Posts about Madison

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 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.
Continue reading

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.

Disrupting the Replication of Bacteria

UW-Madison researchers develop novel method to find new antibiotics:

Filutowicz’s approach involves looking for new drugs that render bacteria harmless by blocking the replication of—and thus eliminating—some of their DNA.

Bacterial DNA comes in two forms: chromosomal DNA, which is required for life, and plasmid DNA, which is not. The nonessential plasmid DNA contains many undesirable bacterial genes, including those that confer antibiotic resistance or lead to the production of toxins.

Filutowicz is seeking antibiotics that would selectively disrupt the replication of plasmid DNA, so that when bacteria reproduce, they would produce plasmid-free offspring that are harmless or susceptible to traditional antibiotics. Such compounds could dramatically alter the character of some of our nastiest microbial adversaries.

Related: How do antibiotics kill bacteria?Entirely New Antibiotic DevelopedTop degree for S&P 500 CEOs? EngineeringAntibiotic Discovery Stagnates
Continue reading

Top degree for S&P 500 CEOs? Engineering

See more recent post with data from 2005-2009: S&P 500 CEO’s: Engineers Stay at the Top

The most common undergraduate degree for CEO’s of Fortune 500 companies is Engineering: with 20% of all CEOs (from 2005 CEO Study: A Statistical Snapshot of Leading CEOs

Another interesting point from the report (at least to those of us who grew up in Madison with a father who taught at the University of Wisconsin (teaching Chemical Engineering, Industrial Engineering and Statistics, in my father’s case, by the way):

For the second year in a row, the University of Wisconsin joins Harvard as the most common undergraduate university attended by S&P 500 CEOs. Prior to 2004, Harvard alone was the most common school attended.

Concentrating Solar Collector wins UW-Madison Engineering Innovation Award

Solar Collector

An inexpensive, modular solar-energy technology that could be used to heat water and generate electricity (see photo) won $12,500 and took first place in both the Schoofs Prize for Creativity and Tong Prototype Prize competitions, held Feb. 9 and 10 during Innovation Days on the UW-Madison College of Engineering campus.

In a package about the size of a small computer desk, the winning system uses a flat Fresnel lens to collect the sun’s energy and focus it onto a copper block. Then a unique spray system removes the energy from the copper block and converts it into steam, says inventor Angie Franzke, an engineering mechanics and astronautics senior from Omro, Wisconsin. The steam either heats water for household use or powers a turbine to generate electricity.

Other 2006 Schoofs Prize for Creativity winners include:

* Second place and $7,000 — William Gregory Knowles, for the OmniPresent Community-Based Response Network, a personal, business or industrial security system that draws on networked users and devices to more efficiently verify burglar alarms, fire alarms or medical emergencies.
* Third place and $4,000 — Garret Fitzpatrick, Jon Oiler, Angie Franzke, Peter Kohlhepp and Greg Hoell for the Self-Leveling Wheelchair Tray, a stowable working surface for wheelchairs that self-levels, even when the wheelchair is tilted or reclined up to a 45-degree angle.

Read more about the 2006 competition

Symbiotic relationship between ants and bacteria

Study reveals classic symbiotic relationship between ants, bacteria

Ants that tend and harvest gardens of fungus have a secret weapon against the parasites that invade their crops: antibiotic-producing bacteria that the insects harbor on their bodies.

“Every ant species [that we have examined] has different, highly modified structures to support different types of bacteria,” says Currie. “This indicates the ants have rapidly adapted to maintain the bacteria. It also indicates that the co-evolution between the bacteria and the ants, as well as the fungus and parasites, has been occurring since very early on, apparently for tens of millions of years.”

Furthermore, Currie says, the fact that the species have coexisted for so long means there might be a mechanism in place to decrease the rate of antibiotic resistance – which could help address a significant problem facing modern medicine. “We can learn a lot about our own use of antibiotics from this system,” he says.

Read more about the overuse of antibiotics

  • Recent Comments:

    • Jason Monroe: Many of my friends do Crossfit and realize how quickly you lose weight when you increase your...
    • Denise Gabbard: Nice! This is the kind of thing we should all embrace. Not only are they helping the planet...
    • Huskar: Thanks your explanation.
    • Mark: Good point, my explanation is as follows. If someones got a better one I’d like to hear it....
    • Asad Wahab: I was just wondering if he can is round in shape then how come the electrons are shifted to one...
    • Sonia Bourke: That’s amazing – such a beautiful animal. I’ve always wondered how a...
    • Anonymous: Hi, Thanks for your nice article. I think India can overtake the China, because engineering...
    • Mark: We just bought one the other day at a plant sale, and it has just begun to flower. I didn’t...
  • Recent Trackbacks:

  • Links