[{"id":917,"date":"2017-02-23T10:20:58","date_gmt":"2017-02-23T15:20:58","guid":{"rendered":"http:\/\/sites.allegheny.edu\/biochem\/?page_id=917"},"modified":"2026-02-27T15:50:33","modified_gmt":"2026-02-27T20:50:33","slug":"department-information","status":"publish","type":"page","link":"https:\/\/sites.allegheny.edu\/biochemistry\/department-information\/","title":{"rendered":"Department Information"},"content":{"rendered":"<h3 class=\"acalog-entity-name\">Biochemistry<\/h3>\n<div class=\"acalog-entity-programs\">\n<p>Professors Humphreys (Chair), Chapp, Coenen, Deckert, Garcia, Hersh, Kadmiel, Murphree, Nelson, Pandey, Persichini<\/p>\n<p>Biochemistry is the science at the interface of Biology, Chemistry, and Physics that deals with the chemical composition of living matter and the molecular nature and physical processes of living systems. The Biochemistry major is part of an interdisciplinary program primarily supported by faculty from the Biology and Chemistry departments. The major is considered a Natural Sciences major. There is no Biochemistry minor.<\/p>\n<div>\n<div><hr><div class=\"box box-info box-align-\"><h4><i class=\"fa fa-info\"><\/i><span>Academic Bulletin<\/span><\/h4>Visit the Academic Bulletinfor information on all majors, minors, and other programs at Allegheny college.\n<p><a target=\"_self\" class=\"button icon button-lg block  yellow\" href=\"http:\/\/catalog.allegheny.edu\"><i class=\"fa fa-book  pull-left\"><\/i>Visit the Allegheny College Academic Bulletin<\/a><\/p><\/div><\/div>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>Biochemistry Professors Humphreys (Chair), Chapp, Coenen, Deckert, Garcia, Hersh, Kadmiel, Murphree, Nelson, Pandey, Persichini Biochemistry is the science at the interface of Biology, Chemistry, and Physics that deals with the chemical composition of living matter and the molecular nature and physical processes of living systems. The Biochemistry major is part of an interdisciplinary program primarily [&#8230;]<\/p>\n<p><a class=\"mt-5\" href=\"https:\/\/sites.allegheny.edu\/biochemistry\/department-information\/\">Continue Reading &#8220;Department Information&#8221;<\/a><\/p>\n","protected":false},"author":546,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"inline_featured_image":false,"footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-917","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages\/917","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/users\/546"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/comments?post=917"}],"version-history":[{"count":1,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages\/917\/revisions"}],"predecessor-version":[{"id":1139,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages\/917\/revisions\/1139"}],"wp:attachment":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/media?parent=917"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":909,"date":"2017-02-23T10:15:05","date_gmt":"2017-02-23T15:15:05","guid":{"rendered":"http:\/\/sites.allegheny.edu\/biochem\/?page_id=909"},"modified":"2024-05-20T09:47:13","modified_gmt":"2024-05-20T13:47:13","slug":"biochemistry-major","status":"publish","type":"page","link":"https:\/\/allegheny.edu\/academics\/programs\/biochemistry\/","title":{"rendered":"Biochemistry Major"},"content":{"rendered":"<p><img decoding=\"async\" class=\"aligncenter\" src=\"https:\/\/sitesmedia.s3.amazonaws.com\/biochem\/files\/2017\/02\/2C7A6882-2-e1487862875159-1024x485.jpg\" alt=\"\" \/><\/p>\n<p><div class=\"dep-info\"><h3 xmlns:h=\"http:\/\/www.w3.org\/1999\/xhtml\">Biochemistry Learning Outcomes<\/h3><p xmlns:h=\"http:\/\/www.w3.org\/1999\/xhtml\">Students who successfully complete a major in Biochemistry are expected to be able to:<\/p><ul xmlns:h=\"http:\/\/www.w3.org\/1999\/xhtml\"><li>Think critically and creatively to develop appropriate biochemical research questions;<\/li>&#13;\n\t<li>Use the scientific method to carry out laboratory investigations that address biochemical questions;<\/li>&#13;\n\t<li>Clearly and persuasively communicate the results of scientific investigations in written and oral forms;<\/li>&#13;\n\t<li>Use an understanding of Biology, Chemistry, and Physics concepts to organize and evaluate the research findings found in the primary Biochemistry literature;<\/li>&#13;\n\t<li>Explain how science and technology impact society, both positively and negatively, with attention to the limitations of science;<\/li>&#13;\n\t<li>Use and synthesize the fundamental concepts of Chemistry, Biology, and Physics to analyze and solve complex problems involving living systems.<\/li>&#13;\n<\/ul><h3 xmlns:h=\"http:\/\/www.w3.org\/1999\/xhtml\">The Biochemistry Major<\/h3><p xmlns:h=\"http:\/\/www.w3.org\/1999\/xhtml\">The Biochemistry major leads to the Bachelor of Science degree and requires a group of introductory and upper level courses from the Biology, Chemistry, Physics, and Mathematics Departments. In addition, majors must take the Junior Seminar offered by one of the participating departments (<a link-id=\"acalog-a-31\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=16847\" type=\"tooltip\">BIO 580<\/a>\u00a0or <a link-id=\"acalog-a-32\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=16882\" type=\"tooltip\"> CHEM 584<\/a>). Students may choose an area of specialty within the major via additional electives and the selection of an appropriate Senior Project (<a link-id=\"acalog-a-33\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=16816\" type=\"tooltip\">BCHEM 600<\/a>\u00a0and <a link-id=\"acalog-a-34\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=16817\" type=\"tooltip\"> BCHEM 610<\/a>). No courses required for the major may be taken on a Credit\/No Credit basis.<\/p><\/div><div class=\"core\"><h3>Requirements:<\/h3><a:content xmlns:a=\"http:\/\/www.w3.org\/2005\/Atom\"\/><br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=20881\">MATH 141\u00a0-\u00a0Calculus I with Precalculus, Part 2<\/a> OR<br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=20882\">MATH 151\u00a0-\u00a0Calculus I<\/a> (students can take either course to fulfill the Calculus I requirement) Placement into MATH 152 satisfies the MATH 141 or 151 requirement for the major.<br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=20883\">MATH 152\u00a0-\u00a0Calculus II<\/a> <br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=17579\">PHYS 110\u00a0-\u00a0Core Concepts in Physics I<\/a> When scheduling permits, students are strongly encouraged to enroll in PHYS 110\u00a0rather than PHYS 101. Note that enrollment in PHYS 110\u00a0is limited to first and second year students. OR<br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=17577\">PHYS 101\u00a0-\u00a0Fundamentals of Physics I<\/a> When scheduling permits, students are strongly encouraged to enroll in PHYS 110\u00a0rather than PHYS 101. Note that enrollment in PHYS 110\u00a0is limited to first and second year students. <br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=16821\">BIO 220\u00a0-\u00a0Organismal Physiology and Ecology<\/a><br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=16822\">BIO 221\u00a0-\u00a0Genetics, Development and Evolution<\/a><br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=16825\">BIO 305\u00a0-\u00a0Molecular Biology<\/a> <br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=16863\">CHEM 120\u00a0-\u00a0Chemical Concepts 1<\/a> Placement into CHEM 122\u00a0satisfies the CHEM 120\u00a0requirement for the major.<br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=16864\">CHEM 122\u00a0-\u00a0Chemical Concepts 2<\/a><br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=16866\">CHEM 231\u00a0-\u00a0Organic Chemistry I: Form and Function<\/a><br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=16868\">CHEM 242\u00a0-\u00a0Physical Chemistry<\/a><br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=16869\">CHEM 253\u00a0-\u00a0Introductory Biochemistry<\/a> <br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=16851\">FSBIO 201\u00a0-\u00a0Investigative Approaches in Biology<\/a> OR<br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=16884\">FSCHE 201\u00a0-\u00a0Research Methods in Chemistry<\/a><\/div><div class=\"core\"><h3>6 Credits of Upper-Level Biology and Chemistry Electives:<\/h3><a:content xmlns:a=\"http:\/\/www.w3.org\/2005\/Atom\" xmlns:h=\"http:\/\/www.w3.org\/1999\/xhtml\"><p xmlns:h=\"http:\/\/www.w3.org\/1999\/xhtml\">One each from Biology and Chemistry*:<\/p><\/a:content><\/div><div class=\"core\"><h4>Upper-Level Elective Options: Biology<\/h4><a:content xmlns:a=\"http:\/\/www.w3.org\/2005\/Atom\"\/><br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=16823\">BIO 300\u00a0-\u00a0Bioinformatics<\/a> OR<br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=16970\">CMPSC 300\u00a0-\u00a0Bioinformatics<\/a> <br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=16826\">BIO 310\u00a0-\u00a0Microbiology<\/a><br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=16827\">BIO 320\u00a0-\u00a0Cell Biology<\/a><br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=16829\">BIO 325\u00a0-\u00a0Genetics<\/a><br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=16838\">BIO 360\u00a0-\u00a0Plant Physiology<\/a><\/div><div class=\"core\"><h4>Upper-Level Elective Options: Chemistry<\/h4><a:content xmlns:a=\"http:\/\/www.w3.org\/2005\/Atom\"\/><br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=17917\">CHEM 354\u00a0-\u00a0Biochemical Metabolism<\/a><br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=16873\">CHEM 357\u00a0-\u00a0Macromolecular Synthesis<\/a><br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=20900\">CHEM 362\u00a0-\u00a0Analytical Chemistry<\/a><br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=16877\">CHEM 432-439\u00a0-\u00a0Current Topics in Organic Chemistry<\/a><br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=16879\">CHEM 452-459\u00a0-\u00a0Current Topics in Biochemistry<\/a><br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=16880\">CHEM 462-469\u00a0-\u00a0Current Topics in Analytical Chemistry<\/a><\/div><div class=\"core\"><h3>Junior Seminar:<\/h3><a:content xmlns:a=\"http:\/\/www.w3.org\/2005\/Atom\"\/><br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=16882\">CHEM 584\u00a0-\u00a0Junior Seminar<\/a> OR Approved section of<br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=16847\">BIO 580\u00a0-\u00a0Junior Seminar<\/a><\/div><div class=\"core\"><h3>Senior Project I and II:<\/h3><a:content xmlns:a=\"http:\/\/www.w3.org\/2005\/Atom\"\/><br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=16816\">BCHEM 600\u00a0-\u00a0Senior Project I<\/a><br><a class=\"course-link\" href=\"http:\/\/catalog.allegheny.edu\/preview_course_nopop.php?catoid=24&coid=16817\">BCHEM 610\u00a0-\u00a0Senior Project II<\/a><\/div><div class=\"core\"><h3>Note:<\/h3><a:content xmlns:a=\"http:\/\/www.w3.org\/2005\/Atom\" xmlns:h=\"http:\/\/www.w3.org\/1999\/xhtml\"><p xmlns:h=\"http:\/\/www.w3.org\/1999\/xhtml\">*Please note that many of the upper-level electives have pre-requisites that must be satisfied prior to enrollment.<\/p><\/a:content><\/div><br \/>\n<hr><div class=\"box box-info box-align-\"><h4><i class=\"fa fa-info\"><\/i><span>Academic Bulletin<\/span><\/h4>Visit the Academic Bulletinfor information on all majors, minors, and other programs at Allegheny college.\n<p><a target=\"_self\" class=\"button icon button-lg block  yellow\" href=\"http:\/\/catalog.allegheny.edu\"><i class=\"fa fa-book  pull-left\"><\/i>Visit the Allegheny College Academic Bulletin<\/a><\/p><\/div><\/p>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":546,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"inline_featured_image":false,"footnotes":"","_links_to":"https:\/\/allegheny.edu\/academics\/programs\/biochemistry\/","_links_to_target":""},"class_list":["post-909","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages\/909","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/users\/546"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/comments?post=909"}],"version-history":[{"count":0,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages\/909\/revisions"}],"wp:attachment":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/media?parent=909"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":851,"date":"2015-05-05T08:42:52","date_gmt":"2015-05-05T12:42:52","guid":{"rendered":"http:\/\/sites.allegheny.edu\/biochem\/?page_id=851"},"modified":"2015-05-05T11:21:53","modified_gmt":"2015-05-05T15:21:53","slug":"senior-project-abstracts-2015","status":"publish","type":"page","link":"https:\/\/sites.allegheny.edu\/biochemistry\/student-research\/senior-project\/senior-project-abstracts-2015\/","title":{"rendered":"Senior Project Abstracts 2015"},"content":{"rendered":"<p><strong>Investigation of Keap1 and Nrf2 Expression in Canine Osteosarcoma Cell Lines<br \/>\n<\/strong>Thomas S. Albanesi, 2015 (Advisor: Dr. Ann Kleinschmidt)<\/p>\n<p style=\"padding-left: 30px\">Osteosarcoma, a primary bone cancer, is a devastating disease that has a poor long-term prognosis and affects adolescent humans as well as <em>Canis lupus familiaris<\/em> (the domestic dog).\u00a0 The profile of the disease is similar between both species, and thus, studying canine osteosarcoma may lead to a better prognosis for dogs as well as humans.\u00a0 The Keap1\/Nrf2 pathway regulates oxidative stress in cells, and through the protection Nrf2 provides, it may act as both a tumor suppressor gene and an oncogene.