests include genome biology and bioinformatics.
Phone: 010-80488703
E-mail: [email protected]
Contribution to the Project:
Wp 2: Evaluation of the harpacticoid copepod Tisbe battagliai as model organism for the evaluation of low level environmental contamination by pharmaceuticals.
Wp 7: Development of molecular and physiological biomarkers for metals in estuarine waters and sediments using the benthic amphipod Melita plumulosa.
Publications (last 5 years):
Dapeng Wang, Yan Xia, and Jun Yu. (2012) Multi-level compositional dynamics along human gene transcription start. In preparation.
Dapeng Wang, Yao Su, Hongxing Le and Jun Yu‡. (2012).Transposon-derived and satellite-derived repetitive sequences play distinct roles in the intron size expansion among mammalian genomes. In preparation
Hao Wu, Lin-Lin Pan, Zhang Zhang, Song-Nian Hu, Jun Yu*. (2012). Evolutionary scenario of bacterial DNA polymerase III α subunits and implications for bacterial evolution. In preparation.
Wei Xu, Chengqi Xin, Qiang Lin, Feng Ding, Jianing Geng, Yaping Chen, JunYu‡, Peng Cui and Songnian Hu. (2012). The most active transcriptome is attributable to adolescence in the postnatal development of the mouse cerebrum. In preparation.
Hangxiao Zhang, Qibin Luo, Jing Sun, Fei Liu, Gang Wu, Jun Yu‡, Weiwei Wang (2012) A comparative analysis on mitochondrial genomes of major Artemia species in China: assessing the effect of high plateau adaptation. In preparation.
Miguel A. Esteban, Lili Hao, Feng Li,et al. (2012). Combined Single Base Resolution-Methylome and RNA-Sequencing Maps to Distinguish between Human Embryonic and Induced Pluripotent Stem Cells. Submitted.
Yu Kang, Lufeng Ren, Jun Yu, and Zhancheng Gao. (2012) Homeostasis of the Human Pharyngeal Microbiome May Play an Active Role in Protecting Lower Respiratory Tract Infections. In preparation.
Gang Wu, Jiang Zhu, Fuhong He, Weiwei Wang, Songnian Hu and Jun Yu‡. (2012) Genome Parameters of Mammalian Circadian and Non-circadian Genes. Submitted to PLoS One.
Shangang Jia, Xiaowei Zhang, Guangyu Zhang, et al., Jun Yu‡. (2012). The intestinal metagenome of red palm weevil (Rhynchophorus ferrugineus). Submitted to IMSB.
Lina Ma, Linghu Nie, Bing Zhang, et al., Jun Yu‡. (2012) A RNA-seq-based gene expression profiling of radiation-induced tumorigenic mammary epithelial cells. Submitted to PLoS One.
Zhenqing Ye, Ke Zhang, Songnian Hu,Jun Yu‡. (2012) A new definition of modularity for community detection in complex networks. In press.
Tongwu Zhang, Songnian Hu, Xiaowei Zhang, Ibrahim S. Al-Mssallem and Jun Yu‡. (2012) The complete chloroplast and mitochondrial genomes of Hassawi rice (Oryza sativa L.) and its hybrid in Saudi Arabia: genome variation and rearrangement and origins. Submitted to PLoS One.
Tongwu Zhang, Yingfeng Luo, Yaping Chen, Xiaonuan Li, Songnian Hu, and Jun Yu‡. (2012). BIGRAS: a genome assembly tool for pyrosequencing-based re-sequencing projects. In press.
Hao Wu, Hong-zhu Qu, Zhang Zhang, Song-nian Hu, and Jun Yu‡. Strand-biased gene distribution (SGD) and nucleotide composition (SNC) in Eubacteria. GBP in press.
Weili Liang, Yongbing Zhao, Chunxia Chen, Xiaoying Cui, Jun Yu, Jingfa Xiao and Biao Kan. (2012). Pan-genomic analysis provides insights into the genomic variation and evolution of Salmonella Paratyphi A. PLoS One in press.
Lei Wang, Xiaowei Zhang, Linlin Pan, Wanfei Liu, Guangyu Zhang, Yuxin Yin, An Yin, Shangang Jia, Xiaoguang Yu, Gaoyuan Sun, Songnian Hu, Ibrahim S. Al-Mssallem, Jun Yu‡. (2012). A Large-scale Gene Discovery for the Red Palm Weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae).
Insect Science in press.
Yu Kang, Jun Yu, Zhancheng Gao. (2012) Etiologic Diagnosis of Lower Respiratory Tract Bacterial Infections Using Sputum Samples and Quantitative Loop-mediated Isothermal Amplification. PLoS One. In press.
Guangyu Zhang, Linlin Pan, Yuxin Yin, Wanfei Liu, Dawei Huang, Tongwu Zhang, Lei Wang, Chengqi Xin, Gaoyuan Sun, Mohammed M. Ba Abdullah, Xiaowei Zhang, Songnian Hu, Ibrahim S. Al-Mssallem, Jun Yu‡. (2012) Large-scale collection and annotation of gene models for date palm (Phoenix dactylifera, L.) Plant Molecular Biology, in press.
Peng Cui, Feng Ding, WanFei Liu, Songnian Hu and Jun Yu‡. (2012) The novel role of H3K4 trimethylation in regulating antisense transcription. GBP in
press.
Jun Yu. (2012). Life in Two Tracks. GPB in press.
Jun Yu. (2012). Challenges to the common dogma. GBP in press.
Peng Cui, Wanfei Liu, Qiang Lin, Feng Ding, Songnian Hu, Jun Yu‡. (2012). Comparative study of chromatin state between mouse cerebrum and testis. GPB in press.
Yan Lu, Xingang Li, Min Wang, Xin Li, Feng Zhang, Yun Li, Meng Zhang, Yuwei Da, Jun Yu‡, Jianping Jia. (2012) A Novel Autosomal Dominant Inclusion Body Myopathy Linked to 7q22.1-31.1. PLoS One. In press.
Yu Kang, Rui Deng, Can Wang,et al., (2012) Etiologic Diagnosis of Lower Respiratory Tract Bacterial Infections Using Sputum Samples and Quantitative Loop-Mediated Isothermal Amplification. PLoS One 7(6): e38743. doi:10.1371/journal.pone.0038743
Dongyu Zhao, Jiayan Wu, Yuanyuan Zhou, Wei Gong, Jingfa Xiao, Jun Yu‡. (2012) WikiCell: a unified resource platform for human transcriptomics research. OMICS: A Journal of Integrative Biology 16(6): 357-362. doi:10.1089/omi.2011.0139.
Mingliang Gu, Xiaoqun Dong, Xuezhi Zhang, XUmin Wang, Yue Qi, Jun Yu, Wenquan Niu. (2012) Strong Association between Two Polymorphisms on 15q25.1 and Lung Cancer Risk: A Meta-Analysis. PLoS One 7(6): e37970. doi:10.1371/journal.pone.0037970.
Chao Jiang, Yuan Yuan, Guiming Liu, Luqi Huang, Xumin Wang, Jun Yu, Min Chen. (2012) Analysis of EST-SSR distribution and development of EST-SSR markers in Lonicera Japonica. Acta Pharmaciutica Sinica 47: 803-810. (in Chinese)
Ping-Yi Li, Bin-Bin Xie, Xi-Ying Zhang, Qi-Long Qin, Hong-Yue Dang, Xu-Min Wang, Xiu-Lan Chen, Jun Yu and Yu-Zhong Zhang. (2012) Genetic structure of three fosmid-fragments encoding 16S rRNA genes of the Miscellaneous Crenarchaeotic Group (MCG): implications for physiology and evolution of marine sedimentary archaea. Environmental Microbiology 2:14.
Yuan Yuan, Lipu Song, Minghui Li, Guiming Liu, Yanan Chu, Luyu Ma, Yuanyuan Zhou, Xiao Wang, Wei Gao, Shuangshuang Qin, Jun Yu, Xumin Wang and Luqi Huang. (2012). Genetic Variation and Metabolic Pathway Intricacy Govern the Active Compound Content and Quality of the Chinese Medicinal Plant Lonicera japonica. BMC Genomics 13:195. doi:10.1186/1471-2164-13-195
Yongjun Fang, Hao Wu, Meng Yang, Tongwu Zhang, Linlin Pan, Quanzheng Yun, Xiaoguang Yu, Xiaowei Zhang, Songnian Hu, Ibrahim Al-Mssalem, and Jun Yu‡.A Complete Sequence and Transcriptomic Analysis of Date Palm (Phoenix dactylifera L.) Mitochondrial Genome. PLoS One 7(5): e37164.
doi:10.1371/journal.pone.0037164.
Yimei Cai, Qing Zhou, Caixia Yu, Xumin Wang, Songnian Hu, Jun Yu‡, Xiaomin Yu. (2012) Transposable-Element Associated Small RNAs in Bombyx mori Genome. PLoS One 7(5): e36599. doi:10.1371/journal.pone.0036599
Yan Ge, Jiayan Wu, Ming Yang, Jingfa Xiao, Jun Yu‡. (2012) Molecular dynamics study of the different binding mode between the drug resistant
Streptococcus suis R61 and non-resistant A7 PBP protein and the cefuroxime. PLoS One 7(4): e35941. doi:10.1371/journal.pone.0035941.
Yang Liu, Bin Wang, Peng Cui, Libo Li, Jia-Yu Xue, Jun Yu, and Yin-Long Qiu. (2012). The mitochondrial genome of the lycophyte Huperzia squarrosa: the most archaic form in vascular plants. PLoS One 7(4): e35168.
Zhang Zhang, Jun Li, Peng Cui, Feng Ding, Ang Li, Jeffrey P. Townsend, Jun Yu‡. (2012).Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance.BMC Bioinformatics 13:43.
Peng Cui, Feng Ding, Lingfang Zhang, Songnian Hu and Jun Yu‡. (2012) Replication and transcription contribute differently in mutation rates of human genome. Geno Proteo & Bioinfo 10(1): 4–10.
Peng Cui, Qiang Lin, Feng Ding, Songnian Hu and Jun Yu‡. (2012) Transcript-centric mutations in human genomes. Geno Proteo & Bioinfo 10(1): 11–22.
Yuxin Yin, Xiaowei Zhang,Yongjun Fang, Linlin Pan, Gaoyuan Sun, Chengqi Xin, Mohammed M. Ba Abdullah, Xiaoguang Yu, Songnian Hu, Ibrahim S. Al-Mssallem, Jun Yu‡. (2012). High-throughput Sequencing-based Gene Profiling on Multi-staged Fruit Development of Date Palm (Phoenix dactylifera, L.). Plant Molecular Biology 78(6):617–626.
Tongwu Zhang, Yongjun Fan, Xin Deng, Xumin Wang, Songnian Hu, Xiaowei Zhang, and Jun Yu‡. (2012) The Complete Chloroplast and Mitochondrial Genome Sequences of resurrection plant Boea hygrometrica: Insights into the Evolution of Plant Organellar genomes. PLoS One 7(1): e30531. doi:10.1371/journal.pone.0030531.
Hao Wu, Zhang Zhang, Songnian Hu, Jun Yu‡. (2012) On the Molecular Mechanism of GC Content Variation among Eubacterial Genomes. Biology Direct 7:2 doi:10.1186/1745-6150-7-2.
Qian Zhao, Jingfa Xiao, Jun Yu.‡(2012) Functional and Evolutionary Analyses of Small Proteins from eight Representative Eukaryotes. PIBB39: 359–367doi:10.1016/j.cell.2011.10.017.
Qiang Lin,Peng Cui, Feng Ding, Songnian Hu and Jun Yu‡. (2011). Replication-Associated Mutational Pressure (RMP) Governs Strand-biased Compositional Asymmetry (SCA) and Gene Organization in Animal Mitochondrial Genomes. Current Genomics 13:28–36.
Yongbing Zhao, Jiayan Wu, Junhui Yang, Shixiang Sun, Jingfa Xiao, and Jun Yu‡. (2011). PGAP: Pan-Genomes Analysis Pipeline. Bioinformatics.
28(3): 416-418.
Wei He, Xin Li, Jialiang Chen, Ling Xu, Feng Zhang, Qiushi Dai, Hao Cui, Duen-Mei Wang, Jun Yu, Songnian Hu, Shan Lu. (2011) Genetic linkage analyses and Cx50 mutation detection in a large multiplex Chinese family with hereditary nuclear cataract. Ophthalmic Genet, 32(1):48–53.
Wanfei Liu, Yuhui Zhao, Peng Cui, Qiang Lin, Feng Ding, Chengqi Xin, Xinyu Tan, Shuhui Song, Jun Yu‡, Songnian Hu. (2011) Thousands of novel transcripts identified in mouse cerebrum, testis, and ES cells based on ribo-minus RNA sequencing.Frontier in Genetics 2:93.
Dapeng Wang, Yubin Zhang, Zhonghua Fan, Guiming Liu and Jun Yu‡. (2011). LCGbase: A Comprehensive Database for Lineage-based Co-regulated Genes. Evolutionary Bioinformatics 2012:8 39–46.
Tongwu Zhang, Xiaowei Zhang, Songnian Hu, Jun Yu‡. (2011)An efficient procedure for organellar genome assembly using whole genome data from 454 GS FLX sequencing platform.Plant Methods 7:38.
Ma Lina, Chen Kaifu, Meng Qingshu, Liu Qingyou, Tang Petrus, Hu Songnian, Yu Jun‡. (2011) An evolutionary analysis of trypanosomatid GP63 proteases. Parasitology Research 109:1075–1084.
Yongjun Fang, Zhaolong Li, Jiucheng Liu, Changlong Shu, Xumin Wang, Xiaowei Zhang, Xiaoguang Yu, Duojun Zhao, Guiming Liu, Songnian Hu, Jie Zhang, Ibrahim Al-Mssalleme, and Jun Yu‡. (2011) A Pangenomic Study of Bacillus thuringiensis. Journal of Genetics and Genomics 38:567–576.
Lina Ma, Yanyan Huang, Wangyu Zhu, Fang Zeng, Yongkui Zhang, Xiaoguang Liu, and Jun Yu‡. (2012). An Integrated Analysis of miRNA and mRNA Expressions in Non-small Cell Lung Cancers. PLoS One 6(10): e26502. doi:10.1371/journal.pone.0026502.
Gang Wu, Hangxiao Zhang, Jing Sun, Fei Liu, Xiaomeng Ge, Weihua Chen, Jun Yu‡and Weiwei Wang. (2011) Late embryogenesis abundant (LEA) genes activated in Artemia franciscana post-diapause embryos subjected to water stress. Com. Biochem. Physiol. B.160:32-39.
Anding Zhang, Ming Yang, Pan Hu, Jiayan Wu, Bo Che , Yafeng Hua, Jun Yu, Huanchun Chen, Jingfa Xiao and Meilin Jin. (2011). Comparative Genomic Analysis of Streptococcus suis reveals significant genomic diversity among different serotypes. BMC Genomics 12:523.
Lina Yuan, Lufeng Ren, Yuntao Li, Weijing Han, Yong Yu, Yanna Chu, Guiming Liu, Dan Yu, Mingjing Teng, Liang Wang, Xumin Wang, Xiaoguang Zhou, Yude Yu and Jun Yu‡. (2011). A Complete Genome Assembly of Glaciecola mesophila sp. nov. Sequenced Using a BIGIS-4 sequencer system. Science in China Series C Life Sciences 54 (9): 835-840.
Peng Cui, Qiang Lin, Zhang L, Feng Ding, Lingfang Zhang, Feng Ding, Chengqi Xin, Daoyong Zhang, Fanglin Sun, Songnian Hu, Jun Yu‡. (2011) The Disequilibrium of Nucleosomes Distribution along Chromosomes Plays a Functional and Evolutionarily Role in Regulating Gene Expression. PLoS One 6(8): e23219.
