Total Pageviews

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?

Tuesday, July 26, 2016

Hooked on Phononics: Spider Silk Sound and Heat

      New discoveries about spider silk could inspire new materials to manipulate heat and sound in the same way semiconducting circuits manipulate electrons, according to scientists at Rice University.

      A paper published yesterday in Nature Materials looks at the microscopic structure of spider silk and reveals unique characteristics in the way it transmits phonons, quasiparticles of sound.

      A phonon (cool moving graphic at this link) is a collective excitation in a periodic, elastic arrangement of atoms or molecules in condensed matter, like solids and some liquids. It represents an excited state in the quantum mechanical quantization of the modes of vibrations of elastic structures of interacting particles.

     The research shows for the first time that spider silk has a phonon band gap. That means it can block phonon waves in certain frequencies in the same way an electronic band gap -- the basic property of semiconducting materials -- allows some electrons to pass and stops others.

     The researchers wrote that their observation is the first discovery of a "hypersonic phononic band gap in a biological material."

      How the spider uses this property remains to be understood, but there are clear implications for materials, according to materials scientist and Rice Engineering Dean Edwin Thomas, who co-authored the paper. He suggested that the crystalline microstructure of spider silk might be replicated in other polymers. That could enable tunable, dynamic metamaterials like phonon waveguides and novel sound or thermal insulation, since heat propagates through solids via phonons.

     "Phonons are mechanical waves," Thomas said, "and if a material has regions of different elastic modulus and density, then the waves sense that and do what waves do: They scatter. The details of the scattering depend on the arrangement and mechanical couplings of the different regions within the material that they're scattering from."

       Spiders are adept at sending and reading vibrations in a web, using them to locate defects and to know when "food" comes calling. Accordingly, the silk has the ability to transmit a wide range of sounds that scientists think the spider can interpret in various ways. But the researchers found silk also has the ability to dampen some sound.

      "(Spider) silk has a lot of different, interesting microstructures, and our group found we could control the position of the band gap by changing the strain in the silk fiber," Thomas said. "There's a range of frequencies that are not allowed to propagate. If you broadcast sound at a particular frequency, it won't go into the material."

     Thomas and other researchers decided to take a more detailed look at dragline silk, shown below in a SEM, which spiders use to construct a web's outer rim and spokes and as a lifeline. (A spider suspended in midair is clinging to a dragline.) Though silk has been studied for thousands of years, it has only recently been analyzed for its acoustic properties.

      "Silk is a hierarchical structure comprised of a protein, which folds into sheets and forms crystals. These hard protein crystals are interconnected by softer, amorphous chains," Thomas said. Stretching or relaxing the interconnecting chains changes the silk's acoustic properties by adjusting the mechanical coupling between the crystals.

       "Right now, we don't know how to do any of this in other macromolecular fiber materials," Thomas said. "There's been a fair amount of investigation on synthetic polymers like nylon, but nobody's ever found a band gap."

Have you ever found a band gap?!

Zoë and her "Camp English" group in Ethiopia this summer:

Wednesday, July 20, 2016

Geological Mystery Feature: Alluvial Platinum from Russia

          Any guesses as to the origin of this circular geomorphic feature?

    It's not a crater and it's not a volcano. . .

      It is in northeast Russia and it's the source of alluvial (think panning for gold) platinum. . .

     This landform is nearly perfectly circular, with a diameter just under 8 kilometers (5 miles) and a ridge about 600 meters tall. A river has eroded through the lip, draining rainwater and runoff out of the center. The ridge is bare rock, with vegetation growing both inside and outside the ring. 

     Any ideas? Guess now or read on. . .
     Kondyor Massif is an igneous intrusion piercing the surrounding sedimentary rock without ever forming a volcano or erupting from a crater. A column originally topped by a dome when it formed, 

the structure has undergone differential erosion so the softer material weathered and eroded first, leaving the harder ring behind with the rest of the column hidden below the surface.

       The Kondyor Massif located in Khabarovsk Krai, Far Eastern Federal District, Russian Federation, roughly 600 km (373 mi) west-to-southwest of Okhotsk, or some 570 km (354 mi) south-east of Yakutsk.  

       Slow cooling produced these valuable platinum specimens which are up to 1.5 cm in diameter. They later weather out of the Massif and are mined alluvially.

       How was you guess; did you use circular reasoning? :-)  Have you ever panned for platinum, silver, or gold?


Wednesday, July 13, 2016

BUM in the Ocean: In Situ Microscopy "Polyps" Into View

           Benthic Underwater Microscopy (BUM) is a new technology for studying coral polyps and other microscopic organisms in situ.

       The exquisite and delicate structures of the benthic ecosystems are analyzed and photographed at the bottom of the sea floor.

      The microscope features an extremely high-resolution camera, an underwater computer with a diver interface, bright LED lights for fast exposure images, and a flexible, tunable lens that allows scientists to view underwater structures in 3D.

     Millions of polyps work together to build coral reefs by secreting calcium carbonate, with the minute animals providing nutrients and color to the reef.


      Using the BUM microscope, scientists were able to position themselves 5 centimeters away from the polyps and watch them as they captured tiny plankton and brine shrimp with tiny swaying tentacles.

     Researchers left the microscopes out overnight in order to record the polyps over an extended period. The images and footage gathered show the polyps’ gentle “dancing” and post-meal "kisses" that scientists say could be a way for polyps to share nutrients throughout the coral colony.

     Images from the Benthic Underwater Microscope also revealed a more violent side to the secret lives of polyps, showing coral of different species conquering weaker specimens. In order to win more reef space, the conquering coral will emit filaments that secrete stomach enzymes to destroy the tissue of their competitors.

     Researchers have used the BUM in two places so far, the waters off of Maui and the coast of Israel. With some of the largest coral bleaching events ever recorded taking place this year, scientists were especially interested to study the hard-hit coral reefs off of Maui.

     With the help of the new microscopic tool, scientists discovered that in bleached areas, there is a honeycomb pattern of algal colonization (like underwater squatters, algae move in when coral is weak from bleaching) and algal growth around individual polyps on the coral.

     When coral are weak, scientists found, algae are able to outgrow and smother the already struggling reefs.

       The new BUM technology is promising for understanding subsea micro-organisms, especially coral polyps.

          Lastly, this unrelated image made me laugh today. Hope you enjoy as well!

Hope you wonder at the new technology that has "polyps" into view.

Any ideas as to what this flower is? Thistle-like. . .but different. It's growing in West Chicago Creek, Colorado.