Researchers at the J. Craig Venter Institute (JCVI) published results today describing the successful construction of the first self-replicating, synthetic bacterial cell. The team synthesised the 1.08 million base pair chromosome of a modified Mycoplasma mycoides genome. The synthetic cell is called Mycoplasma mycoides JCVI-syn1.0 and is the proof of principle that genomes can be designed in the computer, chemically made in the laboratory and transplanted into a recipient cell to produce a new self-replicating cell controlled only by the synthetic genome.

This research will be published by Daniel Gibson et al in the 20th May edition of Science Express and will appear in an upcoming print issue of Science.

‘For nearly 15 years Ham Smith, Clyde Hutchison and the rest of our team have been working toward this publication today – the successful completion of our work to construct a bacterial cell that is fully controlled by a synthetic genome,’ said J. Craig Venter, Ph.D., founder and president, JCVI and senior author on the paper. ‘We have been consumed by this research, but we have also been equally focused on addressing the societal implications of what we believe will be one of the most powerful technologies and industrial drivers for societal good. We look forward to continued review and dialogue about the important applications of this work to ensure that it is used for the benefit of all.’

According to Dr Smith, ‘With this first synthetic bacterial cell and the new tools and technologies we developed to successfully complete this project, we now have the means to dissect the genetic instruction set of a bacterial cell to see and understand how it really works.’

To complete this final stage in the nearly 15 year process to construct and boot up a synthetic cell, JCVI scientists began with the accurate, digitised genome of the bacterium, M. mycoides. The team designed 1,078 specific cassettes of DNA that were 1,080 base pairs long. These cassettes were designed so that the ends of each DNA cassette overlapped each of its neighbours by 80bp. The cassettes were made according to JCVI’s specifications by the DNA synthesis company, Blue Heron Biotechnology.

The JCVI team employed a three stage process using their previously described yeast assembly system to build the genome using the 1,078 cassettes. The first stage involved taking 10 cassettes of DNA at a time to build 110, 10,000 bp segments. In the second stage, these 10,000 bp segments are taken 10 at a time to produce eleven, 100,000 bp segments. In the final step, all 11, 100 kb segments were assembled into the complete synthetic genome in yeast cells and grown as a yeast artificial chromosome.

The complete synthetic M. mycoides genome was isolated from the yeast cell and transplanted into Mycoplasma capricolum recipient cells that have had the genes for its restriction enzyme removed. The synthetic genome DNA was transcribed into messenger RNA, which in turn was translated into new proteins. The M. capricolum genome was either destroyed by M. mycoides restriction enzymes or was lost during cell replication. After two days viable M. mycoides cells, which contained only synthetic DNA, were clearly visible on petri dishes containing bacterial growth medium.

The initial synthesis of the synthetic genome did not result in any viable cells so the JCVI team developed an error correction method to test that each cassette they constructed was biologically functional. They did this by using a combination of 100 kb natural and synthetic segments of DNA to produce semi-synthetic genomes. This approach allowed for the testing of each synthetic segment in combination with 10 natural segments for their capacity to be transplanted and form new cells. Ten out of 11 synthetic fragments resulted in viable cells; therefore the team narrowed the issue down to a single 100 kb cassette. DNA sequencing revealed that a single base pair deletion in an essential gene was responsible for the unsuccessful transplants. Once this one base pair error was corrected, the first viable synthetic cell was produced.

Dr Gibson stated, ‘To produce a synthetic cell, our group had to learn how to sequence, synthesise, and transplant genomes. Many hurdles had to be overcome, but we are now able to combine all of these steps to produce synthetic cells in the laboratory.’ He added, ‘We can now begin working on our ultimate objective of synthesising a minimal cell containing only the genes necessary to sustain life in its simplest form. This will help us better understand how cells work.’

This publication represents the construction of the largest synthetic molecule of a defined structure; the genome is almost double the size of the previous Mycoplasma genitalium synthesis. With this successful proof of principle, the group will now work on creating a minimal genome, which has been a goal since 1995. They will do this by whittling away at the synthetic genome and repeating transplantation experiments until no more genes can be disrupted and the genome is as small as possible. This minimal cell will be a platform for analysing the function of every essential gene in a cell.

According to Dr Hutchison, ‘To me the most remarkable thing about our synthetic cell is that its genome was designed in the computer and brought to life through chemical synthesis, without using any pieces of natural DNA. This involved developing many new and useful methods along the way. We have assembled an amazing group of scientists that have made this possible.’

As in the team’s 2008 publication in which they described the successful synthesis of the M. genitalium genome, they designed and inserted into the genome what they called watermarks. These are specifically designed segments of DNA that use the ‘alphabet’ of genes and proteins that enable the researcher to spell out words and phrases. The watermarks are an essential means to prove that the genome is synthetic and not native, and to identify the laboratory of origin. Encoded in the watermarks is a new DNA code for writing words, sentences and numbers. In addition to the new code there is a web address to send emails to if you can successfully decode the new code, the names of 46 authors and other key contributors and three quotations: ‘TO LIVE, TO ERR, TO FALL, TO TRIUMPH, TO RECREATE LIFE OUT OF LIFE.’ – JAMES JOYCE; ‘SEE THINGS NOT AS THEY ARE, BUT AS THEY MIGHT BE.’ – A quote from the book, ‘American Prometheus’; ‘WHAT I CANNOT BUILD, I CANNOT UNDERSTAND.’ – RICHARD FEYNMAN.

The JCVI scientists envision that the knowledge gained by constructing this first self-replicating synthetic cell, coupled with decreasing costs for DNA synthesis, will give rise to wider use of this powerful technology. This will undoubtedly lead to the development of many important applications and products including biofuels, vaccines, pharmaceuticals, clean water and food products. The group continues to drive and support ethical discussion and review to ensure a positive outcome for society.

Funding for this research came from Synthetic Genomics Inc., a company co-founded by Drs. Venter and Smith.

A team of scientists from Columbia University, Arizona State University, the University of Michigan, and the California Institute of Technology (Caltech) have programmed an autonomous molecular “robot” made out of DNA to start, move, turn, and stop while following a DNA track.

The development could ultimately lead to molecular systems that might one day be used for medical therapeutic devices and molecular-scale reconfigurable robots—robots made of many simple units that can reposition or even rebuild themselves to accomplish different tasks.

A paper describing the work appears in the current issue of the journal Nature.

The traditional view of a robot is that it is “a machine that senses its environment, makes a decision, and then does something—it acts,” says Erik Winfree, associate professor of computer science, computation and neural systems, and bioengineering at Caltech.

Milan N. Stojanovic, a faculty member in the Division of Experimental Therapeutics at Columbia University, led the project and teamed up with Winfree and Hao Yan, professor of chemistry and biochemistry at Arizona State University and an expert in DNA nanotechnology, and with Nils G. Walter, professor of chemistry and director of the Single Molecule Analysis in Real-Time (SMART) Center at the University of Michigan in Ann Arbor, for what became a modern-day self-assembly of like-minded scientists with the complementary areas of expertise needed to tackle a tough problem.

Shrinking robots down to the molecular scale would provide, for molecular processes, the same kinds of benefits that classical robotics and automation provide at the macroscopic scale. Molecular robots, in theory, could be programmed to sense their environment (say, the presence of disease markers on a cell), make a decision (that the cell is cancerous and needs to be neutralized), and act on that decision (deliver a cargo of cancer-killing drugs).

Or, like the robots in a modern-day factory, they could be programmed to assemble complex molecular products. The power of robotics lies in the fact that once programmed, the robots can carry out their tasks autonomously, without further human intervention.

With that promise, however, comes a practical problem: how do you program a molecule to perform complex behaviors?

“In normal robotics, the robot itself contains the knowledge about the commands, but with individual molecules, you can’t store that amount of information, so the idea instead is to store information on the commands on the outside,” says Walter. And you do that, says Stojanovic, “by imbuing the molecule’s environment with informational cues.”

“We were able to create such a programmed or ‘prescribed’ environment using DNA origami,” explains Yan. DNA origami, an invention by Caltech Senior Research Associate Paul W. K. Rothemund, is a type of self-assembled structure made from DNA that can be programmed to form nearly limitless shapes and patterns (such as smiley faces or maps of the Western Hemisphere or even electrical diagrams). Exploiting the sequence-recognition properties of DNA base pairing, DNA origami are created from a long single strand of DNA and a mixture of different short synthetic DNA strands that bind to and “staple” the long DNA into the desired shape. The origami used in the Nature study was a rectangle that was 2 nanometers (nm) thick and roughly 100 nm on each side.

The researchers constructed a trail of molecular “bread crumbs” on the DNA origami track by stringing additional single-stranded DNA molecules, or oligonucleotides, off the ends of the staples. These represent the cues that tell the molecular robots what to do—start, walk, turn left, turn right, or stop, for example—akin to the commands given to traditional robots.

