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Prediction Of Local Quality Of Protein Structure Models Considering Spatial Neighbors In Graphical Models., Woong Hee Shin, Xuejiao Kang, Jian Zhang, Daisuke Kihara

Department of Biological Sciences Faculty Publications

Protein tertiary structure prediction methods have matured in recent years. However, some proteins defy accurate prediction due to factors such as inadequate template structures. While existing model quality assessment methods predict global model quality relatively well, there is substantial room for improvement in local quality assessment, i.e. assessment of the error at each residue position in a model. Local quality is a very important information for practical applications of structure models such as interpreting/designing site-directed mutagenesis of proteins. We have developed a novel local quality assessment method for protein tertiary structure models. The method, named Graph-based Model Quality assessment method …

Population Genetics Of The Giant Red Centipede Along The Appalachian Mountains, Kayla Elayne Ladner

Honors Theses

This study focused on population genetics of the giant red centipede, Scolopocryptops sexpinousus, in the Southern Appalachian Mountains. Two genetic markers were used—the mitochondrial COI gene, and the nuclear RNA Polymerase II gene. The goal of this study was to determine how many genetically distinct populations of this invertebrate species exist within the study area, and to understand the spatial distribution of genetic diversity within and among populations. I hypothesized several genetically distinct populations of S. sexpinosus would be detected because the complex topographic characteristics and historical climate cycles of the region are thought to limit movement of many forest …

Induction Of Haploid Plants In Citrus Through Gamma-Irradiated Pollen And Ascertainment Of Ovule Age For Maximum Recovery Of Haploid Plantlets, Manoj Kundu, Anil Dubey, Manish Srivastav, Surendra Kumar Malik

Turkish Journal of Biology

The present investigation was carried out for the induction of haploid plants in Citrus grandis through in situ parthenogenesis by pollination with gamma-irradiated pollen of C. limetta and C. sinensis, treated with 50, 100, 200, 300, and 400 Gy gamma ray doses followed by in vitro ovule culture. Ovule culture at 50 days after pollination (DAP) was found optimum for the maximum recovery of in vitro-raised plantlets as compared to 35 and 20 DAP. At 50 DAP, irrespective of the pollen parent, plantlet regeneration capacity decreased at 300 and 400 Gy irradiation treatment (0.62% and 0.60%, respectively) with maximum recovery …

A Computational Study Of Vegf Production By Patterned Retinal Epithelial Cell Colonies As A Model For Neovascular Macular Degeneration, Qanita Bani Baker, Gregory J. Podgorski, Elizabeth Vargis, Nicholas Flann

Biology Faculty Publications

Background: The configuration of necrotic areas within the retinal pigmented epithelium is an important element in the progression of age-related macular degeneration (AMD). In the exudative (wet) and non-exudative (dry) forms of the disease, retinal pigment epithelial (RPE) cells respond to adjacent atrophied regions by secreting vascular endothelial growth factor (VEGF) that in turn recruits new blood vessels which lead to a further reduction in retinal function and vision. In vitro models exist for studying VEGF expression in wet AMD (Vargis et al., Biomaterials 35(13):3999–4004, 2014), but are limited in the patterns of necrotic and intact RPE epithelium they can …

Studies On Development In Euphilomedes Ostracods: Embryology, Nervous System Development, And The Genetics Of Sexually Dimorphic Eye Development, Kristina Koyama

University of the Pacific Theses and Dissertations

Model organism studies have been fundamental in understanding evolutionary and developmental biology. However, non-model organisms present opportunities to study unique characteristics and as comparisons to model organisms, leading us toward broader and more relevant perspectives on diversity. The Euphilomedes genus of ostracods is an example of a non-model group with potential for evolutionary and developmental studies.

Ostracoda is an ancient, basally branching lineage of Crustaceans with a complete and prodigious fossil record. Despite the group’s promise for evolutionary studies, much remains unknown about the basic biology of this clade. There are a limited number of embryogenesis studies in Ostracoda; here, …

Recent Diatoms Reported From The Central United States: Register Of Taxa And Synonyms, Mark E. Eberle

Biological Sciences Faculty Publications

This list of diatoms summarizes information for more than 1000 taxa and synonyms reported in published accounts of collections made in the central United States, principally within the states of Kansas, Nebraska, and Oklahoma, but also including adjacent areas in eastern Colorado and western Missouri. The objective was to provide people working on diatom projects in this region with a base reference to help them assess the results of their research. Records from Master’s theses and references focused on fossil diatoms were not incorporated into this list. Specimens were not examined, so taxa presented here are those reported in the …

