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PegnVA

03/08/12 7:22 AM

#169886 RE: F6 #169875

This study was discussed on PBS last night...one of the most interesting findings was that although we closely resemble the ape family, they do not carry the gene for dementia. Why? This is surely a logical question...does diet contribute to dementia?


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F6

06/07/12 3:04 AM

#176874 RE: F6 #169875

Entire DNA of fetus revealed through risk-free testing


A lab technician cuts a DNA fragment under ultraviolet light.
(Wong Maye-e / Associated Press / June 6, 2012)


Researchers use blood from the mother and saliva from the father to determine a fetus' entire DNA sequence. If refined, the technique could provide a risk-free way to screen for genetic disorders.

By Rosie Mestel, Los Angeles Times
June 6, 2012, 5:44 p.m.

Scientists have pieced together the entire DNA sequence [i.e., genome] of an 18-week-old fetus without having to use any invasive tests that could result in a miscarriage — an advance that offers a glimpse of the future of prenatal testing.

Using blood drawn from the mother and a sample of saliva from the father, the researchers were able to scan the fetus' genome and determine whether it contained any of the myriad single-letter changes in the DNA code that can cause a genetic disorder. They could even pinpoint which mutations were inherited from Mom, which came from Dad, and which were brand-new.

If the technique is refined and the technology becomes inexpensive — as many experts anticipate — this type of prenatal testing could provide prospective parents with a simple, risk-free way to screen for a broad array of simple genetic disorders, according to the authors of a report [ http://stm.sciencemag.org/content/4/137/137ra76 ] in Thursday's edition of Science Translational Medicine.

The work is based on the fact that small fragments of fetal DNA circulate in the blood of pregnant women.

Several biotech companies are developing tests that capture those DNA fragments and screen them for signs of Down syndrome and other disorders that result from having an extra copy of an entire chromosome.

But that type of screening is far easier than searching for single-letter variations in individual genes, said senior author Jay Shendure, a geneticist at the University of Washington in Seattle.

An additional chromosome is "the equivalent of an extra chapter in a book," he said. "What we're trying to do is pick up a typo in a word."

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.

Technology like this could lead to more widespread screening of fetuses for genetic disorders that could benefit from early treatment, said Dr. Joe Leigh Simpson, senior vice president for research and global programs for the March of Dimes in White Plains, N.Y. It might even help doctors identify women at heightened risk for problems such as pre-term birth, he said.

rosie.mestel@latimes.com

*

Also

Biologists construct self-assembling tiles of DNA
http://www.latimes.com/news/science/la-sci-dna-shapes-20120602,0,182781.story

Detecting cancers -- from tiny bits of tumor DNA in blood
http://www.latimes.com/health/boostershots/la-heb-detecting-cancers-dna-blood--20120530,0,3112263.story

Turning DNA into a hard drive
http://www.latimes.com/news/science/la-sci-synthetic-biology-q-a-20120526,0,4569181.story

*

Copyright © 2012, Los Angeles Times

http://www.latimes.com/news/science/la-sci-fetal-genome-sequence-20120607,0,7625263.story [with comments]


===


Babies could be tested for 3,500 genetic faults


An ultrasound scan of a human foetus
Photo: ALAMY


Scientists could soon be able to routinely screen unborn babies for thousands of genetic conditions, raising concerns the breakthrough could lead to more abortions.

By Stephen Adams, Medical Correspondent
10:51PM BST 06 Jun 2012

A team has been able to predict the whole genetic code of a foetus by taking a blood sample from a woman who was 18 weeks pregnant, and a swab of saliva from the father.

They believe that, in time, the test will become widely available, enabling doctors to screen unborn babies for some 3,500 genetic disorders.

At the moment the only genetic disorder routinely tested for on the NHS is Down’s syndrome.

This is a large-scale genetic defect caused by having an extra copy of a bundle of DNA, called a chromosome.

Other such faults are sometimes tested for, but usually only when there is a risk of inheriting them from a parent.

By contrast, the scientists say their new test would identify far more conditions, caused by genetic errors.

However, they warned it raised “many ethical questions” because the results could be used as a basis for abortion.