Zongjun Du, Zhewen Zhang, Tingting Miao, Jiayan Wu, Guoqiang Lü, Jun Yu, Jingfa Xiao, and Guanjun Chen. (2011). Draft Genome Sequence of a Novel Agar-Digesting Marine Bacterium HQM9. Journal of Bacteriology 193:4557–4558.
Hu P, Yang M, Zhang A, Wu J, Chen B, Hua Y, Yu J, Chen H, Xiao J, Jin M. (2011) Complete Genome Sequence ofStreptococcus suis Serotype 3 Strain ST3. Journal of Bacteriology 193:3428–3429.
Fei Liu, Hangxiao Zhang, Gang Wu, Jing Sun, Lili Hao, Xiaomeng Ge, Jun Yu‡, Weiwei Wang. (2011) Sequence variation and expression analysis of seed dormancy- and germination-associated ABA- and GA-related genes in rice cultivars. Front Plant Sci 2:17.
Zhang Zhang and Jun Yu.‡ (2011) On the organizational dynamics of the genetic code. Genomics Proteomics Bioinformatics 9:1–9.
Ming Yang, Yan Ge, Jiayan Wu, Jingfa Xiao, Jun Yu. ‡ (2011) Coevolution study of mitochondrial respiratory chain proteins: toward the understanding of protein-protein interaction. Journal of Genetics and Genomics 38:201–207.
Lina Ma, Qingshu Meng, Weihung Cheng, Yunju Sung, Petrus Tang, Songnian Hu and Jun Yu.‡(2011) Involvement of GP63 protease in the infection of Trichomonas vaginalis. Parasitology Research109:71–9.
Huitao Liu, Peng Cui, Kehui Zhan, Qiang Lin, Guoyin Zhuo, Xiaoli Guo, Feng Ding, Wenlong Yang, Dongcheng Liu, Songnian Hu, Jun Yu and Aimin Zhang. (2011) Comparative analysis of mitochondrial genomes between a wheat K-type cytoplasmic male sterility (CMS) line and its maintainer line. BMC
Genomics 12:163.
Dapeng Wang and Jun Yu.‡ (2011) Both size and GC-content of minimal introns are selected in human population. PLoS One 6: e17945.
Binbin Wang, Yong-Biao Zhang, Feng Zhang, Xumin Wang, Hongbin Lin, Ning Wan, Haiyu Weng, Zhenqing Ye, Panpan Wang, Tingting Wu, Lili Zhang, Xin Li, Longfei Cheng, Jing Wang Jiangwei Yan, Duen-Mei Wang, Xu Ma, Jun Yu.‡ (2011) On the Origin of Tibetans and their Genetic Basis in Adapting High-Altitude Environments. PLoS One 6(2): e17002.
Dapeng Wang, Fei Liu, Lei Wang, Shi Huang and Jun Yu. ‡ (2011) Nonsynonymous substitution rate (Ka) is a relatively consistent parameter for defining fast-evolving and slow-evolving protein-coding genes. Biology Direct 6:13.
Qingshu Meng, Kaifu Chen, Lina Ma, Songnian Hu and Jun Yu. ‡ (2011) A systematic identification of Kolobok superfamily transposons in Trichomonas vaginalis and sequence analysis on related transposases. Journal of Genetics and Genomics 38:63–70.
Jianhong An, Haolei Wan, Xiangtian Zhou, Dan-Ning Hu, Ledan Wang, Lili Hao, Dongsheng Yan, Fanjun Shi, Zhonglou Zhou, Jiao Wang, Songnian Hu, Jun Yu‡, Jia Qu. (2011) A Comparative Transcriptomic Analysis of Uveal Melanoma and Normal Uveal Melanocyte. PLoS ONE 6(1): e16516.
Jiehua Ye, Lin-Hui Su, Chyi-Liang Chen, Songnian Hu, Jianbing Wang, Jun Yu, Cheng-Hsun Chiu (2011) Analysis of pSC138, the multidrug resistance plasmid of Salmonella enterica serotype Choleraesuis SC-B67. Plasmid 65:132–140.
Hongzhu Qu, Hao Wu, Tongwu Zhang, Zhang Zhang, Songnian Hu and Jun Yu‡. (2010). Nucleotide compositional asymmetry between the leading and lagging strands of eubacterial genomes. Research in Microbiology 161:838–846.
Guiming Liu, Yongjun Fang, Hongming Zhang, Yan Li, Xingang Li, Jun Yu, and Xumin Wang. (2010) Computational identification and microarray-based validation of microRNAs in Oryctolagus cuniculus. Molecular Biology Reports 37:3575–3581.
Jun Wang, Jianguo Zhang, Ruiqiang, Hongkun Zheng, Jun Li, Yong Zhang, Heng Li, Peixiang Ni, Songgang Li, Shengting Li, Jingqiang Wang, Dongyuan Liu, Jason McDermott, Ram Samudrala, Siqi Liu, Jian Wang, Huanming Yang, Jun Yu,‡ Gane Ka-Shu Wong. (2010) Evolutionary Transients in the Rice Transcriptome. Geno Proteo & Bioinfo 8(4)223–228.
Wanfei Liu, Dawei Huang, Kan Liu, Songnian Hu, Jun Yu, Gang Gao, and Shuhui Song (2010). Discovery, Identification and Comparative Analysis of Non-Specific Lipid Transfer Protein (nsLtp) Family in Solanaceae. Geno Proteo & Bioinfo 8(4): 229–237.
Lili Hao, Xiaomeng Ge, Hao-Lei Wan, Songnian Hu, Martin J Lercher, Jun Yu‡ and Wei-Hua Chen. (2010) Human functional genetic studies are biased against the medically most relevant primate-specific genes. BMC Evolutionary Biology 10:316.
Haiyan Guo, WeiWei Wang, Ning Yang, BaoLin Guo, Sun Zhang, RuiJin Yang, Yuan Ye, JunLin Yu, SongNian Hu, QiShi Sun and Jun Yu. ‡ (2010) DNA barcoding provides distinction between Radix Astragali and its adulterants. Science in China Series C Life Sciences 53: 53 No.8: 992–999.
Peng Cui, Qiang Lin, Feng Ding, Chengqi Xin, Wei Gong, Lingfang Zhang, Jianing Geng, Bing Zhang, Xiaomin Yu, Jin Yang, Songnian Hu and Jun Yu‡. (2010) A Comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing. Genomics 2010 Nov;96(5):259-65.
Meng Yang, Xiaowei Zhang, Yuxin Yin, Guiming Liu, Kaifu Chen, Quanzheng Yun, Duojun Zhao, Ibrahim S. Al-Mssallem, and Jun Yu. ‡ (2010). The
chloroplast genome sequence of date palm (Phoenix dactylifera L.). PLoS One 5(9): e12762.
Zhang Zhang and Jun Yu.‡ (2010) Modeling genome compositional dynamics based on GC and purine contents. Biology Direct 5:63.
Kaifu Chen, Lei Wang, Meng Yang, Jiucheng Liu, Chengqi Xin, Songnian Hu, and Jun Yu.‡(2010) Sequence Signatures of Nucleosome Positioning in Caenorhabditis elegans. Geno Proteo & Bioinfo 8:92–102.
Ximiao He, Shu Tao, Jing Jin, Songnian Hu, and Jun Yu.‡ (2010) The Most Redundant Sequences in Human CpG Island Library Are Derived from Mitochondrial Genome. Geno Proteo & Bioinfo 8:81–91.
Xiaoguang Zhou, Lufeng Ren, Qingshu Meng, Yuntao Li, Yude Yu, and Jun Yu. ‡ (2010) The next-generation sequencing technology and application. Protein & Cell1:520–536.
Meng Yang, Shuhui Song, Xiangjun Tian, Zhizhuang Zhao, Songnian Hu, and Jun Yu‡. (2010). A comprehensive analysis of protein phosphatases in rice and Arabidopsis.Plant Systematics and Evolution 289:111–126.
YANG Yue, GONG Wei, WANG Weiwei, YU Xiaomin, HU Songnian, YU Jun. ‡ (2010). The Alterations of Energy Metabolism-related Protein Patterns in Brown Adipose Tissue of Rats during Cold-induced Thermogenesis. Progress in Biochemistry and Biophysics37:1108–1119.
Peng Cui, Qiang Lin, Chengqi Xin, Lu Han, Lili An, Yulan Wang, Zhishang Hu, Feng Ding, Lingfang Zhang, Songnian Hu, Haiying Hang, and Jun Yu‡. (2010). Hydroxyurea-induced Global Transcriptional Suppression in Mouse ES Cells. Carcinogenesis 31:1661–1668.
Dongyu Zhao, Yan Wang, Di Luo, Xiaohu Shi, Liupu Wang, Dong Xu, Jun Yu and Yanchun Liang. (2010). PMirP: A pre-microRNA prediction method based on structure–sequence hybrid features. Journal Artificial Intelligence in Medicine 49:127–132.
Qi-Long Qin, Xi-Ying Zhang , Xu-Min Wang, Gui-Ming Liu, Xiu-Lan Chen, Bin-Bin Xie, Hong-Yue Dang, Bai-Cheng Zhou, Jun Yu and Yu-Zhong Zhang. (2010). The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation. BMC Genomics 11:247.
Jiang Zhu, Fuhong He, Dapeng Wang, Kan Liu, Dawei Huang, Jingfa Xiao, Jiayan Wu, Songnian Hu and Jun Yu.‡ (2010) A novel role for minimal introns:
routing mRNAs to the cytosol. PLoS One 5(4): e10144.
Yimei Cai, Xiaomin Yu, Qing Zhou, Caixia Yu, Haiyan Hu, Jiucheng Liu, Hongbin Lin, Jin Yang, Bing Zhang, Peng Cui, Songnian Hu and Jun Yu. ‡ (2010). Novel microRNAs in silkworm (Bombyx mori). Funct Integr Genomics 10:405–415.
Dapeng Wang, Yubin Zhanga, Zhang Zhang, Jiang Zhu and Jun Yu. ‡ (2010). KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies. Geno Proteo &Bioinfo. 8:77–80.
XiaoGuang Zhou, Ren LuFeng, Li YunTao, Zhang Meng, Yu YuDe and Yu Jun. ‡ (2010). The next-generation sequencing technology: A technology review and future perspective. Science in China Series C Life Sciences53(1) 1–14.
Liguo Wang, Yuanxin Xi, Jun Yu, Liping Dong, Laising Yen, Wei Li. (2010). A Statistical Method for the Detection of Alternative Splicing Using RNA-Seq. PLoS ONE 5(1): e8529.
Cui Peng, Lingfang Zhang, Qiang Lin, Feng Ding, Chengqi Xin, Xiangdong Fang, Songnian Hu, Jun Yu. ‡ (2010). A novel mechanism of epigenetic regulation: Nucleosome-space occupancy. Biochem Biophys Res Com 391:884–889.
Cui Peng, Huitao Liu, Qiang Lin, Feng Ding, Guoyin Zhuo, Songnian Hu, DongCheng Liu, Wenlong Yang, Kehui Zhan, Aimin Zhang, and Jun Yu. ‡ (2009). A complete mitochondrial genome of wheat (Triticum aestivum cv. Chinese Yumai) and fast evolving mitochondrial genes in higher plants. Journal of Genetics 88:209–307.
Guoqiang Zhang, Lingxia Zhang, Mingcheng Zhang, Linlin Pan, Fengyu Wang, Jun Huang, Guoli Li, Jun Yu, Songnian Hu. (2009). Screening and Assessing 11 Mycobacterium tuberculosis Proteins as Potential Serodiagnostical Markers for Discriminating TB Patients from BCG Vaccinees.Geno Prot & Bioinfo 7:107–115.
Dapeng Wang, Song Zhang, Fuhong He, Jiang Zhu, Songnian Hu, Jun Yu. ‡ (2009). How Do Variable Substitution Rates Influence Ka and Ks Calculations? Geno Prot & Bioinfo 7:116–127.
Jingfa Xiao and Jun Yu.‡ (2009). On the Genetic Code and Its Origin. Science in China Series C39(8):717–726. (in Chinese)
Xiaomin Yu, Qing Zhou, Yimei Cai, Qibin Luo, Hongbin Lin, Songnian Hu, Jun Yu. ‡(2009). A Discovery of Novel microRNAs in the Silkworm (Bombyx mori) Genome. Genomics 94:438–444.
Jun Yu as a listed author f the Schistosoma japonicum Genome Sequencing and Functional Analysis Consortium. (2009) The Schistosoma japonicum genome reveals features of host–parasite interplay. Nature 460: 345–351, doi:10.1038/nature08140.
Jun Li, Zhang Zhang, Søren Vang, Jun Yu, Gane Ka-Shu Wong, Jun Wang. (2009) Correlation between Ka/Ks and Ks is related to substitution model and evolutionary lineage. J Mol Evol 68(4):414-23.
Dapeng Wang, Haolei Wan, Song Zhang, and Jun Yu.‡ (2009) Gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable
substitution rates. Biology Direct 2009, 4:20.
Jingui Zhu, Yongqiao Sun, Faqing Zhao, Jun Yu, Roger Craig and Songnian Hu. (2009) Analysis of tarantula skeletal muscle protein sequences and identification of transcriptional isoforms. BMC Genomics 10:117.
Liang Yang and Jun Yu. ‡ (2009) A Comparative Analysis of Divergently-Paired Genes (DPGs) of Drosophila and Vertebrate Genomes. BMC Evolutionary Biology 9:55.
Feng Ding, Petrus Tang, Mei-Hua Hsu, Peng Cui, Songnian Hu, Jun Yu, Cheng-Hsun Chiu. (2009) Genome Evolution Driven by Host Adaptations Results in a More Virulent and Antimicrobial-Resistant Streptococcus pneumoniae Serotype 14. BMC Genomics 10:158.
Weihua Chen, Xiaomeng Ge, Weiwei Wang, Jun Yu,‡ and Songnian Hu. (2009). A gene catalogue for post-diapause development of an anhydrobiotic arthropod Artemia franciscana. BMC Genomics 10:52.
Ji R, Cui P, Ding F, Geng J, Gao H, Zhang H, Yu J, Hu S, Meng H. (2009) Monophyletic origin of domestic bactrian camel (Camelus bactrianus) and its evolutionary relationship with the extant wild camel (Camelus bactrianus ferus). Anim Genet 2009, 40(4):377–382.
Liguo Wang, Lili Hao, Xianran Li, Songnian Hu, Song Ge, Jun Yu.‡ (2009) SNP deserts of cultivated Asian rice: genomic regions under domestication. J
Evol Biol 22:51–761.
Zejuan Li, Roger T. Luo, Shuangli Mi, et al. (2009) Consistent Deregulation of Gene Expression between Human and Murine MLL Rearrangement Leukemias. Cancer Res 69:1109–1116.
Shuhui Song, Yuefeng Huang, Xuan Wang, Gang Wei, Weiwei Wang, Xiaomeng Ge, Songnian Hu, Yanchun Liang, and Jun Yu.‡ (2009) HRGD: a Database for Heterosis-associated Genes. Plant Mol Biol. 69:255–260.
Toronto 2009 Data Release Workshop Authors (Jun Yu as one of the listed authors). (2009) Benefits and Best Practices of Rapid Pre-Publication Data Release. Nature 461(7261): 168–170.
Wang F, Xiao J, Pan L, Yang M, Zhang G, Jin S, Yu J. ‡(2008) A Systematic Survey of Mini-Proteins in Bacteria and Archaea. PLoS ONE 3(12): e4027.
doi:10.1371/journal.pone.0004027.
Xiaomeng Ge, Weihua Chen, Shuhui Song, Weiwei Wang, Songnian Hu, Jun Yu.‡ (2008) Transcriptomic profiling of mature embryo from an elite super-hybrid rice LYP9 and its parental lines. BMC Plant Biol. 8:114.
Zhenqing Ye, Songnian Hu, Jun Yu.‡ (2008) Adaptive clustering algorithm for community detection in complex networks. Phys. Rev. E 78, 046115.
