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Carla Nunziata via Wikimedia Commons // CC-BY-SA 3.0
Carla Nunziata via Wikimedia Commons // CC-BY-SA 3.0

Organism Designers Hack Biology to Make Smells From Scratch

Carla Nunziata via Wikimedia Commons // CC-BY-SA 3.0
Carla Nunziata via Wikimedia Commons // CC-BY-SA 3.0

We may not have jetpacks just yet, but the future is definitely upon us. The genetic engineers (or “organism designers,” as they prefer to be called) at Ginkgo Bioworks are hard at work brewing up new smells.

The company started back in 2008, right around the time that DNA sequencing technology became more affordable. Scientists were sequencing genomes right and left, which created a wonderful library of genetic information. Biologist Tom Knight saw an opportunity, and teamed up with recent MIT graduates Reshma Shetty, Jason Kelly, Barry Canton, and Austin Che to form Ginkgo Bioworks. Their goal, Ginkgo’s creative director Christina Agapakis told Smithsonian, was “to make biology easier to engineer, and then to look at what that means for industry and technology.”

Ginkgo opened what they call a “foundry”—a laboratory where organism designers can pry apart yeast DNA and insert new and useful traits. “It’s like a rapid prototyping factory,” Agapakis said. “We can run many variants of different pathways and see what works in the right combination.”

Exactly what these organisms produce depends on what their clients are looking for. Some projects involve creating organisms that can capture carbon. Others are aimed at growing better probiotics. At the moment, Ginkgo is focused on making new smells. There’s a big market for synthetic scents and flavors, and innovation is at a premium.

Currently, Ginkgo is working to create a strain of yeast that smells like roses. The foundry was commissioned by French perfumer Robertet to recreate the scent of one particular rose that grows only in Turkey and Bulgaria. The roses must be picked and processed by hand, which is time-consuming and expensive. A yeast that smells like the finicky roses could be a welcome alternative.

“Yeast is awesome,” Agapakis told Smithsonian, “because we as humans are really good at fermenting yeast.” She notes that our species' predilection for beer has yielded all sorts of developments in yeast technology. In fact, Emily Greenhagen, the company’s head of fermentation, co-owns a brewery nearby with her husband. 

Another foundry is in the works, with plans to open up shop in spring or summer of next year. “The foundry is constantly iterating,” Agapakis told Smithsonian. “We’re always thinking about organism design and how to run it more efficiently.”

[h/t Smithsonian]

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Gino Fornaciari, University Of Pisa
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Stones, Bones, and Wrecks
Scientists Accidentally Discover Ancient Hepatitis B in a 16th-Century Mummy
Gino Fornaciari, University Of Pisa
Gino Fornaciari, University Of Pisa

Since the 1980s, a child mummy buried in the Basilica of Saint Domenico Maggiore in Naples, Italy in the 16th century has been known as the earliest recorded case of smallpox in the world. The problem is, the 2-year-old didn’t have smallpox, according to new research spotted by IFLScience. But, as the scientists reexamining the remains discovered, it’s still a landmark study in disease evolution. It appears to be the earliest instance of hepatitis B that researchers have ever found in Italy, giving scientists insight into how the virus has evolved over the last several centuries.

The hepatitis B virus (HBV) attacks the liver and can result in cirrhosis and liver cancer, killing around 887,000 people per year. Though it can now be largely prevented by a vaccine, the World Health Organization estimates that 257 million people around the world live with HBV. It often affects children, spreading from mother to child during birth.

For the current study published in PLOS Pathogens, a team of researchers from McMaster University in Canada set about studying the child mummy with the hopes of continuing their past work nailing down how smallpox spread and evolved over human history. But when they used molecular analysis to study the mummy’s skin and bones, they didn’t find anything that indicated that the toddler had smallpox. Instead, they found the hepatitis B virus—which can cause a rash called Gianotti-Crosti Syndrome that the original researchers studying the mummy may have mistaken for the telltale rash associated with smallpox.

The ancient HBV strain found in the mummy's tissues had a genome closely related to that of the modern virus, which, The New York Times explains, could very well mean that the mummy was contaminated when it was first studied in the 1980s. But after analyzing the genetic material further and studying other examples of older HBV strains, they found that it’s plausible that the virus just hasn’t evolved extensively in the past 500 years. Though the contamination theory is still possible, it’s more likely that the mummy really does carry an ancient version of the virus. Considering that HBV has also been traced back to the 16th century in Asia, it’s likely that Europeans were suffering from it around the same time.

[h/t IFLScience]

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Illustration by Eric S. Carlson in collaboration with Ben A. Potter
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Stones, Bones, and Wrecks
11,500-Year-Old Skeleton Reveals an Unknown Group of Ancient Migrants to the Americas
Illustration by Eric S. Carlson in collaboration with Ben A. Potter
Illustration by Eric S. Carlson in collaboration with Ben A. Potter

In 2013, deep in the forest of central Alaska's remote Tanana River Valley, archaeologists unearthed the remains of a 6-week-old baby at a Late Pleistocene archaeological site. The tiny bones yielded big surprises for researchers, who announced this week that the child's genome—the oldest complete genetic profile of a New World human—reveals the existence of a human lineage that was previously unknown to scientists. Related to yet genetically distinct from modern Native Americans, the infant offers fresh insights into how the Americas were first peopled, National Geographic reports.

Published in the journal Nature on January 3, the study analyzed the DNA of the infant, whom the local Indigenous community named Xach'itee'aanenh T'eede Gaay ("sunrise girl-child" in the local Athabascan language). Then, researchers used genetic analysis and demographic modeling to identify connections between different groups of ancient Americans. This allowed them to figure out where this newly identified population—named Ancient Beringians—fit on the timeline.

University of Alaska Fairbanks professors Ben Potter and Josh Reuther excavate at the Upward Sun River site in central Alaska.
Members of the archaeology field team watch as University of Alaska Fairbanks professors Ben Potter and Josh Reuther excavate at the Upward Sun River site.
UAF photo courtesy of Ben Potter

The study suggests that a single founding group of Native Americans separated from East Asians some 35,000 years ago. This group, in turn, ended up dividing into two distinct sub-groups 15,000 years later, consisting of both the Ancient Beringians and what would eventually become the distant ancestors of all other Native Americans. The division could have occurred either before or after humans crossed over the Bering land bridge around 15,700 years ago.

After arriving in the New World, Ancient Beringians likely remained north, while the other population spread out across the continent. Eventually, the Ancient Beringians either melded with or were replaced by the Athabascan peoples of interior Alaska. 

The study provides "the first direct evidence of the initial founding Native American population, which sheds new light on how these early populations were migrating and settling throughout North America," said Ben Potter, the University of Alaska-Fairbanks archaeologist who discovered the remains, in a news release. Potter was a lead author of the study, along with Eske Willerslev and other researchers at the Center for GeoGenetics at the University of Copenhagen's Natural History Museum of Denmark.

[h/t National Geographic]

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