Biology Commons^™

Revealing Biotic Diversity: How Do Complex Environments Influence Human Schistosomiasis In A Hyperendemic Area, Martina Rose Laidemitt

Biology ETDs

Human schistosomiasis is one of the great neglected tropical diseases (NTDs) of our time with more than 206 million individuals infected and more than 90% of those infected reside in Sub-Saharan Africa (WHO 2017). Chemotherapy based control programs play an essential role in contributing to the elimination of human schistosomiasis; however, there is an increasing consensus that chemotherapy needs to be supplemented by other means if interruption of transmission and elimination are to be achieved. Given this situation, the focus of this dissertation was to better understand transmission dynamics in a hyperendemic setting in western Kenya and to find alternative …

Physical Processes Dictate Early Biogeochemical Dynamics Of Soil Pyrogenic Organic Matter In A Subtropical Forest Ecosystem, Jason Stuart, Russell Anderson, Patrick Lazzarino, Kevin A. Kuehn, Omar R. Harvey

Faculty Publications

Quantifying links between pyOM dynamics, environmental factors and processes is central to predicting ecosystem function and response to future perturbations. In this study, changes in carbon (TC), nitrogen (TN), pH, and relative recalcitrance (R50) for pineand cordgrass-derived pyOM were measured at 3–6 weeks intervals throughout the first year of burial in the soil. Objectives were to (1) identify key environmental factors and processes driving early-stage pyOM dynamics, and (2) develop quantitative relationships between environmental factors and observed changes in pyOM properties. The study was conducted in sandy soils of a forested ecosystem within the Longleaf pine range of the United …

Transcending The Cell Fate Stereotype: Cell Penetrating Peptide Technology Helps Induce Pluripotency In Multiple Cell Types, Kelsey Clearman

Master of Science in Integrative Biology Theses

Induced pluripotent stem cells (iPSCs) are one of the most promising new technologies in the field of regenerative medicine. iPSCs can be generated directly from a patient’s own fibroblast cells then converted into any cell type, thus overcoming challenges associated with embryonic stem cells and graft-vs-host disease that result from current methods. Generation of iPSCs from fibroblasts is traditionally accomplished by ectopic expression of four key transcription factors (TFs): Oct4, Sox2, Klf4, and c-Myc also known as OSKM. These TFs have been shown to be involved in maintaining pluripotency and inhibiting embryonic stem (ES) cell differentiation. Reprogramming fibroblasts into iPSCs …

Exploring The Phenotypic Consequences Of Tissue Specific Gene Expression Variation Inferred From Gwas Summary Statistics, Alvaro N. Barbeira, Scott P. Dickinson, Rodrigo Bonazzola, Jiamao Zheng, Heather E. Wheeler, Jason M. Torres, Eric S. Torstenson, Kaanan P. Shah, Tzintzuni Garcia, Todd L. Edwards, Eli A. Stahl, Laura M. Huckins, Gtex Consortium, Dan L. Nicolae, Nancy J. Cox, Hae Kyung Im

Biology: Faculty Publications and Other Works

Scalable, integrative methods to understand mechanisms that link genetic variants with phenotypes are needed. Here we derive a mathematical expression to compute PrediXcan (a gene mapping approach) results using summary data (S-PrediXcan) and show its accuracy and general robustness to misspecified reference sets. We apply this framework to 44 GTEx tissues and 100+ phenotypes from GWAS and meta-analysis studies, creating a growing public catalog of associations that seeks to capture the effects of gene expression variation on human phenotypes. Replication in an independent cohort is shown. Most of the associations are tissue specific, suggesting context specificity of the trait etiology. …

Characterizing Nab2 Phosphorylation And Its Role In Regulating Egr Transcription Factors, Kimberly Abt

Honors Program Theses and Projects

The early growth response (Egr) family of transcription factors is composed of four members Egr1-4, which play roles in various cell behaviors including proliferation, apoptosis, and differentiation in a cell type and stimulus specific manner. Roles for Egr1-3 are especially well documented in the nervous system: Egr 1 and 3 regulate expression of genes involved in synaptic plasticity and long term potentiation, Egr2 contributes to hindbrain development and peripheral nerve myelination, and Egr 1 and 2 also contribute to the transcriptional network that drives neuronal differentiation in PC12 cells. However, the mechanisms that regulate Egr activity are not fully understood. …

Studying Planarian Regeneration Aboard The International Space Station Within The Student Space Flight Experimental Program, Vista Ssep Mission 11 Team, D. Hagstrom, C. Bartee, Eva-Maria S. Collins

