BayBio Annual Conference 2011 | Bay Area BioGENEius Challenge

The BayBio Institute will host the inaugural Bay Area BioGENEius Challenge on April 20^th, 2011, at its Annual Conference in Burlingame, CA.

High school students who are doing outstanding research in the life sciences will compete to qualify for the National and International BioGENEius Challenges that will be held at the BIO International Convention on June 27-30, 2011, in Washington, D.C.

The BayBio Institute invites high school students who participate in the local International Science and Engineering Fairs to submit a simple 2-page on-line application to qualify for the Bay Area Challenge.

Participation Criteria: Students enrolled in biology or science-related courses (Grade 9 to 12) in any public or private school within the Bay Area who are also participating in a local International Science and Engineering Fair (ISEF). Individual students only may submit only ONE project for this competition. Research presented in 2011 must be NEW research. Projects may be continued research from previous years.

Challenge Finalists: Two finalists in the Bay Area BioGENEius Challenge will go on to compete at the National and International BioGENEius Challenges held at the BIO Conference on June 27-30, 2011, in Washington, D.C. The first place winner of the Bay Area BioGENEius Challenge receives a $7,500 cash award. Other awards include $5,000 for second place, $2,500 for third place, and $1,000 for fourth place. Each remaining finalist will receive a $500 Honorable Mention Award.

Opportunities:

• Participate in educational sesions, network with life science executives and scientists and compete at BayBio’s Annual Conference and the BIO International Convention
• Add the prestigious career-building competition to your resume and college application
• Meet students from across the U.S., Canada and Western Australia

The Bay Area BioGENEius Challenge is a collaboration with the Biotech Institute and the International Science and Engineering Fair (ISEF).

Elliot Akama-Garren
Grade 12
Henry M Gunn High School, Palo Alto CA
From Cancer to Autoimmune Disease: Selective Tyrosine Kinase Inhibition for the Treatment of Multiple Sclerosis
Multiple sclerosis (MS) is a demyelinating disease of the central nervous system that afflicts approximately one million individuals worldwide. Tyrosine kinases such as ErbB-1 and ErbB-2 are critical in inflammatory regulation and are promising targets for the treatment of cancers and autoimmune diseases, as shown in animal models of rheumatoid arthritis. Upon investigating the potential for tyrosine kinase inhibition to treat experimental autoimmune encephalomyelitis (EAE), a murine model of MS, we found that lapatinib (ErbB-1 and ErbB-2 inhibitor) decreases the severity of EAE. To investigate the differential effects of ErbB-1 versus ErbB-2 inhibition, we examined the potential of AG825 (ErbB-2 inhibitor) and AG1478 (ErbB-1 inhibitor) to treat EAE. In vivo, our data suggest that ErbB-2 inhibition decreases EAE severity, whereas ErbB-1 inhibition has no effect. In vitro, we show that ErbB-2 is differentially transcribed in mouse brain endothelial cells, as compared to macrophages and splenoctyes…Truncated at 150 words

Nicole Allen
Grade 12
Granada High School, Livermore CA
The Effects of Hypoxia on C2C12 Stem Cell Differentiation
Muscle cells are exposed to vastly different levels of oxygen throughout their development. In order to investigate the role of oxygen in the differentiation and development of muscle cells, I cultured C2C12 cells, which come from a mesenchyme cell line that was derived from adult muscle stem cells. The cells were grown under both normal (~21% O2) and hypoxic (<0.1% O2) conditions, during which time their differentiation patterns were followed using markers for striated muscle-specific proteins (titin and α-actinin) as well as markers for myogenic transcription factors (MyoD and myogenin). Both groups were cultured in buffered media, fixed, and viewed via immunofluorescence. Even in the near-complete absence of oxygen, the muscle cells grown under hypoxic conditions managed to differentiate. However, this differentiation was found to be suppressed and delayed when compared with the control groups of cells and delayed when compared with the control groups of cells.

Arun Asundi
Grade 12
San Mateo High School, San Mateo CA
Biofuel Production from Cellulose
Bioethanol production from cellulosic biomass is receiving an increasing amount of attention as an alternate fuel source. The process involves several enzymatic steps. Cellulase breaks down cellulose into individual glucose molecules. The glucose thus harvested, undergoes yeast-mediated alcoholic fermentation to produce bioethanol. This project attempts to maximize production of bioethanol by optimizing both the breakdown of cellulose to glucose, and the production of bioethanol by yeast. In addition to process optimization, this project focuses on developing reliable assays to measure the amounts of glucose and ethanol produced in each reaction. Production of glucose by cellulase was successfully optimized by independently testing the type of cellulase used, the concentration of reagents in the reaction, and the optimal ratio of cellulase to cellulose. A new assay has been developed to accurately and quantitatively measure the amount of glucose in a solution. A Benedict's assay is performed on the solution, which produces solid Copper Oxide, proportional to the amount of glucose in solution…Truncated at 150 words

