Scientists find stem cells capable of repairing skull, face bones

February 2, 2016

A team of Rochester scientists has, for the first time, identified and isolated a stem cell population capable of skull formation and craniofacial bone repair in mice–achieving an important step toward using stem cells for bone reconstruction of the face and head in the future, according to a new paper in Nature Communications. Read more

Record warm years almost certainly due to human-made climate change

January 26, 2016

Recent record warm years are with extremely high likelihood caused by human-made climate change. Without greenhouse-gas emissions from burning coal and oil, the odds are vanishingly small that 13 out of the 15 warmest years ever measured would all have happened in the current, still young century. These odds are between 1 in 5000 and 1 in 170.000, a new study by an international team of scientists now shows. Including the data for 2015, which came in after the study was completed, makes the odds even slimmer.

“2015 is again the warmest year on record, and this can hardly be by chance,” says co-author Stefan Rahmstorf of the Potsdam Institute for Climate Impact Research. The scientists performed a sophisticated statistical analysis, combining observational data and comprehensive computer simulations of the climate system. Their new approach allowed them to better separate natural climate variability from human-caused climate change.

“Natural climate variability causes temperatures to wax and wane over a period of several years, rather than varying erratically from one year to the next,” says lead-author Michael Mann, distinguished professor of meteorology and director, Earth System Science Center, Penn State (US). “That makes it more challenging to accurately assess the chance likelihood of temperature records. Given the recent press interest, it just seemed like it was important to do this right, and address, in a defensible way, the interesting and worthwhile question of how unlikely it is that the recent run of record temperatures might have arisen by chance alone.”

Global warming increases risk of local heat extremes

The newly computed odds for experiencing the recent runs of record temperatures by chance, without accounting for human-caused greenhouse gases, are greater than odds previously reported in some media – between 1 in 27 million and 1 in 650 million – but they are still incredibly slim.

In contrast, taking human-caused global warming into account makes the recent record temperatures quite likely, as the study further shows. Rahmstorf sums up the findings: “Natural climate variations just can’t explain the observed recent global heat records, but man-made global warming can.” What is more, the anomalous global average warmth comes with substantial impacts. “It has led to unprecedented local heat waves across the world – sadly resulting in loss of life and aggravating droughts and wildfires,” says Rahmstorf. “The risk of heat extremes has been multiplied due to our interference with the Earth system, as our data analysis shows.”

Physicists propose the first scheme to teleport the memory of an organism

January 13, 2016

In “Star Trek”, a transporter can teleport a person from one location to a remote location without actually making the journey along the way. Such a transporter has fascinated many people. Quantum teleportation shares several features of the transporter and is one of the most important protocols in quantum information. In a recent study, Prof. Tongcang Li at Purdue University and Dr. Zhang-qi Yin at Tsinghua University proposed the first scheme to use electromechanical oscillators and superconducting circuits to teleport the internal quantum state (memory) and center-of-mass motion state of a microorganism. They also proposed a scheme to create a SchrÃdinger’s cat state in which a microorganism can be in two places at the same time. This is an important step towards potentially teleporting an organism in future. Read more

Do we have free will?

January 4, 2016

The background to this new set of experiments lies in the debate regarding conscious will and determinism in human decision-making, which has attracted researchers, psychologists, philosophers and the general public, and which has been ongoing since at least the 1980s. Back then, the American researcher Benjamin Libet studied the nature of cerebral processes of study participants during conscious decision-making. He demonstrated that conscious decisions were initiated by unconscious brain processes, and that a wave of brain activity referred to as a ‘readiness potential’ could be recorded even before the subject had made a conscious decision. Read more

Super-Earths feature ‘Forbidden’ substances

December 27, 2015

Using mathematical models, scientists have ‘looked’ into the interior of super-Earths and discovered that they may contain compounds that are forbidden by the classical rules of chemistry — these substances may increase the heat transfer rate and strengthen the magnetic field on these planets. The findings have been presented in a paper published in the journal Scientific Reports.

