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2016

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Articles 1141 - 1170 of 1869

Full-Text Articles in Biology

Alzheimer’S Disease And The P.V236e Variant In The Apoe Gene, Alton Chad Sorensen, John Kauwe Feb 2016

Alzheimer’S Disease And The P.V236e Variant In The Apoe Gene, Alton Chad Sorensen, John Kauwe

Journal of Undergraduate Research

I was interested in trying to validate the findings of the publication by Medway et al. concerning the SNP rs199768005 using data from the Cache Country data set. Unfortunately, of the 4703 people from our data set, only 10 were carriers. Using R statistical analysis, I found that the p-value for this SNP with an association to protect for Alzheimer’s Disease (AD) was not significant. It was similarly not significant in its association with Any AD. I also ran other models to include for factors such as education or age in conjunction with this SNP and its association with AD …

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Ligament Microstructure Analysis, Michael Gillespie, Jonathan Wisco Feb 2016

Ligament Microstructure Analysis, Michael Gillespie, Jonathan Wisco

Journal of Undergraduate Research

Due to the relatively poor fiber contrast of tendons in comparison with muscles, the anatomical, and therefore, functional relationship of muscle attachments to bones via tendons has not been well mapped. We were interested in mapping the 3D gross anatomical structure of tendons using a MicroScribe 3D digitizer (GoMeasure3D, Amherst, VA), with the goal to compare fibrous architecture between tendons of various types of muscles and muscle classes. We developed a stain made of blue dye and powdered sugar to increase fiber visibility, thus allowing for 3D digitization. This technique was applied to human cadaveric calcaneal tendon and quadriceps tendon.

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Analyzing Structural Differences In Quadriceps Femoris Tendon Fibers Using Microscribe Technology, Nathaniel Hainsworth, Jon Wisco Feb 2016

Analyzing Structural Differences In Quadriceps Femoris Tendon Fibers Using Microscribe Technology, Nathaniel Hainsworth, Jon Wisco

Journal of Undergraduate Research

Not all tendons and ligaments are created equally. Many have different structural characteristics based on functionality or need for stability. This turns out to be true even between different portions of the same tendon. This project’s purpose was to analyze and compare structural differences between tendon fibers of the patellar portion and quadriceps portion of the quadriceps femoris tendon. We hypothesized that there are significant structural differences between these two portions because they act very different biomechanically, as well as different in the amount of tension/strain put on each portion. We mapped individual tendon fibers of both portions using MicroScribe …

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Assessment Of Biodiversity On Mount Timpanogos With A Focus On Flies, Diptera: Agromyzidae, Samantha Smith, Dr. Riley Nelson Feb 2016

Assessment Of Biodiversity On Mount Timpanogos With A Focus On Flies, Diptera: Agromyzidae, Samantha Smith, Dr. Riley Nelson

Journal of Undergraduate Research

Mount Timpanogos, with an elevation of 3,582 meters, is home to an amazing array of insect species. Through much previous effort, many have studied the insects found in American Fork Canyon leading up to Mount Timpanogos. They have still barely scratched the surface of the abundant biodiversity on the mountain. Varied temperature regimes can cause changes in insects’ life cycle and the length of their feeding period, making the collections at different elevations of Mount Timpanogos during different years of particularly great value (Petitt et al 1991). Thus the value of collections along Mount Timpanogos is two-fold; both to study …

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Analysis Of Hmgcr As A Genetic Modifier For Alzheimer’S Disease, Brian Davis, Dr. John S. K. Kauwe Feb 2016

Analysis Of Hmgcr As A Genetic Modifier For Alzheimer’S Disease, Brian Davis, Dr. John S. K. Kauwe

Journal of Undergraduate Research

Alzheimer’s disease (AD) is a chronic neurodegenerative disorder that occurs predominantly later in life and represents the fourth most common cause of death in the developed world. Given the absence of curative treatment, discovering the factors related to the development of AD and the conversion from mild cognitive impairment (MCI) to AD is one of the most urgent medical mysteries affecting the aging population. The search for the identification of genes contributing to AD led to the identification of 695 candidate genes of which a surprising number are directly involved in lipid metabolism at the level of transport, synthesis, storage, …

