A Case Study in Taphonomy from the Phillips Coal Ball Collection

The Pennsylvanian (323–299 million years ago) is a very unique time interval in Earth’s history. The Pennsylvanian tropics have one of the best plant-fossil records due to coal balls. These are carbonate nodules containing anatomically preserved fossil peat—deposits of partially decomposed plant material (Schopf, 1975). The Phillips Coal Ball Collection (PCBC) is one of the largest paleobotanical datasets in existence, containing 50,000 coal balls and 500,000 coal ball peels—thin, acetate sheets. From the peels, 800,000cm2 of plant material have been microscopically analyzed and identified at a tissue/organ level. While these fossils have been studied extensively, the link between plant diversity and taphonomy—the process of fossilization—remains underexplored. My plan is to develop an index of preservation decay and apply it to a case study of peels, examining the link between preservation and diversity. I expect lower species diversity in highly degraded peels. Any correlation I find could have major implications for […]

...Read More about Sydney Booth

The Effect of Deafferentation on the Sensorimotor System

Motor learning – the process of acquiring skilled movements – helps us learn to kick a ball and play piano. Among the many processes that enable motor learning, motor adaptation is of primary importance, enabling us to readily respond to changes in the body (e.g., muscle fatigue) and environment (e.g., a heavy jacket). A large body of work has emphasized how motor adaptation is driven by visual signals; however, the role of proprioception – one’s awareness about the location of the body – has been largely neglected. To fill this gap in the literature, I will examine the role of proprioception on motor adaptation. Through behavioral experiments (in-person and online), as well as a meta-analysis of the literature, I will compare motor performance between patients without proprioception – also known as deafferentation, an extremely rare neurological condition – with those of age-matched controls. These results will not only reveal how […]

...Read More about Anisha Chandy

Gut microbiota for E. faecalis Infection Resistance in C. elegans

The animal gastrointestinal tract is colonized by diverse microorganisms collectively termed the gut microbiota, of which bacteria are the most characterized. Gut bacteria play numerous roles in host physiology, from development to immune homeostasis. In recent years, there has been a significant rise in interest in understanding the role of gut microbiota in protecting the host from pathogen colonization. Past research has uncovered that gut microbiota can prevent pathogenic bacteria from colonizing the host gut by competing for resources, enhancing host immunity, or directly inhibiting pathogen proliferation. Yet, more research is required to better understand the modes in which gut bacteria help their hosts resist infections. I will take advantage of the Caenorhabditis elegans model to identify specific gut bacteria that increase host resistance to the pathogen Enterococcus faecalis, a bacterium responsible for many human infections. I hypothesize that common C. elegans gut microbiota members will confer protection against E. […]

...Read More about Da Kyung Jung

Investigating Genetic Determinants of Growth in C. aerofaciens

The gut bacteria Collinsella aerofaciens has two coexisting growth phenotypes in culture, and my research will identify genes driving these phenotypes. C. aerofaciens is a large component of the human gut microbiome, and is able to ferment and metabolize different carbohydrate sources, making it a crucial part of human nutrient metabolism. Looking at variation in growth (pellet versus suspension) will allow me to better understand the ways in which the bacteria respond to different growing conditions. We will use a combination of gene expression analysis and a forward genetic screen to identify the genetic loci that are responsible for the observed differences in growth. This project will contribute new information regarding C. aerofaciens’ growth as a bacteria crucial for metabolism and digestion of certain compounds, and for repression and modulation of pathogenicity in the human gut. Understanding bacterial growth in the gut will provide information as to the role of […]

...Read More about Haaris Kadri

Front Limb Functional Morphology of Fox Squirrels During Landing

The ability to reliably leap and land on unfamiliar and unstable surfaces is instrumental to squirrels’ survival and navigation of arboreal environments. In previous studies, squirrels quickly learned to modify impulse generation upon repeated leaps from unfamiliar, compliant beams and rapidly adjusted foot placement to compensate for rotating rods. Understanding how squirrels adjust to unexpected landing conditions could not only help us better understand their morphological adaptations but could also provide innovative solutions in developing bio-inspired robots. Current jumping robots, such as UC Berkeley’s SALTO, are only capable of using their point foot to land on flat surfaces. Biological systems like squirrels can help inspire robots that can land on complex terrains. My study aims to quantify the key metrics in squirrel landing foot placement, in particular paw placement angles, contact area, front limb stance width, and toe span over different gap distances and landing rod diameters. By studying prominent […]

