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Molecular Biology of Periodontium
KV Arun
1:
Cells of the Periodontium
BASIC TISSUES
Gingiva
Free gingiva or marginal gingiva
Attached gingiva
Clinical features of gingiva
Color
Contour
Consistency
Surface texture
Size and shape
Position
Histology
Cementum
Acellular afibrillar cementum
Acellular extrinsic fiber cementum
Cellular mixed stratified cementum
Cellular intrinsic fiber cementum
Intermediate cementum
Cementum attachment protein
Cementum growth factor
Periodontal ligament
Transseptal fibers
Alveolar crest group
Oblique fibers
Horizontal group
Apical group
Inter-radicular fibers
Functions
Alveolar bone
CELL ORGANELLES
Plasma membrane
Structure
Membrane lipids
Phospholipids
Cholesterol
Glycolipids
Membrane proteins
Types of membrane proteins
Integral membrane proteins
Channel proteins
Carrier proteins
Coupled carriers
Mitochondria
Structure
Nucleus
Active transport
Golgi complex
Structure
Functional significance
Glycoprotein processing
Proteoglycan processing
Process of glycosylation
Lysosomes
Functional significance
Endoplasmic reticulum
Structure
Functional relevance
CELLS OF PERIODONTIUM
Keratinocytes
Fibroblasts
Origin
Morphology
Cell size
Cytoskeletal elements
Cell proliferation and apoptosis
Functions and structural proteins
Trans membrane proteins
Periodontal ligament fibroblasts
Cementoblasts
Origin
Acellular cementum
Cellular cementum
Morphology
Regulation
Systemic
Local regulators
Amelogenin
Protein secretion
Bone forming cells
Osteoblast
Structure
Osteoclast
Origin
Osteoblast-osteoclast coupling
Osteocytes
Communication in osteocytes
Anabolic responses
Catabolic responses
Epithelial cell rests of malassez
Stem cells
SUMMARY
2:
Organization of the Matrix
GLYCOSAMINOGLYCAN
Chondroitin sulfate
Dermatan sulfate
Heparan sulfate/ Heparan
Keratan sulfate
Hyaluronan
Core protein
PROTEOGLYCAN
COLLAGEN AND NON-COLLAGENEOUS PROTEINS
Collagen
Non-collageneous proteins
Elastin
Fibronectin
Matricellular proteins
Biological functions of matricellular proteins
Functional relevance to gingiva
Cell migration
De-adhesion and cell survival
De-adhesion and differentiation
Molecular pathways of dissembly
Laminin
Nomenclature
Functions
Cell migration
Vitronectin, nidogen
Sibling proteins
Common features
Osteopontin
Bone sialoprotein
Dentin matrix protein
Distribution
Functions
Dentin sialophospho-protein
Distribution
Functions
Matrix extracellular phosphoglycoprotein
Distribution
Functions
Phosphotonins
Cell surface metalloprotease
Extracellular matrix proteins
Molecular mechanisms of phosphate regulation
Relevance to periodontics
Gla proteins
Osteocalcin
Osteonectin
EXTRACELLULAR MATRIX OF GINGIVA
Gingival connective tissue
Unique features of gingival metabolism
Elastin
Fibronectin
Laminin
Other matrix components
EXTRACELLULAR MATRIX OF BONE
Extracellular matrix of periodontal ligament
Periostin
Functions
Maintenance of the periodontal ligament space
Cementum
Acellular extrinsic fiber cementum (AEFC)
Cementum attachment protein (CAP)
Enamel matrix proteins
Cellular intrinsic fiber cementum
Biology of epithelial attachment
Pathology
SUMMARY
3:
Cell Cycle
CELL CYCLE
Phases
G1 phase
S phase
G2 phase
M phase
Prophase
Prometaphase
Metaphase
Anaphase
Telophase
Cytokinesis
Functional relevance to the periodontium
Regulation of cell cycle
Intracellular regulation
Mechanism of action
Regulation of cyclin/Cdk complex
Cdk inhibitory proteins
Cyclin lysis
Extracellular regulation
Mitogens
Growth factors
Survival factors
Estimation of mitotic index
Radioautography
Tritiated thymidine
Fluorescent activated cell sorter (FACS)
PCNA (Proliferating cell nuclear antigen)
Ki 67
Estimation of the individual phases of the cell cycle
Periodontal implications of estimating mitotic index
SUMMARY
CELL DEATH
NECROSIS
Coagulation necrosis
Liquefactive necrosis
Necrotising periodontal diseases
Necrotising ulcerative periodontal disease (NUP)
Acute necrotic lesions