The molecular robot the researchers chose to use—dubbed a “spider”—was invented by Stojanovic several years ago, at which time it was shown to be capable of extended, but undirected, random walks on two-dimensional surfaces, eating through a field of bread crumbs.

To build the 4-nm-diameter molecular robot, the researchers started with a common protein called streptavidin, which has four symmetrically placed binding pockets for a chemical moiety called biotin. Each robot leg is a short biotin-labeled strand of DNA, “so this way we can bind up to four legs to the body of our robot,” Walter says. “It’s a four-legged spider,” quips Stojanovic. Three of the legs are made of enzymatic DNA, which is DNA that binds to and cuts a particular sequence of DNA. The spider also is outfitted with a “start strand”—the fourth leg—that tethers the spider to the start site (one particular oligonucleotide on the DNA origami track). “After the robot is released from its start site by a trigger strand, it follows the track by binding to and then cutting the DNA strands extending off of the staple strands on the molecular track,” Stojanovic explains.

“Once it cleaves,” adds Yan, “the product will dissociate, and the leg will start searching for the next substrate.” In this way, the spider is guided down the path laid out by the researchers. Finally, explains Yan, “the robot stops when it encounters a patch of DNA that it can bind to but that it cannot cut,” which acts as a sort of flypaper.

Although other DNA walkers have been developed before, they’ve never ventured farther than about three steps. “This one,” says Yan, “can walk up to about 100 nanometers. That’s roughly 50 steps.”

“This in itself wasn’t a surprise,” adds Winfree, “since Milan’s original work suggested that spiders can take hundreds if not thousands of processive steps. What’s exciting here is that not only can we directly confirm the spiders’ multistep movement, but we can direct the spiders to follow a specific path, and they do it all by themselves—autonomously.”

In fact, using atomic force microscopy and single-molecule fluorescence microscopy, the researchers were able to watch directly spiders crawling over the origami, showing that they were able to guide their molecular robots to follow four different paths.

“Monitoring this at a single molecule level is very challenging,” says Walter. “This is why we have an interdisciplinary, multi-institute operation. We have people constructing the spider, characterizing the basic spider. We have the capability to assemble the track, and analyze the system with single-molecule imaging. That’s the technical challenge.” The scientific challenges for the future, Yan says, “are how to make the spider walk faster and how to make it more programmable, so it can follow many commands on the track and make more decisions, implementing logical behavior.”

“In the current system,” says Stojanovic, “interactions are restricted to the walker and the environment. Our next step is to add a second walker, so the walkers can communicate with each other directly and via the environment. The spiders will work together to accomplish a goal.” Adds Winfree, “The key is how to learn to program higher-level behaviors through lower-level interactions.”

Such collaboration ultimately could be the basis for developing molecular-scale reconfigurable robots—complicated machines that are made of many simple units that can reorganize themselves into any shape—to accomplish different tasks, or fix themselves if they break. For example, it may be possible to use the robots for medical applications. “The idea is to have molecular robots build a structure or repair damaged tissues,” says Stojanovic.

“You could imagine the spider carrying a drug and bonding to a two-dimensional surface like a cell membrane, finding the receptors and, depending on the local environment,” adds Yan, “triggering the activation of this drug.”

Such applications, while intriguing, are decades or more away. “This may be 100 years in the future,” Stojanovic says. “We’re so far from that right now.”

“But,” Walter adds, “just as researchers self-assemble today to solve a tough problem, molecular nanorobots may do so in the future.”

The other coauthors on the paper, “Molecular robots guided by prescriptive landscapes,” are Kyle Lund and Jeanette Nangreave from Arizona State University; Anthony J. Manzo, Alexander Johnson-Buck, and Nicole Michelotti from the University of Michigan; Nadine Dabby from Caltech; and Steven Taylor and Renjun Pei from Columbia University. The work was supported by the National Science Foundation, the Army Research Office, the Office of Naval Research, the National Institutes of Health, the Department of Energy, the Searle Foundation, the Lymphoma and Leukemia Society, the Juvenile Diabetes Research Foundation, and a Sloan Research Fellowship.

Contact: Kathy Svitil ksvitil@caltech.edu

Image Credit: Courtesy of Paul Michelotti

Sci­en­tists are re­port­ing that they have de­cod­ed more than half the Ne­an­der­thal ge­nome, and that the da­ta sup­ports a the­o­ry that our an­cest­ors in­ter­bred with Ne­an­der­thal peo­ple a lit­tle.

The sci­en­tists de­vised a draft ge­nome se­quence, or a list of the “let­ters” in a crea­ture’s ge­ne­tic code. These “let­ters” con­sist of mo­lec­u­lar un­its called nu­cleotides that make up the DNA. An anal­y­sis of this se­quence can re­veal in­forma­t­ion about an or­gan­is­m’s an­ces­try.

Sci­en­tists used pill-sized sam­ples of pow­der from three bones of Ne­an­der­thals, a stocky an­cient breed of hu­mans that co-ex­isted wth an­ces­tors of mod­ern hu­mans. The find­ings ap­pear in the May 7 is­sue of the re­search jour­nal Sci­ence.

The re­search­ers, led by Svante Pääbo of the Max Planck In­sti­tute for Ev­o­lu­tion­ary An­thro­po­l­ogy in Leip­zig, Ger­ma­ny, com­pared the Ne­an­der­thal ge­nome with ge­nomes of five pre­s­ent-day hu­mans.

The re­sults al­so re­vealed var­i­ous genes that are un­ique to mod­ern peo­ple, the sci­en­tists said, in­clud­ing a hand­ful of genes that spread rap­idly among our spe­cies af­ter we split from a com­mon an­ces­tor we shared with Ne­an­der­thals. Among these genes are three be­lieved to af­fect men­tal and cog­ni­tive de­vel­op­ment; muta­t­ions in these genes are linked to con­di­tions such as Down syn­drome, schiz­o­phre­nia and au­tism.

“For the first time we can now iden­ti­fy ge­net­ic fea­tures that set us apart from all oth­er or­gan­isms, in­clud­ing our clos­est ev­o­lu­tion­ary rel­a­tives,” Ne­an­der­thals, said Pääbo. “This [work] really just hints at what genes one should now stu­dy, and I’m sure we and many oth­er groups will be do­ing that.”

Ne­an­der­thals first ap­peared around 400,000 years ago, ranged across Eu­rope and west­ern Asia, and died out about 30,000 years ago. The draft Ne­an­der­thal ge­nome se­quence be­ing re­ported rep­re­sents about 60 per­cent of the ge­nome; the da­ta was worked out us­ing bones found in a cave in Cro­a­tia.

Pääbo and col­leagues al­so se­quenced the ge­nomes of five pre­s­ent-day hu­mans from south­ern Af­ri­ca, West Af­ri­ca, Pap­ua New Guin­ea, Chi­na and France, to com­pare with the Ne­an­der­thal ge­nome.

The Ne­an­der­thal ge­nome proved slightly more si­m­i­lar to those of the non-Af­ri­can peo­ple than Af­ri­cans, said the in­ves­ti­ga­tors. One of the sim­plest sce­nar­i­os to ex­plain this and some pre­vi­ous da­ta, they added, is that af­ter mod­ern hu­mans mi­grat­ed out of Af­ri­ca, they en­coun­tered and in­ter­bred with Ne­an­der­thals in the Mid­dle East. The han­ky-pan­ky seems to have been fairly lim­it­ed, judg­ing from the extent of the si­m­il­ar­ities, but “it’s cool to think that some of us have a lit­tle Ne­an­der­thal DNA in us,” Pääbo said.

Article Credit: World Science

A California Institute of Technology (Caltech)-led team of researchers and clinicians has published the first proof that a targeted nanoparticle – used as an experimental therapeutic and injected directly into a patient’s bloodstream – can traffic into tumours, deliver double-stranded small interfering RNAs (siRNAs), and turn off an important cancer gene using a mechanism known as RNA interference (RNAi). Moreover, the team provided the first demonstration that this new type of therapy, infused into the bloodstream, can make its way to human tumours in a dose-dependent fashion – i.e., a higher number of nanoparticles sent into the body leads to a higher number of nanoparticles in the tumour cells.

These results, published in the March 21 advance online edition of the journal Nature, demonstrate the feasibility of using both nanoparticles and RNAi-based therapeutics in patients, and open the door for future ‘game-changing’ therapeutics that attack cancer and other diseases at the genetic level, says Mark Davis, the Warren and Katharine Schlinger Professor of Chemical Engineering at Caltech, and the research team’s leader.

