1. From the National Center for Biotechnology Information (NCBI), http://www.ncbi.nlm.nih.gov/
"Understanding nature's mute but elegant language of living cells is the quest of modern molecular biology.
From an alphabet of only four letters representing the chemical subunits of DNA, emerges a syntax of life processes whose most complex expression is man.
The unraveling and use of this ‘alphabet’ to form new ‘words and phrases’ is a central focus of the field of molecular biology. The staggering volume of molecular data and its cryptic and subtle patterns have led to an absolute requirement for computerized databases and analysis tools.
The challenge is in finding new approaches to deal with the volume and complexity of data, and in providing researchers with better access to analysis and computing tools in order to advance understanding of our genetic legacy and its role in health and disease."
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2. This website is a valuable resource in the classroom!!!!
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3. NCBI: Database Search and Retrieval
Entrez
It provides access to:
PubMed
Nucleotides: GenBank, dbEST
Proteins PDB
Structures
Genomes
PopSet
And more………..
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4. NCBI Tools for Data Mining:
BLAST (most popular tool)
program for sequence similarity searching
instrumental in identifying genes and genetic features
BLAST can execute sequence searches against the entire DNA database in less than 15 seconds.
Good for local pairwise alignments but not multiple alignments or global pairwise alignments
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5. TIGR is a good public database for looking at gene sequences from a number of species.. This allows scientists to do comparative genomics (look for similarities in the DNA of other species)
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6. Comparative Genomics will speed the Discovery Process for New Drugs:
Scientific American July 2000
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7. Get Schooled for Bioinformatics:
Biology
Know basics & Have sense of biological experimentation and public databases (NCBI, TIGR, etc.)
Computer Science
Programming (C/C++/Perl scripting)
Database construction (UNIX/LINUX)
Algorithm design
Math/Statistics
Probability, Experiment design, Machine learning
Ethics
“Core Bioinformatics”
LIMS (lab information management sys)
EST clustering
Sequence analysis & annotation, etc
per Russ Altman of Stanford’s Biomedical Informatics Training Program
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8. Bioinformatics – Three Levels
3. DEVELOPERS (PhD)*
of Information
of Tools
of Instrumentation
of Architecture/Storage
of Algorithms
of Modeling Strategies
of Visualization Methods
1. USERS (AS/BS level)
of Information
of Tools
of Instrumentation
In-Silico (Computer) Modeling
2. INTERPRETERS (BS/MS)
Per Pete Smietana, PhD (bioinformaticist)
*These people are in highest demand
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9. Bionformatics is a Hot Topic at UC Davis
The Biotechnology Program with ARC received an NSF grant to teach the basics to Community College instructors.
Dr. Craig Benham was hired in 2001 as the director of Bioinformatics for the new Genome Center.
CGF (Genome Facility for the College of Ag) is a cutting edge facility: microarrays, high through-put analysis, bioinformatics, etc.
Offer a Masters in Medical Informatics, with other degrees in the works.
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10. Per Tina Settineri, Applied Biosystems
Proteomics - What is it?
A proteome is the entire PROTein complement expressed by a genOME or a cell tissue type.
Only one genome for an organism, but the Proteome changes under different expression conditions.
Proteomics is the study of the proteins expressed from a genome. Proteomic researchers determine variations in proteins expressed due to disease, drugs environment, and time course.
Per Tina Settineri, Applied Biosystems
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11. The Challenge of Proteomics
Multiple Proteins for each Gene due to splicing
Varied and fragile nature of proteins
Quantitative and Qualitative changes of the proteome
Structural and Functional Proteomics Studies
Complex Proteome(s)
Per Tina Settineri, Ph.D., Applied Biosystems
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12. Problem is that over 40% of Human genes have Unknown Function!
Of 26,383 gene predictions:
41.7% unknown function
Science v. 291, Feb. 16, 2001
per Dana Haley- Vicente
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Protein Bioinformatics

13. TGT AAT AGT TAT ATT TTC ATT ATA AAT TGT GTT TGT
AGA CAT CAT AAA TTT AAA
ACA TGG CTT TTT AAC CTG
ATA AAT CCT ACG AAT ATT
TGT AAT AGT TAT GTT ATT
GCA GTA AGT ACC GTT TGT
ATT ATA AAT TGT GTT CTG
TGT AAT AGT TAT ATT TTC
ATT ATA AAT TGT GTT TGT
AGA CAT CAT AAA TTT AAA
ACA TGG CTT TTT AAC CTG
ATA AAT CCT ACG AAT ATT
TGT AAT AGT TAT GTT ATT
GCA GTA AGT ACC GTT TGT
ATT ATA AAT TGT GTT CTG
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Which genes are turned off then on ?
Courtesy of Dr. Young Moo Lee

