Biology Commons^™

The Junior Scientist Outreach Program Handbook: A Guide To The Preparation, Execution, And Evaluation Of A Sustainability-Themed Informal Science Education Outreach Program, Martha Josefina Vargas

Biology Faculty & Staff Publications

This handbook is intended to provide the history of and methodology for the preparation, execution and evaluation of an informal science education program that is based in a predominantly Hispanic community in Albuquerque, New Mexico. Because this program, known as The Junior Scientist Outreach Program (JSOP), has already positively impacted the lives of hundreds of students and families, the importance and relevance of its continuation will be highlighted and reiterated throughout the instructions and step-by-step procedures.

Specimen Catalog & Field Notes, Bethany L. Abrahamson

Division of Mammals - Field Notes and Catalogs

No abstract provided.

Preserved Self-Awareness Following Extensive Bilateral Brain Damage To The Insula, Anterior Cingulate, And Medial Prefrontal Cortices, Carissa Philippi, Justin Feinstein, Sahib Khalsa, Antonio Damasio, Daniel Tranel, Gregory Landini, Kenneth Williford, David Rudrauf

Psychology Faculty Works

No abstract provided.

Plant Calcium Content: Ready To Remodel, Jian Yang, Tracy Punshon, Mary Lou Guerinot, Kendal D. Hirschi

Dartmouth Scholarship

By identifying the relationship between calcium location in the plant cell and nutrient bioavailability, the plant characteristics leading to maximal calcium absorption by humans can be identified. Knowledge of plant cellular and molecular targets controlling calcium location in plants is emerging. These insights should allow for better strategies for increasing the nutritional content of foods. In particular, the use of preparation-free elemental imaging technologies such as synchrotron X-ray fluorescence (SXRF) microscopy in plant biology may allow researchers to understand the relationship between subcellular location and nutrient bioavailability. These approaches may lead to better strategies for altering the location of calcium …

Coxsackievirus And Adenovirus Receptor (Car) Mediates Trafficking Of Acid Sensing Ion Channel 3 (Asic3) Via Psd-95, Katherine J.D.A. Excoffon, Abimbola O. Kolawole, Nobuyoshi Kusama, Nicholas D. Gansemer, Priyanka Sharma, Alesia M. Hruska-Hageman, Elena Petroff, Christopher J. Benson

Department of Biology Faculty Scholarship and Creative Works

We have previously shown that the Coxsackievirus and adenovirus receptor (CAR) can interact with post-synaptic density 95 (PSD-95) and localize PSD-95 to cell-cell junctions. We have also shown that activity of the acid sensing ion channel (ASIC3), a H+-gated cation channel that plays a role in mechanosensation and pain signaling, is negatively modulated by PSD-95 through a PDZ-based interaction. We asked whether CAR and ASIC3 simultaneously interact with PSD-95, and if so, whether co-expression of these proteins alters their cellular distribution and localization. Results indicate that CAR and ASIC3 co-immunoprecipitate only when co-expressed with PSD-95. CAR also brings both PSD-95 …

Transcriptome-Based Exon Capture Enables Highly Cost-Effective Comparative Genomic Data Collection At Moderate Evolutionary Scales, Ke Bi, Dan Vanderpool, Sonal Singhal, Tyler Linderoth, Craig Moritz, Jeffrey M. Good

Biological Sciences Faculty Publications

Background: To date, exon capture has largely been restricted to species with fully sequenced genomes, which has precluded its application to lineages that lack high quality genomic resources. We developed a novel strategy for designing array-based exon capture in chipmunks (Tamias) based on de novo transcriptome assemblies. We evaluated the performance of our approach across specimens from four chipmunk species. Results: We selectively targeted 11,975 exons (similar to 4 Mb) on custom capture arrays, and enriched over 99% of the targets in all libraries. The percentage of aligned reads was highly consistent (24.4-29.1%) across all specimens, including in multiplexing up …

Assembly Of The Didymium Iridis Mitochondrial Genome By Genome Walking, Dale Kopp

College of Science and Health Theses and Dissertations

Organelle inheritance and RNA editing has been studied in Didymium iridis even though the genome has not been completely sequenced. Four segments, comprising 66 kb, have been sequenced in the past. Several approaches have been taken to complete the sequence including restriction mapping and southern hybridization, as well as screening clone banks by PCR with the sequence of contig ends. In this study, genome walking was used to uncover sequences connecting the four segments. Using genome walking, approximately 4,113 bp of new sequence was identified. With the new sequence and the characterization of two previously sequenced D. iridis mt regions …

