adaptive specific host defenses immunology overview official educational resources

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adaptive immunity

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https://www.ncbi.nlm.nih.gov/books/NBK7795

mkdir -p "/tmp/workspace/adaptive-host-defenses/src" "/tmp/workspace/adaptive-host-defenses/output" && python -c "from pypdf import PdfReader; p='/tmp/workspace/attachments/c8296e29-6f0c-41aa-b31e-17feab1f0236/Chapter18_Adaptive_Specific_Host_Defenses.pdf'; r=PdfReader(p); print('pages',len(r.pages)); open('/tmp/workspace/adaptive-host-defenses/src/chapter_text.txt','w',encoding='utf-8').write('\\n\\n'.join('--- PAGE %d ---\\n%s'%(i+1,(x.extract_text() or '')) for i,x in enumerate(r.pages)))"

python - <<'PY' from pypdf import PdfReader p='/tmp/workspace/attachments/c8296e29-6f0c-41aa-b31e-17feab1f0236/Chapter18_Adaptive_Specific_Host_Defenses.pdf' r=PdfReader(p) for i,pg in enumerate(r.pages,1): t=(pg.extract_text() or '').replace('\n',' ') print(f'{i:02d}: {t[:380]}') PY

cat > "/tmp/workspace/adaptive-host-defenses/src/create_deck.py" <<'PY' from pptx import Presentation from pptx.util import Inches, Pt from pptx.dml.color import RGBColor from pptx.enum.shapes import MSO_SHAPE, MSO_CONNECTOR from pptx.enum.text import PP_ALIGN, MSO_ANCHOR from pptx.enum.dml import MSO_THEME_COLOR from pptx.enum.text import MSO_AUTO_SIZE OUT='/tmp/workspace/adaptive-host-defenses/output/Adaptive_Specific_Host_Defenses.pptx' prs=Presentation(); prs.slide_width=Inches(13.333); prs.slide_height=Inches(7.5) blank=prs.slide_layouts[6] # palette NAVY=RGBColor(12,38,64); BLUE=RGBColor(24,111,155); TEAL=RGBColor(22,157,146); GOLD=RGBColor(243,181,64); RED=RGBColor(205,77,74); LIGHT=RGBColor(242,247,249); DARK=RGBColor(31,47,61); GRAY=RGBColor(94,110,122); WHITE=RGBColor(255,255,255); PALE=RGBColor(222,239,242) def rect(s,x,y,w,h,fill, radius=False, line=None): sh=s.shapes.add_shape(MSO_SHAPE.ROUNDED_RECTANGLE if radius else MSO_SHAPE.RECTANGLE, Inches(x), Inches(y), Inches(w), Inches(h)); sh.fill.solid(); sh.fill.fore_color.rgb=fill; sh.line.color.rgb=line if line else fill; return sh def text(s,txt,x,y,w,h,size=20,color=DARK,bold=False,align=None, font='Aptos', margin=.08): tb=s.shapes.add_textbox(Inches(x), Inches(y), Inches(w), Inches(h)); tf=tb.text_frame; tf.clear(); tf.word_wrap=True; tf.margin_left=tf.margin_right=Inches(margin); tf.margin_top=tf.margin_bottom=Inches(margin/2); tf.vertical_anchor=MSO_ANCHOR.MIDDLE lines=txt.split('\n') for i,line in enumerate(lines): p=tf.paragraphs[0] if i==0 else tf.add_paragraph(); p.text=line; p.font.name=font; p.font.size=Pt(size); p.font.bold=bold; p.font.color.rgb=color; p.space_after=Pt(4) if align: p.alignment=align return tb def title(s,head,sub=None, num=None): rect(s,0,0,13.333,.32,TEAL); text(s,head,.55,.48,11.8,.55,28,NAVY,True) if sub:text(s,sub,.57,1.04,11.7,.35,11,GRAY) if num is not None:text(s,f'{num:02d}',12.35,.48,.45,.35,13,TEAL,True,PP_ALIGN.RIGHT) def footer(s,source='Source: OpenStax Microbiology, Ch. 18 (supplied chapter)'): rect(s,.55,7.12,12.23,.015,RGBColor(205,216,221)); text(s,source,.55,7.16,10.8,.18,8,GRAY); text(s,'Adaptive Specific Host Defenses',10.85,7.16,1.9,.18,8,GRAY,False,PP_ALIGN.RIGHT) def