pathology, immunology and infection biology

8/12/2019 Pathology, Immunology and Infection Biology

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Biomedicine Course Autumn 2002Pathology, Immunology and Infection biology

Synopses of lecturesMon 26/8 10.00 10.45 (Agneta Richter-Dahlfors)Introduction: Introduction to pathogenic microorganisms and infectious

diseases.

Objectives:this lecture will: provide an historical overview of the origins of microbiology describe the major types of human pathogens and their major biological features review some of the evolutionary, social and economical implication of microbial

diseases review the directions of the microbiological research of today and speculate

about future directions.

Section I Molecular Immunobiology

Aims of this section to review the anatomy and cell composition of the immune system to provide an overview of lymphocyte receptors (LR), their structure and function

to review the main steps of the assembly process of the LRs to review the principal mechanisms of these receptors in induction of adaptive

immune responses to review the regulation of lymphocyte gene expression during development

Tue 27/8 09.00-11.30 (Elena Levitskaya)Anatomy and cells of the immune system

The aim of this lecture is to scrutinize the functional role of red and whiteblood cells for our immune defences. Also, to present the central and peripheralorgans in our immune system, the lymphatic circulation as well as the anatomy of

peripheral lymphoid tissues. Mucosal associated lymphoid tissues are defined.Keywords: direct cytotoxicity, antibody dependent cell-mediated cytotoxicity(ADCC), phagocytosis, pinocytosis, antigen presentation and processing, antigen

presenting cell (APC), costimulation, Langenhans cells (LH), Interdigitating dendriticcells (IDC), Follicular dendritic cells (FDC), cytokines and chemokines, FcR, CR,mediators of inflammation, major basic protein, NK cells and inhibitory (KIR) andactivating (KAR) receptor(s), NKT cells, anti-bacterial peptides. Gut-AssociatedLymphoid Tissue (GALT), Bronchial-Associated Lymphoid Tissue (BALT),Mucosal-Associated Lymphoid Tissue (MALT).

A review article on anti-bacterial peptides will be handed out.


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Tue 27/8 13.00- 14.30 (Benedict Chambers)Innate immunity

The aim of this lecture is to present innate immunity and its major relevancefor signalling, orientation and strengthening of adaptive responses. Previously knownqualities of innate immunity as absence of memory and specificity, are discussed

based on recent knowledge of conserved receptors (pattern of recognition receptors)and conserved patterns associated with the pathogen (pathogen-associated molecular

patterns). The inflammatory response leading to the production of pro-inflammatorycytokines and acute-phase proteins are discussed. Acute-phase proteins are introducedas opsonins. Mannan binding protein and its ability to activate complement cascadewill be discussed. The three pathways for complement activation are introduced.Biochemical reactions leading to C3 convertase and C5 convertase are presented indetail during this lecture.Keywords: barriers to infection, lyzozyme, lactoferin, anti-bacterial peptides, naturalflora, inflammation, increased vascular permeability, cytokines, chemokines,lymphocyte migration, PRR, PAMPS, Toll-like receptors, CRP, SAA. MBP, type Iinterferons, Il-1, Il-6, TNF-a, IL-8, Il-12, C3 tickover, C3, C5 convertases,Membrane-Attack Complex (MAC).

A review article on PRR, PAMPS will be handled out.

Thu 29/8 09.00-11.30 (Elena Levitskaya)

Basic immunological terminology, immunoglobulin structure andfunction of B-cells

Short historical introduction describing the concepts of cellular and humoralimmunity.Humoral immunity as prevailing concept in the early strategies of immunologicalresearch.Basic immunological terms which developed during studies on humoral immunity:

Antigen; Immnogen; Hapten; Antigenic determinant; Adjuvant; Affinity; Avidity; Specificity; Crossreactivity.

Structure of immunoglobulins, Fab, F(ab)2 and Fc fragments.Antigenic determinants of immunoglobulins, idiotypic networks.

Immunoglobulin subclasses and their functional diversity.

Monoclonal and polyclonal antibodies.


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Principles of hybridma technology.Major assays based on Ag/Ab reaction.

B-cell activation. Immunoglobulins as cell surface signal transducing receptors.

Components of the signalling machinery.Immunoglobulin class switch.T-cell dependent and independent antigensRegulation of B-cell activation and maturation by lymphokines and co-stimulatorysignals. Anatomy of the process: follicular dendritic cells, lymphnodes, germinalcenter.B-cells as antigen presenting cells.

Thu 29/8 13.00-14.30 (Elena Levitskaya)Generation diversity of B-cell repertoires

The aim of this lecture is to give understanding to the generation of receptordiversity present in the T and B lymphocytes and their relevance to adaptive immuneresponses. The immunoglobulin receptor (IgR) is used as a model for generearrangement. The IgR is quickly introduced as a surface protein and from the

protein structure we will go into DNA and understand mechanisms behindrearrangement of immunoglobulin genes. 12/23 rule, generation of P and Nnucleotides will be explained. The development of B cells in the bone marrow and itsselection process will be introduced.Keywords: IgR (IgM IgD), VL, VH, CL, CH, Variable, Constant, CDR1,2,3, VDJ/VJ

gene segments, germline DNA, somatic recombination, heptamer, nonamer, RAG-1,RAG-2 complex, hairpin formation, TdT, allelic exclusion, somatic hypermutation,clonal deletion of B cells.

Fri 30/8 09.00-11.30 (Elena Levitskaya)MHC structure and antigen processing and presentation

Antigen processing and presentation machinery, MHC molecules and T-cells ascomponents of the integral system of adoptive immunity.

Short history of major discoveries that have unravelled the structure and function ofMHC molecules. Basic information about MHC class I and class II molecules.

Nomenclature of MHC and MHC encoded molecules in mice and humans. Structureof MHC molecules.Major steps of MHC class I restricted antigen presentation.Major proteases involved in antigen processing.Evolutionary relationship between the proteolyic systems and MHC.Major steps of proteolysis involved in MHC class I restricted presentation. Structureand enzymatic activity of the proteasome.Housekeeping and immunoproteasome.Regulatory complexes (19S, PA28).Other proteases involved in the processing of MHC class I associated peptides.


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Function and selectivity of TAPs. Phenotype of TAP deficient cells. Assembly andtrafficking of MHC class I molecules through ER and Goldgi compartments. Role ofdifferent chaperones.

Assembly and trafficking of MHC class II molecules. Structure and function ofinvariant chain. Degradation of invariant chain and other proteins transported into thelysosomal/endosomal compartment. Cathepsins. CLIP and HLA-DM.

Alternative pathway of MHC class I restricted antigen presentation. Characteristics ofthe pathway in different cell types.

Genetics and structure of TCR. Structural aspects of MHC:TCR interaction.

Fri 30/8 13.00-14.00 (Benedict Chambers)Dendritic cells

The aim of this lecture is to describe the biology of dendritic cells and their role inimmune responses. Topics will be DC precursors and their relation to other cells inthe immune system. Uptake of antigen and trafficking to secondary lymphoid organs,with Langerhans cells in the skin as a model. Signals that induce DC maturation.Interaction between T cells and DC and the molecules involved. Co-stimulation andthe danger hypothesis. Peripheral tolerance versus T cell activation. The difference

between DC and macrophages and B cells as APC.

Tue 3/9 09.00-10.00 (Victor Levitsky)T-cell activation

Role of MHC/TCR interactions in immune regulation. General characteristics of T-cell recognition.Different outcomes of MHC/TCR interaction.Effects of altered peptide ligands on T-cell recognition and activation.TCR serial triggering. Thermodynamic and kinetic characteristics of MHC:TCRinteraction.Models of TCR triggering.Schematic overview of TCR signal transduction, short description of major signalling

pathways.Role of co-stimulation.CR/MHC interaction in space and time. Supramolecular activation complexes.

Tue 3/9 10.30-11.30 (Victor Levitsky)T-cell effector functions

Effector molecules of T-cells. Apoptosis as a major mechanism of CTL killing.

Granule exocytosis.Perforine and granzymes.Caspases: nomenclature, enzymatic activity and function.


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TNF-receptor family of apoptotic and co-stimulatory molecules. Signalling throughFas and TNFalfa-receptor. TRAIL and its receptors.Bactericidal molecules produced by T-cells.Lymphokines and inhibition of viral replication.

Th1 and Th2 subsets of CD4+ T-cells.Role of effector molecules in regulating homeostasis in the immune system.Phenotype of relevant mutant and gene knock-out mouse strains.

Wed 4/9 09.00-11.30 (Victor Levitsky)T-cell selection and tolerance

In this lecture, we will walk through T cell development from the precursors in thebone marrow, via the thymus to the peripheral T cell in secondary lymphoid organs.The role of the thymus will be emphasized and the different steps in thymic selectiondescribed in detail, giving experimental evidence for positive and negative selectionfrom work with superantigens and TCR transgenic mice. Generation of T cell receptordiversity will be described. We will then go into tolerance, discuss clonal deletion inT and B cells and then go into mechanisms for peripheral tolerance, such asignorance, anergy, immunological privileged sites etc. Finally, the development ofgamma/delta T cells and thymus-independent T cell maturation in the gut will bediscussed.

