Musings of a BIOL463 Student

I chose to highlight this assignment because I really enjoy dissecting and answering questions as a group. It really helps me learn and understand the paper a lot better. This assignment also opened my eyes in the importance of studying limb development.

Part I – The study of limb phenotypes (10 min)

What big processes of development are involved in the formation of a human limb?

• Coordinated determination of three axes:

1. Anteroposterrio (AP)- earliest axis to be defined
2. Proximodistal (PD)- controlled by apical ectodermal ridge (AER)
3. Dorsoventral (DV)-

 

• ZPA = important signaling centre = expresses SHH
  • Defines AP axis
• AER produces growth factor and signals needed for PD growth of limb
• Need feedback loop between ZPA and AER that maintains both of them and for coordinated growth along axes and DV polarity maintenance

 

2. Think about human limb development (wild-type or mutant) as a phenotype of interest. From a fundamental research perspective, why is it a useful phenotype to study? Why is it a good model system for the study of development? What are the advantages?

• Helps in categorizing types of malformations, subsequently guides the therapies that may be used to treat the malformation
• Each finger looks different which means each digit had to develop differently to result in these morphologies. Spatial and temporal order is important and can help you understand why specific malformations result.
• Easily observable

 

3. What is the difference between an isolated and a syndromic malformation, and what kinds of mutations are they postulated to be associated with?

• Isolated: mutations in the cis-regulatory regions of a gene (this means that it only affects that location of genes)
• Syndromic: other phenotypes, if there’s an error in the coding region of transcription factor it will affect the regulation of many genes, resulting in the syndrome.

 

Part II – The study of cis-regulatory elements (20 min)

 

4. Select one of the loci discussed in the review by Bhatia and Kleinjan. As a group, prepare a model of its regulation (can be in words, diagrams, a mixture thereof, etc). Then:
   • list the evidence that the authors use as a basis for each part of the model;
   • evaluate the evidence (decide if it is sufficient to support the various parts of the model);
   • if applicable, select a part of the model for which we do not (yet) have much supporting evidence. What additional piece(s) of evidence would help strengthen the model? What experiment(s) could you do to obtain them?

• PAX6: locus on Ch11
  • Haploinsufficiency is cause of congenital eye malformation aniridia
  • ELP4: Multiple enhancers for PAX6 have been identified within ELP4 introns (synteny)
  • SIMO: conserved ocular enhancer involved in autoregulation of PAX6
    • If you have a mutation in SIMO, it interferes with the binding of PAX6
    • Says: “in a patient” – (Bhatia et al. 2013)
      • Not statistically significant
      • Need a larger sample size (more patients)
    • Design in vitro studies to confirm and further understand the relationship between SIMO and PAX6 binding affinity
      • How does a mutation in this enhancer reduce PAX6 binding affinity?
      • What is different about the mutated PAX6 protein? Does the amino acid sequence change?

 

5. What is synteny? How does progress in our identification of cis-regulatory elements help explain some cases of synteny? (And thus making the connection between genome structure, function and evolution relevant?)

• Synteny:
  • Order in which gene is located within a chromosome, that can be passed on
  • Heritable pattern of gene position on a chromosome
  • You can trace evolution through this (eg. If a cat and a dog have a gene in the same location, shows evolutionary relationship)
• If you have the CRE in the intron of one gene regulating the transcription of another gene, it shows their evolutionary relationship
  • You need both genes to be maintained in order for the second to be functional

 

 

Part III – Where do the cases are from, and who is the information for? (10 min)

 

6. Think about all the research conducted on human limb malformation. How do you think the subjects for the study were recruited? How do you think the information gained from these studies was disseminated? Who had access to it? Who could it be useful or interesting for? How are the phenotypes under study depicted?

 

OR: (please answers only one of Q6 or Q7, not both)

 

7. Understanding human “pathologies” that have a genetic basis is almost always listed as one of the benefits of uncovering the genetic and molecular mechanisms that cause a given phenotype. How does the knowledge obtained in this field benefit the patients/subjects? How does it benefit the community at large?

• Patients and Subjects
  • Detection of diseases (diagnostics) and stratification (putting diseases into different categories)
    • Stratification of cancer: can all be in different categories
    • This is important for designing treatment that targets the specific cancer type (ie. Molecular aberrations)
  • Identification of drugs that may be more effective for patients with certain molecular aberrations (ie. Patient specific, personalized medicine)
• Community benefits
  • Understanding the genetic component important for screening and predicting/prevention or at risk (eg. BRCA)