bullets(s,items,x,y,w,h,size=17,color=DARK): tb=s.shapes.add_textbox(Inches(x),Inches(y), Inches(w), Inches(h)); tf=tb.text_frame; tf.clear(); tf.word_wrap=True; tf.margin_left=Inches(.05); tf.margin_top=Inches(.02) for i,item in enumerate(items): p=tf.paragraphs[0] if i==0 else tf.add_paragraph(); p.text=item; p.level=0; p.font.name='Aptos'; p.font.size=Pt(size); p.font.color.rgb=color; p.space_after=Pt(8); p.text='• '+item return tb def card(s,head,body,x,y,w,h,accent=TEAL,body_size=14): rect(s,x,y,w,h,WHITE,True,RGBColor(210,223,228)); rect(s,x,y,.1,h,accent); text(s,head,x+.23,y+.16,w-.38,.35,17,NAVY,True); text(s,body,x+.23,y+.62,w-.38,h-.72,body_size,DARK) def arrow(s,x1,y1,x2,y2,color=TEAL): ln=s.shapes.add_connector(MSO_CONNECTOR.STRAIGHT,Inches(x1),Inches(y1),Inches(x2),Inches(y2)); ln.line.color.rgb=color; ln.line.width=Pt(2); ln.line.end_arrowhead=True def cover(): s=prs.slides.add_slide(blank); rect(s,0,0,13.333,7.5,NAVY); rect(s,0,0,13.333,.18,TEAL); rect(s,.65,.86,.14,4.95,GOLD); text(s,'CHAPTER 18',1.08,.92,3,.35,14,GOLD,True); text(s,'Adaptive Specific\nHost Defenses',1.05,1.42,8.9,1.55,41,WHITE,True); text(s,'How antigen-specific lymphocytes, antibodies, immune memory, and vaccination protect the host',1.08,3.22,8.3,.55,19,RGBColor(207,225,232)); # symbolic cells for x,y,r,c,l in [(10.35,1.5,.7,TEAL,'B'),(11.55,2.58,.55,GOLD,'T'),(9.9,3.28,.42,RED,'Ag'),(11.0,4.25,.72,BLUE,'M')]: sh=s.shapes.add_shape(MSO_SHAPE.OVAL, Inches(x), Inches(y), Inches(r), Inches(r)); sh.fill.solid(); sh.fill.fore_color.rgb=c; sh.line.color.rgb=WHITE; text(s,l,x,y+r*.25,r,r*.38,15,WHITE,True,PP_ALIGN.CENTER) arrow(s,10.9,2.2,11.55,2.82,WHITE); arrow(s,10.3,3.58,10.75,4.23,WHITE) text(s,'Detailed learning presentation | Based on the supplied chapter',1.08,6.28,8,.3,12,RGBColor(176,204,214)); def standard(head,sub='',n=0): s=prs.slides.add_slide(blank); rect(s,0,0,13.333,7.5,LIGHT); title(s,head,sub,n); footer(s); return s cover() # 2 s=standard('Learning roadmap','What this chapter builds, from recognition to lasting protection',2) for i,(h,b,c) in enumerate([('1. Recognition','Antigens, epitopes, antibodies and antigen presentation',TEAL),('2. Cellular immunity','T-cell maturation, activation and effector functions',BLUE),('3. Humoral immunity','B-cell activation, plasma cells and antibody actions',GOLD),('4. Protection over time','Memory, acquired immunity and vaccination',RED)]): card(s,h,b,.75+(i%2)*6.1,1.7+(i//2)*2.05,5.55,1.5,c,16) # 3 s=standard('The two arms of host defense','Innate defense acts first; adaptive defense adds precision and memory',3) card(s,'Innate immunity','Immediate. Recognizes shared microbial patterns. Barriers, phagocytes, complement, inflammation and NK cells.',.75,1.65,5.75,3.8,TEAL,18) card(s,'Adaptive immunity','Slower at first exposure. Recognizes specific epitopes. B and T lymphocytes expand into effector and memory cells.',6.85,1.65,5.75,3.8,BLUE,18) arrow(s,6.5,3.55,6.85,3.55,GOLD); text(s,'Antigen presentation\nlinks the systems',5.25,4.05,2.8,.55,13,GRAY,False,PP_ALIGN.CENTER) #4 s=standard('Defining properties: specificity and memory','These explain why recovery or vaccination can protect against later exposure',4) card(s,'Specificity','Each lymphocyte clone has receptors that recognize one molecular target. The target may be an entire antigen or a particular epitope.',.75,1.62,5.75,3.65,TEAL,18) card(s,'Memory','First exposure creates memory B and T