| One Gene to Whole Pathway: The Role of Norsolorinic Acid in Aflatoxin Research / J.W. Bennett ; P.-K. Chang ; D. Bhatnagar |
| Flavour Compounds in Cheese / P.F. Fox |
| The Role of Micro Organisms in Soy Sauce Production / D.K. OToole |
| Gene Transfer Among Bacteria in Natural Environments / X. Yin ; G. Stotzky |
| Breathing Manganese and Iron: Solid State Respiration / K.H. Nealson ; B. Little |
| Microbial Production of Docosahexaenoic Acid (DHA, C22:6) / O.P. Ward |
| Enzymatic Deinking / P. Bajpai |
| Subject Index |
| Unusual Two-Component Signal Transduction Pathways in the Actinobacteria / Matthew I. Hutchings |
| Introduction / I： |
| Unusual Two-Component Systems in Actinobacteria / II： |
| Orphan Two-Component Proteins / III： |
| Conclusions and Perspectives / IV： |
| References |
| Acyl-HSL Signal Decay: Intrinsic to Bacterial Cell-Cell Communications / Ya-Juan Wang ; Jean Jing Huang ; Jared Renton Leadbetter |
| Acyl-HSL-Degrading Organisms, Enzymes, and Homologues |
| Mechanisms of Acyl-HSL Degradation |
| Specificity of Acyl-HSL-Degrading Enzymes |
| Acyl-HSL Stability in Natural Environments / V： |
| Coevolution of Quorum-Sensing Bacteria with Hosts and Acyl-HSL-Degrading Bacteria / VI： |
| Conclusions / VII： |
| Microbial Exoenzyme Production in Food / Peggy G. Braun |
| Structure and Function of Exoenzymes |
| Classification of Enzymes |
| Enzyme Synthesis |
| Enzyme Activity |
| Conclusion and Future Prospects |
| Biogenetic Diversity of Cyanobacterial Metabolites / Ryan M. Van Wagoner ; Allison K. Drummond ; Jeffrey L. C. Wright |
| Major Biosynthetic Routes in Cyanobacteria |
| Polyketides |
| Cyanopeptides |
| Alkaloids |
| Isoprenoids |
| Other Cyanobacteria] Metabolites |
| Pathways to Discovering New Microbial Metabolism for Functional Genomics and Biotechnology / Lawrence P. Wackett |
| Defining the Hypothesis That Most Metabolic Reactions Are Yet to be Discovered |
| Organization of Existing Metabolic Information |
| Approaches for New Discovery |
| Newly Discovered Microbial Metabolism |
| Significance of New Discoveries in Novel Functional Group Metabolism |
| Use of Recently Discovered Biocatalysis Industrially |
| Biocatalysis by Dehalogenating Enzymes / Dick B. Janssen |
| Halocarboxylic Acid Dehalogenases |
| Haloalkane Dehalogenases |
| Halohydrin Dehalogenases |
| Lipases from Extremophiles and Potential for Industrial Applications / Moh'd Salameh ; Juergen Wiegel |
| Lipases from Extreme Microorganisms |
| Improving Lipases for Efficient Applications |
| Regio- and Stereospecificity of Lipases |
| Applications of Lipases |
| In Situ Bioremediation / Kirsten S. Jorgensen |
| Unsaturated Zone Treatment Methods |
| Saturated Zone Treatment Methods |
| Use of Inocula |
| Monitoring Methods |
| Conclusions and Future Prospects |
| Bacterial Cycling of Methyl Halides / Hendrik Schafer ; Laurence G. Miller ; Ronald S. Oremland ; J. Colin Murrell |
| Methyl Halide-Degrading Organisms |
| Biochemistry and Genetics of Methyl Halide Degradation |
| Microbial Ecology of Methyl Halide-Degrading Bacteria |
| Potential Applications for Bioremediation Using Methyl Halide-Oxidizing Bacteria |
| Outlook |
| Index |
| Contents of Previous Volumes |
| Fungi and Sick Building Syndrome |
| Fungi and the Indoor Environment: Their Impact on Human Health |
| Fungal Contamination as a Major Contributor of Sick Building Syndrome |
| Indoor Moulds and their Associations with Air Distribution Systems |
| Microbial cell wall agents and sick building syndrome |
| The Role of Stachybotrys in the Phenomenon Known as Sick Building Syndrome |
| Moisture Problem Buildings with Molds Causing Work-Related Diseases |
| Possible Role of Fungal Hemolysins in Sick Building Syndrome |
| The Roles of Penicillium and Aspergillus in Sick Building Syndrome |
| Medical Aspects of Fungi and Sick Building Syndrome |
| Pulmonary Effects of Stachybotrys chartarum in Animal Studies |
| Toxic Mold Syndrome |
| Fungal Hypersensitivity: Pathophysiology, Diagnosis, Therapy |
| Indoor Molds and Asthma in AdultsRole of Molds and Mycotoxins in Being Sick in Buildings-Neurobehavioral and Pulmonary Impairment |
| The Diagnosis of Cognitive Impairment Associated with Exposure to Mold |
| Mold and Mycotoxins: Effects on the Neurological and Immune Systems in HumansOther Considerations |
| Identification, Remediation, and Monitoring Processes used in a Mold-Contaminated High School |
| The Microbial Status and Remediation for Contents in Mold |
| Specific Detection of Fungi Associated with SBS using Quantitative Polymerase Chain Reaction (QPCR) |
| Cumulative Subject Index, Volumes 22-42 |
| Contributors |
| Anaerobic Biodegradation of Methyl tert-Butyl Ether (MTBE) and Related Fuel Oxygenates / Max M. Haggblom ; Laura K. G. Youngster ; Piyapawn Somsamak ; Hans H. Richnow1： |
| Fuel Oxygenates as Contaminants of Water Sources |
| Environmental Fate |
| MTBE Biodegradation |
| Monitoring Natural Attenuation |
| Summary |
| Controlled Biomineralization by and Applications of Magnetotactic Bacteria / Dennis A. Bazylinski ; Sabrina Schubbe2： |
| Features of the Magnetotactic Bacteria |
| General features / A： |
| Distribution and ecology / B： |
| Phylogeny and taxonomy / C： |
| Physiology / D： |
| The Magnetosome |
| Composition of magnetosome crystals |
| Size of magnetosome crystals |
| Magnetosome crystal morphologies |
| Arrangement of magnetosomes within cells |
| Biological advantage of magnetotaxis / E： |
| Chemical and Molecular Basis of Magnetosome Synthesis |
| Genomics of magnetotactic bacteria |
| Genetic systems and manipulations in magnetotactic bacteria |
| The magnetosome membrane |
| Physiological conditions under which magnetite magnetosomes are synthesized |
| Regulation of the expression of magnetosome genes |
| Applications of Magnetotactic Bacteria, Magnetosomes, and Magnetosome Crystals |
| Mass cultivation of magnetotactic bacteria |
| Applications of cells of magnetotactic bacteria |
| Applications of magnetosomes and magnetosome crystals |
| Conclusions and Future Research Directions |
| Acknowledgments |
| The Distribution and Diversity of Euryarchaeota in Termite Guts / Kevin J. Purdy3： |
| Euryarchaeota in Termite Guts |
| Termite gut structure and metabolism |
| Detection of Euryarchaeota in Termite Guts |
| Isolated Euryarchaeota from termite guts |
| Uncultured Euryarchaeota in lower termite guts |
| Uncultured Euryarchaeota in higher termite guts |
| Why Are There Different Euryarchaeota in Different Termites? |
| Conclusion |
| Understanding Microbially Active Biogeochemical Environments / Deirdre Gleeson ; Frank McDermott ; Nicholas Clipson4： |
| An Introduction to the Molecular Microbial World |
| 16S approaches |
| rRNA and mRNA |
| Recent technological advances |
| Microorganisms in the Environment |
| Microbes and minerals |
| Silicate minerals |
| Metals |
| Extreme Environments |
| Microbes in iron- and sulfur-rich environments |
| Cave systems |
| The deep subsurface |
| Radioactive environments |
| The Origin of Life on Earth, and Beyond |
| The Scale-Up of Microbial Batch and Fed-Batch Fermentation Processes / Christopher J. Hewitt ; Alvin W. Nienow5： |
| Engineering Considerations Involved in Scale-Up |
| Agitator tasks in the bioreactor |
| Unaerated power draw P (or mean specific energy dissipation rate [epsilon subscript T] W/kg) |
| Aerated power draw P[subscript g] (or aerated ([epsilon subscript T])[subscript g] W/kg) |
| Flow close to the agitator-single phase and air-liquid |
| Variation in local specific energy dissipation rates, [epsilon subscript T]W/kg |
