Summary for the final project

First I came up with two questions that seemed interesting, then after thinking some more I realized that I have always been interested about Planarians, and it is a related topic to developmental genetics. Then reading into planarian regeneration in depth, I managed to come up with a testable hypothesis which tests the possibility for an inhibitory long distance signalling mechanism during regeneration.

 

I sent you my final project in the email. I hope that it got sent correctly because my internet got disconnected !!

Also thanks for the awesome course 🙂

Draft of the final project ..

An inhibitory signalling mechanism is involved in regeneration of planarian eye spots

Question: How is loss of eye spots signalled to the neoblasts to produce optic cup progenitors?

Introduction:

Planarians have been used as a model organism in studies about regeneration for many years due to their astonishing regenerative abilities (Newmark 2001). These flatworms are able to regenerate their full body from a small piece that was cut off from the original planarian (Newmark 2001). This process requires the separated body portion to somehow determine the polarity of the original body and reconstruct itself with the body organs in the right locations (Newmark 2001). Many studies have been done to determine this process in great details and different models have been proposed . The most agreed upon model involves the use of concentration gradients to set up the body axis and determine wound polarity (Newmark 2001). This model also leads to the suggestion of a morphogenic gradient in the embryos during development (Newmark 2001). The mechanisms suggested for this regenerative ability involves the use of neoblasts, cells that possess abilities similar to stem cell in mammals and other organisms (Newmark 2001). During wound regeneration, a blastema is formed with accumulation of undifferentiated cells (neoblasts) (Newmark 2001). One of the unanswered questions

regarding regeneration is how wounding induces regeneration in neoblasts. To answer this question, we will focus on a much specified tissue type, the photoreceptors in the planarian head region. Planarian eyes can regenerate from tissues that are positioned far away from the head region (Newmark 2001). These photoreceptors are formed of a pigment cup (pigment cells), photoreceptor neurons and rhabdomeres (Newmark 2001).

In a study done by Lapan et.al (2011), two genes were identified that were invovled in the formation of optic cups and formation of optic cups occurred after the migration of progressively differentiated progenitors from the neoblasts. This study also suggested that there is a long distance signalling mechanism involved in the induction of progenitors. Another study done by Rand et al. (1926), also provides evidence for a long distance signalling mechanism. In this study they grafted a head excised just behind the eyes of one animal onto the side of the anterior portion of the body of another, then they removed the original head, the regeneration of a new head seemed to become inhibited and the grafted head swung into the body axis. A study was done by Kobayashi et al. (2008) on an eye defective mutant, mensashi, to regenerate eye pigment cells after irradiation (destroys neoblasts) and transplantation of neoblast-rich fraction onto the mutant. In this study, they were able to restore the eye pigment cells in the mensashi and this may suggest that there was a lack of an inhibitory signalling mechanism towards the neoblasts in the mensashi mutants due to having no eye spots (Kobayashi 2008). Finally, a study done by Wenemoser et al. (2010) suggests that injury leads to two miotic peaks in the body. The first mitotic peak is a body-wide response to any injury and the second mitotic peak is a localized neoblast response when the injury causes loss of tissue

(Wenemoser 2010). This second response causes the recruitment of neoblasts to the wound site (Wenemoser 2010). Therefore it is possible that the key determinant to the second mitotic peak is the absence of tissue (Wenemoser 2010). The neoblast accumulation and migration around the wound site suggests that regeneration initiation may involve a signal from injuries (Wenemoser 2010). Based on this evidence, I am proposing the following hypothesis: A long distance signalling mechanism involving changes in concentration gradient of a morphogen(s), which is produced specifically by the eye spots, is responsible in inhibiting the production of optic cup progenitors by the neoblasts closest to the eye spots. My prediction for this hypothesis is that the presence of the eye spots is inhibiting the regeneration of new eye spots by the neoblasts through a long distance signalling mechanism. This question fits into the broader picture of developing a model for planarian regeneration. This model is important because it gives us insight into the process of regeneration and stem cells as there seems to be a parallel between planarian stem cells and the stem cells in mammals (Newmark 2001). This question can give us the opportunity to address problems in development and stem cell differentiation. Another potential impact of this question is gaining a deeper understanding of injury and wound signalling that could also apply to humans. Finally, the findings for this question can be used in stem cell research and health care

Experimental design:

To test the possibility of an inhibitory signal and a concentration gradient produced by the eye spots, we will have 4 treatments. First treatment is to surgically remove the eyespots from a planarian, then transplant them into different locations on the planarian

body and measure the rate of regeneration of new eye spots at each. The second treatment would be to surgically remove the eyespots and then transplant them into their original location; this is a control treatment to observe the effects of moving the eye spots into a different location. The third treatment, also another control, is to surgically remove the eye spots and then measure the rate of regeneration of new eye spots. The fourth treatment would be performed on a ‘menashi’ mutant (unable to form functional black eye spots but forms white spots that contain most of the eye cells), in which the white eye spots are surgically removed and transplanted into different locations on the body and the regeneration time for new eye spots is measured. In the case that the transplantation experiments fail and the eye spots get reabsorbed, a second type of experiment could be performed with mutant planarians with more than 2 eyes (Kyobayashi 2007). In this experiment, the ectopic eye spots could be removed and the regeneration rate of new eye spots could be measured. The tissue transplantation protocol can be found in the study published by Guedelhoefer et al. (2012).

Discussion of possible results:

If eye spots (or the tissue around it that is carried with the eye spots during transplantation) produce a specific inhibitory signal to show their presence and this signal is responsible for inhibiting the neoblasts to produce optic cup progenitors, then the planarians and also the menashi mutants with transplanted eye spot should have a slower eye regeneration rate than the control planarian with completely removed eyes. Furthermore, if this signal is in the form of a concentration gradient, then the planarians that have their eye spots transplanted into a closer to the original eye position should have

a slower regeneration rate. If a slower regeneration rate is observed in these two cases, then this will suggest that the eye spots (or the tissues around it) are producing an inhibitory signal towards the neoblasts to stop the production of eye progenitors before an injury.

Resources:

Guedelhoefer IV. O., Alvarado. A. Planarian Immobilization, Partial Irradiation, and Tissue Transplantation. J Vis Exp. 2012; 66: 405.

Kyobayashi. C., Saito. Y., Ogawa. K., Agata. K.Wnt signaling is required for antero- posterior patterning of the planarian brain. Elsevier. 2007; 306:2.

Kobayashi. K., Hashiguchi. T., Ichikawa. T., Ishino. Y., Hoshi. M., Matsumoto., M. Neoblast-enriched fraction rescues eye formation in eye-defective planarian ‘menashi’ Dugesia ryukyuensis. Development, Growth & Differentiation. 2008; 50 (8).

Newmark, P., Alvarado. A. Regeneration in Planaria. Nature Publishing Group. 2001.

Rand. H., Browne. A. Inhibition of regeneration in planarians by grafting: technique of grafting. PNAS. 1926; 12:9

Wenemoser. D., Reddien. P. Planarian regeneration involves distinct stem cell responses to wounds and tissue absence. Elsevier. 2010; 344:2.

Outline of the final project …

TEMPLATE FOR PROJECT OUTLINE

(please type!)

 Student’s name: Kattie Sepehri

Topic chosen: Planarian regeneration

 

SPECIFIC QUESTION: How is loss of eye spots signalled to the neoblasts to produce optic cup progenitors?

 

 

HYPOTHESIS:A long distance signalling mechanism involving changes in concentration gradient of a morphogen(s), that is produced specifically by the eye spots, is responsible in inhibiting the production of optic cup progenitors by the neoblasts closest to the eye spots.

 

 

EVIDENCE ON WHICH THE HYPOTHESIS IS BASED (INCLUDE REFERENCES):

  • S., Reddien. P. dlxand sp6-9 Control Optic Cup Regeneration in a Prototypic Eye, PLOS. 2011;7.
  • Identified two genes that make TFs, expressed specifically in the optic cup.
  • RNAi of these genes prevented the formation of optic cups
  • Optic cup formation occurred after migration of progressively differentiated progenitor cells from the neoblasts.
  • Suggests that there might be a long distance signaling mechanism

 

  • H., Browne. A. Inhibition of regeneration in planarians by grafting: technique of grafting. PNAS. 1926; 12:9.
  • Graft a head excised just behind the eyes of one animal onto the side of the anterior portion of the body of another, remove the original head, the regeneration of a new head seems to become inhibited and the grafted head swung into the body axis.

