The Fight

After spending a weekend of cooking fun, I was quickly brought back to reality with the preparation of a science research project proposal, a science conference, and the struggle to ascertain funds. Although it was both great and bad, this week did bring me new information and insight into things at hand.

For HHMI, I went to the lab and prepared my presentation on my project. The project centers around the mechanism of transport of a chemical produced by a fungus. The chemical is called Aflatoxin and cause a myriad of effects in people. The effects range from liver cancer to death. This substance is actually common in our foods (though like only 90 ppb of grain). I created the presentation steadfastly and then went to the Jefferson Hotel for the Summit on Systems Biology. This day had the introduction of the heavy hors d'oeuvres for dinner and a meet and greet, basically networking event. I managed to talk to a few people from firms that will help graduates find careers in the life sciences careers. I got an amazing glass cup from a company called illumina, I believe they manufacture these amazing micro array slides that have about 40 million spots on them (on the molecular level) that all take a part in analyzing the genome and sequences.

The next day opened up with the talks and such. I did manage to take quite a few notes:

At 7:00 we had a Continental Breakfast in which, I ate tons of grapes and such, I got so full.

Dr. Eugene P. Traini, the President of VCU spoke and gave us an introduction. He is an amazing speaker. The speakers came immediately thereafter.

The Systems Biology Challenge in the 21st Century Biomedical Research, by Dr. Leroy Hood (famous for the Automated Sequencer)-Systems approach in Biology and Medicine.
In the future he hopes to see that there is a grand convergence of several sciences enabling us to have predictive, personalized, preventive, participatory medicine. He defines biological information as being of two parts, one of digital information (the genome), and those of environmental information.

Perspectives on Systems Biology from the Research Institute, by Dr. Claire Fraser-Liggett (President and Director of TIGR, The Institute of Genomic Research, known for sequencing several genomes). She stated that DNA sequence data is the starting point for genomics based research. She also claimed that science takes place at the interface of computing and biology.

Perspectives on Systems Biology from the NIH (National Institutes of Health) by David Balshaw (works in NIH Environmental Health Sciences). Apart from hearing the word "peculated, I gathered from him that they have a $29.8 billion dollar budget.

Perspectives on Systems Biology from the Academia by Michael Savageau (University of Michigan), He spoke of elucidating and quantifying data. There is one goal of academia and that is to design a system for the coupling of expression in elementary Gene Circuits.

Perspectives on Systems Biology from the Pharmaceutical Industry- Burt Adelman, He basically said that the pharmacy must understand how human population has to understand human pathobiology. They have to focus industry research efforts on making drugs with the full collaboration of the scientific community.

Systems Pharmacology: An Application of Biology by Kieth Elliston, he simply said these few things. Systems biology, translational medicine, and drug development must be combined. Phenotypes are the result of complex network reactions in a biological network. High failures of drugs are due to a primitive understanding of the molecular actions of drugs. A better understanding of molecular reactions will help reduce failures.
Model to note: Casual System Model-rationalize based on knowledge we know-Automated Reasoning (interrogate data with artificial intelligence).

Human Microbial Metagenomics: Understanding Our Microbial Selves, by Clair Faiser-Liggett (she was my favorite speaker of the mix). The science of microbial communities is the systems biology of the biosphere. Microbiome0 A multi-membered community of bacteria that exists within a defined environmental domain. Human Microbiome-The community of bacteria that live on or in the human host (mucosal surfaces). Metagenomics- The culture independent study of the genomes of many organisms simultaneously in order to understand microbial communities as intact systems. In order to put this into practice we must take surveys of community diversity, do whole genome sequencing, and map the community functions back to the cells. (here she used the herculean word, as in a herculean amount of data). In summary, Our 'metagenome' is a composite of Home Sapiens genes and genes present in the genomes of trillions of microbes that colonize our adult bodies.

