Thursday, December 4, 2008

The DNA Network

The DNA Network

Sweet news about a spoonful of sugar [The Navigator - Navigenics Blog]

Posted: 05 Dec 2008 12:15 AM CST

Michael Nierenberg, M.D.

image"All natural sweetener."

"Just like sugar."

"Zero calories."

Artificial sweeteners have been billed as the perfect alternative to sugar – a way for weight-conscious adults to have their cake and eat it, too. Yet more and more, a modicum of restraint is certainly advised when reaching for those packets of aspartame or sucralose.

While it's true that sugar alternatives are much sweeter than table sugar, requiring smaller amounts to achieve the same level of sweetness, they won't necessarily help you lose weight and keep it off. Simply taking the sugar out of a slab of chocolate cake doesn't miraculously transform it into a low-calorie, high-nutrient food. At the end of the day, it's still a slab of chocolate cake, with calories from flour, shortening, eggs, and other ingredients like nuts. So if you eat too much of it, your body will be the worse off from the encounter, regardless of which sweetener is used.

In fact, a growing body of evidence suggests that, when compared with sugar, no-calorie sweeteners may actually make it harder for people to control their body weight.

Scientists a step closer to understanding AIDS immunity [My Biotech Life]

Posted: 04 Dec 2008 08:06 PM CST

HIV colorI don’t usually get my science news from the Portuguese paper but this article caught my eye. Amazingly I didn’t pick this up in the huge amount of science and immunology feeds I subscribe to but I digress.

It seems that researchers are a step closer to understanding how HIV seropositive individuals can live with the virus for years with out taking antiretroviral drugs and contracting AIDS.

This small population of under 0,2 percent happens to have a way to keep their CD4+ count at a normal level while the CD8+ lymphocytes stick to their job maintaining viral levels as low as 50 viruses per milliliter of blood. Normally this is not the case and CD8+ lymphocytes can’t keep up with the viral activity.

I have always thought that the key to understanding how to overcome or prevent HIV/AIDS was to study these individuals that seem to be immune. This is not a simple virus but I do think science is making progress, one small step at a time.

[Image: Wikipedia:HIV]

Scientists a step closer to understanding AIDS immunity

Statistics on next-generation sequencing platforms [Genetic Future]

Posted: 04 Dec 2008 05:37 PM CST

David Dooling from PolITiGenomics has put together a handy little table for genomics nerds like me: statistics on the output of the various iterations of the three major competing second-generation DNA sequencing platforms (Roche's 454, Illumina's Solexa/Genome Analyzer and ABI's SOLiD).

It's probably a little inscrutable for non-genomicists, but it helps to provide some insight into the sheer scale of the DNA sequence data currently being produced by large-scale sequencing facilities. A single Illumina GA II machine, for instance, churns out on the order of 8 gigabases of sequence (that's almost three human genome equivalents) every week. Now consider that my workplace as of this week has 37 Illumina machines, all running hot pretty much 24/7 (well, most of the time), and you have some sense of the quantity of sequence currently being generated - and of the informatics infrastructure required to store, manage and process that volume of data.

Read the comments on this post...

Going (pro)Rogue [Bayblab]

Posted: 04 Dec 2008 01:59 PM CST

With a recent election overshadowed by Obamamania to our south, the Canadian government decided to draw some attention to itself with a recent parliamentary crisis. In that election, the Conservative Party earned more seats than any other single party, but not enough to command a majority of the 308 seats in the House of Commons. Still, they were asked by the Governer General, to form a minority government with Stephen Harper as Prime Minister. This is what normally happens, and what everybody expected (read: took for granted) based on the distribution of seats after the election. Typically for a minority government to last, they have to play nice with the other parties to reach compromises in order to get a majority of votes in the house. Mr. Harper somehow didn't realize he didn't have a majority and pushed an economic statement that was sure to not sit well with the Liberal, NDP and Bloc Quebecois members that make up the majority of the seats in parliament. They didn't like it, decided "hey, we're in the majority, if we band together we topple this government and try to replace it with a coalition made up of the majority of MPs". This was to happen Monday in a vote of confidence on Harper's ability to lead.