14. Tina Settineri, Applied Biosystems
What is Protein Identification and how is it done by mass spectrometry?
Starts with proteins
separated by
2-dimensional
gel electrophoresis:
IEF followed by SDS PAGE
Each black spot is a protein
Spots will excised and analyzed
Tina Settineri, Applied Biosystems
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15. Tina Settineri, Applied Biosystems
GATHER EVIDENCE
Police Officer
1. Interview witnesses
2. Dust for fingerprints
Biospectrometrist
1. Interview biologist who isolated the protein
2. Cleave protein with trypsin to obtain peptide mixture
3. Analyze peptide mixture by MALDI-TOF MS to get peptide molecular weights!
enzyme
Tina Settineri, Applied Biosystems
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16. DATABASE SEARCH Biospectrometrist Police Officer search search
molecular weight: 30,000
Origin: bovine liver
Peptide mass list from MALDI-TOF analysis: , , , ,
Police Officer
Height: 5’7”
Weight: 160 lbs
Gender: male
Age:
Fingerprints
search
search
DATABASE OF
KNOWN FELONS
PEPTIDE MASS
DATABASE
OF KNOWN
PROTEINS
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17. Mass accuracy tolerance = 15 ppm
This means that the mass is within Da at
m/z 1000
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Per Tina Settineri, Ph.D., Applied Biosystems

18. Protein Structure is …
“Protein structure is the key to understanding disease, because proteins (not genes) are the end points of life sciences investigation since proteins ultimately regulate metabolism and disease.”
Chemical & Engineering News, Feb. 19, 2001 p. 30.
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Protein Bioinformatics

19. Similar Function, Similar Structure, Low Sequence Homology
Methyltransferases
Only 5.5 % sequence identity
Molecular Simulations Inc. San Diego, CA WebLab Viewer Pro
Need more than a BLAST search!
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Protein Bioinformatics

20. Protein Structures – Predicted vs. Experimental
Methylglyoxal synthase predicted (bottom) and experimental (top) structures agree exactly (red region)
– NIH National Center for Biotechnology Information
In Silico Modeling is an important skill
C & E News Sept. 2000
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21. Sequence to Structure to Function:
Homology Implies Function
3D Active Site
Most
3D Structure
Secondary Structure
Evolutionary Conservation
Protein Sequence
DNA Sequence
Least
(databases)
Molecular Simulations Inc. San Diego, CA
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22. PubGene - example of use of bioinformatics for genomics & proteomics
PubGene" Solution "PubGene searches for various relationships between subjects such as genes, RNA transcripts, proteins, mutations, chemical compounds,or diseases. "PubGene includes a number of data layers to allow user-defined content display, and presents results as association networks.
PubGene" Package Text Mining Module: proprietary databases of human, mouse, and rat gene and protein names and aliases associations with interface for literature search. Expression Analysis Module to look for gene and protein relationships in a microarray experiment Sequence Homology Module to search for protein homology networks.
Future Products MutationGeneProteinDisease relationships MeltMap (human genome) project   Distributed by Technology Networks:
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23. Metabolomics = metabolism +genomics
Systematic Metabolic profiling may identify how genes regulate a metabolic process, such as cold tolerance or oil production in plants.
Metanomics in Berlin, Germany is creating the MetaMap database for Arabidopsis (see Working Weeds. Scientific Am. April 2003.
Involves genetic modification of organisms versus wild type, then rapidly screening them for chemical or physical changes after a change in experimental conditions.
Lipomics Technologies in West Sacramento is creating lipid profiles in humans and lab animals (health vs. disease or drug therapy)
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24. Pharmacogenomics could lead to personalized medicines.
Ref. Laboratory Medicine. Sept 2003.
It is the study of how an individual’s genetic inheritance affects the body’s response to drugs, with the goal of optimizing therapy and identifying better, safer drugs.
Single Nucleotide Polymorphisms (SNPs) will be the basis of classification (Connect phenotype with genotype).
HapMap is an international project to look at patterns of inheritance of SNP haplotypes.
Although several pharmacogenetic syndromes are monogenetic traits, most are polygenetic.
Example: isoniazid is the therapy for choice for TB, but some develop neuropathy due to a single gene variation.
We need to couple the Human Genome Project with functional genomics and bioinformatics to unravel the puzzle of why some drugs work for some people, while others become toxic..
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25. Nutritional genomics or “Nutrigenomics"
January 21, 2002 – UC, Davis and the Children's Hospital Oakland Research Institute (CHORI) become a National Center of Excellence in Nutritional Genomics. A five-year, $6.5 million grant from the National Center on Minority Health and Health Disparities, a division of the National Institutes of Health.
The Goal of the Center: Explore the links between diet, genes and diseases in minority populations, such as Type 2 diabetes, obesity, heart disease and some cancers.
"The research we'll be doing in the Nutrigenomics Center is one of the first examples of taking the benefits of human genome research from the lab to the home," said Ray Rodriguez, professor of molecular and cellular biology at UC Davis and director of the new center.
Good reference: “We are what we eat”, The Economist, Sept 4, 2003
For more information: Media contact: Raymond Rodriguez- (530) ,
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26. Agricultural Biotechnology is a promising new area of crop science ...
Decrease use of chemicals on farmland.
Enhanced pest and disease resistance.
Increased stress tolerance: drought, salinity, cold, etc.
Improved vitamin and micronutrient composition.
“Pharming” to make vaccines and therapeutics.
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27. They are specialists in Plant Genomics.
Dr. Doug Cook and Dr. Richard Michelmore are the lead researchers for CGF.
They are specialists in Plant Genomics.
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28. “Golden Rice”
High Provitamin A (-carotene) rice is a major advance for plant biotechnology and focuses international attention on the metabolic engineering of output traits.
Institute of Plant Sciences, Swiss Federal Institute of Technology Zurich Switzerland.
Vitamin A deficiency is a serious health problem in 26 countries, putting 124 million children at risk for disease and death. (Night blindness, total blindness, diarrhea, respiratory disease and measles.
Ye et. al., Engineering the Provitamin A (-Carotene) Biosynthetic Pathway into (Carotenoid-Free) Rice Endosperm. Science 287:
Picture of Ingo Potrykus
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29. Increased b-Carotene in Rice Grains
Normal rice
Normal rice
(daffodil)
Introduced
enzyme
(source)
Over 120 million children worldwide are deficient in vitamin A. Rice has been engineered to accumulate b-carotene, which is converted to vitamin A in the body. Incorporation of this trait into rice cultivars and widespread distribution could prevent 1 to 2 million deaths each year.
(bacteria)
“Golden” rice
(daffodil)
Ye et al. (2000) Science 287:
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30. “Pharming” represents the Third Wave of Ag Biotech
Use of Genetically Modified Plants or Livestock as factories, rather than food
Plant derived medicines is not new! Examples: Taxol, digitalis, quinine, etc.
A plant/seed can be a high protein expression system (ex: Large Scale Biology;Ventria Biosciences; Epicyte; Monsanto; Prodigene, etc.)
Proteins can also be expressed in milk, semen or urine of cows, pigs, rabbits, etc. Example: spider silk (Nexia)
Significantly less costly than stainless steel tanks due to low initial capital investment and scalability
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31. Nature Biotechnology Uncorking the biomanufacturing bottleneck Alan Dove, Aug 2002 p777-9
“As biomanufacturing capacity becomes strained, several new methods for producing biologics are being investigated by biotechnology companies”
Spokesperson from GTC Biotherapeutics (formerly Genzyme Transgenics) in Framingham, MA estimates a 200% increase in manufacturing capacity for Mabs alone over the next 10 years. Their solution is milking transgenic animals (“mammary bioreactors”). PPL Therapeutics (UK) and BioProtein (France) have similar projects. Goats, sheep and cows are the most common mammals.
Transgenic chicken eggs may also be feasible, but the research is still in early stages. Companies: Origen Therapeutics (Burlingame, CA); Avigenics (Athens, Ga); TranXenGen (Shrewsbury, MA); GeneWorks (Ann Arbor, MI) and Vivalis (France).
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32. Therapeutic Protein Production in Plants Important Considerations

