Biology Commons^™

A Composite Review Of The Proposed Molecular Mechanisms And Genetic Components Underlying Parkinson’S Disease, Paige Brodrick

Scripps Senior Theses

Parkinson’s disease (PD) is a progressive neurodegenerative disorder characterized by the progressive death of dopaminergic neurons present in the substantia nigra. The clinical presentation of PD includes tremors, slowed movement (bradykinesia), muscle and limb rigidity, and difficulty with walking and balancing. While many environmental factors can affect the onset and progression of the disease, genetic mutations have a large influence. Of the identified PD-linked genetic mutations, mutations in the leucine-rich repeat kinase 2 (LRRK2) are one of the most common genetic causes of PD. Located in endosomes, LRRK2 has been shown to play a role in the sorting and endocytosis …

Experimental And Theoretical Investigation Of Overall Energy Deposition In Surface-Induced Unfolding Of Protein Ions, Micah T. Donor, Austin M. Mroz, James S. Prell

Faculty Publications - Department of Biological & Molecular Science

Recent advances in native mass spectrometry have enabled its use to probe the structure of and interactions within biomolecular complexes. Surface-induced dissociation, in which inter- and intramolecular interactions are disrupted following an energetic ion-surface collision, is a method that can directly interrogate the topology of protein complexes. However, a quantitative relationship between the ion kinetic energy at the moment of surface collision and the internal energy deposited into the ion has not yet been established for proteins. The factors affecting energy deposition in surface-induced unfolding (SIU) of protein monomers were investigated and a calibration relating laboratory-frame kinetic energy to internal …

The Effects Of Medical Marijuana On The Endocannabinoid Systems Of Children With Autism Spectrum Disorders, Maya Eylon

Whittier Scholars Program

50% of children with Autism Spectrum Disorder(ASD) have behavior abnormalities ranging from anxiety, to tantrum, to behavior outbreaks. Of these children, 40% are not responding to the treatment options available today (behavior therapy and medical treatments). There is a need within the ASD community that is not being address and because of that the desperate parents of these children have been turning to unconventional treatments, such as medical marijuana. Although there have been several anecdotes speaking to the power of cannabis, there is a severe slack of scientific data and research to demonstrate the effectiveness of cannabis in treating these …

Radiomic Feature Stability Across 4d Respiratory Phases And Its Impact On Lung Tumor Prognosis Prediction, Qian Du, Michael Baine, Kyle Bavitz, Josiah Mcallister, Xiaoying Liang, Hongfeng Yu, Jeffrey Ryckman, Lina Yu, Hengle Jiang, Sumin Zhou, Sumin Zhou, Chi Zhang, Dandan Zheng

School of Biological Sciences: Faculty Publications

Radiomic analysis has recently demonstrated versatile uses in improving diagnostic and prognostic prediction accuracy for lung cancer. However, since lung tumors are subject to substantial motion due to respiration, the stability of radiomic features over the respiratory cycle of the patient needs to be investigated to better evaluate the robustness of the interpatient feature variability for clinical applications, and its impact in such applications needs to be assessed. A full panel of 841 radiomic features, including tumor intensity, shape, texture, and wavelet features, were extracted from individual phases of a four-dimensional (4D) computed tomography on 20 early-stage non-small-cell lung cancer …

Ecological Pleiotropy And Indirect Effects Alter The Potential For Evolutionary Rescue, John P. Delong, Jonathan Belmaker

School of Biological Sciences: Faculty Publications

Invading predators can negatively affect naïve prey populations due to a lack of evolved defenses. Many species therefore may be at risk of extinction due to overexploitation by exotic predators. Yet the strong selective effect of predation might drive evolution of imperiled prey toward more resistant forms, potentially allowing the prey to persist. We evaluated the potential for evolutionary rescue in an imperiled prey using Gillespie eco‐evolutionary models (GEMs). We focused on a system parameterized for protists where changes in prey body size may influence intrinsic rate of population growth, space clearance rate (initial slope of the functional response), and …

Influenza H1 Mosaic Hemagglutinin Vaccine Induces Broad Immunity And Protection In Mice, Brigette N. Corder, Brianna L. Bullard, Jennifer L. Debeauchamp, Natalia A. Ilyushina, Richard J. Webby, Eric A. Weaver

