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2016

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Articles 1 - 20 of 20

Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

The Chemistry Of The Flint Water Crisis, Ernest M. Oleksy Dec 2016

The Chemistry Of The Flint Water Crisis, Ernest M. Oleksy

The Downtown Review

Politics and science do not always go hand-in-hand. Nowhere was this more clear than in the Flint Water Crisis. Negligence towards growing levels of lead poisoning in drinking water led to incredibly deleterious effects on Flint's citizens. The chemistry of equilibrium and the shortcomings of local leaders led to Flint's water becoming a crisis.

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Expression, Purification, And Crystallization Of An Endoxylanase From Bacteroides Vulgatus, Jesslyn Park, Jason Hurlbert Oct 2016

Expression, Purification, And Crystallization Of An Endoxylanase From Bacteroides Vulgatus, Jesslyn Park, Jason Hurlbert

The Winthrop McNair Research Bulletin

Sustainable sources of energy are growing in demand as fossil fuels are rapidly expended. One such energy source is fuel ethanol generated from the fermentation of plant biomass by engineered bacterial biocatalysts. The creation of a biocatalyst capable of converting nearly any plant matter to fuel ethanol requires the identification of novel enzymes capable of degrading specific carbohydrate polymers and cloning these enzymes into a bacterial host. This study seeks to structurally characterize a novel xylanase of glycosyl hydrolase family 30 (GH30) from Bacteroides vulgatus, a bacterium found in the human gut microbiome, via x-ray crystallography. The gene for …

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Sweating The Small Stuff: Linking Plankton To Climate Change, Brian Kim '18 Makes Conncetions, Stephen Collins Sep 2016

Sweating The Small Stuff: Linking Plankton To Climate Change, Brian Kim '18 Makes Conncetions, Stephen Collins

Colby Magazine

It takes an expansive mind to connect microscopic marine copepods (certain crustacean plankton) unwittingly chomping on floating microplastics with a bigger picture: the planet’s carbon pump and global climate change. But that’s what Brian Kim ’18 decided to investigate during Jan Plan, working with Bigelow Lab Senior Research Scientist David Fields.

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Modeling And Analysis Of Germ Layer Formations Using Finite Dynamical Systems, Alexander Garza, Megan Eberle, Eric A. Eager Aug 2016

Modeling And Analysis Of Germ Layer Formations Using Finite Dynamical Systems, Alexander Garza, Megan Eberle, Eric A. Eager

Spora: A Journal of Biomathematics

The development of an embryo from a fertilised egg to a multicellular organism proceeds through numerous steps, with the formation of the three germ layers (endoderm, mesoderm, ectoderm) being one of the first. In this paper we study the mesendoderm (the tissue that collectively gives rise to both mesoderm and endoderm) gene regulatory network for two species, \textit{Xenopus laevis} and the axolotl (\textit{Ambystoma mexicanum}) using Boolean networks. We find that previously-established bistability found in these networks can be reproduced using this Boolean framework, provided that some assumptions used in previously-published differential equations models are relaxed. We conclude by discussing our …

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Quantifying Greenhouse Gas Flux Of Restored Vs. Unrestored Wetlands: A Case Study At Prairie Wolf Slough, Matthew Connors, Beth Lawrence Jul 2016

Quantifying Greenhouse Gas Flux Of Restored Vs. Unrestored Wetlands: A Case Study At Prairie Wolf Slough, Matthew Connors, Beth Lawrence

DePaul Discoveries

Wetlands provide ecological services such as cleansing the water supply, sequestering carbon, and providing habitat for wildlife, however wetland restoration often alters the greenhouse gas flux of the site. Our study aims to investigate the effects of wetland restoration on greenhouse gas flux at Prairie Wolf Slough. We did this by comparing greenhouse gas flux on matching hydric soil series from the restored wetland with an adjacent abandoned agricultural field. We measured known controls of greenhouse gas flux such as soil moisture and soil temperature. We found that there was no detectable methane and nitrous oxide flux at either site, …

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Required Biochem Class Live-Streamed This Summer: Collaboration With Union College Makes Required Credits Easier To Obtain, Chris Mclean-Wheeler Jun 2016

Required Biochem Class Live-Streamed This Summer: Collaboration With Union College Makes Required Credits Easier To Obtain, Chris Mclean-Wheeler

Andrews Agenda: Campus News

No abstract provided.

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Protein Adsorption Using A Lattice Toy Model, Ari J. Weiland May 2016

Protein Adsorption Using A Lattice Toy Model, Ari J. Weiland

Macalester Journal of Physics and Astronomy

Protein adsorption is an important subfield of Biophysics particularly relevant in medical science. Using a computational simulation with a basic but configurable two-dimensional square lattice model of approximate amino acid interactions, I investigated the entropic effects of protein adsorption on a weakly attractive surface. These simulations allow for a precise calculation of the partition functions of these complex systems, from which I can then analyze other thermodynamic properties.

