Genetics and Genomics Commons^™

Characterization Of Mrna Polyadenylation In The Apicomplexa, Ashley T. Stevens, Daniel K. Howe, Arthur G. Hunt

Plant and Soil Sciences Faculty Publications

Messenger RNA polyadenylation is a universal aspect of gene expression in eukaryotes. In well-established model organisms, this process is mediated by a conserved complex of 15–20 subunits. To better understand this process in apicomplexans, a group of unicellular parasites that causes serious disease in humans and livestock, a computational and high throughput sequencing study of the polyadenylation complex and poly(A) sites in several species was conducted. BLAST-based searches for orthologs of the human polyadenylation complex yielded clear matches to only two—poly(A) polymerase and CPSF73—of the 19 proteins used as queries in this analysis. As the human subunits that recognize the …

Microbial Ecology Of South Florida Surface Waters: Examining The Potential For Anthropogenic Influences, Chase P. Donnelly

HCNSO Student Theses and Dissertations

South Florida contains one of the largest subtropical wetlands in the world, and yet not much is known about the microbes that live in these surface waters. These microbes play an important role in chemical cycling and maintaining good water quality for both human and ecosystem health. The hydrology of Florida’s surface waters is tightly regulated with the use of canal and levee systems run by the US Army Corps of Engineers and The South Florida Water Management District. These canals run through the Everglades, agriculture, and urban environments to control water levels in Lake Okeechobee, the Water Conservation Areas, …

Deciphering The Role Of Human Arylamine N-Acetyltransferase 1 (Nat1) In Breast Cancer Cell Metabolism Using A Systems Biology Approach., Samantha Marie Carlisle

Electronic Theses and Dissertations

Background: Human arylamine N-acetyltransferase 1 (NAT1) is a phase II xenobiotic metabolizing enzyme found in almost all tissues. NAT1 can additionally hydrolyze acetyl-coenzyme A (acetyl-CoA) in the absence of an arylamine substrate. NAT1 expression varies inter-individually and is elevated in several cancers including estrogen receptor positive (ER+) breast cancers. Additionally, multiple studies have shown the knockdown of NAT1, by both small molecule inhibition and siRNA methods, in breast cancer cells leads to decreased invasive ability and proliferation and decreased anchorage-independent colony formation. However, the exact mechanism by which NAT1 expression affects cancer risk and progression remains unclear. Additionally, consequences …

Functional Studies Of The E. Coli Proc And A Putative Ortholog Mrub_1345, Maureen Azar, 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 Escherichia coli and Meiothermus ruber proC genes using the complementation assay. In this research project, mutants of varying severity to the functional state of the protein were developed. The results showed that two or more amino acid deletions reduced or eliminated ProC function. Amino acid substitutions, on the other hand, were not severe enough to impact ProC function. Double and triple mutants …

Copy Number Variation In The Porcine Genome Detected From Whole-Genome Sequence, Rebecca Anderson

Honors Theses

Copy number variations (CNVs) are large insertions, deletions, and duplications in the genome that vary between individuals in a species. These variations are known to impact a broad range of phenotypes from molecular-level traits to higher-order clinical phenotypes. CNVs have been linked to complex traits in humans such as autism, attention deficit hyperactivity disorder, nervous system disorders, and early-onset extreme obesity. In this study, whole-genome sequence was obtained from 72 founders of an intensely phenotyped experimental swine herd at the U.S. Meat Animal Research Center (USMARC) in Clay Center, Nebraska. This included 24 boars (12 Duroc and 12 Landrace) and …

Efficient Alignment Algorithms For Dna Sequencing Data, Nilesh Vinod Khiste

Electronic Thesis and Dissertation Repository

The DNA Next Generation Sequencing (NGS) technologies produce data at a low cost, enabling their application to many ambitious fields such as cancer research, disease control, personalized medicine etc. However, even after a decade of research, the modern aligners and assemblers are far from providing efficient and error free genome alignments and assemblies respectively. This is due to the inherent nature of the genome alignment and assembly problem, which involves many complexities. Many algorithms to address this problem have been proposed over the years, but there still is a huge scope for improvement in this research space.