cells. Re-exposure produces a faster, larger, more effective secondary response.',6.85,1.62,5.75,3.65,GOLD,18) text(s,'Key distinction: immune memory is antigen-specific. Prior exposure to one pathogen does not generally protect against an unrelated pathogen.',.88,5.72,11.55,.6,17,NAVY,True,PP_ALIGN.CENTER) #5 s=standard('Primary versus secondary immune response','The quantitative basis for vaccine protection',5) # graph axes rect(s,1.15,5.65,10.4,.03,DARK); rect(s,1.15,1.55,.03,4.1,DARK); text(s,'Antibody concentration',.25,2.75,.8,.7,12,GRAY,False,PP_ALIGN.CENTER); text(s,'Time after antigen exposure',4.2,6.0,3.7,.3,13,GRAY) # approximate curves via straight connectors pts=[(1.3,5.55),(2.2,5.45),(3.0,4.6),(3.75,3.15),(4.5,3.45),(5.25,4.5),(6.05,5.2)] for a,b in zip(pts,pts[1:]): arrow(s,*a,*b,TEAL) pts2=[(6.15,5.35),(6.7,4.25),(7.45,2.05),(8.3,1.8),(9.25,2.3),(10.55,3.45),(11.3,4.5)] for a,b in zip(pts2,pts2[1:]): arrow(s,*a,*b,GOLD) text(s,'Primary response\nlag + lower peak',2.45,2.1,2.25,.65,14,TEAL,True,PP_ALIGN.CENTER); text(s,'Secondary response\nrapid + higher peak',7.15,.92,2.7,.65,14,RGBColor(180,123,10),True,PP_ALIGN.CENTER); text(s,'1st exposure',2.2,5.7,1,.3,11,GRAY); text(s,'2nd exposure',7.0,5.7,1.1,.3,11,GRAY) #6 s=standard('Antigens, epitopes and haptens','The molecular targets of adaptive recognition',6) card(s,'Antigen','A substance capable of being specifically recognized by antibodies or lymphocyte receptors. Proteins are generally highly antigenic.',.75,1.65,3.75,3.6,TEAL,17) card(s,'Epitope (determinant)','The small, discrete region of an antigen bound by a receptor. One complex antigen commonly contains multiple epitopes.',4.8,1.65,3.75,3.6,BLUE,17) card(s,'Hapten','A small molecule that can bind antibody but is typically not immunogenic alone. Linked to a carrier protein, it can trigger a response.',8.85,1.65,3.75,3.6,GOLD,17) #7 s=standard('Humoral and cellular immunity','Different lymphocytes, complementary roles',7) card(s,'Humoral immunity: B cells','B cells differentiate into plasma cells that release antibodies. Antibodies operate in blood, lymph and mucosal secretions, especially against extracellular microbes and toxins.',.75,1.6,5.75,4.25,TEAL,18) card(s,'Cell-mediated immunity: T cells','Helper T cells coordinate responses with cytokines. Cytotoxic T cells kill infected or abnormal host cells, a major defense against intracellular pathogens.',6.85,1.6,5.75,4.25,BLUE,18) #8 s=standard('Antibody architecture','Immunoglobulins convert antigen binding into effector functions',8) # Y diagram for coords in [(5.65,2.0,6.25,3.75),(6.85,2.0,6.25,3.75),(6.17,3.63,6.75,5.52)]: x1,y1,x2,y2=coords; ln=s.shapes.add_connector(MSO_CONNECTOR.STRAIGHT,Inches(x1),Inches(y1), Inches(x2), Inches(y2)); ln.line.color.rgb=BLUE;ln.line.width=Pt(11) text(s,'Fab regions\nVariable ends bind a specific epitope',.78,1.68,3.85,.7,18,NAVY,True); arrow(s,4.55,2.25,5.55,2.22,TEAL) text(s,'Fc region\nConstant stem binds Fc receptors and complement components',8.65,4.35,3.85,.72,18,NAVY,True); arrow(s,8.55,4.7,6.75,4.65,GOLD) text(s,'Two antigen-binding sites per antibody molecule; antibody class is determined by the constant region of its heavy chain.',2.2,5.95,8.9,.5,15,GRAY,False,PP_ALIGN.CENTER) #9 s=standard('Antibody isotypes: a practical comparison','Same basic architecture, different distribution