roebe 0.5.122

data/lib/roebe/www/immunology/immunology.rb

@@ -0,0 +1,836 @@
+english('Immunology') {
+autoextend
+ruby_favicon
+css_style '
+
+p.default {
+  margin: 0.5em;
+  margin-left: 2em;
+}
+
+a:link {
+  text-decoration: none;
+}
+
+a:hover {
+  text-decoration: underline;
+}
+
+div.default {
+
+  padding: 8px;
+  margin: 4px;
+
+}
+'+TEMPLATE1
+body_css_class 's12px padt4px marpad2px BG_IMG_RUBY NO_REPEAT VERDANAs BG_Black White'
+font_size '1.1em'
+
+doc('mar0px pad0px s0_5em') {
+  # ========================================================================= #
+  # === History of Immunology
+  # ========================================================================= #
+  h2 'History of Immunology',
+     'lightblue'
+  p_default {
+    e 'Nearly 2,500 years ago, in his History of the Peloponnesian War,
+    <b class="gold">Thucydides</b> wrote about a plague epidemic:'
+    br
+    e '<b class="italic">„No one caught the disease twice,“</b> he 
+    said, <b class="italic">„or if he did, the second attack was
+    never fatal.“</b>'
+  }
+  # ========================================================================= #
+  # === MACROPHAGES TAG
+  # ========================================================================= #
+  div(id: 'macrophages'){
+    h4 'Macrophages'
+    p {
+      e '- Macrophages can form <b>multinucleate giant cells</b> (MGCs)'
+    }
+  }
+  # ========================================================================= #
+  # === CD8 versus CD4
+  # ========================================================================= #
+  h2 'MHC-I versus MHC-II','gold'
+  p {
+    e '<b>MHC-I</b>:  bindet an den <b>CD8 Rezeptor</b>.'
+    e '<b>MHC-II</b>: bindet an den <b>CD4 Rezeptor</b>.'
+  }
+  # ========================================================================= #
+  # === Protein A-Chromatographie zur Antikörperreinigung
+  # ========================================================================= #
+  h2 'Protein A-Chromatographie zur Antikörperreinigung',
+     'FI gold'
+  p('s1em ind1em marr2em'){
+    e 'Die Affinitätschromatographie an Protein A-Sepharose ist
+    eine der verbreitetsten Methoden zur Antikörperreinigung.'
+    br
+    e 'Protein A ist ein bakterielles Zellwandprotein von 
+    <b class="gold">Staphylococcus aureus</b> mit einer 
+    spezifischen Affinität zur Fc-Region von Immunglobulinen 
+    der G-Klasse (IgG).'
+    br
+    e 'Protein A hat ein Molekulargewicht von 42 kDa und weist 
+    eine hohe pH-Stabilität von pH 2-10 auf.'
+    br
+    e 'Die Bindungsaffinität zum Fc-Teil von Antikörpern ist 
+    pH-abhängig und nach Bindung von Antikörpern in Gegenwart
+    neutraler oder leicht alkalischer Puffer lassen sich die
+    Immunglobuline mit einem abfallenden pH-Gradienten eluieren.'
+    br
+    e 'Abhängig von Herkunft (Spezies) und Subklasse des Antikörpers 
+    kann die Bindungsstärke von Protein A erheblich variieren.'
+    br
+    e 'Für Antikörper mit geringer Bindungsaffinität zu Protein A, 
+    wie zB IgG aus der Maus, kann eine weitere Affinitätsmatrix, 
+    Protein G-Sepharose, verwendet werden.'
+    br
+    e 'Protein G ist ein Zelloberflächenprotein aus Streptokokken
+    der G-Gruppe und unterscheidet sich in seinem Affinitäts-Spektrum
+    von Protein A'
+  }
+  # ========================================================================= #
+  # === T-Lymphocyten
+  # ========================================================================= #
+  h3 'T-Lymphocyten'
+  p {
+    e 'Die T-Lymphocyten haben den CCR 7 Rezeptor. Damit werden sie
+    in den Paracortex gelockt (homing)'
+  }
+  # ========================================================================= #
+  # === The lymphoid lineage
+  # ========================================================================= #
+  h3 'The lymphoid lineage'
+  p {
+    e 'The <b>lymphoid lineage</b> consists of <b>T‐lymphocytes</b>,
+    <b>B‐lymphocytes</b>, and <b>natural killer (NK) cells</b>.'
+  }
+  # ========================================================================= #
+  # === CYCLOSPORIN
+  # ========================================================================= #
+  h4 'Cyclosporin'
+  div_default {
+    e '<b>Cyclosporin A</b> kommt in Pilzen vor.'
