Life Sciences Commons^™

Hiv Vaccines: Progress, Limitations And A Crispr/Cas9 Vaccine, Omar A. Garcia Martinez

Biology: Student Scholarship & Creative Works

ABSTRACT: The HIV-1 pandemic continues to thrive due to ineffective HIV-1 vaccines. Historically, the world’s most infectious diseases, such as polio and smallpox, have been eradicated or have come close to eradication due to the advent of effective vaccines. Highly active antiretroviral therapy is able to delay the onset of AIDS but can neither rid the body of HIV-1 proviral DNA nor prevent further transmission. A prophylactic vaccine that prevents the various mechanisms HIV-1 has to evade and attack our immune system is needed to end the HIV-1 pandemic. Recent advances in engineered nuclease systems, like the CRISPR/Cas9 system, have …

Impacts From The Use Of Antibiotics In Livestock: Methods Of Transmission Of Antibiotic Resistance From Livestock To Humans, Kristin M. Walden

Biology: Student Scholarship & Creative Works

Antibiotic use in livestock production has been around since the 1950s. Antibiotic feed is used in livestock and other meat producing animals for three reasons: illness prevention, illness treatment, and growth promotion. Unfortunately, since the time that antibiotics were first invented, antibiotic resistant bacteria have become a threat to public health. There are many studies showing methods of transmission of antibiotic resistance from livestock to humans. Antibiotic resistance can spread from livestock to soil, water, insects, and food, which ultimately comes into contact with humans. A proposed study to measure antibiotic resistance when eliminating antibiotic feed will provide a hypothesis …

Mrub_2874 Is Homologous To B3386 And Mrub_1349 Is Homologous To B2914, But Mrub_1349 Is Not Homologous To B4090, Samantha Murad, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

ABSTRACT. This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation – Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_2874 and Mrub_1349. We predict that Mrub_2874 encodes the enzyme ribulose-5-phosphate 3-epimerase (DNA coordinates 2912530..2913204 on the reverse strand), which is the first step of the pentose phosphate pathway (KEGG map number 00030). It catalyzes the conversion of D-ribulose 5-phosphate to D-xylulose 5-phosphate. The E. coli K12 MG1655 ortholog is predicted to be b3386, which has the gene …

Challenges Of Adoptive (T-)Cell Transfer Immunotherapy For Cancer, Aaron Volk

Biology: Student Scholarship & Creative Works

Background and significance: The rebirth of the theory of immunosurveillance in 2001 rejuvenated interest in anticancer immunotherapies. In particular, T-cell-based therapies have garnered substantial interest due to the robustness and tumor antigen-specific cytotoxicity of T-cell anticancer immune responses.

Hypothesis: The efficacy of adoptive cell transfer (ACT) T-cell immunotherapy could significantly improve and gain widespread approval if future innovations in ACT-based approaches account for the pro- and antitumoral properties of non-CD8⁺ lineages of effector T-cells, evasion of T-cell antitumor immunity, and tumor-induced suppression of antitumor immunity.

Problem Analysis: Despite numerous reports of highly successful ACT-based clinical trials, no such therapy …

Bioinformatics Comparison Of M. Ruber Mrub_2507 To E. Coli Pdxk/B1636 And M. Ruber Mrub_2888 To E. Coli Pdxh/B1638 To Determine The Orthologous Nature, Adam Bernardi, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation – Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_2507 and Mrub_2888. We predict that Mrub_2507 encodes the enzyme pyridoxal kinase (DNA coordinates 2555521..2556402), which is in the Vitamin B₆ Metabolism pathway (KEGG map number 00750). It catalyzes the conversion of pyridoxine, pyridoxamine, or pyridoxal to pyridoxine 5’-phosphate, pyridoxamine 5’-phosphate, or pyridoxal 5’-phosphate respectively. The E. coli K12 MG1655 ortholog is predicted to be b1636, which has …

Genomic Analysis Of Meiothermus Ruber Mrub_1907 And Meiothermus Ruber Mrub_1844 With Potential Ortholog Escherichia Coli B3774 Ilvc And Escherichia Coli B3771 Ilvc Gene Through Bioinformatics, Felipe A. Hernandez, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation – Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_1907 and Mrub_1844. We predict that Mrub__1907 encodes the enzyme ketol-acid reductoisomerase (DNA coordinates 1966630..1967649 on the reverse strand), which is the fourth step of the L-isoleucine pathway (from threonine) (KEGG map number 00290). It catalyzes the conversion of (R)-3- Hydroxy-3-methyl-2-oxopentanoate to (R)-2-3 Dihydroxy-3-methylpentanoate. The E. coli K12 MG1655 ortholog is predicted to be b3774, which has the gene …