and roles',9) rows=[('IgM','Pentamer in serum; first prominent antibody in primary response; strong agglutination and complement activation.'),('IgG','Major serum antibody; neutralization, opsonization and complement activity; only class that crosses placenta.'),('IgA','Dimer in secretions such as mucus, tears and breast milk; protects mucosal surfaces.'),('IgE','Binds mast cells/basophils; allergy and defense against parasitic infections.'),('IgD','Mainly membrane-bound B-cell receptor; present only in trace serum amounts.')] for i,(a,b) in enumerate(rows): y=1.38+i*1.04; rect(s,.75,y,1.25,.73,[TEAL,BLUE,GOLD,RED,GRAY][i],True); text(s,a,.83,y+.19,1.07,.28,17,WHITE,True,PP_ALIGN.CENTER); text(s,b,2.23,y+.06,10.0,.62,15,DARK) #10 s=standard('What antibodies do','Five principal ways antibodies limit infection',10) items=[('Neutralization','Blocks attachment of microbes or toxins to host cells.'),('Opsonization','Coats a pathogen so phagocytes bind Fc regions and ingest it more efficiently.'),('Complement activation','Especially IgM and IgG initiate complement-mediated inflammation and microbial clearance.'),('Agglutination','Cross-links particulate antigens, clumping them for easier removal.'),('ADCC','Antibody-coated targets are recognized by Fc receptors on effector cells such as NK cells, which release cytotoxins.')] for i,(a,b) in enumerate(items): card(s,a,b,.75+(i%2)*6.1,1.45+(i//2)*1.55,5.6,1.18,[TEAL,BLUE,GOLD,RED,GRAY][i],13) #11 s=standard('Major histocompatibility complex: the display system','T cells recognize antigen only when it is displayed with an appropriate MHC molecule',11) card(s,'MHC I','Expressed by almost all nucleated cells. Displays intracellular peptides, including viral or abnormal proteins, to CD8 cytotoxic T cells.',.75,1.65,5.75,3.45,BLUE,19) card(s,'MHC II','Expressed by professional antigen-presenting cells: dendritic cells, macrophages and B cells. Displays processed extracellular antigens to CD4 helper T cells.',6.85,1.65,5.75,3.45,TEAL,19) text(s,'Mnemonic: I → CD8; II → CD4. This pairing directs the appropriate arm of cellular immunity.',1.2,5.66,11,.5,16,NAVY,True,PP_ALIGN.CENTER) #12 s=standard('Professional antigen-presenting cells (APCs)','APCs initiate and shape adaptive responses',12) for i,(a,b,c) in enumerate([('Dendritic cells','Highly effective at activating naive T cells; collect antigen in tissues and present it in lymphoid organs.',TEAL),('Macrophages','Phagocytose microbes and present antigen; helper T-cell cytokines strengthen microbicidal activity.',BLUE),('B cells','Bind a specific soluble antigen through BCR, internalize it, and present peptide on MHC II to a matching helper T cell.',GOLD)]): card(s,a,b,.75+i*4.05,1.65,3.65,3.75,c,16) #13 s=standard('T-cell development and self-tolerance','The thymus selects useful T cells and removes dangerous self-reactive cells',13) steps=[('Bone marrow','Precursor forms'),('Thymus','TCR gene rearrangement'),('Positive selection','Keeps cells that recognize self-MHC'),('Negative selection','Eliminates strongly self-reactive clones'),('Peripheral tolerance','Anergy and regulatory T cells restrain self-reactivity')] for i,(a,b) in enumerate(steps): x=.55+i*2.53; rect(s,x,2.25,2.2,1.45,[GRAY,BLUE,TEAL,RED,GOLD][i],True); text(s,a,x+.12,2.46,1.96,.34,15,WHITE,True,PP_ALIGN.CENTER); text(s,b,x+.1,2.93,2,.43,11,WHITE,False,PP_ALIGN.CENTER) if