Jiang Zhu, Fuhong He, Songnian Hu and Jun Yu.‡ (2008) Reevaluating the nature of housekeeping gene. Trends in Genetics 24:481–484.
Xiaomin Yu, Qing Zhou, Sungchou Li, Qibin Luo, Wenchang Lin, Huan Chen, Yue Yang, Songnian Hu, Jun Yu.‡(2008) Computational and experimental
identification of microRNAs in the silkworm (Bombyx mori). PLoS ONE 3(8): e2997.
Weiwei Wang, Bo Meng, Xiaomeng Ge, Xiaomin Yu, Yue Yang, Liguo Wang, Songnian Hu, Siqi Liu, Jun Yu.‡ (2008) Proteomic Profiling of Rice Embryos
from a Hybrid Rice Cultivar and Its Parental Lines. Proteomics 8:4808–4821.
Fengping Wang, Jianbin Wang, Huahua Jian, et al. (2008) Environmental Adaptation: Genomic Analysis of the Piezotolerant and Psychrotolerant Deep-Sea
Iron Reducing Bacterium Shewanella piezotolerans WP3. PLoS ONE 3(4): e1937.
TONG XiaoMei, CHEN Fang, YU Jun, HUA Sang, ASAN Ciren, LUOSANG JiangBai, WANG Wei, YU Liang, ZHENG XiaoGuang, WANG Jian. (2008). Phylogenetic identification and microbial diversity in snow of the summit (8201 m) of Cho Oyu Mountain in Tibet. Chinese Science Bulletin 53: 3317–3323.
Luo Q, Zhou Q, Yu X, Lin H, Hu S,Yu J‡ (2008) Genome-wide mapping of conserved microRNAs and their host transcripts in Tribolium castaneum. J Genet Genomics 35:349–55.
Jiang Zhu, Fuhong He, Jing Wang and Jun Yu.‡(2008) How many human genes can be defined as house-keeping with current expression data? BMC Genomics 9:172.
Liping Wei‡ and Jun Yu.‡(2008) Bioinformatics in China: A Personal Perspective. PLoS Comp Biol 4(4): e1000020.
Jiang Zhu, Fuhong He, Jing Wang, and Jun Yu.‡ (2008) Modeling Transcriptome Based on Transcript-Sampling Data. PLoS ONE 3(2): e1659.
Xiangtian Zhou, Weiwei Wang, Fan Lu, Songnian Hu, Liqin Jiang, Dongsheng Yan, Xiaowei Zhang, Xiaomin Yu, Jun Yu, Jia Qu. (2007) A comparative gene expression profile of the whole eye from human, mouse, and guinea pig. Molecular Vision 13:2214–2221.
Jingfa Xiao and Jun Yu.‡ (2007) A Scenario on the Stepwise Evolution of the Genetic Code. Geno Prot & Bioinfo 5: 143–151.
Ye Feng, Chih-Jung Chen, Lin-Hui Su, Songnian Hu, Jun Yu, Cheng-Hsun Chiu. Evolution and pathogenesis of Staphylococcus aureus: lessons learned from genotyping and comparative genomics. FEMS Microbiology Reviews 32:23–37.
Gorodkin J, Cirera S, Hedegaard J, et al. (2007) Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags. Genome Biol. 8(4):R45.
Weiwei Wang, Bo Meng, Weihua Chen, Xiaomeng Ge, Siqi Liu, and Jun Yu.‡ (2007) A proteomic study on postdiapaused embryonic development of brine shrimp (Artemia franciscana). Proteomics 7:3580–3591.
Frazer, K.A., Ballinger, D.G., Cox, D.R., et al., (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449:851–861.
Sabeti, P.C., Varilly, P., Fry, B., et al. (2007) Genome-wide detection and characterization of positive selection in human populations. Nature 449:913–918.
Shu-hui Song, Hong-Zhu Qu, Chen Chen, Song-Nian Hu, Jun Yu.‡ (2007) Differential Gene Expression in an Elite Hybrid Rice Cultivar (Oryza sativa, L): a Global Transcription Analysis Based on SAGE Data. BMC Plant Biology 7:49.
Jiangwei Yan, Hui Tang, Yacheng Liu, Wanshan Ma, Yin Liu, Qingxia Zhang, Junwei Gao, Zhangping Jiao, Leipeng Shang, Yuting Jing, Songnian Hu, Jun
Yu.‡ (2007) Allele frequencies of mitochondrial D-loop (CA)n repeat polymorphism in six Chinese ethnic groups. Legal Medicine 9:330–331.
Jun Yu. (2007) An Evolutionary Scenario for the Origin of Genetic Code. Communications of Chinese-American Society of Chemistry, Fall Issue of 2007.pp3–7.
Jianfei Hu, Xiaoqian Zhao and Jun Yu.‡(2007) Replication-associated purine asymmetry (PAS) may contribute to strand-biased gene distribution SGD). Genomics 90:186–194.
Jianfei Hu, Xiaoqian Zhao, Zhang Zhang, Jun Yu.‡ (2007) The Compositional Dynamics of the Guanine and Cytosine Content in Prokaryotic Genomes. Research in Microbiology 158:363–370.
Peng Cui, Rimutu Ji, Feng Ding, Dan Qi, Hongwei Gao, He Meng, Jun Yu, Songnian Hu and Heping Zhang. (2007) A complete mitochondrial genome sequence of the wild two-humped camel (Camelus bactrianus ferus): an evolutionary history of camelidae. BMC Genomics 8:241.
Jun Yu. (2007) A content-centric organization of the genetic code. Geno Prot & Bioinfo 5:1–6.
Tian Xiangjun, Jing Zheng, Songnian Hu, Jun Yu.‡ (2007) The discriminatory transfer routes of tRNA genes among organellar and nuclear genomes in flowing plants: a genome-wide investigation on indica rice. Journal of Molecular Evolution 64(3): 299.
Zhonghua Zhang, Yajun Deng, Jun Tan, Songnian Hu, Jun Yu, Qingzhong Xue. (2007) A genome-wide microsatellite polymorphism database for the indica and japonica rice. DNA Research 14:37–45.
Chen C, Tang J, Dong W, et al., Yu J ‡ (2007) A Glimpse of Streptococcal Toxic Shock Syndrome from Comparative Genomics of S. suis 2 Chinese Isolates. PLoS ONE 2(3): e315.
Xiaoqian Zhao, Zhang Zhang, Jiangwei Yan, Jun Yu.‡ (2007) GC Content Variability of Eubacterial Genomes Is Governed by the Alpha Subunit of DNA Polymerase III. Biochem Biophys Res Com 356:20–25.
Jun Yu, G.K. Wong, S. Liu, J. Wang, H. Yang. (2007) A comprehensive crop genome project: the superhybrid rice genome project in China. Philos Trans R Soc Lond B Biol Sci 362(1482):1023–34.
biomedical sciences from New York University Medical School in 1990. He had served as a Research Assistant Professor at NYU since 1990 until he joined University of Washington Genome Center in 1993. Dr. Yu's primary research interests include genome biology and bioinformatics.
Phone: 010-80488703
E-mail: [email protected]
Contribution to the Project:
Wp 2: Evaluation of the harpacticoid copepod Tisbe battagliai as model organism for the evaluation of low level environmental contamination by pharmaceuticals.
Wp 7: Development of molecular and physiological biomarkers for metals in estuarine waters and sediments using the benthic amphipod Melita plumulosa.
Publications (last 5 years):
Dapeng Wang, Yan Xia, and Jun Yu. (2012) Multi-level compositional dynamics along human gene transcription start. In preparation.
Dapeng Wang, Yao Su, Hongxing Le and Jun Yu‡. (2012).Transposon-derived and satellite-derived repetitive sequences play distinct roles in the intron size expansion among mammalian genomes. In preparation
Hao Wu, Lin-Lin Pan, Zhang Zhang, Song-Nian Hu, Jun Yu*. (2012). Evolutionary scenario of bacterial DNA polymerase III α subunits and implications for bacterial evolution. In preparation.
Wei Xu, Chengqi Xin, Qiang Lin, Feng Ding, Jianing Geng, Yaping Chen, JunYu‡, Peng Cui and Songnian Hu. (2012). The most active transcriptome is attributable to adolescence in the postnatal development of the mouse cerebrum. In preparation.
Hangxiao Zhang, Qibin Luo, Jing Sun, Fei Liu, Gang Wu, Jun Yu‡, Weiwei Wang (2012) A comparative analysis on mitochondrial genomes of major Artemia species in China: assessing the effect of high plateau adaptation. In preparation.
Miguel A. Esteban, Lili Hao, Feng Li,et al. (2012). Combined Single Base Resolution-Methylome and RNA-Sequencing Maps to Distinguish between Human Embryonic and Induced Pluripotent Stem Cells. Submitted.
Yu Kang, Lufeng Ren, Jun Yu, and Zhancheng Gao. (2012) Homeostasis of the Human Pharyngeal Microbiome May Play an Active Role in Protecting Lower Respiratory Tract Infections. In preparation.
Gang Wu, Jiang Zhu, Fuhong He, Weiwei Wang, Songnian Hu and Jun Yu‡. (2012) Genome Parameters of Mammalian Circadian and Non-circadian Genes. Submitted to PLoS One.
Shangang Jia, Xiaowei Zhang, Guangyu Zhang, et al., Jun Yu‡. (2012). The intestinal metagenome of red palm weevil (Rhynchophorus ferrugineus). Submitted to IMSB.
Lina Ma, Linghu Nie, Bing Zhang, et al., Jun Yu‡. (2012) A RNA-seq-based gene expression profiling of radiation-induced tumorigenic mammary epithelial cells. Submitted to PLoS One.
Zhenqing Ye, Ke Zhang, Songnian Hu,Jun Yu‡. (2012) A new definition of modularity for community detection in complex networks. In press.
Tongwu Zhang, Songnian Hu, Xiaowei Zhang, Ibrahim S. Al-Mssallem and Jun Yu‡. (2012) The complete chloroplast and mitochondrial genomes of Hassawi rice (Oryza sativa L.) and its hybrid in Saudi Arabia: genome variation and rearrangement and origins. Submitted to PLoS One.
Tongwu Zhang, Yingfeng Luo, Yaping Chen, Xiaonuan Li, Songnian Hu, and Jun Yu‡. (2012). BIGRAS: a genome assembly tool for pyrosequencing-based re-sequencing projects. In press.
Hao Wu, Hong-zhu Qu, Zhang Zhang, Song-nian Hu, and Jun Yu‡. Strand-biased gene distribution (SGD) and nucleotide composition (SNC) in Eubacteria. GBP in press.
Weili Liang, Yongbing Zhao, Chunxia Chen, Xiaoying Cui, Jun Yu, Jingfa Xiao and Biao Kan. (2012). Pan-genomic analysis provides insights into the genomic variation and evolution of Salmonella Paratyphi A. PLoS One in press.
Lei Wang, Xiaowei Zhang, Linlin Pan, Wanfei Liu, Guangyu Zhang, Yuxin Yin, An Yin, Shangang Jia, Xiaoguang Yu, Gaoyuan Sun, Songnian Hu, Ibrahim S. Al-Mssallem, Jun Yu‡. (2012). A Large-scale Gene Discovery for the Red Palm Weevil Rhynchophorus ferrugineus (Coleoptera: Curculionidae).
Insect Science in press.
Yu Kang, Jun Yu, Zhancheng Gao. (2012) Etiologic Diagnosis of Lower Respiratory Tract Bacterial Infections Using Sputum Samples and Quantitative Loop-mediated Isothermal Amplification. PLoS One. In press.
Guangyu Zhang, Linlin Pan, Yuxin Yin, Wanfei Liu, Dawei Huang, Tongwu Zhang, Lei Wang, Chengqi Xin, Gaoyuan Sun, Mohammed M. Ba Abdullah, Xiaowei Zhang, Songnian Hu, Ibrahim S. Al-Mssallem, Jun Yu‡. (2012) Large-scale collection and annotation of gene models for date palm (Phoenix dactylifera, L.) Plant Molecular Biology, in press.
Peng Cui, Feng Ding, WanFei Liu, Songnian Hu and Jun Yu‡. (2012) The novel role of H3K4 trimethylation in regulating antisense transcription. GBP in
press.
Jun Yu. (2012). Life in Two Tracks. GPB in press.
Jun Yu. (2012). Challenges to the common dogma. GBP in press.
Peng Cui, Wanfei Liu, Qiang Lin, Feng Ding, Songnian Hu, Jun Yu‡. (2012). Comparative study of chromatin state between mouse cerebrum and testis. GPB in press.
Yan Lu, Xingang Li, Min Wang, Xin Li, Feng Zhang, Yun Li, Meng Zhang, Yuwei Da, Jun Yu‡, Jianping Jia. (2012) A Novel Autosomal Dominant Inclusion Body Myopathy Linked to 7q22.1-31.1. PLoS One. In press.
Yu Kang, Rui Deng, Can Wang,et al., (2012) Etiologic Diagnosis of Lower Respiratory Tract Bacterial Infections Using Sputum Samples and Quantitative Loop-Mediated Isothermal Amplification. PLoS One 7(6): e38743. doi:10.1371/journal.pone.0038743
Dongyu Zhao, Jiayan Wu, Yuanyuan Zhou, Wei Gong, Jingfa Xiao, Jun Yu‡. (2012) WikiCell: a unified resource platform for human transcriptomics research. OMICS: A Journal of Integrative Biology 16(6): 357-362. doi:10.1089/omi.2011.0139.
Mingliang Gu, Xiaoqun Dong, Xuezhi Zhang, XUmin Wang, Yue Qi, Jun Yu, Wenquan Niu. (2012) Strong Association between Two Polymorphisms on 15q25.1 and Lung Cancer Risk: A Meta-Analysis. PLoS One 7(6): e37970. doi:10.1371/journal.pone.0037970.
Chao Jiang, Yuan Yuan, Guiming Liu, Luqi Huang, Xumin Wang, Jun Yu, Min Chen. (2012) Analysis of EST-SSR distribution and development of EST-SSR markers in Lonicera Japonica. Acta Pharmaciutica Sinica 47: 803-810. (in Chinese)
Ping-Yi Li, Bin-Bin Xie, Xi-Ying Zhang, Qi-Long Qin, Hong-Yue Dang, Xu-Min Wang, Xiu-Lan Chen, Jun Yu and Yu-Zhong Zhang. (2012) Genetic structure of three fosmid-fragments encoding 16S rRNA genes of the Miscellaneous Crenarchaeotic Group (MCG): implications for physiology and evolution of marine sedimentary archaea. Environmental Microbiology 2:14.
Yuan Yuan, Lipu Song, Minghui Li, Guiming Liu, Yanan Chu, Luyu Ma, Yuanyuan Zhou, Xiao Wang, Wei Gao, Shuangshuang Qin, Jun Yu, Xumin Wang and Luqi Huang. (2012). Genetic Variation and Metabolic Pathway Intricacy Govern the Active Compound Content and Quality of the Chinese Medicinal Plant Lonicera japonica. BMC Genomics 13:195. doi:10.1186/1471-2164-13-195
Yongjun Fang, Hao Wu, Meng Yang, Tongwu Zhang, Linlin Pan, Quanzheng Yun, Xiaoguang Yu, Xiaowei Zhang, Songnian Hu, Ibrahim Al-Mssalem, and Jun Yu‡.A Complete Sequence and Transcriptomic Analysis of Date Palm (Phoenix dactylifera L.) Mitochondrial Genome. PLoS One 7(5): e37164.
doi:10.1371/journal.pone.0037164.
Yimei Cai, Qing Zhou, Caixia Yu, Xumin Wang, Songnian Hu, Jun Yu‡, Xiaomin Yu. (2012) Transposable-Element Associated Small RNAs in Bombyx mori Genome. PLoS One 7(5): e36599. doi:10.1371/journal.pone.0036599
Yan Ge, Jiayan Wu, Ming Yang, Jingfa Xiao, Jun Yu‡. (2012) Molecular dynamics study of the different binding mode between the drug resistant
Streptococcus suis R61 and non-resistant A7 PBP protein and the cefuroxime. PLoS One 7(4): e35941. doi:10.1371/journal.pone.0035941.
