This project hopes to identify the metabolites in various buckwheat cultivars and address their anti-microbial properties. Buckwheat is an important grain in Asia and Europe. It is noted for its nutritional use and has applications in East Asian medicines. Based on its merit as a medicinal plant, it is hoped that some compound with anti-microbial properties may be discovered. From studies using soybeans, significant variation in the metabolic compounds present have been found. Previous studies have demonstrated that many plants have metabolites with anti-microbial properties, and buckwheat remains a prime candidate due to its current usage in medicine, affordability, and relative growing ease. As such, the project hopes to identify anti-microbial metabolites present in buckwheat and also address the metabolic variation among cultivars. During the NJC-PAUSD research exchange, it was concluded that the best method to test the efficacy of the extract was to directly place the extract within the agar gel wells. The rationale behind this was because the amount of extract on the plate was much easier to quantify. The first step is to obtain the seeds of various buckwheat cultivars. The project plans on using an extraction kit to extract the metabolites present in the seeds. The extract will then be tested alongside dH2O (control) and standard antibiotics on gram-positive and gram-negative bacteria using a direct agar plate diffusion method. It is uncertain at this stage how many samples of the extract will have to be tested on the bacteria. Based on correspondence with Professor Bjorkman from Cornell University, endophytes are prevalent in buckwheat and their effects on the results is unknown. However, the number of samples that need to be run is quite high as to account for genetic variability in the cultivar in addition to the unforeseen impact of the endophytes. After establishing which extracts are more potent, the project will run combined gas chromatography‐mass spectrometry and ultra‐performance liquid chromatography‐tandem mass spectrometry to identify the metabolites. By analyzing substantial spikes in the concentration of certain metabolites, the project hopes to identify which metabolic compounds contribute to the anti-microbial effect...

The object of this project is to design an enzyme inhibitor for the the enzyme TGF-beta 1 (transforming growth factor beta 1). The design of this inhibitor will improve upon those of other TGF-beta 1 inhibitors that have already been developed, and will do so by optimizing the inhibitor’s potency, solubility, cell membrane permeability, and selectivity. TGF-beta 1 is a cytokine that is involved in cell growth, cell proliferation, and apoptosis. It helps regulate the cell cycle at the end of the gap 1 phase by preventing the cell from growing further. However, in oncogenic cells, TGF-beta 1 is often over expressed, affecting certain biochemical pathways within the body. Thus, inhibiting TGF-beta 1 has been considered as a possible cancer treatment. The ideal outcome of this project would be to develop an inhibitor that can potentially be tested as a treatment for cancer. The first objective of this project will to be to understand the structure of TGF-beta 1. Using the RCSB Protein Data Bank, TGF-beta 1 can be searched and the different aspects of its structure can be examined. The RCSB Protein Data Bank shows different types of affinities and interactions taking place within the protein, which can help determine how an inhibitor may dock to the protein.The next step would be to determine the site at which the inhibitor would be designed to inhibit TGF-beta 1. It would be necessary to determine whether the inhibition site would be at the active site or an allosteric site. If it were to be at an allosteric site, it would be necessary to determine whether the inhibitor would be designed as an uncompetitive or noncompetitive inhibitor. Such decisions will be determined upon further analysis of the protein TGF-beta 1 structure in the RCSB Protein Data Bank interface. After the inhibition site is determined, the actual design of the inhibitor would begin using a certain type of ligand design software, which can be chosen from the database Click2Drug [3]. Using the information on the structure of TGF-beta 1 from the RCSB Protein Data Bank, the inhibitor would be designed to optimize potency, solubility, cellular permeability, and selectivity. Our design would be created by modifying different side groups of previously designed TGF-beta 1 inhibitors, and determining the combination of side chains that are optimal. After designing the inhibitor, its docking
 to TGF-beta 1 would be simulated using molecular docking software in reference [3]. Based on the success of the simulated docking, the design of the inhibitor could be modified and tested again. If the inhibitor shows enough promise
 in the molecular docking simulations to be tested in real life, its efficacy would be tested be tested in vitro, if possible. It would be ideal if a laboratory could test the inhibitor’s potency, solubility, cellular permeability, and selectivity.

How can optimal gene panels be designed for early cancer detection? Cancer has become a popular research topic as more and more people die of cancer and the situation involving it becomes graver. In this study, we will generate effective gene panels that cover the smallest number of mutations and the greatest number of patients. A gene panel is set up so that the mutations found in the patients are listed out, compared, and selected to represent the largest number of patients. By finding the mutations correlated to cancer, we can facilitate early cancer detection, potentially saving lives. The development of liquid biopsy and the CAPP-Seq method are more effective than traditional techniques, and through the use of public data from TCGA, we can expand on previous research and create optimal gene panels. Eventually, these gene panels will be included in a public database...We aim to design gene panels for multiple cancer types by taking advantage of the public data available in The Cancer Genome Atlas (TCGA) consortium, which has already sequenced more than 30 types of cancer with more than 500 patients for each. In our research, we will address the cancers with the highest number of new cases and death rates, including lung, breast, prostate, colon, ovarian, kidney, liver, skin, stomach, brain, thyroid, as well as head and neck cancer.[6] For each cancer type, we aim to design a cancer-specific gene panel; also, we will integrate different cancer types and generate a common gene panel for researchers and clinicians to use...