Morphological Correlates Of A Combat Performance Trait In The Forked Fungus Beetle, Bolitotherus Cornutus, K. M. Benowitz, E. D. Brodie Iii, Vincent A. Formica

Biology Faculty Works

Combat traits are thought to have arisen due to intense male-male competition for access to females. While large and elaborate weapons used in attacking other males have often been the focus of sexual selection studies, defensive traits (both morphological and performance) have received less attention. However, if defensive traits help males restrict access to females, their role in the process of sexual selection could also be important. Here we examine the morphological correlates of grip strength, a defensive combat trait involved in mate guarding, in the tenebrionid beetle Bolitotherus cornutus. We found that grip strength was repeatable and differed between …

Antony Van Leeuwenhoek: Creation “Magnified” Through His Magnificent Microscopes, Alan L. Gillen, Douglas Oliver

Faculty Publications and Presentations

Although van Leeuwenhoek was not the inventor of the microscope, he advanced it more than anyone else for seeing living things.

Antony van Leeuwenhoek1 (Fig. 1) found great joy in God’s smallest creatures. He first discovered protozoans in his youth. The Dutch haberdasher retained a child-like joy of discovery from his youth until his death at age 90. He lived to see tiny microbes though his homemade microscopes. He loved to grind and focus a new lens in order to see the unseen world. Leeuwenhoek spent countless hours grinding tiny lenses and looking through them. This Christian lay biologist …

A Ranksum Statistics Based Framework To Decipher Transcription Regulation, Iuan-Bor Chen

Arts & Sciences Graduate Student Theses and Dissertations

The unbiased generation of specific and meaningful hypotheses from the deluge of data generated by modern genomic methods remains a challenge. These datasets require increasing level of expertise to analyze fully, and are often underutilized even in the originating lab. It would be desirable to have a computational strategy that is easy to implement, robust against outliers and missing data, and broadly applicable to diverse experimental designs. In this dissertation, I present a set of ranksum statistics-based analytical methods as a framework to extract testable hypotheses from large and complex datasets. To illustrate its utility, this framework was applied to …

Characterization Of Microsatellite Loci And Pilot Population Genetic Analysis In Hickory Shad, Alosa Mediocris, Fnu Vishakha

Theses and Dissertations

The hickory shad (Alosa mediocris) is a relatively understudied species of the anadromous fish sub-family Alosinae. This study, the first population genetic analysis of this species, employed 12 neutral microsatellite loci to estimate genetic diversity and population structure in tributaries of lower Chesapeake Bay, Virginia including James River and its tributaries (Appomattox and Chickahominy Rivers), Rappahannock River, and Pamunkey River. Genetic variation was extremely low. Estimates of observed heterozygosity were lower than expected heterozygosity. Significant population structure was detected among the six samples (FST = 0.093, p = 0.01). Effective population sizes were low (Ne ranged from 2 to 134). …

Bone Morphogenetic Protein Signaling In Vascular Disease: Anti-Inflammatory Action Through Myocardin-Related Transcription Factor A, Dahai Wang, Jamunabai Prakash, Peter H. Nguyen, Brandi N. Davis-Dusenbery, Nicholas S. Hill, Matthew D. Layne, Akiko Hata, Giorgio Lagna

Biology

Pulmonary artery hypertension (PAH) patients exhibit elevated levels of inflammatory cytokines and infiltration of inflammatory cells in the lung. Concurrently, mutations of bmpr2, the gene encoding the type II receptor of bone morphogenetic proteins (BMP), are found in ∼75% of patients with familial PAH, but a possible nexus between increased inflammation and diminished BMP signaling has hitherto remained elusive. We previously showed that BMP4 triggers nuclear localization of the Myocardin-related transcription factor A (MRTF-A) in human pulmonary artery smooth muscle cells (PASMC), resulting in the induction of contractile proteins. Here we report the BMPR2-dependent repression of a set of inflammatory …

Analyses Of Chromosome Copy Number And Expression Level Of Four Genes In The Ciliate Chilodonella Uncinata Reveal A Complex Pattern That Suggests Epigenetic Regulation, Laure Bellec, Laura A. Katz

