Basics of biology lectures at verhaert - part 3 - immunology and metabolomics

15.09.2015
Ref: VPS-0036-DOC-A
CONFIDENTIAL
CONFIDENTIAL
Basics of biology – Verhaert lunch lectures
Jef Aernouts

15.09.2015
Ref: VPS-0036-DOC-A
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Chapters
• Building blocks of life
• Genomics
• Proteomics
• Immunology
• Metabolomics

15.09.2015
Ref: VPS-0036-DOC-A
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Part 1: building blocks
of life

CONFIDENTIAL
Biomolecules
Backbone slide
Life
Living organisms
forming
viruses bacteria fungi plants animals
Made up of cell(s):
Prokaryotic Eukaryotic
classes

Single vs. multicellular organisms
Unicellular Multicellular
• Organisms composed of only
1 cell
• Examples:
Bacteria (prokaryotic)
Yeast (fungi, eukaryotic)
Protosoa (eukaryotic), e.g.
plasmodium causing
malaria
• Organisms consisting of many
cells (always eukaryotic)
• Examples:
Plants (autotroph)
Animals (heterotroph)
Fungi (heterotroph)
e.g. mushrooms

Virus - definitions
Parasitism: viruses are dependent on specific host cells; they cannot reproduce on their own but have
to reside in a specific host.
A virus consists of:
• Nucleic acids (DNA or RNA)
• Covered by a protein coat
• Sometimes enclosed by a membrane (= enveloped)
Various hosts:
• Bacteriophages (host = bacterium)
• Animal virus (host = animal), e.g. influenza virus (flu)
• Plant virus (host = plant), e.g. tobacco mosaic virus
Size: 20 - 300 nm
Source: http://www.biology-online.org/dictionary

Virus replication
Example of influenza infection:
Result: viruses take over the
normal cell metabolism
 infected

15.09.2015
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Backbone slide
Immunity: definitions & role
Innate immunity
(=natural, =native)
• First line of defense
• Basic/generic resistance
Adaptive immunity
(=specific, = acquired)
• Induced by invaders
time
Humoral Cell-mediated
extracellular intracellular
interplay

Immunity – intro video
Video: https://youtu.be/8EEJsu3NjQU

Immunity - definitions
Immunity: resistance to infectious disease
Immune (defense) system: collection of cells, tissues and molecules that mediate resistance
Immune response: coordinated reaction to microbes
Pathogen (microbe): infectious agent that can cause disease
• Viruses (e.g. HIV causing AIDS)
• Bacteria (e.g. Anthrax causing)
• Fungi (e.g. Ringworm skin infection)
• Protosoa (e.g. Plasmodium causing Malaria)

Immunity – involved cells
Cell differentiation from stem cells:
White blood cells (leukocytes): cells of the immune system that are involved in protecting the body
against both infectious disease and foreign invaders

15.09.2015
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Immunity - overview
• Also called natural or native
• Always present in healthy individuals
(present before infection)
• Immediate response (first line of defense)
• Basic resistance to disease
• Also called specific or acquired
• Stimulated/induced by microbes
• Lag time between exposure and maximal
response
• Exposure results in immunologic memory
(base for vaccines)
Innate immunity Adaptive immunityinterplay

15.09.2015
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Innate immunity
1. Physical components
• Anatomic/physical:
• Skin (barrier)
• Mucous membranes
• Tears (washing effect)
• Physiological:
• Temperature
e.g. chicken (41 °C) are resistant to anthrax (37-39 °C)
• pH
• Variety of chemicals
2. Phagocytosis: ‘eating invaders’
Ingestion and digestion of foreign cells/molecules through
phagocytosis
• Macrophages
• Neutrophils
• Natural Killer (NK) cells
• Complement system

15.09.2015
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Innate immunity – video phagocytosis
Video: https://youtu.be/r4-g6tVyUAU

Adaptive immunity: intro video
Video: https://youtu.be/Bf2t8n1ibwQ

Adaptive immunity
Although innate immunity can effectively combat infections
 many microbes have evolved to resist innate immunity
 adaptive immunity
Adaptive immune system consists of
lymphocytes (class of white blood
cells) and their products (e.g.
antibodies):
• B lymphocytes
• T lymphocytes

