TOPIC E: DEVELOPMENT Flashcards
what are descriptive studies based on?
- Expression profiles of mRNA
- Non coding RNAs and proteins
- Temporal (when) and spatial (where)
- fate mapping of cells (lineage tracing)
- comparative studies of organisms
What are manipulative studies and 3 examples?
ALTERING SYSTEM AND OBSERVING EFFECTS
- Gene knockout or transgenic overexpression
- Adding drug or tetragon and observing effects
- Translating cells from ONE area to ANOTHER (cell commitment and specification)
What kind of microscopy is a light microscoope used for?
- Brightfiled microscopy
What kind of microscopy is a confocal microscope used for?
- Fluorescence microscopy
What kind of microscopy is an electron microscope used for?
- TEM (Transmission electron microscopy–> can “see” inside cell)
Does temporal gene expression analysis in tissue examine WHEN a gene is expressed?
- YES “when”= time
What does DNA analyis include?
- PCR (promoter and enhancer studies–> plasmids)
- gene cloning (epigenetics–> methylation of DNA, histone modification)
- Southern blotting– >gene knockout or overexpression
What does RNA analysis include?
- gene expression analysis
- RT-PCR
- RNA -seq
- Knockdown of mRNAs using RNA intereference (RNAi)
What does protein analysis include?
- Western blotting and immunostaining of tissues
- Protein structure –> function, phosphorlyation, sumoylation (to do with ubiquitin) , acetylation, glyocsylation
- Protein-protein interactions by co-immunoprecipiation
WHat does bioinformatics include?
- using computer software to understand biologcial data
e. g. constructing whole genomes, comparing data genes or sets
What is real time PCR?
- Quanititative Reverse Transcription -PCR (q RT-PCR)
- converts RNA—> cDNA (via reverse trancription)
- Fluorescent ATCG labells added to mix
What do a lower number of PCR cycling to reach detection indicate?
- More starting RNA
What do a higher number of cycles of PCR cycling to reach detection indciate?
- Less cDNA present therefore less RNA
What does in situ hybridisation look at and what colour stain?
- Study of prenatal development
- temporal and spatial expression of mRNAs in MODEL embryos (fly, fish, chicken, mouse)
- Purple stain for cells with the RNA of interest
What is imunofluorescence to do with?
WHEN and WHERE a protein is epxressed in a tissue (antibodies against protein of interest)
What does Western Blotting show in terms of the proteins?
- The SIZE of the protein and the relative amount present in a tissue
Does the primary antibody for Western blotting or Immunofluorescne have to be made in the same animal or separate animals?
- Separate animals for different cell strucutres
Does a second degree antibody have to be made in separate animals to target different primary antibodies?
- NO
- Can be made in SAME animal
What does a transgenic mice model involve?
- Carrying foreign gene and we observe the phenotype
What are the 2 methods for creating trasngenic mice?
- Pronuclear injection
2. Transforming ES cells (embryonic stem cells)
What does modern developmental bio involve?
- Embryology
- Cytology (cells ) + Histology (tissues)
- genetics
- understands the genetic and cell mechanisms that allow 1 cell–> multicomplex cell
What issues does Dev bio help with?
- Cancers, cell therapy for human disease (stem cells) , developmental disorders `
What is pattern formation?
- Once cell–> many cells–> organised cells–> tissues–> organs
Which two processes does pattern formation require?
- Differential gene expression
2. Signalling between cells
Which 5 things does pattern formation arise from?
- Cell proliferation
- Cell migration
- Changes in cell shape and SIZE
- Cell differentiation
- Cell interaction
- Apoptosis (cell death–> not shown on diagram)
What are epithelial cells characterised by?
- TIGHTLY connected to each other
- don’t move alone (move as a sheet–> mass movement)
- Polarised, cell-cell junctions, cilia,
- Sits on basement membrane
- (Cytokeratin marker gene)
What is the marker gene for epithelial cells?
- Cytokeratin
What are mesenchmyal cells characrterised by?
- Not connected to other cells
- More in ECM
- Not polarised
- No cilia
- (Vimetin marker gene)
What is the marker gene for mesenchymal cells?
- Vimetin
What plays a major role in cancer matastasis and development?
- EMT–> epithelial to mesenchymal transition
What does polarised mean in terms of epithelial and mesenchymal?
- Strucutres (e.g. nucleus) are on one side of cel and not other
- (nucleus on basement membrane side)
What is cell fate defined as?
- Given destination of cell if left undisturbed in embryo
What are two types of cell COMMITMENT?
- Speciifcation
2. Determination `
What occurs in the cell COMMITMENT of specification?
- Cell can autonomously differentiate BUT it can still be REVERSED
e. g. IF forming neuron but then put in different place, can change into different cell type
What occurs in the cell COMMITMENT process of determination?
- Cell differentiates autonomoously if placed in a dish BUT when placed into another tissue CANNOT BE REVERSED
What does cell FATE compose of?
- CELL COMMITMENT (Specification and determination )
- DIFFERENTIATION (Developmental fate –> final phenotypes e.g. neuron developing dendritic processes)
What is an examples of formation of beta islet cells?
- blastomere–> endoderm cell (SPECIFIED)–> pancreatic bud cell –> endocrine pacnreas cell (DETERMINED) –> Beta islet cell
What is cell fate restriction governed by? (3 things)
- Cells genome (gene expression )
- Cells history (factors it has been exposed to–> where it has been moved from)
- Interaction with neighbours
What is an example of a specified cell ?
- Haemotopoetic stem cell
What is an example of a determined cell? (bloodline)
- Common myeloid progenitor
What is an example of a differentiated cell type?
- Myeboblasts (baso neutro eoso)
What is a fate map?
- Diagram that maps adult tissues or structures to regions of embryo that give rise to structure
e. .g lineage tracing (label group of cells and see where they go)
Is embryonic development conserved in animals and if so, what makes it good for?
- YES! Which makes them good model organisms to study development (model human development)
What are advantages of flies and c.elegan worms for model organisms?
Rapid life cycle
- Key genes are known
- fate of cells known
What are disadvantages of using flies and c.elegan worms for model organisms?
- Aspects of anatomy and development NOT conserved in humans
What are the advantages of using zebra fish and the clawed frog (lower vertebrates) as model organisms?
- Vertebrates develop OUTSIDE the maternal body
- Can perform fate mapping in them
- Easy to keep clean and manipulate
What are the diasvantatges of using lower vertebrates (zebra fish and clawed frog) ?
- Don’t share some features of humans such as mammary glands (so can’t use for breast cancer)
What are avain embryos used to study?
- Embryogenesis–> gastrulation, neural crest cells –> GFP positive labelled neural tube put into quail embryo –> cell fate then follwed
What are the advantages of using avian embryos?
- Easy to obtain (from egg) and manipulate
What are the diadvantages of using avian embryos?
- Longer life cycle (4 months)
- Transgenic strategies worse than mouse (over/under expression)
What are the advantages of the mouse (mammalian model)?
- Same organs as humans and also diseases like obesity
- Easy to maintain colonies (good transgenics)
- Transgenic and knockout mice for human disease
What are the disasdvantages of using mammalian model organisms?
- Embryos develop in utero (so harder to access)
- Expensive –> null mutant generation
- Models can show DIFFERENT PHENOTYPES to human disease
Which two factors is development driven by?
- Differential gene expression
2. Interaction b/w TFs and signalling molecules b/w cells
Does each embryo cell retain its own ‘history memory’?
- YES!
What is each gene controlled by?
- Promoters (initate gene expression)
- enhancers (bind activating factors)
- inhibitory (bind inhibitory factors)
What are TFs?
- DNA binding proteins –> regulate a array of target genes
- direct development ‘tell’ other genes what to do
What do transactivation domains on Transcription factors do?
- Activate or repress genes
e. g. homeobox genes
What do homeobox genes encode and what does this form?
- Homeobox proteins
- to form homeodomain
Are genes expressed FIRST in drosophilla more posterior or anterior?
- More anterior
What do mutations in Hox genes cause?
- Homeotic transformations–> one body part develops as a different body part (wrong location) e.g. legs where antenae used to be (antennapedia mutation)
What transformation is where one body part develops as different body part?
- Homeotic trasnsformation
Where are the Hox genes expressed in mice and humans?
- Series along the length of the embryo
- genes determine the vertebrae type
What is induction defined as?
- Change in the cell fate due to signals sent from other cells –> signals LIMITED in space and time (can be turned off) e.g. Glycoproteins
What does signalling equal?
- Things that are secreted from cell
Do all organisms use a limited repertoire of inductive signals?
- Yes!
What is embryonic induction?
- One tissue sends signals to direct the development of ANOTHER tissue
e. g. Newt (ball of cells) –> dorsal blastophere
What does the dorsal blastophere do?
- Acts as the organiser by releasing signals to neighboring tissues
What does the spemann organiser do?
- Can induce a SECOND BODY AXIS through INDUCTION (duplicated neural tube)
What occurs in sequential induction?
- One type of cells (B lets say) can release inductive signals (e.g. glycoproteins) to another type of cells (lets say A) to allow certain cells in A to produce a NEW type of cells (type C) etc until many different cell types form
What determines how cells respond differently to signals? (i.e. what is it based on?) (2 things)
- Other signals that it is receiving (combinatorial combined effects)
- Cell memory (what other signals it has had in the past–> chromatin marks)
Will a cell with a different signalling history respond in the same way to a cell?
- NO!
What is lateral inhibition?
- When cells send inhibitory signals to neighboring cells –> alters behavior of receptive cells
e. g. neuronal differentiation (one cell forms a neuron and other cells don’t)
What is the notch signalling pathway for lateral inhibition?
- DIRECT INTERACTION b/w cell surface receptor (Notch) and ligands (delta or Jagged or Serate)
In the Notch signalling pathway of lateral inhibition, what is the cell surface receptor and what are the most common ligands?
- Cell surface receptor= Notch
- Ligands= delta, Jagged , Serate
A part from the nervous system development, where is the delta notch pathway of lateral inhibition important?
- Heart, kidney and pancreas development
What is an example of autocrine signalling?
- IL-2 in T cell proliferation or IL-1 in monocytes
What are examples of paracrine signalling?
- Diffusable factors, neighboring cells (adjaent cells)
e. g. Fibroblast growth factor (FgF)