THE CHEMISTRY OF NONBENZENOID AROMATIC COMPOUNDS II

By KAREN MILLER

CONTENTS INTRODUCTION TO MICROARRAY-BASED DETECTION METHODS INTRODUCTION TO MICROARRAY TECHNOLOGY TECHNICAL ASPECTS OF MICROARRAY TECHNOLOGY PROBES GENOME FRAGMENTS PCR PRODUCTS OLIGONUCLEOTIDE PROBES SUBSTRATES FOR PRINTING SLIDES WITH POLY-L-LYSINE COATING SLIDES WITH AMINO SILANE COATING SLIDES WITH ALDEHYDE COATING SLIDES WITH EPOXY COATING PROPRIETARY SURFACE CHEMISTRIES PROBE SPACERS TARGETS FOR MICROARRAY ANALYSIS TARGET AMPLI?CATIONS AND SENSITIVITY ISSUES LABELING OF THE TARGETS HYBRIDIZATION AND WASH CONDITIONS CLASSICAL COMMERCIALLY AVAILABLE MICROARRAY FORMATS SPOTTING APPROACHES IN SITU SYNTHESIS ALTERNATIVE METHODS FOR IMPROVING MICROARRAY-BASED DETECTION SENSITIVITY RESONANCE-LIGHT SCATTERING (RLS) PLANAR-WAVEGUIDE TECHNOLOGY (PWT) LIQUID ARRAYS THREE-DIMENSIONAL MICROARRAY FORMATS MARKER GENES USED ON MDMS ANALYSIS AND QUALITY CONTROL ASPECTS APPLICATIONS OF MICROARRAY TECHNOLOGY IN MICROBIAL DIAGNOSTICS GENE EXPRESSION STUDIES COMPARATIVE GENOMIC HYBRIDIZATION (CGH) GENERIC OR UNIVERSAL MICROARRAYS MICROARRAYS FOR SEQUENCE ANALYSIS MICROBIAL DIAGNOSTIC MICROARRAYS (MDMS) FURTHER DEVELOPMENTS AND NEW PERSPECTIVES REGARDING ARRAY SENSITIVITY AND SPECI?CITY CONCLUSIONS REFERENCES PART I METHODS LONG OLIGONUCLEOTIDE MICROARRAY-BASED MICROBIAL DETECTION INTRODUCTION METHOD DNA EXTRACTION F29 AMPLI?CATION KLENOW AMPLI?CATION/LABELING PROBE AND SLIDE PREPARATION SLIDE PROCESSING PROTOCOL (FOR AMINO SURFACES) HYBRIDIZATION AND SLIDE WASHING COMMENTS OUR TEST SYSTEM AND RESULTS SEQUENCE-SPECIFIC END-LABELING OF OLIGONUCLEOTIDES PROBE DESIGN SLIDE PREPARATION (SPOTTING) SLIDE PROCESSING PROTOCOL ( FOR ALDEHYDE SURFACES) DNA EXTRACTION AND PCR AMPLI?CATION OF THE TARGETED GENE SHRIMP ALKALINE PHOSPHATASE TREATMENT LABELING DATA ANALYSIS COSTS MICROARRAY FOR DETECTION OF PATHOGENIC BACTERIA NON-COGNATE APPROACHES FOR PATHOGEN DETECTION ON MICROARRAYS NON-COGNATE HYBRIDIZATION SYSTEM CONCEPT DE?NITION OF THE OPTIMAL PROBE LENGTH VIRTUAL ASSESSMENT OF ARRAY PERFORMANCES (IN SILICO EXPERIMENTS) ARRAY MANUFACTURING AND HYBRIDIZATION (WET-LAB EXPERIMENTS) ANALYSIS PERSPECTIVES PATTERNING TECHNIQUES FOR ARRAY PLATFORMS SOFT LITHOGRAPHY PHOTOLITHOGRAPHY ROBOTIC PRINTING MICRO-SPOTTING INK-JET PRINTING LITHOGRAPHY WITH AFM DIP-PEN LITHOGRAPHY WITH AFM CAFM LITHOGRAPHY NANOSHAVING AND NANOGRAFTING PROBE IMMOBILIZATION TECHNIQUES IN ARRAY TECHNOLOGIES SUPPORT MATERIAL GLASS SILICON GOLD POLYMERS QDS IMMOBILIZATION PART II IDENTIFICATION LOW-COST AND LOW-DENSITY MICROARRAYS – A NOVEL TECHNIQUE FOR IDENTIFICATION AND TYPING OF MICROORGANISMS CHIP DESIGN/ARRAY DESCRIPTION