Biofilms:
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| Other Authors: | , |
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| Format: | Book |
| Language: | English |
| Published: |
London ; Oxford ; San Diego, CA ; Cambridge, MA
Academic Press, an imprint of Elsevier
2023
|
| Edition: | First edition |
| Series: | Methods in microbiology
volume 53 |
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | xviii, 324 Seiten Illustrationen, Diagramme 23 cm |
| ISBN: | 9780323988339 |
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| 245 | 1 | 0 | |a Biofilms |c edited by Volker Gurtler (School of Science, College of Science Engineering and Health, RMIT University, Bundoora, VIC, Australia), Marianna Patrauchan (Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United Stated) |
| 250 | |a First edition | ||
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| adam_text | Contents Contributors............................................................................................................... xiii Preface........................................................................................................................xvii SECTION 1 Plant biofilms_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ CHAPTER 1 Bacterial biofilms as an essential component of rhizosphere plant-microbe interactions.3 Ankita Bhattacharyya, Olga Mavrodi, Niladri Bhowmik, David Weller, Linda Thomashow, and Dmitri Mavrodi 1. Introduction......................................................................................... 4 2. Rhizosphere—A microbial habitat shaped by root exudates........ 6 3. Experimental approaches for studying rhizosphere biofilms...... 11 3.1 Growing biofilms in the presence of root exudates.............. 11 3.2 The use of microfluidics in the rhizosphere biofilm research...................................................................................... 16 3.3 Integration of rhizosphere biofilm research with microscopy................................................................................ 17 3.4 Other emerging approaches for mapping rhizosphere biofilms....................................................................................... 18 4. Sensing the plant host: Bacterial chemotaxis towards plant roots exudates.................................................................................... 19 5. Colonizing the plant root................................................................ 22 5.1 Attachment to plant
roots......................................................... 22 5.2 The rhizosphere biofilm matrix............................................... 24 5.3 Regulatory mechanisms thatgovern the biofilm lifestyle... 26 6. The importance of rhizosphere biofilms....................................... 28 7. Conclusions........ ............................................................................. 31 Acknowledgements................................................................................ 31 References............................................................................................... 32 SECTION 2 Mixed species_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ CHAPTER 2 Monospecies and polymicrobial biofilms in static and flow environment........................ 51 Mohd Hafiz Arzmi, Wan NurHazirah Wan Ahmad Kamil, and Mukarramah Zainal 1. Introduction........................................................................... 52 2. Biofilm and flow environment........................................................ 52 V
Contents Key resources table......................................................................... 53 Materials and equipment................................................................ 55 5. Step-by-step method details........................................................... 55 5.1 Growth of microorganisms...................................................... 55 5.2 Static biofilm formation........................................................... 56 5.3 Crystal violet assay................................................................... 57 5.4 XTT reduction assay........................... 57 5.5 Flow cell preparation................................................................ 58 5.6 Flow-cell biofilm formation..................................................... 58 5.7 Flow-cell gel acrylamide preparation..................................... 59 5.8 In situ hybridization,(FISH) staining...................................... 60 5.9 Confocal laser scanning microscopy andimage analysis.... 60 6. Quantification and statistical analysis............................................ 63 6.1 Advantages..................................................... ........64 6.2 Limitations................................................................................. 64 7. Optimization and troubleshooting...................................................64 7.1 Potential Solution to optimize the procedure......................... 64 8. Safety considerations and standards............................................... 65 9. Alternative
methods/procedures......................................................65 References............................................................................................... 65 Further reading....................................................................................... 66 3. 4. CHAPTER 3 Optimization of protocol for quantification of biofilm formed by pathogenic rapidly-growing nontuberculous mycobacteria for diagnostic screening.............................................................. 67 Ayushi Sharma, Nidhi Tyagi, and Rahul Shrivastava 1. Introduction....................................................................... 69 1.1 Biofilm....................... 69 1.2 The nontuberculous mycobacteria(NTM)...............................71 1.3 NTM biofilm..............................................................................73 1.4 Biofilm estimation methods..................................................... 74 1.5 Outline of the chapter............................................................... 77 2. Biofilm culture of the NTM strain................................................ 78 2.1 Materials, equipment, and reagents......................................... 78 2.2 Protocols..................................................................................... 78 2.3 Safety considerations and standards........................................ 80 2.4 Analysis and statistics............................................................... 80 2.5 Pros and cons............................................................................. 81 2.6
