Biology Commons^™

Genomic Signatures Of Cooperation And Conflict In The Social Amoeba, Elizabeth A. Ostrowski, Yufeng Shen, Xiangjun Tian, Richard Sucgang, Huaiyang Jiang, Jiaxin Qu, Mariko Katoh-Kurasawa, Debra A. Brock, Christopher Dinh, Fremiet Lara-Garduno, Sandra L. Lee, Christie L. Kovar, Huyen H. Dinh, Viktoriya Korchina, Laronda Jackson, Shobha Patil, Yi Han, Lesley Chaboub, Gad Shaulsky, Donna M. Muzny, Kim C. Worley, Richard A. Gibbs, Stephen Richards, Adam Kuspa, Joan E. Strassmann, David C. Queller

Biology Faculty Research

• Molecular evolution analyses reveal the history of social conflict
• Genes that mediate social conflict show signatures of frequency-dependent selection
• Balanced polymorphisms suggest that cheating may be stable and endemic

Cooperative systems are susceptible to invasion by selfish individuals that profit from receiving the social benefits but fail to contribute. These so-called "cheaters" can have a fitness advantage in the laboratory, but it is unclear whether cheating provides an important selective advantage in nature. We used a population genomic approach to examine the history of genes involved in cheating behaviors in the social amoeba Dictyostelium discoideum, testing whether these genes experience …

Complete Genome Sequence Of Listeria Monocytogenes Strain Dpc6895, A Serotype 1/2b Isolate From Bovine Raw Milk, Aidan Casey, Aidan Coffey, Et. Al.

Department of Biological Sciences Publications

Listeria monocytogenes is a foodborne pathogen and is the causative agent of listeriosis among humans and animals. The draft genome sequence of L. monocytogenes DPC6895, a serotype 1/2b strain isolated from the raw milk of a cow with subclinical bovine mastitis, is reported.

Entomophilic Nematode Diversity And Distribution In Beaver Dam Wash Area, Westen Achibald, Dr. Byron Adams

Journal of Undergraduate Research

The Beaver Dam Wash National Conservation Area is considered an important biodiversity hotspot for the Western United States. The wash is an ecotone on the Northeastern edge of the Mojave Desert and is directly adjacent to both the Colorado Plateau and the Great Basin. Thus, this area contains various species of flora and fauna from each of the surrounding biomes. Prior research of the Beaver Dam Wash has documented high aboveground biodiversity for a desert ecosystem however no research has been conducted on belowground diversity. For this reason we chose to characterize the diversity and distribution of entomophilic nematodes, as …

Importance Of Rare Genetic Variants In Alzheimer’S Disease (Ttc3), Devan Bursey, Dr. John S. K. Kauwe

Journal of Undergraduate Research

Alzheimer’s is a neurodegenerative disease caused by the formation of amyloid plaques and neurofibrillary tangles. Most current research on Alzheimer’s disease has focused on using genome-wide association studies to identify common genetic variants however; past research has shown that rare genetic variants play an important role in the development of Alzheimer’s disease. For example, studies have shown that rare genetic variants in APP, PSEN1, and PSEN2 drastically increase an individual’s risk for Alzheimer’s disease (Tanzi). My research focused on specific rare genetic variant in the TTC3 gene (S1966X). This rare variant has a point mutation that causes a premature stop …

Replication Of Gene-Gene Interactions In Large Alzheimer Disease Dataset, Kevin Boehme, Dr. John "Keoni" Kauwe

Journal of Undergraduate Research

Alzheimer’s disease (AD) is a common and complex neurodegenerative disease. It is the most common cause of dementia and is characterized by the accumulation of amyloid plaques and neurofibrillary tangles. To date, many genetic loci have been found that modify AD risk, but collectively, they explain only a fraction of the heritability of the disease. It is hypothesized that rare variants with large effects as well as epistatic interactions account for much of the unexplained heritability in AD.