Biology Faculty Works

The growing possibilities of space travel are quickly moving from science fiction to reality. However, to realize the dream of long-term space travel, we must understand how these conditions affect biological and physiological processes. Planarians are master regenerators, famous for their ability to regenerate from very small parts of the original animal. Understanding how this self-repair works may inspire regenerative therapies in humans. Two studies conducted aboard the International Space Station (ISS) showed that planarian regeneration is possible in microgravity. One study reported no regenerative defects, whereas the other study reported behavioral and microbiome alterations post-space travel and found that …

Morphological Traits As Indicators Of Sexual Dimorphism In Prairie Rattlesnakes (Crotalus Viridis), Colleen Rothe-Groleau, Claudia M. Rauter, James D. Fawcett

Transactions of the Nebraska Academy of Sciences and Affiliated Societies

As humans encroach into areas inhabited by predators, the potential of human-predator confrontations increases and the predators become regarded as dangerous pests. Predators exert a measure of population control over pest species such as small rodents, as well as limit the quantity and scope of diseases (e.g. spread of Hantavirus by these prey species). Control of these small rodent pest species can be aided by conserving and managing their predators like rattlesnakes (Crotalus spp). Management of any population requires detailed information on population composition and the ability to determine the key information (especially age and sex) for each individual …

Same-Sex Marriage And The Baby Carriage: A Post-Obergefell Analysis Of Art Funding For Same-Sex Couples In The United States, Charmaine Mech

Georgia Journal of International & Comparative Law

No abstract provided.

Biosemiotics As An Argument For The Recontextualization Of Biological Discoveries: A Critical Analysis Of The Biosemiotic Model Of Marcello Barbieri., Augustus Morrissey Snyder

Senior Honors Projects, 2010-2019

The primary purpose of this project was to investigate and explain the philosophical approach of biosemiotics to understanding living systems in contrast to the current scientific paradigm. Secondary goals were to evaluate the potential merits and relevance of this approach to biology and to introduce such a topic for discussion to biologists in a formal academic setting. My method consisted of critical textual analysis supplemented by analogy and biological examples where appropriate. In general, contemporary biosemiotics argues for a teleologic recontextualization of biological discoveries in practice and education. This is accomplished in a sophisticated fashion through the application and modification …

Antimicrobial Activity Of Novel Cationic Amphiphiles, Melanie Kusakavitch

Senior Honors Projects, 2010-2019

This project focused on the development of amphiphiles in order to prevent hospital-acquired infections before they have a chance to enter the host, thereby reducing the need for antibiotics. The antibiotic resistance crisis of the 21st century is a dangerous epidemic with global consequences. Therefore, there is a desperate need for novel approaches in antimicrobial research. This would decrease the overall length of stay in hospitals and costs associated with such a stay. In this study, tetracationic amphiphiles with two 12-carbon chains and an aliphatic linker were studied. The MIC value of each amphiphile and strain pair was determined and …

Muscle Synergies And How They Contribute To The Movement Of The Tail During The Nociceptive Withdrawal Response In The Rat’S Tail, Hasti Izadpanah

Senior Honors Projects, 2010-2019

Noxious stimuli can evoke the nociceptive withdrawal response (NWR), which protects the affected part of the body from injury. The rat’s tail, because of the large number of joint (n=84) and muscle (n=300) degrees of freedom, may present a computational challenge to the central nervous system. Previous studies have revealed that synergies act to reduce the number of degrees of freedom across diverse movements in a variety of animals; however, there is little information in mammals on synergistic control of the tail. The long-term specific aim of this project is to test the hypothesis that during the NWR muscle synergies …

Muc4 Based Immunotherapy For Pancreatic Cancer, Kasturi Banerjee

Theses & Dissertations

Pancreatic Cancer (PC) is a lethal disease claiming approximately 45000 lives in the US in 2018, and it establishes an elaborate immunosuppressive tumor microenvironment that aids in disease pathogenesis. Immunotherapy has emerged as a strategy to target tumor cells by reprogramming patient’s immune system. Challenges present in PC immunotherapy are: i) identifying a tumor-associated antigen that could be targeted, ii) identifying adjuvants that could efficiently deliver antigens, iii) eliciting robust anti-tumor responses and iv) overcoming peripheral tolerance and immunosuppression elicited by the tumor.