These concerns were last night amplified by pro-life campaigners, who said widespread use of such a test would “inevitably lead to more abortions”.

The American scientists were able to map the baby’s genetic code principally from tiny traces free-floating DNA, which makes its way into the mother’s blood.

Blood sample DNA from the mother was also studied as well as DNA extracted from the father's saliva.

Fitting pieces of the genetic jigsaw together, scientists in the US were able to reconstruct the entire genetic code of an unborn baby boy.

They were then able to see what spontaneous genetic mutations had arisen.

Such natural mutations - called ‘de novo’ mutations - are responsible for the majority of genetic defects.

By checking their prediction of the baby’s genetic code with actual DNA taken after the birth, the team from the University of Washington in Seattle, found they were able to identify 39 of 44 such mutations in the child.

De novo mutations are thought to play a role in a number of complex conditions such as autism and schizophrenia.

The team also tested their approach on a woman who was earlier in her pregnancy than 18 weeks, and found it still worked.

Dr Jay Shendure, the lead scientist, said: "This work opens up the possibility that we will be able to scan the whole genome of the foetus for more than 3,000 single-gene disorders through a single, non-invasive test."

Jacob Kitzman, who worked on the project, added: “The improved resolution is like going from being able to see that two books are stuck together to being able to notice one word mis-spelled on a page.”

In future, a more refined and less costly version of the procedure could make pre-natal genetic testing far more comprehensive than it is now, the scientists say.

The research is reported in the journal Science Translational Medicine.

The scientists said the test would be a considerable improvement on current techniques, which involve inserting a probe into the womb to take fluid from the foetal sac or placental samples. This can be dangerous for both mother and child.

Such existing methods only enable doctors to check for a relatively small number of genetic disorders.

These include Down's syndrome and cystic fibrosis - which are both large-scale genetic defects - as well as muscular dystrophy and spina bifada, which can have hereditary elements.

As well as testing for thousands of genetic defects, the scientists said their test could give a wealth of information on the baby’s future health.

However, they warned: “The less tangible implication of incorporating this level of information into pre-natal decision-making raises many ethical questions that must be considered carefully within the scientific community and on a societal level.

“As in other areas of clinical genetics, our capacity to generate data is outstripping our ability to interpret it in ways that are useful to physicians and patients.”

Josephine Quintavalle, founder of the Pro-Life Alliance, put it more baldly.

She said: “One always hopes, vainly, that in utero testing will be for the benefit of the unborn child.

“But, whilst this new test may not itself be invasive, given our past track record, it is difficult to imagine that this new test will not lead to more abortions.”

© Copyright of Telegraph Media Group Limited 2012

http://www.telegraph.co.uk/health/healthnews/9315265/Babies-could-be-tested-for-3500-genetic-faults.html [with comments]


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fuagf

07/16/12 9:03 PM

#179626 RE: F6 #169875

A Bone Here, a Bead There: On the Trail of Human Origins


Origins of Modern Humans: John Noble Wilford of The New York Times interviews
the paleoanthropologist Chris Stringer of the Natural History Museum in London.

By JOHN NOBLE WILFORD
Published: July 16, 2012 28 Comments

Who are we, and where did we come from? Scientists studying the origin of modern humans, Homo sapiens, keep reaching deeper in time to answer those questions — toward the last common ancestor of great apes and humans, then forward to the emergence of people more and more like us in body and behavior.

Multimedia


Slide Show - Researching the Origins of Modern Humans
http://www.nytimes.com/slideshow/2012/07/17/science/Conversations.html?ref=science

Audio: Chris Stringer [inside]
John Noble Wilford of The New York Times interviews the paleoanthropologist Chris
Stringer of the Natural History Museum in London. .. 20:48 .. On the origins of modern humans.

Their research is advancing on three fronts. Fossils of skulls and bones expose anatomical changes. Genetics .. http://health.nytimes.com/health/guides/specialtopic/genetics/overview.html?inline=nyt-classifier .. reveals the timing and place of the Eve of modern humans.

And archaeology turns up ancient artifacts reflecting abstract and creative thought, and a growing self-awareness. Just last month, researchers made the startling announcement that Stone Age paintings in Spanish caves were much older than previously thought, .. http://www.nytimes.com/2012/06/15/science/new-dating-puts-cave-art-in-the-age-of-neanderthals.html .. from a time when Neanderthals were still alive.

To help make sense of this cascade of new information, a leading authority on modern human evolution — the British paleoanthropologist Chris Stringer — recently sat for an interview in New York that ranged across many recent developments: the evidence of interbreeding between Neanderthals and Homo sapiens; the puzzling extinct species of little people nicknamed the hobbits; and the implications of a girl’s 40,000-year-old pinkie finger found in a Siberian cave.

Dr. Stringer, an animated man of 64, is an anthropologist at the Natural History Museum in London and a fellow of the Royal Society. But he belies the image of a don: He showed up for our interview wearing a T-shirt and jeans, looking as if he had just come in from the field.

A condensed and edited version of our conversation follows. In it and in a new book, he describes a new wrinkle to the hypothesis of a recent African origin of modern Homo sapiens. His ideas may light up more debate in a contentious science.

First of all, would you explain the title of your new book?

Yes, the title is “Lone Survivors: How We Came to Be the Only Humans on Earth.” And this comes from the fact that if we went back 100,000 years, which is very recent, geologically speaking, there might have been as many as six different kinds of humans on the earth. All those other kinds have disappeared, and left us as the sole survivors.

You wrote that in 1970, when you started doing research in this field, the origin of modern humans
was hardly recognized as a topic worthy of study in science. What has changed since then?


It’s been a fantastic time to be involved in the field, and even when I was writing this book in the last two years, I had to regularly go back and rewrite things I thought I’d finished with, because new developments were coming up all the time. In 1970, for some people, there was no single origin of modern humans: We evolved globally, all over the world. There was a view that in the different regions an earlier species, Homo erectus, evolved relatively seamlessly to modern humans. This idea was known as multiregionalism.

The argument went that we remained one species throughout that evolutionary process, because there was interbreeding among the different populations. It meant that the Neanderthals in Europe, for example, would be the ancestors of modern Europeans; Homo erectus in China would be the ancestor of modern Asians. And Java Man would be a distant ancestor of modern Australian aboriginal populations.

What we have seen since then is a growth in the fossil record, in our ability to date that record and to CT-scan fossils and get minute details out of them. DNA studies have had a huge impact on our field. We now have the genomes of Neanderthals and of these strange people in Siberia called the Denisovans.

Speaking of DNA, what about the African Eve? This established an approximate date for the genetic origin of modern humans, in Africa. As a leading advocate of the recent African origin, in contrast to the multiregional model, did you believe this settled the debate?

To be honest, it’s not been totally resolved, but the Mitochondrial Eve publication of 1987 was a key moment. Up to then, a few of us were arguing for a recent African origin from the fossil and archaeological evidence. But the evidence was pretty skimpy, and the majority opinion was against our view.

When this new genetic technique appeared, it seemed to give clarity to the picture. Here was an independent bit of data, from our mitochondrial DNA, inherited through females, suggesting we originated, all of us, all over the world, from a single ancestral population that lived in Africa maybe 200,000 years ago.

I came to this conclusion gradually, starting with the Neanderthals. They were the best-known ancient humans, and there was a view that they were our ancestors. I tested that model in my Ph.D. research, and I concluded the Neanderthals did not make good ancestors of modern humans, even in Europe, where we had the best data. So gradually my search moved from one region to another, to see where the evidence best fitted the idea of our origins.

It turned out that Africa was the place that had the oldest fossils of modern humans. Africa, for me, was the only place that showed a transition from archaic to modern humans.

In your book you propose that there was not one place in Africa where modern humans originated.

Earlier, influenced by the mitochondrial DNA data, I felt there was one place in Africa, a sort of garden of Eden, where we evolved, where we changed behaviorally and physically to become modern humans.

But the story is much more complicated. Even the DNA data show that essentially each of our genes has a separate evolutionary history. And so, when you look at the total picture, including the fossil data and archaeological data, there is no single spot in Africa that seems to be the place for our origins genetically.

