臺灣博碩士論文加值系統

Metal oxide nanoparticles exhibit unique and diverse applications in biological and biomedical science. The properties of metal oxide nanoparticles and oxide layers on metal surface are attributed to non-stochiometric and quantum size effects. This Ph. D thesis aims exploring the application of bare metal oxide nanoparticles, their fabrication and metal surfaces for biological applications to the detection of biomolecules and bacteria by mass spectrometry. Recently, phosphopeptides have become a critical issue for mapping proteins phosphorylation sites, which are well known as posttranslational modification in proteomics. TiO2 nanoparticles were synthesized and evaluated to serve as multifunctional nanoprobe for microwave-assisted tryptic digestion of phosphoproteins and effective enrichment of phosphopeptides; those were directly analyze by mass spectrometry for phosphopeptides detection. This approach had been applied on α-casein, β-casein and real sample milk phosphopeptides analysis directly by electrospray ionization (ESI) and matrix assisted laser desorption/ionization time of flight (MALDI-TOF) mass spectrometry. High sensitivity and sequence coverage of phophopeptides were obtained using TiO2 NPs as microwave absorbers. This effective digestion of phosphoproteins with TiO2 nanoparticles was observed within 45 seconds. NiO NPs have also been applied as simple and highly sensitive substrates for phosphopeptides enrichment from a trypsin predigested phosphoproteins complex solution within 30 seconds in a microwave oven. Further, this technique was combined with centrifugation on-particle ionization/enrichment of phosphopeptides, and phosphopeptides analyzed by MALDI-TOF mass spectrometry. This approach was applied for sensitive and efficient enrichment of the phosphopeptides from real world complex samples like human blood serum, nonfat milk and egg white, successfully. NiO NPs were further applied for evaluating the heat stress system of Escherichia coli (10^7 cfu/mL) at various temperatures and proteins enrichment using MALDI-TOF mass spectrometry. In the presence of NiO NPs significant number of proteins peaks were obtained. The 10 kDa chaperonin (groES) are the principle proteins that operate for the protection of proteins from heat shocked and work for assembling newly synthesized proteins. During the heat stress response with NiO NPs, 10 kDa chaperonin (groES) proteins were detected using MALDI-TOF mass spectrometry. In addition, heat stress effect on E. coli generate more stable protein ions which can be applied for bacterial detection under high temperature conditions from biological, clinical and environmental samples. Fe3O4-NH2 magnetic nanoparticles were fabricated by amoxicillin drug using carbodiimide chemistry. Staphylococcus aureus and Escherichia coli were used for enrichment based on the β-lactam affinity of Fe3O4-Amox magnetic nanoparticles (MNPs) and separated by a strong external magnet. The affinity between functionalized MNPs and bacterial cell surface was explored by TEM and the capture efficiency was confirmed by plate count method. Fe3O4-Amox MNPs, after attachment of 10^4 -10^3 cfu/mL of S. aureus and E. coli, show multiple bacterial protein ion signals in MALDI-TOF mass spectra. The penicillin binding proteins (PBPs) analysis by MALDI-TOF mass spectrometry was performed based on the β-lactam affinity of Fe3O4-Amox MNPs. Multiple high molecular weight PBPs were observed from E. coli in a range of 20 to 55kDa in MALDI mass spectrum. As per S. aureus bacteria, femAB operon based proteins with molecular weight of 49570.4 Da, were observed by MALDI-TOF mass spectrometry using Fe3O4-Amox MNPs. Biofilm studies have extensive significance since their results can provide insights into the behavior of bacteria on material surfaces when exposed to natural water. In this thesis, MALDI-TOF mass spectrometry had been applied to