Genetic Engineering: Principles and Methods 28 (eBook)

ACKNOWLEDGMENT 6
CONTENTS OF EARLIER VOLUMES 8
CONTENTS 21
REGULATION OF PLANT INTERCELLULAR COMMUNICATION VIA PLASMODESMATA 23
INTRODUCTION 23
PLASMODESMATA: STRUCTURES AND FUNCTIONS 23
MORE APPROACHES TO IDENTIFY PD COMPONENTS 34
PERSPECTIVES 34
ACKNOWLEDGMENTS 35
REFERENCES 35
ROOT-KNOT AND CYST NEMATODE PARASITISM GENES: THE MOLECULAR BASIS OF PLANT PARASITISM 38
INTRODUCTION 38
MAJOR SEDENTARY PHYTONEMATODES 39
ADAPTATIONS FOR PLANT PARASITISM 40
NEMATODE PARASITISM GENES AND THEIR PRODUCTS 43
POTENTIAL ROLES OF PARASITISM PROTEINS 45
PARASITISM GENE IDENTIFICATION 45
KNOWN PARASITISM GENES 46
CURRENT HYPOTHESES OF PARASITISM PROTEIN FUNCTIONS 46
PARASITISM GENES IN A WIDER SENSE 51
DIFFERENCES BETWEEN ROOT-KNOT NEMATODES AND CYST NEMATODES 52
WHICH GLAND HAS WHICH FUNCTION? 53
FUNCTIONAL CHARACTERIZATION OF PARASITISM PROTEINS 54
PRESENT AND FUTURE 59
REFERENCES 61
MUTAGENESIS OF HUMAN p53 TUMOR SUPPRESSOR GENE SEQUENCES IN EMBRYONIC FIBROBLASTS OF GENETICALLY- ENGINEERED MICE 65
INTRODUCTION 65
IMMORTALIZATION MECHANISMS OF MURINE EMBRYONIC FIBROBLASTS( MEFs): CRUCIAL ROLE OF p53 POINT MUTATIONS 67
HUF (HUPKI EMBRYONIC FIBROBLAST) IMMORTALIZATION AS A METHOD TO SELECT FOR DYSFUNCTIONAL POINT MUTATIONS IN HUMAN P53 GENE SEQUENCES 68
P53 MUTAGENESIS ASSAY: SHORT PROTOCOL 70
INDICATORS OF LOSS OF p53 FUNCTION IN HUF CELL LINES 71
PERSPECTIVES 72
REFERENCES 73
SALICYLIC ACID-, JASMONIC ACID- AND ETHYLENE-MEDIATED REGULATION OF PLANT DEFENSE SIGNALING 75
INTRODUCTION 75
EARLY EVENTS FOLLOWING PATHOGEN PERCEPTION 77
THE SALICYLIC ACID PATHWAY 82
THE JASMONIC ACID PATHWAY 87
CONCLUSION 94
ACKNOWLEDGMENTS 95
REFERENCES 95
PROXIMITY LIGATION: A SPECIFIC AND VERSATILE TOOL FOR THE PROTEOMIC ERA 104
ABSTRACT 104
INTRODUCTION 104
PROXIMITY LIGATION 106
PROXIMITY-LIGATION IN SITU ASSAY ( P- LISA) 108
CURRENT METHODS TO DETECT PROTEIN INTERACTIONS 108
DETECTION OF PROTEIN INTERACTIONS AND MODIFICATIONS BY PROXIMITY LIGATION 109
SUMMARY 110
ACKNOWLEDGMENTS 111
REFERENCES 111
PROTEIN OVEREXPRESSION IN MAMMALIAN CELL LINES 113
INTRODUCTION 113
TRANSIENT VS STABLE EXPRESSION 114
EXPRESSION FROM CLONED GENOMIC FRAGMENTS 117
EXPRESSION OF THE HUMAN CXADR GENE IN BAC- TRANSFECTED MOUSE CELLS 118
CONCLUSIONS 120
ACKNOWLEDGMENTS 120
REFERENCES 120
A HIGH-THROUGHPUT APPROACH TO PROTEIN STRUCTURE ANALYSIS 123
INTRODUCTION 124
TARGET SELECTION 128
PROTEIN PRODUCTION AND BIOPHYSICAL ANALYSIS 129
PROTEIN STRUCTURE ANALYSIS 130
HOMOLOGY MODELING OF REPRESENTATIVE PROTEIN FAMILY MEMBERS 137
STRUCTURE TO FUNCTION 138
CONCLUSION 142
REFERENCES 142
NEW MASS-SPECTROMETRY-BASED STRATEGIES FOR LIPIDS 147
ABSTRACT 147
INTRODUCTION 148
MS SAMPLE INTRODUCTION, IONIZATION STRATEGIES, AND SCAN MODES 149
ESI-MS AND ESI-MS/MS APPROACHES TO LIPIDOMIC ANALYSES 155
APCI-MS FOR LIPIDOMICS 157
MALDI-MS FOR LIPIDOMICS 158
MALDI AND TOF-SECONDARY ION MASS SPECTROMETRY ( TOF- SIMS) FOR LIPID IMAGING 159
SPECIALIZED DERIVATIZATION TECHNIQUES THAT CAN AID LIPIDOMIC ANALYSES 164
INFORMATIC CHALLENGES 165
OUTLOOK 167
ACKNOWLEDGMENTS 168
REFERENCES 168
PAIRED-END GENOMIC SIGNATURE TAGS: A METHOD FOR THE FUNCTIONAL ANALYSIS OF GENOMES AND EPIGENOMES 176
INTRODUCTION 176
WHAT ARE GENOMIC SIGNATURE TAGS? 177
SERIAL ANALYSIS OF CHROMATIN OCCUPANCY (SACO) 178
PAIRED-END GENOMIC SIGNATURE TAGS (PE-GST) 180
INCREASING TAG LENGTH AT THE 3' END 183
BSER I DIGESTION TO RELEASE PAIRED- END DITAGS 184
PAIRED-END PROFILING OF THE METHYLOME 184
SUMMARY 187
ACKNOWLEDGMENTS 188
REFERENCES 188
INDEX 191