...Read More about Duyi (Tina) Kuang

Establishing a Mouse Model for Brain Arteriovenous Malformations

This project aims to establish and characterize a novel mouse model for hereditary hemorrhagic telangiectasia (HHT). HHT is an autosomal dominant disorder known to be caused by mutations in the receptor activin receptor-like kinase (ALK1). Arteriovenous malformations (AVMs) are a hallmark of HHT, and brain AVMs (bAVMs) can be particularly risky as they can cause hemorrhagic stroke. HHT-bAVM formation mechanism is not well understood and there are no preventions or treatments. Animal models of Alk1 deficiency can facilitate the study of HHT-bAVM pathogenesis; however, existing HHT-Alk1 mouse models are limited in their ability to recapitulate clinical bAVM features. Thus, I propose to establish a superior HHT-bAVM mouse model, with genetics and symptoms closer to clinical HHT-bAVM and having high bAVM penetrance, as well as characterize the cellular parameters accompanying HHT-bAVM pathogenesis in these mice to better understand HHT-bAVM progression mechanism. Successfully completing this project will provide a crucial system and […]

...Read More about Cynthia Liu

Effects of Wildfire and Invasives on California Grassland Microbiomes

The devastation caused by intensifying wildfires in California over several decades has had increasingly detrimental effects on the diversity of native vegetation and the soil microbiome, which are critical in shaping plant growth and function. However, we still know very little about how native soil microbiomes are affected by wildfire and their role in host plant recovery. Specifically, we do not know how soil microbiomes of California grasslands (which evolved with periodic, low-intensity fires) mediate the recovery of native vegetation and how they may interact with non-native plants. As both fires and non-native plant invasion are major forces shaping grasslands, understanding their interaction is essential to improve restoration practices. In my research, I will investigate how pyrophilic bacteria and native pre-fire taxa change in their abundance in burned and unburned soils on sites that have been invaded or not by non-native plants at Blue Oak Ranch Reserve. Better understanding of […]

...Read More about Laura Powers

Tuning Effects of Plasmid Copy Number on E. coli Biosynthesis

Metabolically engineering living organisms to synthesize chemicals is an exciting alternative to traditional production pipelines, allowing for the sustainable and scalable production of a wide array of useful compounds. However, dramatically altering the fundamental chemical behavior of organisms by introducing new biosynthetic pathways can often have unintended consequences on cellular growth. The expression of an unnatural pathway consumes valuable cellular resources, an effect known as metabolic burden that ultimately limits overall production. My research project seeks to better characterize the effect metabolic burden has on an existing engineered biosynthetic pathway producing butanol, a next-generation biofuel. In order to accomplish this, we propose the development and application of a system to manually tune plasmid copy number within a cell. After examining the butanol pathway, we plan to expand the scope of our system to pathways producing 1,3 butanediol, 4-hydroxy-2-butanone, and amorphadiene. This work will offer a generalizable approach to optimizing production […]

...Read More about Albert Qiang

Expression of RickA and Sca2 in Rickettsia parkeri

The spotted fever group Rickettsiae (SFGR) are a collective group of Gram-negative obligate pathogens from Rickettesia spp. Most bacteria in the SFGR use two effectors to mediate actin-based motility (ABM). This is in contrast to other intracellular pathogens, which utilize only a single effector for ABM. The goal of my research project is to understand how Rickettsia parkeri, a member of the SFGR family, regulates the expression of two effectors that mediate ABM: RickA and Sca2. While both effectors are involved in mediating ABM, the regulation for both effectors and the dynamics of their expression have not been fully characterized. In this project, I will explore the role of transcription of the rickA and sca2 genes with respect to ABM on a single-cell level using live-cell microscopy. To look at the role of translation and secretion in regulating gene expression and activity, I will explore the localization of RickA and […]