Yang Liu, Bin Wang, Peng Cui, Libo Li, Jia-Yu Xue, Jun Yu, and Yin-Long Qiu. (2012). The mitochondrial genome of the lycophyte Huperzia squarrosa: the most archaic form in vascular plants. PLoS One 7(4): e35168.
Zhang Zhang, Jun Li, Peng Cui, Feng Ding, Ang Li, Jeffrey P. Townsend, Jun Yu‡. (2012).Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance.BMC Bioinformatics 13:43.
Peng Cui, Feng Ding, Lingfang Zhang, Songnian Hu and Jun Yu‡. (2012) Replication and transcription contribute differently in mutation rates of human genome. Geno Proteo & Bioinfo 10(1): 4–10.
Peng Cui, Qiang Lin, Feng Ding, Songnian Hu and Jun Yu‡. (2012) Transcript-centric mutations in human genomes. Geno Proteo & Bioinfo 10(1): 11–22.
Yuxin Yin, Xiaowei Zhang,Yongjun Fang, Linlin Pan, Gaoyuan Sun, Chengqi Xin, Mohammed M. Ba Abdullah, Xiaoguang Yu, Songnian Hu, Ibrahim S. Al-Mssallem, Jun Yu‡. (2012). High-throughput Sequencing-based Gene Profiling on Multi-staged Fruit Development of Date Palm (Phoenix dactylifera, L.). Plant Molecular Biology 78(6):617–626.
Tongwu Zhang, Yongjun Fan, Xin Deng, Xumin Wang, Songnian Hu, Xiaowei Zhang, and Jun Yu‡. (2012) The Complete Chloroplast and Mitochondrial Genome Sequences of resurrection plant Boea hygrometrica: Insights into the Evolution of Plant Organellar genomes. PLoS One 7(1): e30531. doi:10.1371/journal.pone.0030531.
Hao Wu, Zhang Zhang, Songnian Hu, Jun Yu‡. (2012) On the Molecular Mechanism of GC Content Variation among Eubacterial Genomes. Biology Direct 7:2 doi:10.1186/1745-6150-7-2.
Qian Zhao, Jingfa Xiao, Jun Yu.‡(2012) Functional and Evolutionary Analyses of Small Proteins from eight Representative Eukaryotes. PIBB39: 359–367doi:10.1016/j.cell.2011.10.017.
Qiang Lin,Peng Cui, Feng Ding, Songnian Hu and Jun Yu‡. (2011). Replication-Associated Mutational Pressure (RMP) Governs Strand-biased Compositional Asymmetry (SCA) and Gene Organization in Animal Mitochondrial Genomes. Current Genomics 13:28–36.
Yongbing Zhao, Jiayan Wu, Junhui Yang, Shixiang Sun, Jingfa Xiao, and Jun Yu‡. (2011). PGAP: Pan-Genomes Analysis Pipeline. Bioinformatics.
28(3): 416-418.
Wei He, Xin Li, Jialiang Chen, Ling Xu, Feng Zhang, Qiushi Dai, Hao Cui, Duen-Mei Wang, Jun Yu, Songnian Hu, Shan Lu. (2011) Genetic linkage analyses and Cx50 mutation detection in a large multiplex Chinese family with hereditary nuclear cataract. Ophthalmic Genet, 32(1):48–53.
Wanfei Liu, Yuhui Zhao, Peng Cui, Qiang Lin, Feng Ding, Chengqi Xin, Xinyu Tan, Shuhui Song, Jun Yu‡, Songnian Hu. (2011) Thousands of novel transcripts identified in mouse cerebrum, testis, and ES cells based on ribo-minus RNA sequencing.Frontier in Genetics 2:93.
Dapeng Wang, Yubin Zhang, Zhonghua Fan, Guiming Liu and Jun Yu‡. (2011). LCGbase: A Comprehensive Database for Lineage-based Co-regulated Genes. Evolutionary Bioinformatics 2012:8 39–46.
Tongwu Zhang, Xiaowei Zhang, Songnian Hu, Jun Yu‡. (2011)An efficient procedure for organellar genome assembly using whole genome data from 454 GS FLX sequencing platform.Plant Methods 7:38.
Ma Lina, Chen Kaifu, Meng Qingshu, Liu Qingyou, Tang Petrus, Hu Songnian, Yu Jun‡. (2011) An evolutionary analysis of trypanosomatid GP63 proteases. Parasitology Research 109:1075–1084.
Yongjun Fang, Zhaolong Li, Jiucheng Liu, Changlong Shu, Xumin Wang, Xiaowei Zhang, Xiaoguang Yu, Duojun Zhao, Guiming Liu, Songnian Hu, Jie Zhang, Ibrahim Al-Mssalleme, and Jun Yu‡. (2011) A Pangenomic Study of Bacillus thuringiensis. Journal of Genetics and Genomics 38:567–576.
Lina Ma, Yanyan Huang, Wangyu Zhu, Fang Zeng, Yongkui Zhang, Xiaoguang Liu, and Jun Yu‡. (2012). An Integrated Analysis of miRNA and mRNA Expressions in Non-small Cell Lung Cancers. PLoS One 6(10): e26502. doi:10.1371/journal.pone.0026502.
Gang Wu, Hangxiao Zhang, Jing Sun, Fei Liu, Xiaomeng Ge, Weihua Chen, Jun Yu‡and Weiwei Wang. (2011) Late embryogenesis abundant (LEA) genes activated in Artemia franciscana post-diapause embryos subjected to water stress. Com. Biochem. Physiol. B.160:32-39.
Anding Zhang, Ming Yang, Pan Hu, Jiayan Wu, Bo Che , Yafeng Hua, Jun Yu, Huanchun Chen, Jingfa Xiao and Meilin Jin. (2011). Comparative Genomic Analysis of Streptococcus suis reveals significant genomic diversity among different serotypes. BMC Genomics 12:523.
Lina Yuan, Lufeng Ren, Yuntao Li, Weijing Han, Yong Yu, Yanna Chu, Guiming Liu, Dan Yu, Mingjing Teng, Liang Wang, Xumin Wang, Xiaoguang Zhou, Yude Yu and Jun Yu‡. (2011). A Complete Genome Assembly of Glaciecola mesophila sp. nov. Sequenced Using a BIGIS-4 sequencer system. Science in China Series C Life Sciences 54 (9): 835-840.
Peng Cui, Qiang Lin, Zhang L, Feng Ding, Lingfang Zhang, Feng Ding, Chengqi Xin, Daoyong Zhang, Fanglin Sun, Songnian Hu, Jun Yu‡. (2011) The Disequilibrium of Nucleosomes Distribution along Chromosomes Plays a Functional and Evolutionarily Role in Regulating Gene Expression. PLoS One 6(8): e23219.
Zongjun Du, Zhewen Zhang, Tingting Miao, Jiayan Wu, Guoqiang Lü, Jun Yu, Jingfa Xiao, and Guanjun Chen. (2011). Draft Genome Sequence of a Novel Agar-Digesting Marine Bacterium HQM9. Journal of Bacteriology 193:4557–4558.
Hu P, Yang M, Zhang A, Wu J, Chen B, Hua Y, Yu J, Chen H, Xiao J, Jin M. (2011) Complete Genome Sequence ofStreptococcus suis Serotype 3 Strain ST3. Journal of Bacteriology 193:3428–3429.
Fei Liu, Hangxiao Zhang, Gang Wu, Jing Sun, Lili Hao, Xiaomeng Ge, Jun Yu‡, Weiwei Wang. (2011) Sequence variation and expression analysis of seed dormancy- and germination-associated ABA- and GA-related genes in rice cultivars. Front Plant Sci 2:17.
Zhang Zhang and Jun Yu.‡ (2011) On the organizational dynamics of the genetic code. Genomics Proteomics Bioinformatics 9:1–9.
Ming Yang, Yan Ge, Jiayan Wu, Jingfa Xiao, Jun Yu. ‡ (2011) Coevolution study of mitochondrial respiratory chain proteins: toward the understanding of protein-protein interaction. Journal of Genetics and Genomics 38:201–207.
Lina Ma, Qingshu Meng, Weihung Cheng, Yunju Sung, Petrus Tang, Songnian Hu and Jun Yu.‡(2011) Involvement of GP63 protease in the infection of Trichomonas vaginalis. Parasitology Research109:71–9.
Huitao Liu, Peng Cui, Kehui Zhan, Qiang Lin, Guoyin Zhuo, Xiaoli Guo, Feng Ding, Wenlong Yang, Dongcheng Liu, Songnian Hu, Jun Yu and Aimin Zhang. (2011) Comparative analysis of mitochondrial genomes between a wheat K-type cytoplasmic male sterility (CMS) line and its maintainer line. BMC
Genomics 12:163.
Dapeng Wang and Jun Yu.‡ (2011) Both size and GC-content of minimal introns are selected in human population. PLoS One 6: e17945.
Binbin Wang, Yong-Biao Zhang, Feng Zhang, Xumin Wang, Hongbin Lin, Ning Wan, Haiyu Weng, Zhenqing Ye, Panpan Wang, Tingting Wu, Lili Zhang, Xin Li, Longfei Cheng, Jing Wang Jiangwei Yan, Duen-Mei Wang, Xu Ma, Jun Yu.‡ (2011) On the Origin of Tibetans and their Genetic Basis in Adapting High-Altitude Environments. PLoS One 6(2): e17002.
Dapeng Wang, Fei Liu, Lei Wang, Shi Huang and Jun Yu. ‡ (2011) Nonsynonymous substitution rate (Ka) is a relatively consistent parameter for defining fast-evolving and slow-evolving protein-coding genes. Biology Direct 6:13.
Qingshu Meng, Kaifu Chen, Lina Ma, Songnian Hu and Jun Yu. ‡ (2011) A systematic identification of Kolobok superfamily transposons in Trichomonas vaginalis and sequence analysis on related transposases. Journal of Genetics and Genomics 38:63–70.
Jianhong An, Haolei Wan, Xiangtian Zhou, Dan-Ning Hu, Ledan Wang, Lili Hao, Dongsheng Yan, Fanjun Shi, Zhonglou Zhou, Jiao Wang, Songnian Hu, Jun Yu‡, Jia Qu. (2011) A Comparative Transcriptomic Analysis of Uveal Melanoma and Normal Uveal Melanocyte. PLoS ONE 6(1): e16516.
Jiehua Ye, Lin-Hui Su, Chyi-Liang Chen, Songnian Hu, Jianbing Wang, Jun Yu, Cheng-Hsun Chiu (2011) Analysis of pSC138, the multidrug resistance plasmid of Salmonella enterica serotype Choleraesuis SC-B67. Plasmid 65:132–140.
Hongzhu Qu, Hao Wu, Tongwu Zhang, Zhang Zhang, Songnian Hu and Jun Yu‡. (2010). Nucleotide compositional asymmetry between the leading and lagging strands of eubacterial genomes. Research in Microbiology 161:838–846.
Guiming Liu, Yongjun Fang, Hongming Zhang, Yan Li, Xingang Li, Jun Yu, and Xumin Wang. (2010) Computational identification and microarray-based validation of microRNAs in Oryctolagus cuniculus. Molecular Biology Reports 37:3575–3581.
Jun Wang, Jianguo Zhang, Ruiqiang, Hongkun Zheng, Jun Li, Yong Zhang, Heng Li, Peixiang Ni, Songgang Li, Shengting Li, Jingqiang Wang, Dongyuan Liu, Jason McDermott, Ram Samudrala, Siqi Liu, Jian Wang, Huanming Yang, Jun Yu,‡ Gane Ka-Shu Wong. (2010) Evolutionary Transients in the Rice Transcriptome. Geno Proteo & Bioinfo 8(4)223–228.
Wanfei Liu, Dawei Huang, Kan Liu, Songnian Hu, Jun Yu, Gang Gao, and Shuhui Song (2010). Discovery, Identification and Comparative Analysis of Non-Specific Lipid Transfer Protein (nsLtp) Family in Solanaceae. Geno Proteo & Bioinfo 8(4): 229–237.
Lili Hao, Xiaomeng Ge, Hao-Lei Wan, Songnian Hu, Martin J Lercher, Jun Yu‡ and Wei-Hua Chen. (2010) Human functional genetic studies are biased against the medically most relevant primate-specific genes. BMC Evolutionary Biology 10:316.
Haiyan Guo, WeiWei Wang, Ning Yang, BaoLin Guo, Sun Zhang, RuiJin Yang, Yuan Ye, JunLin Yu, SongNian Hu, QiShi Sun and Jun Yu. ‡ (2010) DNA barcoding provides distinction between Radix Astragali and its adulterants. Science in China Series C Life Sciences 53: 53 No.8: 992–999.
Peng Cui, Qiang Lin, Feng Ding, Chengqi Xin, Wei Gong, Lingfang Zhang, Jianing Geng, Bing Zhang, Xiaomin Yu, Jin Yang, Songnian Hu and Jun Yu‡. (2010) A Comparison between ribo-minus RNA-sequencing and polyA-selected RNA-sequencing. Genomics 2010 Nov;96(5):259-65.
Meng Yang, Xiaowei Zhang, Yuxin Yin, Guiming Liu, Kaifu Chen, Quanzheng Yun, Duojun Zhao, Ibrahim S. Al-Mssallem, and Jun Yu. ‡ (2010). The
chloroplast genome sequence of date palm (Phoenix dactylifera L.). PLoS One 5(9): e12762.
Zhang Zhang and Jun Yu.‡ (2010) Modeling genome compositional dynamics based on GC and purine contents. Biology Direct 5:63.
Kaifu Chen, Lei Wang, Meng Yang, Jiucheng Liu, Chengqi Xin, Songnian Hu, and Jun Yu.‡(2010) Sequence Signatures of Nucleosome Positioning in Caenorhabditis elegans. Geno Proteo & Bioinfo 8:92–102.
Ximiao He, Shu Tao, Jing Jin, Songnian Hu, and Jun Yu.‡ (2010) The Most Redundant Sequences in Human CpG Island Library Are Derived from Mitochondrial Genome. Geno Proteo & Bioinfo 8:81–91.
Xiaoguang Zhou, Lufeng Ren, Qingshu Meng, Yuntao Li, Yude Yu, and Jun Yu. ‡ (2010) The next-generation sequencing technology and application. Protein & Cell1:520–536.
Meng Yang, Shuhui Song, Xiangjun Tian, Zhizhuang Zhao, Songnian Hu, and Jun Yu‡. (2010). A comprehensive analysis of protein phosphatases in rice and Arabidopsis.Plant Systematics and Evolution 289:111–126.
YANG Yue, GONG Wei, WANG Weiwei, YU Xiaomin, HU Songnian, YU Jun. ‡ (2010). The Alterations of Energy Metabolism-related Protein Patterns in Brown Adipose Tissue of Rats during Cold-induced Thermogenesis. Progress in Biochemistry and Biophysics37:1108–1119.
Peng Cui, Qiang Lin, Chengqi Xin, Lu Han, Lili An, Yulan Wang, Zhishang Hu, Feng Ding, Lingfang Zhang, Songnian Hu, Haiying Hang, and Jun Yu‡. (2010). Hydroxyurea-induced Global Transcriptional Suppression in Mouse ES Cells. Carcinogenesis 31:1661–1668.
Dongyu Zhao, Yan Wang, Di Luo, Xiaohu Shi, Liupu Wang, Dong Xu, Jun Yu and Yanchun Liang. (2010). PMirP: A pre-microRNA prediction method based on structure–sequence hybrid features. Journal Artificial Intelligence in Medicine 49:127–132.