\u00a0 Thus, dysregulation of Keap1 and Nrf2 may contribute to oncogenesis.\u00a0 A form of gene expression regulation, DNA methylation, is a possible causation of such dysregulation.\u00a0 Thus, in this project, the methylation status of the Keap1 promoter and its effects on Keap1 gene expression were analyzed in osteosarcoma cell lines.\u00a0 Quantitative PCR did not show significant differences in the Keap1 mRNA levels between the cell lines, but there was a significant difference in the Nrf2 mRNA levels.\u00a0 Minimizing the variability between the trials, the ratio of Nrf2\/Keap1 mRNA levels showed significant differences between some cell lines.\u00a0 Keap1 promoter methylation was detected in three of the four osteosarcoma cell lines, but the methylation status of the control cell line was inconclusive.\u00a0 The data supports a possible role of Nrf2 and Keap1 in osteosarcomagenesis.\u00a0 However, the results of the DNA methylation analysis were inconclusive.<\/p>\n<hr \/>\n<p><strong>An Investigation of the Thermodynamics of Cytosine Bulges at the Splice Site of Influenza A in the Double Stranded RNA Region of Hairpin Loops<br \/>\n<\/strong>Bethany M. Crile, 2015 (Advisor: Dr. Marty Serra)<\/p>\n<hr \/>\n<p><strong>Biofilm characterization of <em>Haemophilus ducreyi\u2019s<\/em> sexually transmitted versus chronic limb ulcer strains<br \/>\n<\/strong>Andrew J. Crofford, 2015 (Advisor: Dr. Tricia Humphreys)<\/p>\n<p style=\"padding-left: 30px\"><em>Haemophilus ducreyi<\/em>, the causative agent of the sexually transmitted infection chancroid, has two sexually transmitted ulcer strains: class I (35000HP), class II (HMC112), and a newly discovered chronic limb ulcer (CLU) strain (NZS3). CLU are transmitted by non-genital interaction such as casual contact with a limb abrasion. It is unknown if these strains form biofilms, but it is hypothesized the CLU strain has greater biofilm components present because of its seeming ease of transmission. Therefore, the three strains were compared for biofilm growth using real time RT-PCR and fluorescent and confocal microscopy. Three open reading frames within a polycistronic operon that codes for fimbria-like proteins (flp) and tight-adhesion proteins (tad) were compared in biofilm and planktonic cells. Microscopy images identified extracellular DNA and carbohydrates (\u03b1-mannopyranosyl and \u03b1-glucopyranosyl), common biofilm formation indicators, which form a matrix around the cells. HMC112 typically had more proficient growth than 35000HP, which had better growth than NZS3. There was no statistical significance between biofilm and planktonic mRNA levels for flp3, orfB, or tadG between classes (P=0.49, 0.88, and 0.27 respectively). However, HMC112 formed the most prolific biofilm, but it had the least amount of mRNA from the flp\/tad operon. NZS3 did not form as three-dimensional biofilms as the other two strains, but it had the greatest mRNA levels. This study supports the idea that <em>H. ducreyi<\/em> is a biofilm-forming bacteria when observed in a pure liquid culture.<\/p>\n<hr \/>\n<p><strong>Investigation of the Modification of Cysteine Residues in <em>Brassica rapa<\/em> APX1 by CysNO<br \/>\n<\/strong>Patrick P. Ottman, 2015 (Advisor: Dr. Ann Kleinschmidt)<\/p>\n<p style=\"padding-left: 30px\">There is evidence that modification of cysteines by oxidation and nitrosylation affect protein structure and function. While S-nitrosylation of cysteines has been researched, no studies have ever investigated how multiple cysteines in a single protein are differentially nitrosylated and only predictive models exist. It has been shown that nitrosylation at cysteines of the cytosolic ascorbate peroxidase of <em>Arabidopsis thaliana<\/em> (AtAPX1) affects its activity. To investigate the modification of the cysteines on <em>Brassica rapa<\/em> APX1, a protocol including reduction of the protein with TCEP, treatment with different concentrations of CysNO, followed by labeling unmodified cysteines with DyLight 550 were developed. Five transitions of fluorescence were observed between concentration ratios (CysNO\/BrAPX1) 0.08\/1, 0.11\/1, 0.13\/1, 0.22\/1, 0.34\/1, and 3.36\/1. The activity of the corresponding nitrosylation events were also investigated and results showed that as more S-nitrosylation events occurred, the activity of the protein varied. From this research it is theorized that different cysteines are modified at different concentrations of CysNO and thus all the cysteine residues do not have the same redox potential because of differing microenvironments. This could mean that each cysteine modification has its own separate effect on the proteins activity and thus the protein\u2019s activity could be redox controlled.<\/p>\n<p><strong>Disruption of <em>Haemophilus ducreyi<\/em> biofilms by probiotic lactobacilli<br \/>\n<\/strong>Jenna L. Sandala, 2015 (Advisor: Dr. Tricia Humphreys)<\/p>\n<p style=\"padding-left: 30px\"><em>Haemophilus ducreyi<\/em>, an obligate human pathogen, is the etiological agent of the sexually transmitted infection (STI) chancroid, which is marked by soft, erythematous papular lesions that appear on or around the genitals. Though wide-spectrum antibiotics are generally successful in clearing <em>H. ducreyi<\/em> infections, this conventional treatment can be hindered by a variety of factors, including the formation of biofilms, communities of bacterial cells that organize into a matrix of extracellular polymeric substances (EPS).\u00a0 Recently, the introduction of probiotic lactobacilli to other urogenital infections has been shown to not only disrupt biofilm formation, but also clear the infection on the whole.\u00a0 Therefore, the purpose of this study was to determine what effect, if any, the introduction of probiotic <em>Lactobacillus rhamnosus<\/em> GR-1 and <em>Lactobacillus reuteri<\/em> RC-14 had on <em>H.\u00a0ducreyi<\/em> 35000HP biofilm structure. Additionally, the <em>H. ducreyi<\/em> transcriptional response to the presence of lactobacilli was quantified by performing real time RT-PCR of the CpxRA stress response gene products.\u00a0 Analysis of biofilm structures was performed using both light and fluorescent microscopy, and revealed that <em>H. ducreyi<\/em> biofilms that had been challenged with lactobacilli were consistently less dense and exhibited scattered growth in comparison to unchallenged biofilms. Real time RT-PCR analysis of the <em>cpxA<\/em> and <em>cpxR<\/em> gene products showed a decrease in expression of both genes in cells within a biofilm compared to planktonic cells; similarly, cells challenged with lactobacilli exhibited a down-regulation of both genes in comparison to unchallenged cells.\u00a0 Because the CpxRA regulon inhibits transcription of virulence factors under normal conditions, this means that both biofilm formation and challenge with lactobacilli are correlated with an increase in virulence factor expression, suggesting that these conditions are associated with the <em>H. ducreyi<\/em> stress response.\u00a0 Findings from this study support the idea that probiotic bacteria play an integral role in maintaining urogenital health and show promise for the use of probiotic lactobacilli for treating chancroid infections in the future.<\/p>\n<hr \/>\n<p><strong>The Enzymatic Degradation of Diblock Copolymers by <em>Burkholderia cepacia<\/em> lipase<br \/>\n<\/strong>Mark P. Seraly, 2015 (Advisor: Dr. Ryan Van Horn)<\/p>\n<hr \/>\n<p><strong>Oxyfunctionalization via Flavin-Dependent Monooxygenases and their Biomimetic Analogues<\/strong><br \/>\nWill D. Shields, 2015 (Advisor: Dr. Shaun Murphree)<\/p>\n<hr \/>\n<p><strong>Effect of malathion and resveratrol treatment of SH-SY5Y cells on levels of SOD1, SOD2 and CAT mRNA<br \/>\n<\/strong>Katherine M. Shumway, 2015 (Advisor: Dr. Ann Kleinschmidt)<\/p>\n<p style=\"padding-left: 30px\">The effects of malathion with and without resveratrol on mRNA levels of the antioxidant enzymes SOD1, SOD2, and CAT were observed in SH-SY5Y human neuroblastoma cells. Several studies have shown that malathion induces oxidative stress, so it was hypothesized that treatment with malathion would induce oxidative stress and cause increased mRNA levels of the enzymes, and treatment with resveratrol would increase mRNA levels of SOD2 and CAT while SOD1 mRNA would remain unchanged.\u00a0 Treatments with no chemical (control), 100 \u00b5M malathion, and 100 \u00b5M malathion and 100 \u00b5M resveratrol, were performed for 16 hrs, 1 hr, 2 hrs, and 3 hrs.\u00a0 Total RNA was isolated from the cells and analyzed for RNA quality.\u00a0 The 16 hr treatments resulted in degraded RNA, only 1-3 hr treatments were used for reverse transcription.\u00a0 Real-time PCR was performed on resulting cDNA to measure mRNA levels of SOD1, SOD2, and CAT in control cells, those treated with malathion, and those treated with malathion and resveratrol.\u00a0 Results suggest that neither malathion treatment nor malathion and resveratrol treatment had an effect on the levels of mRNA for these antioxidant enzymes.\u00a0 It is possible malathion and resveratrol are unable to regulate the oxidative stress response in SH-SY5Y cells.<\/p>\n<p><strong>Total Synthesis of a Potential Antifouling Furanosesquiterpene and Analogues<\/strong><br \/>\nChad N. Ungarean, 2015 (Advisor: Dr. Shaun Murphree)<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Investigation of Keap1 and Nrf2 Expression in Canine Osteosarcoma Cell Lines Thomas S. Albanesi, 2015 (Advisor: Dr. Ann Kleinschmidt) Osteosarcoma, a primary bone cancer, is a devastating disease that has a poor long-term prognosis and affects adolescent humans as well as Canis lupus familiaris (the domestic dog).\u00a0 The profile of the disease is similar between [&#8230;]<\/p>\n<p><a class=\"mt-5\" href=\"https:\/\/sites.allegheny.edu\/biochemistry\/student-research\/senior-project\/senior-project-abstracts-2015\/\">Continue Reading &#8220;Senior Project Abstracts 2015&#8221;<\/a><\/p>\n","protected":false},"author":183,"featured_media":0,"parent":401,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"nosidebar.php","meta":{"inline_featured_image":false,"footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-851","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages\/851","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/users\/183"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/comments?post=851"}],"version-history":[{"count":0,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages\/851\/revisions"}],"up":[{"embeddable":true,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages\/401"}],"wp:attachment":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/media?parent=851"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":756,"date":"2014-05-01T10:44:08","date_gmt":"2014-05-01T14:44:08","guid":{"rendered":"http:\/\/sites.allegheny.edu\/biochem\/?page_id=756"},"modified":"2015-05-05T09:30:54","modified_gmt":"2015-05-05T13:30:54","slug":"senior-project-abstracts-2014","status":"publish","type":"page","link":"https:\/\/sites.allegheny.edu\/biochemistry\/student-research\/senior-project\/senior-project-abstracts-2014\/","title":{"rendered":"Senior Project Abstracts 2014"},"content":{"rendered":"<p><strong>The effect of altering gap junction activity on <em>Drosophila melanogaster<\/em> survival after bacterial infection<br \/>\n<\/strong>Nicole Guito, 2014 (Advisor: Dr. Brad Hersh)<\/p>\n<p style=\"padding-left: 30px\">The intercellular channels that connect one cell to another are termed gap junctions, and they are responsible for direct communication between neighboring cells. Such cell communication is also important during the immune response, and, therefore, gap junctions are hypothesized to play a role in the immune system. To further investigate this role, we studied viral innexins or vinnexins, which are proteins that are encoded by a Polydnavirus carried by some ichneumonid parasitoid wasps. Vinnexin proteins can be overexpressed in a desired location using the UAS-GAL4 system in order to see their effect on the organism. We first looked at the effects of vinnexin overexpression in the <em>Drosophila<\/em> eye and throughout the body. We hypothesized that vinnexins disrupt host physiology, and we found that while vinnexins do not disrupt proper development, they are lethal when expressed throughout the body. We also looked at the effects of vinnexin overexpression in the gut on <em>Drosophila<\/em> survival after bacterial infection with <em>S. marcescens<\/em>, and we hypothesized that vinnexins disrupt the immune response. We found that vinnexinG overexpression was lethal, but that the parental lines from the original vials had a lower survival rate than the offspring. Therefore, we need to further investigate the levels of gene expression in the offspring in order to interpret these results. This project was beneficial because we have a better understanding of the location in which vinnexin overexpression causes disruption in <em>Drosophila.<\/em><\/p>\n<hr \/>\n<p><strong>An Investigation of the Promoter Region of <em>Arabidopsis thaliana<\/em> Peroxidase Gene 32<\/strong><br \/>\nGabriella Izzo, 2014 (Advisor: Dr. Ann Kleinschmidt)<\/p>\n<p style=\"padding-left: 30px\"><em>Arabidopsis thaliana<\/em> has 73 different full length class III heme peroxidase genes, some of which are expressed throughout each life stage of the plant, and have a variety of functions such as in pathogen defense, and cell wall synthesis.