1 gb display only

The Sierra Nevada yellow-legged frog (Rana sierrae), which has been extirpated from over 90% of its historic range, is one of the most threatened amphibian species in California. In order to develop conservation techniques to promote the recovery of this once abundant species, we closely monitored a population of R. sierrae in the Desolation Wilderness, CA, that continues to persist in spite of infection with the amphibian chytrid fungus, Batrachochytrium dendrobatidis (Bd). We marked all individuals using passive integrated transponder (PIT) tags, and we monitored individual infection levels over the course of two years using qPCR. In addition, we collected bacterial cultures from the skin of 60 individuals, and we conducted in vitro Bd-inhibition trials in order to identify strains of bacteria with anti-fungal properties, which could be used as probiotic treatments in future conservation interventions. Finally, we collected skin microbiome samples from individually marked R. sierrae at four intervals throughout each summer active season, and we used next generation sequencing to analyze changes in species composition and community structure in R. sierrae’s resident skin microbes through time. This longitudinal analysis will contribute to the successful development of future bioaugmentation interventions, since a basic understanding of microbial community dynamics will allow us to better predict the ability of a probiotic treatment to colonize a frog’s skin and persist in the long term.

48 GL

How does participation in the Teen Environmental Education Mentorship Program at NatureBridge Golden Gate impact TEEM participants ans their future?

By: Stephen Kielar

Marine Biology

Faculty Advisor: Dr. Kimberly Tanner

Many informal learning environments such as aquariums, zoos, museums and outdoor education facilities offer programs that aim to expose high school students to careers in science and the environment. The Teen Environmental Education Mentorship, TEEM as it will be referred to, is one of these programs. TEEM is a year-long paid environmental education internship and leadership program for San Francisco Bay Area high school participants. The TEEM program takes high school students out of their urban and suburban communities of San Francisco and Marin counties and into the Marin Headlands, part of the Golden Gate National Recreation Area, once a week. At Naturebridge, TEEM participants teach younger students, currently at the Naturebridge campus, environmentally-themed lessons. TEEM participants work with each other as well as full time educators at Naturebridge who act as mentors for the TEEM participants to help create and assess these lessons. On the weekends, the TEEM participants also take part in stewardship activities throughout the San Francisco Bay Area. Many organizations put a lot of time and resources into these types of high school programs; however, it is difficult for organizations to conduct formal assessments of the impact these programs have on their participants (Owen, 431). The TEEM program has been around in its current form since 2008. During this time there has been no significant assessment of the TEEM program. Our study looks to find what impact, if any, the TEEM Program at Naturebridge Golden Gate has on its participants. / Our research methods include an online survey along with audio-or video-taped interviews. The survey includes open ended as well as closed ended questions and is designed to collect data from as many TEEM alumni from 2008-14 as possible. The interviews are designed to gather more in-depth information about the TEEM experience for its participants. / As TEEM alumni report their recollections of the program and how it impacted them it is anticipated that the most prominent impacts will be observed around the following 3 themes: meeting new people, spending time in the outdoors, and teaching students at Naturebridge. I predict that they will be impacted most by the other team participants, followed by their team manager, and their mentors who are full time educators at Naturebridge. I predict that TEEM alumni will report that coming to the Marin Headlands once a week was a break from the stresses of high school life, as well as a place to reflect and connect with the environment. I predict that the strongest memories the TEEM alumni report about teaching will be the challenges of teaching diverse groups of students and co-teaching with other TEEM participants. I predict the majority of TEEM alumni will report a major benefit of the program was a substantial gain in self-efficacy in regards to communicating with people from different backgrounds. / While programs like TEEM expose high school students to careers in science and the environment, the main benefit of such programs may very well be in making meaningful social connections with peers from different backgrounds while working toward a common goal.

49 GL

Engineering Trypsin for development of Inhibitor Resistant Variants

By: Abriti Sharma

Biochemistry

Faculty Advisor: Dr. Teaster Baird Jr.

