Amit Akula

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 […]

Billal Ahmed

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 […]

Zeerek Ahmad

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 […]

Lawrence Bai

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 […]

Renan Aparicio

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 […]

Eliel Anttila

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 […]

Michelle Antonucci

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.

Travis Bartley

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 […]

Denny Cha

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 […]

Lucas Brenes

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 […]