Thu 5/9 09.00-10.00 (Benedict Chambers)

NK cells

The origin of NK cells will be described, how they were discovered and what isthought to be their main biological role. We will then go into the recognitionmechanisms, focusing on the two step model with an initial positive trigger that is

balanced by negative signals, the missing self model. Next, some of the knownreceptors that mediate positive and negative signals, their signal transduction

pathways and how they are balanced in the cell will be discussed. Finally, we will talkabout NK-T cells and their proposed biological role.

Thu 5/9 10.30-12.00 (Benedict Chambers)Congenital immunodeficiencies

The aim of this lecture is to give a detailed description of congenitalimmunodeficiency disorders and emphasize how they can shed light on immunefunctions. At least one disorder for each major component of the immune system, i.e.T cells, B cells, complement, macrophages etc. will be touched upon, but we will notgo into details of all known diseases. Some epidemiology will be discussed as well.


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Fri 6/9 09.00-11.30 (Victor Levitsky)Regulation of immune responses

The aim of these lectures is to summarize the role of innate and adaptive immunity in

infection. An example of a viral and a bacterial infection will be used. The classshould actively participate in the exercise of mounting an adequate eliminatingresponse to both infectious agents, involving effector cells and molecules in theimmediate early, early and late phases of infection.

Section II Pathology

Aims of this section

Description of basic pathological responses Structural alterations in cells and tissues during cell adaptation, damage and death. Etiological (causative) factors for and pathogenesis of cell adaptation, damage and

death. Structure of and mechanisms involved in tissue repair and regeneration.

Mon 9/9 09.00-10.15 (Lennart Eriksson)Introduction to concept of disease, cell damage and adaptation

Mon 9/9 10.45-12.00 (Jerker Olsson)Cell damage and defence mechanisms

Objectives:You should be able to describe the tissue reactions at the morphologicallevel during reversible (degeneration) and irreversible (necrosis) cell damage. Youshould know common etiological factors and pathogenetic mechanisms for celldamage, in particular due to lack of adequate oxygen supply and following expositionof cytotoxic compounds. You should be able to describe the role of free radicals forthe development of cell damage, how free radicals are formed and the effects of theseradicals on cellular components and functions. Knowledge on the cellular defence

mechanisms towards free radicals, and how cells can learn (adapt) to cope with ahostile environment.

Tue 10/9 9.00-10.15 & 10.45-12.00 (Gran Andersson)Acute and chronic inflammation

Objectives:

Definition of acute and chronic inflammation, innate and adaptive immuneresponse

Regulatory and effector inflammatory cells

Aetiology of inflammation Local and systemic inflammatory symptoms


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Local vascular and cellular responses during inflammation Leukocyte-endothelial interactions, emigration and chemotaxis Vasoactive and chemotactic mediators Phagocytosis and intracellular destruction of inflammatory agents Histopathology of acute and chronic inflammatory exsudate Composition of exsudate and granulation tissue Dissemination of agens (lymfangitis, lymfadenitis, sepsis) Granulomatous inflammation Healing after inflammation

Wed 11/9 09.00-10.15 (Gran Andersson)Tissue regeneration and repair

Objectives: You should be able to describe the structure and composition ofgranulation (repair) tissue, and the essential features of wound healing. Why do sometissues heal damaged areas with a scar while other tissues completely regenerate?Which are the molecular mechanisms involved in tissue regeneration and repair,

particularly the role of growth factors, cell proliferation and cell differentiation. Youshould know the repair mechanisms of specialized tissues, such as epithelia, muscle,nervous tissue and bone.

Fri 13/9 09.00-10.25 (Staffan Strmblad)Cellular ageing and cell death

Objectives: You should be able to describe the mechanisms and characteristics forcellular ageing and different forms of cell death, including necrosis and apoptosis,their regulation, physiological relevance and relation to disease. You should alsoknow the principle for various apoptosis detection methods.

Synopsis:Maximal life span, Age-related changes, Progeria, Mechanisms of ageing,Telomeres and telomerase.

Necrosis; Characteristics of Necrosis, Pyknosis, Karyorrhexis.Apoptosis; Definition, Physiological relevance, Diseases related to apoptosis

regulation, Cellular changes and characteristic morphology during apoptosis, CentralMechanism of apoptosis, Activators and inhibitors of apoptosis, Fas, Caspases, bcl-2family, Methods for detection of apoptosis, Immune evasion by stimulation ofapoptosis.

Section III Clinical Immunology - Autoimmunity

Aims of this section:

To provide clinical examples of autoimmune diseases To review the molecular mechanisms of autoimmune reactions To discuss rational approaches of therapy


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To review the present status of research in autoimmunity

Mon 16/9 08.30-09.15 (Helena Erlandsson Harris)

Introduction to autoimmunity and Rheumatoid Arthritis (RA)

Objectives:By the end of this lecture you should be able to: Define autoimmunity Define autoimmune disease Define the term autoantigen Define the term autoantibody Define organ-specific autoimmune diseases, and give an example Define systemic autoimmune diseases, and give an example Describe B-cell mediated autoimmunity, and give an example of a disease

Describe T-cell mediated autoimmunity, and give an example of a disease Have an idea about these concepts in conjunction with rheumatoid arthritis

Lecture synopsis: A definition of autoimmunity is stated and discussed. Theexistence of autoimmunity in healthy individuals is mentioned and the developmentfrom autoimmunity to autoimmune disease, and factors influencing this, is discussed.Briefly, prevalencies and geographical spread of autoimmune diseases are discussed.Division of autoimmunity in B-cell mediated and T-cell mediated is made, andmechanisms involved described. Antagonistic and agonistic autoantibodies and theiropposite effects discussed. Examples of AD given for each scenario.Division of autoimmunity in systemic and organ-specific is described with examplesof diseases.An introduction of rheumatoid arthritis as an autoimmune disease, and features of RAaccording to previous part of the lecture, is ending this lecture.

Mon 16/9 10.00-10.45 (Tina Trollmo)Autoimmunity evolving to autoimmune disease

Objectives:By the end of this lecture you should be able to:- Discuss possible theoretical explanations to the occurrence of autoimunity and

factors that might influence the induction of autoimmune diseases.

Lecture synopsis: Errors in central or peripheral tolerance mechanisms,immunoprivilige, molecular mimicry, induction of co-stimulatory signals,inappropriate MHC expression, polyclonal activators as autoantigens, oxidative stressas factors triggering/influencing the development of autoimmunity/autoimmunediseases. For the different concepts discussed, examples will be given from human orexperimental systems.

Mon 16/9 11.00-11.45 (Tina Trollmo)

Environment and genetic factors (RA)


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Objectives:After this lecture you should be able to: Give examples of environmental factors known to influence the development

of autoimmune disease, and if known, mechanisms for this. Give examples of genetic factors influencing the development of autoimmune

disease (RA). Describe the theory behind The shared epitope hypothesis.

Lecture synopsis: Current knowledge in the field of environmental and geneticinfluence of AD and RA in particular is reviewed. Concerning environmental factorssuch things as drugs, smoking, diet, sunlight, stress(?), silicone, plastics and solventsare discussed. Concerning genetic factors MHC-linkage and the shared epitopehypothesis will be discussed, as well as other hereditary factors such as sexhormones,TNF-a polymorphisms, Ig-genes, TcR genes, apoptosis genes.

Tue 17/9 08.30-09.30 (Vivi Malmstrm)Experimental models of RA

Objectives:After this lecture you should be able to: Name some examples of different experimental arthritis models Define the term adjuvant Name two cartilage antigens that can induce exp arthritis Name two adjuvants that can cause exp arthritis

Lecture synopsis: Advantages and disadvantages with animal models of human

diseases compared to studies in humans will be discussed, as well as types of studiesthat are/can be performed in animals.Experimental models will be divided into groups according to way of induction,spontaneous, induced with ag, induced with adjuvant and genetically modified.Examples will be discussed in each group. Collagen-induced arthritis and oil-inducedarthritis will then be presented in more detail. Half of the lecture will be used as adiscussion with the students how you can investigate various immunological featuresof these two models, and how it has been done. (T-cell dependence, B-celldependence, type I or type II cytokine pattern, MHC-restriction etc). The idea is totrigger the researchers in the students.

Tue 17/9 10.00-10.45 (Vivi Malmstrm)Future therapeutic strategies for RA

Objectives:After this lecture you should be able to: Discuss oral tolerance as a therapeutic strategy for autoimmune diseases Briefly explain what is meant with bystander suppression Briefly describe the role of TNF-a in RA

Lecture synopsis: TNF-a treatment as a therapy for RA will be discussed, from the

first animal studies to the latest patient trials. Antibodies, soluble receptors, syntheticsubstances.


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Feeding with potential autoantigens to induce tolerance as a therapy for autoimmunediseases. Possible tolerance mechanisms (TGF- production or deletion) will bediscussed. Ameliorating effect of coupling to cholera toxin B. MBP trials in MS andCII trials in RA.

Bystander suppression (tolerance induced to a particular joint-specific antigen willameliorate any form of arthritis, whether induced by the antigen in question orinduced by other means).