Circular Causality: Principles for the Analysis and synthesis of dynamical systems, by Rene Thomas (best known for Discovery of DNA Denaturation in 1951, from Universite Libre de Bruxelles). Two types of circuits exist, positive and negative. Epigenetic differences are those which can be transmitted from cell generation to generation in the absences of any genetic difference. Multi stationarity characterizes systems that can display two or more stable states in identical external systems. Whether a circuit is positive or negative depends on its partial parity. Positive circuits generate multi stationarity. Negative generates periodicity. Differentiative is a regulatory mechanism that happens when two types of extremes must be chosen. When the sign of a circuit depends on the location in phase space, we call it an ambiguous circuit.

Multi-omics analysis and date-driven systems biology by Masaru Tomita from Keio University in Japan. He spoke of the process of Capillary Electrophoresis and Mass spectrometry. He performed research in E. Coli and says that it seems to use complementary strategies that result in a metabolic network that is robust against small perturbations. Biosimulations can confirm if your model is consistent.

Digital Genetics: Unraveling the Genetic Basis of Evolution by Chistoph Adami from California Institute of Technology, created digi life. The origin and dynamics of evolutionary change is evolutionary genetics. Complex genes evolve through the accumulation of function, while the selective target constantly changes.

Student Presentaions Night
Is Reductionism Enough for the -omics hierarchy? by Derek Austin, senior HHMI VCU. Science tries to answer questions about natural phenomenon. Reductionism seeks to express life itself in terms of a dance of isolable chemical fractions (Robert Rosen quote). Conclusion: Purely reductionist study, based on the belief that biological phenomena can be completely explained by chemical phenomena is insufficient to analyze the -omics hierarchy".

Evolutionary neuronal and glial growth on electrospun polarized matrices: bridging the gap in percussive spinal cord injuries, by Woon Chow, graduate PhD student. He discussed and modeled a new method of healing spinal cord injuries, elctrospin the fibers and get straighter regrowth in the spinal cord.

The Human Cytomegalovirus Alkaline Nuclease As An Target by Allison Muchta, PhD student VCU. Current antivirals of HCMV have side effects. Alkaline Nuclease is the possible antiviral target. It is a possible recombinase or debranching enzyme.

Toward a General Approach of Designing Glycosaminoglycan Mimics by Arjun Raghoraman PhD student VCU. GAG's play an important role in the functioning of several proteins in our body.

Complex Analysis of Chromatic Associated Genes in Lung Adenocarcinoma,Sterling Thomas, PhD student VCU.

Day 2


Genome-Scale Models, by Bernhard Palsson, University of California-San Diego (Computational Systems Biologist). Genome-scale reconstruction and constraint based modeling: Enabling in silico (performed on a computer) analysis procedures. RNAP binding and dynamic maps are obtained (experiment).

Genome Design, Engineering and Evolution in Cell Cultures by George Church (known for the creation of the first Direct Genome Sequencing Method and Personal Genome Project) MIT professor and Harvard Medical School professor. He discussed the Personal Genome Project (basically people getting their genomes sequenced and it being available for scientific study).

Function, Design and Evolution of Gene Circuitry by Michael A. Savageau. Graded switches have faster switching times, robust switching times, and robust thresholds. Hysteric switches for irreversible commitment during differentiaion have slow times and act as a filter in the cell.

Identifying Gene Networks in Acute Responses to Ethanol by Expression and Behavioral Genetics by Michael Miles, VCU.

Where Medicine Went Wrong by Bruce West, author of books. Linear implies simple.

Metabolic Profiling of Planned Heart Attacks by Robert E. Gertszten, MD of Harvard Medical School.

Integrative Modeling of Cardiac Function in Health and Disease, Raimond Winsolw of Johns Hopkins University School of Medicine.

The Cell as a Dynamical Information Processing Network by Stuart Kauffman (known for arguing for Biological Complexity) from University of Calgary. Critical Cells maximize correlated behavior of genes over time. Thus they can carry out most complex coordinated behavior.

Genomic Strategies to Cancer Biology and Cancer Therapy by Joseph Nevins of Duke University. Gene expression profiles as surrogates for biological phenotypes.



Basically and in sum, I attended the conference for three days, endured just about every single presentation, and had loads of food to eat. The event was nice and I did get to meet some of the most amazing scientists ever. It really has made me think of my future and my future in research or so. I have to decide on that which I want to do now that i have seen several different areas of Bioinformatics and such in this short time.