+    br
+    e 'Wenn der Wirkstoff vom Körper aufgenommen wird, lagert es sich
+    in den T-Lymphozyten an Rezeptoren an.'
+    br
+    e 'Der Wirkstoff führt in mehreren Reaktionsschritten dazu, dass
+    Interleukin 2 nicht mehr von den T-Zellen hergestellt wird.'
+    br
+    e 'Interleukin 2 ist ein Botenstoff und wird benötigt, um das
+    Immunsystem zu aktivieren. Er ist an der Entstehung einer
+    Entzündungsreaktion beteiligt. Cyclosporin kann somit also
+    auch AutoImmunkrankheiten verursachen, da es die Aptoptose
+    in den Thymocyten unterbindet.'
+  }
+  # ========================================================================= #
+  # === Natürliche Killerzellen steuern die Wundheilung (08.09.2021)
+  #
+  # See: https://www.media.uzh.ch/de/medienmitteilungen/2021/Wundheilung.html
+  # ========================================================================= #
+  h3 'Natürliche Killerzellen steuern die Wundheilung (08.09.2021)'
+  p {
+    e 'Natürliche Killerzellen töten nicht nur Krebszellen oder
+    virusinfizierte Zellen ab. Sie steuern bei Hautverletzungen auch
+    die Balance zwischen Wundheilung und Bakterienabwehr.'
+    br
+    e 'Wird der Heilungsprozess beschleunigt, schwächt dies die Immunabwehr,
+    wie Forschende der Universität Zürich zeigen. Relevant ist dies sowohl
+    für die Behandlung von Hautverletzungen wie auch die Bekämpfung
+    antibiotikaresistenter Keime.'
+    br
+    e 'Natürliche Killerzellen sind ein bestimmter Typ von Immunzellen.
+    Sie erkennen abnormale Körperzellen wie Tumor- und virusinfizierte
+    Zellen und töten diese ab. Ein internationales Forschungsteam unter
+    der Leitung von Christian Stockmann, Professor am Institut für
+    Anatomie der Universität Zürich (UZH), hat nun herausgefunden,
+    dass Killerzellen eine weitere, überraschende Funktion haben:
+    Sie kontrollieren die Wundheilung in der Haut.'
+    br
+    e '«Wir konnten diese Zellen in Mäusen genetisch so verändern,
+    dass das Wachstum von Blutgefässen beschleunigt wird und sich
+    Hautwunden schneller schliessen. Allerdings wird dadurch die
+    Immunabwehr abgeschwächt, was die Anfälligkeit für bakterielle
+    Infektionen erhöht», sagt Stockmann.'
+    br
+    e 'Beschleunigte Wundheilung birgt höheres Infektionsrisiko'
+    br
+    e 'In der Biomedizin wird intensiv nach Möglichkeiten gesucht,
+    um Wundheilungsprozesse zu beeinflussen. Versucht wird vor
+    allem, die Gefässneubildung anzuregen und zu beschleunigen –
+    entweder direkt oder indirekt über die Beeinflussung der
+    Immunantwort. «Unsere Ergebnisse zeigen, dass man bei 
+    solchen Ansätzen möglicherweise ein erhöhtes Infektionsrisiko
+    in Kauf nimmt. Daher ist hier Vorsicht geboten», so
+    Stockmann.'
+    br
+    e 'Eine weitere offene Frage ist, inwiefern Natürliche Killerzellen
+    nicht nur das Tempo, sondern auch die Qualität der Wundheilung –
+    etwa die Zusammensetzung des Bindegewebes oder die Regeneration
+    von Haarfollikel, Drüsen und anderen Hautkomponenten –
+    beeinflussen.'
+    br
+    e '«Die spannendste Frage ist, wie wir es schaffen können,
+    die Wundheilung zu beschleunigen und gleichzeitig die
+    Immunabwehr gegen Wundinfektionen zu stärken», sagt
+    der Anatom und Immunologe Stockmann.'
+    br
+    e 'Killerzellen gegen antibiotikaresistente Bakterien einsetzen'
+    br
+    e 'Der Wissenschaftler sieht aber noch weiteres Potenzial:
+    Bei Krebstherapien werden heute auch Therapeutika
+    eingesetzt, die Killerzellen aktivieren und stimulieren,
+    so dass diese vermehrt die Krebszellen abtöten.'
+    br
+    e '«Unsere Daten weisen darauf hin, dass diese Medikamente
+    auch bei bakteriellen Infektionen nützlich sein könnten –
+    was angesichts der zunehmend antibiotikaresistenten
+    Keime unbedingt weiter erforscht werden sollte», sagt
+    Stockmann.'