The authors of the paper are a group of researchers from MIPT led by Artem Oganov, a professor of the Skolkovo Institute of Science and Technology and the head of the MIPT Laboratory of Computer Design. In a previous study, Oganov and his colleagues used an algorithm created by Oganov called USPEX to identify new compounds of sodium and chlorine, as well as other exotic substances. Read more

Intelligence ‘networks’ discovered in brain for the first time

December 22, 2015

Scientists from Imperial College London have identified for the first time two clusters of genes linked to human intelligence.

Called M1 and M3, these so-called gene networks appear to influence cognitive function – which includes memory, attention, processing speed and reasoning.

Crucially, the scientists have discovered that these two networks – which each contain hundreds of genes – are likely to be under the control of master regulator switches. The researchers are now keen to identify these switches and explore whether it might be feasible to manipulate them. The research is at a very early stage, but the scientists would ultimately like to investigate whether it is possible to use this knowledge of gene networks to boost cognitive function.

Dr Michael Johnson, lead author of the study from the Department of Medicine at Imperial College London, said: “We know that genetics plays a major role in intelligence but until now haven’t known which genes are relevant. This research highlights some of genes involved in human intelligence, and how they interact with each other.

What’s exciting about this is that the genes we have found are likely to share a common regulation, which means that potentially we can manipulate a whole set of genes whose activity is linked to human intelligence. Our research suggests that it might be possible to work with these genes to modify intelligence, but that is only a theoretical possibility at the moment – we have just taken a first step along that road.”

In the study, published in the journal Nature Neuroscience, the international team of researchers looked at samples of human brain from patients who had undergone neurosurgery for epilepsy. The investigators analysed thousands of genes expressed in the human brain, and then combined these results with genetic information from healthy people who had undergone IQ tests and from people with neurological disorders such as autism spectrum disorder and intellectual disability.

They conducted various computational analyses and comparisons in order to identify the gene networks influencing healthy human cognitive abilities. Remarkably, they found that some of the same genes that influence human intelligence in healthy people were also the same genes that cause impaired cognitive ability and epilepsy when mutated.

Dr Johnson added: “Traits such intelligence are governed by large groups of genes working together – like a football team made up of players in different positions. We used computer analysis to identify the genes in the human brain that work together to influence our cognitive ability to make new memories or sensible decisions when faced with lots of complex information. We found that some of these genes overlap with those that cause severe childhood onset epilepsy or intellectual disability.

“This study shows how we can use large genomic datasets to uncover new pathways for human brain function in both health and disease. Eventually, we hope that this sort of analysis will provide new insights into better treatments for neurodevelopmental diseases such as epilepsy, and ameliorate or treat the cognitive impairments associated with these devastating diseases.”

Exposure to violence makes you more likely to lie, cheat

December 4, 2015

Can watching a violent movie make you more likely to lie, cheat or steal? What about reading a violent book? While that may seem like a stretch, a new research study shows it may be the case.

The study, published in the Journal of Business Ethics, finds that exposure to human violence is strongly linked to an increase in cheating for monetary gain. In other words, violence may be making us less ethical.

“Research shows that violent media increases aggressive behavior towards others, but what we’re showing here is that it goes beyond that,” said study coauthor Josh Gubler, a professor of political science at BYU.

Gubler and coauthor David Wood, a professor of accounting in the Marriott School of Management, carried out three experiments with roughly 1,000 participants (recruited from Amazon’s Mechanical Turk) for the study.

In the first experiment, participants were paid to review sentences and edit those with mistakes. Half of the participants were given sentences with violent language. Subjects were told they would be paid whether or not they were correct, providing an incentive to mark all sentences “correct” to earn money quicker. Those who reviewed violent sentences were 24 percent more likely to cheat.

In another experiment, participants were hired to watch and evaluate movie clips. (They were told they needed to watch the entirety of all the clips to be paid.) One clip consisted of 10 minutes of a blue screen with a monotone voiceover. The researchers found those who viewed violent movie clips were more likely to lie about watching all the videos.

Surprisingly, while both male and female test subjects responded to violently worded media (experiment 1), only the men’s ethics were negatively influenced by violent videos.