i<4: arrow(s,x+2.2,2.97,x+2.48,2.97,WHITE) text(s,'Purpose: maintain a T-cell repertoire that can recognize foreign antigen presented by self-MHC while preventing autoimmunity.',1.05,5.02,11.2,.6,18,NAVY,True,PP_ALIGN.CENTER) #14 s=standard('The three major functional classes of T cells','Surface coreceptors and functions distinguish their roles',14) card(s,'Helper T cells (CD4+)','Recognize peptide-MHC II on APCs. Secrete cytokines that help B cells, macrophages and cytotoxic T cells.',.75,1.65,3.75,3.7,TEAL,17) card(s,'Cytotoxic T cells (CD8+)','Recognize peptide-MHC I on infected/abnormal cells. Kill targets with perforin and granzymes, inducing apoptosis.',4.8,1.65,3.75,3.7,RED,17) card(s,'Regulatory T cells','Suppress inappropriate immune activation and help maintain self-tolerance, reducing risk of autoimmune injury.',8.85,1.65,3.75,3.7,BLUE,17) #15 s=standard('T-cell activation needs more than antigen','Signal integration helps prevent accidental immune responses',15) card(s,'Signal 1: specificity','TCR recognizes a particular peptide bound to MHC. CD4 or CD8 stabilizes the interaction with MHC II or MHC I.',.75,1.6,3.7,3.75,TEAL,17) card(s,'Signal 2: costimulation','APC costimulatory molecules confirm a meaningful danger context. Without costimulation, a T cell may become anergic.',4.82,1.6,3.7,3.75,GOLD,17) card(s,'Signal 3: cytokines','Cytokines drive proliferation and guide differentiation into specialized effector and memory subsets.',8.88,1.6,3.7,3.75,BLUE,17) #16 s=standard('Helper T-cell subsets coordinate immune strategy','Cytokine environment drives specialization after activation',16) for i,(a,b,c) in enumerate([('TH1','Supports macrophage activation, intracellular killing and cytotoxic responses.',TEAL),('TH2','Supports B-cell activation, antibody production and class switching.',GOLD),('TH17','Promotes inflammation and recruitment of neutrophils to combat extracellular pathogens.',RED),('Treg','Limits immune responses and maintains tolerance.',BLUE)]): card(s,a,b,.75+(i%2)*6.1,1.55+(i//2)*2,5.55,1.4,c,15) #17 s=standard('Cytotoxic T cells eliminate infected host cells','A focused mechanism for intracellular infection',17) text(s,'Infected nucleated cell',.95,2.65,2.25,.4,16,NAVY,True,PP_ALIGN.CENTER); rect(s,.85,2.05,2.45,1.65,PALE,True,BLUE); text(s,'MHC I +\nforeign peptide',1.3,2.38,1.55,.55,15,BLUE,True,PP_ALIGN.CENTER) arrow(s,3.45,2.87,5.05,2.87,RED); text(s,'recognition',3.7,2.3,1,.27,11,GRAY,False,PP_ALIGN.CENTER) rect(s,5.1,2.05,2.2,1.65,RGBColor(254,230,229),True,RED); text(s,'CD8 CTL\nperforin + granzymes',5.35,2.4,1.7,.6,15,RED,True,PP_ALIGN.CENTER) arrow(s,7.45,2.87,9.0,2.87,RED); rect(s,9.05,2.05,2.6,1.65,RGBColor(245,239,237),True,RED); text(s,'Apoptosis\ncontrolled target-cell death',9.3,2.4,2.1,.58,15,RED,True,PP_ALIGN.CENTER) text(s,'This process avoids indiscriminate damage: the CTL recognizes a specific peptide-MHC I complex before killing.',1.35,5.25,10.6,.55,17,DARK,False,PP_ALIGN.CENTER) #18 s=standard('Superantigens: a harmful shortcut','Nonspecific T-cell activation can produce dangerous cytokine release',18) text(s,'Normal activation: a TCR recognizes a specific peptide nested in the MHC II binding cleft.',.85,1.55,11.5,.45,17,TEAL,True,PP_ALIGN.CENTER) text(s,'Superantigen: bridges MHC II and the variable region