Biology Commons^™

Healthy Skepticism: The Relationship Between Funding Source And Conclusion In Nutrition-Related Scientific Articles On Saturated Fat, Lili Muskal

CMC Senior Theses

Recently published scientific articles have led to mixed nutritional advice on dietary saturated fatty acids. Lesser et. al (2007) identified that mixed conclusions in scientific articles on sweetened beverages might be attributed industry funding, as articles funded by the beverage industry are four to eight times more likely to report conclusions in favor of the sponsor’s products. This thesis applies Lesser’s methods to determine whether industry funding influences the inconsistent conclusions on saturated fatty acids. This thesis analyzes 100 articles on foods high in dietary saturated fatty acids. While studies with food industry funding are more likely to produce favorable …

Put Your Money Where Your Mouth Is: Reforming Organized Dentistry To Address Persistent Oral Health Disparities In The U.S., Aparna Chintapalli

Pomona Senior Theses

The importance of oral health has been largely neglected from the conventional standards of healthcare in terms of public understanding & prioritization, the industrial infrastructure, and the scope of prevention & early-intervention services. Its adjunctive locus to the field of medicine has lead to the bifurcation of the oral cavity from the rest of the human body. As a result of this divide, there have been multiple factors that have allowed socially stratified oral health outcomes to manifest. This thesis examines the determinants of oral health disparities through a multidisciplinary lens (i.e. biology, public policy, infrastructure), and offers evidence of …

Characterization Of A Protozoan Phosducin-Like Protein-3 (Phlp-3) Reveals Conserved Redox Activity, Rachel L. Kooistra, Robin David, Ana C. Ruiz, Kyle J. Haselton, Kaitlyn Kiernan, Andrew M. Blagborough, Ligin Solamen, Kenneth W. Olsen, Catherine Putonti, Stefan M. Kanzok

Biology: Faculty Publications and Other Works

We recently identified three novel thioredoxin-like genes in the genome of the protozoan parasite Plasmodium that belong to the Phosducin-like family of proteins (PhLP). PhLPs are small cytosolic proteins hypothesized to function in G-protein signaling and protein folding. Although PhLPs are highly conserved in eukaryotes from yeast to mammals, only a few representatives have been experimentally characterized to date. In addition, while PhLPs contain a thioredoxin domain, they lack a CXXC motif, a strong indicator for redox activity, and it is unclear whether members of the PhLP family are enzymatically active. Here, we describe PbPhLP-3 as the first phosducin-like protein …

Enabling Precision Medicine Via Standard Communication Of Hts Provenance, Analysis, And Results, Gil Alterovitz, Dennis Dean, Carole Globe, Michael R. Crusoe, Stiam Soiland-Reyes, Amanda Bell, Anais Hayes, Anita Suresh, Anjan Purkkayastha, Charles H. King, Dan Taylor, Elaine Johanson, Elaine E. Thompson, Eric Donaldson, Hiroki Morizono, Hsinyi Tsang, Jeet K. Vora, Jeremy Goecks, Jianchao Yao, Jonas S. Almeida, Jonathon Keeney, Kanakadurga Addepalli, Konstantinos Krampis, Krista M. Smith, Lydia Guo, Mark Walderhaug, Marco Schito, Matthew Ezewudo, Nuria Guimera, Paul Walsh, Robel Kahsay, Srikanth Gottipati, Timothy C. Rodwell, Toby Bloom, Yuching Lai, Vahan Simonyan, Raja Mazumder

Publications and Research

A personalized approach based on a patient's or pathogen’s unique genomic sequence is the foundation of precision medicine. Genomic findings must be robust and reproducible, and experimental data capture should adhere to findable, accessible, interoperable, and reusable (FAIR) guiding principles. Moreover, effective precision medicine requires standardized reporting that extends beyond wet-lab procedures to computational methods. The BioCompute framework (https://w3id.org/biocompute/1.3.0) enables standardized reporting of genomic sequence data provenance, including provenance domain, usability domain, execution domain, verification kit, and error domain. This framework facilitates communication and promotes interoperability. Bioinformatics computation instances that employ the BioCompute framework are easily relayed, repeated …

