Bioinformatics Workshop for Teachers and Students

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Bioinformatics Workshop for Teachers and Students

• By Veronica Almeida

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Gregor Mendel

• In the 1890's, the invention of better
  microscopes allowed biologists to discover the
  basic facts of cell division and sexual
  reproduction.  The focus of genetics research
  then shifted to understanding what really happens
  in the transmission of hereditary traits from
  parents to children.  A number of hypotheses were
  suggested to explain heredity, but Gregor Mendel
  , a little known Central European monk, was the
  only one who got it more or less right.  His
  ideas had been published in 1866 but largely went
  unrecognized until 1900, which was long after his
  death.  His early adult life was spent in
  relative obscurity doing basic genetics research
  and teaching high school mathematics, physics,
  and Greek in Brno (now in the Czech Republic). 
  In his later years, he became the abbot of his
  monastery and put aside his scientific work. He
  also realized that not only did it apply to
  plants but to humans and animals. Mendel picked
  pea plants as his focus for his research because
  they can be grown in large numbers and their
  reproduction can be manipulated. Pea plants have
  both male and female reproductive organs. In his
  experiments, Mendel was able to selectively
  cross-pollinate purebred plants with particular
  traits and observe the outcome over many
  generations.  This was the basis for his
  conclusions about the nature of genetic
  inheritance. He died in 1884.

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Vocabulary
Day 2, June 22 NCBI-The national center for
biotechnology information Molecular genetics-
background for molecular biology Arabidopsis-a
genus of the mustard family having white, yellow,
or purplish flowers easy to grow Oryza sativa-
Cultivated rice yields the stage food of 50 of
worlds population Genus-taxonomic group
containing 1 or more species Patatin- main
protein in potato Query- the search sequence
that is put in Subject- what it hits( sequence
found) Positive sign- similar amino acids have
the same functions Expect value- number of
database hits expected to find by chance BLAST-
Basic Local Alignment Search Tool

• Day 1, June 21
• Deoxyribonucleic acid- DNA
• Insulin- a type of protein that regulates the
  bodies use of sugar
• Genes- segments in chromosomes that represents
  the way your eyes look, hair color, skin color
  etc a unit of heredity
• Double helix- shape of DNA
• ORF- Open Reading Frames
• Nucleotides- 4 bases of DNA(A-Adenine, T-thymine,
  C- Cytosine, G- Guanine)
• GMO- Genetically Modified Organism

• Day 3, June 23
• Annotation- extra information associated with a
  particular point in document or program
• Comparative genomics- comparing how an organism
  is the same and different
• Functional genomics-what the genes encode
• Structural genomics- the sequence and
  identification of genes
• Genomics- entire sequence
• Transcriptomics-all expressed genes
• Proteomics- all proteins
• Metaomics- all compounds
• Pathogen- any disease producing agent (especially
  virus, bacterium, or microorganism)
• EST-expressed sequence tag (sequencing of

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Day 1 Journal/Notes June 21,2004

• DNA divides into 2
  chromosomes. The segments found in a chromosome
  are genes which either represents the genes of
  eyes, mouth, hair and etc. There are 46
  chromosomes in each human cell. Female eggs cells
  have 23 chromosomes. Males sperm cells have 23
  chromosomes too. Some genes are dominant like
  that of being able to roll your tongue or having
  brown hair. Having blonde hair is a recessive
  gene. Men have 2 different chromosomes which are
  X and Y. Females have 2 same chromosomes X and X.
  When a males x chromosome crosses with a females
  x chromosome a baby girl is conceived. When the
  males y chromosome crosses with the females x
  chromosome a baby boy is conceived.
• RNA is translated into proteins. A double
  helix of DNA was formed when A and T was stacked
  above C and G. DNA is the molecule of all living
  things. DNA is a self replicating molecule.
  Proteins are 3rd dimensional and dont work in a
  straight line. There are 30,000 genes in a human
  body.
• Protein always begins with ATG which is the
  abbreviation for methionine. A human nucleus has
  3 billion base pairs and about 35,000 protein
  coding genes.

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Day 2 journalJune 22,2004Steven Pechous
PowerPointpresentation summary

• NCBI was created in 1988 as part of a
  National Library of Medicine at NIH (national
  institutes of health). NCBI creates public
  databases for anyone to use. PubMed has over 1
  million journal articles that are used by doctors
  but can be accessed by anyone too. There are many
  books in the bookshelf that you can print off for
  references or research help. GenBank record has
  many different tables. A very important table is
  Feature Table which gives you the name of the
  gene, name of the organism it comes from, its
  protein ID number, what it does, and the base
  sequence. The NCBI website also has a Primary
  database and derivative database. In the Protein
  database you can find out how much protein there
  is in just about anything. When Steven typed
  potato within organism he got up to 1819 records
  of it There are links, blinks and domains that
  you can search just about anything containing
  protein or anything that has to do with protein
  structures. There are 3D domains that you can
  download and actually see the protein structure.
  There has been over 100,000 bacterial genomes
  submitted into this website.
• The map viewer page shows about all genomes
  available to research on, they include Fungi,
  plants, invertebrates, vertebrates, mammals and
  protozoa. Higher genome map views show what the
  genome is and where its located. You can also
  look for mutations in a gene.
• BLAST is where you can search for Nucleotide
  sequences, protein sequences, genomes and you can
  also align 2 sequences at one time. On BLAST it
  calculates similarity biological sequences, and
  finds best local alignments.
• Protein searches are more sensitive then
  nucleotide searches.
• You can locate any type of gene
• You can identify annotate sequences, assemble
  genomes, and explore evolutionary relationships
  on Sequence Similarity Searching.
• Similar sequence may not have similar functions
• Everything on their website is FREE!!!!!!!!!!!!!!!
  

