New Research in Prenatal DNA Sequencing

I didn’t build in quite enough buffer time to get started on my next reader-initiated travel blog (it’s a secret – I’m not telling until I get there). I’m going to shoot out of the door in this next break. There may be a cat picture for my 3:30pm post. Just to warn you.

If you want to send me somewhere in the Minneapolis area, simply donate $10 to SSA and in the Topic Suggestion box write “Visit” and a place in Minneapolis.

Send MOAR money to the SSA! Put my name in the Blogger spot of the form, and request one of my reader challenges or suggest a topic that you’d like me to write about. Please? I’ll beg. On video. In song if need be. It only gets wackier around here the later we get into this.

We haven’t had any science yet. How about this cool story?

Invasive fetal (or prenatal) testing is serious business. Chorionic villus testing and amniocentesis can be used to help detect chromosomal abnormalities or disorders, but there is a small but noted risk of miscarriage with these procedures. On June 6th the Los Angeles Times reported on research being performed that would allow much less risky sequencing of fetal DNA:

To set about their task, Shendure’s team started by sequencing the genome of an anonymous pregnant woman, using a complete sample of her DNA obtained from her blood cells. They also sequenced free-floating DNA fragments extracted from her blood plasma, repeating their work until they had decoded every part of the human genome 80 times.

That plasma contained a mix of 10% fetal DNA and 90% maternal DNA, all in tiny fragments. The scientists needed to be able to tell which pieces were from the mother and which belonged to the fetus.

To solve that problem, the scientists relied on the fact that genetic material is inherited in long strands of DNA, called chromosomes — and that tiny genetic variations on the same chromosome are usually inherited together, in blocks known as haplotypes. If a given haplotype was present in the fetus as well as in the mother, it would be detected in the plasma in extra amounts.

The scientists also sequenced the father’s DNA, which was extracted from saliva. This allowed the team to figure out whether genetic variations in the fetus that didn’t match the mother were inherited from the father or were new mutations. On average, about 50 new mutations show up in a fetus.

The scientists checked their results against a blood sample taken from the baby’s umbilical cord after birth. Their calculations were more than 98% correct, they found, and they had detected 39 out of the 44 new mutations. None of those mutations had known medical consequences, the researchers said.

This approach could be used to devise a single test to screen for the 3,000 known disorders that are caused by mistakes in single genes. Individually, they are rare, but together they affect about 1% of births.

This is post 19 of 49 in the SSAweek Biodork Blogathon. Donate to the SSA today! Read more about my reader challenges here.

New Research in Prenatal DNA Sequencing

Lyme Disease – Always Learning.

If you’ve ever been camping or hiking or hunting or had an outdoor pet or gone anywhere near a tree or have a TV or know anyone who fits any of these situations, you’ve probably heard of Lyme Disease. I live in Minnesota, land of forests and lakes, big-ass mosquitos and lots and lots of ticks. I think it’s only natural and healthy for me to have an interest in the subject.

Disclaimers: I am not a doctor, nor an infectious disease researcher, nor a specialist on Lyme Disease or post-treatment Lyme disease syndrome (PLDS). I do have experience with serological testing, immunoassays and laboratory science. This blog post was inspired by a press release about antibodies linked to long-term Lyme symptoms. I welcome and appreciate any comments, corrections or conversation that are expressed with respect, and in the case of claims, with references. Also, I hold up the Centers for Disease Control and Prevention (CDC) as the gold standard for dissemination of accurate and reliable public information on infectious disease. If you think that the CDC or “western medicine” is misguided or intentionally evil, or that all American physicians are controlled by the mob (hat tip to an earlier commenter), you should probably stop reading here.

Continue Reading

Lyme Disease – Always Learning.

Social Science and Stuff

Omigosh, I’m so excited to be going tonight to Party with the Pharaohs, the Science Museum of Minnesota’s first Social Science event for adults. I set up a page on Eventbrite to organize all of my fabulous science-minded friends for this evening, and some of y’all even accepted! I’m giddy. It’s going to be a blast, what with the mummies and the movies and the food and the cash bar and the live animal exhibition and the omnitheater and wheee!