Methods To Improve The Remediation Of Polycyclic Aromatic Hydrocarbons (Pahs) In Aerobic And Anaerobic Environments, Brian Wartell

Dissertations

Oil spills occur regularly in terrestrial environments and crude oil can contain many compounds that are highly resistant to degradation. Among these compounds are high levels of polycyclic aromatic hydrocarbons (PAHs) which are not only toxic but can also be carcinogenic and/or mutagenic. The first chapter of this dissertation includes an extensive review chapter on the variables affecting the anaerobic degradation of hydrocarbons, with a particular focus on PAHs. Electron acceptors, electron donors, temperature, salinity, pH all play key roles in determining the possibility effective of effective degradation occurring. Thus, by addressing solutions, such as biostimulation, improving environmental variables for …

Table Of Contents

Journal of the South Carolina Academy of Science

No abstract provided.

Characterization Of A Protozoan Phosducin-Like Protein-3 (Phlp-3) Reveals Conserved Redox Activity, Rachel L. Kooistra, Robin David, Ana C. Ruiz, Sean W. Powers, Kyle J. Haselton, Kaitlyn Kiernan, Andrew M. Blagborough, Ligin Solamen, Kenneth W, Olsen, Catherine Putonti, Stefan M. Kanzok

Bioinformatics Faculty Publications

We recently identified three novel thioredoxin-like genes in the genome of the protozoan parasite Plasmodium that belong to the Phosducin-like family of proteins (PhLP). PhLPs are small cytosolic proteins hypothesized to function in G-protein signaling and protein folding. Although PhLPs are highly conserved in eukaryotes from yeast to mammals, only a few representatives have been experimentally characterized to date. In addition, while PhLPs contain a thioredoxin domain, they lack a CXXC motif, a strong indicator for redox activity, and it is unclear whether members of the PhLP family are enzymatically active. Here, we describe PbPhLP-3 as the first phosducin-like protein …

Characterization Of A Protozoan Phosducin-Like Protein-3 (Phlp-3) Reveals Conserved Redox Activity, Rachel L. Kooistra, Robin David, Ana C. Ruiz, Sean W. Powers, Kyle J. Haselton, Kaitlyn Kiernan, Andrew M. Blagborough, Ken W. Olsen, Catherine Putonti, Stefan M. Kanzok

Chemistry: Faculty Publications and Other Works

We recently identified three novel thioredoxin-like genes in the genome of the protozoan parasite Plasmodium that belong to the Phosducin-like family of proteins (PhLP). PhLPs are small cytosolic proteins hypothesized to function in G-protein signaling and protein folding. Although PhLPs are highly conserved in eukaryotes from yeast to mammals, only a few representatives have been experimentally characterized to date. In addition, while PhLPs contain a thioredoxin domain, they lack a CXXC motif, a strong indicator for redox activity, and it is unclear whether members of the PhLP family are enzymatically active. Here, we describe PbPhLP-3 as the first phosducin-like protein …

Evaluation Of Fermentation At 40°C And 30°C For Cost Effective Lignocellulose To Lipid Conversion, Kyle M. Macewen

Graduate Masters Theses

As the world population continues to grow, the demand for energy will continue to rise. Biofuels have become an attractive alternative to replace fossil fuels as a clean and renewable source of energy. The six- and five-carbon sugars contained in lignocellulosic plant biomass is the largest carbohydrate source in the world, and a key feedstock for sustainable biofuel production. The conversion of lignocellulose to lipids is done by using oleaginous yeast as a biocatalyst. Recently, Arxula adeninivorans has become a yeast of interest because of its unique properties. These include its unusual metabolic flexibility which allows it to utilize a …

An Acoustic Monitoring Method For Assessing River Dolphin Presence And Changes In The Context Of Anthropogenic Development, Charles A. Muirhead

Graduate Masters Theses

Populations of river dolphins throughout Asia are in decline as a direct result of intensified anthropogenic activity along river systems. Water development projects, land use change, contamination, and intensified fishing practices are known factors contributing to the probable extinction of the Yangtze river dolphin (Lipotes vexillifer) and declining populations of the South Asian river dolphin (Platanista gangetica spp.), Irrawady dolphin (Orcaella brevirostris), and finless porpoise (Neophocaena a. asiaeorientalis). Although not yet as extensive, river system development in South America is following a similar path as that of Asia, with impacts on dolphin species likely to follow. Currently, the Amazon river …

