Science Tuesday - Climate Change, Genetics, RetroPathology, Menopause and Heat Waves

[brdgt]

Observatory: Shifting Dunes and an Ancient Drought
By HENRY FOUNTAIN, The New York Times, July 25, 2006

Bob Dylan got it right: you don’t need a weatherman to know which way the wind blows. All you need, really, is a dune.

If that dune has been fixed in place since ancient times, you can know which way the wind blew back then, and by extension what the climate was like.

By analyzing the region of dunes known as the Nebraska Sand Hills, scientists at the University of Nebraska have determined that a major wind shift occurred on the Great Plains from 800 to 1,000 years ago. That shift, which brought dry air from the southwest, led to a prolonged drought that was much more severe than the Dust Bowl.

“That was a drought with a capital D,” said David B. Loope, a professor of geosciences and an author of a paper in the journal Science describing the finding.

The dunes in the Sand Hills are now covered in grasses that keep them in place. A dating method showed that they were last mobile — that is, grassless — from 800 to 1,000 years ago.

Dr. Loope and his colleagues, including Venkataramana Sridhar, the paper’s lead author, first set out to determine what the dunes would look like if they could move now, under current wind conditions. They plugged wind data from the last several decades into a computer program that simulates dune movement, and came up with an answer: the dunes that would have formed are nothing like the actual ones. “They are a completely different orientation,” Dr. Loope said.

Further calculations showed what winds would have formed the existing dunes. Instead of the current prevailing strong northerly and weaker southerly winds, the researchers found that the ancient winds would have been northerly and southwesterly, and of equal strength.

“The southerly vector that we have today couldn’t have been present when the dunes were shaped,” Dr. Loope said. “That’s really important.” Those southerly winds bring moisture from the Gulf of Mexico. “If you have southwesterlies instead of southerlies, you don’t get any moisture,” he said.

There is dry southwesterly air today, Dr. Loope said, but it is higher in the atmosphere. The moist southerly air from the Gulf “wedges in underneath it,” he said.

Ten centuries ago, something caused those southwesterly winds to descend — probably atmospheric mixing brought on by a heating of the land, Dr. Loope said. That mixing would have pushed the dry air toward the surface.

With the possibility of more extreme weather, such mixing could occur in the future. “This is in the system,” Dr. Loope said, “and could happen again.”

Progress on Fish Poisoning

Scientists in Japan report that they have synthesized the two most potent forms of ciguatoxin, a compound responsible for a common form of fish poisoning worldwide.

Ciguatera, as the poisoning is known, occurs among people who eat barracuda, red snapper and other reef fish. While rarely fatal, it can cause vomiting and diarrhea, numbness, tingling and other odd sensations; neurological symptoms can sometimes last for months or years.

The toxin is produced by a tiny dinoflagellate, Gambierdiscus toxicus, and accumulates in the food chain. Along the way the molecules become more oxidized, with the most oxidized versions 10 times as potent as the original toxin.

It takes just a tiny amount of ciguatoxin to cause poisoning, and that creates a problem for researchers: there isn’t enough of the stuff to study. Its basic molecular structure was uncovered only in 1989, and that was after researchers processed nearly 9,000 pounds of moray eel to produce a third of a milligram of the compound, or roughly one ninety-thousandth of an ounce.

So synthesizing it, as Masayuki Inoue and colleagues at Tohoku University have done, should help other researchers discover more about how ciguatoxin affects the nervous system, and perhaps devise drugs to treat the poisoning. Their work is described in a paper to be published next week in The Journal of the American Chemical Society.

The researchers are affiliated with the university’s Research and Analytical Center for Giant Molecules, and ciguatoxin certainly qualifies as a giant molecule — it has a ladderlike structure consisting of 13 ether rings. Fragments had been synthesized before, but even so, assembling the entire molecule was no simple feat. One of the versions synthesized required 9 steps, the other 10.

More Plants, More Bugs?

There are a lot more plant species in the tropics than in temperate regions. There are a lot more plant-eating insects in the tropics, too, and scientists have long wondered why.

The explanation could be relatively simple — more types of plants make for more types of insects. Or it could be more complex — in the tropics, there could be fewer plant species serving as a food source for each insect species, on average, than in temperate zones. This greater “host specificity” among tropical plants — more finely dividing the food supply — would allow more insect species to thrive.

