4^th International Conference and Exhibition on Metabolomics & Systems Biology April 27-29, 2015 Philadelphia, USA

James Gigrich is a PhD candidate at George Washington University. He has an MS in Operation Research from Georgia Institute of Technology and a BS in Electrical Engineering from West Point. He currently is the Senior Director of Government Relations and National Security Programs for Keysight Technologies, the legacy Hewlett-Packard Company and a world leader in measurement technologies.

Systems engineering recognizes that each system is an integrated whole, even though composed of diverse specialized structures and sub-functions. Hepatocytes are complex cells with numerous subsystems, and the interactions among hepatocytes are complex and not completely understood. Systems engineering looks at systems of all types and emphasizes the relationships and interactions between components. Systems engineering can analyze living systems in terms of design, information processing, optimization, and other explicit concepts, by using various quantitative System Engineering tools that include data analysis, modeling and simulation, signaling processing and graph theory. The application of these tools provides new insight into the intricate workings of hepatocytes. Hepatocytes are complex and yet exceedingly connected systems that make it tremendously challenging to understand the underlying signaling pathways and interpreting numerous and varied high dimensional measurement data. Currently, there is a paradigm shift from apical endpoints in animal testing to perturbation of toxicity pathways in human hepatocyte cells. Gene expression data of PPARα binding measured over multiple concentrations and times of GW7647 doses along with downstream phenotypes were examined using multivariate data analysis. Associated phenotype changes to hepatocytes showed a correlation with high-dimensional multivariate genomic data – gene expression profiling data. The use of multivariate techniques like principal components analysis, factor analysis, and cluster analysis to analyze gene expression and phenotype data allows for more informed decision-making in toxicity testing.

Background: 2-Oxoglutarate and ferrous iron dependent oxygenases are involved in a variety of biological processes in aerobic organisms ranging from humans to bacteria. Synthetic N-oxalylglycine has been identified as a broad-spectrum 2OG oxygenase inhibitor. We report the identification of NOG as a natural product present in spinach leaves. Method: To investigate whether NOG and related derivatives naturally occur in spinach leaves, we first developed an analytical method using reversed-phase liquid chromatography mass spectrometry (RP-LC/MS) and an NOG standard. The detection of NOG provided a linear response with concentration in the range 10–1000 µM with a correlation coefficient R²>0.998. The detection limits for NOG were 5 μM and the limit of quantification was13 μM. Results: The LC-MS, LC-MS/MS, NMR, and ESI accurate mass analyses provide positive evidence for the presence of NOG in spinach leaves. The amount of NOG at natural abundance in the spinach leaves sample was calculated to be 0.1681 mg per 3g dry weight of spinach leaves. Conclusions: The results presented here demonstrate that NOG is present as natural products in plant tissues known to contain high levels of oxalic acid, i.e. spinach. We did not detect NOG in E. coli, or human tissue culture cells. Thus, whilst we cannot rule out the possibility that NOG is present in animal cells, there is no evidence for its presence at currently detectable levels. Whether or not the amount of NOG present in spinach leaves is bioavailable in sufficient quantity to elicit a physiological effect upon ingestion remains to be investigated.

Rajan Chaudhari is a final year PhD student in the Department of Chemistry & Biochemistry with specialization in Computer-aided Drug Design at University of the Sciences in Philadelphia. He finished his Bachelors in Pharmacy from Pune University in 2007 and Masters in Bioinformatics from University of the Sciences in 2010. His research interests include improving homology modeling of membrane proteins and developing tools for accelerated drug design. He is a member of ACS and ISCB since 2011. He is also actively involved in organizing regional MACC meetings for computational chemists.

G protein-coupled receptors (GPCRs) are the top ranked drug targets in pharmaceutical industry because of their ability to induce wide variety of cellular responses. Therefore, structural information of such drug targets plays important role in accelerating drug discovery process. Results from GPCR DOCK competitions indicate that homology modeling of GPCRs based on low sequence identity is still a major challenge. To tackle this problem, we developed “refined restraints first-modeling next” approach that extracts unique distance restraints from multiple templates and incorporates them into homology modeling process. This method was applied to improve modeling of human beta 2 adrenergic receptor based on low sequence identity templates of bovine rhodopsin (1u19) and human protease-activated receptor 1 (3vw7). Results showed improvement over standard single-template and multiple-template methods in terms of generating low RMSD models. Our method is easy to implement and can be applied to all alpha helical trans-membrane proteins.

Lauren J Brown has completed her Master degree at the age of 22 at Thomas Jefferson University. From there she went on to work at Thomas Jefferson University Hospital in the Clinical Pathology Department. She is currently a 4th year PhD Graduate student at University of the Sciences in Philadelphia where she is studying natural products research with a focus on plant and fungal metabolites.

