For the first time, scientists have added microscopic tracking devices into the interior of cells, giving a peek into how development starts.
For the first time, scientists have introduced minuscule tracking devices directly into the interior of mammalian cells, giving an unprecedented peek into the processes that govern the beginning of development. This work on one-cell embryos is set to shift our understanding of the mechanisms that underpin cellular behavior in general, and may ultimately provide insights into what goes wrong in aging and disease.The research, led by Professor Tony Perry from the Department of Biology and Biochemistry at the University of Bath, involved injecting a silicon-based nanodevice together with sperm into the egg cell of a mouse. The result was a healthy, fertilized egg containing a tracking device.The tiny devices are a little like spiders, complete with eight highly flexible ‘legs’. The legs measure the ‘pulling and pushing’ forces exerted in the cell interior to a very high level of precision, thereby revealing the cellular forces at play and showing how intracellular matter rearranged itself over time.
Five mouse embryos, each containing a nanodevice that is 22-millionths of a meter long. The film begins when the embryos are 2-hours old and continues for 5 hours. Each embryo is about 100-millionths of a meter in diameter. Credit: Professor Tony Perry
The nanodevices are incredibly thin – similar to some of the cell’s structural components, and measuring 22 nanometres, making them approximately 100,000 times thinner than a pound coin. This means they have the flexibility to register the movement of the cell’s cytoplasm as the one-cell embryo embarks on its voyage towards becoming a two-cell embryo.
“This is the first glimpse of the physics of any cell on this scale from within,” said Professor Perry. “It’s the first time anyone has seen from the inside how cell material moves around and organizes itself.”
Why probe a cell’s mechanical behavior?
The activity within a cell determines how that cell functions, explains Professor Perry. “The behavior of intracellular matter is probably as influential to cell behavior as gene expression,” he said. Until now, however, this complex dance of cellular material has remained largely unstudied. As a result, scientists have been able to identify the elements that make up a cell, but not how the cell interior behaves as a whole.
“From studies in biology and embryology, we know about certain molecules and cellular phenomena, and we have woven this information into a reductionist narrative of how things work, but now this narrative is changing,” said Professor Perry. The narrative was written largely by biologists, who brought with them the questions and tools of biology. What was missing was physics. Physics asks about the forces driving a cell’s behavior, and provides a top-down approach to finding the answer.
“We can now look at the cell as a whole, not just the nuts and bolts that make it.”
Mouse embryos were chosen for the study because of their relatively large size (they measure 100 microns, or 100-millionths of a meter, in diameter, compared to a regular cell which is only 10 microns [10-millionths of a meter] in diameter). This meant that inside each embryo, there was space for a tracking device.
The researchers made their measurements by examining video recordings taken through a microscope as the embryos developed. “Sometimes the devices were pitched and twisted by forces that were even greater than those inside muscle cells,” said Professor Perry. “At other times, the devices moved very little, showing the cell interior had become calm. There was nothing random about these processes – from the moment you have a one-cell embryo, everything is done in a predictable way. The physics is programmed.”
The results add to an emerging picture of biology that suggests material inside a living cell is not static, but instead changes its properties in a pre-ordained way as the cell performs its function or responds to the environment. The work may one day have implications for our understanding of how cells age or stop working as they should, which is what happens in disease.
The study is published this week in Nature Materials and involved a trans-disciplinary partnership between biologists, materials scientists and physicists based in the UK, Spain, and the USA.
Reference: “Tracking intracellular forces and mechanical property changes in mouse one-cell embryo development” by Marta Duch, Núria Torras, Maki Asami, Toru Suzuki, María Isabel Arjona, Rodrigo Gómez-Martínez, Matthew D. VerMilyea, Robert Castilla, José Antonio Plaza and Anthony C. F. Perry, 25 May 2020, Nature Materials.
The study is published this week in Nature Materials and involved a trans-disciplinary partnership between embryologists in Bath and the USA led by Professor Perry, and materials scientists and physicists led by Professor José Antonio Plaza at the Instituto de Microelectrónica de Barcelona (IMB-CNM) in Spain.
A host of international companies will be evaluated next for the free license granted by Caltech.
After receiving more than 100 applications, NASA’s Jet Propulsion Laboratory in Southern California has selected eight U.S. manufacturers to make a new ventilator tailored for coronavirus (COVID-19) patients.
The prototype, which was created by JPL engineers in just 37 days, received an Emergency Use Authorization from the Food and Drug Administration on April 30.
Called VITAL (Ventilator Intervention Technology Accessible Locally), the high-pressure ventilator was designed to use one-seventh the parts of a traditional ventilator, relying on parts already available in supply chains. It offers a simpler, more affordable option for treating critical patients while freeing up traditional ventilators for those with the most severe COVID-19 symptoms. Its flexible design means it also can be modified for use in field hospitals.
The Office of Technology Transfer and Corporate Partnerships at Caltech, which owns the patents and software for VITAL, is offering a free license for the device. Caltech manages JPL for NASA.
The U.S. companies selected for licenses are:
Vacumed, a division of Vacumetrics, Inc. in Ventura, California Stark Industries, LLC in Columbus, Ohio MVent, LLC, a division of Minnetronix Medical, in St. Paul, Minnesota iButtonLink, LLC in Whitewater, Wisconsin Evo Design, LLC in Watertown, Connecticut DesignPlex Biomedical, LLC in Fort Worth, Texas ATRON Group LLC in Dallas Pro-Dex, Inc. in Irvine, California
“The VITAL team is very excited to see their technology licensed,” said Leon Alkalai, manager of the JPL Office of Strategic Partnerships and a member of the VITAL leadership team. “Our hope is to have this technology reach across the world and provide an additional source of solutions to deal with the on-going COVID-19 crisis.”
JPL now is evaluating international manufacturers from countries including Brazil, Mexico, India and Malaysia. A full list of approved manufacturers is available here.
VITAL was developed with input from doctors and medical device manufacturers. A prototype of the JPL device was successfully tested by the Human Simulation Lab in the Department of Anesthesiology, Perioperative and Pain Medicine at Mount Sinai on April 23.
A modified design, which uses compressed air and can be deployed by a greater range of hospitals, was recently tested at the UCLA Simulation Center in Los Angeles. A high-fidelity lung simulator tested almost 20 different ventilator settings, representing a number of scenarios that could be seen in critically ill patients in an intensive care unit.
“VITAL performed well in simulation testing with both precise and reproducible results,” said Dr. Tisha Wang, clinical chief of the UCLA Division of Pulmonary and Critical Care Medicine. “In addition, the setup and operation of the ventilator was quick and user-friendly. The UCLA team commends JPL for actively contributing to the COVID-19 response and successfully addressing one of the key medical needs in the sickest group of patients.”
The compressed-air design also has been submitted to the FDA for a ventilator Emergency Use Authorization and is currently under review.
Ice-blue clouds are drifting high above the Arctic, which means the Northern Hemisphere’s noctilucent cloud season is here.
NASA’s Aeronomy of Ice in the Mesosphere spacecraft — AIM for short — first spotted wisps of these noctilucent, or night-shining, clouds over the Arctic on May 17, 2020. In the week that followed, the ghost-like wisps grew into a blur, quickly filling more of the Arctic sky. This is the second-earliest start of the northern season yet observed, and the season is expected to run through mid-August.
The seasonal clouds hover high above the ground, about 50 miles overhead in a layer of the atmosphere called the mesosphere. Most meteors burn up when they reach the mesosphere; there are enough gases there to slough plummeting meteors into nothing more than dust and smoke. Noctilucent clouds form when water molecules congregate around the fine dust and freeze, forming ice crystals. The icy clouds, reflecting sunlight, shine bright blue and white. They first appear in summer — around mid-May in the Northern Hemisphere and mid-November in the Southern — when the mesosphere is most humid, with the season’s heat lofting moisture up to the sky.
“Every year, twice a year, the start of the season is a big event for us,” said Jim Russell, AIM principal investigator at Hampton University in Virginia. “The reason we’re excited is we’re trying to find out what the causes of the season’s starting are and what does it really mean with regard to the larger picture in the atmosphere.”
Also known as polar mesospheric clouds (because they tend to huddle around Earth’s poles), these clouds help scientists better understand the mesosphere and how it’s connected to the rest of the atmosphere, weather, and climate.
Scientists are eager to see what this Arctic season brings. For the most part, the brilliant clouds usually cling to the polar regions. But sometimes, they stray south. Last year, they were spotted as far south as southern California and Oklahoma — lower latitudes than have ever been seen before, Russell said. The new season is another chance to better understand the fleeting clouds and their possible migration south. Some evidence indicates this could be the result of changing atmospheric conditions.
“With every year, we get new data to help us put together a picture of the atmosphere,” Russell said.
‘Groupie’ galaxies orbiting Milky Way tell us about dark matter, how galaxy formed.
We live in a big-city galaxy. The Milky Way is so big it has satellite galaxies that orbit it, just as the Moon orbits the Earth. These arrangements tell us a great deal about the secrets of the universe—from how galaxies form to the mysterious nature of dark matter.
Two new studies have revealed more and more about these ‘groupie’ galaxies around the Milky Way, including evidence that large satellite galaxies can bring their own small satellites with them when they are sucked into orbit around the Milky Way. Scientists have also extracted information about the halos of dark matter that surround these galaxies, as well as a prediction that our home galaxy should host an additional 100 or so very faint satellite galaxies awaiting discovery.
The research, co-led by University of Chicago Asst. Prof. Alex Drlica-Wagner in collaboration with scientists from SLAC National Accelerator Laboratory and the University of Wisconsin-Madison, was published in the April edition of the The Astrophysical Journal. It relies heavily on data from the Dark Energy Survey, a groundbreaking effort to map the skies led by Fermi National Accelerator Laboratory and the University of Chicago.
“The Dark Energy Survey data gives us unprecedented sensitivity for the smallest, oldest, and most dark-matter-dominated galaxies,” said Drlica-Wagner. “These faint galaxies can teach us a lot about how stars and galaxies form.”
A simulation of the formation of dark matter structures from the early universe until today. Gravity makes dark matter clump into dense halos, indicated by bright patches, where galaxies form. At about 18 seconds into this simulation, a halo like the one that hosts the Milky Way begins to form near the center top of the frame. Shortly afterward, a smaller halo begins to take shape at the top center of the screen. This halo falls into the first, larger halo by about 35 seconds, mimicking the Large Magellanic Cloud’s fall into the Milky Way. SLAC and Stanford researchers, working with collaborators from the Dark Energy Survey, have used simulations like these to better understand the connection between dark matter and galaxy formation. Credit: Ralf Kaehler/SLAC National Accelerator Laboratory
Shining galaxies’ light on dark matter
Astronomers have long known the Milky Way has satellite galaxies—including the notable Large Magellanic Cloud, which can be observed with the naked eye in the southern hemisphere—but thanks to surveys with large telescopes, the list of known satellites has increased to about 60 over the last two decades.
These galaxies tell us much about the cosmos, including how much dark matter it takes to form a galaxy, how many satellite galaxies we should expect to find around the Milky Way, and whether galaxies can bring their own satellites into orbit around our own—a key prediction of the most popular model of dark matter. (The answer to that last question appears to be a resounding “yes.”)
“We wanted to rigorously answer the question: What is the faintest galaxy that our telescopes can detect?” Drlica-Wagner said.
To answer this question, they simulated over a million small satellite galaxies, embedded them into large astronomical data sets, and used their search algorithms to try to re-extract them. This allowed them to determine which galaxies could be detected and which were too faint for current telescopes. They then combined this information with large numerical simulations of dark matter clustering to predict the total population of satellites around the Milky Way (including both those that we can see, and those that we cannot).
The result was a prediction that about 100 more galaxies remain to be discovered orbiting the Milky Way. If the “missing” 100 galaxies are discovered, this would help confirm the researchers’ model linking dark matter and galaxy formation.
“One of the most exciting things about this work is that we will be able to use our measurements of satellite galaxies to understand microscopic properties of dark matter,” Drlica-Wagner said.
The leading model for dark matter is that it’s a subatomic particle, like an electron or a proton, that was formed in the early universe. If these particles of dark matter were very light, they could have had very high velocity, which would make it hard for dark matter to clump and form the galaxies that we see today. Thus, by observing a large number of small galaxies, it is possible to put a lower limit on how much mass a dark matter particle could have, the scientists said.
“The particle nature of dark matter can have observable consequences for the galaxies that we see,” said Drlica-Wagner.
Read Link Between Dark Matter Halos and Galaxy Formation Revealed With Help From the Milky Way’s Satellites for more about this research.
“Milky Way Satellite Census. I. The Observational Selection Function for Milky Way Satellites in DES Y3 and Pan-STARRS DR1” by A. Drlica-Wagner, K. Bechtol, S. Mau, M. McNanna, E. O. Nadler, A. B. Pace, T. S. Li, A. Pieres, E. Rozo, J. D. Simon, A. R. Walker, R. H. Wechsler, T. M. C. Abbott, S. Allam1, J. Annis, E. Bertin, D. Brooks, D. L. Burke, A. Carnero Rosell, M. Carrasco Kind, J. Carretero, M. Costanzi, L. N. da Costa, J. De Vicente, S. Desai, H. T. Diehl, P. Doel, T. F. Eifler, S. Everett, B. Flaugher, J. Frieman, J. García-Bellido, E. Gaztanaga, D. Gruen, R. A. Gruendl, J. Gschwend, G. Gutierrez, K. Honscheid, D. J. James, E. Krause, K. Kuehn, N. Kuropatkin, O. Lahav, M. A. G. Maia, J. L. Marshall, P. Melchior, F. Menanteau, R. Miquel, A. Palmese, A. A. Plazas, E. Sanchez, V. Scarpine, M. Schubnell, S. Serrano, I. Sevilla-Noarbe, M. Smith, E. Suchyta, G. Tarle and (DES Collaboration), 15 April 2020, Astrophysical Journal.
“Milky Way Satellite Census. II. Galaxy–Halo Connection Constraints Including the Impact of the Large Magellanic Cloud” by E. O. Nadler, R. H. Wechsler, K. Bechtol, Y.-Y. Mao, G. Greeng, A. Drlica-Wagner, M. McNanna, S. Mau, A. B. Pace, J. D. Simon, A. Kravtsov, S. Dodelson, T. S. Li,,, A. H. Riley, M. Y. Wang, T. M. C. Abbott, M. Aguena, S. Allam, J. Annis, S. Avila, G. M. Bernstein, E. Bertin, D. Brooks, D. L. Burke, A. Carnero Rosell, M. Carrasco Kind, J. Carretero, M. Costanzi, L. N. da Costa, J. De Vicente, S. Desai, A. E. Evrard, B. Flaugher, P. Fosalba, J. Frieman, J. García-Bellido, E. Gaztanaga, D. W. Gerdes, D. Gruen,, J. Gschwend, G. Gutierrez, W. G. Hartley, S. R. Hinton, K. Honscheid, E. Krause, K. Kuehn, N. Kuropatkin, O. Lahav, M. A. G. Maia, J. L. Marshall, F. Menanteau, R. Miquel, A. Palmese, F. Paz-Chinchón, A. A. Plazas, A. K. Romer, E. Sanchez, B. Santiago, V. Scarpine, S. Serrano, M. Smith, M. Soares-Santos, E. Suchyta, G. Tarle, D. Thomas, T. N. Varga, A. R. Walker and (DES Collaboration), 15 April 2020, Astrophysical Journal.
The research was a collaborative effort within the Dark Energy Survey, led by the Milky Way Working Group, with substantial contributions from junior members including Sidney Mau, an undergraduate at UChicago; and Mitch McNanna, a graduate student at UW-Madison.
A staple in every science classroom is the periodic table of elements, and for many it is their first introduction to the vast mysteries of the natural world.
Now physicists from Kyoto University have unveiled a new table that provides a different perspective on the building blocks of the universe. While the traditional table is based on the behavior of electrons in an atom, this new table is based on the protons in the nucleus.
“The periodic table of the elements is one of the most significant achievements in science, and in its familiar form it is based on the shell structure of electron orbitals in atoms,” explains Yoshiteru Maeno, one of the co-developers of the new table.
“But atoms are comprised of two types of charged particles that designate each element: electrons orbiting the core and protons in the core itself.”
The team’s new ‘Nucletouch’ table — also available as a 3D model — was announced recently in the journal Foundations of Chemistry.
Over 150 years have passed since Dmitri Mendeleev discovered the periodic law that lead him to propose the classic periodic table. He even had the foresight to add space for elements that were still unknown in his time.
“Fundamentally, it comes down to the electrons in each atom. Atoms are considered to be stable when electrons completely fill their ‘shell’ of orbits around the nucleus,” continues Maeno.
“So-called ‘noble gases’, inert elements such as helium, neon, and argon, rarely react with other elements. Their most stable electron numbers are 2, 10, 18, 36, and so on.”
Maeno decribes these as atomic ‘magic numbers’, and importantly the same principle can also be applied to protons. Imagining that protons in a nucleus exist in ‘orbits’ may seem like a stretch, but the discovery of the concept was awarded the 1963 Nobel prize in physics.
Protons have different stable magic numbers: 2, 8, 20, 28, and so on. Among these are familiar elements such at helium, oxygen, and calcium. The Nucletouch table places these ‘magic nuclei’ at its center, providing a new perspective on the elements.
“Similar to electrons, when nuclear orbits are filled with protons, they form stable nuclei, analogous to the noble-gas elements,” says collaborator Kouichi Hagino.
“In our nuclear periodic table, we also see that nuclei tend to be spherically-shaped near the magic numbers, but deformed as you move away from them.”
The team made the table to highlight alternative ways to illustrate the laws of nature, and hopes that enthusiasts and academics alike will find something to enjoy and learn from this fresh new look at an old friend.
Reference: “A nuclear periodic table” by K. Hagino and Y. Maeno, 21 April 2020, Foundations of Chemistry.
On May 29, 2020, a family of sunspots — dark spots that freckle the face of the Sun, representing areas of complex magnetic fields — sported the biggest solar flare since October 2017. Although the sunspots are not yet visible (they will soon rotate into view over the left limb of the Sun), NASA spacecraft spotted the flares high above them.
The flares were too weak to pass the threshold at which NOAA’s Space Weather Prediction Center (which is the U.S. government’s official source for space weather forecasts, watches, warnings and alerts) provides alerts. But after several months of very few sunspots and little solar activity, scientists and space weather forecasters are keeping their eye on this new cluster to see whether they grow or quickly disappear. The sunspots may well be harbingers of the Sun’s solar cycle ramping up and becoming more active.
Or, they may not. It will be a few more months before we know for sure.
As the Sun moves through its natural 11-year cycle, in which its activity rises and falls, sunspots rise and fall in number, too. NASA and NOAA track sunspots in order to determine, and predict, the progress of the solar cycle — and ultimately, solar activity. Currently, scientists are paying close attention to the sunspot number as it’s key to determining the dates of solar minimum, which is the official start of Solar Cycle 25. This new sunspot activity could be a sign that the Sun is possibly revving up to the new cycle and has passed through minimum.
However, it takes at least six months of solar observations and sunspot-counting after a minimum to know when it’s occurred. Because that minimum is defined by the lowest number of sunspots in a cycle, scientists need to see the numbers consistently rising before they can determine when exactly they were at the bottom. That means solar minimum is an instance only recognizable in hindsight: It could take six to 12 months after the fact to confirm when minimum has actually passed.
This is partly because our star is extremely variable. Just because the sunspot numbers go up or down in a given month doesn’t mean it won’t reverse course the next month, only to go back again the month after that. So, scientists need long-term data to build a picture of the Sun’s overall trends through the solar cycle. Commonly, that means the number we use to compare any given month is the average sunspot number from six months both backward and forward in time — meaning that right now, we can confidently characterize what October 2019 looks like compared to the months before it (there were definitely fewer sunspots!), but not yet what November looks like compared to that.
On May 29, at 3:24 a.m. EST, a relatively small M-class solar flare blazed from these sunspots. Solar flares are powerful bursts of radiation. Harmful radiation from a flare cannot pass through Earth’s atmosphere to physically affect humans on the ground, however — when intense enough — they can disturb the atmosphere in the layer where GPS and communications signals travel. The intensity of this flare was below the threshold that could affect geomagnetic space and below the threshold for NOAA to create an alert.
Nonetheless, it was the first M-class flare since October 2017 — and scientists will be watching to see if the Sun is indeed beginning to wake up.
Development of Europe’s first ever lunar lander was agreed upon by ESA Member States in 2019 and now ESA is seeking your ideas for science and robotic missions on the Moon.
Set to launch on an Ariane 64 rocket later this decade and return to the Moon on a regular basis, the large lander will provide unprecedented opportunities for science and robotics on the lunar surface and your mission could be one of the first.
The call for ideas comes hot on the heels of ESA signing an agreement to start building the third European Service Module for NASA’s Artemis program. This module will drive the spacecraft that ferries the next astronauts to the Moon.
Repeat trips to the Moon
The European-led large lunar lander program provides autonomous access to the Moon, delivering 1.5 tonnes of material from Europe’s Spaceport in Kourou, French Guiana – this is roughly the weight of a hippopotamus.
The program, currently known as the European Large Logistics Lander or EL3 for short, is designed to incorporate different types of uncrewed missions, from supply runs for Artemis astronauts, to stand-alone robotic science and technology demonstration missions and even a lunar return mission to bring samples to laboratories on Earth.
“This European lander will be able to access locations all over the Moon from the equator to the poles, from the near side to the far side, opening up tremendous opportunities to deliver science, research technology and infrastructure,” says ESA’s Exploration science and research coordinator James Carpenter, “developing this capability is a hugely important strategic step for Europe. It will allow us to take a lead in future robotic missions and support international activities at the Moon’s surface.”
The best of all worlds
Now that ESA has defined the hardware, launch, and operations side for this unique European program, the agency is looking for outstanding mission ideas that could be delivered by the European Large Logistics Lander.
Examples of what could be proposed include robotic exploration of lunar caves, telescopes on the far side of the Moon, searching for water ice or producing useable products from resources on the Moon.
“We are asking the best minds to submit ideas for this program as we explore our Solar System in collaboration with scientists, engineers, industry, and companies,” James continues, “we really want to extend this call for ideas outside the realm of the usual space players, considering all aspects of lunar exploration.”
The lunar lander program is not a one-shot mission but promises regular launches starting in the later part of this decade and continuing into the 2030s.
We are looking for ideas that align with ESA’s strategy for exploration to inspire, create new knowledge, grow international cooperation and create economic growth and industrial competitiveness.
Any company, organization or person can submit their ideas for the EL3 program. Details and information on how to apply are available here. The deadline for submissions is 3 July 2020.
Breakthrough in Artificial Photosynthetic System That Produces Clean and Renewable Energy From Sunlight and Water
Understanding nature’s process could inform the next generation of artificial photosynthetic systems that produce clean and renewable energy from sunlight and water.
Photosystem II is a protein complex in plants, algae and cyanobacteria that is responsible for splitting water and producing the oxygen we breathe. Over the past few years, an international collaboration between scientists at the Department of Energy’s Lawrence Berkeley National Laboratory, SLAC National Accelerator Laboratory and several other institutions have been able to observe various steps of this water-splitting cycle at the temperature at which it occurs in nature.
Now, the team has used the same method to zero in on a key step in which a water molecule moves in to bridge manganese and calcium atoms in the catalytic complex that splits water to produce breathable oxygen. What they learned brings them one step closer to obtaining a complete picture of this natural process, which could inform the next generation of artificial photosynthetic systems that produce clean and renewable energy from sunlight and water. Their results were published in the Proceedings of the National Academy of Sciences this month.
“We demonstrated that it is possible to make these measurements in previous iterations of this work, but we never had the spatial resolution or enough time points to really drill down into these finer details,” says co-author Uwe Bergmann, a distinguished staff scientist at SLAC. “After carefully optimizing this experiment over many years, we honed our ability to make measurements at high enough quality to see these tiny changes for the first time.”
The bucket brigade
During photosynthesis, the oxygen-evolving complex, a cluster of four manganese atoms and one calcium atom connected by oxygen atoms, cycles through four stable oxidation states, known as S0 through S3, when exposed to sunlight.
On a baseball field, S0 would be the start of the game when a player on home base is ready to go to bat. S1-S3 would be players on first, second, and third. Every time a batter connects with a ball, or the complex absorbs a photon of sunlight, the player on the field advances one base. When the fourth ball is hit, the player slides into home, scoring a run or, in the case of Photosystem II, releasing breathable oxygen. This research focused on the transition from S2 to S3, the last stable intermediate state before an oxygen molecule is produced.
The oxygen-evolving complex is surrounded by water and protein. In the step the scientists looked at, water flows through a pathway into the complex, where one water molecule ultimately forms a bridge between a manganese atom and a calcium atom. This water molecule likely provides one of the oxygen atoms in the oxygen molecule produced at the end of the cycle.
Using SLAC’s Linac Coherent Light Source (LCLS) X-ray laser, the researchers found that water molecules are ferried into the complex as if through a bucket brigade: They move in many small steps from one end of the pathway to the other. They also showed that the calcium atom within the complex could be involved in shuttling the water in.
“It’s like a Newton’s Cradle,” says Vittal Yachandra, one of the authors of the study and a senior scientist at Berkeley Lab who has been working on Photosystem II for more than 35 years. “Usually in liquid water things are constantly moving around, but now we are in this fascinating situation where some of the water molecules around the manganese cluster change their position, while others are actually always in the same place. You can repeat the experiment 10,000 times and they will still be sitting in that same spot.”
Working in tandem
At LCLS, the team zapped samples from cyanobacteria with ultrafast pulses of X-rays to collect both X-ray crystallography and spectroscopy data to map how electrons flow in the oxygen-evolving complex of Photosystem II. Through this technique, they are able to simultaneously map its structure and uncover information about the chemical process at the manganese cluster.
Previously, the researchers had used this technique to make sure the sample was intact and importantly, also in the right intermediate chemical state. This paper marks the first time the researchers were able to merge the two sets of information to see connections between the structural and the chemical changes. This allowed the researchers to watch how the steps unfold in real time, and learn new things about the reaction.
“It is exciting to see the ‘cause and effect’ of changes induced by light absorption as they happen,” Yachandra says.
“It is easy to forget how critical the environment is and how it enables these really complicated processes,” says Junko Yano, one of the authors of the study and a senior scientist at Berkeley Lab. “Life does not happen in a vacuum; all components have to work together to make the reaction possible. These results show us how the protein and water molecules around the catalytic cluster work in tandem for making oxygen. Our results will start a new way of thinking and inspire new kinds of questions.”
Ready, set, action!
Beyond photosynthesis, Yano says, this technique can be applied to other enzymatic systems to make more detailed snapshots of catalytic reactions.
“It allows us to connect the structural biology and chemistry of systems to understand and control complicated chemical reactions,” she says.
The ultimate goal of the project is to piece together an atomic movie using many snapshots made throughout the process, including the elusive transient state at the end that bonds two oxygen atoms from two water molecules to form the oxygen molecule.
“Our dream is to go around the whole reaction cycle and get enough time points and details that you can see the entire process unfold, from the first photon of light coming in to the first molecule of breathable oxygen coming out,” says co-author Jan Kern, a staff scientist at Berkeley Lab. “We’ve been building the set for this movie, establishing our technique and showing what’s possible. Now the cameras are finally rolling and we can start working on the feature film.”
Reference: “Untangling the sequence of events during the S2 → S3 transition in photosystem II and implications for the water oxidation mechanism” by Mohamed Ibrahim, Thomas Fransson, Ruchira Chatterjee, Mun Hon Cheah, Rana Hussein, Louise Lassalle, Kyle D. Sutherlin, Iris D. Young, Franklin D. Fuller, Sheraz Gul, In-Sik Kim, Philipp S. Simon, Casper de Lichtenberg, Petko Chernev, Isabel Bogacz, Cindy C. Pham, Allen M. Orville, Nicholas Saichek, Trent Northen, Alexander Batyuk, Sergio Carbajo, Roberto Alonso-Mori, Kensuke Tono, Shigeki Owada, Asmit Bhowmick, Robert Bolotovsky, Derek Mendez, Nigel W. Moriarty, James M. Holton, Holger Dobbek, Aaron S. Brewster, Paul D. Adams, Nicholas K. Sauter, Uwe Bergmann, Athina Zouni, Johannes Messinger, Jan Kern, Vittal K. Yachandra, and Junko Yano
, 20 May 2020, Proceedings of the National Academy of Sciences.
In addition to SLAC and Berkeley Lab, the collaboration includes researchers from Uppsala University and Umeå University in Sweden; Humboldt University of Berlin and the University of Heidelberg in Germany; the University of California, Berkeley and the University of California, San Francisco; the Diamond Light Source and the Rutherford Appleton Laboratory in the UK; and the Japan Synchrotron Radiation Research Institute and RIKEN SPring-8 Center in Japan.
Key components of this work were carried out at SLAC’s Stanford Synchrotron Radiation Lightsource (SSRL); Berkeley Lab’s Advanced Light Source (ALS) and National Energy Research Scientific Computing Center (NERSC); and the SPring-8 Angstrom Compact Free Electron Laser (SACLA) in Japan. LCLS, SSRL, ALS and NERSC are DOE Office of Science user facilities. This work was supported by the DOE Office of Science and the National Institutes of Health, among other funding agencies.
Two University of Cincinnati students have developed an interactive dashboard that shows COVID-19 cases and deaths in Greater Cincinnati and other major U.S. cities. Known as the COVID-19 Watcher, it joins a list of options available to the public to track the novel coronavirus.
Benjamin Wissel, a student in the UC College of Medicine’s Medical Scientist Training Program, and Pieter-Jan Van Camp, MD, a doctoral student in the Biomedical Informatics Graduate program, developed their app during the spring when there were no options for tracking city data. Since then the New York Times has added this feature to their dashboard as well.
“People are connected and viruses spread through city infrastructures,” says Wissel. “Our app is especially relevant in places like Cincinnati, whose metro area is split between three different states. The public benefits from additional sources that can provide up-to-date COVID-19 data for the country, state, county, and city level.”
Wissel and Van Camp published research on their dashboard recently in the Journal of the American Medical Informatics Association. Their dashboard is also listed on the Centers for Disease and Prevention Control website under the heading Cincinnati Children’s Hospital’s COVID-19 Watcher.
The COVID-19 Watcher displays data from every county and 188 metropolitan areas in the country. Features of the dashboard include ranking of the worst affected areas and auto-generating plots that depict temporal changes in testing capacity, cases and deaths. The COVID-19 Watcher can provide the public with real-time updates of outbreaks in their area.
“The New York Times has been tracking COVID-19 since January, and they released their data to the public in late March of this year,” says Wissel. “Our app pulls in their data, merges it with sources from the U.S. Census Bureau to map cases for each county to metropolitan areas, and then visualizes the data.”
Wissel says users of the dashboard can compare their city with others.
“Outbreaks started at different times in different cities, so it is insightful to compare the progression of the virus spreading in your city compared to other cities who started before you,” explains Wissel. “It is very hard to think of things in terms of exponential growth, but seeing case numbers from a city that is, for example, five days ahead of you can give you an idea of where your city might be in five days.”
Van Camp says users can explore the interactive dashboard’s possibilities.
“I think one of the dashboard’s more interesting features is the option to adjust the data by the size of the population per capita,” says Van Camp. “This way, you can compare the outbreak in different regions, regardless of high or low population, on a relative scale.”
Reference: “An Interactive Online Dashboard for Tracking COVID-19 in U.S. Counties, Cities, and States in Real Time” by Benjamin D Wissel, BS, P J Van Camp, MD, Michal Kouril, PhD, Chad Weis, MS, Tracy A Glauser, MD, Peter S White, PhD, Isaac S Kohane, MD, PhD and Judith W Dexheimer, PhD, 25 April 2020, Journal of the American Medical Informatics Association.
Other co-authors on research include Michal Kouril, PhD, UC assistant professor of pediatrics and Cincinnati Children’s researcher; Chad Weis, senior systems analyst at Cincinnati Children’s; Tracy Glauser, MD, UC professor of pediatrics and associate director of the Cincinnati Children’s Research Foundation; Peter White, PhD, adjunct professor of biomedical informatics at UC; Isaac Kohane, MD, PhD, chair of the Department of Biomedical Informatics Harvard Medical School; and Judith Dexheimer, PhD, UC associate professor of pediatrics and Cincinnati Children’s researcher.