Nov. 22, 2013 — Viruses cannot only cause illnesses in humans, they also infect bacteria. Those protect themselves with a kind of 'immune system' which -- simply put -- consists of specific sequences in the genetic material of the bacteria and a suitable enzyme. It detects foreign DNA, which may originate from a virus, cuts it up and thus makes the invaders harmless.
Scientists from the Helmholtz Centre for Infection Research (HZI) in Braunschweig have now shown that the dual-RNA guided enzyme Cas9, which is involved in the process, has developed independently in various strains of bacteria. This enhances the potential of exploiting the bacterial immune system for genome engineering.
Even though it has only been discovered in recent years the immune system with the cryptic name 'CRISPR-Cas' has been attracting attention of geneticists and biotechnologists as it is a promising tool for genetic engineering. CRISPR is short for Clustered Regularly Interspaced Palindromic Repeats, whereas Cas simply stands for the CRISPR-associated protein. Throughout evolution, this molecule has developed independently in numerous strains of bacteria. This is now shown by Prof Emmanuelle Charpentier and her colleagues at the Helmholtz Centre for Infection Research (HZI) who published their finding in the international open access journal Nucleic Acids Research.
The CRISPR-Cas-system is not only valuable for bacteria but also for working in the laboratory. It detects a specific sequence of letters in the genetic code and cuts the DNA at this point. Thus, scientists can either remove or add genes at the interface. By this, for instance, plants can be cultivated which are resistant against vermins or fungi. Existing technologies doing the same thing are often expensive, time consuming or less accurate. In contrast to them the new method is faster, more precise and cheaper, as fewer components are needed and it can target longer gene sequences.
Additionally, this makes the system more flexible, as small changes allow the technology to adapt to different applications. "The CRISPR-Cas-system is a very powerful tool for genetic engineering," says Emmanuelle Charpentier, who came to the HZI from Umeå and was awarded with the Humboldt Professorship in 2013. "We have analyzed and compared the enzyme Cas9 and the dual-tracrRNAs-crRNAs that guide this enzyme site-specifically to the DNA in various strains of bacteria." Their findings allow them to classify the Cas9 proteins originating from different bacteria into groups. Within those the CRISPR-Cas systems are exchangeable which is not possible between different groups.
This allows for new ways of using the technology in the laboratory: The enzymes can be combined and thereby a variety of changes in the target-DNA can be made at once. Thus, a new therapy for genetic disorders caused by different mutations in the DNA of the patient could be on the horizon. Furthermore, the method could be used to fight the AIDS virus HIV which uses a receptor of the human immune cells to infect them. Using CRISPR-Cas, the gene for the receptor could be removed and the patients could become immune to the virus. However, it is still a long way until this aim will be reached.
Still those examples show the huge potential of the CRISPR-Cas technology. "Some of my colleagues already compare it to the PCR," says Charpentier. This method, developed in the 1980s, allows scientists to 'copy' nucleic acids and therefore to manifold small amounts of DNA to such an extent that they can be analyzed biochemically. Without this ground-breaking technology a lot of experiments we consider to be routine would have never been possible.
Charpentier was not looking for new molecular methods in the first place. "Originally, we were looking for new targets for antibiotics. But we found something completely different," says Charpentier. This is not rare in science. In fact some of the most significant scientific discoveries have been made incidentally or accidentally.
Nov. 22, 2013 — For years scientists have intensely argued over whether increases of potent methane gas concentrations in the atmosphere - from about 5,000 years ago to the start of the industrial revolution - were triggered by natural causes or human activities.
A new study, which will be published Friday in the journal Science, suggests the increase in methane likely was caused by both.
Lead author Logan Mitchell, who coordinated the research as a doctoral student at Oregon State University, said the "early anthropogenic hypothesis," which spawned hundreds of scientific papers as well as books, cannot fully explain on its own the rising levels of atmospheric methane during the past 5,000 years, a time period known as the mid- to late-Holocene. That theory suggests that human activities such as rice agriculture were responsible for the increasing methane concentrations.
Opponents of that theory argue that human activities during that time did not produce significant amounts of methane and thus natural emissions were the dominant cause for the rise in atmospheric CH4.
"We think that both played a role," said Mitchell, who is now a post-doctoral researcher at the University of Utah. "The increase in methane emissions during the late Holocene came primarily from the tropics, with some contribution from the extratropical Northern Hemisphere.
"Neither modeled natural emissions alone, nor hypothesized anthropogenic emissions alone, are able to account for the full increase in methane concentrations," Mitchell added. "Combined, however, they could account for the full increase."
Scientists determine methane levels by examining ice cores from polar regions. Gas bubbles containing ancient air trapped within the ice can be analyzed and correlated with chronological data to determine methane levels on a multidecadal scale. Mitchell and his colleagues examined ice cores from the West Antarctic Ice Sheet Divide and the Greenland Ice Sheet Project and found differences between the two.
Ice cores from Greenland had higher methane levels than those from Antarctica because there are greater methane emissions in the Northern Hemisphere. The difference in methane levels between the hemispheres, called the Inter-Polar Difference, did not change appreciably over time.
"If the methane increase was solely natural or solely anthropogenic, it likely would have tilted the Inter-Polar Difference out of its pattern of relative stability over time," Mitchell said.
Since coming out of the ice age some 10,000 years ago summer solar insolation in the Northern Hemisphere has been decreasing as a result of the Earth's changing orbit, according to Edward Brook, a paleoclimatologist in Oregon State's College of Earth, Ocean, and Atmospheric Sciences and Mitchell's major professor. This decrease affects the strength of Asian summer monsoons, which produce vast wetlands and emit methane into the atmosphere.
Yet some 5,000 years ago, atmospheric methane began rising and had increased about 17 percent by the time the industrial revolution began around 1750.
"Theoretically, methane levels should have decreased with the loss of solar insolation in the Northern Hemisphere, or at least remained stable instead of increasing," said Brook, a co-author on the Science article. "They had been roughly on a parallel track for some 800,000 years."
Mitchell used previous models that hypothesized reasons for the methane increase - both natural and anthropogenic - and compared them to the newly garnered ice core data. None of them alone proved sufficient for explaining the greenhouse gas increase. When he developed his own model combining characteristics of both the natural and anthropogenic hypotheses, it agreed closely with the ice core data.
Other researchers have outlined some of the processes that may have contributed to changes in methane emissions. More than 90 percent of the population lived in the Northern Hemisphere, especially in the lower latitudes, and the development of rice agriculture and cattle domestication likely had an influence on methane emissions. On the natural side, changes in the Earth's orbit could have been responsible for increasing methane emissions from tropical wetlands.
"All of these things likely have played a role," Mitchell said, "but none was sufficient to do it alone."
The study was supported by the National Science Foundation's Office of Polar Programs, with additional support from the Oregon National Aeronautics and Space Administration (NASA) Space Grant Consortium.
Nov. 22, 2013 — Sea-level rise in this century is likely to be 70-120 centimeters by 2100 if greenhouse-gas emissions are not mitigated, a broad assessment of the most active scientific publishers on that topic has revealed. The 90 experts participating in the survey anticipate a median sea-level rise of 200-300 centimeters by the year 2300 for a scenario with unmitigated emissions.
In contrast, for a scenario with strong emissions reductions, experts expect a sea-level rise of 40-60 centimeters by 2100 and 60-100 centimeters by 2300. The survey was conducted by a team of scientists from the USA and Germany.
"While the results for the scenario with climate mitigation suggest a good chance of limiting future sea-level rise to one meter, the high emissions scenario would threaten the survival of some coastal cities and low-lying islands," says Stefan Rahmstorf from the Potsdam Institute for Climate Impact Research. "From a risk management perspective, projections of future sea-level rise are of major importance for coastal planning, and for weighing options of different levels of ambition in reducing greenhouse-gas emissions."
Projecting sea-level rise, however, comes with large uncertainties, since the physical processes causing the rise are complex. They include the expansion of ocean water as it warms, the melting of mountain glaciers and ice caps and of the two large ice sheets in Greenland and Antarctica, and the pumping of ground water for irrigation purposes. Different modeling approaches yield widely differing answers. The recently published IPCC report had to revise its projections upwards by about 60 percent compared to the previous report published in 2007, and other assessments of sea-level rise compiled by groups of scientists resulted in even higher projections. The observed sea-level rise as measured by satellites over the past two decades has exceeded earlier expectations.
Largest elicitation on sea-level rise ever: 90 key experts from 18 countries
"It this therefore useful to know what the larger community of sea-level experts thinks, and we make this transparent to the public," says lead author Benjamin Horton from the Institute of Marine and Coastal Sciences at Rutgers University in New Jersey. "We report the largest elicitation on future sea-level rise conducted from ninety objectively selected experts from 18 countries." The experts were identified from peer-reviewed literature published since 2007 using the publication database 'Web of Science' of Thomson Reuters, an online scientific indexing service, to make sure they are all active researchers in this area. 90 international experts, all of whom published at least six peer-reviewed papers on the topic of sea-level during the past 5 years, provided their probabilistic assessment.
The survey finds most experts expecting a higher rise than the latest IPCC projections of 28-98 centimeters by the year 2100. Two thirds (65%) of the respondents gave a higher value than the IPCC for the upper end of this range, confirming that IPCC reports tend to be conservative in their assessment.
The experts were also asked for a "high-end" estimate below which they expect sea-level to stay with 95 percent certainty until the year 2100. This high-end value is relevant for coastal planning. For unmitigated emissions, half of the experts (51%) gave 1.5 meters or more and a quarter (27%) 2 meters or more. The high-end value in the year 2300 was given as 4.0 meters or higher by the majority of experts (58%).
While we tend to look at projections with a focus on the relatively short period until 2100, sea-level rise will obviously not stop at that date. "Overall, the results for 2300 by the expert survey as well as the IPCC illustrate the risk that temperature increases from unmitigated emissions could commit coastal populations to a long-term, multi-meter sea-level rise," says Rahmstorf. "They do, however, illustrate also the potential for escaping such large sea-level rise through substantial reductions of emissions."
Nov. 22, 2013 — No matter where they live in the world, university students who were spanked as children are more likely to engage in criminal behavior, according to new research by Murray Straus, co-director of University of New Hampshire Family Research Lab. Even young adults whose parents were generally loving and helpful as they were growing up showed higher rates of criminal behavior.
Straus will present the research results, "Crime by University Students in 15 Nations: Links to Spanking and Positive Parenting at Age 10 by Father, Mother, And Both Parents," today at the annual meeting of the American Society of Criminology in Atlanta.
"The results show that spanking is associated with an increase in subsequent misbehavior, which is the opposite of what almost everyone believes. These results are consistent with a large number of high quality peer-reviewed studies," Straus said.
Straus looked at criminality trends of university students in 15 countries using nine measures of criminality. The measures are criminal beliefs, antisocial personality, father assaulted by child in previous year, mother assaulted by child in previous year, physical assault of partner in previous year, severe physical assault of partner in previous year, physically injured partner in previous year, attacked someone intending to seriously injure them, and stolen money from anyone, including family.
The 15 countries are Hong Kong, Taiwan, Belgium, Greece, Italy, Norway, Poland, Russia, Scotland, Slovenia, Spain, Switzerland, Israel, Canada, and the United States. Straus took into account the influence of such factors as parental education, misbehavior as a child, loving and positive approach to correcting misbehavior, student gender, student age, and nation. One of the most interesting findings was related to the effect of parents who took a loving and positive approach but who also spanked their children.
"So many parents and child psychologists believe that if spanking is done by loving and helpful parents, it has no harmful effect," Straus said. "This study and only one other study I know of that empirically investigated this belief found that it is not true. Spanking seems to be associated with an increased probability of subsequent child behavior problems regardless of culture and, regardless of whether it done by loving and helpful parents."
"Children need lots guidance and correction, but not by being physically attacked under the euphemism of 'spanking,' " Straus said.
Straus found that positive parenting decreased the probability of subsequent crime but mainly for nonfamily crime. And even though positive parenting was associated with less crime by students, the relation of spanking to crime remained for all nine aspects of crime.
"Most people will find these results hard to understand because parents spank to correct misbehavior and to teach the child to be law-abiding citizens," Straus said.
Straus also investigated the criminal behavior of university students who were spanked just by their fathers, just by their mothers, or by both parents. He found that university students who were spanked by both parents are associated with the greatest increase in criminality for eight of the nine criminality measures.
In most of the 15 nations, two-thirds of university students said they were hit when they were age 10, and among those who were hit, they said it typically was between once and twice a week. If university students were hit by only one parent, more often than not the mother was the parent carrying out the punishment.
Straus' findings are based on data from the International Parenting Study of 15 nations and 11,408 university students.