directly analyze exopolysaccharides (EPS) of the biofilm formed on aluminum surfaces exposed to seawater. The optimal conditions for MALDI mass spectrometry applied for EPS analysis of biofilm are described. In addition, microbiologically influenced corrosion of aluminum exposed to sea water by a marine fungus was also observed and identity of the fungus established using MALDI-TOF mass spectrometry analysis of EPS. This study introduces a novel, fast, sensitive and selective platform for biofilm study from natural water without the need of tedious culturing steps or complicated sample pretreatment procedures. The last chapter in this thesis highlights the effects of surface pretreatment methodologies on subsequent oxide film formation on titanium metal surfaces by heat treatment at 600 °C, 700 °C, 800 °C and 900 °C. Different pretreatment methods and high temperature treatment on titanium metals were applied to generate different morphological rutile oxide surfaces. Further, the different oxide films were ablated by Nd-YAG laser. The ablated titanium substrates and their influence on bacterial adhesion were studied. The influence of the different titanium oxide surfaces, their hydrophobicity and hydrophilicity based properties on the effective functioning of the bacterial chips are presented and the surface properties characterized by SEM and contact angle measurements. The result shows that Staphylococcus aureus preferred hydrophilic surfaces and also had an affinity for the non-heat treated control surfaces. Pseudomonas aeruginosa, on the other hand did not prefer the titanium surfaces and only modification of the surfaces by heat treatment and laser ablation could lead to enhanced adhesion of this bacterium. Laser ablation resulted in significant improvement in the attachment of both the bacteria and led to establishing a superhydrophilic surface. Bacterial attachment on different titanium based chips was confirmed by epifloresence microscope and these chips were used directly on a homemade aluminum MALDI target plate for the detection of the captured bacterial proteins by MALDI-TOF mass spectrometry.

Chapter-1
Introduction………………………………………………………………………………..
1
1.1.0 General Introduction…………………………………………………………….......... 1
1.2.0 Synthesis techniques of oxide nanoparticles……………………………………......... 2
1.3.0 Oxide nanoparticles and microwave based studies for phosphopeptide
enrichment…………………………………………………………………................. 4
1.4.0 Bacteria Cell Envelope and Components……………………………………….......... 7
1.5.0 Bacterial protein profiling by MALDI-TOF MS………………….………………….. 10
1.6.0 Penicillin Binding proteins and bacteria enrichment…………….………………….... 11
1.7.0 Heat stresses on bacteria………………………………………….…………………... 12
1.8.0 Bacterial adhesion and biofilm formation on metal surface……….……………......... 14
1.9.0 Instrumentation…………………………………………………….………………… 15
1.9.1 Laser Desorption and Ionization techniques for biomolecules and bacteria...... 15
1.9.1.1 MALDI mechanism…………………………………………………… 15
1.9.1.2 MALDI matrix considerations biological molecule and bacteria…….. 19
1.9.2 Other ionization techniques for biomolecule and bacteria analysis………....... 19
1.9.3 Transmission and Scanning electron microscopy (TEM and SEM)………...... 21
1.10 Scope of the thesis…………………………………………………………………... 23
1.11 Reference……………………………………………………………………………. 26
Chapter-2
Two-step on-particle ionization/enrichment via a washing- and
separation-free approach: multifunctional TiO2 nanoparticles as
desalting, accelerating, and affinity probes for microwave-assisted tryptic
digestion of phosphoproteins in ESI-MS and MALDI-MS: comparison
with microscale TiO2…………………………………………………………………………………………… 33
2.1.0 Introduction.................................................................................................................. 33
2.2.0 Experimental methods………………………………………...................................... 35