| Air dispersion capability / F： |
| Bulk fluid-and air-phase mixing / G： |
| Main differences across the scales / H： |
| Process Engineering Considerations for Scale-Up |
| Fluid mechanical stress or so-called "shear damage" |
| Operational constraints at the large scale |
| The physiological response of cells to the large-scale environment |
| Small-scale experimental simulation models of the large scale |
| Results from small-scale experimental trials of large-scale E. coli fed-batch processes |
| Conclusions and Future Perspective |
| Production of Recombinant Proteins in Bacillus subtilis / Wolfgang Schumann6： |
| Vector Systems |
| Rolling circle-type replication vectors |
| Theta-type replication vectors |
| Integrative vectors |
| Bacteriophage vectors |
| Expression Systems |
| Promoter systems |
| Secretion systems |
| Vectors allowing the addition of tags to recombinant proteins |
| DNA elements improving the production of recombinant proteins |
| Transformation Systems |
| Natural competence |
| Protoplasts |
| Electrotransformation |
| Mobilization from E. coli to B. subtilis |
| Chromosomal Mutations Enhancing Production of Native Intra- and Extracellular Proteins |
| Molecular chaperones |
| Cellular factors affecting extracytoplasmic protein folding and degradation |
| Chromosomal mutations enhancing the production of recombinant proteins |
| Production of Recombinant Proteins in B. subtilis and Other Bacilli |
| B. subtilis |
| B. brevis |
| B. megaterium |
| Quorum Sensing: Fact, Fiction, and Everything in Between / Yevgeniy Turovskiy ; Dimitri Kashtanov ; Boris Paskhover ; Michael L. Chikindas7： |
| Preface |
| The Basics of Microbial Linguistics |
| Autoinducers: The language of prokaryotic communication |
| Autoinducers with antimicrobial activity |
| Multiple quorum-sensing systems: Integrating the sensory information |
| The "Environment Sensing" theory: So much for social engagements of bacterial |
| Lost in Translation |
| Al-2: The most talked about molecule in the field |
| The early years of research: Al-2 goes interspecies |
| The pivotal case of EHEC |
| The role of luxS in cell physiology: Activated methyl cycle |
| Isr operon: The missing link...is still missing |
| Multilingual bacteria: Another look at the role of interspecies communication in V. harveyi |
| The recent years: Research involving synthetic Al-2 |
| Al-2 in foods: A few words about the currently accepted Al-2 detection assay |
| Quorum Quenching: All Quiet on the Microbial Front |
| Halogenated furanones: The defense system of algae |
| AHL lactonases and acylases: Too early to judge |
| Quorum quenching: Practical applications |
| The available screening procedures for quorum-sensing inhibitors |
| The Update |
| Concluding Remarks |
| Rhizobacteria and Plant Sulfur Supply / Michael A. Kertesz ; Emma Fellows ; Achim Schmalenberger8： |
| Assimilation of Sulfur by Plants |
| Uptake and assimilation of inorganic sulfate |
| Amino acids/peptides as a source of plant sulfur |
| Plant assimilation of oxidized organosulfur |
| Microbial Transformations of Sulfur in Soil and Rhizosphere |
| Mineralization and immobilization of soil sulfur |
| Transformations of sulfate esters |
| Microbial sulfur transformations in nonaerobic soils |
| Sulfur transformations by fungi |
| Functional Specificity of Bacteria in Soil Sulfur Transformations |
| Sulfonate desulfurization by rhizosphere bacteria |
| Diversity of desulfonation genes in rhizosphere |
| Changes in microbial community with sulfur supply |
| Sulfatase genes in rhizosphere |
| Influence of mycorrhizal interactions on sulfur supply |
| Plant Growth Promotion and the Sulfur Cycle |
| Antibiotics and Resistance Genes: Influencing the Microbial Ecosystem in the Gut / Katarzyna A. Kazimierczak ; Karen P. Scott9： |
| Antibiotic Use and the Emergence of Resistant Bacteria |
| Transfer of Antibiotic Resistance Genes Between Bacteria |
| Mechanisms of transfer |
| Why is the gut a good site for gene transfer |
| In vivo demonstrations of resistance gene transfer |
| Consequences of Antibiotic Use |
| Increased carriage of resistant bacteria and resistance genes and the emergence of bacterial strains carrying multiple resistance genes |
| Evolution of novel forms of resistance genes |
| Impact of antibiotics on the commensal gut microbiota |
| Combination therapy: Antibiotics and pro/prebiotics |
| Antibiotics and the early development of the gut microbiota |
| Color Plate Section |
| A Ferment of Fermentations: Reflections on the Production of Commodity Chemicals Using Microorganisms / Ronald Bentley ; Joan W. Bennett |
| What Is Fermentation? What Is a Fermentation Industry? |
| When Did the Production of Commodity Chemicals by Microorganisms Begin? |
| Initial use of bacteria |
| Initial use of fungi |
| Submerged Cultures |
| An interlude |
| Citric acid-the Wisconsin submerged process |
| World War I Spurs Fermentation Technology to Produce Glycerol and Acetone |
| Glycerol |
| Acetone, butanol, ethanol |
| Gluconic Acid, Kojic Acid |
| Penicillin |
| The work of Harold Raistrick |
| The development of penicillin at Oxford |
| The experience in the Unites States and development of submerged fermentation |
| Submerged fermentation for penicillin |
| Submerged Culture Fermentation of "Higher Fungi": The Macrofungi / Mariana L. Fazenda ; Robert Seviour ; Brian McNeil ; Linda M. Harvey |
| Definition of "higher fungi" |
| General considerations |
| Life cycles |
| Growth in Submerged Culture |
| Solid-substrate fermentation vs. submerged liquid fermentation |
| Isolation and maintenance of the cultures |
| Effects of process variables on growth and product formation |
| Fermentation strategies |
| Optimization of culture conditions |
| Products and Applications |
| General comments |
| Bioprocessing Using Novel Cell Culture Systems / Sarad Parekh ; Venkatesh Srinivasan ; Michael Horn |
| Plant Cell Culture Development for Scale-Up |
| Plant suspension culture initiation and establishment |
| Development of homogeneous cell lines |
| Development of single cell-derived cell lines |
| Development of synchronized cell lines |
| Example of plant cell culture-rice suspension cells |
| Transformation and transgenic cell line development |
| Cell banking and cryopreservation |
| Quality control considerations on plant cell fermentation |
| Industrial-Scale Production with Plant Suspension Cell Cultures |
| Scale-up issues with plant suspension cell cultures |
| Process optimization |
| Product formation |
| Process operation strategies on scale-up |
| Nanotechnology in the Detection and Control of Microorganisms / Pengju G. Luo ; Fred J. Stutzenberger |
| Polymeric Nanomaterials |
| Carbohydrate-biofunctionalized polymeric nanomaterials |
| Carbohydrate- or antibody-conjugated nanotubes |
| Chitosan nanoparticles |
| Nanomaterials for vaccine developments |
| Other polymeric nanomaterials |
| Fluorescence Detection of Microorganisms |
| Dye-doped silica nanoparticles |
| Quantum dots (QDs) for fluorescent detection |
| Carbon-based fluorescent nanoparticles |
| Metallic Nanomaterials |
| Elemental metal nanomaterials |
| Metal oxide nanomaterials |
| Magnetic nanomaterials for the detection of microbes |
| Metabolic Aspects of Aerobic Obligate Methanotrophy / Yuri A. Trotsenko ; John Colin Murrell |
| Milestones in Aerobic Obligate Methanotrophy: A Brief Historical Overview |
| Discovery of aerobic methanotrophs and first impacts on methanotrophy |
