Developmental role of Gremlin2 in the Mouse Dorsal Spinal Cord

Development of the nervous system depends on the migration, differentiation, and axonal projections of neurons to their appropriate targets. In the dorsal spinal cord where many sensory and interneurons are born, signaling cues specify the development of neuronal precursors into an array of cell types. However, the process by which these signals regulate neuronal growth is still unclear. This summer, I will examine the function of the Gremlin2 gene, which is expressed in a specific population of dorsal interneurons. Taking advantage of Gremlin2 knock-out mice, I will use immunocytochemistry to determine the precise anatomical location of Gremlin2 expression and analyze defects in specification, migration, and connectivity of these interneurons.

...Read More about Chung Yan Cheung
L&S Sciences

Physiological Costs for Cabbage Aphids Sequestering Glucosinolates

Studies have shown that cabbage aphids (Brevicoryne brassicae) that eat black mustard (Brassica nigra) can sequester toxic compounds to ward off their predators. This summer, I am building on these studies by examining the eco-physiological costs to aphids of processing and sequestering these toxins. The concentrations of the toxins will be analyzed to determine the difference in chemical load for aphids that eat broccoli (Brassica oleracea) versus mustard. My main goal is to study the physiological costs of this chemical load by examining differences in development and reproduction of aphids on the two food sources. The results of these experiments will be important in discovering methods to study and control agricultural aphid populations in a sustainable manner.

...Read More about Andrea Chiem
L&S Sciences

The origin and evolution of duplicated mitochondrial genes in the parthenogenic gecko, Heteronotia binoei

There are forms of the gecko species, Heteronotia binoei, that reproduce sexually that gave rise to forms that reproduce asexually through the process of parthenogenesis. Parthenogens have sections of duplicated genes in their mitochondrial genome while sexual forms do not. My project is to sequence and compare the mitochondrial genes of the sexual and parthenogenic forms to characterize their evolution since their divergence. I will also compare duplicated gene copies to one another within the parthenogenic individuals to characterize evolution of each gene since the duplication event. Gene duplication and subsequent mutation may lead to gene rearrangements within the parthenogenic gecko. Gene rearrangements are found in many other animal species but a mechanism remains unclear. Heteronotia may provide valuable insight into this phenomenon.

...Read More about Brandon Endo
L&S Sciences

Characterizing the Formation and Phylogenetic History of an 81-Member Tandem Duplicated Pre-tRNA Gene Cluster in Arabidopsis thaliana

My research fuses the disciplines of genomics and phylogenetics in order to characterize the evolution of large gene arrays. My research focuses on an eighty-one member pre-tRNA gene array located on chromosome one of Arabidopsis thaliana. The array itself is subdivided into twenty-seven triplet gene units, each triplet consisting of a single pre-tRNASer gene and two pre-tRNATyr genes, respectively. Using genomic data, such as syntenic analysis with outgroup species, and phylogenetic reconstruction of the evolutionary history of the genes in the array, my research aims to elucidate the history of the arrays formation, and the mechanism that formed, or equally-possible mechanisms that would have formed, the array as it exists today.

...Read More about Joshua Kane
L&S Sciences

Psychiatric Misdiagnosis of Patients with Neurodegenerative Disease

Frontotemporal Dementia patients suffer behavioral disturbances which mimic primary psychiatric illnesses such as bipolar disorder or schizophrenia. Unfortunately, awareness of this neurodegenerative disease is limited in the psychiatric world and often demented patients are misdiagnosed. The Memory and Aging Center (MAC) at the University of California San Francisco conducts one of the largest investigations into the frontal variant dementias in the nation. I plan to systematically review 450 patients research charts at the MAC in order to precisely quantify the rate of psychiatric misdiagnosis for each of the dementia subtypes. This quantification has the potential to reduce psychiatric misdiagnosis and promote better patient care.

...Read More about Baber Khan
L&S Sciences

The role of IGF signaling in cell migration and axon guidance in the developing mouse cerebellum

Growth factors are not traditionally known to play a role in cell migration. However, preliminary data suggest that insulin-like growth factor (Igf) functions in the guidance of granule cells within the cerebellum. The cerebellum is an important structure, responsible for the fine control of balance and movement and also involved in motor learning and memory. The cerebellar granule cell is the most abundant neuron in the brain, and investigating its development and wiring could provide insights into the functioning of the cerebellum and into diseases that affect its function. Using modern genetic techniques, my research approach is to conditionally inactivate the Igf1 receptor in mice cerebella. I will then assay for aberrant granule cell localization and axon pathfinding in these mutant mice.

