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Articles 331 - 360 of 740
Full-Text Articles in Chemistry
Phosphoester Bond Stabilization For Enhanced Cid Phosphoproteomics, Stewart Morley, Dr. John Prince
Phosphoester Bond Stabilization For Enhanced Cid Phosphoproteomics, Stewart Morley, Dr. John Prince
Journal of Undergraduate Research
Proteomics uses highly sensitive mass spectrometers to measure peptide fragment masses from enzymatically digested proteins. Measuring the mass of the peptide and fragments produced in the mass spectrometer allows for identification of its parent protein. Phosphoproteomics analyzes peptides that have been phosphorylated. Phosphoproteomics identifies phosphorylation sites, network relationships between proteins, and how cells respond to changes in their environment. Mass spectrometers typically ionize peptides to carry positive charges. This charge aids to draw molecules into the instrument. Phosphate modifications reduce charge on their molecules, reducing the positive charge on phosphopeptides, creating neutral, or negatively charged species. The lack of charge …
Does Pegylation Increase The Thermodynamic Stability Of The Ww Domain Of Pin1 Via Hydrogen Bonding? A Molecular Dynamics Simulation, Chad Torgerson, Dr. Joshua Price
Does Pegylation Increase The Thermodynamic Stability Of The Ww Domain Of Pin1 Via Hydrogen Bonding? A Molecular Dynamics Simulation, Chad Torgerson, Dr. Joshua Price
Journal of Undergraduate Research
Proteins are complex molecules that have the potential to treat diseases and illnesses that small molecule drugs cannot. However, a significant problem with protein medications is that proteins tend to have short serum half-lives and can be difficult to store for extended periods of time due to their often unstable nature.1 One widely used strategy to circumvent these problems and increase the serum half-life of protein drugs is to attach polyethylene glycol (PEG) oligomers to amino acid residues (i.e., PEGylation) of protein structures.2 The thermodynamic effects of PEGylation are not always positive, however, and currently difficult to predict.3 In order …
Investigate The Function Of The 5′ Leader In The Human At1 Angiotensin Receptor, Erik J. Petersen, Dr. Terry S. Elton
Investigate The Function Of The 5′ Leader In The Human At1 Angiotensin Receptor, Erik J. Petersen, Dr. Terry S. Elton
Journal of Undergraduate Research
A comparison of several published hAT1R cDNA sequences revealed that, although these clones shared an identical open reading frame, they differed in portions of their 5′-UTRs.1 Therefore these data suggest that alternative splicing events combine various 5′-UTR exons with the exon that harbors the hAT I R coding region.
Translational Control Of Poly(A)-Binding Protein Expression, Eliott Spencer, Dr. Roger Kaspar
Translational Control Of Poly(A)-Binding Protein Expression, Eliott Spencer, Dr. Roger Kaspar
Journal of Undergraduate Research
Poly(A)-binding protein or PABP is found in high concentrations in all eukaryotic cells. Cell biologists have speculated for a long time that PABP plays an important role in stabilizing the fragile MRNA molecule so that it can be more effectively translated into its final gene product. PABP does this by binding to the Poly(A) tail at the 3′ end of the MRNA. 1,2
Enantioselective Synthesis Of Hasubanan Alkaloids, Daniel Nielsen, Laura Nielsen, Dr. Steven L. Castle
Enantioselective Synthesis Of Hasubanan Alkaloids, Daniel Nielsen, Laura Nielsen, Dr. Steven L. Castle
Journal of Undergraduate Research
In nature, many molecules exist in two different forms, referred to as enantiomers. These forms are structurally identical, yet they are mirror images of each other. One simple example of this is our hands. While both hands are structurally identical, there is no way that they can be superimposed. Our hands are enantiomers, and interact differently with certain objects. For instance, a left hand cannot fit a right-handed glove. Such a phenomenon occurs on the molecular level as well. A left-handed enantiomer of a drug might react with the receptors in the body in a beneficial way, while the right-handed …
The Planar Ion Trap, Ivan Miller, Dr. Daniel Austin
The Planar Ion Trap, Ivan Miller, Dr. Daniel Austin
Journal of Undergraduate Research