Troubleshooting and optimization........................................... 81
Contents 3. Crystal violet assay of the NTM biofilm....................................... 81 4. 5. 6. 7. 3.1 Materials, equipment, and reagents......................................... 81 3.2 Protocol...................................................................................... 82 3.3 Safety considerations and standards....................................... 82 3.4 Analysis and statistics...............................................................82 3.5 Pros and cons....................................... 82 3.6 Troubleshooting and optimization........................................... 83 Response surface methodology based optimization of culture conditions favouring maximum biofilm formation by NTM....................................................................................... 83 4.1 Materials, equipment, and reagents......................................... 84 4.2 Protocol...................................................................................... 84 4.3 Safety considerations and standards........................................86 4.4 Analysis and statistics............................................................... 86 4.5 Pros and cons............................................................................. 86 4.6 Troubleshooting and optimization........................................... 87 Sonication and colony forming unit (CFU) count of NTM biofilm.......................................................................................... 87 5.1 Materials, equipment, andreagents......................................... 87 5.2
Protocols.....................................................................................87 5.3 Safety considerations and standards........................................89 5.4 Analysis and statistics............................................................... 89 5.5 Pros and cons............................................................................. 90 5.6 Troubleshooting and optimization........................................... 90 Determination of the number of days required for NTM biofilm formation........................................................................ 90 6.1 Materials, equipment, and reagents........................................90 6.2 Protocols................................................................................... 90 6.3 Safety considerations and standards...................................... 91 6.4 Analysis and statistics..............................................................91 6.5 Pros and cons............................................................................91 6.6 Troubleshooting and optimization......................................... 91 Basic fuchsin staining of biofilm-forming cells of the pathogenic NTM strain...............................................................91 7.1 Materials, equipment, and reagents......................................... 91 7.2 Protocol...................................................................................... 92 7.3 Safety considerations and standards........................................92 7.4 Analysis and
statistics............................................................... 92 7.5 Pros and cons............................................................................. 92 7.6 Troubleshooting and optimization.................... 93
viii Contents Scanning electron microscopy (SEM) of NTM planktonic and biofilm-forming cells....................................................... 93 8.1 Materials, equipment, and reagents........ ............................. 93 8.2 Protocols................................................................................ 94 8.3 Safety considerations and standards..................................... 95 8.4 Analysis and statistics....... ................................................... 96 8.5 Pros and cons..................................... 96 8.6 Troubleshooting and optimization........................................ 96 9. Conclusion.................................................................................. 96 Acknowledgement............................................................................. 97 References........................ .·................................................................ 97 8. CHAPTER 4 Investigating inter-kingdom interaction between oral Streptococcus mutans and Candida species in mixed-species biofilms................... 101 Md Mahamudul Haque, Tejas Gupte, Ankita Vaishampayan, Navi Mann, and Kangmin Duan 1. Introduction............................................ :................................... 101 2. Materials and methods................................................................103 2.1 Bacterial strains, media, and growth condition................... 103 2.2 Biofilm formation......................................... ...................... 104 2.3 Staining biofilms grown on a
coverslip.............................. 106 2.4 Biofilm examination and image acquisition....................... 107 2.5 Microbial growth assay....................................................... 108 2.6 pH measurement.................................................................. 109 2.7 Measuring the effect of antimicrobial agents on biofilms ...109 2.8 Statistical analysis............................................................... 110 3. Results and discussions...............................................................110 3.1 Growth of S. mutans and Candida species and experimental conditions...................................................... 110 3.2 Formation of biofilms in the microchannel of the BioFlux plate...................................................................... Ill 3.3 Structural examination of the mono-species and mixed-species biofilms........................................................ 112 3.4 Characteristic comparison of the bacterium-fungal mixed-species biofilms........................................................ 115 3.5 Characterization of antimicrobial activity on co-culture... 116 4. Conclusion.................................................................................. 118 References........................................................................................ 118