Qi-Long Qin, Xi-Ying Zhang , Xu-Min Wang, Gui-Ming Liu, Xiu-Lan Chen, Bin-Bin Xie, Hong-Yue Dang, Bai-Cheng Zhou, Jun Yu and Yu-Zhong Zhang. (2010). The complete genome of Zunongwangia profunda SM-A87 reveals its adaptation to the deep-sea environment and ecological role in sedimentary organic nitrogen degradation. BMC Genomics 11:247.
Jiang Zhu, Fuhong He, Dapeng Wang, Kan Liu, Dawei Huang, Jingfa Xiao, Jiayan Wu, Songnian Hu and Jun Yu.‡ (2010) A novel role for minimal introns:
routing mRNAs to the cytosol. PLoS One 5(4): e10144.
Yimei Cai, Xiaomin Yu, Qing Zhou, Caixia Yu, Haiyan Hu, Jiucheng Liu, Hongbin Lin, Jin Yang, Bing Zhang, Peng Cui, Songnian Hu and Jun Yu. ‡ (2010). Novel microRNAs in silkworm (Bombyx mori). Funct Integr Genomics 10:405–415.
Dapeng Wang, Yubin Zhanga, Zhang Zhang, Jiang Zhu and Jun Yu. ‡ (2010). KaKs_Calculator 2.0: A Toolkit Incorporating Gamma-Series Methods and Sliding Window Strategies. Geno Proteo &Bioinfo. 8:77–80.
XiaoGuang Zhou, Ren LuFeng, Li YunTao, Zhang Meng, Yu YuDe and Yu Jun. ‡ (2010). The next-generation sequencing technology: A technology review and future perspective. Science in China Series C Life Sciences53(1) 1–14.
Liguo Wang, Yuanxin Xi, Jun Yu, Liping Dong, Laising Yen, Wei Li. (2010). A Statistical Method for the Detection of Alternative Splicing Using RNA-Seq. PLoS ONE 5(1): e8529.
Cui Peng, Lingfang Zhang, Qiang Lin, Feng Ding, Chengqi Xin, Xiangdong Fang, Songnian Hu, Jun Yu. ‡ (2010). A novel mechanism of epigenetic regulation: Nucleosome-space occupancy. Biochem Biophys Res Com 391:884–889.
Cui Peng, Huitao Liu, Qiang Lin, Feng Ding, Guoyin Zhuo, Songnian Hu, DongCheng Liu, Wenlong Yang, Kehui Zhan, Aimin Zhang, and Jun Yu. ‡ (2009). A complete mitochondrial genome of wheat (Triticum aestivum cv. Chinese Yumai) and fast evolving mitochondrial genes in higher plants. Journal of Genetics 88:209–307.
Guoqiang Zhang, Lingxia Zhang, Mingcheng Zhang, Linlin Pan, Fengyu Wang, Jun Huang, Guoli Li, Jun Yu, Songnian Hu. (2009). Screening and Assessing 11 Mycobacterium tuberculosis Proteins as Potential Serodiagnostical Markers for Discriminating TB Patients from BCG Vaccinees.Geno Prot & Bioinfo 7:107–115.
Dapeng Wang, Song Zhang, Fuhong He, Jiang Zhu, Songnian Hu, Jun Yu. ‡ (2009). How Do Variable Substitution Rates Influence Ka and Ks Calculations? Geno Prot & Bioinfo 7:116–127.
Jingfa Xiao and Jun Yu.‡ (2009). On the Genetic Code and Its Origin. Science in China Series C39(8):717–726. (in Chinese)
Xiaomin Yu, Qing Zhou, Yimei Cai, Qibin Luo, Hongbin Lin, Songnian Hu, Jun Yu. ‡(2009). A Discovery of Novel microRNAs in the Silkworm (Bombyx mori) Genome. Genomics 94:438–444.
Jun Yu as a listed author f the Schistosoma japonicum Genome Sequencing and Functional Analysis Consortium. (2009) The Schistosoma japonicum genome reveals features of host–parasite interplay. Nature 460: 345–351, doi:10.1038/nature08140.
Jun Li, Zhang Zhang, Søren Vang, Jun Yu, Gane Ka-Shu Wong, Jun Wang. (2009) Correlation between Ka/Ks and Ks is related to substitution model and evolutionary lineage. J Mol Evol 68(4):414-23.
Dapeng Wang, Haolei Wan, Song Zhang, and Jun Yu.‡ (2009) Gamma-MYN: a new algorithm for estimating Ka and Ks with consideration of variable
substitution rates. Biology Direct 2009, 4:20.
Jingui Zhu, Yongqiao Sun, Faqing Zhao, Jun Yu, Roger Craig and Songnian Hu. (2009) Analysis of tarantula skeletal muscle protein sequences and identification of transcriptional isoforms. BMC Genomics 10:117.
Liang Yang and Jun Yu. ‡ (2009) A Comparative Analysis of Divergently-Paired Genes (DPGs) of Drosophila and Vertebrate Genomes. BMC Evolutionary Biology 9:55.
Feng Ding, Petrus Tang, Mei-Hua Hsu, Peng Cui, Songnian Hu, Jun Yu, Cheng-Hsun Chiu. (2009) Genome Evolution Driven by Host Adaptations Results in a More Virulent and Antimicrobial-Resistant Streptococcus pneumoniae Serotype 14. BMC Genomics 10:158.
Weihua Chen, Xiaomeng Ge, Weiwei Wang, Jun Yu,‡ and Songnian Hu. (2009). A gene catalogue for post-diapause development of an anhydrobiotic arthropod Artemia franciscana. BMC Genomics 10:52.
Ji R, Cui P, Ding F, Geng J, Gao H, Zhang H, Yu J, Hu S, Meng H. (2009) Monophyletic origin of domestic bactrian camel (Camelus bactrianus) and its evolutionary relationship with the extant wild camel (Camelus bactrianus ferus). Anim Genet 2009, 40(4):377–382.
Liguo Wang, Lili Hao, Xianran Li, Songnian Hu, Song Ge, Jun Yu.‡ (2009) SNP deserts of cultivated Asian rice: genomic regions under domestication. J
Evol Biol 22:51–761.
Zejuan Li, Roger T. Luo, Shuangli Mi, et al. (2009) Consistent Deregulation of Gene Expression between Human and Murine MLL Rearrangement Leukemias. Cancer Res 69:1109–1116.
Shuhui Song, Yuefeng Huang, Xuan Wang, Gang Wei, Weiwei Wang, Xiaomeng Ge, Songnian Hu, Yanchun Liang, and Jun Yu.‡ (2009) HRGD: a Database for Heterosis-associated Genes. Plant Mol Biol. 69:255–260.
Toronto 2009 Data Release Workshop Authors (Jun Yu as one of the listed authors). (2009) Benefits and Best Practices of Rapid Pre-Publication Data Release. Nature 461(7261): 168–170.
Wang F, Xiao J, Pan L, Yang M, Zhang G, Jin S, Yu J. ‡(2008) A Systematic Survey of Mini-Proteins in Bacteria and Archaea. PLoS ONE 3(12): e4027.
doi:10.1371/journal.pone.0004027.
Xiaomeng Ge, Weihua Chen, Shuhui Song, Weiwei Wang, Songnian Hu, Jun Yu.‡ (2008) Transcriptomic profiling of mature embryo from an elite super-hybrid rice LYP9 and its parental lines. BMC Plant Biol. 8:114.
Zhenqing Ye, Songnian Hu, Jun Yu.‡ (2008) Adaptive clustering algorithm for community detection in complex networks. Phys. Rev. E 78, 046115.
Jiang Zhu, Fuhong He, Songnian Hu and Jun Yu.‡ (2008) Reevaluating the nature of housekeeping gene. Trends in Genetics 24:481–484.
Xiaomin Yu, Qing Zhou, Sungchou Li, Qibin Luo, Wenchang Lin, Huan Chen, Yue Yang, Songnian Hu, Jun Yu.‡(2008) Computational and experimental
identification of microRNAs in the silkworm (Bombyx mori). PLoS ONE 3(8): e2997.
Weiwei Wang, Bo Meng, Xiaomeng Ge, Xiaomin Yu, Yue Yang, Liguo Wang, Songnian Hu, Siqi Liu, Jun Yu.‡ (2008) Proteomic Profiling of Rice Embryos
from a Hybrid Rice Cultivar and Its Parental Lines. Proteomics 8:4808–4821.
Fengping Wang, Jianbin Wang, Huahua Jian, et al. (2008) Environmental Adaptation: Genomic Analysis of the Piezotolerant and Psychrotolerant Deep-Sea
Iron Reducing Bacterium Shewanella piezotolerans WP3. PLoS ONE 3(4): e1937.
TONG XiaoMei, CHEN Fang, YU Jun, HUA Sang, ASAN Ciren, LUOSANG JiangBai, WANG Wei, YU Liang, ZHENG XiaoGuang, WANG Jian. (2008). Phylogenetic identification and microbial diversity in snow of the summit (8201 m) of Cho Oyu Mountain in Tibet. Chinese Science Bulletin 53: 3317–3323.
Luo Q, Zhou Q, Yu X, Lin H, Hu S,Yu J‡ (2008) Genome-wide mapping of conserved microRNAs and their host transcripts in Tribolium castaneum. J Genet Genomics 35:349–55.
Jiang Zhu, Fuhong He, Jing Wang and Jun Yu.‡(2008) How many human genes can be defined as house-keeping with current expression data? BMC Genomics 9:172.
Liping Wei‡ and Jun Yu.‡(2008) Bioinformatics in China: A Personal Perspective. PLoS Comp Biol 4(4): e1000020.
Jiang Zhu, Fuhong He, Jing Wang, and Jun Yu.‡ (2008) Modeling Transcriptome Based on Transcript-Sampling Data. PLoS ONE 3(2): e1659.
Xiangtian Zhou, Weiwei Wang, Fan Lu, Songnian Hu, Liqin Jiang, Dongsheng Yan, Xiaowei Zhang, Xiaomin Yu, Jun Yu, Jia Qu. (2007) A comparative gene expression profile of the whole eye from human, mouse, and guinea pig. Molecular Vision 13:2214–2221.
Jingfa Xiao and Jun Yu.‡ (2007) A Scenario on the Stepwise Evolution of the Genetic Code. Geno Prot & Bioinfo 5: 143–151.
Ye Feng, Chih-Jung Chen, Lin-Hui Su, Songnian Hu, Jun Yu, Cheng-Hsun Chiu. Evolution and pathogenesis of Staphylococcus aureus: lessons learned from genotyping and comparative genomics. FEMS Microbiology Reviews 32:23–37.
Gorodkin J, Cirera S, Hedegaard J, et al. (2007) Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags. Genome Biol. 8(4):R45.
Weiwei Wang, Bo Meng, Weihua Chen, Xiaomeng Ge, Siqi Liu, and Jun Yu.‡ (2007) A proteomic study on postdiapaused embryonic development of brine shrimp (Artemia franciscana). Proteomics 7:3580–3591.
Frazer, K.A., Ballinger, D.G., Cox, D.R., et al., (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449:851–861.
Sabeti, P.C., Varilly, P., Fry, B., et al. (2007) Genome-wide detection and characterization of positive selection in human populations. Nature 449:913–918.
Shu-hui Song, Hong-Zhu Qu, Chen Chen, Song-Nian Hu, Jun Yu.‡ (2007) Differential Gene Expression in an Elite Hybrid Rice Cultivar (Oryza sativa, L): a Global Transcription Analysis Based on SAGE Data. BMC Plant Biology 7:49.
Jiangwei Yan, Hui Tang, Yacheng Liu, Wanshan Ma, Yin Liu, Qingxia Zhang, Junwei Gao, Zhangping Jiao, Leipeng Shang, Yuting Jing, Songnian Hu, Jun
Yu.‡ (2007) Allele frequencies of mitochondrial D-loop (CA)n repeat polymorphism in six Chinese ethnic groups. Legal Medicine 9:330–331.
Jun Yu. (2007) An Evolutionary Scenario for the Origin of Genetic Code. Communications of Chinese-American Society of Chemistry, Fall Issue of 2007.pp3–7.
Jianfei Hu, Xiaoqian Zhao and Jun Yu.‡(2007) Replication-associated purine asymmetry (PAS) may contribute to strand-biased gene distribution SGD). Genomics 90:186–194.
Jianfei Hu, Xiaoqian Zhao, Zhang Zhang, Jun Yu.‡ (2007) The Compositional Dynamics of the Guanine and Cytosine Content in Prokaryotic Genomes. Research in Microbiology 158:363–370.
Peng Cui, Rimutu Ji, Feng Ding, Dan Qi, Hongwei Gao, He Meng, Jun Yu, Songnian Hu and Heping Zhang. (2007) A complete mitochondrial genome sequence of the wild two-humped camel (Camelus bactrianus ferus): an evolutionary history of camelidae. BMC Genomics 8:241.
Jun Yu. (2007) A content-centric organization of the genetic code. Geno Prot & Bioinfo 5:1–6.
Tian Xiangjun, Jing Zheng, Songnian Hu, Jun Yu.‡ (2007) The discriminatory transfer routes of tRNA genes among organellar and nuclear genomes in flowing plants: a genome-wide investigation on indica rice. Journal of Molecular Evolution 64(3): 299.
Zhonghua Zhang, Yajun Deng, Jun Tan, Songnian Hu, Jun Yu, Qingzhong Xue. (2007) A genome-wide microsatellite polymorphism database for the indica and japonica rice. DNA Research 14:37–45.
Chen C, Tang J, Dong W, et al., Yu J ‡ (2007) A Glimpse of Streptococcal Toxic Shock Syndrome from Comparative Genomics of S. suis 2 Chinese Isolates. PLoS ONE 2(3): e315.
Xiaoqian Zhao, Zhang Zhang, Jiangwei Yan, Jun Yu.‡ (2007) GC Content Variability of Eubacterial Genomes Is Governed by the Alpha Subunit of DNA Polymerase III. Biochem Biophys Res Com 356:20–25.
Jun Yu, G.K. Wong, S. Liu, J. Wang, H. Yang. (2007) A comprehensive crop genome project: the superhybrid rice genome project in China. Philos Trans R Soc Lond B Biol Sci 362(1482):1023–34.
Dr Sharon Hook
Commonwealth Scientific and Industrial Research Organisation (CSIRO)
Dr Sharon Hook is a Senior Research Scientist within the Environmental Biogeochemistry Program, CSIRO Land and Water.
Her research on the impacts of environmental contaminants on marine and aquatic organisms as determined via traditional, biomarker dependant and transcriptomic endpoints is delivered through two flagships - Water for a Healthy Country and Wealth from Oceans.
Dr Hook’s research has focused on developing novel techniques to assess the impacts of contaminants, including oil, metals, and endocrine disrupting chemicals, on aquatic organisms. To this end, she has used standardised toxicological tests, cell based bioassays, and measures of gene expression to assess xenobiotic response.
Her research topics of special interest include::
- evaluating biomarker responses as they relate to organism fitness in contaminated field sites.
- determining the impact of environmental contaminants on normal signalling progresses, such as those that ocurr during embryonic or sexual development.
- utilising gene expression data to develop multi variate biomarkers of contaminant exposure and response.
- developing novel molecular techniques for use in ecotoxicology.
- determining how genotoxicity is influenced by repair capacity
- determining how exposure route and contaminant interact to influence toxicological response.
Phone: + 61 2 9710 6839
e-mail: [email protected]
RELATED PUBLICATIONS
Hutchins, DA , I Stupakoff, S Hook, S. Luoma and NS Fisher. 1997. Effects of Arctic temperatures on distribution and retention of the nuclear waste
radionuclides 241Am, 57Co, and 137Cs in the bioindicator bivalve Macoma balthica. Marine Environmental Research. 45:17-28.
Hook, SE and NS Fisher, 2001. Sublethal toxicity of silver in zooplankton: importance of exposure pathways and implications for toxicity testing.
Environmental Toxicology and Chemistry. 20: 568-574.
Hook, SE and NS Fisher, 2001. Reproductive toxicity of metals in calanoid copepods. Marine Biology. 138:1131-1140.
