http://www.loc.gov/mods/v3 http://www.loc.gov/standards/mods/v3/mods-3-2.xsd
1 online resource (xviii, 324 pages) : illustrations (chiefly color).
Biofilms, Volume 53 in the ongoing Methods in Microbiology series, highlights new advances in the field with this new volume presenting interesting chapters on a variety of timely topics, including Monospecies and polymicrobial biofilms in static and flow environment, Methods used to study biofilms, Spatial analysis of bacterial biofilms, Biofilm.
Intro -- Biofilms -- Copyright -- Contents -- Contributors -- Preface -- References -- Section 1: Plant biofilms -- Chapter 1: Bacterial biofilms as an essential component of rhizosphere plant-microbe interactions -- 1. Introduction -- 2. Rhizosphere-A microbial habitat shaped by root exudates -- 3. Experimental approaches for studying rhizosphere biofilms -- 3.1. Growing biofilms in the presence of root exudates -- 3.2. The use of microfluidics in the rhizosphere biofilm research -- 3.3. Integration of rhizosphere biofilm research with microscopy -- 3.4. Other emerging approaches for mapping rhizosphere biofilms -- 4. Sensing the plant host: Bacterial chemotaxis towards plant roots exudates -- 5. Colonizing the plant root -- 5.1. Attachment to plant roots -- 5.2. The rhizosphere biofilm matrix -- 5.3. Regulatory mechanisms that govern the biofilm lifestyle -- 6. The importance of rhizosphere biofilms -- 7. Conclusions -- Acknowledgements -- References -- Section 2: Mixed species -- Chapter 2: Monospecies and polymicrobial biofilms in static and flow environment -- 1. Introduction -- 2. Biofilm and flow environment -- 3. Key resources table -- 4. Materials and equipment -- 5. Step-by-step method details -- 5.1. Growth of microorganisms -- 5.2. Static biofilm formation -- 5.3. Crystal violet assay -- 5.4. XTT reduction assay -- 5.5. Flow cell preparation -- 5.6. Flow-cell biofilm formation -- 5.7. Flow-cell gel acrylamide preparation -- 5.8. In situ hybridization (FISH) staining -- 5.9. Confocal laser scanning microscopy and image analysis -- 5.9.1. Expected outcomes -- 6. Quantification and statistical analysis -- 6.1. Advantages -- 6.2. Limitations -- 7. Optimization and troubleshooting -- 7.1. Potential Solution to optimize the procedure -- 8. Safety considerations and standards -- 9. Alternative methods/procedures -- References.
Further reading -- Chapter 3: Optimization of protocol for quantification of biofilm formed by pathogenic rapidly-growing nontuberculous mycobac -- 1. Introduction -- 1.1. Biofilm -- 1.1.1. Factors influencing biofilm formation -- 1.1.2. Quorum sensing -- 1.2. The nontuberculous mycobacteria (NTM) -- 1.2.1. Transmission of NTM -- 1.2.2. Mycobacterium fortuitum -- 1.2.3. Mycobacterium chelonae -- 1.2.4. Mycobacterium abscessus -- 1.3. NTM biofilm -- 1.4. Biofilm estimation methods -- 1.4.1. Crystal violet assay -- 1.4.2. Viable plate count method (CFU counting) -- 1.4.3. Microscopy -- 1.4.3.1. Light icroscopy -- 1.4.3.2. Scanning electron microscopy (SEM) -- 1.4.3.3. Confocal scanning laser microscopy (CSLM) -- 1.4.3.4. Atomic force microscopy (AFM) -- 1.4.4. Congo red agar method -- 1.4.5. Fluorescent dyes and proteins -- 1.4.6. Next-generation sequencing -- 1.5. Outline of the chapter -- 1.5.1. Notes -- 2. Biofilm culture of the NTM strain -- 2.1. Materials, equipment, and reagents -- 2.2. Protocols -- 2.2.1. Growth of planktonic NTM culture -- 2.2.2. Ziehl-Neelsen staining -- 2.2.3. NTM biofilm formation protocol -- 2.3. Safety considerations and standards -- 2.4. Analysis and statistics -- 2.5. Pros and cons -- 2.6. Troubleshooting and optimization -- 3. Crystal violet assay of the NTM biofilm -- 3.1. Materials, equipment, and reagents -- 3.2. Protocol -- 3.3. Safety considerations and standards -- 3.4. Analysis and statistics -- 3.5. Pros and cons -- 3.6. Troubleshooting and optimization -- 4. Response surface methodology based optimization of culture conditions favouring maximum biofilm formation by NTM -- 4.1. Materials, equipment, and reagents -- 4.2. Protocol -- 4.2.1. RSM design of experiment (DoE) -- 4.2.2. RSM experimental runs -- 4.2.3. RSM ANOVA, regression, and graphical analysis -- 4.2.4. RSM numerical optimization.
