Non-linear Tensegrity Control System Design for the ULTRA Spine

Current robotic designs have limited movement because they involve rigid bodies and links that are connected through restrictive joints. Conventional actuation of these joints is usually achieved through motor and hydraulic control. In contrast, many macroscopic biological systems have evolved to produce locomotion through the actuation of tensile links to control their rigid counterparts. This allows for lighter and better dynamic systems that are capable of safer and more efficient motion. These biological systems can be modeled with a principle known as tensegrity, a combination of tension and integrity. A tensegrity system refers to an internally stable structure that is built from a network of compressive and tensile members. When applied to robotics, tensegrity structures can achieve large degrees of freedom while remaining extremely lightweight and robust. During my fellowship, I will be working in Professor Agoginos Berkeley Emergent Space Tensegrities (BEST) Lab in order to research a control system […]

...Read More about Zeerek Ahmad
Rose Hills

NKG2D Ligand Induction by Viral Proteins

Natural Killer (NK) cells are an important part of the Innate Immune System, surveying the body to recognize and eliminate cells determined to be abnormal. NK Cells can be activated through ligands that bind to excitatory receptors on the cell. The most well-studied excitatory ligands have been the NKG2D family of ligands, which bind to NKG2D receptors on NK Cells. Im using MCMV, Mouse Cytomegalovirus, as a model to study NKG2D ligand regulation in cells infected by viruses. M18, a protein in MCMV, by itself is necessary and sufficient for induction of the Rae-1 family of ligands, which are sub-group of NKG2D ligands. M18 does not exist as one peptide chain, but rather in two forms that are produced by cleavage, and I plan to determine where M18 is cleaved in post-translational modification and how this cleavage potentially affects Rae-1 induction. Discovering the cleavage site and how cleavage affects Rae-1 […]

...Read More about Billal Ahmed
L&S Sciences

Cluster-based parallel processing of DT-MRI acquisitions for real time probabilistic fiber tracking

Using acquisition data from Diffusion Tensor Magnetic Resonance Imaging (DT-MRI), an MRI variant that can map the diffusion of water, medical researchers have been able to image neural bundles in the brain, known as white matter tracts. Fiber tractography has been used extensively for clinical diagnosis of many neurological disorders and is used by neurosurgeons for surgical planning. Dipy, an open source project, provides a rich suite of fiber tracking algorithms accessible to any medical center in the world. Computing the fiber tracks using its probabilistic models, however, are computationally expensive. My project this summer is to integrate standard parallelization frameworks into dipys probabilistic models. I plan on leveraging industry standard cloud computing tools to accelerate the computation of these fiber tracts. The goals of my project are to enhance dipys probabilistic models for richer image processing, to provide real-time fiber tracking analytics to UCSF surgical planners, and to provide […]

...Read More about Amit Akula
Rose Hills

Integration Time in the Avian Auditory System

Temporal discrimination of acoustical signals plays a key role in how we perceive sounds. It affects the perception of loudness, timbre and pitch and it determines the rate at which we can parse phonemes in speech. A robust way to assess temporal integration is to determine the flicker-fusion rate: the rate at which a train of clicks is heard as a continuous sound with a low pitch instead of as a series of short sound elements. This rate is approximately 40Hz in humans corresponding to our lower bound of pitch discrimination and an upper bound for parsing phonemes. Songbirds have been used extensively in neurophysiological and behavioral research designed to understand the perception and production of learned communication calls because they are one of the few animals, other than humans, that are capable of vocal learning. Although it is known that songbirds have frequency resolution similar to humans, it is […]

...Read More about Milan Amin
L&S Sciences

Astigmatism-related Amblyopia Treatment

Vision is a vital sense that many people reply on to navigate through their daily lives, and yet people with amblyopia (commonly referred to as lazy eye) can have their vision and depth perception severely impacted by this condition. With my mentor in the Levi Lab, I sought to develop an effective treatment for astigmatism-related amblyopia and test it in a clinic trial. The treatment is a perceptual learning task where the patient looks at a computer that presents different orientations of a black and white pattern. The task of looking at the pattern repeatedly is done to hopefully train the eye to focus using the astigmatic part of the eye, to ultimately improve the visual input from that eye, and improve their binocular vision.

