•  immunology and molecular biology

• Preface
• Section I. Introduction to immunology and molecular biology
  • 1. Gene expression and regulation
    • Basic elements of gene expression
    • Gene structure
    • Gene expression
    • Transcription
    • Translation
    • Gene expression regulation
    • Events associated with RNA and proteins
    • Epigenetic mechanisms
    • Signal transduction pathways
    • Recommended Lectures
  • 2. Innate immune system
    • Introduction
    • Components of the innate immune system
    • Characteristics of the innate immune system and its recognition mechanisms
    • Inflammation and inflammasome
    • References
  • 3. Toll-like receptors and autoimmunity
    • Introduction
    • TLR molecular structure
    • TLR-mediated recognition mechanisms
    • TLR signaling
    • TLRs and autoimmunity
    • The TLR9 and the CpG ligand
    • TLR and rheumatoid arthritis
    • TLR pathway as a therapeutic target
    • CpG sequences as adjuvant and autoimmunity
    • References
  • 4. The complement system
    • Introduction
    • The complement cascade
    • The complement regulatory factors
    • The complement receptors
    • The complement system and adaptive immunity
    • The complement system and infectious diseases
    • The complement system and dead cell clearance
    • The complement system and diseases
    • The complement system and atherosclerosis
    • The complement system and ischemia-reperfusion injury
    • The complement system and neurodegenerative diseases
    • The complement system and osteoarthritis
    • The complement system and allergy
    • The complement system and cancer
    • The complement system and autoimmune diseases
    • The complement system and therapeutic target
    • References
  • 5. Introduction to T and B lymphocytes
    • Introduction
    • T-lymphocytes (T cells)
    • B lymphocytes (B cells)
    • Anti-B cell therapies
    • References
  • 6. B lymphocytes in autoimmunity
    • Introduction
    • B cell development and the B cell receptor formation
    • B cell tolerance mechanisms and their role in autoimmunity
    • References
  • 7. T lymphocytes in autoimmunity
    • Introduction
    • Generation of T cell receptors
    • Immunologic tolerance
    • Mechanisms of tolerance
    • Role of co-stimulatory signals in maintenance and breakdown of self-tolerance
    • Pathogenetic role of T cells in autoimmunity
    • Pathogenic role of autoreactive CD8+ T cells
    • Cross-tolerance and autoreactive CD8+T cells
    • Antigen driven-dendritic cell activation in autoimmunity
    • References
  • 8. Are autoimmune diseases autoimmune epithelitis?
    • Are autoimmune diseases considered autoimmune epithelitis?
    • Epithelium as the most representative of all tissues present within the animal kingdom
    • Epithelium as the entrance point for microorganisms
    • The majority of organs and tissues affected by autoimmune diseases have fenestrate capillaries
    • Epithelial tissues are the ones which suffer the most apoptosis
    • Epithelium as a target of viral infection
    • Viral infection associated with autoimmune disease
    • Epithelial cells act as antigen presenting cells
    • Epithelial cells select the repertoire of T lymphocytes within the thymus
    • The epithelium is frequently compromised by autoimmune polyglandular syndromes
    • Epigenetics and autoimmunity: Is the epithelial cell an epigenetic target? What are the implications of that?