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Protein BLAST Page
Accession, GI, or sequence
Choose your database
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Day 3 journalJune 23,2004Willem Albert Rensink
PowerPointpresentation summary

• Project TIGR has four different projects that
  they work on. The four are Microbial genomics,
  plant genomics, human and rat genomics, and
  bioinformatics. When it comes to the point of
  working with protein there is a whole new science
  behind that. The most easiest to work with is DNA
  and RNA is a little more difficult. Why do we
  sequence an entire genome? The reason why we do
  that is to accelerate all other research efforts.
  Why we need genomics is because if you find 1
  gene you can find many more with that. Another
  reason is that it is a global analysis of all
  genes. Also most processes are more complex. You
  can also work forwards or backwards on genetics.
  There are also a list of things that can be
  sequenced. For instance, DNA or cDNA can be
  sequenced along with PCR products, plasmids,
  lambdas, BACs, cosmids and bacterial genomic
  DNA. The sequence run can result in 500 to 800
  base pairs of sequence. DNA recombination allows
  you to clone DNA. There are 2 different
  approaches for sequencing. They are directed and
  random shotgun. The difference between these two
  is that directed uses clones and the random
  shotgun doesnt. Sequencing can be done on a
  machine called a Q-bot. There are also 2 types of
  gaps and one is sequencing gaps and the other is
  physical gap. On functional assignment you have
  to name the gene and state its role like what it
  does.
• DNA finger printing is used for many different
  cases. These cases include forensic science,
  paternity testing, historical investigators,
  missing persons investigation, mass disasters,
  and military DNA. The short tandem repeat region
  is variable between samples while flanking
  regions where PCR primers bind are constant. In
  this region you also learn that homozygote means
  both alleles being the same length while
  heterozygote means that alleles differ and can be
  resolved from one another. FBI combined DNA index
  system is used for linking serial crimes and
  unsolved cases with repeat offenders. Eye color
  is know to have a polygenic inheritance pattern
  that is governed by 6 or more genes.

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The Institute for Genomic Research (TIGR)
Washington, D.C.
TIGR is a not-for-profit research institution
located in Rockville, MD about 25 miles NW of
Washington, D.C.
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Day 4 journalJune 24,2004Tim Straub, George
Vandermark and Ted KishaPowerPoint Presentations

• Tim straub.
• Microarrays are miniaturizations of the former
  high density dot blots on nylon membranes.
• PCR is used to amplify the yellow shaded sequence
  of the gene.
• Analysis for this kind of microarray experiment
  is qualitive and very easy.
• George Vandermark
• Aphanomyces euteiches (fungi disease) causes
  severe root rot diseases in alfalfa, peas, and
  beans. It usually causes spores on roots of
  alfalfa. They rate alfalfa for Aphanomyces
  resistance by a scale of 1-5, 1 being the
  healthiest and 5 being dead. Phytophthora root
  rot is familiar to aphanomyces but is a more
  terrible disease. A survival spore can survive
  for decades in soil. The disease is complex with
  aphanomyces and nematodes. Rating Phytopthora is
  based on 2 classes. The 1st one is resistant and
  the 2nd is susceptible.
• Scientists can use a PCR machine to examine
  differences among plants.
  

• Ted Kisha
• National Plant germplasm System is a cooperative
  effort by public and private organizations to
  preserve the genetic diversity of plants.
• World food supply is based on intensive
  agriculture, which relies on genetic uniformity.
• Scientist have to have access to genetic
  diversity to bring out new varieties that can
  resist pests, diseases and environmental
  stresses.
• All important crop species originate outside the
  U.S.
• A genetic marker is an image of representation of
  a specific, heritable DNA sequence which can be
  mapped to a specific locus .
• There are 4 types of genetic markers. They are
  phenotypic, isozymes, restriction fragment length
  polymorphism, and polymerase chain reaction based
  markers.

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Codon Table

• There are 64 codons when using the 4 nucleotides.
• DNA codons for each Amino Acids.
• NAME Abbreviations Codons
• Alanine Ala A
  GCA,GCC,GCG,GCT
• Cysteine Cys C TGC,TGT
• Aspartic Acid Asp D GAC,GAT
• Glutamic Acid Glu E GAA,GAG
• Phenylalanine Phe F TTC,TTT
• Glycine Gly G
  GGA,GGC,GGG,GGT
• Histidine His H CAC,CAT
• Isoleucine Ile I ATA,ATC,ATT
• Lysine Lys K AAA,AAG
• Leucine Leu L
  TTA,TTG,CTA,CTC,CTG,CTT
• Methionine Met M ATG
• Asparagine Asn N AAC,AAT
• Proline Pro P CCA,CCC,CCG,CCT
• Glutamine Gln Q CAA,CAG
• Arginine Arg R CGA,CGC,CGG,CGT
• Serine Ser S TCA,TCC,TCG,TCT,AGC,AGT

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DNA structure

• DNA

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Potatoes have different types of characteristics
such as their color and number of eyes
Pictures of Potatoes

• Potatoes have 12 different chromosomes.

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The people in the workshopA couple were missing