\u00a0 Though overall changes in peroxidase protein activity have been characterized, the functions of the majority of individual peroxidase proteins have not yet been identified.\u00a0 Sequence conservation of the mRNA\u2019s and post-translational modifications of the protein make linking proteins to the mRNA sequences which encode them difficult.\u00a0 One way to gain more information about specific peroxidase proteins is through localization of the activity of the promoter, with the aim of using this information about important regulatory sequences to make predictions about what the protein does.\u00a0 This study used the promoter region of <em>Arabidopsis thaliana<\/em> peroxidase gene 32 to gain more information about the function of\u00a0 the protein the gene encodes, as well as about important regulatory sequences within the promoter.\u00a0 As little has been done to map the peroxidase promoters, different lengths of the promoter were amplified so that conclusions could be made about where important regulatory sequences are located within the promoter region.\u00a0 While the appropriate clones were made, analysis within plants was not completed due to difficulties with the transformation of the plasmid into Agrobacterium tumefaciens.\u00a0 In silico analysis of the promoter was performed, however, and based upon this it could be hypothesized that <em>A. thaliana<\/em> peroxidase gene 32 is inhibits floral organ development and is involved in stress response.<\/p>\n<hr \/>\n<p><strong>Further Investigation of the Cell Proportioning and Spore Formation Phenotype of the <em>fbiA<sup>&#8211;<\/sup><\/em> mutant in <em>Dictyostelium discoideum<\/em><\/strong><br \/>\nRachel Kloecker, 2014 (Advisor: Dr. Margaret Nelson)<\/p>\n<p style=\"padding-left: 30px\"><em>Dictyostelium discoideum<\/em> is a unicellular slime mold used as a model for cell differentiation in more complex organisms due to the role that cell fate and proportioning play in its life cycle. <em>Dictyostelium<\/em> transition from unicellularity to a multicellular fruiting body under conditions of starvation and release spores into an environment with a more abundant food source. FbiA is one protein that may influence cell fate in this process and may be a target of ubiquitination by a previously characterized protein, FbxA. In previous studies, the <em>fbiA<sup>&#8211;<\/sup><\/em> mutant has produced more prestalk cells, fewer prespore cells, and fewer mature spores than the wildtype. However, the wildtype used in those studies was lost in a freezer failure, and follow-up experiments suggested that the mutant phenotype was less marked than originally described. This study aimed to clarify the <em>fbiA<sup>&#8211;<\/sup><\/em> phenotype by quantifying the percent prespore and percent spore using Mud1 immunofluorescence and detergent treatment, respectively. Synergy experiments via <em>actin15-lacz<\/em> transformation were also conducted to determine any mutant preference in proportioning and its degree of autonomy. Reliable conclusions could not be drawn from the percent prespore and spore data due to inconsistencies between trials. However, the synergy experiment images suggest that <em>fbiA<sup>&#8211;<\/sup><\/em> cells tend towards the PstO and PstB fate, especially later in development. Additional trials of all aspects of the experiment need to be conducted to achieve greater consistency and more reliable conclusions.<\/p>\n<hr \/>\n<p><strong>The role of innexins 2 and 5 and vinnexins D and Q1 in the innate immune response of <em>Drosophila<\/em> melanogaster<\/strong><br \/>\nKelsey Sadlek, 2014 (Advisor: Dr. Brad Hersh)<\/p>\n<p style=\"padding-left: 30px\">Innexins are transmembrane proteins that comprise gap junctions, communication channels between cells, in <em>Drosophila melanogaster<\/em> and are speculated to play a vital role in the organism\u2019s cellular immune response.\u00a0 When invaded by the parasitoid wasp, the <em>Drosophila<\/em>\u2019s immune defense system is often compromised.\u00a0 The female parasitoid injects virus particles into the host, which are often associated with a change in hemocyte cell morphology and immune suppression.\u00a0 The polydnavirus, a type of dsDNA virus present in many parasitoid wasps, contains vinnexins, viral homologs of innexins that disrupt the normal immune response of the <em>Drosophila<\/em> by a mechanism that is not completely understood.\u00a0 Though these vinnexins have been found to interact with innexin 2, specifically, in addition to all other vinnexins in previous studies, the role of this interaction and its relation to immune suppression is not clear.\u00a0 Using the UAS-GAL4 express ion system, we knocked-out innexins 2 and 5 to elucidate their role in the <em>Drosophila<\/em> cellular immune response.\u00a0 In addition, we used the yeast 2-hybrid method to investigate specific interactions between innexin 2 and vinnexin D and vinnexin Q1.\u00a0 We were unable to observe a trend between encapsulation and RNAi knock-out genotypes, and we were unable to observe any interactions between innexin 2 and vinnexins, though we gained insight into the molecular techniques that we used.<\/p>\n<hr \/>\n<p><strong>Characterization of UBX binding of <em>Cpr47Ee edge<\/em> in the <em>Drosophila melanogaster<\/em> haltere<\/strong><br \/>\nRachel Stegemann, 2014 (Advisor: Dr. Brad Hersh)<\/p>\n<p style=\"padding-left: 30px\">Hox genes are a highly conserved group of genes that encode transcription factors that regulate various direct and indirect target genes. These genes are essential for anterior to posterior patterning in all bilaterally symmetrical metazoans. Although the mechanism by which they choose their targets is not well understood, Hox proteins bind preferentially to a core DNA sequence of ATTA, which will occur approximately every 256 base pairs in an average genome. We have hypothesized that other DNA sequences, both upstream and downstream of this core site, increase specificity of Hox protein binding. In this experiment, we used the Hox protein Ultrabithorax (UBX) and one of its target binding sites, <em>Cpr47Ee edge<\/em> cis-regulatory element to identify additional sequences important for Hox function. This direct UBX target contains two core ATTA sites, one of which is essential for proper expression. UBXIa protein was induced in BL21(DE3)<em>pLysS E. coli<\/em> bacteria and then purified on a Ni-NTA column. The purified protein was used in electromobility shift assays (EMSA) to determine binding affinity with wild-type and mutated sequences of the <em>Cpr47Ee edge<\/em> regulatory DNA.<\/p>\n<hr \/>\n<p><strong>Isolation and Characterization of the Extracellular Polymeric Substances of <em>Haemophilus ducreyi<\/em><\/strong><br \/>\nJosh Taylor, 2014 (Advisor: Dr. Tricia Humphreys)<\/p>\n<p style=\"padding-left: 30px\">Previous research has suggested that the bacterium <em>Haemophilus ducreyi,<\/em> the etiological agent of the sexually transmitted genital ulcerative disease chancroid, is capable of biofilm formation. Biofilms are surface-adherent communities of microorganisms, oftentimes consisting of multiple species of bacteria. These formations have been specifically noted to augment the virulence and overall pathogenicity of infectious microorganisms. In this way, the possibility of biofilm formation in <em>H. ducreyi<\/em> poses major implications to diagnosis and treatment. This study sought to confirm the secretion of extracellular polymeric substances (EPS) required for successful biofilm formation by <em>H. ducreyi.<\/em> These substances include extracellular DNA (eDNA), extracellular polysaccharides, as well as extracellular amino acids and protein. Observation of eDNA was made through the use of DAPI staining of green fluorescent protein expressing <em>H. ducreyi<\/em> grown on positively charged slides, which were then examined through the use of fluorescent microscopy.\u00a0 The amount of eDNA noted during fluorescent microscopy was relatively extensive in proportion to the number of cells present, indicative of a large amount of extracellular matrix. This matrix was isolated through the use of sonication at various amplitudes, followed by ultracentrifugation and filtration in order to remove large molecule contaminants. The resulting supernatant was tested for nucleic acid, protein, and polysaccharide content via various spectrophotometric methodologies. In this way the presence of DNA, protein, and polysaccharides was observed in the supernatant and their respective concentrations quantified. The fact that <em>H. ducreyi<\/em> possessed all major EPS components further indicates that this microorganism is properly equipped for biofilm formation, a potentially critical factor in the overall pathology, transmission, and persistence of chancroid infection.<\/p>\n<hr \/>\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>The effect of altering gap junction activity on Drosophila melanogaster survival after bacterial infection Nicole Guito, 2014 (Advisor: Dr. Brad Hersh) The intercellular channels that connect one cell to another are termed gap junctions, and they are responsible for direct communication between neighboring cells. Such cell communication is also important during the immune response, and, [&#8230;]<\/p>\n<p><a class=\"mt-5\" href=\"https:\/\/sites.allegheny.edu\/biochemistry\/student-research\/senior-project\/senior-project-abstracts-2014\/\">Continue Reading &#8220;Senior Project Abstracts 2014&#8221;<\/a><\/p>\n","protected":false},"author":183,"featured_media":0,"parent":401,"menu_order":0,"comment_status":"closed","ping_status":"open","template":"nosidebar.php","meta":{"inline_featured_image":false,"footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-756","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages\/756","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/users\/183"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/comments?post=756"}],"version-history":[{"count":0,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages\/756\/revisions"}],"up":[{"embeddable":true,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages\/401"}],"wp:attachment":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/media?parent=756"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":693,"date":"2013-04-25T12:50:06","date_gmt":"2013-04-25T16:50:06","guid":{"rendered":"http:\/\/sites.allegheny.edu\/biochem\/?page_id=693"},"modified":"2015-04-27T15:25:00","modified_gmt":"2015-04-27T19:25:00","slug":"senior-project-abstracts-2013","status":"publish","type":"page","link":"https:\/\/sites.allegheny.edu\/biochemistry\/student-research\/senior-project\/senior-project-abstracts-2013\/","title":{"rendered":"Senior Project Abstracts 2013"},"content":{"rendered":"<p><strong>The effect of 5-methyl cytosine on RNA duplex stability<\/strong><br \/>\nDishler, Abigael, 2013 (Advisor: Dr. Marty Serra)<\/p>\n<hr \/>\n<p><strong>Synthesis of Sodium Sulfonate Auxin Derivatives<\/strong><br \/>\nZachary Einwag, 2013 (Advisor: Dr. Shaun Murphree)<\/p>\n<hr \/>\n<p><strong>Auxin effects on root exudation in tomato <em>(Solanum lycopersicum)<\/em><\/strong><br \/>\nColleen Friel, 2013 (Advisor: \u00a0Dr. Catharina Coenen)<\/p>\n<p style=\"padding-left: 30px\">Plant roots exude a wide range of chemicals into the rhizopshere.\u00a0 These exudates are important for mediating interactions between plants and soil microorganisms and constitute a significant fraction of global carbon transfer into soils.\u00a0 Despite this importance, the regulation of root exudation is currently poorly understood.\u00a0 To test the hypothesis that the plant hormone auxin, which regulates sugar flow between different plant tissues, also regulates root exudation, we are characterizing root exudates in tomato.\u00a0 Exudates from wild-type tomato root seedlings were compared to those of the auxin-resistant tomato mutant <em>diageotropica (dgt).\u00a0<\/em> Sugars in exudates were identified and quantified by HPLC with refractive index detection, and organic acids were identified and quantified by HPLC with UV detection.\u00a0 Exudate profiles suggest that auxin stimulates the exudation of oxalic and citric acid, but does not affect exudation of succinic and fumar ic acid, or sugars.\u00a0 Root colonization\u00a0 of WT and <em>dgt<\/em> seedlings by two strains of the biocontrol bacterium <em>Pseudomonas fluorsecens<\/em>\u00a0 was\u00a0 also quantified.\u00a0 <em>P. fluorescens<\/em> <em>Pf-5<\/em> colonized WT roots at a higher level than <em>dgt<\/em> roots, while there was no difference in colonization between WT and <em>dgt<\/em> by <em>P. fluorescens<\/em> Wayne 1R.\u00a0 When this data is analyzed along with results from similar experiments in root organ culture (ROC), a model for auxin regulation of root exudation can be developed.\u00a0 Auxin appears to upregulate the synthesis or export of specific organic acids that accumulate in the tricarboxylic acid (TCA) cycle.\u00a0 Auxin also appears to promote sugar exudation via invertase stimulation only in high carbon environments, such as ROC.\u00a0 Finally, auxin effects on colonization by biocontrol bacteria appear to be strain-dependent.\u00a0 These results highlight the complexity of auxin effects on carbon flux to the rhizosphere.