of the TCR outside the normal peptide-binding site.',.85,2.5,11.5,.45,17,RED,True,PP_ALIGN.CENTER) text(s,'Result: many T cells activate at once → massive cytokine release → systemic inflammation. Staphylococcal toxic shock syndrome is a classic example.',.95,4.1,11.4,.8,19,NAVY,True,PP_ALIGN.CENTER) #19 s=standard('B-cell development and the B-cell receptor','B cells mature in bone marrow and recognize native antigen directly',19) card(s,'Maturation','B cells develop in bone marrow. Selection preserves cells with functional receptors and removes or inactivates many self-reactive cells.',.75,1.62,5.75,3.65,TEAL,18) card(s,'BCR','Surface immunoglobulin, chiefly membrane IgM and IgD on naive mature B cells. All BCRs on one B cell share the same specificity.',6.85,1.62,5.75,3.65,BLUE,18) #20 s=standard('Two pathways of B-cell activation','The presence or absence of helper T-cell assistance changes the quality of the response',20) card(s,'T-independent activation','Repetitive epitopes, often on nonprotein antigens, cross-link BCRs. Innate signals such as TLR-PAMP interactions supply a second signal. Produces mainly antibody with limited memory.',.75,1.6,5.75,4.0,GOLD,17) card(s,'T-dependent activation','A B cell binds protein antigen, internalizes and presents peptide on MHC II. A cognate helper T cell provides cytokines and contact signals. Promotes class switching and durable memory.',6.85,1.6,5.75,4.0,TEAL,17) #21 s=standard('T-dependent B-cell activation: step by step','A linked-recognition partnership between B cell and helper T cell',21) steps=[('1','BCR binds antigen'),('2','B cell internalizes and processes antigen'),('3','Peptide displayed on MHC II'),('4','Matching CD4 helper T cell engages'),('5','Cytokines/contact activate B cell'),('6','Clonal expansion → plasma + memory cells')] for i,(n,b) in enumerate(steps): x=.5+(i%3)*4.25;y=1.5+(i//3)*2.25; rect(s,x,y,.52,.52,TEAL,True); text(s,n,x,y+.12,.52,.22,14,WHITE,True,PP_ALIGN.CENTER); text(s,b,x+.7,y,3.15,.62,15,NAVY,True); #22 s=standard('From B cell to plasma cell and memory cell','Clonal selection makes the response both large and durable',22) rect(s,.8,2.6,2.25,1.1,PALE,True,TEAL); text(s,'Naive B cell\nwith matching BCR',.98,2.85,1.9,.48,16,TEAL,True,PP_ALIGN.CENTER); arrow(s,3.1,3.15,4.38,3.15,TEAL); rect(s,4.4,2.6,2.25,1.1,RGBColor(232,245,243),True,TEAL); text(s,'Activated B cell\nclonal proliferation',4.6,2.85,1.85,.48,16,TEAL,True,PP_ALIGN.CENTER); arrow(s,6.65,3.15,7.75,2.25,BLUE); arrow(s,6.65,3.15,7.75,4.08,GOLD); rect(s,7.8,1.65,3.5,1.1,RGBColor(230,239,247),True,BLUE); text(s,'Plasma cells\nsecrete large amounts of antibody',8.0,1.9,3.1,.48,16,BLUE,True,PP_ALIGN.CENTER); rect(s,7.8,3.55,3.5,1.1,RGBColor(255,246,222),True,GOLD); text(s,'Memory B cells\nrespond quickly on re-exposure',8.0,3.8,3.1,.48,16,RGBColor(180,123,10),True,PP_ALIGN.CENTER) #23 s=standard('Four ways to acquire immunity','Active immunity creates memory; passive immunity transfers ready-made protection',23) headers=['Natural','Artificial']; labels=[('Active','Infection → host makes own response and memory','Vaccination → host makes own response and memory'),('Passive','Maternal antibodies → immediate, temporary protection','Injected antibodies/antiserum → immediate, temporary protection')] for j,h in enumerate(headers): text(s,h,4.3+j*4.0,1.35,3.1,.35,18,NAVY,True,PP_ALIGN.CENTER) for