Masuda Sharifi

UC LEADS Scholar-Junior

Lab Group: Bill Saxton

Major: Molecular, Cell, and Developmental Biology

Research: Autophagy is a bulk degradation process in which a double membrane vesicle, autophagosome, forms around cytoplasmic components that need to be broken down. This process is essential in most cells, especially in neurons. Neurons are highly asymmetric cells with long axonal extensions that help transmit essential signals throughout the whole body. Because most biosynthesis occurs in the cell body, anterograde transport away from the cell body in the axons is important for the distribution of freshly synthesized components throughout the neuron. Old damaged components are returned retrograde, towards the cell body to be degraded and recycled.  Despite bulk degradation, via autophagy, mechanisms in axons being unknown, this process is still likely dependent on axonal transport which will target autophagosomes to damaged organelles. In order to gain better insight into autophagosome transport, we utilized Drosophila melanogaster as our model organism.  We expressed the autophagosome marker ATG8::mCherry in motor neurons and observed their distribution and transport in whole live drosophila larvae. We found more ATG8::mCherry expression in the motor neuron cell bodies compared to the axon and terminals.  ATG8::mCherry labeled vesicles moved in both direction in the axons and preliminary observation indicates that autophagosomes occur less frequently than other transport vesicles (dense core vesicles) in axons.  Our results suggest that autophagy is maintained at low levels in healthy axons and future work will focus on autophagy in degenerating axons.

Internships/ Presentations/ Awards:

Autophagosome Transport in Drosophilia Motor Neurons. Masuda Sharifi, Angeline Lim, William Saxton. University of California-Santa Cruz, 6th Annual Physical and Biological Sciences Summer Research Symposium, 2015. Poster Presentation.

SACNAS Travel Award Recipient, Summer 2015
Travel scholarship with award that includes travel, lodging and conference registration waiver for the 2015 Washington, DC SACNAS conference

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2014 Spring Dean’s Honors

2014 Winter Dean’s Honors

2013 Fall Dean’s Honors

2013 Fall Oakes Core Award

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Summer Research Experience, University of California-Santa Cruz. Santa Cruz, CA. Summer 2015 


Javier Ruiz

UC LEADS Scholar-Senior

Lab Group: Robotics and Control Lab

Major: Computer Engineering

Research: 

A MinSeg is a small robot whose mechanics are similar to that of an inverted pendulum, with two wheels to drive the base to keep the upper mass upright. It is used for educational purposes in engineering courses. Its design causes the motor to apply torque to both the wheels and the body of the MinSeg. We wish to explore the dynamics of the system, in order to observe how to apply a controller to the system in order for it to balance on its own. To keep the MinSeg upright, we develop a model for its dynamic behavior. A linear quadratic regulator is then applied to the model, and the results are tested in simulation. Testing this controller on the actual MinSeg device, however, produces unstable oscillatory performance. This could be due to certain parameters of the system being unknown. Data pertaining to the states of the system are collected while the MinSeg is running and estimation techniques are used to approximate these parameters.

Internships/ Presentations/ Awards:

Distributed Formation Control for Multi-Agent Swarms. Javier Ruiz, Aaron Ma, Sonia Martinez, Jorge Cortes. University of California San Diego.Summer Research Conference, 2016. Oral Presentation. 
 
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Regent David Lee Scholarship. 2014, 2015

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 Robots in the Real World REU 2015, Oregon State University, Summer 2015


Nicolas Blanc

UC LEADS Scholar-Senior

Lab Group: Quentin Williams

Major: Physics

Research: 

Most geologically important minerals originate deep in the Earth's mantle and crust. The structural and thermodynamic properties of these minerals give a valuable insight to understand their formation and, consequently, the formation and evolution of the Earth as a planet. Using high-temperature diamond anvil cells, a device capable of generating pressures corresponding to those present throughout the depths of the Earth, and in situ Raman and Infrared spectroscopic techniques, the properties of minerals at extreme pressure/temperature conditions are examined and characterized. The pressure- and temperature-dependent structural behavior of minerals are vital in determining the mechanisms of planetary evolutions and the degree to which the Earth has geologically differentiated over time.

Internships/ Presentations/ Awards:

A High-Pressure Infrared Spectroscopic Study of Chromium Pyrophosphate to 18 GPa. Nicolas Blanc and Quentin Williams. University of California-Santa Cruz, 6th Annual Physical and Biological Sciences Summer Research Symposium, 2015. Poster Presentation.

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Summer Research Experience, University of California-Santa Cruz. Santa Cruz, CA. Summer 2015 


 
 

Jenny Anne Maun

UC LEADS Scholar. Class of 2015.

