Search found 38 matches

by G-Do
Tue Jan 02, 2007 2:15 am
Forum: Molecular Biology
Topic: DNA damage
Replies: 5
Views: 3664

The cell can protect itself (meaning all of its molecules, not just DNA) from radical oxygen species using superoxide dismutases, which target R.O.S.s for de-radicalization. Ascorbic acid (vitamin C) also helps. I'm not sure if the cell has preventive measures for pre-emptively protecting itself fro...
by G-Do
Sat Dec 30, 2006 5:41 am
Forum: Evolution
Topic: Life arose "200 million years ago"?!
Replies: 6
Views: 4109

The major reference that supports this assertion is the article by Rosing and Frei. Unfortunately, I don't have access to that at this time. You can try to nab it via an interlibrary loan (ask your local librarian). My appraisal of the site: The short version is, take it with a grain of salt. The lo...
by G-Do
Tue Dec 12, 2006 1:31 am
Forum: Molecular Biology
Topic: DNA the genetic material
Replies: 5
Views: 2887

Hi Victor,

OT, but I always understood that we do this because DNA is insoluble in ethanol (DNA has a negatively charged phosphate backbone and ethanol is an organic solvent). So it has the effect of making the DNA come out of solution.

Cheers.
by G-Do
Sun Dec 10, 2006 9:15 pm
Forum: Zoology Discussion
Topic: Most venomous animal
Replies: 26
Views: 58248

That is an interesting question! I'm guessing it's the poison arrow tree-frogs of South and Central America. However, their poison is secreted through the skin, so if you're using the definition which says that venom is "a toxin delivered by a bite or a sting" I'd have to go with one of th...
by G-Do
Fri Dec 08, 2006 5:19 am
Forum: Bioinformatics
Topic: Protein Interaction Information Visualisation
Replies: 6
Views: 5537

Hi Jimbobbery, A small group of proteins with many interactions between them could represent many things. In a protein interaction network, it probably represents members of a large multimeric complex, like the DNA replicating machinery or the ribosome. In metabolic and regulatory networks, I'm not ...
by G-Do
Tue Nov 28, 2006 6:56 am
Forum: Bioinformatics
Topic: Batch BLASTP
Replies: 2
Views: 4010

You could run the sequence through FGENESB: w To get to FGENESB, mouse over "OPERON & GENE FINDING IN BACTERIA" in the left-hand navigation bar and select FGENESB. This tool lets you annotate genes on an input genome using a Markov chain trained on some similar organism. In the output,...
by G-Do
Tue Nov 28, 2006 6:40 am
Forum: Molecular Biology
Topic: RNA extraction of a very, very small quantity of tissue
Replies: 6
Views: 5457

Hi Tapi, You said: "...and I think that this type of kits amplify preferently the most abundant transcripts so the results wouldnt be valid." That is not categorically true. Some amplification kits are better than others, and new protocols are often put on the market without strong QC (mea...
by G-Do
Thu Nov 23, 2006 6:21 pm
Forum: Bioinformatics
Topic: Protein Interaction Information Visualisation
Replies: 6
Views: 5537

I can't speak very well to the process, as I'm just a beginner at regulatory network / metabolic network / interaction network analysis myself, but one popular free tool is Cytoscape: m You might read their cited literature to get a better handle on this stuff. The major network annotation that most...
by G-Do
Thu Nov 23, 2006 6:12 pm
Forum: Molecular Biology
Topic: RNA extraction of a very, very small quantity of tissue
Replies: 6
Views: 5457

Hey there, Have you already got the RNA? If so, you can amplify it indefinitely using one an mRNA-amplification kit, like the one available from Ambion: m The messageAmp kit will turn a small sample of mRNA into a nigh-limitless amount. I have used it with great success in my own research (going fro...
by G-Do
Thu Nov 23, 2006 6:00 pm
Forum: Bioinformatics
Topic: Want to identify common nucleotide motifs
Replies: 5
Views: 6103

Go to; http://www.ncbi.nlm.nih.gov Then go for BLAST --- Nucleotide compare Progamme or FAST ---- Proteom compare programme You will get results in 15 sec. I oftnely use this site. It is a large database site. One of my favorites. How is that supposed to help find ~100mer motifs in many input oligo...
by G-Do
Sun Nov 19, 2006 5:52 am
Forum: Bioinformatics
Topic: Want to identify common nucleotide motifs
Replies: 5
Views: 6103

Hi biznatch, Do you have any reason to expect that the elements controlling these genes' regulation are 100bp in length? Do you have any reason to expect that the elements controlling these genes' regulation are in the exons/introns, as opposed to the 5'UTR/3'UTR and 10kb promoter? I can tell you no...
by G-Do
Thu Nov 16, 2006 3:33 pm
Forum: Bioinformatics
Topic: Want to identify common nucleotide motifs
Replies: 5
Views: 6103

Hi biznatch, Which motif-finders have you tried? MEME is my favorite. However, I'm not sure that it can be used to discover motifs in such a large sequence set - typically, the bigger your sequences are, the more difficult it is to establish the statistical significance of any particular discovered ...