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Association Of Rare Genetics Variants To The Protection Of Alzheimer’S Disease In The Cache County Data Set, Josue David Gonzalez Murcia, John Kauwe Feb 2016

Association Of Rare Genetics Variants To The Protection Of Alzheimer’S Disease In The Cache County Data Set, Josue David Gonzalez Murcia, John Kauwe

Journal of Undergraduate Research

Alzheimer’s disease is one of the top 10 causes of death in the world and the 6th leading cause of death in the United States, with 5.5 million people diagnosed with the disease. Alzheimer’s cannot be cured, prevented or slowed. Most research with Alzheimer’s disease has been done on SNPs that have a relatively high frequency in the population this has helped facilitate researchers in finding a broad genetic pathway in the development of Alzheimer’s disease (Naj et al. 2011; Harold et al. 2009). Our research will focus on a very rare SNP, with a much lower frequency than previously …

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Expanding The Freshwater Aquatic Invertebrate Identification Guide Cd, Sarah Brown, C. Riley Nelson Feb 2016

Expanding The Freshwater Aquatic Invertebrate Identification Guide Cd, Sarah Brown, C. Riley Nelson

Journal of Undergraduate Research

The Freshwater Aquatic invertebrate Identification Guide (FAIIG) was a computer program created by the C. Riley Nelson lab in 2006 to help students with the identification process of various aquatic invertebrates throughout Utah. It has been used in Bio 100 classes at Brigham Young University to help students successfully identify various aquatic invertebrate specimens from rivers and streams in Utah. The goal of this project was to work on expanding the FAIIG program to include aquatic invertebrates in North America west of the Mississippi River. As well as expanding the breadth of content, we also worked on improving the information …

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Association Of Rs75932628 (R47h) With Vascular Dementia In The Cache County Study, Emily Sears, Dr. John Kauwe Feb 2016

Association Of Rs75932628 (R47h) With Vascular Dementia In The Cache County Study, Emily Sears, Dr. John Kauwe

Journal of Undergraduate Research

Vascular dementia (VaD) is a neurodegenerative disease caused by atherosclerosis, or inadequate blood flow to the brain as a result of the build-up of fat deposits, dead cells, or other cell debris on the inside of arteries. It shortens the lifespan of those affected, and severely impairs their quality of life. VaD is the second most common form of dementia, after Alzheimer’s disease, accounting for 20-30% of dementia cases. Thus far the risk factors that have been determined are non-specific to the brain: high blood pressure, high cholesterol, and high blood sugar (Roman et. al 2003). There has not been …

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Assembling Benchmark Datasets For Machine Learning Classification, Parker Hollingsworth, Stephen Piccolo Feb 2016

Assembling Benchmark Datasets For Machine Learning Classification, Parker Hollingsworth, Stephen Piccolo

Journal of Undergraduate Research

Machine learning classification is a type of artificial intelligence that learns from data and makes predictions. There are many different algorithms that can be used to develop predictive models for machine learning. Generally the algorithm looks for patterns in the data and uses those patterns to make predictions on an additional data set. This type of artificial intelligence is being used increasingly in the biomedical community to predict disease diagnosis and prognosis. Although machine learning has shown to provide promising results, it is far from perfect. The accuracy of the predictive model often depends on arbitrary decisions made by researchers. …

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Investigation Of Visual Systems In A New Species Of Firefly, Yelena Pacheco, Dr. Seth Bybee Feb 2016

Investigation Of Visual Systems In A New Species Of Firefly, Yelena Pacheco, Dr. Seth Bybee

Journal of Undergraduate Research

Fireflies are well known for their bioluminescent flashes causing them to be a particular group of interest concerning insect vision research. Their flashes are used for both sexual communication and as an aposematic warning to predators. Bioluminescent fireflies are known to use either a yellow-green flash or a yellow-orange flash to communicate between sexes in order to find a mate. There have been many studies concerning flash patterns’ role in sexual communication among fireflies; however, the understanding of firefly vision as a whole allows for many more untouched research possibilities. As a member of the Bybee lab I had the …

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Crystal Structure Of Deinococcus Phytochrome In The Photoactivated State Reveals A Cascade Of Structural Rearrangements During Photoconversion, E Sethe Burgie, Junrui Zhang, Richard D. Vierstra Feb 2016

