Genetic work with model organisms, such as fruit flies, mice, and zebrafish, has provided invaluable insights into the mechanisms behind human disease and development. One tool for creating these models is direct modification of the genome. Michael is optimizing the use of reagents, called zinc finger nucleases (ZFNs), in order to create specific and targeted modifications in the DNA sequence of a very genetically tractable system, the zebrafish. Using ZFNs, genes can possibly be directly targeted to express desired proteins, incorporate molecular tags, or can even be repaired by a corrected template. He will develop assays to quantify ZFN-mediated targeting and optimize conditions to improve targeting efficiency, with the goal of making this technology broadly accessible to and widely used within the scientific community.
In this project we plan on using parallelized computation to build realistic sparse coding models for neurons in the primary visual cortex (V1). Sparse coding is a stimulus encoding technique used by V1 neurons that aims to minimize the number active neurons required in encoding any input image. Due to computational constraints, previous sparse coding models have been limited in their ability to match the biology of lateral geniculate nucleus projections to V1. Our models will allow us to better describe recorded biological data and provide further evidence that V1 relies upon sparse coding of input images.
Salmonella is the leading source of food-borne diseases in the United States. Infection by Salmonella Typhimurium causesdiseases ranging from self-limiting gastroenteritis to life-threatening systemic infection, provoking around 1.3 billion cases every year worldwide. Moreover, no vaccine to prevent salmonellosis exists. Recently, 19 small noncoding bacterial RNAs (sRNAs) located in salmonella SPIs were discovered, of which IsrC is one of the newest forms. Bacterial sRNAs regulate the expression of their target genes in pathogenesis, essentially contributing to bacterial invasiveness. My research will focus on the interaction between IsrC and its predicted target, HilE, a global negative regulator of salmonella virulence genes. This research seeks to further clarify the role of sRNAs in the molecular pathogenesis of salmonella virulence as well as increase the possibility of developing new strategies against bacterial infection, thus lowering salmonella infection rates.
Research in alternative energy has become increasingly urgent in recent years due to constantly increasing pollution and depletion of traditional energy sources. One of the most compelling devices in the field is the fuel cell, a means for converting hydrogen and oxygen into useful energy. To contribute to the advancement of the field of alternative energy, this thesis aims to further the characterization of an oxygen reduction catalyst for a PEM fuel cell. Literature has shown that certain first-row transition metal corrole complexes are active for catalytic oxygen reduction, and the projects primary objective is to electrochemically characterize these complexes to determine which compounds are most effective in oxygen reduction catalysis.
Marine-atmosphere gas exchange plays a major role in the global carbon cycle. A key parameter of oceanic CO2 uptake and sequestration is the biological carbon pump (BCP). The BCP is composed of planktonic organisms that fix CO2 in photosynthesis, converting it to food and tissue. The biomass of these organisms turns over about once every week, exporting the carbon they contain away from the ocean-atmospheric interface to greater oceanic depths as they are consumed and expelled in the form of particulate organic carbon aggregates. This process, known as sedimentation, is currently a large mystery to oceanographers and climate modelers. To parameterize the BCP sedimentation process in ocean and climate modeling, the Bishop research group has designed Carbon Flux Explorers (CFEs)–relatively small but powerful robots– to study this rapidly changing system on biologically significant time scales. My research project will design, code, and implement data processing algorithms onto CFEs, thus completing […]
Ethnobotany is defined as the scientific study of the traditional knowledge and customs of a people concerning plants and their medical, religious, and other uses. Given that many active compounds used in pharmaceutical drugs today are extracted from plants, understanding indigenous knowledge regarding medicinal plant use is invaluable to deepen existing knowledge regarding various pharmacological uses of high-value medicinal plants, conservation, and sustainable resource management. My research seeks to document and catalogue the high-value medicinal plants used by the Tamang people in remote villages in rural Sindhupalchok, Nepal, as well as assess the bio-efficacy of the medicinal plants by comparing indigenous use with reported phytochemical and pharmacological properties in literature.
In the burgeoning field of genetic engineering, living systems are engineered to perform desired functions such as fighting cancer, sensing harmful chemicals, or producing useful compounds. However, cellular processes are unpredictable and genes do not always act as expected. In order to find a gene’s optimal setting, scientists currently need to search through “libraries”–large numbers of genetic variants–which is labor and time-intensive. Robert’s research centers on developing a new technology called MiCodes, or Microscopy Codes, which will speed up our ability to perform library screening under the microscope by barcoding cells with fluorescent tags. If successful and adopted by the scientific community, MiCodes would fundamentally change the way library screening is done for many applications, including cancer research, cell culture studies, and biofuels production.
Alternative splicing of pre-mRNA is critical to development and differentiation, allowing metazoans to generate a large amount of protein diversity from a single gene. Despite its importance, our understanding of the factors that influence this process is limited. The objective of Joshs project is to investigate the role of the Fox family of proteins, which have been implicated as splicing regulators. Through experiments with zebrafish he will asses the effect that Fox has on a library of alternatively spliced exons in the hope of better understanding this protein familys role. Hopefully his project will provide insight into the role of Fox and the alternative splicing events it controls, and possibly some insight into the mechanism any of a number of the genetic diseases caused by aberrant splicing.
Thalassemia is a disease common to 60 countries worldwide, with high prevalence in Middle Eastern countries. The Iranian population consists of many who exhibit the beta-thalassemia hemoglobinopathy, which reduces red blood cells ability to carry oxygen, and even more who are carriers of this life-threatening disease. In the past, most of the children born with beta-thalassemia failed to survive during the first decade of life. Medical advances have recognized that placental and umbilical cord blood of a newborn is a rich source of blood stem cells, which can replace the blood of a thalassemic sibling and cure him of the disease for life. In this clinical study, Shahrzad will survey and document the need for a sibling donor cord blood program in Tehran, Iran, evaluating the feasibility of establishing such a program.
Nanocrystalline materials have shown promise in many applications, such as light-emitting diodes, solar cells, biomedicine, optoelectronics, etc. Shape-controlled nanocrystals are important because different geometries of nanocrystals possess various electronic properties which can be tailored to their application. In this project, Yu will conduct synthesis experiments of Cadmium Telluride (CdTe) by varying the amount of solvent. By analyzing nucleation kinetics in the synthesis of the CdTe, Yu hopes to develop a mechanistic explanation for crystal branching and increase the reproducibility of the tetrapods shape syntheses. Moreover, this approach to understanding CdTe tetrapods and their syntheses will contribute to an explanation of thermodynamic and kinetic effects on CdTes structure.