Monthly Archives: January 2015

Homework Monday January 19th

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1. Humans are complicated creatures. The formation of our limbs is just one simple example of how complicated our body can be and what ‘techniques’ it uses to form itself. Our hands develop along three axes: posterior-anterior (thumb to pinky), distal-proximal (tips of fingers to wrist), and dorsal-ventral (back of hand to palm). The first axis (the posterior-anterior axis) allows the formation of your fingers in the correct order. The way it does this is by producing a protein called ‘Sonic hedgehog’ (Shh) which, depending on its gradient, will form all your different digits. Thumbs, for instance, form when Shh concentration is high, whereas pinkies form when Shh concentrations are low. Conditions such as polydactyly (more than 5 fingers) occur when the levels of Shh are abnormal, which can be due to mutations in both the protein itself and DNA sequences that regulate the rate of protein production. Protein production can be controlled in various ways, including using ‘enhancer’ regions that loop DNA and allow the proper machinery to express the proper genes. An example of an enhancer is the area found in the OCA2 system, which controls eye colour in humans. This enhancer was shown to interact with the promoter for OCA2 gene, and that when the enhancer is mutated, there is less interaction with OCA2. Thus, individuals with poor interactions within the OCA2 system have eyes that are blue instead of brown. These two examples are only two of the many ways our bodies can regulate growth, and it is of interest to all kinds of people (patients, physicians, researchers, genetic counsellors) to understand how these pathways work.

2. The hardest part about answering question 1 for me was being able to pick out the ‘main’ points in our discussion. This includes both filtering out the scientifically relevant points, but also knowing which points are important in a “summary for the public”-style paragraph.  It is much easier writing a summary using scientific language because you can use common acronyms, terms, or ideas to help shorten your paragraph. In layman’s words, however, you have to elaborate on each idea in order to fully explain what is happening—which makes it difficult to choose what is worth including or not.

Week 1 Learning Journal

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A. Factual Knowledge

This week, I learned the definitions of  totipotent and pleuripotent. Totipotent refers to the cells formed shortly after fertilization that have the ability to specialize into any kind of cell. It has the most potency of any cell type. Pleuripotent, on the other hand, are the cells that result when totipotent cells first begin to differentiate. Pleuripotent cells can give rise to many different cell types, but is more differentiated than totipotent cells.

I know I have acquired this factual knowledge because I am able to compare and contrast totipotent and pleuripotent cell types (as done above) and also because I am able to apply their definitions to a real-world example. For instance, when C. elegans eggs become fertilized, the resulting zygote is totipotent. Once it divides into 2 cells, the cells are no longer totipotent because they can only grow into their respective ‘sides’ of the worm. In contrast, a human embryo can contain multiple cells but still have identical totipotency in all the cells– which is why an embryo in early developmental stages can split to form two whole individuals rather than two halves of a single person. It is only later in development that the cells become pleuripotent, at which point removal of certain cells may result in physical deformations in the mature fetus.

B. Conceptual knowledge

This week I learned what kinds of information we can obtain from the three broad types of experimental approaches: Look/stain and look, remove something, and add something. From “look” approaches, we can acquire lots of different information such as the location of structure, the appearance of structure, the location or distribution of proteins, the expression pattern of mRNA, the movement of different molecules, and much more. When something is removed. we learn what functions that unit is necessary for. This is in contrast to when you add something, in which case we learn what functions that unit might be sufficient for.

I have acquired this information because I am able to use this conceptual knowledge when analyzing data or exercising my ‘skills’. For example, if you were to present me with a case study in which the deletion of gene Y results in X phenotype, I could tell you that gene Y is necessary for the wild-type phenotype X. Likewise, I would be able to say that in an experiment where you add component A to result in affect B, component A is sufficient to induce affect B.

C. Skills

One skill I have acquired this week is the ability to know how to interpret experimental data– specifically, what data might mean and what limitations certain results have. As an extension of this skill, I also have learned how to identify how one might clarify or resolve the limitations of a particular experiment.