Crystal Structure Of Deinococcus Phytochrome In The Photoactivated State Reveals A Cascade Of Structural Rearrangements During Photoconversion, E Sethe Burgie, Junrui Zhang, Richard D. Vierstra

Biology Faculty Research

Phytochromes are photochromic photoreceptors responsible for a myriad of red/far-red light-dependent processes in plants and microorganisms. Interconversion is initially driven by photoreversible isomerization of bilin, but how this alteration directs the photostate-dependent changes within the protein to actuate signaling is poorly understood. Here, we describe the structure of the Deinococcus phytochrome photosensory module in its near complete far-red light-absorbing Pfr state. In addition to confirming the 180° rotation of the D-pyrrole ring, the dimeric structure clearly identifies downstream rearrangements that trigger large-scale conformational differences between the dark-adapted and photoactivated states. Mutational analyses verified the importance of residues surrounding the bilin …

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Dynamics And Thermal Sensitivity Of Ballistic And Non-Ballistic Feeding In Salamanders, Stephen M, Deban, Jeffrey A. Scales Feb 2016

Dynamics And Thermal Sensitivity Of Ballistic And Non-Ballistic Feeding In Salamanders, Stephen M, Deban, Jeffrey A. Scales

Integrative Biology Faculty and Staff Publications

Low temperature reduces the performance of muscle-powered movements, but in movements powered by elastic recoil mechanisms, this effect can be mitigated and performance can be increased. To better understand the morphological basis of high performance and thermal robustness of elastically powered movements, we compared feeding dynamics at a range of temperatures (5-25°C) in two species of terrestrial plethodontid salamanders, Plethodon metcalfi and Ensatina eschscholtzii, which differ in tongue muscle architecture and the mechanism of tongue projection. We found that Ensatina is capable of ballistic projection with a mean muscle mass-specific power of 2100 W kg(-1), revealing an elastic mechanism. Plethodon, …

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Optogenetic Stimulation Of Drosophila Heart Rate At Different Temperatures And Ca2+ Concentrations, Yuechen Zhu, Henry Uradu, Zana R. Majeed, Robin L. Cooper Feb 2016

Optogenetic Stimulation Of Drosophila Heart Rate At Different Temperatures And Ca2+ Concentrations, Yuechen Zhu, Henry Uradu, Zana R. Majeed, Robin L. Cooper

Biology Faculty Publications

Optogenetics is a revolutionary technique that enables noninvasive activation of electrically excitable cells. In mammals, heart rate has traditionally been modulated with pharmacological agents or direct stimulation of cardiac tissue with electrodes. However, implanted wires have been known to cause physical damage and damage from electrical currents. Here, we describe a proof of concept to optically drive cardiac function in a model organism, Drosophila melanogaster. We expressed the light sensitive channelrhodopsin protein ChR2.XXL in larval Drosophila hearts and examined light‐induced activation of cardiac tissue. After demonstrating optical stimulation of larval heart rate, the approach was tested at low temperature …

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Presenilin E318g Variant And Alzheimer’S Disease Risk: The Cache Country Study, Ariel Hippen, John Kauwe Feb 2016

Presenilin E318g Variant And Alzheimer’S Disease Risk: The Cache Country Study, Ariel Hippen, John Kauwe

Journal of Undergraduate Research

Alzheimer’s disease is the leading cause of dementia in the elderly and the third most common cause of death in the United States. A vast number of genes regulate Alzheimer’s disease, including Presenilin 1 (PSEN1). It is possible that novel variants in the PSEN1 gene have an effect on Alzheimer’s disease status. A recent study suggested that one of these variants, PSEN1 E318G, significantly affects Alzheimer’s disease status in a large case-control dataset, particularly in connection with the APOEε4 allele [1].