Comparison Of Genes In Meiothermus Ruber And Escherichia Coli In The Thiamine Biosynthesis Pathway, Erin E. Frye, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation – Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_2046 and Mrub_2041.We predict that Mrub_2046 encodes the enzyme phosphomethylpyrimidine kinase (DNA coordinates 2082772..2083572 on the reverse strand), which is the second step of the Thiamine Metabolism pathway (KEGG map number mrb00730). It catalyzes the conversion of 4-Amino-2-methyl-5-phosphomethylpyrimidine to 4-Amino-2-methyl-5-hydroxymethyl diphosphate The E. coli K12 MG1655 ortholog is predicted to be b2103, which has the gene identifier thiD. We …

Meiothermus Ruber Mrub_0976 And Mrub_1641 Share The Same Functions As Escherichia Coli B3940 And B3433 In The Biosynthesis Of Homoserine, Cody Stephans, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_0976 and Mrub_1641. We predict that Mrub_0976 encodes the enzyme aspartate kinase (DNA coordinates 964404..965630) which is the 1^st step of the homoserine biosynthesispathway (KEGG map number M00018). It catalyzes the conversion L-aspartate to L-asparyl-4-phospate. The E. coli K12 MG1655 ortholog is predicted to be b3940, which has the gene identifier ‘thrA’. We …

Possible Orthologs Of Trpa And Trpb Genes Between E. Coli (B1260 And B1261) And M. Ruber (Mrub_1512 And Mrub_1511), John J. Stenger, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

Mrub_1512 encodes the enzyme tryptophan A (DNA coordinates 1544300..1545091), which is the 6th step of the Tryptophan Biosynthesis pathway (KEGG map number 00400). It catalyzes the conversion of Chorismate to L-Tryptophan. The E. coli K12 MG1655 ortholog is predicted to be b1260, which has the gene identifier trpA. We predict that Mrub_1512 (DNA coordinates 1544300..1545091) is a alpha subunit of the Tryptophan Synthase (KEGG map number 00400). Mrub_1511 encodes the enzyme tryptophan B (DNA coordinates 1543083..1544303), which is the 7th step of the Tryptophan Biosynthesis pathway (KEGG map number 00400). It catalyzes the conversion of Chorismate to L-Tryptophan. The E. …

Mrub_2765 Is The Version Of E. Coli Fabz In Meiothermus Ruber, While Mrub_0266 Is The Version Of E. Coli Fabi In Meiothermus Ruber, Amanda M. Narkis, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation – Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_2765 and Mrub_0266. We predict that Mrub_2765 encodes the enzyme β-hydroxyacyl-Acyl carrier protein (ACP) dehydratase (DNA coordinates 2805770..2806213 on the reverse strand), which is the 3^rd step of the fatty acid elongation pathway (KEGG map number 00780). It catalyzes the conversion of (3R)-3-hydroxyacyl-[ACP] to trans-2-enoyl-[ACP]. The E. coli K12 MG1655 ortholog is predicted to be …

Pyruvate Metabolism In M. Ruber When Compared To E. Coli, Amanda M. Johnson, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_0476, Mrub_1516, Mrub_1517, Mrub_0477, and Mrub_2322. We predict that Mrub_0476, Mrub_1516, and Mrub_1517 (DNA coordinates 461643..464366, 1548957..1549955, 1549952..1550986, respectively) are a paralogous a subunit of the pyruvate dehydrogenase complex E1(KEGG map number 00620). We predict that Mrub_0477 and Mrub_2322 (DNA coordinates 464402..465697 and 2371690..2373090, respectively) are a paralogous subunit of the pyruvate dehydrogenase complex …

A Bioinformatics Study On Whether Or Not Mrub_2763 Gene In M. Ruber Is Similar To The Lpxb Gene In E. Coli And If Mrub_2768 Is Similar To The Lpxd Gene In E. Coli., Frank J. Habura, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the gene Mrub_2768 and Mrub_2763. We predict that Mrub_2768 (DNA coordinates 2808186..2809178 on the reverse strand) encodes the enzyme UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase (LpxD), which is the third step of the Lipopolysaccharide biosynthesis pathway (KEGG map number 00540). It catalyzes the conversion of UDP-3-O-(3-hydroxymyristoyl)-α-D-glucosamine + a(3R)-3-hydroxymyristoyl-[acp] → a holo-[acyl-carrier protein] + UDP-2-N,3-O-bis[(3R)-3-hydroxytetradecanoyl]-α-D-glucosamine. The E. coli K12 MG1655 ortholog is predicted to be b0179, which …