An effective therapeutic protease has to retain good catalytic efficiency and more resistant to its endogenous inhibitors. Since residues 39, 41 and 60 seem to have interactions with inhibitors that seem to be conserved, variants F41A, Y39A, F41G, Y39A/F41A were designed to have better understanding of enzyme-inhibitor interaction and allow us to make substitution for desired inhibitor binding effect.

50 GP1

Biophysical characterization of hemoglobin derivatives upon photodissociation of molecular oxygen from a cobalt peroxo complex

By: Abraham King Cada

Biochemistry

Faculty Advisor: Dr. Raymond Esquerra

Clarifying enzymatic reaction mechanisms is not only essential to provide insights into the fundamental biochemistry but also toward designing strategies that can inhibit or enhance enzyme function. Despite the recent advances in utilizing low-temperature conditions in capturing transient reaction intermediates, fundamental control of initiation and proper monitor of catalytic reactions remains a challenge. This study demonstrates the feasibility of photoinitiating oxygen dependent reactions using a cobalt complex, (mu-peroxo)(mu-hydroxo)bis[bis(bipyridyl)cobalt(III)]nitrate (HPBC). We show the release of dioxygen by HPBC with ultraviolet light at ambient and cryotemperatures. Deoxyhemoglobin and the formation of oxyhemoglobin upon irradiation of the complex will be monitored using UV/Vis spectroscopy and magnetic circular dichroism spectroscopy. Verification of the viability of HPBC in delivering dioxygen in situ under cryotemperatures combined with temperature-controlled spectroscopy can be used in studying fast reaction mechanisms that involve molecular oxygen.

51 GP1

Experimental Study of Particle Size Reduction in Debris Flows

By: Omid Arabnia

Earth and Climate Sciences

Faculty Advisor: Dr. Leonard Sklar

Rock particles in debris flows are reduced in size through abrasion and fragmentation. Wear of coarse sediments results in production of finer particles, which can alter the bulk material rheology influencing runout distance. Particle wear also affects the size distribution on hillslopes before delivering the sediment to the fluvial channel network. A better understanding of the controls on particle wear in debris flows is needed to infer flow conditions from debris flow deposits, estimate the initial size of sediments entrained in the flow, model debris flow dynamics, and map hazards. I used three rotating drums to create laboratory debris flows across a range of scales. Drum diameters range from 0.2 to 4.0 m, with the largest drum able to accommodate up to 2 Mg of debris, including boulders. I began the experiments with well-sorted, angular coarse particles, which evolved through particle wear in transport. The fluid was initially clear water, which rapidly acquired fine-grained wear products. After each 0.25 km of tangential travel distance, I quantified the particle size distribution. I calculated particle wear rates by fitting the Sternberg equation to the statistics of particle size and mass distributions. Mass wear rates are 2.9, 4.9. and 11%/km in the small, medium, and large drum, respectively. Rates of coarse particle wear and production of fragments and fine particles scale with the rate of energy expenditure per unit bed area, or unit drum power. I use this power scaling to estimate a mass particle breakdown rate of 13%/km at Inyo Creek, CA.

52 GP1

Impacts of Climate Variability on California Groundwater Resources

By: Claudia Corona

Geosciences

Faculty Advisor: Dr. Jason J. Gurdak

Current scientific research aims to better understand how water-resources respond to climate and anthropogenic stresses. However, such research has focused on the visible, accessible surface-water systems. The impact of climate on the subsurface, groundwater levels is poorly understood –an alarming finding, especially in California, where groundwater stores are the largest source of freshwater. The success of our water-resource management plans may rest on understanding climate variability’s effects on groundwater resources. I am a first-year graduate student in Dr. Gurdak’s Hydrogeology and Water Resources Research Lab, working on a National Science Foundation project to better understand the effects of climate variability on groundwater resources in California and beyond. Currently, I am developing models to correlate fluctuations in recharge rates and groundwater-levels to historical and future climate variability and future climate change scenarios. My research progresses our understanding of how climate impacts recharge, data that can be used improve national-scale groundwater models and sustainability studies—tools that help policy-makers, farmers and industrial stakeholders work together to ensure successful water-resource management strategies.

