Elina Wells

Immunosurveillance is the immune system’s ability to detect foreign pathogens, such as bacteria, viruses, and cancerous cells in the body. Many cancers evade immunosurveillance, through the use of mechanisms, which allow them to exist and spread undetected. Checkpoint blockade therapy – an immunotherapy treatment method in part developed at Berkeley – counters the “breaks” of immunosuppressive cells, imposed on inflammatory immune cells within the tumor microenvironment. Many current immunotherapies use Listeria monocytogenes as a way to induce immune cells that were previously exhausted to regain their effector phenotype and control cancer. However, about half of the patients fail to respond to treatment. This may be because immunosuppressive cells within the tumor microenvironment dampen any immune response leading to unresponsive inflammatory cells. I propose that changing the injection method from intravenous (IV) to intratumoral (IT) injection will counter these shortcomings because an immune response will generate directly within the tumor. My […]

Diana Francis

Sleep behavior in Cassiopea, the upside-down jellyfish, challenges the common association between sleep and brain function. In lieu of a brain and centralized nervous system (CNS), Cassiopea has a decentralized net of ganglia that initiate pulsing activity at a slower rate during the night. My project seeks to understand how an animal that lacks a CNS undergoes a whole-body behavioral state change. More specifically, I will examine how this behavior affects the expression of several genes connected to sleep and activity using in situ hybridization and quantitative PCR. These genes encode an acetylcholine receptor subunit, choline acetyltransferase, a GABAergic receptor, a sodium-calcium exchanger, and a glutathione S-transferase. Characterizing the expression of these genes will help illustrate the connection between ganglion usage and sleep behavior. I will silence one gene of interest, the acetylcholine receptor subunit, using RNA interference, and compare the gene expression of sleep-deprived jellyfish to those of jellyfish […]

Allison Zau

Riparian meadows in the Sierra Nevada facilitate access to near-surface groundwater, a resource critical to sustaining the productivity and biodiversity of the larger montane ecosystems. Historically, the groundwater flow is consistently recharged by snowmelt percolating down from snowpack at higher elevation. However, climate change is depleting this critical snowpack, destabilizing the groundwater flow and consequently the ecosystem. Using seismic surveys I conducted last year, I will produce cross-sections of a characteristic meadow. These will provide information on the near-surface groundwater distribution and composition and geometry of the soil and rock bedding. I can then evaluate how the landscape affects the relative volume and movement of groundwater. Understanding these subsurface controls on groundwater availability will inform meadow conservation efforts.

Kenneth Trang

Bacteria inhabit almost every surface on Earth, from tabletop to hydrothermal vents. Thus, it’s unsurprising that a diverse community of microbes also thrives within the human gut. However, these residents aren’t stowaways, as strong evidence has emerged in the last decade that a well-balanced community of gut bacteria is indispensable to human health. And yet, our understanding of the genetic factors involved in selecting what gut microbes can colonize and persist remain limited. This summer, I research the effect of host genetics on the composition of the gut-microbiome, focusing on the effect of individual genes on compositional changes occurring during early development in the model organism Caenorhabditis elegans. This unprecedented work will not only constitute the first experimental investigation into the role of individual genes in the initial establishment of the gut microbiome composition of any animal host, but also contribute more generally to our understanding of the fundamental rules […]

Heidi Yang

Adaptive radiations are rapid bursts of diversification of a single ancestor that give rise to many ecologically different species. While the ecological and evolutionary aspects have been extensively studied, little is known about the genomic mechanisms that produce such high genetic and phenotypic diversity. Transposable elements (TEs), DNA sequences that can change their position within a genome, are one potential genomic component, since they can quickly produce a wide variety of mutations when active. McClintock (1984) first proposed that TE activity may increase in response to “challenges to the genome.” Since adaptive radiations frequently occur when a species colonizes a new area, novel environmental and ecological conditions may trigger the deregulation of the genome and activate TEs. Using the adaptive radiation of Tetragnatha spiders, which display various stages of adaptive radiation across several Hawaiian islands, this project will utilize transcriptome data and genomic sequencing methods to test the expectation that […]

Lilliana Zar

The 26S proteasome is the last stop of the main protein degradation pathway in our cells, and it allows us to keep our bodies healthy by degrading old or non-functional proteins. The motor of the proteasome is responsible for engaging, unraveling and pulling the targeted protein into the core, where it is degraded. The pore loops, six in total, are located on the motor and are the parts of the proteasome that physically interact with the targeted protein. These six pore loops pull the protein to the core like hands pulling a rope downward, switching position like hands would from top to bottom of the protein “rope” by using ATP. When a protein substrate tail is initially engaged by these pore loops, the arrangement of the entire proteasome complex shifts to begin degradation of the targeted protein. My research will explore the effect of pore loop mutations on the shift […]

Owen Doyle

Non-invasive brain stimulation (NIBS) safely manipulates neural excitability in the brain, offering neuroscientists a powerful tool to study the human brain and clinicians a potential treatment for psychiatric and neurological disorders. NIBS methods influence the brain’s electrical activity by generating an electric field over a targeted region of the scalp. For example, directing stimulation over the motor cortex can elicit movement in a muscle of interest. The intensity of movement may reflect the integrity of the nervous system’s motor pathway but measuring electrical changes in the brain proves vital to understanding how the brain responds to stimulation. A new magnetic NIBS device developed at Berkeley requires an investigation of these electrophysiological changes. I will study our device’s effect on neural activity using electroencephalography (EEG), a non-invasive method of monitoring electrical signals in the brain. Using EEG, we hope to understand how the device modulates neural excitability and endogenous neural oscillations.

Alexandra Weiss

Compartmentalization lies at the heart of understanding cell biology. The eukaryotic cell is composed of organelles, each of which carries out a unique function. As the newly discovered complexity of the prokaryotic cell is becoming further understood, bacterial organelles are becoming an essential detail to comprehending how bacteria function. The Komeili group recently discovered a novel membrane-bound organelle called the ferrosome. It is hypothesized that the ferrosome may play a part in iron storage or bacterial stress response. Yet, the question remains: what is the function of the ferrosome? My project seeks to answer this question by employing Random Barcode Transposon Sequencing, a powerful new method used to annotate gene function. I will determine which genes become conditionally essential in the absence of ferrosomes. Finding out the ferrosome’s function can reveal how bacteria produce, use, and store iron. It can also have broader implications in organelle biogenesis and bacterial stress […]

Eden McEwen

The twinkling of stars and other astronomical targets due to the Earth’s atmosphere is a long-standing disadvantage that ground-based telescopes face compared to their space-based peers. Large observatories have used adaptive optics (AO) to correct for atmospheric blurring, producing nearly diffraction-limited images. Ground layer AO (GLAO) seeks to apply corrections to a wider field of view than traditional AO by selectively targeting lower atmospheric layers. My SURF project will look at the last three years of data from the ‘imaka GLAO experiment to characterize the instrument’s correction over a variety of conditions and over multiple wavelengths. Better corrections over larger fields and shorter wavelengths enables observations of extended targets in multiple spectrums. The results from this work will inform GLAO systems in the next generation of ground based telescopes.

Andy Chen

The retina is the neural tissue lining the back of the eye that senses incoming light and relays this information to the brain, allowing for vision to occur. During development, “waves” of neural activity propagate across the retina, and to areas of the brain that receive retinal input. Retinal waves play an important role in establishing the organization of retinal inputs to the brain, but there is only limited evidence that they play a role in the development of the retina itself. I am exploring the role of waves in the development of a class of output neurons of the retina called intrinsically photosensitive Retinal Ganglion Cells (ipRGCs), which express the light-sensitive protein Melanopsin. These ipRGCs themselves participate in retinal waves during a period of development in which they undergo a significant amount of cell death. By comparing the densities and connectivity of ipRGCs in wild type mice and mice […]