Tue 17/9 11.00-12.00 (Helena Erlandsson Harris)The hopes and wishes of a RA patient

Objectives: After this lecture you should hopefully feel that you have gained inunderstanding of how it can be to live with an autoimmune disease, and the restraintsit puts on everyday life. It is also my hope that you, after listening to thisextraordinary woman, feel filled with enthusiasm to do research about autoimmunediseases (and arthritis in particular!).

Lecture synopsis: Margareta Bckskog, 1:e vice chairman in the patientsorganisation Reumatikerfrbundet, has promised to come and tell us about herRheumatoid arthritis and how it affects her life. She will also tell us about her hopesof how research might improve her situation.

Section III Clinical Immunology - Allergy

Aims of this session

- to review the principle mechanisms of the IgE-mediated reaction- to give an overview of the mechanisms of T-cell mediated allergic reactions- to provide an overview of structure and function of IgE- to describe the use of DNA technology in allergy- to review novel strategies for allergy treatment

Wed 18/9 8.30-9.15 (Marianne van Hage-Hamsten)Mechanisms in IgE-mediated allergic reactions

Objectives

By the end of this lecture you should be able to:- understand the mechanisms of the IgE-mediated reaction- give examples of different allergens- indicate the relevant diagnostic tools- briefly discuss some possible reasons for the increase in allergy

Lecture synopsis: The aim of this lecture is to present the IgE-mediated allergic

reactions and describe their mechanisms. The atopic march will be mentioned. Themost common allergens, which are small antigens that provoke an IgE-antibodyresponse, will be summarised and their properties discussed. The different tools for


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diagnosis of allergy will be reviewed as well as their advantages and disadvantages.The increase in allergic diseases and some possible reasons for this will be describedand protective mechanisms discussed.

Wed 18/9 9.20 10.05 (Magnus Lindberg)Mechanisms of contact dermatitis

Objectives

By the end of this lecture you should be able to:- understand the mechanisms of the T-cell mediated allergic reaction- give examples of different haptens/allergens- indicate the relevant diagnostic tools present today and the need of additional ones- discuss preventive strategies-Lecture Synopsis

The aim of this lecture is to present the T-cell mediated allergic reactions and describetheir mechanisms. The most common haptens/allergens, which are causing contactallergy will be presented. The method for diagnosis of allergic contact dermatitis will

be reviewed, its advantages and disadvantages, and the need for additional methodswill be discussed. In addition, the social and economic problems related to allergiccontact dermatitis and different strategies for prevention will be described.

Wed 18/9 10.30 - 11.15 (Cecilia Hellman)

Airway inflammation

Objectives

After this lecture you should be able to: Describe the key events in the early and late phase of an allergic reaction Describe the role of mast cells, Th2-lymphocytes and eosinophils in the initiation

and maintenance of airway inflammation Identify some cytokines / chemokines, and explain their specific role in the

initiation and maintenance of airway inflammation

Lecture synopsis

This lecture will focus on the late phase of the allergic reaction. The biology andintegrated function of mast cells, Th2-lymphocytes and eosinophils, as well as theimportance of different cytokines / chemokines in the initiation and maintenance ofairway inflammation will be discussed.

Wed 18/9 11.15 - 12.00 (Omid Rasool)Experimental allergy - DNA technology

Lecture synopsis: For the last 100 years, allergists have relied on natural allergenic

products (crude extracts) for the diagnosis and treatment of allergic diseases.Although the quality of natural allergen extracts has improved during the last 20years, allergens prepared from such materials remain heterogeneous products and vary


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in allergen composition and content. Furthermore, natural products may becomecontaminated with allergens from other sources. Therefore, production of moreconsistent products, such as recombinant allergens, has become of great importance toimprove the quality of allergens used as tools for diagnosis and treatment of type I

allergies.Techniques of molecular biology and genetic engineering applied to allergens haveenabled the production of recombinant allergens, which can be produced as pure

proteins and in large amounts. Several techniques have been used for allergenidentification and cloning. Strategies based on PCR (RACE-PCR, also calledanchored PCR) offer opportunity to directly select, amplify and isolate a message ofinterest. This approach needs a small amount of sequence information. ExpressioncDNA libraries, such as lambda and phage display libraries, prepared from theallergen source, are other tools used for allergen identification. Once the allergen iscloned, it will be necessary to express the protein in order to analyse it further. Theexpression system of choice, either prokaryotic or eukaryotic, will be very muchdependent on the nature and properties of the protein. Mapping of the B- and T-cellepitopes of the allergen together with the study of its three-dimensional structure willgive important information regarding the properties of the allergen and its molecularinteractions.

Wed 18/9 13.00 - 13.45 (Caroline Nilsson)The asthmatic patient

Lecture synopsis

The lecture will cover definition, diagnosis and clinical aspects of asthma. Theselection and the utility of different direct and indirect challenge models ofasthma will be presented as well as the possibilities of sampling biologicalfluids and tissues.

Questions on "The asthmatic patient"1. Name the most common trigger factors of airway obstruction in asthma.Distinguish between allergens and unspecific trigger factors.2. Discuss the different levels of action of the allergen bronchoprovocation, theleukotriene bronchoprovocation and the exercise challenge.Briefly explain what is meant by a "biomarker" in the context of asthma and

give some examples.

Thu 19/9 8.30-9.30 (Mauro DAmato)Susceptibility genes for asthma and allergy

Lecture Synopsis: Asthma and allergy are complex disorders, which are due to theinteraction of an unknown number of genes with strong environmental factors.Segregation analysis, twin studies and, more recently, linkage studies suggest the

presence of major genes conferring susceptibility to these pathological conditions.Identifying such genetic predisposing factors will improve our understanding of itsaetiology and will hopefully lead to a better treatment of patients and the developmentof prevention strategies.


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A serious impediment to the study of the genetics of asthma and allergy is thedifficulty in defining their phenotype, for which a uniform definition still does notexist. Indeed, it has become clear that the choice of the phenotype is of paramountimportance in the ability to discover predisposing genes or to replicate previous

positive findings. To overcome this problem, there is now a general tendency todissect these complex phenotypes into their major components, by the analysis ofquantitative traits rather than the diseases in their whole manifestation. Theseinclude total and specific serum IgE levels, skin prick tests for hypersensitivity,

bronchial hyperresponsiveness (BHR), eosinophil count etc., which are moreamenable to objective measurement than clinician diagnosed asthma/allergy.

As for other complex disorders, the identification of predisposing genes canbe assessed by two different approaches: examining candidate genes or by geneticlinkage followed by positional cloning. The first approach is generally used whensome hypothesis can be made regarding disease pathogenesis and the role of acandidate gene is tested by allele-association (case-control) studies. By geneticlinkage and positional cloning, genes are identified based on their position on thegenetic map. This approach has the advantage of not requiring any prior knowledge ofthe pathophysiology of the disease. The prerequisite is the collection of a largenumber of families and accurate phenotyping of the individuals. Genetic linkage relieson the demonstration of a co-inheritance of the disease with genetic polymorphicmarkers of known chromosomal localization. This results in the disease gene beingmapped to an approximate position on the genome. The power of this approach issuch that if an appropriate number of markers are typed in several hundreds offamilies a whole-genome screen is possible. Several association and linkage studies(three whole-genome screens) have been performed in the last few years and a number

of genes have been consistently reported to be involved in the inherited susceptibilityto asthma. Moreover,For the sole didactic purpose we will arrange these genes into three major

groups comprising genes involved in mechanisms of general inflammation andmaintenance of the Th1/Th2 balance, genes contributing to specific responses againstallergens, and genes acting at the level of target organs, influencing their reactivityand function. A few examples for each group will be discussed and data from recentliterature will be covered.

Thu 19/9 10.00 - 11.00 (Guro Gafvelin)

Novel strategies for allergy treatment

Objectives: By the end of the lecture you should be able to: describe different general approaches for allergy treatment explain differences between pharmacological treatment, specific immunotherapy

and new general treatments of allergy account for advantages and drawbacks with different allergy treatments describe how an allergy vaccine could be designed

Lecture Synopsis: There are several efficient pharmacological agents in use today,

which relieve the symptoms of allergy. Among these are specific inhibitors ofmediators released by mast cells e.g. antihistamins, and general anti-inflammatoryagents like corticosteroids. The only curative treatment for allergy in use today is


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specific immunotherapy. Immunotherapy involves administering increasing quantitiesof allergen over a period of time to induce allergen specific tolerance. Duringimmunotherapy, T-cells are affected and may either become anergic or deviate from aTh2 to a Th0/Th1 response. It has also been shown that allergen specific IgG-

antibodies are synthesised during immunotherapy, which may act as blockingantibodies.A main interest is to reduce the risks associated with injecting allergens to

patients. This may be achieved by the use of recombinant allergens. Modifiedrecombinant allergens with decreased IgE binding but retained T-cell epitopesovercome problems such as sensitisation to new components and anaphylactic sideeffects and are ideal candidates for specific immunotherapy. Another promisingapproach in immunotherapy, which has so far only been tested in animal models, isthe application of naked DNA vaccination. In this case, DNA encoding the allergen isgiven as plasmid DNA also containing immunostimulatory sequences that stimulate acellular immune response. Molecular biology techniques have also been used todevelop other new treatments of allergy. A humanised monoclonal anti-IgE antibody

blocking the binding of IgE to its high affinity receptor FcRI has been constructedand tested on patients. Another target for allergy treatment is cytokines involved inthe allergic response. For example, Th2 cytokines like IL-4 and IL-5 may beinactivated by specific antibodies or receptor fragments and Th1 cytokines like IL-12may be given to enhance the effect of immunotherapy. Chemokines and costimulatorymolecules are other possible targets for treatment of allergic disease.

