Meeting Minutes: 27th June 2007

We welcomed our newest BiRG member "Kimberly Holmes"
The discussion today was about Working with a single DNA sequence : the slides are available in the Shared Folder
David began his presentation with the statement "Not everything that can be counted counts and not everything that counts can be counted"

Topics covered in detail included

- PCR
- Cloning
- Cleaning a DNA sequence (removing contamination)
- Restriction Map
- FIRTSMARKET website (use Netscape browser)
- Primer Design (MIT Website)
- Emboss
- Gene Prediction [ prokaryotes -> GeneMark ]
- Gene Prediction [ eukaryotes -> Genomescan ]
- BLAST
- Shotgun sequencing/contigs/assemble/homology
- read pieces
- PHRAP assembly program
- CAP3 program for joining small sequences

We have a nice discussion with Dr. Ramachandran explaining several concepts during the presentation. We also discussed about gene expression and Hidden Markov Models

Lastly, we do not meet next week - Independence Day - July 4

BiRG MINUTES June 13, 2008

Protein and specialized Sequence Databases

 Types of Organisms: Prokaryotic, Eukaryotic, and Archea

Protein Maturation

Deciphering a Swiss-Prot entry

Specialized protein databases: KEGG (the metabolic pathways database) or PDB (structure database)

2 ways to predict genetics

1.       Genes to proteins or translation (genomics)

2.       DNA

We must merge the two

From Gene to functional Protein

                DNA > mRNA > proteins > upon maturing > transportation > destination

Protein Maturation:

                -removal of some fragments

                -specific protein cleavage

                -chemical modifications

                -Phosphorylation (addition of phosphate that gives the protein its shape)

                -adition of lipids or sugars (glycosylation)

-Proteins are often modified to make them active

www.ebi.ac.uk/RESID

-Modification can imply attaching a lipid or a sugar

www.glycosuite.com

-Use these resources to determine the details of the modification

www.lipidbank.jp

Swiss-Prot Database – (British) entries describe all proteins that have known functions

                tremble contains the 4 mill putative proteins found in GenBank

                Swiss-Prot contains the subset of tremble with a known function

                This is redundant to create many databases using the same information

                A Swiss-Prot entry: www.expasy.org/uniprot/P00533

Gen Info (accession number), References, Commments, Cross-reference, feature table,  sequence

General Information: Entry Name, Primary Accession Number (PXXXX [P is for protein]), Last Modified, Protein name and synonyms, from/taxonomy fields (tells where protein came from), references section

                Comments section lists all the known functions of the protein

                Features Section localizes precisely every known function of your protein, each on its sequence

•                      TRANSMEM: Transmembrane domain (something that passes through the membrane)

•                      ACT_SITE: Active sites    (where chemicals can bond)

•                      BINDING: Binding sites

•                      DISULPHID: Bridge of cysteines

•          EMBL: GenBank original DNA sequence

•          PDB: Experimental structure of your protein

•          DIP: Proteins interacting with your protein

•          GlycoSuiteDB: Glycolsylations

•          MIM: List of genetic diseases involving your protein

•          Ontologies: Function of your protein

•          Profiles: Known protein domains in your protein

•          ENSEMBL: Genomic location of your protein

 
By alternative splicing, the protein can have MANY functions

•          To find out about the function of your protein, you will need to determine

–        Where your protein works

–        Metabolic pathway in which the protein is involved

–        The protein's 3D structure

–        Which protein family it belongs to

Where do proteins work?

                Part of the metabolic pathway

                                Chain of production linking several different proteins

                                Modify metabolites by passing them from one enzyme to the next

                                On KEGG pathway, each enzyme appears w/its EC number

•          www.genome.ad.jp/kegg

–        KEGG is the most extensive database of metabolic pathways

–        You can use it to compare species    Japan

•          www.chem.qmul.ac.uk/iubmb

–        The IUBMD assigns the EC numbers used to describe an enzyme activity   UK

•          www.ecocy.org

–        An exhaustive list of all known metabolic pathways in E. coli and other bacteria

Some important Protein Families

•          www.kinasenet.org

–        Kinases control everything in us; their deregulation is the cause of many cancers

•          imgt.cines.fr

–        Immunoglobulins are key elements of our natural defenses

•          rebase.neb.com

–        This site is a key resource on restriction enzymes

      Predicting protein function is a central goal in biology

•          Protein databases help organize knowledge

•          They provide the material for

–        Developing new biological experiments

–        Developing new prediction algorithms

–        Extrapolating experimental data to unknown sequences

June 6, 2008 MINUTES by William Apple

We discussed Nucleotide Sequence Databases

Distinguishing structure of eukaryotic and prokaryotic proteins
Eukaryotic DNA in nucleus, nuclear DNA
mRNA-photocopy of DNA that is carried to Ribosomes
alternative splicing-introns "comment" out segments of exons (information) to generate many types of proteins
Eukaryotes (1 gene/1Kb) are very complex compared to Prokaryotes (1 gene/100Kb)
GenBank – housed by national Center of Biotechnoloies
memory of biological science; many biologists send genes they find to keep the database up-to-date
Reading a Prokaryotic GenBank entry (p75)
    ACESSION is the accession number
    LOCUS contains information on gene size
    ORGANISM defines the organism containing the gene
    REFERNECE indicates who produces the gene
    FEATURES
Reading a Eukaryotic GenBank entry
Gene-centric databases: pieces genes together to work with; uses GenBank data; Entrez Gene genome
ENSEMBLE visualization of human chromosomes – can click and zoom on various parts of a chromosome
TIGR Institute
DoE Joint Genome Institute
University of California – good alternative to ENSEMBL; is a mirror site

We had many good discussions.  The meeting was very productive.

Minutes from 30 MAY 08

- David brought along a very informative video on Bioinformatics
- The video is a "must see" and is on the SHARED Folder of the BiRG server.
- David continued to discuss about the different avenues with BioInformatics research directions
- William raised a few interesting questions, Dr. Ramachandran explained the concepts about introns and exons with genes.

- John Lannon submitted his digital version of the paper titled "Investigating Alu Distribution by Family across Human Chromosome Sequences" for inclusion in the Undergraduate Research Journal.
This work had won the Chancellor's Award for Interdisciplinary Achievement in this year's Celebrating Success Student Conference held on April 17-18, 2008

23 MAY 08 - Meeting Minutes

- The BiRG lab welcomed another new member William Apple.
- William is our new  Undergraduate Research Assistant working on Flash Animations and Social Informatics.
- David continued with his presentations about Bioinformatics and Proteomics
- BiRG accounts were set-up for William and David
- The Lab had coffee and chocolates again for the BiRGers

Meeting Minutes: 05/16/2008

- The BiRG lab welcomed our new member David Olayemi. David was awarded the Undergraduate Research Fellowship Award for Summer 2008.
- The BiRG lab celebrated the the Success of fellow BiRGer John Lannon with coffee, soda and chocolates.
- David started his tenure with the BiRG Lab with a very informative discussion on Bioinformatics.( His presentation slides are available on the BiRG Server in the Presentation Folder)

Very interesting discussion followed - with Prof Manwani sharing with us his insights on Karma and DNA.
Theresa and Shawn also kept the discussion active. At the end Dr. Ramachandran informed the lab about available resources and one-one-one appointment time available for scheduling.