Digital Commons Network^™

Ngasp - The Nematode Genome Annotation Assessment Project, Avril Coghlan, Tristan J. Fiedler, Sheldon J. Mckay, Paul R. Flicek, Todd W. Harris, Darin Blasiar, Lincoln D. Stein

Biomedical Engineering and Sciences Faculty Publications

While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets across 10 Mb of the C. elegans genome. Predictions were compared to reference gene sets consisting of confirmed or manually curated gene models from WormBase. Results: The most accurate gene-finders were …

Estimating Total Phosphorus And Total Suspended Solids Loads From High Frequency Data, Amber Spackman Jones

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Frequently measured turbidity was examined as a surrogate for total phosphorus (TP) and total suspended solids (TSS) loads at two locations in the Little Bear River, Utah, USA. Using regression techniques, equations were developed for TP and TSS as functions of turbidity. The equations accounted for censored data, and additional explanatory variables to represent hydrological conditions were considered for inclusion in the equations. By using the resulting surrogate relationships with high frequency turbidity measurements, high frequency estimates of TP and TSS concentrations were calculated. To examine the effect of sampling frequency, reference loads were determined from the concentration records for …

Community-Based Inquiry Improves Critical Thinking In General Education Biology, Ian J. Quitadamo, Celia L. Faiola, James E. Johnson, Martha J. Kurtz

All Faculty Scholarship for the College of the Sciences

National stakeholders are becoming increasingly concerned about the inability of college graduates to think critically. Research shows that, while both faculty and students deem critical thinking essential, only a small fraction of graduates can demonstrate the thinking skills necessary for academic and professional success. Many faculty are considering nontraditional teaching methods that incorporate undergraduate research because they more closely align with the process of doing investigative science. This study compared a research-focused teaching method called community-based inquiry (CBI) with traditional lecture/laboratory in general education biology to discover which method would elicit greater gains in critical thinking. Results showed significant critical-thinking …

Evolution Of The Holozoan Ribosome Biogenesis Regulon, Seth J. Brown, Michael D. Cole, Albert J. Erives

Dartmouth Scholarship

The ribosome biogenesis (RiBi) genes encode a highly-conserved eukaryotic set of nucleolar proteins involved in rRNA transcription, assembly, processing, and export from the nucleus. While the mode of regulation of this suite of genes has been studied in the yeast, Saccharomyces cerevisiae, how this gene set is coordinately regulated in the larger and more complex metazoan genomes is not understood. Here we present genome-wide analyses indicating that a distinct mode of RiBi regulation co-evolved with the E(CG)-binding, Myc:Max bHLH heterodimer complex in a stem-holozoan, the ancestor of both Metazoa and Choanoflagellata, the protozoan group most closely related to animals. These …

Lis1 And Ndel1 Influence The Timing Of Nuclear Envelope Breakdown In Neural Stem Cells, Sachin Hebbar, Mariano T. Mesngon, Aimee M. Guillotte, Bhavim Desai, Ramses Ayala, Deanna S. Smith

Faculty Publications

Lis1 and Ndel1 are essential for animal development. They interact directly with one another and with cytoplasmic dynein. The developing brain is especially sensitive to reduced Lis1 or Ndel1 levels, as both proteins influence spindle orientation, neural cell fate decisions, and neuronal migration. We report here that Lis1 and Ndel1 reduction in a mitotic cell line impairs prophase nuclear envelope (NE) invagination (PNEI). This dyneindependent process facilitates NE breakdown (NEBD) and occurs before the establishment of the bipolar spindle. Ndel1 phosphorylation is important for this function, regulating binding to both Lis1 and dynein. Prophase cells in the ventricular zone (VZ) …

Darwin At The Drugstore? Testing The Biological Fitness Of Antibiotic Resistant Bacteria, Alan L. Gillen, Sarah Anderson

Faculty Publications and Presentations

The issue of antibiotic resistance in bacteria is growing. For example, methicillin-resistant Staphylococcus aureus (MRSA) is a leading human pathogen. New strains of MRSA are resistant to methicillin and numerous other antibiotics, placing the patient in significant danger. Indeed, the Centers for Disease Control revealed in 2007 that the number of deaths due to MRSA exceeded that of AIDS in the United States. It is no wonder that antibiotic resistance is one of the most significant and important health care issues. The ability of bacterial pathogens to evade traditional antibiotics is faster than the drug makers’ ability to make new …

Dna Sequence Analysis Of A Bioluminescent Marine Bacterium, Benjamin Ryder

Master's Theses, Dissertations, Graduate Research and Major Papers Overview

Studies the sequencing of the DNA fragment containing the gene phaC (PHA synthase) and undertakes the search for open reading frames and putative gene matches in a bioluminescent marine bacterium.

