One Species' Genome Discovered Inside Another's

Bacterial to Animal Gene Transfers Now Shown to be Widespread, with Implications for Evolution and Control of Diseases and Pests

MEDIA CONTACT: Jonathan Sherwood (585) 273-4726

Scientists at the University of Rochester and the J. Craig Venter Institute have discovered a copy of the genome of a bacterial parasite residing inside the genome of its host species.

The research, reported in today's Science, also shows that lateral gene transfer—the movement of genes between unrelated species—may happen much more frequently between bacteria and multicellular organisms than scientists previously believed, posing dramatic implications for evolution.

Such large-scale heritable gene transfers may allow species to acquire new genes and functions extremely quickly, says Jack Werren, a principle investigator of the study. If such genes provide new abilities in species that cause or transmit disease, they could provide new targets for fighting these diseases.

The results also have serious repercussions for genome-sequencing projects. Bacterial DNA is routinely discarded when scientists are assembling invertebrate genomes, yet these genes may very well be part of the organism's genome, and might even be responsible for functioning traits.

"This study establishes the widespread occurrence and high frequency of a process that we would have dismissed as science fiction until just a few years ago," says W. Ford Doolittle, Canada Research Chair in Comparative Microbial Genomics at Dalhousie University, who is not connected to the study. "This is stunning evidence for increased frequency of gene transfer."

"It didn't seem possible at first," says Werren, professor of biology at the University of Rochester and a world-leading authority on the parasite, called Wolbachia. "This parasite has implanted itself inside the cells of 70 percent of the world's invertebrates, coevolving with them. And now, we've found at least one species where the parasite's entire or nearly entire genome has been absorbed and integrated into the host's. The host's genes actually hold the coding information for a completely separate species."

Wolbachia may be the most prolific parasite in the world—a "pandemic," as Werren calls it. The bacterium invades a member of a species, most often an insect, and eventually makes its way into the host's eggs or sperm. Once there, the Wolbachia is ensured passage to the next generation of its host, and any genetic exchanges between it and the host also are much more likely to be passed on.

Since Wolbachia typically live within the reproductive organs of their hosts, Werren reasoned that gene exchanges between the two would frequently pass on to subsequent generations. Based on this and an earlier discovery of a Wolbachia gene in a beetle by the Fukatsu team at the University of Tokyo, Japan, the researchers in Werren's lab and collaborators at J. Craig Venter Institute (JCVI) decided to systematically screen invertebrates. Julie Dunning-Hotopp at JCVI found evidence that some of the Wolbachia genes seemed to be fused to the genes of the fruitfly, Drosophila ananassae, as if they were part of the same genome.

Michael Clark, a research associate at Rochester then brought a colony of ananassae into Werren's lab to look into the mystery. To isolate the fly's genome from the parasite's, Clark fed the flies a simple antibiotic, killing the Wolbachia. To confirm the ananassae flies were indeed cured of the wolbachia, Clark tested a few samples of DNA for the presence of several Wolbachia genes.

To his dismay, he found them.

"For several months, I thought I was just failing," says Clark. "I kept administering antibiotics, but every single Wolbachia gene I tested for was still there. I started thinking maybe the strain had grown antibiotic resistance. After months of this I finally went back and looked at the tissue again, and there was no Wolbachia there at all."

Clark had cured the fly of the parasite, but a copy of the parasite's genome was still present in the fly's genome. Clark was able to see that Wolbachia genes were present on the second chromosome of the insect.

Clark confirmed that the Wolbachia genes are inherited like "normal" insect genes in the chromosomes, and Dunning-Hotopp showed that some of the genes are "transcribed" in uninfected flies, meaning that copies of the gene sequence are made in cells that could be used to make Wolbachia proteins.

Werren doesn't believe that the Wolbachia "intentionally" insert their genes into the hosts. Rather, it is a consequence of cells routinely repairing their damaged DNA. As cells go about their regular business, they can accidentally absorb bits of DNA into their nuclei, often sewing those foreign genes into their own DNA. But integrating an entire genome was definitely an unexpected find.

"The question is, are these foreign genes providing new functions for the host? This is something we need to figure out."

Werren and Clark are now looking further into the huge insert found in the fruitfly, and whether it is providing a benefit. "The chance that a chunk of DNA of this magnitude is totally neutral, I think, is pretty small, so the implication is that it has imparted of some selective advantage to the host," says Werren. "The question is, are these foreign genes providing new functions for the host? This is something we need to figure out."

Evolutionary biologists will certainly take note of this discovery, but scientists conducting genome-sequencing projects around the world also may have to readjust their thinking.

Before this study, geneticists knew of examples where genes from a parasite had crossed into the host, but such an event was considered a rare anomaly except in very simple organisms. Bacterial DNA is very conspicuous in its structure, so if scientists sequencing a nematode genome, for example, come across bacterial DNA, they would likely discard it, reasonably assuming that it was merely contamination—perhaps a bit of bacteria in the gut of the animal, or on its skin.

But those genes may not be contamination. They may very well be in the host's own genome. This is exactly what happened with the original sequencing of the genome of the anannassae fruitfly—the huge Wolbachia insert was discarded from the final assembly, despite the fact that it is part of the fly's genome.

In the early days of the Human Genome Project, some studies appeared to show bacterial DNA residing in our own genome, but those were shown indeed to be caused by contamination. Wolbachia is not known to infect any vertebrates such as humans.

"Such transfers have happened before in the distant past" notes Werren. "In our very own cells and those of nearly all plants and animals are mitochondria, special structures responsible for generating most of our cells' supply of chemical energy. These were once bacteria that lived inside cells, much like Wolbachia does today. Mitochondria still retain their own, albeit tiny, DNA, and most of the genes moved into the nucleus in the very distant past. Like wolbachia, they have passively exchanged DNA with their host cells. It's possible wolbachia may follow in the path of mitochondria, eventually becoming a necessary and useful part of a cell.

"In a way, wolbachia could be the next mitochondria," says Werren. "A hundred million years from now, everyone may have a wolbachia organelle."

"Well, not us," he laughs. "We'll be long gone, but wolbachia will still be around."

This research was funded by the National Science Foundation's Frontiers in Integrative Biological Research program, which supports large, integrative projects addressing major questions in biology.

Where have all the dolphins gone?

The alarming drop in numbers of the Bay's three most common species of dolphin -- the striped, bottlenose and common -- can be attributed to one or both of two causes, Clive Martin, senior wildlife officer for the Biscay Dolphin Research Programme, told AFP.

"We know for a fact that by-catch is killing thousands of dolphins every year," he said, referring to commercial fishing operations in the bay, which is formed by the northern coast of Spain and the eastern French seaboard up to the tip of Brittany.

Martin singled out French "pair trawlers" that sweep the ocean with huge nets twice the size of a football pitch strung out between them as being especially lethal to the marine mammals.

"Dolphins are sometimes trapped hundreds at a time, and are asphyxiated" when they cannot come up for air, he said. Most dolphins typically replenish their lungs with fresh air every five minutes or so, he explained.

The second -- and probably more important -- reason that dolphins have disappeared is that there is simply very little left for them to eat.

"Anchovy fishing in the Bay of Biscay has progressively failed, and this year there is a complete ban by Spain, France and the United Kingdom on the fishing of anchovies," a principal food source for dolphins, Clive said.

He speculated that the roving sea mammals -- which swim in pods numbering in the dozens for bottlenose dolphins, and sometimes in the thousands for the common dolphin -- had moved west toward the mid-Atlantic looking for food.

A sharp decrease in the presence of many seabirds that also feed on fish -- such as auks, shearwaters and gannets -- lends support to this explanation.

The Bay of Biscay Research Programme has been systematically recording dolphin sightings along the same route from Bilbao, Spain to Portsmouth, England for 13 years.

Compared to the comparable period in 2004 and 2005, dolphin sightings in 2007 have decreased by 50 percent, he said.

The Bay of Biscay hosts a greater variety of dolphin populations than any other part of the world's oceans. Clive suggested that policy makers should consider transforming the area into a sanctuary for marine life.

© 2007 AFP

Unravelling The Random Fluctuations Of Nothing

Science Daily — The dream of theoretical physics is to unite behind a common theory that explains everything, but that goal has remained highly elusive. String theory emerged 40 years ago as one of the most promising candidates for such a theory, and has since slipped in and out of favour as new innovations have occurred.

Now Europe is fortunate to have one of the world’s leading experts in string theory working on an ambitious project that could make significant progress towards a unified theory, and at least help resolve two mysteries. One is how the universe emerged in the beginning as a random fluctuation of a vacuum state, and the other is a common explanation for all sub-atomic particles.

Czech physicist Dr. Martin Schnabl has been selected to receive a EURYI Award by the European science Foundation (ESF) and the European Heads of Research Councils (EuroHORCS) to help him pursue his project and build on five years of hard work culminating in the solution of an equation in string field theory that had gone unsolved for 20 years.

The elegance and beauty of the solution have been widely praised in a field that is highly regarded for its aesthetic appeal, drawing together many important concepts in mathematics and physics. The EURYI Awards scheme, entering its fourth and final year, aims to attract outstanding young researchers from anywhere in the world to work in Europe for the further development of European science, contributing to building up the next generation of leading European researchers.

String theory was developed in an attempt to bring together the physics of the big and the small, represented respectively by general relativity and quantum mechanics. It replaces the idea of elementary particles occupying a single zero point with a one dimensional string joining two points. In this sense a string, like a particle, is a model designed to represent or predict particular fundamental properties of the physical universe.

But while the number of particles continued to grow, the string was an attempt to join them all together, leading to the idea of a string field. This field represents all particles as vibrations of a string at given frequencies. The string field is then the sum total of all vibrations, elegantly bringing all particles together into one, so that physicists no longer need to be embarrassed by the discovery of yet another particle type.

“It's a sort of field theory for the infinite tower of oscillatory modes of a string, each of them representing different particle species,” Schnabl said. As Schnabl observed, string field theory, by explaining also how quantum mechanics is compatible with general relativity, is essential for understanding what goes on in situations where both of these are playing together.

“It is important in the regimes where quantum gravity is important, such as black holes and the beginning of the universe,” added Schnabl. In both cases, dimensions can be small, requiring quantum mechanics, but energies and mass are enormous, creating huge gravitational fields that currently can only be dealt with by general relativity.

One of the problems of string field theory lies in conducting experiments that test predictions or help inspire new theoretical developments. The theory predicts that the universe has 10 dimensions, of which four are the ones we observe in spacetime. Yet in 40 years no better candidate has emerged to explain the properties of the universe, or all universes, at all scales of time and distance. Furthermore the string field has a habit of feeding the rest of physics and mathematics by virtue of lying at the cutting edge of analytical reason. This is why it should interest lay people as well, insisted Schnabl. “The very general public can be interested if they enjoy watching mankind's advances in understanding some of the deepest questions about the nature of our universe.”

Schnabl, a 34 year-old Czech scientist, is a member of Princeton’s Institute for Advanced Study. He will be conducting his research at the Institute of Physics Academy of Sciences of the Czech Republic after receiving his award in Helsinki, Finland on 27 September 2007 with other 19 young researchers.

After wiretapping victory, Bush says he wants more authority from Congress

Michael Roston
Published: Monday August 6, 2007

The day after President George W. Bush marshaled political forces in Congress to grant him greater authority to engage in counterterrorism-related spying, the president stated that he would seek greater changes to the Foreign Intelligence Surveillance Act when the legislative branch returns to work in September.

"While I appreciate the leadership it took to pass this bill, we must remember that our work is not done," the President said in his Sunday statement. "This bill is a temporary, narrowly focused statute to deal with the most immediate shortcomings in the law."

The President said next month he would focus on further immunizing private companies that cooperate with government wiretapping. However, he used complicated language to describe these activities.

"When Congress returns in September the Intelligence committees and leaders in both parties will need to complete work on the comprehensive reforms requested by Director McConnell, including the important issue of providing meaningful liability protection to those who are alleged to have assisted our Nation following the attacks of September 11, 2001," he said.

One constitutional scholar derided Bush's reasoning, particularly the tortuous language in his statement.

"Apparently 'allegedly helped us stay safe' is Bush Administration code for telecom companies and government officials who participated in a conspiracy to perform illegal surveillance," wrote Yale Law Professor Jack Balkin in a Monday morning blog post. "Because what they did is illegal, we do not admit that they actually did it, we only say that they are alleged to have done it."

Balkin also offered another amusing interpretation of Bush's words.

"Or perhaps the Administration is suggesting that although such parties are alleged to have helped the country stay safe, there's no evidence that their repeated violations of federal law actually did much to promote our security," he quipped.

Last week, National Intelligence Director Mike McConnell made a related appeal, appearing to acknowledge that telecommunications companies had not only 'allegedly' assisted the government in its wiretapping activities.

"[T]hose who assist the Government in protecting us from harm must be protected from liability," he said in a Friday statement. "This includes those who are alleged to have assisted the Government after September 11, 2001 and have helped keep the country safe....I appreciate the commitment of the congressional leadership to address this particular issue immediately upon the return of Congress in September 2007."

And for one top Congressional advocate of Bush's proposed wiretapping 'reforms,' the participation of telecommunication companies in government spying was not described as an allegation at all.

"These are companies who were doing the patriotic thing," said Rep. Pete Hoekstra (R-MI), Ranking Republican on the House Permanent Select Committee on Intelligence, in an interview with Paul Gigot for Fox News's Journal Editorial Report on Saturday night. "They were helping the U.S. government, the American people, get the information that we believe we needed to keep us safe. They voluntarily participated, and now that the program is exposed, they've been open to all kinds of lawsuits."

Meanwhile, pundits were already building the case for expanding liability protections for telecommunications companies that help the government spy.

"The new legislation does not go far enough because, while it addresses liability for telecommunications companies under FISA, it does not look at companies' liabilities under other laws," wrote Harold Furchtgott-Roth, a former Federal Communications Commission commisioner, in a Monday article in the New York Sun. "This is an important point because the American Civil Liberties Union and other groups have many legal cases against various communications companies for cooperating with the federal government on many matters outside FISA."

Hoekstra in a statement released to RAW STORY Saturday night after the House passed his legislation said that, "he would use momentum from Congressional Republicans’ efforts to fix FISA to push for comprehensive reform of the law to...obtain retroactive liability for parties who may have aided the government."

But Democratic House Speaker Nancy Pelosi also stated her own plan to pass legislation in September with the intention of countering the changes enacted by the President's allies in Congress.

"Tonight, the House passed S. 1927, a bill approved by the Senate yesterday, which is an interim response to the Administration’s request for changes in FISA, and which was sought to fill an intelligence gap which is asserted to exist," the Speaker said in a Saturday letter to the House Intelligence and Judiciary Committees. "Many provisions of this legislation are unacceptable, and, although the bill has a six month sunset clause, I do not believe the American people will want to wait that long before corrective action is taken."

She therefore called on the committees, "as soon as possible after Congress reconvenes," to pass "legislation which responds comprehensively to the Administration’s proposal while addressing the many deficiencies in S. 1927."

Why Media have little time, tolerance for 'second-tier' candidates

Clear the Stage

By Peter Hart

With the public still many months away from choosing major-party presidential candidates, robust public debates with a wide sampling from across the political spectrum would seem to be an empowering democratic exercise. And for a press corps so often complaining about the scripted and stilted tedium of day-to-day political campaigning, wide-open debates and a freewheeling exchange of ideas might make for good TV.

But many journalists seem not to agree. In the coverage of the early candidate debates, the media have fallen into a familiar pattern of trying to “weed out” candidates who do not meet the press corps’ ideological preferences (Extra!, 9–10/03). The most vigorous weeding, as usual, has been directed at left-leaning Democrats, but the media outrage when Rep. Ron Paul (R.-Texas) raised questions about the “war on terror” demonstrated that the media’s insistence on ideological orthodoxy is unfortunately bipartisan.

In the wake of the first Democratic candidates’ debate (MSNBC, 4/26/07), many media outlets and commentators seemed annoyed that the so-called “second-tier” candidates were even bothering to run. As FAIR has noted (Extra! Update, 6/07), early election polls are very bad at predicting the eventual nominee, so it’s unwise to use them to determine which candidates are viable front-runners and which campaigns are merely a nuisance.

That’s not the way it’s seen by many Washington pundits, though—at least when it comes to Democrats. The Los Angeles Times argued (4/27/07) that the wide format of one Democrats’ debate “allowed each candidate a total of 11 minutes to talk—giving [Ohio Rep. Dennis] Kucinich and [former Senator of Alaska Mike] Gravel, both of whom have a negligible showing in polls, equal time with the front-runners, which they used to take aggressive hits at [New York Sen. Hillary] Clinton and [Illinois Sen. Barack] Obama.”

It’s not merely about polling, of course—if that were true, the media would be just as scornful of New Mexico Gov. Bill Richardson or Sen. Joe Biden (D.-Del.), who both lurk near the bottom in national surveys. The problem is that the press sees some of the lesser candidates as potentially shifting the debate. As Washington Post columnist David Broder lamented (6/7/07):

Prodded by four long shots for the nomination and threatened by the rhetoric of former senator John Edwards, a serious contender, the two front-runners, Hillary Rodham Clinton and Barack Obama, have abandoned their cautious advocacy of a phased withdrawal of U.S. forces and now are defending votes to cut off support for troops fighting insurgents in Iraq.

Broder can take comfort in the fact that this “threatening” rhetoric isn’t actually given much debate time; while Kucinich and Gravel were asked only eight questions in the April 26 debate, “front-runners” Clinton, Obama and former vice presidential candidate John Edwards each received 12. No doubt aware of this disparity, Sen. Chris Dodd’s campaign took the unusual approach of counting up airtime in the June 3 debate. The disparities were more or less in line with the polling—top-tier candidates spoke more than the also-rans, with the debate moderator—CNN’s Wolf Blitzer—logging 13 minutes of time, more than all candidates except Clinton and Obama.

After that debate, CNN’s Howard Kurtz (4/29/07) seemed annoyed media were paying any attention at all to Gravel: “He was sort of a bomb-thrower on that stage. Why should a network allow somebody with, say, zero chance of becoming president into these debates?”

CBS’s Bob Schieffer lodged a similar complaint (Face the Nation, 4/29/07): “Is it fair to have all these people out there? I mean, it is a free country. Everybody [who] wants to run for president should have that opportunity and does. But clearly, somebody like former Sen. Mike Gravel is not going to be a serious candidate, and yet he gets equal time, and . . . I would just say it honestly: In my view, it just wastes time.”

While Schieffer may see an inclusive debate as time wasted, MSNBC host Chris Matthews pinpointed the importance of including “second-tier” candidates when he asked Obama campaign adviser David Axelrod (4/26/07) if he thought his candidate “was hampered” by Gravel and Kucinich’s “radical critique . . . it made your guy seem more like he was part of the establishment than he would like to have seemed?”

Often reporters and pundits act, when they’re trying to winnow the field, as if they’re only aiming to improve the democratic process. But Matthews’ question recognizes that there is a sizable segment of the population whose dissatisfaction with mainstream party politics wouldn’t be included at all in the national debate if it weren’t for the “second tier.”

The initial reaction to lesser-known Republican candidates appearing in debates was quite different. After the GOP debate, the L. A. Times editorialized (5/4/07), “The breadth of small-fries in the field makes it hard to define a coherent Republican message, but that’s a sign of intellectual ferment in the troubled GOP.”

When three of the GOP contenders signaled their doubts about evolution, the Washington Post helpfully noted (5/6/07) that “a look at public polling on the issue reveals that the three men aren’t far from the mainstream in that belief.” And in an online column, Newsweek’s Howard Fineman declared (5/3/07): “Let’s hear it for the ‘second-’ and ‘third-’ tier presidential candidates. . . . If you know, as I do, some of the other, putatively lesser, GOP contenders, you have to be impressed with the depth of their political passion, their knowledge and even their track records. They represent, in undiluted form, the vivid primary colors of the conservative movement.”