i,(r,a,b) in enumerate(labels): text(s,r,.85,2.35+i*2.05,2.1,.35,18,[TEAL,GOLD][i],True); card(s,'',a,3.0,1.95+i*2.05,3.65,1.25,TEAL if i==0 else GOLD,14); card(s,'',b,7.0,1.95+i*2.05,3.65,1.25,BLUE if i==0 else RED,14) #24 s=standard('Vaccines create protective immune memory','They simulate antigen exposure without requiring the disease itself',24) text(s,'Vaccine antigen',.75,2.7,1.55,.35,17,NAVY,True,PP_ALIGN.CENTER); arrow(s,2.3,2.88,3.35,2.88,TEAL); text(s,'Primary adaptive response\nB and T activation',3.4,2.45,2.3,.7,17,TEAL,True,PP_ALIGN.CENTER); arrow(s,5.8,2.88,6.85,2.88,TEAL); text(s,'Memory B and T cells',6.9,2.7,2.2,.35,17,GOLD,True,PP_ALIGN.CENTER); arrow(s,9.15,2.88,10.15,2.88,GOLD); text(s,'Later exposure:\nfast secondary response',10.15,2.45,2.5,.7,17,RED,True,PP_ALIGN.CENTER) text(s,'The desired outcome is immunity with much less risk than experiencing the natural infection.',1.25,5.3,10.8,.5,19,NAVY,True,PP_ALIGN.CENTER) #25 s=standard('Vaccine platforms','Different designs present antigen in different ways',25) items=[('Live attenuated','Weakened pathogen. Often strong, broad immunity; requires care because it can replicate.'),('Inactivated','Killed pathogen. Cannot cause active infection; often requires boosters and higher doses.'),('Subunit / toxoid','Selected antigen components or inactivated toxin. Safer, focused antigen exposure; adjuvants/boosters may be needed.'),('Nucleic-acid / vector','Genetic instructions or viral vector cause host cells to produce antigen, stimulating adaptive responses.')] for i,(a,b) in enumerate(items): card(s,a,b,.75+(i%2)*6.1,1.5+(i//2)*2.05,5.55,1.5,[TEAL,BLUE,GOLD,RED][i],15) #26 s=standard('Why boosters and schedules matter','Population protection depends on individual responses and timely public-health guidance',26) bullets(s,['Immune responses vary by vaccine platform, age, immune status and prior exposure.','Boosters can restore or broaden protection when antibody levels or immune protection decline.','National schedules are updated as evidence, disease burden and products change. Use current public-health guidance for decisions.','High vaccine uptake reduces opportunities for transmission and helps protect people unable to be vaccinated.'],.85,1.55,11.55,4.6,19) #27 s=standard('Clinical connections and safety checkpoints','Adaptive immunity is protective, but dysregulation can cause disease',27) for i,(a,b,c) in enumerate([('Autoimmunity','Failed central or peripheral tolerance allows harmful responses to self.',RED),('Allergy','IgE-mediated activation of mast cells and basophils drives immediate hypersensitivity.',GOLD),('Immunodeficiency','Defects in B cells, T cells or their signaling can cause recurrent or unusual infections.',BLUE),('Superantigen disease','Nonspecific, widespread T-cell stimulation can cause cytokine-mediated shock.',TEAL)]): card(s,a,b,.75+(i%2)*6.1,1.55+(i//2)*1.95,5.55,1.35,c,15) #28 s=standard('High-yield integration map','Trace one pathogen through the adaptive response',28) steps=[('Pathogen enters','Innate cells capture antigen'),('APC presents','MHC II activates CD4 helper cell'),('T-cell help','Cytokines coordinate B cells and cytotoxic responses'),('B cells respond','Antibody neutralizes, opsonizes and activates complement'),('CD8 response','MHC I-guided killing of infected cells'),('Memory remains','Rapid protection at the next encounter')] for i,(a,b) in enumerate(steps): x=.55+(i%3)*4.25;y=1.4+(i//3)*2.25; rect(s,x,y,3.75,1.35,[TEAL,BLUE,GOLD,RED,BLUE,TEAL][i],True); text(s,a,x+.2,y+.16,3.35,.28,16,WHITE,True,PP_ALIGN.CENTER); text(s,b,x+.2,y+.6,3.35,.35,12,WHITE,False,PP_ALIGN.CENTER) #29 s=standard('Exam-style self-check','Use these prompts to verify that the mechanisms connect',29) bullets(s,['Why is a secondary response faster and larger than a primary response?','How do MHC I and MHC II determine which T-cell class responds?','Compare IgM, IgG, IgA and IgE by location and major function.','What extra steps make a T-dependent B-cell response more durable than a T-independent one?','What happens if a T cell recognizes antigen without costimulation?','Differentiate active from passive immunity, and natural from artificial acquisition.'],.88,1.43,11.25,4.9,18) #30 s=standard('Take-home messages','A concise synthesis of adaptive specific host defense',30) for i,t in enumerate(['Adaptive immunity is antigen-specific and develops memory.','B cells and antibodies provide humoral protection; T cells coordinate and kill infected cells.','MHC I presents intracellular peptides to CD8 cells; MHC II presents extracellular peptides to CD4 cells.','Effective lymphocyte activation requires antigen recognition plus context, including costimulation and cytokines.','Vaccines safely establish immunologic memory, enabling a rapid response later.']): rect(s,.82,1.36+i*.93,.42,.42,[TEAL,BLUE,GOLD,RED,TEAL][i],True); text(s,str(i+1),.82,1.45+i*.93,.42,.17,12,WHITE,True,PP_ALIGN.CENTER); text(s,t,1.48,1.32+i*.93,10.8,.5,18,NAVY,True) #31 references s=standard('Sources and scope','Primary teaching source and update note',31) text(s,'Primary source',.85,1.55,2.6,.35,20,TEAL,True); text(s,'OpenStax Microbiology, Chapter 18: Adaptive Specific Host Defenses (user-supplied PDF). Content, terminology, diagrams and learning sequence in this deck follow the chapter.',.85,2.0,11.2,.75,17,DARK) text(s,'Supplementary textbook check',.85,3.15,3.2,.35,20,BLUE,True); text(s,'Cellular and Molecular Immunology: adaptive immune responses are mediated by B and T lymphocytes; defining properties include specificity, diversity and memory.',.85,3.6,11.2,.65,17,DARK) text(s,'Scope note',.85,4.85,2.3,.35,20,GOLD,True); text(s,'This is an educational presentation, not individualized medical advice. Vaccine decisions and schedules should use current guidance from local public-health authorities.',.85,5.3,11.2,.55,17,DARK) # set core properties prs.core_properties.title='Adaptive Specific Host Defenses' prs.core_properties.subject='Detailed educational presentation based on supplied Chapter 18' prs.core_properties.author='Orris' prs.save(OUT) print(OUT, len(prs.slides)) PY python "/tmp/workspace/adaptive-host-defenses/src/create_deck.py"

python - <<'PY' from pptx import Presentation p='/tmp/workspace/adaptive-host-defenses/output/Adaptive_Specific_Host_Defenses.pptx' prs=Presentation(p) print('slides:',len(prs.slides)) for i,s in enumerate(prs.slides,1): texts=[] for sh in s.shapes: if getattr(sh,'has_text_frame',False) and sh.text.strip(): texts.append(sh.text.replace('\n',' | ')) print(i, ' :: '.join(texts[:3])) PY ls -lh "/tmp/workspace/adaptive-host-defenses/output/Adaptive_Specific_Host_Defenses.pptx"