Mass spectrometry has been a common analytical procedure for over fifty years. Today it is most commonly used to characterize and quantify unknown solutions, solids, and vapors in chemical and biochemical environments by determining the specific masses of atoms and molecules. Ion traps have become standard methods in analysis as they have dramatically improved the selectivity and resolution of mass spectrometers. Ion traps use applied voltages to create electrical fields in a small trapping volume. These fields interact with the molecules in the mass analyzer by trapping ionized molecules over a broad mass range. The trapped ions are eventually ejected …
Investigation Of The Structure Of Quinoa Saponins By Hplc And Mass-Spec, Samuel Swainhart, Dr. Steve Wood
Investigation Of The Structure Of Quinoa Saponins By Hplc And Mass-Spec, Samuel Swainhart, Dr. Steve Wood
Journal of Undergraduate Research
Quinoa is a grain grown mainly by Natives in diverse areas throughout Latin America that is considered by many nutritional scientists as possibly the most nourishing grain available. Its contents include high levels of protein, an exceptional composition of amino acids, and many carbohydrates. Unfortunately, quinoa is very climate sensitive, and currently can only be grown in certain areas of the world, due to a low tolerance for intense heat. For this reason, quinoa is not grown everywhere and its annual yields are nowhere near the enormous quantities of rice and grain harvested annually. There are many different known varieties …
Homocitric Acid In Nitrogenase: Interactions With The Cofactor Of The Molybdenum-Iron Protein, Christopher M. Lee, Dr. G. D. Watt
Homocitric Acid In Nitrogenase: Interactions With The Cofactor Of The Molybdenum-Iron Protein, Christopher M. Lee, Dr. G. D. Watt
Journal of Undergraduate Research
Ammonia is extremely valuable in the industrial production of fertilizer, plastics, explosives, dyes, and other compounds. The most plentiful and common source of ammonia comes from the conversion of atmospheric nitrogen gas to ammonia. In industry the 80-year-old Haber method is used, which is a costly process that relies on very high temperatures and pressures to catalyze the reaction.
Redox Properties Of Horse Spleen Ferritin, D. Cope Norcross, Dr. Gerald D. Watt
Redox Properties Of Horse Spleen Ferritin, D. Cope Norcross, Dr. Gerald D. Watt
Journal of Undergraduate Research
Iron is essential to all forms of life. Yet, free iron is toxic unless sequestered and regulated. Organisms use the protein ferritin to perform this function. Ferritin is found storing and releasing iron in almost all living organisms. Ferritin is a large, nearly spherical, hollow protein composed of twenty-four nearly identical subunits (Harrison, et. al., 1991; Theil, 1990). The structure of this protein has been characterized and is well known, yet relating this form to its function is still an active area of research. Although there have been many studies done and many models proposed, very little is known about …
Applications Of Meta 1,3-Photocyclizations Using Silicon As A Tether, Bradley Nilsson
Applications Of Meta 1,3-Photocyclizations Using Silicon As A Tether, Bradley Nilsson
Journal of Undergraduate Research
Current literature contains many examples of the use of light to induce the synthesis of novel compounds and natural compounds. One reaction that has been extensively studied is the meta photocycloaddition of arenes to alkenes. Commonly this is experimentally treated as an inten-nolecular reaction. Problems with this approach to the photocycloaddition include low yields and extensive side reactions with competing regioselectivities. We felt that bringing the alkene and the arene together via a molecular tether prior to irradiation with UV light would increase yields and limit side reactions. Our goal is to find a way to make this reaction more …
Lithium-Halogen Exchange In Non-Ethereal Solvent: Efficient Preparation Of 2-Bromo-6-Lithiopyridine In Dichloromethane, Jared R. Mitchell, Dr. Matt A. Peterson
Lithium-Halogen Exchange In Non-Ethereal Solvent: Efficient Preparation Of 2-Bromo-6-Lithiopyridine In Dichloromethane, Jared R. Mitchell, Dr. Matt A. Peterson
Journal of Undergraduate Research
Organolithium reagents have long been known as useful reagents for carbon-carbon bond formation in synthetic organic chemistry. Although a variety of techniques have been developed for their generation, one of the most frequently used methods involves treating either an alkyl or aryl halide (R-X, X = halogen) with a commercially available organolithium such as nbutyllithium (nBuLi). When these reactions are carried out at low temperature in inert solvents, the lithium atom of nBuLi and the halogen atom of the alkyl or aryl halide are exchanged, hence this process is referred to as a lithium-halogen exchange reaction (Figure 1).
