Tag Archives: Students

Printing Bone, Muscle and More

A Pittsburgh-based research team has created and used an innovative ink-jet system to print “bio-ink” patterns that direct muscle-derived stem cells from adult mice to differentiate into both muscle cells and bone cells.

The custom-built ink-jet printer, developed at Carnegie Mellon’s Robotics Institute, can deposit and immobilize growth factors in virtually any design, pattern or concentration, laying down patterns on native extracellular matrix-coated slides (such as fibrin). These slides are then placed in culture dishes and topped with muscle-derived stem cells (MDSCs). Based on pattern, dose or factor printed by the ink-jet, the MDSCs can be directed to differentiate down various cell-fate differentiation pathways (e.g. bone- or muscle-like).

“This system provides an unprecedented means to engineer replacement tissues derived from muscle stem cells,” said Johnny Huard, professor of orthopedic surgery at the University of Pittsburgh School of Medicine and director of the Stem Cell Research Center at Children’s Hospital of UPMC. Huard has long-standing research findings that show how muscle-derived stem cells (MDSCs) from mice can repair muscle in a model for Duchenne Muscular Dystrophy, improve cardiac function following heart failure, and heal large bone and articular cartilage defects.

Weiss and Campbell, along with graduate student Eric Miller, previously demonstrated the use of ink-jet printing to pattern growth factor “bio-inks” to control cell fates. For their current research, they teamed with Phillippi, Huard and biologists of the Stem Cell Research Center at Children’s Hospital to gain experience in using growth factors to control differentiation in populations of MDSCs from mice.

The team envisions the ink-jet technology as potentially useful for engineering stem cell-based therapies for repairing defects where multiple tissues are involved, such as joints where bone, tendon, cartilage and muscle interface. Patients afflicted with conditions like osteoarthritis might benefit from these therapies, which incorporate the needs of multiple tissues and may improve post-treatment clinical outcomes.

The long-term promise of this new technology could be the tailoring of tissue-engineered regenerative therapies. In preparation for preclinical studies, the Pittsburgh researchers are combining the versatile ink-jet system with advanced real-time live cell image analysis developed at the Robotics Institute and Molecular Biosensor and Imaging Center to further understand how stem cells differentiate into bone, muscle and other cell types.

Microcosm by Carl Zimmer

cover of Microcosm by Carl Zimmer

Microcosm: E. Coli and the New Science of Life by Carl Zimmer is an excellent book. It is full of fascinating information and as usual Carl Zimmer’s writing is engaging and makes complex topics clear.

E-coli keep the level of oxygen low in the gut making the resident microbes comfortable. At any time a person will have as many as 30 strains of E. coli in their gut and it is very rare for someone ever to be free of E. coli. [page 53]

In 1943, Luria and Delbruck published the results that won them the 1969 Nobel Prize in Physiology or Medicine in which they showed that bacteria and viruses pass down their traits using genes (though it took quite some time for the scientific community at large to accept this). [page 70]

during a crisis E coli’s mutation rates could soar a hundred – or even a thousandfold… Normally, natural selection favors low mutation rates, since most mutations are harmful. But in times of stress extra mutations may raise the odds that organisms will hit on a way out of their crisis… [alternatively, perhaps] In times of stress, E coli. may not be able to afford the luxury of accurate DNA repair. Instead, it turns to the cheaper lo-fi polymerases. While they may do a sloppier job, E coli. comes out ahead [page 106]
Hybridization is not the only way foreign DNA got into our cells. Some 3 billion years ago our single-celled ancestors engulfed oxygen-breathing bacteria, which became the mitochondria on which we depend. And, like E. coli, our genomes have taken in virus upon virus. Scientists have identified more than 98,000 viruses in the human genome, along with our mutant vestiges of 150,00 others… If we were to strip out all our transgenic DNA, we would become extinct.

I highly recommend Microcosm, just as I highly recommend Parasite Rex, by Carl Zimmer.