Thu 19/9 11.15 - 12.00 Anne RenstrmPrevention in allergy research

Allergy and asthma may influence quality of life in many ways. Besides personalhealth, both the lifestyle of the patient and often his family may be affected. Theschool work of a student, or the career an occupational asthmatic may suffer. Theeconomical consequences of occupational allergy or asthma may affect both the

patient (sick leave, medical costs, rehabilitation, change of job/new education (newstudent loans), unemployment) and the employer (loss of competence and time,recruitment of new staff, costs for/investments in prevention). The costs of allergy andasthma in Western countries are indeed great.

Much research has been focused on the development of pharmaceuticalapproaches to combat allergy and asthma in patients. However, other strategies can be

employed both to limit the consequences of disease and to prevent recurrence:screening, early intervention, education, reduction of exposure to the allergen andadjuvants (eg smoking, pollution), rehabilitation etc. Primary prevention: preventingor minimising the development of allergy or asthma by identifying individuals at riskor risk occupations/situations, and by developing prevention strategies, is even moredesirable. Such efforts aimed at primary or secondary prevention must be properlyevaluated.

Several prevention strategies have recently been tested, such as Lactobacilliintake, occupational health activities, or various allergen exposure reductionmeasures. To study where, in which situations and to what levels subjects are exposed

to allergens, and to evaluate the effectiveness of exposure reduction strategies, it isnecessary to measure the allergens. A number of methods to sample and assess


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allergen exposure have been developed over the last decade, making it both possibleand necessary to choose between methods.Some studies aimed at primary or secondary prevention will be presented.

Section IV Microbiology - Virology

Aims of this section:

to provide an overview of virus structures and genome types to review the main steps of the virus cycle to provide an overview of the main strategies of RNA and DNA virus replication

and to explain the concept of viral latency to review the principal mechanisms of viral pathogenesis

to discuss why and how viruses interfere with the cell cycle to review viral strategies to prevent apoptosis to describe viral functions affecting

host immune responses to discuss the origin of new viruses to review the factors contributing to the emergence of new viral diseases and the

national and international programs for monitoring disease outbreaks to illustrate the principles and strategies for development of new antiviral drugs

Section IV Microbiology- Epidemiology


to provide an overview of the epidemiology of infectious diseases to review the impact of infectious diseases to review the transmission routes to review the principal types of surveillance

Mon 23/9 9.30 11.00 (Karl Ekdahl)Epidemiology of Infectious Diseases

Objectives:by the end of this lecture you should be able to: define the most important concepts used in infectious disease epidemiology describe the different variables needed to understand the transmission of

diseases give examples of factors influencing the emergence of new infections

Lecture Synopsis: The impact of acute infectious diseases on mortality patternsin Sweden has changed dramatically during the last 100 years: from a situationsimilar to the one we find in developing countries today to one where the role finfectious diseases seems negligible. A number of factors have contributed tothis - many of them outside the medical sphere. However, most of the deadly

diseases remain under control only through a never-ending work in manysectors of society to keep them at bay. One of the important components in thecombat against infectious diseases has been the establishment of routine


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surveillance systems. The basic Swedish surveillance system will be describedas well as the possibilities for intervention it supplies. There are a number ofterms that need to be grasped in order to understand infectious diseaseepidemiology: attack rate, asymptomatic infection, immunity, secondary case,

latency period, incubation time, etc. These will be covered. The propensity of adisease to spread in a population depends not only on biological characteristicsof the pathogen and the host, but also on contact patterns in society. Models will

be discussed for how these factors co-operate. Against this background, it willbe underlined that infectious diseases keep evolving and emerging, and thatthere is every reason to believe that this will never stop.

Tue 24/9 9.00-10.00 (Anders Bergqvist)Virus structure and classification

Objectives: Part I- by the end of this lecture you should be able to: define a virus describe the basic components of a virus list the different types of viral genomes giving examples for each type describe the basic principles of virion assembly and architecture name the main criteria for classification of viruses

Lecture Synopsis: A virus is a subcellular organism with a parasitic intracellular lifecycle that, unlike cells, contains either DNA or RNA and multiply by assembly of

preformed components rather than division. A virus particle (virion) consist of a

nucleic acid genome surrounded by a proteinaceous shell (capsid). In some virusesthis core structure is covered by a lipid membrane of cellular origin (envelope).Viruses may be subdivided by genome type into: 1. double stranded (ds) DNAgenomes, typically large viruses; 2. single stranded (ss) DNA genomes, typicallysmall viruses; 3. ds RNA genomes that consist of between 2 and 12 differentmolecules of RNA (segmented genomes); 4. ssRNA genomes of positive sense and 5.SsRNA genomes of negative sense genomes; 6. Viruses with RNA genomes that use aDNA (retroviruses); 7. viruses with DNA genomes that used a RNA intermediate(hepadnaviruses). Virions are assembled to protect the nucleic acids from physicalchemical or enzymatic damage. The outer surface is also responsible for recognitionand interaction with the host cells. The capsid is made up of multiple protein subunitsthat are held together by hydrophobic and electrostatic interactions resulting inenergetically stable ordered structures with helical or icosahedral symmetry. Helicalcapsids are formed by basic nuclocapsid proteins (N) regularly spaced around thenucleic acid. All animal viruses with helical symmetries are enveloped with singlestranded, negative sense RNA genomes. Icosahedral capsids are composed oftriangular faces arranged around the surface of a sphere. Each face is built by threesubunits (protomers). The five subunits around each vertex form the capsomers.Complex capsids use scaffolding proteins as a mold for assembly. Very large viruseslike poxviruses have a more complex structure. The classification of viruses intofamilies and genera is bases on structural properties such as size, nucleocapsid

symmetry, and presence of an envelope membrane and type of genome. Otherclassifications are based on epidemiological and clinical criteria. Sequencing of viralgenomes has revealed phylogenetic relationships between viruses based on genome


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organisation and gene arrangement. Many viruses have gained functional genes fromtheir hosts.

Objectives: Part II- By the end of this lecture you should be able to:

define the concept of cell tropism describe the different phases of the virus cycle give examples of viral receptors list different modes of virus entry and uncoating describe how viruses inhibit cellular protein synthesis describe the general strategies of viral replication describe the basic principles of virus maturation and exit explain the main differences between productive/lytic, persistent, transforming and

latent infection.

Lecture Synopsis: Animal cells show restricted susceptibility to virus infection. Inresistant cells the infection is blocked due to lack of surface receptors or specificfactors required for viral replication. The replication of viruses in susceptible cells can

be divided into eight stages: attachment, penetration, uncoating, gene expression andgenome replication, assembly, maturation and exit. Many examples of surface

proteins, carbohydrate residues on glycoproteins or glycolipids that serves as virusreceptors are know. Penetration of the virus is an energy-dependent process that mayoccur via: 1. translocation of the entire virus particle across the cytoplasmicmembrane; 2. endocytosis into intracellular vacuoles; 3. fusion of the virus envelopewith the cell membrane. The product and intracellular site of uncoating depends onthe structure of the virus nuleocapsid. The nature of the viral genome determines the

strategy of replication. Shut off cellular protein synthesis is achieved: i. a cleavage ofa 200 kD cap-binding protein, ii. elongation block of the initiation complex, iii. blockstranscription initiation. The site of virus assembly depends on the site of replicationand on the mechanism of release. The maturation of naked viruses involves assemblyof the empty procapsid, its association with the nucleic acid and further processing ofthe capsid proteins to prevent exit of the viral genome. The virus envelope is formed

by budding of cellular membranes (plasma membrane, ER or Golgi). Envelopeproteins displace host proteins. Matrix proteins connect the cytoplasmic side of thenucleocapsid with the cytoplasmic domain of the envelope protein and direct virionassembly. The rapid release of large numbers of mature non enveloped virus particles

causes cell lysis. Naked DNA viruses that mature in the nucleus tend to accumulateand are released when the cell undergo autolysis. Budding from the cell surface or incytoplasmic vesicles is compatible with cell survival. The outcome of infectiondepends on the virus and on the type of infected cells. Infection of permissive cellsresults in high levels of virus production followed by cell lysis. In less permissivecells virus production may persist at low levels without causing cell death. Intransformed cells the infection is abortive, only few viral genes are expressed andtheir products induce cell growth. The viral genome is not expressed or only very fewviral products are expressed in latently infected cells.


