Biology Commons^™

Robust Detection Of Rare Species Using Environmental Dna: The Importance Of Primer Specificity, Taylor M. Wilcox, Kevin S. Mckelvey, Michael K. Young, Stephen F. Jane, Winsor H. Lowe, Andrew R. Whiteley, Michael K. Schwartz

Biological Sciences Faculty Publications

Environmental DNA (eDNA) is being rapidly adopted as a tool to detect rare animals. Quantitative PCR (qPCR) using probe-based chemistries may represent a particularly powerful tool because of the method's sensitivity, specificity, and potential to quantify target DNA. However, there has been little work understanding the performance of these assays in the presence of closely related, sympatric taxa. If related species cause any cross-amplification or interference, false positives and negatives may be generated. These errors can be disastrous if false positives lead to overestimate the abundance of an endangered species or if false negatives prevent detection of an invasive species. …

Melanin Concentration Gradients In Modern And Fossil Feathers, Daniel J. Field, Liliana D’Alba, Jakob Vinther, Samuel M. Webb, William Gearty, Matthew D. Shawkey

School of Biological Sciences: Faculty Publications

In birds and feathered non-avian dinosaurs, within-feather pigmentation patterns range from discrete spots and stripes to more subtle patterns, but the latter remain largely unstudied. A ,55 million year old fossil contour feather with a dark distal tip grading into a lighter base was recovered from the Fur Formation in Denmark. SEM and synchrotron-based trace metal mapping confirmed that this gradient was caused by differential concentration of melanin. To assess the potential ecological and phylogenetic prevalence of this pattern, we evaluated 321 modern samples from 18 orders within Aves. We observed that the pattern was found most frequently in distantly …

Sugar Promotes Vegetative Phase Change In Arabidopsis Thaliana By Repressing The Expression Of Mir156a And Mir156c, Li Yang, Mingli Xu, Yeonjong Koo, Jia He, R. Scott Poethig

Faculty Publications

Nutrients shape the growth, maturation, and aging of plants and animals. In plants, the juvenile to adult transition (vegetative phase change) is initiated by a decrease in miR156. In Arabidopsis, we found that exogenous sugar decreased the abundance of miR156, whereas reduced photosynthesis increased the level of this miRNA. This effect was correlated with a change in the timing of vegetative phase change, and was primarily attributable to a change in the expression of two genes, MIR156A and MIR156C, which were found to play dominant roles in this transition. The glucose-induced repression of miR156 was dependent on the …

Trans-Species Activity Of A Nonself Recognition Domain, Robert P. Smith, Kenji Wellman, Myron L. Smith

Biology Faculty Articles

Background: The ability to distinguish nonself from self is a fundamental characteristic of biological systems. In the filamentous fungus Neurospora crassa, multiple incompatibility genes mediate nonself recognition during vegetative growth. One of these genes, un-24, encodes both nonself recognition function and the large subunit of a type I ribonucleotide reductase, an evolutionarily conserved enzyme that is essential for the conversion of NDP precursors into dNDPs for use in DNA synthesis. Previous studies have shown that co-expression of the two allelic forms of un-24, Oakridge (OR) and Panama (PA), in the same cell results …

Plant Diversity At Home And Abroad, Dr. Leigh Johnson

Journal of Undergraduate Research

This award supported a multifaceted mentoring environment for students with a focus on plant biodiversity. The objectives were to provide support for two students participating in a focused, study abroad program sponsored by an NSF Partnerships in Research and Education award for which the PI is a participant, and support for multifaceted research that includes training in herbarium curation and contemporary plant systematics. The goal for all participants was to provide training and skills useful for successful graduate study or employment. Because the project was extended beyond one year, this mentoring award serviced more students than originally anticipated. Beyond the …

Glycoconjugates Prevent Bacterial Dissemination And Cellular Death During B. Cereus/ B. Anthracis Infection, Mohamed Hassen Lahiani

Theses and Dissertations

Bacillus cereus group species including Bacillus cereus and Bacillus anthracis produce highly resistant spores. Dormant spores can survive for long period in harsh environmental conditions. Spores are engulfed by macrophages. Mammalian macrophages are the first line defenders immune cells through its phagocytic activity. Glycoconjugates (GCs) are a family of synthetic carbohydrates that possesses numerous bactericidal and immunodulatory properties. In my study, I used a multivariate approach to study the effects of GCs on B. cereus and B. anthracis Sterne phagocytosis. During in vitro study, I found that GC1 and GC3 were the best candidates that inhibited B. cereus and B. …

Patagonian Field Study: An International, Cross-Cultural Mentoring Experience, Dr. Jerry Johnson

Journal of Undergraduate Research

This mentoring environment grant was awarded in 2008. The purpose of the project was twofold: (1) to help support BYU undergraduate students to participate in our Patagonia PIRE international field study program in Argentina and Chile; and (2) to support undergraduate participation in research on evolution of fishes in Mexico. Here I report on the outcomes of this project, specifically addressing the five points requested by the ORCA for MEG final reports.

Mitochondrial Genetics Of Alzheimer's Disease And Aging, Perry Gene Ridge

Theses and Dissertations

Mitochondria are essential cellular organelles and the location of the electron transport chain, the site of the majority of energy production in the cell. Mitochondria contain their own circular genome approximately 16,000 base pairs in length. The mitochondrial genome (mtDNA) encodes 11 protein-coding genes essential for the electron transport chain, 22 tRNA genes, and two rRNA genes. Mitochondrial malfunction occurs in many diseases, and changes in the mitochondrial genome lead to numerous disorders. Multiple mitochondrial haplotypes and sequence features are associated with Alzheimer's disease. In this dissertation we utilized TreeScanning, an evolutionary-based haplotype approach to identify haplotypes and sequence variation …

Phosphatidic Acid Binds To Cytosolic Glyceraldehyde-3-Phosphate Dehydrogenase And Promotes Its Cleavage In Arabidopsis, Xuemin Wang, Sang-Chul Kim, Liang Guo

Biology Department Faculty Works

Phosphatidic acid (PA) is a class of lipid messengers involved in a variety of physiological processes. To understand how PA mediates cell functions in plants, we used a PA affinity membrane assay to isolate PA-binding proteins from Camelina sativa followed by mass spectrometric sequencing. A cytosolic glyceraldehyde-3-phosphate dehydrogenase (GAPC) was identified to bind to PA, and detailed analysis was carried out subsequently using GAPC1 and GAPC1 from Arabidopsis. The PA and GAPC binding was abolished by the cation zinc whereas oxidation of GAPCs promoted the PA binding. PA had little impact on the GAPC catalytic activity in vitro, but the …

Keeping Abreast With Liberal Arts And Science Through Steam, Tanya Rivas, Gregory Knotts

The Transdisciplinary STEAM+ Journal

The integrated unit on breast cancer described here includes biological science and visual art standards and was targeted at high school juniors and seniors. The goal was to make a potentially controversial and taboo subject relatable through an art-science approach

Metabolic Rescue Of “Glucose Addicted” Cancer Cells In Vitro, Paolo Vignali

Pursuit - The Journal of Undergraduate Research at The University of Tennessee

Transformations in the glycolytic metabolism of neoplasms modulate their robust cellular division. This characteristic leads to an “addiction” to glucose for continued proliferation and viability. This study investigated whether glucose metabolites could rescue cellular viability in glucose-starvation conditions, a model of the inter-tumoral nutrient-deficient environment. Findings illustrated potential cellular viability rescue with pyruvate addition in glucose-deprived conditions, yet the same potential was not observed with lactic acid, a metabolite that exists at characteristically high concentrations within the intertumoral microenvironment. These results could implicate a predominance of certain metabolic pathways in nutrient-starved cells. Molecular transport capacities across plasma membranes are tied …

Hematopoietic Stem Cells And Progenitors In Murine Autoimmune Arthritis, Kwadwo Asare Oduro Jr.

All Theses and Dissertations (ETDs)

Although the physiological role of stem cells in generating and maintaining a functional biological system is widely appreciated, very little is known about the behavior of these cells in pathological conditions. If and how these primitive cells are affected by a disease process or may contribute to the disease process has not been adequately explored. We have studied the Hematopoietic System, with particular emphasis on Hematopoietic Stem Cells: HSCs) and Progenitors, in a spontaneous murine autoimmune arthritis model. We found that these mice have a systemic increase in myeloid cells, which correlated with an increased frequency of granulocyte-monocyte progenitors relative …

Under Graduate Curriculum Integration: Bringing Students Together Through Research, Clay Runck, James Russell, Allison D’Costa

Interdisciplinary STEM Teaching & Learning Conference (2012-2019) (Archived)

At Georgia Gwinnett College we are integrating the undergraduate educational experience for our Bachelor of Science students in the Biology discipline. We are using the opportunities presented by the genetic information revolution to combine biology courses in a longitudinal and integrative research project aimed at cataloguing biological diversity over space and time on the developing Georgia Gwinnett College campus.

