Molecular paradigms of infectious disease a bacterial perspective

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Veröffentlicht: New York, NY Springer 2006
Schriftenreihe:Emerging infectious diseases of the 21st century
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adam_text Contents Preface vii Contributors ix Chapter 1: Genetic Analysis of Bacterial Pathogenesis 1 James M. Slauch Chapter 2: Genetic Exchange in Bacteria and the 34 Modular Structure of Mobile DNA Elements James W. Wilson Chapter 3: Genomics and the Use of Genomic Tools to 78 Study Pathogenic Bacteria Barry S. Goldman and Conrad Hailing Chapter 4: Pathogenicity Islands and Bacterial Virulence 115 Michael Hensel Chapter 5: Capsules 138 Robert T. Cartee and Janet Yother Chapter 6: Bacterial Cell Walls 176 Jennifer K. Wolf and Joanna B. Goldberg Chapter 7: Mechanisms of Bacterial Adhesion and 207 Consequences of Attachment Gregory G. Anderson, Yvonne M. Lee, Craig L. Smith, and Scott J. Hultgren Chapter 8: Bacterial Invasion into Non Phagocytic Cells 247 Daoguo Zhou Chapter 9: Bacterial Protein Secretion Mechanisms 274 James W. Wilson Chapter 10: Toxins as Host Cell Modulators 321 Dan Ye and Steven R. Blanke Chapter 11: Quorum Sensing: Coordinating Group 404 Behavior Through Intercellular Signals Joshua D. Shrout and Matthew R. Parsek xii Contents Chapter 12: The Role of Sigma Factors in Regulating 438 Bacterial Stress Responses and Pathogenesis Clint Coleman, Chasity Baker, and Cheryl A. Nickerson Chapter 13: Two Component Regulatory Systems 502 Lisa A. Morici, Anders Frisk, and Michael J. Schurr Chapter 14: Oxidative Stress Systems in Bacteria: 544 Four Model Organisms Daniel J. Hassett and James A. Imlay Chapter 15: Bacterial Biowarfare Agents 575 Mark Soboleski, Audrey Glynn, and Lucy Cardenas Freytag Index 619 Chapter 1 Genetic Analysis of Bacterial Pathogenesis James M. Slauch 1. Introduction 2 2. Fusion based Techniques for Identification of Virulence Genes .... 3 2.1. TnPhoA 3 2.2. In vivo Expression Technology 5 2.3. Variations on the IVET Theme 13 3. Transposon based Techniques for Identification of Virulence Genes 14 3.1. Signature tagged Mutagenesis 16 3.2. Genomic Analysis and Mapping by in vitro Transposition. . . 17 3.3. Transposon Site Hybridization 19 4. Classic Bacterial Genetics in an Animal Model 22 5. Conclusions 25 Chapter 2 Genetic Exchange in Bacteria and the Modular Structure of Mobile DNA Elements James W. Wilson 1. Introduction 36 1.1. Vehicles that Mediate Horizontal Gene Transfer 38 1.2. The Four Major Horizontal Transfer Paradigms: Transformation, Conjugation, Transduction, and Transposition 39 2. Transformation Mechanisms 40 2.1. Gram positive Transformation 40 2.2. Gram negative Transformation 42 2.3. The Helicobacter pylori DNA Uptake Mechanism Is Related to Type IV Secretion 42 2.4. Competence Induction 44 3. Plasmid Replication, Conjugation, and Maintenance 45 3.1. Plasmid Replication 45 3.2. Plasmid Conjugation 49 3.3. Plasmid Maintenance Functions 53 3.4. Example of a Virulence Plasmid from Yersinia pestis 55 4. Bacteriophages and Transduction 55 4.1. Lytic and Lysogenic Bacteriophages 55 4.2. Generalized and Specialized Transduction 58 4.3. Regulation of Phage encoded Toxins by Host encoded Regulators: Diphtheria Toxin and Cholera Toxin 59 5. Transposons and the Transposition of DNA 61 5.1. Insertion Sequences, Composite Transposons, and Noncomposite Transposons 62 5.2. Cut and paste Versus Replicative Transposition 64 Department of Microbiology