Lab Group:

Major: Bioengineering

Research: My research is about the study of pathological synergies of the affected upper-limb acquired from stroke. We study the kinematics of upper-limb movements but in particular we study the muscle co-activations, or the muscles that the brain signals to contract, in every day movements such as elbow flexion, shoulder abduction, wrist pronation, and other common motions. Our goal is to compare these stroke synergies with the healthy synergies that our non-stroke subjects have and see which particular muscle groups are and are not activated. A technique we are using to analyze data is called Non-Negative Matrix Factorization (NMF). This is an algorithm which searches and sorts for items that may have similarities. We want to find these similarities and differences to see if there are any pattern recognitions. We are using a measuring tool called variability accounted for (VAF) to compare how approximate our model created by the NMF is to our original data in terms of muscle activation, controls, force, and length.

Internships/ Presentations/ Awards:

Effects of Load on Wear of Cartilage in the Rabbit Hemi-Condyle. Jenny Anne C Maun, Michele M Temple-Wong, Koichi Masuda, Robert L Sah, UC San Diego Summer Research Conference, August 2014.

Comparing Simple-Isolated Joint Movement to Complicated Multi-Joint Movement in Stroke Synergies. Jenny Anne Maun, Matt Simkins, and Jacob Rosen. UC LEADS 2014 Statewide Symposium, Riverside, CA.

Non-Negative Matrix Factorization on Stroke Synergies. Jenny Anne Maun, Matt Simkins, and Jacob Rosen. ABRCMS 2013, Nashville, TN.

Non-negative Matrix Factorization on Stroke Synergies. Jenny Anne Maun, Matt Simkins, and Jacob Rosen. Summer Research Symposium, Univeristy of California-Santa Cruz, 2013

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Outstanding Research Poster 2014 UC LEADS Research and Leadership Symposium.

ABRCMS (Annual Biomedical Research Conference for Minority Students) Poster Presentation Award Recipient 2013 - Engineering, Physics, Mathematics Awardee.

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Summer Training Academy for Research in the Sciences (STARS), UC San Diego, Summer 2014.

Summer Research Experience, UC Santa Cruz, Summer 2013


Georgia Sheppard

UC LEADS Scholar-Junior

Lab Group: Bin Chen

Major: Molecular, Cell, and Developmental Biology

Research: 

Internships/ Presentations/ Awards:

Laminar Fate Determination of Neocortical Progenitor Cells. Georgia Sheppard, Ton Nguyen, Alyssa Perry, Kendy Huang, Bin Chen. University of California-Santa Cruz, 6th Annual Physical and Biological Sciences Summer Research Symposium, 2015. Poster Presentation.

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Summer Research Experience, University of California-Santa Cruz. Santa Cruz, CA. Summer 2015 


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Javier Portillo

UC LEADS Scholar. Class of 2015. Transfer Student from Riverside Community College

Lab Group: Camilia Forsberg Lab

Major: Neuroscience

Research: 

Internships/ Presentations/ Awards:

 


 

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Andrea Reyes-Ortiz

UC LEADS ScholarClass of 2015.

Major: Bioengineering

Research Group: Jonathan Zehr Group

Research: Approximately 78% of Earth’s atmosphere is made up of nitrogen, but atmospheric nitrogen has limited availability for biological use. This nitrogen limitation affects the rate of important biogeochemical processes. Ammonia-oxidizing archaea (AOA) are involved in a key step of the oceanic nitrogen cycle, nitrification. In the Monterey Bay region, a correlation between chlorophyll concentration and AOA has been documented during a phytoplankton bloom. Since ammonia was never measured in this study, it remains undetermined whether AOA were abundant due to increased ammonia in those waters, or due to a specific relationship between AOA and phytoplankton. Such a relationship would result in decreased ammonia uptake by the associated phytoplankton and have implications for carbon fixation rates. In order to investigate this potential relationship, quantitative PCR was used to quantify AOA distributions using the ammonia monooxygenase (amoA) genes within samples taken from an Autonomous Underwater Vehicle (AUV) in 2011 and the Environmental Sample Processor (ESP) in 2012. Data from AUV samples taken in high ammonia, low chlorophyll regions and the reverse, show a positive correlation between AOA and ammonia and an unexpected negative correlation with chlorophyll. We contribute this to the intermediate upwelling conditions during sampling and hypothesize that a positive correlation with chlorophyll may only exist during high stratification or bloom conditions.  Therefore we will also present amoAassays optimized on the ESP for deployment in more stratified conditions in Monterey Bay in September 2012 as well as AOA data from AUV samples collected during this same field program. A specific bloom-dependent positive correlation between AOA and chlorophyll would implicate ammonia oxidation activity as an important negative feedback to phytoplankton blooms.

