Posts about Madison

Image of the Common Cold Virus

image of the rhino virus (human cold)image created by Dr. Jean-Yves Sgro, Institute for Molecular Virology, University of Wisconsin-Madison, from published X-ray data. larger image

Sequences capture the code of the common cold

Conducted by teams at the University of Maryland School of Medicine, UW-Madison and the J. Craig Venter Institute, the work to sequence and analyze the cold virus genomes lays a foundation for understanding the virus, its evolution and three-dimensional structure and, most importantly, for exposing vulnerabilities that could lead to the first effective cold remedies.

“We’ve had bits and pieces of these things for a long time,” says Ann Palmenberg, of UW-Madison’s Institute for Molecular Virology and the lead author of the new study. “Now, we have the full genome sequences and we can put them into evolutionary perspective.”

As its name implies, the common cold is an inescapable, highly contagious pathogen. Humans are constantly exposed to cold viruses, and each year adults may endure two to four infections, while schoolchildren can catch as many as 10 colds.

“We know a lot about the common cold virus,” Palmenberg explains, “but we didn’t know how their genomes encoded all that information. Now we do, and all kinds of new things are falling out.”

The newly sequenced viruses also show, says Palmenberg, why it is unlikely we will ever have an effective, all-purpose cold vaccine: The existing reservoir of viruses worldwide is huge and, according to the new study, they have a tendency to swap genetic sequences when cells are infected by more than one virus, a phenomenon that can lead to new virus strains and clinical manifestations.

The ability of different cold virus strains to swap genes and make entirely new strains was thought to be impossible, notes Claire M. Fraser-Liggett, a co-author of the new study and director of the Institute for Genome Sciences and professor of medicine and microbiology at the University of Maryland School of Medicine. “There is the possibility that this could lead to the emergence of a new rhinovirus strain with fairly dramatic properties,” says Fraser-Liggett.

Related: Common Cold Alters the Activity of GenesLearning How Viruses Evade the Immune SystemLethal Secrets of 1918 Flu Virusimages of snowflakes

Promoting Bio-Literacy

Wisconsin State Herbarium tries to ‘counteract bio-illiteracy’

“In a past century people could go outside and name the flowers or trees,” said Ken Cameron, the herbarium’s director. “Now you take a kid outside and the most they can say is, ‘It’s a tree.’ If we can get students in and get them excited, then I think we’ve helped to counteract bio-illiteracy.”

Herbaria are becoming more of a rarity. And the UW-Madison has the third largest collection of any public university in the country, behind the universities of California and Michigan. At many universities, botany has been absorbed into large biology departments, and collections put into storage. That has not happened at UW-Madison.

“The combination of having a botany department and a big herbarium is getting pretty rare,” said David Baum, botany department chairman. “And more and more herbaria are closing or making the decision to move off campus into storage, which has a real negative effect on research.”

The University of Wisconsin-Madison Herbarium, founded in 1849 (the year the University was founded), is a museum collection of dried, labeled plants of state, national and international importance, which is used extensively for taxonomic and ecological research, as well as for teaching and public service. It contains the world’s largest collection of Wisconsin plants, about one-third of its 1,000,000 specimens having been collected within the state. Most of the world’s floras are well represented, and the holdings from certain areas, such as the Upper Midwest, eastern North America and western Mexico, are widely recognized as resources of global significance.

Related: Plants can Signal Microbial Friends for Helpposts on plantsRainforestsThe Avocado

Soil Mineral Degrades the Nearly Indestructible Prion

Warped pathogens that lack both DNA and RNA, prions are believed to cause such fatal brain ailments as chronic wasting disease (CWD) in deer and moose, mad cow disease in cattle, scrapie in sheep and Creutzfeldt-Jakob disease in humans. In addition to being perhaps the weirdest infectious agent know to science, the prion is also the most durable. It resists almost every method of destruction from fire and ionizing radiation to chemical disinfectants and autoclaving, which reduce prion infectivity but fail to completely eliminate it.

Other studies have shown that prions can survive in the soil for at least three years, and that soil is a plausible route of transmission for some animals, says Joel Pedersen, a UW-Madison environmental chemist. “We know that environmental contamination occurs in deer and sheep at least,” he notes.