Hook, SE and NS Fisher, 2002. Relating the reproductive toxicity of five ingested metals in calanoid copepods with sulfur affinity. Marine Environmental Research. 53:161-174.
Hook, SE and NS Fisher, 2002. Toxicology tests with aquatic animals need to consider the trophic transfer of metals Toxicology. 181/182:531-536.
Hook, SE and RF Lee, 2004. Genotoxicant induced DNA damage and repair in early and late developmental stages of the grass shrimp Paleomonetes pugio embryo as measured by the Comet Assay. Aquatic Toxicology. 66:1-14.
Hook, SE and RF Lee, 2004. Interactive effects of UV, Benzo [a] pyrene, and Cadmium on DNA damage and repair in embryos of the grass shrimp
Paleomonetes pugio, Marine Environmental Research. 58: 735-739.
Handy, R., McGeer, J., Allen, H., Drevnick, P., Gorsuch, J., Green, A., Hook, S, Lundebye, A-K., Mount, D., Stubblefield. 2005. Toxic Effects of Dietary Metal Exposure: Laboratory Studies W. In: Toxicity of Dietborne Metals to Aquatic Biota, J.S. Meyer, W.J. Adams, K.V. Brix, S.N. Luoma, D.R. Mount,
W.A. Stubblefield and C.M. Wood (eds.), SETAC Press.
Muirhead, E.K., Skillman, A.D., Hook, S. and I.R. Schultz. 2006. Oral Exposure of PBDE-47 in Fish: Toxicokinetics and Reproductive Effects in Japanese Medaka (Oryzias latipes) and Fathead Minnows (Pimephales promelas). Environmental Science & Technology. 40:523-528.
Hook SE, AD Skillman, JA Small, and IR Schultz. 2006. Gene expression patterns in Rainbow Trout, Onorhynchus mykiss, exposed to a suite of model
toxicants. Aquatic Toxicology 77: 372-385
Hook SE, AD Skillman, JA Small, and IR Schultz. 2006. Dose response relationships in gene expression profiles in Rainbow Trout, Onorhynchus mykiss exposed to Ethinylestradiol. Marine Environmental Research. 62: S151-154
Skillman, AD, Nagler, JJ, Hook, SE Small, JA. Schultz.IR. 2006. Dynamics of Ethynylestradiol Exposure in Rainbow Trout (Oncorhynchus mykiss):
Absorption, Tissue Distribution and Hepatic Gene Expression Patterns. Environmental Toxicology and Chemistry. 25: 2297-3005
Hook SE, AD Skillman, JA Small, and IR Schultz. 2007. Temporal Changes in Gene Expression in Rainbow Trout Exposed to Ethynyl Estradiol. Comparative Biochemistry and Physiology. 145: 73-85.
Hook SE, AD Skillman, JA Small, and IR Schultz. 2008. Gene expression profiles in rainbow trout, Onorhyncus mykiss, exposed to a chemical mixture. Toxicological Sciences 102: 42-60
Hook, SE, Cobb, ME, Oris, JT, Anderson, JW. 2008. Gene sequences for Cytochromes p450 1A1 and 1A2: The need for biomarker Development in Sea otters (Enhydra lutris). Comparative Biochemistry and Physiology 151:336-348.
Hook, SE, Lampi, MA, Febbo, EJ, Ward, JA, Parkerton TJ (2010). Hepatic Gene Expression in Rainbow Trout (Oncorhynchus mykiss) Exposed to Different Hydrocarbon Mixtures. Environmental Chemistry and Toxicology 29: 2034-2043.
Hook, SE, Lampi, MA, Febbo, EJ, Ward, JA, Parkerton TJ (2010). Temporal patterns in the transcriptomic response of rainbow trout, Oncorhynchus mykiss, to crude oil. AquaticToxicology 99: 320-329.
Hook, SE. (2010) Promise and progress in environmental genomics: a status report on the applications of microarray studies in ecologically relevant fish species. Journal of Fish Biology 77: 1999- 2022.
Hook SE, Nagler, JJ, Cavileer, T, Verducci, J, Liu, Y., Hayton, W, Schultz, IR. (2011) Relationships between hormone levels and transcriptomic profiles during a normal reproductive period in female rainbow trout Environmental Chemistry and Toxicology 30: 309-318.
Pearson, W.H., Deriso, R.B., Elston, R.A., Hook, S.E., Parker, K.R., Anderson, J.W. (2012). Hypotheses concerning the decline and poor recovery of Pacific herring in Prince William Sound, Alaska. Reviews in Fish Biology and Fisheries 22: 95-135.
Her research on the impacts of environmental contaminants on marine and aquatic organisms as determined via traditional, biomarker dependant and transcriptomic endpoints is delivered through two flagships - Water for a Healthy Country and Wealth from Oceans.
Dr Hook’s research has focused on developing novel techniques to assess the impacts of contaminants, including oil, metals, and endocrine disrupting chemicals, on aquatic organisms. To this end, she has used standardised toxicological tests, cell based bioassays, and measures of gene expression to assess xenobiotic response.
Her research topics of special interest include::
- evaluating biomarker responses as they relate to organism fitness in contaminated field sites.
- determining the impact of environmental contaminants on normal signalling progresses, such as those that ocurr during embryonic or sexual development.
- utilising gene expression data to develop multi variate biomarkers of contaminant exposure and response.
- developing novel molecular techniques for use in ecotoxicology.
- determining how genotoxicity is influenced by repair capacity
- determining how exposure route and contaminant interact to influence toxicological response.
Phone: + 61 2 9710 6839
e-mail: [email protected]
RELATED PUBLICATIONS
Hutchins, DA , I Stupakoff, S Hook, S. Luoma and NS Fisher. 1997. Effects of Arctic temperatures on distribution and retention of the nuclear waste
radionuclides 241Am, 57Co, and 137Cs in the bioindicator bivalve Macoma balthica. Marine Environmental Research. 45:17-28.
Hook, SE and NS Fisher, 2001. Sublethal toxicity of silver in zooplankton: importance of exposure pathways and implications for toxicity testing.
Environmental Toxicology and Chemistry. 20: 568-574.
Hook, SE and NS Fisher, 2001. Reproductive toxicity of metals in calanoid copepods. Marine Biology. 138:1131-1140.
Hook, SE and NS Fisher, 2002. Relating the reproductive toxicity of five ingested metals in calanoid copepods with sulfur affinity. Marine Environmental Research. 53:161-174.
Hook, SE and NS Fisher, 2002. Toxicology tests with aquatic animals need to consider the trophic transfer of metals Toxicology. 181/182:531-536.
Hook, SE and RF Lee, 2004. Genotoxicant induced DNA damage and repair in early and late developmental stages of the grass shrimp Paleomonetes pugio embryo as measured by the Comet Assay. Aquatic Toxicology. 66:1-14.
Hook, SE and RF Lee, 2004. Interactive effects of UV, Benzo [a] pyrene, and Cadmium on DNA damage and repair in embryos of the grass shrimp
Paleomonetes pugio, Marine Environmental Research. 58: 735-739.
Handy, R., McGeer, J., Allen, H., Drevnick, P., Gorsuch, J., Green, A., Hook, S, Lundebye, A-K., Mount, D., Stubblefield. 2005. Toxic Effects of Dietary Metal Exposure: Laboratory Studies W. In: Toxicity of Dietborne Metals to Aquatic Biota, J.S. Meyer, W.J. Adams, K.V. Brix, S.N. Luoma, D.R. Mount,
W.A. Stubblefield and C.M. Wood (eds.), SETAC Press.
Muirhead, E.K., Skillman, A.D., Hook, S. and I.R. Schultz. 2006. Oral Exposure of PBDE-47 in Fish: Toxicokinetics and Reproductive Effects in Japanese Medaka (Oryzias latipes) and Fathead Minnows (Pimephales promelas). Environmental Science & Technology. 40:523-528.
Hook SE, AD Skillman, JA Small, and IR Schultz. 2006. Gene expression patterns in Rainbow Trout, Onorhynchus mykiss, exposed to a suite of model
toxicants. Aquatic Toxicology 77: 372-385
Hook SE, AD Skillman, JA Small, and IR Schultz. 2006. Dose response relationships in gene expression profiles in Rainbow Trout, Onorhynchus mykiss exposed to Ethinylestradiol. Marine Environmental Research. 62: S151-154
Skillman, AD, Nagler, JJ, Hook, SE Small, JA. Schultz.IR. 2006. Dynamics of Ethynylestradiol Exposure in Rainbow Trout (Oncorhynchus mykiss):
Absorption, Tissue Distribution and Hepatic Gene Expression Patterns. Environmental Toxicology and Chemistry. 25: 2297-3005
Hook SE, AD Skillman, JA Small, and IR Schultz. 2007. Temporal Changes in Gene Expression in Rainbow Trout Exposed to Ethynyl Estradiol. Comparative Biochemistry and Physiology. 145: 73-85.
Hook SE, AD Skillman, JA Small, and IR Schultz. 2008. Gene expression profiles in rainbow trout, Onorhyncus mykiss, exposed to a chemical mixture. Toxicological Sciences 102: 42-60
Hook, SE, Cobb, ME, Oris, JT, Anderson, JW. 2008. Gene sequences for Cytochromes p450 1A1 and 1A2: The need for biomarker Development in Sea otters (Enhydra lutris). Comparative Biochemistry and Physiology 151:336-348.
Hook, SE, Lampi, MA, Febbo, EJ, Ward, JA, Parkerton TJ (2010). Hepatic Gene Expression in Rainbow Trout (Oncorhynchus mykiss) Exposed to Different Hydrocarbon Mixtures. Environmental Chemistry and Toxicology 29: 2034-2043.
Hook, SE, Lampi, MA, Febbo, EJ, Ward, JA, Parkerton TJ (2010). Temporal patterns in the transcriptomic response of rainbow trout, Oncorhynchus mykiss, to crude oil. AquaticToxicology 99: 320-329.
Hook, SE. (2010) Promise and progress in environmental genomics: a status report on the applications of microarray studies in ecologically relevant fish species. Journal of Fish Biology 77: 1999- 2022.
Hook SE, Nagler, JJ, Cavileer, T, Verducci, J, Liu, Y., Hayton, W, Schultz, IR. (2011) Relationships between hormone levels and transcriptomic profiles during a normal reproductive period in female rainbow trout Environmental Chemistry and Toxicology 30: 309-318.
Pearson, W.H., Deriso, R.B., Elston, R.A., Hook, S.E., Parker, K.R., Anderson, J.W. (2012). Hypotheses concerning the decline and poor recovery of Pacific herring in Prince William Sound, Alaska. Reviews in Fish Biology and Fisheries 22: 95-135.
Dr Afonso Bainy
Universidade Federal de Santa Catarina (UFSC)
Afonso Celso Dias BAINY
graduated in Biological Oceanography by the Federal University of Rio Grande in 1986, completed master's degree in Biological Sciences (Biochemistry) from the Federal University of Rio Grande do Sul in 1990 and completed his doctorate in Biological Sciences (Biochemistry), University Sao Paulo in 1995. Done internships in short-term linked to the Biology Department Woods Hole Oceanographic Institution, Woods Hole, MA, USA, from 11/1995 to 02/1996, the place he returned to perform his post-doctoral period of 11 / 2001-12 / 2002. Since August 1993 is Professor, Department of Biochemistry, Federal University of Santa Catarina. He is currently Associate Professor 2. Participated in the creation of the Laboratory for Biomarkers of Aquatic Contamination and Immunochemistry, local headquarters where he developed most of their research projects. He is coordinator of the research group registered in the CNPq entitled “Systems biochemical and molecular defenses in aquatic organisms”. He has published 66 articles in professional journals and has one accepted for publication. Presented over 179 papers in conference proceedings, has published five book chapters, organized nine national and international scientific events. In particular, in October 2004 chaired the Organizing Committee of the VIII Brazilian Congress of Ecotoxicology, held in Florianópolis, SC, and in May 2007, chaired the 14th International Symposium on Pollutant Responses in Marine Organisms (PRIMO 14). Has advised 60 people between post-doctoral, masters and doctoral graduates of undergraduate students. Currently 12 people are focusing on these different levels. He received five honors. Coordinated several research projects and is currently coordinating a research project in this same area, with emphasis on the development of new biomarkers of aquatic contamination and adaptive systems of aquatic organisms to environmental contamination. In addition, is Vice-Coordinator of the National Institute of Science and Technology- Aquatic Toxicology, based in FURG, and involves the following institutions: FURG, UFSC, Universidade Federal do Paraná, UEL, UFSCAR, UFPE.
Phone +55-48-3721 6391
Emails [email protected] or [email protected]
Contribution to the project:
WP 4 – Protein expression profiles in mussels Mytilus galloprovincialisexposed to three representative pharmaceuticals
WP 5 - Differential gene and protein expression profiles in mussels Mytilus galloprovincialis exposed to metal nanoparticles
WP8 – Expression analysis of susceptible genes in target tissues liver and brain of Danio rerio and Poecilia vivipara exposed to three pharmaceutical compounds and hospital effluent mixtures.
WP9- Interspecific varioation in gene expression in oysters Crassostrea brasiliana and Crassostrea gigasexposed to Linear Alkyl Benzenes (LABs)
Related publications:
Gonçalves-Soares, D.; Seiffert, W.Q.; Schlindwein, A.D.; Toledo-Silva, G.; Zanette, J.; Marques, M.R.F. ; Bainy, A.C.D. Identification of differentially transcribed genes in shrimp Litopenaeus vannamei exposed to osmotic stress and challenged with WSSV virus. Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics, v. 7, p. 73-81, 2012.
Gonçalves-Soares, Daniela ; ZANETTE, Juliano ; Yunes, João S. ; Yepiz-Plascencia, Gloria M. ; Bainy, A.C.D.. Expression and activity of glutathione
S-transferases and catalase in the shrimp Litopenaeus vannamei inoculated with a toxic Microcystis aeruginosa strain. Marine Environmental Research, v. 75, p. 54-61, 2012.
Ferreira, R.S. ; Monserrat, José Maria ; Ferreira, J.L.R. ; Kalb, A.C.; Stegeman, John J ; Bainy, A.C.D.; Zanette, Juliano . Biomarkers of Organic contamination in the South-American Fishes Poecilia vivipara and Jenynsia multidentata. Journal of Toxicology and Environmental Health. Part A, v. 75, p. 1-11, 2012.
Lüchmann, Karim H.; Mattos, Jacó J.; Siebert, Marí lia N. ; Dorrington, Tarquin S. ; Toledo-Silva, Guilherme ; Stoco, Patricia H.; Grisard, Edmundo C.; Bainy, A.C.D. Suppressive subtractive hybridization libraries prepared from the digestive gland of the oyster Crassostrea brasiliana exposed to a diesel fuel water-accommodated fraction. Environmental Toxicology and Chemistry, v.31, p.1249-1253, 2012.
Carriquiriborde, P. ; Bainy, A.C.D. Environmental toxicology and chemistry in Latin America. Environmental Toxicology and Chemistry, v. 31, p. 931-934,
2012.
Pereira, C. D. S. ; Martín-Díaz, M. L. ; Catharino, M. G. M. ; Cesar, A. ; Choueri, R. B. ; Taniguchi, S.; Abessa, D. M. S. ; Bícego, M. C. ; Vasconcellos, M. B. A. ; Bainy, A. C. D. ; Souza, E. C. P. M. ; DelValls, T. A. . Chronic contamination assessment integrating biomarkers responses in transplanted mussels-A seasonal monitoring. Environmental Toxicology, v. 27, p. 257-267, 2012.
Zanette, J.; Almeida, Eduardo A.; Silva, Angela Z.; Guzenski, J.; Ferreira, Jaime F.; Di Mascio, P. ; Marques, Maria R.F.; Bainy, Afonso C.D. Salinity influences glutathione S-transferase activity and lipid peroxidation responses in the Crassostrea gigas oyster exposed to diesel oil. Science of the Total Environment, v. 409, p. 1976-1983, 2011.