The story is dominated by East Africa, because that’s the area that has the best preservation of the fossil record. You could say southern Africa is giving scientists the best record of behavioral evolution. They are finding evidence pretty early of processing marine resources, the use of red ocher for symbolic purposes, self-adornment with shell beads.

In my view, different parts of Africa were important at different times, to distinct human species, and this was being controlled by the climate. Africa is a huge place influenced by many different factors: the Mediterranean, the North Atlantic, the South Atlantic, the Southern Ocean, the monsoons coming off the Indian Ocean. At different times this would have produced good areas for humans and bad areas.

Populations in different areas would have flourished briefly, developed new ideas, and then maybe those populations could have died out, even — but not before exchanging genes, tools and behavioral strategies. This kept happening until we get to within the last 100,000 years, and then finally we start to see the modern pattern behaviorally and physically coalescing from these different regions to become what we call modern humans by about 60,000 years ago.

Previously, the splendid cave art of Europe influenced the view that modern behavior began there some 40,000 years ago. How firm is the new interpretation that Homo sapiens developed modern behavior as well as modern anatomy in Africa?

There were remarkable things happening in Europe at least 40,000 years ago, with the painted caves, with flutes, with the statuettes and so on. But the seeds of that revolution were sown in Africa more than 100,000 years ago. I would argue that when modern humans came out of Africa, say 60,000 years ago, fundamentally they were behaviorally modern. They took that into Europe. They took that into Asia and into Australia. So there was no single revolutionary event in Europe; this was something that was in modern humans when they came out of Africa, and the ones who stayed behind as well.

How does the discovery in Indonesia, on the island of Flores, fit in with current thinking about
human migrations and lineage? Are the so-called hobbits really members of our genus Homo?


The hobbit, Homo floresiensis, .. http://topics.nytimes.com/top/news/science/topics/archaeology_and_anthropology/homo_floresiensis/index.html?inline=nyt-classifier .. is a really challenging find for everyone. There’s still a minority of scientists who don’t accept that it is a distinct human species; it’s some kind of a weird, maybe diseased form of modern human. But I think it is a genuine distinct form, and actually a very primitive form.

It’s either derived from a very primitive form of Homo erectus, maybe similar to the ones at Dmanisi in the Republic of Georgia, or it’s evidence of an earlier Africa exit, maybe before two million years ago, by something that’s pre-erectus that somehow got all the way over to the Far East and survived there in isolation, evolving for more than a million years. It’s an extraordinary story, if that’s true. And again, further evidence of how little we know about much of Asia in terms of this story.

The more you learn, the more fascinating the subject becomes.

Absolutely, and that’s how I found it right through my career.

In your earlier career, you concentrated on Neanderthals. Do you now accept the new evidence of Neanderthal-Homo sapiens interbreeding, which seems to establish that we are more than 2 percent Neanderthal?

This is one of the remarkable bits of news of the last couple of years. We’ve had the genomes of Neanderthals reconstructed, and yes, indeed, it shows that people outside of Africa have, on average, about 2.5 percent of an input of Neanderthal DNA in them. And, of course, it’s led to a rethinking of our relationship with them; clearly there was viable interbreeding.

We don’t know the circumstances. Maybe a parsimonious view is that there was a single interbreeding period when modern humans came out of Africa. They met some Neanderthals in the Middle East. There was some interbreeding, under circumstances we don’t know yet, and that input of Neanderthal DNA was then transferred as those populations spread to Europe and to China, down to New Guinea, into the Americas; they took that bit of Neanderthal with them.

Archaeologists have found evidence that Neanderthals and Homo sapiens
occupied the same caves in Israel. Could this have been an interbreeding contact?


Western Asia becomes a critical area for this possibility of interbreeding. It could have been 25 Neanderthals mixing with 1,000 modern humans. It doesn’t have to be a lot of Neanderthals, but clearly there might have been interbreeding somewhere like Israel or Lebanon or Syria — all possible places where we know Neanderthals lived, and at times modern humans also lived.

There’s also a view that the interbreeding was more widespread, but that either cultural or physiological factors limited the successful births. For example, we know that the pelvic shape of Neanderthal females is different from the pelvic shape of modern human females. If a modern human female was giving birth to a hybrid baby, part Neanderthal, could there have been obstetric problems? We don’t know the circumstances of these encounters: if it was a peaceful mixing and merging of these people, or if the circumstances were violent.