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Tue 24/9 10.15-11.15 (Anders Bergqvist)Wed 25/9 10.15-11.00 (Anders Bergqvist)

Viral replication strategies I & II

Objectives: Part I- By the end of this section you should be able to: Understand the main differences between RNA and DNA viruses List two problems with animal cells that an RNA virus has to solve List two differences between +RNA viruses and the other RNA viruses (- and ds) List three basic strategies that RNA viruses use to produce their proteins. Name two RNA viruses, which produce more structural proteins than ns proteins,

and one that does not. Illustrate how this is done.

Lecture Synopsis: RNA is much more mutable than DNA. It follows that RNAviruses tend to be smaller and more compact than DNA viruses (smaller target size for

mutation). Most RNA viruses do not require the nucleus of the cell, and no RNAviruses (except retroviruses) integrate into the genome of the host; RNA viruses cancause acute or persistent infections, but are never latent. Animal cells only have aDNA dependent RNA polymerase function; RNA viruses must carry their own

polymerase (RDRP). Animal cells also use monocystronic messages. The RNA virusmust find a way to produce individual proteins from their genome. They can do this

by using subgenomic messages, polyprotein processing, or segmentation of thegenome. RNA viruses produce either a single or multiple subgenomic messages, ornested set transcripts. Some RNA viruses have devised strategies for producing moreof the structural proteins than non-structural proteins. In general +RNA viruses beginthe infectious cycle with translation, while - and ds RNA viruses begin with

transcription. Naked +RNA virus genome is often infectious. The lecture will cover inmore detail the replication strategy of poliovirus, rabdovirus, influenza virus, androtavirus.

Objectives: Part II- By the end of this section you should be able to: explain the molecular basis of permissive and non-permissive infection define the various steps of temporally organised transcription (immediate early,

early, late) describe different strategies of DNA virus replication

Lecture Synopsis: Not all virus infections result in virus replication and productionof progeny virus. Progression of the virus cycle may be limited by lack of specificcellular factors that are not expressed in the particular cell type or are expressed in adifferentiation-dependent fashion (Papillomavirus). Transcriptions of viral genesoccurs in the nucleous of the infected cells, except in Poxviruses that encode theirown RNA polymerase, and is temporally organised. Only a fraction of the genome istranscribed into early genes that are required for initiation the synthesis of viral DNA.Late genes encode for structural components of the virus. Complex viruses haveimmediate early genes, which are expressed in the presence of inhibitors of proteinsynthesis. and delayed early genes (Herpesviruses). Regulation is carried out by

proteins present in the virion or specified by viral or cellular genes, interacting with

regulatory sequences in the 5end of the genes. Adenovirus, Herpesvirus,Papovavirus, Parvovirus, Poxvirus and Hepatitis B virus use different strategies forviral DNA replication. These strategies depend on the type of viral genome (linear,


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circular, single stranded, double stranded, partially double stranded) and on theamount of genetic information carried by the virus (parvovirus, poxvirus).

Objectives: Part III- By the end of this section you should be able to:

define the concept of latency and give examples of DNA viruses that establishlatency

explain how latency may be established explain why viruses that establish latency can cause disease long after primary

infection

Lecture Synopsis: Certain viruses can persist in the host organism by latent infectionin which no infectious virus is produced. Latent DNA viruses hide in specific celltypes where they express very few or no viral products (neuronal cells, hematopoyeticstem cells, and lymphoid cells). Different forms of latent Epstein-Barr virus infection

are discussed to illustrate the molecular events involved (downregulation of viralpromoters, use of alternative promoters). Latently infected cells that still express viralproteins must evade recognition by the host immune system. Latency may occur atimmunologically privileged sites (nervous system, non immunogenic cells). Certainviral proteins are protected from recognition (EBNA1). Various types of stimuli (UVlight, hormonal changes etc.) induce the reactivation of latent viral infections bylargely unknown mechanisms. Reactivation that occurs in immunocompetent hosts isusually limited and may be asymptomatic. Massive reactivation may occur inimmunosuppressed patients with consequent reappearance of clinical symptoms.

Wed 25/9 11.15-12.30 (Anneka Ehrnst)Viral pathogenesis

Objectives: - By the end of this lecture you should be able to: list the possible routes of virus entry and give examples of viruses using these

routes describe different routes of virus spread explain various mechanisms of viral pathogenesis (cytopathic effect, cell damage

associated with chronic inflammation, transformation)

Lecture Synopsis: Viral pathogenesis is an abnormal situation of no value to thevirus. The first factor that influences the course of infection is the mechanisms andsite of entry into the body. Few viruses enter through the skin (herpes simplex,

papilloma viruses) and this probably still requires some form of disruption. Themucosal membranes of the eye and genitourinary tract are more favourable route ofaccess, thus many viruses are sexually transmitted. Transmission through thealimentary channel requires survival through the stomach, many of these viruses arenaked. Transmission through the respiratory tract occurs via aerosol or exchange ofsaliva. Some viruses use insect or arthropod vectors to avoid environmental stress.Following primary replication at the site of infection the virus may spread through theinfected host. This occurs via cell-cell contact (localised infections Papillomavirus,

Rhinovirus, Rotavirus), via the blood stream (as free virus or in association with redcells, platelets, lymphocytes or monocytes) or via the nervous system. After entry viathe synaptic junctions the virus spread by axonal transport. Some viruses use different


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pathways of spread at different stages of the infections (Varicella zoster). Virusinfection causes phenotypic changes in the infected cells including: altered shape,membrane permeability, detachment from the substrate, membrane fusion, inclusion

bodies, lysis, apoptosis. Cell lysis causes inflammation that may result in additional

damage of the infected tissue (Hepatitis viruses). Immune responses to viral antigensmay favour virus infection (Dengue) or initiate autoimmune responses (Measles,CMV, Coxackie). Cell transformation is a risk factor for tumor development. Innateand adaptive immunity contribute to the control of virus infections. Cell mediateresponses play a predominant role in the control of most virus infections. Innateimmune responses involve cytokines (interferon) natural killer cells (NK) andcomplement responses. Adaptive cellular immune responses are directed to viralantigens expressed in infected cells by cells and result in cell lysis and production ofregulatory or antiviral cytokines (CTL and TH cells). Neutralising antibody directedto surface structures prevent infection or target the virus to other elements of theimmune system (phagocytosis, ADCC, complement system). Antibodies directed toviral antigens may serve as markers of disease progression.

Fri 27/9 08.30-10.00 (Elisabeth Aurelius, Annika Linde)Herpes viruses: classification and principles of diagnosis

Objectives:by the end of this lecture you should be able to: name and describe the eight human herpes-viruses describe the transmission, sites for primary infection and latency of the human

herpes-viruses

describe the clinical outcome of primary and reactivated infection in previouslyhealthy and in immune-compromised hosts

name some principles for diagnosis and treatment

Lecture synopsis: The herpes-viruses are large enveloped DNA viruses, characterisedby their ability to establish latency, with more or less frequent reactivations. Thesereactivations are often asymptomatic, and an efficient means for viral spread. Allhuman herpes-viruses apart from VZV are spread by close contact. The herpes-virusesare divided into three subfamilies, a, b and g herpes-viruses. The division is based on

biological properties and genomic organisation. So far eight herpes-viruses withhumans as their main host have been identified: Herpes simplex type 1 (HSV1);Herpes simplex type 2 (HSV2); Varicella-zoster virus (VZV); Epstein-Barr virus(EBV); Cytomegalovirus (CMV); Human herpesvirus-6 (HHV-6); Humanherpesvirus-7 (HHV-7); Human herpesvirus-8 (HHV-8). HSV1, 2 and VZV belong tothe -herpesvirusgroup. They primarily infect the skin and mucous membranes, andestablish latency in the sensory neural ganglia. More than 70% of the adult Swedish

population have antibodies against HSV as a sign of infection. Primary infection withHSV1 and 2 may be asymptomatic or cause painful blisters in the skin and mucousmembranes. HSV1 is mainly associated with labial and HSV2 with genital lesions.Twenty-30% of infected persons will experience recurrent blisters. Infection of thenervous system may occur in primary as well as in reactivated infections. HSV1 then

preferably causes encephalitis and HSV2 meningitis. In newborn and other immune-compromised hosts HSV may cause life-threatening, disseminated disease. VZV isspread airborne and is one of the most contagious viruses existing today. At 30 years