Comparing Meiothermus Ruber And Myxococcus Xanthus In The Purine Metabolism Pathway, Linnea J. Ritchie, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation – Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. I investigated the biological functions of Mrub_1053 Mrub_2281 and Mrub_2299. I predicted that Mrub_1053 and Mrub_2281 (DNA coordinates 1053364..1054359 on the forward strand and 2333172..2334113 on the forward strand respectively) encodes the enzyme phosphoribose-1-pyrophosphate synthetase (PRS) which is the first step of the purine synthesis pathway (KEGG). I also predicted that Mrub_2299 (DNA coordinates: 2352378..2353775 on the forward strand) encodes for Phosphoribosyl pyrophosphate (PRPP) amidotransferase, which is …

Valine Biosynthesis: Mrub_2994 Is Orthologous To E. Coli B3770 And Mrub_1844 Is Orthologous To E. Coli B3771, Bennett A. Hartmann, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation – Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_2994 and Mrub_1844. We predict that Mrub_1884 encodes the enzyme dihydroxy-acid dehydratase (DNA coordinates 1901362..1903026 on the forward strand), which is the third step of the valine biosynthesis pathway (KEGG map number 00290). It catalyzes the conversion of 2,3-dihydroxy-3methylbutanoate to 3-methyl-2-oxobutanoate. The E. coli K12 MG1655 ortholog is predicted to be b3771, which has the gene identifier ilvD. …

Bioinformatic Comparison Of Genes In The Leucine Biosynthesis Pathway Of Escherichia Coli To Meiothermus Ruber, Isaac D. Schmied, Benjamin T. Ryan, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

We predict that Mrub_1905 and Mrub_1906 encode the enzyme 2-isopropylmalate synthase (Mrub_1906 DNA coordinates complement(1965044..1966603) Mrub_1905 DNA coordinates complement(1963455..1965041)), which is the first step of the leucine biosynthesis pathway (KEGG map number 00290). It catalyzes the conversion of (2S)-2-isopropylmalate to 2-isopropylmaleate. The E. coli K12 MG1655 ortholog is predicted to be b0074, which has the gene identifier leuA. We predict that Mrub_1846 encodes the enzyme 3-isopropylmalate dehydrogenase (DNA coordinates complement(1903909..1904961)), which is the third step of the leucine biosynthesis pathway (KEGG map number 00290). It catalyzes the conversion of (2R,3S)-3-isopropylmalate to (2S)-2-isopropyl-3-oxosuccinate. The E. coli K12 MG1655 ortholog is predicted …

Riboflavin Metabolism: A Study To See If Mrub_1256 Is Orthologous To E. Coli B0415, And If Mrub_1254 Is Orthologous To E. Coli B1662, Anish Sora Reddy, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_1256 and Mrub_1254. We predict that Mrub_1256 encodes the enzyme 6,7-dimethyl-8-ribityllumazine synthase (Dna Coordinates 1282509..1282982 forward strand), which is part of the Riboflavin Metabolism pathway (KEGG map number 00740). It catalyzes the conversion of 3,4-Dihydroxy-2-butanone-4-phosphate or 5-amino-6-ribityl-aminouracil to Quinone. The E. coli K12 MG1655 ortholog is predicted to be E. coli b0415, which has the gene identifier …

The Meiothermus Ruber Mrub_2572 Gene Is An Ortholog Of The Escherichia Coli Pyre B3642 Gene And The Meiothermus Ruber Mrub_2071 Gene Is An Ortholog Of The Escherichia Coli Pyrf B1281 Gene, Cale J. Mccormick, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_2572 and Mrub_2071. We predict that Mrub_2572 encodes the enzyme orotate phosphoribosyltransferase (DNA coordinates 2617545..2618096 on the forward strand), which is the 5^th step of the UMP biosynthesis pathway (KEGG map number 00240). It catalyzes the conversion of orotate + PRPP to orotidine 5’-phosphate. The E. coli K12 MG1655 ortholog is predicted to be b3642, which has the gene …

Bioinformatics Indicates That Meiothermus Ruber Genes Mrub_1710 And Mrub_1712 Are Homologs Of The Escherichia Coli Genes B2903 (P-Protein; Glycine Dehydrogenase) And B2905 (T-Protein; Aminomethyltransferase), Respectively, Malory J. Groen, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation – Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_1710 and Mrub_1712. We predict that Mrub_1710 encodes the enzyme glycine dehydrogenase (DNA coordinates 3046168.. 3049041 on the reverse strand), which is the first step of the glycine degradation pathway (KEGG map number 00260). It catalyzes the conversion of glycine to S-Amino-methyldihydro-lipoylprotein. The E. coli K12 MG1655 ortholog is predicted to be b2903, which has the gene identifier gcvP. …