A study in the journal Science that directly compares communities of leaf-eating insects in a temperate climate (in the Czech Republic and Slovakia) and in a tropical one (Papua New Guinea) suggests that host specificity does not play a role.

The researchers, led by Vojtech Novotny of the University of South Bohemia in the Czech Republic, collected all the insect species feeding on 22 tree species at the Czech and Slovak sites and 22 species in Papua New Guinea. (In all, some 850 insect species were represented.) A critical aspect of the study was controlling for phylogenetic relationships — how closely or distantly related the tree species are — so they were equivalent between the two regions.

The researchers found no significant difference between the two regions in how many plant species were host to each insect. So the simpler explanation — that diversity of plant species leads to diversity of insects — would seem to apply.

Fossilized Frog Marrow

Scientists have discovered fossilized bone marrow in 10-million-year-old frogs and salamanders found in east-central Spain.

Normally soft tissues disappear in the fossilization process, though last year paleontologists at North Carolina State University found a soft form of bone tissue in the leg bone of a Tyrannosaurus rex. The bone marrow was discovered by Maria E. McNamara and Patrick J. Orr of University College Dublin and colleagues and was reported in the journal Geology; they say it is the first example of fossilized marrow ever found.

The marrow is similar in texture and color (red and yellow) to modern marrow.





Scientists Say They’ve Found a Code Beyond Genetics in DNA
By NICHOLAS WADE, The New York Times, July 25, 2006

Researchers believe they have found a second code in DNA in addition to the genetic code.

The genetic code specifies all the proteins that a cell makes. The second code, superimposed on the first, sets the placement of the nucleosomes, miniature protein spools around which the DNA is looped. The spools both protect and control access to the DNA itself.

The discovery, if confirmed, could open new insights into the higher order control of the genes, like the critical but still mysterious process by which each type of human cell is allowed to activate the genes it needs but cannot access the genes used by other types of cell.

The new code is described in the current issue of Nature by Eran Segal of the Weizmann Institute in Israel and Jonathan Widom of Northwestern University in Illinois and their colleagues.

There are about 30 million nucleosomes in each human cell. So many are needed because the DNA strand wraps around each one only 1.65 times, in a twist containing 147 of its units, and the DNA molecule in a single chromosome can be up to 225 million units in length.

Biologists have suspected for years that some positions on the DNA, notably those where it bends most easily, might be more favorable for nucleosomes than others, but no overall pattern was apparent. Drs. Segal and Widom analyzed the sequence at some 200 sites in the yeast genome where nucleosomes are known to bind, and discovered that there is indeed a hidden pattern.

Knowing the pattern, they were able to predict the placement of about 50 percent of the nucleosomes in other organisms.

The pattern is a combination of sequences that makes it easier for the DNA to bend itself and wrap tightly around a nucleosome. But the pattern requires only some of the sequences to be present in each nucleosome binding site, so it is not obvious. The looseness of its requirements is presumably the reason it does not conflict with the genetic code, which also has a little bit of redundancy or wiggle room built into it.

Having the sequence of units in DNA determine the placement of nucleosomes would explain a puzzling feature of transcription factors, the proteins that activate genes. The transcription factors recognize short sequences of DNA, about six to eight units in length, which lie just in front of the gene to be transcribed.

But these short sequences occur so often in the DNA that the transcription factors, it seemed, must often bind to the wrong ones. Dr. Segal, a computational biologist, believes that the wrong sites are in fact inaccessible because they lie in the part of the DNA wrapped around a nucleosome. The transcription factors can only see sites in the naked DNA that lies between two nucleosomes.

The nucleosomes frequently move around, letting the DNA float free when a gene has to be transcribed. Given this constant flux, Dr. Segal said he was surprised they could predict as many as half of the preferred nucleosome positions. But having broken the code, “We think that for the first time we have a real quantitative handle” on exploring how the nucleosomes and other proteins interact to control the DNA, he said.

The other 50 percent of the positions may be determined by competition between the nucleosomes and other proteins, Dr. Segal suggested.

Several experts said the new result was plausible because it generalized the longstanding idea that DNA is more bendable at certain sequences, which should therefore favor nucleosome positioning.

“I think it’s really interesting,” said Bradley Bernstein, a biologist at Massachusetts General Hospital.

Jerry Workman of the Stowers Institute in Kansas City said the detection of the nucleosome code was “a profound insight if true,” because it would explain many aspects of how the DNA is controlled.