and Immunology, Tulane University Health Sciences Center, 1430 Tulane Avenue, New Orleans, LA 70112; Present address: Center for Infectious Diseases and Vaccinology, BioDesign Institute, Arizona State University, PO Box 875401, Tempe, AZ 85287 1A Chapter 2. Genetic Exchange in Bacteria 35 6. The Modular Structure of Mobile Genetic Elements 65 6.1. Genetic Modules Found in Mobile DNA Elements 65 6.2. Other Types of Mobile Genetic Elements that Are Combinations of Modules 67 7. Conclusions—A World of Genetic Modules 73 Chapter 3 Genomics and the Use of Genomic Tools to Study Pathogenic Bacteria Barry S. Goldman and Conrad Halling 1. Introduction 80 2. Genome Sequencing and Assembly 81 2.1. Required Resources 81 2.2. Whole Genome Shotgun Sequencing 82 2.3. Creating a Shotgun Library 82 2.4. Generating Sequence Reads 84 2.5. Assembling the Sequence of the Genome 84 3. Genome Annotation 85 3.1. Identification of Open Reading Frames 85 3.2. Identification of Other Elements 86 3.3. Protein Domain based Annotation 86 3.4. Metabolic Pathway based Annotation 87 3.5. Annotation Error 87 3.6. Problems in Annotation Methodology 89 3.7. Removing Annotation Errors 89 4. Microarray Technologies 90 4.1. Transcriptional Profiling Methodologies 90 4.2. Sources of Variability 92 4.3. Statistical Analysis of Microarray Data 93 4.4. Microarray based Findings 93 4.5. Identifying Genomic Variation using DNA Microarrays .... 94 4.6. Problems with Microarray Technology 95 5. Comparative Genomics 95 5.1. Pre genomics Taxonomy 95 5.2. 16S rRNA based Taxonomy 96 5.3. Horizontal Gene Transfer 96 5.4. Methods for Detecting Horizontal Transfer 97 6. Themes of Pathogenicity Determined from Genomic Analysis.... 99 6.1. Evolution Driven by Horizontal Gene Transfer 99 6.2. Pathogenicity Islands 100 Monsanto Company, 800 N. Lindbergh Blvd., St Louis MO 63167 Chapter 3. Genomics and the Use of Genomic Tools 79 6.3. Plasmids as Mobile Pathogenicity Islands 100 6.4. Hypervariable Regions 100 6.5. Reduced Horizontal Transfer in Intracellular Pathogens ... 101 7. Genomic Rearrangements—Syntenic Maps Give a View of Vertical Descent 101 8. Conclusions 104 8.1. Genomic Space 104 Chapter 4 Pathogenicity Islands and Bacterial Virulence Michael Hensel 1. Introduction 116 2. How Did Bacteria Learn to Infect and Colonize Host Organisms? . . 116 2.1. Horizontal Gene Transfer 117 3. Features of Pathogenicity Islands 117 3.1. Pathogenicity Islands form Insertions in the Genome of Bacteria 118 3.2. Virulence Genes in Pathogenicity Islands 118 3.3. Base Composition of Pathogenicity Islands 121 3.4. Genetic Instability of Pathogenicity Islands 122 3.5. Pathogenicity Islands and Genes for tRNAs 123 4. Identification of New Pathogenicity Islands 123 5. Evolution and Transfer of Pathogenicity Islands 124 5.1. Transformation and Pathogenicity Islands 124 5.2. Bacteriophages and Pathogenicity Islands 125 5.3. Pathogenicity Islands and Virulence Plasmids 125 6. Paradigms of Pathogenicity Islands and Their Role in Bacterial Pathogenesis 126 6.1. Pathogenicity Islands of Pathogenic Escherichia coli 127 6.2. The cag Pathogenicity Islands of Helicohacter pylori 127 6.3. The High Pathogenicity Island of Yersinia spp 128 6.4. Pathogenicity Islands in Salmonella spp 128 6.5. Pathogenicity Islands in Staphylococcus aureus 129 7. Specific Aspects of Pathogenicity Islands 132 7.1. Mosaic Pathogenicity Islands 132 7.2. Regulation of Virulence Genes in Pathogenicity Islands ... 132 7.3. Black Holes: Virulence Due to the Lack of Genes? 