Effects Of Metabolic Rate On Muscle Cell Phospholipid Profile, Aaron Miller, Danny Sims, Dr. Steven Wood
Effects Of Metabolic Rate On Muscle Cell Phospholipid Profile, Aaron Miller, Danny Sims, Dr. Steven Wood
Journal of Undergraduate Research
Animal and human cell membranes are composed primarily of phospholipids that form a bi-layer around the cell. Phospholipids play a crucial role in cell membrane function by regulating fluidity and structure. Alterations in the cell membrane composition can drastically affect cell function and metabolism. The purpose of our research study was to identify muscle cell membrane compositional changes due to exercise and muscular dystrophy. Also, we sought to identify the specific chemical changes occurring in the cell membrane by characterizing the structures of the cell membrane phospholipids using mass spectrometry.
Strategic Isolation Of A Putative Cox Enzyme Honors Thesis, Jacob Orme, Dr. Daniel Simmons
Strategic Isolation Of A Putative Cox Enzyme Honors Thesis, Jacob Orme, Dr. Daniel Simmons
Journal of Undergraduate Research
Most of the results of my work are confidential pending publication. This also applies to the public availability of my honors thesis, which will not be printed until later this year as a result. This fact highlights two important points: 1) I will be unable to offer many specifics in this report-although I will offer as much information as possible1-and 2) more importantly, this ORCA project has been extraordinarily successful.
Diversity Of Hiv, Jacob Venesky, Dr. Greg F. Burton
Diversity Of Hiv, Jacob Venesky, Dr. Greg F. Burton
Journal of Undergraduate Research
My ORCA research project was designed to assess the level of diversity found in a patient’s body. When a doctor prescribes drugs to combat HIV, he or she must first assess whether the patient houses drug-resistant strains. This is usually done by extracting blood from the patient and sampling the HIV found within. There is a general assumption made that if there are no drugresistant strains of HIV found in the blood, then the prescribed drugs will be effective at controlling the virus. However, if the HIV found in the blood of the patient was not fully representative of the …
Finding Interactions Between Smpb And Tmrna During Trans-Translation, David Healey, Dr. Allen Buskirk
Finding Interactions Between Smpb And Tmrna During Trans-Translation, David Healey, Dr. Allen Buskirk
Journal of Undergraduate Research
During the last year, I have worked in collaboration with Allen Buskirk and DeAnna Cazier to study the interactions between SmpB and tmRNA during a process called bacterial trans-translation. To understand our experiments, it is necessary to know a little about what trans-translation is, and how it works.
Kurasoin B Analogues, Jason Nielson, Dr. Merritt Andrus
Kurasoin B Analogues, Jason Nielson, Dr. Merritt Andrus
Journal of Undergraduate Research
During the past year, I have actively worked at developing analogues of the anti-cancer agent kurasoin B. I have included the synthetic path that we have followed during the past year as a reminder of the proposed plan I submitted. Included in the general synthetic pathway are the percent yields that I was able to obtain for each reaction.
Total Synthesis Of 12-Hete Using Asymmetric Phase-Transfer Catalyst, Adam Calvert, Dr. Merritt Andrus
Total Synthesis Of 12-Hete Using Asymmetric Phase-Transfer Catalyst, Adam Calvert, Dr. Merritt Andrus
Journal of Undergraduate Research
Natural compounds can be found throughout the world in an essentially limitless variety. By discovering compounds and investigating their properties, we can unlock the mysteries to cure rare diseases and alleviate common ailments. There are however many challenges with using natural compounds in such ways. The first problem is that most biological molecules are found in very small amounts. This not only poses as a problem with identifying their unique properties, but also stands in the way of their pharmaceutical use. A key solution to this challenge is organic total synthesis.
Synthesis Of (S)-Equol, Aaron Butler, Dr. Merritt Andrus
Synthesis Of (S)-Equol, Aaron Butler, Dr. Merritt Andrus
Journal of Undergraduate Research
S-equol is a soy isoflavone metabolized from the isoflavone daidzein by intestinal microflora. Isoflavones are a class of nonsteroidal estrogens. A study conducted by DellaPenna indicates that populations with isoflavone-rich diets have fewer incidences of cardiovascular disease, osteoporosis, and some cancers including breast, prostate, and colon cancers (1). A study by Setchell et al suggests that the health benefits seen in populations whose diets are rich in isoflavones may be correlated with people’s ability to produce s-equol (2). Despite encouraging preliminary studies regarding s-equol, there has yet to be extensive studies done with s-equol in vivo. This is due to …
Orca Report, Jacob Voelkel
Orca Report, Jacob Voelkel
Journal of Undergraduate Research
As a researcher in the Dearden Lab, I researched the selective binding properties of metal ions to members of the cucurbituril family.