Reproductive Isolation In The Elegans-Group Of Caenorhabditis, Scott Everet Baird, Sara Rose Seibert

Biological Sciences Faculty Publications

Reproductive isolation is the basis of the Biological Species Definition and can be a driving force of speciation. Theoretical studies have provided models of how reproductive isolation can arise within individual species. Genetic tests of these models are limited to populations in which reproductive isolation is present but not complete. Here, reproductive isolation in the Elgans-Group of the nematode genus Caenorhabditis is reviewed. Pre-mating barriers, assortative fertilization and post-zygotic barriers all have been observed in this clade. In some combinations of species, fertile F1 hybrids can be obtained. Therefore, the Elegans-Group of Caenorhabditis is poised to become an important experimental …

Molecular Chaperoning Function Of Ric-8 Is To Fold Nascent Heterotrimeric G Protein Α Subunits, Puiyee Chan, Celestine J. Thomas, Stephen R. Sprang, Gregory G. Tall

Biological Sciences Faculty Publications

We have shown that resistance to inhibitors of cholinesterase 8 (Ric-8) proteins regulate an early step of heterotrimeric G protein α (Gα) subunit biosynthesis. Here, mammalian and plant cell-free translation systems were used to study Ric-8A action during Gα subunit translation and protein folding. Gα translation rates and overall produced protein amounts were equivalent in mock and Ric-8A-immunodepleted rabbit reticulocyte lysate (RRL). GDP-AlF4(-)-bound Gαi, Gαq, Gα13, and Gαs produced in mock-depleted RRL had characteristic resistance to limited trypsinolysis, showing that these G proteins were folded properly. Gαi, Gαq, and Gα13, but not Gαs produced from Ric-8A-depleted RRL were not protected …

Sequencing And De Novo Transcriptome Assembly Of Brachypodium Sylvaticum (Poaceae), Samuel E. Fox, Justin Preece, Jeffrey A. Kimbrel, Gina L. Marchini, Abigail Sage, Ken Youens-Clark, Mitchell B. Cruzan, Pankaj Jaiswal

Biology Faculty Publications and Presentations

Premise of the study: We report the de novo assembly and characterization of the transcriptomes of Brachypodium sylvaticum (slender false-brome) accessions from native populations of Spain and Greece, and an invasive population west of Corvallis, Oregon, USA. Methods and Results: More than 350 million sequence reads from the mRNA libraries prepared from three B. sylvaticum genotypes were assembled into 120,091 (Corvallis), 104,950 (Spain), and 177,682 (Greece) transcript contigs. In comparison with the B. distachyon Bd21 reference genome and GenBank protein sequences, we estimate >90% exome coverage for B. sylvaticum . The transcripts were assigned Gene Ontology and InterPro annotations. Brachypodium …

Antioxidative Properties Of Bitter Gourd (Momordica Charantia) And Zucchini (Cucurbita Pepo), Mijitaba Hamissou, Amanda C. Smith, Robert E. Carter Jr., Jimmy K. Triplett Ii

Research, Publications & Creative Work

The enzymatic and non-enzymatic antioxidative capacities of bitter gourd (Momordica charantia) and zucchini (Cucurbita pepo) were investigated in water extracts and chemical buffer extracts. Bitter gourd and zucchini fruits were purchased from a farmer’s market and homogenized separately in water and in a native enzyme extraction buffer. Total phenolic compounds, free radical DPPH scavenging activity, SOD activity and β- glucosidase activity were assayed in the extracts. The average total phenolic compounds recorded in bitter gourd were 13.28 GAE/g fresh weights while in zucchini, the average was 8.67GAE/g fresh weight. This study also found that bitter gourd was 82.05% as effective …

Mechanistic Studies Of Intracellular Delivery Of Proteins By Cell-Penetrating Peptides In Cyanobacteria, Betty Revon Liu, Yue-Wern Huang, Han-Jung Lee

Biological Sciences Faculty Research & Creative Works

Background: The plasma membrane plays an essential role in selective permeability, compartmentalization, osmotic balance, and cellular uptake. The characteristics and functions of cyanobacterial membranes have been extensively investigated in recent years. Cell-penetrating peptides (CPPs) are special nanocarriers that can overcome the plasma membrane barrier and enter cells directly, either alone or with associated cargoes. However, the cellular entry mechanisms of CPPs in cyanobacteria have not been studied.

Results: In the present study, we determine CPP-mediated transduction efficiency and internalization mechanisms in cyanobacteria using a combination of biological and biophysical methods. We demonstrate that both Synechocystis sp. PCC 6803 and Synechococcus …

Prevalence And Comparative Analysis Of Cutaneous Leishmaniasis In Dargai Region In Pakistan, Clarence Lee

Department of Biology Faculty Publications

In the present study, 102 samples of exudates from cutaneous leishmanial lesions were collected from local Pakistanis and Afghan refugees residing in Dargai Tehsil of Malakand Agency Pakistan, and were analyzed. The lesions were more prevalent among the locals (60.79%) compared to refugees (49.21%), and 70.58% male compared to 30.42% female were infected with Leishmania. Infection was more prevalent among youth's ages of 11-20 year old (34.32%) compared to older adults. Exposed parts of the body (face, hands, legs, neck, ears and feet) were the main affected areas. Faces experienced more bites (36.28%), followed by legs (26.48%), and hands (21.57%). …

Evaluating Tradeoffs Among Ecosystem Services To Inform Marine Spatial Planning, Sarah E. Lester, Christopher Costello, Benjamin S. Halpern, Steven D. Gaines, Crow White, John A. Barth

Biological Sciences

A central challenge for natural resource management is developing rigorous yet practical approaches for balancing the costs and benefits of diverse human uses of ecosystems. Economic theory has a long history of evaluating tradeoffs in returns from different assets to identify optimal investment strategies. There has been recent progress applying this framework to the delivery of ecosystem services in land use planning. However, despite growing national and international interest in marine spatial planning, there is a lack of parallel frameworks in the marine realm. This paper reviews an ecosystem service tradeoff analysis framework and provides a more comprehensive synthesis for …

Marine Protected Areas And Resilience To Sedimentation In The Solomon Islands, B. S. Halpern, K. A. Selkoe, Crow White, S. Albert, S. Aswani, M. Lauer

Biological Sciences

The ability of marine protected areas (MPAs) to provide protection from indirect stressors, via increased resilience afforded by decreased impact from direct stressors, remains an important and unresolved question about the role MPAs can play in broader conservation and resource management goals. Over a five-year period, we evaluated coral and fish community responses inside and outside three MPAs within the Roviana Lagoon system in Solomon Islands, where sedimentation pressure from upland logging is substantial. We found little evidence that MPAs decrease impact or improve conditions and instead found some potential declines in fish abundance. We also documented modest to high …

Recurrent Rearrangement During Adaptive Evolution In An Interspecific Yeast Hybrid Suggests A Model For Rapid Introgression, Barbara Dunn, Terry Paulish, Alison Stanbery, Jeff Piotrowski, Gregory Koniges, Evgueny Kroll, Edward J. Louis, Gianni Liti, Gavin Sherlock, Frank Rosenzweig

Biological Sciences Faculty Publications

Genome rearrangements are associated with eukaryotic evolutionary processes ranging from tumorigenesis to speciation. Rearrangements are especially common following interspecific hybridization, and some of these could be expected to have strong selective value. To test this expectation we created de novo interspecific yeast hybrids between two diverged but largely syntenic Saccharomyces species, S. cerevisiae and S. uvarum, then experimentally evolved them under continuous ammonium limitation. We discovered that a characteristic interspecific genome rearrangement arose multiple times in independently evolved populations. We uncovered nine different breakpoints, all occurring in a narrow similar to 1-kb region of chromosome 14, and all producing an …

Ontogenetic Variation In Cold Tolerance Plasticity In Drosophila: Is The Bogert Effect Bogus?, Katherine A Mitchell, Brent J Sinclair, John S Terblanche

Biology Publications

Ontogenetic variation in plasticity is important to understanding mechanisms and patterns of thermal tolerance variation. The Bogert effect postulates that, to compensate for their inability to behaviourally thermoregulate, less-mobile life stages of ectotherms are expected to show greater plasticity of thermal tolerance than more-mobile life stages. We test this general prediction by comparing plasticity of thermal tolerance (rapid cold-hardening, RCH) between mobile adults and less-mobile larvae of 16 Drosophila species. We find an RCH response in adults of 13 species but only in larvae of four species. Thus, the Bogert effect is not as widespread as expected.