The discovery of RNA interference, the mechanism by which double strands of RNA silence genes, won researchers Andrew Fire and Craig Mello the 2006 Nobel Prize in Physiology or Medicine. The scientists first reported finding this novel mechanism in worms in a 1998 Nature paper. Since then, the potential for this type of gene inhibition to lead to new therapies for diseases like cancer has been highly touted.

‘RNAi is a new way to stop the production of proteins,’ says Davis. What makes it such a potentially powerful tool, he adds, is the fact that its target is not a protein. The vulnerable areas of a protein may be hidden within its three-dimensional folds, making it difficult for many therapeutics to reach them. In contrast, RNA interference targets the messenger RNA (mRNA) that encodes the information needed to make a protein in the first place.

‘In principle,’ says Davis, ‘that means every protein now is druggable because its inhibition is accomplished by destroying the mRNA. And we can go after mRNAs in a very designed way given all the genomic data that are and will become available.’

Still, there have been numerous potential roadblocks to the application of RNAi technology as therapy in humans. One of the most problematic has been finding a way to ferry the therapeutics, which are made up of fragile siRNAs, into tumour cells after direct injection into the bloodstream. Davis, however, had a solution. Even before the discovery of RNAi, he and his team had begun working on ways to deliver nucleic acids into cells via systemic administration. They eventually created a four-component system – featuring a unique polymer – that can self-assemble into a targeted, siRNA-containing nanoparticle. The siRNA delivery system is under clinical development by Calando Pharmaceuticals, Inc., a Pasadena-based nanobiotech company.

‘These nanoparticles are able to take the siRNAs to the targeted site within the body,’ says Davis. Once they reach their target – in this case, the cancer cells within tumours – the nanoparticles enter the cells and release the siRNAs.

The scientific results described in the Nature paper are from a Phase I clinical trial of these nanoparticles that began treating patients in May 2008. Phase I trials are, by definition, safety trials; the idea is to see if and at what level the drug or other therapy turns harmful or toxic. These trials can also provide an in-human scientific proof of concept – which is exactly what is being reported in the Nature paper.

Using a new technique developed at Caltech, the team was able to detect and image nanoparticles inside cells biopsied from the tumours of several of the trial’s participants. In addition, Davis and his colleagues were able to show that the higher the nanoparticle dose administered to the patient, the higher the number of particles found inside the tumour cells – the first example of this kind of dose-dependent response using targeted nanoparticles.

Even better, Davis says, the evidence showed the siRNAs had done their job. In the tumour cells analysed by the researchers, the mRNA encoding the cell-growth protein ribonucleotide reductase had been degraded. This degradation, in turn, led to a loss of the protein.

More to the point, the mRNA fragments found were exactly the length and sequence they should be if they’d been cleaved in the spot targeted by the siRNA, notes Davis. ‘It’s the first time anyone has found an RNA fragment from a patient’s cells showing the mRNA was cut at exactly the right base via the RNAi mechanism,’ he says. ‘It proves that the RNAi mechanism can happen using siRNA in a human.’

‘There are many cancer targets that can be efficiently blocked in the laboratory using siRNA, but blocking them in the clinic has been elusive,’ says Antoni Ribas, associate professor of medicine and surgery at UCLA’s Jonsson Comprehensive Cancer Centre. ‘This is because many of these targets are not amenable to be blocked by traditionally designed anti-cancer drugs. This research provides the first evidence that what works in the lab could help patients in the future by the specific delivery of siRNA using targeted nanoparticles. We can start thinking about targeting the untargetable.’

‘Although these data are very early and more research is needed, this is a promising study of a novel cancer agent, and we are proud of our contribution to the initial clinical development of siRNA for the treatment of cancer,’ says Anthony Tolcher, director of clinical research at South Texas Accelerated Research Therapeutics (START).

‘Promising data from the clinical trials validates our years of research at City of Hope into ribonucleotide reductase as a target for novel gene-based therapies for cancer,’ adds coauthor Yun Yen, associate director for translational research at City of Hope. ‘We are seeing for the first time the utility of siRNA as a cancer therapy and how nanotechnology can target cancer cells specifically.’

The Phase I trial – sponsored by Calando Pharmaceuticals – is proceeding at START and UCLA’s Jonsson Comprehensive Cancer Centre, and the clinical results of the trial will be presented at a later time. ‘At the very least, we’ve proven that the RNAi mechanism can be used in humans for therapy and that the targeted delivery of siRNA allows for systemic administration,’ Davis says. ‘It is a very exciting time.’

Imagine if your fear of spiders, heights or flying could be cured with a simple injection. Research published in BioMed Central’s open access journal, Behavioural and Brain Functions suggests that one day this could be a reality.

The cerebellum, an area of the brain thought to be involved with the development of our fears, was studied in goldfish by researchers at the University of Hiroshima in Japan. Using classical conditioning, Masayuki Yoshida and Ruriko Hirano taught their fish to become afraid of a light flashed in their eyes. By administering a low voltage electric shock every time a light was shone, the fish were taught to associate the light with being shocked, which slowed their hearts – the typical fish reaction to a fright. Yoshida explains, ‘As you would expect, the goldfish we used in our study soon became afraid of the flash of light because, whether or not we actually gave them a shock, they had quickly learned to expect one. Fear was demonstrated by their heart beats decreasing, in a similar way to how our heart rate increases when someone gives us a fright.’

Humans can also be ‘trained’ to become afraid, and in fact, simple classical conditioning rooted in our childhood and early development can explain many of our behaviours. In this study however, the team discovered that fish that had first been injected in the cerebellum with lidocaine had stable heart rates and showed no fear when the light was shone – they were unable to learn to become afraid.

Since the brains of goldfish show many similarities with those of mammals, including humans, it is hoped that with further study it may soon be possible to understand more about the biological and chemical processes that cause us to become afraid. For the goldfish, the effect of lidocaine is only temporary – fearless fish return to being frightened fish as soon as the anaesthetic has worn off. Nevertheless, one day, our irrational phobias could become a thing of the past.

A research team led by the University of Colorado at Boulder has discovered a previously unknown cellular ’switch’ that may provide researchers with a new means of triggering programmed cell death, findings with implications for treating cancer.

The new results are a big step forward in understanding programmed cell death, or apoptosis, a cell suicide process that involves a series of biochemical events leading to changes like cell body shrinkage, mitochondria destruction and chromosome fragmentation, said CU-Boulder Professor Ding Xue. But unlike traumatic cell death from injury, programmed cell death is a naturally occurring aspect of animal development that may help prevent human diseases like cancer and autoimmune disorders, said Xue, lead author on the new study.

In the new study, Xue and his team found that a well-known cellular molecule called caspase – known as the ‘executioner enzyme’ for apoptosis because of its primary role of cutting up and destroying cellular proteins – has an entirely different effect on a particular enzyme called Dicer. The team found that when caspase cleaves Dicer, it does not kill it but instead changes its function, causing Dicer to break up chromosomes – pieces of coiled DNA containing thousands of genes – and kill the cells that house them.

‘This finding was totally unexpected,’ said Xue of CU-Boulder’s molecular, cellular and developmental biology department. ‘We believe that by understanding this mechanism, we may be able to develop a new way to trigger cell death in a controlled manner as a way to treat disease.’

A paper on the subject appears in the March 12 issue of Science. Co-authors on the study included CU-Boulder postdoctoral researchers Akihisa Nakagawa and Yong Shi and Tokyo Women’s Medical University researchers Eriko Kage-Nakadai and Shohei Mitani.

The normal function of Dicer is to snip strands of RNA into smaller pieces that attach to messenger RNA molecules – which carry DNA’s genetic messages from the nucleus of cells to make specific proteins in cell cytoplasm – and silence their activity, said Xue. But when caspase comes in contact with Dicer, it takes away Dicer’s ability to cleave RNA and it replaces it with the ability to snip up and destroy DNA-laden chromosomes.

The experiments were undertaken on a common, eyelash-sized nematode known as Caenorhabditis elegans, a popular laboratory organism for genetic and biomedical experiments. The study of cell death in C. elegans is providing critical information to scientists trying to understand cell death mechanisms in humans and identify ways to combat human diseases caused by ‘inappropriate apoptosis,’ Xue said.

‘There are many enzymes whose job it is to cut RNA, and many unrelated enzymes whose job it is to cut DNA,’ said CU-Boulder MCD Biology Department Chair Tom Blumenthal, who studies RNA processing in C. elegans and who was not involved in the study. ‘But this is the first time that anyone has shown that it is possible to cleave an RNA-cutter enzyme and thereby convert it to a DNA-cutter enzyme.’

As part of the study, the team ‘knocked out’ the C. elegans gene that encodes the Dicer enzyme. The removal of the gene compromised the apoptosis process and blocked the fragmentation of chromosomes, said Xue.