Discovery And Functional Implication Of Genetic Alterations Associated With Clonal Hematopoietic Expansion, Mingchao Xie

Arts & Sciences Graduate Student Theses and Dissertations

Cancers, including hematologic malignancies, arise as a result of the stepwise accumulation of mutations. Some early mutations that potentially initiate clonal expansion might exist in patients many years before they develop obvious disease symptoms. Therefore, identifying and characterizing these early mutations are critical to understanding the genetic basis of tumorigenesis. Here, we analyzed blood-derived DNA sequencing data from 2,728 individuals without apparent hematologic malignancies and identified 77 blood-specific mutations in 31 cancer-associated genes. Importantly, 83% of all mutations occurred in 19 genes that have been previously linked to hematological malignancies, such as DNMT3A, TET2, JAK2, and ASXL1. By investigating these …

Synthetic Ion Channels: A New Class Of Membrane Disruptor And Efflux Pump Inhibitor For The Recovery Of Antibiotic Potency, Mohit Bharatkumar Patel

Dissertations

Antibiotic resistance has become a world-wide health care crisis. In 2013 there were 50,000 deaths in U.S. and EU, associated with hospital acquired bacterial infections. This problem is exacerbated by the lack of new antibiotics in development. Here, we report that synthetic amphiphiles represent a new class of adjuvants that rescue antibiotic potency against multidrug resistant bacteria. Hydraphiles are amphiphiles, designed and synthesized in Gokel lab, that show many of the same properties as protein ion channels. Hydraphiles were previously shown to have antimicrobial activity against Escherichia coli, Bacillus subtilis and Saccharomyces cerevisiae. Here, we report that hydraphiles recover the …

How To Assess Your Cure: A Practical Guide For Instructors Of Course-Based Undergraduate Research Experiences, Erin Shortlidge, Sara Brownell

Biology Faculty Publications and Presentations

Integrating research experiences into undergraduate life sciences curricula in the form of course-based undergraduate research experiences (CUREs) can meet national calls for education reform by giving students the chance to “do science.” In this article, we provide a step-by-step practical guide to help instructors assess their CUREs using best practices in assessment. We recommend that instructors first identify their anticipated CURE learning outcomes, then work to identify an assessment instrument that aligns to those learning outcomes and critically evaluate the results from their course assessment. To aid instructors in becoming aware of what instruments have been developed, we have also …

Red Flour Beetle, Tribolium Castaneum, Development On Rice Fractions And Oviposition Preference, Brook A. Hale

Student Theses and Dissertations

The red flour beetle (RFB), Tribolium castaneum (Herbst), is a stored-product insect commonly found in rice mills. To understand how RFBs develop on different types of rice fractions occurring in a rice mill, I conducted three studies. I examined egg to adult development on nine rice fractions (rough rice, rice hulls, paddy rice dust, brown rice, rice bran, milled broken kernels, milled whole kernels, milled rice dust and rice flour) and identified brown rice, bran, milled kernels and rice flour were best for development. A second study examined neonate adult development using rice fractions and temperature as variables and found …

The Effects Of Drought On Diets Of Apex Predators In The South African Lowveld Inferred By Fecal Hair Analysis, Shelby Wade

Mahurin Honors College Capstone Experience/Thesis Projects

To properly manage offtake quotas and conservation efforts, Balule Nature Reserve (South Africa) instituted a study in 2014 to determine prey species selection by megapredators. In 2015, Balule Nature Reserve received about 190 mm less rainfall between the months of January and June than in 2014 (116 mm less than average). This study compares the diets of lions and hyaenas between 2014 and 2015. Prey species consumed were determined by fecal analysis, and results were compared to prey availability. Sixteen, 1 km2 plots were chosen from the 400 km2 Reserve. Between June and August 2015, we walked three, 1 km …

The Role Of Epidermal Enhancer 923 In The Chromatin Architecture And Transcriptional Regulation Of The Epidermal Differentiation Complex, Inez Oh

Arts & Sciences Graduate Student Theses and Dissertations

The epidermis covers the surface of the skin and provides a functional barrier across the entire body. Epidermal cells or keratinocytes proliferate in the innermost basal layer and migrate upwards into the suprabasal spinous and granular layers as they differentiate, and finally into the terminally differentiated outermost stratum corneum. Keratinocytes undergoing terminal differentiation are marked by tissue-specific concomitant expression of genes encoded in the Epidermal Differentiation Complex (EDC) locus. The EDC genes are organized into four gene families - S100, Sprr, Lce, and Flg-like, which are coordinately expressed upon activation of the terminal differentiation program in keratinocytes. The molecular mechanisms …