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of age practically everyone in Sweden has experienced primary VZV infection. Theprimary infection causes chickenpox with fever and generalised blisters. The severityof the symptoms varies. Neonates infected by their mothers in utero and immune-compromised patients frequently contract severe disease. When the cellular immune

control of the latent virus diminishes, with age or with immune-suppression for otherreasons reactivation may occur. This results in localised, painful blisters; herpeszoster. Demonstration of virus in lesions by virus isolation, antigen detection or PCRis the most efficient means for diagnosis, but serology may also be used. CMV,human herpesvirus-6 and -7 (HHV-6 and HHV-7) belong to the -herpesviruses.They primarily infect lymphoid tissue, but may infect a variety of cells throughout the

body. Latency is probably established in monocytes. Primary infection with CMV inearly childhood is mainly transferred via breast-milk, and does normally not cause anysymptoms. A second wave of infections occurs with the onset of sexual activity, andalso these infections are often asymptomatic, but fever and inflammation of lymphoidglands and liver may occur. CMV infects 0.5% of foetuses in Sweden, and is the mainviral cause of congenital defects, mainly hearing loss and various CNS defects. CMVis also a main infectious complication in immune-compromised patients. HHV-6 andHHV-7 infect via saliva, and almost everyone is infected by three years of age. HHV-6 infection causes exanthema subitum, characterised by three days of high feverfollowed by a rash. Neurological complications are sometimes seen. Also HHV-7 maycause exanthema subitum, but the clinical importance of this virus is otherwise stillunclear. Diagnosis is made mainly by serology and PCR. The human -herpes-viruses are Epstein-Barr virus (EBV) and human herpesvirus-8 (HHV-8). EBVreplicates in epithelial cells, and has its latency in B-lymphocytes. HHV-8 has beenidentified in B-cells, but whether this is the site of latency is not known. EBV infects

via saliva and sexually, and >95% of the population is infected at the age of 30. Theclinical outcome of primary EBV infection becomes more severe with increasing age.EBV is the main cause of mononucleosis; long standing fever, tonsillitis andinflammation of other lymph glands as well the liver. EBV is involved in thedevelopment of lymphatic and nasopharyngeal carcinomas. Diagnosis of primaryEBV infection is made serologically, In atypical cases PCR may be useful. HHV-8was recently detected and is associated with a skin cancer of mainly AIDS patients,Kaposis sarcoma. It is spread sexually in Western countries, but reports concerningseroprevalence vary considerably, and the true rate of infection is unknown. Diagnosisis made by serology and PCR on blood cells or tumour material. There are antiviraldrugs effective against all herpesviruses. They target either the virus specific

thymidine kinase and/or the DNA. The effect of treatment varies, and it is mostsuccessful against the a-herpesviruses.

Fri 27/9 10.30-12.30 (Marie Henriksson)Subversion of cellular functions: cell cycle and apoptosis

Objectives:- by the end of this lecture students should: know the major effector mechanisms of antiviral adoptive immunity understand the relationship between the life-stile of the virus and the effective

mechanisms of antiviral immune response understand the difference between immune responses to persistent and non-persistent viruses


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induction of apoptosis. DNA tumour viruses have virus specific proteins, i.e. there areno cellular homologues, that activate the host cell replication. The strategy used is toattack, bind to and thereby inhibiting the function of the key players in cell cycleregulation, pRb and p53. The binding of viral proteins to Rb releases the transcription

factor E2F from Rb which than can activate S-phase genes. Binding of viral proteinsto p53 has a dual effect, no G1 arrest and no induction of apoptosis. Different forms ofapoptosis can be distinguished, e.g. Fas induced apoptosis. The mechanism is thefollowing: the death stimuli, Fas ligand (FasL), binds to the Fas receptor (FasR)leading to a trimerisation of receptors. Adaptor proteins (FADDs) then bind to thecytoplasmic part of the R, the so called the death domain (DD). The adaptor in turnrecruits and binds FLICE (caspase8) which results in self activation of the proteasedomain. Caspases are cystein proteases that need to be cleaved in order to be active.The active FLICE then cleaves another pro-protease and starts a chain reactionleading to apoptosis of the cell. Damage of mitochondria is a central co-ordinationfactor in apoptosis. The Bcl-2 family of proteins are located in the mitochondria.There is a balance of activating and inhibiting proteins where the Bcl-2 is the

prototype for the inhibition and Bax for the induction of apoptosis, respectively. Theexact mechanism for Bcl-2 function is not known. Viruses have established strategiesto interfere with almost all stages of apoptosis.

Mon 30/9 13.00 14.00 (ke Lundqvist)Emerging viruses

Objectives:By the end of this lecture you should be able to:

Understand the concept emerging viruses, and what the main viral threats are atpresent Understand the influence of the modern life-style on entry and spread of new

viruses into the human population. Understand the concept species specificity, and its limiting effect on viral spread Briefly describe some methods by which unknown viruses have been identified Briefly describe some surveillance programmes Briefly describe existing means for prevention of spread

Lecture Synopsis: The term emerging viruses is used to describe viruses thatrepresent a new epidemiological threat to humans. It may refer to the causative agentsof diseases that have not previously been described in humans, as HIV in the

beginning of the 80-ies, old viruses that spread in new regions, like dengue fever inthe 90-ies, or old viruses that have changed immunogenicity and pathogenicity, likeinfluenza has done a few times during this century. In a wider sense it can also includeviruses which are detected by chance, until the role and pathogenicity of the agent isdefined. An example of this is human herpesvirus- 6, detected in the 80-ies andinitially thought to be a rare infection but later verified to be the cause of a commonchildhood disease. The appearance of a completely new virus is probably anextremely rare event. Re-assortment of duck and human influenza virus genes in pigs,giving rise to new influenza variants is probably the closest we will come to a new

virus in our times. In most instances an emerging virus is an animal virus that has forsome reasons managed to infect the human host. Many of these viruses are monkeyviruses, mainly emerging in the African continent, such as Ebola and HIV. There are,


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however examples of other natural hosts such as sin nombre virus spread from thedeer mouse in the US, pneumonia in Australia caused by a morbilli-virus in horsesand a chicken influenza infecting humans in Hong-Kong. Fortunately, these emergingviruses seldom get truly adapted to the human host. HIV is a remarkable exception.

The fact that it probably has emerged from monkeys, genetically closely related tohumans, and that it only kills its infected host after many years from primary infectionmay explain its success. In old ages poor hygienic conditions, crowded living and lackof epidemiological and medical control measures may have facilitated the spread ofsome emerging viruses. In modern times the increased population, urbanisation, rapidglobal contacts, environmental destruction possibly affecting our immune systems andchanges in natural habits may facilitate virus spread. The rapid spread of HIV is oneexample, the spread of Dengue to new regions in the world another. New viruses may

be identified as a result of continuos surveillance of regions where threats areexpected. The isolation and typing of the chicken flu in Hong-Kong is one example.The appearance of an unknown disease usually initiates the search for the agent. Avariety of conventional and modern methods are used, including electron microscopy,virus isolation, genome detection and serology. Electron microscopy is the onlymethod that can be used without any prior knowledge of the nature of the infectiousagent. All other methods are more specific, and lots of various antigens, primers andcell cultures may have to be tried before the agent is identified. By restrictiondifference analysis (RDA) foreign genetic material can be deduced from the normalcellular background. This method was used to identify the probable agent causingKaposis sarcoma (HHV-8), and may be developed to be used in other conditionssuspected to be caused by unidentified agents. The identification of emerging virusesis primarily under national control. Centres such as Center for Disease Control (CDC)

in the USA, Collindale in the UK and Swedish Institute for Infectious Disease Controlare initiating investigations as soon as something unexpected is reported in theircountries. CDC is also helping a lot internationally, and has teams that can travelanywhere for investigations on short notice. The EU is trying to build up improvedfacilities for Paneuropean epidemiological control. In the developing countries thenational organisations often have very limited resources and WHO is working hard tostrengthen the epidemiological surveillance in such countries. WHO also spreadsinformation to all its collaborating centres as soon as something unexpected happens.Internet has become a source of information, for good and for bad, which oftenspreads information more effectively than WHO. One good source of information isPromed where mostly serious information on most emerging infections can be found.

The first measure to prevent a serious viral threat is epidemiological control measures,such as isolation of an area where a potentially dangerous agent is detected. In modernsocieties this is a very difficult measure, since world-wide travel is part of our dailylife and our societies and economies are therefore extremely vulnerable. Decision withmajor effects on society life must be taken by our political leaders, but few othermeans to protect large populations groups are available even today. Antiviral and

preventive hyperimmune-globulins effective against various viruses exist only to alimited extent. They can possibly be given to special risk groups, but are at present notavailable in amounts sufficient to meet the needs of a large epidemic. The mosteffective measure against viral spread is vaccination, though this approach has failedso far for many viruses such as HIV and RSV. Live vaccines are today given against avariety of viruses. Such vaccines demand strict controls for safety, and will probablynever be the first line vaccines against newly emerging viruses. Killed purified virus


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preparations are still the most suitable first line vaccine. However, the rapidproduction of large amounts of virus is restricted to those viruses that can grow ineggs. Recombinant proteins could be another source of vaccine, but demands that thegene product giving protective immune response is identified, and often good

adjuvants are necessary to elicit a sufficient immune response. Much hope is givetoday to DNA-vaccines. Viral genes inserted into plasmids and administered byvarious routes are taken up by cells. Proteins are produced and presented to theimmune system in such a way that both cellular and humoral immune responses areelicited. There is still a long way to go concerning the efficacy and safety of these newmethods, but they may represent our main future hope for the rapid production of aneffective vaccine that may protect a whole population from a serious viral threat.