Genetic studies of C. elegans have identified many genes that are important for the five sequential steps of programmed cell death, Xue said. They include the specification of which cells should die, the activation of the cell death program, the onset of the killing process, the engulfment of cell ‘corpses’ and the degradation of cellular debris, said Xue.

‘Our findings initially seemed too good to be true,’ said Xue, who said the team has been working on the project for five years. ‘We wound up looking at the results from a number of angles, including genetics, cell biology and biochemistry. Eventually we reached the only logical conclusions we could make.’

‘This is a completely novel finding, and all of the players in this story are well known, well studied aspects of a very important process in our lives,’ said Blumenthal. ‘The minute I saw the results, I knew it was a very, very important finding with wide implications.’

Since the failure of apoptosis is one of the main contributors to the development of tumours, many biomedical researchers believe that a better understanding of the programmed cell death process could lead to potential therapeutic agents for those suffering from a number of diseases caused by abnormal apoptosis, said Xue. ‘The biomedical potential here is for researchers to be able turn a pro-survival enzyme into an enzyme that is pro-death,’ Xue said.

The Science study by Xue and his team was funded by the Burroughs Wellcome Fund and the National Institutes of Health.

The researchers are now investigating whether human cells have the mechanisms to convert the function of Dicer enzyme in the same manner as C. elegans cells, said Xue. Nearly half of the genes found in C. elegans are believed to have functional counterparts in humans, he said.

C. elegans is a key organism for scientists to study for several reasons, according to Xue. It was the first organism whose genome was completely sequenced, and its transparency under microscopes has allowed scientists to study many aspects of cellular and developmental biology, as well as genetics. Nobel prizes for C. elegans biomedical research were awarded in 2002, 2006 and 2008.

In a world first an international team of researchers have successfully extracted ancient DNA from the eggshells of various species of extinct birds.

The research, published in scientific journal Proceedings of the Royal Society B, shows that fossil eggshell is a previously unrecognised source of ancient DNA and can provide exceptional long-term preservation of DNA in warmer climates. The findings will boost research in archaeology and biology where species identifications can add significantly to our understanding of biodiversity, evolutionary processes, past environmental change and dispersal of animal and human populations.

The study includes samples of Aepyornis sp, the giant Madagascan elephant bird collected by Dr Jean-Luc Schwenninger, a Quaternary geochronologist based at the Research Laboratory for Archaeology and the History of Art (RLAHA) at Oxford University. The bird looked like an outsized ostrich, standing about three metres high and weighing in excess of half a tonne. It was the heaviest bird to have ever existed and produced eggs with a capacity of 11L (equivalent to over two hundred chicken eggs or seven ostrich eggs). Its eggs are the largest eggs ever known.

Since 1991, Schwenninger and a team from Sheffield University, the University of Colorado, and Antananarivo’s National Museum of Art and Archaeology in Madagascar have conducted large scale archaeological surveys of the Southern region of Madagascar and studied the timing of extinction of these giant flightless birds. Whilst scouring the coastal dunes of Southern Madagascar they have found evidence of many of the bird’s former nesting sites from concentrations of eggshell debris. They have also excavated archaeological sites which document the rise and fall of a lost civilization with long-distance trade contacts to Africa’s Swahili coast, the Persian Gulf and China.

Dr Schwenninger and his colleague Professor Michael Parker Pearson, from the University of Sheffield, believe that by the time this civilization flourished, from the 11th to the 13th century, the population of elephant birds was in serious decline. The precise cause of extinction is not yet fully understood but it is probably linked to the arrival of humans.

AMS radiocarbon dating of eggshell remains, carried out at the Oxford Radiocarbon Accelerator Unit based at RLAHA, indicate that most of the birds seem to have died out at about the same time as large numbers of settlements appear in the archaeological record at around AD 1000. The French governor Etienne de Flacourt refers to indigenous sightings of the Aepyornis in 1650 which describe the bird as a ‘type of ostrich which people cannot catch and which searches out the most deserted places’.

The DNA breakthrough was achieved when Dr Schwenninger and doctoral student James Haile, based at Oxford’s Ancient Biomolecules Centre considered analysing samples of sediment for his research. Dr Shwenninger said: ‘This time last year, I gave James a few samples from several of our archaeological and subfossil sites in Madagascar to see if any plant or animal DNA could be extracted. I also mentioned to him that I had some eggshell which might be worth looking at. In fact, we had already tried this back in 1998 and again in 2003 but without success. He was very keen to give it another go and he succeeded where others, including his thesis supervisor had previously failed.’

How much do we now know about the human genome? What can genes tell us about how we, and other species, evolved? How much of our DNA actually does something, and how much is just non-functional ‘junk’? Join Professor Chris Ponting as he discusses how evolution has shaped our genes, and what we know about our own genetic makeup.

Further Information
Professor Chris Ponting was trained in particle physics before being entranced by the analysis of DNA, genes and genomes. He was a major participant in the international project that sequenced the human genome, and then performed similar roles in projects that sequenced the genomes of the lab mouse, rat, dog, opossum, chicken, and platypus genomes. Once in a while, he has unearthed a nugget of information that tells us something new about human disease. This, in itself, will not immediately help those suffering from health problems. Instead, once this information is published, it provides someone else with a missing piece in their own research puzzle which – when complete – leads to improved diagnoses, drugs or therapy. His most recent research focuses on several human diseases, including learning disability, asthma, obesity, Alzheimer’s and muscular dystrophy.

Two teams of Oxford University researchers led by Professors Judith Armitage and David Stuart have made the first steps towards being able to engineer a bacterial cell that can sense and respond to novel environmental cues. The groups demonstrated that it should be possible to design synthetic signalling circuits inside a cell, ultimately enabling the development of new biosensors.

The ability of bacteria to respond to environmental cues is a universal feature of living cells. Evolution has created a vast array of signalling mechanisms that enable cells to react in many ways to changes in their surroundings. One of the most important of these is a two-component signalling circuit which is widely used by bacteria. It comprises a protein kinase, which acts as the sensor, and its partner protein known as a response regulator. Some species of bacteria have over 150 different sensor-response regulator pairs in a single cell, so the specificity between these pairs has to be tightly controlled to prevent ‘crossed wires’ between signalling pathways.

The two Oxford groups combined their expertise in structural biology and biochemistry to address where this specificity comes from. They used extremely bright pinpoints of light produced by the UK’s national synchrotron facility, Diamond Light Source in south Oxfordshire, to carry out X-ray crystallography, a method that allows visualization of proteins at an atomic level. Using this approach, the researchers solved the three-dimensional structure of one of these two-component complexes found in the bacterium Rhodobacter sphaeroides. This complex is crucial for a process known as chemotaxis which controls the movement of a bacterium when it senses a chemical or nutrient gradient in its environment. Based on the crystallography results, the researchers were able to pinpoint the specific amino acids that are required for this molecular recognition. They found that one amino acid on the response regulator pointed out like a finger towards a pocket on the sensor, enabling the two proteins to fit snugly together. By introducing this finger into other response regulator proteins, which do not normally partner this specific sensor, they were able to change their specificity and re-engineer the chemotaxis pathway.

This is the first time that researchers have re-designed the intracellular part of the chemotaxis circuitry. This re-engineering paves the way for producing custom-designed circuits for applications in systems biology.

“This is a significant step on the road to identifying the critical amino acid interface that allows discrimination between apparently related proteins and their partners, and a step along the road to rational design of protein signalling networks.”
Professor Judith Armitage, Department of Biochemistry

“The aim is to understand the system so well that you’re able to change it in any way you like”, says Christian Bell, the postgraduate student who worked on the project in both labs. “The dream will be a synthetic cell that does exactly what you want.”

In adult fe­male mice, switch­ing off one gene seems to start turn­ing the ovaries in­to tes­ti­cles and trig­gers the pro­duct­ion of male hor­mones at nor­mal male levels, sci­en­tists say.

The cu­ri­ous find­ings have led two re­search­ers to re­mark in a pub­lished pa­per that, bi­o­log­ic­ally speak­ing, fe­males may be en­gaged in a life­long “bat­tle to sup­press their in­ner ma­le.”

Both pa­pers ap­pear in the Dec. 11 is­sue of the re­search jour­nal Cell.

The new results echo a pre­vious study that found that fe­male ovar­ian tissues in mice start to con­vert to male-like tis­sues in the ab­sence of sig­nals from es­tro­gen, a fe­male sex hor­mone. That stu­dy ap­peared in the Dec. 17, 1999 is­sue of the jour­nal Science.

In the newer re­search, N. Hen­ri­ette Uh­len­haut of the Eu­ro­pe­an Mo­lec­u­lar Bi­ol­o­gy Lab­o­r­a­to­ry in Hei­del­berg, Ger­ma­ny, and col­leagues were stu­dy­ing genes that dur­ing de­vel­op­ment are re­spon­si­ble for con­vert­ing glands called go­nads in­to ei­ther ovaries or tes­ti­cles, de­pend­ing on the sex.