Dna Inside, Lori B. Andrews

Lori B. Andrews

The Reproductive Ecology Of Graptemys Geographica In The Central Canal, Kati Keppen Rush

Undergraduate Honors Thesis Collection

Life for all organisms involves carefully managing a limited amount of resources. In many cases these resources affect how organisms Jive on a daily basis. In addition to competition from other species, organisms face competition within their own species, populations, and niches. Those individuals that manage their resources effectively will increase their chances of survival, reproduction, and the continuation of their genes in the gene pool. Studies that focus on life history characteristics of organisms aim to understand the mechanisms used by organisms to increase the chances that their genes will remain in thegenepoolpasttheirown Iifetime.Thegoal ofthesemechanisms istoensuresurvival and maximize reproduction. …

Characterization Of The Interaction Between The Fanconi Anemia (Fa) D2 Protein And Proliferating Cell Nuclear Antigen (Pcna), Carolyn Schmiedel

Senior Honors Projects

No abstract provided.

Stomatal Conductance Of Malosma Laurina In Frequently Burned And Non-Frequently Burned Sites, Kamron A. King, Matthew T. Bender, Stephen D. Davis

Featured Research

In the months following the Malibu fires, the fire zones have experienced and abundance of new growth. Among this new growth, there are differences that can be observed when comparing the top of the Malibu hill (frequent fire zone) to the base of the hill (nonfrequent fire zone). As the chaparral resprouted we noticed the behavior of the Malosma laurina in both frequent and non-frequent fire zones and stomatal conductance, height, and water potential were tested for plants in the two varying zones, with plants in the non-frequent fire zone outperforming their counterparts.

Soil Moisture Adjacent The Roots Of Post-Fire Ceanothus Megacarpus And Malosma Laurina, Kristi Holly, Kelly Sayre, Anson Snow

Featured Research

Hydraulic lift is a passive process in which a plant will bring water from subsoil to topsoil levels through its roots. In this experiment, we compared the soil moisture levels in the area surrounding two different chaparral species C. megacarpus, a shallow rooted nonsprouter, and M. laurina, a deep-rooted obligate sprouter, in order to determine the hydraulic lift patterns of chaparral as they regrow after fire. Furthermore, the C. Megacarpus had died due to the Malibu fire, while the M. Laurina was resprouting. Therefore, using a Hydrosense Soil Water Measurement System, we measured soil moisture percentages, and the results showed …

The Effect Of Fire Frequency On The Presence Of Native And Nonnative Species In The Santa Monica Mountains, Bobby Boss, Simone Ross, Taryn Thompson

Featured Research

We surveyed two sites in the Santa Monica Mountains of Southern California that experienced both high and low fire frequency (Figure 1). Our objective was to find out if increased fire frequency allowed for the invasion of non-native species. We collected data on herbaceous coverage and point to plant distance of woody chaparral species. A series of random points were used, and each area was divided up into four equal quadrants using two meter sticks. The individual nearest to the center in each quadrant was then identified and measured. To measure herbaceous coverage, percentages were took of cover of each …

Physiological Performance In Full-Sun Vs. Shaded Post-Fire Malosma Laurina Seedlings, Lindsey A. Murphy, David C. Valencia, Catherine D. Drummond

Featured Research

Post-fire Malosma laurina regenerates both by resprouting and by disseminating seeds. The objective of this study is to assess seedling performance either in full-sunlight or in artificially shaded treatments. By identifying under which conditions Malosma laurina seedlings grow more effectively, one can predict where post-fire M. laurina seedling communities will thrive. The methodology employed throughout this experiment began by covering existing seedlings with shade cloth held by wooden stakes. These treatments were adjacent to full-sun environments; each of which contained at least two Malosma laurina seedlings. Six experimental sites were set up, and the seedlings in question were monitored for …

Reproductive Biology Of The Coyote (Canis Latrans): Integration Of Behavior And Physiology, Debra Anne Carlson

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Wild Canis species possess a unique suite of reproductive traits including social monogamy, copulatory lock/tie, and biparental care. Females are seasonally monestrous and experience an obligatory pseudopregnancy after spontaneous ovulation. While these characteristics have been ascribed to coyotes, an integrated profile of behavior and physiology has not yet been described. In this study, temporal correlations between steroid hormone levels and socio-sexual mating behaviors were documented, as were changes in vaginal epithelium. Pseudopregnancy was compared to pregnancy by contrasting hormone (progesterone, estradiol, prolactin and relaxin) profiles of unmated females to patterns obtained in alternate years when they bred. Meanwhile, social interactions …

Foraging Preference By Wild Deer On Toyon (Heteromeles Arbutifolia) From Santa Catalina Island Versus Malibu, Amelia I. Clark, Brett Smith, Courtney Smith, Stephen D. Davis

Featured Research

Our group collected samples of Heteromeles Arbutifolia from both Santa Catalina Island and Pepperdine University’s campus in Malibu, CA in order to compare the morphological differences and deer preference between them. In our experiment, we planted the H. Arbutifolia from both locations side by side on a hillside overlooked by the Thorton Administration Center building on Pepperdine’s campus. In the first trial the deer did not consume either of the samples; we believe this was due to the length of time from when the branches were collected from the island to when they were introduced to the deer on campus. …

Comparison Of Post-Fire Growth Rates Between Elymus Condensatus And Yucca Whipplei In Coastal Chaparral, Jae K. Chung, Andrew J. Ishibashi, Francisco B. Sapigao