+    br
+    e 'Natürliche Killerzellen kommunizieren laufend mit anderen
+    Abwehrzellen und beeinflussen deren Aktivität. Dazu sondern
+    sie Botenstoffe ab, sogenannte Zytokine. In ihrer Studie
+    stellten die Forschenden fest, dass Killerzellen auch
+    Hautverletzungen infiltrieren, in denen sehr niedrige
+    Sauerstoffkonzentrationen herrschen. In solchen Geweben
+    stellen Killerzellen ihre Genaktivität um und passen
+    sich so dem Sauerstoffmangel an. Verantwortlich für
+    diese Umstellung sind sogenannte HIF-Signalfaktoren.'
+    br
+    e 'Fehlt in Mäusen einer dieser Signalfaktoren namens
+    HIF-1α, ist die Ausschüttung bestimmter Zytokine beeinträchtigt.
+    Als Reaktion darauf wird das Wachstum von Blutgefässen in der
+    Haut und damit die Wundheilung beschleunigt, während die
+    Bekämpfung bakterieller Infektionen gedrosselt wird.
+    Die Balance verschiebt sich so in Richtung Wundheilung.'
+  }
+  # ========================================================================= #
+  # === interferon tag
+  # ========================================================================= #
+  div_default {
+    h2 'Interferon'
+    p {
+      e 'Interferon Alpha hat (mind.) 15 Gene, Beta und Gamma nur je
+      1. Die Alpha-Varianten zeigen <b>unterschiedliche Spezifität</b>.'
+    }
+  }
+  # ========================================================================= #
+  # === PRR
+  # ========================================================================= #
+  h2 'PRR: <i>pattern recognition receptors</i>'
+  div(id: 'PRR') {
+    e 'PRRs sind auf der Oberfläche von Phagocyten zu finden - sie werden
+    dort auch exprimiert. Dies hilft den Immunzellen Pathogene zu erkennen
+    und die Phagocytose zu ermöglichen.' 
+  }
+  # ========================================================================= #
+  # === IKAROS TAG
+  # ========================================================================= #
+  div(id: 'ikaros'){
+    h4 'Ikaros','','ikaros'
+    p {
+      e 'Ikaros ist ein "<i>differentiation factor</i>" der <b>leukocyte lineage</b>.'
+      br
+      e 'Ikaros interagiert mit Aiolos (einem <i>lymphoid restricted
+      transcription factor</i>, der gemeinsam mit Ikaros die 
+      <b>Lymphocyte Differentiation</b> steuert)'
+      br
+      e '<b>Ikaros</b> besitzt einen Zinkfinger:'
+      br
+      dimg 'science/biology/IKAROS.jpg',
+           'marl2em bblack1'
+    }
+  }
+  # ========================================================================= #
+  # === Exam questions
+  # ========================================================================= #
+  h2 'Exam questions'
+  div_default {
+    e 'Describe the receptors, their ligands and soluble molecules that provide
+    three distinct signals for full T cell activation, including their
+    functional relevance.'
+    br
+    e 'Polarizing cytokines can be secreted, which in turn causes
+    T cells to specialize.'
+    br
+    e 'IL-1α and IL-1β are pro-inflammatory cytokines, produced following
+    damage to the host (release of DAMPs) or upon innate recognition of
+    PAMPs.'
+    br
+    e 'The activities of IL-1 form a <b>direct bridge between innate
+    and adaptive immunity</b>.'
+    br
+    e 'Sources used:'
+    br
+    abr_self 'https://www.frontiersin.org/articles/10.3389/fimmu.2020.621931/full'
+  }
+  # ========================================================================= #
+  # === Describe the differences between a naïve T cell and an effector T cell.
+  # ========================================================================= #
+  div_default {
+    e 'Describe the differences between a naïve T cell and an effector T
+    cell.'
+    br
+    e 'If a naive T cell encounters an appropriate antigen then said
+    naïve cell is activated into different types of T cells.'
+    br
+    e 'Each naïve T cell has a unique T cell receptor (TCR) that
+    recognizes a specific antigen.'
+    br
+    e 'Sources used:'
+    br
+    abr_self 'https://www.akadeum.com/blog/what-are-naive-cells/'
+  }
+  # ========================================================================= #
+  # === Q3: Name two co-stimulatory molecules expressed on naïve T cells,
+  #     including their ligands and their function
+  # ========================================================================= #
+  div_default {
+    e 'Q3: Name two co-stimulatory molecules expressed on naïve T cells,
+    including their ligands and their function'
+    br
+    e 'The most prominent co-stimulatory molecule is <b>CD28</b>, which
+    controls the activation of naïve and memory T cells by antigen
+    presented on professional antigen-presenting cells.'