APOPTOSIS
Events in apoptosis
Process of apoptosis
Extrinsic pathway
Intrinsic pathway
Regulation of apoptosis
Periodontal implications
Tissue homeostasis
Inflammatory cells
Periodontal cells
Methods used to assess apoptosis
p53 antibody
TUNEL Method
SUMMARY
4:
Cell Cytoskeleton
MICROFILAMENT
Structure
ACTIN FILAMENT
Microfilaments in gingiva
Gingival keratinocytes
Cell motility
Receptor activation and intracellular signaling
WASp family of proteins
Role of ABP's in actin polymerization
Cell polarity
Adhesion
Disassembly of adhesion
Retraction of the rear end
Neutrophil migration
Motility of fibroblasts
MICROTUBULES
Structure
Microtubules in gingiva
Fluid transport
Motor proteins in microtubules
INTERMEDIATE FILAMENT
Structure
Organization within the cell
Intermediate filaments in gingiva
CYTOKERATINS IN EPITHELIUM
Functional relevance in gingiva
Mechanical integrity
Principle of cellular tensegrity
Regulation of tissue growth and regeneration
Intermediate filaments and apoptosis
Vesicular transport and polarity
Oral gingival epithelium
Junctional epithelium
Regulation
SUMMARY
5:
Cell Adhesions
OCCLUDING JUNCTIONS
Necessity for occluding junctions
Methods of studying the occluding junctions
Principle of freeze fracture method
Technique
Occluding junctions in gingiva
Functional relevance of the occluding junctions to gingiva
Structural Proteins of the Occluding Junctions
Integral membrane proteins
Claudins
Functions
Occludins
Function
Junction adhesion molecule (JAM)
Plaque associated proteins
Functions
Regulation of tight junctions
Disruption of the tight junctions
Anchoring junctions
Necessity of anchoring junctions
Methods to study anchoring junctions
Anchoring junctions in gingival epithelium
Functional relevance of anchoring junctions in gingiva
Classification of anchoring junctions
Structural proteins of anchoring junctions
Transmembrane adhesion protein (TMAP)
Intracellular component
Intracellular anchor proteins
Extracellular ligand
ADHERENS JUNCTION
DESMOSOMES
Structure
Proteins present in the desmosome
Protein interaction
Functional relevance to the gingiva
CELL-MATRIX JUNCTIONS
HEMIDESMOSOMES
FOCAL ADHESIONS
COMMUNICATING JUNCTIONS – GAP JUNCTIONS
Structural proteins of gap junctions
Gap junctions in the gingiva
Functional relevance of gap junctions
CELL ADHESION MOLECULES
Cadherins
Structure
Functional relevance to gingiva
Selectins
Integrins
Structure
Function
Adhesion
Differentiation
Mechanosensory function
Classification
β1 integrins
β2 integrins
β3 integrins
β4 integrins
β6 integrin
IMMUNOGLOBULIN SUPER FAMILY
SUMMARY
6:
Cell Signaling and Communications
COMPONENTS OF COMMUNICATION SYSTEM
Signal
Classification of signals
Distant signals
Neural signals
Endocrine signals
Locally generated signals
RECEPTOR PROTEINS
TRANSCRIPTION FACTORS
AP-1
NFKB (Nuclear factor kappa B)
NFAT (Nuclear factor of activated T cell)
Structural relation to the Rel/NFκB family
Ets
SUMMARY
7:
Genetic Basis of the Periodontium
DEOXYRIBONUCLEIC ACID
STRUCTURE
Chromosomes
Structure of chromosome
Packaging of DNA into the chromosome
Structure of nucleosome
Chromatin fibers
Euchromatin and heterochromatin
Centromeres
Telomere
Protein formation
DNA REPLICATION
TRANSCRIPTION
Process of transcription
RNA processing
RNA splicing
5′ end capping
Poly A tail
TRANSLATION
Start and stop codon
Start codon
Stop codon
AMINO ACIDS
General structure
Classification of amino acids
A. Based on structure
B. Classification based on polarity
PROTEINS
Structure of proteins
Organization of protein
1. Primary structure
2. Secondary structure
Alpha helix
Beta sheet
Tertiary structure
Quaternary structure
Classification of proteins
Genetic influences in periodontal disease
POLYMORPHISMS THAT AFFECT THE IMMUNE SYSTEM
Cytokine polymorphisms
Interleukin-1 gene polymorphisms
IL-2 polymorphism
IL-4 polymorphism
IL-6 polymorphism
IL-10 polymorphism
TNF polymorphisms
Other cytokine polymorphism
MMP polymorphisms
