Posts Tagged ‘biology’

Photo: Franco Folini, CC BY-SA 2.0/flickr.
Says Atlas Obscura, “Genetic research indicates that the turnip was likely the first Brassica rapa crop, originating up to 6,000 years ago in Central Asia.”

For something a little bit different, consider “the vegetable that took over the world.” It turns out that different cultures not only develop their own versions of music and art but their own versions of the same edible plant. It helps that the plant in question has triplicated genes.

Gemma Tarlach reports at Atlas Obscura about “the single species that gives us turnips, bok choy, broccoli rabe” …

“The plant known as Brassica rapa has quite the history, one that, after decades of debate, is finally emerging. The single species, which humans have turned into turnips, bok choy, broccoli rabe (also known as rapini), and other residents of the produce aisle, began up to 6,000 years ago in Central Asia.

“[In June] Molecular Biology and Evolution published findings from an unprecedented study of B. rapa that pulled together genetic sequencing, environmental modeling, and the largest number of wild, feral, and cultivated samples ever collected. … The paper is a significant step forward in understanding how one of the planet’s most important agricultural species might weather climate change.

“ ‘This study is really great. I like the approaches they took, and the framework they placed it in,’ says Nora Mitchell, a plant evolutionary biologist at the University of Wisconsin-Eau Claire. Mitchell, who was not involved in the research. … She says the new paper’s environmental modeling — reconstructing conditions under which B. rapa was adapted to different locations, as well as forecasting what changing conditions might mean for its future — makes the study particularly compelling. …

” ‘The work is a particular achievement when you consider both the diversity and global spread of B. rapa crops, wild relatives, and feral varieties that have escaped farmers’ fields’ … says Alex McAlvay, lead author of the study and a botanist at the New York Botanical Garden. Now, he says, B. rapa, in various forms, ‘grows from Alaska to Tierra del Fuego. They grow in Oceania, they grow from Spain to Japan.’ …

B. rapa’s ability to survive as a feral plant worldwide had created a lot of uncertainty about its origins. Botanists often look to wild relatives of crops to help understand where the plants were first domesticated. But B. rapa is everywhere and, before the new research, distinguishing truly wild species from feral escapees was almost impossible. …

“While genetic detective work is always a complex undertaking, McAlvay says he and his colleagues were particularly challenged by a ‘crazy mess’ of genes that originated in the ancestor of both B. rapa and its close relative B. oleracea, another single species that provides multiple vegetables: broccoli, cauliflower, cabbage, kale, and more.

‘One reason we think these species have this incredible diversity is that their ancestor had not only a duplication of their genome, but a triplication,’ says botanist Makenzie Mabry, who coauthored the new paper. …

“While humans and many other organisms inherit a single set of chromosomes, one half from each parent, some plants inherit double sets. The Brassica ancestor had three sets that, says Mabry. …

“ ‘There’s an additional layer of weirdness,’ on the road to domestication and diversification, adds McAlvay: Different cultures selected for certain traits in different parts of the plant. For example, we’re familiar with tomatoes in all colors, sizes, and flavor profiles, but they’re all the fruit of the plant Solanum lycopersicum. For B. rapa, however, ‘with turnip, you’re looking at the root, the underground stem of the plant. Tatsoi is the leaves. Broccoli rabe is the flowers,’ says McAlvay.

“ ‘In China, people saw the same kind of raw material, the turnip, and they did something totally different than the Italians and Spanish did,’ he adds, running down a list of water-rich bok choy, chunky turnips, bitter greens, jagged-leaf mizuna, and other B. rapa permutations worldwide. …

“Digging up B. rapa’s roots is more than an exercise in botanical history. … ‘Food security is a big issue, especially global food security. And with Brassica having so many crops, not only vegetables but for oils as well, it’s really important to continue producing these crop species in the face of climate change, increased drought, and nutrient changes, as well as crop blights and crop diseases,’ Mitchell explains. ‘It’s important to understand not only what happened in the past but how these plants might respond in the future, and to know what kind of genetic resources could increase diversity.’

“McAlvay believes the paper’s findings on weedy, feral varieties may prove particularly significant for breeding better B. rapa crops in the future. ‘For most of recent history, people have dismissed the stray dogs of the plant world as not particularly useful,’ he says. ‘But because they’re already adapted to really rough, tough environments, there’s some push, with the advent of gene editing, to be inspired by those turnips gone wild.’ ”

What a miracle is Nature! More at Atlas Obscura, here.

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Photo: Steve Atwood
The wrybill uses its laterally curved bill to reach insect larvae under rounded riverbed stones.

I was intrigued by new research showing that some cells in nature have a left or right orientation and, when disrupted, are able to repair themselves. The Quanta Magazine article reposted at Wired is long and technical. I’m hoping to capture the basics here.

Tim Vernimmen writes, “In 2009, after she was diagnosed with stage 3 breast cancer, Ann Ramsdell began to search the scientific literature to see if someone with her diagnosis could make a full recovery. Ramsdell, a developmental biologist at the University of South Carolina, soon found something strange: The odds of recovery differed for women who had cancer in the left breast versus the right. Even more surprisingly, she found research suggesting that women with asymmetric breast tissue are more likely to develop cancer.

“Asymmetry is not readily apparent. Yet below the skin, asymmetric structures are common. Consider … how our heart, born from two identical structures fused together, twists itself into an asymmetrical pump that can simultaneously push oxygen-rich blood around the body and draw in a new swig from the lungs, all in a heartbeat. …

“In her early years as a scientist, Ramsdell never gave asymmetry much thought. But … after her recovery, Ramsdell decided … to start looking for asymmetry in the mammary glands of mammals.

In marsupials like wallabies and kangaroos, she read, the left and the right glands produce a different kind of milk, geared toward offspring of different ages. …

“Research from [the lab of Michael Levin, a biologist at Tufts University] suggests that communication among cells may be an under-explored factor in the development of asymmetry.

“The cellular skeleton also directs the transport of specialized proteins to the cell surface, Levin said. Some of these allow cells to communicate by exchanging electrical charges. This electrical communication, his research suggests, may direct the movements of cells as well as how the cells express their genes.

“ ‘If we block the [communication] channels, asymmetrical development always goes awry,’ he said. ‘And by manipulating this system, we’ve been able to guide development in surprising but predictable directions, creating six-legged frogs, four-headed worms or froglets with an eye for a gut, without changing their genomes at all.’

“The apparent ability of developing organisms to detect and correct their own shape fuels Levin’s belief that self-repair might one day be an option for humans as well.

“ ‘Under every rock, there is a creature that can repair its complex body all by itself,’ he points out. ‘If we can figure out how this works,’ Levin said, ‘it might revolutionize medicine. Many people think I’m too optimistic, but I have the engineering view on this: Anything that’s not forbidden by the laws of physics is possible.’ ”

The original story appeared in Quanta Magazine. Check the Wired reprint here.

Photo: SEFSC Pascagoula Laboratory; Collection of Brandi Noble, NOAA/NMFS/SEFSC
The twospot flounder lies on the seafloor on its right side, with both eyes on its left side.

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Our friend Mika is back in Hokkaido these days, after several years in New York working in restaurants and perfecting her “house” dancing. But every once in a while she ventures out to help on a street art project. Here is her friend Florence Blanchard’s mural for CBM Network (Crossing Biological Membranes) at the University of Sheffield in England.

At her WordPress site, Florence explains what the art represents, “I am delighted to present my newest mural here – a collaboration with CBMNet at the University Of Sheffield, in conjunction with Festival Of The Mind 2016 / Fear of the Unseen: Engineering Good Bacteria.

“The ‘Crossing Biological Membranes Network’ is composed of scientists working to understand the mechanisms by which substances are transported into, within, and out of cells. Their ultimate aim is to produce knowledge which will enable the development of new technologies in the Industrial Biotechnology and Bioenergy sector (eg: producing biofuels using E coli bacteria).

“My role in this collaboration has been to translate the CBMNet area of work into a large outdoor mural located within the university campus. For this occasion I have presented my interpretation of a detail of a cell membrane as seen under an electron microscope, having undergone a cryofracture.

“A cryofracture is a procedure in which the sample is frozen quickly and then  broken with a sharp blow so you are able to study its structure in very close detail – Imagine breaking a bar of chocolate with hazelnuts, this way you can see how hazelnuts are positioned inside the bar.”

“For an online animation of a biomembrane cryofracture follow this link: http://www.sciencephoto.com/media/530082/view.”

Check out the WordPress post.

Photo: Florence Ema Blanchard
Blanchard’s street art is tied to a scientific quest: “Engineering Good Bacteria.”

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With every new discovery of fossils, it seems, the first appearance of life on Earth is earlier.


There is always controversy, and your belief about the earliest date may depend on just how hellish you think the Hadean period was, when asteroids bombarded the planet and life probably would have been impossible.

Nicholas Wade writes at the New York Times, “Geologists have discovered in Greenland evidence for ancient life in rocks that are 3.7 billion years old. The find, if confirmed, would make these fossils the oldest on Earth and may change scientific understanding of the origins of life.

“Experts are likely to debate whether the structures described in the new report were formed biologically or through natural processes. If biological, the great age of the fossils complicates the task of reconstructing the evolution of life from the chemicals naturally present on the early Earth. It leaves comparatively little time for evolution to have occurred and puts the process close to a time when Earth was being bombarded by destructive asteroids. …

“Certain features ‘are fairly credible hallmarks of microbial activity,’ Abigail C. Allwood of Caltech’s Jet Propulsion Laboratory wrote in a commentary accompanying the Nature article [by Allen P. Nutman et al.]. They have a few features that make them ‘interesting and possibly biological,’ she added in an email.

“Another expert in the early Earth’s environment, Tanja Bosak of M.I.T., said the structures do resemble modern stromatolites but their origin ‘will be hotly debated.’ …

“Dr. Nutman argues that life must therefore have originated even earlier, probably in the late Hadean stage of Earth’s history, which lasted from 4.65 billion years ago — when the planet formed from debris in orbit around the sun — to 4 billion years ago.

“But the Hadean was so called because of the hellish conditions thought to have prevailed, including cataclysmic meteorite impacts that boiled the oceans into steam and turned Earth’s surface into molten lava. The largest of these impacts, at 4.5 billion years ago, tore a piece from Earth that became the moon. It is difficult to see how life could have begun under such circumstances.”

Weigh in on the controversy here.

Photo: Allen Nutman
Stromatolites from Greenland may be evidence of the oldest life on earth.

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It’s amazing what you can learn from DNA. Recently, scientists have been collecting insights from camel DNA about how camel ancestors were used on ancient trade routes.

Victoria Gill writes at the BBC, “Scientists examined DNA samples from more than 1,000 one-humped camels. Despite populations being hundreds of miles apart, they were genetically very similar. Scientists explained that centuries of cross-continental trade had led to this ‘blurring’ of genetics.

“The findings are published in the Proceedings of the National Academy of Sciences.

“One of the team, Prof Olivier Hanotte, from Nottingham University, explained that what made the dromedary so biologically fascinating was its close link to human history.

” ‘They have moved with people, through trading,’ he told BBC News. ‘So by analysing dromedaries, we can find a signature of our own past. … Our international collaboration meant we were able to get samples from West Africa, Pakistan, Oman and even Syria.’ …

” ‘People would travel hundreds of miles with their camels carrying all their precious goods. And when they reached the Mediterranean, the animals would be exhausted.

” ‘So they would leave those animals to recover and take new animals for their return journey.’

“This caused centuries of genetic ‘shuffling’, making dromedaries that are separated by entire continents remarkably similar.

“Crucially, this has also ensured that the animals maintained their genetic diversity — constantly mixing up the population. This means that dromedaries are likely to be much more adaptable in the face of a changing environment. …

” ‘The dromedary will be our better option for livestock production of meat and milk. It could replace cattle and even sheep and goats that are less well-adapted.’ ”

More at the BBC website, here.

Photo: Mark Payne/Gill/NPL
Ships of the desert: camels provide transport, milk and food in arid, hostile environments

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I’m hearing more and more these days about “good bacteria,” including in a song by singer-composer Will McMillan on the friendly bacteria we humans carry around.

Now, it seems, bacteria found in soil may help to save amphibians from dangerous fungal epidemics. Public Radio International’s environmental news program, Living on Earth, has the story.

“Around the world, fungal diseases have been killing millions of frogs and bats and snakes. And a newly emerging disease in salamanders in Europe is scaring biologists here, so the US Fish and Wildlife Service has introduced a ban on their import to try to protect amphibians in the US.

“But now scientists see some hope in soil bacteria that get onto the salamanders and frogs and apparently protect them. Doug Woodhams is an assistant professor of biology at UMass Boston, who’s been working with amphibians in Panama – and he explained what his team has found to Living on Earth’s Helen Palmer.

“WOODHAMS: Some of the amphibians have beneficial bacteria that live on their skin and these have antifungal properties.

“PALMER: This is kind of like having good bacteria in your gut, for instance, that stop you from getting sick. … Is there any evidence that  good bacteria actually work against devastating funguses?

“WOODHAMS: Yeah, there’s quite a bit of evidence. Many of the bacteria that we can culture from some amphibian species are able to inhibit the fungus in culture. We also have some population-level data that shows populations that tend to have these antifungal bacteria can persist with Bd in the environment and survive. …

“Bd is the chytrid fungus that’s been spreading around the world and devastating amphibian populations. So salamanders, frogs, toads. Populations that tend to have more of these beneficial bacteria seem to be surviving, and populations that don’t have as many of the individuals that have these bacteria seem to disappear. …

“The next thing we want to try is adding some of these bacteria, not just to petri dishes, but to soil and see if infected amphibians can be cleared of their infection by being housed on soil that’s been inoculated with these bacteria. …

“There are other fungal pathogens, so it could be something that you could apply in a cave that could reduce White-nosed syndrome [in bats]. Also, rattlesnakes have been recently affected by fungal disease during hibernation, so it could be applied into a rattlesnake den.”

More on the science here.

Photo: Matt Becker
The Appalachian Mountains are home to this Cow Knob Salamander, Plethodon punctatus, from George Washington National Forest, Virginia.


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I like win-win stories like this one from National Public Radio. It’s about a new crop with a lot of monetary potential — and distinct advantages for the environment.

“It doesn’t require any land or fertilizer. Farming it improves the environment, and it can be used in a number of ways. So what is this miracle cash crop of the future? It’s seaweed.

“Charlie Yarish, professor of ecology and evolutionary biology at the University of Connecticut, loves seaweed. In nature, he says, when seaweed turns a rich chocolate color, that means the plant is picking up nitrogen, a process called nutrient bioextraction. …

“Many plants and animals cannot survive when there is too much nitrogen in the water, but seaweed is able to ‘capture’ the nitrogen, as well as contaminants in the water.

“A United Nations report says that nearly 16 million tons of seaweed were farmed in 2008 — most of it in Asia. Yarish helped a company called Ocean Approved start the United States’ first open-water kelp farm in the Gulf of Maine in 2006 … Now, he’s helping to create a seaweed farm off the coast of Connecticut.

“Bren Smith owns and runs the Thimble Island Oyster Company, off the coast of Branford, Conn. After his business was hit hard by Tropical Storm Irene last year, ruining about 80 percent of the shellfish crop, Smith started looking around for something more resilient to farm. That’s when he found Yarish, who agreed to help set him up in the seaweed farming business. …

” ‘There’s no barns, there’s no tractors. This is what’s so special about ocean farming. It’s that it’s got a small footprint and it’s under the water. I mean, we’re so lucky; I feel like I stumbled on this just great secret that we then can model and spread out to other places,’ ” Smith says. …

” ‘The plan is to actually split it into a couple different experimental markets — one for food, one for fertilizer, one for fish food. I’m [also] working with a skin care company in Connecticut, and then one for biofuel,’ Smith says. He’s even hoping he can someday fuel his own boat with biofuel from the seaweed.”

Craig LeMoult has the whole story here at NPR, where you also can listen to the audio.

Photograph by Ron Gautreau
Oyster fisherman Bren Smith on his boat.

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Kirk Johnson writes in today’s NY Times about efforts to make time in prison more constructive, both in terms of sustainable practices that control prison costs and in terms of inmate improvement.​ The endangered frog program in Oregon, which requires perfect behavior from participating prisoners, is especially intriguing.

Johnson writes, “Mat Henson, 25, serving a four-and-a-half-year sentence for robbery and assault, and his research partner, Taylor Davis, 29, who landed in the Cedar Creek Corrections Center here in central Washington for stealing cars, raised about 250 Oregon spotted frogs in the prison yard this summer.

“Working with biologists, Mr. Henson is now helping write a scientific curriculum for other frog-raisers, in prison or out. A previous inmate in the program, released some years ago, is finishing his Ph.D. in molecular biology. …

“The program’s broader goal of bringing nature and sustainable practices to prisons is echoed across the nation as states seek ways to run prisons more cost-effectively.

“Utilitarian practicality led Wisconsin in 2008 to begin having inmates grow much of their own food. And federal energy rules are pushing the goal of zero-net energy use in federal prisons by 2030.

“Indiana and Massachusetts have become aggressive in reducing energy and water consumption and waste in their prisons, and tough renewable energy mandates in California are pushing alternative generation and conservation at prisons there, said Paul Sheldon, a senior adviser at Natural Capitalism Solutions, a Colorado-based nonprofit that works with government agencies and companies on sustainability issues. …

“There may be some intangible benefits for inmates who are being exposed to the scientific process, many of them for the first time, said Carri LeRoy, a professor of ecology at Evergreen State College in Olympia, and co-director of the Sustainability in Prisons project.

“Science, she said, is about procedural order, point A to point B, with every step measured and marked for others to check and follow. And when the focus of that work is a creature that undergoes a profound metamorphosis from egg to tadpole to adult, the lesson is also one about the possibilities of change. In a prison, Professor LeRoy said, that is a big deal.

“ ‘This image of transformation, I think, allows them maybe to understand their own transformation,’ Professor LeRoy said.”

Read more.

Photograph: Matthew Ryan Williams for The New York Times

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