MiCodes: Enabling Library Screens with Microscopy by Connecting Genotypes to Observable Phenotypes

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.

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Sciences

Neurally Inspired Self-Organizing Maps for Image Coding

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.

...Read More about S. Zayd Enam
Sciences

Automation of Carbon Flux Explorers for the Study of the Ocean Biological Carbon Pump

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 […]

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Sciences

Electrochemical Characterization of First-Row Transition Metal Corrole Complexes for Use as Oxygen Reduction Catalysts

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.

...Read More about Brendon McNicholas
Sciences

Characterization of Fine Genetic Regulatory Mechanisms of a Bacterial sRNA in the Virulence of a Foodborne Pathogen Salmonella Typhimurium

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.

...Read More about Laura Carolina Rodriguez-Adjunta
Sciences

Indigenous Knowledge and Bio-efficacy of Medicinal Plant Use: An Ethnobotancial Study of Sindhupalchok, Nepal

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.

...Read More about Sikai Song
Sciences