53 GP1

Bio-hydro-micrometeorology of a Sierra Nevada montane meadow

By: Suzanne Maher

Earth Sciences

Faculty Advisors: Dr. Andrew Oliphant and Dr. Jerry Davis

Montane meadows are common geomorphological features of the Sierra Nevada. They store, filter and regulate water and support wetland and riparian plant communities, which in turn provide unique wildlife habitat. Many of these meadows have been degraded by enhanced runoff and gullying primarily due to agricultural and extractive industries. Restoration techniques are being utilized in select meadows to redress the gullying and return the water table to pre-disturbance levels. The objective of this study is to examine the role of restoration practices on the ecohydrology of meadow ecosystems, particularly atmospheric exchanges of water, carbon, and energy. The rate and sign of these exchanges were measured using eddy covariance in a restored Sierra Nevada montane meadow during the growing season. Sampling and analysis of vegetation and soil was also conducted both within the measurement footprint and in a degraded meadow for comparison. The restored meadow ecosystem provides a sink for atmospheric carbon and source of atmospheric water, and has a high ratio of latent to sensible heat flux. There was also significantly higher soil moisture and organic content, vegetation diversity and density, and above- and below-ground biomass in the restored meadow as compared to the degraded meadow. /

54 GP1

Developing a Miniature Weighing Lysimeter for Measuring Plant-Atmosphere Water and Energy Exchanges on Living Roofs

By: Rubaya Pervin, Ian Santos, and Sergey Dusheyko

Geographic Information Science

Faculty Advisors: Dr. Andrew Oliphant and Dr. Hao Jiang

A miniature weighing lysimeter is a device for automated measurement of plant-atmosphere water exchanges through processes of evapotranspiration, dewfall, fog deposition and rainfall or irrigation. It can measure small changes in weight (<1 g) of plants and soil over periods of 30-minutes or less. The goal of this project is to develop a prototype network of accurate, low-profile, low-power and low-cost miniature weighing lysimeters for use in estimating water and energy budgets of living roofs. In this interdepartmental research and educational collaboration, we have combined expertise in bio-micrometeorology with electrical engineering and software development. In the presentation, we will display a prototype lysimeter system and present the design and test results from its development to date. /

55 GP1

Classification, vegetation-environment relationships, and distribution of plant communities on Southeast Farallon Island, California

By: Jamie Hawk

Resource Management & Env. Planning

Faculty Advisors: Dr. Barbara A. Holzman and Dr. Ellen Hines

We present the plant communities of Southeast Farallon Island and describe their relationships to environmental variables and disturbance factors. We sampled a total of 42 vegetation plots containing 26 taxa with a stratified random design across the 70-acre island. To classify the herbaceous communities we applied agglomerative hierarchical clustering, while the influence of site parameters was obtained using Nonmetric Multidimensional Scaling (NMDS) ordination. A total of five plant communities were classified, including two native plant assemblages (Spergularia macrotheca type and Lasthenia maritima type) and three invaded communities (Tetragonia tetragonioides type, Plantago coronopus type, and Mixed vegetation type). The strongest gradients in vegetation composition can be explained by solar heat load, dominance of substrate type, and edaphic factors (soil pH, salinity, depth). Physical disturbance and proximity to anthropogenic land use also influence plant community composition. A map of the classified vegetation types and other mapping units were created to better understand current patterns in vegetation and assist in long-term management of the island’s resources. Southeast Farallon Island is the largest seabird breeding colony south of Alaska and management is planning for intensive habitat restoration, therefore, a clear understanding of native and invaded plant communities and their vegetation-environment relationships is required.

56 GP1

Radar Studies of Coherent Waves at Ocean Beach, S.F.