Contents SECTION 3 Nano techniques_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ CHAPTER 5 Programming bacterial adhesion to functionalized surfaces through cellular display of recombinant nanobodies.............. 123 Sofia Fraile, Esteban Veiga, Victor de Lorenzo, and Esteban Martinez-Garcia 1. Introduction.................................................................................... 124 2. Materials......................................................................................... 126 2.1 Strains and plasmids......................... 126 2.2 Bacterial growth media........................................................... 126 2.3 Chemicals and reagents.......................................................... 126 2.4 DNA and protein techniques.................................................. 127 2.5 Other laboratory material........................................................128 3. Methods.......................................................................................... 129 3.1 Introducing the recombinant adhesin expression plasmid into E. coli....................................................... ......... 129 3.2 Testing the expressionof the recombinant adhesin.............. 131 3.3 Assaying the display of the recombinant adhesin................133 3.4 Evaluating the functionality of the recombinant adhesin... 134 4. Notes/troubleshooting.................................................................... 137 Acknowledgements.............................................................................. 138
References............................................................................................. 138 CHAPTER 6 Micro- and nanoscale techniques for studying biofilm-mineral interactions............. 143 Luca Stigliano, Jeanne Caumartin, and Karim Benzerara 1. Introduction......................................................................................144 2. Confocal laser scanning microscopy (CLSM) to image biofilm-minerals assemblages in situ, at the submicrometer scale............................................................................................ 148 3. Optical coherence tomography (OCT) to in situ characterize the structure of thick biofilms at the micrometre scale over large areas.................................................................................. 151 4. Atomic force microscopy (AFM) to image the topography, and mechanical, electrical and chemical properties of biofilm-mineral assemblages at the sub-nanometre scale... 153 5, Vertical scanning interferometry (VSI) to quantify dissolution rates of mineral substrates covered by biofilms...... 157
x Contents 6. Analyses of biofilm-mineral interactions down to the nanometre scale by scanning electron microscopy and helium ion microscopy............................. ,.............................. 161 7. Focused ion beam milling for ТЕМ sample preparation and 3D nanoscale investigation of biofilm-mineral interactions......................... .-...................................................... 164 8. Transmission electron microscopy (ТЕМ) to study biofilm-mineral interactions..................................................... 168 9. Characterizing chemical element distribution and speciation in biofilm-mineral assemblages by spectroscopies................171 Acknowledgements..........:.·.................................................................. 176 References............................................................................................. 176 SECTION 4 Genetics and microfluidics_ _ _ _ _ _ _ _ _ _ _ _ _ CHAPTER 7 Methods for studying biofilms: Microfluidics and translation in the clinical context...... 195 Júlia Alcàcer-Almansa, Betsy Verónica Arévalo-Jaimes, Núria Blanco-Cabra, and Eduard Torrents Introduction.................................................................................... 196 General in vitro methods to study biofilms................................ 197 2.1 Static or closed models........................................................... 199 2.2 Dynamic or open models........................................................201 3. Microfluidics for biofilm study.................................... ................ 204 3.1
Microfluidics for biofilm fluid mechanics characterization and biofilm modelling............................... 212 3.2 Microfluidics for studying the environmental influences on biofilm development..................... 213 3.3 Microfluidics for detecting biofilm adhesion, monitoring biofilm growth and testing antibiofilm activity...................................................................................... 214 4. From bench to bedside................................................................... 215 4.1 General overview of biofilm research translation............... 215 4.2 Translation of biofilm devices............................................... 216 4.3 Limitations and considerations.............................................. 220 Acknowledgements.............................................................................. 222 Author contribution.............................................................................. 222 References............................................................................................. 223 1. 2.
Contents CHAPTER 8 Studying gene expression in biofilms................... 235 Nasibeh Arabameri and Boo Shan Tseng 1. Why study gene expression of biofilm cells?............................. 236 2. Methods for studying individual genes........................................ 237 2.1 Northern blot analysis............................................................ 237 2.2 RT-qPCR................................................... ........................... 238 2.3 Reporter gene assay................................................................ 241 2.4 mRNA-FISH........................................................................... 246 2.5 Advantages and limitations of thesemethods..................... 247 3. Methods for studying transcriptomes........................................... 249 3.1 DNA microarray analysis...................................................... 249 3.2 RNA-seq.................................................................................. 251 3.3 Advantages and limitations of thesemethods..................... 254 4. Methods for studying heterogeneity of geneexpression............. 254 4.1 Thin sectioning........................................................................ 254 4.2 LCM......................................................................................... 255 4.3 Single-cell analysis................................................................. 255 4.4 Fluorescence microscopy....................................................... 256 4.5 Advantages and limitations of thesemethods..................... 256 5.