    • References
  • 9. Cytokines, chemokines and growth factors
    • Introduction
    • Fundamental classification
    • Cytokines and cytokine-receptors general characteristics and properties
    • Cytokines, cytokine receptors, and their signaling pathways specific characteristics and properties
    • Cytokine family signaling through class II cytokine receptors (IL-10/IFN superfamily)
    • Cytokine family signaling through immunoglobulin cytokine receptor superfamily
    • Cytokines families signaling through immunoglobulin cytokine receptors superfamily non-receptor tyrosine-kinase (RTK)-class
    • Cytokines from TNF Family signal through TNF receptor family, other cytokines with TNF-domains and non TNF-ligands
    • Chemokine superfamily
    • Orphan or other cytokine family members
    • References
    • Suggested bibliographic sources
  • 10. Major histocompatibility complex: Antigen processing and presentation
    • Inroduction
    • History
    • Genetic organization of HLA
    • Regulation of gene expression
    • Origin and evolution of HLA
    • HLA characteristics
    • Structure of HLA class I and class II
    • Functions of HLA class I and class II
    • Antigen processing and presentation
    • References
  • 11. Immunosenescence
    • Introduction
    • Aging
    • Telomeres and aging
    • Epigenetics and aging
    • Immune aging
    • Infection and immunosenescence
    • Autoimmune disease
    • Concluding remarks
    • References
  • 12. The endocrine system and autoimmunity
    • Introduction
    • Immune-neuro-endocrine interaction and risk of developing an autoimmune disease
    • Immune–neuro-endocrine interaction in rheumatoid arthritis
    • Immune-neuro-endocrine interaction in systemic lupus erythematosus
    • Immune neuroendocrine interaction in autoimmune uveitis
    • Circadian rhythm from hormones and cytokines in health/disease processes
    • Concluding remarks
    • Abbreviation list
    • References
  • 13. Cell Death
    • Introduction
    • Apoptosis
    • Apoptotic cell clearance
    • Apoptosis and the homeostasis of the immune system
    • Apoptosis and autoimmune diseases
    • Granzymes
    • Netosis
    • Netosis and autoimmunity
    • Cross-talk between the subroutines
    • References
• Section II. From the mosaic of autoimmunity to the autoimmune tautology
  • 14. From the Mosaic of Autoimmunity to the Autoimmune Tautology
    • Introduction
    • Women are more prone to autoimmunity
    • Shared subphenotypes
    • Polyautoimmunity
    • Familial aggregation
    • Age of onset influences severity
    • Similar pathophysiology
    • Similar environmental agents (The autoimmune ecology)
    • Influence of ancestry
    • Common genetic factors
    • Similar treatment
    • References
  • 15. Evolution and Autoimmunity
    • Introduction
    • Evolutionary theories that may explain autoimmune phenomena development in humans
    • Influence of the first form of evolutionary memory on the autoimmune phenomena
    • Influence of the second form of evolutionary memory in autoimmune phenomena
    • Influence of the third form of evolutionary memory in the autoimmune phenomena
    • Influence of the fourth form of evolutionary memory in the autoimmune phenomena
    • Conclusion
    • References
  • 16. Introduction to Genetics of Autoimmune Diseases
    • Introduction
    • Genetic epidemiology
    • Perspectives
    • References
  • 17. HLA Association with Autoimmune Diseases
    • Introduction
    • Epidemiological analysis
    • Molecular interaction: MHC-peptides and autoimmune diseases
    • HLA commonalities among autoimmune diseases
    • References
  • 18. Non-HLA genes and autoimmune diseases
    • Introduction
    • Shared genetic variants among ADs
    • Shared genetic factors
    • Translational autoimmunity
    • References
  • 19. Infection and autoimmune diseases
    • Introduction
    • Infectious agents and ADs
    • Infections: A trigger mechanism for ADs
    • Microbiota and ADs
    • Metagenomics
    • Conclusion
    • Abbreviation list
    • References
  • 20. Autoimmune ecology
    • Introduction
    • Cigarette smoking
    • Organic solvents
    • Silica
    • Berrilyum
    • Adulterated rapesed oil
    • Drugs
    • Vaccines and autoimmunity
    • Hormones and autoimmunity
    • Conclusions
    • Abbreviation list
    • References
  • 21. Molecular mimicry in autoimmunity and vaccinations
    • Introduction
    • Induction/triggering of autoimmunity by molecular mimicry
    • References
  • 22. Epigenetics and autoimmune diseases
    • Introduction
    • Epigenetic mechanisms
    • Epigenetics and autoimmunity
    • Conclusions
    • References
  • 23. Immunological computation
    • Introduction
    • Basic concepts on immunolgy
    • History of AISs
    • Main artificial immune system algorithms
    • Applications
    • Perspectives
    • References
• Section III. Autoimmune Diseases
  • 24. Rheumatoid arthritis
    • Introduction
    • Epidemiology
    • Etiology and risk factors
    • Pathogenesis
    • Clinical features
    • Monitoring patients with rheumatoid arthritis
    • Imaging techniques
    • Treatment
    • References
  • 25. Systemic lupus erythematosus
    • Introduction
    • Epidemiology
    • Physiopathology
    • Clinical manifestations
    • Classification and diagnosis
    • Treatment
    • References
  • 26. Antiphospholipid syndrome
    • Introduction
    • Epidemiology
    • Clinical manifestations
    • Treatment
    • Current treatment of thrombosis
    • Obstetric considerations
    • Caps
    • References
  • 27. Systemic autoimmune diseases and pregnancy
    • Introduction
    • Antiphospholipid syndrome
    • Systemic lupus erythematosus
    • Rheumatoid arthritis
    • Undifferentiated connective tissue disease
    • Sjögren’s syndrome
    • Systemic sclerosis
    • Polymyositis and dermatomyositis
    • Mixed connective tissue disease
    • Systemic necrotizing vasculitides
    • Takayasu’s arteritis
    • Granulomatosis with angiitis
    • Microscopic polyangiitis
    • Churg-Strauss syndrome
    • Behçet’s disease
    • Disease modifying anti-rheumatic drugs and its use during pregnancy and breastfeeding
    • References
  • 28. Sjögren’s syndrome
    • Introduction
    • Geo-epidemiology and burden of the disease
    • Approach of patients with sicca syndrome and differential diagnosis
    • The clinical spectrum of SS
    • Patient assessment
    • Course and activity of SS
    • Physiopathology
    • Treatment
    • Translational research in SS
    • Perspectives
    • Abbreviation list
    • References
  • 29. Autoimmune diabetes mellitus (Type 1A)
    • Introduction
    • Epidemiology
    • Genetics
    • Environmental aspects
    • Autoantibodies
    • Pathogenesis
    • Clinical presentation
    • Laboratory findings
    • Prediction of disease
    • Immune therapy in type 1 diabetes
    • Prevention targets and immune therapy interventions
    • Vaccination
    • Treatment
    • Abbreviations
    • References
  • 30. Thyroid disease and autoimmune diseases
    • Introduction
    • Genetics
    • Epigenetics
    • Environmental factors
    • Autoantibodies
    • Autoimmune thyroid diseases
    • Polyautoimmunity
    • Conclusions
    • Abbreviation list
    • References
  • 31. Autoimmune hepatitis
    • Introduction
    • Autoimmune hepatitis (AIH)
    • Treatment of AIH-I
    • Immunopathogenesis of AIH-I
    • Regulatory T cells in AIH-IN
    • Conclusions
    • References
  • 32. Primary biliary cirrhosis
    • Introduction
    • Epidemiology
    • Etiology and pathogenesis
    • Clinical features
    • Diagnosis
    • Natural history and prognosis
    • Treatment
    • References
  • 33. Celiac disease
    • Introduction
    • Epidemiology
    • Pathogenesis
    • Genetic factors
    • Environmental factors
    • Natural history
    • Clinical manifestations
    • Diagnosis
    • Treatment
    • References
  • 34. Dermatological autoimmune diseases
    • Introduction
    • The origin of the skin
    • Cell junctions relevant for autoimmunity
    • Autoimmunity
    • Pemphigus
    • Bullous penphigoid (bp) diseases
    • Dermatitis herpetiformis (DH)
    • Epidermolysis bullosa acquisita (EBA)
    • Vitiligo
    • Psoriasis
    • Concluding remarks
    • References
  • 35. Systemic sclerosis
    • Introduction
    • Case report 1
    • Case report 2
    • Case report 3
    • References
  • 36. Systemic vasculitis
    • Introduction
    • Classification of vasculitis
    • Pathogenesis
    • Approach to the patient with suspected vasculitis
    • Disease activity assessment
    • Giant cell arteritis
    • Takayasu arteritis
    • Polyarteritis nodosa
    • Kawasaki disease
    • Cryoglobuilinemic vasculitis
    • Anca-associated vasculitis (AAV)
    • Iga vasculitis (henoch-schönlein purpura)
    • Hypersensitivity vasculitis
    • Behçet’s disease
    • Cogan syndrome
    • Single-organ vasculitis
    • Vasculitis associated with systemic disease
