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Recent transcriptome data from yeast, worm, plants, and humans has shown that alternative polyadenylation (APA), a mechanism that enables expression of multiple 3′UTR isoforms for the same gene, is widespread in eukaryotic organisms. It is still poorly understood why metazoans require multiple 3′UTRs for the same gene, but accumulating evidence suggests that APA is largely regulated at a tissue-specific level. APA may direct combinatorial variation between cis-elements and microRNAs, perhaps to regulate gene expression in a tissue-specific manner. Apart from a few single gene anecdotes, this idea has not been systematically explored.
This dissertation research employs a systems biology approach to study the somatic tissue dynamics of APA and its impact on microRNA targeting networks in the small nematode C. elegans. In the first aim, tools were developed and applied to isolate and sequence mRNA from worm intestine and muscle tissues, which revealed pervasive tissue-specific APA correlated with microRNA regulation. The second aim provides genetic evidence that two worm genes use APA to escape repression by microRNAs in the body muscle. Finally, in aim three, mRNA from five additional somatic worm tissues was sequenced and their 3′ends mapped, allowing for an integrative study of APA and microRNA targeting dynamics in worms. Together, this work provides evidence that APA is a pervasive mechanism operating in somatic tissues of C. elegans with the potential to significantly rearrange their microRNA regulatory networks and precisely dose their gene expression.
This project utilized computational tools to analyze large data sets and interpreted the results from historical and philosophical perspectives. Tools deployed were derived from scientometrics, corpus linguistics, text-based analysis, network analysis, and GIS analysis to analyze more than 9000 articles (metadata and text) on systems biology. The application of these tools to a HPS project represents a novel approach.
The dissertation shows that systems biology has transitioned from a more mathematical, computational, and engineering-oriented discipline focusing on modeling to a more biology-oriented discipline that uses modeling as a means to address real biological problems. Also, the results show that bioengineering and medical research has increased within systems biology. This is reflected in the increase of the centrality of biology-related concepts such as cancer, over time. The dissertation also compares the development of systems biology in China with some other parts of the world, and reveals regional differences, such as a unique trajectory of systems biology in China related to a focus on traditional Chinese medicine.
This dissertation adds to the historiography of modern biology where few studies have focused on systems biology compared with the history of molecular biology and evolutionary biology.
The first chapter revisits some of the key experiments that contributed to the development of the repression model of genetic regulation in the lac operon and concludes that the early research on gene expression and genetic regulation depict an iterative and integrative process, which was neither reductionist nor holist. In doing so, it challenges a common application of a conceptual framework in the history of biology and offers an alternative framework. The second chapter argues that the concept of emergence in the history and philosophy of biology is too ambiguous to account for the current research in post-genomic molecular biology and it is often erroneously used to argue against some reductionist theses. The third chapter investigates the use of network representations of gene expression in developmental evolution research and takes up some of the conceptual and methodological problems it has generated. The concluding comments present potential avenues for future research arising from each substantial chapter.
In sum, this dissertation argues that the epistemic practices of gene expression research are an iterative and integrative process, which produces theoretical representations of the complex interactions in gene expression as networks. Moreover, conceptualizing these interactions as networks constrains empirical research strategies by the limited number of ways in which gene expression can be controlled through general rules of network interactions. Making these strategies explicit helps to clarify how they can explain the dynamic and adaptive features of genomes.
Human Papillomavirus, or HPV, is a viral pathogen that most commonly spreads through sexual contact. HPV strains 6 and 11 normally cause genital warts, while HPV strains 16 and 18 commonly cause cervical cancer, which causes cancerous cells to spread in the cervix. Physicians can detect those HPV strains, using a Pap smear, which is a diagnostic test that collects cells from the female cervix.
Johann Gregor Mendel studied patterns of trait inheritance in plants during the nineteenth century. Mendel, an Augustinian monk, conducted experiments on pea plants at St. Thomas’ Abbey in what is now Brno, Czech Republic. Twentieth century scientists used Mendel’s recorded observations to create theories about genetics.
In the 1930s, George Beadle and Boris Ephrussi discovered factors that affect eye colors in developing fruit flies. They did so while working at the California Institute of Technology in Pasadena, California. (1) They took optic discs (colored fuchsia in the image) from fruit fly larvae in the third instar stage of development. Had the flies not been manipulated, they would have developed into adults with vermilion eyes. (2) Beadle and Ephrussi transplanted the donor optic discs into the bodies of several types of larvae, including those that would develop with normal colored eyes (brick red), and those that would develop eyes with other shades of red, such as claret, carmine, peach, and ruby (grouped together and colored black in the image). (3a) When implanted into normal hosts that would develop brick red eyes, the transplanted optic disc developed into an eye that also was brick red. (3b) When implanted into abnormal hosts that would develop eyes of some other shade of red, the transplanted optic discs developed into eyes that were vermilion. Beadle and Ephrussi concluded that there was a factor, such as an enzyme or some other protein, produced outside of the optic disc that influenced the color of the eye that developed from the disc.
This illustration shows George Beadle and Edward Tatum's experiments with Neurospora crassa that indicated that single genes produce single enzymes. The pair conducted the experiments at Stanford University in Palo Alto, California. Enzymes are types of proteins that can catalyze reactions inside cells, reactions that produce a number of things, including nutrients that the cell needs. Neurospora crassa is a species of mold that grows on bread. In the early 1940s, Beadle and Tatum conducted an experiment to discover the abnormal genes in Neurospora mutants, which failed to produce specific nutrients needed to survive. (1) Beadle and Tatum used X-rays to cause mutations in the DNA of Neurospora, and then they grew the mutated Neurospora cells in glassware. (2) They grew several strains, represented in four groups of paired test tubes. For each group, Neurospora was grown in one of two types of growth media. One medium contained all the essential nutrients that the Neurospora needed to survive, which Beadle and Tatum called a complete medium. The second medium was a minimal medium and lacked nutrients that Neurospora needed to survive. If functioning normally and in the right conditions, however, Neurospora can produce these absent nutrients. (3) When Beadle and Tatum grew the mutated mold strains on both the complete and on the minimal media, all of the molds survived on the complete media, but not all of the molds survived on the minimal media (strain highlighted in yellow). (4) For the next step, the researchers added nutrients to the minimal media such that some glassware received an amino acid mixture (represented as colored squares) and other glassware received a vitamin mixture (represented as colored triangles) in an attempt to figure out which kind of nutrients the mutated molds needed. The researchers then took mold from the mutant mold strain that had survived on a complete medium and added that mold to the supplemented minimal media. They found that in some cases the mutated mold grew on media supplemented only with vitamins but not on media supplemented only with amino acids. (5) To discover which vitamins the mutant molds needed, Beadle and Tatum used several tubes with the minimal media, supplementing each one with a different vitamin, and then they attempted to grow the mutant mold in each tube. They found that different mutant strains of the mold grew only on media supplemented with different kinds of vitamins, for instance vitamin B6 for one strain, and vitamin B1 for another. In experiments not pictured, Beadle and Tatum found in step (4) that other strains of mutant mold grew on minimal media supplemented only with amino acids but not on minimal media supplemented only with vitamins. When they repeated step (5) on those strains and with specific kinds of amino acids in the different test tubes, they found that the some mutated mold strains grew on minimal media supplemented solely with one kind of amino acid, and others strains grew only on minimal media supplemented with other kinds of amino acids. For both the vitamins and amino acid cases, Beadle and Tatum concluded that the X-rays had mutated different genes in Neurospora, resulting in different mutant strains of Neurospora cells. In a cell of a given strain, the X-rays had changed the gene normally responsible for producing an enzyme that catalyzed a vitamin or an amino acid. As a result, the Neurospora cell could no longer produce that enzyme, and thus couldn't catalyze a specific nutrient.