Pereira, C.D.S.; Martin-Díaz, M.L.; Zanette, J. Cesar, A.; Choueri, R.B. ; Abessa, D.M.S.; Catharino, M.G.M. ; Vasconcellos, M.B.A. ; Bainy, A.C.D.; Sousa, E.C.P.M.; Del Valls, T.A. Integrated biomarker responses as environmental status descriptors of a coastal zone (São Paulo, Brazil). Ecotoxicology and Environmental Safety, v. 74, p. 1257-1264, 2011.
Lüchmann, K.H. ; Mattos, J.J. ; Siebert, M.N. ; Granucci, N.; Dorrington, T.S. ; Bícego, M.C. ; Taniguchi, S.; Sasaki, S.T. ; Daura-Jorge, F.G. ; Bainy, A.C.D. Biochemical biomarkers and hydrocarbons concentrations in the mangrove oyster Crassostrea brasiliana following exposure to diesel fuel water-accommodated fraction. Aquatic Toxicology, v. 105, p. 652-660, 2011.
Sáenz, L.A.; Seibert, E.L.; Zanette, J.; Fiedler, H.D.; Curtius, A.J.; Ferreira, J.F.; Almeida, E.A.; Marques, M.R.F. ; Bainy, A.C.D. Biochemical biomarkers and metals in Perna pernamussels from mariculture zones of Santa Catarina, Brazil. Ecotoxicology and Environmental Safety, v. 73, p. 796-804, 2010.
Mattos, J.J. ; Siebert, M.N. ; Luchmann, K.H. ; Granucci, N.; Dorrington, T. ; Stoco, P.H. ; Grisard, E.C. ; Bainy, A.C.D. Differential gene expression in Poecilia vivipara exposed to diesel oil water accommodated fraction. Marine Environmental Research, v. 69, p. S31-S33, 2010.
Zanette, J.; Goldstone, J.V. ; Bainy, A.C.D. ; Stegeman, John J. Identification of CYP genes in Mytilus (mussel) and Crassostrea (oyster) species: First approach to the full complement of cytochrome P450 genes in bivalves. Marine Environmental Research, v. 69, p. S1-S3, 2010.
Zanette, J.; Jenny, M.J. ; Goldstone, J.V. ; Woodin, B.R. ; Watka, L.A. ; Bainy, A.C.D. ; Stegeman, J.J. New cytochrome P450 1B1, 1C2 and 1D1 genes in the killifish Fundulus heteroclitus: Basal expression and response of five killifish CYP1s to the AHR agonist PCB126. Aquatic Toxicology, v. 93, p. 234-243, 2009.
Toledo-Silva, G. ; Siebert, M. ; Medeiros, I. ; Sincero, T. ; Moraes, M.O. ; Goldstone, J ; Bainy, A.C.D. Cloning a new cytochrome P450 isoform (CYP356A1) from oyster Crassostrea gigas. Marine Environmental Research, v. 66, p. 15-18, 2008.
Medeiros, I. ; Siebert, M.N. ; Toledo-Silva, G ; Moraes, M.O. ; Marques, M.R.F. ; Bainy, A .C.D. Differential gene expression in oyster exposed to sewage. Marine Environmental Research, v. 66, p. 156-157, 2008.
Zanette, J ; Nuner, F. F. ; Medeiros, I.D. ; Siebert, M.N. ; Mattos, J.J. ; Luchmann, K.H.; Melo, C.M.R.; Bainy, A.C.D. Comparison of the antioxidant defense system in Crassostrea rhizophorae and Crassostrea gigas exposed to domestic sewage discharges. Marine Environmental Research, v. 66, p. 196-198, 2008.
Bainy, A.C.D. ; Medeiros, I.D.; Siebert, M.N.; Toledo-Silva, G.; Rodrigues, T.B.; Marques, M.R.F. Induced gene expression in oyster Crassostrea gigas exposed to sewage. Environmental Toxicology and Pharmacology, v. 26, p. 362-365, 2008.
Almeida, E.A.; Bainy, A.C.D.; Loureiro, A.P.M. ; Martinez, G.R. ; Miyamoto, S. ; Onuki, J. ; Barcbosa, L.F.; Garcia, C.C.M.; Prado, F.M. et al. Oxidative stress in Perna perna and other bivalves as indicators of environmental stress in the Brazilian marine environment: Antioxidants, lipid peroxidation and DNA damage. Comparative Biochemistry and Physiology. A, Molecular & Integrative Physiology, v. 146, p. 588-600, 2007.
Bainy, A.C.D. Nuclear receptors and susceptibility to chemical exposure in aquatic organisms. Environment International, v. 33, p. 571-575, 2007.
Pereira, C.D.S.; Abessa, D.M.S.; Bainy, A.C.D. ; Zaroni, L.P.; Gasparro, M.R.; Bícego, M.C. ; Taniguchi, S.; Furley, T.Heid ; Sousa, E.C.P.M. Integrated assessment of multilevels biomarker responses and chemical analysis in mussels from São Sebastião, São Paulo, Brazil. Environmental Toxicology and Chemistry, v. 26, p. 462, 2007.
Almeida, E.A.; Bainy, A.C.D. Effects of aerial exposure on antioxidant defenses in the brown mussel Perna perna. Brazilian Archives of Biology and Technology, Curitiba, Paraná, v. 49, n. 2, p. 225-229, 2006.
Franco, J.L. ; Trivella, D.B.B. ; Trevisan, R.; Dinslaken, D. ; Marques, M.R.F.; Bainy, A.C.D. ; Dafre, A.L. Antioxidant status and stress proteins in the gills of the brown mussel Perna perna exposed to zinc. Chemico-Biological Interactions, v. 160, n. 3, p. 232-240, 2006.
Almeida, E.A; Bainy, A.C.D. ; Dafré, A.L. ; Gomes, O.; Medeiros, M.H.G.; DiMascio, P. Oxidative stress in digestive gland and gill of the brown mussel () exposed to air and re-submersed. Journal of Experimental Marine Biology and Ecology, v. 318, n. 1, p. 21-30, 2005.
Silva, A.Z.; Zanette, J.; Ferreira, J.F. ; Guzenski, J.; Marques, M.R.F.; Bainy, A.C.D. Effects of salinity on biomarker responses in (Mollusca, Bivalvia) exposed to diesel oil. Ecotoxicology and Environmental Safety, v. 62, p. 376-382, 2005.
Bresolin, T.; Rebelo, M.F.; Bainy, A.C.D. Expression of PXR, CYP3A and MDR1 genes in liver of zebrafish. Comparative Biochemistry and Physiology.
C, Toxicology & Pharmacology, Irlanda, v. 140, n. 3-4, p. 403-407, 2005.
Dafré, A.L.; Medeiros, I.D.; Muller, I.C.; Ventura, E.C.; Bainy, A.C.D. Antioxidant enzymes and thiol/disulfide status in the digestive gland of the
brown mussel exposed to lead and paraquat. Chemico-Biological Interactions, Irlanda, v. 149, n. 2-3, p. 97-105, 2004.
Almeida, E.A.; Bainy, A.C.D. ; Miyamoto, S.; Medeiros, M.H.G. ; DiMascio, P. Protective effect of phospholipid hydroperoxide glutathione peroxidase (PHGPx) against lipid peroxidation in mussels Perna perna exposed to different metals. Marine Pollution Bulletin, v. 49, p. 386-392, 2004.
Almeida, E. A. ; Bainy, A.C.D. ; Loureiro, A.P.M. ; Medeiros, M.H. G. ; DiMascio, P. DNA and Lipid Damage in the brown mussel Perna perna from a
contaminated site. Bulletin of Environmental Contamination and Toxicology, v. 71, p. 270-275, 2003.
Almeida, E.A. ; Bainy, A.C.D. ; Medeiros, M.H.G. ; DiMascio, P. Effects of heavy metal and air exposure on serotonin and dopamine levels in tissues of the mussel Perna perna. Marine Pollution Bulletin, v. 46, p. 1485-1490, 2003.
graduated in Biological Oceanography by the Federal University of Rio Grande in 1986, completed master's degree in Biological Sciences (Biochemistry) from the Federal University of Rio Grande do Sul in 1990 and completed his doctorate in Biological Sciences (Biochemistry), University Sao Paulo in 1995. Done internships in short-term linked to the Biology Department Woods Hole Oceanographic Institution, Woods Hole, MA, USA, from 11/1995 to 02/1996, the place he returned to perform his post-doctoral period of 11 / 2001-12 / 2002. Since August 1993 is Professor, Department of Biochemistry, Federal University of Santa Catarina. He is currently Associate Professor 2. Participated in the creation of the Laboratory for Biomarkers of Aquatic Contamination and Immunochemistry, local headquarters where he developed most of their research projects. He is coordinator of the research group registered in the CNPq entitled “Systems biochemical and molecular defenses in aquatic organisms”. He has published 66 articles in professional journals and has one accepted for publication. Presented over 179 papers in conference proceedings, has published five book chapters, organized nine national and international scientific events. In particular, in October 2004 chaired the Organizing Committee of the VIII Brazilian Congress of Ecotoxicology, held in Florianópolis, SC, and in May 2007, chaired the 14th International Symposium on Pollutant Responses in Marine Organisms (PRIMO 14). Has advised 60 people between post-doctoral, masters and doctoral graduates of undergraduate students. Currently 12 people are focusing on these different levels. He received five honors. Coordinated several research projects and is currently coordinating a research project in this same area, with emphasis on the development of new biomarkers of aquatic contamination and adaptive systems of aquatic organisms to environmental contamination. In addition, is Vice-Coordinator of the National Institute of Science and Technology- Aquatic Toxicology, based in FURG, and involves the following institutions: FURG, UFSC, Universidade Federal do Paraná, UEL, UFSCAR, UFPE.
Phone +55-48-3721 6391
Emails [email protected] or [email protected]
Contribution to the project:
WP 4 – Protein expression profiles in mussels Mytilus galloprovincialisexposed to three representative pharmaceuticals
WP 5 - Differential gene and protein expression profiles in mussels Mytilus galloprovincialis exposed to metal nanoparticles
WP8 – Expression analysis of susceptible genes in target tissues liver and brain of Danio rerio and Poecilia vivipara exposed to three pharmaceutical compounds and hospital effluent mixtures.
WP9- Interspecific varioation in gene expression in oysters Crassostrea brasiliana and Crassostrea gigasexposed to Linear Alkyl Benzenes (LABs)
Related publications:
Gonçalves-Soares, D.; Seiffert, W.Q.; Schlindwein, A.D.; Toledo-Silva, G.; Zanette, J.; Marques, M.R.F. ; Bainy, A.C.D. Identification of differentially transcribed genes in shrimp Litopenaeus vannamei exposed to osmotic stress and challenged with WSSV virus. Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics, v. 7, p. 73-81, 2012.
Gonçalves-Soares, Daniela ; ZANETTE, Juliano ; Yunes, João S. ; Yepiz-Plascencia, Gloria M. ; Bainy, A.C.D.. Expression and activity of glutathione
S-transferases and catalase in the shrimp Litopenaeus vannamei inoculated with a toxic Microcystis aeruginosa strain. Marine Environmental Research, v. 75, p. 54-61, 2012.
Ferreira, R.S. ; Monserrat, José Maria ; Ferreira, J.L.R. ; Kalb, A.C.; Stegeman, John J ; Bainy, A.C.D.; Zanette, Juliano . Biomarkers of Organic contamination in the South-American Fishes Poecilia vivipara and Jenynsia multidentata. Journal of Toxicology and Environmental Health. Part A, v. 75, p. 1-11, 2012.
Lüchmann, Karim H.; Mattos, Jacó J.; Siebert, Marí lia N. ; Dorrington, Tarquin S. ; Toledo-Silva, Guilherme ; Stoco, Patricia H.; Grisard, Edmundo C.; Bainy, A.C.D. Suppressive subtractive hybridization libraries prepared from the digestive gland of the oyster Crassostrea brasiliana exposed to a diesel fuel water-accommodated fraction. Environmental Toxicology and Chemistry, v.31, p.1249-1253, 2012.
Carriquiriborde, P. ; Bainy, A.C.D. Environmental toxicology and chemistry in Latin America. Environmental Toxicology and Chemistry, v. 31, p. 931-934,
2012.
Pereira, C. D. S. ; Martín-Díaz, M. L. ; Catharino, M. G. M. ; Cesar, A. ; Choueri, R. B. ; Taniguchi, S.; Abessa, D. M. S. ; Bícego, M. C. ; Vasconcellos, M. B. A. ; Bainy, A. C. D. ; Souza, E. C. P. M. ; DelValls, T. A. . Chronic contamination assessment integrating biomarkers responses in transplanted mussels-A seasonal monitoring. Environmental Toxicology, v. 27, p. 257-267, 2012.
Zanette, J.; Almeida, Eduardo A.; Silva, Angela Z.; Guzenski, J.; Ferreira, Jaime F.; Di Mascio, P. ; Marques, Maria R.F.; Bainy, Afonso C.D. Salinity influences glutathione S-transferase activity and lipid peroxidation responses in the Crassostrea gigas oyster exposed to diesel oil. Science of the Total Environment, v. 409, p. 1976-1983, 2011.
Pereira, C.D.S.; Martin-Díaz, M.L.; Zanette, J. Cesar, A.; Choueri, R.B. ; Abessa, D.M.S.; Catharino, M.G.M. ; Vasconcellos, M.B.A. ; Bainy, A.C.D.; Sousa, E.C.P.M.; Del Valls, T.A. Integrated biomarker responses as environmental status descriptors of a coastal zone (São Paulo, Brazil). Ecotoxicology and Environmental Safety, v. 74, p. 1257-1264, 2011.
Lüchmann, K.H. ; Mattos, J.J. ; Siebert, M.N. ; Granucci, N.; Dorrington, T.S. ; Bícego, M.C. ; Taniguchi, S.; Sasaki, S.T. ; Daura-Jorge, F.G. ; Bainy, A.C.D. Biochemical biomarkers and hydrocarbons concentrations in the mangrove oyster Crassostrea brasiliana following exposure to diesel fuel water-accommodated fraction. Aquatic Toxicology, v. 105, p. 652-660, 2011.
Sáenz, L.A.; Seibert, E.L.; Zanette, J.; Fiedler, H.D.; Curtius, A.J.; Ferreira, J.F.; Almeida, E.A.; Marques, M.R.F. ; Bainy, A.C.D. Biochemical biomarkers and metals in Perna pernamussels from mariculture zones of Santa Catarina, Brazil. Ecotoxicology and Environmental Safety, v. 73, p. 796-804, 2010.
Mattos, J.J. ; Siebert, M.N. ; Luchmann, K.H. ; Granucci, N.; Dorrington, T. ; Stoco, P.H. ; Grisard, E.C. ; Bainy, A.C.D. Differential gene expression in Poecilia vivipara exposed to diesel oil water accommodated fraction. Marine Environmental Research, v. 69, p. S31-S33, 2010.
Zanette, J.; Goldstone, J.V. ; Bainy, A.C.D. ; Stegeman, John J. Identification of CYP genes in Mytilus (mussel) and Crassostrea (oyster) species: First approach to the full complement of cytochrome P450 genes in bivalves. Marine Environmental Research, v. 69, p. S1-S3, 2010.
Zanette, J.; Jenny, M.J. ; Goldstone, J.V. ; Woodin, B.R. ; Watka, L.A. ; Bainy, A.C.D. ; Stegeman, J.J. New cytochrome P450 1B1, 1C2 and 1D1 genes in the killifish Fundulus heteroclitus: Basal expression and response of five killifish CYP1s to the AHR agonist PCB126. Aquatic Toxicology, v. 93, p. 234-243, 2009.
Toledo-Silva, G. ; Siebert, M. ; Medeiros, I. ; Sincero, T. ; Moraes, M.O. ; Goldstone, J ; Bainy, A.C.D. Cloning a new cytochrome P450 isoform (CYP356A1) from oyster Crassostrea gigas. Marine Environmental Research, v. 66, p. 15-18, 2008.