School of Biological Sciences: Faculty Publications

Annually, influenza A virus (IAV) infects ~5–10% of adults and 20–30% of children worldwide. The primary resource to protect against infection is by vaccination. However, vaccination only induces strain-specific and transient immunity. Vaccine strategies that induce cross-protective immunity against the broad diversity of IAV are needed. Here we developed and tested a novel mosaic H1 HA immunogen. The mosaic immunogen was optimized in silico to include the most potential B and T cell epitopes (PBTE) across a diverse population of human H1 IAV. Phylogenetic analysis showed that the mosaic HA localizes towards the non-pandemic 2009 strains which encompasses the broadest …

Life Ascending: Mechanism And Process In Physiological Adaptation To High-Altitude Hypoxia, Jay F. Storz, Graham R. Scott

School of Biological Sciences: Faculty Publications

To cope with the reduced availability of O2 at high altitude, air-breathing vertebrates have evolved myriad adjustments in the cardiorespiratory system to match tissue O2 delivery with metabolic O2 demand. We explain how changes at interacting steps of the O2 transport pathway contribute to plastic and evolved changes in whole-animal aerobic performance under hypoxia. In vertebrates native to high altitude, enhancements of aerobic performance under hypoxia are attributable to a combination of environ- mentally induced and evolved changes in multiple steps of the pathway. Additionally, evidence suggests that many high-altitude natives have evolved mechanisms for attenuating maladaptive acclimatization responses to …

Testing The Competition-Colonization Trade-Off And Its Correlations With Functional Trait Variations Among Subtropical Tree Species, Yue Bin, Guojun Lin, Sabrina E. Russo, Zhongliang Huang, Yong Shen, Honglin Cao, Juyu Lian, Wanhui Ye

School of Biological Sciences: Faculty Publications

The competition-colonization trade-off, by which species can partition spatial niches, is a potentially important mechanism allowing the maintenance of species diversity in plant communities. We examined whether there was evidence for this trade-off among tree species in a subtropical forest and how it correlated with eight functional traits. We developed and estimated a metric for colonization ability that incorporates both fecundity and seed dispersal based on seed trap data and the sizes and distributions of adult trees. Competitive ability was estimated as survival probability under high crowding conditions based on neighborhood models. Although we found no significant relationship between colonization …

Gravid Tetragnathid Spiders Show An Increased Functional Response, Mary E. Boswell, John P. Delong

School of Biological Sciences: Faculty Publications

Spiders in the genus Tetragnatha feed on emerging aquatic insects, including mosquitoes and midges, but there is little known about the foraging behavior of these spiders. We hypothesized that female spiders actively developing egg sacs would increase food consumption to provide more energy to produce and provision their eggs. We tested this hypothesis by measuring foraging rates of Tetragnatha spiders kept in jars and provisioned with different levels of midges. We then tested for a difference in the functional response of spiders that did or did not lay egg sacs in their jars. Egg-laying and non-egg-laying spiders showed significantly different …

Modeling Genomes To Phenomes To Populations In A Changing Climate: The Need For Collaborative Networks, Nika Galic, Allyson G. Hindle, John P. Delong, Karen Watanabe, Valery Forbes, C. Loren Buck

School of Biological Sciences: Faculty Publications

Condensed Abstract

Climate is changing globally and its impacts can arise at different levels of biological organization; yet, cross-level consequences of climate change are still poorly understood. Designing effective environmental management and adaptation plans requires implementation of mechanistic models that span the biological hierarchy. Because biological systems are inherently complex and dynamic in nature, dealing with complexities efficiently necessitates simplification of systems or approximation of relevant processes, but there is little consensus on mathematical approaches to scale from genes to populations. Here we present an effort that aims to bring together groups that often do not interact, but that are …

Body Condition Helps To Explain Metabolic Rate Variation In Wolf Spiders, Stella F. Uiterwaal, John P. Delong

School of Biological Sciences: Faculty Publications

1. Metabolism is the fundamental process that powers life. Understanding what drives metabolism is therefore critical to our understanding of the ecology and behavior of organisms in nature.

2. Metabolic rate generally scales with body size according to a power law. However, considerable unexplained variation in metabolic rate remains after accounting for body mass with scaling functions.

3. We measured resting metabolic rates (oxygen consumption) of 227 field-caught wolf spiders. Then, we tested for effects of body mass, species, and body condition on metabolic rate.

4. Metabolic rate scales with body mass to the 0.85 power in these wolf spiders, …

Large Expert-Curated Database For Benchmarking Document Similarity Detection In Biomedical Literature Search, Peter Brown, Relish Consortium, Yaoqi Zhou, Chi Zhang, Tian Gao

School of Biological Sciences: Faculty Publications

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were …

A Rapid And Accurate Minion-Based Workflow For Tracking Species Biodiversity In The Field, Hendrik Freitag, Simone Maestri, Emanuela Cosentino, Marta Paterno, Jhoana M. Garces, Luca Marcolungo, Massimiliano Alfano, Iva Njunjić, Menno Schilthuizen, Ferry Slik, Michele Menegon, Marzia Rossato, Massimo Delledonne

Biology Faculty Publications

Genetic markers (DNA barcodes) are often used to support and confirm species identification. Barcode sequences can be generated in the field using portable systems based on the Oxford Nanopore Technologies (ONT) MinION sequencer. However, to achieve a broader application, current proof-of-principle workflows for on-site barcoding analysis must be standardized to ensure a reliable and robust performance under suboptimal field conditions without increasing costs. Here, we demonstrate the implementation of a new on-site workflow for DNA extraction, PCR-based barcoding, and the generation of consensus sequences. The portable laboratory features inexpensive instruments that can be carried as hand luggage and uses standard …

Multiscale Model Of Regional Population Decline In Little Brown Bats Due To White-Nose Syndrome, Andrew M. Kramer, Claire S. Teitelbaum, Ashton Griffin, John M. Drake

Integrative Biology Faculty and Staff Publications

1. The introduced fungal pathogen Pseudogymnoascus destructans is causing decline of several species of bats in North America, with some even at risk of extinction or extirpation. The severity of the epidemic of white-nose syndrome caused by P. destructans has prompted investigation of the transmission and virulence of infection at multiple scales, but linking these scales is necessary to quantify the mechanisms of transmission and assess population-scale declines.
2. We built a model connecting within-hibernaculum disease dynamics of little brown bats to regional-scale dispersal, reproduction, and disease spread, including multiple plausible mechanisms of transmission.
3. We parameterized the model using the approach of …

A Ctenophore (Comb Jelly) Employs Vortex Rebound Dynamics And Outperforms Other Gelatinous Swimmers, Brad J. Gemmell, Sean P. Colin, John H. Costello, Kelly R. Sutherland

Integrative Biology Faculty and Staff Publications

Gelatinous zooplankton exhibit a wide range of propulsive swimming modes. One of the most energetically efficient is the rowing behaviour exhibited by many species of schyphomedusae, which employ vortex interactions to achieve this result. Ctenophores (comb jellies) typically use a slow swimming, cilia-based mode of propulsion. However, species within the genus Ocyropsis have developed an additional propulsive strategy of rowing the lobes, which are normally used for feeding, in order to rapidly escape from predators. In this study, we used high-speed digital particle image velocimetry to examine the kinematics and fluid dynamics of this rarely studied propulsive mechanism. This mechanism …

4dee—What's Next? Designing Instruction And Assessing Student Learning, Luanna Prevost, Amanda E. Sorensen, Jennifer H. Doherty, Diane Ebert-May, Bob Pohlad

Integrative Biology Faculty and Staff Publications

No abstract provided.

Multiscale Model Of Regional Population Decline In Little Brown Bats Due To White-Nose Syndrome, Andrew M. Kramer, Claire S. Teitelbaum, Ashton Griffin, John M. Drake

Integrative Biology Faculty and Staff Publications

1. The introduced fungal pathogen Pseudogymnoascus destructans is causing decline of several species of bats in North America, with some even at risk of extinction or extirpation. The severity of the epidemic of white-nose syndrome caused by P. destructans has prompted investigation of the transmission and virulence of infection at multiple scales, but linking these scales is necessary to quantify the mechanisms of transmission and assess population-scale declines.
2. We built a model connecting within-hibernaculum disease dynamics of little brown bats to regional-scale dispersal, reproduction, and disease spread, including multiple plausible mechanisms of transmission.
3. We parameterized the model using the approach of …

How Do Trait-Mediated Non-Lethal Effects Of Predation Affect Population-Level Performance Of Mosquitoes?, Karthikeyan Chandrasegaran, Steven A. Juliano