Many new genome …

Examination Of Orthologous Genes (Mrub_2518 And B3728, Mrub_2519 And B3727, Mrub_2520 And B3726, Mrub_2521 And B3725) Responsible For Abc Phosphate Transporters In Two Species M. Ruber And E. Coli, Margaret Meyer, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes b3725, b3726, b3727, b3728 and Mrub_2518, Mrub_2519, Mrub_2520 and Mrub_2521 (KEGG map number 02010). We predict that these genes encode the components of a Phosphate ABC transporter: Orthologous genes Mrub_2518 (DNA coordinates 2565359..2566438) and b3728 encodes the periplasmic phosphate binding component; Orthologous genes Mrub_2519 (DNA coordinates 2566499..2567485) and b3727, and Mrub_2520 (DNA coordinates 2567496..2568326) and b3726 encode for the two transmembrane proteins; Orthologous genes Mrub_2521 (DNA coordinates 2568338..2569159) and b3725 encode for the ATP binding protein within the cytoplasm. Within the two species, M. ruber and E. coli, …

Mrub_1325, Mrub_1326, Mrub_1327, And Mrub_1328 Are Orthologs Of B_3454, B_3455, B_3457, B_3458, Respectively Found In Escherichia Coli Coding For A Branched Chain Amino Acid Atp Binding Cassette (Abc) Transporter System, Bennett Tomlin, Adam Buric, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes Mrub_1325, Mrub_1326, Mrub_1327, and Mrub_1328 (KEGG map number 02010). We predict these genes encode components of a Branched Chain Amino Acid ATP Binding Cassette (ABC) transporter: 1) Mrub_1325 (DNA coordinates 1357399-1358130 on the reverse strand) encodes the ATP binding domain; 2) Mrub_1326 (DNA coordinates 1358127-1359899 on the reverse strand) encodes the ATP-binding domain and permease domain; 3) Mrub_1327 (DNA coordinates 1359899-1360930 on the reverse strand) encodes a permease domain; and 4)Mrub_1328 (DNA coordinates 1711022-1712185 on the reverse strand) encodes the substrate binding domain. This system is not predicted to …

Predicted Ortholog Pairs Between E. Coli And M. Ruber Are B3456 And Mrub_2379, B3457 And Mrub_2378, B3456 And Mrub_2374, B3455 And Mrub_2376, And B3454 And Mrub2377, Which Each Code For Components Of A Prokaryotic-Type Abc Transporter For Branched-Chain Amino Acids, Elizabeth Paris, Tony Steinle, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes Mrub_2379, Mrub_2378, Mrub_2374, Mrub_2376, and Mrub_2377 (KEGG map number 02010). We predict these genes encode components of a branched-chain amino acid ATP Binding Cassette (ABC) transporter: 1) Mrub_2374 (DNA coordinates 2424832-2425902 on the reverse strand) encodes one permease component (aka transmembrane domain); 2) Mrub_2378 (DNA coordinates 2429525-2430439 on the reverse strand) encodes the second permease component (aka transmembrane domain); 3) Mrub_2376 (DNA coordinates 2427858-2428613 on the reverse strand) encodes one of the ATP-binding domain (aka nucleotide binding domain); 4) Mrub_2377 (DNA coordinates 2428704-2429489 on the reverse strand) …

