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How many synthetic genes does it take to sustain life?

Syn 3.0 bacterial cells magnified about 15,000 times by an electron microscope. This is the world’s first minimal bacterial cell. Its synthetic genome contains only 473 genes. Surprisingly, the functions of 149 of those genes are unknown. Photo by Tom Deerinck and Mark Ellisman of the National Center for Imaging and Microscopy Research at the University of California at San Diego

How many genes does it take to survive and grow strong? 473..if you’re bacteria. Synthetic biologists based in California have nailed down the essential genes for life in a species of bacteria, Mycoplasma mycoides. Engineered by many of the same people who sequenced the human genome, this minimalist microbe may serve as the broth for cooking up the core functions of life.

For example, scientists have cataloged the genomes of thousands of species, yet despite this prior research, no one knows the functions for 31 percent of the genes needed to sustain life in this synthetic germ.

“I think we’re showing how complex life is, even in the simplest of organisms,” geneticist and study co-author Craig Venter said of the work published today in the journal Science. One open question is whether the essential, yet mysterious genes of this synthetic microbe can reveal why so much of human genome — 85 to 92 percent — has lacked a discernible function so far.

This landmark find has been 20 years in the making at the J. Craig Venter Institute, and its origins formed the basis for the human genome project. In 1995, scientists at this institute sequenced the first genome for a free-living organism, Haemophilus influenzae. Later that year, the institute would partner with Clyde A. Hutchison III, a microbiologist at the University of North Carolina at Chapel Hill, and publish the smallest genome ever found for a self-replicating organism. Its owner: the bacteria Mycoplasma genitalium. Everything to follow came from this diminutive collection of genetic code.

Venter, Hutchinson and their colleagues realized if they wanted to solve the basic questions of life, they would need to work with the most minimal genome.

“The only way to do that would be by trying to synthesize a genome, and that started our 20-year quest to do this,” Venter said. In other words, they would need to create synthetic life.

Mycoplasma provided the ideal starting ground, given these bacteria contain so few genes. In 2010, the institute announced that they had completed step one in this mission. The scientists had assembled nucleotides, the building blocks of DNA, into a working synthetic genome for Mycoplasma mycoides. Mycoplasma mycoides is a relative of bacterial species that launched this project, but it grows faster, which expedites this brand of work.

That’s important because creating synthetic life requires numerous rounds of trial-and-error. To start, they had to stitch together 1.07 million DNA base pairs — the railroad tracks of genomic code — inside of a test tube. Each rail is chemically added one by one, but there’s a margin of error. The team wanted to create a precise replica, so they had to repeat the process until a facsimile of the microbe’s natural genome emerged. Six years ago, they announced their initial success and named this synthetic genome Syn 1.0. They named this genome Syn 1.0.

Steps in creating Syn 3.0. Major advances in DNA technologies have made it possible for biologists to now behave as software engineers and rewrite entire genomes to program new biological operating systems. Illustration and caption by J. Craig Venter Institute

Today, the researchers introduced Syn 3.0, which they created by introducing mutations, one by one, into 901 genes of Syn 1.0. Through multiple iterations, this process exposed which genes were truly essential for the survival of Mycoplasma mycoides. The team landed on 473 genes that maintained the cells replication.

Some genes initially thought of as non-essential, because of what’s known about their jobs in other species, turned out to perform the same critical function as a second gene. In other words, the cell could survive without one of these genes, but not without both of them.

“I love their approach; people can argue over scientific results about whether or not a gene is essential, but the synthesis of this genome draws a line in the sand, and shows unequivocally what is possible,” University of California Los Angeles biochemist Sriram Kosuri, who wasn’t involved in the research, told GENeS.

It’s worth emphasizing that Venter and his team didn’t create new life. In essence, they cut spokes from a bike wheel in order to see how many are required to keep rolling.

“[Syn 3.0] displayed substantial defects in growth and morphology that suggest it is extremely unlikely that such a cell would survive outside of the laboratory. Hence any potential risks associated with [Syn 3.0] are minimal,” Samuel Deutsch, head of DNA synthesis and Assembly at the U.S. Department of Energy Joint Genome Institute, told GENeS.

Also, the 473 genes that are essential for Mycoplasma mycoides are not likely to be the same crucial genes for human life — or even other species of bacteria.

Still, there’s something special about starting from scratch. Syn 3.0 offers a foundation for adding new genes and seeing what they do, and the applications could be widespread, if not a long way from fruition.

“Our long-term vision has been to design and build synthetic organisms on demand where you can add in specific functions and predict what the outcome is going to be,” said Daniel Gibson, vice president of DNA Technologies at Synthetic Genomics who partnered on the project. “So we believe that these cells would be very useful for many industrial applications, from medicine to biochemicals, biofuels, nutrition and agriculture.”

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UN: Women and girls are ‘currency’ in South Sudan’s civil war

In a Skype interview, David Marshall of the U.N. describes findings in a new report on violence in South Sudan.

South Sudan’s government forces are encouraging its armed militias to take women and girls as “currency” in place of wages, a new U.N. report found.

