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Wednesday, August 31, 2016

One-Syllable State of Maine Rocks: Underappreciated Silurian Age Stones

      Take a close look at these exquisite Silurian rocks from the state of Maine, USA. (How did I just realize Maine is our only monosyllabic state?) The Silurian, an underappreciated time period, without the cachet of say, the younger Jurassic, is part of the Paleozoic era between the Ordovician and Devonian. Silurian rocks are 443 million years to 416 million years old.

A significant evolutionary milestone during the Silurian was the diversification of jawed and bony fishes. 

       Life also began to appear on land during the Silurian in the form of moss-like, vascular land plants that grew beside bodies of water. Small terrestrial arthropods also began to appear.

       These Maine rocks of the Kittery Formation are old. They show the results of millions of years of deposition, igneous activity, faulting, tectonics, and metamorphism. 

      However, in researching this week's topic, I discovered the "Silurians," a fictional race of reptile-like humanoids in the long-running British science fiction tv series Doctor Who? Those first Silurians are depicted as prehistoric and scientifically advanced sentient humanoids who predate the evolution of man.

      The creatures were called Silurians, after their supposed origins in the Silurian period. However, author John Pertwee claims that "properly speaking", the Silurians should have been called the "Eocenes" (part of the much more recent Cenozoic era.)
     Perhaps Dr. Who needed a geologic consultant to the tv show. E. O. Seen and heard? Background music by Diana Ross and the Eocenes?!

Just call me,
Silurian Steph

Bonus question: without googling or duck duck going, name all current countries of only one syllable.

Thursday, August 25, 2016

CRISPR Technology: Palindromic AHA!

      As we discussed last week, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are segments of prokaryotic DNA containing short repetitions of base sequences. 


       CRISPR’s powerful possibilities — even the controversial notions of creating “designer babies” and eradicating entire species — are stunning and sometimes disconcerting.

     So far CRISPR’s biggest impact has been felt in biology labs around the world. The inexpensive, easy-to-use gene editor has made it possible for researchers to delve into fundamental mysteries of life in ways that had been difficult or impossible. Developmental biologist Dr. Robert Reed likens CRISPR to a computer mouse.

       “You can just point it at a place in the genome and you can do anything you want at that spot.”
Anything, that is, as long as it involves cutting DNA. CRISPR/Cas9 in its original incarnation is a homing device (the CRISPR part) that guides molecular scissors (the Cas9 enzyme) to a target section of DNA. Together, they work as a genetic-engineering cruise missile that disables or repairs a gene, or inserts something new where it cuts.

      Even with all the genetic feats the CRISPR/Cas9 system can do, “there were shortcomings. There were things we wanted to do better,” says MIT molecular biologist Dr. Feng Zhang, one of the first scientists to wield the molecular scissors. From his earliest report in 2013 of using CRISPR/Cas9 to cut genes in human and mouse cells, Zhang has described ways to make the system work more precisely and efficiently.

      He isn’t alone. A flurry of papers in the last three years have detailed improvements to the editor. Going even further, a group of scientists, including Zhang, have dreamed up ways to make CRISPR do a toolbox’s worth of jobs.

      Turning CRISPR into a multitasker often starts with dulling the cutting-edge technology’s cutting edge. In many of its new adaptations, the “dead” Cas9

scissors can’t snip DNA. Broken scissors may sound useless, but scientists have upcycled them into chromosome painters, typo-correctors, gene activity stimulators and inhibitors and general genome tinkerers.

      “The original Cas9 is like a Swiss army knife with only one application: It’s a knife,”

      says Dr. Gene Yeo, an RNA biologist at the University of California, San Diego. But Yeo and other researchers have bolted other proteins and chemicals to the dulled blades and transformed the knife into a multifunctional tool.

      Zhang and colleagues are also exploring trading the Cas9 part of the system for other enzymes that might expand the types of manipulations scientists can perform on DNA and other molecules. With the expanded toolbox, researchers may have the power to pry open secrets of cancer and other diseases and answer new questions about biology.
     The genome is like a piano, says Dr. Jonathan Weissman, a biochemist at the University of California, San Francisco. “You can play a huge variety of different music with only 88 keys by how hard you hit the keys, what keys you mix up and the timing.” By dialing down or turning up the activity of combinations of genes at precise times during development, cells are coaxed into becoming hundreds of different types of body cells.

     For the last 20 years, researchers have been learning more about that process by watching when certain genes turn on and off in different cells. Gene activity is controlled by a large variety of proteins known as transcription factors. When and where a transcription factor acts is at least partly determined by chemical tags on DNA and the histone proteins that package it. Those tags are known collectively as epigenetic marks. They work something like the musical score for an orchestra, telling the transcription factor “musicians” which notes to hit and how loudly or softly to play. So far, scientists have only been able to listen to the music.

      With this new research, researchers can create molecules that will change epigenetic notes at any place in the score, Weissman says, allowing researchers to arrange their own music.
Epigenetic marks are alleged to be involved in addiction, cancer, mental illness, obesity, diabetes and heart disease. Scientists haven’t been able to prove that epigenetic marks are really behind these and other ailments, because they could never go into a cell and change just one mark on one gene to see if it really produced a sour note.

      The explosion of new ways to use CRISPR hasn’t ended. “The field is advancing so rapidly,” says Zhang. “Just looking at how far we have come in the last three and a half years, I think what we’ll see coming in the next few years will just be amazing,” according to an article published this week.

What a difference the past 4 years have made in epigenetics!


Wednesday, August 17, 2016

From Fish Fin Rays to Fingers: The Digit-al Age

      One of the major transformations required for the descendants of fish to become creatures that could walk on land was the replacement of long, elegant fin rays by fingers and toes. In the August 17, 2016, issue of Nature, scientists from the U. of Chicago show that the same cells that make fin rays in fish play a central role in forming the fingers and toes of four-legged creatures.

      After 3 years of experiments using new gene-editing techniques and sensitive mapping to label and track developing cells in fish, the researchers describe how the small flexible bones found at the ends of fins are related to fingers and toes, which are more suitable for life on land.

     "When I first saw these results you could have knocked me over with a feather," said the study's senior author, Dr. Neil Shubin, an authority on the transition from fins to limbs.

      "For years," he said, "scientists have thought that fin rays were completely unrelated to fingers and toes, completely dissimilar because one kind of bone is initially formed out of cartilage and the other is formed in simple connective tissue. Our results change that whole idea. We now have a lot of things to rethink."

     To unravel how fins might have transformed into wrists and fingers, the researchers worked mostly with standard zebrafish.

     Dr.Tetsuya Nakamura, used a gene-editing technique, CRISPR/Cas, in zebrafish to delete important genes linked to limb-building, and then selectively bred zebrafish with multiple targeted deletions. He cross bred the fish mutants, a project that began at Woods Hole, Massachusetts.

     The researchers simultaneously refined cell-labeling techniques to map out when and where specific embryonic cells migrated as the animals developed.

     "It was one of those eureka moments," Dr. Andrew Gehrke said. "We found that the cells that mark the wrists and fingers of mice and people were exclusively in the fin rays of fish."

     The team focused on Hox genes, which control the body plan of a growing embryo along the head-to-tail, or shoulder-to-fingertip, axis. Many of these genes are crucial for limb development.
They studied the development of cells, beginning soon after fertilization and followed them as they became part of an adult fin. Previous work has shown that when Hox genes, specifically those related to the wrists and digits of mice (HoxD and HoxA), were deleted, the mice did not develop those structures. When Nakamura deleted those same genes in zebrafish, the long fins rays were greatly reduced.

     "What matters is not what happens when you knock out a single gene but when you do it in combination," Dr. Nakamura explained. "That's where the magic happens."

     The researchers also used a high-energy CT scanner to see the minute structures within the adult zebrafish fin. These can be invisible, even to most traditional microscopes. The scans revealed that fish lacking certain genes lost fin rays, but the small bones made of cartilage fin increased in number.

     The authors hypothesize that the mutants that Nakamura made caused cells to stop migrating from the base of the fin to their usual position near the tip. This inability to migrate meant that there were fewer cells to make fin rays, leaving more cells at the fin base to produce cartilage elements.

     "It really took the combination of labeling and knockouts to convince us that this cellular relationship between fins and limbs was real," Dr. Gehrke said.

     Future research includes new expeditions to find more fossil intermediates -- such as Tiktaalik, a link between primitive fish and the first four-legged animals, discovered by Shubin and others in 2006 -- in the transition from fins to limbs. 

     The researchers are also planning experiments with Hox genes to learn how a common population of cells can form such different structures in fish and humans.

Anything fishy about this story? It's certainly not fin-ished yet. . .

Happy 23rd birthday today, Zoë (8/20/16)! Photo of Zoë in northern Ethiopia, safe and sound.

Wednesday, August 10, 2016

Young Sunflowers Follow the Sun, Mature Sunflowers Face East for the Warmth and Bugs (Florida Anyone?)

      Young sunflowers, as you may have observed, are heliotropic and appear to follow the sun (cue The Beatles!). However, mature sunflowers continue to face east once the stalk has matured to gather maximum warmth and pollinators (cue the Beetles!).

       Young sunflowers (Helianthus annuus) grow better when they track the sun’s daily motion from east to west across the sky. An internal clock helps control the behavior, Dr. Stacey Harmer and researchers report in 8/5/16 issue of Science.

      Depending on the time of day, certain growth genes appear to be activated to different degrees on opposing sides of young sunflowers’ stems. The east side of their stems grow faster during the day, causing the stems to gradually bend from east to west. The west side grows faster at night, reorienting the plants to prepare them for the next morning. “At dawn, they’re already facing east again,” says Harmer, University of California, Davis. The behavior helped sunflowers grow bigger.

     Young plants continued to grow from east to west each day even when their light source didn’t move. So Harmer and her colleagues concluded that the behavior was influenced by an internal clock like the one that controls human sleep/wake cycles, instead of being solely in response to available light. 

     That’s probably advantageous, Harmer says, “because you have a system that’s set up to run even if the environment changes transiently.” A cloudy morning doesn’t stop the plants from tracking the sun, for instance.

     Contrary to popular belief, mature sunflowers don’t track the sun — they perpetually face east. That’s probably because their stems have stopped growing. But Harmer and her colleagues found an advantage for the fixed orientation, too: Eastern-facing heads get warmer in the sun than westward-facing ones and attract more insects.

       I was happy to find a sunny topic for this week's PEOTS. This one is for Zoë.  


Tuesday, August 2, 2016

Failure to Launch: Andes, Lava Coulée, and Chao Baby!

       Geologists from
Heidelberg University have discovered deposits of magma in the Andes sufficient to have set off a super-eruption but which, in fact, did not. 

     Researchers discovered that magma volumes of supervolcanic proportions have been continuously accumulating in the Altiplano-Puna region of the Andes since the last super-eruption nearly 2.9 million years ago. 

     These magmas, however, did not reach the surface to trigger a catastrophic eruption but instead slowly cooled at depth and hardened into plutonic rock, similar to the area we discussed in Russia two weeks ago. The results of the research were published in the journal Geology.

      Unlike the pluton they describe, the Chao volcano in northern Chile with a lava coulée (or flow) approximately 14.5 km long in the center of the image above flowed at the surface. The composition of the lava matches that of deposits of adjacent supervolcanic calderas. Chao erupted about 75,000 years ago, but zircon crystals in the lava were already forming in a subterranean magma reservoir for nearly three million years.

     "A supervolcanic eruption spews out more than 1,000 cubic kilometers of magma, which accumulated over time in reservoirs close the earth's surface," explains Dr. Axel Schmitt.

       "In turn, these reservoirs are fed from deeper layers in the earth's crust and the underlying mantle. During an eruption, the overlying rock layers collapse into the empty magma chamber and form depressions, known as calderas, of up to 100 kilometers in diameter." Schmitt indicates that there have been at least seven super-eruptions in the Altiplano-Puna region within the last ten million years, the most recent one about 2.9 million years ago. We don't understand why no further major eruptions have occurred since then and whether the region can now be considered inactive for such events.

      Using samples from five small lava domes in northern Chile and southeast Bolivia, the researchers investigated the most recent eruptions whose chemical composition matches the supervolcanic magmas from the region. They determined the age of very small zircon crystals from these lava flows with the aid of a high-spatial-resolution mass spectrometer. 

      "The mineral zircon forms almost exclusively in magmas, so its age reveals when those magmas were present under the volcano," explains Schmitt. "The astonishing result was that the ages of the zircons measured from all five of the smaller volcanoes extended continuously from the time of the eruption 75,000 years ago back to the last supervolcanic eruption."

     Dr. Schmitt reports that model calculations demonstrated that zircon formation is only possible over such long durations if the inflow of magma amounted to approximately one cubic kilometer over 1,000 years, which is unusually high for a relatively small volcano. The volcanologist explains that the lack of a major volcanic eruption does not necessarily indicate that magmatic activity has come to a complete halt. Perhaps the rise in magma from deeper regions merely slowed during the last 2.9 million years, forming a pluton.

      "However, our results also show that a relatively small increase in the long-term magma recharge from about one to five cubic kilometers in 1,000 years would recreate conditions favoring a catastrophic supervolcanic eruption. A new super-eruption in the Altiplano-Puna region would be possible, but only after a long lead time," said Dr.Schmitt.

Have you ever seen anything so (lava) coulée?