Conclusions..................................................................................... 257 Acknowledgement............................................................................... 258 References.............................................................................................258 SECTION 5 Microsocopy_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ CHAPTER 9 Spatial analysis of multispecies bacterial biofilms.......................................... 275 Virgile Guéneau, Raphaël Charron, Vlad Costache, Arnaud Bridier, and Romain Briandet 1. Introduction..................................................................................... 275 2. General workflow for biofilms spatial analysis........................... 277 2.1 Generating and capturingbiofilms for spatial analysis....... 277 2.2 Biofilm labelling for fluorescencemicroscopy..................... 280 2.3 Imaging biofilms..................................................................... 285 2.4 Image analysis......................................................................... 288 3. Experimental protocol.................................................................... 291 3.1 Before you begin..................................................................... 292 3.2 Materials...................................................................................293 3.3 Methods.................................................................................... 293 Acknowledgements............................................................................. 297
References............................................................................................ 297 xi
xii Contents CHAPTER 10 Use of epifluorescence widefield deconvolution microscopy for imaging and three-dimensional rendering of Pseudomonas aeruginosa biofilms and extracellular matrix materials.... 309 Heidi J. Smith and Michael J. Franklin 1. Introduction............................................................................... 309 2. Materials and methods.............................................................. 312 2.1 Strains and biofilmgrowth conditions................................. 312 2.2 Biofilm staining...................................................................312 2.3 Biofilm imaging and image processing using wide-field deconvolution microscopy.................................................. 313 3. Results and discussion.............................................................. 314 3.1 Imaging early biofilm formation by P. aeruginosa PAO1 using epifluorescence wide-field deconvolution microscopy......................................................................... 314 3.2 Effect of calcium addition on initial P. aeruginosa PAO1 biofilm formation............................................. 316 3.3 Effect of PSL extracellular matrix polysaccharide on early P. aeruginosa PAO1 biofilm formation............. 317 3.4 Biovolume analysis of biofilms before and after computational clearing................................................. 319 4. Conclusions................................................................................ 320 Acknowledgements......................................................................... 322
References........................................................................................ 322
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| adam_txt |
Contents Contributors. xiii Preface.xvii SECTION 1 Plant biofilms_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ CHAPTER 1 Bacterial biofilms as an essential component of rhizosphere plant-microbe interactions.3 Ankita Bhattacharyya, Olga Mavrodi, Niladri Bhowmik, David Weller, Linda Thomashow, and Dmitri Mavrodi 1. Introduction. 4 2. Rhizosphere—A microbial habitat shaped by root exudates. 6 3. Experimental approaches for studying rhizosphere biofilms. 11 3.1 Growing biofilms in the presence of root exudates. 11 3.2 The use of microfluidics in the rhizosphere biofilm research. 16 3.3 Integration of rhizosphere biofilm research with microscopy. 17 3.4 Other emerging approaches for mapping rhizosphere biofilms. 18 4. Sensing the plant host: Bacterial chemotaxis towards plant roots exudates. 19 5. Colonizing the plant root. 22 5.1 Attachment to plant