The Explorations Program: Benefits Of Single-Session, Research- Focused Classes For Students And Postdoctoral Instructors, Jeremy L. Hsu, Anna M. Wrona, Sarah E. Brownell, Waheeda Khalfan

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We present an update to Explorations, a program at Stanford University that allows undergraduates in an introductory biology course to explore specialized topics in the biological sciences while providing graduate students and postdoctoral scholars the unique opportunity to develop and teach single-session, research-focused classes. We provide an assessment of eight iterations of the program, using program attendance, student and instructor evaluations, senior exit surveys, course grades, and completion of undergraduate honors theses to assess the impact of our program on students and instructors. Students rated their experiences highly, and most reported that the program had a positive impact on their …

Assessment Of Behavior And Social Dynamics In A Newly-Forming Group Of Captive Western Lowland Gorillas, Sarah Murphey Huskisson

Graduate Theses

This study presents behavioral data of a recently-formed western lowland gorilla (Gorilla gorilla gorilla) group at Riverbanks Zoo and Garden in Columbia, South Carolina, from the initial stages of group formation through the first several months after introduction. The group consists of a male (19 years), two half-sisters (both 10 years), and an unrelated female (20 years). I collected 15-minute focal animal samples for three hours twice a week in two observation blocks, the first lasting from 7/17/15 to 9/11/15, and the second lasting from 10/30/15 to 1/3/16. A total of 99.25 observation hours were collected. It was predicted that …

Species-Recognition Program: A Computer-Assisted Approach To Recognizing Species, Steve Kelsch, Jeffrey Carmichael

Biology Faculty Publications

Species recognition is a crucial component for many types of biological studies. To that end, broadly trained students must be able to accurately identify many different types of organisms. Courses that focus on learning the names of different species traditionally rely on preserved specimens viewed during class or laboratory time. Unfortunately, reliance on preserved specimens comes with many challenges in providing students with an optimal learning experience. The curriculum activity described here uses a modified PowerPoint file (species-recognition program—SRP) as a means of helping students learn to recognize and identify fishes based on subtle visual cues. Our results indicate that …

Molecular Mechanisms Regulating Pathogen Defense: The Role Of Jmj3 In Arabidopsis Thaliana, Nelson Trysler

Renée Crown University Honors Thesis Projects - All

The Raina lab studies plant-pathogen interactions through genetics and molecular biology by using the model organism, Arabidopsis thaliana. A group of genes in A. thaliana, the Jumonji gene family, regulates gene expression by epigenetic mechanisms. Jumonji genes influence histone demethylation. Previous research in the Raina lab has shown that some Jumonji (JMJ) genes play a role in immune signaling in A. thaliana in response to pathogens. My project is to characterize JMJ3 gene, and see if there was any role that JMJ3 played in pathogen defense in A. thaliana.

The goal of my study was …

Evaluating College Biology Laboratory Accommodations For Students With Blindness And Visual Impairments, Barbara Rae Heard

All Theses And Dissertations

Studies show that active participation in science laboratory activities promotes student learning. However, students with blindness and visual impairments (BVI) often confront obstacles to active participation in the required activities of the college biology laboratory. Legislation requires institutions of higher education to provide accommodations for students with disabilities, yet the institutions must also maintain the academic integrity of their courses and programs. While college biology instructors provide specific accommodations, such as tactile models and audible devices, to enable active participation by students with BVI, they do so without research-supported guidelines for best practices. This mixed methods study sought to evaluate …

Section Abstracts: Biology

Virginia Journal of Science

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

Is Metabolism Goal-Directed? Investigating The Validity Of Modeling Biological Systems With Cybernetic Control Via Omic Data, Frank T. Devilbiss

Open Access Dissertations

Cybernetic models are uniquely juxtaposed to other metabolic modeling frameworks in that they describe the time-dependent regulation of cellular reactions in terms of dynamic "metabolic goals." This approach contrasts starkly with purely mechanistic descriptions of metabolic regulation which seek to explain metabolic processes in high resolution — a clearly daunting undertaking. Over a span of three decades, cybernetic models have been used to predict metabolic phenomena ranging from resource consumption in mixed-substrate environments to intracellular reaction fluxes of intricate metabolic networks. While the cybernetic approach has been validated in its utility for the prediction of metabolic phenomena, its central feature, …

The Effects Of Low Dam Removal And Kayak Run Installation On The Biodiversity Of Fish And Macroinvertebrates In The Great Miami River In Downtown Dayton, Ohio, Sarah Anne Stalder

Honors Theses

Five Rivers Metroparks and the Miami Conservancy District have made plans to remove the upper portion of the Monument Avenue low-head dam in downtown Dayton due to the hazard it poses for recreation on the river and its negative impact on water quality and biodiversity. The plans also include modifying the dam with “kayak drops” and the construction of a second kayak drop slightly upstream of the location of the current low dam to enhance recreational opportunities on the river. Typically, low dam removal alter the flow and depth of a river, especially above the dam in the impounded area …

Integrative Analyses Reveal Signaling Pathways Underlying Familial Breast Cancer Susceptibility, Stephen R. Piccolo, Laura M. Hoffman, Thomas Conner, Gajendra Shrestha, Adam L. Cohen, Jeffrey R. Marks, Leigh A. Neumayer, Cori A. Agarwal, Mary C. Beckerle, Irene L. Andrulis, Avrum E. Spira, Philip J. Moos, Saundra S. Buys, William Evan Johnson, Andrea H. Bild

Faculty Publications

The signaling events that drive familial breast cancer (FBC) risk remain poorly understood. While the majority of genomic studies have focused on genetic risk variants, known risk variants account for at most 30% of FBC cases. Considering that multiple genes may influence FBC risk, we hypothesized that a pathway‐based strategy examining different data types from multiple tissues could elucidate the biological basis for FBC. In this study, we performed integrated analyses of gene expression and exome‐sequencing data from peripheral blood mononuclear cells and showed that cell adhesion pathways are significantly and consistently dysregulated in women who develop FBC. The dysregulation …

Conversations With Gunanurang, Lawrence Smith

Landscapes: the Journal of the International Centre for Landscape and Language

Gunanurang (the Ord River) nurtured some of the original Australians productively for millennia. In less than 150 years, their relationship with the river valley and surrounding land was almost destroyed by the effects of the east Kimberley cattle industry commenced in the 1880s. The biological and archaeological surveys before and during the filling of the Lake Argyle dam were a belated attempt to understand what was being lost in the way of ecosystems and aboriginal sites. This short essay encapsulates the impact of the pastoral industry in the Ord valley.

Hydrodynamic Loading In Concomitance With Exogenous Cytokine Stimulation Modulates Differentiation Of Bovine Mesenchymal Stem Cells Towards Osteochondral Lineages, Stephen M. Goldman, Gilda A. Barabino

Publications and Research

Background: Mesenchymal stem cells (MSCs) are viewed as a having significant potential for tissue engineering and regenerative medicine therapies. Clinical implementation of MSCs, however, demands that their preparation be stable and reproducible. Given that environmental and bioprocessing parameters such as substrate stiffness, seeding densities, culture medium composition, and mechanical loading can result in undirected differentiation of the MSC population, the objective of this study was to systematically investigate how hydrodynamic loading influences the differentiation of bone marrow-derived mesenchymal stem cells (MSCs) towards the osteochondral lineages both in the presence and absence of exogenous, inductive factors.

Methods: Expanded bovine MSCs were …

The Effect Of In Vitro Cultivation On The Transcriptome Of Adult Brugia Malayi, Cristina Ballesteros, Lucienne Tritten, Maeghan O'Neill, Erica Burkman, Weam I. Zaky, Jianguo Xia, Andrew Moorhead, Steven A. Williams, Timothy G. Geary

Biological Sciences: Faculty Publications

Filarial nematodes cause serious and debilitating infections in human populations of tropical countries, contributing to an entrenched cycle of poverty. Only one human filarial parasite, Brugia malayi, can be maintained in rodents in the laboratory setting. It has been a widely used model organism in experiments that employ culture systems, the impact of which on the worms is unknown.