+    br
+    e 'This has a practical implication as well, as blocking of the
+    CD28-CD80/86 pathway can be used to induce tolerance in autoimmune
+    diseases where the disease-inducing autoantigens are not known.'
+    br
+    e 'APCs need activation signals to provide co-stimulatory ligands,
+    for example through the activation of Toll-like receptors.'
+    br
+    e 'Sources used:'
+    br
+    abr_self 'https://arthritis-research.biomedcentral.com/articles/10.1186/ar2414'
+    abr_self 'https://www.youtube.com/watch?v=1FVAFy6qruY'
+  }
+  # ========================================================================= #
+  # === Q4: Name cytotoxic effector proteins and their action on target cells?
+  # ========================================================================= #
+  div_default {
+    e 'Q4: Name cytotoxic effector proteins and their action on target cells.'
+    br
+    e 'Sources used:'
+    br
+    abr_self ''
+  }
+  # ========================================================================= #
+  # === Q5: Name the major functional CD4+ T-cell subsets in the current
+  #     immunological paradigm on CD4+ T-cell differentiation, including
+  #     master-regulator transcription factors involved in their development
+  #     and cytokines relevant for their polarization.
+  # ========================================================================= #
+  div_default {
+    e 'Q5: Name the major functional CD4+ T-cell subsets in the current 
+    immunological paradigm on CD4+ T-cell differentiation, including
+    master-regulator transcription factors involved in their development
+    and cytokines relevant for their polarization.'
+    br
+    e 'Sources used:'
+    br
+    abr_self ''
+  }
+  # ========================================================================= #
+  # === Q6: Imagine you are member in a research team that is supposed to
+  #     develop vaccines against extracellular bacteria: which functional
+  #     subtype of CD4+ T cells should be induced by such vaccines and
+  #     what effector functions would this CD4+ T cell subtype perform?
+  # ========================================================================= #
+  div_default {
+    e 'Q6: Imagine you are member in a research team that is supposed to
+    develop vaccines against extracellular bacteria: which functional
+    subtype of CD4+ T cells should be induced by such vaccines and
+    what effector functions would this CD4+ T cell subtype perform?'
+    br
+    e 'Sources used:'
+    br
+    abr_self ''
+  }
+  # ========================================================================= #
+  # === Q7: What are the main functions exerted by Interleukin-2? Which
+  #         molecules form the IL-2 receptor?
+  # ========================================================================= #
+  div_default {
+    e 'Q7: What are the main functions exerted by Interleukin-2? Which
+    molecules form the IL-2 receptor?'
+    br
+    e 'Sources used:'
+    br
+    abr_self ''
+  }
+  # ========================================================================= #
+  # === Q8: What are the main functions exerted by Interleukin-4?
+  # ========================================================================= #
+  div_default {
+    e 'Q8: What are the main functions exerted by Interleukin-4?'
+    br
+    e 'Sources used:'
+    br
+    abr_self ''
+  }
+  # ========================================================================= #
+  # === Q9: Describe the major suppressive mechanisms that Tregs can perform.
+  # ========================================================================= #
+  div_default {
+    e 'Q9: Describe the major suppressive mechanisms that Tregs can perform.'
+    br
+    e 'Sources used:'
+    br
+    abr_self ''
+  }
+  # ========================================================================= #
+  # === Q10: Describe briefly the major pathways how cytotoxic T cells kill
+  #          their target cells (extrinsic and intrinsic): which molecules
+  #          are involved, how do they act?
+  # ========================================================================= #
+  div_default {
+    e 'Q10: Describe briefly the major pathways how cytotoxic T cells kill 
+    their target cells (extrinsic and intrinsic): which molecules are
+    involved, how do they act?'
+    br
+    e 'Sources used:'
+    br
+    abr_self ''
+  }
+  # ========================================================================= #
+  # === Q11: How can CD4+ T cells co-stimulate CD8+ T cells (name
+  #          involved molecules and required cell-cell interactions)?
+  # ========================================================================= #
+  div_default {
+    e 'Q11: How can CD4+ T cells co-stimulate CD8+ T cells (name involved
+    molecules and required cell-cell interactions)?'
+    br
+    e 'Sources used:'
+    br
+    abr_self ''
+  }
+e 'Q12: What are TH1 effector functions in infections by intracellular bacteria?
+
+Q13: Name TH2 cell effector functions in helminth infections?
+Q14: What is immunological synapse and how it is formed?