The nucleosome is made up of proteins known as histones, which are among the most highly conserved in evolution, meaning that they change very little from one species to another. A histone of peas and cows differs in just 2 of its 102 amino acid units. The conservation is usually attributed to the precise fit required between the histones and the DNA wound around them. But another reason, Dr. Segal suggested, could be that any change would interfere with the nucleosomes’ ability to find their assigned positions on the DNA.

In the genetic code, sets of three DNA units specify various kinds of amino acid, the units of proteins. A curious feature of the code is that it is redundant, meaning that a given amino acid can be defined by any of several different triplets. Biologists have long speculated that the redundancy may have been designed so as to coexist with some other kind of code, and this, Dr. Segal said, could be the nucleosome code.







A President Felled by an Assassin and 1880’s Medical Care
By AMANDA SCHAFFER, The New York Times, July 25, 2006

WASHINGTON — Three vertebrae, removed from the body of President James A. Garfield, sit on a stretch of blue satin. A red plastic probe running through them marks the path of his assassin’s bullet, fired on July 2, 1881.

The vertebrae form the centerpiece of a new exhibit, commemorating the 125th anniversary of Garfield’s assassination. The exhibit also features photographs and other images that tell the story of the shooting and its aftermath, in which Garfield lingered on his deathbed for 80 days. Located at the National Museum of Health and Medicine, on the campus of the Walter Reed Army Medical Center, the exhibit opened on July 2 and will close, 80 days later, on Sept. 19.

Garfield was waiting at the Baltimore and Potomac Railroad Station in Washington, about to leave for New England, when he was shot twice by the assassin, Charles J. Guiteau.

The first bullet grazed Garfield’s arm, said Lenore Barbian, anatomical collections curator for the museum. But the second struck him in the right side of the back and lodged deep in the body.

“No one expected Garfield to live through the night,” Dr. Barbian said.

As the display makes clear, the second bullet pierced Garfield’s first lumbar vertebra, crossing from right to left.

At the time, however, without the benefit of modern diagnostics, Garfield’s doctors could not determine the location of the bullet. “Trying to understand its pathway became their primary concern,” Dr. Barbian said.

At least a dozen medical experts probed the president’s wound, often with unsterilized metal instruments or bare hands, as was common at the time.

Sterile technique, developed by the British surgeon Joseph Lister in the mid-1860’s, was not yet widely appreciated in the United States, although it was accepted in France, Germany and other parts of Europe. Historians agree that massive infection, which resulted from unsterile practices, contributed to Garfield’s death.

The exhibit describes how the president’s fluctuating medical condition became a national obsession in the summer of 1881. His doctors issued daily medical briefings, which were rapidly disseminated by telegraph and published in newspapers across the country. In response, the White House received letters by the bushel basket.

“One man suggested that they turn the president upside down and see if the bullet would just fall out,” Dr. Barbian said.

The exhibit also includes an image of the metal detector designed by Alexander Graham Bell to search for the bullet. It was composed of a battery and several metal coils positioned on a wooden platform and was connected to an earpiece.

Jeffrey S. Reznick, senior curator at the museum, said the device was designed to create an electromagnetic field, which would be disrupted in the presence of a metal object. The disruption would cause the device to emit a clicking sound through the earpiece.

“Electricity and magnetism were just being appreciated as ways to explore the body’s interior,” Dr. Reznick said.

Bell’s invention failed on two occasions to pinpoint the bullet’s location. Historians say this may have been because the device picked up metal coils in the president’s mattress, or because Bell searched only on the right side of Garfield’s body, where the lead physician, Dr. Doctor Willard Bliss — Doctor was his given name — had come to believe the bullet was lodged.

In early September, the president was moved from the White House to a cottage in Elberon, N.J., on the shore.

Also in the exhibit is an image of the president on his deathbed, lying on his back draped in a sheet and surrounded by friends and family, including his wife, Lucretia, and his daughter, Mollie. Garfield died in New Jersey on Sept. 19, 1881.

Photographs of Drs. Daniel S. Lamb and Joseph J. Woodward, who led the autopsy, are shown in the exhibit as well. Dr. Lamb and Dr. Woodward were affiliated with the Army Medical Museum in Washington, which later became the National Museum of Health and Medicine.

At the autopsy, it became evident that the bullet had pierced Garfield’s vertebra but missed his spinal cord. The bullet had not struck any major organs, arteries or veins, and had come to rest in adipose tissue on the left side of the president’s back, just below the pancreas.