So, less than two months after a federal election, and even less time sitting, Harper saw the writing on the wall and decided instead of letting government, you know, govern (during this worst economic downturn since the Great Depression, yadda, yadda) to take his ball and go home, suspending parliament (called proroguing) to buy time to figure a way out of this mess. The Governer General agreed to his request this morning. So until Jan. 26, this parliamentary showdown has been averted, as well as the ability of parliament to do anything. But it has made for interesting times, one of the most interesting parts being the revelation of how few Canadians understand how their government works. Hopefully this has been an opportunity for learning. Larry Moran at Sandwalk has been following what he calls Conservative Lies more closely, and hopefully we can also clear up some misconceptions here at the Bayblab. First an explanation of our parliamentary system (from a Sandwalk commenter):
Let me refresh your memory as to how a Westminster-style Parliamentary system works. The people of Canada do NOT elect a government; they elect members of the House of Commons. The members of the House choose the government. By tradition, the legal Head of State (the Governor-General, in our case) asks the leader of the party with the most seats in the HoC to form a government; that is, to form a cabinet to try to pass laws.

If the majority of the members of the HoC lose confidence in the ability of the minority, they have the right to express this through non-confidence votes or votes against bills that deal with government's ability to spend money.

In this case, the Prime Minister must ask the GG to dissolve Parliament and call an election (remember, the GG is our head of state, and the only one who can call an election). The GG has the legal option to ask another party or parties to form a government, if he or she feels that this party or parties has the confidence of the majority of the HoC (for instance, if a majority of the legally elected members of parliament got together and forged a formal agreement...).

This proposed coalition is absolutely in keeping with Parliamentary law and tradition. It has been forged by people who have been legally elected by the people of Canada. Of course, the GG is completely within her rights to call an election at the request of the Prime Minister. She will have to decide whether it is in Canada's best interest to hold the 4th election in 4 years, and second election in 3 months, or if it is in Canada's best interest to bring in a duly-elected government that has the pledged support of the majority of the HoC, and has proposed specific measures to rectify certain issues currently facing us.
Some of the misconceptions that have been repeated during this debacle:
I voted for Stephen Harper for Prime Minister.
In Canada, a federal election is a series of local elections. Unless you live in a specific riding you never cast your vote for Harper (or Dion, Layton, Duceppe). Yes, many people vote based on party affiliation and pretty much all the time the Prime Minister is the leader of the party with the most seats but the reality is that you vote for a parliament, not a governement.

The Liberal/NDP/Bloc coalition...
The Bloc Quebecois would not be part of a coalition governement (they would have no cabinet positions, for example). They have simply agreed not to bring down a proposed coalition government within 18 months (which some reservations, I would imagine). Furthermore, the accusations of the coalition 'being in bed with separatists' are divisive, offensive appeals to emotion. It suggests that the duly elected officials from Quebec shouldn't have a role in government and that votes from that province shouldn't carry as much weight as from the rest of the country.

A coalition government is undemocratic
Which is more undemocratic: a broad, cross-party agreement between elected MPs who represent the majority of Canadian voters, or shutting down government and locking them out? A coalition government (common in many other democracies where minority governments are the norm) or a PM going (pro)rogue?

Read the coalition agreement here and their economic plan here [pdf]

McClendon: Home for the Holidays Thanks to DNA Testing [DNA Testing Blog]

Posted: 04 Dec 2008 01:53 PM CST

Robert McClendon, exonerated by DNA testing performed by DDC, is home for the holidays for the first time in 18 years. He was released August 11 after DNA evidence cleared him of a child rape charge. McClendon is the 7th Ohio exoneree (read about the other six in this Columbus Dispatch article) and his is the [...]