The contrast was striking: The lesser-known (and generally more conservative) Republican candidates were cheered for participating in the process, while the Democratic candidates who represent more progressive ideals were derided for taking up the time of other, more worthy candidates. And once a candidate is deemed worthy of the “top tier,” they’re more often given a pass on things that might sink a lesser rival. When GOP contender Mitt Romney, for example, made a bizarre claim during a June 5 debate about Saddam Hussein barring weapons inspectors from Iraq prior to the March 2003 invasion, the gaffe was all but invisible in the post-debate press (FAIR Media Advisory, 6/8/07).

But there are still ideological pitfalls for a Republican lesser-known, as Ron Paul discovered during another Republican debate (5/15/07). Paul dared to raise a taboo subject: al Qaeda’s stated reasons for the September 11 attacks. “They attack us because we’ve been over there, we’ve been bombing Iraq for 10 years,” Paul said. “We’ve been in the Middle East. . . . Have you ever read about the reasons they attacked us?”

GOP front-runner Rudy Giuliani responded by saying he’d never heard such an “absurd explanation” for the September 11 attacks, “that we invited the attack because we were attacking Iraq”—a response that got sustained applause from the audience, and much the same from the press corps.

The media reacted strongly in support of Giuliani. Fox News Channel’s John Gibson scored a twofer (5/17/07) by mangling Paul’s words (“Paul suggested that the U.S. actually had a hand in the terrorist attacks”) and then linking him to the Democratic Party, citing a poll that claims many Democrats “think President Bush knew about the 9/11 attacks beforehand. . . . It wouldn’t have stunned me had it come up in the Democratic debate, but it’s a jaw-dropper to see it in the Republican debate.” Time magazine’s Joe Klein (5/17/07) declared it to be Paul’s “singular moment of weirdness,” and stated that Giuliani “reduced Paul to history.”

Lost amidst the media excitement over Giuliani’s response was whether or not Paul was correct. The Nation’s John Nichols wrote a column (5/16/07) pointing out that Paul’s argument more or less echoed the findings of the 9/11 Commission, which noted that Osama bin Laden had called in 1996 for Muslims to drive U.S. troops out of Saudi Arabia—whose mission there was largely to support air patrols over Iraq—and that subsequent statements rallied followers to oppose U.S. policy in Israel/Palestine and Iraq. Such discussions are common in academic and policy circles, but not so in the mainstream media.

MSNBC host Chris Matthews declared (5/16/07) that “Ron Paul has a big problem,” saying that while it was important for Americans to “understand the simmering hatred and the hostility, the sea of hostility, over there,” Paul’s comments were unacceptable on factual grounds: “You can’t say it’s because we put troops in Iraq, over the no-fly zone, because they tried to blow up that same building back in ’93, before all these skirmishes over the no-fly zone. You can’t say that particular argument.”

Paul actually made no reference to the no-fly zones in his debate remarks. But if that’s what Matthews thought Paul was referring to, the cable news host should be aware that the no-fly policy was first declared in 1991, and that there was an extensive series of air raids in support of the no-fly zones in January 1993—a month before the 1993 attack.

When Paul convened a press conference on May 24 at the National Press Club featuring former CIA terrorism expert Michael Scheuer, the press ignored the event, although reporters have interviewed Scheurer regularly for several years. The fact that Scheuer essentially agrees with Paul’s premise, as he explained to AntiWar radio (5/18/07), might explain the media’s fickleness.

CNN host Howard Kurtz (5/20/07) slammed Paul’s “unorthodox theory” about the September 11 attacks, declaring that “news organizations are allowing ego-driven fringe candidates to muck up debates among those with an actual shot at the White House.” The real problem isn’t that Ron Paul can’t win the White House, or that progressive candidates might “muck up” a debate; if anything, they’ve started a debate the media don’t want to have.