POLYMORPHISMS AFFECTING THE INNATE IMMUNE RESPONSE
TLR polymorphisms
FPR polymorphism
DG kinase gene polymorphism
Fc γ receptor polymorphism
HLADR polymorphism
VDR gene polymorphism
SUMMARY
8:
Molecular Diagnostic Procedures
PROTEIN SEQUENCING
Conceptual translation
BLAST ANALYSIS
Necessity for BLAST analysis
Method
Types of BLAST
Relevance to periodontium
Bacteria
Host
Protein quantification
IMMUNOHISTOCHEMISTRY
Principle
Direct methods
Indirect methods
Multistage methods
Tissue processing
Antigen retrieval methods
Microwave pretreatment
Reporter and linkage molecules
Controls
Applications in periodontium
Limitations of IHC
PCR
Method
Applications in Periodontics
Limitations
AFLP PCR
Periodontal application of AFLP PCR
Inverse PCR
Inverse PCR Steps
Periodontal applications of inverse PCR
Nested PCR
Periodontal applications of Nested PCR
Reverse Transcription Polymerase Chain Reaction [RT-PCR]
Method
First strand reaction
Second strand reaction
Periodontal applications of RT-PCR
Real-Time PCR
Periodontal applications of Real-Time PCR
ELISA
Principle
Method
Periodontal applications
Types of ELISA
Indirect ELISA
Sandwich ELISA
Competitive ELISA
WESTERN BLOT
Principle
Method
Gel electrophoresis
Antibody detection
Two-step method
Periodontal applications
SDS-PAGE: Sodium dodecyl sulfate polyacrylamide gel electrophoresis
Principle
Procedure
Periodontal Applications
FLOW CYTOMETRY
Principle
Method
Display and interpretation of flow cytometry data
Periodontal applications
Protein purification
Ultracentrifugation
Principle
Periodontal applications
CHROMATOGRAPHY
Principle
Thin layer chromatography
HPLC
GAS CHROMATOGRAPHY
Periodontal applications
Electrophoresis
Protein sequencing
MASS SPECTROMETRY
Principle
Method
Tandem mass spectrometry
Periodontal applications
Protein structure
X-ray crystallography
Principle
Procedure
Periodontal applications
NMR spectroscopy
Principle
Method
Periodontal applications
SUMMARY
9:
Microbiology of the Periodontium: Molecular Aspects
MOLECULAR METHODS TO ANALYZE PERIODONTAL MICROFLORA
DNA probes
Whole genomic probe
Checker board DNA
Randomly cloned probes
Oligonucleotide probes
Polymerase chain reaction
Static 96 cell microtiter plate assay
Static 12-well microtiter plate assay
Flow-cell system
MOLECULAR STRUCTURES INVOLVED IN PATHOGENECITY
ADHESINS
(I) Adhesion to host surfaces
Porphyromonas gingivalis
Fimbriae
Treponema denticola
Tanerella forsythia
(II) Coaggregation
P. gingivalis
Treponema denticola
Tanerella forsythia
Bacterial invasion
T. denticola
T. forsythia
SUSTENINS
P. gingivalis
Proteases
Iron utilization
T. denticola
Iron and other minor nutrients
Chemotaxins
End products of metabolism
T. forsythia
Proteinase
End products of metabolism
EVASINS
Autoimmune reactions induced by the pathogens
Aggregatibacter actinomycetemcomitans
Capsule
In vitro induced antigen technology
SUMMARY
10:
Tissue Engineering: Molecular Aspects
MATRICES IN TISSUE ENGINEERING
Ideal properties of a matrix
Surface roughness
Surface energy
Surface chemistry
Surface porosity
SCAFFOLDS/ MATRICES
Non-resorbable barriers
Expanded PTFE
Porous ceramic scaffolds
β-TCP
Titanium mesh
Resorbable scaffolds
Resorbable barriers
Synthetic
Polymer matrices
Alginate
Natural products
Collagen
Advantages
Limitations
Hyaluronan
Limitations
Nanotechnology based scaffolds
Self assembly
Chitosan
EXTRACELLULAR MATRIX PRODUCTS
Signaling molecules
Surface receptors
α2β1 integrin
Heparan sulfate proteoglycan
Chondroitin sulfate
Cytokines
Fibroblast growth factor
Transforming growth factor-β
Insulin like growth factor
Platelet derived growth factor
Platelet rich plasma
Bone morphogenetic protein
Action of BMP's
Transcription factors/genes involved in osteoblast differentiation
Inflammatory mediators
Interleukin-1
Prostaglandin (PGE2)
Effects of mechanical loading and angiogenesis on bone
Mechanical loading
Angiogenesis
SUMMARY
INDEX
TOC
Index
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