Such molecules are often found in plants and other organisms, and many are considered desirable starting points for developing potential new drugs. But they also tend to be highly challenging for chemists to construct and modify in the lab — a process called synthesis.

The team used computer modeling and a theoretical framework centered on the concept of “information density” to illuminate chemistry principles underlying their landmark 2019 synthesis of the molecule bilobalide, which is produced in the leaves of the ginkgo tree, Ginkgo biloba. Bilobalide is a particularly complex and compact molecule that has shown promise as a potential neurological or psychiatric drug.

The scientists believe that the theoretical fruits of their new study, published in the Journal of the American Chemical Society, will enable chemists to devise more efficient syntheses of such challenging natural molecules — potentially opening up a new realm of powerfully bioactive compounds for development into medicines and other products.

“When we initially achieved our synthesis of bilobalide, we were essentially following our intuition, but in this new study we dug down to understand how the chemistry actually works and developed principles that we think can be applied to other challenges in organic synthesis,” says Ryan Shenvi, PhD, a professor of chemistry at Scripps Research and the senior author of the study.

Creating a valuable natural compound

Bilobalide — which evolved in the ginkgo tree, likely to protect its leaves from insects — blocks an insect nerve-cell receptor called RDL. The fact that the molecule kills insects yet seems quite safe in mammals and dissipates quickly in the environment has attracted interest for safe crop protection.

Bilobalide holds strong promise for medicinal use, with evidence that it’s relatively safe for humans. It blocks human brain-cell receptors called GABAA receptors, which are evolutionary cousins of insect RDL receptors. An intriguing 2007 study found that the compound could reverse cognitive and memory deficits in mice with a neurological condition modeling human Down syndrome, while other studies have suggested it may protect brain cells from certain kinds of harm.

Although natural bilobalide is synthesized by specialized enzymes in the ginkgo tree’s cells, chemists would like to be able to make it in the lab with organic chemistry techniques. In this way, they could obtain large quantities of the compound and modify it to explore and optimize its properties.

But the synthesis of bilobalide has always been a major challenge for scientists, because the molecule packs a relatively complex set of atoms — including eight reactive oxygens — into an odd and highly compact chemical structure. If they could overcome that challenge, chemists would have a way to make molecules of potentially enormous value.

“When you have complexity that is condensed to that extent, you start to see interesting emergent properties,” Shenvi says.

‘Information density’ brings deep understanding

In the study, Shenvi and his colleagues evaluated their 11-step synthesis of bilobalide, achieved in 2019, as well as two longer bilobalide syntheses that had been published previously.

With the help of computational modeling from collaborator Kendall Houk, PhD, the Saul Winstein Distinguished Research Chair in Organic Chemistry at UCLA, and a formal theory of “molecular information content” published in 2016 by German researcher Thomas Böttcher, they developed a concept of “information density” — essentially, complexity divided by molecular volume — and used that to analyze the bilobalide syntheses.

Their analysis showed that bilobalide, even compared with other naturally derived, compact and biologically active molecules, has a very high information density, and that its information content comes principally from its oxygen atoms and asymmetric carbon backbone.

The work revealed that the Shenvi lab’s synthesis of bilobalide was efficient due to fragment coupling — merging already-complex oxygen-containing molecules — and then making careful modifications to overcome the unusual emergent properties of the system.

The chemistry principles the team developed make sense of their bilobalide synthesis and its greater efficiency over prior syntheses, but are also applicable to many other unsolved problems involving natural-molecule synthesis, the researchers say.

As part of the work, co-author Stefano Forli, PhD, wrote a computer script in the Python coding language to automate the calculation of molecular information, which can be otherwise laborious, at the rate of more than 100,000 molecules per minute. (The script is available for download.) Forli is assistant professor in Scripps Research’s Department of Integrative Structural and Computational Biology.

Collaborating investigator Marisa Roberto, PhD, professor in the Department of Molecular Medicine at Scripps Research, studied the activity of bilobalide and another information-dense molecule, jiadifenolide, which Shenvi’s team also recently synthesized. In rodent studies, she found that both bilobalide and jiadifenolide showed promise as relatively potent and safe GABAA blockers, suggesting the potential for being translated into drugs for psychiatric conditions involving abnormal GABAA activity.

“The GABA system is dramatically altered in neuropsychiatric disorders such as alcoholism and other forms of addiction, for which one or both of these compounds might one day prove useful,” Roberto says.

A new study led by researchers at the University of Miami (UM) Rosenstiel School of Marine and Atmospheric Science looked at the immune system of elkhorn coral (Acropora palmata), an important reef-building coral in the Caribbean, to better understand its response to diseases such as white band disease and rapid tissue loss.

In the experiment, healthy corals were grafted to diseased ones. After one week, the corals were analyzed to study the coral’s overall gene expression in response to disease, if they exhibited an immune response, and whether there were different signatures of gene expression for corals that didn’t show signs of disease transmission. The researchers found that A. palmata has a core immune response to disease regardless of the type of disease, indicating that this particular coral species mounts an immune response to disease exposure despite differences in the disease type and virulence.

“Our results show that elkhorn coral is not immunocompromised but instead is actually actively trying to fight off disease,” said Nikki Traylor-Knowles, an assistant professor of marine biology and ecology at the UM Rosenstiel School and senior author of the study. “This gives me hope that the corals are fighting back with their immune system.”

Based upon these findings, the researchers suggest that corals that did not get disease may have tougher epithelia, a protective layer of cells covering external surfaces of their body. And, that the symbiotic dinoflagellate, Symbiodiniaceae, that live inside corals did not have differences in gene expression in response to disease, but over the course of the two-year study did develop differences.

Coral disease is considered one of the major causes of coral mortality and disease outbreaks are expected to increase in frequency and severity due to climate change and other human-made stressors. The Caribbean branching coral Acropora palmata which has already seen an 80 percent decrease on reefs primarily due to disease, which has resulted in them being classified as threatened under the US Endangered Species Act.

“These corals are keystone species for Florida reefs, so understanding that their immune systems are active is an important component that can be useful for protecting reefs,” said Traylor-Knowles.

Story Source:

Materials provided by University of Miami Rosenstiel School of Marine & Atmospheric Science. Original written by Diana Udel. Note: Content may be edited for style and length.

Cosmic dust

The novel device, designed to duplicate the process that causes swirling clouds of cosmic dust and plasma to collapse into stars and planets, consists of two fluid-filled concentric cylinders that rotate at different speeds. The device seeks to replicate the instabilities that are thought to cause the swirling clouds to gradually shed what is called their angular momentum and collapse into the growing bodies that they orbit. Such momentum keeps the Earth and other planets firmly within their orbits.

“In our simulations we can actually see the MRI develop in experiments,” said Himawan Winarto, a graduate student in the Princeton Program in Plasma Physics at PPPL and lead author of a paper in Physical Review E interest in the subject began as an intern in the University of Tokyo-Princeton University Partnership on Plasma Physics while an undergraduate at Princeton University.

The suggested system would measure the strength of the radial, or circular, magnetic field that the rotating inner cylinder generates in experiments. Since the strength of the field correlates strongly with expected turbulent instabilities, the measurements could help pinpoint the source of the turbulence.

“Our overall objective is to show the world that we’ve unambiguously seen the MRI effect in the lab,” said physicist Erik Gilson, one of Himawan’s mentors on the project and a coauthor of the paper. “What Himawan is proposing is a new way to look at our measurements to get at the essence of MRI.”

Surprising results

The simulations have shown some surprising results. While MRI is normally observable only at a sufficiently high rate of cylinder rotation, the new findings indicate that instabilities can likely be seen well before the upper limit of the experimental rotation rate is reached. “That means speeds much closer to the rates we are running now,” Winarto said, “and projects to the rotational speed that we should aim for to see MRI.”

A key challenge to spotting the source of MRI is the existence of other effects that can act like MRI but are not in fact the process. Prominent among these deceptive effects are what are called Rayleigh instabilities that break up fluids into smaller packets, and Ekman circulation that alters the profile of fluid flow. The new simulations clearly indicate “that MRI, rather than Ekman circulation or Rayleigh instability, dominates the fluid behavior in the region where MRI is expected,” Winarto said.

The findings thus shed new light on the growth of stars and planets that populate the universe. “Simulations are very useful to point you in the right direction to help interpret some of the diagnostic results of experiments,” Gilson said. “What we see from these results is that the signals for MRI look like they should be able to be seen more easily in experiments than we had previously thought.”

Story Source:

Materials provided by DOE/Princeton Plasma Physics Laboratory. Original written by John Greenwald. Note: Content may be edited for style and length.

A 14,000-year paleoecological reconstruction of the sub-Antarctic islands led by University of Maine researchers has found that seabird establishment occurred during a period of regional cooling 5,000 years ago. Their populations, in turn, shifted the Falkland Islands ecosystems through the deposit of high concentrations of guano that helped nourish tussac, produce peat and increase the incidence of fire.

This terrestrial-marine link is critical to the islands’ grasslands conservation efforts going forward, says Dulcinea Groff, who led the research as a UMaine Ph.D. student in ecology and environmental sciences, and part of a National Science Foundation-funded Interdisciplinary Graduate Education Research Traineeship (IGERT) in Adaptation to Abrupt Climate Change (A2C2). The connection of nutrients originating in the marine ecosystem that are transferred to the terrestrial ecosystem enrich the islands’ nutrient-poor soil, thereby making the Falkland Islands sensitive to changes in climate and land use.

The terrestrial-marine linkage in the Falkland Islands was the focus of Groff’s dissertation in 2018.

“Our work emphasizes just how important the nutrients in seabird poop are for the ongoing efforts to restore and conserve their grassland habitats. It also raises the question about where seabirds will go as the climate continues to warm,” says Groff, who conducted the research in the Falkland Islands during expeditions in 2014 and 2016 led by Jacquelyn Gill, an associate professor of paleoecology and plant ecology in the UMaine Climate Change Institute.

“Our 14,000-year record shows that seabirds established at Surf Bay during cooler climates. Seabird conservation efforts in the South Atlantic should be prepared for these species to move to new breeding grounds in a warmer world, and those locations may not be protected,” says Groff, who is now a postdoctoral research scientist at the University of Wyoming.

The UMaine expedition team, which included Kit Hamley, then a master’s student in Quaternary studies and a Climate Change Institute Fellow, collected a 476-centimeter peat column from Surf Bay, East Falkland. The 14,000-year record revealed in the undecomposed tussac leaves of the peat column “captures the development of a terrestrial-marine linkage that supports some of the most important breeding colonies of seabirds in the Southern Ocean today,” according to the research team, which published its findings in the journal Science Advances.

The absence of seabirds at the East Falklands site prior to 5,000 years ago suggests that seabirds may be sensitive to warmer mediated sea surface temperatures, which can impact their food supply, according to the research team. With a warming South Atlantic today, the question is whether the Falkland Islands, about 300 miles east of South America, will continue to be a seabird breeding “hot spot.”

“Our work suggests that as the Southern Ocean continues to warm in the coming decades, the Falkland Islands seabird communities may undergo abrupt turnover or collapse, which could happen on the order of decades,” according to the research team, which, in addition to Groff, Hamley (now a UMaine doctoral student) and Gill, involved Trevor Lessard and Kayla Greenawalt of UMaine, Moriaki Yasuhara of the University of Hong Kong, and Paul Brickle of the South Atlantic Environmental Research Institute, all co-authors on the American Association for the Advancement of Science journal article.

The Falkland Islands are at the boundary of a number of potential climate drivers, note the researchers. And P. flabellata peatlands have the world’s highest accumulation rates, “providing an unusually high-resolution record capable of recording abrupt change” — preserved charcoal, seabird guano and pollen data that can be used to analyze fire history, seabird population abundance and vegetation composition, respectively.

In the Falklands, where there are no native mammals or trees, settlers introduced sheep in the 17th century. Today, residents make their livelihoods from fishing, sheep farming and tourism.

The 14,000-year record from East Falkland revealed that for 9,000 years before the arrival of seabirds, the region was dominated by low levels of grasses, a heathland of ferns and dwarf Ericaceous shrubs. About 5,000 years ago, the researchers say, an “abrupt transition” appears to occur. Concentrations in bio-elements such as phosphorus and zinc increase. Grass pollen accumulation rates skyrocket, indicating the establishment of tussac grasslands within 200 years of the establishment of seabird colonies on the island. Also found in the core: increased accumulation rates of peat and charcoal.

It’s clear that the addition of seabird populations bringing nutrients from the marine environment to the island drove changes in the terrestrial plant community structure, composition and function, according to the researchers, as well as increased fire activity and nutrient cycling.

What remains unclear is what drove the abrupt ecosystem shift, says Gill, one of the world’s leading authorities on paleo-ecosystems, including the impacts of climate change and extinction, and the geographical distribution of living things through space and time.

“We know seabirds arrived at Surf Bay during a time when the climate was becoming cooler in the South Atlantic, though we still don’t know for sure what it was they were tracking. We also don’t know where these birds took refuge when climates were warmer, and that’s concerning as the South Atlantic gets hotter into the future,” says Gill, an NSF CAREER researcher who most recently was named a 2020 Friend of the Planet by the National Center for Science Education.