\u00a0 Auxin effects on root exudation are of major importance for carbon transfer to agricultural soils, because many green revolution crops carry mutations in auxin transport proteins, suggesting that use of these crops on large land areas may affect soil microbial communities and patterns of carbon flow.<\/p>\n<hr \/>\n<p><strong>Comparison of Spectral and Kinetic Characteristics of the <em>Brassica rapa<\/em> and<em> Pisum sativum<\/em> Cytoplasmic Ascorbate Peroxidases<\/strong><br \/>\nSilas Hartley, 2013 (Advisor:\u00a0 Dr. Ann Kleinschmidt)<\/p>\n<p style=\"padding-left: 30px\">Ascorbate peroxidases are important for regulating hydrogen peroxide in plants. Soybean and pea ascorbate peroxidases (APXs) have been extensively studied, whereas APXs from other plant families have not. To determine whether peroxidases from different plant families share similar spectral and kinetic properties, <i>Pisum sativum<\/i> (Ps) and <i>Brassica rapa<\/i> (Br) APXs were compared. Using second order conditions, the APX reaction with hydrogen peroxide, the oxidation from resting state enzyme to compound I, was monitored using stopped-flow methods. Using a derived second-order equation, values were determined for the reaction rate constant, k<sub>1<\/sub>, to be (3.44\u00b10.346)x10<sup>7<\/sup>M<sup>-1<\/sup>s<sup>-1 <\/sup>for Ps APX and (3.97\u00b10.324)x10<sup>7<\/sup>M<sup>-1<\/sup>s<sup>-1<\/sup> for Br APX, when only observing the decrease in absorbance. When the enzyme was reacted with hydrogen peroxide while observing the decrease and increase in absorbance, the k<sub>1<\/sub> values were (3.52\u00b10.0975)x10<sup>7<\/sup>M<sup>-1<\/sup>s<sup>-1<\/sup> and (3.88\u00b10.144)x10<sup>7<\/sup>M<sup>-1<\/sup>s<sup>-1<\/sup> for Ps and Br APX respectively. The k<sub>2<\/sub> values, without the addition of substrate, were (0.646\u00b10.0204)s<sup>-1<\/sup> for Ps APX and (0.698\u00b10.00705)s<sup>-1<\/sup> for Br APX. The k<sub>1<\/sub> value for Ps APX was lower than the previously found value for recombinant APX (rAPX). When ascorbate was used as a reductant, Br APX showed a higher steady-state reaction rate than Ps APX. However, when pyrogallol was used as the reductant, Br APX displayed lower k<sub>cat<\/sub> values compared to Ps APX. Both Ps and Br APXs had similar K<sub>m<\/sub> and n values when reduced by pyrogallol, but Ps APX had a v<sub>max<\/sub> rate nearly twice as large as the rate found for Br APX. These data suggested that Br APX used hydrogen peroxide and ascorbate at faster rates than Ps APX, while Ps APX uses pyrogallol at faster rates than Br APX. These results appear to reinforce the idea of two different binding sites for ionic compounds, such as ascorbate, and non-ionic phenyl reducing agents, such as pyrogallol.<\/p>\n<hr \/>\n<p><strong>Expression of Genes Involved in the Regulation of the Intrinsic Apoptotic Pathway in <em>IRBP<sup>&#8211;<\/sup>\/<sup>&#8211;<\/sup><\/em><\/strong><em><strong> Mus musculus<\/strong><br \/>\n<\/em>Linnea Homa, 2013 (Advisor: Dr. Christy Donmoyer)<\/p>\n<p style=\"padding-left: 30px\">Apoptosis, or programmed cell death, is a vital process for survival and proper development of certain tissues. When apoptosis occurs in adult neuronal tissue it can have detrimental effects. Apoptosis can occur through the intrinsic pathway, which is activated at the mitochondrial level. Mice deficient in interphotoreceptor retinoid-binding protein <em>(IRBP<sup>&#8211;<\/sup>\/<sup>&#8211;<\/sup>)<\/em> experience photoreceptor loss via apoptosis starting around 18 days after birth (P18) and peaking at P23. These mice exhibit elongated eyeballs, and by 30\u00a0days after birth, 50% of their photoreceptors have died. The purpose of this study was to investigate whether two genes found in the intrinsic apoptotic pathway (pro-apoptotic, <em>Bax<\/em>, and anti-apoptotic, <em>Bcl-2<\/em>) are involved in retinal apoptosis in <em>IRBP<sup>&#8211;<\/sup>\/<sup>&#8211;<\/sup> <\/em>mice<em>. <\/em>Mice overexpressing<em> Bcl-2<\/em> and mice deficient for <em>Bax<\/em> have shown that these proteins play important roles as regulators of photoreceptor cell death in retinal degeneration. To investigate the role of these genes in <em>IRBP<sup>&#8211;<\/sup>\/<sup>&#8211;<\/sup> <\/em>mice, relative gene expression was measured by quantitative real-time PCR 23 days after birth (P23) in <em>IRBP<sup>&#8211;<\/sup>\/<sup>&#8211;<\/sup><\/em> mouse retinas and compared with age-matched <em>IRBP<sup>&#8211;<\/sup>\/<sup>&#8211;<\/sup> <\/em>(wild-type) mice (n=3). To observe the occurrence of apoptosis, DNA fragments were observed on a 1.2% agarose gel at P26 in <em>IRBP<sup>&#8211;<\/sup>\/<sup>&#8211;<\/sup><\/em> and P23 in <em>IRBP<sup>&#8211;<\/sup>\/<sup>&#8211;<\/sup><\/em> mice. I hypothesized that expression of the pro-apoptotic gene <em>Bax<\/em> would be higher in the retinas of the <em>IRBP<sup>&#8211;<\/sup>\/<sup>&#8211;<\/sup><\/em> mice compared to wild-type mice, and expression of the anti-apoptotic gene <em>Bcl-2<\/em> would be higher in wild-type versus <em>IRBP<sup>&#8211;<\/sup>\/<sup>&#8211;<\/sup> <\/em>retinas. Results of this study showed that there was not a significant difference in expression for either pro-apoptotic or anti-apoptotic gene between strains, indicating that at P23, the expression of <em>Bcl-2<\/em> and <em>Bax<\/em> may not be altered in the <em>IRBP<sup>&#8211;<\/sup>\/<sup>&#8211;<\/sup><\/em>mice. DNA laddering showed that there were not enough apoptotic cells in retina samples for the <em>IRBP<sup>&#8211;<\/sup>\/<sup>&#8211;<\/sup><\/em> mice to observe with this assay.<\/p>\n<hr \/>\n<p><strong>A Thermodynamic Investigation of the Effects of GU Wobble Base Pairs on Group II Bulges in RNA<\/strong><br \/>\nRyan Kotecki, 2013 (Advisor: Dr. Marty Serra)<\/p>\n<hr \/>\n<p><strong>Comparative Expression of <em>Brassica rapa<\/em> Peroxidase Ohnologs<br \/>\n<\/strong>Christina Mucci, 2013 (Advisor: Dr. Ann Kleinschmidt)<\/p>\n<p style=\"padding-left: 30px\">Peroxidases are a versatile group of enzymes that consist of three classes; the third of which is found in all land plants, including <em>Brassica rapa<\/em>, which is unique for the genome triplication event in the evolution of <em>B. rapa<\/em> from <em>A. thaliana<\/em> that resulted in varying copies of numerous <em>B. rapa<\/em> peroxidase genes.\u00a0 Not enough is known about peroxidase functional pathways to be able to classify them in many circumstances.\u00a0 The quantification of peroxidase ohnolog expression levels in a variety of <em>B. rapa<\/em> tissue types will help to elucidate the circumstances under which different peroxidase ohnologs function.\u00a0 Ohnolog specific primers will be designed and used in real time PCR to quantify the levels of four peroxidase ohnolog pairs in the stems, roots, leaves, and flower buds of <em>B. rapa<\/em>.<\/p>\n<hr \/>\n<p><strong>Investigation of the Effect of Salicylic Acid on Ascorbate Peroxidase in <em>Brassica rapa<\/em> Leaves<br \/>\n<\/strong>Ryan Vietmeier, 2013 (Advisor: Dr. Ann Kleinschmidt)<\/p>\n<p style=\"padding-left: 30px\">Reactive oxygen species (ROS) play a key role in plant cells as a signaling molecule in stress response, but at high concentrations ROS can cause damage to cells.\u00a0 Ascorbate peroxidase (APX) is a ROS scavenging enzyme that regulates ROS levels by converting hydrogen peroxide (H<sub>2<\/sub>O<sub>2<\/sub>) to water, at the expense of oxidation of ascorbate.\u00a0 During pathogen response, increases in ROS are observed, and it has been shown that one of the major components of induction of this is salicylic acid.\u00a0 Thus, the effect of salicylic acid (SA) treatment on total APX activity, and cytosolic APX (cAPX) activity, protein levels, and relative mRNA levels in eight-day-old <em>Brassica rapa<\/em> plants was investigated.\u00a0 Techniques used were reverse transcription polymerase chain reaction (cAPX relative mRNA levels), AXP spectrophotometric assay (total APX activity), native gel analysis (cAPX activity), and western blot (cAPX protein levels).\u00a0 While differences in the level of cAPX mRNA were observed in the 30 minute treatment as compared to that at 0 minutes, there were no significant difference between the level of cAPX in control and SA treated plants at those time points. There was also an observed increase in total APX activity at 0 min for leaves treated with SA, and overall an increase at 30 minutes with increased activity for SA treated leaves.\u00a0 Also, there was an increase in cAPX activity and protein level at the 30-minute time point for SA treated leaves compared to the control.\u00a0 These results suggest that in response to SA treatment results in an increase in cAPX activity which in due to increased production of cAPX protein.<\/p>\n<hr \/>\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"<p>The effect of 5-methyl cytosine on RNA duplex stability Dishler, Abigael, 2013 (Advisor: Dr. Marty Serra) Synthesis of Sodium Sulfonate Auxin Derivatives Zachary Einwag, 2013 (Advisor: Dr. Shaun Murphree) Auxin effects on root exudation in tomato (Solanum lycopersicum) Colleen Friel, 2013 (Advisor: \u00a0Dr. Catharina Coenen) Plant roots exude a wide range of chemicals into the [&#8230;]<\/p>\n<p><a class=\"mt-5\" href=\"https:\/\/sites.allegheny.edu\/biochemistry\/student-research\/senior-project\/senior-project-abstracts-2013\/\">Continue Reading &#8220;Senior Project Abstracts 2013&#8221;<\/a><\/p>\n","protected":false},"author":183,"featured_media":0,"parent":401,"menu_order":0,"comment_status":"closed","ping_status":"open","template":"nosidebar.php","meta":{"inline_featured_image":false,"footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-693","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages\/693","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/users\/183"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/comments?post=693"}],"version-history":[{"count":0,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages\/693\/revisions"}],"up":[{"embeddable":true,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages\/401"}],"wp:attachment":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/media?parent=693"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":685,"date":"2013-04-12T15:42:32","date_gmt":"2013-04-12T19:42:32","guid":{"rendered":"http:\/\/sites.allegheny.edu\/biochem\/?page_id=685"},"modified":"2023-06-21T15:40:38","modified_gmt":"2023-06-21T19:40:38","slug":"news-updates","status":"publish","type":"page","link":"https:\/\/sites.allegheny.edu\/biochemistry\/news-updates\/","title":{"rendered":"News &#038; Updates"},"content":{"rendered":"\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":562,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"inline_featured_image":false,"footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-685","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages\/685","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/users\/562"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/comments?post=685"}],"version-history":[{"count":0,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages\/685\/revisions"}],"wp:attachment":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/media?parent=685"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":659,"date":"2012-09-21T16:06:07","date_gmt":"2012-09-21T20:06:07","guid":{"rendered":"http:\/\/sites.allegheny.edu\/biochem\/?page_id=659"},"modified":"2015-04-27T15:24:59","modified_gmt":"2015-04-27T19:24:59","slug":"colleen-friel","status":"publish","type":"page","link":"https:\/\/sites.allegheny.edu\/biochemistry\/student-profiles\/colleen-friel\/","title":{"rendered":"Colleen Friel"},"content":{"rendered":"<p class=\"profilequote\">\u201cI love being able to conduct research while learning to better understand the natural world around me.\u201d<\/p>\n<p class=\"profilename\">\u2014 Colleen Friel<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/sitesmedia.s3.amazonaws.com\/biochem\/files\/2012\/09\/friel.jpg\" alt=\"\" title=\"friel\" width=\"204\" height=\"150\" class=\"alignright size-full wp-image-661\" \/>\u201cI enjoy Biochemistry because it gives you a wide range of opportunities to get involved with science and become a well-rounded student,\u201d Colleen Friel explains. \u201cI love being able to conduct research while learning to better understand the natural world around me.\u201d<\/p>\n<p>As a Biochemistry major, Colleen has focused her studies on agricultural plant-microbe interactions &#8211; a combination of plant biology and microbiology. She has fulfilled multiple research internships by working with various Allegheny professors, and she has also performed research at the South Dakota State University Department of Biology and Microbiology. Along the way, Colleen claims that she has received much guidance from her academic advisor and professors.<\/p>\n<p>\u201cAllegheny\u2019s faculty has been wonderful in helping me to figure out what expectations I need to live up to in order to succeed as a college student,\u201d Colleen says. \u201cAnd my advisor has been absolutely amazing in doing things such as helping me pick my classes, go to graduate school expos and conferences, proofread my research abstracts and applications, and research internship opportunities. I feel like that kind of student\/faculty connection is one you can\u2019t get anywhere else.