Firstly, we detected circulating autoantibodies to MUC4 present in PC patients and observed that IgM autoantibodies to …

Reconstruction Of The Tail Nociceptive Withdrawal Response From Combinations Of Movement Primitives Associated With Individual Muscles In The Rat, Justin Nguyen

Senior Honors Projects, 2010-2019

Abstract

One type of involuntary movement is the nociceptive withdrawal response (NWR), in which mammals move a part of their body away from noxious, or tissue damaging, stimuli. Previous studies have evoked the limb NWR in diverse animals such as cats, frogs, and humans. However, there is minimal information on how complex movement arising from numerous muscles and joints, such as in the tail of the rat, is effectively coordinated.

The specific aim was to identify the contribution of movement from individual extrinsic muscles to the tail NWR utilizing a new technique. From previous studies, extrinsic muscles in the pelvis …

Connexin32: Sorting, Endocytosis And Assembly, Anuttoma Ray

Theses & Dissertations

Gap junctions (GJ)s are conglomeration of several cell-cell channels at cell-to-cell contact sites involved in the direct intercellular exchange of small growth regulatory molecules. Defects in assembly of GJ-forming proteins, called connexins (Cxs), are observed in many cancers, yet the molecular basis of this defect remains unknown. Connexin32 (Cx32) is expressed by the polarized cells in epithelia. The carboxyl-terminal tail (CT) of Cx32, although not required to initiate GJ formation, orchestrates several aspects of GJ dynamics, function and growth. Our studies have discovered that the CT of Cx32 harbors a tyrosine-based [YXXØ]-type and two dileucine-based [DE]XXXL[LI]-type motifs, which govern the …

Inventory Of The Genus Craterellus Persoon From Kigoma Region, Tanzania, Donatha D Tibuhwa

Tanzania Journal of Science

There is scanty knowledge on macro fungi diversity in Kigoma region. Bioprospecting survey was undertaken in Miombo woodlands, Kigoma region of Tanzania that has never been explored. The survey sought to conduct an inventory of Craterellus Persoon. Conventional taxonomic techniques were used during the survey to characterize the collected materials. Both macro and micro morphological features including basidiocarp size, colour, shape, spore size and print colour were examined. High diversity of reputed macrofungi was observed. This study presents a preliminary inventory of the genus Craterellus Persoon in the country. Three species were described; two namely Craterellus cornucopioides (Linnaeus) Persoon and …

The Influence Of Agricultural Activities On The Diversity Of Rodents In Kindoroko Forest Reserve And Surrounding Areas, North Pare Mountains, Tanzania, Remmy Lema, Flora J Magige

Tanzania Journal of Science

The patterns of richness, diversity and similarity in rodent communities in agricultural areas and in adjacent Kindoroko Forest Reserve in the North Pare Mountains, Tanzania were assessed. By using a capture-mark-recapture method, 289 individuals of nine rodent species in March and May 2011 were captured. Seven species were recorded in agricultural area and 5 species in the Forest Reserve. Multimammate Rat (Mastomys natalensis) was abundant in agricultural area while soft-furred mouse (Praomys delectorum) was dominant in the Forest Reserve. Species diversity was greater outside than inside the forest, supporting results of earlier studies. Species similarity between the two habitats was …

Distribution Patterns Of Gastrointestinal Parasites In Vervet Monkeys (Chlorocebus Pygerythrus) At Gombe National Park, Tanzania, Jared S. Bakuza

Tanzania Journal of Science

Vervet monkeys at Gombe National Park in western Tanzania constitute a key component of the park’s ecosystem through interactions with other animals and people in the area. However, the parasite fauna of these animals has not been investigated. Thus, 21 faecal samples obtained from the animals in September 2010 were examined for parasites using formol-ethyl technique. The parasites observed included Trichuris spp., Physaloptera spp., hookworms and unidentified nematodes. While egg counts for unidentified nematodes did not vary with vervet monkey communities (z = 0.759, p = 0.448), other parasites were significantly higher among vervets at north of the park near …

In Vitro Antimicrobial Activity Of Extracts Of Some Plant Species Used In The Management Of Hiv/Aids In Tanzania, Cyprian Beda Mpinda, Debra Meyer, Sylvester Leonard Lyantagaye