E. Coli B3639 And B3634 Are Orthologs Of Mrub_2047 And Mrub_1372, Rong Zheng, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_2047 and Mrub_1372. We predict that Mrub_2047 encodes the enzyme fused 4'-phosphopantothenoylcysteine decarboxylase/phosphopantothenoylcysteine synthetase, FMN-binding (DNA coordinates 2083590..2084816 on the forward strand), which is the first and the second steps of the CoA biosynthesis pathway (KEGG map number 00770). It catalyzes the conversion of (R)-4’-phosphopantothenate to (R)-4’-phosphopantothenoyl-L-cysteine and the conversion of (R)-4’-phosphopantothenoyl-L-cysteine to 4’-phosphopantetheine. The E. coli K12 MG1655 ortholog …

Mrub_0258 Gene Is An Ortholog Of The B4226 Gene (Ppa) Found In Escherichia Coli; Mrub_1198 Gene Is An Ortholog Of The B2501 Gene (Ppk) Found In Escherichia Coli;, Brandon M. Wills, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of the genes Mrub_0258 and Mrub_1198. We predict that Mrub_0258 encodes the enzyme inorganic pyrophosphatase (226403..226942), which is indirectly involved with the oxidative phosphorylation pathway (KEGG map number 00190). It catalyzes the conversion of the diphosphate ions made by Mrub_1198 into two orthophosphate ions, which can then be used by ATP synthase to produce energy. The E. coli K12 MG1655 ortholog is predicted …

Can The Insertion Of An E. Coli Shine-Dalgarno Sequence Upstream Of M. Ruber Proa Of The Proba Operon Enhance Its Expression, As Measured By A Complementation Assay Using E. Coli Null Strains?, Matthew D. Murphy, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

The process by which the thermophilic bacteria Meiothermus ruber (M. ruber) synthesizes the amino acid proline is examined in this paper. In the well-studied E. coli system, proline biosynthesis involves three enzymes ProA, ProB and ProC; proA and proB form the proBA operon and both proA and proB possess an upstream Shine-Delgarno sequence; and ProB is functionally dependent on ProA as components of a ProBA complex. In previous studies in Dr. Scott’s lab, the putative M. ruber proA (locus tag Mrub1079), proB (Mrub1080) and proC (Mrub1345) genes were cloned into the pKt1 expression vector, transformed into the corresponding …

Detection Of Fecal Contamination Using Molecular Methods, Kristina K. Bowen

Independent Research Projects

This study explores the process of designing a molecular method to detect fecal contamination in the urban watersheds of Rock Island and Moline, Illinois. These urban watersheds are known to contain high ammonia levels and total dissolved solids based on previous studies. Additionally there is concern about the aging combined sewer and storm water system. Therefore, these watersheds are thought to have poor water quality including fecal contamination. Existing molecular methods used for detecting fecal contamination require a considerable amount of resources in the laboratory. Our goal was to design a molecular method that requires fewer resources and can continue …

Using Social Justice And Intersectionality To Improve Stakeholder Conflict In Conservation: A Transdisciplinary Solution, Ana V. Gomez

Biology: Student Scholarship & Creative Works

The social sciences can help to further our causes and help limit conflict within conservation efforts.

Studying Macroinvertebrate Diversity In An Urbanized Watershed Of Rock Island, Illinois., Brittany A. Poynor

Biology: Student Scholarship & Creative Works

Urban land-use covers millions of hectares in the United States. Rock Island is an urbanized city in Illinois, U.S.A. that currently has issues with their stormwater system due to being an urban area. For the past few years, the water quality of the streams in this watershed has been examined, but the biodiversity which can also contribute to water quality knowledge, has not been studied in depth.

The study proposed in this paper is based on the amount of biodiversity in the streams at ten sites in the Rock Island watershed and the water quality at those same sites. It …

Ex-Situ Conservation Programs: Worthwhile?, Nicolette Sliwa, Aaron Sieve

Biology: Student Scholarship & Creative Works

The effectiveness of conservation programs was researched, specifically within zoos, and their attempts to repopulate areas with captive-born individuals of endangered species. There are major biological and economic concerns with these programs focused on, including potential genetic adaptation to captivity, effects of inbreeding, and if this is a truly worthwhile use of funds to restore a species. Looking at the black-footed ferret, the whooping crane, and other supposed successful captive-breeding programs, it is explored whether reintroduced individuals thrive in their new habitats sufficiently enough to contribute to the restoration of the species, and more broadly, their ecosystems.