Brevard Belcina
Grade 12
San Mateo High School, San Mateo CA
Amylase Precipitation and Crystallization
Amylase is a protein that breaks starch down into sugar. Pure protein crystals such as amylase are used for X-ray crystallography for protein structure determination. To attain protein crystals, the hanging-drop vapor diffusion technique is used to supersaturate the drop to cause the amylase to solidify and fall out of solution. Testing different pH and different salt and organic compound mixtures and concentrations is done to find optimal amylase precipitation and crystallization. Data is obtained by using a stereo microscope of magnification ranging from 1X ‑ 20X. The project goal is to determine conditions that yield amylase precipitation and large, well-formed amylase crystals. The first step was to run an initial crystal screen, which is the starting point for the trial and error process for determining the precipitation and crystallization conditions for a protein. The initial screen was a modification of the Hampton Research commercial kit (each test solution was prepared by the investigator)… Truncated at 150 words

Christine Chang
Grade 10
Palo Alto High School, Palo Alto CA
A Novel Method for Fast Identification of Tag Single Nucleotide Polymorphisms (SNP)
Single Nucleotide Polymorphisms (SNPs) determine a person's genetic traits and therefore are important in genetic research. However, there are 10 million SNPs; finding all of these SNPs will be very time consuming and expensive. Tag SNPs, an important subset of the SNPs, can be used to identify haplotypes, which can help us understand how SNPs and other genetic variants are organized on chromosomes. These tag SNPs, however, are not easy to find. This project devised a simple algorithm for finding a minimum set of tag SNPs. This algorithm first removed any duplicate samples, as well as any incomplete SNP sample with missing information. Then the algorithm identified "unconditionally required" positions. These "unconditionally required" positions were verified to see if they were enough to identify the whole set of haplotype patterns. If so, then a minimum set of tag SNPs has been identified. If not, then the positions that weren't "unconditionally required"... Truncated at 150 words

Jennifer Chen
Grade 12
Lynbrook High School, San Jose CA
Massively Parallel DNA Sequencing-Based Human Identification
The forensic DNA backlog represents the accumulation of unanalyzed samples that have the potential to convict the guilty, exonerate the innocent, and protect the general population from repeat offenders, making the reduction of such a backlog critically important. My project proposed a human identification method based on massively parallel DNA sequencing (MPDS) to process a large number of samples at the same time. However, such an economy of scale depends on large-scale barcoding of the samples that are batched together so that they can later be sorted to determine individual profiles. I therefore designed a linking primer strategy, using a two-stage barcoding process to reduce the total number of PCR primers needed. I tested the MPDS-based method with the linking strategy on three reference DNA samples (K562, 9947A, and 9948). I also developed a UNIX-based method of determining the DNA profiles since there is no existing software to analyze such a massive number of sequences for forensic purposes… Truncated at 150 words

Shirley (Yun Qi) Jiang
Grade 12
San Mateo High School, San Mateo CA
Curing Pulmonary Hypertension: Can Inhibition of P38 Attenuate Inflammation and Prevent Experimental Pulmonary Arterial Hypertension?
The association between chronic inflammation and pulmonary arterial hypertension (PAH) is well recognized. PAH is a syndrome in which PA obstruction increases pulmonary vascular resistance that, in turn, leads to right ventricular (RV) failure. Inflammatory cells, e.g. dendritic cells, macrophages, mast cells, T and B lymphocytes and elevated pro-inflammatory cytokines and chemokines are reported to contribute to the vascular pathology of PAH. Specifically, 5-Lipoxygenase (5-LO) and its downstream leukotriene products have been implicated in PAH pathogenesis. In this study, we examined the phosphorylation and activity of 5-LO in the experimental PAH setting using a rat model. We hypothesized that the prevention of 5-LO phosphorylation by P38 inhibition attenuates inflammation and early PAH, modulates the expression of pro- and anti- inflammatory cytokines and chemokines, and lowers right ventricular systolic pressure (RVSP) and RV hypertrophy. PAH was induced by injecting rats with SU5416, a vascular endothelial growth receptor inhibitor, and negative control rats were injected with vehicle control (DMSO)…Truncated at 150 words

Revanth Kosaraju
Grade 11
The Harker School, San Jose CA
A Novel Perfusion-Based Protocol for Decellularization of Adipose Tissue on a Bioreactor
Emerging tissue engineering research has focused on three crucial steps: harvesting of a tissue sample, decellularization, and stem cell growth. Decellularization is necessary for removing cells and cellular antigens, which can cause rejection in a whole organ or tissue transplant, and also preserving the ECM and vasculature as a location of stem cell seeding and growth. Adipose tissue, or fat tissue, has become very crucial due to its high vascularization, a necessity for long-term viability of manufactured tissues and organs. However, none of the existing protocols for adipose tissue decellularization use a perfusion-based method. Such a method would have several benefits, including a more thorough decellularization for successful transplantation of tissues and organs. This study sought to develop a novel protocol employing peracetic acid to decellularize adipose tissue on a bioreactor through perfusion. In repeated trials (n=3), the decellularization efficacy of the novel protocol was compared with that of two existing detergent-based protocols using…Truncated at 150 words