“Our study is also a powerful reminder of why we need to understand how different ecosystems are connected as the world warms,” says Gill. “We know that many seabirds in the South Atlantic rely on these unique coastal grasslands, but it turns out that the grasses also depend on the nutrients seabirds provide. Because they rely on ecosystems in the ocean and on land for their survival, seabirds are really good sentinels of global change. We just don’t have good long-term monitoring data for most of these species, so we don’t know enough about how sensitive they are to climate change. The fossil record can help us fill in the gaps.”

Both the platform and the protein could be highly useful to synthetic biologists and biomedical researchers. They often need to single out cells with specific visual phenotypes like shape or activity determined by their genetic or epigenetic makeup or their developmental history.

Rice graduate student Jihwan (James) Lee and François St-Pierre, an assistant professor of neuroscience at Baylor College of Medicine and an adjunct assistant professor of electrical and computer engineering at Rice, and their team reported their results in Science Advances.

Lee and his colleagues dubbed their platform SPOTlight, short for Single-cell Phenotypic Observation and Tagging with Light. It addresses the limitations of existing sorting techniques to isolate single live cells with unique profiles from heterogenous populations.

They then leveraged the method for protein engineering to develop the most photostable yellow fluorescent protein reported to date.

“We basically developed a platform that allows one to screen for spatial and temporal properties of individual cells,” said Lee, the first author and a student in Rice’s Systems, Synthetic and Physical Biology program working in St-Pierre’s Baylor lab.

“This is done by first observing the cells under a microscope,” he said. “The cells express a special protein so that shining a spot of light on desired cells make them go red. We can then easily separate red cells from the rest using a common device called a flow cytometer.”

That “special” photoactivatable fluorescent protein irreversibly transitions from dark to bright after being zapped by violet light. Photoactivatable dyes can also be used instead of proteins. In effect, cells are left with a long-lasting tag.

To only tag cells of interest, the team used a digital micromirror device, an array of tiny motor-driven mirrors also used in digital projectors, to give it the ability to light up single cells. “These micromirrors rotate and turn to define a region of your sample, down to single cells,” Lee said. “This is all automated. There’s a motorized microscope stage that moves the cells on an imaging plate around a predefined zone, and the DMD will shine light only on a particular cell.”

Through SPOTlight, a researcher can observe a population of hundreds of thousands of human or yeast cells over time to find those with desirable cellular dynamics, subcellular structures or shapes. Custom software can then be used to identify all cells with the desired profile, and instruct the light source and the DMD to photoactivate them with violet light.

“Then we use a flow cytometer or cell-sorting machine that can detect and recover the cells we tagged while throwing away the rest,” Lee said. “After we’ve recovered our cells of interest, we can send them for sequencing or conduct further studies.”

Lee said the prototype tags individual cells in 45 seconds to a minute. “That depends on the power of the light,” he said. “With a stronger light source, we should be able to do this even faster, maybe down to a few seconds per cell.”

To demonstrate the utility of SPOTlight, Lee and his colleagues used it to screen 3 million mutant cells expressing a library of fluorescent proteins, ultimately identifying and refining a yellow fluorescent protein they call mGold.

“It’s a variant of an existing fluorescent probe called mVenus,” Lee said. “The problem with mVenus is that it photobleaches very fast. It becomes dimmer and dimmer as you keep shining light on it. If you’re monitoring cells expressing mVenus for a long time, there comes a time where the fluorescent protein is no longer detectable. So we decided to screen for mVenus mutants with better fluorescent stability.”

He said researchers typically engineer fluorescent proteins by shining light on bacterial colonies expressing the proteins to see which one is brightest. With SPOTlight, “we can screen for brightness and photostability at the same time,” Lee said. “This isn’t something people commonly did, but biology isn’t static. It’s moving in time and space, so it’s important to have these temporal properties as well.

“Compared with commonly used yellow fluorescent proteins, mGold was four to five times more stable,” he said.

“Important developmental events and behaviors require monitoring for many minutes, hours or days and it’s frustrating when the probes we use to image these processes go dark before we’ve been able to capture the whole story,” St-Pierre said.

“It’s like having a power outage in the middle of watching a good movie,” he said. “Building on our work with mGold, we now want to use SPOTlight to develop probes that will enable us to watch full movies.

“Similarly, SPOTlight can enable synthetic biologists to engineer new proteins, nucleic acids or cells,” St-Pierre said. “More broadly, this method can help any researcher seeking to unravel the genetic or epigenetic determinants of an interesting cellular phenotype, including such clinically relevant properties as resistance to disease or treatment.”