Ovaries produce eggs, the fe­male sex cells, while tes­ti­cles produce sperm.

Uh­len­haut and col­leagues ge­net­ic­ally en­gi­neered mice in which the ac­ti­vity of a called Fox2L could be chem­ic­ally sup­pressed in the ovaries.

Fox2L, in turn, is a reg­u­la­tor gene that in­flu­ences the lev­el of ac­ti­vity of an ar­ray of oth­er genes. Among oth­er things, it keeps in check genes that tend to pro­mote tes­ti­cle de­vel­op­ment, ac­cord­ing to Uh­len­haut’s group.

Switch­ing off Fox2L had the im­me­di­ate ef­fect of in­creas­ing the lev­el of ac­ti­vity of some of these “tes­tis-specific” genes, the sci­en­tists re­ported. Crit­i­cal among these, they iden­ti­fied one called Sox9.

Con­com­i­tant with the boost in Sox9 ac­ti­vity was a “re­pro­gram­ming” of cer­tain ovar­i­an cell lin­eages in­to what ap­peared to be tes­tis cell lin­eages, Uh­len­haut and col­leagues found. Mean­while, the mod­i­fied ovaries be­gan pro­duc­ing nor­mal ma­le-like lev­els of the hor­mone tes­tos­ter­one.

“Our re­sults show that main­te­nance of the ovar­i­an phe­no­type [form] is an ac­tive pro­cess through­out life,” the sci­en­tists wrote.

It’s un­clear wheth­er the find­ings would trans­late to hu­mans, but be­cause mice share over 90 per­cent of their genes with hu­mans, it very of­ten hap­pens that mouse pro­cesses have par­al­lels in hu­mans.

It would seem “tes­tic­u­lar de­vel­op­ment is ac­tively re­pressed through­out the life of fe­ma­les,” added An­drew Sin­clair and Craig Smith of the Mur­doch Chil­dren’s Re­search In­sti­tute in Mel­bourne, Aus­tral­ia, in a pa­per pub­lished in the same is­sue of Cell. Sin­clair and Smith—the re­search­ers who in their ar­ti­cle metaphoric­ally sug­gested an “in­ner ma­le” may lurk with­in all fe­ma­les—also not­ed the find­ings go against “con­ven­tional wis­dom” that the ova­ry and tes­tis are “ter­mi­nally dif­fer­en­ti­ated,” or ir­re­versibly de­vel­oped to their ma­ture state.

Why does a human baby need a full year before it can start walking, while a newborn foal gets up on its legs almost directly after birth? Scientist have assumed that human motor development is unique because our brain is unusually complex and because it is particularly challenging to walk on two legs. But now a research group at Lund University in Sweden has shown that human babies in fact start walking at the same stage in brain development as most other walking mammals, from small rodents to elephants. The findings are published in the prestigious journal PNAS.

The Lund group consists of neurophysiologists Martin Garwicz and Maria Christensson and developmental psychologist Elia Psouni. Contrary to convention, they used conception and not birth as the starting point of motor development in their comparison between different mammals. This revealed astonishing similarities among species that diverged in evolution as much as 100 million years ago.
- Humans certainly have more brain cells and bigger brains than most other terrestrial mammalian species, but with respect to walking, brain development appears to be similar for us and other mammals. Our study demonstrates that the difference is quantitative, not qualitative, says Martin Garwicz.

Based on knowledge about development in other mammals it is therefore possible to actually predict with high precision when human babies will start to walk. This is a very unexpected and provocative finding. The notion that humans have a unique position among mammals is not only deeply rooted among lay people, but is also reflected in fundamental assumptions in different research fields related to human development and human brain evolution.- Our study strongly contradicts this assumption and thereby sheds new light on theories in, for instance, evolutionary and developmental biology, says Martin Garwicz
- On the other hand, our findings fit well with the substantial similarities between the genomes of different mammals. Perhaps these similarities are after all not that surprising – although the end products ‘human’ and ‘rat’ may be very different, our study suggests that the building blocks and principles for how these building blocks interact with one another during development could be the same.
The study originated in an attempt by the group to translate behavioral milestones of motor development between two distantly related species. The similarities in relative developmental time courses between the two species were so striking that the scientists started to wonder whether the regularity applied to other mammals and ultimately also to humans.

The Lund group has now compared 24 species, which together represent the majority of existing walking mammals. Some, like the great apes, are closely related to us evolutionarily while others, such as rodents, hoofed animals, and elephants, diverged from our evolutionary path about 90-100 million years ago.

Despite this, and regardless of differences in various species’ brain and body size, gestation time, and brain maturity at birth, the comparison shows that the young from all species start walking at the same relative time point in brain development. Humans may be unique, but not in this particular way. When the nervous system has reached a given level of maturity, you learn to walk, whether you are a hedgehog, a foal, or a human baby…

Article Credit: AlphaGalileo

Researchers in Japan have found that female mice produced by using genetic material from two mothers but no father live significantly longer than mice with the normal mix of maternal and paternal genes. Their findings provide the first evidence that sperm genes may have a detrimental effect on lifespan in mammals.

The research, which is published online on Wednesday 2 December in Europe’s leading reproductive medicine journal Human Reproduction [1], found that mice created from two female genomes (bi-maternal (BM) mice) lived an average of 186 days longer than control mice created from the normal combination of a male and female genome. The average lifespan for the type of mice used in the study is between about 600-700 days, meaning that the BM mice lived approximately a third longer than normal.

Professor Tomohiro Kono (PhD), from the Department of Bioscience, Tokyo University of Agriculture, and Director of the Nodai Research Institute (Tokyo, Japan), and Dr Manabu Kawahara (PhD), associate professor at the Laboratory of Animal Resource Development, Faculty of Agriculture, Saga University (Japan), carried out the research. They believe the reason for the difference in longevity could relate to a gene on chromosome 9 associated with post-natal growth.

Prof Kono said: “We have known for some time that women tend to live longer than men in almost all countries worldwide, and that these sex-related differences in longevity also occur in many other mammalian species. However, the reason for this difference was unclear and, in particular, it was not known whether longevity in mammals was controlled by the genome composition of only one or both parents.”

To answer this question, Prof Kono and Dr Kawahara set out to study the life span of mice produced without sperm. To do this, they collected non-growing oocytes (eggs) from day-old mice, manipulated the genetic material in these eggs so that the genes behaved like sperm genes, and then transplanted this manipulated genetic material into the fully grown, unfertilised oocytes of adult mice that had their nuclei removed (enucleated oocytes). These reconstructed oocytes developed into embryos, which were transferred into surrogate mother mice. The mice that were born as a result were bi-maternal, having genetic material from two mothers, but no father.

The researchers created control mice through natural mating that were genetically identical to the BM mice, apart from the fact that they were created in the normal way with genes from male and female mice.
There were 13 BM mice and 13 control mice born between October 2005 and March 2006, and Prof Kono found that the average lifespan was 186 days longer in the BM mice than in the controls (841.5 days versus 655.5 days). The longest time that any of the control mice lived was 996 days, with all but one of them dying by 800 days, while the longest time alive for the BM mice was 1045 days, with all but three of them living for more than 800 days. The researchers checked the weight of the mice at 49 days and 600 days (around 20 months after birth) and found that the BM mice were significantly lighter and smaller than the control mice. The BM mice also seemed to have better immune systems, with a significant increase in one
type of white blood cell, eosinophil.

Both sets of mice were kept in the same, infection-free environments, with free access to food, making it unlikely that some external environmental factor was the cause of the difference in life spans.
Prof Kono said: “We believe that the most likely reason for the differences in longevity relates to the repression of a gene called Rasgrf1 in the BM mice. This gene normally expresses from the paternally inherited chromosome and is an imprinted gene on chromosome 9 associated with post-natal growth. Thus far, it’s not clear whether Rasgrf1 is definitively associated with mouse longevity, but it is one of the strong candidates for a responsible gene. Furthermore, we cannot eliminate the possibility that other, unknown genes that rely on their paternal inheritance to function normally may be responsible for the extended longevity of the BM mice.”

Imprinted genes are genes that are turned on, or “expressed”, according to whether they are inherited from the mother or the father.

The researchers write: “Our results are consistent with models based on sex-specific selection of reproductive strategies, e.g. male individuals maximizing fitness by an intense investment in reproduction by way of a larger body size in order to achieve more breeding opportunities, resulting in shorter longevity…. In contrast, female individuals usually do not engage in such costly male behaviours and instead tend to optimize their reproductive output by conserving energy for delivery, providing for offspring, foraging and predator avoidance. Our results further suggested sex differences in longevity originating at the genome level, implying that the sperm genome has a detrimental effect on longevity in mammals.”