2.2.1 Reagents and materials……………………………………................................ 35
2.2.2 Preparation of solutions ………………………………………......................... 35
2.2.3 Synthesis and preparation of the TiO2 NPs solution …………………………. 36
2.2.4 Preparation of microscale TiO2 solution …………………………………........ 36
2.2.5 Procedures for microwave-assisted tryptic digestion of phosphoproteins
using nanoscale and microscale TiO2 particles in ESI-MS and MALDI MS…. 36
2.2.6 Procedures for two-step on-particle ionization/enrichment of TiO2 NPs
assisted microwave-assisted tryptic digestion of milk………………………….. 37
2.2.7 Instruments……………………………………………………………………... 38
2.2.7.1 Microwave used………………………………………………………… 38
2.2.7.2 ESI-MS analysis…………………………………………………........... 38
2.2.7.3 MALDI time of flight MS analysis…………………………………….. 39
2.2.8 Matching the mass spectral data of ESI-MS and MALDI TOF- MS with the
results of MS-Fit and BioTools……………………………………………....... 39
2.3.0 Results and discussion………………………………………………………………. 39
2.3.1 Characterization of TiO2 NPs ………………………………………………….. 39
2.3.2 Determination of the optimal conditions for TiO2 NPs assisted microwave
assisted tryptic digestions of phosphoproteins…………………………………. 40
2.3.3 Probing the microwave absorbing property of TiO2 NPs and microscale
TiO2 particles in microwave-assisted tryptic digestion of phosphoproteins……. 41
2.3.4 Two-step on-particle ionization / enrichment of TiO2 NPs assisted
microwave-assisted tryptic digestion of α-casein and enrichment of
phosphopeptides in ESI-MS………………………………………………….. 42
2.3.5 Two-step approach for TiO2 NPs assisted microwave assisted tryptic
digestion of α-casein and enrichment of phosphopeptides in MALDI-
TOF-MS………………………………………………………………………… 45
2.3.6 Application of the two-step approach of TiO2 NPs for acceleration and
enrichment of phosphopeptides from milk……………………………………. 48
2.3.7 Application of the two-step approach of TiO2 NPs assisted microwave-
assisted tryptic digestion of phosphoproteins from protein mixtures………..... 50
2.3.8 Detection sensitivity for the two-step approach of TiO2 NPs assisted
microwave-assisted tryptic digestions of phosphoprotein and enrichment
of phosphopeptides in ESI-MS and MALDI-MS……………………………. 51
2.3.9 Principle of two-step on-particle ionization/enrichment of TiO2 NPs
assisted microwave-assisted tryptic digestions of phosphoproteins in ESI-
MS and MALDI-MS………………………………………………………….. 54
2.4.0 Conclusions………………………………………………………………………….. 55
2.5.0 References…………………………………………………………………………… 56
Chapter-3
Highly selective and sensitive enrichment of phosphopeptides via NiO
nanoparticles using a microwave-assisted centrifugation on-particle
ionization/enrichment approach in MALDI-MS………………………....... 60
3.1.0 Introduction………………………………………………………………………….. 60
3.2.0 Experimental………………………………………………………………………… 62
3.2.1 Reagent and materials………………………………………………………… 62
3.2.2 Preparation of NiO NPs………………………………………………………. 63
3.2.3 Tryptic digestion of standard phosphoproteins……………………………..... 63
3.2.4 Procedures for tryptic digestion of nonfat milk and egg white………………. 64
3.2.5 Procedure for enrichment of phosphopeptides on NiO NPs using a
microwave and CF-OPIE approach…………………………………………… 64
3.2.6 Instrumentation and database searches……………………………………...... 65
3.3.0 Results and discussion……………………………………………………………… 66
3.3.1 Characterization of the NiO NPs and the CF-OPIE approach……………….. 66
3.3.2 Optimization of microwave irradiation time in the CF-OPIE approach on
NiO NPs for phosphopetide analysis….……………………………………… 68
3.3.3 Performance of the microwave-assisted CF-OPIE approach for the
isolation of phosphopeptides via NiO NPs..………………………………….. 69
3.3.4 Application of NiO NPs for real sample phosphoproteome analysis………… 78
3.4.0 Conclusions………………………………………………………………………… 83
3.5.0 References………………………………………………………………………….. 84
Chapter-4
Monitoring the heat stress response of Escherichia coli via NiO
nanoparticle assisted MALDI–TOF mass spectrometry……………….....