By: Bruce Laughlin

Physics

Faculty Advisor: Dr. Roger Bland

Using data collected by a radar system installed at the south end of Ocean Beach, the phase relationships between waves arriving at the beach from different directions were studied. A method of observing constant phase relationships between waves was developed, allowing the identification of coherent waves arriving at the beach. This study quantifies a fundamental aspect of ocean gravity wave refraction around a bathymetric features (in this case the San Francisco Bar, a sandbar formed by tidal sediment deposition from the Golden Gate).

57 GP1

Fabrication of Hyperuniform Disordered Photonic Bandgap Materials

By: Francisco Baltazar

Physics

Faculty Advisor: Dr. Weining Man

We are fabricating hyperuniform disordered structures on silicon chips at the nanometer scale. Within these structures, we create waveguides through which light can propagate. Essentially, these structures allow us to control the propagation of light. This has great potential in creating a new era of photonic materials. Notice that all of your electronics work by manipulating the flow of electrons, or electricity, through silicon. Achieving the same result with photons (light particles), has the advantage that light travels much faster than electrons can, as well as carry a larger amount of information per second. It is our hope that integrating all-optical circuits in our technology is in the near future.

58 GP1

The Stability Of Circumbinary Planetesimal Disks

By: Michael Quinn Parkinson

Physics

Faculty Advisor: Dr. Joseph Barranco

A new type planetary system was observed using the Kepler space telescope. These systems have planets orbiting the center of mass of a binary with a very small separation, colloquially known as Tatooines. This new class of exoplanets is intriguing from the perspective of protoplanet accretion within a planetesimal disk because these systems involve dynamically active stellar binaries. The binary interacts with a planetesimal disk through strong gravitational perturbations potentially causing disk instability. This work is an Toomre stability analysis on circumbinary planetesimal disks. I seek the orbital parameter space in which a circumbinary planetesimal disk will remain stable on timescales associated with planet formation.

59 GP1

Guiding Invisible Light by Plasmonic Resonant Solitons in Metallic Nanosuspensions

By: Trevor Kelly

Physics

Faculty Advisor: Dr. Zhigang Chen

We demonstrate the guiding of invisible light by visible light in plasmonic nanosuspensions. A low-power (40-60mW) visible light beam at 532nm (pump beam) penetrates through colloidal suspensions of gold spheres by nonlinear self-trapping into an optical soliton, which in turn creates a waveguide that allows guidance of an invisible infrared laser beam (probe beam) at 1064nm of different power levels (20-500mW). Interestingly, although the probe beam itself has very weak or no nonlinear self-action, the pump beam undergoes self-trapping at an even lower power due to the presence of and possible interaction with the probe beam, which certainly merits further investigation.

60 GP1

Mining the Mitelman Database to Analyze Cancer Karyotypes

By: Angel Pilar

Mathematics

Faculty Advisors: Dr. Javier Arsuaga and Dr. Hernando Martinez Vergara (EMBL)

Gene fusion events may drive cells to become cancerous. We develop a method for identifying chromosomal regions where gene fusion events occur. We study T-cell and NK-cell neoplasms, particularly because there is a known gene fusion event between chromosomes 5 and 2. Our method uses mathematical analysis of chromosome interaction data extracted from the Mitelman Database. We find that there is a significant interaction between chromosomes 5 and 2 as previous research found. Our methods also found that gene-fusions events might be occurring between chromosome pairs 13-17, 4-12, 21-22, and 14-18.

61 GP1

Classifying Gestures Using Neural Trees and Random Forests

By: David Rodriguez

Mathematics

Faculty Advisors: Dr. Alexandra Piryatinska and Dr. Xiaorong Zhang

Using a wireless device attached to the arm we collect sensor data resulting in 18 streams as you make various gestures. For each gesture these signals are then decomposed into time domain features which a neural tree and random forest algorithm are trained to identify the various gestures. We compare the performance of both neural tree and random forest algorithms on future unseen instances of gestures remarking on their differences in speed and accuracy.