Featured Research

The two monocot species, Yucca whippelei and Elymus condensata chosen for this study are two co-occurring species on the Pepperdine campus. We chose 6 samples of each species and looked at parameters that would allow us to compare their post fire growth rates. These parameters included leaf area index, internal CO2 levels, transpiration rate, and photosynthetic rate. We used the Students T-test on the means of each parameter and found significant differences in leaf area index, internal CO2 levels, and transpiration rate. All of these were greater in the Yucca except for the leaf area index. We concluded that, because …

Growth Sequence Of Post-Fire Chaparral Resprouts In California’S Santa Monica Mountains, Iolana N. Kaneakua, Kelly L. Reynolds, Luke S. Walsh

Featured Research

The post-fire resprout succession of California Chaparral was surveyed in Corral Canyon of the Santa Monica Mountains. The primary objective of this investigation was to determine the sequence of Chaparral post-fire resprouts and possible correlations to the life histories of those species. Over a three month period, four designated study sites were visited every two weeks, surveying the number of adults, the number of resprouts and the height of the resprouts. It was found that both the facultative and the obligate typed species were successful in post-fire resprout. Facultative species were the first to resprout and obligate species displayed the …

Effects Of Shading On Post-Fire Seedlings Of Laurel Sumac (Malosma Laurina) In The Santa Monica Mountains, Anastasia N. Fry, Jennifer A. Sledge, Drew A. Almodovar

Featured Research

The interactions between post-fire plants is crucial directly after fire. A recent fire on Pepperdine campus allowed for a study to be performed on these interactions. The dominant chapparal plant, Malosma lauraina, laural sumac, both re-sprouts and grows from seeds after fire. Marah Macrocarpus, wild cucumber, grows rapidly after rain following a fire. Some M. lauraina seedlings end up under the M. Macrocarpus yet survive. This study aimed to find differences between those seedlings interacting with M. Macrocarpus and those that are not. Three groups of specimen were used. One control group grew in the sun, one control group in …

Peer Review In An Undergraduate Biology Curriculum: Effects On Students’ Scientific Reasoning, Writing And Attitudes, Briana Eileen Timmerman

Faculty Publications

Scientific reasoning and writing skills are ubiquitous processes in science and therefore common goals of science curricula, particularly in higher education. Providing the individualized feedback necessary for the development of these skills is often costly in terms of faculty time, particularly in large science courses common at research universities. Past educational research literature suggests that the use of peer review may accelerate students’ scientific reasoning skills without a concurrent demand on faculty time per student. Peer review contains many elements of effective pedagogy such as peer-peer collaboration, repeated practice at evaluation and critical thinking, formative feedback, multiple contrasting examples, and …

A Tale Of Two Investigations In Molecular Biology: The Use Of Pcr Technology To Identify Bacteria Containing Genes For Pha Synthesis And The Antibiotic Sensitivity Profile Of Vibrio Species B-18, Diana B. Lizarazo

Honors Projects

The Vibrio species, B-18, produces PHA, a bacterial storage material with application as a biodegradable plastic. Phase one of this project aimed at determining if PCR technology could be used to find other bacteria that produce a similar type of PHA. Results showed that the primer sets utilized were not able to identify bacteria with PHA genes. Phase two hoped to discover if it would be possible to introduce Escherichia coli plasmids into B-18 using electroporation. Results demonstrated that electroporation was not useful for introducing plasmids into B-18.

The Biology, Nymphal Stages, And Life Habits Of The Endemic Sand Dune Cricket Schizodactylus Inexpectatus (Werner, 1901) (Orthoptera: Schizodactylidae), Gökhan Aydin, Andrey Khomutov

Turkish Journal of Zoology

The biology, nymphal stages, and life habits of the endemic dune cricket Schizodactylus inexpectatus (Werner, 1901) (Orthoptera: Schizodactylidae) were investigated in this study carried out between 2000 and 2007 in the Çukurova delta (Adana province) and in Alata (Mersin province), Turkey. The study showed that S. inexpectatus, which is a nocturnal insect, passes through 9 nymphal stages, each characterised by its own body size. The present study showed that certain properties of burrows, such as their depths, do not depend on either adult or immature stages of the insect. Food preferences of cannibalistic species of S. inexpectatus were also investigated …

Proper Cellular Reorganization During Drosophila Spermatid Individualization Depends On Actin Structures Composed Of Two Domains, Bundles And Meshwork, That Are Differentially Regulated And Have Different Functions, Tatsuhiko Noguchi, Marta Lenartowska, Aaron D. Rogat, Deborah J. Frank, Kathryn G. Miller

Biology Faculty Publications & Presentations

During spermatid individualization in Drosophila, actin structures (cones) mediate cellular remodeling that separates the syncytial spermatids into individual cells. These actin cones are composed of two structural domains, a front meshwork and a rear region of parallel bundles. We show here that the two domains form separately in time, are regulated by different sets of actin-associated proteins, can be formed independently, and have different roles. Newly forming cones were composed only of bundles, whereas the meshwork formed later, coincident with the onset of cone movement. Polarized distributions of myosin VI, Arp2/3 complex, and the actin-bundling proteins, singed (fascin) and quail …