Hunting the next killer virus: Joe DeRisi

Attribution - http://www.ted.com/

Abstract:

Joe DeRisi wanted to aid medicine and detect viruses. DeRisi wanted to make a chip to screen for different pathogens. He discovered identical sequences in genomes to other viruses that make a marker to other viruses. The less the markers have income the less similar they are to another type of virus. DeRisi used DNA and RNA regions to be represented on the chip as detection agents. The DNA was printed on glass to make these chips and would be the markers for the pathogens. If there were a virus in the DNA on the chip it would be florescent under the machine. Each of the spots on the chip represented a different virus or species of viruses. When the virus is individually looked at each virus comes up in a barcode like manner, which could be referred to as a fingerprint of the virus. No one stripe in the barcode is equivalent to a virus but it is the sequence of stripes that make the fingerprint. Each virus has a different barcode combination. For the final large chip they put every virus known to man from plants, animals and humans, to make the ultimate virus chip.

Biography on Joe DeRisi

Joe DeRisi is a biochemist who specialized in molecular biology, parasitology, genomics, virology, and computational biology. He received a B.A. from the Univeristy of California, Santa Cruz, in molecular biology; and a Ph.D. in biochemistry from Stanford University. Joe is a Howard Hughes Medical Investigator and a professor at the University of California, San Francisco. He also is the 2008 winner of the Heinz Award for Technology. On top of that he is a Macarther grant recipient for his interests with viruses, more specifically the detection of the virus. Joe Derisi is known for his achievements on the work of gene profiling throughout the lifecycle of the malaria and his analysis of the SARS virus. One of DeRisi's biggest successes is his work inventing the ViroChip, which accelerated the ability of researchers to discover viral infections. Joe worked to make a microarray chip that applied to viral discovery instead of cancer and toxicology. This chip makes what would be like a fingerprint for every virus. He looks and turns it in to a bar code or signature for each of the specific virus. Joe has now built a chip that has every known virus discovered on it.

Attribution- http://en.wikipedia.org/wiki/Joseph_DeRisi

http://www.nytimes.com/2008/10/07/health/research/07conv.html

http://www.ethanzuckerman.com/blog/2006/02/23/joe-derisi-and-virus-detection/

Vocabulary

Virus - a small infectious agent that can replicate only inside the living cells of organisms. Most viruses are too small to be seen directly with a light microscope. Viruses infect all types of organisms, from animals and plants to bacteria and archaea.

Diagnosis - the identification of the nature and cause of anything, to determine the cause and effect relationships.

Evolution - is the change in the inherited traits in a population of organisms through successive generations. Over time variants with particular heritable traits become more, or less, common.

DNA - Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms. The main role of DNA molecules is the long-term storage of information. DNA is often compared to a set of blueprints, like a recipe or a code, since it contains the instructions needed to construct other components of cells, such as proteins and RNA molecules.

RNA - Ribonucleic acid is one of the three major that are essential for all known forms of life. RNA is made up of a long chain of components called nucleotides. Each nucleotide consists of a nucleobase, a ribose sugar and a phosphate group. The sequence of nucleotides allows RNA to encode genetic information.

Pathogen - more commonly known as a germ, is a biological agent such as a virus, bacteria, or fungus that causes disease to its host.

Cell culture - is the complex process by which cells are grown under controlled conditions.

Antibodies - are gamma globulin proteins that are found in blood or other bodily fluids of vertebrates, and are used by the immune system to identify and neutralize foreign objects, such as bacteria and viruses. Anti bodies are produced by a kind of white blood cells called a plasma cells.

Epidemiology - is the study of patterns of health and illness and associated factors at the population level. It is the cornerstone method of public health research, and helps inform evidence-based medicine for identifying risk factors for disease and determining optimal treatment approaches to clinical practice and for preventative medicine.