 

  • K., Hashiguchi. T., Ichikawa. T., Ishino. Y., Hoshi. M., Matsumoto., M. Neoblast-enriched fraction rescues eye formation in eye-defective planarian ‘menashi’ Dugesia ryukyuensis. Development, Growth & Differentiation. 2008; 50 (8).
  • An eye defective mutant, mensashi, was able to regenerate eye pigment cells after irradiation and transplantation of neoblast-rich fraction.
  • May suggest a lack of an inhibitory signalling mechanism that is not present in the mensashi mutants due to having no eye spots.

·         Wenemoser. D., Reddien. P. Planarian regeneration involves distinct stem cell responses to wounds and tissue absence. Elsevier. 2010; 344:2.

o   Suggests that injury leads to two miotic peaks in the body. The  first mitotic peak is a body-wide response to any injury and the second mitotic peak is a localized neoblast response when the injury causes loss of tissue. This second response causes the recruitment of neoblasts to the wound site. Therefore it is possible that the key determinant to the second mitotic peak is the absence of tissue.

o   The neoblast accumulation and migration around the wound site suggests that regeneration initiation may involve a signal from injuries.

 

 

 

PREDICTION(S):

 

  • The regeneration rate of the eye spots will change/stay the same when more eye spots are removed or displaced due to a possible inhibitory signal that is produced by the eyes that stops the formation of progenitors by the neoblasts.

 

 

EXPERIMENTAL APPROACH TO TEST PREDICTION (INCLUDE ANY DETAILS THAT YOU HAVE WORKED OUT SO FAR):

 

First approach: To test the possibility of a signal and a concentration gradient produced by the eye spots, we will surgically remove the eyespots and at the same time we will transplant eye spots into a different location. If eye spots have a specific signal to show their presence and this signal is responsible in inducing the optic cup progenitors, then the planarian with transplanted eye spot should have a slower eye regeneration rate.

 

Second approach: Another method to test the presence of a signal is to remove ectopic eye spots from mutant planarians with more than 2 eyes, these mutants should have slower eye regeneration than wild type planarians as there will be a smaller change in signal.

 

Third approach: Transplant eye regions from a defective mutant planarian ‘menashi’ (unable to form functional black eye spots but forms white spots that contain most of the eye cells) into a wild type planarian that has its eye spots removed. If an inhibitory long distance signal is produced by these cells then the planarian should not regenerate new eye spots.

 

 

 

 

 

 

LIST OF RELEVANT PRIMARY AND REVIEW ARTICLES READ, AND SUMMARY OF RELEVANT INFORMATION FROM EACH (this is the start of an annotated bibliography):

 

  • F. Studies on transplantation in planaria. Biological Bulletin. 1929; 57:188-197.
  • Transplanting different areas of the planarian, including the areas around the eyes

 

  • Guedelhoefer IV. O., Alvarado. A. Planarian Immobilization, Partial Irradiation, and Tissue Transplantation. J Vis Exp. 2012; 66: 405.
  • Detailed protocols for tissue transplantation

 

  • C., Saito. Y., Ogawa. K., Agata. K.Wnt signaling is required for antero-posterior patterning of the planarian brain. Elsevier. 2007; 306:2.
  • The mutants created in this study have more than 2 eye spots and can be used in my experiment.

 

·         Cebria. F., Newmark . P. Morphogenesis defects are associated with abnormal nervous system regeneration following roboA RNAi in planarians. Development. 2007; 134.

o   Role of nervous system in regulating morphogenesis during the regeneration of the anterior part of planarian. Smed-roboA is important in guidance of visual axons, and the RNAi mutants of this gene have ectopic projections and visual defects. In the case of my question this could suggest that the long distance signal is carried by the nervous system.

  • R., Newmark. P. The cell biology of regeneration. The Journal of Cell Biology. 2012; 196: 5.
  • Discussion of regeneration in other organisms such and also planarians. Evidence suggests conservation of regenerative abilities through evolution.

 

·         Adell. T., Cebria. F., Salo. E. Gradients in Planarian Regeneration and Homeostasis. CSH Perspectives. 2012; 2:1.

o   Discusses the gradients that are involved in planarian regeneration and polarity, such as BMP, Wnt and FGF. These gradients could also be important in my experiment and should be taken into consideration.

  • Newmark, P., Alvarado. A. Regeneration in Planaria. Nature Publishing Group. 2001.
  • Contains an introduction to regeneration in planarian and some histroy of research in this field. Also a proposed mechanism in regeneration such as the role of neoblasts is discussed.