Podophyllotoxin is an active cytotoxic natural product that is precursor to important anti-cancer drugs. My laboratory has a fungal endophyte, PPE7 derived from the Podophyllum peltatum plant, both sources of the compound. Multiple locations of P. peltatum colonies have been mapped throughout the south eastern portion of Pennsylvania, some with slightly different phenotypic representations. Preliminary data suggests aneuploidy in the plant genome. Research has begun to confirm the aneuploid state and determine the implications for podophyllotoxin production. Plant nuclei were isolated and treated as single cells in flow analysis. I have perfected this protocol using both Vicia faba as an internal standard (Fava bean) and Podophyllum peltatum (American Mayapple). The nuclear isolation buffer, buffer volume and plant biomass amount have been optimized to produce an appropriate number of nuclei in a volume suitable for analysis. By these methods, I have determined the genome size of Podophyllum peltatum to be approximately 52.6327±0.5877 Gbp (mean±SD, n=6). With these findings I will next determine if aneuploidy is prevalent throughout all mapped colonies and the podophyllotoxin production implications.

The up regulation of apoptosis, reactive oxygen species (ROS) and disturbances of autophagy may involve in brain aging process. Exercise plays an important role to enhance human health. Resveratrol is a natural polyphenol primarily found in grapes and red wine that offers multiple beneficial effects including neuroprotection and metabolic improvement. In this study, we tested effects of resveratrol supplementation (15 mg/kg/day, 4 weeks, IG), swimming exercise training (40 mins/day, 4 weeks) or resveratrol with swimming exercise training on the apoptosis and autophagy pathways in the cerebral cortex of aging rats (24-month-old). Exercise training and resveratrol supplementation up regulate beclin-1, Atg7 and LC3B expression. On the other hand down regulate apoptosis proteins such as BAX, BAD and caspase 3. The results suggest that exercise training and resveratrol not only enhance autophagy but also reduce the apoptosis pathway which may benefit the aging brain.

Ubeydullah is 4th year medical student at Ataturk University in Turkey. He joined Weljie Lab at Department of Medical Pharmacology, University of Pennsylvania in July 2014 for one year as an intern student. His research interests include identification of molecular signatures of sleep restriction and deprivation, discovery of biomarkers for various diseases using metabolomics platforms, and identification of lipidomic and transcriptomic alterations in insomnia patients. He is studying on insomnia metabolomics by H1 Nuclear Magnetic Resonancespectroscopy (H1NMR). And he worked on metabolomics of lung cancer by H1NMR spectroscopy at summer research. He also attended Department of Clinical Biology and Genetic Lab for summer research at Ataturk University in 2012-2013.

Sleep related disorders such as insomnia, parasomnias, sleep apnea and narcolepsy could be better understood by studying Brain activity during sleep and wakefulness. Increasing evidence also points to the bidirectional interaction of sleep and metabolism. However, simple and quantitative test to estimate brain function related to sleep and metabolism is still absent. We profiled the blood serum metabolome of healthy individuals every 2 hours over a period of 48 hours that included regular sleep and wakefulness periods using NMR spectroscopy. Brain activity of the participants was monitored via overnight polysomnography. Multivariate regression modelling was used to correlate these two different data sets. Encouraging results were observed suggesting the possibility of estimation of brain activity during sleep. These results have the potential to uncover the connection of altered brain function and metabolic biochemistry in dysregulated sleep

Nikita Panov was born in Russia and moved to the United States in 1997. After high school, he worked at a chemical company, specializing in ion exchange resin regeneration and water treatment services. Having decided to pursue higher education, Nikita enrolled in Delaware County Community College, where he focused his studies on the fundamental sciences; Chemistry, Biology, and Physics. Having transferred to West Chester University of Pennsylvania, Nikita decided to focus on the study of Cell and Molecular Biology. He joined the Pisciotta Lab in late fall of 2013 and focused his work on the study of microbial electrochemistry and the ability of exploiting certain exoelectrogenic bacteria for their metabolic output. Additionally, Nikita is interested in alternative bio-fuel production from algae and other lipid accumulating microorganisms. After earning his bachelor's in biology, Nikita will pursue his Ph.D in Biochemistry at the City University of New York.

The finite nature of fossil fuels presents an unsustainable long-term model for energy sourcing compounded by climate change. Sustainable, alternative methods for producing energy-rich fuel are needed. Deriving biodiesel from algae is one option. However, the low concentration of carbon dioxide in air (0.04%) poses a challenge for maximizing the anabolic potential of algae. Strategically sourcing cheap CO2 to reduce input costs could give momentum to the nascent algal bio-product industry. Developments in bio-electrochemically catalyzed anaerobic digestion technology have enabled accelerated gaseous metabolite production from waste. Utilizing biogas for its high carbon dioxide content (up to 40%) can facilitate growth of algae, while cutting operational costs. This study evaluated whether algae can be grown on gas metabolites bio-electrochemically [BEC] generated by pure culture Geobacter sulfurreducens. We examined the effect of [BEC] biogas on the growth rate of Chlorella sp. grown for 21 days with 12:12 daily light dark cycles in BG-11 media. Growth rate on BEC-derived biogas was significantly greater than on air alone and comparable to growth of Chlorella sp. on 5% carbon dioxide. These results support further exploration into the use of bio-electrochemically formed gas metabolites for cultivation of phototrophs.

