leonardo

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bio	website	guizzetti.ca
	location	London, Ontario
	age	26
visits	member for	1 year, 2 months
	seen	May 19 at 3:03
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I'm Leo and I'm passionately involved in biology and running, and interested in programming and cooking.

	3,816 reputation	bio	website	guizzetti.ca	visits	member for	1 year, 2 months
528 badges		location	London, Ontario		seen	May 19 at 3:03

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May 3	comment	How is gene expression estimated? @SteveLianoglou: MS is not my expertise, but that is not my understanding (this may vary with the type of MS used, e.g., TOF-SIM, GC). Successful identification of proteins via MS is dependent on abundance but also peptide fragment length (read: experimental optimization). MS can theoretically get down to 1 fmol resolution. Check this out for more information: lab.rockefeller.edu/chait/pdf/08/08_eriksson_wiley.pdf
May 1	comment	How is gene expression estimated? @WYSIWYG: no, I guess not, but it is certainly quantitative and highly sensitive, so I'm (lazily) throwing it in with the more traditional methods. ;)
Apr 30	comment	How is gene expression estimated? It's my understanding that scientists often use these microarray experiments as high-throughput screening methods to identify either candidate genes or gene networks. If the data from one such experiment is truly to be trusted, it must always be followed up by traditional biochemical methods (mass spec, western blot, ELISA/RIA, microscopy).
Mar 30	comment	205 nm UV-Vis readings You would appear to be correct. What is not shown is relative absorbance of protein and nucleic acid at 205 nm. NB: I have not followed up with the two references linked from that page I posted.
Mar 22	comment	Complexity in creating transgenic animals (e.g., mice) Hmm...I forgot to mention the obvious problem with combinatorial effects that you brought up. I was assuming that the effects of single mutations were already known. These are interesting points you bring up.
Mar 21	comment	What are usable Sum formulas for Proteins? Hi mart, I would say the edit was better, but (to me) you still don't seem clear about what you need. Considering sulfur in proteins, only cysteine (Cys) and methionine (Met) use S, and a subset of proteins are sulfonated. The proportion of Cys/Met in proteins varies widely, so 11-19% seems reasonable, and maybe even on the high end. Also keep in mind proteins are not static entities in a cell, they are always in flux, being broken down and synthesized. I'm not certain you can reduce it to a static chemical formula.
Mar 18	comment	Sequencing rtPCR product Theoretically, you will still end up with a specific PCR amplicon, so you can sequence it with the same primers used for rt-PCR. By the way, do you mean real-time or reverse transcriptase PCR?
Mar 12	comment	Are descriptive statistics sometimes more useful than tests of significance? I think this is a valid question to as Biology because the standards of publication are different between fields of study. I'm sure any statistician will have problems with biological literature. You may have found an important, and biological effect which you can describe qualitatively. When it comes time to publish, if you cannot show the different quantitatively (and likely with a stats test), you limit yourself to publishing in a lower-tier journal.
Mar 11	comment	Alternatives to TBE buffer for denaturing polyacrylamide gel electrophoresis of DNA and RNA? A neighbouring lab uses the sodium borate buffer for genotyping in agarose gels. They can run the gels at 10% higher voltages than what I push my TAE buffer at (95V; 20 mA max). Is there a particular reason to use denaturing poly-acrylamide or to run them super fast?
Feb 16	comment	Does ethanol destroy RNase? In short, RNA contamination and degradation are super easy in a lab setting. We have an RNA-only dedicated workbench in our lab which gets treated with a "broad spectrum" RNAse-degrading solution before any RNA work is conducted.
Jan 14	comment	How should I ship plasmids? This is the best way to go. You can also wrap the filter paper in a bit of cling wrap just in case.
Jan 6	comment	What is the purpose of the adrenal medulla? I think we're agreed then: the adrenal medulla is a complementary organ to the mass response of the SNS. It is also more than that, acting as an endocrine tissue, which does take input from other endocrine tissues to modulate any sustained responses to stress.
Jan 5	comment	Is there any difference in terms of personal healthcare between complete DNA sequencing and SNPs genotyping? Genotyping can tell you more information than just SNP, for instance you could easily amplify a region of a gene for sequencing to determine if there are more serious errors.
Jan 4	comment	Is every part of a virus important for replication? That's right. Everything works together. What @Alan Boyd has pointed out is that 3 genes can be removed, and that HIV virus can still make more viral particles that are capable of replicating and reinfecting. Those 3 genes seem to play more nuanced roles in the dynamics of an HIV infection cycle.
Jan 4	comment	Is every part of a virus important for replication? That's correct. The RNA genome of HIV encodes genes for the 9 proteins mentioned above. These proteins each serve some function. These proteins together with the viral envelope, let the virus enter a susceptible cell, integrate with the host's genome and later replicate itself. For example, you couldn't just inject someone with the RNA genome and expect to see HIV virus production.
Jan 3	comment	Atomic force microscopy: depth penetration? I was under the impression that AFM works superficially on specimens.
Jan 3	comment	Is every part of a virus important for replication? @Alan Boyd has given a detailed answer regarding HIV.
Jan 2	comment	Simulating Cell differentiation There is plenty of literature that shows information is stored in at least 3 major places. DNA is the lowest level of information (raw 'bits' of storage), then you have epigenetic modifications which can modulate the level of DNA accessibility and expresion (which are still not fully understood how these are inherited). The last important information encoding is at the level of protein and can be as trivial as a protein switched on/off, or embodied in the behaviour of a whole network of protein interactions. We are just starting to grasp the latter.
Jan 2	comment	Simulating Cell differentiation Basically to answer this question, people are devoting entire careers towards this goal. Even a simplified simulation can quickly become a PhD thesis if you so choose. I will assume you want a simulation which takes into account some level of biochemistry since the simple calculation of dividing cells is trivial. What you should decide on up front is to what depth of information do you want to simulate (eg, can you make some simplifications to make your model less realistic but more manageable)?
Dec 30	comment	Bradford Protein Assay Hello there. This looks like a homework problem. Before one of us helps you, what have you tried so far?