Optimization Of Anti-Cancer Agents Discovered At Byu, Chris Cutler, Dr. Matt Peterson
Optimization Of Anti-Cancer Agents Discovered At Byu, Chris Cutler, Dr. Matt Peterson
Journal of Undergraduate Research
The goal of this project was to prepare a library of adenine-based anticancer agents in order to help understand which properties of the molecules contribute to the anticancer activity. I worked in Dr. Peterson’s organic chemistry laboratory for the duration of 2009, synthesizing compounds for anticancer testing. Some were submitted to the NIH for screening against a large panel of cancer cell lines, while others were sent to a collaborator for similar testing. While the results of most of these tests are still forthcoming, the data we have received so far is promising. My work contributed to a publication in …
Thin Film Solutions To Widespread Hospital Infection: Optimization Of Ceragenin-Containing Thin Films, Jeffrey Clark, Dr. Paul B. Savage
Thin Film Solutions To Widespread Hospital Infection: Optimization Of Ceragenin-Containing Thin Films, Jeffrey Clark, Dr. Paul B. Savage
Journal of Undergraduate Research
One current problem in medicine is the accumulation of biofilm on medical devices. Bacterial colonization of endotracheal tubes and urinary catheters is the leading cause of hospital-acquired infections. These infections contribute significantly to patient mortality rates and care costs1. Ceragenin-containing thin films have the potential to prevent these infections. Our lab and collaborators have recently shown that the ceragenin CSA-13 in thin films derived from polyurethane undergo sustained release and prevent bacterial colonization of a coated device2. Optimization of this technology has the potential to yield coatings for a variety of medical devices including endotracheal tubes and urinary catheters.
Ion Beam Mapping Inside An Inductively Coupled Plasma Mass Spectrometer Using Laser Induced Fluorescence, Brett S. Duersch, Dr. Paul B. Farnsworth
Ion Beam Mapping Inside An Inductively Coupled Plasma Mass Spectrometer Using Laser Induced Fluorescence, Brett S. Duersch, Dr. Paul B. Farnsworth
Journal of Undergraduate Research
Inductively coupled plasma mass spectrometry (ICP-MS) is one of the fastest growing fields in analytical chemistry. This discipline combines the powerful detection of mass spectrometry (MS) with the almost universal ionization capabilities of the inductively coupled plasma (ICP) . Combing these two techniques is not a trivial matter, since ions must be extracted from a plasma operating at atmospheric pressures and at temperatures ranging from 6,000 to 10,000 C into a mass spectrometer which operates at vacuum pressures(10 -10 torr). At present the ICP and -3 -6 the MS are typically interfaced with a series of two cones. The first …
Membrane Depolarization Due To Cationic Steroid Antibiotics, Jonathan O. Wright, Dr. Paul Savage
Membrane Depolarization Due To Cationic Steroid Antibiotics, Jonathan O. Wright, Dr. Paul Savage
Journal of Undergraduate Research
The project that I have worked on this past year has been focused on a novel group of antibiotics developed in the lab of Dr. Savage. The antibiotics, called ceragenins or cationic steroid antibiotics (CSA’s), are molecules synthesized from cholic acid, a common bile acid, and they mimic the structure and functionality of antimicrobial peptides found in nature. Although the CSA’s are much smaller than the peptides, they have similar structural aspects, a hydrophobic side as well as a cationic side, and are believed to have a similar mechanism of action. They, like the antimicrobial peptides, have been found to …
Composite Teflon And Polymer Inclusion Membranes For Use In Ion Chromatography Suppressors, Tyler L. Crawford, Dr. John D. Lamb
Composite Teflon And Polymer Inclusion Membranes For Use In Ion Chromatography Suppressors, Tyler L. Crawford, Dr. John D. Lamb
Journal of Undergraduate Research
Ion chromatography (IC) has a need for a suppressor which would allow the simultaneous conductitnetric detection of both cations and anions. Such a suppressor’s membrane would need to exhibit a large flux and a high level of selectivity. Polymer inclusion membranes (PIMS) containing macrocycles have been shown to exhibit high selectivity over a long period of time. The structure of the macrocycle 1 determines the affinity these Ugands exhibit toward cations. By completing metal salts, the macrocycles are able to extract ionic species into solvents that these metal salts would not be soluble in alone. The macrocycle can then transport …
