Category: DNA

Creating a Synthetic Human Genome

On By A.P.In DNA, gene, The FutureLeave a comment


Sixty trays can contain the entire human genome as 23,040 different fragments of cloned DNA. Credit James King-Holmes/Science Source

By ANDREW POLLACK

Scientists are now contemplating the fabrication of a human genome, meaning they would use chemicals to manufacture all the DNA contained in human chromosomes.

The prospect is spurring both intrigue and concern in the life sciences community because it might be possible, such as through cloning, to use a synthetic genome to create human beings without biological parents.

While the project is still in the idea phase, and also involves efforts to improve DNA synthesis in general.

Organizers said the project could have a big scientific payoff and would be a follow-up to the original Human Genome Project, which was aimed at reading the sequence of the three billion chemical letters in the DNA blueprint of human life. The new project, by contrast, would involve not reading, but rather writing the human genome — synthesizing all three billion units from chemicals.

But such an attempt would raise numerous ethical issues. Could scientists create humans with certain kinds of traits, perhaps people born and bred to be soldiers? Or might it be possible to make copies of specific people?

“Would it be O.K., for example, to sequence and then synthesize Einstein’s genome?” Drew Endy, a bioengineer at Stanford, and Laurie Zoloth, a bioethicist at Northwestern University, wrote in an essay criticizing the proposed project. “If so how many Einstein genomes should be made and installed in cells, and who would get to make them?”

The project was initially called HGP2: The Human Genome Synthesis Project, with HGP referring to the Human Genome Project. An invitation to the meeting at Harvard said that the primary goal “would be to synthesize a complete human genome in a cell line within a period of 10 years.”

But by the time the meeting was held, the name had been changed to “HGP-Write: Testing Large Synthetic Genomes in Cells.”

The project does not yet have funding, Dr. Church said, though various companies and foundations would be invited to contribute, and some have indicated interest. The federal government will also be asked. A spokeswoman for the National Institutes of Health declined to comment, saying the project was in too early a stage.

Besides Dr. Church, the organizers include Jef Boeke, director of the institute for systems genetics at NYU Langone Medical Center, and Andrew Hessel, a self-described futurist who works at the Bay Area software company Autodesk and who first proposed such a project in 2012.

Scientists and companies can now change the DNA in cells, for example, by adding foreign genes or changing the letters in the existing genes. This technique is routinely used to make drugs, such as insulin for diabetes, inside genetically modified cells, as well as to make genetically modified crops. And scientists are now debating the ethics of new technology that might allow genetic changes to be made in embryos.

But synthesizing a gene, or an entire genome, would provide the opportunity to make even more extensive changes in DNA.

For instance, companies are now using organisms like yeast to make complex chemicals, like flavorings and fragrances. That requires adding not just one gene to the yeast, like to make insulin, but numerous genes in order to create an entire chemical production process within the cell. With that much tinkering needed, it can be easier to synthesize the DNA from scratch.

Right now, synthesizing DNA is difficult and error-prone. Existing techniques can reliably make strands that are only about 200 base pairs long, with the base pairs being the chemical units in DNA. A single gene can be hundreds or thousands of base pairs long. To synthesize one of those, multiple 200-unit segments have to be spliced together.

But the cost and capabilities are rapidly improving. Dr. Endy of Stanford, who is a co-founder of a DNA synthesis company called Gen9, said the cost of synthesizing genes has plummeted from $4 per base pair in 2003 to 3 cents now. But even at that rate, the cost for three billion letters would be $90 million. He said if costs continued to decline at the same pace, that figure could reach $100,000 in 20 years.

J. Craig Venter, the genetic scientist, synthesized a bacterial genome consisting of about a million base pairs. The synthetic genome was inserted into a cell and took control of that cell. While his first synthetic genome was mainly a copy of an existing genome, Dr. Venter and colleagues this year synthesized a more original bacterial genome, about 500,000 base pairs long.

Dr. Boeke is leading an international consortium that is synthesizing the genome of yeast, which consists of about 12 million base pairs. The scientists are making changes, such as deleting stretches of DNA that do not have any function, in an attempt to make a more streamlined and stable genome.

But the human genome is more than 200 times as large as that of yeast and it is not clear if such a synthesis would be feasible.

Jeremy Minshull, chief executive of DNA2.0, a DNA synthesis company, questioned if the effort would be worth it.

“Our ability to understand what to build is so far behind what we can build,” said Dr. Minshull, who was invited to the meeting at Harvard but did not attend. “I just don’t think that being able to make more and more and more and cheaper and cheaper and cheaper is going to get us the understanding we need.”