\u201d<\/p>\n<p>Along with her Biochemistry studies, Colleen is also an Economics minor and has taken various Music courses. This unusual combination of classes will allow Colleen to obtain a unique undergraduate degree without having to ignore any of her interests.<\/p>\n<p>\u201cEconomics doesn\u2019t usually get paired together with science, but I\u2019ve found that it allows me to better understand the process of gaining funding for grants that I will rely on to perform research in my future career,\u201d Colleen explains. \u201cAnd even though it is not my major or minor, I spend quite a bit of time in the music department. Music allows me to step back from all of my analytical tendencies and embrace my creative side.\u201d<\/p>\n<p>On campus, Colleen is also the Secretary of the Equestrian Club, the Treasurer of the Beta Beta Beta National Biology Honor Society, a Research Assistant for the Environmental Science department, and a Teaching Assistant for both the Biology Freshman Seminar and the Physics department. Her future plans are to obtain a Ph.D. in plant pathology and conduct research on biocontrol bacteria. She claims her key to success at Allegheny is all about taking advantage of the chances offered to students.<\/p>\n<p>\u201cThe ideal Allegheny student is motivated, inquisitive, and tenacious,\u201d Colleen explains. \u201cNo matter what horizon you want to expand your learning toward, Allegheny can offer you the opportunity to do so. It\u2019s a school where you don\u2019t have to be afraid to push the envelope a little bit.\u201d<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u201cI love being able to conduct research while learning to better understand the natural world around me.\u201d \u2014 Colleen Friel \u201cI enjoy Biochemistry because it gives you a wide range of opportunities to get involved with science and become a well-rounded student,\u201d Colleen Friel explains. \u201cI love being able to conduct research while learning to [&#8230;]<\/p>\n<p><a class=\"mt-5\" href=\"https:\/\/sites.allegheny.edu\/biochemistry\/student-profiles\/colleen-friel\/\">Continue Reading &#8220;Colleen Friel&#8221;<\/a><\/p>\n","protected":false},"author":169,"featured_media":0,"parent":664,"menu_order":0,"comment_status":"closed","ping_status":"open","template":"nosidebar.php","meta":{"inline_featured_image":false,"footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-659","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages\/659","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/users\/169"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/comments?post=659"}],"version-history":[{"count":0,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages\/659\/revisions"}],"up":[{"embeddable":true,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages\/664"}],"wp:attachment":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/media?parent=659"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":610,"date":"2012-04-16T10:35:47","date_gmt":"2012-04-16T14:35:47","guid":{"rendered":"http:\/\/sites.allegheny.edu\/biochem\/?page_id=610"},"modified":"2016-01-27T10:03:37","modified_gmt":"2016-01-27T15:03:37","slug":"senior-project-abstracts-2012","status":"publish","type":"page","link":"https:\/\/sites.allegheny.edu\/biochemistry\/student-research\/senior-project\/senior-project-abstracts-2012\/","title":{"rendered":"Senior Project Abstracts 2012"},"content":{"rendered":"<p><strong>Whole Genome Analysis Reveals That Conservation and Duplication Gave Rise to the Current V2R Gene Repertoire in Mammals<\/strong><br \/>\nAlexander\u00a0Berry, 2012 (Advisor: Dr. Kristen Webb)<\/p>\n<p style=\"padding-left: 30px\">The vomeronasal organ (VNO) is the part of the olfactory system that detects specific semiochemicals known as pheromones, which allow for communication between members of a species, and also affect social and reproductive behaviors. The chemodetection function of the VNO in mammals is facilitated by G protein-coupled receptors (GPCRs) encoded by members of two gene superfamilies: vomeronasal 1 receptor (V1R) and vomeronasal 2 receptor (V2R). Previously, members of the V2R gene family from eight mammalian genomes had been identified and their evolutionary relationships reconstructed. The objective of this study was to use bioinformatics techniques to survey four additional mammalian genomes from the African savannah elephant <em>(Loxodonta africana)<\/em>, the European rabbit <em>(Oryctolagus cuniculus)<\/em>, the guinea pig <em>(Cavia porcellus)<\/em>, and the domestic horse <em>(Equus caballus)<\/em> for V2R genes and to include these genes in evolutionary analyses. These four mammals were chosen to diversify the group of mammals surveyed for V2R genes. Ninety and fifty-two intact genes were identified in <em>O. cuniculus<\/em> and <em>C. porcellus<\/em>, respectively, and these genes appear to have mostly evolved through duplications after the rodent lineages diverged. Two and five intact genes were found in <em>E. caballus<\/em> and <em>L. africana<\/em>, respectively, and appear to be conserved, as they are also present in several other species.<\/p>\n<hr \/>\n<p><strong>Thermodynamic Investigation of Group III Single Nucleotide Bulge Loops and Group II Single Nucleotide Bulge Loops with Adjacent GU Wobble Base Pairs in RNA Duplexes<\/strong><br \/>\nAnthony\u00a0Blaszczyk, 2012 (Advisor: Dr. Marty Serra)<\/p>\n<p style=\"padding-left: 30px\">Four Group III and seven Group II RNA duplexes containing a single nucleotide bulge loop adjacent to a GU wobble base pair were optically melted, and the thermodynamic parameters (\u0394G\u00b037, \u0394H\u00b0, \u0394S\u00b0, and TM) were determined for each sequence. Data from this study were combined with data from previous thermodynamic investigations to compare the stability of Group II and Group III bulge loops with an adjacent GU wobble base pair (McMichael, unpublished; Serra, unpublished). The current model to predict the thermodynamic influence of a bulge loop does not consider Group II or Group III bulges with an adjacent GU wobble base pair. In this study Group II and Group III sequences with bulges adjacent to a GU wobble were analyzed and compared to previously studied Group I bulges with an adjacent GU wobble base pair. The identity of the bulge is ambiguous in both Group II and Group III sequences, but the nucleotides that could be bulged were shown to have no influence on the stability of the duplex. Group III bulges were the only group that saw a thermodynamically favorable influence by adding an adjacent GU wobble base pair in place of a Watson-Crick base pair. Group II bulges were shown to only be thermodynamically favorable when the sequence had the potential to form a tandem GU motif. For both Group II and Group III bulges, the potential to form a tandem GU motif was seen to be more important than both the position and orientation of the neighboring GU base pair.<\/p>\n<hr \/>\n<p><strong>Sequence Comparison and Analysis of the <em>Haemophiulus ducreyi<\/em> homologue to <em>Escherichia coli<\/em> tolB<\/strong><br \/>\nColleen\u00a0Dailey, 2012 (Advisor: Dr. Tricia Humphreys)<\/p>\n<p style=\"padding-left: 30px\"><em>Haemophilus ducreyi<\/em> is a gram-negative bacterium that causes the sexually transmitted disease chancroid. Despite several attempts, a vaccine for <em>H. ducreyi<\/em> has not been developed. Because the bacteria are resistant to phagocytosis, research is being directed towards the cellular envelope. By weakening the envelope, the bacteria may become more susceptible to attacks by the human immune system. Outer membrane integrity and structure is maintained in part by the Tol-PAL protein complex. This study focuses on TolB, a protein of this complex. PCR and sequencing were used to isolate and analyze the nucleotides that code for this protein from four strains of <em>H. ducreyi<\/em>. Phyre 2 was then used to determine the three dimensional structure of the protein. The amino acid sequences were identical for three of the four strains tested. The structure was also found to be comparable to the known TolB structure obtained from <em>E. coli<\/em>. This indicates that To lB is partially conserved across gram-negative bacteria. Further studies would help to clarify the importance of this conservation as related to protein structure and function.<\/p>\n<hr \/>\n<p><strong>Kinetic Studies of Glutathione S-Transferase<\/strong><br \/>\nTabitha\u00a0Davis, 2012 (Advisor: Dr. Alice Deckert)<\/p>\n<p style=\"padding-left: 30px\">This study focuses on Glutathione S-Tranferase (GST) and the kinetics of the reaction it catalyzes: nucleophilic aromatic substitution. This enzyme is found in many different organisms including plants, animals, and humans and their basic function is to detoxify cells. The two binding sites of GST, the G site and the H site are specific for glutathione (GSH) and toxins (in this study, 2,4-dinitro-chlorobenzene (CDNB)), respectively. The catalyzed reaction was monitored at pH 6.5 using a stopped flow spectrophotometer to determine the rate constants for the reaction. The uncatalyzed reaction was monitored at pH 6.5 and 9 using an Ocean Optics UV-VIS spectrophotometer to compare to the catalyzed reaction. The uncatalyzed and catalyzed reactions showed similar kinetic profile shapes. By fitting the kinetic profiles with a bi-exponential (burst) fit (derived from the proposed mechanism) the uncatalyzed reaction showed very slow carbon-sulfur bond formation while the catalyzed reaction showed a much faster rate. The fitted data indicates that one of the rate constants is dependent on GSH concentration, while the other is not. By comparing the catalyzed and uncatalyzed reactions, it is apparent that GST is catalyzing both the ionization of GSH and the formation of the carbon-sulfur bond. The implications of this study in cancer research indicate that the ability to inhibit the ionization and stabilization power of the GST would inhibit its ability to metabolize chemotherapy agents.<\/p>\n<hr \/>\n<p><strong>The Enantiomeric Behavioral Effects of \u03ba-opioid Agonist U-50488<br \/>\n<\/strong>Amon Manekul, 2012 (Advisor: Dr. Rodney Clark)<\/p>\n<p style=\"padding-left: 30px\">A recent study revealed the potency of U-50488, a \u03ba-opioid agonist as an up-regulating agent of the immune system. The purpose of the present examine was to examine the differential effects the enantiomers of U-50488. Testing was done using 6 Sprague-Dawley rats on a Multiple, Fixed Ratio 10 Fixed Interval 90\u201d schedule of water presentation, and sessions lasted for 25 minutes. Each enantiomer and the racemate were administered intraperitoneally in volumes of 1 mL\/kg body weight and the dose varied from 0.3 mg\/kg to 3.0 mg\/kg. The results of the experiment show that (+) U-50488 is responsible for the longevity of response suppression whereas (-) U-50488 is responsible for the magnitude of response suppression.<\/p>\n<hr \/>\n<p><strong>A Thermodynamic Study of Multiple Single-Nucleotide Bulge Loops in RNA Duplexes<\/strong><br \/>\nEric\u00a0Mastrogiacomo, 2012 (Advisor: Dr. Marty Serra)<\/p>\n<p style=\"padding-left: 30px\">RNA duplexes containing multiple single-nucleotide bulge loops were evaluated<br \/>\nvia optical melting in 1M NaCl to determine the thermodynamic parameters (\u0394Ho, \u0394So, \u0394G37o , and TM). Nine duplexes containing multiple bulge loops located in the same strand of the RNA duplex were analyzed. The distance of the bulge from the 5\u2019 and 3\u2019 end was varied while the inner duplex remained constant. Within the entire data set, the\u00a0inner duplex varied in length as well as composition. The inner duplex was made up of 3\u00a0to 4 nucleotides and the identity of the nucleotides was varied as well. This thermodynamic data was added to previous research performed by Jones and compared to\u00a0the revised Blose model (McCann et al., 2011). The revised Blose model does not\u00a0accurately predict the effect of multiple single nucleotide bulges because the second\u00a0bulge affects the duplex in a related but different manner than the first bulge. However,\u00a0the revised Blose model does accurately predict that the bulge becomes less destabilizing\u00a0as the stability of the less stable stem decreases. The trends found were not statistically\u00a0different from each other, which is a result of the small data set. A larger data set of\u00a0multiple nucleotide bulge loops should be studied in the future.