+
+Immunological memory (Clara Pernold)
+Q1) Explain the benefits of immune memory in comparison to primary response.
+Contrast the features of an antibody response during a primary infection with
+that during a memory response.
+Q1) Describe the roles of B cells in immunological memory: What is the difference
+between “constitutive” and “reactive” humoral memory and the cell types
+responsible?
+Q1) What are the different stages of B cell related memory?
+Q1) What is the role of CD40/CD40L and BLIMP-1?
+Q1) What is the role of IL-7 receptor during the memory response?
+Q1) CD45 is a molecule, which is often used to discern between T cell phenotypic
+subsets.
+a) What is the differential expression pattern of this molecule?
+b) How do such molecular variants arise?
+c) What are the relevant cellular phenotypes elucidated using CD45 as a
+marker and how do these phenotypes relate to function?
+Q1) Outline the major differences between a primary and secondary T cell
+response.
+Q1) Memory T cells can be divided into two main subsets, describe their
+phenotype. How does the expression of molecules relate to cellular function?
+Describe the biological relevance of Tcm and Tem when controlling
+previously encountered antigen over the time course of a secondary
+infection.
+Describe the phenotypes of Tcm, Tem and Trm
+What is the function of the following cell surface molecules: CD62L, CCR7,
+CD103, CD69?
+What leads to T-cell exhaustion and how do the functional and phenotypic
+characteristics of exhausted cells change over time?
+'
+
+  p_default {
+    e 'What is immune senescence? How would the phenotype of an immune
+    cell change?'
+    br
+    e 'Older adults are predisposed to a higher risk of latent virus
+    reactivation.'
+  }
+  # ========================================================================= #
+  # === Q2: What is the meaning of “autofluorescence” in flow cytometry? What is causing
+  #     “autofluorescence”? How is autofluorescence determined in a
+  #     flow cytometry experiment – e.g. draw an example as histogram? 
+  # ========================================================================= #
+  div_default {
+    e 'Immunological Methods (Kerstin Mair)'
+    br
+    e 'Q1: Interpret this pseudocolor plot showing flow cytometry data: what phenotypes
+    of lymphocytes can you identify? What can be concluded about the abundance of
+    individual phenotypes?'
+    br
+    embed_remote_image 'https://i.imgur.com/5xZgcfZ.png'
+  }
+  # ========================================================================= #
+  # === Q2: What is the meaning of “autofluorescence” in flow cytometry? What is causing
+  #     “autofluorescence”? How is autofluorescence determined in a
+  #     flow cytometry experiment – e.g. draw an example as histogram? 
+  # ========================================================================= #
+  div_default {
+    e 'Q2: What is the meaning of '+squote('autofluorescence')+' in flow
+    cytometry? What is causing '+squote('autofluorescence')+'? How is
+    autofluorescence determined in a flow cytometry experiment – e.g.
+    draw an example as histogram?'
+    br
+  }
+  # ========================================================================= #
+  # === Q3: Name a) similarities and b) differences between flow cytometry
+  #         and mass cytometry. 
+  # ========================================================================= #
+  div_default {
+    e 'Q3: Name a) similarities and b) differences between flow cytometry
+    and mass cytometry.'
+    br
+    e 'Let us first define these two methods.'
+    br
+    e 'Flow Cytometry (FC) is a technique used to examine the
+    chemical and physical properties of a population of cells.
+    This is done with the help of a laser beam. The cells will
+    flow through that laser beam.'
+    br
+    e 'Mass cytometry (MC) is a variation of flow cytometry in which
+    antibodies are labeled with heavy metal ion tags rather
+    than fluorochromes. The advantage here is that we can combine
+    many more antibody specificities in a single sample.
+    The cells used in MC are incubated with a cocktail of antibodies
+    that have been previously conjugated with heavy metal isotopes
+    via a polymer chain of chelating groups.'
+    br
+    abr_self 'https://imperialbiosciencereview.com/2020/09/25/flow-cytometry-vs-mass-cytometry-cytof/'
+  }
+  # ========================================================================= #
+  # === Q4: For what reasons might it be relevant to sort lymphocyte
+  #         subsets? 
+  # ========================================================================= #
+  div_default {
+    e 'Q4: For what reasons might it be relevant to sort lymphocyte
+    subsets?','lightblue'
+    br
+    e 'This may be useful to determine
+    Which T cell populations mediate highly effective
+    adoptive immunotherapy.'
+    br
+    e 'Adoptive cell transfer (ACT) is an ex-vivo expansion and
+    re-infusion of antigen (Ag)-specific T cells to patients.'