33. Why Make Pharmaceuticals in Plants?
Supply the increasing demand for new biotech drugs (esp. antibodies)
50 Mabs by 2008
Significantly decrease unit costs
Improve patients’ access to biotech medicines
Plants are an efficient producer of proteins
Plants are scalable bioreactors
Plants provide cost advantages to mammalian cell culture systems
3-5 times faster than mammalian systems
Plant cells are similar to human cells
Similar protein synthesis machinery
Read the same genetic code
Assemble, fold and secrete complex proteins
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34. Transgenic Maize Provides High-Capacity, Low Cost Option for Large Scale Mab Manufacturing
Significant cost associated with Mammalian Cell systems
Transgenics provide a cost effective method at large scales
Example: Maize
7 x 15,000L Tanks
~ Acres
Plant transgenics realize a significant savings in facility costs by replacing traditional biosynthesis in tanks with plants…Mamm requires significant capitol and infrastructure expense
Reduced facility cost translates into reduced COGS
MN also brings a unique set of talents that provide significant enablement…We understand how to design, build, validate and operate MT facilities…Corn seed enables you to decouple manufacturing from DSP…a huge advantage
Mn knows how to “ring the Rag” with respect to cost savings operating MT plants
Transgenic plants offer lower capitol costs and ability to produce MT scale production cost effectively
~$ M Construction
~$80-120M Construction
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35. Use Tobacco to make medicines
RNA
“Personalized medicine”
Large Scale Biology (Aka Biosource) in Vacaville, Ca is using the tobacco plant as a production system for human vaccines, cancer therapies (ex: lymphoma) and other pharmaceuticals. “Pharming in Plants” but no gene flow!
(Transient expression of mRNA of vaccine gene)
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36. Engineers are involved in Biotech too!
Bioprocessing
Nanotechnology
Biophotonics
Biosensors
Biomedical Engineering
Tissue engineering
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37. Motto: Shining Light on Life
NSF Center for Biophotonics Science and
Technology (CBST)
Motto: Shining Light on Life
Lead campus
Will be located across from the UCD Med Center
~100 participants
$52M over 10 yrs
Dennis Matthews, Director
Emphasis on integrative research,
education, and knowledge transfer
in biophotonics
~20 research projects