    • Vasculitis mimics
    • References
  • 37. Autoimmune uveitis
    • Introduction
    • Classification
    • Approach to uveitis
    • Epidemiology
    • Associated diseases
    • Other associated diseases
    • Treatment
    • Biological therapies
    • Follow-up
    • Keypoints
    • Acknowledgements
    • References
  • 38. Cardiovascular involvement in autoimmune diseases
    • Introduction
    • Atherosclerosis
    • Rheumatoid arthritis
    • Systemic lupus erythematosus
    • Antiphospholipid syndrome
    • CVD in others ADS
    • Conclusions
    • Abreviations
    • References
  • 39. Autoimmune diseases and cancer
    • Introduction
    • Rheumatoid arthritis and cancer
    • Sjogren’s syndrome (SS) and cancer
    • SLE and cancer
    • Polymyositis (PM) / Dermatomyositis (DM) and cancer
    • Scleroderma and cancer
    • Systemic vasculitis and cancer
    • References
  • 40. The early autoimmune disease clinic. The case of rheumatoid arthritis
    • Introduction
    • Results
    • Discussion
    • Conclusions and perspectives
    • References
• Section IV. Innovative therapies
  • 41. Intravenous immunoglobulin-customized therapy
    • Introduction
    • Mechanisms
    • IVIG sources and extraction
    • Dose and route
    • Adverse events
    • Benefit
    • Specific IVIG for different Diseases
    • Conclusions
    • References
  • 42. Autologous peripheral hematopoietic stem cell transplantation
    • Introduction
    • Hematopoietic stem cell transplantation
    • Types of HSCT
    • Autologous peripheral hematopoietic stem cell transplantation (AHSCT)
    • Stem cell collection
    • Conditioning regimens
    • Aplastic phase and engraftment
    • Candidate selection
    • Post-Transplant care
    • Rational use and therapeutic mechanisms of HSCT in AD
    • Preclinical data
    • Clinical data
    • Indications for autologous HSCT in ADs
    • Results of HSCT in ADs
    • Multiple sclerosis (MS)
    • Systemic sclerosis (SSc)
    • Systemic lupus erythematosus (SLE)
    • Rheumatoid arthritis (RA)
    • Juvenile idiopathic arthritis (JIA)
    • Type 1 diabetes mellitus (T1D)
    • Other ADs
    • Complications of HSCT
    • Conclusions
    • References
  • 43. RNAi and autoimmunity
    • Introduction
    • Types of RNAi
    • RNAi precursor biogenesis
    • Development of RNAis active forms from their pre-RNAi precursor
    • Gene regulation of the RNAi
    • Mechanisms of action of miRNA and siRNA
    • RNAi and the immune system
    • RNAi and autoimmune diseases
    • miRNA and RA
    • miRNA in SLE
    • Other autoimmune diseases
    • Conclusion
    • References
  • 44. Nanotechnology and autoimmunity
    • Introduction
    • Nanotechnology in autoimmune diseases
    • Diagnostic approaches
    • Therapeutic approaches
    • Theranostic approach
    • Benefits and disadvantages of NPS and engineered nanomaterials
    • Ethical considerations
    • Abbreviation list
    • References
• Section V. Basic principles of laboratory
  • 45. Cell culture and cell analysis
    • Introduction
    • Development of cell culture
    • Preliminary preparation and sampling
    • Blood cell storage: cryopreservation and thawing process
    • Characterization and separation of cells by cellular markers
    • Affinity separation by magnetic particles
    • Count and cell viability
    • Recommended readings
  • 46. Analysis of nucleic acids
    • Isolation of DNA and RNA from eukaryotic cells
    • Cell-Based DNA cloning
    • Polymerase chain reaction (PCR)
    • Real time PCR
    • Other techniques to analyze DNA or RNA
    • Recomended readings
    • Cell-based DNA cloning
    • PCR and real time PCR
    • Recommended Web sites
  • 47. A primer on current and common sequencing technologies
    • Introduction
    • Background
    • Fundamentals of sequencing platforms
    • Next generation sequencing (NGS) platforms
    • NGS data analysis
    • Recommended readings
  • 48. Analysis of proteins and antibodies
    • Introduction
    • General antibody characteristics
    • ELISA
    • Principle of the method
    • Western blotting
    • Immunofluorescence and immunohistochemistry
    • Concluding remarks
    • Recommended readings
  • 49. Epigenetic tools in autoimmune diseases
    • Introduction
    • Methylation analysis
    • Histone modification analysis
    • Concluding remarks
    • Recommended readings
• Contributors

source https://www.ncbi.nlm.nih.gov/books/NBK459466/

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