Tanzania Journal of Science

Six plants species (Harungana madagascariensis, Sapium ellipticum, Teclea nobilis, Pseudospondias microcarpa, Rauvolfia vomitoria and Psorospermum febrifugum) which are used in managing HIV/AIDS in Bukoba, Tanzania were screened for their antimicrobial effect on the selected representatives of infectious bacterial and fungal species. Gram-positive bacteria Streptococcus lactis, Gram-negative bacteria Klebsiella pneumoniae and a fungus Candida albicans were tested for their sensitivity to the treatment with selected plants extracts using disc diffusion and broth dilution techniques. Extracts of S. ellipticum, P. febrifegum and P. microcarpa demonstrated growth inhibition of S. lactis with the MIC ranging from 3.2 to 100 mg/ml. The extracts of …

Diet Composition Of The Golden Jackal (Canis Aureus) In The Ngorongoro Crater, Tanzania, Se Temu, Cuthbert L Nahonyo, Pd Moehlman

Tanzania Journal of Science

The Ngorongoro crater is known for having the highest density of carnivores in the world. In the past, most of the research focused on large carnivores such as lions and spotted hyenas. Medium sized carnivores such as jackals have received very little attention and the information on these carnivores including their diet composition is limited. Diet composition of golden jackal(Canis aureus) was studied in the Ngorongoro crater from July 2014 to May 2015 covering both dry and wet seasons using focal animal observation (direct method) and  collection (and analysis) of faecal/scat samples from known individuals in the field (indirect method). …

Elucidating The Roles Of Lunatic Fringe In Pancreatic Ductal Adenocarcinoma, Prathamesh Patil

Theses & Dissertations

Pancreatic cancer is an aggressive form of cancer that is very difficult to detect, treat resulting in a high rate of mortality. Understanding the molecular basis of pancreatic cancer and identifying new molecular targets for designing therapeutic interventions is paramount for improving outcomes in this disease. Notch signaling is a vital developmental signaling pathway that has been implicated to play both oncogenic and tumor suppressive roles in pancreatic cancer. Previous studies from other groups have shown that O-linked glycosylation of Notch signaling plays a key role in the regulation of Notch signaling. Lunatic fringe (Lfng) is one of the glycosyltransferases …

Analysis Of Genes Encoded By A Chromosomal Insert In Rickettsia Philipii, Sydney A. Wright

Honors College Theses

Background: Spotted Fever group rickettsiae are obligate intracellular arthropod-borne bacteria. Rickettsiae are globally distributed yet typically confined to the distribution of their vector(s). Rickettsia rickettsii and Rickettsia philipii are closely related human pathogens endemic to the United States and cause similar febrile illness with differing morbidity and mortality. Genomic comparison found the presence of a 19 kilobase insert containing eleven genes in Rickettsia philipii. The functions of proteins encoded by this insert are speculated to affect virulence and pathogenicity.

Materials and Methods: Bioinformatic analysis was performed to identify functional motifs in four proteins encoded by the insert. Homologous proteins …

The Behavioral Response Of Mosquitoes To Different Snake Odors, Caitlyn E. Hicks

Honors College Theses

Due to it causing high mortality rates, Eastern Equine Encephalitis (EEEV) is considered to be one of the most medically important encephalitic viruses in the Eastern United States. In order to be able to control the transmission of this virus, understanding of vector behavior and feeding preferences is necessary. In this study, the response of Culex nigripalpus to different snake skin odors was tested to determine if this species of mosquito responded to particular snake species. Culex nigripalpus showed the greatest response to Copperhead (Agkistrodon contortrix) and Cottonmouth (A. piscivorus) snakes, as compared to other venomous …

Morphological Comparison Of Fourth-Instar Larvae From Various Populations Of Wyeomyia Smithii, Kendra D. Moore

Honors College Theses

Populations of pitcher plant mosquitoes, Wyeomyia smithii, have exhibited recent shifts in blood-feeding behavior, likely in response to changes in climate and food availability. A comparison of various morphological structures in fourth-instar larvae was conducted to investigate the hypothesis that geographic and temporal dietary differences are reflected in changes in organismal size.