Dr. Ira Rutkow, a professor of surgery at the University of Medicine and Dentistry of New Jersey and a medical historian, said: “Garfield had such a nonlethal wound. In today’s world, he would have gone home in a matter or two or three days.”

In addition to causing sepsis by probing the wound with unsterile hands and instruments, Garfield’s doctors did him a disservice by strictly limiting his solid food intake, believing that the bullet might have pierced his intestines, said Dr. Rutkow, the author of “James A. Garfield,” a book in the American Presidents Series.

In mid-August, the doctors insisted that Garfield be fed rectally, and he received beef bouillon, egg yolks, milk, whiskey and drops of opium in this manner.

“They basically starved him to death,” said Dr. Rutkow, noting that the president lost over 100 pounds from July to September.

Garfield’s assassination occurred at a time of transition in American medicine. There was little standardization of medical practice, and various sects — including homeopaths and allopaths, who took opposite approaches to treatment — competed for patients.

Behind the scenes, relations between Garfield’s physicians were acrimonious, historians say. While the head physician, Dr. Bliss, released optimistic reports to the press, his rivals, including Dr. Silas Boynton, repeatedly leaked negative — and ultimately more truthful — information. (Dr. Bliss was an allopath and Dr. Boynton was a homeopath, which partly accounts for their rivalry.)

Medical journals also published scathing editorials criticizing the president’s care. “You wouldn’t see that kind of bickering in medical journals today,” Dr. Rutkow said.

Dr. Rutkow said that sterile practice was widely accepted in the United States by the early 1890’s. X-rays, which would also have been helpful to the president, were discovered in the 1890’s as well.

The Garfield exhibit is on display alongside the museum’s permanent Civil War exhibit, which includes the bullet that killed President Abraham Lincoln and fragments of his skull, as well as bone saws, artificial limbs and various other Civil War artifacts. The museum also holds the spleen, the brain and most of the skeleton of Garfield’s assassin, Guiteau, although these artifacts are not part of the current exhibit.

Sarah Vowell, the author of “Assassination Vacation,” which explores the assassinations of Lincoln, Garfield and President William McKinley, says Garfield’s vertebrae were passed around to the jurors at Guiteau’s trial.

The assassin’s lawyers tried to argue that their client was not guilty by reason of insanity. The defense was unsuccessful, and he was hanged on June 30, 1882.

Guiteau himself repeatedly criticized Garfield’s doctors, suggesting that they were the ones who had killed the president.

“I just shot him,” Guiteau said.





Research Finds Little Proof on Menopause Treatments
By NICHOLAS BAKALAR, The New York Times, July 25, 2006

Almost half of American women seek alternative or complementary treatments for the unpleasant symptoms of menopause. But a systematic review of the evidence has found little proof that any of them work.

Researchers reviewed 70 randomized controlled trials of alternative treatments and found insufficient scientific evidence to support the effectiveness of any of the commonly used remedies: herbs, mind-body techniques, energy therapies using magnets or electrical nerve stimulation, homeopathy, naturopathy or culturally based non-Western medical treatments. The review was published yesterday in The Archives of Internal Medicine.

Most of the studies were of poor quality, but even those judged by the researchers to be “fair” or “good” on a three-point scale most often demonstrated little difference between alternative treatments and placebo. For example, a study that compared 56 patients given a soy drink with 55 who drank a medically inactive liquid found no difference between the groups, although both groups got some symptom relief.

Three of four trials of the herb black cohosh, a common alternative treatment for menopausal symptoms, showed no improvement, but the studies suffered from poor methodology. The fourth, judged “fair” by the researchers, enrolled 304 women, half of whom took black cohosh and the other half a placebo for 12 weeks. Compared with placebo, there was greater improvement in the treatment group as measured by the participants’ own reports. Dr. Anne Nedrow, the lead author of the review, said the study “did show some benefits, but we had to balance it with studies that showed none.”

The scientists examined nine studies of mind-body therapies, treatments that focus on the ways in which emotional, mental, social, spiritual and behavioral factors can affect health. While they varied considerably in quality, none found a significant improvement compared with placebo treatment using stress-management techniques, meditation, relaxation exercises, audiotape relaxation or supportive counseling.