A Novel Body Coloration Phenotype In Anolis Sagrei: Implications For Physiology, Fitness, And Predation, Yasmeen Erritouni, Beth Reinke, Ryan Calsbeek

Beth Reinke

Small Rna Mgrr Regulates Sensitivity Of Escherichia Fergusonii To Oxidative Stress, Austin Paul Wright

Dissertations and Theses

Non-coding small RNAs (sRNAs) are integral to post-transcriptional gene regulation in bacteria. The function of an sRNA is dependent on both secondary structure and the sequence of its unstructured seed region. The sRNA seed region typically base-pairs with target mRNAs to down-regulate the expression of target genes by blocking the ribosome-binding site or by promoting RNase-mediated degradation of the sRNA-mRNA complex. sRNAs have also been shown to increase expression of target genes by releasing RNA secondary structures that block ribosome-binding sites. Selective pressure to maintain sRNA function conserves the sequence of the sRNA seed region, but mutations in mRNA sequences …

Phenotypic And Transcriptomic Characterization Of Colonial Phase Variation In The Cholera Pathogen Reveals A Novel Smooth Biofilm-Defective Form, Bliss Nicole Lambert

LSU Doctoral Dissertations

Biofilm formation, through the production of Vibrio polysaccharide (VPS), greatly enhances the environmental fitness and pathogenic success of Vibrio cholerae. As a result of phase variation, V. cholerae can switch from a smooth form to rugose, whose cells produce excess VPS, resulting in highly structured biofilms and greater resistance to stress. To further characterize the reversible process of phase variation, we isolated three colonial lineages. Each lineage began with a smooth parent, N16961, and contained a rugose variant derived from the parent, N16961R, as well as a smooth revertant of the rugose, N16961SD. We found clear phenotypic and transcriptomic …

Comparative Transcriptome Analysis Reveals An Efficient Mechanism For Α-Linolenic Acid Synthesis In Tree Peony Seeds, Qingyu Zhang, Rui Yu, Daoyang Sun, Mahbubur Rahman, Lihang Xie, Jiayuan Hu, Lixia He, Aruna Kilaru, Lixin Niu, Yanlong Zhang

ETSU Faculty Works

Tree peony (Paeonia section Moutan DC.) species are woody oil crops with high unsaturated fatty acid content, including α-linolenic acid (ALA/18:3; >40% of the total fatty acid). Comparative transcriptome analyses were carried out to uncover the underlying mechanisms responsible for high and low ALA content in the developing seeds of P. rockii and P. lutea, respectively. Expression analysis of acyl lipid metabolism genes revealed upregulation of select genes involved in plastidial fatty acid synthesis, acyl editing, desaturation, and triacylglycerol assembly in seeds of P. rockiirelative to P. lutea. Also, in association with ALA content in seeds, …

Ne Stem 4u Afterschool Intervention Leads To Gains In Stem Content Knowledge For Middle School Youth, Christine E. Cutucache, Taylor Boham, Jamie Luhr, Amie Sommers, Nikolaus Stevenson, Erkko Sointu, Kati Mäkitalo‐Siegl, Sirpa Kärkkäinen, Teemu Valtonen, Neal Grandgenett, William Tapprich

Biology Faculty Publications

Afterschool interventions in STEM are linked to learning gains during the school day. These opportunities engage and excite students about STEM concepts since they observe a more hands-on, project-oriented approach. Often these opportunities for afterschool interventions are infrequent in nature and leave gaps for students in their maturation and understanding. Herein we describe the first report of an afterschool intervention, named NE STEM 4U, targeting socioeconomically disadvantaged middle school youth via a twice weekly, year-long intervention, studied across two years. We assessed the impact of this program on i.) short-term, individual student gains in STEM content knowledge and ii.) delivery …

Living Shoreline Stabilization To Increase Resiliency At De Soto National Memorial, Linda Walters, Melinda Donnelly, Christian Pilato, Suzanne Connor