The Effect Of In Vitro Cultivation On The Transcriptome Of Adult Brugia Malayi, Cristina Ballesteros, Lucienne Tritten, Maeghan O’Neill, Erica Burkman, Weam I. Zaky, Jianguo Xia, Andrew Moorhead, Steven A. Williams, Timothy G. Geary

Biological Sciences: Faculty Publications

Infections with filarial worms cause serious physical impairment and affect tens of millions of people in tropical and subtropical countries. To better understand the biology and phar- macology of these parasites, Brugia malayi is often used as a model. This parasite can be maintained in the laboratory in Mongolian jirds, enabling researchers to test drugs in vivoand in vitro, among other studies. The effects of removing worms from their hosts and cul- turing them may affect many aspects of their physiology, including response to drugs, but the extent to which the worms undergo changes during culture has remained unknown. Using …

Lycium Barbarum L. (Goji Berry) Fruits Improve Anxiety, Depression-Like Behaviors, And Learning Performance: The Moderating Role Of Sex, Fatma Pehli̇van Karakaş, Hami̇t Coşkun, Kadi̇r Sağlam, Bi̇hter Gökçe Bozat

Turkish Journal of Biology

The aim of this research was to investigate the effects of the methanol extract obtained from Lycium barbarum fruits on anxiety, depression-like behaviors, and spatial memory in Wistar albino rats. A total of 28 rats were selected, randomly assigned to four experimental groups, and tested by means of the open field and elevated plus maze tests for anxiety-like behaviors, the forced swim test for depression-like behaviors, and the Morris water maze test for spatial memory. The findings demonstrated that in the open field, L. Barbarum-administered rats spent more time at the center and showed more mobility and velocity than controls. …

Underlying Mechanisms And Prospects Of Heart Regeneration, Gali̇p Servet Aslan, Dudu Gonca Misir, Fati̇h Kocabaş

Turkish Journal of Biology

Findings in the last decade suggest that there is a considerable amount of cardiomyocyte turnover in the human heart throughout life, albeit not sufficient for heart regeneration following myocardial infarctions. Only a few species are known to be remarkably efficient in cardiac regeneration. They restore lost cardiomyocytes via a process of cardiomyocyte dedifferentiation, which is followed by robust proliferation of cardiomyocytes and incorporation into the myocardium. Similarly, neonatal mice have been recently shown to regenerate their heart following myocardial injuries. Studies with a neonatal cardiac regeneration mouse model suggest that the major source of new cardiomyocytes is likely to be …

Histopathological And Biochemical Changes In The Liver, Kidney, And Bloodof Amphibians Intoxicated With Cadmium, Marcela Fátima Medina, Maria Elina González, Sandra Maria Roxana Klyver, Iris Maria Aybar Odstrcil

Turkish Journal of Biology

The worldwide decline in amphibian populations has made heavy metal pollution a subject of interest. The aim of this work was to analyze the effect of sublethal doses of cadmium (Cd) on the liver, kidney, and blood of Rhinella arenarum specimens. Serum markers indicative of hepatic injury (gamma glutamyltransferase, alkaline phosphatase, pseudo cholinesterase, and total cholesterol) and markers of renal dysfunction (blood urea nitrogen, serum creatinine, calcium, and glucose) showed variation in animals treated with a 0.5 mg/kg dose compared to controls. Histopathological images revealed alterations in the liver (hepatocyte ballooning and hyperplasia of Kupffer cells) and kidney (renal tubular …

The Confluence Of Philosophy And Biology: An Excavation Of Philosophical Issues In Molecular And Developmental Biology, Patrick Johnson Mendie, Emmanuel Bassey Eyo (Ph.D)

Journal of Health Ethics

Philosophical evaluations have played an influential role in the growth and development of molecular and developmental biology to ensure that every individual is born healthy, born wanted and has the privilege to fulfil his or her potentials for a life free from disease and disability. This is why it becomes necessary for biologists to carefully understand human genes, evolution, cells and general human anatomy to fulfil this project. During this process, they are faced with challenges where they also lack the foundation on how to solve them. This challenge gave birth to a philosophical excavation of molecular and developmental biology. …

3: "The Current Extinction: Defaunation & Ecosystem Disruption", Sarah O'Leary-Driscoll, Crystal Randall

Ecosystem Disruption & Climate Change

Information taken from: Dirzo, R. et al (2014). Defaunation in the Anthropocene. Science, 345(401).

Scientists estimate, conservatively, that there are 5 to 9 million different animal species on the planet. But that number is continually changing, and unfortunately, dropping, as we are likely losing 11,000- 58,000 species annually, and evidence suggests that on average, there has been a decline of about 28% in terms of numbers of individuals within a species over the last four decades. Both of these statistics are vitally important. The critical nature of the first is perhaps more obvious, as total loss of a species is …