The Emerald Ash Borer: Beautifully Deadly, Preston Arnold, Dr. S. M. Bybee, Dr. N. P. Lord

Journal of Undergraduate Research

The Jewel Beetles (Coleoptera: Buprestidae) contain ~15,000 of the most stunning yet least understood species in the animal kingdom (Fig. 1; Bellamy and Nelson, 2002). Although it is the 8th largest beetle family and contains many species of biological interest and economic importance, the family is poorly studied. To date, only one molecular phylogeny has been published for the family, and the six subfamilial classifications are still in flux (Evans et al. 2014). Of particular interest within the family Buprestidae is the Emerald Ash Borer; (EAB; Agrilus planipennis) a destructive pest of great economic importance (Fairmare). The EAB was …

Retinoic Acid Regulation Of Aromatase Expression In The Ovary, Sarah Persaud

College of Science and Health Theses and Dissertations

Retinoic acid is the active derivative of vitamin-A in the body. Retinoic acid is essential in normal embryonic development, and studies from the Kipp laboratory have also demonstrated its importance in the developing ovary. Aromatase, encoded by the gene Cyp19a1, is an enzyme that converts androgens to estrogens, and is primarily expressed in the granulosa cells of the ovary. Previous studies have suggested that retinoic acid influences aromatase expression in a few different tissue types; however, how retinoic acid may regulate aromatase expression in the ovary is not known. Therefore, the purpose of this study was to examine the role …

Specific Intensity Direct Current (Dc) Electric Field Improves Neural Stem Cell Migration And Enhances Differentiation Towards Βiii-Tubulin+ Neurons, Huiping Zhao, Amanda Steiger, Mitch Nohner, Hui Ye

Biology: Faculty Publications and Other Works

Control of stem cell migration and differentiation is vital for efficient stem cell therapy. Literature reporting electric field–guided migration and differentiation is emerging. However, it is unknown if a field that causes cell migration is also capable of guiding cell differentiation— and the mechanisms for these processes remain unclear. Here, we report that a 115 V/m direct current (DC) electric field can induce directional migration of neural precursor cells (NPCs). Whole cell patching revealed that the cell membrane depolarized in the electric field, and buffering of extracellular calcium via EGTA prevented cell migration under these conditions. Immunocytochemical staining indicated that …

Ecological, Localization And Functional Analysis Of Two Lysosomal Enzymes In Dictyostelium Discoideum, Sanaa Talib Jawed

Theses and Dissertations

Dictyostelium discoideum is a primitive eukaryote that has recognized useful in studying various aspects of lysosomal enzymes as well as development since it can differentiate from unicellular amoebae into a multicellular.In this study, we investigated the localization, ecological and molecular function of two lysosomal enzymes, hexosaminidase (NagA) and,,-glucosidase (GluA) proteins, by overexpressing the genes encoding them in D. discoideum. Separate cell-lines overexpressing a GFP-tagged versions of the full length DdNagA gene (GFP-NagA), mutant version of the NagA gene (GFP-NagA (N214S)), a GFP-tagged version of the full length DdGluA gene (GFP-GluA) and a mutant version of first 83 amino acids DdGluA …

Behavioral Immunity Suppresses An Epizootic In Caribbean Spiny Lobsters, Mark J. Butler Iv, Donald C. Behringer Jr., Thomas W. Dolan Iii, Jessica Moss, Jeffrey D. Shields

Biological Sciences Faculty Publications

Sociality has evolved in a wide range of animal taxa but infectious diseases spread rapidly in populations of aggregated individuals, potentially negating the advantages of their social interactions. To disengage from the coevolutionary struggle with pathogens, some hosts have evolved various forms of "behavioral immunity"; yet, the effectiveness of such behaviors in controlling epizootics in the wild is untested. Here we show how one form of behavioral immunity (i.e., the aversion of diseased conspecifics) practiced by Caribbean spiny lobsters (Panulirus argus) when subject to the socially transmitted PaV1 virus, appears to have prevented an epizootic over a large seascape. We …

Investigations Of Larval Pacific Lamprey Entosphenus Tridentatus Osmotic Stress Tolerance And Occurrence In A Tidally-Influenced Estuarine Stream, Gregory Shell Silver

Dissertations and Theses

Pacific lamprey is a culturally valuable species to indigenous people, and has significant ecological importance in freshwater and marine ecosystems. Over the past several decades, constrictions in range and reductions in Pacific lamprey abundance have been observed in Western North America, and may be indicators of range-wide declines. In the face of declining populations, the U.S. Fish and Wildlife Service has partnered with tribal, state, federal, and local entities to implement a regional Pacific lamprey conservation agreement aimed at reducing threats to Pacific lamprey and improving their habitats and population status. Research needs identified in the conservation agreement include assessing …

Neurotranscriptome Profiles Of Multiple Zebrafish Strains, Ryan Y. Wong, John Godwin

Biology Faculty Publications

Behavioral displays or physiological responses are often influenced by intrinsic and extrinsic mechanisms in the context of the organism's evolutionary history. Understanding differences in transcriptome profiles can give insight into adaptive or pathological responses.We utilize high throughput sequencing (RNA-sequencing) to characterize the neurotranscriptome profiles in both males and females across four strains of zebrafish (Danio rerio). Strains varied by previously documented differences in stress and anxiety-like behavioral responses, and generations removed from wild-caught individuals. Here we describe detailed methodologies and quality controls in generating the rawRNA-sequencing reads that are publically available in NCBI's Gene Expression Omnibus database (GSE61108).

The Effects Of Arginine Vasopressin On Maternal Behavior And Aggression In Peromyscus Californicus Mothers, Nathaniel Ng

Honors Projects

Research studies since the 1950s have shown that a chemical within the brain called arginine vasopressin (AVP) is associated with the modulation of many different social behaviors in mammals. Some of these behaviors are related to parenting, such as parental care initiation, aggression, social recognition, depression and anxiety. Understanding the physiology behind AVP regulation could allow for the creation of new therapies for treating human social disorders, such as using an AVP receptor antagonist to attenuate anxiety. This project examines how neural injections of AVP and an AVP receptor antagonist affect both maternal care and aggression in female Peromyscus californicus …

The Varying Role Of Water Column Nutrient Removal Along River Continua In Contrasting Landscapes, Alexander J. Reisinger, Jennifer L. Tank, Emma J. Rosi-Marshall, Robert O. Hall Jr, Michelle A. Baker

Biology Faculty Publications

Nutrient transformation processes such as assimilation, dissimilatory transformation, and sorption to sediments are prevalent in benthic zones of headwater streams, but may also occur in the water column. The river continuum concept (RCC) predicts that water column processes become increasingly important with increasing stream size. We predicted that water column nutrient uptake increases with stream size, mirroring carbon/energy dynamics predicted by the RCC. We measured water column uptake of ammonium ( NH+4NH4+ ), nitrate ( NO−3NO3− ), and soluble reactive phosphorus (SRP) in 1st through 5th order stream and river reaches (discharge: 50–68,000 L s−1) in three watersheds ranging from …

Factors Constraining The Reproductive Output Of Baptisia Alba Macrophylla, Ashley Morgan Hembrough

Theses and Dissertations

Baptisia alba macrophylla, a native, herbaceous perennial legume, produces inflorescences with a large number of flowers, yet matures relatively few fruits. We hypothesized that the number of seeds matured by B. alba macrophylla is maximized based on resource availability at each stage of development, but this optimal number is further compromised by extrinsic factors including pollen limitation and pre-dispersal seed predation by the weevils Apion rostrum and Tychius sordidus. To test this hypothesis, we conducted a field experiment at two sites: (i) the John English Prairie, located in Hudson, IL, and also (ii) the Sugar Grove Nature Center and Funks …

Analysis Of Plant Lignin Formation And Engineering For Biofuels Production, Deborah Lynn Petrik

Theses and Dissertations

ANALYSIS OF PLANT LIGNIN FORMATION AND ENGINEERING FOR BIOFUELS PRODUCTION

Deborah L. Petrik

149 Pages August 2015

Grasses such as switchgrass and Miscanthus are attractive feedstock candidates for second generation biofuels because they are perennials that can grow on less fertile or "marginal" lands not used for food crops, require little fertilizer and modest pest and disease management, and are not a human food source. Releasing the energy potential contained in plant-based cellulosic material requires either conversion to a liquid biofuel such as ethanol or burning. Thus, much of the current research focuses on not only understanding grass development as …

Modeling Mammalian Carboxypeptidase O Expression Patterns With The Thirteen-Lined Ground Squirrel (Ictidomys Tridecemlineatus), Christian Bardan, Peter Lyons

Posters, Presentations, and Papers

Carboxypeptidase O (CPO) is a protease that cuts acidic amino acids from the carboxyl terminus of a substrate protein. Besides its potential digestive application, not much else is known about its other activities in the body. This study aims to describe the expression pattern of CPO using the thirteen-lined ground squirrel as a model mammalian system. Thus far we have sampled tissue from one ground squirrel and analyzed those samples via Western blot. Immunoreactive bands likely to be CPO (molecular weight approximately 42 kDa) were seen in kidney, liver, and small intestine tissue samples. Further investigation will include immunohistochemical analysis.