Briggs-Rauscher Oscillating Reaction

video showing the Briggs-Rauscher Oscillating Reaction. From Wikipedia:

The first known homogeneous oscillating chemical reaction, reported by W. C. Bray in 1921, was between hydrogen peroxide (H₂O₂) and iodate (IO₃^âˆ’) in acidic solution. Due to experimental difficulty, it attracted little attention and was unsuitable as a demonstration. In 1958 B. P. Belousov in the Soviet Union discovered the Belousov–Zhabotinsky reaction (BZ reaction), is suitable as a demonstration, but it too met with skepticism (largely because such oscillatory behavior was unheard of up to that time) until A. M. Zhabotinsky, also in the USSR, learned of it and in 1964 published his research. In May of 1972 a pair of articles in the Journal of Chemical Education brought it to the attention of two science instructors at Galileo High School in San Francisco. They discovered the Briggs–Rauscher oscillating reaction by replacing bromate (BrO₃^âˆ’) in the BZ reaction by iodate and adding hydrogen peroxide. They produced the striking visual demonstration by adding starch indicator.

The detailed mechanism of this reaction is quite complex. Nevertheless, a good general explanation can be given.
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10 Simple Science Tricks for Parties

Fun video by Richard Wiseman on his top 10 science stunts for Christmas parties.

Science Explained: RNA Interference

Explained: RNA interference

Every high school biology student learns the basics of how genes are expressed: DNA, the cell’s master information keeper, is copied into messenger RNA, which carries protein-building instructions to the ribosome, the part of the cell where proteins are assembled.

But it turns out the picture is far more complicated than that. In recent years, biologists have discovered a myriad of other molecules that fine-tune this process, including several types of RNA (ribonucleic acid). Through a naturally occurring phenomenon known as RNA interference, short strands of RNA can selectively intercept and destroy messenger RNA before it delivers its instructions.
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Double-stranded RNA molecules called siRNA (short interfering RNA) bind to complementary messenger RNA, then enlist the help of proteins, the RNA-induced silencing complex. Those proteins cleave the chemical bonds holding messenger RNA together and prevent it from delivering its protein-building instructions.

This article from MIT is one, of many, showing MIT’s commitment to science education of the public. Good job, MIT.

Engineered Circuits That can Count Cellular Events

Engineered circuits can count cellular events by Anne Trafton

MIT and Boston University engineers have designed cells that can count and “remember” cellular events, using simple circuits in which a series of genes are activated in a specific order.
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The first counter, dubbed the RTC (Riboregulated Transcriptional Cascade) Counter, consists of a series of genes, each of which produces a protein that activates the next gene in the sequence.

With the first stimulus — for example, an influx of sugar into the cell — the cell produces the first protein in the sequence, an RNA polymerase (an enzyme that controls transcription of another gene). During the second influx, the first RNA polymerase initiates production of the second protein, a different RNA polymerase.

The number of steps in the sequence is, in theory, limited only by the number of distinct bacterial RNA polymerases. “Our goal is to use a library of these genes to create larger and larger cascades,” said Lu.

The counter’s timescale is minutes or hours, making it suitable for keeping track of cell divisions. Such a counter would be potentially useful in studies of aging.

The RTC Counter can be “reset” to start counting the same series over again, but it has no way to “remember” what it has counted. The team’s second counter, called the DIC (DNA Invertase Cascade) Counter, can encode digital memory, storing a series of “bits” of information.

The process relies on an enzyme known as invertase, which chops out a specific section of double-stranded DNA, flips it over and re-inserts it, altering the sequence in a predictable way.

The DIC Counter consists of a series of DNA sequences. Each sequence includes a gene for a different invertase enzyme. When the first activation occurs, the first invertase gene is transcribed and assembled. It then binds the DNA and flips it over, ending its own transcription and setting up the gene for the second invertase to be transcribed next.

When the second stimulus is received, the cycle repeats: The second invertase is produced, then flips the DNA, setting up the third invertase gene for transcription. The output of the system can be determined when an output gene, such as the gene for green fluorescent protein, is inserted into the cascade and is produced after a certain number of inputs or by sequencing the cell’s DNA.

This circuit could in theory go up to 100 steps (the number of different invertases that have been identified). Because it tracks a specific sequence of stimuli, such a counter could be useful for studying the unfolding of events that occur during embryonic development, said Lu.

Other potential applications include programming cells to act as environmental sensors for pollutants such as arsenic. Engineers would also be able to specify the length of time an input needs to be present to be counted, and the length of time that can fall between two inputs so they are counted as two events instead of one.

Movie Aims to Inspire College Students With Tales of Successful Minority Scientists

African American women are still rare in many science professions, despite their increasing representation in undergraduate science classes. The documentary – Roots to STEM: Spelman Women in Science—seeks to explore how these women were able to succeed and to hold them up as role models.

