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This netcast explores the rapidly changing world of biotech, with a penchant towards getting a better understanding of who we are and where we are going. The living world will soon be a true substrate for engineering. Our world will change, and so will we. 
We bring a first hand account from the scientists that are moving us into this new technological era: the era of biotech. 

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    « FiB Episode 003 - Tackling Genomes with Dr. Marc Vidal (Part I) | Main | FiB Episode 002 - The Genetics of Youth with Dr. Leonard Guarente. »

    Some Basics

    Great questions! From Wizard of Aus

    What is a homolog?
    A gene that is a homolog to another means that it shares a common ancestral DNA sequence. If you were to compare the DNA sequences, you would see regions were the sequence is identical. This could include genes that were duplicated within an organism or simply comparable genes between two different species.

    What is a ortholog?
    A gene that is an ortholog to another means that it is from a different species, and (1) it shares a common ancestral DNA sequence, and (2) the protein generated from the genetic code has retained its properties and function. You can verify this by taking a human homolog of a yeast gene, and introducing it into a yeast. If it restores a mutant yeast to behaving normally, you know that it is has retained it's function and would be considered an ortholog.

    What is an enzyme?
    An enzyme is a protein that acts like a chemical catalyst, that is it speeds up or facilitates a chemical reaction. An enzyme called glucosidase for example would break a chemical bond found in a sugar, or a protease woud cut a protein, a kinase adds a phosphate (PO4) to a protein etc... Enzymes are involved in metabolism, molecular signaling etc..

    I hope this helps. It may require a couple reads through. When I first read about this stuff it didn't sink in right away.

    Try the following:

    (1) copy this DNA sequence (it's human):
    1 ggcacgtgac ggtcgggccg cctccgcctc tctctttact gcggcgcggg gcaagatcat
    61 ggaagggaag tggttgctgt gtatgttact ggtgcttgga actgctattg ttgaggctca
    121 tgatggacat gatgatgatg tgattgatat tgaggatgac cttgacgatg tcattgaaga
    181 ggtagaagac tcaaaaccag ataccactgc tcctccttca tctcccaagg ttacttacaa
    241 agctccagtt ccaacagggg aagtatattt tgctgattct tttgacagag gaactctgtc
    301 agggtggatt ttatccaaag ccaagaaaga cgataccgat gatgaaattg ccaaatatga
    361 tggaaagtgg gaggtagagg aaatgaagga gtcaaagctt ccaggtgata aaggacttgt
    421 gttgatgtct cgggccaagc atcatgccat ctctgctaaa ctgaacaagc ccttcctgtt
    481 tgacaccaag cctctcattg ttcagtatga ggttaatttc caaaatggaa tagaatgtgg
    541 tggtgcctat gtgaaactgc tttctaaaac accagaactc aacctggatc agttccatga
    601 caagacccct tatacgatta tgtttggtcc agataaatgt ggagaggact ataaactgca
    661 cttcatcttc cgacacaaaa accccaaaac gggtatctat gaagaaaaac atgctaagag
    721 gccagatgca gatctgaaga cctattttac tgataagaaa acacatcttt acacactaat
    781 cttgaatcca gataatagtt ttgaaatact ggttgaccaa tctgtggtga atagtggaaa
    841 tctgctcaat gacatgactc ctcctgtaaa tccttcacgt gaaattgagg acccagaaga
    901 ccggaagccc gaggattggg atgaaagacc aaaaatccca gatccagaag ctgtcaagcc
    961 agatgactgg gatgaagatg cccctgctaa gattccagat gaagaggcca caaaacccga

    (2) go to the national center for biotechnology information database
    http://www.ncbi.nlm.nih.gov/BLAST/

    then click on (in the first box):

    Nucleotide-nucleotide BLAST (blastn)

    (3) Paste the sequence in the search box and click on BLAST.
    (4) On the new page, click on Format

    This allows you to compare the human gene to all the genes in the database. There will be mouse, rat, chicken versions... If the sequences are really close, they could be experimentally verified to see if they retain function, hence orthologs...