Our research involves study of two-dimensional materials which are crystalline structure of single layer of atoms. The aim of the study is to detect thermodynamic properties of these 2D gaseous sensor material at low concentrations as they interact with other molecules. More specifically, the adsorption energies and their influence on the band structure of the material were calculated through Density Function Theory using Qunatum Expresso. The interactions between sheets graphene and molecules including carbon monoxide (CO) and nitrogen monoxide (NO) were calculated. Further more, analysis of single and multiple molecule adsorptions on both pristine and defective sheets in various positions and orientations were analyzed. Currently, we have over one hundred models of various combinations of the aforementioned variables....

The most recent statistics state that there were approximately 230,480 new cases of breast cancer and 39,520 breast cancer deaths in the United States in 2011. Over the years, irregularities have been noticed in the statistics regarding breast cancer occurrences in women of different races and ethnicities. Many other factors come into play, including age, amount of exercise done, weight, smoking history, and many more, but race and ethnicity seem to represent an important factor in the probability that a woman will develop breast cancer and whether or not she will be able to fight it off. They are not always consistent, but scientists and researchers have been able to find patterns in the data concerning breast cancer occurrence. Although there has been an important decrease in mortality rates over the years, it has not been equal among the various racial/ethnic groups either, and has been found to vary. This raises an important question: are women from certain races/ethnicities more prone to developing breast cancer? Do the statistics change accordingly to a woman’s race/ethnicity? And if so, in what ways do they differ? In my research, I will try to find answers to these questions by studying existing statistics about this topic and by collecting new data. In order to be consistent, this study will focus only on non-Hispanic white, non-Hispanic black, Hispanic and Asian women...Many studies and projects have already been done on this subject, so the first step in my research would be to try to find as much already existing information about ethnicity and race as a factor in breast cancer as possible. Some potential data sources could be the school's library and databases. For example, Ebsco includes many academic journals and newspaper articles on a broad domain of medicine topics. Another source would be medical databases, such as the CDC (Centers for Disease Control and Prevention) database, the ACOG (American Congress of Obstetricians and Gynecologists) database, the World Health Organization database, and the US National Library of Medicine (PubMed.gov) website, which all include many data and statistics as public information....

What type of water properties are optimal for Quagga Mussels? In Southern California bodies of water, do the water properties adversely affect the reproductive viability of the Quagga Mussels? Quagga and Zebra mussels are mainly found in the Great Lakes area, but have made their way to California and Nevada. These mussels invade pipes, boats, docks and can cause damage to water treatment facilities. They also interrupt the food chain by absorbing nutrients that would normally be consumed by other species. By absorbing these plants, the mussels cause the water to become clear. The mussels absorb all of the plankton in the water. Plankton performs photosynthesis and creates food for other species. In the Great Lakes they have decreased the populations of salmon and whitefish, and even native mussel species. The invasive mussels are filter feeders meaning they promote water clarity allowing sunlight to reach the bottom benthic layer of the water and create a perfect environment for algae blooms.Algae blooms in the great lakes have killed many fish and aquatic birds in the Great Lakes region.  Quaggas and zebra mussels will also colonize beds of native clams and other invertebrates. The feeding abilities of the colonized native organisms are affected to the point of stressing and killing populations of other species....I will collect water using 45 gallon buckets. The water will be from a lake in Nevada, or Southern California because the water is contaminated. I will then measure the temperature, salinity, calcium levels, and pH of the water in order to get accurate data. I will track the life of the veligers, the babies, through their life and their reproductive viability. Each day I must record the water properties and the size and weight of the mussels. I will need to paint the mussels in order to track each one...

This project will analyze the effect of obesity on the pharmacokinetics and pharmacodynamics of propofol.  Propofol is the most commonly used intravenous drug for induction of anesthesia.  Currently, all recommended dosing regimens are based upon work done in normal weight subjects.  To data, very little is published on the necessary dose or weight-based scalar to use in bariatric patients.  This is troublesome as propofol has a very narrow therapeutic window.  If too little drug is given, subjects have an increased risk for awareness during anesthesia.  If too much drug is given, adverse side effects such as hypotension are likely.  This study will analyze the proper dosing regimen for propofol in this patient population.  Results of this study will allow clinicians to administer propofol safely and more effectively in this patient population...