| Renaissance of interest in the biology and biochemistry of methanotrophs |
| New findings (insights) in methanotrophy assessed by molecular approaches |
| Pathways of Sequential Oxidation of Methane to CO[subscript 2] |
| Enzymes of primary methane oxidation |
| Soluble methane monooxygenase |
| Particulate methane monooxygenase (pMMO) |
| Oxidation of methanol by methanol dehydrogenase |
| Oxidation of formaldehyde by a linear pathway |
| Pterin-dependent oxidation of formaldehyde |
| Oxidation of formate to CO[subscript 2] |
| Pathways of Primary C[subscript 1] Assimilation and Intermediary Metabolism |
| Assimilation of formaldehyde via the Quayle ribulosemonophosphate and serine pathways |
| Pathways of nitrogen assimilation |
| Biochemical basis/rationale of obligate methanotrophy |
| Conclusions and Outlook |
| Note Added in Proof |
| Bacterial Efflux Transport in Biotechnology / Tina K. Van Dyk |
| Important Efflux Transport Protein Families |
| Energy sources and physiological roles |
| Functions in gram negative and gram positive bacteria |
| Substrate specificity |
| Internet resources |
| Discovery of Efflux Transport Function |
| Global gene expression analyses |
| Genetic selections and screens |
| Engineering Efflux Transport to Improve Amino Acid Production |
| L-Lysine |
| L-Threonine |
| L-Phenylalanine |
| L-Cysteine |
| Efflux Transport in Whole Cell Biotransformations |
| Solvent tolerant bacteria |
| Mitigation of substrate and product toxicity |
| Limits on Efflux Transport Utility in Metabolic Engineering |
| Hydrophobicity considerations |
| Availability of known transporters and protein engineering |
| Future Prospects for Efflux Transport in Biotechnology |
| Antibiotic Resistance in the Environment, with Particular Reference to MRSA / William Gaze ; Colette O'Neill ; Elizabeth Wellington ; Peter Hawkey |
| Evolution of Resistance |
| Origins of antibiotic resistance genes |
| Mechanisms of resistance |
| Mechanisms of Horizontal Gene Transfer |
| The role of integrons in resistance gene mobility |
| Coselection for resistance genes |
| Antibiotics and Resistance Genes in the Environment |
| Sewage sludge |
| Farm animals |
| Transfer from the environment to the clinic |
| MRSA in the Nonclinical Environment |
| Methicillin resistance in Staphylococcus aureus |
| Environmental reservoirs of MRSA |
| Pig associated MRSA |
| Cattle associated MRSA |
| Horse associated MRSA |
| MRSA in companion animals |
| Host Defense Peptides in the Oral Cavity / Deirdre A. Devine ; Celine Cosseau |
| Host-Microbe Interactions in the Mouth |
| The normal oral microbiota |
| Microbiota associated with disease |
| HDP Expression in the Mouth |
| Innate defenses in the mouth |
| Histatins |
| Defensins |
| Cathelicidin LL-37 |
| Functions of HDPs in the Mouth |
| Antibacterial functions |
| Antifungal activities |
| Antiviral activities |
| Non-antimicrobial functions |
| Roles of HDPs in Oral Health and Disease |
| Microbial induction of oral HDP expression |
| Expression in oral health and disease |
| Therapeutic Applications |
| Diversity of Microbial Toluene Degradation Pathways / R. E. Parales ; J. V. Parales ; D. A. Pelletier ; J. L. Ditty |
| Dioxygenase Mediated Pathway: Pseudomonas putida F1 |
| Pathway details and enzymology |
| Genetics and regulation |
| Toluene 2-Monooxygenase Pathway: Burkholderia vietnamiensis G4 |
| Genetics and pathway regulation |
| Toluene-3-monooxygenase Pathway: Ralstonia pickettii PKO1 |
| Toluene-4-monooxygenase Pathway: Pseudomonas mendocina KR1 |
| A Strain with Multiple Toluene Degradation Pathways: Burkholderia sp. Strain JS150 |
| A Nonspecific Toluene Monooxygenase Pathway: Pseudomonas stutzeri OX1 |
| Pathway regulation |
| TOL Pathway: Pseudomonas putida mt-2 / VIII： |
| Pathway and enzymology |
| A Fungal Toluene Degradation Pathway / IX： |
| Anaerobic Toluene Pathway: Thauera aromatica K172 / X： |
| Microbial Endocrinology: Experimental Design Issues in the Study of Interkingdom Signalling in Infectious Disease / Primrose P. E. Freestone ; Mark LyteXI： |
| Microbial Endocrinology as a New Scientific Discipline |
| Overview and goal of review |
| The stress response and its influence on the immune system and the infectious agent |
| Mechanisms by which stress-related neuroendocrine hormones can enhance bacterial growth and virulence |
| The spectrum of catecholamine responsive bacteria |
| Catecholamine specificity in enteric bacteria |
| Molecular analyses of bacterial catecholamine responsiveness |
| Experimental Design Issues in the Study of Microbial Endocrinology |
| Medium comparability |
| Bacterial inoculum size and its influence on stress neurohormone responsiveness |
| The importance of neuroendocrine hormone concentration |
| Neuroendocrine stress neurohormone assay methodologies |
| Conclusions and Future Directions |
| Molecular Genetics of Selenate Reduction by Enterobacter cloacae SLD1a-1 / Nathan Yee ; Donald Y. Kobayashi |
| Physiology and Biochemistry of E. cloacae SLD1a-1 |
| Basic Systems of Molecular Genetics in Facultative Se-reducing Bacteria |
| Growth of E. cloacae SLD1a-1 on selenate-containing agar plates |
| Direct cloning experiments |
| Gene specific mutagenesis |
| Random mutagenesis using transposons |
| Genetic Analysis of Selenate Reduction in E. cloacae SLD1a-1 |
| A Molecular Model for Selenate Reduction in E. cloacae SLD1a-1 |
| Metagenomics of Dental Biofilms / Peter Mullany ; Stephanie Hunter ; Elaine Allan |
| Isolation of Metagenomic DNA |
| Sample Collection and Processing |
| DNA Extraction |
| Preparation of the Insert DNA for Cloning |
| Partial restriction digestion |
| Mechanical shearing of the DNA |
| Removal of Human DNA |
| Metagenomic Library Construction |
| Construction of large insert metagenomic libraries |
| Construction of small insert libraries |
| Phage display |
| Limitations of Metagenomics |
| Conclusions and Future Perspectives |
| Biosensors for Ligand Detection / Alison K. East ; Tim H. Mauchline ; Philip S. Poole |
| Induction Biosensors |
| General considerations for use of induction biosensors |
| Reporter genes |
| Molecular Biosensors |
| Optical biosensors |
| Electrical biosensors |
| Islands Shaping Thought in Microbial Ecology / Christopher J. van der Gast |
| The Importance of Islands |
| Biogeographic islands for studies of bacterial diversity |
| Island biogeography |
| Species-Area Relationships |
| Microbial biogeography |
| Island size and bacterial diversity |
| Beta Diversity |
| Smaller islands are less stable than larger ones |
| Species-time relationships |
| Distance-decay relationships |
| Opposing Perspectives on Community Assembly |
| Human Pathogens and the Phyllosphere / John M. Whipps ; Paul Hand ; David A. C. Pink ; Gary D. Bending |
| Food Poisoning Outbreaks Associated with Consumption of Fresh and Minimally Processed Fresh Vegetables, Salads, and Fruit |
| Sources of Human Pathogens on Plants |
| Ecology of Human Pathogens in Relation to Phyllosphere Contamination |
| Ecology and survival in sewage, manure, soil, and water |
| Ecology and survival in association with plants |
| Ecology and survival during processing |
| Conclusions and Future |
| Microbial Retention on Open Food Contact Surfaces and Implications for Food Contamination / Joanna Verran ; Paul Airey ; Adele Packer ; Kathryn A. Whitehead |
| Microbial Attachment, Biofilm Formation, and Cell Retention |
| Surfaces (substrata) Encountered |
| Factors Affecting Retention |
| Surface topography |
| Surface chemistry |
| Presence of organic material |