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Investigation Of Parasympathetic Effects Of Lavender Essential Oil In Humans, Haakon Robert Nelson, Rachel Ann Burkhart, Daniel Morin, Nicole Grace Weissenfluh, Michael R. Korn Apr 2016

Investigation Of Parasympathetic Effects Of Lavender Essential Oil In Humans, Haakon Robert Nelson, Rachel Ann Burkhart, Daniel Morin, Nicole Grace Weissenfluh, Michael R. Korn

Montview Journal of Research & Scholarship

The purpose of this study will be to investigate the claim that administration of lavender (Lavandula angustifolia) essential oil (topically, orally, and/or respiratorily) produces a relaxative effect in human subjects. This investigation will theoretically be conducted in two stages. Stage one will focus primarily on determining the presence of therapeutic effects and the relative effectiveness of lavender in several application modalities. Stage two will proceed based on findings from stage one. If significant parasympathetic effects are observed in relation to one or more of the lavender oil modalities described above, a more focused investigation will be conducted in stage two …

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Poster: Embryonic Stem Cell Research, Emillie Partridge Apr 2016

Poster: Embryonic Stem Cell Research, Emillie Partridge

Best Integrated Writing

This poster presentation by Partridge provides information about stem cell research and the controversy surrounding it.

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Section Abstracts: Structural Biology, Biochemistry, And Biophysics Apr 2016

Section Abstracts: Structural Biology, Biochemistry, And Biophysics

Virginia Journal of Science

Abstracts of the Structural Biology, Biochemistry, and Biophysics Section for the 94th Annual Virginia Academy of Science Meeting, May 18-20, 2016, at University of Mary Washington, Fredericksburg, VA.

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Developing A Microfluidic Lab-On-A-Chip Device To Assess The Correlation Between The Ratio Of H And L Ferritin In Maternal Serum And Preterm Birth, Kaitlyn Brower, Adam Woolley Feb 2016

Developing A Microfluidic Lab-On-A-Chip Device To Assess The Correlation Between The Ratio Of H And L Ferritin In Maternal Serum And Preterm Birth, Kaitlyn Brower, Adam Woolley

Journal of Undergraduate Research

Preterm birth is the leading cause of death in children under the age of 51 and is defined by the Centers for Disease Control as birth before 37 weeks gestation.2 It is estimated that 15 million babies are born premature annually and that PTB kills nearly 1 million babies every year. Currently, accurate detection of PTB risk isn’t possible and extrauterine treatments and interventions are insufficient.

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Targeting Superoxide Dismutase-¬1 In Cancer, Laura Oh, Josh Andersen Feb 2016

Targeting Superoxide Dismutase-¬1 In Cancer, Laura Oh, Josh Andersen

Journal of Undergraduate Research

SOD1 is overexpressed in many cancers such as lung adenocarcinoma, non-­ small-­cell lung cancer, and 70% of primary breast cancers. Traditionally, SOD1 is known as an antioxidant in the human body, but only 1% of SOD1 expressed in cells is necessary to keep superoxide radicals below cytotoxic levels, suggesting that SOD1 may have undiscovered functions. One of the known trademarks of cancer is the Warburg Effect defined by up-­regulated glycolysis and down-­ regulated respiration. It is thought that this unique mode of metabolism promotes cancer cell growth. A recent study demonstrated that SOD1 functions to repress respiration through the casein …

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Learning Chemistry Through Experimentation, Kyle Long, Jennifer Nielson Feb 2016

Learning Chemistry Through Experimentation, Kyle Long, Jennifer Nielson

Journal of Undergraduate Research

For the past five years, Dr. Jennifer Nielson has conducted research in Kampala, Uganda, located in south-central Africa. I have been able to join her for two of the five years, including this past year for nearly three weeks in August. Our research focuses on teaching basic chemistry principle that are difficult to comprehend by using experiments that demonstrate the general concept of atomic structures and functions.

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Solving The Structure Of The Raptor-Cct Complex, Grant Ludlam, Barry Willardson Feb 2016

Solving The Structure Of The Raptor-Cct Complex, Grant Ludlam, Barry Willardson

Journal of Undergraduate Research

The protein Raptor is an essential component of the mechanistic target of rapamycin (mTOR) cell signaling complex 1 (mTORC1) (1). The mTORC1 complex is a master regulator of cell growth, making it a high-priority target in cancer and inflammation research (2). Before Raptor can be assembled into the mTORC1, it is first folded by the chaperone protein cytosolic chaperonin containing TCP1 (CCT). CCT is composed of two rings of 8 different subunits, which together form a barrel shape. CCT substrates are folded in the 85 Å wide folding cavity inside the barrel.