Faculty Publications – Biological Sciences

Non-lethal, trait-mediated effects of predation impact prey behavior and life-history traits. Studying how these effects in turn influence prey demography is crucial to understand prey life-history evolution. Mosquitoes are important vectors that claim several million lives every year worldwide by transmitting a range of pathogens. Several ecological factors affect life-history traits of both larval and adult mosquitoes, creating effects that cascade to population-level consequences. Few studies have comprehensively explored the non-lethal effects of predation and its interactions with resources and competition on larval, adult, and population traits of mosquitoes. Understanding these interactions is important because the effects of predation are …

Lagosinema Tenuis Gen. Et Sp. Nov. (Prochlorotrichaceae, Cyanobacteria): A New Brackish Water Genus From Tropical Africa, Sandra C. Akagha, Jeffrey R. Johansen, Dike I. Nwankwo, Kedong Yin

2019 Faculty Bibliography

A novel filamentous, nonheterocytous cyanobacterium was isolated from Lagos Lagoon, Nigeria. The isolate was <3.0 μm wide, untapered, with small rounded polar bodies (aerotopes or cyanophycin granules) visible at the crosswalls, and consequently fit the morphological description of Limnothrix planctonica. Although morphologically inseparable from that species, it was molecularly distant from that taxon, with genetic identities between the two taxa ranging 90.73–92.49%, a degree of separation typical of different genera. Both taxa, as well as Limnothrix rosea, are phylogenetically in the Prochlorotrichaceae, distant from the type species of Limnothrix, L. redekei, which is in the Pseudanabaenaceae. The isolate is herein described as Lagosinema tenuis gen. et sp. nov.

A Field-Based Survey Of Fluorescence In Tropical Tree Frogs Using An Led Uv-B Flashlight, Michelle E. Thompson, Ralph Saporito, Diego H. Ruiz-Valderrama4, Guido F. Medina-Rangel, Maureen A. Donnelly

2019 Faculty Bibliography

No abstract provided.

Alcohol Induced Bacterial Changes In The Setting Of Colitis, Paulius Kuprys

Dissertations

Inflammatory bowel diseases (IBD) affect a large number of individuals around the world. This group of diseases is largely composed of two types: Crohn's disease (CD) and ulcerative colitis (UC). Upon development of IBD, patients experience cyclical episodes of inflammation, known as flares. Flare induction appears to arise from multiple factors, which can also vary on a person-to-person basis. Alcohol has been shown to trigger IBD flares and onset, though the underlying mechanism has not been established.Defining factors of the IBD intestinal environment include an altered microbiome, bacterial infiltration of the intestinal epithelium, and increased leakage of proinflammatory bacterial byproducts. …

Utilization Of Homoplasy-Free Sine Markers To Resolve The Phylogeny Of Peromyscus Species, Alec Wroblewski

Senior Honors Theses and Projects

The Peromyscus genus consists of over 50 recognized species, providing a rare opportunity to study evolutionary mechanisms of mammalian speciation, which is enhanced by phylogenetic analyses. We propose utilizing short interspersed DNA elements (SINEs) to assess the evolutionary history of Peromyscus as these markers provide a "molecular fossil record" since shared genomic integrations of elements correspond to descent from common ancestors. We have identified "young" SINEs from sequences of P. aztecus to advance our study by assessing for the presence of elements at fourteen orthologous loci among twelve species, including three separate P. aztecus individuals, one of which was used …

Coaggregation Patterns And Surface Characteristics Of Lactobacillus Rhamnosus Gg Under Varying Nutrient Conditions, Amanda Rielinger

Senior Honors Theses and Projects

Lactobacillus rhamnosus GG (LGG) is one of the best studied probiotic organisms. The ability of probiotics to adhere to other microorganisms and the intestinal epithelium is thought to play a major role in their protective functions. Coaggregation is an important mechanism for biofilm formation by microorganisms. The goals of this study were to examine the ways in which nutrient variation affects intercellular interactions between LGG and other gut microbes and the hydrophobic character of LGG. We hypothesized that nutritional variation may affect the ability of LGG to coaggregate and form biofilms and thus affect its probiotic characteristics and ability to …

Characterization Of Reproductive Tumors In Caenorhabditis Elegans, Shanti Nicole Gunda Bernstein

Senior Honors Theses and Projects

Tumors are characterized by over-proliferation of cells. However, not all tumors behave the same or have the same effects on surrounding non-tumorous tissues. Using the model organism C. elegans, we established tumor rupture trends in tumorous animals of three different genotypes. The characteristics studied include the effect of a germline tumor on the distribution of intermediate filament proteins in the endotube of the intestine, rate of tumor rupture between the hermaphrodites of each genotype, and tumor nuclear morphology of males and hermaphrodites of two genotypes. We conclude that tumors in C. elegans behave differently among the genotypes studied and the …