Widely considered the foremost researcher in his field, Straus is the co-director of the Family Research Laboratory and professor emeritus of sociology at UNH. He has studied spanking by large and representative samples of American parents since 1969. His newest book is "The Primordial Violence: Spanking Children, Psychological Development, Violence, and Crime" (Routledge, 2013). He also is the author of "Beating The Devil Out Of Them: Corporal Punishment In American Families And Its Effects On Children" (Transaction, 2006).
He has been president of three scientific societies including the National Council on Family Relations, and has been an advisor to the National Institutes of Health and the National Science Foundation. Much of his research on spanking can be downloaded from http://pubpages.unh.edu/~mas2.
Straus's research was supported, in part, by a grant from the National Institute of Mental Health.
Archaeologists discover largest, oldest wine cellar in Near East: 3,700 year-old store room held 2,000 liters of strong, sweet wine
Nov. 22, 2013 — Would you drink wine flavored with mint, honey and a dash of psychotropic resins? Ancient Canaanites did more than 3,000 years ago.
Archaeologists have unearthed what may be the oldest -- and largest -- ancient wine cellar in the Near East, containing forty jars, each of which would have held fifty liters of strong, sweet wine. The cellar was discovered in the ruined palace of a sprawling Canaanite city in northern Israel, called Tel Kabri. The site dates to about 1,700 B.C. and isn't far from many of Israel's modern-day wineries.
"This is a hugely significant discovery -- it's a wine cellar that, to our knowledge, is largely unmatched in age and size," says Eric Cline chair of the Department of Classical and Near Eastern Languages and Civilizations of at The George Washington University. Cline and Assaf Yasur-Landau, chair of the Department of Maritime Civilizations at the University of Haifa, co-directed the excavation. Andrew Koh, assistant professor of classical studies at Brandeis University, was an associate director.
The team's findings will be presented this Friday in Baltimore at the annual meeting of the American Schools of Oriental Research.
Koh, an archaeological scientist, analyzed the jar fragments using organic residue analysis. He found molecular traces of tartaric and syringic acid, both key components in wine, as well as compounds suggesting ingredients popular in ancient wine-making, including honey, mint, cinnamon bark, juniper berries and resins. The recipe is similar to medicinal wines used in ancient Egypt for two thousand years.
Koh also analyzed the proportions of each diagnostic compound and discovered remarkable consistency between jars.
"This wasn't moonshine that someone was brewing in their basement, eyeballing the measurements," Koh notes. "This wine's recipe was strictly followed in each and every jar."
Important guests drank this wine, notes Yasur-Landau.
"The wine cellar was located near a hall where banquets took place, a place where the Kabri elite and possibly foreign guests consumed goat meat and wine," he says.
At the end of the season, the team discovered two doors leading out of the wine cellar -- one to the south, and one to the west. Both probably lead to additional storage rooms. They'll have to wait until 2015 to find out for sure.
Nov. 22, 2013 — A new species of carnivorous dinosaur -- one of the three largest ever discovered in North America -- lived alongside and competed with small-bodied tyrannosaurs 98 million years ago. This newly discovered species, Siats meekerorum, (pronounced see-atch) was the apex predator of its time, and kept tyrannosaurs from assuming top predator roles for millions of years.
Named after a cannibalistic man-eating monster from Ute tribal legend, Siats is a species of carcharodontosaur, a group of giant meat-eaters that includes some of the largest predatory dinosaurs ever discovered. The only other carcharodontosaur known from North America is Acrocanthosaurus, which roamed eastern North America more than 10 million years earlier. Siats is only the second carcharodontosaur ever discovered in North America; Acrocanthosaurus, discovered in 1950, was the first.
"It's been 63 years since a predator of this size has been named from North America," says Lindsay Zanno, a North Carolina State University paleontologist with a joint appointment at the North Carolina Museum of Natural Sciences, and lead author of a Nature Communications paper describing the find. "You can't imagine how thrilled we were to see the bones of this behemoth poking out of the hillside."
Zanno and colleague Peter Makovicky, from Chicago's Field Museum of Natural History, discovered the partial skeleton of the new predator in Utah's Cedar Mountain Formation in 2008. The species name acknowledges the Meeker family for its support of early career paleontologists at the Field Museum, including Zanno.
The recovered specimen belonged to an individual that would have been more than 30 feet long and weighed at least four tons. Despite its giant size, these bones are from a juvenile. Zanno and Makovicky theorize that an adult Siats might have reached the size of Acrocanthosaurus, meaning the two species vie for the second largest predator ever discovered in North America. Tyrannosaurus rex, which holds first place, came along 30 million years later and weighed in at more than twice that amount.
Although Siats and Acrocanthosaurus are both carcharodontosaurs, they belong to different sub-groups. Siats is a member of Neovenatoridae, a more slender-bodied group of carcharodontosaurs. Neovenatorids have been found in Europe, South America, China, Japan and Australia. However, this is the first time a neovenatorid has ever been found in North America.
Siats terrorized what is now Utah during the Late Cretaceous period (100 million years ago to 66 million years ago). It was previously unknown who the top meat-eater was in North America during this period. "Carcharodontosaurs reigned for much longer in North America than we expected," says Zanno. In fact, Siats fills a gap of more than 30 million years in the fossil record, during which time the top predator role changed hands from carcharodontosaurs in the Early Cretaceous to tyrannosaurs in the Late Cretaceous.
The lack of fossils left paleontologists unsure about when this change happened and if tyrannosaurs outcompeted carcharodontosaurs, or were simply able to assume apex predator roles following carcharodontosaur extinction. It is now clear that Siats' large size would have prevented smaller tyrannosaurs from taking their place atop the food chain.
"The huge size difference certainly suggests that tyrannosaurs were held in check by carcharodontosaurs, and only evolved into enormous apex predators after the carcharodontosaurs disappeared," says Makovicky. Zanno adds, "Contemporary tyrannosaurs would have been no more than a nuisance to Siats, like jackals at a lion kill. It wasn't until carcharodontosaurs bowed out that the stage could be set for the evolution of T. rex."
At the time Siats reigned, the landscape was lush, with abundant vegetation and water supporting a variety of plant-eating dinosaurs, turtles, crocodiles, and giant lungfish. Other predators inhabited this ecosystem, including early tyrannosaurs and several species of other feathered dinosaurs that have yet to be described by the team. "We have made more exciting discoveries including two new species of dinosaur," Makovicky says.
"Stay tuned," adds Zanno. "There are a lot more cool critters where Siats came from."
All fieldwork was conducted under permits through the Bureau of Land Management and funded by the Field Museum. Research was funded by North Carolina State University, North Carolina Museum of Natural Sciences and the Field Museum.
Nov. 21, 2013 — Obesity may alter the way we taste at the most fundamental level: by changing how our tongues react to different foods.
In a Nov. 13 study in the journal PLOS ONE, University at Buffalo biologists report that being severely overweight impaired the ability of mice to detect sweets.
Compared with slimmer counterparts, the plump mice had fewer taste cells that responded to sweet stimuli. What's more, the cells that did respond to sweetness reacted relatively weakly.
The findings peel back a new layer of the mystery of how obesity alters our relationship to food.
"Studies have shown that obesity can lead to alterations in the brain, as well as the nerves that control the peripheral taste system, but no one had ever looked at the cells on the tongue that make contact with food," said lead scientist Kathryn Medler, PhD, UB associate professor of biological sciences.
"What we see is that even at this level -- at the first step in the taste pathway -- the taste receptor cells themselves are affected by obesity," Medler said. "The obese mice have fewer taste cells that respond to sweet stimuli, and they don't respond as well."
The research matters because taste plays an important role in regulating appetite: what we eat, and how much we consume.
How an inability to detect sweetness might encourage weight gain is unclear, but past research has shown that obese people yearn for sweet and savory foods though they may not taste these flavors as well as thinner people.
Medler said it's possible that trouble detecting sweetness may lead obese mice to eat more than their leaner counterparts to get the same payoff.
Learning more about the connection between taste, appetite and obesity is important, she said, because it could lead to new methods for encouraging healthy eating.
"If we understand how these taste cells are affected and how we can get these cells back to normal, it could lead to new treatments," Medler said. "These cells are out on your tongue and are more accessible than cells in other parts of your body, like your brain."
The new PLOS ONE study compared 25 normal mice to 25 of their littermates who were fed a high-fat diet and became obese.
To measure the animals' response to different tastes, the research team looked at a process called calcium signaling. When cells "recognize" a certain taste, there is a temporary increase in the calcium levels inside the cells, and the scientists measured this change.
The results: Taste cells from the obese mice responded more weakly not only to sweetness but, surprisingly, to bitterness as well. Taste cells from both groups of animals reacted similarly to umami, a flavor associated with savory and meaty foods.
Medler's co-authors on the study were former UB graduate student Amanda Maliphol and former UB undergraduate Deborah Garth.