Chinese researchers report first-ever gene editing of human embryos

On By A.P.In DNA, gene, Medicine, Michael Moore, Science, The FutureLeave a comment

In an ethically charged first, Chinese researchers have used gene editing to modify human embryos obtained from an in-vitro fertilization clinic.

The 16-person scientific team, based at the Sun Yat-Sen University in Guangzhou, China, set out to see whether it could correct the gene defect that causes beta-thalassemia, a blood disease, by editing the DNA of fertilized eggs.

The team’s report showed the method is not yet very accurate, confirming scientific doubts around whether gene editing could be practical in human embryos, and whether genetically engineered people are going to be born anytime soon.

The authors’ report appeared on April 18 in a low-profile scientific journal called Protein & Cell. The authors, led by Junjiu Huang, say there is a “pressing need” to improve the accuracy of gene editing before it can be applied clinically, for instance to produce children with repaired genes.

The team did not try to establish a pregnancy and say for ethical reasons they did their tests only in embryos that were abnormal.

“These authors did a very good job pointing out the challenges,” says Dieter Egli, a researcher at the New York Stem Cell Foundation in Manhattan. “They say themselves this type of technology is not ready for any kind of application.”

The paper had previously circulated among researchers and had provoked concern by highlighting how close medical science may be to tinkering with the human gene pool.

n March, an industry group called for a complete moratorium on experiments of the kind being reported from China, citing risks and the chance they would open the door to eugenics, or changing nonmedical traits in embryos, such as stature or intelligence.

Other scientists recommended high-level meetings of experts, regulators, and ethicists to debate if there are acceptable uses for such engineering.

The Chinese team reported editing the genes of more than 80 embryos using a technology called CRISPR-Cas9. While in some cases they were successful, in others the CRISPR technology didn’t work or introduced unexpected mutations. Some of the embryos ended up being mosaics, with a repaired gene in some cells, but not in others.

Parents who are carriers of beta-thalassemia could choose to test their IVF embryos, selecting those that have not inherited the disease-causing mutation. However, gene editing opens the possibility of germline modification, or permanently repairing the gene in an embryo, egg, or sperm in a way that is passed onto the offspring and to future generations.

That idea is the subject of intense debate, since some think the human gene pool is sacrosanct and should never be the subject of technological alteration, even for medical reasons. Others allow that germline engineering might one day be useful, but needs much more testing. “You can’t discount it,” says Egli. “It’s very interesting.”

The Chinese team performed the gene editing in eggs that had been fertilized in an IVF clinic but were abnormal because they had been fertilized by two sperm, not one. “Ethical reasons precluded studies of gene editing in normal embryos,” they said.

Abnormal embryos are widely available for research, both in China and the U.S. At least one U.S. genetics center is also using CRISPR in abnormal embryos rejected by IVF clinics. That group described aspects of its work on the condition that it would not be identified, since the procedure remains controversial.

Making repairs using CRISPR harnesses a cell’s own DNA repair machinery to correct genes. The technology guides a cutting protein to a particular site on the DNA molecule, chopping it open. If a DNA “repair template” is provided—in this case a correct version of the beta-globin gene—the DNA will mend itself using the healthy sequence.

The Chinese group says that among the problems they encountered, the embryo sometimes ignored the template, and instead repaired itself using similar genes from its own genome, “leading to untoward mutations.”

Huang said he stopped the research after the poor results. “If you want to do it in normal embryos, you need to be close to 100 percent,” Huang told Nature News. “That’s why we stopped. We still think it’s too immature.”

http://www.technologyreview.com/news/536971/chinese-team-reports-gene-editing-human-embryo/

Thanks to Michael Moore for bringing this to the It’s Interesting community.

The eternity drive: Why DNA could be the future of data storage

On By A.P.In data storage, DNA, Science, Technology, The FutureLeave a comment

By Peter Shadbolt, for CNN

How long will the data last in your hard-drive or USB stick? Five years? 10 years? Longer?

Already a storage company called Backblaze is running 25,000 hard drives simultaneously to get to the bottom of the question. As each hard drive coughs its last, the company replaces it and logs its lifespan.

While this census has only been running five years, the statistics show a 22% attrition rate over four years.

Some may last longer than a decade, the company says, others may last little more than a year; but the short answer is that storage devices don’t last forever.

Science is now looking to nature, however, to find the best way to store data in a way that will make it last for millions of years.

Researchers at ETH Zurich, in Switzerland, believe the answer may lie in the data storage system that exists in every living cell: DNA.

So compact and complex are its strands that just 1 gram of DNA is theoretically capable of containing all the data of internet giants such as Google and Facebook, with room to spare.

In data storage terms, that gram would be capable of holding 455 exabytes, where one exabyte is equivalent to a billion gigabytes.