Therapies involving reflexology, bone manipulation and magnetic devices were found to be almost completely useless. In one small study of magnets, the placebo group showed more improvement than the group that received the magnet treatment.

Acupuncture was also ineffective. The reviewers examined four trials; three demonstrated no difference between real and sham procedures. The fourth, judged by the reviewers to be of fair quality, compared standard estrogen therapy, sham acupuncture and electroacupuncture, a variation on the practice in which continuous electrical pulses are delivered through the needles. Only the estrogen group improved.

None of six trials of traditional Chinese medicinal herbs, three using a combination of medicines, showed a significant benefit over controls for menopausal symptoms.

Studies of biological therapies like kava, primrose oil, guar gum, wild yam cream and red clover showed little or no difference in symptoms between those who used the substances and those given a placebo.

Still, Dr. Nedrow said, “We don’t have proof these therapies don’t work, either, because the studies are not of the length, quality and size that you can draw those conclusions.” Dr. Nedrow is an assistant professor of medicine at the Oregon Health and Science University.

Most of the trials lacked consistent or clear reporting of adverse effects, although one five-year follow-up study of soy indicated that it increased the risk for endometrial hyperplasia, a usually benign thickening of the lining of the uterus that can cause abnormal bleeding. Liver toxicity has been reported with both black cohosh and kava.

Dr. Nedrow is not opposed to her patients’ using these treatments.

“I think the placebo is a powerful thing and underutilized,” she said. “If they’re taking a product and they like it and it is safe, I say great, and I won’t spend the time to read my article to them.”

And she added, “I think that some of these treatments, if the research was better, might show benefits.”





Heat Wave Claims Lives in Europe, and Hottest Days Are Still to Come
By AGENCE FRANCE-PRESSE, The New York Times, July 19, 2006

PARIS, July 18 (Agence France-Presse) — Much of Europe baked Tuesday in temperatures reaching as high as 104 degrees in some places, in a heat wave that has claimed at least six lives.

Five deaths related to the oppressive heat were recorded on Tuesday alone, after the death on Sunday of a man in Murcia, in southern Spain.

In the Netherlands, two people succumbed to the heat on Tuesday during the opening day of an annual four-day walk in the eastern Nijmegen region, the Dutch news agency ANP reported.

In France’s southwest Bordeaux region, local authorities said two octogenarians fell victim to hyperthermia, or abnormally high body temperature. In Spain, a 44-year-old man died of heat exhaustion at Orense, in the northwestern region of Galicia, regional officials said, after he had reportedly been working outside.

Britain, already suffering the hottest day of the year on Tuesday, braced itself for what could be the nation’s hottest day on record as forecasters predicted that temperatures could surpass 102 degrees in parts of England on Wednesday.

Already, the London Underground system, the oldest subway system in the world, was a furnace on Tuesday with a record temperature of almost 117 degrees.

Meteorologists in Germany were warning residents that Thursday could be the hottest day of the year at more than 100 degrees, and July as a whole could be the hottest month in a century.

The high temperatures revived the specter of the 2003 heat wave, which killed 30,000 people in Europe, half of them in France.

Cyclists competing in the Tour de France sweated through the 116-mile stage in the Alps, which includes four notorious climbs.

French authorities, who were accused of reacting too slowly to the 2003 heat wave, were leaving little to chance this year, and hospitals and retirement homes were on high alert.

In Italy, the main farmers’ union said the country was suffering one of the worst droughts in 30 years with the situation in the north and the center particularly bad.

Comments

[monkeyhouse.livejournal.com]

they fed the president rectally?
*boggle*

[brdgt.livejournal.com]

Oh that loved that stuff back then, especially with water.

[antarcticlust.livejournal.com]

I took a class on optically stimulated luminescence dating, where we worked with the University of Nebraska professor who does a lot of work on the Nebraska sandhills with Joe Mason, a prof here in geography. It's really cool work- they can tell when the dunes moved, and where they came from, and how fast they formed and moved. We drove around Illinois looking at dunes- it's funny, because many of the houses are built on them because it's a nice high place, and I'm pretty sure there's no such thing as dune insurance.

That story about Garfield is mindboggling. I always wondered how he managed to survive for 80 days. How sad.

[brdgt.livejournal.com]

It's fascinating how quickly biology/genetics/genomics is changing right now.

[brdgt.livejournal.com]

I saw that one, but it kept getting bumped down in my posting order. Rats purring, huh? That's either creepy or sweet.