...Read More about Michelle Antonucci
Rose Hills

Neoproterozoic carbon anomalies in the rock record

A worldwide abundance of glacially deposited sediments in early Neoproterozoic strata suggests the onset of a great global cooling event that began approximately 720 million years ago. Sometimes referred to as the Snowball Earth Hypothesis, this period of massive climactic change resulted in the propagation of glaciers at very low latitudes, and potentially covered the entire surface of the planet with ice. Determining the geographical, climatological, and biological changes that happened prior to the onset of this event can allow us to better understand the processes that led to such a dramatic climate anomaly. This summer, I will be mapping, sampling, and analyzing pre-glacial Neoproterozoic rocks in the region around Negash, Ethiopia. By combining data from 13C ratios from carbonate rocks with radiometrically-dated ages gleaned from multiple volcanic ashes interspersed among the carbonates, we will be able to better constrain and determine the speed and duration of significant climactic anomalies […]

...Read More about Eliel Anttila
L&S Sciences

Analysis of neurodegeneration-associated TREM2

The prevalence of neurodegenerative diseases has reached an unprecedented level and is now a prominent threat to the health and wellbeing of our aging population. As a result, the demand for effective therapies has become of paramount importance. Studying proteins involved in neurodegeneration allows researchers to outline cellular pathways leading to disease, which in turn helps provide targets for drug molecules. Recently, scientists discovered a link between different neurodegenerative diseases and specific point mutations in triggering receptor expressed on myeloid cells 2 (TREM2). TREM2 is normally expressed at the cell surface and is believed to play a key role in the immune response of the brain. Recent studies suggest that mutant versions of TREM2 are defective in the transport of the protein to the cell surface. This summer, I will analyze mutant forms of TREM2 to determine where in the cell these defects are present in an attempt to understand […]

...Read More about Renan Aparicio
Rose Hills

Mechanism of DNA Spacer Acquisition during CRISPRCas Adaptive Immunity

Found in many species of bacteria and archaea, the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR associated (Cas) proteins provide an adaptive defense mechanism against foreign invaders such as viruses and plasmids. By integrating segments of the foreign DNA into the CRISPR locus of the host genome, the bacteria remember the invaders and can subsequently produce CRISPR RNAs (crRNAs) to destroy the foreign DNA complementary to the crRNA. In particular, Cas9 plays a major role in using the short RNA as a guide to search for any DNA sequences in viruses and plasmids that match the RNA sequence, cleaving and destroying them. Although the CRISPR pathway has been extensively studied, the mechanism of new spacer acquisition is still poorly understood. In 2015, it was discovered that four proteins Cas1, Cas2, Csn2 and Cas9 are involved in acquiring these spacers in the bacteria Streptococcus pyogenes. Using a combination of […]

...Read More about Lawrence Bai
Rose Hills

The Remediated Bakhtin: Heteroglossia and New Media

According to the 20th century theorist Mikhail Bakhtin, the distinguishing feature of the novel lies in its ability to incorporate multiple dialects and forms of language into itself and better mirror the diversity of language that naturally occurs in reality. In his argument for this theory, Bakhtin relies on a cultural analysis of the genres development and ignores the impact of technological innovation in media that may have crucially affected the development of the genre. My project seeks to analyze Bakhtins theory in relation to similar studies that incorporate the development of media and extrapolate these relations in regards to the internet. In doing so I seek to answer the following questions: What has been the impact of the internet on heteroglossia, diversity, of language? Does Bakhtins theory of the novel still hold in consequence of this impact? And ultimately, what is the relationship of the novel genre to the […]

...Read More about Travis Bartley
Humanities and Social Science

Building a Movement from the Inside: An Organizational History of the Prisoner Hunger Strike Solidarity Network to Support Prisoner-Led Resistance at Pelican Bay

In Spring of 2011, prisoners inside Pelican Bay State Prison contacted prisoner-rights and anti-prison activist organizations announcing prisoners would be beginning a rolling hunger strike and that they needed support making sure their voices and demands were heard and acted on outside prison walls. The Prisoner Hunger Strike Solidarity coalition (PHSS)- originating in the Bay Area and made up of grassroots organizations, family members, formerly incarcerated people, lawyers, and individuals- to amplify the voices of CA prisoners on hunger strike was formed. Though the hunger strike has ended, the demands of the prisoners have not been met, and prisoners alongside PHSS continue to fight to get these demands met. My research will create an organizational history of PHSS in order to determine whether this model of prisoner-led resistance can be replicated elsewhere, keeping in mind the unique history of radical bay area social movements. I hope to aid organizers and […]

...Read More about Rosella Bearden
Humanities and Social Science

U.S Public Perception of Measles, 1900 - Present

Measles was once a nearly ubiquitous childhood plague, a rite of passage with sometimes deadly outcomes. However, the disease has all but disappeared in the vaccination era – few people cross paths with the measles, few know anyone who has been infected. The veritable erasure of the disease from public life stems from widespread use of the measles vaccine, whose success effectively revolutionized societys relationship with measles from one of grudging resignation, to a near ignorance. It is the nature and details of this change in perception that I will explore this summer. Via a case study of the measles experience in 20th century United States, I will investigate how the introduction of preventative health measures moderates the publics relationship with disease, transforming perceptions of harm and danger previously inherent to the illness. I will systematically survey the dynamic public attitude toward measles throughout the last century, as presented in […]

...Read More about Marina Blum
Humanities and Social Science

Modern Science and Tibetan Buddhism

Over the past two decades Tibetan Buddhism and modern Science have been seriously engaging each other in topics of consciousness, origins, and happiness. The excitement of the possible convergence between science and spirituality in a conversation that has been historically polarized between secular and religious values has overshadowed investigative research that aims to understand the quality and impact of the interaction. To start this process, I will look at the lasting effects of two programs; Science For Monks (SFM) and the Emory Tibet Science Initiative (ETSI) on Tibetan Buddhist communities in India. I will do this by investigating and documenting the existence and utility of science in major Tibetan Buddhist monasteries in South India, specifically Sera, Drepung, and Gaden. At each location I will document physical changes to the monastery that have resulted from SFM and ETSI and conduct interviews with monks who have attended their workshops. What is the […]

...Read More about Kathryn Boden
Humanities and Social Science

Investigating Age Related Decline of Germline Regeneration in an Amphipod Crustacean

Regeneration is an organisms ability to regrow and compensate for damage to specific cell lineages, and the extent to which it can occur varies greatly among species. My research focuses on the germline, which is the cell lineage entrusted with producing and maintaining gametes that contribute to the creation of offspring. The ability to regenerate the germline is predominately observed in species that can undergo total body plan regeneration such as flatworms and sponges. Parhyale hawaiensis however, is an amphipod crustacean that has been shown to regenerate its germline post-hatching despite not having full body plan regenerative capabilities. I am testing the limits of this novel process by ablating the germline in adults and observing if mature Parhyale retain this ability. In order to investigate this pathway I am using the CRISPR/Cas9 genome editing system and the NTR/Mtz cell ablation method to create a transgenic lineage that I will use […]

...Read More about Lucas Brenes
Rose Hills

Identification of Interactor Binding Domains on Usp44

Ubiquitin is a protein that serves as a molecular tag for either degradation of its targets by the 26S proteasomes or for a wide variety of other functions such as DNA repair, transcription, endocytosis, membrane transport, or protein localization in a proteasome independent manner by covalently attaching to its target proteins. Deubiquitinases (DUBs) are proteins that mediate ubiquitin removal and processing to play regulatory roles in multiple cellular processes. The deubiquitinase (DUB) Usp44 is a critical regulator of cell division that acts as a tumor suppressor by preventing premature anaphase during mitosis. During cell division, Usp44 protects mitotic checkpoint complex from the anaphase-promoting complex (APC)-driven disassembly, which allows it to regulate transition from metaphase to anaphase. Beside this well-known function, Usp44 may also play a significant role in regulating stem cell pluripotency and differentiation in neuronal lineages. Previous work has identified and characterized Usp44 binding partners. Most of the binding […]

...Read More about Denny Cha
L&S Sciences

Pseudomonas aeruginosa Hijacks Cell Death Pathways

Pseudomonas aeruginosa is an opportunistic pathogen responsible for a significant number of antibiotic resistant infections. It can infect almost any site of the body, but typically targets damaged epithelial tissues such as corneas of contact lens wearers, potentially leading to blindness. P. aeruginosa uses a Type 3 Secretion System, a needle-like structure, to introduce bacterial exotoxins into host cells which can cause cell death. P. aeruginosa has also been found to replicate intracellularly and occupy protrusions in the plasma membrane known as blebs. Previous studies from the Fleiszig lab have shown that caspase 1, an enzyme that can induce pyroptotic cell death, plays a role in initiating bleb formation. We hypothesize that caspase 1 activity and the induction of pyroptosis is needed for bacterial intracellular survival and replication to occur.

...Read More about Stephanie Chang
Rose Hills

Evaluation of Post ACL Injured Knees

Injuries to the ACL are very common in the young and active population, and this can often lead to posttraumatic osteoarthritis (OA), sometimes as early as in their third decade of life. Like idiopathic OA seen in older individuals, posttraumatic OA causes pain, impaired function, and overall decreased quality of life, but occurs at a much younger age after injury. ACL injuries are commonly treated with surgical reconstruction of the ligament, replacing the torn ACL with a graft. However, surgical reconstruction does not perfectly correct for tibiofemoral joint kinematics. Moreover, these subtle changes in knee kinematics can lead to early joint degeneration overtime. Since the mechanism behind OA development after ACL injuries is poorly understood, there is little development of preventive measures that could help this particular population. The purpose of my project is to correlate biomechanical alterations after ACL injuries and articular cartilage changes to better understand how ACL […]

...Read More about Ellison Chen
Rose Hills

The role of Gpr75 in the beta cell response to autoimmunity

Despite the growing prevalence of diabetes, the exact biological mechanisms leading to the onset of this disease still remain painfully unclear. Type 1 diabetes in particular is caused by an autoimmune attack to an individuals insulin secreting beta cells; this cell population cannot be regenerated and an adverse condition known as hyperglycemia ensues. The immune cells and chemokines present in the pancreas at the onset of this autoimmune response are of interest when considering this disease. Recent studies have suggested that the activity of a particular G-coupled protein receptor may influence the onset and progression of beta cell destruction. The goal of my project is to study this G-coupled protein receptors role in regulating beta cell function, as well as investigate any potential interactions between this receptors and the molecules of the immune system present in type 1 diabetes.

...Read More about Justin Choe
Rose Hills

Imitation, Emulation, and the Meaning of Originality in Painting Versus Cinema

How do issues of authorship and originality function within fine art and cinema? What are the similarities between painting and film? What are the fundamental differences, especially those relating to the meaning and worth of emulation within the two mediums? My research will attempt to answer these questions using two case studies: Orson Welles’ 1973 film F for Fake, and the paintings of the infamous Elmyr de Hory, Hungarian art forger extraordinaire who imitated the style of countless painters (Degas, Derain, Dufy, Matisse, Modigliani, Picasso, and Vlaminck to name a few), and traveled the world painting counterfeits in hotel rooms along the way, prompting a manhunt for one of art history’s greatest and most prolific art forgers. Using postmodernist texts as a foundation and employing rigorous filmic and formal analyses of F for Fake and Elmyr de Hory’s forgeries respectively, my research will challenge prevailing conceptions of the integrity of […]

...Read More about Scarlet Cummings
Humanities and Social Science

Investigating Alzheimer's: Network Theory Approach

The leading hypothesis suggests that the progression of Alzheimers disease (AD), the major cause of dementia, is driven by the accumulation of misfolded amyloidB proteins into plaques within the brain. The presence of these plaques in some cognitively healthy adults has complicated our understanding of AD and has raised the question of what exactly triggers cognitive decline. Recent studies employing network theory have revealed that the answer may lie in the details of the disruption of the brain network by the amyloidB plaques. This summer I will use fMRI and PET imaging data to simulate the progressive effects of plaque deposition on the topology of the functional brain network.

...Read More about Leonardino Digma
Rose Hills

Characterization of Gene Flow Through Experimental Secondary Contact by Molecular Assay

Speciation has long been studied in the field of evolutionary biology, but many questions remain regarding the specific genomic interactions between diverging species. To study the genetic events involved in the development of reproductive isolation and speciation, I will focus on the Drosophila nasuta fruit fly clade which is currently in the process of diverging. I will use molecular assays to characterize gene flow through experimental secondary contact between recently diverged Drosophina nasuta subspecies and draw conclusions about the level and type of reproductive isolation between the subspecies pairs. My results will ultimately be analyzed alongside the results of mating and fertility assays and whole genomic sequencing conducted within the Bachtrog lab to facilitate a better understanding of the extent and kind of reproductive isolation between recently diverged subspecies. This research will provide a framework for future investigations of the genetic and phenotypic reasons behind genetic incompatibilities and their role […]

...Read More about Jennifer Ding
Rose Hills