The Effect Of Varying Sound Intensities On Phonotactic Selectivity In Female Acheta Domesticus, Re'jeanne Greene, Benjamin Navia Ph.D.

Posters, Presentations, and Papers

Female cricket Acheta domesticus recognize and respond to the call of the conspecific male by walking towards it (phonotaxis). Such phonotactic response has been described as selective, e. g. females are more likely to respond phonotactically to calls with syllable periods typical of the males’ calling song than they are to respond to calls with unattractive syllable periods (Stout et al., 1983). A previous study by Popov and Shuvalov (1977) concluded that phonotaxis can be altered by internal and external conditions. One internal condition that can modify selective phonotaxis is age (Henley et al. 1992; Stout et al. 2010). …

Plant Community Associations Of Two Invasive Thistles, Emily S.J. Rauschert, Katriona Shea, Sarah Goslee

Biological, Geological, and Environmental Faculty Publications

In order to combat the growing problems associated with biological invasions, many researchers have focused on identifying which communities are most vulnerable to invasion by exotic species. However, once established, invasive species can significantly change the composition of the communities that they invade. The first step to disentangling the direction of causality is to discern whether a relationship with other vegetation exists at all. Carduus nutans and C. acanthoides are similar invasive thistles, which have caused substantial economic damage worldwide. We assessed the associations between the thistles and the standing flora in four sites in central Pennsylvania in which they …

Characterizing The Neurotranscriptomic States In Alternative Stress Coping Styles, Ryan Y. Wong, Melissa S. Lamm, John Godwin

Biology Faculty Publications

Background: Animals experience stress in many contexts and often successfully cope. Individuals exhibiting the proactive versus reactive stress coping styles display qualitatively different behavioral and neuroendocrine responses to stressors. The predisposition to exhibiting a particular coping style is due to genetic and environmental factors. In this study we explore the neurotranscriptomic and gene network biases that are associated with differences between zebrafish (Danio rerio) lines selected for proactive and reactive coping styles and reared in a common garden environment.

Results: Using RNA-sequencing we quantified the basal transcriptomes from the brains of wild-derived zebrafish lines selectively bred to exhibit the proactive …

Suspension Model For Blood Flow Through A Tapering Catheterized Inclined Artery With Asymmetric Stenosis, Devajyoti Biswas, Moumita Paul

Applications and Applied Mathematics: An International Journal (AAM)

We intend to study a particle fluid suspension model for blood flow through an axially asymmetric but radially symmetric mild stenosis in the annular region of an inclined tapered artery and a co-axial catheter in a suitable flow geometry has been considered to investigate the influence of velocity slip at the stenotic wall as well as hematocrit, shape parameter. The model also includes the tapering effect and inclination of the artery. Expressions for the flow variables have been derived analytically and their variations with various flow parameters are represented graphically. The results for the different values of the parameters involved …

Mathematical Modeling And Analysis Of Leukemia: Effect Of External Engineered T Cells Infusion, Manju Agarwal, Archana S. Bhadauria

Applications and Applied Mathematics: An International Journal (AAM)

In this paper, a nonlinear model is proposed and analyzed to study the spread of Leukemia by considering the effect of genetically engineered patients T cells to attack cancer cells. The model is governed by four dependent variables namely; naive or susceptible blood cells, infected or dysfunctional blood cells, cancer cells and immune cells. The model is analyzed by using the stability theory of differential equations and numerical simulation. We have observed that the system is stable in the local and global sense if antigenicity rate or rate of stimulation of immune cells is greater than a threshold value dependent …

Population Structure Of Mitochondrial Genomes In Saccharomyces Cerevisiae, John F. Wolters, Kenneth Chiu, Heather L. Fiumera

Biological Sciences Faculty Scholarship

Background: Rigorous study of mitochondrial functions and cell biology in the budding yeast, Saccharomyces cerevisiae has advanced our understanding of mitochondrial genetics. This yeast is now a powerful model for population genetics, owing to large genetic diversity and highly structured populations among wild isolates. Comparative mitochondrial genomic analyses between yeast species have revealed broad evolutionary changes in genome organization and architecture. A fine-scale view of recent evolutionary changes within S. cerevisiae has not been possible due to low numbers of complete mitochondrial sequences.