Fossilization has been known to preserve DNA in strands long enough to gain an animal’s entire genome — the complete set of genes present in a cell or organism.

So far, scientists have extracted and sequenced the genome of a 110,000-year-old polar bear and more recently a 700,000-year-old horse.

Robert Grass, lecturer at the Department of Chemistry and Applied Biosciences, said the problem with DNA is that it degrades quickly. The project, he said, wanted to find ways of combining the possibility of the large storage density in DNA with the stability of the DNA found in fossils.

“We have found elegant ways of making DNA very stable,” he told CNN. “So we wanted to combine these two stories — to get the high storage density of DNA and combine it with the archaeological aspects of DNA.”

The synthetic process of preserving DNA actually mimics processes found in nature.

As with fossils, keeping the DNA cool, dry and encased — in this case, with microscopic spheres of glass – could keep the information contained in its strands intact for thousands of years.

“The time limit with DNA in fossils is about 700,000 years but people speculate about finding one-million-year storage of genomic material in fossil bones,” he said.

“We were able to show that decay of our DNA and store of information decays at the same rate as the fossil DNA so we get to similar time frames of close to a million years.”

Fresh fossil discoveries are throwing up new surprises about the preservation of DNA.

Human bones discovered in the Sima de los Huesos cave network in Spain show maternally inherited “mitochondrial” DNA that is 400,000 years old – a new record for human remains.

The fact that the DNA survived in the relatively cool climate of a cave — rather than in a frozen environment as with the DNA extracted from mammoth remains in Siberia – has added to the mystery about DNA longevity.

“A lot of it is not really known,” Grass says. “What we’re trying to understand is how DNA decays and what the mechanisms are to get more insight into that.”

What is known is that water and oxygen are the enemy of DNA survival. DNA in a test tube and exposed to air will last little more than two to three years. Encasing it in glass — an inert, neutral agent – and cooling it increases its chances of survival.

Grass says sol-gel technology, which produces solid materials from small molecules, has made it a relatively easy process to get the glass around the DNA molecules.

While the team’s work invites immediate comparison with Jurassic Park, where DNA was extracted from amber fossils, Grass says that prehistoric insects encased in amber are a poor source of prehistoric DNA.

“The best DNA comes from sources that are ceramic and dry — so teeth, bones and even eggshells,” he said.

So far the team has tested their storage method by preserving just 83 kilobytes of data.

“The first is the Swiss Federal Charter of 1291 — it’s like the Swiss Magna Carta — and the other was the Archimedes Palimpsest; a copy of an Ancient Greek mathematics treatise made by a monk in the 10th century but which had been overwritten by other monks in the 15th century.

“We wanted to preserve these documents to show not just that the method works, but that the method is important too,” he said.

He estimates that the information will be readable in 10,000 years’ time, and if frozen, as long as a million years.

The cost of encoding just 83Kb of data cost about $2,000, making it a relatively expensive process, but Grass is optimistic that price will come down over time. Advances in technology for medical analysis, he said, are likely to help with this.

“Already the prices for human genome sequences have dropped from several millions of dollars a few years ago to just hundreds of dollars now,” Grass said.

“It makes sense to integrate these advances in medical and genome analysis into the world of IT.”

http://www.cnn.com/2015/02/25/tech/make-create-innovate-fossil-dna-data-storage/index.html?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+rss%2Fcnn_latest+%28RSS%3A+Most+Recent%29

Protein That Can Edit Other Proteins Without DNA Blueprint Discovered

On By A.P.In DNA, gene, Kebmodee, protein, ScienceLeave a comment

In our cells, proteins are the tiny machines that do most of the work. And the instructions for making proteins — and for piecing together their building blocks, called amino acids — are laid out by DNA, then relayed through RNA. But now, researchers show for the first time that amino acids can be assembled by another protein — without genetic instructions. These surprising findings were published in Science this week.

If a cell is an automobile-making factory, then ribosomes are the machines on the protein assembly line that links together amino acids in an order specified by DNA and messenger RNA (mRNA), an intermediate template. If something goes awry and a ribosome stalls, the quality control team shows up to disassemble the ribosome, discard that bit of genetic blueprint, and recycle the partially-made protein.

Turns out, that assembly line can keep going even if it loses its genetic instructions, according to a large U.S. team led by University of Utah, University of California, San Francisco, and Stanford researchers. They discovered an unexpected mechanism of protein synthesis where a protein, and not the normal genetic blueprint, specifies which amino acids are added.

“In this case, we have a protein playing a role normally filled by mRNA,” UCSF’s Adam Frost says in a news release. “I love this story because it blurs the lines of what we thought proteins could do.”

Frost and colleagues found a never-before-seen role for one member of the quality control team: a protein named Rqc2, which helps recruit transfer RNA (tRNA) to sites of ribosomal breakdowns (tRNA is responsible for bringing amino acids to the protein assembly line). Before the incomplete protein gets recycled, Rqc2 prompts the stalled ribosomes to add two amino acids — alanine and threonine — over and over. And that’s because the Rqc2–ribosome complex binds tRNAs that carry those two specific amino acids. In the auto analogy, the assembly line keeps going despite having lost its instructions, picking up whatever it can and attaching it in no particular order: horn-wheel-wheel-horn-wheel-wheel-wheel-wheel-horn, for example.

Pictured above, Rqc2 (yellow) binds tRNAs (blue and teal), which add amino acids (bright sot in the middle) to a partially-made protein (green). The complex binds the ribosome (white). A truncated protein with a seemingly random sequence of alanines and threonines probably doesn’t work properly, and that tail could be a code that signals for the malformed protein to be destroyed.

http://www.iflscience.com/health-and-medicine/protein-directs-protein-synthesis-without-dna-blueprint

Thanks to Kebmodee for bringing this to the attention of the It’s Interesting community.

Rapid-DNA technology that profiles DNA in about 90 minutes for law enforcement

On By A.P.In DNA, Kebmodee, ScienceLeave a comment


Rapid-DNA technology makes it easier than ever to grab and store your genetic profile. G-men, cops, and Homeland Security can’t wait to see it everywhere.

Robert Schueren shook my hand firmly, handed me his business card, and flipped it over, revealing a short list of letters and numbers. “Here is my DNA profile.” He smiled. “I have nothing to hide.” I had come to meet Schueren, the CEO of IntegenX, at his company’s headquarters in Pleasanton, California, to see its signature product: a machine the size of a large desktop printer that can unravel your genetic code in the time it takes to watch a movie.

Schueren grabbed a cotton swab and dropped it into a plastic cartridge. That’s what, say, a police officer would use to wipe the inside of your cheek to collect a DNA sample after an arrest, he explained. Other bits of material with traces of DNA on them, like cigarette butts or fabric, could work too. He inserted the cartridge into the machine and pressed a green button on its touch screen: “It’s that simple.” Ninety minutes later, the RapidHIT 200 would generate a DNA profile, check it against a database, and report on whether it found a match.

The RapidHIT represents a major technological leap—testing a DNA sample in a forensics lab normally takes at least two days. This has government agencies very excited. The Department of Homeland Security, the Department of Defense, and the Justice Department funded the initial research for “rapid DNA” technology, and after just a year on the market, the $250,000 RapidHIT is already being used in a few states, as well as China, Russia, Australia, and countries in Africa and Europe.

“We’re not always aware of how it’s being used,” Schueren said. “All we can say is that it’s used to give an accurate identification of an individual.” Civil liberties advocates worry that rapid DNA will spur new efforts by the FBI and police to collect ordinary citizens’ genetic code.

The US government will soon test the machine in refugee camps in Turkey and possibly Thailand on families seeking asylum in the United States, according to Chris Miles, manager of the Department of Homeland Security’s biometrics program. “We have all these families that claim they are related, but we don’t have any way to verify that,” he says. Miles says that rapid DNA testing will be voluntary, though refusing a test could cause an asylum application to be rejected.

Miles also says that federal immigration officials are interested in using rapid DNA to curb trafficking by ensuring that children entering the country are related to the adults with them. Jeff Heimburger, the vice president of marketing at IntegenX, says the government has also inquired about using rapid DNA to screen green-card applicants. (An Immigration and Customs Enforcement spokesman said he was not aware that the agency was pursuing the technology.)

Meanwhile, police have started using rapid DNA in Arizona, Florida, and South Carolina. In August, sheriffs in Columbia, South Carolina, used a RapidHIT to nab an attempted murder suspect. The machine’s speed provides a major “investigative lead,” said Vince Figarelli, superintendent of the Arizona Department of Public Safety crime lab, which is using a RapidHIT to compare DNA evidence from property crimes against the state’s database of 300,000 samples. Heimburger notes that the system can also prevent false arrests and wrongful convictions: “There is great value in finding out that somebody is not a suspect.”

But the technology is not a silver bullet for DNA evidence. The IntegenX executives brought up rape kits so often that it sounded like their product could make a serious dent in the backlog of half a million untested kits. Yet when I pressed Schueren on this, he conceded that the RapidHIT is not actually capable of processing rape kits since it can’t discern individual DNA in commingled bodily fluids.