Tue 1/10 08.30-10.00 (Olle Reichard/Madeleine von Sdow)Hepatitis viruses: - classification and principles of diagnosis

Objectives- by the end of this lecture you should be able to: describe the overall structure and classification of hepatitis A,B, and C viruses describe different diagnostic methods for hepatitis A, B, and C in general terms describe the clinical picture and the natural course of acute and

chronic viral hepatitis discuss possible explanations for chronicity in hepatitis discuss treatment possibilities of chronic hepatitis

Lecture synopsis: Hepatitis A, B, and C viruses (HAV, HBV, and HCV) all cause

inflammation in the liver, but the viruses are not related virologically. HAV is a RNAvirus within the picornavirus family, and is spread by the faecal-oral route. HAVcause acute infections, usually subclinical in children and clinical in adults, thatalways resolve. Thus, there is no carrier state. Acute and resolved infections arediagnosed by anti-IgM and anti-IgG antibodies, respectively. No antiviral treatment isavailable. A vaccine exist. HBV is a DNA virus within the hepadnavirus family and isspread by the parenteral route, mostly by blood. The acute infection resolves inapproximately 95% of the cases, and thus becomes chronic in 5%. Chronicity is morecommon in new-borns and in immunocompromised persons. The chronic hepatis Bcarrier state is characterised by 3 phases; the immunotolerant- (highly replicative),immunoactive- (diminished viral replication) or low-replicative phases. Chroniccarriers risk liver cirrhosis and hepatocellular carcinoma over time. HBV infectionsare diagnosed by serology (HBsAg and HBeAg with their corresponding antibodies,and anti-HBc) and by detection of HBV DNA by PCR or dot-blot methods. Antiviraltreatment (alfa-interferons and nucleoside analogues) of chronic HBV infection is

possible. A HBsAg based vaccine has been developed. HCV is a RNA virus withinthe flavi/pesti virus family. It is transmitted mainly by blood, and causes chronicinfections in approximately 85% of the cases. The reason for the high chronicity rateis not fully known but depends at least in part to escape mutations within thehypervariable region of the virus. Approximately 20% of the chronic carriers willdevelop liver cirrhosis or hepatocellular carcinoma within 20-25 years. Treatment

with a combination of Alfa-interferon and the nucleoside analogue ribavirin eradicateHCV in a proportion of patients, and approximately 50% of treated patients seem tobe cured by the treatment. The reason why some patients respond to treatment, while


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others do not, is not known. Probably both viral and host factors are important. Novaccine is available.

Tue 1/10 13.00-14.00 (Monica Grandien)Prions

Objectives:

- The biology of prions.- Mechanisms of spread of prions to and within the infected host- Prion diseases : transmissible spongiform encephalopathies (TSE)- Neurohistopathological correlates of prioninfections in man and animals- Genetics: mutation and polymorphism of the gene for normal prion protein

Lecture synopsis:Definition of prions: small proteinaceous infectious particles that resist inactivation

by procedures modifying nucleic acids and that contain an abnormal isoform of acellular protein which is a major and necessary component ( S. B..Prusiner ).The presence of normal prion protein, its size and structure. Conformational changeof isoform from normal (PrPcell) to the disease-causing (PrPsc or PrPres) prion protein.Prion strains and the possibilities to differentiate between them. The species barrier.

The prion diseases or TSEs have the following characteristics:1. they are progressive fatal brain diseases with long incubation periods2. there is no detectable immune response

3. the brain shows a spongiform picture caused by neuronal vacuolisation andastocytic gliosis. Amyloid plaques occur in the brain in a varying degree.

Prion diseases inhumans:a. sporadic : Creutzfeldt - Jakob disease (CJD)

b. inherited : familial CJD.,Gerstmann-Strussler-Scheinkers syndrom, (GSS)fatal familial insomnia (FFI)

c. transmitted : iatrogen CJDKuru variant CJD ( v CJD)

Prion diseases inanimals:a. scrapie, in sheep and goats

b. bovine spongiform encephalopathy ( BSE ) in cattlec. mink encephalopathyd. chronic wasting disease in mule deer and elk in USA.

Wed 2/10 09.00-9.45 (Britta Wahren)Chemotherapy of viral infections

Targets for antiviral effects can be specific molecules or can be quite general. In thelecture you will learn about clinical useful antiviral drugs for retroviruses, herpes


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viruses and influenza. The properties of antiviral compounds that affect distincttargets as well as the influence of dosing and ad routes will be described. Antiviralresistance and the phenomena of synergy and antagonism between antivirals are otherimportant factors. The field develops rapidly due to new methodology for identifying

molecules that cause inhibition of viral replication.

Specific molecules consist of viral-specific enzymes such as polymerases, reversetranscriptases, proteases, and other enzymes that are unique for the virus type, for thevirus family or for several viral families. They should be distinct enough for the hostenzymes so that inhibitory molecules cause little or no damage to the hostmetabolism. Such molecules can be used as monotherapy or in combination with oneanother. By combination of compounds one can obtain synergistic effects, which

benefit the host both by the effectiveness and by less side effects. Other importantissues are bolus doses and repeated therapy.

A danger in treatment is the induction or selection of resistant virus. The mostcommon phenomenon with viral specific drugs is a selection among many replicatingquasispecies. Toxic drugs that affect also host enzymes or host DNA/RNA can causenew mutations that form a drug resistant virus population. Resistant viral populationshave begun to spread through patient patient contact or by transmission from motherto the newborn child.

General antivirals affect host cell DNA or RNA as well as viral nucleotides and canbe mutagenic. They induce or can constitute interferons, cytokines or chemokines andindirectly affect the immune system. Direct resistance is uncommon but may occur

through escape mechanisms in effector molecules.

Wed 2/10 10.00 - 10.45 (Britta Wahren)Antiviral vaccines

Objectives: by the end of this lecture you should have understood the followingconcepts Passive/active vaccination. Live/attenuated vaccines. Adjuvants. Side effects. Vaccination of children. Vaccination of adults/travel vaccinations.

Section IV Microbiology - Bacteriology


to define the general, outermost host anatomical and physical defence barriers to define the role of these barriers in preventing infections

to describe innate defence mechanisms, phagocytic cells, the complement systemand antibacterial peptides


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to describe how bacteria may overcome the effects of host defences to provide an overview of adhesion mechanisms to understand the cross-talk between bacteria and host cells upon adherence to review bacterial invasion of epithelial cells and uptake of phagocytic cells to define the global and domestic impact of bacterial gastrointestinal infections to define routes and sources of these infections to define the infection pathogenesis of a toxigenic gastrointestinal infection to define the infection pathogenesis of an invasive gastrointestinal infection

Thu 3/10 09.00-10.00 & 10.00-11.00 (Staffan Arvidson)Bacteria-host interaction

Objectives: Part I - by the end of this lecture you should be able to:

list the components of our innate defence list different antimicrobial strategies and effectors understand the how these substances may act and function describe the initial phases of an inflammatory response

Lecture synopsis: The anatomical linings of our bodies consists of the skin and, forexample in the nasopharynx, lungs and gastrointestinal tract, mucosal surfaces. Theskin is protective much due to its rigid structure and antibacterial substances. Themucosal surface is thin as thus apparently more vulnerable. To be protective, mucosalmembranes are equipped with additional defence systems. These include a persistentarrangement of flow out from the host, e.g. through peristalsis and the action ofciliated cells. The secretions covering mucous membranes are themselvesantimicrobial (due to lysozyme, secretory IgA, low pH, bile acids, antibacterial

peptides, lactoferrin) and prevents colonisation (due to adhesion receptor analogues).A pathogen successful enough to penetrate the mucosal barrier will have to faceinnate defence mechanisms operating in the parenteral space or in conjunction withepithelial linings. These include the action of the complement system, phagocyticcells (macrophages), and initiation of inflammation and neutrofil infiltration.

Objectives: Part II - by the end of this lecture you should be able to:

understand what strategies bacteria use to overcome host defence barriers name virulence factors of bacteria name some important bacterial pathogens, and link them to a particular disease

Lecture synopsis: Interference with mucous membrane function may be achieved byintoxication of ciliated cells (Bordetella pertussis). Peristalsis can be coped withthrough strong bacterial motility, enabling penetration of the mucin layer, and throughsubsequent adhesion to mucosal cells (Vibrio cholerae). Bacteria may adapt to low pHthrough so called acid tolerance responses (Shigellasp., Salmonellasp.). Penetrationof the epithelial cells can be achieved through expression of bacterial invasionfunctions enabling bacteria to enter the parenteral space (Listeria monocytogenes,Salmonellasp., Yersiniasp.). In the parenteral space, expression of particular surfaceantigens may prevent complement activation (Streptococcus pyogenes M proteins)


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which may interfere with normal complement regulation. Special bacterial toxins oreffector molecules interfere with macrophage functions preventing phagocytosis(Yersinia pseudotuberculosis) or enabling bacterial growth within macrophages.

Fri 4/10 09.00-10.45 (Roland Mllby)Bacterial microecology

Objectives:

By the end of this lecture you will understand the origin of life, the evolutionaryrelations between all life on earth, including bacteria and man as well as thecomplexity of the human microecology in relation to health and disease.The message is that bacteria were here first and that every other living creature has toadapt to this fact.