...Read More about Alix Mary Lacoste
L&S Sciences

DNA Damage Checkpoint Activation in Heterochromatin

It is essential that the cell preserves the integrity of its DNA by initiating a proper response when there is damage to its genome. As a fellow of the Summer Undergraduate Research Fellowships, I am utilizing this summer and the senior academic year to study the DNA repair pathway in heterochromatin. Using Drosophila melanogaster as a model system, I propose to fluorescently tag different DNA repair proteins and conduct experiments to understand the kinetics of these proteins following DNA damage induced by X-ray treatment. This research is promising: knowledge of how cells repair DNA damage in heterochromatin can contribute to a better understanding, and therefore, potential treatments of diseases associated with damage to our genome (e.g., cancers).

...Read More about Hai Le
L&S Sciences

Differential response of wild-type and mutant small heat shock protein alpha-crystallin to chemical and thermal stresses

Cataracts, caused by the aggregation of proteins inside lens cells, are the leading cause of blindness in the world. Alpha-crystallins, members of the small heat shock protein family, are essential for eye lens transparency in humans and mice. Using mouse models with different mutations in aA-crystallin, I am investigating the mechanisms for establishing and maintaining lifelong lens transparency. This summer I will be challenging these cells with a compound called Withaferin A, a chemical that causes changes in cell architecture. By observing the response of intracellular proteins to this compound, I will be able to explore some of the causes of protein aggregation and malfunction inside lens cells. If successful, my research may provide clues for preventing or treating cataract formation.

...Read More about James Lee
L&S Sciences

Systematically Detect Fine Scale Crossover Breakpoints with High Density SNP Markers in Three Generation Tri-Trio Pedigrees

The importance of studying genetic variants in humans has given rise to the worldwide HapMap Project, which can potentially lead to techniques to diagnose, treat, or prevent illnesses according to each persons different genetic makeup, thus enhancing efficacy. This project tests a method to identify crossover breakpoint regions at a higher resolution than previous studies have. Because single nucleotide polymorphisms are bi-allele, their limited number of states can be analyzed case by case in advance; studying families of three generations using tri-trio pedigree charts allows for the deduction of information about the child, thus enabling the detection of crossover breakpoints regions within chromosomes. An automation in R language is being developed, which can test larger data sets efficiently.

...Read More about Janet Luo
L&S Sciences

Elucidating the structure and function of lens protein Lim2

The human lens is made up of two types of cells: a monolayer of lens epithelial cells, and its differentiated progeny, lens fiber cells. The differentiation process is a complex sequence of events in which lens epithelial cells slowly lose all their organelles, and elongate into lens fiber cells. There is a lens membrane protein called Lim2 that appears to exist only in lens fiber cells, and not in lens epithelial cells. Lim2 is known to be critically important for maintaining the integrity of the lens, and its role will be the focus of my summer research project. I will be conducting various in vitro experiments to determine the structure and functional domain of this protein.

...Read More about Vibha Mahendra
L&S Sciences

Neurogenesis from Neuroglia

Neurogenesis, the process by which new neurons form, was thought to be impossible in mature brains for most of the 20th century. However, recent studies have found that neurogenesis in intact adult brains does occur in specific regions. I will be studying neurogenesis in vitro using neuroglial cells, which are neuron supporting cells, by treating them with Epidermal Growth Factor (EGF) and Fibroblast Growth Factor (FGF). Following treatment, I will perform functional tests to evaluate the extent to which these factors were able to promote the transdifferentiation of these neuroglial cells into functional neurons. Learning the pathway to inducing neurogenesis could ultimately lead to important implications for the treatments of countless neurodegenerative diseases, such as Alzheimers and Parkinsons disease.

...Read More about Shila Manandhar
L&S Sciences

Thermal Ecology and Physiology of two Cryptic Skinks, Emoia cyanura and E. impar, on Mo'orea, French Polynesia

I am interested in the thermal ecology of two tropical skinks, Emoia cyanura and E. impar, in Tahiti, French Polynesia. Since these skinks are so similar in morphology and ecology, they likely compete for essential resources, including sources of heat. So far, through field observations and lab experiments, I have found that E. cyanura prefers open canopy habitats and warmer body temperature relative to E. impar. To expand my study, I will test sprint speed of each species at different body temperatures to see if they are thermal “generalists” or “specialists”. My investigation into thermal niche partitioning of these two lizards provides an important test case for how tropical lizards might change their behavior and habitat usage during climate change in the near future.

...Read More about Matthew McElroy
L&S Sciences

Screening for Silence: Bypassing Sir2 deacetylation in yeast

Because any given cell carries an overwhelming excess of genetic information, they need a way to selectively pinpoint what they need, when they need it. Silencing entire regions of the genome via chromatin modifications is one method that eukaryotes have developed to great effect. The four SIR (Silent Information Regulator) genes are absolutely critical to silencing in yeast. Wild-type Sir3 typically requires Sir2s deacetylation activity, and not just the deacetylation itself, in a mechanism that is still unclear. I will use sequencing and protein structural analysis to study PCR generated point mutations in the SIR3 gene that recover silencing in order to help me identify key functional regions in the Sir3 protein.

