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Apr
2
comment Why do women live longer than men?
Depression is more common in women not in men: nimh.nih.gov/health/publications/depression/… Also, I would say that the roots of different behaviors are most likely to be in the genes since lifespan of men are shorter than women in most cultures. My guess would be the effect of testosterone. Men are more prone to take risks - even the life threatening ones - because of this hormone while women are more likely to choose the safer path.
Mar
22
comment Does DNA Ligase look for complementarity in sticky ends?
I have solved the problem by increasing the time of digestion and preparing new plates. Now I get only a few colonies when there is no insert - probably there are still some single digests and ligase repairs the nick- and it is not a major problem anymore. I have read about your suggestion elsewhere but there was only one such site between my sites and the enzyme for that was rare & expensive so I followed another approach as I mentioned. Apparently I got false positives because my enzymes were sloppy and my plates were a bit old.
Mar
21
comment Oligonucleotide purification with desalting
Well, people do ligate annealed oligos directly to cut vectors. Actually it has been said that cloning small inserts is much easier than large inserts but I have no experience on this of course. If you are not familiar with oligonucleotide annealing for ligation and cloning, this may help you: addgene.org/plasmid-protocols/annealed-oligo-cloning
Mar
19
comment Are restriction enzymes active at −20 °C?
I do not know, I have never had star activity before. Your answer makes sense and I think like that too but I posted the question here because there was no answer to this on the internet and I thought maybe someone here has an experience on this.
Feb
17
comment Does DNA Ligase look for complementarity in sticky ends?
I use around 300ng plasmid for transformation. Some say use less but they have no logical explanation unfortunately. Regarding incomplete digestion: I have thought of it too. However, since the sites of two enzymes are very close (only 31bp in between the sites whereas the vector is around 6kb) when I extract the cut band from the gel, I also extract single digests and there seems to be no way to be sure if I am extracting only the double digests or not. I can give phosphatase treatment a shot but do you have any idea about the question regarding ligase ?
Feb
17
comment Does DNA Ligase look for complementarity in sticky ends?
Unfortunately I am not doing that because some people can make cloning work without phosphatase treatment in our lab and I am mostly following their procedures. At least so far.
Dec
3
comment How to find miRNA binding sites on a specific gene?
Bioinformatic part of your answer may be better that is why i did not give full credit. For those who also would like to know more about tools for finding miRNA target site they could check this article. It is really good: journal.frontiersin.org/Journal/10.3389/fgene.2014.00023/full Thanks for reminding me of the question by the way.
Oct
26
comment How to find miRNA binding sites on a specific gene?
yes "For the time being i am just looking for a good candidate list of miRNAs for a specific gene (the gene of my choice)". So, i want to choose a specific gene in the database and i want that database to show me a list of mirna's that can bind to that gene's 3'UTR . Also, I want to see the accountability of mirna binding via a scoring method such as mirSVR. I have so far found only mirSVR and the mentioned website but are there other ways and what is the best way to search for that in the literature? sorry if i am not maintaining correct terminology, i am relatively new in this.
Oct
26
comment How to find miRNA binding sites on a specific gene?
Thank you for the answer but my question was actually a lot more simpler. For the time being i am just looking for a good candidate list of miRNAs. I have found a website (microrna.org/microrna/home.do) for this and it is based on mirSVR score. Is this a good way of picking candidate miRNA's? Are there other ways of finding candidate miRNA's that are based on different scoring algorithm?
Jun
18
comment what is the difference between “cistron” and “gene”
off the top of my head: cistron and gene are equivalent to each other but cistron is a bit old-fashioned. Consider two phenotypes in different individuals belonging to certain organism; let's say both of them are recessive and you cross these phenotypes with one another. If you see wild type phenotype in the next offspring then it means your phenotypes reside in different regions in the genome and these regions were first defined as cistrons. Of course it then turned out to be much more complicated than that and people started using the term gene more often
Jun
13
comment What is Pan for in pan-caspase?
there is no specific context but i now realized that it is usually used as pan-caspase inhibitor in the articles i was looking at. just to be sure: can we then say that pan is the opposite of specific?