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Evolution and Development - Biology UvA
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Summary of the lectures given during the course Evolution and Development of the Bachelor Biology at the University of Amsterdam.
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Regulation of Gene ExpressionHow to recognize/detect an mRNA with a specific sequence?
Rna-gel blot
Rt-pcr
In situ hybridisation
Rna sequencing
RT-pcr: isolate mrna, convert to cdna, amplify by pcr, run products on a gel
RNA-seq: isolate mrna, convert to cdna, sequence individual cdna
Possibilities to regulate the expression of a gene
Gene expression can be regulated at multiple levels
regulation of transcription initiation
transacting TFs specifically bind to sis-regulatory gene elements
o Sis regulatory elements often cluster in regions called enhancers
o enhancers come be very far away from the transcribed region
many TFs are part of families
Methods
Measuring RNA levels is most versatile and commonly used
o Few genes -> RNA gel blot, RT PCR, Q PCR, in situ hybridization
o Many genes -> microarray, RNA-seq
protein DNA interactions
o EMSA, footprinting, chromatin IP (ChiP-seq)
Promoter-reporter genes
o trans genes that mimic expression of endogenous genes
Gene regulatory networks (GRNs)
transcription of TF's genes is activated/repressed by TF’s
All genes operate within complex regulatory networks
combinatorial control
o multiple TF's needed
, o one TF may have multiple roles
Hierarchical relations
o example -> MyoD, Eyeless
mutant phenotypes reveals roles of a gene in development
Lose it -> gene necessary for process X?
Move it -> gene sufficient for process X?
Mechanisms that create cell memory
DNA methylation
chromatin -> metalation
histone modification
recruitment of de novo DNA methylase
where a C is placed next to a G methylation is possible -> CpG
Half methylation -> methylase recognizes it
no metalation -> methylase doesn't recognize it
auto regulation of TRX factors genes -> widely
used
positive feedback loops -> stable gene
expression
negative feedback loops -> oscillators
DNA rearrangements -> specific cases
Antibodies: immunoglobin's (Ig), excreted or
membrane bound. Two heavy chains and two
light chains.
how can you recognize so many different
antigens?
multiple combinations are possible by distinct IG domains on the DNA. This comes
for the heavy chain but with the light chain there's VJ joining.
The intervening DNA has TIRs (Terminal inverted repeat)
RAG1 and RAG2 resemble transposases
Enzymes with similar structures and sequence
RAG1 and RAG2 genes are linked
cloning IPS cells
stem cell: not fully differentiated and self-renewing
zygote: fully totipotent
, ES cells
isolated from inner cell mass
undifferentiated
pluripotent
adult stem cells
limited capacity, not toti- or pluripotent
they live in stem cell niches (bone marrow)
o there are cells around them that stimulate them to act as stem cells
organoids:
organ like structures
they are made in vitro from adult stem cells
they are living representation of the organ they originated from
Between in vivo and in vitro
clinical relevance
Embryogenesis
Gastrulation: massive cell movement to the inside
zygote -> blastula -> gastrula
ectoderm:
epidermal cells of skin
the nervous system
pigment cell
endoderm:
digestive tube
pharynx
respiratory tube
mesoderm:
noto chord
bone tissue
kidney
blood cells
facial muscle
germ cells
sperm
egg
neurulation: invagination in embryos where the neural plate closes itself to form the neural
tube, the embryo is now called the neurula
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