Tarsha Ward remembers begging her mother for a stethoscope so she could be the star of career day at her kindergarten class in Charleston, S.C. Her mother presented her with something that proved more prophetic: a white lab coat.

“For me that was the beginning of a career,” said Ward, who is working toward her doctorate in biomedical sciences at Morehouse School of Medicine in Atlanta, Ga., focused on cancer research. “Ever since then everything was about science.”

“If you get into a bind you have to think it out yourself,” she said. “A Ph.D. has really taught me to think on my own. You’re here thinking in the midnight hours and there’s no book to tell you what’s right. You just have to see if it works.”

Such struggles have already paid off. “In seven months, I published my first paper. I worked on it day and night,” said Ward, a 2004 Spelman graduate. “I (loved) the fact that I could find something no one else could find and actually publish it.”

Read the full press release

How to Stay Healthy: Avoiding the Flu

It is no secret that washing your hands is a great strategy to stay healthy. Still few people take care to wash their hands thoroughly frequently during each day. The H1N1 Flu is just the latest sickness that washing your hands protects you from.

The CDC recommends you take these everyday steps to protect your health to protect yourself from the flu:

Wash your hands often with soap and water, especially after you cough or sneeze. Alcohol-based hand cleaners are also effective. Though the scientific evidence is not as extensive as that on hand washing and alcohol-based sanitizers, other hand sanitizers that do not contain alcohol may be useful for killing flu germs on hands.
Avoid touching your eyes, nose or mouth. Germs spread this way.
Try to avoid close contact with sick people.

And to keep others healthy you should

Cover your nose and mouth with a tissue when you cough or sneeze. Throw the tissue in the trash after you use it. [others also suggest coughing into you elbow instead of your hands, again to reduce the spread of germs.]
If you are sick with flu-like illness, CDC recommends that you stay home for at least 24 hours after your fever is gone except to get medical care or for other necessities. (Your fever should be gone without the use of a fever-reducing medicine.) Keep away from others as much as possible to keep from making others sick.

The spread of this 2009 H1N1 flu is thought to be happening in the same way that seasonal flu spreads. Flu viruses are spread mainly from person to person through coughing or sneezing of people with influenza. Sometimes people may become infected by touching something with flu viruses on it and then touching their mouth or nose.

The incidence of H1N1flu is likely to be high this flu season based on results in the Southern Hemishpere. Symptoms are those of the flu: fever, cough, sore throat, runny or stuffy nose, body aches, headache, chills and fatigue; can include diarrhea and vomiting.

The CDC includes weekly flu statistics on their web site. Since mid-April to August 30, 2009, a total of 9,079 hospitalizations and 593 deaths associated with 2009 influenza A (H1N1) viruses have been reported to CDC an increase from 8,843 hospitalizations and 556 deaths from the prior week.

The Value of Displaying Data Well

Anscombe’s quartet: all four sets are identical when examined statistically, but vary considerably when graphed. Image via Wikipedia.

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Anscombe’s quartet comprises four datasets that have identical simple statistical properties, yet are revealed to be very different when inspected graphically. Each dataset consists of eleven (x,y) points. They were constructed in 1973 by the statistician F.J. Anscombe to demonstrate the importance of graphing data before analyzing it, and of the effect of outliers on the statistical properties of a dataset.

Of course we also have to be careful of drawing incorrect conclusions from visual displays.

For all four datasets:

Property	Value
Mean of each x variable	9.0
Variance of each x variable	10.0
Mean of each y variable	7.5
Variance of each y variable	3.75
Correlation between each x and y variable	0.816
Linear regression line	$y = 3 + 0.5 x$

Edward Tufte uses the quartet to emphasize the importance of looking at one’s data before analyzing it in the first page of the first chapter of his book, The Visual Display of Quantitative Information.

Here Comes Science by They Might Be Giants

They Might Be Giants creates great music and has moved into creating music aimed at kids, of any age, over the last few years. They are releasing a new Album and animated DVD Here Comes Science, is being released tomorrow. Their music is both enjoyable to listen to and educational, something that is often attempted but rarely done as successfully as they do.

The release include the following songs and videos:

1. Science Is Real
2. Meet the Elements
3. I Am a Paleontologist w/Danny Weinkauf
4. The Bloodmobile
5. Electric Car w/Robin Goldwasser
6. My Brother the Ape
7. What Is a Shooting Star?
8. How Many Planets?
9. Why Does the Sun Shine?
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