Biological Sciences: Faculty Publications

Chilodonella uncinata, like all ciliates, contains two distinct nuclei in every cell: a germline micronucleus and a somatic macronucleus. The macronucleus develops from the zygotic nucleus through a series of chromosomal rearrangements. Macronuclear development in C. uncinata yields a nucleus with highly amplified gene-sized chromosomes. The macronucleus is transcriptionally active during vegetative growth while there is no expression in the micronucleus except during a brief period following conjugation. Gene family evolution in ciliates occurs through complex processes including gene duplication and an alternative processing of scrambled genes. Here we use quantitative PCR to compare relative expression levels of eight genes …

Methylene Blue Modulates Huntingtin Aggregation Intermediates And Is Protective In Huntington's Disease Models, Emily M. Sontag, Gregor P. Lotz, Namita Agrawal, Andrew Tran, Rebecca Aron, Guocheng Yang, Mihaela Necula, Alice Lau, Steven Finkbeiner, Charles G. Glabe, J. Lawrence Marsh, Paul J. Muchowski, Leslie M. Thompson

Biological Sciences Faculty Research and Publications

Huntington's disease (HD) is a devastating neurodegenerative disorder with no disease-modifying treatments available. The disease is caused by expansion of a CAG trinucleotide repeat and manifests with progressive motor abnormalities, psychiatric symptoms, and cognitive decline. Expression of an expanded polyglutamine repeat within the Huntingtin (Htt) protein impacts numerous cellular processes, including protein folding and clearance. A hallmark of the disease is the progressive formation of inclusions that represent the culmination of a complex aggregation process. Methylene blue (MB), has been shown to modulate aggregation of amyloidogenic disease proteins. We investigated whether MB could impact mutant Htt-mediated aggregation and neurotoxicity. MB …

Transient Expression Of Ova Antigen: Rtb Fusions In Plants For Production Of Improved Subunit Vaccines, Lana Elkins

Student Theses and Dissertations

Plant-based production systems may provide a solution to the safety, cost, and scalability limitations of traditional vaccine production. While subunit vaccines offer several advantages, challenges of low immunogenicity need to be addressed. The nontoxic B subunit of ricin (RTB) may provide a novel platform for effective delivery and immune presentation for subunit vaccines. The RTB lectin binds sugars on the surface of mammalian cells to facilitate uptake/transport of fused antigen. The natural cell trafficking of RTB may allow differential presentation to the two major arms of the animal immune system, antibody- and cell-mediated using an RTB and RTBKDEL fusion vaccine …

Circadian Rhythm In Yeast, Jake Yablonowski, Michael Borchert

Symposium on Research and Creative Expression (SORCE)

Circadian rhythms are found in a variety of organisms and are involved in controlling activity of the organism. However, a circadian rhythm for yeast has not been discovered yet. The goal of this study is to find evidence for a circadian rhythm in yeast by looking for changes in GAPDH concentrations and peroxiredoxin levels. GAPDH and peroxiredoxin have been shown to be controlled by the circadian clock in many organisms. A continuous yeast culture is sampled every two hours over a period of about 104 hours. Each sample is processed and tested for the concentration of GAPDH using GAPDH reagent. …

Effects Of Invasion By The Common Reed (Phragmites Australis) On Carbon Transformations In A Great Lakes Marsh, Shawn Trevor Duke

Master's Theses and Doctoral Dissertations

The common reed (Phragmites australis) is a highly productive invasive grass that alters the wetland physiochemical environment and produces toxic secondary metabolites. Plant litter decomposition, effects of water level on soil microbes, and soil microbial response to leachate additions were investigated in Phragmites invaded and pre-invaded Typha sites. Less litter mass was lost from Phragmites than Typha in both sites during the initial 144 days. Annual mass loss from both species’ litter was greater in the Phragmites site. Lower water levels resulted in greater CO₂ than CH₄ production in both Phragmites and Typha soils. Higher water …

Ocean Acidification: Understanding The Coastal Carbon Pump In A High Co2 World, Rachel Cooper

Theses and Dissertations

Since the 1800s, carbon dioxide emissions due to human activities have contributed significantly to the amount of carbon in the atmosphere. Approximately a third of this carbon is absorbed by the ocean, through air-sea fluxes at the ocean surface (Sabine, 2004). Increased CO2 has changed the carbon chemistry of the ocean and hence the pH. pH is expected to drop by 0.4 by the year 2100. It is unclear how this lower pH will affect carbon cycling and sequestration with respect to the biological carbon pump. Most studies have focused on open ocean phytoplankton or bacterial communities in large, stationary …

The Role Of Individual Behavior Type In Mediating Indirect Interactions, Blaine D. Griffen, Benjamin J. Toscano, John Gatto

Faculty Publications

Trait-mediated indirect interactions (TMII) play an important role in structuring natural communities, and numerous studies have experimentally demonstrated their presence in a variety of systems. However, these studies have largely examined the presence or absence of traits that are responsible for these interactions, without considering natural variation between individuals in the extent to which these traits are manifested. We used a well-documented TMII to investigate the importance of individual behavior type for determining the strength of the TMII. The toadfish Opsanus tau has an indirect positive influence on bivalve survival because the mud crab Panopeus herbstii, a consumer of bivalves, …

Birds In Residential Metropolitan New Orleans Neighborhoods And Their Relationships To The Batture And Yard Vegetation, Ruth A. Guymon

LSU New Orleans Theses and Dissertations

Metropolitan New Orleans Neighborhoods were surveyed in order to determine how bird populations responded to distance from the batture, percent canopy cover, stem counts, and understory vegetation. Surveys were conducted in the spring and summer of 2010. It was found that batture birds, urban birds, and pooled birds all had greater species richness and abundance in the spring in areas with more canopy cover, higher stem counts, more understory vegetation, and distances closer to the batture. In the summer, batture birds had greater richness and abundance in areas with more canopy cover, higher stem counts, and more understory cover. This …

Improving The Efficiency Of Homologous Gene Replacement By Disrupting Non-Homologous End Joining Pathway Gene Kusa In The Oleaginous Fungus Mortierella Alpina, Kathleen T. Krueger, Ziyu Dai Dr, Ugur Uzuner, Scott E. Baker Dr

STAR Program Research Presentations

Mortierella alpina , a oleaginous filamentous fungus, is one of industrial fungal strains known for the production of arachidonic acid. It is also of particular interest for hydrocarbon biofuel production since it is able to produce up to 50% of its mass in rich, long-chain polyunsaturated fatty acids [PUFA’s]. In addition to high fatty acid production, M. alpina like many other oleaginous fungi, already have mechanisms for accumulating significant concentrations of hydrophobic compounds making it a naturally equipped candidate to handle potential toxic concentrations of hydrocarbons. To date, three different transformation methods have been established for M. alpina that are …

Functional Response Of Protected Larval Stage Delta Smelt (Hypomesus Transpacificus), Jorge Ruiz, Lindsay Sullivan, Wim Kimmerer, Joan Lindberg

STAR Program Research Presentations

Delta smelt (Hypomesus transpacificus) is a protected slender-bodied fish endemic to the San Francisco Estuary. Smelt prey upon various zooplankton including the copepods such as Pseudodiaptomus forbesi. This experiment studied the prey maximum feeding rate of 2 larval stages (21 DHP, 35 DPH) of Delta smelt on various concentrations of P. forbesi. The copepod prey was offered at 7 different concentrations (2No./L–120No./L). After feeding was terminated the free prey and ingested prey were counted and analyzed to find the feeding rate of Delta smelt. Maximum feeding rate was found to be at much higher prey densities …

Analyzing Environmental Microbes For Genomic Regions Promoting Ionic Liquid Tolerance In E. Coli, Ann Nguyen, Alison Richins, Thomas Rüegg, Steven Singer, Michael Thelen

STAR Program Research Presentations

Ionic liquids (ILs) are promising as solvents to increase the efficiency of biofuel production; however, ILs are toxic to microbes used in the fermentation of liquid fuels. To engineer IL resistant biofuel hosts, environmental bacteria were screened for tolerance, and these were used to create gene libraries to test in E. coli. Future characterization of these libraries using molecular techniques will be used to identify genes that contribute IL-tolerance to transformed microbes.

Developing Monitoring Methods For Leptasterias Spp. As Sentinel Species In Detecting Local Environmental Changes, Zachary Sturbaum, Kathryn Nuessly, Riley J. Smith, C. Sarah Cohen

STAR Program Research Presentations

Leptasterias spp., a six-rayed sea star, is found in rocky intertidal habitats ranging from Alaska to central California. Leptasterias spp. can be monitored on a broad scale throughout their range by a variety of means using timed counts and random plot censusing in order to detect both large-scale and local-level changes in the environment due to climate change, land-based human activity, or other environmental events. Leptasterias brood their young externally until the embryos grow into fully developed juveniles. These juveniles disperse by crawling away, limiting their dispersal potential. This localized dispersal provides an opportunity to use Leptasterias spp …

Quantitative Evaluation Of Reciprocal Herkogamy In The Distylous Species, Hedyotis Caerulea (Rubiaceae), Dennis A. Sampson, Robert A. Krebs

Biological, Geological, and Environmental Faculty Publications

Hedyotis caerulea possesses two distinct floral morphs that are generally found in equal numbers in naturally occurring populations. Flowers either possess a relatively long style and short anthers, called a “pin,” or a short style and long anthers, called a “thrum.” This placement of reproductive organs is considered herkogamous and distylous, as it encourages outcrossing by restricting pollination to individuals of the alternate morph. Numerous species have been described as distylous without quantitative data establishing stigma-anther reciprocity. Here we assess those assumptions in H. caerulea by measuring stigma height, anther height and a suite of additional floral traits across multiple …

Study Of Cellular Responses Under Chemically Induced Hypoxia, George Coricor

Theses

No abstract provided.

Size And Weight Changes Of Leatherback Hatchlings Among Emergence Groups, Shane Morales, Kelly Stewart

STAR Program Research Presentations

In ideal leatherback sea turtle nests, all the hatchlings move together as a single group through the sand to leave the nest. Often, though, hatchlings emerge in two separate groups hours or days apart while others remain stuck in the sand where they may die unless they are dug out (excavation). First emergence groups spend the shortest amount of time in the sand while excavated hatchlings spend the longest amount of time in the sand (typically three days longer than first emergence hatchlings). Individuals from each of the separate emergences were weighed and measured (carapace only) in order to compare …

Endoplasmic Reticulum Involvement In Yeast Cell Death, Nicanor Austriaco

Biology Faculty Publications

Yeast cells undergo programed cell death (PCD) with characteristic markers associated with apoptosis in mammalian cells including chromatin breakage, nuclear fragmentation, reactive oxygen species generation, and metacaspase activation. Though significant research has focused on mitochondrial involvement in this phenomenon, more recent work with both Saccharomyces cerevisiae and Schizosaccharomyces pombe has also implicated the endoplasmic reticulum (ER) in yeast PCD. This minireview provides an overview of ER stress-associated cell death (ER-SAD) in yeast. It begins with a description of ER structure and function in yeast before moving to a discussion of ER-SAD in both mammalian and yeast cells. Three examples of …

Long-Term Survival Of Anoxia Despite Rapid Atp Decline In Embryos Of The Annual Killifish Austrofundulus Limnaeus, Jason E. Podrabsky, Michael A. Menze, Steven C. Hand

Faculty Research & Creative Activity

Embryos of the annual killifish Austrofundulus limnaeus can survive for months in the complete absence of oxygen. Survival of anoxia is associated with entry into a state of metabolic dormancy known as diapause. However, extreme tolerance of anoxia is retained for several days of post-diapause development. Rates of heat dissipation in diapause II and 4 days post-diapause II embryos were measured under aerobic conditions and during the transition into anoxia. Phosphorylated adenylate compounds were quantified in embryos during entry into anoxia and after 12 hr of aerobic recovery. Rates of heat dissipation were not affected by exposure to anoxia in …

Greater Galagos Near Mt. Kasigau, Kenya: Population Density Estimates, Andrea Falcetto

Masters Theses & Specialist Projects

This study examined population density and habitat use of a species of greater galago, genus Otolemur, around Mt. Kasigau, Kenya. Mt. Kasigau has a unique regional microclimate, a cloud forest, which provides many different flora and fauna a home. To examine population density, two different methods were used. The first method was using line transects and analyzing results using Distance 6.0. These surveys were conducted during both dry and wet season and results were compared after the study. The second method was to trap individuals and use mark-recapture to determine population density. When caught in a trap, individuals were …