Genetics: Simplified!

Four years of biology summed up in one picture! If only it was this easy ...

 

Amanda

email: manda147@interchange.ubc.ca | Student Number: 92681071

Assignment #3

This assignment was to summarize Distinct physiological and behavioural functions for parental alleles of imprinted Grb10 by Garfield et al. published in Letters to Nature 2011. Enjoy!

Garfield Paper Summary

Garfield et al. discuss the first known imprinted gene (Grb10) that is shown to implicate regulation of social behaviour. To show this, the researchers created a knock out Grb10 mouse model that proved Grb10 was entirely paternally derived in the CNS proper, and maternally derived in the ventricular layers of the brain. Their studies showed that the brain and kidneys were similar in size to that of wildtype mice, but the pups entire bodies and liver were enlarged. Expression of the paternal allele in the CNS of M/+ and +/P type endogenous analysis indicated that expression of Grb10 was established in embryogenesis and maintained until adulthood. However, in +/P models, there was no evidence of brain overgrowth, even though maternal Grb10 had been shown to be a regulator of fetal growth. This indicated that paternal genes were the imprinted genes regulating things such as exploratory behaviour and circadian rhythm. Other behavioural changes observed was that the M/+ mice were more passive in social behaviour than the +/P mice. These studies have shown that differences in genome representation between social groups create different behavioural patterns and change tolerance. This is indicative that Grb10 expression could be related to levels of serotonin and dopamine metabolites, since they both show a strong correlation with dominant/submissive behaviours. This paper demonstrated how two parental alleles of Grb10 have distinctive patterns of imprinted expression and are found especially on different tissues with little to none overlap. I think this paper was considered broad enough interest to be reported in the news because it is both scientific and eludes to sociality. To know that at least part of our behavioural patterns and personality is genomically derived sparks quite an interest to most people. 

Amanda

email: manda147@interchange.ubc.ca | Student Number: 92681071

Some Thoughts about Genetics ...

It's nice how most of my courses (science courses at least) this year are interrelated. I find myself applying the genetics knowledge I got from this class to my project in my Genetics and Cell Biology of Cancer class, and vice versa which will be evident in my final project since it has a lot to do about the genetics of cancer. I find experimental biology to be much more satisfying and interesting than theoretical stuff simply  because I'm a 'need to see it to believe it' type of person. I hope to work in clinical trials with medicine, or experimenting with mouse models as it's cool to me how small genotypic alterations can affect phenotype in such a huge way.

Amanda

email: manda147@interchange.ubc.ca | Student Number: 92681071

VISTA Discussion Posts

Subject: Re:List of things I have found confusing thus far... Topic: General questions
Author: Amanda Wong

Q5 -
- Western blotting is the most common one, so I don't know if it would be the 'superior' method, but it's the easiest and relatively cheapest.
- ELISA can be used to measure concentration of the protein, by calculating the quantity of the protein present proportional to the reagents to proteins used
- Mass spec can determine protein mass by measuring TOF (time of flight) when the ionized atoms of the protein is shot through an electrical field
- Protein assays can be used to determine the protein concentration in a solution. ie. Lowry protein assay uses colorimetrics or Bradford protein assay uses spectroscopy

Hope that helps! 
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Subject: Aging  Topic: Progeria projects Author: Amanda Wong

For those who are interested, I learned in another class that telomere length are responsible for aging. As telomeres shorten (due to the end-replication problem), they correlate to aging at a cellular level. The end replication problem is because transcription only occurs 5'-3', so there's always a 3' overhang that can't be replicated. The telomere hypothesis is that immortal cells maintain telomeres, so if telomere length can be retained, aging can potentially stop (at a cellular level). However, this is also linked to cancer formation, but I think this could maybe be explored if people want to slow down aging.

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Subject: Developmental Biology Questions
Topic: Assignment week 1--post your three questions here! Author: Amanda Wong

Since I'm hoping to get into genetic studies related to cancer research, some developmental biology questions I'd like to ask include:

1. What are the most common defects in gene control or morphogenesis that give rise to tumors?
2. Can signalling pathways, such as those that are disrupted by mutation in cancer, be manipulated to change cell growth and differentiation?
3 What's the difference between tumorigenic cancer stem cells and normal stem cells? 

Amanda

email: manda147@interchange.ubc.ca | Student Number: 92681071

Life of a Drosophila

Amanda

email: manda147@interchange.ubc.ca | Student Number: 92681071

Assignment #2

This next assignment was Problem Set 1, which was given to us during the third week of classes. Here, we studied maternal effect genes, the A-P and D-V asymmetry. We also looked as some cool effects and consequences when concentration gradients are skewed incorrectly, such as mRNAs gurken, oskar and bicoid which are all normally asymmetrically distributed in the cytoplasm - very bad for drosophila, poor things!

Patterning in the early fly embryo

1.         Drosophila embryos produced by torso mutant mothers lack their terminal parts (acron and telson), regardless of the genotype of their fathers. Homozygous torso^-/torso^- embryos from heterozygous mothers develop normal acrons and telsons. What conclusions can be made about:

a) The nature of the torso gene? it is a maternal effect gene since all embryos from mutant mothers are affected

b) The function of the torso gene? it is a response to or is necessary for development of terminal parts (acrons and telsons)

By now you know the molecular nature of the Torso protein. Imagine that you did not have that information, and you thought it could be either a soluble, diffusible protein (like Spz or Bcd), or a membrane-associated protein. What experiment/manipulation could help you distinguish between these two possibilities?

c) If it were a diffusible protein, what would you expect to observe?

If it was diffusible protein, we can try transferring cytoplasm to a different cell to see what effect.