“We have whole industries that glorify violence–in video games, in media, in Hollywood–and then, on the opposite side, we have a significant body of research showing very serious effects to this,” Wood said. “There is a disconnect between what science is saying and what we choose to do in society.”

One such study, published in 2009, found that subjects who played violent video games for only 20 minutes took five times longer to help a person in need. The study also found that people who had just seen a violent film took 26 percent longer to help an injured woman.

Last year the journal, Psychology of Popular Media Culture, published a study showing the majority of media researchers, not to mention parents and pediatricians, see the link between violent media and increased aggression.

Wood believes our society needs to have a “really serious gut check” and ask why we tolerate and glorify violence. He and Gubler said their study is the latest to show that violent media has more negative impacts than most people imagine.

“We hope this provides another piece of evidence to the debate we’re having within western society of the effects of media on behavior,” Gubler said. “We hope this information informs parents and communities as they make decisions about what types of media they consume.”

Scientists discover new system for human genome editing

September 27, 2015

A team including the scientist who first harnessed the revolutionary CRISPR-Cas9 system for mammalian genome editing has now identified a different CRISPR system with the potential for even simpler and more precise genome engineering.

In a study published today in Cell, Feng Zhang and his colleagues at the Broad Institute of MIT and Harvard and the McGovern Institute for Brain Research at MIT, with co-authors Eugene Koonin at the National Institutes of Health, Aviv Regev of the Broad Institute and the MIT Department of Biology, and John van der Oost at Wageningen University, describe the unexpected biological features of this new system and demonstrate that it can be engineered to edit the genomes of human cells.

“This has dramatic potential to advance genetic engineering,” said Eric Lander, Director of the Broad Institute and one of the principal leaders of the human genome project. “The paper not only reveals the function of a previously uncharacterized CRISPR system, but also shows that Cpf1 can be harnessed for human genome editing and has remarkable and powerful features. The Cpf1 system represents a new generation of genome editing technology.”

CRISPR sequences were first described in 1987 and their natural biological function was initially described in 2010 and 2011. The application of the CRISPR-Cas9 system for mammalian genome editing was first reported in 2013, by Zhang and separately by George Church at Harvard.

In the new study, Zhang and his collaborators searched through hundreds of CRISPR systems in different types of bacteria, searching for enzymes with useful properties that could be engineered for use in human cells. Two promising candidates were the Cpf1 enzymes from bacterial species Acidaminococcus and Lachnospiraceae, which Zhang and his colleagues then showed can target genomic loci in human cells.

“We were thrilled to discover completely different CRISPR enzymes that can be harnessed for advancing research and human health,” Zhang said.

The newly described Cpf1 system differs in several important ways from the previously described Cas9, with significant implications for research and therapeutics, as well as for business and intellectual property:

 

  • First: In its natural form, the DNA-cutting enzyme Cas9 forms a complex with two small RNAs, both of which are required for the cutting activity. The Cpf1 system is simpler in that it requires only a single RNA. The Cpf1 enzyme is also smaller than the standard SpCas9, making it easier to deliver into cells and tissues. 

     

  • Second, and perhaps most significantly: Cpf1 cuts DNA in a different manner than Cas9. When the Cas9 complex cuts DNA, it cuts both strands at the same place, leaving ‘blunt ends’ that often undergo mutations as they are rejoined. With the Cpf1 complex the cuts in the two strands are offset, leaving short overhangs on the exposed ends. This is expected to help with precise insertion, allowing researchers to integrate a piece of DNA more efficiently and accurately. 

     

  • Third: Cpf1 cuts far away from the recognition site, meaning that even if the targeted gene becomes mutated at the cut site, it can likely still be re-cut, allowing multiple opportunities for correct editing to occur. 

     

  • Fourth: the Cpf1 system provides new flexibility in choosing target sites. Like Cas9, the Cpf1 complex must first attach to a short sequence known as a PAM, and targets must be chosen that are adjacent to naturally occurring PAM sequences. The Cpf1 complex recognizes very different PAM sequences from those of Cas9. This could be an advantage in targeting some genomes, such as in the malaria parasite as well as in humans. 

“The unexpected properties of Cpf1 and more precise editing open the door to all sorts of applications, including in cancer research,” said Levi Garraway, an institute member of the Broad Institute, and the inaugural director of the Joint Center for Cancer Precision Medicine at the Dana-Farber Cancer Institute, Brigham and Women’s Hospital, and the Broad Institute. Garraway was not involved in the research.

Zhang, Broad Institute, and MIT plan to share the Cpf1 system widely. As with earlier Cas9 tools, these groups will make this technology freely available for academic research via the Zhang lab’s page on the plasmid-sharing-website Addgene, through which the Zhang lab has already shared Cas9 reagents more than 23,000 times to researchers worldwide to accelerate research. The Zhang lab also offers free online tools and resources for researchers through its website, http://www.genome-engineering.org.

The Broad Institute and MIT plan to offer non-exclusive licenses to enable commercial tool and service providers to add this enzyme to their CRISPR pipeline and services, further ensuring availability of this new enzyme to empower research. These groups plan to offer licenses that best support rapid and safe development for appropriate and important therapeutic uses. “We are committed to making the CRISPR-Cpf1 technology widely accessible,” Zhang said.

“Our goal is to develop tools that can accelerate research and eventually lead to new therapeutic applications. We see much more to come, even beyond Cpf1 and Cas9, with other enzymes that may be repurposed for further genome editing advances.”

The missing link of lizard evolution

August 26, 2015

University of Alberta paleontologists have discovered a new species of lizard, namedGueragama sulamericana, in the municipality of Cruzeiro do Oeste in Southern Brazil in the rock outcrops of a Late Cretaceous desert, dated approximately 80 million years ago.

“The roughly 1700 species of iguanas are almost without exception restricted to the New World, primarily the Southern United States down to the tip of South America,” says Michael Caldwell, biological sciences professor from the University of Alberta and one of the study’s authors. Oddly however, iguanas closest relatives, including chameleons and bearded dragons, are all Old World. As one of the most diverse groups of extant lizards, spanning from acrodontan iguanians (meaning the teeth are fused to the top of their jaws) dominating the Old World to non-acrodontans in the New World, this new lizard species is the first acrodontan found in South America, suggesting both groups of ancient iguanians achieved a worldwide distribution before the final break up of Pangaea.

A terrestrial Noah’s Arc

“This fossil is an 80 million year old specimen of an acrodontan in the New World,” explains Caldwell. “It’s a missing link in the sense of the paleobiogeography and possibly the origins of the group, so it’s pretty good evidence to suggest that back in the lower part of the Cretaceous, the southern part of Pangaea was still a kind of single continental chunk.”

Distributions of plants and animals from the Late Cretaceous reflect the ancestry of Pangaea when it was whole. “This Gueragama sulamericana fossil indicates that the group is old, that it’s probably Southern Pangaean in its origin, and that after the break up, the acrodontans and chameleon group dominated in the Old World, and the iguanid side arose out of this acrodontan lineage that was left alone on South America,” says Caldwell. “South America remained isolated until about 5 million years ago. That’s when it bumps into North America, and we see this exchange of organism north and south. It was kind of like a floating Noah’s Arc for a very long time, about 100 million years. This is an Old World lizard in the new world at a time when we weren’t expecting to find it. It answers a few questions about iguanid lizards and their origin.”

The University of Alberta is a world leader in paleontology. This study was a collaboration between the University of Alberta and scientists in Brazil. Caldwell says of the collaboration, “It’s providing an opportunity for our students and research groups to expand our expertise and interests into an ever-increasing diversity of organisms within this group of animals called snakes and lizards.”

The lead author of the paper is Caldwell’s PhD student, Tiago Simoes, a Vanier scholar. “As with many other scientific findings, this one raises a number of questions we haven’t previously considered,” says Simoes. “This finding raises a number of biogeographic and faunal turnover questions of great interest to both paleontologists and herpetologists that we hope to answer in the future.”

