Take home exam number 3! Here is one of my responses....
Much of the information known today about biology comes from scientists craving a deeper understanding of the world around us and the fundamental workings of living things. Basic research that started with curiosity and aimed at understanding has led to the discovery of DNA structure, the central dogma, genetics, regulatory mechanisms and much, much more. Unfortunately today, many politicians and grant providers believe that the slow rate of successful applications to medical diagnosis and therapy is due to a lack of willingness to focus solely on human health and are trying to narrow the focus of scientific research to "translational research" that can be directly applied to human health. However, basic research is essential to continue growing our fundamental base of knowledge. History shows that our solid scientific foundation is the result of the work done by thousands of basic scientists whose biggest goal was to understand the fundamental workings of living things.
There are many reasons basic scientific research is important. One reason is that it helps identify the universal aspects of life but also helps identify where things are different. When universal aspects are discovered it gives us a basis for developing theories and laws that we can then apply to other various systems. For example fly research has led to the discovery of many tool box genes/ proteins and a deeper understanding of regulatory mechanisms some of which can also be found in other species, including humans. Finding genes and mechanisms that have been conserved throughout evolution can also give us insight to our evolutionary past, help construct phylogeny trees and see how all living things are related. As many historians say "the key to a bright future is understanding the past."
Another reason basic scientific research is important is that it can help us discover, design, and utilize new research methods and tools. Many methods we use today were designed conducting basic scientific research, examples being transformation, vectors, mutational analysis, and more. Studying different animal systems that can be applied to humans is also very important because for some studies it would be unethical to perform the treatments on humans. For developmental studies specifically it is difficult to work with humans because of the long gestation period as well, therefore its logical to study other "model" organisms.
Lastly, basic scientific research may contribute to advances in other fields such as food, fishery, pest control, resource management, conservation, and engineering. Science isn't just about finding medical cures, although that is very important, it is also important to understand how the world works around us. By further developing these fields we can improve the standard of life for many.
Overall, basic research is what has built our founding knowledge. If we would like to continue to grow and learn as a scientific community it is important to continuing doing basic scientific research. By doing basic research we will continue to identify aspects of life that have been conserved through evolution, develop laws and theories that can be applied to various systems, develop new scientific methods, and contribute to advancement in other fields aside from medicine. Rather than trying to investigate very specific aspects of certain diseases and illnesses we should be broadening our scope and trying to understand general mechanisms and then eventually "the cures" will present themselves.
Recently in class we have been studying fly development, for lab we were asked to create a video of a development stage. This has proven to be a difficult and frustrating assignment... either our technology isn't working, or the flies don't do what we want them to! In an attempt to catch fly mating behavior my lab partner and I recorded this video of fly behavior.
Two weeks ago I wrote about the central dogma and how the analogy of computer technology relates. This week, I would like to further that analogy and talk about some of the regulation mechanisms, and also point out some areas where this analogy could be misleading.
Selective protein production is important in cell differentiation, so it is also important to look at how protein production is regulated. One mechanism called enzyme induction was intensively studied in E. Coli, a type of bacteria. E. Coli metabolizes glucose as an energy source, but also has that ability to break down more complex sugars like lactose using an enzyme called β-galactosidase. Scientists discovered that when E. Coli was grown on a medium including glucose, little of the enzyme B-galactosidase was produced, but when there was no glucose present, only lactose, this enzyme was produced in large quantities. Carroll deems this "gene logic," meaning that enzymes are only produced when they are needed. When lactose is present it binds to the repressor (a molecule blocking the transcription of the gene when it is not needed), and makes the repressor fall off which allows the gene to be transcribed and translated to produce the B-galactosidase enzyme to break down lactose. The repressor of the B-galactosidase gene is an example of one of many DNA-binding proteins that bind to genetic switches in bacteria and yeast. Very similar to the "Boolean logic" used in computer technology where essentially all "decisions" made by the computer are either 0 or 1, these systems are deemed either "on" or "off."
A gene may have one of these switches, or may have various switches. It is also possible that one protein may control multiple switches. In order to coordinate development of an organism, the switches of different genes may share multiple inputs or similar sequences. For specific cell types, it is often found that the genes for certain proteins are activated by switches with common sequences and utilize the same "tool kit" protein. The developmental steps performed by these individual switches and proteins are connected to the switches and proteins of other genes, in essence creating a large "cascade," which can be diagramed in a similar way to electrical circuits and networks. Each switch is a decision point, like one node in an electrical circuit; the activators and repressors act on the switches to turn them on/off. There are multiple "tiers" of a circuit that define the cascade. Each one of these "circuits" can represent one structure with-in the organism. It takes multiple circuits connected to form a network in order to produce a whole and complete, complex organism.
Although modern computer technology provides a good analogy for the cascade of regulatory mechanism within complex organisms, no metaphor is perfect. Modern computer technology and computer programming is strict, if one code is entered improperly the program simply doesn't work. However, with biological systems there are mechanisms for repair and essentially "room for error," in most cases. If a wrong base is added to a sequence the cell has multiple mechanisms to excise this base, or minimize the effects the error will cause. There are lethal mutations, that are more similar to the mis-coding of a computer, but again there are many mechanisms in place to avoid these mutations. Another area that this metaphor fails to address is reproduction and evolution. Obviously a computer system is absolute and does not pass on its hard-disk information to future progeny, but it is crucial to understand this process when talking about mutations, natural selection, evolution, divergence of species and how this relates to the central dogma. Overall, comparing the central dogma to the computer technology analogy may be helpful in understanding the mechanical operations of producing and regulating different proteins, but it lacks the "big picture" view when looking at the effects of mutations and the divergence of species.
This past weekend we were assigned a take home exam. One of the prompts addressed an article that I had commented on two weeks ago. Here is the prompt:
We went over the experiment to test the role of enhancers of the Prx1 locus which showed their role in regulating limb length in bats and mice. Explain it again, going over the details of the experiment, the results, and the interpretation...but without using any scientific jargon. If you do use any jargon (like "locus", "regulation", "enhancer"), you must also define it in simple English. Make the story comprehensible to a non-biologist!
And here was my response:
The article "Regulatory divergence modifies limb length between mammals" by Chris J. Cretekos et al. set out to investigate the cause of length differences between the limbs of short-tail fruit bats and mice. These organisms represent the two largest orders of mammals and it is thought that they shared a common ancestor between 80 and 100 million years ago. The "lay-out" of their limbs is extremely similar and includes the general one-bone, two-bones, cluster of bones, digits pattern (as also seen in our limbs). However, there are also differences in their limb structure such as the relative length of the digits, the presences or absence of tissue between digits (similar to "webbing") and between limbs (forming wings). In the development of bat and mice embryos the initial formation of the fore-limb show similar timing and position, however as the embryo grows and develops these differences become more apparent.
So what causes this difference in development between mice and bats? Well, before I address this question it is also important to consider the two types of changes that can cause morphological differences. First, it is possible that there are changes in the DNA sequence itself (that code for the parts of the limbs). Second, it is possible that there are changes in the DNA sequence that are non-coding (do not code for limb itself) but are rather the regulatory elements in limb development. A regulatory element is a molecule that helps control the development of some aspect of the organism (in this case the forelimb). This second type of mutation is called a cis-mutation, and can cause modification in specific aspects of the patterns or the level of gene expression.
Prx1 is a gene that is found in both mice and bats and it is a developmental control gene that has been shown to increase skeletal elongation in limbs. When scientists deleted this gene in mice, the resulting embryo initially developed normally, however, the long bones of limbs were significantly shorter and these mutants died at birth. This suggests that Prx1 is essential in regulating long bone elongation. Cretekos et al. hypothesized that because bats have significantly longer long bones, and mice lacking this gene showed significantly shorter long bones that this gene may be what is causing the morphological difference between bat and mice fore-limbs. To further investigate they looked at the expression of this gene in embryos of both mice and bats. They found that Prx1 is initially expressed consistently throughout the budding limb, however later on Prx1 is up-regulated (more is produced) in the end of the bat limb compared to the mouse. These differences in Prx1 gene expression correspond with the physical differences observed.
Next, researchers investigated the cis-regulation of Prx1 (the regulatory sequence of the gene that is non-coding). By deleting certain sections upstream of the Prx1 gene they found a region that acted as a transcription enhancer. A transcription enhancer is a sequence of the gene that an activating protein binds in order to turn the gene on (this helps increase the amount of Prx1 transcripts produced). This enhancer region was similar in both bats and mice. In order to examine the function of this enhancer sequence researchers replaced the mouse enhancer sequence with the bat enhancer (leaving the original Prx1 gene intact in the mice). What they found was that the bat Prx1 enhancer sequence increased the forelimb length during the development of the mice but the pattern was maintained (it still looked like a mouse forelimb). It was also interesting that when the mouse Prx1 enhancer was simply deleted (and not replaced) limb development in the mice was normal. These results show that there must be multiple enhancers that perform the same function aside from the one that was replaced or deleted in this study.
Overall, this study showed further support that changes in the non-coding region of the gene (cis-mutations) can play a role in the physical changes that have occurred and allowed for the divergence of species such as bats and mice.
In the book "Endless Forms Most Beautiful," by Sean Carroll the process by which genetic information is stored, copied, and decoded is related to the analogy of modern computer technology. DNA is comparable to the information stored on a computer's hard disk-drive; it is like a long term hard copy of genetic information. It is universal and is the basis of all kingdoms of life, from a tiny microscopic bacterium to a 6 ton elephant in Africa. DNA is the beginning of the central dogma. The central dogma is describing the process of protein production; from DNA to RNA to protein. To continue with our computer analogy, RNA is similar to the information stored in a cache because the lifetime of RNA is much shorter than that of DNA. RNA is simply used as a "messenger" to relay the genetic information for protein production, and the proteins are in essences the "programs" of the computer.
In complex organisms like humans, we have cells that perform different functions. For example we have red blood cells that carry oxygen, and these cells are different from our muscle cells. However, even though these cells have completely different structures and functions they are based upon an identical DNA sequence. How is this possible? Well, it is in the regulation of these genes and differential protein production that allows these cells to perform different roles in our bodies. The genetic information found in DNA is essentially "decoded" in two steps to produce different proteins. DNA is made up of two strands that consist of nucleotides with four distinct bases; complimentary base pair bonding is what holds the two strands together. Each "gene" occupies a certain region along the DNA strand. The gene is decoded in two steps, the first called transcription. During transcription a polymerase produces an RNA strand that is based on the DNA template. This RNA transcript is single stranded, based on the complimentary sequence of the DNA template and is termed "messenger RNA." In the second decoding step the messenger RNA (mRNA) is directly translated into an amino acid sequence that forms a protein. The amino acid sequence corresponds directly with the original DNA sequence, and that determines the specific folding, structure, and chemical properties of the protein which determines the protein's function. Although I am no computer expert, using Sean Carroll's metaphor, this decoding process can be related to the "decoding" of the information put into computer. The information or "code" is given to the computer, and the sequence of that code will be processed by multiple mechanisms in the computer and a "result" will be produced.
This week in class we explored a paper written by Chris J. Cretekos et al. The article was called "Regulatory divergence modifies limb length between mammals," and looked at the limb-specific transcriptional enhancer Prx1 found in mice and compared it to the orthologous gene found in bats. What they found was that when the bat sequence of Prx1 was inserted into the mice, transcript levels in developing forelimbs was much higher and that the forelimbs themselves were also longer compared to the controls. It was also found that when the Prx1 gene was deleted in mice normal forelimbs developed. Overall, this article supports the claim that cis-regulatory are important in generating morphological differences between species.
This week I would like to return to a topic that I discussed in week 6; Mosaicism vs. Regulation. After reading Chelsae's Blog I decided it's worth discussing which of these processes is "more important" or the "right way." To elaborate I do not think either of these mechanism is more important or "better" than the other but rather they both play an important role in development. It is a combination of all these process that contribute to the complexity of development. For Weismann's theory about nuclear determinates, there are developmentally important proteins/RNA's that are unevenly distributed during cell division that lead to the fates of the daughter cells. These factors were termed cytoplasmic determinates. Now the term "mosaic" refers to eggs/embryos that develop as if their pattern of development was determined very early by the differential distribution of different molecules. This determines cell fate at an early stage. Examples that have a significant amount of mosaic development are Caenorhabditis and ascidian embryos. The biggest difference between regulative and mosaic embryos in the importance/amount of cell-cell interactions. In regulative development the cell-cell interactions are absolutely necessary to recognize and restore "the missing cell".
In conclusion, I feel that it is nearly impossible to sum up the phenomenon of development with just one of these terms because the development of an embryo is a complex process in itself and is regulated by even more complex processes.
One of the key concepts to understanding how a single celled organism can develop into a differentiated multicellular organism is to understand the central dogma. The central dogma is a term that describes how cells use DNA to produce mRNA to produce proteins. To produce a particular protein, the gene must be turned on and transcribed into mRNA, which then must be translated into protein. It is also important to distinguish between genotype and phenotype. The genotype of an organism is the genetic information (genes) it acquired from its parents. The phenotype describes how the organism appears physically, including its internal structure, and the biochemistry of its cell(s). The dynamic relationship between the genotype and phenotype is what attributes to the development of specialized and different cells. For example, consider why one of your liver cell looks different, and functions different from one of your heart cells. If the DNA in these cells is the same, how is it possible that they look and function differently?
The answer to this question is regulation. Although this liver and heart cell contain the same exact DNA sequence, not all of the genes in the DNA are turned on and producing the same exact proteins. What a cell can do is largely determined by what proteins it contains. In order to "turn on" a gene, a combination of steps must happen, which may include the binding of a specialized gene-regulatory protein to the control regions of the DNA. Both transcription and translation are regulated by multiple other mechanisms as well. For example, some mRNA may get degraded before it has a chance to be translated (preventing the protein from being produced.) Another example is called RNA Processing. After the gene is transcribed to RNA, the RNA may be cut and spliced in different ways to give rise to many different mRNAs (and proteins, all from the same gene). Alternatively, the proteins produced can be modified after translation as well (called post-translational modifications) before they become active proteins. One last mechanism is a category of genes that produces microRNAs. These are little RNA fragments that prevent the translation of specific mRNAs.
Together, all of these mechanisms mean that one gene can produce a multitude of functionally different proteins. So although the liver cell and the heart cell have the same DNA sequence, this does not necessarily mean they will be producing the exact same proteins. By controlling which proteins are made in the cell, the genes (DNA) can control the properties and behaviors of the cells, which determine the course of development. Genes control the development of the organism by determining where and when proteins are made (there are many genes involved in this process). The interactions between proteins and genes and between proteins and proteins also contribute to the properties of the cell.
One of these properties is cell-cell interactions, which is the ability of a cell to communicate with, and respond to, the cells around it. Their response to signals for cell movement, or change in cell shape brings about morphological (physical) changes in the developing organism. The cell-cell interactions are what determine how the organism develops (where the heart goes in relationship to the liver, arm, etc.) so therefore no developmental processes can be due to the function of a single gene or protein. Aside from just a single cell influencing the actions of another single cell, this can also happen in groups. One group of cells can influence the development of an adjacent group of cells. This signal can be sent through many cells, or be localized to a few cells.
Overall, the differences between cells must be generated by differences in gene activity which would lead to the production of different proteins. This leads to differences in cell properties and functions. Different proteins located on the outside of the cell, or being released from the cell provide a mechanism for cell-cell interactions/ or communication between cells. Responses to these signals can bring about physical changes in the developing organism, thus producing two cells with different physical properties and functions, but that still contain the same exact DNA sequence.
While investigating how cells became different from one another during development, two ideas were originally proposed. One of these was called Mosaicism and the other Regulation. Mosaicism is a model of development proposed by Weismann in the 1880's, where the adult is mapped out on the embryo by a pattern of nuclear determinants. It suggested that the nucleus of the zygote contained a number of special factors, and when the fertilized egg underwent rapid cell division these special factors (determinates) were distributed unevenly to the daughter cells. The uneven distribution is what determined the fate of each cell. Initial support for the Mosaic model came from experiments performed by Wilhelm Roux on frog embryos. During the first cleavage of a fertilized egg, he used a hot needle to destroy one of the two cells, and what he found was that the remaining cell developed into a half-larva which supports the mosaic mechanism.
However, Hans Driesch repeated a similar experiment on sea urchin eggs and found a completely different result. After separating the cells at the two-cell stage he found they developed into two normal larvas that were just smaller. This lead to the other proposed model termed Regulation. This refers to the ability of the embryo to develop normally even if there are parts that have been removed or rearranged suggesting that the early embryo is unspecified and that all cells are equivalent and contain the same cytoplasmic factors. A key factor that differentiates between the experiments done by Driesch and Roux were that during Roux's experiment he left the killed cell attached. The embryo didn't "know" the other cell was dead; it still developed a functional dorsal organizer, and developed as if the other cell was still there. If the dead cell at the two cell stage had been removed, it would have resulted in whole, but small embryos.