Some examples that I have to demonstrate this ability is:

  • Be able to look at the relationships between cell potency and time/stage after fertilization, when transplanting genetic material into egg cells. In this case, it is important to realize that while we can conclude that as time increases potency decreases, we do NOT know that DNA is necessarily being deactivated. It may be that DNA is gradually being discarded as cells become more differentiated. In order to determine whether it is DNA being inactivated, or `DNA being discarded (or something else entirely), DNA could be quantified or sequenced to compare the DNA content between cell stages.
  • Be able to conclude the phenotypic effects of the loss of the Rspo2 gene in frogs. Although the results show asymmetrical facial and limb development, it would be best to say that Rspo2 is involved in general facial and lib development, rather than say “it results in the right leg and left face being deformed”. This is because the asymmetrical deformations may be due in part to environmental effects, and that the asymmetry might be partially stochastic (random) regarding which side it effects.

 

Assignment 1

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  1. Are the cells found in the protonema of bryophytes all considered pluripotent, or are there particular sections of the protonema destined to become differentiated into the gametophyte stage? Furthermore, how does Methylobacterium induce faster growth of protonema in Funaria ? Does it prevent further cell differentiation, or does it simply increase nutrient availability?
  2. How similar is the development of stomata on tracheophyte sporophytes and the stomata on bryophyte sporangia? Are they homologous, or are they converging?
  3. What structural/biochemical mechanisms surround Paramecium aureli’s ability to change its tolerance to heat, salt, and arsenic, and why does this tolerance disappear after several generations?

As a bryo-enthusiast, I would love to be able to study the development, history, and relevance of bryophytes to humans because I think they are amazing organisms that deserve far more credit that they receive. One of the things that attracts me to them is their simplicity and the way they are able to thrive in such diverse habitats despite having relatively simple structure, physiology, and development. Furthermore, I am particularly interested in looking at host-microbe relationships. Considering we know so little about the complex microbial world and how communities of microbes change ( or are changed by) other organisms, I believe this topic is a marriage of my two passions.

If the results of my potential experiment showed that protonema (specifically, caulonema, which is the stage of protonema right before gametophyte and rhizoid differentiation) consisted of a large collection of identical cells (that is, there is no pre-determined stem cell from which the gametophyte grows), it would suggest that there are some factors or signals that induce further differentiation. I believe this would be fascinating to the world of developmental genetics because it would be an example of how plants signal cell differentiation and specificity. conversely, if it is revealed that the point of cell differentiation is pre-determined in the early protonemal stages, I could investigate what causes particular cells to be ‘chosen’ and how one might manipulate this.

Additionally, I would want to investigate the effect of  Methylobacterium (a protonema-associated microbe) has on protonemal growth. I would want to investigate why Methylobacterium-associated hosts tend to grow more extensive protonema– for example, whether it grows faster because of increased induction of growth genes, of if it is because there is a repression of differentiation genes. This could be important in understanding how to induce faster stem cell growth or how to prevent stem cells from further differentiating. Either option could provide useful knowledge about how to manipulate cell growth and differentiation, and it may lead to us using Methylobacterium as a tool to study stem cells in other organisms.

In the world of science, the ability to understand how plants sustain pluripotent cell stages (like protonema), what triggers differentiation, and what external factors may prevent differentiation could be used in many different fields. Cell cultures used for other experiments could be sustained better due to increased knowledge of how to prolong cell stages. Experimental organisms could be grown at faster rates if we were to understand how to speed up the development process. In society, we may even be able to extend the tools and concepts gained from these results into treating human disease and illness. For example, if studies on Methylobacterium were to reveal that the bacteria produced a compound that prevents the expression of certain genes in development, one could potentially use similar compounds in tumour therapy to control rapidly dividing cells. Although my proposed question may not directly affect society, there are many ways its results could influence new ideas that would eventually lead to better medicinal practices.