+    br
+    e 'A straightforward and functionally significant means of
+    classifying T cell subsets can be accomplished by assessing
+    for the co-expression of the lymphoid homing molecules
+    L-selectin (CD62L) and CC-chemokine receptor 7 (CCR7).
+    T cells which display these 2 molecules have a
+    propensity to home to secondary lymphoid structures
+    where they can actively survey professional
+    antigen presenting cells for the presence of cognate
+    Antigenes.'
+    br
+    e 'Human lymphocytes can be divided into:'
+    br
+    cmd '  T lymphocytes (CD3+, CD4+, CD8+),'
+    cmd '  B lymphocytes (CD19+), and'
+    cmd '  Natural Killer (NK) lymphocytes (CD16+, CD56+).'
+    br
+    e 'Sources:'
+    br
+    abr_self 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3501135/'
+  }
+  # ========================================================================= #
+  # === Q5: Name two methodologies that are used to sort lymphocyte
+  #         subsets and explain briefly their functional principle. 
+  # ========================================================================= #
+  div_default {
+    e 'Q5: Name two methodologies that are used to sort lymphocyte
+    subsets and explain briefly their functional principle.',
+    'lightblue'
+    br
+  }
+  # ========================================================================= #
+  # === Q6: How does the proliferation dye CFSE (also named CFDA-SE) allow the
+  #     differentiation of individual daughter cell generations in
+  #     proliferation assays analysed by flow cytometry? Briefly describe
+  #     the principle.
+  # ========================================================================= #
+  div_default {
+    e 'Q6: How does the proliferation dye CFSE (also named CFDA-SE) allow the
+    differentiation of individual daughter cell generations in proliferation
+    assays analysed by flow cytometry? Briefly describe the principle.',
+    'lightblue'
+    br
+    e 'This dye allows us to monitor the <b>proliferation of
+    lymphocytes</b>.'
+    br
+    e 'CFSE stands short for carboxyfluorescein diacetate succinimidyl
+    ester.'
+    br
+    e 'The idea is for CFSE to covalently label long-lived intracellular
+    molecules with the highly fluorescent dye, carboxyfluorescein.'
+    br
+    e 'CFSE can go through membranes.'
+    br
+    e 'Its succinimidyl group covalently binds to intracellular
+    lysine residues and other free primary amines, producing
+    green fluorescence.'
+    br
+    e 'This stable linkage ensures retention of the dye within
+    the cell once incorporated, without leaching onto
+    surrounding cells. This feat of CFSE has led to widespread
+    use in fluorescence microscopy or flow cytometry to
+    study cell division, proliferation and migration. The
+    dye has an excitation wavelength around 492 nm and
+    an emission wavelength around 517 nm.'
+    br
+    e 'Note that <b>CFDA-SE</b> is NOT fluorescent.'
+    br
+    e 'Each cell division can be assessed by measuring the
+    corresponding decrease in cell fluorescence via Flow
+    cytometry.'
+    br
+    e 'Sources:'
+    br
+    abr_self 'https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3185625/'
+  }
+  # ========================================================================= #
+  # === Q7: Name two methods to analyze cell lysis and briefly describe one of the
+  #         methods.
+  # ========================================================================= #
+  div_default {
+    e 'Q7: Name two methods to analyze cell lysis and briefly describe one of
+    the methods.','lightblue'
+    br
+  }
+  # ========================================================================= #
+  # === Q8: What are the requirements for intracellular cytokine staining
+  #         by flow cytometry.
+  # ========================================================================= #
+  div_default {
+    e 'Q8: What are the requirements for intracellular cytokine staining
+    by flow cytometry?','lightblue'
+    br
+    e '<b class="lightgreen">Intracellular cytokine staining</b>
+    (ICS) is a method of cytokine analysis that provides information
+    on the type of cytokines that are produced upon (antigen-specific)
+    stimulation of T cells and B cells. We can detect immunological
+    biomarkers in the form of expressed cytokines.'
+    br
+    e 'ICS can reveal which subtype of CD4+ T helper cell is induced
+    under certain culture conditions, and indicates whether a
+    biological or compound alters T cell polarization in vitro.
+    Rather than looking at the total amount of secreted cytokines
+    produced by all the cells in culture, which is generally
+    analyzed by ELISA or CBA, ICS will provide information on
+    cytokine production by each individual cell. This allows
+    us to analyze the proportion of cells that produce a
+    cytokine of interest, or allows for quantification of
+    the amount of cells producing multiple cytokines (i.e.
+    the rate of polyfunctionality).'