...Read More about Tania Sodhi

Functional Significance of hox3 in Leech Posterior Growth Zone

In arthropods and vertebrates, Hox genes determine how an organism develops along the axis running from its head to its tail. Little is known of Hox function outside of these standard animal models, but studies in annelids (segmented worms) suggest that Hox genes not only play a conserved role in embryonic patterning, but are also deployed in ways specific to annelids. For example, hox3 is expressed around the posterior growth zone (PGZ), from which all new segments arise. I hypothesize that hox3 is a stem cell marker in annelids that is necessary for PGZ activity. I will examine this hypothesis with expression analysis and CRISPR mutagenesis of hox3 in Helobdella austinensis, a leech. My proposed research represents one of the first analyses of Hox function in a segmented animal that is not an arthropod or a vertebrate; it thus adds to our understanding of how developmental mechanisms evolved during the […]

...Read More about Tannya Tang

The Role of Psychedelics in Associative Learning

  Psychedelics have been used medicinally for thousands of years by Native Americans, but research into their clinical effects and mechanisms was prematurely halted in the 1960s. Exploration of the effects of psychedelics is long overdue. Recent studies have found that single doses of psychedelics can have positive, long-lasting effects, but very few studies examine psychedelic effects on behavior. My project aims to discover how psychedelics influence associative learning behavior. Associative learning involves learning the association between a cue and an outcome. I hypothesize that mice treated with psychedelics will become better at associative learning. To test this hypothesis, I will condition mice in an enriched environment with novel flooring and then condition them in a non-enriched environment with a different flooring. Both conditions will isolate the mouse; the enriched environment is like a moude playground, whereas the non-enriched environment is a boring empty cage. If mice have learned the […]

...Read More about Katrina White

Identifying Essential Periaxin Domains for Proper Lens Function

  Cataract, a clouding of the eye lens, is the leading cause of blindness worldwide. Periaxin (Prx) is a scaffold protein interacting with membrane/cytoskeletal networks in the lens and other cell types and has been implicated in cataract development. My project will investigate the functions of Prx variants in lens cells. Recent studies in the Gong Lab suggest that Prx is a genetic modifier regulating cataract severity in connexin 46 knockout (Cx46KO) mice. Four Prx missense variants have been identified between the 129SvJae (129) and the C57BL/6J (B6) mouse strains. Based on Prxs structural importance, I hypothesize that Prx variants interact differently with lens cytoskeletal proteins and subsequently affect their cellular distribution and lens cell structure integrity. I will determine how different Prx gene variants alter the distribution and function of cytoskeletal proteins in cultured lens cells, which will reveal new molecular information about how substituted amino acid residues in […]

...Read More about Jianxiang Zhang

VIP-SOM Disinhibitory Circuit in V1 during Figure-Ground Perception

The perception of a stimulus is strongly influenced by the background surrounding it. In mammals, this figure-ground perception to identify stimuli from the environment is crucial for survival, such as detecting predators. My project aims to explore the neural mechanisms behind figure-ground perception, especially focusing on the role of vasointestinal peptide positive (VIP) and somatostatin (SOM) interneurons in the primary visual cortex (V1). To explore the mechanism, I will first develop a novel mice behavioral task that can accurately quantify figure-ground modulation. Then, I will use optogenetics to activate or silence VIP and SOM neurons to explore how these perturbations affect mices performance in the task. In doing so, I aim to uncover how VIP-SOM disinhibitory circuit contributes to figure-ground perception.

...Read More about Xiaozhou Zhang

Functional Genetic Analysis of Foxc1 on Tooth Regeneration

  Understanding the genetic basis of organ regeneration remains a central challenge in the field of developmental biology. Teeth are a classic model for organogenesis, since many homologous ectodermal organs (e.g., teeth and hair) follow similar patterns of development and regeneration. Threespine stickleback fish are a powerful model organism for studying tooth regeneration in vertebrates because they possess the ancestral dental phenotype of polyphyodonty, in which teeth are continuously replaced throughout adult life. Past research has shown that Foxc1 regulates Bmp6, a gene important for viability, growth, and tooth patterning in threespine stickleback fish, and maintaining quiescence, a period of rest, in mouse hair follicle stem cells. My project aims to study whether Foxc1a and Foxc1b are required for regulating tooth regeneration in threespine sticklebacks. I hypothesize that Foxc1a and Foxc1b play homologous roles in reestablishing quiescence in fish tooth stem cells as Foxc1 does in past studies of mouse […]

...Read More about Emily Zhao