| Characterization of Surfaces |
| Topography |
| Chemistry |
| Measuring Retention and Assessing Cleaning and Disinfection |
| Substratum preparation |
| Amount of retention |
| Strength of retention |
| Quantifying organic material |
| Capsular Polysaccharides in Escherichia coli / David Corbett ; Ian S. Roberts |
| Functions of Bacterial Capsules |
| Capsular Polysaccharides in E. coli |
| E. coli Group 1 Capsules |
| E. coli Group 4 Capsules |
| E. coli Group 3 Capsules |
| E. coli Group 2 capsules |
| Genetics and evolution of E. coli Group 2 capsules |
| Biosynthesis of E. coli Group 2 capsular polysaccharides |
| Export of E. coli Group 2 Polysaccharides |
| Group 2 capsular polysaccharide synthesis and export are linked |
| Regulation of Capsule Expression in E. coli |
| Regulation of the E. coli K30 capsule and expression of colanic acid (Slime) in E. coli K-12 strains |
| Regulation of expression of Group 2 (K5) capsule gene clusters |
| Microbial PAH Degradation / Evelyn Doyle ; Lorraine Muckian ; Anne Marie Hickey |
| Polycyclic Aromatic Hydrocarbons (PAHs) |
| Toxicity |
| Sources of PAHs |
| Environmental contamination |
| Degradation of PAHs |
| Pure culture studies |
| Culture-independent analysis |
| Marker genes |
| Bioremediation of PAH Contaminated Environments |
| Factors affecting bioremediation |
| Acid Stress Responses in Listeria monocytogenes / Sheila Ryan ; Colin Hill ; Cormac G.M. Gahan |
| Listeriosis |
| Acid Tolerance Response (ATR) and Cross Protection |
| Acid Resistance and Listerial Survival in Foods |
| Acid Resistance and L. monocytogenes Pathogenesis |
| Listerial Mechanisms of Acid Resistance |
| GAD system |
| Arginine and agmatine deiminase systems |
| F[subscript 0]F[subscript 1]-ATPase |
| Macromolecular protection and repair |
| Cell membrane changes |
| Sigma B |
| LisRK two-component regulatory system |
| Global Regulators of Transcription in Escherichia coli: Mechanisms of Action and Methods for Study / David C. Grainger ; Stephen J. W. Busby |
| An overview of the bacterial multi-subunit RNA polymerase |
| DNA recognition by RNA polymerase |
| Regulation by Transcription Factors |
| An overview of transcription regulators |
| Global transcription factors |
| Regulation of Transcription by Nucleoid-Associated Proteins |
| The nucleoid-associated proteins |
| Mechanisms of transcription regulation by Fis, H-NS, and IHF |
| A Novel Method for Studying Transcription on a Global Scale |
| Overview of chromatin immunoprecipitation |
| Application of ChIP-chip to the study of sequence specific transcription factors |
| Application of ChIP-chip to the study of nucleoid-associated proteins |
| RNA polymerase-omics |
| Protocols for ChIP-chip experiments with E. coli |
| The Role of Sigma B ([sigma superscript B]) in the Stress Adaptations of Listeria monocytogenes: Overlaps Between Stress Adaptation and Virulence / Conor P. O'Byrne ; Kimon A. G. Karatzas |
| Listeria monocytogenes: An Adaptable Pathogen |
| The Sigma Factors of L. monocytogenes |
| Sigma B ([sigma superscript B]) |
| Complex protein-protein interactions control [sigma superscript B] activity |
| Elucidation of the [sigma superscript B] regulon by proteomics and transcriptomics |
| A Central Role for [sigma superscript B] in Adaptation to Stress |
| [sigma superscript B] and osmoregulation |
| [sigma superscript B] and acid resistance |
| [sigma superscript B] is involved in cryotolerance |
| [sigma superscript B] affects piezotolerance |
| Antimicrobial resistance and [sigma superscript B] |
| The role of [sigma superscript B] in resistance to bile |
| Does Competition between Sigma Factors Influence Growth Rate in L. monocytogenes? |
| Role of [sigma superscript B] in Metabolism |
| [sigma superscript B] Plays Important Role in Virulence |
| PrfA and the intracellular stages of infection |
| Early and extracellular stages of infection |
| Protein Secretion and Membrane Insertion Systems in Bacteria and Eukaryotic Organelles / Milton H. Saier ; Chin Hong Ma ; Loren Rodgers ; Dorjee G. Tamang ; Ming Ren Yen |
| Introduction: Transport Protein Classification |
| The Diversity of Protein Translocases in Bacteria and Eukaryotic Organelles |
| Complex Inner Membrane Secretory Systems in Bacteria |
| Type I (ABC-MFP-OMF-type) protein exporters (Fig. 6.1) |
| General secretory translocases (Sec systems; Fig. 6.2) |
| Type III flagellar and pathogenicity-related systems (Fig. 6.3) |
| Type IV conjugation- and virulence-related (IVSP) systems (Fig. 6.4) |
| The putative type VI symbiosis/virulence secretory systems (TC #9.A.34) |
| Twin arginine translocation (Tat) systems (Fig. 6.5) |
| OMP Translocases of Gram-Negative Bacteria |
| The MTB (Fig. 6.6) |
| FUP systems |
| Autotransporter-1 (AT-1) systems |
| Autotransporter-2 (AT-2) systems |
| The Intimin/Invasin or Autotransporter-3 Systems |
| Two-partner secretion (TPS) systems |
| OMP insertion porins (OmpIP) |
| Protein Translocases of Eukaryotic Organelles |
| MPT complexes (TIM-TOM; TC #3.A.8; Fig. 6.7) |
| The CEPT complex (Tic-Toc; TC #3.A.9; Fig. 6.9) |
| Comparisons and Overview |
| Metabolic Behavior of Bacterial Biological Control Agents in Soil and Plant Rhizospheres / Cynthia A. Pielach ; Daniel P. Roberts |
| Techniques for Studying the Metabolic Behavior of Bacterial Biological Control Agents |
| Impact of Soil Edaphic Factors and Indigenous Microbes on Introduced Microbes in the Soil Environment |
| Plant Influences on Microbial Metabolism in the Soil Environment |
| Copper Homeostasis in Bacteria / Deenah Osman ; Jennifer S. Cavet |
| The properties of copper |
| Copper requiring proteins |
| Principles of copper homeostasis |
| Mechanisms of Copper Trafficking and Resistance |
| P[subscript 1B]-type ATPases |
| Copper acquisition |
| Copper detoxification |
| Sensors of elevated copper levels |
| Copper-chaperones |
| Copper and Bacterial Pathogenicity |
| Copper as a Biocide |
| Pathogen Surveillance Through Monitoring of Sewer Systems / Ryan G. Sinclair ; Christopher Y. Choi ; Mark R. Riley ; Charles P. Gerba |
| Monitoring for human pathogens in sewage |
| Potential Biological Agents in Sewage |
| Human pathogens secreted in bodily fluids |
| Duration of release and concentration in bodily fluids and skin |
| Concentration of Biological Agents in Sewage |
| Laboratory Methods and Detection |
| Detection of pathogens |
| Survival of pathogens in sewer systems |
| Lessons learned from poliovirus: Monitoring as an early warning system |
| Differentiation of vaccine and virulent strains |
| Conclusions: The Probability of Detection |
| The Molecular Basis of pH Sensing, Signalling and Homeostasis in Fungi / Elaine Bignell |
| Barriers to Horizontal Gene Transfer in Campylobacter jejuni / Susan P. Gardner ; Jonathan W. Olson |
| Innate Immunity to Intracellular Pathogens: Lessons Learned From Legionella pneumophila / Sunny Shin |
| Culture Collections / David Smith |
| Phage Therapy Pharmacology: Phage Cocktails / Benjamin K. Chan ; Stephen T. Abedon |
| Utility of Greater Wax Moth Larva (Galleria mellonella) for Evaluating the Toxicity and Efficacy of New Antimicrobial Agents / Andrew P. Desbois ; Peter J. Coote |
| Bacteriophages and Nanostructured Materials / Paul Hyman |
| Microbial Communities Associated With House Dust / Helena Rintala ; Miia Pitkäranta ; Martin Täubel |
| Serpula lacrymans, Wood and Buildings / S.C.Watkinson ; D.C.Eastwood |
| Table of Contents (Tentative) |
| Zones of Inhibition? The Transfer of Information Relating to Penicillin in Europe during World War II / Gilbert Shama |
| Biogenesis of the cell wall and other glycoconjugates of Mycobacterium tuberculosis / Devinder Kaur ; Marcelo E. Guerin ; Henrieta skovierová ; Patrick J. Brennan ; Mary Jackson |
| Variation in form and function: The Helix-turn-Helix regulators of the GntR superfamily / Paul A Hoskisson ; Sébastien Rigali |
| Bacterial L-Forms / E. J. Allan ; C. Hoischen ; J. Gumpert |
| Definition and Characteristics of L-Forms |
| Definition of L-forms |
| Induction and cultivation |
| Significance of L-Forms |
| Contributions to bacterial cell division |
| Contributions to membrane organization |
| Biotechnology |
| L-form interaction and association with eukaryotes |
| Biochemistry, Physiology and Biotechnology of Sulfate-Reducing Bacteria / Larry L. Barton ; Guy D. Fauque |
| Diversity of SRB |
| Distribution in the environment |
| Major characteristics |
| Central Metabolic Pathways of SRB |
| Sulfur metabolism |
| Nitrogen metabolism |
| Hydrogen metabolism |
| Oxygen metabolism |
| Fermentation of organic substrates |
| Fermentation of inorganic sulfur compounds |
| Carbon metabolism |
| Characteristics of Electron Transfer Proteins |
| Soluble electron transfer proteins |
| Membrane-associated electron transport complexes |
| Environmental Impact of SRB |
| Biocorrosion of ferrous metals |
| Corrosion of concrete and stonework |
| Impact on the petroleum industry |
| Biotechnology of SRB |
| Bioremediation of organic compounds |
| Immobilization of toxic metals |
| Reduction of azo dyes |
| Recovery of precious metals |
| Perspective |
| Biotechnological Applications of Recombinant Microbial Prolidases / Casey M. Theriot ; Sherry R. Tove ; Amy M. Grunden |
| Prolidase |
| Mechanism of substrate specificity and catalysis |
| Proposed reaction mechanism |
| Structure-function information provided by the solved Pyrococcus furiosus prolidase structure |
| Molecular and catalytic properties of recombinant prolidases |
| Applications of Prolidases |
| Detoxification of OP compounds |
| Uses in the food industry |
| Impact on human health |
| Advances in and Limitations of the Use of Prolidase for Biotechnological Applications |
| The Capsule of the Fungal Pathogen Cryptococcus neoformans / Oscar Zaragoza ; Marcio L. Rodrigues ; Magdia De Jesus ; Susana Frases ; Ekaterina Dadachova ; Arturo Casadevall |
| Capsule Components and Structure |
| Structure of capsular components |
| Capsule dynamics |
| Capsule Synthesis in Cryptococcus |
| Genes, enzymes and signaling pathways |
| GXM traffic in C. neoformans |
| Polysaccharide connections at the C. neoformans surface |
| Capsule Functions in C. neoformans: The Capsule as a Virulence Factor: Function During the Interaction with the Host |
| Role of the capsule during Interaction with the host |
| Role of the exopolysaccharides during infection |
| Origin of the capsule as virulence factor |
| Use of Capsular Components as Antifungal Targets and Vaccine |
| Capsule as an antifungal target: mAbs to the capsule as therapeutic alternative |
| Use of capsular components as vaccine |
| Future Perspectives |
| Baculovirus Interaction In Vitro and In Vivo / Xiao-Wen Cheng ; Dwight E. Lynn |
| Baculovirus Infection Process |
| Baculovirus Interactions |
| Baculovirus Interactions In Vitro |
| Antagonistic interactions |
| Neutralistic interactions |
| Baculoviruses Interactions In Vivo |
| Neutralism |
| Mutualism |
| Antagonism |
| Future Prospects |
| Posttranscriptional Gene Regulation in Kaposi's Sarcoma-Associated Herpesvirus / Nicholas K. Conrad |
| KSHV-Encoded miRNAs |
| Discovery and conservation of KSHV-encoded miRNAs |
| Targets of KSHV miRNAs |
| KSHV miR-K12-11 is an ortholog of miR-155 |
| ORF57, A Multifunctional Regulator of Gene Expression |
| ORF57 stimulates the export of introless viral mRNAs |
| ORF57 affects transcription and RNA stability |
| ORF57 enhances viral pre-mRNA splicing |
| SOX Destabilizes Cellular mRNAs |
| Kaposin B Stabilizes AU-Rich mRNAs |
| The PAN-ENE is a cis-acting RNA Stability Element |
| Phage Evolution and Ecology |
| Bacteriophage Types |
| Phage Ecology |
| Phage organismal and population ecology |
| Phage community ecology |
| Phage ecosystem ecology |
| Phage Evolutionary Biology |
| Microevolution versus macroevolution |
| Fitness and natural selection |
| Mutation |
| Genetic drift |
| Migration (Introgression) |
| Recombination |
| Phage Evolutionary Ecology |
| Life history evolution |
| Adsorption |
| Infection, prereproductive period |
| Infection, reproductive period |
| Burst |
| Phage Genome Evolution |
| Horizontal gene transfer |
| Genomics and mosaicism |
| "All the world's a phage" |
| Nucleoid-Associated Proteins and Bacterial Physiology / Charles J. Dorman |
| The Multifunctional Fis Protein |
| The Fis Protein and Bacterial Physiology |
| The Characteristic Expression Pattern of Fis |
| Fis and the Global Transcription Pattern |
| The H-NS Protein, a Universal Repressor |
| Proteins HU and IHF |
| RpoS as a Regulatory Target of NAPs |
| Biodegradation of Pharmaceutical and Personal Care Products / Jeanne Kagle ; Abigail W. Porter ; Robert W. Murdoch ; Giomar Rivera-Cancel ; Anthony G. Hay |
| What are PPCPs? |
| Human Interactions With PPCPs |
| Biological Transformation of PPCPs During Wastewater Treatment |
| Biological Transformation of PPCPs in the Environment |
| Growth on PPCPs |
| Pathways for the Degradation of Selected PPCPs |
| Octylphenol degradation by Sphingomonas sp. strain PWEI |
| Ibuprofen degradation by Sphingomonas sp. strain Ibu-2 |
| Deet degradation by P. putida DTB |
| Bioremediation of Cyanotoxins / Christine Edwards ; Linda A. Lawton |
| Hepatoxic Peptides-Microcystins and Nodularins |
| Persistence and biodegradation |
| Biodegrading bacteria |
| Characterization of MC-LR degradation pathway |
| Exploitation of Microcystin-degrading bacteria |
| Other Toxins |
| Saxitoxins |
| Cylindrospermopsin |
| Anatoxin-a |
| Virulence in Cryptococcus Species / Hansong Ma ; Robin C. May |
| Cryptococcus and Cryptococcosis |
| C neoformans |
| C gattii |
| Other species |
| Cryptococcosis |
| Genome sequencing project |
| Virulence Factors |
| Capsule |
| Melanin |
| Ability to grow at physiological temperature |
| Degradative enzymes |
| Mating type |
| Phenotypic switching |
| The origin and maintenance of virulence factors |
| Signaling Pathways Regulating Pathogenicity |
| cAMP-PKA |
| MAP kinase pathway |
| Cryptococcus and the Host Response |
| Immunocompromised host |
| Immunocompetent host |
| Current Understanding on How Cryptococcus Crosses the Blood-Brain Barrier |
| Animal Models |
| Perspectives |
| Molecular Networks in the Fungal Pathogen Candida albicans / Rebecca A. Hall ; Fabien Cottier ; Fritz A. Mühlschlegel |
| Rasl Interrelated Networks |
| Mitogen-activated protein kinase signaling |
| Cyclic AMP-dependent PKA pathway |
| Carbon Dioxide Sensing |
| Quorum Sensing and its Effects on C. albicans Morphology |
| Farnesol exerts its effects through cAMP signaling cascades |
| Tuplp is involved in quorum sensing in C. albicans |
| Transcriptional analysis of quorum sensing in C albicans |
| pH Regulation of Cell Morphology |
| Other Pathways Affecting Morphology |
| Temperature Sensors of Eubacteria |
| Thermosensors |
| Nucleoid modulators |
| RNA |
| Proteins |
| Responses to Sudden Changes in the Growth Temperature |
| The high temperature response |
| The heat shock response |
| The low temperature response |
| The cold shock response |
| Sensors of the HTR |
| Nucleoid modulators as thermosensor |