Examination Of Behavioral Lateralizations In Juvenile Tarantulas In The Presence Of Prey Odors, Matthew Angelosanto

Senior Honors Theses and Projects

The functional and/or structural specialization of the left or right side of the brain (behavioral lateralization) has substantial impacts on the interactions an animal makes with other organisms and its surroundings. While this has been extensively shown throughout vertebrates, it has recently been demonstrated in various taxa of invertebrates. Despite this, its presence in arachnids, and specifically tarantulas, remains poorly understood. The purpose of this study was to determine whether behavioral lateralization is present in the juvenile tarantulas Pterinochilus murinus and Brachypelma albopilosum in response to prey odors. If behavioral lateralization was found, I aimed to detennine how it differed …

Strain-Specific Protein Interaction And Localization Of Two Strains Of Potato Yellow Dwarf Virus And Functional Domains Of Their Matrix Protein, Chanyong Jang

Theses and Dissertations--Plant Pathology

Potato yellow dwarf virus (PYDV) is the type species of the genus nucleorhabdovirus which is typified by its nucleotropic characters of the members. The virus accomplishes its replication and morphogenesis in the nuclei of infected cells. Two strains, Constricta strain (CYDV) and Sanguinolenta strain (SYDV) have been described at the level of vector-specificity. CYDV is vectored by Agallia constricta and SYDV is transmitted by Aceratagllia sanguinolenta. The full-length genome of CYDV was sequenced. The 12,792 nt antisense genome encodes seven open reading frames in the order of, nucleocapsid protein (N), unknown protein (X), phosphoprotein (P), movement protein (Y), matrix …

Effects Of Suv39h1 And Suv420h1/H2 On Programmed Genome Rearrangement In Petromyzon Marinus, Claire A. Scott

Oswald Research and Creativity Competition

The sea lamprey (Petromyzon marinus), diverged from the vertebrate lineage roughly 550 million years ago, prior to the evolution of several major morphological features such as jaws and paired fins/appendages. Lamprey therefore provides a comparative perspective that can be used to study the evolution of differences in genome regulation, including epigenetics and programmed genome rearrangement (PGR). Programmed genome rearrangement is a unique regulatory mechanism wherein specific genes are effectively turned off by completely eliminating their sequences from the genome. Through PGR, lamprey delete approximately 20% of their genome from all somatic cells, with these specific sequences being only …

Plant Hormone Signaling Lab Module, Olivia Snyder

Williams Honors College, Honors Research Projects

Course material for universities constantly needs updating and refinement. One area that required new material at The University of Akron was the Principles of Biology II course, specifically in the laboratory section. A new laboratory module was created and centered around hormone signaling in Arabidopsis thaliana. Brassinosteroid mutants were used to show students the event hormones had on plants. Students were to test root lengths by completing growth plate analysis.

The Caricomp Network Of Caribbean Marine Laboratories (1985–2007): History, Key Findings, And Lessons Learned, Jorge Cortes, Hazel A. Oxenford, Brigitta I. Van Tussenbroek, Eric Jordan-Dahlgren, Aldo Croquer, Carolina Bastidas, John C. Ogden

Integrative Biology Faculty and Staff Publications

Caribbean Coastal Marine Productivity (CARICOMP) was a basin-wide cooperative, international network of marine laboratories established in 1985. Recognizing major trends of change in coastal ecosystems and the importance of the linkages among them, our goal was to monitor synoptically with standardized methods the physical environment and to document trends in measures of the structure and functioning of coral reefs, seagrasses and mangroves. Between 1985 and 1993, the CARICOMP Steering Committee established a data management center and wrote a methods manual. Marine laboratories joined the program by appointing a Site Director and signing an agreement specifying the cost sharing and responsibilities …

Comparison Of Dna Methylation In Vibrio Vulnificus Cells Grown In Human Serum With Those Grown In Seawater, James W. Conrad, Valerie J. Harwood

Integrative Biology Faculty and Staff Publications

The chromosomal methylation statuses of the highly virulent Vibrio vulnificus strain CMCP6 grown in human serum and in seawater are compared here. Growth in seawater resulted in ∼4 times as much methylation as that in human serum, primarily N⁴-methylcytosines.