 

 

 

HOW DOES THE QUESTION FIT INTO THE BROADER PICTURE, AND WHAT IS ITS IMPACT?

 

  • This question fits into the broader picture of developing a model for planarian regeneration. This model is important because it gives us insight into the process of regeneration and stem cells.
  • This question can give us the opportunity to address problems in development and stem cell differentiation.
  • Another potential impact of this question is gaining a deeper understanding of injury and wound signalling that could also apply to humans.
  • There seems to be a parallel between planarian stem cells and the stem cells in mammals.

 

 

 

POTENTIAL WAYS TO MAKE YOUR QUESTION KNOWN TO THE PUBLIC AT LARGE (OR TO YOUR NON-BIOLOGIST FAMILY AND FRIENDS):

  • The findings for this question can be used in stem cell research and health care. Also the concept of planarian regeneration is very easy to demonstrate without having a significant knowledge about biology.
  • Demonstrations of the cool regenerative powers of planarians can easily be shown by cutting them into tinny pieces and letting them form a new organism.  This demonstration could raise the curiosity of the public about this complex process.

 

 

ANY OTHER PARTS OF THE PROJECT COMPLETED SO FAR:

 

 

ANYTHING YOU WOULD LIKE SPECIFIC FEEDBACK ON:

  • The experimental procedure, since I have doubts about whether it is possible to transplant an eye spot – cannot find any research that successfully transplanted an eye spot into another part of the body, but there is some research/techniques on transplantation of the eye spots and the tissue around it. Therefore my 1st and 3rd approaches  could lead to failure if the transplanted eyes spots are simply reabsorbed….
  • Ways to make my question known to the public…

 

 

 

 

 

 

 

 

 

 

Initial questions…

Initial questions for final project … they were very broad

1) The human heart is initially similar to a fish heart in the embryo and the hands are initially formed as paddles. Is this a necessary step or is this simply a remainder of the evolutionary history ?

2) When are maternal RNA or proteins deposited into the embryo? Is it before fertilization or after? If it is before fertilization, then at what stage of the egg development are they deposited? If it is after fertilization then what are the mechanisms that signals the mother to deposit them, and how would this work in the case of external fertilization?

 

MURC …

This term I had the opportunity of being part of the MURC organizing committee, and I got the chance to read many different abstracts from students in different faculties. (This year we actually managed to get presentations/posters from non-science faculties too!!). Part of my job was to categorize the abstracts into related topics.

While reading the abstracts, I realized that it was relatively easy for me to understand the topics related to science/biology. I guess this is a good sign and it shows that I have actually learnt something in my 4 years of education. The difficulty however, was understanding and categorizing the topics that did not relate to life sciences. The individual words made sense … but putting the words together and making sense of it did not make any sense and I had to actually use Google/wikipedia.

This reminded me of our discussion about the general public and how research will apply/translate  to them. I can imagine the difficulty for someone with no background in life sciences if they ever tried to read a research paper. Therefore I think it becomes important for researchers, reviewers, journalists, teachers and anyone involved with the communication of the knowledge to not have any bias towards a specific conclusion. This could help the general public to be able to integrate/use the information found in research in their everyday choices.

GMO (babies)????

So this happened some time ago …

http://www.iflscience.com/health-and-medicine/uk-allows-ivf-using-dna-three-parents

And started a huge argument between my friends, regarding “genetically modified babies”. My friend who is not a biology major, was set against the idea because she felt that genetically manipulating babies is immoral.  In my opinion, since this technique is being used to treat a vital disease, then it should not be publicly discouraged and be labelled as “genetically modifying” (which carries a negative connotation already). Since they are simply changing the cytoplasm of the cell and only the mitochondrial genes will get replaced, which is only 37 genes (http://ghr.nlm.nih.gov/mitochondrial-dna), then can this really be called genetically modifying? It seems to me that many people have found a fear of anything that is labelled as genetically modified, however I think that this fear is not scientifically accurate because this term can have a very wide range of applications, for example even selectively breading dogs can be termed genetically modifying.

So what does genetically modifying really mean to the general public … ?

 

 

BIOL 463: Speed-Dating Presentation

Contributors:
Sam Livingston, Elkie Fung, Kattie Sepehri, Grace Lin, Jordan Whittier

Technique Chosen:
Flow cytometry

 

What does this technique do?