Despite the new technology’s crime-solving potential, privacy advocates are wary of its spread. If rapid-DNA machines can be used in a refugee camp, “they can certainly be used in the back of a squad car,” says Jennifer Lynch, a senior staff attorney at the Electronic Frontier Foundation. “I could see that happening in the future as the prices of these machines go down.”

Lynch is particularly concerned that law enforcement agencies will use the devices to scoop up and store ever more DNA profiles. Every state already has a forensic DNA database, and while these systems were initially set up to track convicted violent offenders, their collection thresholds have steadily broadened. Today, at least 28 include data from anyone arrested for certain felonies, even if they are not convicted; some store the DNA of people who have committed misdemeanors as well. The FBI’s National DNA Index System has more than 11 million profiles of offenders plus 2 million people who have been arrested but not necessarily convicted of a crime.

For its part, Homeland Security will not hang onto refugees’ DNA records, insists Miles. (“They aren’t criminals,” he pointed out.) However, undocumented immigrants in custody may be required to provide DNA samples, which are put in the FBI’s database. DHS documents obtained by the Electronic Frontier Foundation say there may even be a legal case for “mandating collection of DNA” from anyone granted legal status under a future immigration amnesty. (The documents also state that intelligence agencies and the military are interested in using rapid DNA to identify sex, race, and other factors the machines currently do not reveal.)

The FBI is the only federal agency allowed to keep a national DNA database. Currently, police must use a lab to upload genetic profiles to it. But that could change. The FBI’s website says it is eager to see rapid DNA in wide use and that it supports the “legislative changes necessary” to make that happen. IntegenX’s Heimburger says the FBI is almost finished working with members of Congress on a bill that would give “tens of thousands” of police stations rapid-DNA machines that could search the FBI’s system and add arrestees’ profiles to it. (The RapitHIT is already designed to do this.) IntegenX has spent $70,000 lobbying the FBI, DHS, and Congress over the last two years.

The FBI declined to comment, and Heimburger wouldn’t say which lawmakers might sponsor the bill. But some have already given rapid DNA their blessing. Rep. Eric Swalwell, a former prosecutor who represents the district where IntegenX is based, says he’d like to see the technology “put to use quickly to help law enforcement”—while protecting civil liberties. In March, he and seven other Democratic members of Congress, including progressive stalwart Rep. Barbara Lee of California, urged the FBI to assess rapid DNA’s “viability for broad deployment” in police departments across the country.

Thanks to Kebmodee for bringing this to the attention of the It’s Interesting community.

The FBI Is Very Excited About This Machine That Can Scan Your DNA in 90 Minutes

Ebola’s Family Tree: Disease May Have Existed For 23 Million Years, Much Longer Than Previously Believed

On By A.P.In DNA, ebola, Medicine, ScienceLeave a comment

A family of viruses that Ebola belongs to may have existed over 20 million years ago, according to a new study published in the journal PeerJ.

Researchers from the University of Buffalo found that Filoviruses did not begin appearing 10,000 years ago as previously thought, but in fact have been around for much longer. The Ebola virus belongs to the family of filoviruses, also known as the Filoviridae family. “Filoviruses are far more ancient than previously thought,” said Derek Taylor, lead author of the study and a professor of biological sciences at the University of Buffalo, in the press release. “These things have been interacting with mammals for a long time, several million years.”

Despite the fact that scientists around the world are frantically searching for a cure and better treatment for Ebola, there’s still much to learn about the deadly virus. The authors of the study argue that better understanding Ebola’s evolutionary roots could “affect design of vaccines and programs that identify emerging pathogens.”

The study focused not on Ebola specifically, but the ancestors and family of Ebola to better understand where it may have come from. Both the Ebola virus and Marburg virus — also a hemorrhagic fever virus that belongs to the Filoviridae family — were found to be tied to ancient evolutionary lines, and they shared a common ancestor 16 to 23 million years ago. The authors discovered this by examining viral fossil genes, which are bits of genetic material that animals acquire from viruses during infection. They found Filovirus-like genes in rodents, particularly hamsters and voles, which means that the filovirus family is likely as old as these rodents’ common ancestor. The genetic material in these fossils were more closely related to Ebola than Marburg, meaning the two lines had already begun to diverge during the Miocene Epoch, a time period that occurred five to 23 million years ago. During this time, there were also warmer climates, as well as the first appearances of kelp forests and grasslands on Earth.

“These rodents have billions of base pairs in their genomes, so the odds of a viral gene inserting itself at the same position in different species at different times are very small,” Taylor said. “It’s likely that the insertion was present in the common ancestor of these rodents.”

The Filoviridae family is defined by viruses that form virions, or filamentous infectious viral particles. The Ebola virus and Marburg virus are the most well-known among this group, and they are both severe viruses that cause hemorrhagic fevers in both animals and humans (essentially, they’re deadly diseases that lead to fever and bleeding).

Taylor believes that the study may help in the fight against Ebola by widening our knowledge about its history, and identifying what species are most likely to be hosts of the virus. “When they first started looking for reservoirs for Ebola, they were crashing through the rainforest, looking at everything — mammals, insects, other organisms,” Taylor said. “The more we know about the evolution of filovirus-host interactions, the more we can learn about who the players might be in the system.”

Source: Taylor D, Ballinger M, Zhan J, Hanzly L, Bruenn J. Evidence that ebolaviruses and cuevaviruses have been diverging from marburgviruses since the Miocene. PeerJ. 2014.

http://www.medicaldaily.com/ebolas-family-tree-disease-may-have-existed-23-million-years-much-longer-previously-307958

Genetically Modified Mosquitos Could Eradicate Wild Populations By Only Producing Male Offspring

On By A.P.In Andrea Crisanti, Anopheles gambiae, cloning, DNA, gene, genetic modification, genetically modified, Imperial College London, Lisa Winter, malaria, Medicine, mosquito, Nature, Nature Communications, Nikolai Windbichler, Roberto Galizi, Science1 Comment

by Lisa Winter

Over 200 million people are infected by malaria each year, and the majority of the 627,000 deaths per year are children younger than five. The disease is carried by mosquitos who act as vectors for the parasite. It’s only transmitted to humans by female mosquitoes, as they’re the only ones who bite. A team of researchers led by Andrea Crisanti of the Imperial College London managed to genetically modify mosquitos to produce 95% male offspring, eliminating mosquito populations along with the risk of malaria. The results of the study were published in Nature Communications.

In most species of mosquito, the females need a blood meal in order to acquire the nutrients to create viable eggs. When she does, she can lay about 200 eggs at a time in water, and up to 3,000 eggs over the course of her lifetime. About half of those offspring will be daughters, many of whom will live long enough to produce that amount of offspring also. For humans living near mosquitos carrying the parasite that causes malaria, those numbers of female mosquitos present a very real threat.

But what if the numbers could be skewed so that the sex ratio favors males, who are harmless to humans? This is exactly what Crisanti’s team set out to do with Anopheles gambiae, a species of mosquito endemic to sub-Saharan Africa, where 95% of malaria deaths occur. The researchers modified the males with the enzyme I-Ppol, which excises the X chromosome during spermatogenesis. This renders sperm that would produce daughters to be non-functional, while the sperm that will create male offspring are unaffected. As a result, about 95% of the resulting offspring are male.

Next, modified males were introduced to five caged wild-type populations. As the males mated with the females, they passed along the same mutation until it dominated the population. For four of the five populations, it took only six generations for the mosquitos to die out due to a lack of females.

“What is most promising about our results is that they are self-sustaining,” co-author Nikolai Windbichler said in a press release. “Once modified mosquitoes are introduced, males will start to produce mainly sons, and their sons will do the same, so essentially the mosquitoes carry out the work for us.”

This study was the first to successfully manipulate mosquito sex ratios, and it was done in a big way. The researchers hope that this information will be used to develop genetic mutations to be used in the wild, bringing large populations of mosquitos to their knees.

“The research is still in its early days, but I am really hopeful that this new approach could ultimately lead to a cheap and effective way to eliminate malaria from entire regions,” added lead author Roberto Galizi. “Our goal is to enable people to live freely without the threat of this deadly disease.”

Of course, while eradicating the mosquitos would be fantastic for eliminating the threat of malaria, what other affects would it have? Wouldn’t there be harsh consequences for the ecosystem? After all, mosquitos have been on the planet for about 100 million years and represent 3,500 species. As it turns out, mosquitos wouldn’t really be missed if they were to disappear (http://www.nature.com/news/2010/100721/pdf/466432a.pdf). While mosquitos can act as pollinators as well as a food source for other animals, their absence would be merely a temporary setback before another species filled the niche. Of course, there is a gamble in assuming the replacement organism would be harmless.

“Malaria is debilitating and often fatal and we need to find new ways of tackling it. We think our innovative approach is a huge step forward. For the very first time, we have been able to inhibit the production of female offspring in the laboratory and this provides a new means to eliminate the disease,” Crisanti explained.

Each year, sub-Saharan Africa loses about $12 billion in economic productivity due to malarial infections. Considering developed areas in these countries have per capita incomes of about US$1500, this would have very real implications for the quality of life for people in those areas. Eliminating that disease would also allow doctors and hospitals to address other health concerns, and the environment would likely benefit from not having to use insecticides.

http://www.iflscience.com/health-and-medicine/gm-mosquitos-could-eradicate-wild-populations-only-producing-male-offspring

Termite Genome Reveals Details of “Caste System”

On By A.P.In Arizona State University, caste system, DNA, gene, Hymenoptera, Jürgen Liebig, LiveScience, Nature, Nature Communications, Science, termiteLeave a comment

The genome of the termite has just been sequenced, and it is revealing several clues about how the pests create their rigid social order.

For instance, the new genome, detailed today (May 20) in the journal Nature Communications, uncovers some of the underpinnings of termites’ caste system, as well as the roots of the males’ sexual staying power.

Like other social insects— such as ants, honeybees and some wasps — termites live in highly structured “caste systems,” with each creature programmed to perform a rigidly defined job. A select few termite kings and queens reproduce, while drones and soldiers work, defend the colony or care for young.

Yet termites evolved their social structure independently from ants and bees, which belong to an order known as Hymenoptera.

To understand how this happened, Jürgen Liebig, a behavioral biologist at Arizona State University, and his colleagues collected dampwood termites(Zootermopsis nevadensis nuttingi) that lived in Monterey, California. The researchers then sequenced the genome of the insects and measured how those genes were expressed, or turned on and off.

The research revealed several insights about termite sexual and social behavior.

Termite society is roughly half males and half females. Termites have sexually active kings as well as queens, and kings make sperm throughout their lifetimes. Dampwood termite males also have testes that shrivel and grow seasonally.

Ants and honeybees, in contrast, live in predominantly female societies, and ant sex is a one-time affair.

“Their societies generally consist of females — the males are only there to fly out, mate and die,” Liebig told Live Science.

Sure enough, the termites had more gene variants associated with sperm production and degradation, and those genes were expressed to a greater extent than in ants, Liebig said. That finding suggested those genetic differences contributed to male termites’ sexual longevity.

The termite genome also contains a high fraction of genes that are turned off by chemical tags, or methyl groups, the researchers found. In honeybees, this process of methylation sets the fate of individual animals, determining their place in the caste system. The new findings suggest a similar process may be at play in termites.

In addition, both ants and termites communicate via chemical smell signals sensed by receptors on their antennas.

But while ants venture out for food, these particular termites spend their whole lives dining on one piece of wood.

The new analysis revealed that the termites have far fewer cell types for recognizing individual chemicals, probably because they rarely face off against foreign termites or search for food. They simply don’t need to recognize as many smells, Liebig said.

However, some termite species, such as Australian mound-building termites, do forage and encounter foreigners along the way, so as a follow-up, the team would like to see if those termites can detect a greater array of chemicals, Liebig said.

http://www.scientificamerican.com/article/termite-genome-reveals-details-of-caste-system/

New research shows that whales and dolphins can’t taste anything except salt

On By A.P.In bitter, cetacean, China, Danielle Reed, DNA, dolphin, Dolphins, Dr. Rajadhyaksha, Evolution, Evolutionary Biology, gene, Genome Biology and Evolution, Huabin Zhao, Jianzhi Zhang, Monell Chemical Senses Center, Nature, raoellid, Salt, salty, savory, Science, sour, sweet, taste, taste receptor, umami, University of Michigan, whale, Whales, Wuhan University, zoologyLeave a comment

Tastes are a privilege. The oral sensations not only satisfy foodies, but also on a primal level, protect animals from toxic substances. Yet cetaceans—whales and dolphins—may lack this crucial ability, according to a new study. Mutations in a cetacean ancestor obliterated their basic machinery for four of the five primary tastes, making them the first group of mammals to have lost the majority of this sensory system.

The five primary tastes are sweet, bitter, umami (savory), sour, and salty. These flavors are recognized by taste receptors—proteins that coat neurons embedded in the tongue. For the most part, taste receptor genes present across all vertebrates.

Except, it seems, cetaceans. Researchers uncovered a massive loss of taste receptors in these animals by screening the genomes of 15 species. The investigation spanned the two major lineages of cetaceans: Krill-loving baleen whales—such as bowheads and minkes—were surveyed along with those with teeth, like bottlenose dolphins and sperm whales.

The taste genes weren’t gone per se, but were irreparably damaged by mutations, the team reports online this month in Genome Biology and Evolution. Genes encode proteins, which in turn execute certain functions in cells. Certain errors in the code can derail protein production—at which point the gene becomes a “pseudogene” or a lingering shell of a trait forgotten. Identical pseudogene corpses were discovered across the different cetacean species for sweet, bitter, umami, and sour taste receptors. Salty tastes were the only exception.

“The loss of bitter taste is a complete surprise, because natural toxins typically taste bitter,” says zoologist Huabin Zhao of Wuhan University in China who led the study. All whales likely descend from raccoon-esque raoellids, a group of herbivorous land mammals that transitioned to the sea where they became fish eaters. Plants range in flavors—from sugary apples to tart, poisonous rhubarb leaves—and to survive, primitive animals learned the taste cues that signal whether food is delicious or dangerous. Based on the findings, taste dissipated after this common ancestor became fully aquatic—53 million years ago—but before the group split 36 million years ago into toothed and baleen whales.

“Pseudogenes arise when a trait is no longer needed,” says evolutionary biologist Jianzhi Zhang of the University of Michigan, Ann Arbor, who was not involved in the study. “So it still raises the question as to why whales could afford to lose four of the five primary tastes.” The retention of salty taste receptors suggests that they have other vital roles, such as maintaining sodium levels and blood pressure.

But dulled taste perception might be dangerous if noxious substances spill into the water. Orcas have unwittingly migrated into oil spills, while algal toxins created by fertilizer runoff consistently seep into the fish prey of dolphins living off the Florida coast.

“When you have a sense of taste, it dictates whether you swallow or not,” says Danielle Reed, a geneticist at the Monell Chemical Senses Center in Philadelphia, Pennsylvania. She was not involved with the current work, but co-authored a 2012 paper that found the first genetic inklings that umami and sweet taste receptors were missing in cetaceans, albeit in only one species—bottlenose dolphins.

Flavors are typically released by chewing, but cetaceans tend to swallow their food whole. “The message seems clear. If you don’t chew your food and prefer swallowing food whole, then taste really becomes irrelevant,” Reed says.

http://news.sciencemag.org/biology/2014/05/whales-cant-taste-anything-salt

Thanks to Dr. Rajadhyaksha for bringing this to the attention of the It’s Interesting community.

DNA mugshot: Computer sketch program can reconstruct faces from DNA

On By A.P.In computer, Crime, DNA, DNA mugshot, facial morphology, gene, New Scientist, Philip Ross, PLoS Genetics, Science, The Future1 Comment


Workflow for 3D face scan processing, including the A) original surface, B) trimmed to exclude non-face parts, C) reflected to make mirror image, D) anthropometric mask of quasi-landmarks, E) remapped, F) reflected remapped, G) symmetrized and H) reconstructed.

By Philip Ross

Could a single hair be used to make an accurate 3D model of a criminal suspect’s face? Researchers from the U.S. and Belgium have developed a computer program that renders a crude genetic “mugshot” from a small sample of DNA.

Forensics can already predict eye and hair color relatively easily. Io9 notes that criminal investigators can even use maggots to extract a victim’s DNA from their unidentifiable body or find hidden faces by zooming into hi-res photos of eyes. But the face is a complex structure that’s more difficult to map from just one DNA sample.

According to New Scientist, researchers used a stereoscopic camera to make 3D images of roughly 600 volunteers with mixed European and West African ancestry. They identified more than 7,000 distinct points on the face to see how sex and racial ancestry affect the position of these points. The variations were used to develop a statistical model that reconstructs the overall shape of a person’s face.

The team also isolated 24 genetic variants, called single nucleotide polymorphisms, which play a role in shaping a face, such as those that shape the head during embryonic development. Lastly, researchers had volunteers rate the 600 faces on perceived ethnicity as well as on a scale of masculinity and femininity.

The new study, published in the journal PLOS Genetics, says this process could allow investigators to make computer-generated mugshots from genetic material left at a crime scene.

“We show that facial variation with regard to sex, ancestry, and genes can be systematically studied with our methods, allowing us to lay the foundation for predictive modeling of faces,” the authors note. “Such predictive modeling could be forensically useful; for example, DNA left at crime scenes could be tested and faces predicted in order to help to narrow the pool of potential suspects. Further, our methods could be used to predict the facial features of descendants, deceased ancestors, and even extinct human species. In addition, these methods could prove to be useful diagnostic tools.”

Any 3D renderings created using the new technology wouldn’t be used in a court of law – any person identified via the DNA mugshots would still have his DNA compared to the crime scene sample – but it could at least narrow the search for a suspected criminal. And there are still a few kinks to work out in the process before the technology is ever used in the field.

“I believe that in five to 10 years’ time, we will be able to computationally predict a face,” Peter Claes of the Catholic University of Leuven in Belgium told New Scientist.

http://www.ibtimes.com/dna-mugshot-how-crime-fighting-computer-sketch-program-can-predict-face-your-genes-1563049

Thanks to Da Brayn for bringing this to the attention of the It’s Interesting community.