+    br
+    e 'This can help, for example, to unravel the polarization,
+    strength and specificity of immune responses upon
+    immune-modulating therapies.'
+  }
+  # ========================================================================= #
+  # === Q9: Describe the steps that have to be done for an ELISpot assay.
+  # ========================================================================= #
+  div_default {
+    e 'Q9: Describe the steps that have to be done for an ELISpot assay. '+
+      DONE_IMAGE,'lightblue'
+    br
+    e 'The ELISPOT assay can be used to assess cytokine secretion,
+    that is, to enumerate cytokine-secreting cells.'
+    br
+    e 'ELISPOT is an abbreviation towards <b>Enzyme-Linked Immunospot
+    assay</b>.'
+    br
+    e 'The ELISpot assay represents the convergence of
+    plate-based Enzyme Linked Immunosorbent Assays (ELISAs)
+    with membrane-based Western blotting technologies. It is
+    is a common method for the measurement of cellular immunity.
+    ELISPOT was developed for the detection of secreted proteins,
+    such as cytokines and growth factors.'
+    br
+    e 'ELISPOT evaluates the strength of T cell-mediated immune
+    activity. The limit of detection in an ELISPOT assay is
+    typically 1 cell in 100000 cells.'
+    br
+    e 'The ELISPOT method was first reported by Czerkinsky et al.,
+    in 1983. The method was originally developed to quantify
+    immunoglobulin-secreting cells.'
+    br
+    e 'Parameters that can be evaluated include:'
+    br
+    le 'spot number','gold'
+    le 'spot size','gold'
+    le 'spot intensity','gold'
+    br
+    e 'ELISPOT enables the comprehensive screening of patient
+    derived peripheral blood mononuclear cells to reveal
+    the antigenic restriction of T-cell responses.'
+    br
+    e 'The majority of Elispots are performed on polyvinylidene
+    fluoride (PVDF) membrane plates. Alternatively a 
+    nitrocellulose membrane can be used.'
+    br
+    e 'The <b class="lightgreen">steps</b> for an
+    ELISPOT (standard assay variant) include:'
+    br
+    le '- Coat the membrane with the capture antibody. These
+    antibodies are often cytokine-specific and they are now
+    immobilized on membrane-bottomed 96-well plates. The 
+    antibody thus is the first layer in the individual 
+    wells, so they can be found on the bottom of the
+    wells. The capture antibody must be specific to the
+    secreted (target) protein.'
+    le '- Add the cells, usually peripheral blood mononuclear
+    cells, also called PBMCs). These are seeded in the presence
+    or absence of stimulating antigens.'
+    le '- Over time, activated cells (also called "responding
+    cells") begin to secrete cytokines, which bind to the
+    capture Antibody in the immediate vicinity of
+    the expressing cell.'
+    le '- Wash to remove away the cells.'
+    le '- Add a second cytokine-specific biotinylated
+    Ab which binds to the cytokine-Ab complex.
+    This is called the <b>detection antibody</b> and
+    it will bind specifically to the bound protein.'
+    le '- Add streptavidin-enzyme conjugate. Spot detection
+    is accomplished through substrate deposition following
+    either a one-step (enzyme-conjugated, cytokine-specific
+    Ab) or two-step (biotinylated Ab/streptavidin-enzyme)
+    antibody binding process. Once the signals are
+    developed, spot numbers can be tallied manually
+    or through use of image-based spot readers with
+    accompanying analysis software. The frequency
+    and total number of responder cells is determined
+    by comparing the number of spots between
+    stimulated and untreated/control wells.'
+    br 
+    e 'Sources used:'
+    br
+    abr_self 'https://www.future-science.com/doi/10.4155/bio-2022-0010'
+    abr_self 'https://www.sciencedirect.com/topics/immunology-and-microbiology/enzyme-linked-immunospot-assay'
+  }
+  # ========================================================================= #
+  # === Inflammation
+  # ========================================================================= #
+  h2 'Inflammation',
+     'gold'
+  div_default {
+    e '<b>Inflammation</b> is a series of events that surround an immune
+    response and display a number of characteristic features, including
+    local swelling (edema), redness (due to capillary dilation), pain,
+    and <b>heat</b>.'
+  }
+  # ========================================================================= #
+  # === Peyersche Plaques
+  # ========================================================================= #
+  h2 'Peyersche Plaques',
+     'gold'
+  div_default {
+    e '<b>Plasmazellen</b>, die mit Peyersche Plaques assoziiert vorliegen,
+    sezernieren in der Regel Antikörper der Klasse 
+    <b class="lightblue">IgA</b>.'
