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 |