Just who were the Denisovans?

It’s an extraordinary discovery. Two or three years ago I vaguely knew there was an archaeological site in Siberia called Denisova Cave. And then a few teeth, a finger bone have produced a really high-quality genome now that’s posted on the Web site of the Max Planck Institute for Evolutionary Biology .. http://www.evolbio.mpg.de/english/index.html .. in Leipzig, Germany. The preservation of the DNA is exceptional, and well beyond anything we have from Neanderthals. It seems these Denisovans were related to the Neanderthals, an early branch off the Neanderthal line.

We know a lot about the Denisovans genetically, but physically we know very little about them. These fossils are so fragmentary. The even more remarkable thing is they are only known from one site in Siberia, and their DNA turns up in people only in really one region today — not in Siberia, or Asia, but down in Australia and New Guinea. That’s extraordinary.

This is difficult to explain, because we thought that the ancestors of the Australian Aborigines and New Guineans must have got to their regions through southern Asia. Somewhere in Southeast Asia is the most likely place they would have had interbreeding with the Denisovans. That also implies the Denisovans were not just in Siberia; they must have been a widespread group.

This raises one more question: Could we ever clone these extinct people?

Science is moving on so fast. The first bit of Neanderthal mitochondrial DNA was recovered in 1997. No one then could have believed that 10 years later we might have most of the genome. And a few years after that, we’d have whole Denisovan and Neanderthal genomes available. So no one would have thought cloning was a possibility. Now, at least theoretically, if someone had enough money, and I’d say stupidity, to do it, you could cut and paste those Denisovan mutations into a modern human genome, and then implant that into an egg and then grow a Denisovan.

I think it would be completely unethical to do anything like that, but unfortunately someone with enough money, and vanity and arrogance, might attempt it one day. These creatures lived in the past in their own environments, in their own social groups. Bringing isolated individuals back, for our own curiosity or arrogant purposes, would be completely wrong.

In the introduction to your book, you list the kinds of questions you’re always getting from
people. One of them will be the closing question: What is the future of human evolution?


That’s a tough one to answer. There’s a lot of data, not my research, but mainly geneticists have been working on this, and they’ve showed just how many genetic changes there have been in the last few thousand years in the human genome. And this is because we’ve undergone great changes with urbanization, with agriculture, very big changes in lifestyles. And this has influenced our genetic makeup as much as living in the Paleolithic had done. We’ve seen, if anything, an acceleration of genetic changes in humans due to these lifestyle changes. So, I think human evolution has been going on quite rapidly recently, and it’s going to carry on.

Not everyone agrees. My colleague in London, Steve Jones, has argued essentially that evolution has stopped in humans because we are in control of it. We have medical care. Nearly everyone reaches reproductive age. Everyone has enough food and water. So natural selection has been nullified in humans. I disagree with him because, of course, there are still a lot of people in the world who don’t have the best medical care, who don’t have enough food and water. Think of the impact of AIDS .. http://health.nytimes.com/health/guides/disease/aids/overview.html?inline=nyt-classifier .. in Africa.

So selection is still operating on many human populations just as much as it ever has done, really. Also, all of us probably have 50 mutations in our DNA compared with our parents. So that’s going on every generation as well. We are still evolving. We will continue to evolve.

http://www.nytimes.com/2012/07/17/science/chris-stringer-on-the-origins-and-rise-of-modern-humans.html?pagewanted=all
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fuagf

09/17/12 3:26 AM

#185235 RE: F6 #169875

Human Muscle, Regrown on Animal Scaffolding


Damon Winter/The New York Times

Sgt. Ron Strang exercising with his girlfriend, Monica Michna. He lost part of his left quadriceps to a bomb in Afghanistan.

By HENRY FOUNTAIN - Published: September 16, 2012 10 Comments

PITTSBURGH — In the months after a roadside bomb in Afghanistan blew off part of his left thigh, Sgt. Ron Strang wondered if he would ever be able to walk normally again.

Body Builders - Second of three articles.