roots. 22 5.2 The rhizosphere biofilm matrix. 24 5.3 Regulatory mechanisms thatgovern the biofilm lifestyle. 26 6. The importance of rhizosphere biofilms. 28 7. Conclusions. . 31 Acknowledgements. 31 References. 32 SECTION 2 Mixed species_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ CHAPTER 2 Monospecies and polymicrobial biofilms in static and flow environment. 51 Mohd Hafiz Arzmi, Wan NurHazirah Wan Ahmad Kamil, and Mukarramah Zainal 1. Introduction. 52 2. Biofilm and flow environment. 52 V
Contents Key resources table. 53 Materials and equipment. 55 5. Step-by-step method details. 55 5.1 Growth of microorganisms. 55 5.2 Static biofilm formation. 56 5.3 Crystal violet assay. 57 5.4 XTT reduction assay. 57 5.5 Flow cell preparation. 58 5.6 Flow-cell biofilm formation. 58 5.7 Flow-cell gel acrylamide preparation. 59 5.8 In situ hybridization,(FISH) staining. 60 5.9 Confocal laser scanning microscopy andimage analysis. 60 6. Quantification and statistical analysis. 63 6.1 Advantages. '.64 6.2 Limitations. 64 7. Optimization and troubleshooting.64 7.1 Potential Solution to optimize the procedure. 64 8. Safety considerations and standards. 65 9. Alternative
methods/procedures.65 References. 65 Further reading. 66 3. 4. CHAPTER 3 Optimization of protocol for quantification of biofilm formed by pathogenic rapidly-growing nontuberculous mycobacteria for diagnostic screening. 67 Ayushi Sharma, Nidhi Tyagi, and Rahul Shrivastava 1. Introduction. 69 1.1 Biofilm. 69 1.2 The nontuberculous mycobacteria(NTM).71 1.3 NTM biofilm.73 1.4 Biofilm estimation methods. 74 1.5 Outline of the chapter. 77 2. Biofilm culture of the NTM strain. 78 2.1 Materials, equipment, and reagents. 78 2.2 Protocols. 78 2.3 Safety considerations and standards. 80 2.4 Analysis and statistics. 80 2.5 Pros and cons. 81 2.6
Troubleshooting and optimization. 81
Contents 3. Crystal violet assay of the NTM biofilm. 81 4. 5. 6. 7. 3.1 Materials, equipment, and reagents. 81 3.2 Protocol. 82 3.3 Safety considerations and standards. 82 3.4 Analysis and statistics.82 3.5 Pros and cons. 82 3.6 Troubleshooting and optimization. 83 Response surface methodology based optimization of culture conditions favouring maximum biofilm formation by NTM. 83 4.1 Materials, equipment, and reagents. 84 4.2 Protocol. 84 4.3 Safety considerations and standards.86 4.4 Analysis and statistics. 86 4.5 Pros and cons. 86 4.6 Troubleshooting and optimization. 87 Sonication and colony forming unit (CFU) count of NTM biofilm. 87 5.1 Materials, equipment, andreagents. 87 5.2
Protocols.87 5.3 Safety considerations and standards.89 5.4 Analysis and statistics. 89 5.5 Pros and cons. 90 5.6 Troubleshooting and optimization. 90 Determination of the number of days required for NTM biofilm formation. 90 6.1 Materials, equipment, and reagents.90 6.2 Protocols. 90 6.3 Safety considerations and standards. 91 6.4 Analysis and statistics.91 6.5 Pros and cons.91 6.6 Troubleshooting and optimization. 91 Basic fuchsin staining of biofilm-forming cells of the pathogenic NTM strain.91 7.1 Materials, equipment, and reagents. 91 7.2 Protocol. 92 7.3 Safety considerations and standards.92 7.4 Analysis and
statistics. 92 7.5 Pros and cons. 92 7.6 Troubleshooting and optimization. 93
viii Contents Scanning electron microscopy (SEM) of NTM planktonic and biofilm-forming cells. 93 8.1 Materials, equipment, and reagents. . 93 8.2 Protocols. 94 8.3 Safety considerations and standards. 95 8.4 Analysis and statistics. . 96 8.5 Pros and cons. 96 8.6 Troubleshooting and optimization. 96 9. Conclusion. 96 Acknowledgement. 97 References. .·. 97 8. CHAPTER 4 Investigating inter-kingdom interaction between oral Streptococcus mutans and Candida species in mixed-species biofilms. 101 Md Mahamudul Haque, Tejas Gupte, Ankita Vaishampayan, Navi Mann, and Kangmin Duan 1. Introduction. :. 101 2. Materials and methods.103 2.1 Bacterial strains, media, and growth condition. 103 2.2 Biofilm formation. . 104 2.3 Staining biofilms grown on a
