Geoff's story links

I was recently alerted to this paper from PLoS about the deletion of ultraconserved elements. The researchers knocked out four different ultraconserved elements and it had no effect on the mice. Under normal conditions these sequences of DNA don't seem to matter, so why has there been enough evolutionary pressure for them to be so perfectly conserved?

Interesting article on a novel way of selectively killing cancer cells based on homozygous deletions. There are some interesting ideas in this paper, but what is really unique is that ideas are all that is in the paper. I think the "idea" paper is becoming more and more rare, but even as recently as a few decades ago, these sorts of papers were an important part of moving science forward. I'm glad PNAS will still publish this type of paper.

Zotero is a new extension for Firefox that looks like a great new challenger to EndNote. It is a free, open-source, platform-independent reference mananger that looks like it has a lot of great features. I haven't played around with it much yet, but when I do I will post a review in the blog section. I'd be interested to hear an opinion from anyone who has tried it.

Big tech players are starting a big push into healthcare. It may take some time, but overall this is a very good outcome for patients.

Funny blog post about people "borrowing" reagents in the lab during grad school. My favorite experience with this was discovering that the "lab stock" of protease inhibitors was actually a post doc's private stock. This was discovered after I asked her if I could borrow some since the lab stock was gone. She promptly went to the same box I had been looking in (and taking from) and found that it was gone. My famous last words were, "Oops, I thought that was the lab stock......."

This is an interesting editorial in Nature about performance enhancing drugs in sports. They basically comment that maybe it would be better if they just let athletes use performance enhancing drugs. I have brought this up a few times as well just to get a rise out of people, but the author makes some valid points. The idea does bring to mind the old Saturday Night Live sketch, the All Drug Olympics.

This is great news! I don't need to diet, I can just hang out with skinny people. Curtis has volunteered for anyone in need of skinny friends.

Finally I can cut back on my 20 servings of fruit and vegetables a day. The one main caveat to this study is that it is based on differences in literature distribution and counseling that was given to the two groups. As brought up in the article, just giving someone literature doesn't mean they are actually following it.

This PNAS article describes using a lectin microarray to analyze the various changes that occur in the glycosylation status of cells. This powerful new approach opens up the world of glycosylation to global analysis. Such an approach could be a source of new biomarkers and treatment targets in a wide variety of diseases, such as inflammation and cancer.

This paper from Craig Venter's lab came out a few couple of weeks ago in Science Express. Many people have declared this a great breakthrough for science, while others have tried to downplay it's significance. I think it is a promising step forward in synthetic biology, as genome transplantation is key to the whole process.

Yet another stem cell bill that eases restrictions on stem cell research has passed in both the House and Senate. Will it get vetoed?

Three independent labs are reporting this week that they have confirmed last year's finding that inserting 4 genes into mouse skin cells is sufficient to convert them into embryonic stem cells. This is a huge advance, especially now that it has been confirmed by so many indepenent labs. Irving Weissman is quoted as saying, “From the point of view of moving biomedicine and regenerative medicine faster, this is about as big a deal as you could imagine." I'll follow up with more links, etc. as I find them.

The American Society of Clinical Oncology (ASCO) Meeting was held last weekend. This link hits the winners/losers of this year's ASCO meeting.

There isn't really anything new in this article, but I think it's crazy that removing half of someone's brain is possible.

This article in the May issue of Cancer Cell describes, "bacterially derived nano-sized particles (minicells) for encapsulation of a range of different chemotherapeutic drugs." This is another derivative of liposome technology to deliver higher doses of traditional chemotherapeutics. This technology is exciting because it appears to be effective at even lower doses of drug than current liposome technology.

This series of articles from Science includes a wide range of advice for PhD students, from attending meetings to planning and time management. Some of the articles may not be relevant for everyone, but there are some good suggestions.

The FDA yet again shows that their drug approval process has no consistency. This new breast cancer drug from Glaxo Smith Kline was approved without any data showing it improved patient survival. I'm in favor of the FDA approving more drugs, but how can they approve this drug a week after putting a black box warning on an entire drug family due to media hype over a very small trial (erythropoiesis-stimulating agents)?

Rats self-administering intravenous cocaine.......I'm not sure what else needs to be said. The study does seem to provide some nice data supporting a biological explanation for impulsiveness.

Cool new paper from the Mullins lab at UCSF. Be sure to check out the supplementary movies.

Cool paper in the latest issue of PNAS. They demonstrate site-specific knock-in of a gene in human cells. This would be really great if it works well.

It is generally thought that the inactive X chromosome (Xi) in female cells is silenced through methylation of CpG islands. This paper demonstrates that on a global level the Xi is actually hypomethylated and the active X is hypermethylated. I haven't made it all the way through the paper, but it seemed controversial enough to post now.

This paper reveals that smelling nutrients shortens the life-span extending effects of caloric-restriction in fruit flies. Although caloric restriction to increase life-span is not common practice right now in humans, it is interesting to think that smell could be involved in determining how long we live.

This review in the latest issue of Science attmepts to synthesize data from a number of studies on standardized tests. Their conclusion is that standardized tests are effective at predictiing success. The problem is, you have to go to the articles they are citing to determine if this is really true. I still have a hard time believing that the GRE is really going to determine if people are going to succeed in a PhD program.

This article proposes a novel model for regulating organ size. It also describes the differences between organ size regulation in pancreas and liver. I'd be interested to know what a person with more stem cell bakground than me thinks of this paper.

A nice feature for the 10 year anniversary of Dolly, the cloned sheep.