Photo session [Mailund on the Internet]

Posted: 04 Dec 2008 01:45 PM CST

Hi, sorry I haven’t written anything in ages.  I’ve been completely swamped in work on a genome project, but one I don’t think I can write about until the paper is out, and since I haven’t thought about much else the last couple of weeks I’ve been silent here.

Don’t worry, I’ll tell all about it when we are getting closer to publication.

Anyway, a few days ago I had a photo session related to the project (and a previous project) and you can see some of the pics below.

(Photographs by Jesper Voldgaard).

As you can no doubt guess from the pictures, some abes are involved in the project…

Science nerds can't score [Bayblab]

Posted: 04 Dec 2008 12:49 PM CST

A recent study in the journal of sexual health (castration or institutional subscription required) looking at the prevalence of chlamydia screening uncovered some interesting facts about university student sexuality:

"Arts students were younger, more likely to be sexually active and to report having little or no knowledge of chlamydia. Males in the study were less likely to have had sex as a group compared to the group of females in the sample. Science students were also less likely to have had sex compared to their counterparts in other faculties."

So why are science boys unable to seal the deal? According to the authors:

"Boys also start having sex later than girls, [...] And who are the people at unis that go to the rave parties and the bar? ... it's not the nerdy boy science students. They're carrying on doing their experiments, going to the library or doing their assignments."

Ouch. Is that true? I thought that was only the engineers!

Also while you're there, you can check out these papers on understanding oral sex or on how impotent males feel vibrators, in the same issue of the journal.

"Free" large scale sequencing for Department of Energy related projects ... [The Tree of Life]

Posted: 04 Dec 2008 12:19 PM CST

Interested in Department of Energy-related missions such as global carbon cycling, alternative energy production, and biogeochemistry? And want some genomes, metagenomes, or other things sequenced that are relevant to these topic areas? All you have to do is write a proposal to the Joint Genome Institute (JGI) Community Sequencing Program, get it selected by the review committee, and then the JGI will do the sequencing and some analysis for you.

Go to this web site to learn more ....JGI - CSP Overview.

Doubts on the Cancer Stem Cell Hypothesis [Bayblab]

Posted: 04 Dec 2008 10:46 AM CST

The cancer stem cell hypothesis states that a tumour consists of a subpopulation of cells that give rise to all the heterogeneity found in the cancerous tissue. These cells have some common markers and characteristics of normal stem cells. These, the hypothesis suggests, give rise to the tumour and are therefore the best target for cancer therapeutics.
A recent paper in Nature seems to have caused a bit of a stir in the cancer stem cell field. (first born child or expensive subscription required). Part of the evidence for the cancer stem cell hypothesis is that when human tumour cells are implanted into an immunocompromised host mouse only a small percentage of these cells are capable of reproducing a tumour. This new paper demonstrates that if the host is more immunocompromised then a larger number of cells are capable of reproducing a tumour, instead of only as low as one in a million cells to as many as one in four.
A wired artcle on the work really tries to stir the pot:(free)
"The controversial idea that all tumors are created by cancer stem cells received a setback Wednesday."
There are also some great summaries of what the impact of this paper may be in this field of research in Nature. News and Views. Nature News. Again you will have to sell organs or have an institutional subscription.

I can't say that I know much about cancer stem cells, only that I find the hypothesis interesting. As the summaries suggest, I would not find it surprising that some cancers do indeed consist of a subpopulation of cancer stem cells wereas others do not. I also don't know if specifically targetting cancer stem cells is going to cure a patient since these cells, while capable of causing a recurrance don't cause the symptoms of cancer.
I also don't follow the logic that the cancer stem cells are the reason that chemoresistance occurs, and other hypothesis that have come out of the cancer stem cell hypothesis.
That being said I certainly don't find this study to be blow to the cancer stem cell hypothesis.

ABRF 2009 is just around the corner [FinchTalk]

Posted: 02 Dec 2008 09:11 AM CST

Karen Jonscher said it best, "Reminder - register now for the [ABRF] Satellite Educational Workshops!" In her email to the ABRF email forum, Karen reminded us that the ABRF Education Committee is...

No comments: