Open Access. Powered by Scholars. Published by Universities.®
- Keyword
-
- Annotation (8)
- Bioinformatics (8)
- Genome (8)
- Meiothermus ruber (8)
- CRISPR-Cas (6)
-
- Prokaryotic defense (6)
- B2755 (2)
- Cas1 (2)
- Mrub_3013 (2)
- B2756 (1)
- B2757 (1)
- B2759 (1)
- B2760 (1)
- Biology (1)
- CRISPR-Cas prokaryotic defense (1)
- CRISPR/Cas (1)
- CRISPR/Cas adaptive immune system (1)
- Cas3 gene (1)
- Cas5 (1)
- CasA (1)
- CasB (1)
- CasC (1)
- CasD (1)
- CasE (1)
- Cascade complex (1)
- E. coli b2761 (1)
- Escherichia coli (1)
- Field Research (1)
- Field work (1)
- Forest (1)
- Publication
- Publication Type
Articles 1 - 14 of 14
Full-Text Articles in Life Sciences
Ecological Researcher, Alex Demmers
Ecological Researcher, Alex Demmers
Celebration of Learning
This is my field research I complete during the summer of 2018.
Snake Fungal Disease In Lake Eerie Water Snakes And Its Affect On Attitude And Behavior During Treatment, Kelcie Fredrickson
Snake Fungal Disease In Lake Eerie Water Snakes And Its Affect On Attitude And Behavior During Treatment, Kelcie Fredrickson
Celebration of Learning
Snake fungal disease (SFD) is caused by the fungus Ophidiomyces ophiodiicola. Infection occurs when the outer skin is breached, and the organism enters the epidermis. The epidermis becomes necrotic and produces a yellow/brown crust. When the crust breaks off, ulcerations/lesions are formed along the snake’s body, head and tail. It has been found that SFD can be treated with a terbinafine nebulization treatment. Ellen Haynes, a PhD student, created a study in which 26 Lake Eerie water snakes are separated into treatment and control groups to determine the effectiveness of the nebulization treatment. Through daily observations, this research aimed …
Tracking Residual-Yolk Energy In Dormant Hatchling Turtles, Tom Pham, Dr. Tim J. Muir, Samira Radi, Jacob Wyco
Tracking Residual-Yolk Energy In Dormant Hatchling Turtles, Tom Pham, Dr. Tim J. Muir, Samira Radi, Jacob Wyco
Celebration of Learning
Hatchling painted turtles (Chrysemys picta) spend their first winter inside natal nests without food and must rely on maternally derived energy in the form of residual yolk for up to nine months. In this study, we take a closer look at the use and movement of residual-yolk energy during the first 33 weeks (~8 mo.) after hatching by measuring changes in mass, lipid content, & protein content of yolk, liver, small intestine, and carcass. Our data showed a significant decrease in yolk mass by 64% and significant increases in carcass & liver masses of 9% & 16%, respectively, …
Invertebrate Diversity Of Ponds Within Gremel Wildlife Sanctuary And Amboy Marsh, Dalton Howard, Madison Lape
Invertebrate Diversity Of Ponds Within Gremel Wildlife Sanctuary And Amboy Marsh, Dalton Howard, Madison Lape
Celebration of Learning
This project tested the water quality of different ponds and used macroinvertebrates as the overall indicator. The invertebrates give us a lot of knowledge about the health of the ecosystem and possible pollutants that could be harming the environments.
Do Stands Of Native Trees Harbor Different Invasive Species Than Stands Of Planted Pine?, Carly Mccameron, John Mccarthy, Dr. Kevin Geedey
Do Stands Of Native Trees Harbor Different Invasive Species Than Stands Of Planted Pine?, Carly Mccameron, John Mccarthy, Dr. Kevin Geedey
Celebration of Learning
The most outstanding invasive species that can be found at Augustana’s Green Wing Environmental Laboratory are honeysuckle, buckthorn, multiflora rose, garlic mustard, autumn olive, and oriental bittersweet. These plants are not only disrupting the ecosystem at Green Wing, but they are doing it all over the country. The result of their disruption is that they have taken over entire habitats and left natural species with no way to compete for survival. To study this we used the line-point method as well as other forms of data collection to compare a non-native pine tree habitat to an area dominated by native …
Mrub_3019 Casa Gene Is An Ortholog To E. Coli B2760, Kelsey Heiland, Dr. Lori Scott
Mrub_3019 Casa Gene Is An Ortholog To E. Coli B2760, Kelsey Heiland, Dr. Lori Scott
Meiothermus ruber Genome Analysis Project
This research is part of the Meiothermus ruber genome annotation project which aims to predict gene function with various bioinformatics tools. We investigated the function of Mrub_3019, which encodes the CasA protein involved in the multi-subunit effector complex for the CRISPR-Cas immunity system and predicted it to be an ortholog of E. coli K12 MG1655 b2760 (casA). We predicted that Mrub_3019 encodes the protein CasA, which is involved in PAM recognition of CRISPR interference pathway. Foreign DNA will bind to CasA, which signals Cas3 for helicase-mediated DNA degradation. Our hypothesis is supported by low E-values for pairwise alignment in NCBI …
Mrub_3015 Is Orthologous To The B2757 Gene Found In Escherichia Coli Coding For Casd, Ramona Collins, Dr. Lori Scott
Mrub_3015 Is Orthologous To The B2757 Gene Found In Escherichia Coli Coding For Casd, Ramona Collins, Dr. Lori Scott
Meiothermus ruber Genome Analysis Project
This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the biological function of the gene Mrub_3015, which we hypothesize is a component of the CRISPR-Cas prokaryotic defense system. We predict that Mrub_3015 (DNA coordinates 3055550...3056245) encodes the the CRISPR-associated protein cas5, which is integral in maintaining the crRNA-DNA structure, keeping the complex from base pairing with the target phage DNA. Our hypothesis is supported by identical hits for Mrub_3015 and b2527 to the KEGG, Pfam, TIGRfam, CDD and PDB databases as well as a …
Mrub_3018 Is Orthologous To E. Coli B2759 (Casb), Kyle Parker, Dr. Lori Scott
Mrub_3018 Is Orthologous To E. Coli B2759 (Casb), Kyle Parker, Dr. Lori Scott
Meiothermus ruber Genome Analysis Project
This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We studied the biological activity of the Mrub_3018 gene, which we hypothesize is orthologous to E. coli gene B2759. We predicted that Mrub_3018(DNA coordinates 3057916… 3058524) encodes the protein CasB. CasB is a protein in the CRISPR CASCADE that will function as a structural protein. When the rest of the proteins form an “S” formation CasB will connect the front and back of the “S” creating a back bone for the structure. It will help bind DNA …
Mrub_3014 Is Orthologous To B2756, Samir Abdelkarim, Dr. Lori Scott
Mrub_3014 Is Orthologous To B2756, Samir Abdelkarim, Dr. Lori Scott
Meiothermus ruber Genome Analysis Project
This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the biological function of the gene Mrub_3014, which we hypothesize is a component of the CRISPR-Cas prokaryotic defense system. We predict that Mrub_3014 (DNA coordinates 3054943..3055575) encodes CRISPR-associated protein Cse3/case which function as an endonuclease. Our hypothesis is supported by identical hits for Mrub_3014 and b2756 to the KEGG, Pfam, TIGRfam, CDD and PDB databases, as well as a low E-value for a pairwise NCBI BLAST comparison. Both protein products are predicted to be localized …