- Do a rescue experiment to see if you can transfer cytoplasm to give the phenotype

- Do cytoplasm fractionation. 

d) If it were a membrane-associated protein, what would you expect to observe?

If it was a membrane protein, transfer the membrane and see what effects it has. If the protein does not function without the membrane, we know its a membrane protein, and if it does we know it is independent of the membrane. 

2.         In loppins (small, diploid animals increasingly popular in several genetics courses), five different LOF mutations in the nan gene have been isolated. Homozygosity for any of the LOF nan alleles results in a complete lack of antennae.

a) What can you conclude regarding the function of the nan gene product?

It is required for the formation of the antennae

b) Based on the current loppins literature, you suspect the Nan protein to be part of a larger, multi-protein complex that also contains the protein Js. Your colleague, on the other hand, is convinced that Nan acts alone and downstream of the Js-containing multi-protein complex, in a signalling pathway.

i) If you are correct, what should you observe in a nan mutant with respect to the Js protein? (Think about the distribution/localization of the protein and well as its concentration and function).

Both phenotype of nan mutant and Js mutant would have same phenotype. Use EMSA to determine whether or not they form a complex. 

ii) If your colleague is correct, what should you observe in a nan mutant with respect to the Js protein?

The Js protein should stay the same, if Nan is independent AND downstream of Js

iii) Assuming that your ‘suspicion’ (i.e. hypothesis) is correct, predict the phenotype of a js^- (complete LOF) mutant (think about as many aspects of its phenotype as you can, such as general morphological aspect, gene expression patterns, etc).

Complete lack of antennae, which would be the same as nan^- mutant, since I believe that Js is dependent of Nan

iv) Would your prediction be different if it turned out that your colleague’s hypothesis, and not yours, is the correct one?

If not, what experiment could you do to determine which hypothesis is correct?

Predict the outcomes of your experiment if your hypothesis was correct and if your colleague’s was correct.

You can do a loss of function of Nan with wildtype Js, and compare this phenotype to a loss of function Nan and Js to determine whether Js alone alters the phenotype. If they show the same phenotype, it is likely that Js is dependent of Nan, however it is possible for the phenotype to be the same, assuming that the Js doesn’t change the phenotype by itself.

Patterning in a vertebrate limb bud-refer to the attached figures and to the Bastida and Ros (2008) review paper for help, information and inspiration.

3. SHH s essential for a number of processes (pretty much everything…). What do we need to be able to do if we want to study its role in limb development, specifically?

Make lots of mutants with LOF of SHH receptors, and identify the phenotypes individually. Stain the SHH and identify the localization. Use RNAi to try and disrupt the mRNA expression at a controlled stage.

4.a) What would be the phenotype of an individual with a complete LOF mutation in Shh in the cells that give rise to the limbs? Propose a reasonable hypothesis.

The individual would not have any limbs since SHH is responsible for patterning and development of most limbs.

b) In fact, researchers have carried out this experiment, and they observed that the individuals with this mutation had abnormal autopods (including absent or severely malformed d2-d5), yet their first digits were developed normally. What can we conclude from this information?

Digit 1 is independent of SHH, but is necessary for d2-d5

5. If we injected lots of SHH in the anteriormost region of a chicken's limb bud, what phenotype should we obtain? (Explain your reasoning)

Dependent on which stage we inject the SHH. SHH are very time dependent, location dependent, and concentration dependent.

6. Predict what phenotypes we would see if we stopped the limb bud expression of Shh precisely, at the following time points:

a) Very early in the development of the limb bud

Loss of posterior digit

b) About halfway through the development of the limb bud

Malformed digits that are associated with Shh, very time dependent.

c) Late in the development of the limb bud –

 Possibly no effect, dependent of the time

Amanda

email: manda147@interchange.ubc.ca | Student Number: 92681071

Assignment #1

This is our Fundamental Facts about Gene Regulation assignment. I found that while completing it, there were concepts from first year, and even high school, that I had to review before this class! Nevertheless, it was a good start to the course. 

Q&A:

Qa, b, c: labelled on diagram

Qd: RNA polymerase complex will dissociate from the DNA at the end of an exon when the newly synthesized RNA molecule forms a G-C-rich hairpin loop followed by a run of Us, or in eukaryotes, where the 3’ end is polyadenylated.

Qe: Translation will start and stop at the start/stop codon of the mRNA

Qf: Proteins that are needed for transcription include RNA polymerase, transcription factors such as TFIID (transcription factor), helicase, TATA-binding protein, activators, repressors, Rho for termination

Qg: Some cis-regulatory elements that have been omitted from the diagram include a frameshift element that regulates alternative frame use with mRNAs and IRES (internal ribosome entry site) which initiates translation in the middle of an RNA. 

Amanda

email: manda147@interchange.ubc.ca | Student Number: 92681071 

 

About me :)

Hi Dr. Kalas & whoever may be reading this,

This is my blog for my individual portfolio that I'll be putting together. A little bit about myself:
I'm in my 4th year at UBC, and my major is Integrated Science where I chose to do Microbiology and Medical Genetics. I'll be graduating this year (exciting/scary!) and hopefully attending grad school preferably doing a project in regards to genetics and cancer, as I want to work in oncology or cancer research eventually. I chose to take BIOL 463 to further my understanding of gene regulation and the elements that are necessary for proper functionality of all these genes that control us. It has been a great class and has definitely shed some new light on gene regulation, especially in embryogenesis, that I can apply to my other studies and in the future. I hope to share a bit of what I learned this semester through this blog, and hope you enjoy it!

Amanda

email: manda147@interchange.ubc.ca | Student Number: 92681071