Matching Items (17)
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Proteins are a fundamental unit in biology. Although proteins have been extensively studied, there is still much to investigate. The mechanism by which proteins fold into their native state, how evolution shapes structural dynamics, and the dynamic mechanisms of many diseases are not well understood. In this thesis, protein folding

Proteins are a fundamental unit in biology. Although proteins have been extensively studied, there is still much to investigate. The mechanism by which proteins fold into their native state, how evolution shapes structural dynamics, and the dynamic mechanisms of many diseases are not well understood. In this thesis, protein folding is explored using a multi-scale modeling method including (i) geometric constraint based simulations that efficiently search for native like topologies and (ii) reservoir replica exchange molecular dynamics, which identify the low free energy structures and refines these structures toward the native conformation. A test set of eight proteins and three ancestral steroid receptor proteins are folded to 2.7Å all-atom RMSD from their experimental crystal structures. Protein evolution and disease associated mutations (DAMs) are most commonly studied by in silico multiple sequence alignment methods. Here, however, the structural dynamics are incorporated to give insight into the evolution of three ancestral proteins and the mechanism of several diseases in human ferritin protein. The differences in conformational dynamics of these evolutionary related, functionally diverged ancestral steroid receptor proteins are investigated by obtaining the most collective motion through essential dynamics. Strikingly, this analysis shows that evolutionary diverged proteins of the same family do not share the same dynamic subspace. Rather, those sharing the same function are simultaneously clustered together and distant from those functionally diverged homologs. This dynamics analysis also identifies 77% of mutations (functional and permissive) necessary to evolve new function. In silico methods for prediction of DAMs rely on differences in evolution rate due to purifying selection and therefore the accuracy of DAM prediction decreases at fast and slow evolvable sites. Here, we investigate structural dynamics through computing the contribution of each residue to the biologically relevant fluctuations and from this define a metric: the dynamic stability index (DSI). Using DSI we study the mechanism for three diseases observed in the human ferritin protein. The T30I and R40G DAMs show a loss of dynamic stability at the C-terminus helix and nearby regulatory loop, agreeing with experimental results implicating the same regulatory loop as a cause in cataracts syndrome.
ContributorsGlembo, Tyler J (Author) / Ozkan, Sefika B (Thesis advisor) / Thorpe, Michael F (Committee member) / Ros, Robert (Committee member) / Kumar, Sudhir (Committee member) / Shumway, John (Committee member) / Arizona State University (Publisher)
Created2011
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Among wild rodent populations, vertical transmission is believed to constitute the primary route of infection for Lymphocytic Choriomeningitis Virus (LCMV), a non-lytic arenavirus with both acute and chronic forms. When carrier mice infected at birth with the acute Armstrong strain reproduce, they generate congenital carrier offspring containing a quasispecies of

Among wild rodent populations, vertical transmission is believed to constitute the primary route of infection for Lymphocytic Choriomeningitis Virus (LCMV), a non-lytic arenavirus with both acute and chronic forms. When carrier mice infected at birth with the acute Armstrong strain reproduce, they generate congenital carrier offspring containing a quasispecies of LCMV that includes Armstrong as well as its chronic Clone-13 variant. This study examined the genetic trends in the vertical transmission of LCMV from mothers infected perinatally with Clone-13. Viral isolates obtained from the serum of congenital carrier offspring were partially sequenced to reveal residue 260 in the glycoprotein-encoding region of their S segment, the site of a major amino acid change differentiating the chronic and acute strains. It was found that the phenylalanine-to-leucine mutation associated with Clone-13 was present in 100% of the isolates, strongly indicating that the offspring of Clone-13 carriers contain exclusively the chronic variant. This research has broad implications for the epidemiology of the virus, and, given the predominance of Armstrong in the wild, suggests that there must be a biological cost associated with Clone-13 infection in non-carriers.
ContributorsFrear, Cody Christian (Author) / Blattman, Joseph (Thesis director) / Hogue, Brenda (Committee member) / Holechek, Susan (Committee member) / Barrett, The Honors College (Contributor) / School of Human Evolution and Social Change (Contributor) / School of Life Sciences (Contributor)
Created2015-05
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Despite the 40-year war on cancer, very limited progress has been made in developing a cure for the disease. This failure has prompted the reevaluation of the causes and development of cancer. One resulting model, coined the atavistic model of cancer, posits that cancer is a default phenotype of the

Despite the 40-year war on cancer, very limited progress has been made in developing a cure for the disease. This failure has prompted the reevaluation of the causes and development of cancer. One resulting model, coined the atavistic model of cancer, posits that cancer is a default phenotype of the cells of multicellular organisms which arises when the cell is subjected to an unusual amount of stress. Since this default phenotype is similar across cell types and even organisms, it seems it must be an evolutionarily ancestral phenotype. We take a phylostratigraphical approach, but systematically add species divergence time data to estimate gene ages numerically and use these ages to investigate the ages of genes involved in cancer. We find that ancient disease-recessive cancer genes are significantly enriched for DNA repair and SOS activity, which seems to imply that a core component of cancer development is not the regulation of growth, but the regulation of mutation. Verification of this finding could drastically improve cancer treatment and prevention.
ContributorsOrr, Adam James (Author) / Davies, Paul (Thesis director) / Bussey, Kimberly (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2015-05
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Calvin Blackman Bridges studied chromosomes and heredity in the US throughout the early twentieth century. Bridges performed research with Thomas Hunt Morgan at Columbia University in New York City, New York, and at the California Institute of Technology in Pasadena, California. Bridges and Morgan studied heredity in Drosophila, the common

Calvin Blackman Bridges studied chromosomes and heredity in the US throughout the early twentieth century. Bridges performed research with Thomas Hunt Morgan at Columbia University in New York City, New York, and at the California Institute of Technology in Pasadena, California. Bridges and Morgan studied heredity in Drosophila, the common fruit fly. Throughout the early twentieth century, researchers were gathering evidence that genes, or what Gregor Mendel had called the factors that control heredity, are located on chromosomes. At Columbia, Morgan disputed the theory, but in 1916, Calvin Bridges published evidence that, according to Morgan, did much to convince skeptics of that theory. Bridges also established that specific chromosomes function in determining sex in Drosophila.

Created2017-05-19
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Alfred Henry Sturtevant studied heredity in fruit flies in the US throughout the twentieth century. From 1910 to 1928, Sturtevant worked in Thomas Hunt Morgan’s research lab in New York City, New York. Sturtevant, Morgan, and other researchers established that chromosomes play a role in the inheritance of traits. In

Alfred Henry Sturtevant studied heredity in fruit flies in the US throughout the twentieth century. From 1910 to 1928, Sturtevant worked in Thomas Hunt Morgan’s research lab in New York City, New York. Sturtevant, Morgan, and other researchers established that chromosomes play a role in the inheritance of traits. In 1913, as an undergraduate, Sturtevant created one of the earliest genetic maps of a fruit fly chromosome, which showed the relative positions of genes along the chromosome. At the California Institute of Technology in Pasadena, California, he later created one of the first fate maps, which tracks embryonic cells throughout their development into an adult organism. Sturtevant’s contributions helped scientists explain genetic and cellular processes that affect early organismal development.

Created2017-05-20
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From 1913 to 1916, Calvin Bridges performed experiments that indicated genes are found on chromosomes. His experiments were a part of his doctoral thesis advised by Thomas Hunt Morgan in New York, New York. In his experiments, Bridges studied Drosophila, the common fruit fly, and by doing so showed that

From 1913 to 1916, Calvin Bridges performed experiments that indicated genes are found on chromosomes. His experiments were a part of his doctoral thesis advised by Thomas Hunt Morgan in New York, New York. In his experiments, Bridges studied Drosophila, the common fruit fly, and by doing so showed that a process called nondisjunction caused chromosomes, under some circumstances, to fail to separate when forming sperm and egg cells. Nondisjunction, as described by Bridges, caused sperm or egg cells to contain abnormal amounts of chromosomes. In some cases, that caused the offspring produced by the sperm or eggs to display traits that they would typically not have. His research on nondisjunction provided evidence that chromosomes carry genetic traits, including those that determine the sex of an organism.

Created2017-05-18
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In 1910, Thomas Hunt Morgan performed an experiment at Columbia University, in New York City, New York, that helped identify the role chromosomes play in heredity. That year, Morgan was breeding Drosophila, or fruit flies. After observing thousands of fruit fly offspring with red eyes, he obtained one that had

In 1910, Thomas Hunt Morgan performed an experiment at Columbia University, in New York City, New York, that helped identify the role chromosomes play in heredity. That year, Morgan was breeding Drosophila, or fruit flies. After observing thousands of fruit fly offspring with red eyes, he obtained one that had white eyes. Morgan began breeding the white-eyed mutant fly and found that in one generation of flies, the trait was only present in males. Through more breeding analysis, Morgan found that the genetic factor controlling eye color in the flies was on the same chromosome that determined sex. That result indicated that eye color and sex were both tied to chromosomes and helped Morgan and colleagues establish that chromosomes carry the genes that allow offspring to inherit traits from their parents.

Created2017-05-22
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In 1913, Alfred Henry Sturtevant published the results of experiments in which he showed how genes are arranged along a chromosome. Sturtevant performed those experiments as an undergraduate at Columbia University, in New York, New York, under the guidance of Nobel laureate Thomas Hunt Morgan. Sturtevant studied heredity using Drosophila,

In 1913, Alfred Henry Sturtevant published the results of experiments in which he showed how genes are arranged along a chromosome. Sturtevant performed those experiments as an undergraduate at Columbia University, in New York, New York, under the guidance of Nobel laureate Thomas Hunt Morgan. Sturtevant studied heredity using Drosophila, the common fruit fly. In his experiments, Sturtevant determined the relative positions of six genetic factors on a fly’s chromosome by creating a process called gene mapping. Sturtevant’s work on gene mapping inspired later mapping techniques in the twentieth and twenty-first centuries, techniques that helped scientists identify regions of the chromosome that when mutated cause organisms to develop abnormally and to create treatments to cure those kinds of disorders.

Created2017-05-22
Description

Hermann Joseph Muller conducted three experiments in 1926 and 1927 that demonstrated that exposure to x-rays, a form of high-energy radiation, can cause genetic mutations, changes to an organism's genome, particularly in egg and sperm cells. In his experiments, Muller exposed fruit flies (Drosophila) to x-rays, mated the flies, and

Hermann Joseph Muller conducted three experiments in 1926 and 1927 that demonstrated that exposure to x-rays, a form of high-energy radiation, can cause genetic mutations, changes to an organism's genome, particularly in egg and sperm cells. In his experiments, Muller exposed fruit flies (Drosophila) to x-rays, mated the flies, and observed the number of mutations in the offspring. In 1927, Muller described the results of his experiments in "Artificial Transmutation of the Gene" and "The Problem of Genic Modification". His discovery indicated the causes of mutation and for that research he later received the Nobel Prize in Physiology or Medicine in 1946. Muller's experiments with x-rays established that x-rays mutated genes and that egg and sperm cells are especially susceptible to such genetic mutations.

Created2017-03-07
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In 2015, Junjiu Huang and his colleagues reported their attempt to enable CRISPR/cas 9-mediated gene editing in nonviable human zygotes for the first time at Sun Yat-Sen University in Guangzhou, China. Their article, CRISPR /Cas9-mediated Gene Editing in Human Tripronuclear Zygotes, was published in Protein and Cell. Nonviable zygotes are

In 2015, Junjiu Huang and his colleagues reported their attempt to enable CRISPR/cas 9-mediated gene editing in nonviable human zygotes for the first time at Sun Yat-Sen University in Guangzhou, China. Their article, CRISPR /Cas9-mediated Gene Editing in Human Tripronuclear Zygotes, was published in Protein and Cell. Nonviable zygotes are sperm-fertilized eggs that cannot develop into a fetus. Researchers previously developed the CRISPR/cas 9 gene editing tool, which is a system that originated from bacteria as a defense mechanism against viruses. In their article, Huang and his team demonstrate that CRISPR/cas-9 gene editing can be used to correct a mutation in zygotes, or sperm-fertilized egg cells. However, they report that using CRISPR/cas 9 to edit those nonviable human zygotes led to off-target changes and, therefore, to unintended mutations in the human genome. Before Huang and his colleagues' experiment, CRISPR/cas 9 had never been used on human zygotes. In their article, Huang and his colleagues demonstrated the need to improve CRISPR/cas 9 gene editing accuracy before using it for gene therapy to treat and correct genetic diseases in humans.

Created2017-11-08