Tag: Biology

Genetic Basis of Evolution of Armor Phenotypes in Threespine Stickleback

Presenter: Taylor Wilson, Biology

Poster: D-6

Mentor: William Cresko, Biology

Differences in physical traits among species arise first as variations within and among populations. Studying this intraspecific variation provides important new knowledge about the process that gives rise to biodiversity. To better understand this variation and its genetic and developmental basis I am studying a small fish, the threespine stickleback (Gasteroseus aculeatus). The threespine stickleback is undergoing rapid evolution in bodies of water recently formed by uplift and glacial melt, diverging into very different anadromous and freshwater life history forms. With each saltwater-to-freshwater evolutionary transition, there is a reduction in the stickleback’s bony armor plates and characteristic spines. In order to discover the genetic basis for the diversity of armor phenotypes, I am measuring variation in the size and number of lateral and pelvic armor structures of 148 stickleback collected from the McKenzie River in Springfield, OR. The genetic variation in these same individuals has been measured using high-throughput sequencing techniques.

We are correlating these genetic data with specific aspects of the armor variation, such as spine lengths and plate sizes. This is the first such study in stickleback, and is providing us with key information on which genes are responsible for the rapid evolution in some of the phenotypes of the threespine stickleback. My results will have general importance beyond stickleback by providing new knowledge about the genetic and genome basis of evolution in the wild.

Effect of Mutations Within the DNA Binding Domain on Ancestral Steroid Hormone Receptors’ Specificity to DNA Response Elements and Protein Stability

Presenter: Greg Hanak, Biology

Poster: B-3

Mentor: Joe Thornton, Biology

The steroid hormone receptor (SR) family is a group of proteins that activate transcription via the binding of DNA response elements. We believe that the present day SRs found in animals, which include the estrogen, androgen, progestagen, mineralocorticoid and glucocorticoid receptor, all evolved from one ancestral receptor protein (ancSR1). The ancSR1, which had the ability to activate transcription via the binding of DNA estrogen response elements (EREs) in response to estrogens, gave rise to another ancestral receptor (ancSR2) that carried the ability to bind the DNA response elements associated with all the SRs except the EREs that were recognized by ancSR1. Examination of the ancSR1 and ancSR2 on a molecular level showed a number of differences in the amino acid sequence between the two receptors, some being within the P-box of the DNA binding domain (DBD). The question then becomes how are these P-box mutations contributing to the specificity of the ancSR2 protein. We predict that the derived P-box in ancSR2 is eliminating positive contact with EREs. To prove this, biophysical and biochemical experiments such as thermal melts, guanidine melts and DNA binding assays will be run on the DBDs of these two ancestral proteins and two different supposed intermediates of ancSR1 and ancSR2. The data gained from these experiments and the inferences made will help us better understand the series of events leading up to the formation of the current, distinct SRs and, more importantly, how and why they function as they do.

Enhancer-GAL4 Database Yields Subsets of Gene Expression

Presenter: David Bauer, Kris Haenderson, Allison Wilbur, Biology

Poster: A-2

Mentor: Chris Doe, Biology

Enhancers and suppressors are major controls in the tempro-spatial expression of a gene. Prior work has shown that enhancers may be made up of small modules, each driving only a small subset of expression in an overall pattern that we associate with a gene. The Rubin lab at Janelia Farms Research Center created over 70,000 fragment sequences from more than 1,100 neural gene regions. These fragment enhancer sequences were used to generate site-specific transgenic GAL4 expressing Drosophila lines. These lines are currently being screened by several collaborating labs for their ability to function as transcriptional enhancers to drive limited subsets of UAS-GFP expression. Our lab’s role is to screen Drosophila embryos for neural expression patterns of the transgenic enhancer fragment lines. As a test analysis, we took a subset of 82 individual fragment enhancer lines derived from seven gene regions in embryonic nerve cords (VNC). These 82 lines produced 77% of fragments with expression in the VNC. Within that expressing set, 62% drove small patterns of less than ten cells per hemisegment. This data complements the screening results collaborative labs are finding in Drosophila larval brains. Together, these results show that the theory of enhancers being a set of modules acting in concert to yield an overall pattern of gene expression seems quite likely. The end result should be a valuable tool that can be used for studies of gene control, patterning, and neuronal circuitry.