PROTOCOL FOR A LCD ARRAY EXPERIMENT AMPLI?CATION SHORT PROTOCOL FOR HYBRIDIZATION AND LABELING RESULTS AND DISCUSSION DNA MICROARRAY TECHNIQUE FOR DETECTION AND IDENTIFICATION OF VIRUSES CAUSING ENCEPHALITIS AND HEMORRHAGIC FEVER PRINCIPLE OF APPLYING MICROARRAY TECHNOLOGY FOR VIRUS DETECTION AND IDENTI?CATION VIRUSES AND THE IMPORTANCE OF RAPID DIAGNOSTICS ADVANTAGES AND DRAWBACKS OF USING THE MICROARRAY TECHNIQUE KEY FACTORS FOR DEVELOPMENT OF A MICROARRAY-BASED TEST HANTAVIRUS MICROARRAY FLAVIVIRUS MICROARRAY HEMORRHAGIC FEVER VIRUSES MICROARRAYS FOR GENOMOTYPING OF PATHOGENS AIM AND APPROACH FRANCISELLA GENOMOTYPING BRUCELLA GENOMOTYPING PART III TYPING SINGLE NUCLEOTIDE POLYMORPHISMS AS TARGETS FOR DNA-BASED IDENTIFICATION AND TYPING OF BIOSAFETY LEVEL 3 BACTERIA REAL-TIME POLYMERASE CHAIN REACTION: MORE THAN A SIMPLE POLYMERASE CHAIN REACTION RESULTS OF DIFFERENT SNP TYPING METHODS LOCKED NUCLEIC ACID-CONTAINING TAQMAN PROBES AS SNP TYPING TOOLS USE OF TAQMAN LNA PROBES FOR THE TYPING OF BRUCELLA SUIS SUBSPECIES TYPING SNPS WITH MOLECULAR BEACONS USE OF MOLECULAR BEACONS FOR TYPING BURKHOLDERIA PSEUDOMALLEI SUBSPECIES TYPING LARGE NUMBER OF SNPS BY LIGATION DETECTION REACTION USE OF LDR PROBES AND LOW-DENSITY MICROARRAYS FOR THE MULTIPLEX DIAGNOSTIC OF BSL3 BACTERIA USE OF A MICROCHIP TO DETECT ANTIBIOTIC RESISTANCE GENES IN BACILLUS ANTHRACIS CONJUGAL TRANSFER OF ANTIBIOTIC RESISTANCE GENES BETWEEN ENTEROCOCCUS SPECIES AND AVIRULENT STRAINS OF B ANTHRACIS DETERMINATION OF THE MICS OF DIFFERENT ANTIBIOTICS FOR THE B ANTHRACIS TRANSCONJUGANTS DETECTION OF ANTIBIOTIC RESISTANCE GENES IN B ANTHRACIS BY MICROCHIP-BASED HYBRIDIZATION SYSTEM (ARRAYTUBE) PART IV QUALITY CONTROL PROGRESS TOWARDS DEVELOPMENT OF MICROARRAYS FOR ROUTINE DIAGNOSTIC USE MATERIALS AND METHODS BACTERIAL STRAINS, CULTURE AND NUCLEIC ACID PURI?CATION DESIGN AND PRINTING OF OLIGONUCLEOTIDE PROBES RANDOM AMPLI?CATION AND CY3-LABELING OF NUCLEIC ACID HYBRIDIZATION OF LABELED TARGETS AND DATA PROCESSING RESULTS RANDOM AMPLI?CATION AND HYBRIDIZATION OF CY3-LABELED PATHOGEN DNA TARGETS QUALITY ASSESSMENT OF INTRA- AND INTER-OPERATOR VARIATION SOURCES OF INTRA-OPERATOR EXPERIMENTAL VARIATION SOURCES OF INTER-OPERATOR EXPERIMENTAL VARIATION DISCUSSION INTRODUCTION TO MICROARRAY TECHNOLOGY MICROARRAYS CONSIST OF AN ORDERLY ARRANGEMENT OF PROBES (OLIGONUCLEOTIDES, DNA FRAGMENTS, PROTEINS, SUGARS OR LECTINS) ATTACHED TO A SOLID SURFACE THE MAIN ADVANTAGES OF MICROARRAY TECHNOLOGY ARE HIGH THROUGHPUT, PARALLELISM, MINIATURIZA- TION, SPEED AND AUTOMATION DESPITE THE FACT THAT MICROARRAY ANALYSIS IS A RELATIVELY NOVEL TECHNOLOGY, WITH THE PUBLICATION OF THE ?RST MICROARRAY STUDIES IN