...Read More about Jane O
L&S Sciences

Development of Cryogenic Si-Ge Amplifier for L and X Bands

My project is to design, test and construct an electronic amplifier customized for data-taking in low temperature experiments (liquid helium cooled) at the Quantum Nanoelectronics Laboratory. Electrical signals from experiment samples are too weak to be measured directly, so this amplifier will make the signals stronger. For the transistor, the essential part of the amplifier, I will use a commercial Silicon-Germanium transistor, which is known for its low cost. Using computer simulations and testing of the amplifier characteristics, amplifiers for various experiments in the lab demanding different frequency ranges can be made (for example 5-6GHz, 1-3GHz). I will optimize the amplifier to work at cryogenic temperatures with minimum power dissipation and noise for maximum gain.

...Read More about Seita Onishi
L&S Sciences

Single-molecule analysis of the AMPA receptor2 TARP interaction

This summer I will be researching the interaction between Transmembrane AMPA-receptor regulatory proteins (TARPS) and AMPA glutamate receptors at the single molecule level. In order to do this I will have to make constructs containing fluorescent proteins paired with various members of the TARP family and AMPA glutamate receptor family. The interaction between TARPs and AMPA receptors particularly interesting because TARPs play a critical role in the regulation of synaptic AMPA receptor trafficing. While TARPs are not the only protein involved in this regulation it is believed that the regulation of these receptors underlies some forms of synaptic plasticity, a molecular correlate of learning and memory.

...Read More about Eric Pang
L&S Sciences

Economic Preference Parameters for Ambiguous Decision-Making

Cognitive control is the mechanism of coordinating actions with internal goals. I am primarily interested in the role of cognitive control in decision-making, particularly how internal states such as economic preferences can influence decision-making under probabilistic outcomes. Individuals differ in their tolerance for the amount of uncertainty in decision-making, and behavioral economic models, such as expected utility functions can create parameters that capture preference or aversion for risk and ambiguity. Using the choice history of each subject between pairs of gambles, my project will investigate how economic preference parameters may change for ambiguous conditions if probabilities are fixed. Will people show the same aversion for ambiguity if they believe experience with ambiguous conditions can help them learn the probability of outcomes?

...Read More about Karina Sakanaka
L&S Sciences

Characterizing Drug-Resistance Determinants in Gram-negative Bacteria from Blood Stream Infection

The core goal is to identify the origin of antibiotic drug-resistance determinants, with the hypothesis that drug-resistance determinants, in particular integrons carrying gene cassettes coding for drug resistance, from bacteria that is ingested through uncooked food (spinach, animal meat) can horizontally transfer to commensal bacteria in the human intestine, and under selective pressure of antibiotics, and ultimately lead to complicated multi-drug resistant bloodstream or urinary tract infections. Integrons are mobile genetic elements, found on transposons, plasmids and chromosomes that capture and express gene cassettes by site-specific recombination. This summer I will analyze bacteria isolated from bacteremia samples for prevalence of integrons using PCR, sequence and identify gene cassettes using bioinformatics such as BLAST, and compare results with those from spinach and animal studies.

...Read More about Julia Selezneva
L&S Sciences

Mathematical analysis of DNA unknotting by type II topiosomerases

Type II topoisomerases are enzymes that can change the topology of circular DNA molecules. These enzymes are essential to every living organism, which makes them good targets for anti-cancer and anti-bacterial drugs. DNA topology assays are used to determine the efficiency of topoisomerase inhibitors in drug design. In my research, I focus on the unknotting probability of knots by type II topoisomerases. In our previous study, our group built a mathematical model in simple cubic lattice to simulate how random strand passages generate the knotting distribution. We intended to use a sophisticated theoretical framework and efficient computer simulations to test and compare some of the existing models and propose new ones. I aim to implement the random strand-passage model in the Dowker code level to discover how topo II simplifies knots under the thermal dynamic equilibrium level.

...Read More about Yannan Shen
L&S Sciences

Probing the Necessity of Intestinal Stem Cells for Renewal of the Adult Drosophila Midgut

In adult animals, many tissues undergo continuous renewal, a process in which older cells die and are replaced by newly born cells. These new cells are generated by the proliferation of tissue stem cells, which divide continuously throughout the animal’s lifetime. The process of tissue self-renewal has long been thought essential for the maintenance of tissue structure and function; however, this presumption has never been explicitly examined. In my SURF project, I will explore the necessity of tissue renewal using the Drosophila epithelial midgut as a model system. Specifically, my research entails the genetic elimination of Drosophila intestinal stem cells and determining the effects of stem cell loss on the structure and function of the midgut.

...Read More about Sarah Soliman
L&S Sciences

The vascular organization of the cat inferior colliculus

I am analyzing the vascular organization of the cat inferior colliculus (IC), a major auditory structure in the midtbrain, to determine whether its divisions share a common pattern. The IC consists of the central nucleus (CN), the dorsal cortex (DC), and the lateral cortex (LC), each with different roles in auditory behavior and perception. I am comparing the IC capillary distribution to quantify differences between subdivisions using plastic-embedded material from two adult cats in 1 m-thick semithin sections stained with toluidine blue. Ten non-overlapping random 200 x 200 m2 samples will be selected from each CN, DC, and LC for analysis. The purpose of this study is to demarcate the borders of these subdivisions based on the vasculature. Inconsistent anatomical definitions may be the basis for past contradictory findings on the IC.

...Read More about Yohan Song
L&S Sciences

Use of chemical olfactory cues in colonial tuco-tucos, Ctenomys sociabilis

I work in Professor Eileen Laceys lab with a colony of tuco-tucos, which are subterranean rodents in the family Ctenomyidae. Although there are more than 50 species of tuco-tucos in South America, the species I am studying is unique in that they live in groups and related females share a single burrow system. As a result, social relationships between females are very important in this species. I am studying chemical communication between females. Specifically, I am testing the hypothesis that olfactory cues in urine may serve as indicators of individual identity. The results of my work may yield new insights into the role of olfactory communication in the social structure of this unusual species.

...Read More about Maressa Takahashi
L&S Sciences

Mapping Curly in Xenopus tropicalis Using Gynogenesis and Natural Mating Techniques

It has been discovered that Curly, the early developmental mutation in Xenopus tropicalis, a frog model for human biology, leads to an abnormal number of Mitotic cells during the cell cycle. The mutant phenotype is possibly due to the abnormal expression of cell cycle factors. Mapping the location allows us to study these factors, creating a greater understanding of cancer. My project focuses on using primers to map the Curly mutation by using a combination of two methods. One involves natural mating between hybrid Curly carriers, and the other generates diploid mutant embryos from only Curly mother DNA, a process called gynogenesis. Testing the fraction of mutants per embryos allows us to calculate the mutation’s genetic location from the centromere.

...Read More about Toral Trivedi
L&S Sciences

Food Origins of Multi-Drug Resistant Hospital-Acquired Infections

This summer, the aim of my project is to investigate the origin of drug resistance in hospital acquired, multi-drug resistant bacteria. This project challenges the idea that human overuse of antibiotics is dominant in selecting for drug resistance in bacteria, and instead investigates the role of food as the primary source of new drug resistance for bacteria in our body. This is a particularly dangerous and has wide public health implications because of the ability for pathogenic bacteria in hospitals to rapidly acquire new drug resistances. Bacteria can harbor drug resistance through mobile genetic elements such as integrons and plasmids. This summer I will work on identifying such drug-resistance determinants on saprophytic sources and compare those sequences with drug resistant bacteria found in human blood stream infections.

...Read More about Lisa Wong
L&S Sciences

Exploring the Difference between Thermophilic and Mesophilic Proteins Using Protein Engineering

T. thermophilus RNase H (TthRNase H) is a protein that is stable at high temperatures. In my project, I will examine how the amino acid sequence of TthRNase H determines its folding properties that lead to its thermostability. To approach this question, I am going to construct two proteins, one containing the core of C. tepidum RNase H (a protein stable at moderate temperatures) and the periphery of TthRNase H and another containing the core of C. tepidum RNase H and the the periphery of E. coli RNase H (a protein stable only at low temperatures). Using CD spectroscopy to analyze these proteins, I hope I will be able to get more insights on folding mechanisms of proteins.

...Read More about Wing Shing Yip
L&S Sciences

The Effect of Birth Order on the Induction of Mixis in the Rotifer B. calyciflorus

The basis of sexual reproduction is a perennial topic of interest in evolutionary biology. The rotifer, Brachionus Calyciflorus, is an interesting system to compare sexual and asexual reproduction because it is cyclically parthenogenetic, meaning it alternates between generations produced sexually and asexually. By understanding the mechanisms controlling the timing of sexual reproduction in such organisms, we can better understand how natural selection determines the balance between asexual and sexual reproduction. In this study I look at the contributions of three related factors in determining the proportion of sexually reproducing daughters a female produces. This study aims to answer how birth order, days since mictic egg and generations since mictic egg and/or their interactions, best explains the patterns of mixis inducibility.

...Read More about Lauren Zerbib
L&S Sciences