M. Ruber Mrub_3013 Is Orthologous To E. Coli B2755, Laura Butcher, Dr. Lori Scott
M. Ruber Mrub_3013 Is Orthologous To E. Coli B2755, Laura Butcher, Dr. Lori Scott
Meiothermus ruber Genome Analysis Project
This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the biological function of gene Mrub_3013, which we hypothesize is orthologous to b2755 in E. coli K12 MG1655 (a.k.a. Cas1). We investigated the biological function of a gene with the M. ruber locus tag of Mrub_3013, which we hypothesize is a component of the CRISPR-Cas prokaryotic defense system in M. ruber. We predict that Mrub_3013 (DNA coordinates 3,053,978-3,054,940) encodes the protein Cas1 which as part of the CRISPR-Cas system, selects and cuts the foreign …
Mrub_3020, A Paralog Of Mrub_1489, Is Orthologous To E. Coli Casc (Locus Tag B2761), Alfred Dei-Ampeh, Dr. Lori Scott
Mrub_3020, A Paralog Of Mrub_1489, Is Orthologous To E. Coli Casc (Locus Tag B2761), Alfred Dei-Ampeh, Dr. Lori Scott
Meiothermus ruber Genome Analysis Project
This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the biological functions of two genes: mrub_3020 and mrub_1489. We make two hypotheses in this investigation: a) mrub_3020 is orthologous to the gene b2761 in E. coli K12 MG1655 (a.k.a. casC); b) mrub_1489 is a paralog of mrub_3020. We also predict that the two genes encode unique proteins: mrub_3020 with DNA coordinates 3060491…3063190 encodes a CRISPR – associated helicase (Cas3) that supports the Cascade complex of the CRISPR – Cas adaptive immune system …
Effects Of Temperature On Crispr/Cas System, Eddie Beckom, Dr. Lori Scott
Effects Of Temperature On Crispr/Cas System, Eddie Beckom, Dr. Lori Scott
Meiothermus ruber Genome Analysis Project
This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the effect of temperature on the complexity of CRISPR/Cas systems in bacterial organisms across temperature classifications. We predict that temperature extremes would result in CRISPR/Cas systems with multiple operons, repeating cas genes, and complex systems. CRISPR/Cas systems can be classified into three types with a number of subtypes based on the CRISPR-associated genes, cas genes, present in a given organism. Our hypothesis is supported by the presence of multiple operons in thermophilic organisms based on …
An Investigation Into The Relationship Between Mrub_3013, Mrub_1477, And Mrub_0224: Are They Paralogs?, Melette Devore, Dr. Lori Scott
An Investigation Into The Relationship Between Mrub_3013, Mrub_1477, And Mrub_0224: Are They Paralogs?, Melette Devore, Dr. Lori Scott
Meiothermus ruber Genome Analysis Project
This project is part of the Meiothermus ruber genome analysis project, which uses a collection of online bioinformatics tools to predict gene function. We investigated the biological function of mrub_3013 and the nature of its relationship with mrub_1477 and mrub_0224. We hypothesized that mrub_3013 is orthologous to b2755 in E. coli K12 MG1655 (a.k.a. cas1). We predict that mrub_3013 encodes the enzyme Cas1, which is involved in spacer acquisition in the CRISPR-Cas prokaryotic defense system. Our hypothesis is supported by identical hits for b2755, mrub_3013, mrub_1477, and mrub_0224 from the CDD and Pfam databases and highly similar hits from …
Smoking Cessation Treatments Varenicline (Chantix®️), Nrts, And Nicotine Dependence, Marley Vea Devoss
Smoking Cessation Treatments Varenicline (Chantix®️), Nrts, And Nicotine Dependence, Marley Vea Devoss
Biology: Student Scholarship & Creative Works
Varenicline was approved in 2006 by the FDA as an effective smoking cessation drug. Varenicline was designed to bind with α4β2 nicotinic acetylcholine receptors (nAChR) to work as both an agonist and antagonist. Other drugs like nicotine replacement therapies (NRTs) have also contributed to the decreasing rate of active smokers in the United States. The mechanisms of varenicline and its role in addiction are reviewed in this paper. With NRTs and recent trends in electronic smoking devices, nicotine dependence is still a cause for concern due to studies connecting nicotine with cell proliferation and heart disease.