Identification Of Cold-Responsive Genes In A New Zealand Alpine Stick Insect Using Rna-Seq., Luke T Dunning, Alice B Dennis, Duckchul Park, Brent J Sinclair, Richard D Newcomb, Thomas R Buckley

Biology Publications

The endemic New Zealand alpine stick insect Micrarchus nov. sp. 2 regularly experiences sub-zero temperatures in the wild. 454-based RNA-Seq was used to generate a de novo transcriptome and differentiate between treatments to investigate the genetic basis of cold tolerance. Non cold-treated individuals were compared to those exposed to 0°C for 1 h followed by a 1 h recovery period at 20°C. We aligned 607,410 Roche 454 reads, generating a transcriptome of 5235 contigs. Differential expression analysis ranked candidate cold responsive genes for qPCR validation by P-value. The top nine up-regulated candidates, together with eight a priori targets identified from …

The Triggering Receptor Expressed On Myeloid Cells 2: “Trem-Ming” The Inflammatory Component Associated With Alzheimer's Disease, Troy T. Rohn

Biology Faculty Publications and Presentations

Alzheimer's disease (AD) is an age-related neurodegenerative disorder characterized by a progressive loss of memory and cognitive skills. Although much attention has been devoted concerning the contribution of the microscopic lesions, senile plaques, and neurofibrillary tangles to the disease process, inflammation has long been suspected to play a major role in the etiology of AD. Recently, a novel variant in the gene encoding the triggering receptor expressed on myeloid cells 2 (TREM2) has been identified that has refocused the spotlight back onto inflammation as a major contributing factor in AD. Variants in TREM2 triple one's risk of developing late-onset AD. …

First Bacterial Endosymbionts Found In The Phylum Ascomycota, Eileen Elizabeth Fitzpatrick

Dissertations and Theses

Organisms belonging to the Kingdom Fungi are known to occupy a wide variety of ecological niches and are found globally in virtually all environments. Two members of the smallest of the fungal phylum, the Zygomycota, have also been found to harbor intercellular bacteria initially described as being from or closely related to organisms from the Genus Burkholderia. In this study two microaerophilic members of the species Verticilium from the phyla Ascomycota were characterized. Both appear to carry two bacterial endosymbionts. This is the first evidence of bacterial endosymbionts found within a member of the Ascomycota. Through the use of fluorescent …

Home Range And Habitat Use Of Santa Rosa Island Foxes (Urocyon Littoralis Santarosae), Elizabeth Marie Drake

Master's Theses

Island foxes (Urocyon littoralis) are currently listed as federally endangered on four of the six Channel Islands to which they are endemic. The Santa Rosa Island (SRI) population declined by 99% during the 1990’s due to non-native golden eagle (Aguila chrysaetos) predation and is currently the lowest fox population (~280) and density (0.86 foxes/km²) of any of the Channel Islands. The goals of this study were to assess new miniaturized GPS technology and to quantify home range and habitat use of the SRI population. This is only the second use of Global Positioning System (GPS) …

Sexual Dimorphism And Behavioral Responses To Conspecific Chemical Cues In Pagurus Samuelis, Maria Kim

Loma Linda University Electronic Theses, Dissertations & Projects

Anatomical differences were observed between sexes of P. samuelis. We measured the major cheliped and carapace lengths of hermit crabs caught off the coast of Southern California and found that male chelipeds were significantly larger relative to their carapace length than female chelipeds. Average male cheliped:carapace ratios were 1.86 while average female cheliped:carapace ratios were 1.32. We predicted that males and females would respond differently to cue waters created from their own sex. Females were exposed to female cue treatment odors and males were exposed to male cue treatment odors. We recorded hermit crabs exposed to cue treatment waters and …

Rectal Transmission Of Transmitted/Founder Hiv-1 Is Efficiently Prevented By Topical 1% Tenofovir In Blt Humanized Mice, Morgan L. Chateau, Paul W. Denton, Michael D. Swanson, Ian Mcgowan, J. Victor Garcia

Biology Faculty Publications

Rectal microbicides are being developed to prevent new HIV infections in both men and women. We focused our in vivo preclinical efficacy study on rectally-applied tenofovir. BLT humanized mice (n = 43) were rectally inoculated with either the primary isolate HIV-1JRCSF or the MSM-derived transmitted/founder (T/F) virus HIV-1THRO within 30 minutes following treatment with topical 1% tenofovir or vehicle. Under our experimental conditions, in the absence of drug treatment we observed 50% and 60% rectal transmission by HIV-1JRCSF and HIV-1THRO, respectively. Topical tenofovir reduced rectal transmission to 8% (1/12; log rank p = 0.03) for HIV-1JRCSF and 0% (0/6; log …

Parsimony And Model-Based Analyses Of Indels In Avian Nuclear Genes Reveal Congruent And Incongruent Phylogenetic Signals, Tamaki Yuri, Rebecca T. Kimball, John Harshman, Rauri Ck Bowie, Michael J. Braun

Biology: Faculty Publications and Other Works

Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven …