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 […]

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 […]

Lilou Redon-Gabel

Particulate air pollution contributes to millions of premature deaths worldwide annually and has major climate feedback effects. This is particularly true of black carbon (BC), a component of particulate matter (PM) that results from incomplete combustion sources and has not been as thoroughly assessed as other air pollutants. Gathering particulate air pollution data within communities most affected by industrial activities and vehicle traffic is necessary in developing solutions to mitigate the social and health inequities that result from exposure. My team at LBNL aims to analyze spatiotemporal trends of PM and BC concentrations in vulnerable California communities using our low-cost sensor technology. Our goal is to use high-density air sensor networks to understand the trends in BC concentrations and BC/PM ratios over daily, weekly, and seasonal periods. This will allow us to identify localized regions where air pollution levels are highest as well as the magnitude of different pollutant sources. […]

Samantha Lieberman

In tropical regions around the world, the cassava plant’s starchy tuberous roots are relied on as a staple source of calories. The crop is naturally drought tolerant and can be stored underground for extended periods of time – preventing the need for immediate harvesting and storage. However, prior to consumption, cassava requires significant processing due to the cyanogenic glucosides that it naturally produces. The cyanogenic glucosides linamarin and lotaustralin are synthesized in the leaves of the cassava plant and transported basipetal in the plant to the tuberous roots. The cassava genes CYP79D1 and CYP79D2 encode the enzyme responsible for the first step of the cyanogenic glucoside biosynthetic pathway. Downregulation of these genes should lead to a reduction in cyanide content in cassava leaves and tuberous roots. Therefore: the goal of this project is to use CRISPR-Cas9 gene editing technology to engineer non-toxic varieties of cassava by causing knockouts in the […]

Xavier Tao

Polyketide synthases (PKSs) are a family of enzyme complexes that synthesize a diverse class of secondary metabolites including clinically important antibiotic, antifungal, and anticancer compounds. In order to accomplish this, PKSs utilize a modular assembly with a wide variety of catalytic building blocks, passing molecular intermediates between modules until a product is finished. Due to their unique modular nature and deterministic mechanisms, PKSs have inspired engineering efforts to biosynthesize various useful new molecules. However, designing active variants still face difficulties due to a lack of understanding for the reasons behind successful or inactive enzymes, frequently resulting in nonfunctional systems. For this reason, my project will expand ClusterCAD, a computational platform that provides sequence and structure search tools useful for identifying parts necessary to build new chimeric PKSs. Specifically, I will annotate new database entries and implement support for irregular catalytic modules. The addition of novel mechanism elucidations and support for […]

Evan Juan

With an estimated 105 million infections globally, dengue virus (DENV), the causative agent of dengue fever, places a severe burden upon global public health. Severe manifestations of dengue fever are characterized by leak of plasma from the vascular system; these symptoms can develop into hypovolemic shock and organ failure if left untreated. The Harris laboratory and others have discovered that DENV non-structural protein 1 (NS1) is critical to dengue pathogenesis and can directly trigger vascular leak. The exact mechanism of NS1-induced vascular leak is still unknown, but recent work has shown that the DENV NS1 can activate inflammasomes, an innate immune sensor within cells. Inflammasome activation causes the release of inflammatory mediators which can lead to the disruption of the endothelium. However, it is currently unknown how NS1 activates the inflammasome. My project will focus on investigating this mechanism and its importance in causing vascular leak. Thus, I aim to […]

Sara Smith

Microbial communities are ubiquitous and intimately involved in environmental cycles, human health, and industrial processes. Despite the fact that microbes live in diverse microbiomes, much of our knowledge about them comes from studying isolates. This creates gaps in understanding of how microbes interact with each other in communities. One such interaction is the production of siderophores in low iron environments. Iron is required for essential functions such as respiration and DNA synthesis. Siderophores, small iron chelating molecules excreted into the environment, are the most prevalent method bacteria use to scavenge iron. This process is dependent on community interaction because some microorganisms are able to acquire iron using siderophores produced by a different species. My project will investigate this siderophore “cheating” and its effect on the fitness of members in the microbial community of the cheese rind. This work will be conducted through observational sequence-based approaches as well as perturbing the […]

Tina Li

Cellular aging is a nearly universal trait of all organisms and is a risk factor for a variety of human diseases. Cellular rejuvenation occurs in every human body during gametogenesis, the process by which we form gametes, also known as sperm and egg. In yeast, overexpression of a gametogenesis-specific transcription factor, Ndt80, has been shown to extend lifespan and rejuvenate the nucleolus in aging cells. Using genome-wide screening of gametogenesis genes, the Ünal lab has identified 86 rejuvenation candidates that can extend yeast lifespan. My research will focus on characterizing a subset of these candidates and identifying those that can counteract age-associated expansion of the nucleolus, a common biomarker of cellular age. Using fluorescence microscopy, I will determine how aging affects different nucleolar proteins in a wild-type context and then determine which rejuvenation candidates can reverse these age-related nucleolar phenotypes. My research will give insight into how aging affects the […]