Prion reservoirs in the soil, Pedersen explains, are likely critical links in the chain of infection because the agent does not appear to depend on vectors — intermediate organisms like mosquitoes or ticks — to spread from animal to animal.

That the birnessite family of minerals possessed the capacity to degrade prions was a surprise, Pedersen says. Manganese oxides like birnessite are commonly used in such things as batteries and are among the most potent oxidants occurring naturally in soils, capable of chemically transforming a substance by adding oxygen atoms and stripping away electrons. The mineral is most abundant in soils that are seasonally waterlogged or poorly drained.

full press release

Related: Clues to Prion InfectivityScientists Knock-out Prion Gene in CowsCurious Cat Science and Engineering Search

Correlation is Not Causation: “Fat is Catching” Theory Exposed

“Fat is catching” theory exposed

Their study was reported to have shown that you can “catch” obesity from having fat friends and that obesity is so contagious, it can be spread long-distance by email and instant messaging. Even healthcare professionals, who didn’t understand the etiology of true obesity or how statistics can be misused, failed to detect the implausibility of “second-hand obesity.” In fact, some doctors became so enamored with the new “science of networking” they believed it should be a new medical specialty: network medicine.

Jason M. Fletcher, Ph.D., assistant professor at the Yale School of Public Health in New Haven, Connecticut, along with Boston economist, Ethan Cohen-Cole, Ph.D., designed an ingenious study. They selected conditions that no one would seriously believe were spread by social networking and online friendships: height, headaches and acne. They then applied the same standard statistical methods used in Christakis and Fowler’s social networking research to “find” that acne, height and headaches have the same “social network effect.”

As they explained, patterns of association among people can lead to correlations in health conditions between friends that are not caused by direct social network effects at all.

There is a need for caution when attributing causality to correlations in health outcomes between friends using non-experimental data. Confounding is only one of many empirical challenges to estimating social network effects.

Excellent reminder of the risks of analyzing data for correlations. We continue to, far to often, fail to interpret data properly. Both authors of the study, received PhD’s from the University of Wisconsin-Madison which strengthens my belief that it is teaching students well (just kidding).

Also another example of the scientific inquiry process where scientists challenge the conclusions drawn by other scientists. It is a wonderful system, even if confusing and not the clean idea so many have of how science works.

Related: Correlation is Not CausationSeeing Patterns Where None ExistsStatistics for Experimenters500 Year FloodsPlaying Dice and Children’s NumeracyThe Illusion of UnderstandingAll Models Are Wrong But Some Are UsefulData Doesn’t Lie But People Can Draw Faulty Conclusions from Data

Making Embryonic Stem Cells

photo of Junying Yuphoto of Junying Yu, an assistant scientist with the University of Wisconsin-Madison by Bryce Richter, 2007.

Holy Grail of stem cell research within reach by Mark Johnson

It was time to test the 14 genes she had selected as the best candidates to reprogram a cell.

Using viruses to deliver the genes, she inserted all 14 at once into human cells. On the morning of July 1, 2006, Yu arrived at the lab and examined the culture dishes. Her eyes focused on a few colonies, each resembling a crowded city viewed from space. They looked like embryonic stem cells.

Cells must pass certain tests. They must multiply for weeks while remaining in their delicate, primitive state. When they are allowed to develop, they must turn into all the other cell types.

Bad things happen. Cells develop too soon. Cells die. There is no “aha!” moment, Thomson has said, only stress. He looked at the colonies and suppressed any excitement. He told Yu, essentially: OK, well get back to me in a couple of weeks.

In the fall of 2006, Yu was preparing to whittle down her list of genes when she fell ill. The pain in her gut was awful. She struggled to eat. Her doctor thought it was a stomach flu. Instead, in late October, Yu’s appendix burst. She was laid up for a month. When she returned to the lab, the problem with the culture medium struck again.

Not until January 2007 was she able to begin narrowing the list of genes. She spent several months testing subsets of them, finally arriving at four. Two, Oct4 and Sox2, were “Yamanaka factors,” the name given to the genes the Japanese scientist had used to reprogram mouse cells. Two, Nanog and Lin28, were not.