Attributions-

http://dictionary.reference.com/

http://www.wikipedia.org/

Theme 1 – Evolution

Evolution is any process of formation or growth. It is the development of life that lets anything evolve. In Joe DeRisi’s creation of a viral chip, he learned of the constant evolution that a virus goes through. The reason his chip is so large is for the amount of viruses that are placed on it. Each virus could be passed to another person whose body is infected with it and mutates the virus into a whole new kind of virus. This mutation can occur over and over again, making the first to the last virus a long line of unknown new viruses. The identical sequences found in the virus is what shows scientist like DeRisi that each virus has the capability of evolving, even in to something more deadly then the first. In some cases the process of evolution is a good thing like that of animals or plants, but in some cases like the creation of new viruses it’s not.

Theme 2 – science, Technology and society

Sometimes society and science don’t mix; we have seen it throughout history. In some cases science along side technology create new ideas and understandings and sometimes is creates chaos. For instance when the human genome project was in action many people were unable to decide if they would want to know “what was wrong with them”. In this case of creating a machine that could read a chip containing decoded viruses it is a work of genus. Because of this new machine many new viruses are being coded and detecting faster. And because viruses were being detected earlier each patient could be treated faster and more efficiently. The use of technology saves many people not just in surgical tools but also in ways that can prevent the need for those other tools.

reflections over trimester 1

What I have learned this trimester-

This trimester I have been able to really comprehend the process of osmosis in relation to water diffusion. There are two types of solutions a hypertonic and a hypotonic solution. In the hypertonic solution there is less solute in the cell forcing the cell to want to balance out by pulling all of the water out of the cell and into the solution. In a hypotonic solution the cell would be considered a hypertonic cell because there is more solute in the cell then the solution forcing all the water into the cell making it swell and eventually burst. There is differences in a plant cells like the ideal state. in a plant the ideal state would be a hypotonic solution but in an animal cell it would be an isotonic solution.

What I have found difficult this trimester-

This trimester I have been struggling with meiosis and how mitosis is part of meiosis. I find it difficult to understand how any of the first phases would be different from when it does it again. I get that you have to end up with four haploid cells to make the sex cells but I guess I just don't get the process of getting there, and how it is different then normal reproduction of cells.

How do biological systems regulate?

Biological systems are constantly regulating themselves whether it is by regenerating new cells, or the process of transferring things through the phospholipid bilayer. Some times the cell is not able to regulate enough and a deformity might occur like in the reproduction of cells. If a cell is disrupted it could cause cancer cells to form whether benign or malignant.

reflections on 6.2 and 6.3

What I have learned - I have learned about cell membranes and how they function differently then a cell wall. The cell membrane allows for transportation of substances across the boundary where cell walls don't. There are three types of ways that substances can move through the membrane, either with a selectively permeable membrane which allows substances to pass easily, a passive transport where no energy is need to pass through the membrane or a facilitated diffusion where the substance are not all allowed to move through.

What I have found difficult - I don't quite understand osmosis in relation to water and being hypertonic or hypotonic. I am unable to understand the diffusion of water to really understand the way it works.

How does structure relate to function? - The structure of the a membrane allows for the membrane to carry out certain functions. If the protein was not embedded in the membrane the membrane wouldn't have the signals it needed to make sure the function of the membrane is properly working.

jello... what's in it?

• jello's main binding agent is Gelatin, a protein produced from collagen extracted from the boiled bones, connective tissues, and intestines of animals
• Gelatin is just a processed version of a structural protein called collagen that is found in many animals, including humans.
• Gelatin is a fibrous molecule that makes skin, bones, and tendons both strong and somewhat elastic
• To make gelatin, manufacturers grind up these various parts and pre-treat them with either a strong acid or a strong base to break down cellular structures and release proteins like collagen. After pre-treatment, the resulting mixture is boiled. During this process, the large collagen protein ends up being partially broken down, and the resulting product is called gelatin. The gelatin is easily extracted because it forms a layer on the surface of the boiling mixture.
• At room temperature, the gelatin protein is in the form of a triple helix.

http://recipes.howstuffworks.com/question5571.htm