| RNA as thermosensor |
| Proteins as thermosensor |
| Sensors of the HSR |
| Molecular chaperones as thermosensors |
| Proteases as thermosensors |
| Sensors of the LTR |
| Proteins as thermosensors |
| Sensors of the CSR |
| RNA as sensor |
| Proteins as sensor |
| The Thermotactic Response |
| Acknowledgment |
| Deciphering Bacterial Flagellar Gene Regulatory Networks in the Genomic Era / Todd G. Smith ; Timothy R. Hoover |
| Master Regulators |
| FlhDC |
| CtrA |
| VisNR |
| Other master regulators |
| FlbD |
| FleR/FlrC |
| FlgR |
| FleT |
| SignD and other systems |
| Genetic Tools to Study Gene Expression During Bacterial Pathogen Infection / Ansel Hsiao ; Jun Zhu |
| In Vivo Expression Technology |
| Selection by Selection for complementation of auxotrophy in Salmonella |
| Antibiotic-based IVET selection for ivi genes |
| Recombinase-mediated IVET and analysis of Vibrio cholerae gene regulation |
| DFI: S. typhimurium Genes Induced By Low-ph and Intracellular Growth Conditions In Vitro and In Vivo |
| Repression of An Anti-Colonization Factor in V. cholerae |
| Multiple Effector Mechanisms Induced by Recombinant Listeria monocytogenes Anticancer Immunotherapeutics / Anu Wallecha ; Kyla Driscoll Carroll ; Paulo Cesar Maciag ; Sandra Rivera ; Vafa Shahabi ; Yvonne Paterson |
| Molecular Determinants of L. monocytogenes Virulence |
| Virulence factors associated with L. monocytogenes invasion |
| L. monocytogenes survival in the macrophage |
| Immune Response to L. monocytogenes Infection |
| Innate immunity |
| Cellular immune responses |
| Recombinant L. monocytogenes as a Vaccine Vector |
| Construction of recombinant L. monocytogenes strains |
| LLO and ACTA as adjuvants in L. monocytogenes based immunotherapy |
| The Pleiotropic Effects of L. monocytogenes on the Tumor Microenvironment |
| Protective and therapeutic tumor immunity |
| L. monocytogenes promotes a favorable intratumoral milieu |
| Effect of L. monocytogenes vaccination on regulatory T cells in the tumors |
| Implication of the immune response to L. monocytogenes infection: L. monocytogenes within the tumor |
| Diagnosis of Clinically Relevant Fungi in Medicine and Veterinary Sciences / Olivier Sparagano ; Sam Foggett |
| The general structure of fungi |
| Clinically relevant species of fungi |
| Non molecular Methods of Fungal Diagnosis |
| Microscopy |
| Culture |
| UV wood's Lamp |
| Radiology |
| Spectroscopy |
| Molecular Techniques for Fungal Diagnosis |
| Polymerase chain reaction (PCR) |
| Serological methods |
| Diversity in Bacterial Chemotactic Responses and Niche Adaptation / Lance D. Miller ; Matthew H. Russell ; Gladys Alexandre |
| Molecular Mechanisms of Bacterial Chemotaxis |
| Chemotaxis: Control of the motility pattern |
| Molecular mechanisms of chemotaxis: The E. coli paradigm |
| Bacillus subtilis, another model for chemotaxis signal transduction |
| Diversity in Chemotaxis |
| Complete genome sequencing projects and the diversity in chemotaxis |
| Chemotaxis in bacterial species colonizing diverse niches |
| Characterizing the Chemotaxis Response: Qualitative and Quantitative Assays |
| Temporal gradient assays |
| Spatial gradient assays |
| Use of chemotaxis assays to characterize new microbial functions |
| Cutinases: Properties and Industrial Applications / Tatiana Fontes Pio ; Gabriela Alves Macedo |
| Cutinase Characteristics |
| Applications of Cutinase |
| Oil and dairy products |
| Flavor compounds |
| Phenolic compounds production |
| Insecticide and pesticide degradation |
| Textile industry and laundry |
| Polymer chemistry |
| Enantioselective esterification reactions |
| Food industry |
| Acknowledgements |
| Microbial Deterioration of Stone Monuments-An Updated Overview / Stefanie Scheerer ; Otto Ortega-Morales ; Christine Gaylarde |
| Microbial Ecology of Outdoor Stone Surfaces |
| Molecular biology in the study of epi- and endo-lithic microorganisms |
| Effect of climate and substrate on microflora |
| Mechanisms of Microbial Biodeterioration |
| Biofilms |
| Discoloration |
| Salting |
| Physical damage |
| Inorganic acids |
| Organic acids |
| Osmolytes |
| Microorganisms Detected on Historic Monuments |
| Phototrophic microorganisms |
| Chemoorganotrophic microorganisms |
| Chemolithotrophic microorganisms |
| Control of Biodeteriorating Microorganisms |
| Microbial Processes in Oil Fields: Culprits, Problems, and Opportunities / Noha Youssef ; Mostafa S. Elshahed ; Michael J. Mclnerney |
| Factors Governing Oil Recovery |
| Microbial Ecology of Oil Reservoirs |
| Origins of microorganisms recovered from oil reservoirs |
| Microorganisms isolated from oil reservoirs |
| Culture-independent analysis of microbial communities in oil reservoirs |
| Deleterious Microbial Activities: Hydrogen Sulfide Production (or Souring) |
| Current souring control approaches |
| Microbial control of souring |
| Microbial Activities and Products Useful For Oil Recovery |
| Paraffin control |
| Biogenic acid, solvent, and gas production |
| Biosurfactant production |
| Emulsifiers |
| Exopolymer production and selective plugging |
| In situ hydrocarbon metabolism |
| Implementation of Meor |
| Treatment strategies |
| Nutrients selection |
| Monitoring the success of MEOR field trials |
| Current and Future Directions |
| Biosurfactant formulations |
| Understanding the microbial ecology of oil reservoirs |
| The Bacterial Etiology of Preterm Birth / Kimberly K. Jefferson |
| The Future of Taxonomy / Amanda L. Jones |
| Mathematics Make Microbes Beautiful, Beneficial, and Bountiful / John R. Jungck |
| Pleiomorphism in Mycobacterium / Leif A. Kirsebom ; Santanu Dasgupta ; B.M. Fredrik Pettersson |
| Metal Based NanoParticles; Size, Function and Areas for Advancement in Applied Microbiology / Michael J. Sweet ; Ashley Chesher ; Ian Singleton |
| Thermostable Enzymes as Biocatatysts in the Biofuel industry / Carl J. Yeoman ; Yejun Han ; Dylan Dodd ; Charles M. Schroeder ; Roderick I. Mackie ; Isaac K. O. Cann |
| Thermostable Cellutases |
| Exoglucanases |
| Endoglucanases |
| Glucosidases and Cellodextrinases |
| Thermostable Hemicellulases |
| Xylanases |
| Xylosidases |
| Glucuronidases |
| Endoarabinanases |
| ?-L-Arabinofuranosidases |
| Esterases |
| Mannanases, mannosidases, and other auxiliary enzymes |
| Structural Basis for Thermostability |
| Improving Thermostability and Biotechnological Applicability |
| Discussion and Future Prospects |
| Production of Biofuels from Synthesis Gas Using Microbial Catalysts / Oscar Tirado-Acevedo ; Mari S. Chinn |
| Biomass Gasification |
| Gasifiers |
| Syngas Chemical Catalytic Conversion |
| Ethanol synthesis |
| Hydrogen synthesis |
| Butanol synthesis |
| Syngas Biotransformation |
| Acetyl-CoA pathway and carbon monoxide dehydrogenase |
| Ethanol from syngas |
| Hydrogen from syngas |
| Butanol from syngas |
| Metabolic Engineering of Syngas Biotransformation Processes |
| Microbial Naphthenic Acid Degradation / Corinne Whitby |
| Naphthenic Acids |
| Chemical and physical properties |
| Sources of NAs |
| Biodegradation of NAs |
| Biodegradation of model and commercial NAs |
| Biodegradation of NAs found in the environment |
| Metabolic pathways involved in aerobic NA degradation |
| Bioremediation of NA-Contaminated Environments |
| Factors affecting NA bioremediation |
| Surface and Adhesion Properties of Lactobacilli / G. Deepika ; D. Charalampopoulos |
| Cell Wall of Lactobacilli |
| Physicochemical Properties of the Lactobacillus Surface |
| Models to Study Bacterial Adhesion |