Multimedia [ more inside ]

Body Builders: A First: Organs Tailor-Made With Body’s Own Cells (September 16, 2012)
http://www.nytimes.com/2012/09/16/health/research/scientists-make-progress-in-tailor-made-organs.html?ref=research


Damon Winter/The New York Times
Sgt. Ron Strang’s left thigh is still missing
a lot of muscle, but the little that regrew
helped improve his movement significantly.

The explosion and subsequent rounds of surgery left Sergeant Strang, 28, a Marine, with a huge divot in his upper thigh where the quadriceps muscle had been. He could move the leg backward, but with so much of the muscle gone he could not kick it forward. He could walk, but only awkwardly.

“I got really good at falling,” he said of his efforts. And Sergeant Strang, a tall, athletic man, had to give up running.

But that was two years ago. Now he walks easily, can run on a treadmill and is thinking of a post-military career as a police officer. “If you know me, or know to look for it, you can see a slight limp,” he said. “But everybody else, they go, ‘I would never have guessed.’ ”

There is something else they would never have guessed: Sergeant Strang has grown new muscle thanks to a thin sheet of material from a pig.

The material, called extracellular matrix, is the natural scaffolding that underlies all tissues and organs, in people as well as animals. It is produced by cells, and for years scientists thought that its main role was to hold them in their proper position.

But researchers now know that this scaffolding also signals the body to grow and repair those tissues and organs. Armed with that knowledge, the new body builders are using this material from pigs and other animals to engineer the growth of replacement tissue in humans.

The technique used on Sergeant Strang, though still in development, holds particular promise for some of the thousands of veterans of the Iraq and Afghanistan wars who have been maimed by explosives and have lost so much muscle from an arm or a leg that amputation is sometimes the best alternative.

Sergeant Strang’s is one of the first cases in what will eventually be an 80-patient trial to grow limb muscle. It is financed by the Defense Department’s Office of Technology Transition, but it will include civilians as well.

Dr. Peter Rubin .. http://www.mirm.pitt.edu/people/bios/RubinJP1.asp, a plastic surgeon at the University of Pittsburgh Medical Center who is a leader of the study, said that early results with Sergeant Strang and a handful of other patients showed that the animal scaffolding was spurring muscle growth. “We are seeing evidence of remodeling of tissues,” he said.

Last fall, Dr. Rubin cut out the scar .. http://health.nytimes.com/health/guides/disease/keloids/overview.html?inline=nyt-classifier .. tissue from Sergeant Strang’s leg and stitched a sheet resembling a thick piece of parchment paper — extracellular matrix from a pig urinary bladder, which had shown excellent results in lab studies — into the remaining healthy thigh muscle.

His body immediately started breaking down the matrix, which consists largely of collagen and other proteins. But the doctors expected, and wanted, that to happen — by degrading into smaller compounds, the matrix started the signaling process, recruiting stem cells .. http://topics.nytimes.com/top/news/health/diseasesconditionsandhealthtopics/stemcells/index.html?inline=nyt-classifier .. to come to the site where they could become muscle cells.

“We’re trying to work with nature rather than fight nature,” said another leader of the study, Dr. Stephen Badylak .. http://www.pitt.edu/~msrc/personnel/faculty/steven_badylak.html, deputy director of the McGowan Institute for Regenerative Medicine .. http://www.mirm.pitt.edu/ .. at the university.

Dr. Badylak is a pioneer in the use of extracellular matrix, having discovered many of its properties more than two decades ago while performing biomedical engineering research at Purdue University. As part of his work on a mechanical heart device, he was looking for a way to move blood from one part of the body to another but wanted to avoid synthetic materials, which can cause blood clots.

“I thought, what looks like a tube?” he recalled. “A piece of intestine.” So using a research dog named Rocky, he replaced its main artery near its heart with a section of its small intestine. (“I’d have a tough time getting that experiment approved today,” Dr. Badylak said.)

When he arrived at work the next morning, he was expecting all sorts of problems. “But Rocky is standing up in his cage, wanting breakfast and wagging his tail,” Dr. Badylak said. “I thought, well, this is pretty cool.”