Content

Following areas will be covered: The origin of life, the development of an oxygenated atmosphere, the development

of multicellular organisms up to man. The relations between micro-organisms and life in general. The relations between micro-organisms and host organisms, including symbiosis,

commensalism and parasitism. The composition and complex ecology of microbial populations, specially the

normal flora of man. How to measure this flora, its development and composition during a human life.

Relations between the intestinal flora and the development of the intestinalfunctions Positive and negative effects of the normal flora in health and in disease. Examples of diseases related to the microecology of the normal flora. Examples of pre- and probiotic drugs and effects thereof.

Questions

How can the normal flora be disturbed ? Restored ?Do you know anyone that regularly uses probiotics ? Positive effects ?Is it true that a good defecation is the best sleeping pillow* ?

*Elvira Krank in Krlek och lavemang, 2001

Fri 4/10 11.00-11.45 (Staffan Arvidson)Mon 7/10 13.00-14.45 (Staffan Arvidson)

Antibiotics and antibiotic resistance

When we have an infection, antibiotic treatment may be needed to supplement thebodys natural defences. This was not possible before the 1940ies when the antibioticera started. Antibiotics have saved many lives but in the past decades an increasing

number of bacteria have become resistant to one or several antibiotics. This is a


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serious problem. Will the antibiotic era come to an end? This, and other questions willbe discussed in this lecture

After attending this lecture you should be able to:

Describe the principles for antibiotic action Describe different mechanisms of antibiotic resistance Specify how bacteria become resistant to antibiotics. Suggest means to limit the development of antibiotic resistance

Antibiotics are synthesized and secreted by both procaryotic and eucaryoticmicroorganisms, e.g., Streptomyces, Bacillus,Cephalosporium, and Penicillium .Todays antibiotics are manufactured as semi-synthetic or completely synthetic

products. Most antibiotics have 4-6 membered hydrocarbon ring structures,sometimes with nitrogen and sulphur, in various arrangements and with various side

chains. Examples: beta-lactams, tetracyclines, aminoglycosides, glycopeptides.The following definitions will be discussed: Antibiotic sensitivity and resistance.Bacteriostatic and bactericidal effect. Minimal inhibitory concentration (MIC).Minimal bactericidal activity (MBC). Antibacterial spectrum.The principles of antibiotic sensitivity testing will be described.Which are the cellular targets attacked by antibiotics? For obvious reasons antibioticsmust attack essential structures and functions. The major targets for the antibioticsused today are: the cell wall biosynthesis, protein synthesis, and synthesis of nucleicacids.The mechanisms of action of some major antibiotics will be described.The emergence of antibiotic resistant super bugs such as multi-resistant

Mycobacterium tuberculosis, vancomycin resistant pneumococci and staphylococci,and penicillin resistant pneumococci has prompted alarming headlines in both lay andscientific press. However, antibiotic resistance is not a new phenomenon. Forexample, penicillin resistant S. aureusdeveloped soon after penicillin was introducedin the mid 1940s, and by the 1960s penicillin resistance had become the rule ratherthan the exception in hospital isolates of S.aureus. For a long time antibiotic discoverykept ahead of bacterial resistance and there was little concern about the problem thatwhenever antibiotics are used it means a selection of resistant clones. However, todayantibiotic resistance has become a major medical and economical problem. Resistancecan be due to enzymes that inactivate antibiotics, pumps that remove antibiotics fromthe bacteria, alterations of bacterial target molecules leading to decreased affinity forantibiotics, or a decreased uptake of antibiotics.Bacteria may acquire antibiotic resistance through spontaneous mutations that altersthe target of the drug, or by the uptake of DNA coding for specific proteins thatmediate resistance.

Tue 8/10 13.00 14.45 (Ann-Beth Jonsson)Bacterial adhesion

Objectives: Part I-by the end of this lecture you should be able to:

describe a pilus adhesin and a non-pilus adhesin give examples of bacterial receptors define the two-component system in bacteria


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Lecture synopsis: A necessary step in successful colonisation and production ofdisease by bacterial pathogens is the ability to adhere to host cell surfaces. The

bacterial adhesin binds to a specific target molecule - the receptor. Both cell surface

molecules and/or extracellular matrix protein may act as receptors of bacterialadhesins. The adhesion-receptor interaction is specific. Adherence occurs in twosteps:- Step 1: initial adherence to host cell surfaces.- Step 2: tight adherence to host cells, - this may lead to invasion.Adhesins: Pili (or fimbriae) extend from the bacterial surface in order to reachthe host cell pilus receptor. There are different types of pili, for example type-1

pili, P-pili, type-IV pili. Non-pilus adhesins are usually involved in tight binding.The two component system in bacteria:- Sensor = transmembrane protein that responds to an extracellular signal.- Transducer = cytoplasmic protein that is activated by the sensor (by

phosphorylation). The activated form of the transducer activates gene expression.

Objectives: Part II-by the end of this lecture you should be able to: describe how the bacteria can manipulate the host cell describe the use of type III secretion systems in bacterial adherence describe molecular mechanisms for modulation of adherence and

invasion

Lecture synopsis: The contact between bacteria and host cells leads to asophisticated cross-talk. Bacteria induce signal transduction pathways, stimulate

production of inflammatory cytokines, and trigger changes of the host cellsurface, etc. Invasion is a directed uptake of bacteria by nonphagocytic cells. The

process involves rearrangements of the actin cytoskeleton. Inside the cell thebacteria are in a protected cellular niche to replicate and persist. Bacteria enterfirst in a membrane bound vacuole. After entry they may stay in the vacuole and

prevent fusion with lysozomes or escape from the vacuole. Phagocytic cells:bacteria may survive in macrophages, or escape.- EPEC: Bundle forming pili mediate the initial attachment.Type III secretion machinery: insertion of its own receptor into the host cell.Cause pedestals = actin rearrangements.- Neisseria: Type-IV pili mediate the initial attachment. The pili induce signaltransduction pathways in the host cell that lead to stable and tight adherence.Outer membrane proteins such as Opa mediate efficient invasion. Opa proteins

bind to heparan sulphate proteoglucans or to CD66 molecules on epithelial andendothelial cells.- Uropathogenic E. coli: P pili mediate the initial attachment to target cells. ThePapG adhesin binds to Gal1-4 )Gal. Pilus retraction is a possible mechanism oftight binding.

Tue 8/10 15.00 15.45 (Staffan Arvidson)

Wed 9/10 13.00 13.45 (Staffan Arvidson)Bacterial toxins


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Objectives:By the end of the lectures you should be able to list the various types of toxins and give examples of bacteria that produce them describe the molecular mechanism of action of representatives of each type of

toxin

explain the specific symptoms related to the toxins

Lecture synopsis: Many bacteria secrete protein (exo)toxins which can kill or alterthe function of specific host cells, tissues or organs, at the site of infection or faraway from it. Depending on their biological effects exotoxins are divided incytolysins (hemolysins), enterotoxins , neurotoxins, cytotoxins, superantigens andothers. Cytolysins damage or kill cells by forming pores in the cell membrane, or bydegrading membrane phospholipids. Depending on the kind of target cells, cytolysinsmay cause local tissue damages, specific organ failure, or protection of the bacteriafrom the immunsystem. Enterotoxins, neurotoxins and cytotoxins act inside target

cells. They consist of two parts , or domains, one which is necessary forinternalisation and an other which is toxic. The toxic part has enzymatic activity,which inactivates specific intracellular target proteins by ADP-ribosylation,glycosylation or proteolysis. Depending on which cells are attacked and which target

protein is affected different effects are seen, such as increased synthesis of cAMPleading altered ion transport (diarrhoea), impaired release of neurotransmittors(tetanus or paralysis), inhibition of protein synthesis (cell death), or disruption of thecytoskeleton (immobilisation of cells and cell death).A number of bacterial toxins act as superantigens, which non-specifically activatelarge subsets of T-cells and induce cytokine production that may produce the signsseptic shock.

Examples of cytolysins: Alpha-toxin from Staphylococcus aureus, alpha-toxin fromClostridium perfringens and Escherichia coli hemolysin A. Enterotoxins: Choleratoxin and cholera-like toxins from enteric bacteria. Neurotoxins: Tetanus toxin and

botulinus toxin. Cytotoxins: Diphtheria toxin, Clostridium dificille toxin A, shigatoxin , pertussis toxin. Superantigens: S. aureus TSST-1 and enterotoxins,Streptococcus pyogenespyrogenic toxin.

Wed 9/10 14.00 14.45 (Staffan Arvidson)Skin and soft tissue infections

Wed 9/10 15.00 15.45 (Staffan Arvidson)Sepsis

Objectives:by the end of this lecture you should be able to: Describe the major routes of invasion Define bacteremia, septicemia and septic shock Give examples of the most prominent bacterial pathogens causing systemic

infection Describe the major bacterial components causing septic shock

Describe the major host cells and effector molecules leading to septic shock


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Lecture synopsis:Systemic bacterial infections are caused by bacteria entering theblood stream. The bacteria usually have their origin in a localised infection, eg in thegastrointestinal tract (gastroenteritis), the urinary tract (pyelonephritis), the respiratorytract (pneumonia, otitis media), skin (wounds, surgical instrumentation, catheters).

Septicemia is defined a

pathology, immunology and infection biology

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