Osteoporosis is a bone disease affecting 70% of white people over 80 years old. It is characterized by a loss in bone mass and thinning bone structures, and is defined as having a bone density of 2.5 standard deviations below that of a normal adult. Normally, white and Asian people are at greater risk, and women have far higher risk of osteoporosis than men. A loss in bone mass causes many complications. It is the most common reason for broken bones among the elderly. It can cause micro-fractures that lead to acute or chronic pain that may interfere with daily activities. These fractures can lead to a stooped posture and loss of height. Blood clots, particularly deep vein thrombosis, are associated with osteoporosis. It also leads to falls, as bones are too weak to support the body weight, which in turn leads to more injury and further exacerbates the symptoms of the disease...It has been shown that osteoporosis tends to run in families. This, combined with the fact that certain races are more susceptible to the disease than others, leads scientists to suspect a genetic factor behind the disease. In our research, we are trying to isolate the genes that may be associated with the disease. If we have a specific gene or number of genes that are specifically related to the disease, we can target these genes for future research into developing a cure or treatment...The first step of research is to identify all genes that are possibly associated with the disease. This step has already been done for us. Researchers at Dr. Wu’s lab have identified around 20 genes that may be related with the loss of bone mass in osteoporotic lab rats, which have been shown already to have a link to bones and are expressed in blood samples taken from the bone. The next step would be to identify primer sequences for these genes. Our eventual goal is to isolate these sequences and measure their prevalence, so this is necessary to locate these genes. The idea of the primer is to provide two segments of around 20 nucleotides, which represent the beginning and end of the target gene. We will first go through scientific literature to see which primers we can find from past research, and then check the primers for validity by using the BLAST program to backwards-derive the gene. If we cannot locate the primer in past research, our next step would be to design primers using programs and algorithms available to us. Once we have the primer sequences, we plan to use Quantitative Real-Time PCR (qPCR) to obtain a count of the relative amounts of each gene there is in a sample from osteoporotic rats. This process first uses enzymes to locate the primer sequences, and then transcribes the target gene, effectively duplicating it. At the end, we have a measurable amount of each gene, and we can then mathematically derive how many of the gene were present in the original sample. We hope to be able to isolate a specific gene or group of genes at this step in order to identify a target for future treatment of the disease.

What is the genetic correlation between local viruses and foreign viruses caused by mosquitoes? Mosquitoes cause more human suffering than any other organism, as more than one million people worldwide die from mosquito-borne diseases on a daily basis. Not only can mosquitoes affect humans, but they can also transmit several diseases and parasites through other animals. The skin’s allergic reaction to mosquito bites due to the tissue’s interaction with the insect’s saliva leads to severe itching and pain. Vectored diseases from mosquitoes include malaria, dog heartworm, dengue, encephalitis, and yellow fever. My research will take mosquitoes out of their local context and compare them to their foreign counterparts in order to discover a genetic correlation between them. A team of medical researchers at Purdue University have already found a connection between 12-15 species in Indiana that are of significance to the country’s public health. My research project’s purpose is to pinpoint the correlation between local viruses and foreign viruses caused by mosquitoes, and to analyze how this relationship affects the public health of humans so significantly.

Doxorubicin (DOX) is one of the most effective chemotherapeutic drugs used against cancer. It works by preventing tumor cells from replicating through the inhibition of topoisomerase α (Top2α), an enzyme that regulates the coiling of DNA. However, it has been found that use of the drug has cardiotoxic side effects, increasing the risk of heart disorders such as severe dilated cardiomyopathy (DCM), the weakening of heart muscle in the left ventricle. DCM causes a reduction in the heart’s ability to pump blood efficiently, thus causing congestive heart failure among cancer patients who receive DOX during chemotherapy. Because congestive heart disease essentially hampers the ventricle’s ability to fill with or eject blood, the patient’s heart is severely weakened and its pumping efficiency is reduced. Among the 60% of pediatric cancer patients who receive DOX, 10% of them will develop DOX-induced cardiomyopathy (DIC) as a result up to fifteen years after they complete chemo. There is currently no pharmacological cure for DIC, leaving many of those afflicted with a heart transplant as their only option for treatment...Research on DIC using animal models is limited by inherent interspecies differences of reaction to DOX; using cancer patients currently going DOX treatment as human models is equally difficult due to their multi-drug treatments that would make it nearly impossible to isolate the effects of DOX alone, as well as the invasive procedures that would be necessary to extract cardiomyocytes from the heart. However, human induced pluripotent stem cell-induced-cardiomyocytes (hiPSC-CMs) have proved to be a valuable tool for modeling cardiovascular disease. Pioneered by Shinya Yamanaka in 2006, iPSCs are a type of stem cell that can be obtained by essentially transforming fully differentiated adult somatic cells into pluripotent stem cells through the introduction of four specific genes encoding for transcription factors. This technique has allowed researchers to generate in vitro functional, beating cardiomyocyte models to study the effects of DOX...