Fractionation And Isolation Of The Anti-Tumoral Activity Of An Indigenous Tongan Medicinal Extract, Steven D. Christenson, Dr. Gary M. Booth, Dr. Steven G. Wood
Fractionation And Isolation Of The Anti-Tumoral Activity Of An Indigenous Tongan Medicinal Extract, Steven D. Christenson, Dr. Gary M. Booth, Dr. Steven G. Wood
Journal of Undergraduate Research
Vai Haka is the Tongan name given to a medicinal extract prepared and prescribed by indigenous healers on the island kingdom of Tonga. Used as a treatment for morning sickness (hyper-emesis), the mixture is prepared by boiling the barks of four different rainforest tree species. These species are Tarrena sambucina, Syzigium malaccense, Alphitonia zizyphoides, and Macaranga harveyana. Studies by Cox (et al) demonstrated biological activity in each of these species from a Guinea Pig Ileum assay.1 Further work by Cox documented that each species is used individually by Samoan healers to treat internal distress.2 Thus bioactivity is well documented through …
Pixe Analysis Of Human Hair From An Egyptian Cemetery, Rafael Casellas, Dr. Nolan F. Mangelson, Dr. Lawrence B. Rees
Pixe Analysis Of Human Hair From An Egyptian Cemetery, Rafael Casellas, Dr. Nolan F. Mangelson, Dr. Lawrence B. Rees
Journal of Undergraduate Research
Human hair is considered to be a minor excretory organ for trace elements. The literature suggests that in some cases trace elemental concentration varies in different races of people. In addition, hair analysis has been used to assess nutritional status in humans. These characteristics attracted archeologists because of the potential of using hair analysis to understand past cultures.1
Researching Molecular Mechanics, Kent Bower
Researching Molecular Mechanics, Kent Bower
Journal of Undergraduate Research
The use of Molecular Mechanics has taken a strong foothold in the world of computational chemistry today. Molecular Mechanics methods offer quick solutions to complex molecular conformation calculations that could take up to days or even months to perform on supercomputers using more exact methods, such as ab initio calculations. For this speed the price of accuracy is often paid when using Molecular Mechanics methods, particularly when the system under inspection is very specialized. For example, much current research centers on the conformations of crown-ether systems with metal-cation ligands. The C-C-O-C-C pattern in these ethers exhibits specific properties which make …
Development Of New Lipid A-Binding Agents, Mark Benson, Dr. Paul B. Savage
Development Of New Lipid A-Binding Agents, Mark Benson, Dr. Paul B. Savage
Journal of Undergraduate Research
The aim of this project is to synthesize a non-peptide lipid A-binding agent which is less toxic and simpler than polymyxin B. Such a binding agent could be used to fight sepsis, a toxic condition where the body overreacts to the lipid A portion of bacterial endotoxin released by Gram-negative bacteria.
Synthesis Of Lipid A Analogues And The Study Of Their Interactions With Antibiotics, Glade E. Roper, Dr. Paul B. Savage
Synthesis Of Lipid A Analogues And The Study Of Their Interactions With Antibiotics, Glade E. Roper, Dr. Paul B. Savage
Journal of Undergraduate Research
Septic shock is a disease that kills over 100,000 hospitalized patients in the United States every year. The mortality rate for those who fall into septic shock is between fifty and eighty percent, and despite advances in medicine this rate has remained constant over the years.1 Septic shock is caused by an inflammatory response to Gram–negative endotoxin, also known as lipopolysaccharide (LPS).
Annotated Chromatographic Isotope Features From A Highly Complex Mass Spectrometry Proteomic Dataset (Mouse) For Feature Detection Algorithm Evaluation, John T. Prince, Christoper Conley
Annotated Chromatographic Isotope Features From A Highly Complex Mass Spectrometry Proteomic Dataset (Mouse) For Feature Detection Algorithm Evaluation, John T. Prince, Christoper Conley
ScholarsArchive Data
This data set and accompanying annotations, referred to as the MOUSE data set, were used for feature detection algorithm evaluation (FDAE) as described in "Massifquant: open-source Kalman filter based XC-MS feature detection". Bioinformatics. 2013. (additional citation details available after publication). Existing and future feature detection and quantitation methods designed for LC-MS are welcome to make use of the data. Since the annotation has isotopic information, users are encouraged to develop other meaningful algorithm evaluations at the isotopic-level. Finally, it serves as an example to be improved upon for future manual-annotation efforts undertaken by the XC-MS community.