62 GP1

Representation Varieties

By: Justin Davis

Mathematics

Faculty Advisor: Dr. Joseph Gubeladze

We introduce the varieties of modules over a ground k-algebra A on a finite dimensional k-vector space, called the module variety. For two such vector spaces we introduce the variety of homomorphisms of all possible module structures - the Hom-variety, and the analogous Ext-, and tensor-varieties. These constructions can be carried out for all higher Ext- and Tor-groups. This suggested novel fusion of representation theory, algebraic geometry, and homological algebra allows us to study various properties of the induced representations by employing the machinery of affine algebraic geometry.

63 GP1

Oriented Connected Digraph Processes

By: Mark Rogers

Mathematics

Faculty Advisor: Dr. Serkan Hosten

The brain constructs a model of the universe to navigate and reason about the environment. At one level of complexity, it is a directed graph in which each neuron is a vertex and each synapse is an edge. One can infer that the universe, therefore, has a directed graph structure that Nature discovered in its evolutionary design of the human brain. A new mathematical object called the Oriented Connected Digraph (OCD) Process is invented to model the universe and self-similar subgraphs that correspond to intelligent agents such as humans. This theory can be tested by comparing the network structure of an OCD with the number of edges equal to the number of synapses in the neocortex to that of the human connectome.

64 GP1

Generalized Permutohedra

By: Matthew Cadier Kim

Mathematics

Faculty Advisor: Dr. Federico Ardila

Generalized Permutohedra are a family of polytopes whose normal fan is refined by the type A hyperplane arrangement, also known as the Braid arrangement. They are deformations of usual permutohedra: orbit polytopes of the type A reflection group. This family of of polytopes can be characterized by: polytopes whose normal fan is refined by the Braid arrangement, Submodular Base polytopes. The relation to the Symmetric group means that we capture many sub families of polytopes that have type A symmetries such as matroid polytopes, associahedra, graphical zonotopes, Bruhat order polytopes, and nestohedra.

65 GP1

Statistic of Topological invariant for inferring chromosomes positioning

By: Maxime Pouokam

Mathematics

Faculty Advisor:

The 3D architecture of chromatin plays an important role in processes such as gene regulation and cancer-driving gene fusions. By using contact data obtained from recent sequencing technologies, such as chromatin conformation capture assays (CCC), it has become possible to obtain high resolution 3D reconstructions of chromosome configurations. One obvious question one may ask is how do we assess accuracy of the reconstructions. In other word, given two reconstructions, how do we tell whether they are the same or not. Here we propose a topological analysis that helps analyzing the chromosomes positioning of yeast genome during interphase.

66 GP1 DISPLAY ONLY

An Overlap Criterion for the Tiling Problem of the Littlewood Conjecture

By: Lucy Odom

Mathematics

Faculty Advisor: Dr. Yitwah Cheung

The Littlewood Conjecture is an open problem in number theory, particularly in Diophantine approximation. We will look at the continued fractions of a pair of real numbers that is analogous to the Farey tiling of the plane. We offer an extension to the work already done in Samantha Lui's thesis, where we will do analysis in the case where the pair of real numbers is rational. We will address some issues that arise in this case, in particular the overlapping of tiles, and illustrate a criterion in which the Farey tilings do not overlap.

67 GP1 DISPLAY ONLY

Multidimensional Continued Fractions, Farey Tilings, and Roots of Unity

By: Therese-Marie B. Landry

Mathematics

Faculty Advisor: Dr. Yitwah Cheung

First formulated around 1930, the Littlewood Conjecture claims that for any pair of real numbers, (alpha, beta), and any positive epsilon, there are integers (p_1,p_2,q) such that q |q alpha - p_1| |q beta - p_2| is less than epsilon. Elon Lindenstrauss recently showed that the set of exceptions has Hausdorff dimension zero. The Littlewood Conjecture can be geometrically reformulated as a problem in Farey tilings of the plane. The edges of a Farey tiling take on at most three slopes and third order cyclic symmetry can occur in the pattern of slopes along the boundary tiles. Every Farey tiling is associated to a lattice and we completely classify an infinite family of lattices that gives rise to tilings with such symmetry. In the process, we develop a lexicon we hope will be especially useful in the study of multidimensional continued fractions.