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図書

図書
edited by W. Umbreit and H. Molitor = herausgegeben von W. Umbreit and H. Molitor = rédigé par W. Umbreit et H. Molitor
出版情報: London : Published for and on behalf of the Organizers and the International Union of Biochemistry by the Symposium Publications Division, Pergamon Press, c1960  xiii, 373 p. ; 24 cm
シリーズ名: Proceedings of the Fourth International Congress of Biochemistry, Vienna, 1-6 September 1958 / general editor, O. Hoffmann-Ostenhof = Veröffentlichungen des vierten Internationalen Kongresses für Biochemie, Wien, 1.-6. September 1958 / Gesamtherausgeber, O. Hoffmann-Ostenhof = Comptes rendus des travaux du quatrième congrès international de biochimie, Vienne, 1-6 Septembre, 1958 / publié par O. Hoffmann-Ostenhof ; v. 11, symposium 11
I.U.B. symposium series ; v. 13
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図書

図書
edited by Allen I. Laskin
出版情報: Orlando ; Tokyo : Academic Press, 1959-  v. ; 24 cm
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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
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
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