  • Cell counting, identification, and sorting based on the analysis of laser light scattering from individual cells.

 

What applications is this technique employed for?

Cell counting: Detect relative population sizes of different cell types within a sample

  • Eg. Analyze composition of cells in blood

Cell sorting: physically separating cells or particles of interest from a heterogeneous mixture

  • Biomarker detection – Identification of cells based on a specific molecular characteristic (protein, lipid, DNA/RNA etc.)
  • Apoptosis detection – identification of cell state by detecting DNA damage, caspase activation, or other apoptotic characteristics
  • Protein engineering – rapid sorting of cells expressing desirable proteins
  • Cancer detection – identification of many blood cancers by using antibodies that stick to only one type of cell

 

Cell identification: Identify cells based on external and internal characteristics using light scatter and/or fluorescence (eg. antibody tagging)

 

What questions (give a couple of examples) relating to gene regulation and/or development can be addressed using this technique?

  • Are the cells of a shrinking tissue/organs the result of cellular ‘shrinkage’, apoptosis, or necrosis?
    • Useful for identifying degenerative conditions and abnormalities in normal organ/tissue homeostasis
  • Can the development of cancerous tissue be analyzed through this technique? Useful in identify proteins with improper folding or cells that have passed through stages of the cell cycle which they shouldn’t have.
  • Which cells have progressed to a certain cell fate during a specific time period in development?
  • How many/which cells of a tissue/organ produce my biomarker of interest?

 

What critical reagents are required to use this technique?

  • A flow cytometer
  • fluorescent labels ( eg. specific antibodies or probes)
  • solution to suspend cells – usually PBS
  • Propidium Iodide for non-specific DNA labelling of apoptotic cells

 

What critical information is required to be able to employ this technique?

  • What particle is being detected and how to tag it (eg. antibody tagging)
  • Predicted size of the cell and their surface morphology that can be observed as forward and side scatter by the detectors of the flow cytometer
  • Surface properties for tagging/ internal properties for tagging

References

Davies, D. Flow Cytometry. London: Humana Press, 2007. Ebook.

 

Gasol, Josep M., et al. “Significance of size and nucleic acid content heterogeneity as measured by flow cytometry in natural planktonic bacteria.”Applied and Environmental Microbiology 65.10 (1999): 4475-4483.

Hodge, Sandra J., et al. “Flow cytometric characterization of cell populations in bronchoalveolar lavage and bronchial brushings from patients with chronic obstructive pulmonary disease.” Cytometry Part B: Clinical Cytometry 61.1 (2004): 27-34.

 

Wittrup, K.D. “Protein engineering by cell surface display.” Elsevier  12.4 (2001): 395-392.

 

Janossy, George, et al. “Affordable CD4+ T cell counts by flow cytometry: II. The use of fixed whole blood in resource-poor settings.” Journal of immunological methods 257.1 (2001): 145-154.

Macey, Marion G. Flow Cytometry. Humana Press Incorporated, 2007.

Sosik, Heidi M., et al. “Growth rates of coastal phytoplankton from time‐series measurements with a submersible flow cytometer.” Limnology and Oceanography 48.5 (2003): 1756-1765.

 

 

Reasons for choosing the 4 assignments…

Honey bees-  I have always found honey bees and their community structure very fascinating. Since this lecture I have been thinking about what can actually happen to you if you ingest royal jelly …

Limb Malformations –  Before this lecture I had never heard about limb malformations in mammals, so it was really interesting to get more information about human genetic diseases.

SRS and BWS – This article was quiet challenging to understand, however I liked the way that the study was done, based on pedigrees and on phenotypes seen in humans (not animals).

LacZ transgene – The way that LacZ was used to stain the embryos was a really cool/ smart way of looking at gene expression. I did not know that LacZ can be used even in mammals…

 

Honeyyyyy Beeeeeees

Epigenetics and Development

Our Goals:

* To build our own definition of “epigenetics”;

* To classify the major mechanisms of chromatin remodeling;

* To investigate how external environment/behaviour can trigger a completely different developmental fate

* To propose, and interpret some experiments that allow us to shed light on this phenomenon (in a specific case)

1. What could be the underlying mechanism driving the different developmental trajectory of the organisms studied in today’s class?