    References (1)

    References allow you to track sources for this article, as well as articles that were written in response to this article.
    • Response
      Response: essay help
      Both the bioinformatics and biotech are becoming the important subjects. The technology is involved in all the things which encouraged the tempted guys to read them and explore the new things in them. Thanks for providing the information about the basics of the many terms.

    Reader Comments (5)

    Wonderful! Thanks for taking the time.

    July 27, 2006 | Unregistered Commenterboc

    Love both episodes so far. Love any science blogs, podcasts etc. 2 very interesting topics have been chosen so far. Well done guys

    July 30, 2006 | Unregistered CommenterSteven

    Mark,

    this is amazing work. I've only last year gotten a little closer to molecular biology, but from a somewhat different angle, by reading most of Richard Dawkins' work. It almost seems like you (or your interview partners) are beginning their work where Dawkins stops. It's going to be interesting to see if we can ever get a fully reductionistic view of the mechanisms behind genetics. Even though I agree with Dr. Vidal that we have to see the cellular machinery work at many levels, it's lowest chemical level is where it all happens. It somewhat reminds me of the ant fugue Douglas Hofstadter wrote to explain how complex systems can be built of distinct layers that in themselves are purposeless.
    This podcasts connects to many fields that I've been reading about over the last months and provokes a lot of connecting ideas.
    As a suggestion: I would appreciate if you could give a literature list either by your interview partners or for the specific fild they're working in, because obviously, the podcast can only be a starting point. If you provide links to amazon, you may actually make a nickel or two off that as well.

    Thanks for the work

    pj

    August 11, 2006 | Unregistered Commenterpj

    Mark,

    this is amazing work. I've only last year gotten a little closer to molecular biology, but from a somewhat different angle, by reading most of Richard Dawkins' work. It almost seems like you (or your interview partners) are beginning their work where Dawkins stops. It's going to be interesting to see if we can ever get a fully reductionistic view of the mechanisms behind genetics. Even though I agree with Dr. Vidal that we have to see the cellular machinery work at many levels, it's lowest chemical level is where it all happens. It somewhat reminds me of the ant fugue Douglas Hofstadter wrote to explain how complex systems can be built of distinct layers that in themselves are purposeless.
    This podcasts connects to many fields that I've been reading about over the last months and provokes a lot of connecting ideas.
    As a suggestion: I would appreciate if you could give a literature list either by your interview partners or for the specific fild they're working in, because obviously, the podcast can only be a starting point. If you provide links to amazon, you may actually make a nickel or two off that as well.

    Thanks for the work

    pj

    August 11, 2006 | Unregistered Commenterpj

    Hi,

    I did this and got 112 hits. That is great. Don't understand the lines that came back tho. Here is the first 7 lines:

    BLASTN 2.2.14 [May-07-2006]
    # Query:
    # Database: nr
    # Fields: query id, subject ids, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
    # 112 hits found
    1_24245 gi|66933004|ref|NM_001024649.1| 100.00 843 0 0 178 1020 244 1086 0.0 1557
    1_24245 gi|66933004|ref|NM_001024649.1| 100.00 119 0 0 1 119 67 185 6e-54 220
    1_24245 gi|66933003|ref|NM_001746.3| 100.00 843 0 0 178 1020 297 1139 0.0 1557
    1_24245 gi|66933003|ref|NM_001746.3| 100.00 66 0 0 54 119 173 238 2e-24 122
    1_24245 gi|66933003|ref|NM_001746.3| 100.00 55 0 0 1 55 67 121 2e-18 102
    1_24245 gi|27502676|gb|BC042843.1| 100.00 843 0 0 178 1020 178 1020 0.0 1557
    1_24245 gi|27502676|gb|BC042843.1| 100.00 119 0 0 1 119 1 119 6e-54 220

    September 3, 2006 | Unregistered CommenterAnonymous

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