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New Way To Reproduce A Black Hole?

ScienceDaily (Aug. 22, 2009) — Despite their popularity in the science fiction genre, there is much to be learned about black holes, the mysterious regions in space once thought to be absent of light. In a paper published in the August 20 issue of Physical Review Letters, Dartmouth researchers propose a new way of creating a reproduction black hole in the laboratory on a much-tinier scale than their celestial counterparts.
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The new method to create a tiny quantum sized black hole would allow researchers to better understand what physicist Stephen Hawking proposed more than 35 years ago: black holes are not totally void of activity; they emit photons, which is now known as Hawking radiation.

"Hawking famously showed that black holes radiate energy according to a thermal spectrum," said Paul Nation, an author on the paper and a graduate student at Dartmouth. "His calculations relied on assumptions about the physics of ultra-high energies and quantum gravity. Because we can't yet take measurements from real black holes, we need a way to recreate this phenomenon in the lab in order to study it, to validate it."

In this paper, the researchers show that a magnetic field-pulsed microwave transmission line containing an array of superconducting quantum interference devices, or SQUIDs, not only reproduces physics analogous to that of a radiating black hole, but does so in a system where the high energy and quantum mechanical properties are well understood and can be directly controlled in the laboratory. The paper states, "Thus, in principle, this setup enables the exploration of analogue quantum gravitational effects."

"We can also manipulate the strength of the applied magnetic field so that the SQUID array can be used to probe black hole radiation beyond what was considered by Hawking," said Miles Blencowe, another author on the paper and a professor of physics and astronomy at Dartmouth.

This is not the first proposed imitation black hole, says Nation. Other proposed analogue schemes have considered using supersonic fluid flows, ultracold bose-einstein condensates and nonlinear fiber optic cables. However, the predicted Hawking radiation in these schemes is incredibly weak or otherwise masked by commonplace radiation due to unavoidable heating of the device, making the Hawking radiation very difficult to detect. "In addition to being able to study analogue quantum gravity effects, the new, SQUID-based proposal may be a more straightforward method to detect the Hawking radiation," says Blencowe.

In addition to Nation and Blencowe, other authors on the paper include Alexander Rimberg at Dartmouth and Eyal Buks at Technion in Haifa, Israel.
Adapted from materials provided by Dartmouth College.
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Illustration of a binary black hole system. (Credit: NASA/JPL)
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Artificial Life One Step Closer: Scientists Clone And Engineer Bacterial Genomes In Yeast And Transplant Genomes Back Into Bacterial Cells

ScienceDaily (Aug. 22, 2009) — Researchers at the J. Craig Venter Institute (JCVI), a not-for-profit genomic research organization, have just published results describing new methods in which the entire bacterial genome from Mycoplasma mycoides was cloned in a yeast cell by adding yeast centromeric plasmid sequence to the bacterial chromosome. Researchers modified it in yeast using yeast genetic systems. This modified bacterial chromosome was then isolated from yeast and transplanted into a related species of bacteria, Mycoplasma capricolum, to create a new type of M. mycoides cell.
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This is the first time that genomes have been transferred between branches of life—from a prokaryote to eukaryote and back to a prokaryote. The research was published by Carole Lartigue et al in the journal Science on August 21.

Hamilton Smith, M.D., one of the leaders of the JCVI team said, “I believe this work has important implications in better understanding the fundamentals of biology to enable the final stages of our work in creating and booting up a synthetic genome. This is possibly one of the most important new findings in the field of synthetic genomics.”

The research published today was made possible by previous breakthroughs at JCVI. In 2007 the team published results from the transplantation of the native M. mycoides genome into the M. capricolum cell which resulted in the M. capricolum cell being transformed into M. mycoides. This work established the notion that DNA is the software of life and that it is the DNA that dictates the cell phenotype.

In 2008 the same team reported on the construction of the first synthetic bacterial genome by assembling DNA fragments made from the four chemicals of life—ACGT. The final assembly of DNA fragments into the whole genome was performed in yeast by making use of the yeast genetic systems. However, when the team attempted to transplant the synthetic bacterial genome out of yeast into a recipient bacterial cell, all the experiments failed.

The researchers had previously established that no proteins were required for chromosome transplantations, however they reasoned that DNA methylation (a chemical modification of DNA that bacterial cells use to protect their genome from degradation by restriction enzymes, which are the proteins that cut DNA at specific sites) might be required for transplantation. When the chromosome was isolated direct from the bacterial cells it was likely already methylated and therefore transplantable due to it being protected from the cells restriction enzymes.

In this study, the team began by cloning the native M. mycoides genome into yeast by adding a yeast centromere to the bacterial genome. This is the first time a native bacterial genome has been grown successfully in yeast. Specific methylase enzymes were isolated from M. mycoides and used to methylate the M. mycoides genome isolated from yeast. When the DNA was methylated the chromosome was able to be successfully transplanted into a wild type species of M. capricolum. However, if the DNA was not first methylated the transplant experiments were not successful. To prove that the restriction enzymes in the M. capricolum cell were responsible for the destruction of the transplanted genome the team removed the restriction enzyme genes from the M. capricolum genome. When genome transplantations were performed using the restriction enzyme minus recipient cells, all the genome transplantations worked regardless of if the DNA was methylated or not.

“The ability to modify bacterial genomes in yeast is an important advance that extends yeast genetic tools to bacteria. If this is extendable to other bacteria we believe that these methods may be used in general laboratory practice to modify organisms,” said Sanjay Vashee, Ph.D., JCVI researcher and corresponding author on the paper.

The team now has a complete cycle of cloning a bacterial genome in yeast, modifying the bacterial genome as though it were a yeast chromosome and transplanting the genome back into a recipient bacterial cell to create a new bacterial strain. These new methods and knowledge should allow the team to now transplant and boot up the synthetic bacterial genome successfully.

The research published August 21 by JCVI researchers was funded by the company Synthetic Genomics Inc., a company co-founded by Drs. Smith and Venter.

Journal reference:

1. Lartigue et al. Creating Bacterial Strains from Genomes That Have Been Cloned and Engineered in Yeast. Science, August 20, 2009; DOI: 10.1126/science.1173759

Adapted from materials provided by J. Craig Venter Institute.
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J. Craig Venter Institute (2009, August 22). Artificial Life One Step Closer: Scientists Clone And Engineer Bacterial Genomes In Yeast And Transplant Genomes Back Into Bacterial Cells. ScienceDaily. Retrieved August 23, 2009, from http://www.sciencedaily.com­ /releases/2009/08/090821205730.htm
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Yeast. The entire bacterial genome from Mycoplasma mycoides was cloned in a yeast cell by adding yeast centromeric plasmid sequence to the bacterial chromosome and modifying it in yeast using yeast genetic systems. This modified bacterial chromosome was then isolated from yeast and transplanted into a related species of bacteria, Mycoplasma capricolum, to create a new type of M. mycoides cell. (Credit: Wikimedia Commons. Public Domain Image)
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Orchids And Fungi -- Partners For Life

ScienceDaily (Aug. 22, 2009) — Three Thai orchids have been found to rely on a wide range of fungi to help them take carbon out of the soil instead of producing their own organic carbon. A detailed study of the relationship, published in the open access journal BMC Biology, also features stunning pictures of the plants.
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* Plant cell

Marc-André Selosse and Mélanie Roy, from the Centre d'Ecologie Fonctionnelle et Evolutive, Montpellier, France, studied Aphyllorchis montana, A. caudata and Cephalanthera exigua orchids with Suyanee Vessabutr and Santi Watthana from the Queen Sirikit Botanic Garden, Thailand. These orchids have no chlorophyll and rely on fungi colonizing their roots for their carbon supply.

The plants, which grow on the ground in mountain forests, were collected from 10 different sampling sites in diverse parts of Thailand. The two Aphyllorchis orchids studied were found to associate with a wide range of fungi, while the Cephalanthera was much more specific.

Selosse said: "We show for the first time that certain tropical orchids associate with highly diverse soil fungi colonizing their roots; using stable isotopes, we show that they are likely to use these fungi as a carbon source." Most importantly for conservation concerns, all these fungi associate in turn with the roots of nearby green trees, where they collect carbon for the orchids.