Using a virus to deliver the four genes, she reprogrammed a line of fetal cells, then repeated the experiments with more mature cells. Although the process was inefficient, succeeding with only a small fraction of cells, it did work.

Dr. Junying Yu, an American trained scientist who entered the US as a foreign student from China. Which is somewhat ironic given the movement of USA based stem cell researches to China. Great article showing the process of scientific inquiry.

Related: Junying Yu, James Thomson and Shinya Yamanaka (Time people who mattered 2007) – Discovery leaps legal, financial and ethical hurdles facing stem cellsEdinburgh University $115 Million Stem Cell CenterStanford Gets $75 Million for Stem Cell Centerposts relating to Madison, Wisconsin

Backyard Wildlife: Crows

bird dives at crow

Here is an action shot of a bird diving at a crow in my backyard, presumably to get the crow to leave. I noticed this for going on for several weeks (follow link for better view of the dive-bombing bird). The crow didn’t seem to mind too much most of the time.

I visited Madison this week and saw 4 wild turkeys wandering around in a residential area. I didn’t have my camera handy however, so I didn’t get a photo 🙁 It was a strange and cool site.

Related: Cool Crow ResearchBackyard Wildlife: Sharpshinned Hawkposts on birds

Crows Carry Cameras for Science:

The cameras look through the legs of the birds, transmitting what they record to a person holding a receiver several hundred meters away.

To understand more about how and why the crows use tools, researchers need a lot of details about their lives in the wild

Videos included footage of the crows using plant stems as tools to probe for food and even carrying a tool from one place to another. The images showed that birds on the ground pick up just 8 bits of food an hour.

Photos of Parfrey’s Glen, Wisconsin

John Hunter Durwood Glen

photo of Yellow Flower in Parfreys Glen

See more photos from my visit to Parfrey’s Glen Natural Area in Wisconsin, about an hour outside of Madison. It really was amazingly beautiful – the pictures do not do it justice. The Parfrey’s Glen trail is under a mile but well worth visiting. If you want to hike more try the Ice Age National Scenic Trail or nearby Devil’s Lake State Park. The top photo is of me (John Hunter) at nearby Durwood’s Glen. The yellow flower is from Parfrey’s Glen.

Photo of yellow flower by John Hunter is available for use: Creative Commons Attribution-Share Alike (see requirements for use).

Related: Hoh Rain Forest and Ruby Beach, Olympic National parkC&O Towpath – Monocacy Aqueduct, MarylandNature Recreation DecliningCurious Cat photo traveloguesBull Run Trail, Virginia

Parfrey’s Glen is Wisconsin’s first State Natural Area, is a spectacular gorge deeply incised into the sandstone conglomerate of the south flank of the Baraboo Hills. The exposed Cambrian strata provide excellent opportunities for geological interpretation. The walls of the glen – a Scottish word for a narrow, rocky ravine – are sandstone with embedded pebbles and boulders of quartzite.

Finding the Host Genes Viruses Require

Flu-infected fly cells reveal dependencies of the virus

The new study is important because it demonstrates a rapid-fire technique for identifying host factors such as proteins and carbohydrates that a virus commandeers to successfully infect a cell. By exposing the virus’s dependencies, the Wisconsin team has uncovered a target-rich environment for influenza drug developers.

By working in fly cells, the Wisconsin team was able to deploy a technique to rapidly and selectively silence thousands of genes to see which were used by the flu virus. Screening a library of some 13,000 genes, the group identified more than 100 whose suppression in fly cells hindered the virus’s ability to successfully take over the cell and make new viruses.

S&P 500 CEOs are Engineering Graduates

2007 Data from Spencer Stuart on S&P 500 CEO (they deleted the link so the link was removed – yet another website proves to be unreliable without basic web usability principles being followed) shows once again more have undergraduate degrees in engineering than any other field.