Zebrafish and Related Species as a Model of Evolutionary Development

Presenter: Andrew Delapaz, Biology

Poster: A-6

Mentor: Braedan McCluskey, Biology

Out of the nearly 60,000 species of known vertebrates, fish comprise nearly half of the group. Natural selection has created the spectrum of sizes, shapes, and colors seen in fish. However, the developmental mechanisms underlying these differences are still unknown. The zebrafish (Danio rerio) is a common model for development and genetics. Our specific purpose is to understand differences in anatomical structure development between zebrafish and related species. The sensory “whiskers” found on fish, also known as barbels, differ greatly within this genus and therefore are ideal to study. To investigate the genetics behind barbel development in Danio, we measured and compared barbel size and number in different species and hybrids between these species. These hybrids can be used to determine if a characteristic is inherited in a dominant or additive fashion. The species we used were zebrafish (D. rerio), and dwarf zebrafish (D. nigrofasciatus). We chose these species because in addition to clear differences in body size, D. rerio has two pairs of barbels, while D. nigrofasciatus has only one. The hybrids obtained from crossing these species had a single set of barbels, which were intermediate in length compared to the two parent species. These data indicate that barbel length and number are not determined by the same mechanism. By further researching barbels and other traits among this genus, we can deepen our understanding of how species diversity of vertebrates evolves.

Deciduous Teeth Show Close Relationships Between Oreodont Genera (Eucrotaphus, Merycochoerus and Promerycochoerus)

Presenter : Kendra Walters

Mentor : Edward Davis

Major : Biology

Poster 27

Oreodonts lived during the Cenozoic Era, particularly from the Eocene to Miocene Epochs. They were abundant in the past but have no modern descendants. Classifying oreodonts is a difficult task because there is disagreement on the species, genus and subfamily classifications of many individual oreodont groups. The three genera of oreodonts we examined (Promerycochoerus, Merycochoerus, and Eucrotaphus) have experienced this problem and are divided between two to three different subfamilies. Our examination of the deciduous teeth of four individuals from these three genera found great morphological similarity, indicating a closer relationship than is currently recognized. We examined two individuals of Eucrotaphus trigonocephalus, one individual of Merycochoerus sp., and one of Promerycochoerus carrikeri from the collection at the University of California Museum of Paleontology. The deciduous premolars from all three genera are tellingly similar, varying only in size, and match previous descriptions of Promerycochoerus carrikeri. Simi- larities are especially evident in the last two deciduous premolars. These similar characters contradict the current subfamily divisions, indicating a close relationship between all three genera. We propose a re-division of oreodont subfamilies that reflects this close deciduous morphology. We also recognize synonymy of Promerycochoerus and Merycochoerus, as our examination primarily found size differences between them that we do not accept as genus-level distinctions.

Do Distinct Types of Progenitors Contribute to Enteric Nervous System Development?

Presenter : Charlotte Taylor

Major : Biology

Mentor : Judith Elsen

Poster 10

The enteric nervous system (ENS), the largest component of the peripheral nervous system, provides intrinsic innervation of the intestinal tract and modulates gut function. The ENS forms a complex network of different neuronal subtypes and glial cells. ENS progenitors originate in the hindbrain, migrate to the gut, migrate caudally along the gut in two parallel streams, and eventually encircle the gut. ENS progenitors express different marker genes, e.g. phox2b, sox10, and ret. Our goal is to take advantage of the zebrafish model to learn whether expression of these marker genes designates distinct ENS progenitor populations. We used a phox2b:GFP transgenic line that expresses in ENS progenitors and double fluorescent in situ hybridization to quantify progenitor marker gene expression and colocalization in GFP+ cells. Our analysis suggests that subpopulations of enteric progenitors are present during zebrafish ENS development. These subpopulations are characterized by the following marker combinations: phox2b/sox10/ret, phox2b/ret, and phox2b. Our data also suggest that phox2b and sox10 expression is consistent along the length of the gut and ret expression is higher caudally. Our next step is to conduct lineage tracing studies to learn if distinct ENS progenitor subpopulations give rise to different ENS cell types, by tracing the offspring of genetically labeled subpopulations of progenitors. Traditionally, the Supreme Court has deferred to the President in times of war; however, following 9/11 the Court took an active role in placing limits on the President’s unilateral pow- ers. The Court’s decisions in these cases were effective in restraining Executive power, but they only somewhat protected and restored the detainees’ civil liberties. The protection of certain individual rights has been followed by the curtailment of others. Currently, the Obama Administration is facing criticism for the indefinite detention of detainees, and this study provides a framework which outlines how civil liberties can again begin to be restored.

The Role of the BAF Chromatin Remodeling Complex during Heart Valve Development

Presenter : Maithri Sarangam

Mentor : Kryn Stankunas

Major : Biology

Poster 56

Human heart valves are remarkable structures that open and close billions of time during a lifetime. Like any structure under constant mechanical strain, their shape and molecular composition are finely tuned to maximize efficiency and longevity. The development of these valves must also be finely tuned to produce proper the shape and composition, or dangerous health consequences may arise. We are studying the developmental processes of valve formation. Particularly, we are interested in the role of the BAF chromatin remodel- ing complex. Chromatin refers to the complex of DNA and histone proteins. Cell nuclei contain a series of cylindrical histone com- plexes, around which DNA is wrapped. The structure resembles a single thread wrapped around a series of spools with approximately
2 loops per spool. The BAF complex regulates gene expression by altering nucleosome positioning. We believe the BAF complex is required for the proper development of the aortic and pulmonic valves. We used mouse models and complex mouse genetic techniques to study the role of the BAF complex on mammalian heart valve development. Using a crelox system, we caused a loss of function of the BAF complex by knocking out Brg1, the key ATP-ase required for the complex to function. We then used various staining methods to study the resulting phenotype at different time points during the later stages of development. The results suggest that the BAF complex is required for proper organization of the valve shape and molecular composition.

Altered Lung Development in Growth Restricted Offspring from Hypertensive Pregnant Rats

Presenter : Alice Rear

Mentor : Jeffrey Gilbert

Major : Biology and Human Physiology

Poster 37

Recent studies suggest that angiogenic dysregulation in utero impairs fetal pulmonary vascular development and arrests normal alveolarization, potentially contributing to the pathogenesis of bronchopulmonary dysplasia (BPD). Since reduced utero-placental perfusion (RUPP) induced hypertension is associated with angiogenic imbalance (soluble fms-like tyrosine kinase-1, sFlt-1; and vascular endothelial growth factor, VEGF) in the maternal circulation and amniotic fluid, we hypothesized it would result in abnormal alveolarization, diminished pulmonary vascular development, and impaired VEGF signaling in the fetal rat lung. Fetal lung tissue and amniotic fluid were collected on day 19 of gestation from RUPP and normal pregnancies (NP). A second cohort delivered pups that were weighed at birth and lungs were collected at 10 weeks of age. Fetuses from RUPP pregnancies were smaller at day 19 (2.1 vs. 2.6 g; P<0.05) of gestation and at birth (6.1 vs. 6.7 g; P<0.05) than NP offspring. Preliminary data suggests that RUPP offspring may have reduced (20% decrease) pulmonary vascularity and alveolar simplification (45% decrease in alveolar space) when compared to normal pregnant controls. VEGF receptor-2 was decreased (48%; P< 0.05) in the lungs of day 19 RUPP offspring. These data suggest that chronic placental insufficiency has detrimental effects on the developing pulmonary vasculature and alveoli, and support the hypoth- esis that angiogenic imbalance in utero may play an important role in the pathogenesis of BPD

Variation Through Tooth Wear Obscures the Differential Diagnoses of the Fossil Beavers Dipoides stirtoni and Dipoides smithi

Presenter : Savannah Olroyd

Mentor : Sam Hopkins

Major : Biology

Poster 30

Diagnostic features that show variation can be problematic when their variation interferes with clear distinction between species. Fossil identification can be further confounded when highly variable supposedly diagnostic dental characters change with tooth wear. The fossil beavers Dipoides stirtoni and Dipoides smithi are distinguished from one another by the presence or absence of striations on the fourth premolars. D. stirtoni has a parastria running down the cheek side of the upper P4 and a parastriid on the tongue side of the lower p4 in all wear stages. D. smithi lacks the parastria and only occasionally has a parastriid in later wear stages.

We have reviewed this diagnosis by examining over 200 cheek teeth of both species. No well-worn upper P4s of D. smithi have a para- stria, but the parastria is present in the earlier wear stages of all upper cheek teeth. Approximately 25% of the lower p4s of D. smithi studied have a parastriid in later wear stages, and one D. stirtoni lower p4 had no parastriid. We investigated other dental characters to see if other features were diagnostic to these species. The two are indistinguishable in tooth size, molar shape, and wear stages. The cur- rent diagnosis makes confident identification of new specimens difficult unless the specimen includes a well-worn upper P4. Complex series of tooth wear can produce a large amount of apparent dental variation in mammals with high-crowned teeth. Caution should be taken when using dental characters to assign diagnoses to such taxa.

Examination of Executive Function Measurements in Healthy Adolescents and Young Adults

Presenter : Madison Murray

Mentor : Li-Shan

Major : Biology

Poster 42

Executive function has been defined as the ability to utilize external stimuli in order to plan purposeful action. It is thought to be im- portant for tasks like problem solving and decision-making. As the adolescent brain has not yet reached full maturation and is under- going rapid development particularly in the frontal lobe, where executive function is considered to take place, it may be vulnerable to trauma during this time of life. Due to the continued development of the frontal lobe in the adolescent brain it was hypothesized that healthy adolescent individuals would have decreased executive function ability when compared to healthy young adults. The Attention- al Network Test and the Task Switching Test were administered to 14 healthy individuals (7 adolescents, 7 young adults) five times over a period of two months. Testing was carried out 1 week, 2 weeks, 1 month, and 2 months after the initial testing. Testing was performed in a computer lab to free from noise or visual distractions. Young adults displayed faster overall reaction times, however contrary to our hypothesis; preliminary data has shown that adolescents have increased executive function ability compared to young adults. Further research will examine the effects of concussion of the adolescent brain compared with an adult brain. In order to make an accurate comparison between concussed individuals we must first compare healthy individuals.