Speaking about the results of the study, Selosse said: "Plants really interact with fungi in an unexpectedly diverse way - the impression one gains is that there is a great need for more research on biological interactions in the tropics to unravel this diversity."

Journal reference:

1. Mélanie Roy, Santi Watthana, Anna Stier, Franck Richard, Suyanee Vessabutr and Marc-André Selosse. Two mycoheterotrophic orchids from Thailand tropical dipterocarpacean forests associate with a broad diversity of ectomycorrhizal fungi. BMC Biology, 2009; (in press) [link]

Adapted from materials provided by BioMed Central, via EurekAlert!, a service of AAAS.
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This is an Aphyllorchis montana orchid. (Credit: Roy et al., BMC Biology)
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Aphids Saved From Gruesome Death By Virus-infected Bacteria

ScienceDaily (Aug. 22, 2009) — The term "beneficial virus" sounds like an oxymoron.
See also:
Plants & Animals

* Bacteria
* Insects (and Butterflies)
* Microbes and More

Earth & Climate

* Geochemistry
* Exotic Species
* Pollution

Reference

* Biological pest control
* Colostrum
* Vector (biology)
* Parasitism

But for pea aphids under attack by parasitic wasps, carrying infected bacteria is the difference between life and a slow death, according to new research.

The wasps lay eggs inside the aphids, and the wasp larvae eat the living aphids from the inside out.

"A parasitoid death would be a very gruesome death," said first author Kerry M. Oliver. "It's like the movie 'Alien' where this thing grows inside of you and then ruptures out of you and kills you."

In laboratory experiments, about eighty percent of aphids carrying uninfected Hamiltonella defensa bacteria died as a result of wasp attacks.

However, most of the aphids whose H. defensa bacteria had a particular virus did survive wasp attacks.

The research is the first demonstration that a virus that infects bacteria can help rather than harm the bacteria's animal host, Oliver said.

He and his colleagues conducted the research at The University of Arizona in Tucson.

The researchers also tested strains of aphids whose bacteria had once been infected but were no longer.

"In every instance where the virus was lost, protection was lost almost completely," said Oliver, now an assistant professor at the University of Georgia in Athens.

The virus, known as APSE, carries genes that code for toxins the researchers think are involved in the anti-wasp defense.

By contrast, being infected by viruses toting toxin codes often makes disease-causing bacteria such as E. coli more, not less, harmful to their human hosts.

Biologists call the part of the APSE viral DNA that codes for toxins a "mobile genetic element." The virus can and does move that mobile genetic element between individual bacteria and between different species of bacteria, Moran said.

The mobile genetic element can become incorporated into the recipient's DNA, giving the recipient the ability to make the toxin.

Species-to-species transmission of DNA via mobile genetic element is quite different from the well-known means by which parents pass on their genetic material to their offspring. In animals, pieces of DNA typically cannot jump from one adult organism's genetic material to another adult organism's genetic material.

"The coolest thing to me is that you can have selection and adaptation for (wasp) resistance that occurs in one species and then, whoosh, it could suddenly appear in another species," Moran said.

Pea aphids can be agricultural pests and Aphidius ervi, the wasp the researchers tested, is used to control aphid populations.

The team's research may also reveal why biological control of aphids with wasps works sometimes but not others, she said.

"Our work suggests it depends which virus the bacteria have."

Oliver and his UA colleagues Patrick H. Degnan, Martha S. Hunter and Nancy A. Moran, will publish their paper in the journal Science.

Moran, a UA Regents' Professor of ecology and evolutionary biology, has been investigating the role internal symbiotic bacteria play in the lives of the pea aphid Acyrthosiphon pisum for more than 15 years.

Aphids and other insects that feed on sap often house several species of such bacteria. Some, known as primary symbionts, provide aphids with essential nutrients that are not available in the nutrient-poor plant sap.

Aphids cannot survive without their primary symbionts, and those symbionts cannot survive outside of aphids.

The aphid-primary symbiont relationship is so close that the bacteria live inside specialized cells within the aphid.

In addition, aphids often carry other bacteria known as secondary symbionts. Those are symbionts that are needed for survival and reproduction only under certain conditions, such as the presence of particular enemies.

Oliver, working with Hunter and Moran, discovered that aphids carrying the secondary symbiont Hamiltonella defensa were wasp-resistant, but aphids without H. defensa were susceptible.

But when aphids were kept in the laboratory for generations without being exposed to the wasps, some strains lost their ability to resist wasp attacks, the researchers found.

It turned out that the susceptible aphids still carried the H. defensa bacteria, but the bacteria had lost the APSE virus.

To rule out genetic differences between aphids or bacteria as the source of wasp susceptibility, the researchers needed to do another experiment.

The team compared aphids that had H. defensa with APSE virus to the same strain of aphids carrying the same strain of H. defensa but without the virus.

When exposed to the wasps, about 90 percent of aphids with infected bacteria survived wasp attacks. Aphids without infected bacteria were pretty much doomed.

"It really shows how complicated life is," Oliver said. "It's really a microbial world."

The National Science Foundation, the U.S. Department of Agriculture and the National Institutes of Health funded the research.

Journal reference:

1. Kerry M. Oliver et al. Bacteriophages Encode Factors Required for Protection in a Symbiotic Mutualism. Science, August 21, 2009

Adapted from materials provided by University of Arizona, via EurekAlert!, a service of AAAS.
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A parasitoid wasp, Aphidius ervi, stalks pea aphids so she can lay eggs in them. The wasp is a tad bigger than 0.01 inches long. (Credit: 2005 Kerry M. Oliver)
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Niche Differences In Biodiversity: Species' Differences Are Responsible For Their Coexistence

ScienceDaily (Aug. 22, 2009) — Scientists at UC Santa Barbara have found strong evidence that niche differences are critical to biodiversity. Their findings are published online in this week's issue of the journal Nature.
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Plants & Animals

* Nature
* Ecology Research
* New Species

Earth & Climate

* Ecology
* Biodiversity
* Exotic Species

Reference

* Competitive exclusion in ecology
* Ecological niche
* Speciation
* Ecological succession

"Ecologists have long assumed that species differences in how they use the environment are key to explaining the large number of species we see all around us, but the importance of such niches have never been field tested," said first author Jonathan M. Levine, associate professor in UCSB's Department of Ecology, Evolution, and Marine Biology.

Levine and his co-author Janneke HilleRisLambers, a former postdoctoral fellow at UCSB, who is now an assistant professor at the University of Washington, did field testing of small plants. These plants were found in northern Santa Barbara County on rocky outcrops, where diversity is very high. They used a combination of mathematical techniques, as well as experimental approaches, to remove niche differences from these experimental communities.

"Our work is important because it resolves a century-old biodiversity puzzle," said Levine. "Why doesn't the single best competitor exclude all others in the community?"

Ecological theory has posed two possible answers to the coexistence conundrum. "The classic argument is that niche differences allow species to divide up the environment, much like different products cater to consumers of different tastes or incomes," he said. "The alternative is that competitors are so evenly matched that no single species can win –– as occurs when different airlines offer the same route for the same price."

Conflict between these hypotheses has formed the single greatest controversy in ecology over the last decade. The new study provides the first strong evidence that species' differences are responsible for their coexistence.

Although the study's primary importance is in advancing pure ecological science, understanding how biodiversity works is critical. It is in those communities in which niche differences maintain diversity that species loss has the greatest impact on plant production, and other ecosystem services to mankind –– from economic to aesthetic.

Journal reference:

1. Jonathan M. Levine & Janneke HilleRisLambers. The importance of niches for the maintenance of species diversity. Nature, 2009; DOI: 10.1038/nature08251

Adapted from materials provided by University of California - Santa Barbara.
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University of California - Santa Barbara (2009, August 22). Niche Differences In Biodiversity: Species' Differences Are Responsible For Their Coexistence. ScienceDaily. Retrieved August 23, 2009, from http://www.sciencedaily.com­ /releases/2009/08/090812163802.htm
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Jonathan Levine conducting his biodiversity research. (Credit: George Foulsham, Office of Public Affairs, UCSB)
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