Synthetic Biology Approach to Drive Oxygen-Dependent Biochemical Pathways Under Anaerobic Conditions

Hydrocarbon contamination can be extremely detrimental to affected ecosystems and bioremediation, the use of microorganisms to detoxify and remove environmental pollutants, presents an effective solution. Specifically, oxygenases are required to perform hydroxylation or carboxylation reactions that cleave aromatic rings into less inert intermediates. Oxygen is an essential co-substrate for many aromatic hydrocarbon degradation pathways. However, bioremediation of aromatic hydrocarbons is often constrained by limited oxygen levels, which can be attributed to oxygens low solubility and rapid depletion during cellular respiration. Bioreactor-mediated hydrocarbon degradation similarly faces oxygen limitation issues, and solutions like increasing the bioreactors retention time or continuously pumping in pure oxygen are extremely costly and inefficient. My project aims to synthetically develop recombinant organisms that can drive naturally oxygen-dependent biochemical pathways under anaerobic conditions.

...Read More about Nazar Akhverdyan
Rose Hills

Reprogramming of Mller Glial Cells by Adeno-Associated Viral mediated delivery of split dCAS9-VP64-MS2-p65

Retinitis Pigmentosa (RP) is a set of genetically inherited neurodegenerative disorders that leads to degeneration of photoreceptor neurons and loss of vision. While onset of RP can be detected early, there are currently no treatments to prevent disease progression. Cellular reprogramming is a promising approach to replenishing photoreceptors after retinal degeneration. In zebrafish, Mller glial cells can dedifferentiate and reprogram into photoreceptor cells upon retinal damage. However, this restorative activity of Mller glial cells is limited in mammals. A CAS9 mediated genome wide activation screen offers the potential to identify genes important in reprogramming Mller glial cells into photoreceptor neurons. My project aims to test whether the delivery of a split dCAS9-VP64-MS2-p65 by adeno-associated virus (AAV) can be used to activate and identify genes which promote reprogramming of mammalian Mller glial cells to photoreceptor-like cells. I plan to test whether splitting the CRISPR-CAS9 system for viral packaging can activate these […]

...Read More about Annika Anderson
L&S Sciences

Stability maintenance in reaction-diffusion systems

Interplay between spatial organization and interconversion of different molecules leads to complex pattern formation in simple chemical systems. Some have suggested implications for biological systems, especially in the context of embryonic development. However, unlike idealized chemical systems, biological systems are characterized by complex and dynamic environments. Nevertheless, biological pattern formation appears to be largely stable. This stands in stark contrast to current theories, which predict extreme sensitivity to fluctuations and initial conditions in systems with feedback delays – delays in the response of a system to a stimulus. A comprehensive theory must account for stability despite such time delays, which are common in biological systems. My goal is to develop a theoretical description of pattern formation in the presence of perturbations. Using theory and computer simulation, I will contribute to a quantitative description of stability maintenance in the face of feedback delays. A mathematical description of such systems is valuable […]

...Read More about Easun Arunachalam
Rose Hills

Discerning Anonymity: Characterizing Female Voice in Middle English Literature

There is no doubt that finding a professed author in our surviving Middle English texts is both incredibly valuable and extremely difficult. An author, no matter his or her intentions, often cannot help but bring a rich array of individual complexities into their work. However, when an overwhelming majority of the surviving Middle English poetry we have today is expressly author-less, authorial intention becomes an aspect we can only speculate on without any real confidence. Without a name, the basis for determining many aspects of authorial voice has tended to fall rather problematically on a poems content, and just how far we can extrapolate poetic content as indicative of individual character and authorial presence remains an unanswered question. My research seeks to come to stronger conclusions about such issues, largely focusing on how we can and should determine the poetic female voice, especially in cases of anonymous works where no […]

...Read More about Sarah Barnett
Humanities and Social Science

Controls on trace element incorporation into travertine carbonates

A multitude of different trace metals can readily incorporate into the crystal lattice of calcite, depending on factors like solution chemistry, temperature, and growth rate. Measurements of these elemental abundances in calcite can be an effective means of understanding rates and environments of crystal growth and have been widely utilized over the past decades to decode paleo-environmental growth conditions and, to some extent, in environmental remediation of polluted systems. Much of the present understanding of microscale controls on trace element incorporation into carbonates is based on laboratory experiments and studies of marine or cave carbonates. However, these studies are limited in their ability to precisely describe conditions at the time of carbonate deposition, which limits our understanding of growth mechanism acting at the time of precipitation. Travertines, or continentally-deposited limestones, provide the opportunity to study trace element incorporation in a modern system where source fluids and other system characteristics are […]

...Read More about Holly Barnhart
Rose Hills

Silk Gene Expression Associated with Loss of Web-Building in Tetragnatha Spiders

Discovering how traits evolve or are lost is key to understanding the processes underlying biodiversity. Web-building is an ancestral trait in orb-weaving spiders, but several taxa have secondarily lost the ability to build webs. Among the long-jawed spiders of the genus Tetragnatha, there are species that exhibit a range of web-building phenotypes, including the total loss of web-building and the construction of reduced webs. My research will use Scanning Electron Microscopy (SEM) to investigate the silk organs of these species, which will provide a clear picture of the morphologies associated with the varying levels of web-building. Then, I will use RNA sequencing (RNA-seq) techniques to analyze the complement of expressed silk genes, or transcriptomes, in each species. This comparison across closely related species will provide a greater understanding of the mechanisms underlying the evolution and loss of web-building.

...Read More about Cory Berger
L&S Sciences

Preventing Post-Surgical Amniotic Sac Rupture

During pregnancy, complex birth defects can arise, and fetal surgery can correct or drastically ameliorate these conditions. The largest unmet need of the field is a method to seal the amniotic sac, as it does not heal following surgery and can rupture, leading to preterm birth. I hope to develop self-sealing needles and instrument sheaths to seal defects in the amniotic sac during and after surgery. Hopefully these new methods will help fetal surgery become a viable and safe option for growing families.

...Read More about Sarah Bhattacharjee
Rose Hills

Reshaping Gender: Exploring Godard and Varda's Disruption of Traditional Cinematic Gender Representation during the French New Wave and Beyond

The French New Wave, a cinematic movement which shifted the paradigm of narrative storytelling, was based on an engagement with radical social upheavals. By rejecting the literary, political, and societal standards and expectations of their era, New Wave directors were responsible for groundbreaking representations of modern social issues. In my research project, I am examining the ways in which two particular New Wave directors (Jean-Luc Godard and Agns Varda) interact with and comment on gender roles in their films. Both Godard and Varda employ subversive representations of gender which give their films a reputation of challenging the heteronormative gender structures of contemporary French society. My focus in this project is to identify the intersections between the technical cinematographic and narrative aspects of these New Wave films that give us reason to believe that these two filmmakers actively sought to redefine and reinvent the ways in which spectators view gender relations. […]

...Read More about Jacob Bjorseth
Humanities and Social Science

Buscando Tun Tzaj Chbinchey Qey J: Comparing Perceptions of Access to and Experiences Within Healthcare Between Mayan and Latina Women in East Oakland

Woven into the intricate fabric of Oaklands Latinx population is a community of Maya immigrants. Many arrived as refugees, escaping genocide during the Guatemalan Civil War, and in part because of this traumatic history and their indigenous identity, Maya individuals face unique challenges in accessing health care. While both Latinx and Mayan populations may perceive a lack of access, no existing research analyzes how these perceptions differ, allowing for the assumption that both groups face the same challenges. My research investigates the distinct challenges that the Maya perceive in accessing healthcare and their experiences within the healthcare system of the United States. I will use concurrent mixed methods interviews, nonparticipant observation, and focus groups to conduct my study, which will culminate in a 60-80 page independent thesis and a published paper that pushes us to rethink how our healthcare system interacts with the indigenous immigrant community.

...Read More about Dylan Bush
Humanities and Social Science

Investigation of the Effects of LisH Domain Proteins on the Drosophila Melanogaster Histone Cluster

Many tandemly repeated histone gene clusters exist in the Drosophila Melanogaster genome and are subjected to complex regulation during the cell cycle. However, the exact mechanism of this regulation remains elusive. Using a variant of the CRISPR/Cas9 system, we have developed a DNA-pulldown technique that, when coupled to mass-spectrometry, is capable of identifying bound proteins on a given promoter, enhancer, or any other regulatory DNA sequence. Applying this technique to the D. Melanogaster histone cluster, the pulldown samples interestingly showed an enrichment of a particular protein domain – LisH. Found in the Saccharomyces cerevisiae SIF2 protein, this LisH domain is thought to be responsible for the formation of dimer/tetramers and could be an integral part of the recruitment complex necessary for efficient and proper histone gene transcription. Indeed, one of the LisH proteins identified in the pulldown, Multi sex combs (Mxc), has been shown previously to be involved in the […]

...Read More about Andrew C. Lu
L&S Sciences

Development of Ferritin-iron Redistribution to Ion Channels (FeRIC) Technology

For decades, researchers have been experimenting with tools used for neural stimulation, modulation, and therapy. A greatly used and helpful tool includes optogenetics, which utilizes light waves to control cells expressing light-sensitive channels. While optogenetics is not an invasive recording technology, due to its dependence on visible light it cannot penetrate deep into the organisms tissue. The purpose of this project is to develop a wireless method similar to optogenetics which can overcome the issues optogenetics encounters. Rather than using light to manipulate neuronal behavior, an electromagnetic field will be provided as the stimulus source. The electromagnetic field will target specific cells that express heat-sensitive proteins, specifically the transient receptor potential channel TRPV1. This method of neural stimulation is ideal as it will reach cells deep within the tissue, and it will not expose the subject to exogenous particles.

...Read More about Chelsey Campillo Rodriguez
L&S Sciences

CD36-mediated CoQ uptake is integral to normal BAT function

CoQ is an essential molecule in the electron transport chain (ETC) which acts as an electron carrier to help generate adenosine triphosphate (ATP) in the mitochondria. Therefore, without CoQ or under conditions of severe CoQ deficiency, the redox reactions required for efficient energy production are greatly hampered. The inordinately high levels of mitochondria in brown adipose tissue (BAT) also suggest that a CoQ deficiency could negatively and significantly impact the unique BAT function of thermoregulation through nonshivering thermogenesis. Defective BAT function could then lead to excess fat deposition, obesity, and other serious metabolic diseases. This summer, I will be exploring the scavenger receptor protein CD36 as a fatty acid transporter and its role in facilitating CoQ uptake into cells. I will be using BAT-specific CD36 Knockout mice to improve understanding of the physiological effects of CoQ deficiency in BAT, and subsequently, its effects on overall metabolic health. We aim to […]

...Read More about Jazlyn Chong
Rose Hills

Investigating the role of HERVH in human embryonic stem cell pluripotency

The non-coding genome has traditionally been viewed as junk, with little to no significance in everyday biological functions. However, recent advances have demonstrated clear functional importance of the non-coding genome in both development and disease. Of particular interest are the retrotransposons (RTs), mobile genetic elements that copy themselves through RNA intermediates. One class of RT, the Endogenous Retroviruses (ERVs), occupies nearly 8% of the human genome, yet has lost its to ability to retrotranspose or jump throughout the genome. The inactivity of ERVs despite their high density within the human genome poses the question: what is their significance and impact in human development? Our research seeks to address this question by studying the mechanisms of Human Endogenous Retrovirus H (HERVH), a primate-specific RT that has been previously shown to have significant implications in the maintenance of pluripotency in human embryonic stem cells (hESCs). In this project, I will be focusing […]

...Read More about Jonathan Chu
Rose Hills

Investigating the Molecular Mechanism of Heterochromatic Gene Silencing

The heterochromatin domain is an essential component of the eukaryotic genome, which contains many repetitive non-protein-coding sequences that must be transcriptionally silenced to maintain genomic integrity. Heterochromatic sequences from multiple chromosomes are organized into nuclear domains that concentrate heterochromatic proteins and exclude euchromatic factors. These domains prevent transcription and recombination of the sequences inside, perhaps because of the density of chromatin packing in the domain. However, this chromatin compaction model is inconsistent with other observations, including high mobility of proteins inside the heterochromatin domain. Recent studies have shown that biological phase separation can result in distinct cellular compartments without bounding membranes, which leads us to ask if phase separation is the selective mechanism that explains how the heterochromatin domain is transcriptionally silenced while maintaining mobility of internal components. To study this, I will employ single molecule tracking to directly image the path of euchromatic molecules to determine how they are […]

...Read More about Ryan Chung
Rose Hills

Diurnal variation in robotic observations of carbon export in California coastal waters

One of the most interesting components of the global carbon cycle is the movement of carbon from the atmosphere to the deep ocean, where it is deposited as particulates, a process called the Biological Carbon Pump (BCP). The BCP combines physical oceanography and biology, as the majority of the carbon dioxide that is pulled from the atmosphere into our oceans for biological processes in the photic zone, and then moves from the surface to the deep ocean as zooplankton excrement. Using robotic devices to monitor this chemical and biological cycle, I hope to better understand the diurnal fluctuations in the BCP from the atmosphere to the deep ocean, and therefore better understand how surface zooplankton contribute to carbon cycling on our planet.

...Read More about Beth Connors
L&S Sciences

Role of GPR183 in EET-signaling

My project centers on epoxyeicosatrienoic acids (EETs) which are located in endothelial and vascular smooth muscle cells. From previous studies, they have been shown to be potent vasodilators and though the receptor is not known, their mechanism is believed to rely on calcium activated potassium channels and the hyperpolarization of smooth muscle. In addition to vasodilation, EETs are known to help maintain cardiovascular homeostasis through anti-inflammatory effects and can protect against ischemia and hypertension. Discovering the receptors that control the potential benefits of EETs could lead to new therapeutic options for patients with cardiovascular disease. Based on my preliminary studies using a transfection-based screening strategy in a line of cells expressing fluorescent calcium sensors, my hypothesis is that GPR183 is the receptor through which EET mediates vascular relaxation.

...Read More about Kayleigh Cook
Rose Hills

Morphological Changes in Dopamine Neurons Resulting From Tsc1 deletion

Dopamine is an important neuromodulator, and dysregulation of dopaminergic function is involved in many neurological disorders, from Parkinsons disease to addiction. The mTOR pathway, a ubiquitous signaling pathway which regulates cell growth and survival, plays an important role in dopamine neuron fate. By manipulating mTOR signaling in dopamine neurons via cell-type specific deletion of the Tsc1 gene, a negative regulator of the mTOR complex, I am examining how changes in cell morphology and protein expression levels are impacted by mTOR hyper-activation. This work can contribute to a better understanding of the mechanism governing several neurological diseases, including tuberous sclerosis complex and autism spectrum disorder.

...Read More about Malcolm Crawford
Rose Hills

Roman Amphoras of North Africa: Markers of a Pan-Mediterranean Economy

The Crisis of the Third Century (AD 235-284) nearly saw the complete collapse of the Roman Empire due to a combination of foreign invaders, plague, civil war, and economic depression. While there is a considerable amount of scholarship on the 3rd Century, I am hoping to re-examine this scholarship with an archaeological lens. I am focusing my research on the study of Roman trade amphoras. These ceramic vessels will give me a good picture of the consumption and trade patterns of Rome during the Late Empire. I am focusing my research even further on trade amphoras originating from North Africa. North Africa was a known in the ancient world as the bread basket of Rome, so it will prove a large sample of amphoras for me to work with. In using a combination of historical texts and archaeology I am hoping that my research provides a new perspective on the […]

...Read More about Amanda Dobrov
Humanities and Social Science

Horizontal Gene Transfer of a tet(C)-containing casette between Chlamydia suis and Chlamydia trachomatis

Many strains of Chlamydia suis, a bacteria that infects the intestinal tracts of pigs, are resistant to an antibiotic called tetracycline. My project studies whether the gene conferring tetracycline resistance can be transferred from Chlamydia suis to a different species – for example, Chlamydia trachomatis. C. trachomatis is the leading cause of bacterial sexually transmitted diseases and preventable blindness (or trachoma) in the world today, and tetracycline is one of the main antibiotics used to treat those infections. Because C. suis is genetically similar to C. trachomatis and both can co-infect the same anatomic tissues in humans, it is a huge concern that the gene conferring tetracycline resistance will be transferred to C. trachomatis, making it more difficult to treat this pathogen. This project has implications for public health and our ability to effectively treat C. trachomatis infections now and in the future.

...Read More about Stacey Dojiri
Rose Hills

Understanding the Effect of a Necroptotic Cancer Vaccine on Anti-tumor Immunity

The activation of the adaptive immune system in host-tumor interaction mediates the efficiency and strength of the host anti-tumor response. Necroptosis, a form of programmed cell death, has the ability to moderate the development of antitumor tolerance versus immunity due to its pro-inflammatory properties. However, in what ways and to what extent do the products of necroptosis trigger the activation of the immune system is not well understood. I am interested in using a necroptotic tumor vaccine overexpressing RIP3, a cell death protein, to study the effect of necroptosis on the adaptive immune systems ability to detect and fight cancer cells. Through transduction of cancer cell lines, tumor injections in mice, and flow cytometry, I will investigate the effect of a necroptotic vaccine on the adaptive immune systems tumor response by characterizing APC and T-cell function.

...Read More about Emily Duan
L&S Sciences