Results: To address challenges of sequencing AT-rich and repetitive mitochondrial DNAs (mtDNAs), we sequenced two divergent S. …

Mathematical Model: Comparative Study Of Thermal Effects Of Laser In Corneal Refractive Surgeries, Gokul Kc, Dil B. Gurung, Pushpa R. Adhikary

Applications and Applied Mathematics: An International Journal (AAM)

Lasers have been widely used in ophthalmology. Refractive errors are some of the most common ophthalmic abnormalities worldwide. Laser refractive surgery was developed to correct refractive errors myopia, hyperopia and astigmatism. Two types of laser surgical techniques: lamellar and thermal are available to reshape the corneal curvature. Ultraviolet (UV) emitting argon fluoride (ArF) excimer laser is used to sculpt cornea in lamellar procedures, whereas, infrared (IR) emitting holmium yttrium aluminum garnet (Ho: YAG) laser is used to shrink cornea in thermal procedure. Tissue heating is common in all types of laser surgical techniques. Hence, in this paper, a finite element …

Data From: Migration And The Evolution Of Sexual Dichromatism: Evolutionary Loss Of Female Coloration With Migration Among Wood-Warblers, Richard K. Simpson, Michele A. Johnson, Troy G. Murphy

Biology Faculty Research

No abstract provided.

Questionable Validity Of The Catheter-Associated Urinary Tract Infection Metric Used For Value-Based Purchasing, Lindsay E. Calderon, Kevin T. Kavanagh, Mara K. Rice

Biological Sciences Faculty and Staff Research

Catheter-associated urinary tract infections (CAUTIs) occur in 290,000 US hospital patients annually, with an estimated cost of $290 million. Two different measurement systems are being used to track the US health care system's performance in lowering the rate of CAUTIs. Since 2010, the Agency for Healthcare Research and Quality (AHRQ) metric has shown a 28.2% decrease in CAUTI, whereas the Centers for Disease Control and Prevention metric has shown a 3%-6% increase in CAUTI since 2009. Differences in data acquisition and the definition of the denominator may explain this discrepancy. The AHRQ metric analyzes chart-audited data and reflects both catheter …

Introduction Next Contents Vol 63(4) Global Research On Ultramafic (Serpentine) Ecosystems (8th International Conference On Serpentine Ecology In Sabah, Malaysia), Antony Van Der Ent, Nishanta Rajakaruna, Robert Boyd, Guillaume Echevarria, Rimi Repin, Dick Williams

Biological Sciences

Since 1991, researchers from approximately 45 nations have participated in eight International Conferences on Serpentine Ecology (ICSE). The ICSE conferences are coordinated by the International Serpentine Ecology Society (ISES), a formal research society whose members study geological, pedological, biological and applied aspects of ultramafic ecosystems worldwide. These conferences have provided an international forum to discuss and synthesise multidisciplinary research, and have provided opportunities for scientists in distinct fields and from different regions of the world to conduct collaborative and interdisciplinary research. The 8th ICSE was hosted by Sabah Parks in Malaysia, on the island of Borneo, and attracted the largest …

West Coast Deep Sea Crustacean Resources Harvest Strategy : 2015 – 2020 : Version 1.0 : West Coast Deep Sea Crustacean Managed Fishery, Department Of Fisheries

Fisheries Management Papers

No abstract provided.

Harvest Strategy Policy And Operational Guidelines For The Aquatic Resources Of Western Australia, Department Of Agriculture And Food, Western Australia

Fisheries Management Papers

No abstract provided.

On The Stability Of A Three Species Syn-Eco-System With Mortality Rate For The Third Species, B. H. Prasad

Applications and Applied Mathematics: An International Journal (AAM)

The system comprises of a commensal (S₁) common to two hosts S₂ and S₃ with mortality rate for the host (S₃). Here all the three species posses limited resources. The model equations constitute a set of three first order non-linear simultaneous coupled differential equations. Criteria for the asymptotic stability of all the eight equilibrium states are established. Trajectories of the perturbations over the equilibrium states are illustrated. Further the global stability of the system is established with the aid of suitably constructed Liapunov’s function and the numerical solutions for the growth rate equations are …