15.09.2015
Ref: VPS-0036-DOC-A
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Adaptive immunity: humoral vs. cell-mediated
 Extracellular microbes
(e.g. bacterium in blood)
 Invaders have antigens on its outer surface
(antibody generators): they are recognized
as foreign by B-cells that attach to it
 B-cells differentiate to plasma cells that
produce antibodies
 Antibodies bind temporarily to the pathogen:
 Temporarily inactivate
 Mark for digestion by phagocytes
 Also, some B cells differentiate to memory
cells: respond to secondary encounter
 Intracellular microbes
(e.g. a virus in a host cell)
 Defense mediated by T-cells
(T-Lymphocytes)
 T-cells recognizes antigens
 T-cells transform to antigen-specific cells,
and differentiate into effector cells
 Effector cells act against target cell
 Directly by killing infected cells
(phagocytic)
 Indirectly by releasing chemicals
(cytotoxic)
Humoral immunity Cell-mediated immunity

15.09.2015
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Adaptive immunity: humoral vs. cell-mediated
Also cross-talk between 2 pathways:

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Immunity: active vs. passive & natural vs. artificial
Video: https://youtu.be/njNdANeRK3A

15.09.2015
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Immunity: active vs. passive & natural vs. artificial

15.09.2015
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Example: immuno-assay

05.03.2014
Slide 26
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Immunometry
• Definition:
The measurement of amounts of substances by the use of specific antigen‐antibody reactions.

05.03.2014
Slide 27
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Immunometry
• Definition:
Substances are biomarkers
• Proteins that are present in the blood, urine … The
amount is an indicator of a disease, risk …
• e.g. the use of PSA (prostate specific antigen)
in the screening of prostate cancer
• Also possible to measure markers that reflect the
concentration of active drugs in the blood circulation,
i.e. therapeutic drug monitoring (TDM)
• e.g. monitoring Everolimus, drug to prevent
rejection of organ transplants

05.03.2014
Slide 28
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Immunometry
• Definition:
Basics of immunity:
1. A foreign object enters the bloodstream. The outer surface contains proteins that are not
recognized by the host. These little portions of proteins are called antigens (coming from
ANTIbody GENerator)
2. The white blood cells recognize the antigens as foreign, and specific white blood cells
initialize the production of antibodies (which typically takes a couple of days). For each
antigen, a specific antibody!
3. The produced antibodies are able to bind very specifically to
the antigen. This results in a coating of the foreign object
with antibody(ies). This will initiate the destruction of the object.
4. After infection is eradicated, the specific white blood cells will
hide in the bone marrow and will go in a standby modus.
Immunity is build up in this way.
antigen B
antigen A
antibody B
antibody A

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Slide 29
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Immunometry – making assays
1. Extracting the protein of interest
Collect human blood samples Extract and purify protein
of interest (e.g. PSA)
PSA
PSA
PSA
PSA
PSA
PSA: biomarker for
prostate cancer

05.03.2014
Slide 30
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2. Generate mouse antibodies
Insert the human proteins of
interest (e.g. PSA) in a
mouse. Since these proteins
are foreign, mouse white blood
cells initiate the formation of
mouse antibodies.
The specific white blood
cells are extracted, and
used as fabrics for the
formation of mouse
antibodies for human PSA.
PSAPSA
PSA
PSA
WBC for
antibody A
WBC for
antibody B
human
antigen A
mouse
antibody B
white blood cell
mouse
antibody A
human
antigen BPSA

05.03.2014
Slide 31
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3. Typical lab assay that is a measure of the specific human protein (e.g. PSA)
Strip with mouse “capture”
antibodies A for human PSA
Blood sample with protein
of interest (e.g. PSA)
PS
A
PS
A
PS
A
PS
A
PS
A
PS
A
PS
A
+
Mix with “label” anti-
bodies B with a color
particle attached
After washing the strip:
the more the strip is filled,
the more color is produced

05.03.2014
Slide 32
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3. Typical lab assay that is a measure of the specific human protein
This principle is also used in a pregnancy test (detection of HCG):

15.09.2015
Ref: VPS-0036-DOC-A
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Part 3: metabolism

15.09.2015
Ref: VPS-0036-DOC-A
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Metabolism
Video: https://youtu.be/yiuPCSYBdJk

15.09.2015
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Definitions
Metabolism: the sum of all chemical interactions inside a cell
• Catabolic: degrade into smaller compounds
 release of energy
e.g. proteins (food, muscles) to amino-acids
• Anabolic: linking smaller compounds to a bigger molecule (synthesis)
 requires energy
e.g. protein synthesis
Metabolomics: study of metabolism (includes techniques…)
Cf.: genetics vs. genomics
Catabolic Anabolic
Anabolic steroids:
excessive muscle
buildup
Starvation

15.09.2015
Ref: VPS-0036-DOC-A
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Metabolic pathways
To study in life sciences … 

15.09.2015
Ref: VPS-0036-DOC-A
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