132 7.4. Do all Pathogens Possess Pathogenicity Islands? 133 7.5. Genomic Islands in Nonpathogenic Bacteria and Fitness Islands 133 8. Conclusions 134 Institut fur Klinische Mikrobiologie, Immunologie und Hygiene Universitat Erlangen N iimberg Erlangen, Germany Chapter 5 Capsules Robert T. Cartee and Janet Yother 1. Introduction 139 2. Roles of Capsules in Pathogenesis 140 2.1. Interference with Complement mediated Effects 142 2.2. Adherence and Colonization 143 2.3. Other Functions 144 2.4. Protective Immune Responses 144 3. Genetics and Classification of Capsules 145 3.1. Surface Polysaccharides of E. coli 146 3.2. Group 1 Capsules of E. coli 146 3.3. Groups 2 and 3 Capsules of E. coli 148 3.4. Group 4 Capsules of E. coli 149 3.5. Capsules of Gram positive Bacteria 150 4. Mechanisms of Capsule Synthesis 150 4.1. Block type, or Wzy dependent, Pathway 152 4.2. ABC 2 Transporter dependent Pathway 158 4.3. Synthase dependent Pathway 161 5. Nonpolysaccharide Capsules 164 6. Conclusions 165 Chapter 6 Bacterial Cell Walls Jennifer K. Wolf and Joanna B. Goldberg 1. Introduction 177 2. The Gram Stain 177 3. Gram positive Bacteria 179 4. Gram negative Bacteria 182 5. Notable Exceptions 188 5.1. Acid fast Bacteria 188 5.2. Mycoplasmas 189 6. Cytoplasmic Membrane Components 189 7. Externally Exposed Structures 190 7.1. Flagella 191 7.2. Pili 192 7.3. Type III Secretion Apparatus 194 7.4. Porins 195 7.5. Outer Membrane Transporters 196 7.6. Efflux Pumps 196 8. Cell Wall Antibiotics 197 8.1. Antibiotics Affecting Early Steps in Peptidoglycan Synthesis 197 8.2. (i Lactam Antibiotics 198 8.3. Isoniazid 198 9. Antibiotic Resistance 198 10. Innate Immune Response to Cell Wall Components 200 11. Conclusions 201 Chapter 7 Mechanisms of Bacterial Adhesion and Consequences of Attachment Gregory G. Anderson, Yvonne M. Lee, Craig L. Smith, and Scott J. Hultgren 1. Introduction 208 2. Diversity of Adhesins 209 2.1. The Chaperone/Usher Pathway of Adhesin Assembly .... 209 2.2. TypelVPili 215 2.3. Afimbrial Adhesive Structures 218 2.4. Gram positive Adhesins 222 2.5. Other Adhesins 225 3. Consequences of Adhesion 226 3.1. Activation of Bacterial Signaling Pathways 226 3.2. Colonization of the Host 227 3.3. Biofilm Formation 228 3.4. Bacterial Invasion of Host Tissues 229 3.5. Uropathogenic Escherichia coli Pathogenesis 232 4. Adhesin based Technology 235 4.1. Vaccine Strategies 236 4.2. Receptor Analogues 237 5. Conclusions 237 Chapter 8 Bacterial Invasion into Non Phagocytic Cells Daoguo Zhou 1. Introduction 248 2. Salmonella Invasion 251 2.1. Pathogenicity Islands and Type III Protein Secretion Systems 251 2.2. Actin Cytoskeleton Rearrangements and Salmonella Entry into Host Cells 253 2.3. Role of Salmonella Actin modulating Proteins in Invasion . . 256 2.4. Salmonella induced Host Cell Signaling 258 3. Listeria monocytogenes Invasion 259 3.1. The Internalin Gene Family 259 3.2. Host Factors Involved in L. monocytogenes Entry 261 4. Conclusions 264 Chapter 9 Bacterial Protein Secretion Mechanisms James W. Wilson 1. Introduction 275 1.1. Protein Secretion Mechanisms Are Essential for the Interaction of Bacteria with Host Cells 275 1.2. There Are Sec dependent and Sec independent Secretion Pathways 276 2. The Sec System (The General Secretory Pathway) 276 2.1. The Gram negative Sec System 278 2.2. The Gram positive Sec System 283 3. Sec dependent Secretion Systems 283 3.1. Type V Secretion: Autotransporters 284 3.2. Two partner Secretion (TPS) Pathway 285 3.3. Chaperone/Usher Pathway 285 3.4. Type II Secretion Pathway 289 4. Sec independent Secretion Systems 292 4.1. Type I Secretion: ABC Transporters 292 4.2. Type III Secretion Systems 294 4.3. The Twin Arginine (TAT) Pathway 303 5. A Dual Sec dependent and Sec independent Secretion System: Type IV Secretion 306 5.1. Type IV Secretion Systems Are Related to DNA Conjugation Systems and Mediate the Transport of DNA and Proteins 306 5.2. The Type IV Secretion Apparatus Is a Multiprotein Complex that Spans the Bacterial Cell Envelope 307 6. Conclusions: Examples of Protein Secretion Systems in Different Pathogens 311 Chapter 10 Toxins as Host Cell Modulators Dan Ye and Steven R. Blanke 1. Introduction 323 2. The Importance of Toxins in Bacterial Pathogenesis 324 3. What do Toxins Do? An Overview of Toxins at the Cellular and Molecular Level 324 3.1. An Overview of Toxin Classes and Names 326 3.2. An Overview of Cellular Intoxication Mechanisms 327 3.3. An Overview of Eukaryotic Targets 329 3.4. An Overview of Toxin Structure and Function 331 4. Genomic Considerations 336 4.1. The Organization and Nature of Toxin Genes 336 4.2. Where Do Bacterial Toxins Come From 338 5. Timing and Location is Everything: Bacteria Regulate When and Where Toxins are Produced 339 5.1. Two Component Regulatory Systems of Toxin Production . 340 5.2. Regulation of Toxin Production by Environmental Iron. . . 341 5.3. Regulatory Systems Shared by Virulence and Nonvirulence Genes 341 5.4. Quorum Sensing 342 5.5. Posttranslational Regulation of Toxin Activity 343 6. Delivering the Goods: Exporting Toxins Out of Bacterial Cells. • . 343 6.1. Export of Toxins into the Extracellular Host Environment . 345 6.2. Direct Export of Toxins into the Host Cell Cytosol 348 6.3. Toxins Secretion from Gram positive Bacteria 349 7. Toxin Interactions with Host Target Cells 349 7.1. Host Cell Receptors Mediate Toxin Interactions with Target Cells 350 7.2. Portals and Pathways: Entry of Intracellular acting Toxins into Cells 355 7.3. Portals for Toxin Entry into the Cytosol 358 7.4. Some Bacterial Toxins Cross Mucosal Barriers by the Process of Transcytosis 361 322 Dan Ye and Steven R. Blanke 7.5. Gram positive Large Pore forming Toxins: A Novel Mechanism for the Delivery of Virulence Factors into the Cytosol of Target Cells? 362 8. Modulation of Target Cell Function 363 8.1. Extracellular acting Toxins 364 8.2. Intracellular acting Toxins 371 9. How do Bacterial Toxins Contribute to the Virulence of Pathogenic Bacteria 386 9.1. Toxins that Facilitate the Acquisition of Nutrients for Bacterial Colonization 386 9.2. Toxins that Facilitate Bacterial Infection and Dissemination by Remodeling of Host Colonization Niches 387 9.3. Toxins that Facilitate Colonization and Persistence Through Modulation of the Immune Response 388 9.4. Toxins that Facilitate Intracellular Lifestyles 388 10. The Beneficial Manipulation of Toxins as Molecular Tools in Medicine and Basic Science 389 10.1. The Use of Toxins as Vaccine Adjuvants 389 10.2. The Use of Toxins as Magic Bullets 389 10.3. The Use of Toxins as Delivery Vectors 390 10.4. Toxins as Molecular Reagents in Cell Biology and Pharmacology 391 11. Novel Countermeasures Against the Insidious Uses of Toxins and Toxin producing Microbes for Biological Warfare 391 12. Conclusions 392 Chapter 11 Quorum Sensing: Coordinating Group Behavior Through Intercellular Signals Joshua D. Shrout and Matthew R. Parsek 1. Introduction 406 1.1. Quorum Sensing (QS) is a form of Cell to cell Communication that Coordinates Gene Expression Among Groups of Cells 406 1.2. QS Involves Production of an Extracellular Signal that Affects a Concentration dependent Response... 406 2. Acyl Homoserine Lactone (AHL) QS in Gram negative Bacterial Species 406 2.1. A Common Type of Gram negative QS Involves AHL Signal Molecules 406 2.2. Luxl family members are AHL Synthases ^ 2.3. LuxR family members are AHL Signal Receptors 4 2.4. The Basic Molecular Scheme for AHL mediated QS 41° 2.5. QS as a Global Regulatory System 41° 2.6. AHL QS Controls Virulence Functions for Many Pathogens 4 3. Non AHL QS Systems in Gram negative Species 3.1. The Plant Pathogen Ralstonia solanacearum Utilizes a Volatile Signaling Molecule to Regulate Virulence 4 3.2. Myxococcus xanthus and Other Myxococcus species Use QS to Form Fruiting Bodies • ¦ 4 Chapter 11. Quorum Sensing: Coordinating Group Behavior 405 4. Peptide based QS in Gram positive Bacterial Species 416 4.1. Many Gram positive QS Systems Use Peptide Signals .... 416 4.2. Signal Peptide Structures are Highly Variable 418 4.3. Some Signal Peptides also Function as Bacteriocins 420 4.4. QS Controls Competence in Streptococcus pneumoniae 420 4.5. Staphylococcus aureus Virulence is Controlled by QS 421 5. Nonpeptide based QS Systems in Gram positive species 422 5.1. The A factor of Streptomyces species is a y Butyrolactone Signal 422 6. AI 2QS 423 6.1. One Form of Interspecies QS Utilizes a Signal Called AI 2 423 6.2. AI 2 is a Furanosyl Borate Diester that Binds with Two Proteins to Initiate a Signaling Cascade 423 6.3. AI 2 dependent QS Regulates Virulence Factors in many Species 426 7. Conclusions 427 7.1. QS Coordinates Gene Expression through Extracellular Signaling Molecules 427 7.2. Many Gram negative Species Utilize AHL Signaling Molecules 427 7.3. QS in Gram positive Species Commonly Uses Peptide Signals 427 7.4. QS Controls Virulence functions in many Bacterial Species 427 Chapter 12 The Role of Sigma Factors in Regulating Bacterial Stress Responses and Pathogenesis Clint Coleman1, Chasity Baker2, and Cheryl A. Nickerson13 1. Introduction 439 1.1. Bacterial Stress Responses and Sigma Factors 439 1.2. Bacteria Use Sigma Factors to Activate Transcription of Genes 441 1.3. Alternative Sigma Factors Activate Expression of Specialized Gene Sets in Response to Environmental Stimuli 444 2. Bacteria Use Alternative Sigma Factors to Regulate the Expression of Virulence Genes 449 2.1. Sigma 38—The Major Stress Response Regulator 449 2.2. Sigma B—The General Stress Response Regulator in Gram positive Bacteria 457 2.3. Sigma 32—Heat Shock 462 2.4. Sigma 24—Periplasmic Stress 468 2.5. Sigma 28—Motility and Chemotaxis Genes 472 2.6. In a Class by Itself: o54—Nitrogen Metabolism and So Much More! 476 3. Conclusions 479 4. Questions to Consider 480 Chapter 13 Two Component Regulatory Systems Lisa A. Morici, Anders Frisk and Michael J. Schurr 1. Introduction 503 2. Structure, Function, and Classification of Histidine Kinases .... 505 2.1. Sensing Domains of Histidine Kinases 506 2.2. Linker Domains of Histidine Kinases 507 2.3. Histidine Phosphotransfer Domains of Histidine Kinases . . 507 2.4. Kinase Catalytic Core of Histidine Kinases 508 3. Structure and Function of Response Regulators 508 3.1. Phosphoryl Aspartate Receiver Domains 510 3.2. Output Domains of Response Regulators 510 4. Role of the Two Component Regulators in Pathogenesis 512 4.1. The Gram negative Two Component Regulatory System PhoPQ 512 4.2. BvgAS, a Two Component Regulatory System in Bordetella pertussis 523 5. Conclusions 529 Chapter 14 Oxidative Stress Systems in Bacteria: Four Model Organisms Daniel J. Hassett1 and James A. Imlay2 1. Introduction 547 2. Oxygen Toxicity and Reactive Oxygen Species 547 3. How Do O2 and H2O2 Arise Inside Escherichia coif! 549 4. How Does O2 Injure Cells? 551 5. How Does H2O2 Injure Cells? 552 6. Inducible Cell Defenses Against O2 and H2O, 553 7. Oxidative Stress in the Escherichia coli Periplasmic Space 554 8. Pseudomonas aeruginosa: An Obligate Respirer 554 9. Oxidative Stress Systems in Pseudomonas aeruginosa 555 10. SOD 555 10.1. Fe SOD 555 10.2. Mn SOD 556 11. Catalase 557 11.1. KatA 557 11.2. KatBandAnkB 558 11.3. KatC 559 12. Alkyl Hydroperoxide Reductase 561 13. OxyR 561 14. Glucose 6 Phosphate Dehydrogenase 563 15. The Phagocytic Respiratory Burst: Two Important Pathogens that Resist Killing 563 15.1. Salmonella typhimurium Oxidative Stress Systems 563 16. Mycobacterium tuberculosis Oxidative Stress Systems 564 17. Conclusions 565 Chapter 15 Bacterial Biowarfare Agents Mark Soboleski, Audrey Glynn, and Lucy CArdenas Freytag 1. Biowarfare Agents and Historical Perspective 576 2. Anthrax 577 2.1. Introduction 577 2.2. Pathogenesis 578 2.3. Virulence 581 2.4. Treatment and Prevention 586 2.5. Vaccines and Immunity 587 3. Plague 589 3.1. Introduction 589 3.2. Pathogenesis 590 3.3. Virulence 592 3.4. Treatment 595 3.5. Vaccines and Immunity 595 4. Tularemia 598 4.1. Introduction 598 4.2. Pathogenesis 599 4.3. Virulence 599 4.4. Vaccines and Immunity 601
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id DE-604.BV022890638
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indexdate 2024-12-23T20:41:59Z
institution BVB
isbn 0387309179
0387329013
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9780387309170
language English
oai_aleph_id oai:aleph.bib-bvb.de:BVB01-016095488
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physical 1 Online-Ressource
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publishDate 2006
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publisher Springer
record_format marc
series2 Emerging infectious diseases of the 21st century
spellingShingle Molecular paradigms of infectious disease a bacterial perspective
Molekulare Medizin (DE-588)4543844-4 gnd
Infektionskrankheit (DE-588)4026879-2 gnd
subject_GND (DE-588)4543844-4
(DE-588)4026879-2
title Molecular paradigms of infectious disease a bacterial perspective
title_auth Molecular paradigms of infectious disease a bacterial perspective
title_exact_search Molecular paradigms of infectious disease a bacterial perspective
title_full Molecular paradigms of infectious disease a bacterial perspective Cheryl A. Nickerson ... eds.
title_fullStr Molecular paradigms of infectious disease a bacterial perspective Cheryl A. Nickerson ... eds.
title_full_unstemmed Molecular paradigms of infectious disease a bacterial perspective Cheryl A. Nickerson ... eds.
title_short Molecular paradigms of infectious disease
title_sort molecular paradigms of infectious disease a bacterial perspective
title_sub a bacterial perspective
topic Molekulare Medizin (DE-588)4543844-4 gnd
Infektionskrankheit (DE-588)4026879-2 gnd
topic_facet Molekulare Medizin
Infektionskrankheit
url https://doi.org/10.1007/978-0-387-32901-7
http://d-nb.info/985631082/34
https://nbn-resolving.org/urn:nbn:de:1111-200708024422
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work_keys_str_mv AT nickersoncheryla molecularparadigmsofinfectiousdiseaseabacterialperspective