| Bacterial Adhesion to Intestinal Mucosa |
| Factors Influencing the Surface Properties of Lactobacillus Cells |
| Shining Light on the Microbial World: The Application of Raman Microspectroscopy / Wei E. Huang ; Mengqiu Li ; Roger M. Jarvis ; Royston Goodacre ; Steven A. Banwart |
| Identification of Microbial Species Using Single Cell Raman Spectra |
| Linking Microbial Species, Spatial Distribution, and their Functions |
| Raman Tweezers to Measure and Manipulate Single Microbial Cells |
| Surface-Enhanced Raman Scattering (SERS) |
| Single Cell Raman Spectroscopy and Measuring Microbial Metabolic Potential |
| Raman Spectra Data Analysis |
| Detection of Invasive Aspergillosis / Christopher R. Thornton |
| Human Immune Serum and Diagnosis of A. fumigatus-Associated Diseases |
| Somatic and purified antigens |
| Mitogillin and other enzymes |
| Mannoproteins and galactomannoproteins |
| Galactomannan |
| Polyclonal Antibody-Based Detection Systems |
| Hybridoma Technology and MAb-Based Detection Systems |
| Galactomannan immunoassays |
| Next-generation monoclonal antibodies |
| Lateral-flow technology |
| Nucleic Acid-Based Detection Systems |
| Bacteriophage Host Range and Bacterial Resistance |
| Host-Range Determination |
| Plaquing and efficiency of plating |
| Efficiency of center of infection |
| Spot testing |
| Broth-based host-range determination |
| Breadth of Host Range |
| Intergeneric transduction |
| Intergeneric killing |
| Intergeneric propagation |
| Adsorption Resistance |
| Phage-encounter blocks |
| Receptor loss |
| Prevention of Host Takeover |
| Uptake blocks |
| Restriction-modification |
| CRISPR |
| Abortive Infection |
| Phage resistance to abortive infection |
| Reduced phage productivity |
| Influence of Escherichia coli Shiga Toxin on the Mammalian Central Nervous System / Fumiko Obata |
| STEC Infection in Human Patients |
| Symptoms |
| Relation between D + HUS and CNS occurrences |
| CNS histopathology from autopsy |
| CNS pathology from MRI |
| CSF contents |
| Serum proteins and electrolytes |
| Types of animal models |
| Stx purification and LPS removal |
| CNS symptoms of animal models |
| CNS histopathology of animal models |
| Pathologies by MRI (rabbit) |
| CSF contents of animal models |
| Hematology and serum of animal models |
| Similarities Between Human Patients and Animal Models |
| Relation Between Renal Failure and CNS Failure |
| Stx Route from Blood to CNS Parenchyma |
| Future Directions |
| Natural Products for Type II Diabetes Treatment / Amruta Bedekar ; Karan Shah ; Mattheos Koffas |
| Acarbose |
| Mechanism of action and pharmacokinetics |
| Manufacturing of acarbose |
| Biosynthesis of acarbose in Actinoplanes sp. SE50/110 |
| Effect on hyperglycemia |
| Miglitol |
| Biosynthesis and large-scale production of miglitol |
| Voglibose |
| Anthocyanins |
| Anthocyanin metabolism |
| Novel production technique |
| Mechanism of action |
| Pine Bark Extract |
| Other Extracts of Plant Origin |
| Known active compounds |
| Unknown active compounds |
| Metformin |
| Pharmacokinetics and other effects |
| Adverse effects |
| Metformin in combination therapy |
| Experimental Models Used to Study Human Tuberculosis / Ronan O'Toole |
| Use of Surrogate Models to Study Tuberculosis |
| In vitro Models of Mycobacteriology |
| Fast-growing mycobacterial species |
| The M. tuberculosis complex |
| In vivo Models of Tuberculosis |
| Macrophages and cell cultures |
| Rodent models |
| Nonhuman primates |
| The Study of Tuberculosis Pathogenesis in Human Patients |
| Biosynthesis of Peptide Signals in Gram-Positive Bacteria / Matthew Thoendel ; Alexander R. Horswill |
| Bacillus Intracellular Signaling Peptides |
| B. subtilis CSF |
| Bacillus cereus PapR |
| Enterococcus Pheromones |
| S. aureus Autoinducing Peptides |
| The agr system and AIP signal |
| AgrD and AgrB properties |
| AIP biosynthetic mechanism |
| Other Cyclic Peptide Signaling Systems |
| E. faecaiis fsr system |
| Listeria monocytogenes agr system |
| Clostridium perfringens agr system |
| Lactobacillus plantarum agr system |
| B. subtilis Competence Pheromones |
| Quenching Signal Biosynthesis |
| Cell Immobilization for Production of Lactic Acid: Biofilms Do It Naturally / Suzanne F. Dagher ; Alicia L. Ragout ; Faustino Siñeriz ; José M. Bruno-Bárcena |
| Biofilm Formation |
| Application of Biofilms to Lactic Acid Production |
| Host Organisms |
| Optical purity of the product |
| Cell Immobilization |
| Cell immobilization by entrapment and attachment |
| Natural cell attachment |
| Free and adhered biomass |
| Cultivation Media |
| Biofilm Apparatus and Operation |
| Comparison between productivities of L rhamnosus cells immobilized through natural adhesion to different supports in an identical reactor design |
| Comparison between productivities L. rhamnosus cells immobilized with polyethyleneimine (PEI) or by natural adhesion in different reactor designs |
| Lactic Acid Volumetric Productivity Versus Concentration |
| How much will cells pay for a good nitrogen source? |
| Microbial Fingerprinting using Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS): Applications and Challenges / R. Giebel ; C. Worden ; S. M. Rust ; G. T. Kleinheinz ; M. Robbins ; T. R. Sandrin |
| Need for a rapid and accurate tool to identify microorganisms |
| Characteristics of an ideal method |
| Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) |
| Applications |
| Bacteria |
| Fungi |
| Viruses |
| Current applications |
| Challenges |
| Reproducibility |
| Effects of culture conditions |
| Effects of technical variability |
| Phage Therapy Pharmacology: Calculating Phage Dosing / Stephen Abedon |
| Standard Antibacterial In Vitro Metrics |
| Killing Titer and MBC Calculation |
| Reduction Times and Dosing |
| Bacterial Density and Phage Population Growth |
| Effective Dose Revisited |
| From Rio Tinto to Mars: The Terrestrial and Extraterrestrial Ecology of Acidophiles / R. Amils ; E. González-Toril ; A. Aguilera ; N. Rodríguez ; D. Fernández-Remolar ; F. Gómez ; A. García-Moyano ; M. Malki ; M. Oggerin|cI. Sánchez-Andrea ; J. L. Sanz |
| Extremophiles |
| Acidophiles |
| Geomicrobiology of Rio Tinto |
| Subsurface Geomicrobiology of the Iberian Pyrite Belt |
| Methanogenesis in Nonmethanogenic Conditions |
| Rio Tinto as a Geochemical Analogue of Mars |
| Future Trends |
| Fungal Adaptation to Extremely High Salt Concentrations / Cene Gostincar ; Metka Lenassi ; Nina Gunde-Cimerman ; Ana Plemenitaš |
| Halotolerant and Halophilic Fungi: An Introduction |
| Hortaea werneckii-A Model for Extreme Halotolerance |
| Wallemia ichthyophaga-Alternative Halophilic Solutions |
| The Next Step: Genomics, Transcriptomics, and Beyond |
| Conclusions: An Integrated Model of Extreme Halotolerance |
| Resistance of Yeasts to Weak Organic Acid Food Preservatives / Peter W. Piper |
| The Monocarboxylate Preservatives |
| The Physiological Action of Weak Organic Carboxylic Acids on Yeast |
| Resistance Mechanisms |
| Silver Nanoparticles: A Microbial Perspective / M. J. Sweet ; I. Singleton |
| NP Types |
| Microbial-related Applications of NPs |
| Mechanism of Antimicrobial Action of AgNP |
| Environmental Implications of AgNP-Microbial Considerations |
| Bacterial strategies for growth on aromatic compounds / Kevin W. George |
| Recent Advances In Hantavirus Molecular Biology And Disease Islam / T. M. Hussein ; Abdul Haseeb ; Absarul Haque ; Mohammad A Mir |
| Antigenic variation and the genetics and epigenetics of the PfEMP1 erythrocyte surface antigens in Plasmodium falciparum malaria / David E. Arnot ; Anja T.R. Jensen |