  • Signalling pathway -> Hormones
  • on/off genes -> methylation

2. a) With one or two partners, take two minutes to come up with a definition of “epigenetics”:

  • Factors that influence gene expression and development that is not directly related to the pattern of nucleic acid or DNA of the individual

b) After listening to other classmates’ ideas, provide a more complete (if necessary) definition of “epigenetics”:

  • Heritable modifications of DNA
  • inheritance of a phenotype that is not explained by differences in DNA sequence

3. a) What are different mechanisms that can affect developmental trajectory, and that could be affected/directed by an “outside factor”?

  • Methylation/acetylation
  • Histone modifications and the mechanisms involved -> turn on/off areas of the genome
  • The environment, for example nutrients
  • Developmental pathways

b) What are the mechanisms that can affect chromatin structure?

  • Chromatin remodelling factors
  • Different histones
  • Methylation/acetylation of histones
  • Coiling of chromatin
  • Methylation of DNA

4. What would you predict about gene expression patterns in the two distinct developmental trajectories if epigenetics is driving the phenotype?

  • Worker bees have reproduction related genes shut down

5. Researchers (Grozinger et al., 2007) actually checked… what do you notice about the gene expression patterns in individuals following each of the two developmental trajectories?

  • There is up regulation of foraging genes and down regulation of reproductive genes in worker bees, and queens bees show the opposite pattern

6. What kind of protein/factor could be a key component of the epigenetic control of developmental trajectories? How would you test your hypothesis?

  • methylation -> can test with ChiP analysis, or inject methyl transferase inhibitors into larva
  • Test other suspected  proteins by injection of RNAi into larva

7. What did Kucharski and colleagues find, and what does their experiment suggest?

  • DNA Methyl transferases are important
  • Knock down of Dnmt3 mimics royal jelly – induces queen bee development
  • Workers have more of their DNA methylated

8. a) What component of the food in question is most likely to affect gene regulation?

  • lipid, 10HDA, Royal Jelly Acid

b) How does the food in question activate a transcriptionally silenced gene?

  • Activates Fas expression
  • Overall increase in acetylation of histones when treatment with Royal Jelly acid

9. ***optional*** Using these pieces of data that we just discussed, construct a model of how consumption of the food in question leads to each of the developmental trajectories.

Week 2 In Class Questions – cis-Regulatory Mutations Are a Genetic Cause of Human Limb Malformations

In-class questions (group)

Discuss these questions with members of your group, come to a consensus answer fro each question (you may incorporate several opinions/ideas into one answer), and hand in your groups answers via email after class (ONE set of answers per group, please include the first names of all contributors). Please also send a copy to all contributors, and if you feel so inclined, please feel free to include this piece of work in your portfolio.

 

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

 

  1. What big processes of development are involved in the formation of a human limb?
  • Pattern formation, differential gene expression, timing

 

  1. 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?
  • Easy to see and compare at early stages
  • Expression mechanism can explain phenotype/genotype
  • Developmental problem, possible solution for disorders/illnesses

 

  1. What is the difference between an isolated and a syndromic malformation, and what kinds of mutations are they postulated to be associated with?
  • Isolated malformation is a defect in a single system and can have many causes, while syndromic malformation is a pattern of anomalies that have a single cause (made some corrections from the group discussion).

 

 

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

 

  1. 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?
  • ZRS enhancer controls Shh expression in developing limb bud
  • single base pair substitutions or duplications that encompasses the ZRS region
  • The point mutation results in a wrong 3D structure that affects level of  Shh expression. Ex. it regulates the Shh because it binds to other regulatory protein at higher affinity. The change in Shh causes the bud to express extera digits (at the phenotype – Cuban and Belgian mutation)

 

  1. 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 is the degree to which the patterns/orders of genes are similar in 2 compared genomes. Some Cis-resulatory regions have been conserved in evolution. Recent common ancestors will have more synteny between their chromosomes.

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

 

  1. 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?
  • Subjects could be recruited via
    • Volunteers
    • Direct request from researchers
    • Paid
    • Anonymous information from hospitals
    • Depending on the researchers doing the study it could be free access on the web, in journals, or sold in a journal. The researchers and medical institutions could all have access to the information. It could be interesting for physicians, other researchers working in the same area and other individuals with the genetic condition. The phenotypes under study are depicted as descriptions, pictures or experimental data.

 

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

 

  1. 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?