Later experiments showed that over time the tube had lost the internal cells that are specific to intestines and gained cells specific to blood vessels. “It had morphed into a blood-vessel-like structure, which we thought was incredible,” he said. “Eventually we figured out that it was not the whole intestine but just the extracellular matrix that was responsible.”

Extracellular matrix from pigs, sheep and other animals has been used in the past decade as a reinforcing layer to help repair rotator cuff damage, hernias .. http://health.nytimes.com/health/guides/disease/hernia/overview.html?inline=nyt-classifier .. and other injuries. “Surgeons think of them as meshes that hold things together,” Dr. Badylak said. Most of them do not understand the matrix’s role in signaling and repair. “They don’t get it,” he said. “We didn’t either at first.”

The scaffolding is isolated by stripping out all of the living cells from a tissue or organ, leaving an intricate three-dimensional web of proteins and other compounds. Removing the cells eliminates the possibility that the material, of animal origin, will be rejected outright by the body when it is implanted. But the matrix does provoke a less intense immune response .. http://health.nytimes.com/health/guides/specialtopic/immune-response/overview.html?inline=nyt-classifier, Dr. Badylak said, which is necessary for it to work. “You actually need the immune system to recognize the material.”

“The body can say, ‘This is not me,’ but the signals that are there are actually telling me that I need to rebuild that tissue,” he added.

The matrix has to be in contact with healthy tissue, which is why scar tissue must be removed first. “If it’s put in the middle of a scar, it doesn’t remodel because it’s not exposed to the bloodstream and sources of cells,” Dr. Badylak said.

Stitching it directly to the muscle also ensures that it will be stretched when the muscle is activated, beginning the day after surgery, when patients start an intensive program of physical therapy .. http://topics.nytimes.com/top/news/health/diseasesconditionsandhealthtopics/physicaltherapy/index.html?inline=nyt-classifier. Putting a mechanical load on the matrix tells the body, in effect, that this should become muscle and not some other kind of tissue.

Sergeant Strang was skeptical when he first signed up for the trial and cleared all the physical hurdles to qualify for it — among other things, patients must have some muscle remaining and enough undamaged nerves so the muscle can work. But at that point he was willing to try anything to be able to walk normally again.

Ten soldiers, American and Afghan, were wounded on the road in Helmand Province that Easter Sunday, Sergeant Strang the most severely. He was given 42 units of blood, airlifted to Germany and then treated for a month at Walter Reed Army Medical Center in Bethesda, Md.

Sergeant Strang returned to his home outside Pittsburgh, where he underwent outpatient physical therapy for months. When he walked he favored his right leg, which caused pain in his knees, back, hip and neck. “Everything was torqued to the side,” he said.

When the doctors told him what they planned to do, “I kind of didn’t believe it at first,” Sergeant Strang said. “It strikes you as science fiction stuff when they explain it to you.”

Dr. Badylak said it was important not to set unrealistic expectations.

“We tell them, this isn’t magic. It’s not a miracle,” he said. “We’re not going to restore your 100 percent normal anatomy. But we think we’re going to be able to make a difference for you. You’ll be able to do things you can’t do now.”

There is still a big divot in Sergeant Strang’s leg, graphically illustrating how just a little new muscle tissue can make a difference.

“It was amazing,” he said. “Right off the bat I could do a full stride, I could bend my knee, kick it out a little bit, just enough to get that initial spring where gravity would take it the rest of the way.” Two weeks later he was out in the woods hunting with friends.

Some of the initial improvement may be from the mechanical connection between the matrix and the existing muscle, the doctors said. But as the matrix has degraded, Sergeant Strang has continued to improve, although there are signs that his progress is slowing down.

The improvement had a psychological effect, too, Sergeant Strang said. Before, if he went to a busy restaurant or other crowded place, he would spend time planning where to sit, because he knew he would not be able to move quickly in the event of danger. “It was always in the back of my mind,” he said.

But now, he said, “I don’t have to sit by the door.”

Tuesday: Growing a Spare Part Inside the Body.

http://www.nytimes.com/2012/09/17/health/research/human-muscle-regenerated-with-animal-help.html?_r=1&hp&pagewanted=all