Internships/Presentations/Awards:

Examining the relationship of ammonia-oxidizing archaea to ammonia and phytoplankton in Monterey Bay using autonomous instrumentation. Andrea Reyes-Ortiz, Julie Robidart, Jonathan Zehr. UC LEADS 2013 Statewide Symposium, Santa Cruz, CA.

Summer Undergraduate Research Symposium. Summer 2012.  UC Santa Cruz.


 

Osmar Aguirre

UC LEADS Scholar-Junior

Lab Group: Roberto Bogomolni Lab

Major: Cognitive Science

Research: Investigations on the crystal structure of the light sensitive protein, EL222, lead us to believe that its photocycle can be further optimized as a DNA binding optogenetic tool.

Internships/ Presentations/ Awards:

LOV Dynamics: Tryptophan Time Resolved Spectrocopy for EL222 Photoactivation. Osmar F. Aguirre, Rafael y de la Vega, Roberto Bogomolni. UC Santa Cruz. August 5, 2014

Optogenetics as a high speed neural modulation practice. Osmar F. Aguirre & Abdiel Lopez . Santa Rosa Junior College.  May 16, 2013.

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SACNAS Travel Award Recipient: Paid travel and living expenses to present research on light sensitive proteins at the 2014 SACNAS L.A. Conference.

CHASE Music and Language Summer School Travel Award Recipient: Paid travel and living expenses to participate in a week intensive, graduate level summer school at Yosemite and UC Merced.

Latinos Unidos del Condado de Sonoma Scholarship Recipient:  Scholarship awarded due to academic excellence and participation in the Hispanic community of Sonoma County.

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Summer Research Experience 2014, UC Santa Cruz, Summer 2014 

Center for Human Adaptive Systems and Environments Summer School for Music and Language Cognition at UC Merced - Yosemite/UC Merced - May 18 to May 24, 2014.

C.A. Connects at Santa Rosa Junior College - Santa Rosa, C.A.- Fall 2012.

Lab techniques and publishing internship at Sonoma State University - Rohnert Park, C.A.- Summer 2012.


 

Cecilia Im

UC LEADS Scholar-Junior

Lab Group: Barry Bowman Lab

Major: Molecular, Cell, and Developmental Biology

Research: 

Internships/ Presentations/ Awards:

Summer Research Experience 2014, UC Santa Cruz, Summer 2014 

 
 

Ian Weaver

UC LEADS Scholar-Junior

Lab Group: Enrico Ramirez-Ruiz

Major: Physics (Astrophysics)

Research: AMR Accretion Disk Simulation

Internships/ Presentations/ Awards:

Simulating Accretion Disk and Stream Interaction in Exoplanetary System WASP-12/b. Ian Weaver, Philip Macias, Enrico Ramirez-Ruiz. University of California-Santa Cruz, Summer Research Symposium, 2015. Poster Presentation.

Applying a Hydrodynamical Treatment of Stream Flow and Accretion Disk Formation in WASP 12/b Exoplanetary System. Ian Weaver, Aaron Lopez, Phil Macias, UCSC

Modeling of Mass Transfer in Semi-Detached Binary System, WASP-12b. Ian Weaver, Ivan Alvarado, Rodolfo Navarrete Perez, UCSC, UCI, Indianapolis NSBE Convention

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Ron Ruby Scholarship: For demonstrating potential for leadership in promoting cross-cultural understanding.

California Space Grant Consortium Undergraduate Research Opportunity Program (CaSGC) Scholarship: California’s implementation arm of NASAs National Space Grant College and Fellowship Program.

CAMP Symposium Honorable Mention: Awarded for distinguished poster presentation at the statewide CAMP research symposium.

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LAMAT/UC LEADS: UCSC, 2014

CAMP: UCSC, 2013

High school internship program: American University, 2011


Luz Lule Camargo

UC LEADS Scholar-Sophomore 

Lab Group: Ali A. Yanik Lab

Major: Electrical Engineering

Research: Microfluidic devices have emerged as an easy tool for biological and chemical research. Microfluidics is a field of study that aims to control and manipulate fluids at a small scale. The fluids are geometrically constrained to small volumes for instance miclroliters or nanoliters. Microfluidic devices are used multiple assays in order to enhance efficiency and reduce the amount of material needed for the experiments. The objective of my research is to create a microfluidic device that can generate water droplets act as single-cell BioReactors.