In terms of next steps, Caldwell notes “Each answer only rattles the questions harder. The evolution of the group is much older than has been previously thought, which means we can push an acrodontan to 80 million years in South America. We now need to focus on much older units of of rock if we’re going to find the next step in the process.”

The findings, “A stem acrodontan lizard in the Cretaceous of Brazil revises early lizard evolution in Gondwana,” were published in the journal Nature Communications, one of the world’s top multidisciplinary scientific journals.

Apes may be closer to speaking than many scientists think

August 16, 2015

Koko the gorilla is best known for a lifelong study to teach her a silent form of communication, American Sign Language. But some of the simple sounds she has learned may change the perception that humans are the only primates with the capacity for speech.

In 2010, Marcus Perlman started research work at The Gorilla Foundation, where Koko has spent more than 40 years living immersed with humans — interacting for many hours each day with psychologist Penny Patterson and biologist Ron Cohn.

“I went there with the idea of studying Koko’s gestures, but as I got into watching videos of her, I saw her performing all these amazing vocal behaviors,” says Perlman, now a postdoctoral researcher in the lab of University of Wisconsin-Madison psychology Professor Gary Lupyan.

The vocal and breathing behaviors Koko had developed were not necessarily supposed to be possible.

“Decades ago, in the 1930s and ’40s, a couple of husband-and-wife teams of psychologists tried to raise chimpanzees as much as possible like human children and teach them to speak. Their efforts were deemed a total failure,” Perlman says. “Since then, there is an idea that apes are not able to voluntarily control their vocalizations or even their breathing.”

Instead, the thinking went, the calls apes make pop out almost reflexively in response to their environment — the appearance of a dangerous snake, for example.

And the particular vocal repertoire of each ape species was thought to be fixed. They didn’t really have the ability to learn new vocal and breathing-related behaviors.

These limits fit a theory on the evolution of language, that the human ability to speak is entirely unique among the nonhuman primate species still around today.

“This idea says there’s nothing that apes can do that is remotely similar to speech,” Perlman says. “And, therefore, speech essentially evolved — completely new — along the human line since our last common ancestor with chimpanzees.”

However, in a study published online in July in the journal Animal Cognition, Perlman and collaborator Nathaniel Clark of the University of California, Santa Cruz, sifted 71 hours of video of Koko interacting with Patterson and Cohn and others, and found repeated examples of Koko performing nine different, voluntary behaviors that required control over her vocalization and breathing. These were learned behaviors, not part of the typical gorilla repertoire.

Among other things, Perlman and Clark watched Koko blow a raspberry (or blow into her hand) when she wanted a treat, blow her nose into a tissue, play wind instruments, huff moisture onto a pair of glasses before wiping them with a cloth and mimic phone conversations by chattering wordlessly into a telephone cradled between her ear and the crook of an elbow.

“She doesn’t produce a pretty, periodic sound when she performs these behaviors, like we do when we speak,” Perlman says. “But she can control her larynx enough to produce a controlled grunting sound.”

Koko can also cough on command — not particularly groundbreaking human behavior, but impressive for a gorilla because it requires her to close off her larynx.

“The motivation for the behaviors varies,” Perlman says. “She often looks like she plays her wind instruments for her own amusement, but she tends to do the cough at the request of Penny and Ron.”

These behaviors are all learned, Perlman figures, and the result of living with humans since Koko was just six months old.

“Presumably, she is no more gifted than other gorillas,” he says. “The difference is just her environmental circumstances. You obviously don’t see things like this in wild populations.”

This suggests that some of the evolutionary groundwork for the human ability to speak was in place at least by the time of our last common ancestor with gorillas, estimated to be around 10 million years ago.

“Koko bridges a gap,” Perlman says. “She shows the potential under the right environmental conditions for apes to develop quite a bit of flexible control over their vocal tract. It’s not as fine as human control, but it is certainly control.”

Orangutans have also demonstrated some impressive vocal and breathing-related behavior, according to Perlman, indicating the whole great ape family may share the abilities Koko has learned to tap.

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