coverslip. 106 2.4 Biofilm examination and image acquisition. 107 2.5 Microbial growth assay. 108 2.6 pH measurement. 109 2.7 Measuring the effect of antimicrobial agents on biofilms .109 2.8 Statistical analysis. 110 3. Results and discussions.110 3.1 Growth of S. mutans and Candida species and experimental conditions. 110 3.2 Formation of biofilms in the microchannel of the BioFlux plate. Ill 3.3 Structural examination of the mono-species and mixed-species biofilms. 112 3.4 Characteristic comparison of the bacterium-fungal mixed-species biofilms. 115 3.5 Characterization of antimicrobial activity on co-culture. 116 4. Conclusion. 118 References. 118
Contents SECTION 3 Nano techniques_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ CHAPTER 5 Programming bacterial adhesion to functionalized surfaces through cellular display of recombinant nanobodies. 123 Sofia Fraile, Esteban Veiga, Victor de Lorenzo, and Esteban Martinez-Garcia 1. Introduction. 124 2. Materials. 126 2.1 Strains and plasmids. 126 2.2 Bacterial growth media. 126 2.3 Chemicals and reagents. 126 2.4 DNA and protein techniques. 127 2.5 Other laboratory material.128 3. Methods. 129 3.1 Introducing the recombinant adhesin expression plasmid into E. coli. . 129 3.2 Testing the expressionof the recombinant adhesin. 131 3.3 Assaying the display of the recombinant adhesin.133 3.4 Evaluating the functionality of the recombinant adhesin. 134 4. Notes/troubleshooting. 137 Acknowledgements. 138
References. 138 CHAPTER 6 Micro- and nanoscale techniques for studying biofilm-mineral interactions. 143 Luca Stigliano, Jeanne Caumartin, and Karim Benzerara 1. Introduction.144 2. Confocal laser scanning microscopy (CLSM) to image biofilm-minerals assemblages in situ, at the submicrometer scale. 148 3. Optical coherence tomography (OCT) to in situ characterize the structure of thick biofilms at the micrometre scale over large areas. 151 4. Atomic force microscopy (AFM) to image the topography, and mechanical, electrical and chemical properties of biofilm-mineral assemblages at the sub-nanometre scale. 153 5, Vertical scanning interferometry (VSI) to quantify dissolution rates of mineral substrates covered by biofilms. 157
x Contents 6. Analyses of biofilm-mineral interactions down to the nanometre scale by scanning electron microscopy and helium ion microscopy. ,. 161 7. Focused ion beam milling for ТЕМ sample preparation and 3D nanoscale investigation of biofilm-mineral interactions. .-. 164 8. Transmission electron microscopy (ТЕМ) to study biofilm-mineral interactions. 168 9. Characterizing chemical element distribution and speciation in biofilm-mineral assemblages by spectroscopies.171 Acknowledgements.:.·. 176 References. 176 SECTION 4 Genetics and microfluidics_ _ _ _ _ _ _ _ _ _ _ _ _ CHAPTER 7 Methods for studying biofilms: Microfluidics and translation in the clinical context. 195 Júlia Alcàcer-Almansa, Betsy Verónica Arévalo-Jaimes, Núria Blanco-Cabra, and Eduard Torrents Introduction. 196 General in vitro methods to study biofilms. 197 2.1 Static or closed models. 199 2.2 Dynamic or open models.201 3. Microfluidics for biofilm study. . 204 3.1
Microfluidics for biofilm fluid mechanics characterization and biofilm modelling. 212 3.2 Microfluidics for studying the environmental influences on biofilm development. 213 3.3 Microfluidics for detecting biofilm adhesion, monitoring biofilm growth and testing antibiofilm activity. 214 4. From bench to bedside. 215 4.1 General overview of biofilm research translation. 215 4.2 Translation of biofilm devices. 216 4.3 Limitations and considerations. 220 Acknowledgements. 222 Author contribution. 222 References. 223 1. 2.
Contents CHAPTER 8 Studying gene expression in biofilms. 235 Nasibeh Arabameri and Boo Shan Tseng 1. Why study gene expression of biofilm cells?. 236 2. Methods for studying individual genes. 237 2.1 Northern blot analysis. 237 2.2 RT-qPCR. . 238 2.3 Reporter gene assay. 241 2.4 mRNA-FISH. 246 2.5 Advantages and limitations of thesemethods. 247 3. Methods for studying transcriptomes. 249 3.1 DNA microarray analysis. 249 3.2 RNA-seq. 251 3.3 Advantages and limitations of thesemethods. 254 4. Methods for studying heterogeneity of geneexpression. 254 4.1 Thin sectioning. 254 4.2 LCM. 255 4.3 Single-cell analysis. 255 4.4 Fluorescence microscopy. 256 4.5 Advantages and limitations of thesemethods. 256 5.