So until tomorrow when I can tell you about how all of that went, here are some articles that caught my interest today:

  • Verbal and physical attacks on students are encourged by extremist animal rights group, Negotiation is Over. Reported on by Pharyngula, Respectful Insolence and Speaking of Research.
  • SlutWalk – A Toronto event that is speaking out against the idea that women who dress like “sluts” get what is coming to them. Covered by Almost Diamonds.
  • Abortion Crackers – What happened when a pro-choice store owner in a small town encountered an anti-choice consumer. Written by Liberal House on the Prairie.
Social Science and Stuff

Secret Powers of Time

Last night I was reintroduced to the name of Professor Philip Zimbardo.  I remember discussing his Stanford Prison Experiment in college, but I couldn’t have told you that he was the one involved with it.

I saw this video of one of his lectures yesterday.  It was remarkably engaging!  The lecture is fast-paced – he jumps from topic to topic, and along the way manages to hit on differences in world and regional cultures, teaching theory, business, multi-tasking, family values, and many more.  The visuals are unique and kept me rooted to my seat.  After it was over, I couldn’t believe that I had been watching this video for 10 minutes.

A cursory google search tells me that Dr. Philip Zimbardo has only worked on about a gazillion and a half projects, including a couple dozen books and articles.  A youtube search for “Philip Zimbardo” brings up 237 videos about the man.  So I know what I’ll be doing tonight!*

Thanks to Aaron M. for posting the Secret Powers of Time video on Facebook.

*Well, tomorrow night, maybe.  Tonight I’m going to see Michael Shermer at the University of Minnesota!

Secret Powers of Time

Would you like some powdered water with that?

Dry Water!

Military Intelligence!

Honest Politicians!

Amateur Expert!

Living Dead!

You get the idea. 

How the heck does one make dry water?  Well, they cheat, sort of.  The powdered water is one drop of “wet” water surrounded by modified silica.  So the water itself isn’t powdered, but it’s stored in a way that keeps the water droplets from coalescing.

Did I mention that the headlines about this story are pun-ishingly horrible?  “Dry water making waves!” “Dry water could make a splash commercially”  *shudder*

I heard about this story on Skeptic’s Guide to the Universe (SGU – episode #267) in the Science or Fiction segment.  Several news sources have done a decent job of summarizing the American Chemical Society (ACS) presentation by Dr. Ben Carter (a researcher for study lead, Dr. Andrew Cooper) .  

According to Science 2.0 silica-encapsulated water was first discovered in 1968 by the cosmetic industry.  An article in Scientific American describes the “discovery” of a process to create dry water by coating water in a “hydrophobic powder” in 2001.  It sounds like the technology has been here for a while, but we haven’t yet figured out what to do with it. 

The current focus is on developing dry water technology for use in commercial applications and perhaps in carbon dioxide absorption, which could be useful for that little global warming problem we’re not dealing with.

From an ACS news release:

BOSTON, Aug. 25, 2010 — An unusual substance known as “dry water,” which resembles powdered sugar, could provide a new way to absorb and store carbon dioxide, the major greenhouse gas that contributes to global warming, scientists reported here today at the 240th National Meeting of the American Chemical Society.

The powder shows bright promise for a number of other uses, they said. It may, for instance, be a greener, more energy-efficient way of jump-starting the chemical reactions used to make hundreds of consumer products. Dry water also could provide a safer way to store and transport potentially harmful industrial materials.

and later in the article:

Dry water was discovered in 1968 and got attention for its potential use in cosmetics. Scientists at the University of Hull, U.K. rediscovered it in 2006 in order to study its structure, and Cooper’s group at the University of Liverpool has since expanded its range of potential applications.

One of the most recent involves using dry water as a storage material for gases, including carbon dioxide. In laboratory-scale research, Cooper and co-workers found that dry water absorbed over three times as much carbon dioxide as ordinary, uncombined water and silica in the same space of time. This ability to absorb large amounts of carbon dioxide gas as a hydrate could make it useful in helping to reduce global warming, the scientists suggested.

Cooper and colleagues demonstrated in previous studies that dry water is also useful for storing methane, a component of natural gas, and may help expand its use as a future energy source. In particular, they hope that engineers can use the powder to collect and transport stranded deposits of natural gas.

It sounds like things are proceeding along…


Would you like some powdered water with that?