Biology Commons^™

Evolution Of Thrips (Thysanoptera) Phylogenetic Patterns And Mitochondrial Genome Evolution, Mark Terry, Dr. Michael Whiting

Journal of Undergraduate Research

Thysanoptera (thrips) is an order of insects currently comprised of 7400 species, 1200 genus-groups, and nine living families with three fossil families (Mound, 2005). Two major suborders are recognized in Thysanoptera: Tubulifera (thrips with abdominal segment 10 tubular in shape) and Terebrantia (thrips with abdominal segment 10 subdivided ventrally).

Geneworkshop: A Dynamic, Developing Environment For Biologists, Computer Scientists, And Bioinformaticians, Joshua Sailsbery, Dr. David Mcclellan

Journal of Undergraduate Research

The GeneWorkshop project had one goal, to enable biologists to better utilize bioinformatic tools. Generally, bioinformatic tools have a large learning curve and are not very robust as to the data they accept. In order to meet these criteria, GeneWorkshop was separated into two main objectives. The first objective was the obtaining and maintaining of genetic data. The second objective was interpreting and implementing various bioinformatic software packages.

Conservation Genetics Of Mexican Deer Mice, Melina C. Walden, Dr. Duke S. Rogers

Journal of Undergraduate Research

In the field of biology, the job of documenting, describing, and defining the species of the world is a critical, yet overwhelming task. By focusing research in a specific area of interest, however, scientists work to contribute one small piece at a time to the much larger puzzle. In researching the biological relationships between the Mexican deer mice Peromyscus megalops and P. melanurus, my project contributes to one of the primary goals of biology.

In Quest Of Scientific Literacy And Civic Engagement: Innovations In Biology 100, Timothy Larsen, Dr. Gary M. Booth

Journal of Undergraduate Research

Scientific literacy is increasingly becoming a concern for citizens and consumers in a scientifically and medically advancing world. Service-Learning, Inquiry-Based Learning, and Concept Mapping have been implemented as a means of helping students to adopt deeper approaches to learning. It is the goal of my mentor, Dr. Gary Booth, to use these instructional methods to better prepare BYU students to participate as informed citizens and consumers in society.

Cheatgrass, Scott A. Davis, Dr. Bruce Roundy

Journal of Undergraduate Research

The invasion of non-native species, mainly cheatgrass (Bromus tectorum), into our rangelands, especially following the destruction caused by wildfires, has made it necessary to find viable options for the restoration of native plant species to these areas. The aim of this project was to determine whether or not it was possible to create models for the germination and seminal root growth of a suite of species using heat accumulation. By creating these models, we hoped to be able to discover other native species that not only compete with cheatgrass by establishing early, but provide a good food source for native …

Population Structure Of The Cuttlefish Sepia Officinalis From The North Atlantic-Mediterranean Region, Mark Joseph Nolte, Dr. Keith Crandall, Marcos Pérez-Losada

Journal of Undergraduate Research

An understanding of the relatedness of a population of organisms, or their phylogeny, combined with knowledge of that population’s geographical distribution, can illuminate which geographic forces and events may have played a role in forming the “family tree” of that organism. Therefore past speciation events and the incipient stages of speciation can be discerned when phylogenetic and geographic information is merged. This process, broadly known as the practice of phylogeography or biogeography, is important because it permits researchers to visualize the evolutionary interplay between environment and organism. Additionally, an understanding of an organism’s population structure, or family tree, enables scientists …

Correctly Assigning Dna Barcodes To Organisms, James B. Finlay, Dr. Keith A. Crandall

Journal of Undergraduate Research

Harvard biologist Edward O. Wilson suggested that what makes humans unique is our innate need for closeness to other forms of life. This “biophilia” has been evident since recorded history and was brought to the forefront of science with Darwin’s famous writings about the origin of species. Since that time there has been a major thrust to categorize all life into groups and subgroups in a field known as taxonomy. There are an estimated 10-15 million extant species (Hammond, 1992) on the earth. Taxonomists have classified roughly 1.6 million of these organisms (Wilson, 1992), indicating that much work needs to …

The Significance Of Isotopic Ratios In Migratory Pathways, Rachel Hart, Kent Hatch

Journal of Undergraduate Research

Stable isotope research is an important asset in securing the migratory paths of birds. By matching elemental isotopic ratios in different parts of a bird’s body to the water it drinks, important stopover sites may be conserved and the biological phenomenon of migration may be preserved. Thus far, such research among migratory birds has suggested a positive correlation between certain elemental isotopic ratios found in water sources and those in the composition of bird feathers. Hydrogen (δD) and oxygen (18O and 16O) isotopes have been examined in scientific literature but have not been tested thoroughly, as there are still many …

Phylogeny Of Sap Beetles (Coleoptera: Nitidulidae) Deciphering Patterns Of Host Shift, Matthew Moulton, Dr. Michael F. Whiting

Journal of Undergraduate Research

Nitidulids are a moderately diverse family of beetles, but the evolution of their feeding specializations was poorly understood. They are important in agroecosystems as pests of fruit crops, stored grains, honey production, biocontrol of aphids and scale insects, and transmission of plant viral pathogens. The phylogeny produced helped answer questions pertaining to the evolution of nitidulid host specialization, and provided insights into the diversification of this group. I conducted the first subfamilial phylogenetic analysis based on molecular data. Specific goals were: (1) Perform a phylogenetic analysis using molecular data from eight genes; 2) Use the phylogeny to infer the ancestral …

A New Species Of Blackish Deer Mouse, Jared B. Lee, Dr. Duke S. Rogers

Journal of Undergraduate Research

Biodiversity is a hallmark of our planet. We can see this everyday in the various habitats and environments that we live in, from the desert in Utah to the lush rain forests of South America. These great ecosystems provide a diversity of life in plants and animals. Biologists study and classify these organisms to better understand how this world came into being. All the time new species are being described and discovered in areas throughout the world. In this research project, we used traditional and modern techniques to better understand the diversity and variation in populations of a rodent in …

Patterns Of Genetic Diversity In The Galapagos Archipelago: Identifying And Preserving Evolutionary Processes, Rebecca Baum, Dr. Jack W. Sites

Journal of Undergraduate Research

The Galapagos Archipelago, located 1000 km off the coast of Ecuador, arose 1-5 million years ago by the eruption of underwater volcanoes. It consists of 13 larger islands, 6 smaller islands, and numerous islets. The Archipelago is a national park and a UNESCO World Heritage site, yet very little is known about its “hotspots” of genetic diversity or the processes that generate this diversity. The identification of areas of high genetic diversity provides information not only about lizards but also other native species. This information can be used to prioritize conservation efforts such as non-native (i.e. cats, rats, goats) species …

Matrixgen: Customized Amino Acid Change Matrices To Study Protein Family Evolution, John J. Bowers, Dr. Keith A. Crandall

Journal of Undergraduate Research

Background: Algorithms for aligning protein and DNA sequences are dependent upon the scoring matrix used to generate accurate alignments. Most alignment applications offer only a few choices for such scoring matrices (typically PAM and BLOSUM series matrices).

Hedgehog Signaling Regulates Telomerase Reverse Transcriptase In Human Cancer Cells, Tapati Mazumdar, Ranjodh Sandhu, Maha Qadan, Jennifer Devecchio, Victoria Magloire, Akwasi Agyeman, Bibo Li Ph.D., Janet A. Houghton

Biological, Geological, and Environmental Faculty Publications

The Hedgehog (HH) signaling pathway is critical for normal embryonic development, tissue patterning and cell differentiation. Aberrant HH signaling is involved in multiple human cancers. HH signaling involves a multi-protein cascade activating the GLI proteins that transcriptionally regulate HH target genes. We have previously reported that HH signaling is essential for human colon cancer cell survival and inhibition of this signal induces DNA damage and extensive cell death. Here we report that the HH/GLI axis regulates human telomerase reverse transcriptase (hTERT), which determines the replication potential of cancer cells. Suppression of GLI1/GLI2 functions by a C-terminus truncated GLI3 repressor mutant …

Effects Of 17Β-Estradiol Exposure On Gamete Development And Viability In Freshwater Unionids, David Sovic, Kody F. Kuehnl, Roman Lanno, G. Thomas Watters

Scholarship Forum 2013

Evidence of a functional role for vertebrate steroids has been demonstrated in a number of invertebrate species, including molluscs. This knowledge has generated interest into the possibility of invertebrate endocrine disruption due to exposure to both exogenous steroid hormones and xenobiotics which can mimic the action of these compounds. Exposure to the natural vertebrate estrogen, 17β-estradiol (E2), for example, has been shown to induce accelerated gamete development in multiple mollusc species. Little information exists, however, for freshwater mussels, a group of exceptional conservation interest.

Here, Daniel Sovic, Raoman Lanno, Dr. Kody Kuehnl, and G. Thomas Watters report the findings of …

Molecular Assessment Of Three Reproducing Populations Of The Clubshell Mussel (Pleurobema Clava) Reveals Historic Hybridization With Pleurobema Sintoxia, Kody F. Kuehnl, Michael G. Sovic

Scholarship Forum 2013

The clubshell (Pleurobema clava) is a federally endangered species of freshwater mussel endemic to Ohio that is currently found in fewer than ten river systems in the United States (>85% range reduction). Two of the USFWS’s (1993) recovery goals are to establish ten viable populations and maintain any existing genetic viability. In order to recover the clubshell, conservation efforts including translocation and captive propagation have been used to augment existing populations. In order to maintain the genetic diversity and population level specificity, a molecular assessment is needed. In this study, we generated nuclear microsatellite data and mitochondrial (mtDNA) sequence …

Freshwater Mussels As Biological Indicators, Vera Kazaniwskyj, Y. Zhang, G. Thomas Watters, Kody F. Kuehnl, Barbara A. Wolfe

Scholarship Forum 2013

Viral hemorrhagic septicemia virus (VHSV) is a devastating rhabdovirus affecting freshwater fishes worldwide. In 2005, a new genotype of VHSV (IVb) was discovered in Lake St. Clair and has consequently spread throughout the Laurentian Great Lakes. While it is widely known that freshwater fishes are hosts and transmitters of VHSV, little is known about the ability of invertebrates to take up and carry the virus. Our (Vera Kazaniwskyj, Y. Zhang, G. Thomas Watters, Dr. Kody Kuehnl, and Barbara Wolfe) objective in this study was to investigate the ability of freshwater mussels to accumulate and transmit VHSV by using two commonly …

Mitochondrial Dna Suggests Stonerollers (Campostoma Anomalum) From Upper Shavers Fork Have Strong Genetic Similarities With The Recently Identified New River Form, Michael G. Sovic, Kody F. Kuehnl

Scholarship Forum 2013

A recent analysis of cytochrome b sequence data suggested the presence of two distinct lineages of stoneroller (Campostoma anomalum) in West Virginia: one form that occurs throughout most waters of the Ohio and Potomac River basins, and a second that is restricted to the New River basin.

In Michael Sovic and Dr. Kody Kuehnl's study, cytochrome b data are presented for individuals sampled from the upper reaches of Shavers Fork, a tributary of the Cheat River that is geographically proximate to, but not within the New River drainage. Haplotypes observed in the individuals from Shavers Fork are most similar to …

Upland Habitat Quality And Historic Landscape Composition Influence Genetic Variation Of A Pond-Breeding Salamander, Stephen C. Richter, Steve J. Price, Chelsea S. Kross, Jeremiah R. Alexander, Michael E. Dorcas

Forestry and Natural Resources Faculty Publications

Understanding the temporal and spatial scale at which habitat alteration impacts populations is important for conservation and management. Amphibians have declined more than other vertebrates, and pond-breeding species are particularly susceptible to habitat loss and fragmentation because they have terrestrial and aquatic life stages. One approach to management of pond-breeding species is protection of core upland habitat surrounding the breeding pond. We used genetic variation as an indicator of population status in a common amphibian species, spotted salamanders (Ambystoma maculatum), to determine how amount of suitable upland habitat relates to population status in the greater Charlotte, North Carolina, …

Microclimate Moderates Plant Responses To Macroclimate Warming, Pieter De Frenne, Francisco Rodríguez-Sánchez, David Anthony Coomes, Lander Baeten, Gorik Verstraeten, Mark Vellend, Markus Bernhardt-Römermann, Carissa D. Brownd, Jörg Brunet, Johnny Cornelis, Guillaume M. Decocq, Hartmut Dierschke, Ove Eriksson, Frank S. Gilliam, Radim Hédl, Thilo Heinken, Martin Hermy, Patrick Hommel, Michael A. Jenkins, Daniel L. Kelly, Keith J. Kirby, Fraser J. G. Mitchell, Tobias Naaf, Miles Newman, George Peterken, Petr Petrík, Jan Schultz, Grégory Sonnier, Hans Van Calster, Donald M. Waller, Gian-Reto Walther, Peter S. White, Kerry D. Woods, Monika Wulf, Bente Jessen Graae, Kris Verheyen

Biological Sciences Faculty Research

Recent global warming is acting across marine, freshwater, and terrestrial ecosystems to favor species adapted to warmer conditions and/or reduce the abundance of cold-adapted organisms (i.e., “thermophilization” of communities). Lack of community responses to increased temperature, however, has also been reported for several taxa and regions, suggesting that “climatic lags” may be frequent. Here we show that microclimatic effects brought about by forest canopy closure can buffer biotic responses to macroclimate warming, thus explaining an apparent climatic lag. Using data from 1,409 vegetation plots in European and North American temperate forests, each surveyed at least twice over an interval of …

Rov-Based Tracking Of A Shallow Water Nocturnal Squid, Samuel Yim, Christopher M. Clark, Timothy Peters, Vladimir Prodanov, Pat Fidopiastis

Biological Sciences

This paper describes the use of a Remotely Operated Vehicle (ROV) equipped with a monocular vision system to find and track the squid Euprymna scolopes, so that motion behaviors of the squid could be characterized through the use of off-line image processing and state estimation. The ROV was deployed for several nights at several nearshore locations off Oahu, resulting in 10 hours of squid footage. Using blob-tracking image processing techniques and a Particle Filter state estimator, the squid can be detected and tracked. The position, velocity, and acceleration of the squid relative to the stationary ROV can be determined. Experiment …

Model Of Gene Expression In Extreme Cold - Reference Transcriptome For The High-Antarctic Cryopelagic Notothenioid Fish Pagothenia Borchgrevinki, Kevin T. Bilyk, C. H.Christina Cheng

Department of Biology Faculty Scholarship and Creative Works

Background: Among the cold-adapted Antarctic notothenioid fishes, the high-latitude bald notothen Pagothenia borchgrevinki is particularly notable as the sole cryopelagic species, exploiting the coldest and iciest waters of the Southern Ocean. Because P. borchgrevinki is a frequent model for investigating notothenioid cold-adaptation and specialization, it is imperative that " omic" tools be developed for this species. In the absence of a sequenced genome, a well annotated reference transcriptome of the bald notothen will serve as a model of gene expression in the coldest and harshest of all polar marine environments, useful for future comparative studies of cold adaptation and thermal …

Incorporating Satellite Derived Cloud Climatologies To Improve High Resolution Interpolation Of Daily Precipitation., Adam M. Wilson, Benoit Parmentier, Brian Mcgill, Rob Guralnick, Walter Jetz

Yale Day of Data

Conservation of biodiversity demands comprehension of evolutionary and ecological patterns and processes that occur over vast spatial and temporal scales. A central goal of ecology is to understand the factors that control the spatial distribution of species and this has become even more important in the face of climate change. However, at global scales there can be enormous uncertainty in environmental data used to model species distributions. Even ‘simple’ metrics such as mean annual precipitation are difficult to estimate in areas with few weather stations and available data sets do not quantify uncertainty in these surfaces. We are developing a …

Avoidance Of Apoptosis In Embryonic Cells Of The Annual Killifish Austrofundulus Limnaeus Exposed To Anoxia, Camie Lynn Meller, Jason E. Podrabsky

Biology Faculty Publications and Presentations

Embryos of the annual killifish Austrofundulus limnaeus have unequalled ability among vertebrates to survive long-term anoxia. Surprisingly, these embryos can survive for months in anoxia despite a large-scale decrease in ATP levels during the initial hours of anoxic exposure. These conditions are known to trigger apoptotic cell death in mammalian cells as a result of ischemia or anoxia. Anoxia-induced induction of apoptosis was investigated in four developmental stages of A. limnaeus that differ in their tolerance of anoxia, and thus may respond to anoxia uniquely. Exposure to staurosporine was used to determine if A. limnaeus cells were competent …

Comt1 Gene Fiber-Specific Promoter Elements From Poplar, Chung-Jui Tsai, Edward Odhiambo Anino

Michigan Tech Patents

Polynucleotide constructs contain fiber-specific elements which are used to target expression of polynucleotides and polypeptides to the vascular fibers of a plant. The constructs can be contained within a vector. Transgenic plants transformed with the fiber-specific elements can e made which have expression of polynucleotide or polypeptide directed to the plant fibers.

Phylogeny Of The Tribe Psoraleae In North America, Rebecca Schaeffer, Dr. Keith Crandall

Journal of Undergraduate Research

Many species of plants in the Leguminosae family are important economically, but many of these plants are now considered rare, threatened, or endangered. Seventy percent of the species in the genus Pediomelum are highly limited in geographic distribution, which influences conservation status. In addition to this, very little work with phylogenetic studies has been done on this group. Learning about evolutionary relationships within these species is a first step to understanding more about their conservation status.

Radiological Analysis Of Osteoarthritis In The Mouse Knee Joint, Mark Newcomer, Dr. Robert Seegmiller

Journal of Undergraduate Research

The U.S. Department of Health and Human Services cites that nearly 21 million Americans currently suffer from osteoarthritis (OA) and has recently issued a news release which states that, “Today, 35 million people, 13 percent of the U.S. population, are 65 and older, and more than half of them have radiological evidence of osteoarthritis in at least one joint. By 2030, an estimated 20% of Americans – about 70 million people – will have passed their 65th birthday and will be at increased risk of OA.” Arthritis can present itself in many ways and degrees of severity. Osteoarthritis is by …

Members Of The Church Of Jesus Christ Of Latter-Day Saints In The Middle Missouri River Valley (1846-1853) Recreating A Legacy Of Faith, Tiffany Taylor, Dr. Shauna C. Anderson

Journal of Undergraduate Research

In 1846, after escaping mob persecution in Nauvoo, Illinois, members of The Church of Jesus Christ of Latter-day Saints established communities along the Missouri River in both Iowa and Nebraska. Approximately 90 settlements were created within seven years, with the most well-known being Winter Quarters.

The Use Of 13c/12c And 15n/14n Stable Isotope Ratio Analysis To Determine Carnivory Level In Gender Identified Free-Ranging Utah American Black Bears (Ursus Americanus), Eric Olsen, Beverly Roeder

Journal of Undergraduate Research

Stable isotope analysis of carbon (13C/12C or d13C) and nitrogen (15N/14N or d15N) has been shown to provide a more accurate estimate of overall diet in various mammalian species (Sponheimer et al. 2003). This technique was used to determine the amount of vegetation and animal protein in the nutritional uptake of free ranging Utah black bears (Ursus americanus). Samples were obtained from harvested bears taken during the fall 2005 and spring 2006 hunt from various regions of Utah via the Utah Division of Wildlife Resources (UDWR). Gender was reported by the hunters at time of harvest. Age was determined by …

Meeting The Needs Of Diabetic Patients: An Examination Of Type 2 Diabetes Treatments In Ghana, Ashley Valdivieso, Dr. Melinda Ostraff

Journal of Undergraduate Research

Diabetes is an escalating health risk in Ghana, and it is estimated that approximately 22% of Ghanaians who develop the disease will die of it.1 While government programs intended to provide treatment for diabetes patients have focused on traditional western medicine, Dr. Kwabena Beecham, President of the Ghana Diabetes Association reports that “over 50% of people with diabetes do not experience full health and quality of life despite the availability of medicine.” 3 Studies have also shown that some diabetics have chosen not to treat the disease at all.4 This apparent failure to meet the needs of diabetes patients indicates …

A Higher Resolution Multiplexed Microsatellite Marker Set For Reliable, Cost Effective Genotyping, Robert J. Kolts, Elliott G. Richards, Sam Ashby, Will D. Brubaker, Aaron C. Ferguson, Paul Fjeldsted, Derek Hatch, Dr. Edward R. Wilcox

Journal of Undergraduate Research

We are creating a new microsatellite marker set for public use. Because many projects involving genetic disorders in humans depend on microsatellite markers, there is an existing need for a reliable and cost-effective marker set that provides higher-quality statistical data while still being affordable. Our proposed set will consist of approximately 800 markers and currently has a rough spacing of one marker every 4.1 cM. The average heterozygosity is currently 0.85. To further reduce costs to users, we are arranging markers and corresponding PCR primers into ~178 multiplexed groups consisting of 4-5 markers each. These multiplexed groups will allow research …