<\/p>\n<hr \/>\n<p><strong>Structural and Thermodynamic Analysis of Group III Single Nucleotide Bulge Loops in a Hairpin in RNA and a Thermodynamic Analysis of Group IV Single Nucleotide Bulge Loops in Duplex in RNA<\/strong><br \/>\nMichael\u00a0McCann, 2012 (Advisor: Dr. Marty Serra)<\/p>\n<p style=\"padding-left: 30px\">Single nucleotide bulge loops occur when one nucleotide is unpaired in RNA duplexes. The bulge loops embedded in a hairpin studied in this investigation were of the group III variety, where ambiguity exists as to which nucleotide is bulged since the nearest neighbor can assume GU wobble base pairing instead of canonical Watson-Crick base pairing. The previous investigation of the thermodynamic parameters \u2206H\u00b0, \u2206S\u00b0, \u2206G\u00b037, and TM of thirty-five RNA duplexes containing group III single nucleotide bulge loops by optical melting in 1 M NaCl was completed and used to develop a model to predict the free energy of the destabilization of the duplex by the bulge. The thermodynamic data suggests that canonical Watson-Crick base pairing occurs instead of GU wobble base pairing, allowing a free energy model of group III bulge loops in duplex to be developed by treating them as group I bulge loops. The free energy model for predicting the stability of group I and group II bulge loops in a duplex is \u0394G\u00ba37,bulge = -0.53 \u0394G\u00bastem + 0.7, where \u0394G\u00bastem is the least stable stem for group I bulge loops and is the second-least stable stem for group II bulge loops (McCann et. al, 2011). Since group III bulge loops can be considered group I bulge loops in a duplex if Watson-Crick base pairing takes place, single nucleotides of the group III variety can be predicted by the model. In this investigation, a structural analysis of RNA group III single nucleotide bulge loops embedded in a hairpin was utilized to complement the thermodynamic model of the stability of group III single nucleotide bulge loops in RNA duplexes and structurally solve the ambiguity. In-line structure probing of the hairpins with group III bulge loops suggest the position of the bulged nucleotide is the nucleotide further from the hairpin loop, which was similar to that of group II single nucleotide bulge loops embedded in a hairpin (McCann et al, 2011). The stability of hairpin sequences with group III single nucleotide bulge loops were compared to the stability model of hairpin sequences with group I and group II single nucleotide bulge loops to find that the group III bulge loops in a hairpin can predicted in the same manner that group I and II bulge loops in a hairpin are predicted. The destabilization of the hairpin structure with group I and group II bulge loops is related the stability of the stem opposite the hairpin from the bulge (Lim et al., 2012). Fourteen duplexes containing group IV single nucleotide bulge loops, which have a bulge environment that combines that of group II and III bulge loops, were optically melted in 1 M NaCl to obtain the thermodynamic parameters \u2206H\u00b0, \u2206S\u00b0, \u2206G\u00b037, and TM. The thermodynamic parameters were combined with a set of twenty-three duplexes with a group IV bulge loop to compare it to the model used to predict group I, II, and III single nucleotide bulge loops (McCann et al., in preparation). The free energy of any group of single nucleotide bulge loop in a duplex is \u0394G\u00ba37,bulge = -0.65 \u0394G\u00bastem + 0.34 where the \u0394G\u00bastem is the \u0394G\u00ba of the least stable stem for group I bulge loops, the \u0394G\u00ba of the second least stable stem for group II and III bulge loops, and the \u0394G\u00ba of the third least stable stem for group IV bulge loops.<\/p>\n<hr \/>\n<p><strong>Single Bulge Mutations Affecting the Rate of DNA:RNA Duplexing<\/strong><br \/>\nAmanda\u00a0McClelland, 2012 (Advisor: Dr. Alice Deckert)<\/p>\n<p style=\"padding-left: 30px\">DNA:RNA duplexes are significant in many biological processes. To understand these processes better, a simple system was created with sequences of DNA and RNA with varying parameters. Parameters include a bulge mutation, reactant concentration, and concentration of salt in solution. All three are important in the processes because the rate of duplex formation is affected based on the changes. In order to study this phenomenon, sequences of DNA and RNA were created with a single bulge mutation. The rates were observed using a Stopped-Flow instrument and the data was analyzed to determine if the mutation in the sequence affected the rate at which DNA and RNA form a duplex.<\/p>\n<hr \/>\n<p><strong>A Thermodynamic Investigation of the Stability of RNA-DNA Hybrid Duplexes Under Varying NaCl Conditions<\/strong><br \/>\nElizabeth McMichael, 2012 (Advisor: Dr. Marty Serra)<\/p>\n<p style=\"padding-left: 30px\">Thermodynamic parameters (\u0394G, \u0394H, \u0394S, and TM) were determined for four RNA octomers, their homologous DNA strands, and complementary RNA-DNA hybrid duplexes through optical melting. The stability of duplex formation was investigated under varying NaCl concentrations ranging from 1.0M-0.01M. It has been previously shown that RNA-RNA duplexes are the most stable than corresponding DNA-DNA and RNA-DNA duplexes. The relative stability of DNA-DNA and DNA-RNA duplexes vary based on oligomer composition (Sugimoto et al., 1995). As expected, the RNA-RNA duplex had a greater stability than DNA-DNA duplex in 1.0M NaCl. In most cases, the stability of the hybrid duplexes fell between the RNA-RNA duplex and the DNA-DNA duplex. This study utilizes two sets of RNAs that differ in GC content, 62% to 75%. In all cases, the stability of the 75% GC content duplexes was greater than that of the 62% GC duplexes. The concentration of NaCl further destabilizes duplex formation in all of the oligomers, where greater thermodynamic stability is obtained at higher concentrations of NaCl . The overall purpose of this study is to obtain the thermal data of duplex formation for RNA-RNA, DNA-DNA, and RNA-DNA duplexes in order to compare to the kinetic data of duplex formation in the same duplexes under similar conditions.<\/p>\n<hr \/>\n<p><strong>Regulation of the HOX target gene <em>CG13222<\/em> by Ultrabithorax<\/strong><br \/>\nOlivia\u00a0Mesoras, 2012 (Advisor: Dr. Brad Hersh)<\/p>\n<p style=\"padding-left: 30px\">HOX genes are found in all bilateral animals and are responsible for the regulation of anterior-posterior body patterning. HOX proteins regulate target genes by turning them on or off in specific tissues. The purpose of this study is to look at the regulation of the HOX target gene <em>CG13222<\/em>, which encodes a cuticle protein. <em>CG13222<\/em> requires the HOX protein Ultrabithorax (UBX), which plays a role in haltere (hindwing) development, to bind its cis-regulatory element (CRE) for expression. Ultrabithorax requires two TAAT sequences in the <em>CG13222<\/em> CRE for expression. However, this is likely not the only signal for UBX to bind, as TAAT is common in the genome. This study aimed to discover the other sequence information needed for UBX to bind to the CRE of <em>CG13222<\/em>. This was accomplished by mutating base pairs in the CRE near one required TAAT sequence. The mutations were generated using PCR sewing to mutate two base pairs at a time.<\/p>\n<hr \/>\n<p><strong>Analysis of Peptidoglycan Structure in Two Classes of <em>Haemophilus ducreyi<\/em> Using IR Spectroscopy and HPLC<\/strong><br \/>\nSarah\u00a0Petrovich, 2012 (Advisor: Dr. Tricia Humphreys)<\/p>\n<p style=\"padding-left: 30px\"><em>Haemophilus ducreyi<\/em> is the Gram-negative bacterium that causes the sexually transmitted disease, chancroid. There are two populations of <em>H. ducreyi<\/em>, class I and class II, which vary in outer membrane proteins and therefore have different pathogenic properties and elicit different immune responses. Peptidoglycan is the main target of some antibiotics, such as vancomycin. Because vancomycin is a drug used primarily for the treatment of Gram-positive bacterial infections, it should not be sensitive to this antibiotic. Class II strains have been found to be sensitive to vancomycin, where class I strains are resistant, which suggests differences in the primary structure of peptidoglycan. Infrared spectroscopy was used to observe similarities and differences between the classes. IR spectroscopy only showed differences in the fingerprint region (1500-600 cm-1) of the spectra. High pressure liquid chromatography was also used, but the parameters were not able to be optimized and no peaks were obtained. It cannot be determined from the IR results if there are any significant differences in peptidoglycan structure between class I and class II <em>H. ducreyi.<br \/>\n<\/em><\/p>\n<hr \/>\n<p><strong>Computer Simulation Analysis for Electron Paramagnetic Resonance Spectroscopy Spectra of the Tetraheme Protein Cytochrome c554<\/strong><br \/>\nAlicia\u00a0Seggelink, 2012 (Advisor:\u00a0Dr. Doros Petasis)<\/p>\n<p style=\"padding-left: 30px\">Cytochrome c554 is a tetraheme protein found in the nitrifying bacteria Nitrosomonas europaea and functions as an electron transport mechanism. The four Fe(III) ions, each coordinated within a Protoporphyrin IX ring, make up the active site of this metalloprotein. These iron ions are also paramagnetic species, meaning they have an unpaired electron that can interact with surrounding magnetic fields, whether they are from surrounding ligands and molecules or from an artificially applied magnetic field. This paramagnetic character makes this active site ideal for Electron Paramagnetic Resonance (EPR) spectroscopy. Initial studies of this protein have revealed the complexity of Cyt c554 in terms of its magnetic interactions and electrostatic behavior. In EPR, these characteristics lead to complicated spectra that cannot always be easily deciphered to extrapolate data and information about the electronic structure of the species under investigation. However, the use of computer simulations has been very helpful in terms of modeling a system.<\/p>\n<p style=\"padding-left: 30px\">This project focused mainly on refining a set of parameters that are used in the Spin-Hamiltonian, which is an operator that is used to define the possible energy states of a system as well as give information about the nature of the system. A program called SpinCount can evaluate the Spin-Hamiltonian according to the parameters that are input into the program to yield a simulation of those parameters, which will be an EPR spectrum. The goal of this study was to refine the parameter set until simulations visually agreed with the experimental spectrum of Cyt c554.<\/p>\n<p style=\"padding-left: 30px\">Three spectra were simulated that seem to correspond quite well with the experimental spectrum. According to the parameters used to create the simulations and the interactions that are observed, it is concluded that heme II and heme IV of Cyt c554 are ferromagnetically coupled and do not appear to have either strong nor weak coupling interactions. This investigation suggests that some intermediate level of coupling is occurring even though the parameters may hint towards weak coupling but the energy level diagrams and energy state transitions hint at a stronger coupling of the two heme irons. Further investigation of this system will certainly need to be conducted to fully characterize the electronic configuration and behavior of this heme protein, but the results obtained here could certainly be meaningful for that cause.<\/p>\n<hr \/>\n<p><strong>Kinetics of DNA Duplex Formation<br \/>\n<\/strong>Radek\u00a0Stratil, 2012 (Advisor: Dr. Alice Deckert)<\/p>\n<p style=\"padding-left: 30px\">Kinetic profiles for renaturation of two DNA 10-mers (5\u2019-GCATGTACGC\/GCGTACATGC-3\u2019 and 5\u2019-GAAGGCTCTC\/GAGAGCCTTC-3\u2019) were recorded at a temperature range of 7\u00baC-35\u00baC\u00a0and sodium chloride concentrations of 0.1M-1.0M using stopped-flow method. The profiles were\u00a0fitted to a second-order integrated rate equation to derive the observed reaction rates. The change\u00a0in entropy, \u0394S\u29e7, and the change in enthalpy, \u0394H\u29e7, of activation were derived from Eyring plots.\u00a0The study was focused on determining the effect of alternating and stacked purine-pyrimidine\u00a0sequences on the rate of renaturation. The \u0394S\u29e7 for renaturation of the stacked strands decreased\u00a0from approximately 25 kcal\/molK at 0.01M NaCl to approximately 0 kcal\/molK at 0.03M-1.0M\u00a0NaCl indicating approximately equal levels of disorder in the single strands and the transition\u00a0state. The \u0394H\u29e7 followed the same trend with approximately 20 kcal\/mol at 0.01M NaCl and 10\u00a0kcal\/mol at 0.03M-1.0M NaCl. This trend indicates that at NaCl concentrations above 0.03M, the\u00a0sodium ions shield the negative charges on the sugar-phosphate backbone decreasing the energy\u00a0need for the association of the single strands to form the transition state. The \u0394S\u29e7 for renaturation\u00a0of the alternating strands was recorded to be approximately 40 kcal\/molK for all sodium chloride\u00a0concentrations indicating that the single strands are more highly organized than the transition\u00a0state. This suggests the existence of a stable secondary structure formed by the single strands\u00a0which was proposed to be a hairpin. The \u0394H\u29e7 profile follows the same pattern as the \u0394S\u29e7 and was\u00a0recorded at approximately 21 kcal\/mol for all the NaCl concentration indicating that there is\u00a0substantial energy required to disrupt the secondary structure formed by the single strands in\u00a0order to form the transition state which has lower order. Analysis of hyperchromicities indicated\u00a0secondary structure in the alternating strand. The existence of this structure prevented\u00a0comparison of the rates of renaturation between the alternating and stacked strands.<\/p>\n<hr \/>\n<p><strong>FbxA mediated ubiquitination of FbiA in <em>Dictyostelium discoideum<\/em><\/strong><br \/>\nChristine\u00a0Wachnowsky, 2012 (Advisor: Dr. Margaret Nelson)<\/p>\n<p style=\"padding-left: 30px\">The highly conserved ubiquitin proteasome system (UPS) regulates the cell cycle, transcription factors and tumor suppressor proteins, like p53, by regulating protein levels. In order for ubiquitin mediated protein degradation to occur, the target must bind to an F-box protein, which is part of the Skp, Cullin, Fbox (SCF) complex of the E3 enzyme. Once bound, the target protein is polyubiquitinated and degraded by the proteasome. Since this process is highly conserved, it is often beneficial to study it in model organisms, such as <em>Dictyostelium discoideum<\/em>, in order to gain an understanding of the process that can be applied to more complex organisms. Two SCF complexes and their target proteins have been identified in <em>D. discoideum<\/em>\u00b8 but a second potential target for the F-box protein FbxA has recently been identified as <span style=\"text-decoration: underline\">Fb<\/span>xA <span style=\"text-decoration: underline\"><\/span>Interacting protein (FbiA). Based on this suggested interaction, I hypothesized that the FbiA protein fused to the reporter green fluorescent protein (GFP) should be ubiquitinated in wild type <em>D. discoideum<\/em> Ax2 cells as detected using immunopurification and Western analysis by probing with anti-GFP and anti-ubiquitin antibodies. I also hypothesized that by constructing an epitope-tagged version of ubiquitin, a more specific probe for ubiquitin can be used in the Western analysis to better detect ubiquitinated FbiA. Immunopurification and Western analysis demonstrated no detectable levels of bound protein when probed with anti-ubiquitin, so optimization of the protocol could enable detection. The plasmid was constructed using a vector containing a hemaglutinin tag and the <em>D. discoideum<\/em> gene for ubiquitin D; however further characterization of the plasmid and possibly the construction of a better plasmid will need to be conducted before it can be used to detect ubiquitinated FbiA. Continued analysis to look for ubiquitinated FbiA in <em>D. discoideum<\/em> can continue to provide insight into the role of the UPS in higher systems.<\/p>\n<hr \/>\n<p><strong>Identification of Glucose-inducible Indolic Metabolites Produced by <em>Pseudomonas fluorescens<\/em><\/strong><br \/>\nAmber Wetzel, 2012 (Advisor: Dr. Catharina Coenen)<\/p>\n<p style=\"padding-left: 30px\"><em>Pseudomonas fluorescens<\/em> is a root-associated bacterium that increases crop yield and protects plants against disease. In addition, some strains of <em>P. fluorescens<\/em> promote plant growth, most likely by colonizing roots and producing indole-3-acetic acid (IAA), the most common form of the plant growth hormone auxin. IAA production in <em>P. fluorescens<\/em> grown in Castric media supplemented with tryptophan, a precursor of IAA, can be quantified spectrophotometrically after reacting bacterial supernatants with the Salkowski\u2019s reagent. Two biocontrol strains of <em>P. fluorescens<\/em>, Clinton and Eaton, produce IAA only when glucose is absent from the growth medium. In the presence of glucose, a different metabolite is produced, which also reacts with the Salkowski\u2019s reagent, but has a different absorption maximum. To identify this metabolite, methods involving the analysis of products extracted with ethyl acetate from bacterial supernatant were being developed, including: further analysis with the Salkowski reagent, thin layer chromatography (TLC) and the van Urk-Salkowski\u2019s reagent, and high performance liquid chromatography (HPLC). The conflicting results from these methods prevented the identification of unknown indole as any of the standard indoles: indole-3-acetonitrile (IAN), indole-3-pyruvid acid (IPyA), indole-3-acetaldehyde (IAAld), 1-methylindole (1-MI), and indole-3-carboxaldehyde (ICAld). Further analysis is important because the regulation of bacterial indole production by availability of plant-secreted sugars is an essential component of plant growth regulation by root-associated bacteria.<\/p>\n<hr \/>\n<p><strong>Interaction Between FbiA and FbxA in <em>Dictyostelium discoideum<\/em><\/strong><br \/>\nMichelle\u00a0Williams, 2012 (Advisor: Dr. Margaret Nelson)<\/p>\n<p style=\"padding-left: 30px\"><em>Dictyostelium discoideum<\/em> is a valuable model system for the study of cellular processes, like cellular differentiation and cellular proportioning. <em>Dictyostelium<\/em> is thus used to observe the ubiquitin proteasome system (UPS), which functions through a pathway to target and mark proteins for degradation. FbxA is thought to be a F-box protein and functions in the UPS by specifically binding to target proteins. A yeast-two hybrid analysis suggests that FbxA targets FbiA for degradation (Christman, 1999). Previous research has attempted to further suggest that these two proteins interact by using co-immunoprecipitation to isolate FbxA and FbiA. However, these attempts have been unsuccessful. The goal of this study was to make modifications to the previous co-immunoprecipitation procedure, such as using a different negative control cell line, to successfully isolate FbxA and FbiA. A suggested interaction between FbxA and FbiA was seen in a co-immunoprecipitation of the experimental cell line, Ax2\/Myc-FbxA;GFP-741. A co-immunopreciptation was not completed with the negative control cell line, Ax2\/Myc-FbxA;GFP-\u03b1tubulin, due to complications developing these cells. Without a negative control, the suggestion that Myc-FbxA and GFP-741 interact is not definitive, for Myc-FbxA could be pulled out of solution independent of an interaction with GFP-741. In order to further determine if Myc-FbxA and GFP-741 interact in <em>Dictyostelium discodium<\/em> and further increase the efficiency of this co-immunoprecipitation, this experiment needs to be repeated for the negative control and modifications need to be made to the current experimental design.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Whole Genome Analysis Reveals That Conservation and Duplication Gave Rise to the Current V2R Gene Repertoire in Mammals Alexander\u00a0Berry, 2012 (Advisor: Dr. Kristen Webb) The vomeronasal organ (VNO) is the part of the olfactory system that detects specific semiochemicals known as pheromones, which allow for communication between members of a species, and also affect social [&#8230;]<\/p>\n<p><a class=\"mt-5\" href=\"https:\/\/sites.allegheny.edu\/biochemistry\/student-research\/senior-project\/senior-project-abstracts-2012\/\">Continue Reading &#8220;Senior Project Abstracts 2012&#8221;<\/a><\/p>\n","protected":false},"author":183,"featured_media":0,"parent":401,"menu_order":0,"comment_status":"closed","ping_status":"open","template":"nosidebar.php","meta":{"inline_featured_image":false,"footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-610","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages\/610","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/users\/183"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/comments?post=610"}],"version-history":[{"count":0,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages\/610\/revisions"}],"up":[{"embeddable":true,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages\/401"}],"wp:attachment":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/media?parent=610"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":557,"date":"2012-02-20T10:34:14","date_gmt":"2012-02-20T14:34:14","guid":{"rendered":"http:\/\/sites.allegheny.edu\/biochem\/?page_id=557"},"modified":"2020-04-14T15:57:53","modified_gmt":"2020-04-14T19:57:53","slug":"funding-opportunities-for-student-research","status":"publish","type":"page","link":"https:\/\/sites.allegheny.edu\/biochemistry\/student-research\/funding-opportunities-for-student-research\/","title":{"rendered":"Funding Opportunities for Student Research"},"content":{"rendered":"<p><\/p>\n<p><a href=\"https:\/\/sites.allegheny.edu\/research\/on-campus-student-research-events\/\">Funding for Conference Presentations<\/a> is coordinated through the office of Undergraduate Research, Scholarship, and Creative Activities (URSCA).<\/p>\n<p><strong>The Harold M. State Research Fellowship<\/strong> was established in honor of Professor Harold M. State, Emeritus of the Department of Chemistry, by an appreciative student, Harry E. Bonner, Class of 1956. It is awarded annually to third-year (rising senior) students majoring in any one of the natural science departments.<\/p>\n<p>The award may be used to support student summer research and research conducted during the academic year in collaboration with a faculty member. It may also be used for supplies, materials, and other expenses related to the research project. Monies may support travel for the student and his or her faculty member to conduct research or present research findings.<\/p>\n<p>Students, in conjunction with their advisor, send a proposal of their research project to the Chair of the Chemistry Department. The proposal should indicate whether they are receiving funding from other sources (department, faculty grants, etc.), and it should include a budget.<\/p>\n<p>A committee comprised of the science department chairs will consider the research proposals and determine the award recipient(s). The State Fellow will be selected in the spring semester; the award will be formally announced at the annual Honors Convocation. The application deadline is March 1.<\/p>\n<p><strong><a href=\"https:\/\/sites.allegheny.edu\/biochem\/files\/2019\/11\/The-Class-of-1939-Senior-Research-Fund-Funding-Application-7-18-19.pdf\">The Class of 1939 Senior Research Fund<\/a><\/strong> was established by the Class of 1939 on the occasion of its 50th reunion. The income from this fund shall be used to support student research in all departments in conjunction with the senior project.<\/p>\n<p><strong>Student\/Faculty Collaborative Research<br \/>\n<\/strong><\/p>\n<p>Student\/Faculty Summer Collaborative Research funding offers students and faculty the opportunity to work together on a research project of mutual interest. The Provost and Dean of the College Office coordinates this endeavor.<\/p>\n<p>The project must not be directly related to the student\u2019s senior project, though it can serve as preparation. This funding is not available for independent studies, summer internships, assistantships, or summer employment opportunities. Students interested in obtaining summer employment should contact the Financial Aid Office for a list of positions available during the summer. In order to be eligible for funding, student research must be conducted in collaboration with an Allegheny faculty member and the applicant must be a continuing student in good academic standing. Students must consult with their professor to confirm the specifics of the proposed project, including number of weeks, planned number of hours worked per week, and materials budget, before submitting the application form.<\/p>\n<p>Announcements as well as the link for the application will be posted on My Allegheny in early March each year.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Funding for Conference Presentations is coordinated through the office of Undergraduate Research, Scholarship, and Creative Activities (URSCA). The Harold M. State Research Fellowship was established in honor of Professor Harold M. State, Emeritus of the Department of Chemistry, by an appreciative student, Harry E. Bonner, Class of 1956. It is awarded annually to third-year (rising [&#8230;]<\/p>\n<p><a class=\"mt-5\" href=\"https:\/\/sites.allegheny.edu\/biochemistry\/student-research\/funding-opportunities-for-student-research\/\">Continue Reading &#8220;Funding Opportunities for Student Research&#8221;<\/a><\/p>\n","protected":false},"author":246,"featured_media":0,"parent":54,"menu_order":0,"comment_status":"closed","ping_status":"open","template":"","meta":{"inline_featured_image":false,"footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-557","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages\/557","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/users\/246"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/comments?post=557"}],"version-history":[{"count":0,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages\/557\/revisions"}],"up":[{"embeddable":true,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages\/54"}],"wp:attachment":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/media?parent=557"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":445,"date":"2012-02-17T11:36:21","date_gmt":"2012-02-17T15:36:21","guid":{"rendered":"http:\/\/sites.allegheny.edu\/biochem\/?page_id=445"},"modified":"2023-01-18T12:35:59","modified_gmt":"2023-01-18T17:35:59","slug":"faculty-research-interests","status":"publish","type":"page","link":"https:\/\/sites.allegheny.edu\/biochemistry\/faculty\/faculty-research-interests\/","title":{"rendered":"Faculty Research Interests"},"content":{"rendered":"<hr \/>\n<h4>Dr. Catharina Coenen<\/h4>\n<p>My research focuses on the action of the hormone auxin in plant growth and development and in the interaction between plant roots and soil microbes.\u00a0 My students and I have been characterizing the role of auxin in mycorrhiza, an agriculturally and ecologically important symbiotic association between plant roots and fungi.\u00a0 We have also begun to explore auxin as a communication signal between plant-protective bacteria and the roots these bacteria colonize.\u00a0 These projects have implications for organic agriculture, because the fungi and bacteria we study reduce the need for toxic fungicides and fertilizers.<\/p>\n<p>The methods my students use to study auxin responses include genetics, molecular, biochemical and physiological experiments.