4.3. Safety considerations and standards -- 4.4. Analysis and statistics -- 4.5. Pros and cons -- 4.6. Troubleshooting and optimization -- 5. Sonication and colony forming unit (CFU) count of NTM biofilm -- 5.1. Materials, equipment, and reagents -- 5.2. Protocols -- 5.2.1. Sonication of NTM biofilm -- 5.2.2. Serial dilution and plating -- 5.3. Safety considerations and standards -- 5.4. Analysis and statistics -- 5.5. Pros and cons -- 5.6. Troubleshooting and optimization -- 6. Determination of the number of days required for NTM biofilm formation -- 6.1. Materials, equipment, and reagents -- 6.2. Protocols -- 6.2.1. Crystal violet assay of the NTM biofilm -- 6.2.2. Sonication and CFU count of NTM biofilm -- 6.3. Safety considerations and standards -- 6.4. Analysis and statistics -- 6.5. Pros and cons -- 6.6. Troubleshooting and optimization -- 7. Basic fuchsin staining of biofilm-forming cells of the pathogenic NTM strain -- 7.1. Materials, equipment, and reagents -- 7.2. Protocol -- 7.3. Safety considerations and standards -- 7.4. Analysis and statistics -- 7.5. Pros and cons -- 7.6. Troubleshooting and optimization -- 8. Scanning electron microscopy (SEM) of NTM planktonic and biofilm-forming cells -- 8.1. Materials, equipment, and reagents -- 8.2. Protocols -- 8.2.1. Culture and growth of NTM biofilm -- 8.2.2. Preparation of 1L 0.1M phosphate buffered saline (PBS) (pH 7.4) -- 8.2.3. NTM biofilm cell-fixation -- 8.2.4. Dehydration of NTM biofilm-forming cells using ethanol gradient -- 8.2.5. FEGSEM of NTM biofilm-forming cells -- 8.2.6. SEM of planktonic NTM cells -- 8.3. Safety considerations and standards -- 8.4. Analysis and statistics -- 8.5. Pros and cons -- 8.6. Troubleshooting and optimization -- 9. Conclusion -- Acknowledgement -- References.
Chapter 4: Investigating inter-kingdom interaction between oral Streptococcus mutans and Candida species in mixed -- 1. Introduction -- 2. Materials and methods -- 2.1. Bacterial strains, media, and growth condition -- 2.2. Biofilm formation -- 2.2.1. Preparing the inoculum -- 2.2.2. Biofilm formation on coverslips -- 2.2.3. Biofilms initiated by shear flow -- 2.3. Staining biofilms grown on a coverslip -- 2.4. Biofilm examination and image acquisition -- 2.4.1. Extracellular polymeric substance (EPS) formation in the biofilm by microscopy -- 2.4.2. Examination of the biofilms formed on coverslips by confocal microscopy -- 2.4.3. Examination of the biofilms formed on the BioFlux plate by fluorescence microscopy -- 2.5. Microbial growth assay -- 2.6. pH measurement -- 2.7. Measuring the effect of antimicrobial agents on biofilms -- 2.8. Statistical analysis -- 3. Results and discussions -- 3.1. Growth of S. mutans and Candida species and experimental conditions -- 3.2. Formation of biofilms in the microchannel of the BioFlux plate -- 3.3. Structural examination of the mono-species and mixed-species biofilms -- 3.4. Characteristic comparison of the bacterium-fungal mixed-species biofilms -- 3.5. Characterization of antimicrobial activity on co-culture -- 4. Conclusion -- References -- Section 3: Nano techniques -- Chapter 5: Programming bacterial adhesion to functionalized surfaces through cellular display of recombinant nanobodies -- 1. Introduction -- 2. Materials -- 2.1. Strains and plasmids -- 2.2. Bacterial growth media -- 2.3. Chemicals and reagents -- 2.4. DNA and protein techniques -- 2.5. Other laboratory material -- 3. Methods -- 3.1. Introducing the recombinant adhesin expression plasmid into E. coli -- 3.1.1. Preparation of E. coli competent cells -- 3.1.2. Plasmid transformation -- 3.2. Testing the expression of the recombinant adhesin.
3.2.1. Recombinant protein expression, purification and SDS-PAGE -- 3.2.2. Detection of recombinant fusion proteins by western blot -- 3.3. Assaying the display of the recombinant adhesin -- 3.4. Evaluating the functionality of the recombinant adhesin -- 3.4.1. Functionalization of surfaces with protein of interest -- 3.4.2. Bacterial attachment visualization -- 3.4.3. Bacterial attachment quantification -- 4. Notes/troubleshooting -- Acknowledgements -- References -- Chapter 6: Micro- and nanoscale techniques for studying biofilm-mineral interactions -- 1. Introduction -- 2. Confocal laser scanning microscopy (CLSM) to image biofilm-minerals assemblages in situ, at the submicrometer scale -- 3. Optical coherence tomography (OCT) to in situ characterize the structure of thick biofilms at the micrometre scale ove ... -- 4. Atomic force microscopy (AFM) to image the topography, and mechanical, electrical and chemical properties of biofilm-m ... -- 5. Vertical scanning interferometry (VSI) to quantify dissolution rates of mineral substrates covered by biofilms -- 6. Analyses of biofilm-mineral interactions down to the nanometre scale by scanning electron microscopy and helium ion mi ... -- 7. Focused ion beam milling for TEM sample preparation and 3D nanoscale investigation of biofilm-mineral interactions -- 8. Transmission electron microscopy (TEM) to study biofilm-mineral interactions -- 9. Characterizing chemical element distribution and speciation in biofilm-mineral assemblages by spectroscopies -- Acknowledgements -- References -- Section 4: Genetics and microfluidics -- Chapter 7: Methods for studying biofilms: Microfluidics and translation in the clinical context -- 1. Introduction -- 2. General in vitro methods to study biofilms -- 2.1. Static or closed models -- 2.1.1. Classic static models -- 2.1.2. Novel static models.
edited by Volker Gurtler, Marianna Patrauchan.