MBS1001 BIOMEDICAL
CHALLENGES
September-October 2019
MASTER BIOMEDICAL SCIENCES
MBS1001
Cases, journal clubs, lectures (for exam) and relevant practicals and workshops
,CONTENTS
Mitochondrial theme
Lecture 1 Introduction The scientific method ......................................................................................................... 2
Lecture 2 Mitochondria: challenges in understanding cellular energy production ................................................ 3
Practical 1 & 2computer: COX20 variant ................................................................................................................ 7
Case ..................................................................................................................................................................... 7
Preparations ........................................................................................................................................................ 8
practicals ........................................................................................................................................................... 13
Journal club 1: Legati et al ..................................................................................................................................... 23
Deepening Lecture: Connecting mitochiondrial disease, stem cell therapy and cell fate (not for exam) ............ 31
Lecture 3 Mitochondrial Genetics ......................................................................................................................... 37
Lecture 4 Molecular cloning, a tool for functional analysis of genetic variants .................................................... 43
Case 1 Ellen’s problems (mitochondrial disease) .................................................................................................. 49
Lecture 4 mitochondrial and neuromuscular disease, mechanisms diagnostics and prevention ........................ 62
Journal club 2: Mutation in FAM36 gene .............................................................................................................. 70
Case 2 the blind photographer ............................................................................................................................. 78
Neurological theme
Journal club 3 Suwanjang et al (stress in a dish) ................................................................................................... 87
Case 3 PTSD ........................................................................................................................................................... 93
Lecture 5 neurological theme: PTSD ..................................................................................................................... 99
Journal club 4 Khan-Kirby et al ............................................................................................................................ 111
Case 4 Comparison between epilepsy and schizophrenia .................................................................................. 120
Lecture 6 Epilepsy ............................................................................................................................................... 132
metabolic theme
Journal club 5 Regional differences in cellular mechanisms of adipose tissue gain with overfeeding ............... 128
Case 5 too fat or not too fat ................................................................................................................................ 140
Journal club 6 Pellegrinelli V et al ....................................................................................................................... 147
Lecture 7 link between obesity, BMI and health ................................................................................................ 156
Case 6 foie gras (non-alcoholic fatty lover disease & obesitas) .......................................................................... 162
Lecture 8 type 2 diabetes (T2D) and NAFLD ....................................................................................................... 169
Workshops included:
Workshop Study design causality; (lecture theoretic part) ................................................................................ 177
Statistics workshop (lecture and practical) ......................................................................................................... 178
,INTRODUCTION THE SCIENTIFIC METHOD
SCIENTIFIC METHOD AND SCIENTIFIC THINKING
What is science: method of investigating nature and wants to discover reliable knowledge about nature.
what is reliable knowledge:
1. Empiric: using empirical evidence, evidence that we can feel without senses, is measurable, repeatable and
independent from the observer.
2. Rationalism: using reasoning and logic, not emotional hopeful or wishful thinking.
3. Skepticism: constant questioning of your beliefs and conclusion, good scientists constantly examine the
evidence, arguments and reasons for their believe, science treats new ideas skeptically.
THE SCIENTIFIC METHOD:
1. Observe something and ask a question why does that happen. A problem of question
must be identified, and it needs to be broken down to one question at a
time. (you can’t test everything at once).
2 break down to find hypothesis: possible explanation to the question or
problem. A prediction that can be tested. A theory is already being tested and
believed to be true based on many experiments and a hypothesis is an
educated guess (could be because of that).
3 design controlled experiment: comparison between control and
experimental group. Groups are identical except for one factor, both
groups should be treated the same variable can change in the group, and
the experimental group shows the effect of the variable that is being tested.
Variables:
1. Independent: can be changed by the scientist. Good experiment has only one.
2. Dependent variable: observed in the experiment, can be more than one,
descriptions/characteristics that cannot be counted
Data: qualitative: cannot be counted (color/ shape of liver e.g.), more characteristics like
quantitative data: can be counted (e.g. liver function values (ALT))
4 record and analyze results: no documentation means no results, data analysis → statistics. Proper data
management (reproduction, one test is not enough).
5 draw conclusions → modify hypothesis. The experiment is done to determine if hypothesis is proven /
disproven. Experiments must be repeated, minimal statistic power → no real conclusion can be made.
Scientific attitude: curiosity: passion for exploration and skepticism: doubting and questioning competing ideas
and open minded.
, LECTURE 2 MITOCHONDRIA: CHALLENGES IN UNDERSTANDING CELLULAR ENERGY
PRODUCTION
RECAP, WHAT ARE MITOCHONDRIA?
Mitochondria are the powerhouses of a cell, they produce 90% of energy
for an eukaryotic cell.
During the process of glycolysis (which happens outside the mitochondria),
one sugar molecule is able to yield 4 ATP molecules. The product of
glycolysis can be used, in the mitochondria, to make 32 ATP molecules!
Total yield is 36 ATP molecules from one glucose molecule.
HOW DOES THE ORGANELLE LOOK LIKE:
-Outer membrane / outer shell, this membrane is porous/ has a lot of
holes through which molecules can cross, (not a crucial membrane for
energy production).
- Intermembrane space: between the inner and outer membrane
- Cristae: Inside the mitochondria there is a folded inner-membrane: this is where everything happens
regarding energy production. Energy producing complexes to produce energy, in the form of ATP are present
here. The folds in this membrane create a large surface area. This membrane does not have pores, is tight, so
hardly any molecules can cross without a channel or special mechanism. Even proton cannot cross it. Not a lot
of diffusion happens here.
- Matrix: inside of the mitochondria. Mitochondrial DNA is present inside the mitochondria. It has its own DNA
((alphaproteo) bacteria ended up in human cells→ own DNA). In this mtDNA, 16 thousand nucleotides are
present, compared to 4 billion nucleotides in the nucleus. mtDNA is inherited almost exclusively from mothers.
This tiny amount DNA contains very important genes, which translated into the proteins that mostly reside on
the inner membrane for energy production.
The mitochondria make us eukaryotes (prokaryotes don’t have them), mitochondria originate from the fusion
of bacteria and archaea. This led to the development of eukaryotes. Most eukaryotes are fungi and
multicellular animals.
IN THE MITOCHONDRIA A LOT HAPPENS: S YSTEMS OF THE MITOCHONDRIA INCLUDE:
• Calcium buffering/ homeostasis: restore healthy ca2+ levels in the cells.
• Mitochondria are involved in apoptosis
• The most important function has nothing to do with energy production: Iron Sulphur
(FE-S) clustering: FE-S clusters are small clusters that are inserted into many types of
proteins (including ribosomes), and these are all produced in mitochondria.
-Why is it considered that important?: Some eukaryotes (parasites) don’t have the
oxidative phosphorylation system or ribosomes or even DNA, these functions were
lost in evolution. The only function it retained is FE-S clustering. This is the only not
replaceable function of mitochondria.
• Electron transport chain: oxidative phosphorylation, this ‘chain’ contains 5 protein complexes.
• Mitochondria have their own ribosomes which produce proteins from RNA. It produces proteins from
the mtDNA for the electron transport chain, these proteins are inserted into the inner membrane to
produce energy. The genes on mtDNA all have a bacterial origin. The mitochondrial ribosome contains
a lot of proteins (it is very large) and that while it only encodes a tiny amount of genes from the
mtDNA (+- 12 mitochondrial genes).
CHALLENGES
September-October 2019
MASTER BIOMEDICAL SCIENCES
MBS1001
Cases, journal clubs, lectures (for exam) and relevant practicals and workshops
,CONTENTS
Mitochondrial theme
Lecture 1 Introduction The scientific method ......................................................................................................... 2
Lecture 2 Mitochondria: challenges in understanding cellular energy production ................................................ 3
Practical 1 & 2computer: COX20 variant ................................................................................................................ 7
Case ..................................................................................................................................................................... 7
Preparations ........................................................................................................................................................ 8
practicals ........................................................................................................................................................... 13
Journal club 1: Legati et al ..................................................................................................................................... 23
Deepening Lecture: Connecting mitochiondrial disease, stem cell therapy and cell fate (not for exam) ............ 31
Lecture 3 Mitochondrial Genetics ......................................................................................................................... 37
Lecture 4 Molecular cloning, a tool for functional analysis of genetic variants .................................................... 43
Case 1 Ellen’s problems (mitochondrial disease) .................................................................................................. 49
Lecture 4 mitochondrial and neuromuscular disease, mechanisms diagnostics and prevention ........................ 62
Journal club 2: Mutation in FAM36 gene .............................................................................................................. 70
Case 2 the blind photographer ............................................................................................................................. 78
Neurological theme
Journal club 3 Suwanjang et al (stress in a dish) ................................................................................................... 87
Case 3 PTSD ........................................................................................................................................................... 93
Lecture 5 neurological theme: PTSD ..................................................................................................................... 99
Journal club 4 Khan-Kirby et al ............................................................................................................................ 111
Case 4 Comparison between epilepsy and schizophrenia .................................................................................. 120
Lecture 6 Epilepsy ............................................................................................................................................... 132
metabolic theme
Journal club 5 Regional differences in cellular mechanisms of adipose tissue gain with overfeeding ............... 128
Case 5 too fat or not too fat ................................................................................................................................ 140
Journal club 6 Pellegrinelli V et al ....................................................................................................................... 147
Lecture 7 link between obesity, BMI and health ................................................................................................ 156
Case 6 foie gras (non-alcoholic fatty lover disease & obesitas) .......................................................................... 162
Lecture 8 type 2 diabetes (T2D) and NAFLD ....................................................................................................... 169
Workshops included:
Workshop Study design causality; (lecture theoretic part) ................................................................................ 177
Statistics workshop (lecture and practical) ......................................................................................................... 178
,INTRODUCTION THE SCIENTIFIC METHOD
SCIENTIFIC METHOD AND SCIENTIFIC THINKING
What is science: method of investigating nature and wants to discover reliable knowledge about nature.
what is reliable knowledge:
1. Empiric: using empirical evidence, evidence that we can feel without senses, is measurable, repeatable and
independent from the observer.