+  }
+  # ========================================================================= #
+  # === Erkältung
+  # ========================================================================= #
+  h2 'Erkältung',
+     'gold'
+  div_default {
+    e 'Man kann eine Erkältung unter Umständen durch folgende
+    Maßnahmen verkürzen:'
+    br
+    e '- Ausruhen und viel Schlaf'
+    e '- Tee und ausreichend Wasser'
+    br
+    e 'In der Regel dauert es zwischen drei bis zehn Tage, bis
+    eine Erkältung überwunden ist.'
+  }
+  # ========================================================================= #
+  # === Slogans tag. Slogan tag.
+  # ========================================================================= #
+  h2 'Immuno-Slogans',
+     'gold'
+  p_default {
+    e '- Innate and adaptive immune signaling are heavily Ub-mediated.'
+    e '- <b>Cytokines</b> can act in an autocrine manner.'
+    e '- IgM is particular useful because it shows a high potential for
+    cross-linking antigens.'
+    e '- The Microbiome educates the immune system.'
+    e '- The human body, curiously enough, acts as an incubator of
+    a unique microbiome.'
+    e '- Jedes Toxin ist potenziell in der Forschung nützlich, da
+    Toxine an Proteine binden können und man so, im Prinzip, auch
+    das zugehörige Bindungsprotein finden kann. Daduch erhält man
+    eventuell einen Hinweis auf dessen Rolle im Kommunikationssystem
+    des Körpers.'
+    e '- Antikörper in der späten Immunantwort haben eine höhere Affinität
+    zum Antigen.'
+    e '- Inflammataion is a general, nospecific reaction to noxious
+    stimuli such as toxins and pathogens.'
+    e '- <b>Bacterial pathogens</b> sense their environment, and in
+    response, virulence genes are induced or repressed through
+    spatial and temporal regulation.'
+    e '- Chemokine and cytokine mediators are released by
+    injured cells.'
+    e '- A basic tenet of multicellularity is that one does not go
+    around randomly killing good cellular citizen.'
+    e '- Converting Actin Nucleation to a motile force is
+    done by <i class="lightgreen">Listeria monocytogenes</i>.'
+    e '- The miasma theory was the leading theory of disease
+    origin, until it was eventually displaced in the 19th
+    century by the germ theory of disease.'
+    e '- Neutrophils expel extracellular traps (NETs) to entrap
+    and exterminate micro-organisms.'
+    e '- An allergic reaction results from the immune system
+    being oversensitive, treating essentially harmless
+    invaders as dangerous enemies that must be fought down.'
+    e "- In some types of <b>hepatitis</b> people die not from
+    the hepatitis virus itself, but from the immune system's
+    <b>destruction of the liver</b>."
+    e "- Macrophages are the body's natural scavengers: they are
+    the <b>all-purpose trash disposal units</b> of the body."
+    e '- Parasites have forced organisms to evolve immune
+    systems. Examples are the restriction enzymes bacteria use
+    to cut up invading viruses, as well as the CRISPR/Cas 
+    defence system and the white blood cells in the human
+    body to destry bacteria.'
+    e '- Antigene können die Bildung von Antikörpern
+    hervorrufen.'
+    e '- The immune system has been shaped by genetic evolution. It
+    meets threats shaped by genetic evolution.'
+    e '- The total number of combinatorial arrangements of
+    immunoglobulins (Ig) in an individual is greater than
+    10⁹ (Jerne 1993).'
+    e '- Infectious agents may see humans as a rich sanctuary
+    for propagating their genome.'
+    e '- Initiation and escalation of an immune response carries
+    a significant metabolic cost to the cell.'
+    e '- The relatively invariant nature of PRRs is a strength,
+    as well as a weakness, of the innate immune system.'
+    e '- The PRRs are <b>hard‐wired receptors</b>.'
+    e '- Pathogens vary greatly in size and lifestyle.'
+    e '- Anatomic and chemical barriers are the initial
+    defenses against infection.'
+    e '- The average human requires the production of almost
+    4 × 10¹¹ leukocytes (400 billion) per day.'
+  }
+  # ========================================================================= #
+  # === Links
+  # ========================================================================= #
+  h2 'Links',
+     'gold'
+  p_default {
+    abr_self :local_bioinformatics,
+             css_class: 'steelblue BOLD'
+    abr_self :local_cellbiology,
+             css_class: 'steelblue BOLD'
+    abr_self :local_genetics,
+             css_class: 'steelblue BOLD'
+    abr_self :local_biotechnology,
+             css_class: 'steelblue BOLD'
+    abr_self :local_molecular_therapies,
+             css_class: 'steelblue BOLD'
+  }
+}}