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Contrasting Soil Nitrogen Dynamics Across A Montane Meadow And Urban Lawn In A Semi-Arid Watershed, Steven J. Hall, Michelle A. Baker, Scott B. Jones, John M. Stark, David R. Bowling Feb 2016

Contrasting Soil Nitrogen Dynamics Across A Montane Meadow And Urban Lawn In A Semi-Arid Watershed, Steven J. Hall, Michelle A. Baker, Scott B. Jones, John M. Stark, David R. Bowling

Biology Faculty Publications

Urbanization substantially increases nitrogen (N) inputs and hydrologic losses relative to wildland ecosystems, although the fate of N additions to lawns and remnant grasslands remains contested. In montane semi-arid ecosystems, N cycling is often closely coupled to snowmelt (the dominant period of infiltration) and snow cover, which impact soil temperature and moisture. Here, we compared soil N dynamics between a fertilized and irrigated urban lawn and nearby riparian meadow in Salt Lake City, Utah during a snow manipulation experiment. Snow removal increased freeze/thaw events but did not affect N pools, microbial biomass, denitrification potential, or soil oxygen (O2). Mineral N …

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Late Pleistocene Fishes Of The Tennessee River Basin: An Analysis Of A Late Pleistocene Freshwater Fish Fauna From Bell Cave (Site Acb-2) In Colbert County, Alabama, Usa, Stephen J. Jacquemin, Jun A. Ebersole, William C. Dickenson, Charles Ciampaglio Feb 2016

Late Pleistocene Fishes Of The Tennessee River Basin: An Analysis Of A Late Pleistocene Freshwater Fish Fauna From Bell Cave (Site Acb-2) In Colbert County, Alabama, Usa, Stephen J. Jacquemin, Jun A. Ebersole, William C. Dickenson, Charles Ciampaglio

Biological Sciences Faculty Publications

The Tennessee River Basin is considered one of the most important regions for freshwater biodiversity anywhere on the globe. The Tennessee River Basin currently includes populations of at least half of the described contemporary diversity of extant North American freshwater fishes, crayfish, mussel, and gastropod species. However, comparatively little is known about the biodiversity of this basin from the Pleistocene Epoch, particularly the late Pleistocene (∼10,000 to 30,000 years B.P.) leading to modern Holocene fish diversity patterns. The objective of this study was to describe the fish assemblages of the Tennessee River Basin from the late Pleistocene using a series …

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Rab8 Directs Furrow Ingression And Membrane Addition During Epithelial Formation In Drosophila Melanogaster, Lauren M. Mavor, Hui Miao, Zhongyuan Zuo, Ryan M. Holly, Yi Xie, Dinah Loerke, J Todd Blankenship Feb 2016

Rab8 Directs Furrow Ingression And Membrane Addition During Epithelial Formation In Drosophila Melanogaster, Lauren M. Mavor, Hui Miao, Zhongyuan Zuo, Ryan M. Holly, Yi Xie, Dinah Loerke, J Todd Blankenship

Biological Sciences: Faculty Scholarship

One of the most fundamental changes in cell morphology is the ingression of a plasma membrane furrow. The Drosophila embryo undergoes several cycles of rapid furrow ingression during early development that culminate in the formation of an epithelial sheet. Previous studies have demonstrated the requirement for intracellular trafficking pathways in furrow ingression; however, the pathways that link compartmental behaviors with cortical furrow ingression events are unclear. Here, we show that Rab8 has striking dynamic behaviors in vivo. As furrows ingress, cytoplasmic Rab8 puncta are depleted and Rab8 accumulates at the plasma membrane in a location that coincides with known regions …

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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 Feb 2016

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 …

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Comparison Of Genes In Meiothermus Ruber And Escherichia Coli In The Thiamine Biosynthesis Pathway, Erin E. Frye, Dr. Lori Scott Feb 2016

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 …

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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 Feb 2016

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 1st 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 …

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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 Feb 2016

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. …

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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 Feb 2016

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 3rd 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 …

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Pyruvate Metabolism In M. Ruber When Compared To E. Coli, Amanda M. Johnson, Dr. Lori Scott Feb 2016

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 …

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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 Feb 2016

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 …

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Comparing Meiothermus Ruber And Myxococcus Xanthus In The Purine Metabolism Pathway, Linnea J. Ritchie, Dr. Lori Scott Feb 2016

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 …

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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 Feb 2016

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. …

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Bioinformatic Comparison Of Genes In The Leucine Biosynthesis Pathway Of Escherichia Coli To Meiothermus Ruber, Isaac D. Schmied, Benjamin T. Ryan, Dr. Lori Scott Feb 2016

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 …

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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 Feb 2016

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 …

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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 Feb 2016

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 5th 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 …

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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 Feb 2016

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. …

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