Morpho: Expectations & Mutations, Lynda Bostrom

Masters Theses, 2010-2019

Morpho: Expectations & Mutations is a written document accompanying the culmination of my three years painting at a graduate level. The result of which is an autobiographical body of work navigating the tension of being a human with an invisible disease, while straining to understand Western societal constructs of women. I simultaneously reject these fairy tales as a standard recipe for happiness, yet identify with its visual language that is rooted in the vernacular of my generation. Redefining the elements I reject or embrace helps me to look beyond the boundaries of these constructs, and adopt an attitude of curiosity …

Potential Vectors Of Dog Heartworm, Dirofilaria Immitis, In Arkansas And Seasonal Transmission In The United States, Sofija Todorovic

Student Theses and Dissertations

Dirofilaria immitis (Leidy), is a mosquito-borne, parasitic filarid responsible for heartworm disease in vertebrates. A mosquito survey, focusing on diurnal species, was conducted from May to December 2016 to identify the prevalence of D. immitis in mosquitoes collected at residential entryways in Jonesboro, AR. Aedes albopictus (Skuse), a diurnal mosquito, was collected in low abundance (3.4%) with 16.7% mosquitoes positive for heartworm microfilariae. Dirofilaria immitis was observed in 11.2% of the total mosquitoes collected. The second study estimated the seasonality of heartworm disease in four high-risk US cities. Daily average and hourly temperatures were used to predict the presence of …

Water Quality And Freshwater Mussel Assemblages In The Strawberry River Watershed, Arkansas, Irene Sanchez Gonzalez

Student Theses and Dissertations

Contamination of freshwater resources is an environmental issue worldwide. Habitat alteration and degradation cause water quality decreases and loss of aquatic biodiversity. The Strawberry River in Northeast Arkansas is an example of a highly diverse watershed presenting water quality impairments due to siltation caused by land use alteration. This thesis provides a better understanding of water quality in the tributaries contributing to the Strawberry River and of the freshwater mussel biodiversity of the river. Overall, the Strawberry River tributaries do not exceed criteria assessment but show increased sediment and nutrient concentrations in more agriculturally intense areas. The diversity of freshwater …

Creating A Predictive Model For Flowering Of Virginia Orchid, Cypripedium Pubescens, Emily Horton

Undergraduate Theses and Capstone Projects

This research investigates the native Virginia orchid, Cyprepedium pubescens, or the large yellow lady-slipper. Researchers at Lynchburg College, located in central Virginia, collected orchid activity data over the span of nine years from 2006-2014. This data included the following information: when the first sprout appeared, the number of leaves, the number of flowers, and the number of flowers per each plant. Using collected data about nine orchids on the campus of Lynchburg College as a basis, we wanted create a model that would predict when we might see flowering on a yearly basis. Flowering is important because researchers are investigating …

Interstrand Crosslink Resistance In Escherichia Coli, Jedidiah D. Acott, Jessica M. Cole, Charmain Courcelle, Justin Courcelle

Student Research Symposium

8-methoxypsoralen is a photoactivated DNA-intercalating agent, which after absorbing two high-energy UVA photons, covalently binds pyrimidine bases on both DNA strands, to form an interstrand crosslink (ICL). These lesions completely block replication and transcription, and are widely used in chemotherapies; yet the mechanism by which they are processed remains poorly understood. In 1985, Ahmed and Holland reported an Escherichia coli mutant demonstrating hyper-resistance to ICL-inducing agents. The mutation was mapped to 57.2 minutes on the chromosome, and potentially encoded a 55-kDa protein that was induced as part of the SOS response. Although these genes remain unidentified, hscA and hscB map …

Waking Students Up With Explorations Of Metabolic Dormancy: A Pilot Study Of The Killifish Cure, Emma Goodwin, Daniel E. Zajic, Jason E. Podrabsky, Erin E. Shortlidge

Student Research Symposium

A national goal for education reform is to provide opportunities for all biology undergraduates to participate in research. Traditionally, undergraduates gain research experience by apprenticing in faculty-led research labs; however, only a fraction of undergraduates have access to these opportunities. Course-based Undergraduate Research Experiences (CUREs) are a type of laboratory course where students conduct experiments to answer relevant research questions, thus allowing undergraduates to gain authentic research experience at a large scale. To increase equity in opportunities for biology undergraduates to participate in authentic scientific research at Portland State University (PSU), we have designed and implemented a CURE to pilot …

Unique E3 Ligase Complexes Regulate Levels Of Cyclin E, Katia De Oliveira Rebola, Jeffrey Dean Simger

Student Research Symposium

Cyclin E is an evolutionarily conserved protein whose essential function is to promote the cell cycle transition from G1 to S phase. Cul3 is the main component of the pathway that controls Cyclin E ubiquitination, playing an important role in the normal cell cycle regulation in vivo. The binding between Cul3 and Cyclin E does not occur directly and requires a BTB domain protein to act as a substrate adaptor. The substrate linker responsible for this binding is known as RhoBTB3. Muf1, a largely uncharacterized protein of unknown function, is able to bind to RhoBTB3 directly indicating that it might …