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Software Package For Mass Spectrometry Isotope Analysis And Extraction, Michael Porter, Dr. John Price Feb 2016

Software Package For Mass Spectrometry Isotope Analysis And Extraction, Michael Porter, Dr. John Price

Journal of Undergraduate Research

Proteins are involved in nearly every cellular process. They transport molecules, replicate DNA, catalyze reactions, respond to stimuli, and form the structural framework of the cell. The diversity of protein function has led to an interest in understanding the cellular production and control of individual proteins which in turn is key to understanding how the cell responds to the environment and what occurs on a molecular level during disease.

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Microbial Pretreatment Of Waste For Anaerobic Digestion, Braden Myers, Jaron Hansen Jan 2016

Microbial Pretreatment Of Waste For Anaerobic Digestion, Braden Myers, Jaron Hansen

Journal of Undergraduate Research

The aim of this research was to demonstrate Caldicellulosiruptor bescii is a feasible microbial pretreatment of lignocellulose for enhanced production of biogas when coupled with secondary anaerobic digestion. Before anaerobic digestion of waste can reach its maximum energy production potential, economically sound methods for pretreatments that allow increased digestion of waste materials must be developed. Many types of waste cannot be broken down sufficiently by anaerobic digestion alone. Overcoming this hurdle through successful feedstock pretreatment would unlock a vast potential supply of renewable energy feedstock materials.

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Analysis Of Alternative Storage Conditions For Dna Recovery From Field Samples, Alison Schutt, Emily Stricklin, Britta Ten Haken, Joseph Tolsma, Laurie Furlong, Sara S. Tolsma Jan 2016

Analysis Of Alternative Storage Conditions For Dna Recovery From Field Samples, Alison Schutt, Emily Stricklin, Britta Ten Haken, Joseph Tolsma, Laurie Furlong, Sara S. Tolsma

Northwestern Review

As ecologists increasingly employ molecular methods, they find that tried and true preservation solutions (e.g. ethanol or formalin) may not be optimal when samples are targeted for genetic analyses. Before traveling to remote sample sites, researchers need to consider which preservation methods are likely to yield the largest quantity and highest quality of DNA based on their travel times and field conditions. They also need to consider whether they will have access to preservatives at remote sites and whether those preservatives can be safely transported. To determine which preservation methods would most reliably preserve tissue for genetic analysis under a …

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Understanding The Interaction Between Ulk1 And Atg9 And Autophagy, Ryan Hyatt, Joshua L. Andersen Jan 2016

Understanding The Interaction Between Ulk1 And Atg9 And Autophagy, Ryan Hyatt, Joshua L. Andersen

Journal of Undergraduate Research

Autophagy is an adaptive catabolic process of self-digestion, a process by which the cell recycles aged organelles and other structures. Interestingly, changes in the regulation of autophagy have been linked to infections, cancers, neurodegeneration, aging, and heart disease (Arroyo, Daniela S. et al. 2014). Understanding the mechanisms which control autophagy will aid in better treatment of those diseases, specifically in the development of effective pharmaceuticals.

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The Mechanism Of Homogeneous Hg-Catalyzed Methane Partial Oxidation, Steven Butler, Daniel Ess Jan 2016

The Mechanism Of Homogeneous Hg-Catalyzed Methane Partial Oxidation, Steven Butler, Daniel Ess

Journal of Undergraduate Research

There is now access to vast amounts of inexpensive natural gas, due in part to shale gas discoveries. Abundant natural gas provides significant motivation to develop methods for methane partial oxidation. One major target for methane oxidation is methanol. Natural gas is principally methane, but also includes significant amounts of ethane and propane. Methanol can be produced from natural gas via high-temperature generation of syngas (mixture of H2 and CO).

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Identification Of Compounds Of Allelopathic Extracts From Two Species Of Metapeyssonnelia (Rhodophyta) Growing On The Hydrocoral, Millepora Complanata, In Puerto Rico, Maria I. Reyes-Contreras, Aniuska Kazandjian, David L. Ballantine Jan 2016

Identification Of Compounds Of Allelopathic Extracts From Two Species Of Metapeyssonnelia (Rhodophyta) Growing On The Hydrocoral, Millepora Complanata, In Puerto Rico, Maria I. Reyes-Contreras, Aniuska Kazandjian, David L. Ballantine

Gulf and Caribbean Research

Two Puerto Rican species of the encrusting red alga Metapeyssonnelia are known to overgrow and kill the hydrocoral Millepora complanata. The overgrowth is accompanied by bleaching or tissue lightening regions surrounding the growing margin of the algae on the coral tissue. Lipophilic and hydrophilic extracts from Metapeyssonnelia corallepida and M. milleporoides were obtained and analyzed by GC-MS. The following compounds were identified from M. corallepida: squalene and 5-(hydroxymethyl)-2-(dimethoxymethyl)-furan3-methoxycarbonyl-1,1-diethyl-2-buten-4-olide and from M. milleporoides: 2,4-dit-butyl phenol, 2(3H)-furanone and dihydro-4,4-dimethyl-(CAS), terpenes, furanones and phenol. Aliquots of crude extracts of both Metapeyssonnelia species applied to coral fragments resulted in visible changes …

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