Field
   
% of CEOs
2007 2006 2005

Engineering 21 23 20
Economics 15 13 11
Business Administration 13 12 15
Accounting 8 8 7
Liberal Arts 6 8 9
No degree or no data 3 3

The report does not show the fields for the rest of the CEO’s. 40% of S&P CEOs have MBAs. 27% have other advanced degrees. The University of Wisconsin-Madison, Princeton and Harvard tied for the most CEO’s with undergraduate degrees from their universities at 12. University of Texas has 10 and Stanford has 9.

Data for previous years is also from Spencer Stuart: 2006 S&P 500 CEO Education StudyTop degree for S&P 500 CEOs? Engineering (2005 study)

Related: Engineering Education Study Debateposts on science and engineering careersScience and Engineering Degrees lead to Career SuccessThe Future is Engineering

Nobel Laureate Initiates Symposia for Student Scientists

   
The video shows a portion of Oliver Smithies’ Nobel acceptance lecture. See the rest of the speech, and more info, on the Nobel Prize site.

As an undergraduate student at Oxford University in the 1940s, Oliver Smithies attended a series of lectures by Linus Pauling, one of the most influential chemists of the 20th century. It was a powerful experience, one that sparked the young scientist’s ambitions and helped launch his own eminent career.

“It was tremendously inspiring,” says Smithies, one of three scientists who shared the Nobel Prize in Medicine in 2007. “People were sitting in the aisles to listen to him.”

Now Smithies, who was a genetics professor at the University of Wisconsin-Madison from 1960-88, is taking it upon himself to expose a new generation of undergraduates to this sort of experience. Using the prize money that came with his Nobel Prize, Smithies is funding symposia at all four universities he has been affiliated with throughout his scientific career: Oxford, the University of Toronto, UW-Madison and the University of North Carolina, where he is currently the Excellence Professor of Pathology and Laboratory Medicine. Each university will receive about $130,000 to get things started.

“He wants the symposium to be a day when we bring the very best in biology to campus to interact with the students,” says geneticist Fred Blattner, who is in charge of organizing the symposium at UW-Madison and who collaborated with Smithies when their careers paths overlapped in Wisconsin.

The first of two speakers at the UW-Madison’s inaugural Oliver Smithies Symposium will be Leroy Hood, director of the Institute for Systems Biology, located in Seattle. Hood is a pioneer of high-throughput technologies and was instrumental in developing the technology used to sequence the human genome. More recently, Hood has focused his efforts on systems biology, the field of science in which researchers create computer models to describe complex biological processes, such as the development of cancer in the body. He is also at the forefront of efforts to use computer models to help doctors tailor drugs and dosages to an individual’s genetic makeup.
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Playing Dice and Children’s Numeracy

My father, Willaim Hunter, a professor of statistics and of Chemical Engineering at the University of Wisconsin, was a guest speaker for my second grade class (I think it was 2nd) to teach us about numbers – using dice. He gave every kid a die. I remember he asked all the kids what number do you think will show up when you roll the die. 6 was the answer from about 80% of them (which I knew was wrong – so I was feeling very smart).

Then he had the kids roll the die and he stood up at the front to create a frequency distribution of what was actually rolled. He was all ready for them to see how wrong they were and learn it was just as likely for any of the numbers on the die to be rolled. But as he asked each kid about what they rolled something like 5 out of the first 6 said they rolled a 6. He then modified the exercise a bit and had the kid come up to the front and roll the die on the teachers desk. Then my Dad read the number off the die and wrote on the chart 🙂

This nice blog post, reminded me of that story: Kids’ misconceptions about numbers — and how they fix them

in the real study, conducted by John Opfer and Rober Siegler, the kids used lines with just 0 and 1000 labeled. They were then given numbers within that range and asked to draw a vertical line through the number line where each number fell (they used a new, blank number line each time). The figure above represents (in red) the average results for a few of the numbers used in the study. As you can see, the second graders are way off, especially for lower numbers. They typically placed the number 150 almost halfway across the number line! Fourth graders perform nearly as well as adults on the task, putting all the numbers in just about the right spot.

But there’s a pattern to the second-graders’ responses. Nearly all the kids (93 were tested) understood that 750 was a larger number than 366; they just squeezed too many large numbers on the far-right side of the number line. In fact, their results show more of a logarithmic pattern than the proper linear pattern.