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Capstone Outline Presentation

Includes basic information on the focus and details of the theme, mentors, and planned track activities.

Essay One: Angiogenesis Overview

First Draft of the first essay on angiogenesis. This is a short overview that covers the basics of the process of angiogenesis as well as the variety of molecules and cells involved.

First Draft of the second essay written about Schistosomiasis. It was at this point that the topic had been changed from angiogenesis.

Essay Two: Schistosomiasis Intro
Essay Three: Schistosomiasis Details

First Draft of the third essay. This essay focuses more on the details of the disease and some of the possibilities for long term treatment.

First Draft of the final essay on Schistosomiasis. It is the culmination of all of the completed research and includes edited portions of all other written papers.

Complete Research Paper

Snail Tale: A Study of Schistosomiasis

With the recent outbreaks of dangerous borderless virus’ like Ebola and Zika taking over mass media, it comes as no surprise that the developed world has very little interest in the growth of tropical illness’ that we perceive to be isolated. With the public's focus stuck on the unlikely possibility of contracting one of these media-hyped diseases, research funds are subverted from curing more common tropical illness in favor of appeasing the overblown fears of the developed world. Schistosomiasis is one of these debilitating parasitic diseases, and it’s taking over the tropics at a rate that is only second to malaria, yet despite the growing threat that this disease poses to both the developed and undeveloped world, the study and drive to cure the illness in an effective and permanent way is lacking.

 

Stopping the reproduction or the life cycle of the parasite is imperative due to the large impact that the sickness has on the world’s population. When looking at the mortality rate of people who have caught schistosomiasis, this parasitic fluke has been called the worst human helminth that is currently out in the world. With a classification as the most deadly parasitic disease combined with the fact that schistosomiasis has infected nearly 200 million individuals and leaves over 779 million more at risk for the cancers and kidney diseases that come from long term exposure, there needs to be some urgency in finding a long term solution to this widespread problem (Siddiqui) (McManus). With such a large number of affected people, schistosomiasis is clearly not bounded to one or two countries, but rather has the scope to reach into and affect individuals in 74 out of the 196 countries of the world (Siddiqui). The area that snail fever is affecting is also growing, and this is particularly threatening to the livelihoods of rural communities. According to the Center for Disease Control, schistosomiasis is considered to be a neglected tropical disease that is most commonly contracted by people in regions like the Brazilian rainforests, the rural communities of sub-Saharan Africa, and the Chinese and southeast asian rice paddies (Schistosomiasis FAQ’s). It is in these regions where contact with the schistosome contaminated water is inevitable. The rivers and lakes that hold these parasites are integral in the way of life of the small villages and indigenous groups that live in the surrounding areas. When these people go to get water or need to bathe, they are exposed to the blood flukes with such a high frequency that current vaccines have proven to be ineffective in stopping the cycle of the worms spread because the people always go back to the same contaminated pools to live their lives. Rice University professor, Dr. Daniel Wagner believes that the issue with current schistosomiasis treatments is that they lack in their ability to follow through with stopping the disease. This opinion is also shared by Dr. McManus from the Molecular Parasitology Laboratory, who states that the current immunization out on the market, praziquantel, has many limitations and despite it’s ability to get rid of the parasite in an individual's body, it is not a long term solution and has not been able to prevent the spread of the disease to new geographical areas. The current actions of humanitarian groups to give mass immunizations in fluke prone regions is not something that prevents the real danger, reinfections. After being immunized, the population of temporarily immune individuals would relive their previous ailments, but when the medicine wears off in a few months and they continue to return back to the same infested water source, they perpetuate the disease cycle and become infected yet again. In addition, praziquantel, as with any other temporary treatment, will become obsolete as the fast reproductive cycle of the Schistosoma mansoni worms garners enough genetic variation and mutations to find a way to surpass the fight that the medication is making against it. Once this happens, new drugs will have to be made for stronger and more chemically resistant flukes, and no real change has been made for the at risk populations. Schistosomiasis is still a threat. A threat that is endangering several hundred million individuals with cancers and death. At such high stakes, focus needs to turn away from temporary solutions such as the vaccine praziquantel, and shift to searching for a solid long term plan to end the perpetual spread of the illness.

 

With the threat of this parasitic disease growing in underdeveloped areas and slowly encroaching on developed nations, it has become a necessity to find a way to permanently change the pattern of life that the blood flukes must take to reach their human hosts. To do this, it is absolutely necessary to try to work out the details of the parasite-host relationship with the Biomphalaria glabrata snails and the Schistosoma mansoni worms. This can be done through researching the snails genome and possible outlying controls of snail population and susceptibility. The main three aspects of the slow process to stopping schistosomiasis include, careful analysis of the micro-interactions of the snail and the worm, transgenics, and gene compatability searching. With the help of detailed analysis of data from these three projects, it will be possible to create transgenic immune snails that could break the cycle that Schistosoma mansoni takes to reach and infect humans preventing the blood flukes from ever even having the ability to reproduce.

 

Aligning with the goals of any pathological experiment, the desire to experiment is driven by the urgent need to stop the spread of the so called “snail fever” before it enters and damages the human body. In order to do this, it is absolutely necessary to understand how schistosomes and snails interact with one another to pass along the disease. Schistosomes are a type of blood fluke or worm, that have two distinct hosts that they utilize for different purposes. One host is the Biomphalaria glabrata snails that are used for the laying of parasite eggs as well as sporocyst development, while the other host is the human which provides a great way to grow and receive nutrients as well as travel to new uninfected regions (Schistosomiasis FAQs). Because of the close interconnectedness that the parasite has with both humans and snails, it is very important that we understand the way that the parasite reproduces and what factors it can exert over the snail's ability to resist its takeover. It is important to take note of the life cycle of the parasite so that we have the ability to locate areas of interest and weakness that would allow us to halt its reproduction. The World Health Organization reported in a publication that once schistosome eggs reach the water supply of a community, “they hatch to release a tiny parasite (a miracidium) that swims actively through the water by means of fine hairs (cilia) covering its body” (Rozendaal). From here these miracidium enter the snail, reproduce asexually (a more rapid process than sexual reproduction) and form cercariae (Rozendaal). Scientists have the potential to exploit this and many other Schistosoma mansoni biological weaknesses to find an enzyme that has the ability to tear away or degrade the cilia of the miracidium. If performed successfully, these actions could have the ability to stop the spread of the fluke. By locating these steps of interaction with the host body, scientists are able to narrow the focus of what genes and processes we may want to use as targets for potentially finding a cure. Building off of that, many potential ways to stop the spread of these dangerous flukes make themselves present when we look at the biological structures of the worms. Alongside this, another widely recognized option for stopping the spread of snail fever  is to try to up the innate immune response of the snails to prevent reproduction of the schistosomes in a particular subset of genetically modified clean hosts. From even the most basic of analytical biological structures, the life cycle, doors can be opened to locate new avenues of pathological cures.

 

Yet even with the basic overarching tools of macroscopic morphology at our disposal, it is always necessary to dig a little deeper and attempt to understand the internal structures and molecules that have an impact on the increasing population of the parasite. One very unique process that occurs in the snail during the encroachment of the parasite is that the “schistosomes have evolved a mechanism that is capable of manipulating the genome of a compatible snail host, thereby orchestrating changes in the snail’s cell nuclei that alters gene expression in the parasite’s favor” (Knight). Even though these changes to gene expression have yet to be fully identified, it is an interesting concept that has the potential to be a great tool for attempting to decrease the reproduction of the parasite. By locating and knowing the chemical components that the flukes release to perform these tasks, it makes it much easier to discover ways to halt the power the parasite has over the nucleus of individual snails.  This can be achieved by finding ways to denature schistosome exclusive proteins or by creating ways to block their signal transduction pathways. Now, there are still many more biological factors that play large roles in how this disease is passed around at alarmingly high rates, but even locating just a few possibilities for treatment allows for the expansion of ideas to find more accurate and useful tests to stop the spread of schistosomiasis.

 

It is important when looking at a disease started by an organism, to study the molecular as well as the macroscopic host-parasite interactions in order to find effective targets for halting disease continuation. Macroscopically, the snail host is used by the Schistosoma mansoni worms as a way to gain the nutrients that they need to develop from miracidia to cercariae. When the miracidia invade the snail host they “form a mother sporocyst near the site of penetration. Daughter sporocysts are produced 2-6 weeks after infection and they migrate to other organs in the snail” (Schistosoma). From here thousands of cercariae are released into the water, and after a period of four weeks they have the ability to grow and infect humans (Schistosoma). Small details like the time frame of the sporocysts cercariae production are surprisingly critical, because they highlight some of the timing weaknesses of the worm that come from it’s long periods of in-snail growth. Looking at the details of these stages, we can see some clear weaknesses in the structure of the organism that can be targeted by the upregulation or downregulation of various genes in the snail to halt reproduction. One such viable target is the sporocyst stage of schistosoma development. It is here that there are two distinct variances of sporocysts in use. The first sporocyst derives from the miracarde that originally invades the snail’s head foot where it then divides and reproduces to create several more ‘daughter’ sporocysts that travel through the blood of the Biomphalaria glabrata snails to reach the gonads and other glands (Moen & Olivier). Targeting of the pathways involved in sporocyst reproduction would stop the worms growth before they can even reach any of the adult stages of development. All that would need to be done to achieve a goal such as this would be to begin to study the different pathways in the snail that cause the sporocyst reproduction and division and find a gene or enzyme that can be put into the snails and upregulated to stop the fluke reproductive cycle, thus protecting millions from these parasites. Another way to stop the spread of the deadly Schistosoma mansoni is by the use of siRNAs, small interfering RNAs. The parasite upon invasion requires purine, a nucleic acid, for the division of it’s cells. It has been found that the “parasite is unable to synthesize purines de novo; therefore, it [must] use precursors obtained from the host's blood” in order to grow (Pereira). Small microscopic details such as the fact that the worms can’t produce purines on their own, provide scientists with an idea of where they might want to start experimenting. In this case, there has been a lot of experimentation with siRNA’s in the past so they are relatively easy to use once you can find the desired sequence. All it really takes to overcome the micro and macro interactions of the two organisms involved in schistosomiasis is the fine focus of locating details in their genomes and protein synthesis. Overall, there are so many more interactions that can be focused on in the developmental pathways of the snails to stop schistosomiasis at it’s roots, in development.

 

Continuing our look at the even finer details of our host species, the Biomphalaria glabrata snail’s genome, allows scientists to begin to see what the snail is lacking to make them immune to the parasite. It is necessary to look at the relationships between the two organisms alongside the possible internal and external immunity controls, as they supply laboratories with appropriate information from which to begin testing the creation of snails that can’t take in the parasite. As mentioned earlier, it is impossible to solve this problem in it’s entirety by just using a variety of recursive human administered medications. Solving a complex and vexatious issue requires a more permanent long term solution. One such alternative for this process is the usage of transgenics. From the dictionary of Merriam-Webster, transgenics is “a branch of biotechnology concerned with the production of transgenic plants, animals, and foods” where you change “an organism or cell of one species [by incorporation of] one or more genes [from] another species”(Transgenic). Genetic experiments have been decided by much of the scientific community to be tedious and often have a high degree of uncertainty, especially when dealing with an organism like the Biomphalaria glabrata that has a genome that is highly under labeled (Rozendaal). Due to this relatively underdeveloped genome, it is necessary to find scientists that are willing to look into tracking down specific proteins and gene sequences in the snail that match other more documented organisms. This technique is a part of the process for comparing genes across species that is commonly used for discovering new facts about bodily processes like angiogenesis or the effects of specific diseases. In a similar experimental fashion, mollusk dedicated scientist Dr. Mulvey, believed that one of the most promising avenues for stopping schistosomiasis is cross-species gene comparisons. He has expressed his confidence in this process by saying that “locating and characterizing the genes for controlling [certain] traits could have important consequences for disease control and for the understanding of the snail-schistosome coevolution” (Mulvey).  So far in this endeavor, the best organisms to keep an eye on for comparison include Homo sapiens, Drosophila melanogaster, and other varieties of mollusks.

 

These techniques have been the cornerstone of a study that is being performed at Rice University. Currently, I am involved in the beginnings of this experiment where the end goal is to create viable transgenic snails that are able to fend off invasion of the Schistosoma mansoni worms on their own. As a part of this study, scientists are focusing on the pathways that code for innate immunity in humans and fruit flies. Locating all of these pieces and protein isoforms for the signal transduction pathways in the variety of organisms, allows us to look at the snail and see if any of these sequences was conserved during evolution when these various organisms split apart. To put the idea into more tangible terms, the selection of the genome that codes for innate immunity in both humans and flies, the NF-κB signalling pathway, has had a split in usage since the common ancestor of the two organisms. This means that in both the base organism and the flies, these sequences can also be used in an alternative manner to code for dorsal ventral patterning during morphological development. In humans, this particular ability was lost by the gene and now we only use NF-κB to regulate our immune response (Silverman). Noting these splits in usage for all of the proteins involved in this pathway are absolutely necessary in seeing where the snail fits in the cladogram, as well as for noting the existence of specific sequences that can be altered or suppressed in the future to monitor the spread and development of schistosomes. The end game for tedious research like this, is to take genes from other animals and add them to the genome of the snail or to suppress and support these unique coding patterns in the hopes that we might be able to decrease the ability of the parasite to take over the host and reproduce.

 

There are several steps to the complex process of transgenic comparisons, but none can be achieved without the usage of gene compatability searching, or the searching for genes from model organisms with well documented genomes like humans, other mollusks, or even fruit flies. This is all done with the express purpose in mind to locate a variety of genes that code for parts of vital biological pathways in the Biomphalaria glabrata genome. These are the chosen model organisms because each species has highly labeled genomes that by use of a genome database, can easily tell you what each and every gene produces from its many introns and exons. One of the gene databases is the government ran National Center for Biotechnology Information (NCBI) online database. In this particular database you are able to locate the specific proteins that are involved in the pathways that you want to change and from there you can use a BLAST search to compare the gene that you have located in a model organism to the entire genome of the target organism, the snail. The database will search through all of the ordered bases and amino acids to try to find you several sites that have a high rate of similarity. It is important to note that amongst all of the organisms in the world, it is highly unlikely to ever find a perfect match for one specific protein due to the genetic drift and mutations that cause evolution. Once the database has located the top sites in the target genome for the protein that you had BLAST searched then it is finally time to crunch some numbers and look into the details of how close in amino acid sequence these two really are so that conclusions could be extrapolated from the data collected to show whether or not the Biomphalaria glabrata genome contains a necessary protein that other non-susceptible animals have or lack.

 

Scientists perform and repeat these actions in an experiment because they are looking for one of two specific things. They either want to learn if the organism in question even has these genes in their bodies or they desire to know if the gene exists in the target organism, but performs a different biological function. In this particular experiment for solving the mysteries of schistosomiasis, both of these factors are important in understanding why the snail can’t currently stop the invasion of the incoming Schistosoma mansoni worms. The immune response is one of the major focuses of researchers everywhere because understanding why the snail can’t fight off the worm while other organisms can, is a possible way to start looking at creating immune snails that can’t transmit the disease. Innate immunity “generates antigen-specific receptors, antibodies, and T-cell receptors by somatic cell DNA rearrangement. These receptors, found only in higher eukaryotes, recognize specific pathogen-encoded proteins” (Silverman). At the moment, the path being studied by researchers at Rice University is the NF-kB genetic pathway, as it codes for innate immunity in both humans and flies. Looking at details in the genome of the Biomphalaria glabrata snails is very important because if it is possible to locate regions in immune response that are lacking but have the potential to be regulated to stop schistosome invasion, then that will be one of the major paths taken by modern researchers. After targets are found and compatible genes have been located,like those in the NF-kB pathway, it becomes a viable next step to move on to the transgenic process of replacing, adding, and promoting genes in the body of our hosts. Transgenics have been a hotbed topic, especially in pharming where science “[has] experienced much success, and it is predicted that in the future a plethora of protein products will be made using these ‘natural’ bioreactors” (Larrick).  Many organisms around the world can produce very specific, unique substances that are not found elsewhere in the environment. In cases like this transgenics are used to transfer the genes used to produce these positive and necessary substances from the original carriers to a population of more abundant, easier to reproduce, or simpler to take care of organisms. The desired chemicals are then extracted from the bodies of these organisms to be used in the production of pharmaceuticals in the world. Besides just being used for the commercial world, trans-species genetics is a very important tool used by researchers everywhere. It is used in the study of angiogenesis, the growth of blood vessels in response to hypoxia, and vital to our experiments, it will be used for finding a cure to schistosomiasis.

 

Looking beyond the internal structure of the Biomphalaria glabrata as well as its interactions with the schistosome parasite, several external factors have made themselves apparent for the creation of immune snails that would no longer be able to spread the disease. One factor that is currently under experimentation is to study the effects that their environments have on them. This includes looking at the effects of very minute temperature differences or plant and algae varieties that are common in the tropical regions that host schistosomes and their hosts. In some of the tropical rivers where the freshwater snails develop, there are several key chemicals released by the environment, baby snails, and the food that they consume that may play a role in how the snails develop over time as well as what genes end up being expressed (Thomas). Now this is important to note because of the highly selective nature of schistosomes that derives from their limited window of opportunity for picking viable hosts. Schistosoma mansoni only has the ability to spread and infect more humans when there are an abundance of viable hosts nearby for their reproductive process. The multiplication of these organisms is limited by a window of snail development due to the fact that older snails of reproductive age have a “singular dominant trait that can be passed down where as when the snail is juvenile it has a complex system of about 6 genes” (Knight). The snails have more complex systems of protection as juveniles because they want to reach reproductive age without dying in order to achieve high reproductive rates. The difference makes itself apparent when viewing the genetic expression of adult snails. At this point in their lifestyles, reproductive roles have already been fulfilled and these extra genes are then unnecessary and left unused. Looking for a way to keep the expression of all six original genes over time is yet another possible way to protect the world from the human helminth, schistosomiasis. These differences in gene expression over time and in different environments are just one more factor that need to be taken into consideration when creating a preventative measure for the spread of flukes.

 

Even though all of these targets look promising after extensive research and development, it is important to note that even if any of these processes were able to work in a way that would breed a less susceptible snail, we would still need to consider the environmental impact, rapid genetic variation of the parasite, and competition of the ‘clean’ snails with the non-transgenic snails. Yet even with these concerns in the back of the minds of scientists everywhere, tropical illnesses like schistosomiasis need to be focused on and studied, in order to protect the livelihoods of thousands of world citizens.

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