87
4.1.0 Introduction……………………………………………………………………….... 87
4.2.0 Material and methods……………………………………………………………..... 90
4.2.1 Chemical and reagents………………………………………………………... 90
4.2.2 Bacterial strain and cells culture preparation ……………………………....... 90
4.2.3 Synthesis of NiO nanoparticles ……………………………………………… 91
4.2.4 Procedure of heat treatment to E. coli bacterial cells………………………… 91
4.2.5 Measurement of cells grows that different temperatures treatment................. 92
4.2.6 Sample preparation for transmission electron microscopy................................ 93
4.2.7 Heat treated bacterial cell samples for MALDI–TOF MS analysis………...... 93
4.2.8 MALDI–TOF MS instrumentation and acquisition………………………...... 93
4.3.0 Results and discussion……………………………………………………………… 94
4.4.0 Conclusion………………………………………………………………………..... 106
4.5.0 References………………………………………………………………………...... 107
Chapter 5
Amoxicillin functionalized Fe3O4 magnetic nanoparticles for bacteria
enrichment and large proteins analysis by MALDI-TOF mass
spectrometry………………………………………………………………..... 110
5.1.0 Introduction………………………………………………………………………… 110
5.2.0 Experimental……………………………………………………………................... 112
5.2.1 Materials……………………………………………………………………… 112
5.2.2 Equipment…………………………………………………………………..... 112
5.2.3 Preparation of APTES functionalized Fe3O4 MNPs…………………………. 113
5.2.4 Preparation of amoxicillin functionalized Fe3O4-APTES MNPs……………. 114
5.2.5 Bacterial strain and cells culture preparation………………………………… 115
5.2.6 Bacterial sample preparation, affinity and separation with MNPs analysis
by MALDI TOF mass spectrometry…………………………………….……. 115
5.2.7 Bacterial capture efficiency of Fe3O4-APTES and Fe3O4-Amox MNPs……... 116
5.2.8 Penicillin binding proteins enrichment on Fe3O4-Amox MNPs………….….. 116
5.3.0 Results and discussion………………………………………………………….….. 117
5.3.1 FT-IR spectrum……………………………………………………………...... 117
5.3.2 Thermogravimetric analysis (TGA)………………………………………...... 120
5.3.3 TEM data……………………………………………………………………... 121
5.3.4 MALDI-TOF mass spectrometric analysis of bacteria……………………….. 124
5.3.5 Large Proteins (PBPs) analysis by MALDI MS……………………………… 129
5.4.0 Conclusion …………………………………………………………………………. 132
5.5.0 References………………………………………………………………………….. 133
Chapter-6
Rapid, sensitive and direct analysis of exopolysaccharides from biofilm on
aluminum surfaces exposed to sea water using MALDI-TOF MS…… 136
6.1.0 Introduction………………………………………………………………………… 136
6.2.0 Experimental section……………………………………………………………...... 138
6.2.1 Chemicals and methods………………………………………………………. 138
6.2.2 Preparation of aluminum coupons for biofilm formation…………………… 139
6.2.3 Biofilm formation in seawater………………………………………………. 139
6.2.4 Biofilm sample preparation prior to MS detection…………………………… 139
6.2.5 Preparation of matrix solution……………………………………………….. 140
6.2.6 MALDI-TOF MS and ESI-MS analysis……………………………………… 140
6.3.0 Results and discussion……………………………………………………………. 141
6.3.1 Detection of supernatant and precipitate from biofilm……………………….. 145
6.3.2 Effect of matrix and positive or negative ion mode for detection…………..... 146
6.3.3 Observation of microbiologically influenced corrosion……………………… 150
6.4.0 Conclusion………………………………………………………………………..... 153
6.5.0 References………………………………………………………………………….. 154
Chapter 7
MALDI-MS probing the influence of surface pretreatment, laser ablation
induced hydrophobicity/hydrophilicity of titanium surfaces on the
attachment/inhibition of bacteria…………………………………………………
157
7.1.0 Introduction………………………………………………………………………… 157
7.2.0 Material and Methods……………………………………………………………… 159
7.2.1 Material …………………………………………………………………….... 159
7.2.2 Sample pretreatment………………………………………………………..... 159
7.2.3 Heat treatment and ablation of bacterial chip using Nd-YAG LASER…….... 160
7.2.4 Exposure to bacterial solutions………………………………………………. 160
7.3.0 Result and discussion……………………………………………………………..... 162
7.3.1 Morphological variation in biochip surfaces…………………………………. 162
7.3.2 Surface hydrophobicity/hydrophilicity……………………………………… 165
7.3.3 Effect of pretreatment on bacterial biochip…………………………………... 169
7.3.4 Effect of laser ablation on bacterial biochip…………………………………. 180
7.4.0 Conclusion………………………………………………………………………..... 189
7.5.0 References……………………………………………. 189
Chapter 8, Conclusion of thesis…………192
Appendix-1…………………………...........195
Appendix-2…………………………………197

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