Andrew Liu
Grade 12
Henry M. Gunn High School, Palo Alto CA
Accounting for Cross-Talk between Signaling Pathways Identifies Novel Model for Early and Late Post-transplant Acute Rejection
Long-term allograft survival in transplantation has stalled for 25 years. One reason is the lack of systems-biology-level pathway analysis to identify rejection-causing mechanisms, as existing methods ignore inter-pathway interactions causing rejection. To analyze rejection at systems-biology-level, I developed a novel pathway analysis method – inter-pathway impact factor (IPIF) analysis. Using IPIF, I analyzed renal transplant biopsy data. Comparing IPIF with existing methods demonstrated IPIF's higher statistical power and identification of more biologically relevant pathways. I also identified novel p38- and IL12/23-mediated pathways, prompting proposal of novel mechanisms incorporating monocytes and IL12/23 which were validated by whole blood gene deconvolution. I then identified an existing drug to inhibit IPIF-predicted pathways; this drug reduced graft injury in mouse model. In sum, I developed a powerful method to analyze existing data from conditions such as rejection, identify injury pathways, and generate hypotheses. Using it, I proposed time-specific mechanisms and novel treatment for long-term rejection.

Katie Shao
Grade 11
Davis Senior High School, Davis CA
Protein Genetics: an Investigation into the Dependency of Bacteriorhodopsin's Light-Absorbency on Residue Substitutions
The transmembrane ion-pump Bacteriorhodopsin (bR) from Halobacterium salinarum has long been investigated as a substrate for the construction of protein-based nanodevices. Current methods employed for creating mutant bRs with specific biophysical qualities that could make bR useful for commercial application have focused on traditional protein engineering tools like single-point and random mutagenesis. Evolutionary Genetics offers a complementary approach that takes advantage of nature's successful mutations in bR. By analyzing the protein sequences and phylogenetic relationship between bRs derived from multiple newly sequenced species of haloarchaea, I have identified several potentially key amino acids responsible that distinguish bR variants into phylogenetically distant groups. These mutations may be important for encoding specific functional qualities in bR variants and studying them may yield empirical guidelines designed to improve the efficiency of future attempts at bioengineering bRs. In this project, I cloned bR variants in an SD23 strain of haloarchaea by isolating a few hand-selected bR genes...Truncated at 150 words

Angela Zhang
Grade 11
Vista High School, Cupertino CA
New Smart Weapons: Theranostics — A Novel NanoMedicine Approach to Combat Cancer
Despite our knowledge about cancer, 11 million people in the US live with this incurable disease. Thus, I propose a new generation of nanoparticles(NPs) with electronic-magnetic optical-acoustical-thermal multimodality imaging, targeted drug delivery through near infrared light (NIR) triggering of thermal therapy and drug release, and effective monitoring of treatment response through utilizing both therapeutics and diagnostics (theranostics) in a single platform. A new class of magnetic–gold core-shell nanoparticles was synthesized with conjugation of EGFR-binding affibody for specific targeting of cancer cells, resulted in significant treatment efficacy. The novel multifunctional nanoparticles enables multimodality imaging, with novel magnetomotive photoacoustic imaging of remarkable contrast enhancement. It also provides an innovative smart platform of simultaneous targeted photothermal-therapy and photo-triggered chemotherapy for cancers. The knowledge gained from this work can be applied to many cancers and other diseases and represents a … Truncated at 150 words

Ray Zhou
Grade 11
Amador Valley High School, Pleasanton CA
Near-Infrared Light Biostimulation: a Novel Approach to the Optimization of Industrial Biosynthesis
Near-infrared light biostimulation is a biological mechanism which describes the enhancement of cellular activity via near-infrared irradiation. In this study, it was speculated that such a phenomenon could exist in the microorganisms currently grown for the mass production of biopharmaceuticals. The effects of near-infrared LED irradiation on cellular respiration were assessed by measuring CO2 release as a byproduct of respiration in S. cerevisiae over time. Cell cultures exposed to near-infrared LED light reported a two-to-threefold increase in total respiration, compared to cultures kept in darkness. Moreover, the existence of a photoacceptor complex for near-infrared light was confirmed in both prokaryotic and eukaryotic microbial species, suggesting that the mechanisms of light biostimulation are universal to all microorganisms. As near-infrared LEDs can be obtained today at low cost, it is believed that light biostimulation has the potential to provide a versatile and cost-effective approach to the optimization of industrial biosynthesis.