CEELAB Research Data

De Soto National Memorial (Bradenton, FL) is an important location where both Native Americans and De Soto's army of soldiers once lived. We have been working closely with the National Park Service and the University of Central Florida to understand how to best stabilize this shoreline using living shoreline techniques combined with long-term natural recruitment. Stabilizing De Soto's shoreline is essential to decrease erosion and shoreline loss to protect the Park's cultural and natural resources, especially the numerous historically significant shell middens. Through pre-restoration monitoring, we determined that high-energy boat wakes were limiting natural mangrove recruitment. Lack of retention of …

Atypical Activation Of The G Protein Gα By The Oncogenic Mutation Q209p, Marcin Maziarz, Anthony Leyme, Arthur Marivin, Alex Luebbers, Prachi P. Patel, Zhe Chen, Stephen R. Sprang, Mikel Garcia-Marcos

Biological Sciences Faculty Publications

The causative role of G protein-coupled receptor (GPCR) pathway mutations in uveal melanoma (UM) has been well-established. Nearly all UMs bear an activating mutation in a GPCR pathway mediated by G proteins of the G family, driving tumor initiation and possibly metastatic progression. Thus, targeting this pathway holds therapeutic promise for managing UM. However, direct targeting of oncogenic Gα mutants, present in ∼90% of UMs, is complicated by the belief that these mutants structurally resemble active Gα WT. This notion is solidly founded on previous studies characterizing Gα mutants in which a conserved catalytic glutamine (Gln-209 in Gα) is replaced …

A Generic Pixel-To-Point Comparison For Simulated Large-Scale Ecosystem Properties And Ground-Based Observations: An Example From The Amazon Region, Anja Rammig, Jens Heinke, Florian Hofhansl, Hans Verbeeck, Timothy R. Baker, Bradley O. Christoffersen, Philippe Ciais, Hannes De Deurwaerder, Katrin Fleischer, David Galbraith

Biology Faculty Publications and Presentations

Comparing model output and observed data is an important step for assessing model performance and quality of simulation results. However, such comparisons are often hampered by differences in spatial scales between local point observations and large-scale simulations of grid cells or pixels. In this study, we propose a generic approach for a pixel-to-point comparison and provide statistical measures accounting for the uncertainty resulting from landscape variability and measurement errors in ecosystem variables. The basic concept of our approach is to determine the statistical properties of small-scale (within-pixel) variability and observational errors, and to use this information to correct for their …

A Structural And Dynamic Model For The Assembly Of Replication Protein A On Single-Stranded Dna, Luke A. Yates, Ricardo J. Aramayo, Nilisha Pokhrel, Colleen C. Caldwell, Joshua A. Kaplan, Rajika L. Perera, Maria Spies, Edwin Antony, Xiaodong Zhang

Biological Sciences Faculty Research and Publications

Replication Protein A (RPA), the major eukaryotic single stranded DNA-binding protein, binds to exposed ssDNA to protect it from nucleases, participates in a myriad of nucleic acid transactions and coordinates the recruitment of other important players. RPA is a heterotrimer and coats long stretches of single-stranded DNA (ssDNA). The precise molecular architecture of the RPA subunits and its DNA binding domains (DBDs) during assembly is poorly understood. Using cryo electron microscopy we obtained a 3D reconstruction of the RPA trimerisation core bound with ssDNA (∼55 kDa) at ∼4.7 Å resolution and a dimeric RPA assembly on ssDNA. FRET-based solution studies …

Legacy Habitat Suitability Of Eastern Oysters (Crassostrea Virginica) In Louisiana: A Prelude To Mississippi River Delta Freshwater Diversions, Tasia Mv Denapolis

University of New Orleans Theses and Dissertations

The Louisiana oyster industry is greatly impacted by freshwater and sediment diversions that are part of the effort to restore the state’s coastline. A habitat suitability index (HSI) proposes species-habitat relationships that can be instrumental in creating impact assessments and suitability predictions for management as new diversions are implemented. An oyster (Crassostrea virginica) HSI was developed using three variables crucial to oyster sustainability: average annual salinity, minimum monthly salinity, and average salinity during the spawning season. These Legacy HSI visualizations show annual fluctuations in the distribution of zones suitable for oyster cultivation prior to proposed diversions in Pontchartrain …