Prof Kono concluded: “The study may give an answer to the fundamental questions: that is, whether longevity in mammals is controlled by the genome composition of only one or both parents, and just maybe, why women are at an advantage over men with regard to the lifespan.”

An international group of scientists is proposing to generate whole genome sequences for 10,000 vertebrate species using technology so new it hasn’t yet been invented. But the scientists say new genome sequencing instruments that will allow them to embark on the project may be available within a year or two.

In preparation, they are identifying collaborators who can help assemble a collection of frozen or otherwise suitably preserved tissues or DNA samples from these species.

Their proposal, called “Genome 10K,” will be published this week in the Journal of Heredity.

“The idea behind the project is to prepare for this third generation of DNA sequencing technology that began with the Humane Genome Project,” said Oregon State University’s Scott Baker, who edits the Journal of Heredity. “Whereas that project took nearly 10 years at a cost of more than $3 billion, the goal now is to sequence an entire genome in less than a week, for a cost of less than $1,000.

“If that happens, the impact would be remarkable,” added Baker. “And it will happen – the only question is, how soon?”

Baker, who is associate director of OSU’s Marine Mammal Institute, is one of more than 50 scientists from around the world who is collaborating on the proposal. He is coordinating the effort to assemble DNA samples for all known species of cetaceans – whales, dolphins and porpoises – a task made more difficult because the exact number of species keeps changing.

As DNA analysis becomes more sophisticated, Baker said, molecular differences are emerging among some animals thought to belong to the same species.

“We are adding a new species every year or two,” Baker said, “and there is some disagreement about what criteria we should use to describe new species. But to date, more than 90 species have been identified and officially recognized that will require tissue or DNA samples.”

Thus far, Baker and his colleagues have viable DNA samples from 87 of those species, stored at OSU’s Hatfield Marine Science Center in Newport, Ore., at the University of Auckland in New Zealand, and at NOAA’s Southwest Fisheries Science Center in La Jolla, Calif., which holds the largest repository of cetacean tissues.

One of the challenges is to obtain samples for rare, endangered and even extinct species, Baker said.

“We have thousands of samples from humpback whales, for example,” he pointed out. “But there are a few cetacean species that are known literally from only a single skull, and it can be tough to extract DNA from that.”

The feasibility of sequencing 10,000 vertebrate genomes “requires only one more order of magnitude reduction in the cost of DNA sequencing, following the four orders of magnitude reduction we have seen in the last 10 years,” the scientists write in their article.

The variety of species identified will present different challenges for genome sequencing, Baker says, and whales, dolphins and porpoises could be among the most difficult.

“With some species of mammals, the computational assembly process is relatively simple – you start with one DNA sequence and stitch it together with an existing sequence that is similar, but not identical,” Baker said. “With whales, though, it is what’s called a ‘de-novo’ assembly. There is no template to follow.

“It’s like a gigantic jigsaw puzzle and you have to figure out where the pieces go,” he added.

Baker and his colleagues have been working for nearly 20 years on creating DNA barcodes for different cetacean species. The ability to create entire genome sequences would be of enormous benefits to conservation and basic scientific understanding of cetaceans, he said.

“It would give us tremendous new insight into a group of mammals that went through one of the most remarkable adaptations in evolutionary history,” Baker pointed out. “Cetaceans represent an incredible range of ‘extremophiles,’ including the blue whale, which can reach up to 100 feet in length, the bowhead whale, thought to live up to 200 years of age, and the sperm whales, capable of diving to more than a mile in depth.

“Yet despite this rapid adaptation in physiology and physical form, the molecular evolution of whales is 10 times slower than in other mammals,” Baked added. “This may help us find out why. The more we learn about how whales and dolphins have evolved – and how they are similar or different in genetic diversity – the better we will be able to protect species driven to the verge of extinction.”

The Genome 10K proposal is available free online at the Journal of Heredity, http://jhered.oxfordjournals.org

Further information is available from the Genome 10K Community of Scientists, http://www.genome10k.org

A painstaking analysis of thousands of genes and the proteins they encode shows that human beings are biologically complex, at least in part, because of the way humans evolved to cope with redundancies arising from duplicate genes.

‘We have found a specific evolutionary mechanism to account for a portion of the intricate biological complexity of our species,’ said Ariel Fernandez, professor of bioengineering at Rice University. ‘It is a coping mechanism, a process that enables us to deal with the fitness consequences of inefficient selection. It enables some of our proteins to become more specialised over time, and in turn makes us more complex.’

Fernandez is the lead author of a paper slated to appear in the December issue of the journal Genome Research. The research is available online now.

Fernandez said the study drew from previous findings by his own research group and from seminal work of Michael Lynch, Distinguished Professor of Biology at Indiana University and a recently elected a fellow of the National Academy of Science. Lynch’s work has shown that natural selection is less efficient in humans as compared with simpler creatures like bacteria. This ’selection inefficiency’ arises from the smaller population size of humans as compared with unicellular organisms.

‘In all organisms, genes get duplicated every so often, for reasons we don’t fully understand,’ Fernandez said. ‘When working efficiently, natural selection eliminates many of these duplicates, which are called ‘paralogs.’ In our earlier work, we saw that an unusual number of gene duplicates had survived in the human genome, which makes sense given selection inefficiency in humans.’

In prior research on protein structure, Fernandez’s team found that some proteins are packaged more poorly than others. Moreover, they found that the least-efficiently packed proteins are structurally stable only when they bind with partner proteins to form complexes.

‘These poorly packed proteins are potential troublemakers when gene duplication occurs,’ Fernandez said. ‘The paralog encodes more copies of the protein than the body needs. This is called a ‘dosage imbalance,’ and it can make us sick. For instance, dosage imbalance has been implicated in Alzheimer’s and other diseases.’

Given selection inefficiency, Fernandez knew that paralogs encoding poorly packed proteins could remain in the human genome for quite a while. So he and graduate student Jianpeng Chen decided to examine whether gene duplicates had remained in the genome long enough for random genetic mutations to affect the paralogs dissimilarly. Fernandez and Chen, now a senior researcher in Beijing, China, cross-analysed databases on genomics, protein structure, microRNA regulation and protein expression in such troublesome paralogs.

‘The longer these duplicate genes stick around due to inefficient selection, the more likely they are to suffer a random mutation,’ Fernandez said. ‘Portions of every gene act to regulate protein expression – by binding with microRNA, for example. We found numerous instances where random mutations had caused paralogs to be expressed dissimilarly, in ways that removed detrimental dosage imbalances.’

Lynch said one aspect of Fernandez’s research that is potentially groundbreaking is the observed tendency of proteins to evolve a more open structure in complex organisms.

‘This observation fits with the general theory that large organisms with relatively small population sizes – compared to microbes – are subject to the vagaries of random genetic drift and hence the accumulation of very mildly deleterious mutations,’ Lynch said.

In principle, he said, the accumulation of such mutations may encourage a slight breakdown in protein stability. This, in turn, opens the door to interactions with other proteins that can return a measure of that lost stability.

‘These are the potential roots for the emergence of novel protein-protein interactions, which are the hallmark of evolution in complex, multicellular species,’ Lynch said. ‘In other words, the origins of some key aspects of the evolution of complexity may have their origins in completely nonadaptive processes.’

Fernandez said the research reveals how increasingly specialised proteins can evolve. He drew an analogy to a business that hires two delivery drivers that initially cover the same parts of town but eventually specialise to deliver only to specific neighbourhoods.

‘Eventually, even if times become tough, you cannot lay off either of them because they each became so specialised that your company needs them both,’ he said.

The more simple a creature is, the fewer specialised proteins it possesses. Humans and other higher-order mammals need many specialised proteins to build the specialised tissues in their skin, skeleton and organs. Even more specialised proteins are needed to maintain and regulate them. This complexity requires that the duplicates of the original jack-of-all-trades gene be retained, but this does not happen unless selection is inefficient. This is frequently a point of contention between proponents of evolution and intelligent design.

Fernandez and Chen looked at duplicate genes across the human genome and found that the more poorly packed a protein was, the more likely it was to be distinguished through paralog specialisation.

‘This supports the case for evolution because it shows that you can drive complexity with random mutations in duplicate genes,’ Fernandez said. ‘But this also implies that random drift must prevail over Darwinian selection. In other words, if Darwinian selection were ruthlessly efficient in humans – as it is in bacteria and unicellular eukaryotes – then our level of complexity would not be possible.’

Drunk­en fruit flies have helped re­search­ers iden­ti­fy whole net­works of genes—al­so found in hu­man­s—that play a key role in al­co­hol drink­ing be­hav­ior, ac­cord­ing to a stu­dy.

Sci­en­tists said the in­ves­ti­ga­t­ion iden­ti­fied mo­le­cules in the body that could serve as tar­gets on which drugs against al­co­holism might act.

The work al­so sheds light on many of the neg­a­tive side ef­fects of drink­ing, such as liv­er dam­age, and on why some peo­ple tol­er­ate al­co­hol bet­ter than oth­ers, said the re­search­ers, from North Car­o­li­na State and Bos­ton un­ivers­i­ties

Stud­ies “in which dis­cov­er­ies from mod­el or­gan­isms can be ap­plied to in­sights in hu­man bi­ol­o­gy, can make us un­der­stand the bal­ance be­tween na­ture and nur­ture, why we be­have the way we do,” said Rob­ert An­holt, a ge­net­i­cist at North Car­o­li­na State in­volved with the proj­ect.

An­holt and col­leagues timed how long it took for fruit flies to lose pos­tur­al con­trol af­ter ex­po­sure to al­co­hol. Mean­while, the re­search­ers meas­ured lev­els of ac­ti­vity in the in­sects’ genes. Us­ing sta­tis­ti­cal meth­ods to iden­ti­fy genes that work to­geth­er, the sci­en­tists pin­pointed ones that played a cru­cial role in the re­sponse to al­co­hol ex­po­sure.

The sci­en­tists then stud­ied wheth­er the same genes con­trib­ute to al­co­hol drink­ing habits in hu­mans. In­deed they do: ac­ti­vity in the hu­man coun­ter­part of a crit­i­cal gene in fruit flies could be di­rectly tied to al­co­hol con­sump­tion in hu­mans, said mem­bers of An­holt’s group.

The find­ings are pub­lished in the Oc­to­ber is­sue of the re­search jour­nal Ge­net­ics.

“From a sci­en­tif­ic point of view, re­search like this is al­most in­tox­i­cat­ing,” said Mark John­ston, editor-in-chief of the jour­nal. “We’ve known for a while now that ge­net­ics played a role in al­co­hol con­sump­tion, but now, we ac­tu­ally know some of the genes that are in­volved. As a re­sult of this work, we have a po­ten­tial drug tar­get for cur­ing this in­sid­i­ous con­di­tion.”

By breaking the human genome into millions of pieces and reverse-engineering their arrangement, researchers have produced the highest-resolution picture ever of the genome’s three-dimensional structure.

The picture is one of mind-blowing fractal glory, and the technique could help scientists investigate how the very shape of the genome, and not just its DNA content, affects human development and disease.

“It’s become clear that the spatial organization of chromosomes is critical for regulating the genome,” said study co-author Job Dekker, a molecular biologist at the University of Massachusetts Medical School. “This opens up new aspects of gene regulation that weren’t open to investigation before. It’s going to lead to a lot of new questions.”

As depicted in basic biology textbooks and the public imagination, the human genome is packaged in bundles of DNA and protein on 23 chromosomes, arrayed in a neatly X-shaped form inside each cell nucleus. But that’s only true during the fleeting few moments when cells are poised to divide. The rest of the time, those chromosomes exist in a dense and ever-shifting clump. Of course their constituent DNA strings are clumped, too: If the genome could be laid out end-to-end, it’d be six feet long.

For decades, some cell biologists suspected that the genome’s compression wasn’t just an efficient storage mechanism, but linked to the very function and interaction of its genes. But this wasn’t easy to study: Sequencing the genome destroys its shape, and electron microscopes can barely penetrate its active surface. Though its constituent parts are known, the genome’s true shape has been a mystery.

In April, a paper published in the Proceedings of the National Academy of Sciences linked patterns of gene activation to their physical proximity on chromosomes. It still provided the most persuasive evidence to date that genome shape matters, even though the researchers’ chromosome map was relatively low-resolution. The topography described in the latest research, published Thursday in Science, is far more detailed.

“It’s going to change the way that people study chromosomes. It will open up the black box. We didn’t know the internal organization. Now we can look at it in high resolution, try to link that structure to the activity of genes, and see how that structure changes in cells and over time,” said Dekker.

To determine genome structure without being able to directly see it, the researchers first soaked cell nuclei in formaldehyde, which interacts with DNA like glue. The formaldehyde stuck together genes that are distant from each other in linear genomic sequences, but adjacent to each other in actual three-dimensional genomic space.

The researchers then added a chemical that dissolved the gene-by-gene linear sequence bonds, but left the formaldehyde links intact. The result was a pool of paired genes, something like a frozen ball of noodles that had been sliced into a million fragmentary layers and mixed.

By studying the pairs, the researchers could tell which genes had been near each other in the original genome. With the aid of software that cross-referenced the gene pairs with their known sequences on the genome, they assembled a digital sculpture of the genome. And what a marvelous sculpture it is.

“There’s no knots. It’s totally unentangled. It’s like an incredibly dense noodle ball, but you can pull out some of the noodles and put them back in, without disturbing the structure at all,” said Harvard University computational biologist Erez Lieberman-Aiden, also a study co-author.

In mathematical terms, the pieces of the genome are folded into something similar to a Hilbert curve, one of a family of shapes that can fill a two-dimensional space without ever overlapping — and then do the same trick in three dimensions.

How evolution arrived at this solution to the challenge of genome storage is unknown. It might be an intrinsic property of chromatin, the DNA-and-protein mix from which chromosomes are made. But whatever the origin, it’s more than mathematically elegant. The researchers also found that chromosomes have two regions, one for active genes and another for inactive genes, and the unentangled curvatures allow genes to be moved easily between them.

Lieberman-Aiden likened the configuration to the compressed rows of mechanized bookshelves found in large libraries. “They’re like stacks, side-by-side and on top of each other, with no space between them. And when the genome wants to use a bunch of genes, it opens up the stack. But not only does it open the stack, it moves it to a new section of the library,” he said.

The segregation of active and inactive genes adds to evidence that genome structure affects gene function.

“It’s a great description of the structure of the nucleus, and if you put that on top of what we did, it forms the big picture,” said Steven Kosak, a Northwestern University cell biologist and co-author of the April PNAS paper that linked rough outlines of chromosome arrangement to gene activation. Whereas that study only looked at a few chromosomes, the Science paper “looks at fine resolution over the whole genome,” said Kosak.

“Now you can produce these genome maps, and superimpose them with genome-wide analyses of gene expression. You can really start asking how changes in spatial organization relate to changes in genes turning on and off,” said Tom Misteli, a National Cancer Institute cell biologist who studies how glitches in chromosome structure may turn cells cancerous. Neither Misteli nor Kosak were involved in the Science study.

Connecting genome shape to gene function could also help explain the connection between genes and disease, which remain largely unexplained by traditional, sequence-focused genomics.

“It’s perfectly reasonable and almost inevitable that the 3-D structure of DNA is going to influence how it functions,” said Teri Manolio, director of the National Human Genome Research Institute’s Office of Population Genomics.

Researchers also want to study how genome shape is altered. That appears to happen constantly during the transition from stem cell to adult cell, and then during cell function.

“How much variation is there in structure across cell types? What controls it? Exactly how important is it? We don’t know,” said Dekker. “This is a new area of science.”

[Image: From Science, a two-dimensional Hilbert curve, and the three-dimensional shape of a genome.]
Article Credit: Wired Science

Behavioural ecologists working in Bolivia have found that wild spider monkeys control their diets in a similar way to humans, contrary to what has been thought up to now. Rather than trying to maximize their daily energy intake, the monkeys tightly regulate their daily protein intake, so that it stays at the same level regardless of seasonal variation in the availability of different foods.

Tight regulation of daily protein intake is known to play a role in the development of obesity in humans, and the findings from this research suggest that the evolutionary origins of these eating patterns in humans may be far older than suspected. Until now it was thought humans’ eating patterns originated in the Palaeolithic era (between 2.4 million and 10,000 years ago).

The research, published online today (Wednesday 20 May) in the journal Behavioral Ecology [1], also provides valuable information about which trees are important for the monkeys’ diet, which is relevant to conservation; in addition, it may help to improve the care of captive primates, which can be prone to obesity and related health problems due to their diet.

Dr Annika Felton, a Departmental Visitor at the Fenner School of Environment and Society, The Australian National University, Canberra, Australia, spent a year in the Bolivian rainforest (in Departmento Santa Cruz) familiarising the Peruvian spider monkeys (Ateles chamek) to her presence and then observing their feeding habits.

She followed 15 individual monkeys (7 adult males, 8 adult females), conducting continuous observations of the same animal from dawn to dusk, and following each of the monkeys for at least one whole day a month. During observations she recorded everything they did and ate and for how long. Where possible, she counted every fruit and leaf they ate, and collected samples of what they had eaten from the actual trees the monkeys had chosen. The samples were then dried and sent to the laboratory in Australia where they were analysed for their nutritional content. It is unusual for a study of feeding habits in wild primates to be conducted in this detailed way. It enabled Dr Felton and her colleagues to calculate how much an individual monkey had consumed and the nutrients involved; usually, other field studies are only able to calculate averages for a group of animals.

Dr Felton said: “We found that the pattern of nutrient intake by wild spider monkeys, which are primarily fruit eaters, was almost identical to humans, which are omnivores. What spider monkeys and humans have in common is that they tightly regulate their daily protein intake, i.e. they appear to aim for a target amount of protein each day, regardless of whether they only ate ripe fruit or mixed in other vegetable matter as well. Finding this result in spider monkeys was unexpected because, previously, ripe fruit specialists were thought to be ‘energy maximisers’. In other words, they would aim to maximise their daily energy intake. Our findings show this is not the case.

“The consequence of tight protein regulation is the same for monkeys and humans: if the diet is poor in protein but rich in carbohydrates and fats (energy dense food) individuals will end up ingesting a great deal of energy in order to obtain their protein target, which can lead to weight gain. This ‘protein leverage effect’ is thought to play a significant role in the human obesity problem found in modern western societies. Our results suggest that an adjustment of the nutritional balance of diets as a means to manage human obesity might similarly be an option for mitigating obesity in captive primates.

“Our findings are also interesting from an evolutionary point of view. Similarity in the regulatory pattern of protein intake between distantly related species, such as humans and spider monkeys, possessing very different dietary habits, may indicate that the evolutionary origins of such regulatory patterns are quite old, potentially far older than the Palaeolithic era. If we are not dealing with convergent evolution here – in other words that spider monkeys and humans have evolved this trait independently – then this trait may have been shared by our common ancestor. Spider monkeys are New World primates that split from the Old World primates about
40 million years ago.

“Finally, our research shows that nutritionally-balanced food sources that are used extensively by a wild population may need special attention in terms of conservation planning, perhaps by regulating logging and selecting certain tree species for re-planting. The majority of the monkeys’ nourishment was sourced from a species of fig tree, Ficus boliviana, that is currently being harvested for timber in Bolivia.”

Dr Felton and her colleagues found that the monkeys ate a wide variety of fruit and vegetables – 105 different plants belonging to 63 species during the 12 months of observation. Figs were particularly popular. The monkeys rarely ate insects, which are rich in protein.

The spider monkeys did not specifically select either the most energy-rich or the most proteinrich foods that were available, and the daily amount of food they ate varied quite widely, averaging about 1 kg a day, but sometimes as much as 2.4 kg a day. However, they maintained their daily protein intake around 0.2 MJ (11 grams), whereas their intake of carbohydrates and fats varied between 0.7-6.2 MJ. The availability of sweet, ripe fruit was significantly related to the variation in their daily energy intake – the more there was, the more they ate.

“To maintain a stable intake of protein, spider monkeys consumed large amounts of carbohydrates and fats when protein content in the food was low, for instance when their diet consisted entirely of ripe fruit, and consumed far fewer carbohydrates and fats when feeding on items rich in protein,” said Dr Felton.

She concluded: “What is perhaps most fascinating about our paper is not the answers we provide, but the questions that our findings raise. For example, why do these frugivores have the same pattern of nutritional intake as human omnivores? Is this due to convergent evolution or is it a remaining trait from a common ancestor?

“I am also pleased that our findings can be applied to the management of captive primates (where obesity is a problem), and possibly the management of spider monkey forest habitat.

“Also, importantly, we have shown that the combination of intensive data collection and the application of an innovative analytical framework can dramatically change our perceptions of the nutritional ecology of a species.”

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Each of the world’s 40,000 spider species survives by hunting and killing — except, that is, for Bagheera kiplingi, the world’s first vegetarian arachnid.

Found in Central America, the order-defying jumping spider eats nutrient-rich structures called Beltian bodies, which are found on the tips of Acacia trees. Trees produce the bodies to feed ants that defend them, which is a textbook example of what’s called co-evolutionary mutalism, and one that B. kiplingi has evolved to exploit.

In a paper published Monday in Current Biology, researchers describe the spider’s ant-evading habits and provide a molecular analysis of its body composition, proving that B. kiplingi is indeed what it eats: plants, with a few larval ants on the side. (After all, 400 million years of evolutionary habits die hard.)

A few other spiders have been documented consuming nectar, but only as a snack. No other spider is so predominantly vegetarian. And that’s not all: It looks like B. kiplingi males help care for eggs and young — something entirely unprecedented in the spider world.

The researchers are now studying whether there’s a link between B. kiplingi’s predilection for plants and parental concern. Maybe going veggie softened its heart.

Article Credit: Wired Science

Scientists have managed to induce cells from pigs to transform into pluripotent stem cells – cells that, like embryonic stem cells, are capable of developing into any type of cell in the body. It is the first time in the world that this has been achieved using somatic cells (cells that are not sperm or egg cells) from any animal with hooves (known as ungulates).

The implications of this achievement are far-reaching; the research could open the way to creating models for human genetic diseases, genetically engineering animals for organ transplants for humans, and for developing pigs that are resistant to diseases such as swine flu.

The work is the first research paper to be published online today (Wednesday 3 June) in the newly launched Journal of Molecular Cell Biology [1].
Dr Lei Xiao, who led the research, said: “To date, many efforts have been made to establish ungulate pluripotent embryonic stem cells from early embryos without success. This is the first report in the world of the creation of domesticated ungulate pluripotent stem cells.

Therefore, it is entirely new, very important and has a number of applications for both human and animal health.”

Dr Xiao, who heads the stem cell lab at the Shanghai Institute of Biochemistry and Cell Biology (Shanghai, China), and colleagues succeeded in generating induced pluripotent stem cells by using transcription factors to reprogramme cells taken from a pig’s ear and bone marrow. After the cocktail of reprogramming factors had been introduced into the cells via a virus, the cells changed and developed in the laboratory into colonies of embryonic-like stem cells. Further tests confirmed that they were, in fact, stem cells capable of differentiating into the cell types that make up the three layers in an embryo – endoderm, mesoderm and ectoderm – a quality that all embryonic stem cells have. The information gained from successfully inducing pluripotent stem cells (iPS cells) means that it will be much easier for researchers to go on to develop embryonic stem cells (ES cells) that originate from pig or other ungulate embryos.

Dr Xiao said: “Pig pluripotent stem cells would be useful in a number of ways, such as precisely engineering transgenic animals for organ transplantation therapies. The pig species is significantly similar to humans in its form and function, and the organ dimensions are largely similar to human organs. We could use embryonic stem cells or induced stem cells to modify the immune-related genes in the pig to make the pig organ compatible to the human immune system. Then we could use these pigs as organ donors to provide organs for patients that won’t trigger an adverse reaction from the patient’s own immune system.

“Pig pluripotent stem cell lines could also be used to create models for human genetic diseases. Many human diseases, such as diabetes, are caused by a disorder of gene expression. We could modify the pig gene in the stem cells and generate pigs carrying the same gene disorder so that they would have a similar syndrome to that seen in human patients. Then it would be possible to use the pig model to develop therapies to treat the disease.

“To combat swine flu, for instance, we could make a precise, gene-modified pig to improve the animal’s resistance to the disease. We would do this by first, finding a gene that has antiswine flu activity, or inhibits the proliferation of the swine flu virus; second, we can introduce this gene to the pig via pluripotent stem cells – a process known as gene ‘knock-in’.

Alternatively, because the swine flu virus needs to bind with a receptor on the cell membrane of the pig to enter the cells and proliferate, we could knock out this receptor in the pig via gene targeting in the pig induced pluripotent stem cell. If the receptor is missing, the virus will not infect the pig.”

In addition to medical applications for pigs and humans, Dr Xiao said his discovery could be used to improve animal farming, not only by making the pigs healthier, but also by modifying the growth-related genes to change and improve the way the pigs grow.

However, Dr Xiao warned that it could take several years before some of the potential medical applications of his research could be used in the clinic.
The next stage of his research is to use the pig iPS cells to generate gene-modified pigs that could provide organs for patients, improve the pig species or be used for disease resistance.
The modified animals would be either “knock in” pigs where the iPS or ES cells have been used to transfer an additional bit of genetic material (such as a piece of human DNA) into the pig’s genome, or “knock out” pigs where the technology is used to prevent a particular gene functioning.

Commenting on the study, the journal’s editor-in-chief, Professor Dangsheng Li, said: “This research is very exciting because it represents the first rigorous demonstration of the establishment of pluripotent stem cell in ungulate species, which will open up interesting opportunities for creating precise, gene-modified animals for research, therapeutic and agricultural purposes.”

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