Mrub_1199 & Mrub_2272 Of Meiothermus Ruber Are Orthologous Genes To The B0262 Gene In Escherichia Coli While Mrub_1200, Mrub_1201, Mrub_2015 & Mrub_2271 Are Not Orthologous To The B0262 Gene Coding For The Iron (Fe3+) Abc Transport System, Kumail Hussain, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes Mrub_1199, Mrub_1200, Mrub_1201, Mrub_2015, Mrub_2271 and Mrub_2272 (KEGG map number 02010). We predict these genes encode components of an Iron (Fe3+) ATP Binding Cassette (ABC) transporter: 1) Mrub_1199 (DNA coordinates [1211595-1212572] on the reverse strand) encodes the permease component (aka transmembrane domain); and 2) Mrub_1200 (DNA coordinates [1212612-1214093] on the reverse strand) encodes the ATP-binding domain (aka nucleotide binding domain); and 3) Mrub_1201 (DNA coordinates [1214347-1215309] on the reverse strand) encodes the substrate binding protein (aka the periplasmic component); and Mrub_2015 ( DNA coordinates [2053963-2054949] on the reverse strand) …

Confirmation That Mrub_1751 Is Homologous To E. Coli Xylf, Mrub_1752 Is Homologous To E. Coli Xylh, And Mrub_1753 Is Homologous To E. Coli Xylg, Ben Price, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes Mrub_1751, Mrub_1752 and Mrub_1753 (KEGG map number 02010). We predict these genes encode components of a D-xylose ATP Binding Cassette (ABC) transporter: 1) Mrub_1752 (DNA coordinates 1809004-1810224 on the forward strand) encodes the permease component (aka transmembrane domain), predicted to be an ortholog and 2) Mrub_1753 (DNA coordinates 1810227-1811000 on the forward strand) encodes the ATP-binding domain (aka nucleotide binding domain); and 3) Mrub_1751 (DNA coordinates 1807855-1808892 on the forward strand) encodes the solute binding protein. The ABC-transporter for M. ruber to transport D-xylose is homologous with the transporter …

Mrub_1283, Mrub_1284 And Mrub_1285 Encode For A Glycine/Betaine Abc Transporter And Are Orthologs Of E. Coli Prov, Prow And Prox, Lan Dang, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

ABC transporters are essential for cellular transport; contribute to maintain the homeostasis of the cells. Generally, ABC transporters are multi-subunit; contain essential cytoplasmic factors which are critical to ATP hydrolysis activity. In this paper, we would like to take a closer look to Mrub_1283, Mrub_1284 and Mrub_1285, three consecutive genes in Meiothermus ruber genome. We hypothesize that these genes are in the same operon and encode for ABC glycine/ betaine transporters. To confirm our hypothesis, we utilizes several bioinformatics tools to predict the potential function of Mrub_1283, Mrub_1284 and Mrub_1285 and to search for their orthologs in Escherichia coli genome. …

Mrub_2836, Mrub_1595, And Mrub_1596 Are Orthologs Of B_1857, B_1859 And B_1858 In Escherichia Coli Coding For A Zinc Uptake Abc Transporter System, Austin J. Dollmeyer, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes Mrub_2836, Mrub_1595, and Mrub_1596 (KEGG map number 02010). We predict these genes encode components of a Zn²⁺ ATP Binding Cassette (ABC) transporter: 1) Mrub_2836 (DNA coordinates 1878670-2879569 on the complement strand) encodes the substrate binding protein (aka periplasmic protein), predicted to be an ortho; and 2) Mrub_1595 (DNA coordinates 1628074-1628865 on the complement strand) encodes the permease component (aka transmembrane domain); and 3) Mrub_1596 (DNA coordinates 1628867-1629637 on the complement strand) encodes the ATP-binding protein (aka nucleotide binding domain). This is an ATP transport …

Mrub_2120, Mrub_2121, Mrub_2122, Mrub_2123 And Mrub_2124 Are Orthologs Of E. Coli Genes B3458, B3457, B3456, B3455 And B3454, Respectively, And Make Up An Operon That Codes For The Branched-Chain Amino Acid Abc Transporter In Meiothermus Ruber Dsm 1279, Aaron Jones, Madelyn Huber, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes Mrub_2120, Mrub_2121, Mrub_2122, Mrub_2123 and Mrub_2124 (KEGG map number 02010). We predict these genes encode components of a branched-chain amino acid ATP Binding Cassette (ABC) transporter: 1) Mrub_2120 (DNA coordinates 2169247-2170416 on the reverse strand) encodes the branched-chain amino acid binding protein that is localized to the periplasm; 2) Mrub_2121 (DNA coordinates 2170433..2171353 on the reverse strand) encodes the first TMD; 3) Mrub_2122 (DNA coordinates 2171365..2172279 on the reverse strand) encodes the second TMD; 4) Mrub_2123 (DNA coordinates 2172276..2173028 on the reverse strand) encodes the first NBD; 5) Mrub_2124 …

Mrub_1675, Mrub_1676, Mrub_1677, And Mrub_1679 Genes Are Orthologs Of B_3458, B_3457, B_3456, And B_3454 Genes In E. Coli, Respectively, Coding For Abc Transporters. Mrub_1678 And B_3455, Though Perform Similar Tasks, Are Not Orthologous, Ravi Patel, Alaina Hofmann, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes Mrub_1675, Mrub_1676, Mrub_1677, and Mrub_1679 (KEGG map number 02010). We predict these genes encode components of a Branched chain amino acid (ABC) transporter: Mrub_1675 (DNA coordinates 1711022..1712185 on the reverse strand) encodes the permease component, Mrub_1676 (DNA coordinates 1712313..1713170) encodes for the NBD (aka nucleotide binding domain), Mrub_1677 (DNA coordinates 1713167..1714075 on the reverse strand) encodes the NBD (aka nucleotide binding domain), Mrub_1678 (DNA coordinates 1713167..1714075 on the reverse strand) encodes the TMD (aka transmembrane domain) and Mrub_1679 (DNA coordinates 1714781..1715485 on the reverse strand) encodes …

Mrub_0680, Mrub_0836, And Mrub_0837 Found To Be Orthologous To E. Coli Ccma, Ccmb, And Ccmc, Respectively, Coding For Abc-Transport Proteins Involved In Cytochrome-C Biogenesis, Sarah N. Church, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes Mrub_0680, Mrub_0836 and Mrub_0837(KEGG map number 02010). We predict these genes encode components of a Heme ATP Binding Cassette (ABC) transporter: 1) Mrub_0836 (DNA coordinates 823734..824399on the reverse strand) encodes the permease component (aka transmembrane domain), predicted to be an ortho; and 2) Mrub_0680(DNA coordinates 659484..660071 on the reverse strand) encodes the ATP-binding domain (aka nucleotide binding domain); and 3) Mrub_0837(DNA coordinates 824570..825262on the reverse strand) encodes the solute binding protein. This gene system encodes a transmembrane exporter and helper proteins which are thought to …

Meiothermus Ruber Mrub_0320 Gene Is An Ortholog Of The B3452 Gene, Mrub_0321 Gene Is An Ortholog Of The B3451 Gene, Mrub_0322 Gene Is An Ortholog Of The B3453 Gene, Mrub_2366 Gene Is An Ortholog Of The B3450 Gene Found In Escherichia Coli, Which Encode For Components Of An Abc Transporter Involved In Sn-Glycerol - 3-Phosphate, Jenna Hall, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

In this project we investigated the biological function of the genes mrub_0320, mrub_0321, mrub_0322, and mrub_2366 (KEGG map number 02010). We predict these genes encode components of a sn-glycerol-3-phosphate (ABC) transporter: 1) mrub_0320 (DNA coordinates 288469..289401) encodes the permease component (aka transmembrane domain), predicted to be an ortholog; 2) mrub_0321 (DNA coordinates 289394..290218) encodes another permease domain, and also contains a transcriptional regular; ATP-binding domain (aka nucleotide binding domain); 3) mrub_0322 (DNA coordinates 290234..291541) encodes the solute binding protein; and 4) mrub_2366 (DNA coordinates 2418207..2419352 on the reverse strand) encodes for an ATP-binding domain for multiple sugar-related ABC transport systems …