| Biological Warfare Of The Spiny Plant: Introducing Pathogenic Microorganisms Into Herbivore's Tissues / Malka Halpern ; Avivit Waissler ; Adi Dror ; Simcha Lev-Yadun |
| Milliliter scale fermentations / Ing. Dirk Weuster-Botz |
| Morphology and productivity in filamentous fungi / Rainer Krull |
| Heterologous protein secretion from Bacillus subtilis / C.R. Harwood |
| Adhesive Nanostructured Reactive Microbial Coatings / Michael Flickinger |
| Evolution of the Probiotic Concept: From Conception to Validation and Acceptance in Medical Science / Walter J. Dobrogosz ; Trent J. Peacock ; Hosni M. Hassan |
| Early Stages in Development of the Probiotic Concept |
| The Validation Stage in Development of the Probiotic Concept |
| Evolution in Probiotic Perspectives and Definitions |
| Emergence of the microbiome concept |
| Alternative definitions proposed for probiotics |
| Multiple roles played by specific microbiomic components |
| New Perspectives on host-microbiome interrelationships |
| Probiotic Efficacy-Clinical Trials |
| Efficacy for rotavirus-induced diarrhea in children |
| Treatment of infantile colic, feeding tolerance, bowel habits, and gastrointestinal motility in preterm newborns |
| Protection of infants from infections in child care centers |
| Effects during anti-Helicobacter pylori treatment |
| Increase work-place healthiness in adults |
| Improvements on oral health |
| Probiotics as Immunomodulatory Agents |
| In vitro and ex vivo immunomodulatory activities |
| Adjuvanticity for vaccine effectiveness |
| Modulation of delayed-type hypersensitivity responses |
| Genetically Modified Probiotics (i.e., Designer Probiotics) |
| Genetic enhancement of probiotic efficacy |
| Developing probiotics for vaccine and drug delivery |
| Prokaryotic and Eukaryotic Diversity of the Human Gut / Julian R. Marchesi |
| Prokaryotic Diversity in the Gut |
| Diversity in the large intestine |
| Oral, stomach, and small intestine microbiota |
| Eukaryotic and Viral Diversity in the Human Gut |
| Oxalate-Degrading Bacteria of the Human Gut as Probiotics in the Management of Kidney Stone Disease / Valerie R. Abratt ; Sharon J. Reid |
| Oxalate homeostasis in the gut: Sources of oxalate |
| Oxalate assimilation in the gut |
| Hyperoxaluria and kidney stone disease |
| Oxalate Utilization by Anaerobic and Facultative Gut Bacteria |
| Mechanisms of Oxalate Catabolism in Anaerobic Bacteria of the Human Gut |
| Oxalobacter formigenes |
| Enterococcus faecalis |
| Providencia rettgeri |
| Eubacterium lentum |
| Escherichia coli |
| Lactobacillus and Bifidobacterium species |
| Phylogeny and Genetic Organization of the Genes Involved in Oxalate Degradation |
| Phylogeny of the Oxc and Frc proteins |
| Genetic organization of the oxalate loci |
| Detection and Quantification of Oxalate-Degrading Bacteria in the GIT and Links to Kidney Stone Disease |
| Probiotic Potential of Oxalate-Degrading Bacteria in Vivo |
| Concluding Comments |
| Morphology and Rheology in Filamentous Cultivations / T. Wucherpfennig ; K. A. Kiep ; H. Driouch ; C. Wittmann ; R. Krull |
| Growth of Filamentous Organisms |
| Micromorphology |
| Macromorphology |
| Pellet growth and mass transfer |
| Image analysis as a tool to determine morphology |
| Rheology |
| Rheological models |
| Characterization of important parameters and viscosity in filamentous processes |
| Estimation of rheology |
| The Impact of the Environom on Morphology and Productivity |
| Methanogenic Degradation of Petroleum Hydrocarbons in Subsurface Environments: Remediation, Heavy Oil Formation, and Energy Recovery / N. D. Gray ; A. Sherry ; C. Hubert ; J. Dolfing ; I. M. Head |
| Formation, Reactivity, Distribution, and Composition of Hydrocarbons in Subsurface Environments |
| Ecophysiology of Methanogenic Hydrocarbon Degradation |
| Evidence of Anaerobic Hydrocarbon Biodegradation in Near-Surface Environments |
| Evidence for Hydrocarbon Biodegradation in Petroleum Reservoirs and the Formation of Heavy Oils |
| Methanogenic Hydrocarbon-Degrading Communities: Organisms and Mechanisms |
| Putting Methanogenic Hydrocarbon-Degrading Communities to Good Use |
| Heterologous Gene Expression in Filamentous Fungi / Xiaoyun Su ; George Schmitz ; Meiling Zhang |
| Transformation |
| Global Defenses Against Foreign Genes |
| Impact of Transcription Regulation on Heterologous Gene Expression |
| Engineering Introns in Heterologous Gene Expression in Filamentous Fungi |
| mRNA Stability |
| Signal Peptides |
| Optimization of Codon Usage |
| Fusion of Heterologous Proteins to Native Proteins |
| Coupling of Secretion with Polarized Growth of Filamentous Fungi / 10： |
| Engineering the Glycosylation Pathway for Heterologous Gene Expression / 11： |
| Protein Quality Control / 12： |
| Heterologous Protein Degradation by Extracellular Proteases / 13： |
| Staphylococcal Biofilms: Quest for the Magic Bullet / Jamie L. Brooks14： |
| Targeting the Staphylococcal Biofilm |
| Climate Change and Defense against Pathogens in Plants / Adrian C. Newton ; Lesley Torrance ; Nicola Holden ; Ian K. Toth ; David E. L. Cooke ; Vivian Blok ; Eleanor M. Gilroy |
| Host Defense Genes, Germplasm, and Environmental Interactions |
| Host Defense Mechanisms and Environmental Interactions |
| Limiting Epidemiological Parameters |
| Strategies for Expressing Climate-Durable Resistance |
| Conclusions and Prospects |
| Advances in the In-Field Detection of Microorganisms in Ice / Megan J. Barnett ; David A. Pearce ; David C. Cullen |
| The Case for In-Field Analysis |
| Core Techniques Already Adapted for In-Field Use |
| Future Potential-Technology |
| Future Potential-Techniques |
| Key Target Environments |
| Microsatellites for Microbiologists / Lucinda A. Scriven |
| What are Microsatellites? |
| Why Use Microsatellites Instead of Other Genetic Markers? |
| How to Use Microsatellites |
| Drawbacks of Microsatellite Markers |
| Previous Use of Microsatellites by Microbiologists |
| Modern Advances against Plague / Petra C.F. Oyston ; E. Diane Williamson |
| Genomic Analysis of Yersinia pestis |
| Molecular Basis of Pathogenesis |
| Fighting Plague |
| Salmonella Enteritidis in Shell Eggs: Evolving Concerns and Innovative Control Measures / Jennifer J. Perry ; Ahmed E. Yousef |
| Antimicrobial Features of Egg |
| Egg Contamination |
| Introduction of Salmonella into Laying Environment-Risk Factors |
| Salmonella Enteritidis in Eggs |
| Superior Fitness of Salmonella Enteritidis for Hen Tissue Colonization and Transmission to Eggs |
| Egg Safety Initiatives |
| Regulations |
| Treatments for Enhanced Egg Safety |
| Staphylococcus aureus Aggregation and Coagulation Mechanisms, and Their Function in Host-Pathogen Interactions / H.A. Crosby ; J. Kwiecinski ; A.R. Horswill |
| Fibrinogen/Fibrin-Mediated Clumping |
| Role of Clumping/Agglutination in Disease |
| Antidumping Mechanisms |
| Polysaccharide-Based Aggregation |
| In Sickness and in Health: The Relationships Between Bacteria and Bile in the Human Gut / A.J. Hay ; J. Zhu |
| Bile in Digestion |
| Bile as a Barrier |
| Bacterial Responses to Bile |
| The Role of the Gut Microbiome on Chronic Kidney Disease / B. Sampaio-Mala ; L. Simoes-Silva ; M. Pestana ; R. Araujo ; I.J. Soares-Silva |
| Gut Dysbiosis in Chronic Kidney Disease |
| Uremic Toxins and the Gut Microbiome |
| Intestinal Translocation, Inflammation, and Cardiovascular Risk in Chronic Kidney Disease Patients |
| Prevention Strategies of Gut Dysbiosis in Chronic Kidney Disease |
