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Universita' Degli Studi Di Parma UNIVERSITA’ DEGLI STUDI DI PARMA DOTTORATO DI RICERCA IN BIOTECNOLOGIE XXIII° CICLO FUNCTIONAL ANALYSIS OF POPLAR (Populus nigra L. and P. nigra x P. deltoids) DURING ENVIRONMENTAL EXPOSURE TO METALS Coordinatore: Chiar.mo Prof. Nelson Marmiroli Relatore: Chiar.mo Prof. Nelson Marmiroli Tutor: Dott.ssa Marta Marmiroli Dott.ssa Giovanna Visioli Dottorando: Dott. Davide Imperiale CONTENTS 1 GENERAL INTRODUCTION .................................................................................................................................. 4 1.1 HEAVY METALS POLLUTION....................................................................................................................................... 4 1.2 REMEDIATION TECHNOLOGIES AND PHYTOREMEDIATION ............................................................................................... 7 1.3 HYPERACCUMULATION .......................................................................................................................................... 10 1.4 MECHANISM OF BIOACCUMULATION IN PLANTS .......................................................................................................... 14 1.5 PHYTOREMEDIATION USING WOODY TREES ................................................................................................................ 17 1.6 PROTEOMICS ....................................................................................................................................................... 21 1.7 PROTEIN SEPARATION TECHNIQUES .......................................................................................................................... 22 1.7.1 Two-dimensional electrophoresis ............................................................................................................... 22 1.7.2 Two-dimensional liquid cromatography ..................................................................................................... 27 1.7.3 Liquid cromatography by “ProteomeLab PF 2D” ........................................................................................ 27 1.7.4 Advantages and disadvantages of 2D-gel electrophoresis vs 2D liquid chromatography .......................... 28 1.8 PROTEIN IDENTIFICATION BY MASS SPECTROMETRY .................................................................................................... 30 1.8.1 MALDI/TOF Mass spectrometry .................................................................................................................. 30 1.8.2 Peptide mass fingerprinting (PMF) ............................................................................................................. 32 1.9 REFERENCES ........................................................................................................................................................ 34 2 FUNCTIONAL ANALYSIS OF POPLAR (POPULUS NIGRA L. AND P. NIGRA X P. DELTOIDS) DURING ENVIRONMENTAL EXPOSURE TO METALS .................................................................................................................70 2.1 INTRODUCTION .................................................................................................................................................... 70 2.1.1 Poplar .......................................................................................................................................................... 70 2.1.2 Cadmium in the environment ..................................................................................................................... 73 2.1.3 Effects of cadmium toxicity in plants .......................................................................................................... 75 2.1.4 Plants responses to Cd ................................................................................................................................ 79 2.1.5 Plant proteomics and cadmium .................................................................................................................. 80 2.1.6 Objectives .................................................................................................................................................... 82 2.2 MATERIALS AND METHODS .................................................................................................................................... 83 2.2.1 Plant Material ............................................................................................................................................. 83 2.2.2 Hydroponic culture and treatments ............................................................................................................ 83 2.2.3 Physiological measures and statistical analysis .......................................................................................... 84 2.2.4 Elemental analysis by Atomic Absorption Spectroscopy (AAS) ................................................................... 84 2.2.5 Scanning Electron Microscopy with microanalysis (SEM/EDX) ................................................................... 85 2.2.6 Protein Samples Preparation ...................................................................................................................... 85 2.2.7 Protein Quantification ................................................................................................................................. 86 2.2.8 PD10 desalting column ............................................................................................................................... 86 2.2.9 Two dimensional liquid chromatography "Proteome Lab PF2D" ............................................................... 86 2.2.10 MALDI-TOF Analysis................................................................................................................................ 88 2.2.11 Software and statistical analysis ............................................................................................................ 89 2.3 RESULTS AND DISCUSSION ..................................................................................................................................... 90 2.3.1 Plant morphology and growth analysis ...................................................................................................... 90 2.3.2 Mineral analysis .......................................................................................................................................... 94 2.3.3 Scanning Electron Microscopy with microanalysis (SEM/EDX) ................................................................... 98 2.3.4 Proteomic Analysis .................................................................................................................................... 110 2.3.5 Proteins identification ............................................................................................................................... 119 2.4 CONCLUSION ..................................................................................................................................................... 151 2.5 REFERENCES ...................................................................................................................................................... 157 3 ACKNOWLEDGEMENTS ................................................................................................................................... 180 4 LIST OF PAPERS ............................................................................................................................................... 181 2 CHAPTER 1 3 1 GENERAL INTRODUCTION 1.1 Heavy metals pollution Heavy metals are commonly defined as elements with atomic number >20 and metallic proprieties (ductility, stability as cations, ligand specificity, conductivity, etc.). Metals are natural components in soil but the industrial revolution has accelerated drastically the pollution of the biosphere due to heavy metals mining and utilization. Soil pollution by metals differs from air or water pollution, because heavy metals persist in soil much longer than in other compartments of the biosphere (Lasat et al., 2002). Sources of heavy metal contamination in soils include point sources such as emission, effluents and solid discharge from industries, metals from smelting and mining, warfare and military training and vehicle exhaustion, and nonpoint sources such as soluble salt, disposal of industrial and municipal wastes, use of insecticides and pesticides in agriculture, and excessive use of fertilizers (McGrath et al., 2001; Nriagu, 1979; Alloway et al., 1995). For example, mine tailings rich in sulphide minerals may form acid mine drainage (AMD) through reaction with atmospheric oxygen and water, and AMD contains elevated levels of metals that could be harmful to animals and plants (Stoltz, 2004). Ground-transportation also causes metal contamination. Highway traffic, road maintenance, and de- icing operations generate continuous surface and ground water contamination. Tread ware, brake abrasion, and corrosion are well documented heavy metal sources associated with highway traffic (Ho and Tai, 1988; Fatoki, 1996; García and Millán, 1998; Sánchez Martín et al., 2000). Heavy metal contaminants in roadside soils originate from engine and brake pad wear (Cd, Cu, and Ni) (Viklander, 1998); lubricants (Cd, Cu and Zn) (Birch and Scollen, 2003; Turer et al., 2001); exhaust emissions, (Pb) (Gulson et al., 1981; Al-Chalabi and Hawker, 2000; Sutherland et al., 2003); and tire abrasion (Zn) (Smolders
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