Conclusions. 257 Acknowledgement. 258 References.258 SECTION 5 Microsocopy_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ CHAPTER 9 Spatial analysis of multispecies bacterial biofilms. 275 Virgile Guéneau, Raphaël Charron, Vlad Costache, Arnaud Bridier, and Romain Briandet 1. Introduction. 275 2. General workflow for biofilms spatial analysis. 277 2.1 Generating and capturingbiofilms for spatial analysis. 277 2.2 Biofilm labelling for fluorescencemicroscopy. 280 2.3 Imaging biofilms. 285 2.4 Image analysis. 288 3. Experimental protocol. 291 3.1 Before you begin. 292 3.2 Materials.293 3.3 Methods. 293 Acknowledgements. 297
References. 297 xi
xii Contents CHAPTER 10 Use of epifluorescence widefield deconvolution microscopy for imaging and three-dimensional rendering of Pseudomonas aeruginosa biofilms and extracellular matrix materials. 309 Heidi J. Smith and Michael J. Franklin 1. Introduction. 309 2. Materials and methods. 312 2.1 Strains and biofilmgrowth conditions. 312 2.2 Biofilm staining.312 2.3 Biofilm imaging and image processing using wide-field deconvolution microscopy. 313 3. Results and discussion. 314 3.1 Imaging early biofilm formation by P. aeruginosa PAO1 using epifluorescence wide-field deconvolution microscopy. 314 3.2 Effect of calcium addition on initial P. aeruginosa PAO1 biofilm formation. 316 3.3 Effect of PSL extracellular matrix polysaccharide on early P. aeruginosa PAO1 biofilm formation. 317 3.4 Biovolume analysis of biofilms before and after computational clearing. 319 4. Conclusions. 320 Acknowledgements. 322
References. 322 |
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| genre | (DE-588)4143413-4 Aufsatzsammlung gnd-content |
| genre_facet | Aufsatzsammlung |
| id | DE-604.BV049300663 |
| illustrated | Illustrated |
| index_date | 2024-07-03T22:39:05Z |
| indexdate | 2024-07-10T10:00:55Z |
| institution | BVB |
| isbn | 9780323988339 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-034561912 |
| oclc_num | 1393311416 |
| open_access_boolean | |
| owner | DE-355 DE-BY-UBR |
| owner_facet | DE-355 DE-BY-UBR |
| physical | xviii, 324 Seiten Illustrationen, Diagramme 23 cm |
| publishDate | 2023 |
| publishDateSearch | 2023 |
| publishDateSort | 2023 |
| publisher | Academic Press, an imprint of Elsevier |
| record_format | marc |
| series | Methods in microbiology |
| series2 | Methods in microbiology |
| spelling | Biofilms edited by Volker Gurtler (School of Science, College of Science Engineering and Health, RMIT University, Bundoora, VIC, Australia), Marianna Patrauchan (Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United Stated) First edition London ; Oxford ; San Diego, CA ; Cambridge, MA Academic Press, an imprint of Elsevier 2023 xviii, 324 Seiten Illustrationen, Diagramme 23 cm txt rdacontent n rdamedia nc rdacarrier Methods in microbiology volume 53 Biofilm (DE-588)4232790-8 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Biofilm (DE-588)4232790-8 s DE-604 Gurtler, Volker (DE-588)1179720652 edt Patrauchan, Marianna (DE-588)1299125719 edt Methods in microbiology volume 53 (DE-604)BV000899780 53 Digitalisierung UB Regensburg - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=034561912&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Biofilms Methods in microbiology Biofilm (DE-588)4232790-8 gnd |
| subject_GND | (DE-588)4232790-8 (DE-588)4143413-4 |
| title | Biofilms |
| title_auth | Biofilms |
| title_exact_search | Biofilms |
| title_exact_search_txtP | Biofilms |
| title_full | Biofilms edited by Volker Gurtler (School of Science, College of Science Engineering and Health, RMIT University, Bundoora, VIC, Australia), Marianna Patrauchan (Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United Stated) |
| title_fullStr | Biofilms edited by Volker Gurtler (School of Science, College of Science Engineering and Health, RMIT University, Bundoora, VIC, Australia), Marianna Patrauchan (Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United Stated) |
| title_full_unstemmed | Biofilms edited by Volker Gurtler (School of Science, College of Science Engineering and Health, RMIT University, Bundoora, VIC, Australia), Marianna Patrauchan (Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK, United Stated) |
| title_short | Biofilms |
| title_sort | biofilms |
| topic | Biofilm (DE-588)4232790-8 gnd |
| topic_facet | Biofilm Aufsatzsammlung |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=034561912&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV000899780 |
| work_keys_str_mv | AT gurtlervolker biofilms AT patrauchanmarianna biofilms |