Seeds develop by absorbing nutrients from their mother plant, and using these to synthesize a combination of starch, protein and lipid. The size and number of seeds which finally develop determines the crop's yield, while their composition determines the end-use quality of the crop. A combination of metabolomics, enzyme activity profiling, 13C-based metabolic flux analysis (MFA) and computational analysis is made as part of an attempt to understand regulation of central metabolism of the developing plant seed. Targeted metabolite profiling using LC-MS/MS succeeded in identifying ~100 intermediates within the central metabolism, including sugars, amino acids, nucleotides and their sugars, signaling molecules and intermediates of glycolysis and citric acid cycle. Some of these metabolites differed quantitatively between the accessions and displayed a significant shift corresponding to flux. With increasing flux through glycolysis and lipid synthesis across the genotype accessions, levels of several glycolytic intermediates decrease significantly. Our data indicate that mechanisms of allosteric control are of major importance in controlling the flux partitioning between starch and lipid, specifically the feedback inhibition of phosphofructokinase and ADP-glucose pyrophosphorylase by phosphoenolpyruvate and phosphoglycerate, respectively. In addition, other compounds like cyclic AMP and sucrose-6-phosphate were identified to be potentially involved in so far unknown mechanisms of metabolic control.

Paolo Schiavini has completed his Bachelor and Master’s degree in Chemistry at “Università degli studi di Pavia”, in Italy. At the age of 24 he moved to Montreal to pursue a PhD in Chemistry at McGill University under the supervision of Nicolas Moitessier and Karine Auclair. He is currently working on several areas at the interface between chemistry and biochemistry, including computer-aided drug design, drug metabolism and biocatalysis

Liquid chromatography coupled to mass spectrometry (LC-MS) is undoubtedly the most widely used tool for metabolite identification. Despite of its extensive use, there are cases where LC-MS fully automated analyses are not sufficient to predict or to explain a metabolic profile. In this context, we will describe a study where the presence of multiple stereogenic centres and the possibility of epimerization can lead to unexpected chemical transformations. Through a combination of mass spectrometry, synthetic work, deuterium exchange studies and computational predictions we were able to solve a complicated puzzle and to elucidate the dynamic behavior of our metabolites in solution.

Ningning Zheng has completed her Master’s degree at the age of 27 years from Shanghai University of Traditional Chinese Medicine. She is the Research Assistant of Center for Traditional Chinese Medicine and systems biology. She has published 3 papers inevidence-based complementary and alternative medicine. Her major research field is the study of drug effect based on metabolomics.

In the clinical practice of Traditional Chinese Medicine (TCM), vinegar processing (also called CuZhi in Chinese) is a common procedure for improving the efficacy or decreasing the toxicity of certain TCMs. Radix Bupleuri is a widely used TCM with various potent activities such as anti-inflammation, improving immune and liver functions. Radix Bupleuri is usually processed with vinegar prior to the application in treating fatty liver disease. However, little is known about the exact biological impacts of vinegar processing of Radix Bupleuri on body. In current study, we first compared the contents of saikosaponin a, d, and b2, the active components of Radix Bupleuri, between raw Radix Bupleuri and vinegar processed Radix Bupleuri with HPLC, and found that vinegar processing resulted in higher level of saikosaponin b2, but lower level of saikosaponin a and d, suggesting that vinegar processing could cause the alteration in contents of components, as well as their ratios. Then, we investigated the biological effects of both raw Radix Bupleuri and vinegar processed Radix Bupleuri in high-fat-diet (HFD) induced nonalcoholic fatty liver rats by using GC/MS-based metabolomics profile of urine, serum and liver samples. Although there were no significant differences in traditional biochemical parameters of serum such as TG, TC, LDL, ALT, and AST between the two types of TCM treated groups, we observed that vinegar processed Radix Bupleuri treated rats showed better improvement in liver histology. Meanwhile, the metabolomics results indicated that vinegar processed Radix Bupleuri exerted more profound changes in metabolism of amino acids, vitamins and lipids, suggesting that the biological effects of vinegar processed Radix Bupleuri were different with raw Radix Bupleuri on rats. In summary, our current results indicated that vinegar processing of Radix Bupleuri could lead to the alteration in contents and ratio of chemical components, as well as the biological effects on living body.