Internships/ Presentations/ Awards:

"Droplet Microfluidics and Single-Cell BioReactors" Luz Lule Camargo, Imran Hossain and Ahmet Ali Yanik. Summer Research Symposium, Univeristy of California-Santa Cruz, Summer 2014

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Summer Research Experience 2014, UC Santa Cruz, Summer 2014


 

Hanh Truong

UC LEADS Scholar-Junior

Lab Group: Ro Kamakaka Lab

Major: Biochemistry

Research: Only a subset of genes in any organism is active at any given time while the rest are silenced. Insulators are DNA sequence elements that recruit proteins that help separate silenced regions from highly transcribed regions. Many things are still not known about the mechanism of boundary function of insulators. The purpose of this study is to elucidate the role of Sen 1 in insulation and to determine if Sen1 interacts with other repair proteins (Srs2, Rad51, and Xrs2) in this process. Sen1 is a highly conserved gene, which codes for a DNA helicase that prevents malfunctions that happen during DNA replication. In eukaryotes, DNA strands can be replicated and transcribed at the same time. However often this leads to problems such as collisions between the RNA and DNA polymerases. This result in the formation of DNA-RNA hybrids (called R loops). Sen1 interacts with other DNA repair proteins to resolve such issues. Since R-loops are often found at or near insulator elements, we hypothesize that Sen1 functions in insulator function. In order to test this hypothesis, we will create a yeast strain that is mutated for Sen1 using PCR products. After we create the mutant strain, we will cross it with a strain containing reporter genes that will allow us to monitor function of the barrier insulator. We will then do an assay on whether the Sen1 mutant has an effect on barrier function.

Internships/ Presentations/ Awards:

Dean's Honor

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Undergraduate Summer Research Symposium. UC Santa Cruz. August 2014. 


Diana Lucas Baca

UC LEADS Scholar-Junior

Lab Group: Raskatov Lab

Major: Chemistry

Research: 

Alzheimer’s Disease (AD) is a neurodegenerative disease that causes memory loss and worsens over time affecting crucial synaptic functions, ultimately leading to a significant decrease in brain tissue. AD typically affects people at the age of 60 and older, but it can also affect people as young as 40 and 50 years of age. The loss of brain tissue is associated to two neuronal proteins, the tau protein that occurs intracellular and the amyloid-beta protein that occurs extracellular, which take part in the pathological aspect of Alzheimer’s that leads to the death of the neuron. We focus our research in the amyloid-beta protein, consisting of 40 – 42 amino acids, which has been found to self-aggregate forming toxic oligomeric species, fibrils and consequently neurofibrillary plaques. Its short sequence allows us to synthesize it and purify it to perform a series of biophysical experiments that will provide mechanistic details of great interest to better understand this protein structure and toxicity.

Internships/ Presentations/ Awards:

Synthesis and Biophysical Techniques for Alzheimer's A-Beta Peptide. University of California, Santa Cruz, 7th Annual Physical and Biological Sciences Summer Research Symposium, 2016. Poster Presentation  

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Summer Research Experience, University of California-Santa Cruz. Santa Cruz, CA. Summer 2016 


Valentin Urena Baltazar

UC LEADS Scholar-Senior 

Lab Group: Frank Bridges Lab

Major: Physics

Research: 

In our lab we conduct analysis of local structure in the various metal compounds using Extended X-ray Absorption Fine Structure (EXAFS) Spectroscopy. This summer I examined the local structure of Cu10Zn2Sb4S13, or more formally known as Tetrahedrite. Tetrahedrites are a class of naturally occurring minerals with high thermoelectric efficiency. Thermoelectric materials are used in devices which convert heat to electricity directly via the Seebeck effect, and also for cooling without a refrigerant via the Peltier effect. We examine pure Cu12Sb4S13 and  zinc doped Cu10Zn2Sb4S13 tetrahedrite to better understand the metal to semiconductor transition at T~90K in the pure tetrahedrite. The copper atoms in the crystal are arranged in a tetrahedral structure (Cu1) neighboring four sulfur atoms and in a triangle (Cu2) neighboring three sulfurs. Understanding why the transition is suppressed upon doping will shed light on the structural properties of the tetrahedrite. To probe the crystal structure, X-ray spectroscopy data of the tetrahedrite Cu10Zn2Sb4S13 were collected at the Stanford Synchrotron Radiation Lightsource (SSRL). The photoelectrons ejected by the x-rays are used to probe the local structure of around the excited zinc atom. We then analyze the data from the zinc absorption edge using the EXAFS method. Preliminary results suggest that the zinc atoms mostly occupy Cu1 sites and a smaller fraction of the zinc replaces Cu2 sites.

Internships/ Presentations/ Awards:

Analysis of Local Structure in Tetrahedrite Using Extended X-Ray Absorption Fine Structure (EXAFS) Spectroscopy. Long Beach, SACNAS National Conference, 2016. Poster Presentation.

Analysis of Local Structure in Tetrahedrite Using Extended X-Ray Absorption Fine Structure (EXAFS) Spectroscopy. University of California, Santa Cruz. 7th Annual Physics and Biological Sciences Summer Research Symposium, 2016. Poster Presentation.

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Summer Research Experience, University of California-Santa Cruz. Santa Cruz, CA. Summer 2016


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