Medeiros, I. ; Siebert, M.N. ; Toledo-Silva, G ; Moraes, M.O. ; Marques, M.R.F. ; Bainy, A .C.D. Differential gene expression in oyster exposed to sewage. Marine Environmental Research, v. 66, p. 156-157, 2008.
Zanette, J ; Nuner, F. F. ; Medeiros, I.D. ; Siebert, M.N. ; Mattos, J.J. ; Luchmann, K.H.; Melo, C.M.R.; Bainy, A.C.D. Comparison of the antioxidant defense system in Crassostrea rhizophorae and Crassostrea gigas exposed to domestic sewage discharges. Marine Environmental Research, v. 66, p. 196-198, 2008.
Bainy, A.C.D. ; Medeiros, I.D.; Siebert, M.N.; Toledo-Silva, G.; Rodrigues, T.B.; Marques, M.R.F. Induced gene expression in oyster Crassostrea gigas exposed to sewage. Environmental Toxicology and Pharmacology, v. 26, p. 362-365, 2008.
Almeida, E.A.; Bainy, A.C.D.; Loureiro, A.P.M. ; Martinez, G.R. ; Miyamoto, S. ; Onuki, J. ; Barcbosa, L.F.; Garcia, C.C.M.; Prado, F.M. et al. Oxidative stress in Perna perna and other bivalves as indicators of environmental stress in the Brazilian marine environment: Antioxidants, lipid peroxidation and DNA damage. Comparative Biochemistry and Physiology. A, Molecular & Integrative Physiology, v. 146, p. 588-600, 2007.
Bainy, A.C.D. Nuclear receptors and susceptibility to chemical exposure in aquatic organisms. Environment International, v. 33, p. 571-575, 2007.
Pereira, C.D.S.; Abessa, D.M.S.; Bainy, A.C.D. ; Zaroni, L.P.; Gasparro, M.R.; Bícego, M.C. ; Taniguchi, S.; Furley, T.Heid ; Sousa, E.C.P.M. Integrated assessment of multilevels biomarker responses and chemical analysis in mussels from São Sebastião, São Paulo, Brazil. Environmental Toxicology and Chemistry, v. 26, p. 462, 2007.
Almeida, E.A.; Bainy, A.C.D. Effects of aerial exposure on antioxidant defenses in the brown mussel Perna perna. Brazilian Archives of Biology and Technology, Curitiba, Paraná, v. 49, n. 2, p. 225-229, 2006.
Franco, J.L. ; Trivella, D.B.B. ; Trevisan, R.; Dinslaken, D. ; Marques, M.R.F.; Bainy, A.C.D. ; Dafre, A.L. Antioxidant status and stress proteins in the gills of the brown mussel Perna perna exposed to zinc. Chemico-Biological Interactions, v. 160, n. 3, p. 232-240, 2006.
Almeida, E.A; Bainy, A.C.D. ; Dafré, A.L. ; Gomes, O.; Medeiros, M.H.G.; DiMascio, P. Oxidative stress in digestive gland and gill of the brown mussel () exposed to air and re-submersed. Journal of Experimental Marine Biology and Ecology, v. 318, n. 1, p. 21-30, 2005.
Silva, A.Z.; Zanette, J.; Ferreira, J.F. ; Guzenski, J.; Marques, M.R.F.; Bainy, A.C.D. Effects of salinity on biomarker responses in (Mollusca, Bivalvia) exposed to diesel oil. Ecotoxicology and Environmental Safety, v. 62, p. 376-382, 2005.
Bresolin, T.; Rebelo, M.F.; Bainy, A.C.D. Expression of PXR, CYP3A and MDR1 genes in liver of zebrafish. Comparative Biochemistry and Physiology.
C, Toxicology & Pharmacology, Irlanda, v. 140, n. 3-4, p. 403-407, 2005.
Dafré, A.L.; Medeiros, I.D.; Muller, I.C.; Ventura, E.C.; Bainy, A.C.D. Antioxidant enzymes and thiol/disulfide status in the digestive gland of the
brown mussel exposed to lead and paraquat. Chemico-Biological Interactions, Irlanda, v. 149, n. 2-3, p. 97-105, 2004.
Almeida, E.A.; Bainy, A.C.D. ; Miyamoto, S.; Medeiros, M.H.G. ; DiMascio, P. Protective effect of phospholipid hydroperoxide glutathione peroxidase (PHGPx) against lipid peroxidation in mussels Perna perna exposed to different metals. Marine Pollution Bulletin, v. 49, p. 386-392, 2004.
Almeida, E. A. ; Bainy, A.C.D. ; Loureiro, A.P.M. ; Medeiros, M.H. G. ; DiMascio, P. DNA and Lipid Damage in the brown mussel Perna perna from a
contaminated site. Bulletin of Environmental Contamination and Toxicology, v. 71, p. 270-275, 2003.
Almeida, E.A. ; Bainy, A.C.D. ; Medeiros, M.H.G. ; DiMascio, P. Effects of heavy metal and air exposure on serotonin and dopamine levels in tissues of the mussel Perna perna. Marine Pollution Bulletin, v. 46, p. 1485-1490, 2003.
Dr. Jae-Seong Lee
Hanyang University (UH)
Jae-Seong Lee is full Professor at the College of Natural Sciences, Department of Chemistry of the University of Hanyang (South Korea) since 2009. His main research topics include:
Marine molecular biology and biochemistry,
Marine aquatic toxicology,
Molecular and biochemical approaches using aquatic organisms (e.g. fish, copepod, jellyfish, etc.),
OligoChip approaches,
Environmental systems biology,
Enzyme characteristics
Before joining the Hanyang University in 2001, he has been working at the National Institute for Environmental Studies, Tsukuba, Ibaraki,
Japan (1999-2001); Seoul National University,South Korea (1998-1999); the Department of Biochemistry and Molecular Biology at the Indiana University, USA (1997-1998); the School of Biosciences at the University of Birmingham, UK (1995-1997) and the College of Medicine at the Pennsylvania
State University, USA (1994-1995). He has published more than 157 SCI papers.
Phone: +82-2-2220-0769
e-mail: [email protected]
Contribution to the project:
WP 1: Expression profiling in the intertidal copepod Tigriopus japonicus exposed to four representative pharmaceutical compounds.
WP2: Evaluation of the harpacticoid copepod Tisbe battagliaias model organism for the evaluation of low level environmental contamination by
pharmaceuticals.
RELATED PUBLICATIONS
Kim, B.-M., J.-S. Rhee, J.S. Seo, I.-C. Kim, Y.-M. Lee, and J.-S. Lee, 2012. 8-oxoguanine DNA glycosylase 1 (OGG1) from the copepod Tigriopus japonicus: molecular characterization and its expression in response to UV-B and heavy metals. Comp. Biochem. Physiol., Part C, 155: 290-299.
Won, E.-J., J.-S.Rhee, R.-O. Kim, K. Ra, K.-T.Kim, K.-H. Shin, andJ.-S. Lee, 2012. Susceptibility to oxidative stress and modulated expression of
antioxidant genes in the copper-exposed polychaete, Perinereis nuntia. Comp. Biochem. Physiol., Part C, 155: 344-351.
Rhee, J.-S., E.-J. Won, R.-O. Kim, B.-S. Choi, I.-Y. Choi, G.S. Park, K.-H. Shin, Y.-M. Lee, and J.-S. Lee, 2012. The polychaete, Perinereis
nuntia ESTs and its use to uncover potential biomarker genes for molecular ecotoxicological studies. Environ. Res., 112: 48-57.
Rhee, J.-S., C.-B. Jeong, B.-M. Kim, and J.-S. Lee, 2012. P-glycoprotein (P-gp) in the monogonont rotifer, Brachionus koreanus: Molecular characterization and expression in response to pharmaceuticals. Aquat. Toxicol., 114/115: 104–118.
Kim, J.-H., J.-S. Rhee, H.-U. Dahms, Y.-M. Lee, K.-N. Han, and J.-S. Lee, 2012. The yellow catfish, Pelteobagrus fulvidraco (Siluriformes)
metallothionein cDNA: molecular cloning and transcript expression level in response to exposure to the heavy metals Cd, Cu, and Zn. Fish Physiol. Biochem., in press.
Yi, A.X.L., K.M.Y.,Leung, M.H.W.Lam, J.-S. Lee, and J.P. Giesy, 2012. Review of concentrations of triphenyltin compounds in marine ecosystems and meta-analysis of their risks to human and the environment. Chemosphere, submitted. [review paper]
Rhee, J.-S., B.-M. Kim, C.J. Lee, Y.-D. Yoon, Y.-M. Lee, and J.-S. Lee, 2011. Bisphenol A modulates expression of sex differentiation genes in the self-fertilizing fish, Kryptolebias marmoratus. Aquat. Toxicol., 104: 218– 229.
Won, E.-J., R.-O. Kim, J.-S. Rhee, G.S. Park, J. Lee, K.-H. Shin, Y.-M. Lee, and J.-S. Lee, 2011. Response of glutathione S-transferase (GST) genes to cadmium exposure in the marine pollution indicator worm, Perinereis nuntia. Comp. Biochem. Physiol.,Part C, 154: 82-92.
Rhee, J.-S., E.-J. Won, R.-O. Kim, J. Lee, K.-H. Shin, and J.-S. Lee, 2011. Expression of superoxide dismutase (SOD) genes from the
copper-exposed polychaete, Neanthes succinea. Mar. Pollut. Bull., 63: 277–286.
Kang, S.-W., J. Seo, J. Han,J.-S. Lee, and J. Jung, 2011. A comparative study of toxicity identification using Daphnia magna and Tigriopus japonicus:
implications of establishing effluent discharge limits in Korea. Mar. Pollut. Bull., 63: 370–375.
Marine molecular biology and biochemistry,
Marine aquatic toxicology,
Molecular and biochemical approaches using aquatic organisms (e.g. fish, copepod, jellyfish, etc.),
OligoChip approaches,
Environmental systems biology,
Enzyme characteristics
Before joining the Hanyang University in 2001, he has been working at the National Institute for Environmental Studies, Tsukuba, Ibaraki,
Japan (1999-2001); Seoul National University,South Korea (1998-1999); the Department of Biochemistry and Molecular Biology at the Indiana University, USA (1997-1998); the School of Biosciences at the University of Birmingham, UK (1995-1997) and the College of Medicine at the Pennsylvania
State University, USA (1994-1995). He has published more than 157 SCI papers.
Phone: +82-2-2220-0769
e-mail: [email protected]
Contribution to the project:
WP 1: Expression profiling in the intertidal copepod Tigriopus japonicus exposed to four representative pharmaceutical compounds.
WP2: Evaluation of the harpacticoid copepod Tisbe battagliaias model organism for the evaluation of low level environmental contamination by
pharmaceuticals.
RELATED PUBLICATIONS
Kim, B.-M., J.-S. Rhee, J.S. Seo, I.-C. Kim, Y.-M. Lee, and J.-S. Lee, 2012. 8-oxoguanine DNA glycosylase 1 (OGG1) from the copepod Tigriopus japonicus: molecular characterization and its expression in response to UV-B and heavy metals. Comp. Biochem. Physiol., Part C, 155: 290-299.
Won, E.-J., J.-S.Rhee, R.-O. Kim, K. Ra, K.-T.Kim, K.-H. Shin, andJ.-S. Lee, 2012. Susceptibility to oxidative stress and modulated expression of
antioxidant genes in the copper-exposed polychaete, Perinereis nuntia. Comp. Biochem. Physiol., Part C, 155: 344-351.
Rhee, J.-S., E.-J. Won, R.-O. Kim, B.-S. Choi, I.-Y. Choi, G.S. Park, K.-H. Shin, Y.-M. Lee, and J.-S. Lee, 2012. The polychaete, Perinereis
nuntia ESTs and its use to uncover potential biomarker genes for molecular ecotoxicological studies. Environ. Res., 112: 48-57.
Rhee, J.-S., C.-B. Jeong, B.-M. Kim, and J.-S. Lee, 2012. P-glycoprotein (P-gp) in the monogonont rotifer, Brachionus koreanus: Molecular characterization and expression in response to pharmaceuticals. Aquat. Toxicol., 114/115: 104–118.
Kim, J.-H., J.-S. Rhee, H.-U. Dahms, Y.-M. Lee, K.-N. Han, and J.-S. Lee, 2012. The yellow catfish, Pelteobagrus fulvidraco (Siluriformes)
metallothionein cDNA: molecular cloning and transcript expression level in response to exposure to the heavy metals Cd, Cu, and Zn. Fish Physiol. Biochem., in press.
Yi, A.X.L., K.M.Y.,Leung, M.H.W.Lam, J.-S. Lee, and J.P. Giesy, 2012. Review of concentrations of triphenyltin compounds in marine ecosystems and meta-analysis of their risks to human and the environment. Chemosphere, submitted. [review paper]
Rhee, J.-S., B.-M. Kim, C.J. Lee, Y.-D. Yoon, Y.-M. Lee, and J.-S. Lee, 2011. Bisphenol A modulates expression of sex differentiation genes in the self-fertilizing fish, Kryptolebias marmoratus. Aquat. Toxicol., 104: 218– 229.
Won, E.-J., R.-O. Kim, J.-S. Rhee, G.S. Park, J. Lee, K.-H. Shin, Y.-M. Lee, and J.-S. Lee, 2011. Response of glutathione S-transferase (GST) genes to cadmium exposure in the marine pollution indicator worm, Perinereis nuntia. Comp. Biochem. Physiol.,Part C, 154: 82-92.
Rhee, J.-S., E.-J. Won, R.-O. Kim, J. Lee, K.-H. Shin, and J.-S. Lee, 2011. Expression of superoxide dismutase (SOD) genes from the
copper-exposed polychaete, Neanthes succinea. Mar. Pollut. Bull., 63: 277–286.
Kang, S.-W., J. Seo, J. Han,J.-S. Lee, and J. Jung, 2011. A comparative study of toxicity identification using Daphnia magna and Tigriopus japonicus:
implications of establishing effluent discharge limits in Korea. Mar. Pollut. Bull., 63: 370–375.
Dr. Amel Hamza-Chaffai
Sfax University (USFAX)
Born in August 25th 1965 (Sfax-Tunisia), Amel Chaffai graduated with a Baccalaureate of mathematical Science (1984), an Engineering Diploma in Food science and technology, a Master degree in food and analytical chemistry, a PhD in Biology engineering, and an Accreditation to supervise research in Ecotoxicology. In 2007, she obtained a presidential award of Science Research and Education. She is full Professor at SFAX University since 2005, teaching Zoology and Ecotoxicology and she is author of an online course of Zoology with the Virtual University of Tunis. She also occupied the post of invited Professor in Akita university (Japan), University of Technology (Malaysia), French universities. In research, she is the leader of the research group UR09-03. She, published more than 40 papers in specialized revues of Food Science and ecotoxicology. She was responsible of many international programs with France, Portugal, USA, Japan, Sweden…and expert for national and international environmental projects. Her main research area include Biomonotoring pollution in the marine ecosystems, Pollution and reproduction, Endocrine disruptors, Toxic metal and cancer disease.
Phone: +21674241403
e-mail: [email protected]
Contribution to the project:
WP 6: The use of two bivalves Ruditapes decussates and Cerastoderma galucum in pollution biomonitoring: Effect of metals and endocrine disruptors on the stress response and reproduction based on biomarkers.
WP11: Gathering of obtained biomarker data and identification of common inter-species biomarkers for the different groups of contaminants.
Phone: +21674241403
e-mail: [email protected]
Contribution to the project:
WP 6: The use of two bivalves Ruditapes decussates and Cerastoderma galucum in pollution biomonitoring: Effect of metals and endocrine disruptors on the stress response and reproduction based on biomarkers.
WP11: Gathering of obtained biomarker data and identification of common inter-species biomarkers for the different groups of contaminants.