2. Rationalism: using reasoning and logic, not emotional hopeful or wishful thinking.
3. Skepticism: constant questioning of your beliefs and conclusion, good scientists constantly examine the
evidence, arguments and reasons for their believe, science treats new ideas skeptically.
THE SCIENTIFIC METHOD:
1. Observe something and ask a question why does that happen. A problem of question
must be identified, and it needs to be broken down to one question at a
time. (you can’t test everything at once).
2 break down to find hypothesis: possible explanation to the question or
problem. A prediction that can be tested. A theory is already being tested and
believed to be true based on many experiments and a hypothesis is an
educated guess (could be because of that).
3 design controlled experiment: comparison between control and
experimental group. Groups are identical except for one factor, both
groups should be treated the same variable can change in the group, and
the experimental group shows the effect of the variable that is being tested.
Variables:
1. Independent: can be changed by the scientist. Good experiment has only one.
2. Dependent variable: observed in the experiment, can be more than one,
descriptions/characteristics that cannot be counted
Data: qualitative: cannot be counted (color/ shape of liver e.g.), more characteristics like
quantitative data: can be counted (e.g. liver function values (ALT))
4 record and analyze results: no documentation means no results, data analysis → statistics. Proper data
management (reproduction, one test is not enough).
5 draw conclusions → modify hypothesis. The experiment is done to determine if hypothesis is proven /
disproven. Experiments must be repeated, minimal statistic power → no real conclusion can be made.
Scientific attitude: curiosity: passion for exploration and skepticism: doubting and questioning competing ideas
and open minded.
, LECTURE 2 MITOCHONDRIA: CHALLENGES IN UNDERSTANDING CELLULAR ENERGY
PRODUCTION
RECAP, WHAT ARE MITOCHONDRIA?
Mitochondria are the powerhouses of a cell, they produce 90% of energy
for an eukaryotic cell.
During the process of glycolysis (which happens outside the mitochondria),
one sugar molecule is able to yield 4 ATP molecules. The product of
glycolysis can be used, in the mitochondria, to make 32 ATP molecules!
Total yield is 36 ATP molecules from one glucose molecule.
HOW DOES THE ORGANELLE LOOK LIKE:
-Outer membrane / outer shell, this membrane is porous/ has a lot of
holes through which molecules can cross, (not a crucial membrane for
energy production).
- Intermembrane space: between the inner and outer membrane
- Cristae: Inside the mitochondria there is a folded inner-membrane: this is where everything happens
regarding energy production. Energy producing complexes to produce energy, in the form of ATP are present
here. The folds in this membrane create a large surface area. This membrane does not have pores, is tight, so
hardly any molecules can cross without a channel or special mechanism. Even proton cannot cross it. Not a lot
of diffusion happens here.
- Matrix: inside of the mitochondria. Mitochondrial DNA is present inside the mitochondria. It has its own DNA
((alphaproteo) bacteria ended up in human cells→ own DNA). In this mtDNA, 16 thousand nucleotides are
present, compared to 4 billion nucleotides in the nucleus. mtDNA is inherited almost exclusively from mothers.
This tiny amount DNA contains very important genes, which translated into the proteins that mostly reside on
the inner membrane for energy production.
The mitochondria make us eukaryotes (prokaryotes don’t have them), mitochondria originate from the fusion
of bacteria and archaea. This led to the development of eukaryotes. Most eukaryotes are fungi and
multicellular animals.
IN THE MITOCHONDRIA A LOT HAPPENS: S YSTEMS OF THE MITOCHONDRIA INCLUDE:
• Calcium buffering/ homeostasis: restore healthy ca2+ levels in the cells.
• Mitochondria are involved in apoptosis
• The most important function has nothing to do with energy production: Iron Sulphur
(FE-S) clustering: FE-S clusters are small clusters that are inserted into many types of
proteins (including ribosomes), and these are all produced in mitochondria.
-Why is it considered that important?: Some eukaryotes (parasites) don’t have the
oxidative phosphorylation system or ribosomes or even DNA, these functions were
lost in evolution. The only function it retained is FE-S clustering. This is the only not
replaceable function of mitochondria.
• Electron transport chain: oxidative phosphorylation, this ‘chain’ contains 5 protein complexes.
• Mitochondria have their own ribosomes which produce proteins from RNA. It produces proteins from
the mtDNA for the electron transport chain, these proteins are inserted into the inner membrane to
produce energy. The genes on mtDNA all have a bacterial origin. The mitochondrial ribosome contains
a lot of proteins (it is very large) and that while it only encodes a tiny amount of genes from the
mtDNA (+- 12 mitochondrial genes).