\u00a0 As long as you enjoy working with plants, fungi, or bacteria, there are lots of different experimental approaches to choose from.\u00a0 Even if you may not be interested in staying in plant research in the long term, you will find valuable techniques and analysis methods to learn here that transfer to other systems.<\/p>\n<hr \/>\n<h4 class=\"bt\">Dr. Alice Deckert<\/h4>\n<p>My general research interests lie in the area of interfacial chemical kinetics.\u00a0 My investigations of interfacial kinetics utilize assembled systems such as Langmuir-Blodgett (LB) films and self-assembled monolayers (SAM).\u00a0 These films consist of well-ordered mono- or multilayers and can be fabricated from almost any amphiphillic molecule.\u00a0 The ordered nature of these films provides a unique opportunity to study reactions in organized media.<\/p>\n<p>We employ several analytical techniques to monitor reactions.\u00a0 These include, UV-visible spectroscopy, ATR-FTIR, surface-enhanced Raman spectroscopy (SERS), microgravimetry and surface plasmon resonance (spr).<\/p>\n<p>My primary interest is in reactions between the surface of the film and molecules from the solution or gas phase.\u00a0 In this case only one reactant is \u201corganized\u201d or constrained while the other reactant is free to move in three-dimensions.\u00a0 An understanding of this class of reactions is important when designing chemical sensors or biosensor technology.<\/p>\n<p>Recent senior projects:<\/p>\n<ul>\n<li>&#8220;Oxygen binding of myoglobin immobilized on self-assembled monolayers&#8221;<\/li>\n<li>&#8220;Investigation of the kinetics for activation of 4-mercaptobenzoic acid with N-hydroxysuccinimide and 1-[3-(dimethylamino)propyl]-3]ethylcarbodiimide hydrochloride and displacement by histidine&#8221;<\/li>\n<li>&#8220;Kinetics of DNA duplexing and denaturation studied using surface plasmon resonance&#8221;<\/li>\n<li>&#8220;Kinetic investigation of glucose oxidase binding to a gold organosulfur self-assembled monolayer using surface plasmon resonance (spr) and contact angle (CA)&#8221;<\/li>\n<\/ul>\n<hr \/>\n<h4 class=\"bt\">Dr. Ivy Garcia<\/h4>\n<p>RNA plays a crucial structural and catalytic role in a variety of important cellular processes. They are synthesized as single-stranded chains and must fold into defined complex structures, like proteins, to accomplish their diverse functions. Structural versatility is a challenge for most RNAs due to the difficulty of reaching the native folding state. Hence, protein cofactors are usually necessary to stabilize or modulate RNA folding. One type of RNA protein cofactors are the ubiquitous DEAD-box proteins. DEAD-box proteins are essential in all aspects of RNA metabolism including pre-mRNA splicing, ribosome biogenesis, RNA interference, translation, mRNA transport, and decay. These motor proteins modulate RNA-RNA, RNA-protein, and\/or protein-protein interactions by utilizing nine conserved motifs to convert RNA binding and ATP hydrolysis into distinct conformational changes. As part of the helicase superfamily 2 (SF2), DEAD-box proteins are formally putative RNA helicases. However, ATP driven unwinding of RNA duplexes has only been illustrated for few proteins. The main focus and motivation of my research has been to biochemically understand the structural interactions and the role that proteins play in RNA catalysis and folding in eukaryotic RNA metabolism.<\/p>\n<hr \/>\n<h4 class=\"bt\">Dr. Brad Hersh<\/h4>\n<p>Though virtually all cells in an animal contain the same DNA sequences, different cell types (e.g., muscle cells and nerve cells) have distinct physical properties.\u00a0 These differences are achieved during growth and development of the organism by switching on and off specific sets of genes within the common DNA sequence.\u00a0 My research focuses on identifying and characterizing the DNA sequences that control when, where, and at what level gene expression is switched on and off in the developing animal body.\u00a0 The long term goal of my research is to understand the mechanisms by which Hox proteins, involved in shaping the head-to-tail patterning of all animals, regulate their target genes.\u00a0 We use the fruit fly, <em>Drosophila melanogaster<\/em>, to examine the DNA sequences that respond to the Hox protein Ultrabithorax and either activate or repress gene expression the <em>Drosophila<\/em> hindwing.\u00a0 The lab uses molecular biological techniques to generate variants of sequences shown to be important for gene expression, and then tests the function of these variants in transgenic animals by looking at fluorescent reporter gene activity.\u00a0 In addition, we are interested in identifying the genes that are important for morphological differences between insect species so\u00a0that we may understand evolutionary changes that occur in the developmental processes that produce animal shape.<\/p>\n<hr \/>\n<h4 class=\"bt\">Dr. Tricia Humphreys<\/h4>\n<p>My research focuses on the obligate human pathogen <em>Haemophilus ducreyi<\/em>, the causative agent of the sexually transmitted disease chancroid.\u00a0 Like other genital ulcer diseases, chancroid facilitates the acquisition and transmission of HIV.\u00a0 The long term goal of my research is to understand host-pathogen interactions between <em>H. ducreyi<\/em> and humans.\u00a0 Projects in my lab examine this interaction from the bacterial side of the interaction, including defining differences between the recently described two classes of <em>H. ducreyi<\/em>.\u00a0 Class I and class II <em>H. ducreyi<\/em> are known to differ in outer membrane components, but not much is known about genetic differences.\u00a0 Students in my lab discovered that the two classes have multiple point mutations in key virulence genes (<em>pal<\/em>, <em>wecA<\/em>, <em>lspA2<\/em>) as well as a gene commonly used to understand phylogenetic relationships (<em>recA<\/em>).\u00a0 When these genes are used to generate phylogenetic trees, the class I and II strains split consistently into two groups.\u00a0 Future research will focus on studying phylogenetic relationships using housekeeping genes and mutli-locus sequence analysis.<\/p>\n<hr \/>\n<p><strong>Dr. Mahita Kadmiel<\/strong><\/p>\n<p>My research aims at understanding the molecular basis of human diseases. Too little or too much of stress hormones (glucocorticoids) and changes in sex hormone levels (estrogen and testosterone) have been linked to vision problems. I am investigating the function of these hormones in cornea and retina using rodent models and cells derived from human eyes. I am also interested in investigating the role of hormone-mimicking chemicals (more commonly called Endocrine Disrupting Chemicals) on ocular cells and tissues and how they might influence ocular health.<\/p>\n<hr \/>\n<h4 class=\"bt\">Dr. Shaun Murphree<\/h4>\n<p>Research in the Murphree group focuses mainly on synthetic methodology, particularly through the use of sulfones. For example, the sulfone-based reagent 2,3-dibromo-1-(phenylsulfonyl)-1-propene, or DBP, reacts with 1,3-diketones to form 2,4-disubstituted furans, a structural motif found in some naturally occurring products of biological and industrial interest.<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"aligncenter size-full wp-image-446 imgnoborder\" src=\"https:\/\/sitesmedia.s3.amazonaws.com\/biochem\/files\/2012\/02\/facultyresearch_01.jpg\" alt=\"\" width=\"213\" height=\"150\" \/><\/p>\n<p>Ongoing projects are exploring the synthetic utility of this methodology, as well as the chemistry of other novel sulfonyl-substituted small molecules.<\/p>\n<p>An additional research interest involves the development of more environmentally benign modifications of classical industrial syntheses through the use of catalytic methods.<\/p>\n<hr \/>\n<h4 class=\"bt\">Dr. Margaret Nelson<\/h4>\n<p>I am interested in the way in which signal transduction pathways allow cells to interpret and respond to external cues during development. My research is currently focused on the role that two proteins, FbxA and FbiA, play in the development of <em>Dictyostelium discoideum<\/em>. FbxA is a member of an evolutionarily conserved protein family that regulates cell behavior by targeting specific components of signal transduction pathways for degradation. Malfunctions in this degradation system have been implicated as a potential causative agent in several human diseases, including Alzheimer\u2019s disease, Parkinson\u2019s disease, and cancer. Data from former comp projects suggest that FbiA may be a target of FbxA-mediated degradation. Proteins homologous to FbiA are found in a wide array of eukaryotes, including fungi, plants, <em>C. elegans, Drosophila<\/em>, mice, and humans. The function of these FbiA homologues is, however, unknown. Hence, further characterization of FbiA\u2019s role in <em>Dictyostelium <\/em>development may shed light on the function of this conserved protein family.<\/p>\n<p>Work in the near future will address questions such as: (i) when and where the FbiA protein is expressed, (ii) what signaling pathway(s) are responsible for the complex, developmentally regulated pattern of <em>fbiA<\/em> RNA expression, (iii) why the absence of FbiA disrupts pattern formation, and (iv) whether FbxA &amp; FbiA interact in a biologically relevant fashion. Depending upon the project you choose, you might employ any of the following techniques: restriction digests, agarose gel electrophoresis, plasmid &amp; genomic DNA preps, PCR, introduction of recombinant DNA molecules into cells (bacteria, <em>Dictyostelium<\/em>), cell propagation and sterile technique (bacteria, <em>Dictyostelium<\/em>), protein purification, protein gels, Western blots, histochemical staining, phase contrast microscopy, immunofluorescent microscopy, bright-field microscopy (stereozoom scope), and digital photography.<\/p>\n<p>Recent senior projects:<\/p>\n<ul>\n<li>&#8220;<em>Dictyostelium fbiA<\/em> mRNA expression analysis via <em>in situ<\/em> hybridization&#8221;<\/li>\n<li>&#8220;Characterizing the relationship between the proteins FbxA and FbiA in <em>Dictyostelium discoideum<\/em>&#8220;<\/li>\n<li>&#8220;Regulation of FbiA protein levels via ubiquitination-mediated proteolysis in <em>Dictyostelium discoideum<\/em>&#8220;<\/li>\n<li>&#8220;Characterization of <em>Dictyostelium discoideum<\/em> mutants overexpressing FbiA&#8221;<\/li>\n<li>&#8220;Creating and Characterizing the <em>fbiA<\/em><sup>&#8211;<\/sup> mutant in <em>Dictyostelium discoideum<\/em>&#8220;<\/li>\n<\/ul>\n<hr \/>\n<p><b>YEE MON THU<\/b><\/p>\n<p><span style=\"font-weight: 400;\">Research projects in my lab cover topics in molecular signaling, cell biology, genetics and cancer biology. Overarching theme of my lab is to understand cellular communications elicited by genome instability and their implications in cancer. One such communication is through a type of post-translational modification called sumoylation. Currently, there are two major goals in my lab:<\/span><\/p>\n<p><span style=\"font-weight: 400;\">1) To understand the biological significance of proteins sumoylated in response to genome instability. To this end, we use molecular biology, genetic and biochemical tools compatible with a simple model eukaryote, <\/span><i><span style=\"font-weight: 400;\">Saccharomyces cerevisiae<\/span><\/i><span style=\"font-weight: 400;\">. We generate mutants that cannot be sumoylated or are constitutively sumoylated to determine if altering sumoylation dynamics changes cells\u2019 sensitivity to genotoxic agents.<\/span><\/p>\n<p><span style=\"font-weight: 400;\">2) To characterize the role of a ubiquitin ligase that targets sumoylated proteins for proteasomal degradation in the context of genome stability. We use molecular and cell biology techniques to understand if the ligase causes double-strand breaks and other forms of genome instability. These questions are addressed using both <\/span><i><span style=\"font-weight: 400;\">S. cerevisiae<\/span><\/i><span style=\"font-weight: 400;\"> and human cancer cell lines.<\/span><\/p>\n<hr \/>\n","protected":false},"excerpt":{"rendered":"<p>Dr. Catharina Coenen My research focuses on the action of the hormone auxin in plant growth and development and in the interaction between plant roots and soil microbes.\u00a0 My students and I have been characterizing the role of auxin in mycorrhiza, an agriculturally and ecologically important symbiotic association between plant roots and fungi.\u00a0 We have [&#8230;]<\/p>\n<p><a class=\"mt-5\" href=\"https:\/\/sites.allegheny.edu\/biochemistry\/faculty\/faculty-research-interests\/\">Continue Reading &#8220;Faculty Research Interests&#8221;<\/a><\/p>\n","protected":false},"author":562,"featured_media":0,"parent":20,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"inline_featured_image":false,"footnotes":"","_links_to":"","_links_to_target":""},"class_list":["post-445","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages\/445","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/users\/562"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/comments?post=445"}],"version-history":[{"count":0,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages\/445\/revisions"}],"up":[{"embeddable":true,"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/pages\/20"}],"wp:attachment":[{"href":"https:\/\/sites.allegheny.edu\/biochemistry\/wp-json\/wp\/v2\/media?parent=445"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}]