Human rights atrocities, including rape, killings and looting, are taking place on both sides of South Sudan’s civil war, which has been raging for more than two years, according to the report released on Friday.

“In South Sudan, the reality is you’re either a loyalist (to the government) or you’re not. And if you’re not, you’re in peril of harassment, detention and death,” said David Marshall, coordinator of the U.N. human rights agency’s recent assessment of South Sudan.

“The youth (in government-aligned militias) were told by the army commanders to take what you can, including women and girls” since the fighters couldn’t be paid wages, Marshall told the PBS NewsHour’s Hari Sreenivasan. The government sends its armed forces into areas thought to contain the opposition in order to take the residents’ cattle and destroy civilian property including homes, hospitals and schools. Government officials have denied the findings.

Both sides accuse the other of targeting places of refuge, including churches, hospitals and U.N. bases. U.N. forces sent into South Sudan to protect civilians were blocked by warring parties from certain areas.

A woman reported being tied to a tree as her child was gang-raped, said Marshall. “For me, one of the most shocking findings is after two-and-a-half years of extreme sexual violence, how it’s corroding … the fabric of the community. So mothers have seen children gang-raped, they’ve lost their husbands, they’re on the run, they’re starving. And the communities are broken.”

The campaign of violence has continued even though South Sudan’s President Salva Kiir and opposition leader Riek Machar signed a comprehensive peace agreement in August. “There appears to be little political will to explore issues of truth, justice and accountability,” according to the report.

Since the fighting began in December 2013, more than 600,000 have fled to camps in Uganda, Kenya and Ethiopia, and 1.5 million people have been displaced within South Sudan, putting them in danger of severe food shortages and possible famine, the report said.

In Sudan, and now South Sudan, over decades there have been cycles of extreme violence followed by reconciliation, forgiveness and amnesties, followed by more violence, said Marshall. “There’s no meaningful justice and this is clearly the problem.”

The U.N. report recommends the political and military leadership are removed from power, investigated, prosecuted and punished. And a transitional government should not include anyone who orchestrated the violence and commit to justice, he said.

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Results from 58th Annual Science and Engineering Fair

Winners were announced on Thursday at the San Joaquin County Office of Education of the 58th annual Science and Engineering Fair.

Judges had spent the last two days reviewing 300 individual, group and whole-class projects, submitted by more than 600 K-12 students in the county. Overall, 26 schools from eight school districts, three private schools and three charter schools participated.

Several winners of the fair will proudly represent San Joaquin County in the California State Science Fair in Los Angeles in May. The winners are listed below:

Kindergarten through second grade:

• Class winner: Mrs. Hoptry’s class for “Pop Goes the Kernel” (Bethany Elementary; Lammersville Unified)


• 1st place (tie): Cade Riesenbeck for “Hot Marshmallows” (Dent Elementary; Escalon Unified)


• 1st place (tie): Theodore Harp for “There is More Than One Way to Crack a Nut” (Dent Elementary; Escalon Unified)


• 2nd place: Wyatt Riesenbeck for “Operation Parachute” (Dent Elementary; Escalon Unified)


• 3rd place: Elijah Gori for “Let’s Race” (Lammersville Elementary; Lammersville Unified)

Third through fifth grade:

• 1st place Science: Jordan Prawira for “Egg-cellent Parachute” (Altamont Elementary; Lammersville Unified)


• 1st place Engineering: Genevieve Casazza for “Preventing a Water Pipe from Freezing Without Electricity” (Dent Elementary; Escalon Unified)


• 2nd place: Mathilde Beckman-Forman for “Superhydrophobia Coating” (Wicklund Elementary; Lammersville Unified)


• 3rd place: Jake Bowen for “The Effects of Video Games on Children’s Eyesight” (Bella Vista Christian Academy)

Sixth through eighth grade:

• 1st place Science: Jacqueline Prawira for “Coffee-Doh Battery” (Altamont Elementary; Lammersville Unified)


• 1st place Engineering: Anna Matthews for “Going Green-Water Detector” (Elkhorn School; Lodi Unified)


• 2nd place: Alicia and Ashlyn Roice for “Cure the Burning Heart” (Altamont Elementary; Lammersville Unified)


• 3rd place: Ashley Teele for “Save the Avocado!” (Bethany Elementary; Lammersville Unified)

Ninth through 12th grade:

• 1st place: Baani Minhas for “The Effect of Honey on Shelf Life and Vitamin C Content of Fruits” (Mountain House High School; Lammersville Unified)

Environmental Awards

Environmental Award winners receive cash prizes donated by the San Joaquin County Audubon Society and the Synopsys Outreach Foundation.

• Sanskriti Singh for “Does the Ocean Ever Freeze?” (Altamont Elementary; Lammersville Unified)


• Miles McCarthy for “Filtration Station” (Tom Hawkins Elementary; Jefferson Elementary School District)


• Bernice Lozasa for “Recycling Gray Water” (Questa Elementary; Lammersville Unified)