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The critically endangered vaquita has survived in low numbers in its native Gulf of California for hundreds of thousands of years, a new genetic analysis has found. The study found little sign of inbreeding or other risks often associated with small populations.

Gillnet fisheries have entangled and killed thousands of vaquitas in recent years and scientists believe that fewer than 20 of the small porpoises survive today. The new analysis demonstrates that the species’ small numbers do not doom it to extinction, however, and so gives hope for the small remaining population. Vaquitas have long survived and even thrived without falling into an “extinction vortex,” the new study showed. That’s a scenario in which their limited genetic diversity makes it impossible to recover.

“The species, even now, is probably capable of surviving,” said Phil Morin, research geneticist at NOAA Fisheries’ Southwest Fisheries Science Center and lead author of the new study published this week in Molecular Ecology Resources. “We can now see that genetic factors are not its downfall. There’s a very good chance it could recover fully if we can get the nets out of the water.”

Small but Stable Populations

An increasing number of species in addition to the vaquita have maintained small but stable populations for long periods without suffering from inbreeding depression. Other species include the narwhal, mountain gorilla, and native foxes in California’s Channel Islands. Long periods of small population sizes may have given them time to purge harmful mutations that might otherwise jeopardize the health of their populations.

“It’s appearing to be more common than we thought that species can survive at low numbers over long periods,” said Morin, who credited the vaquita findings to genetic experts around the world who contributed to the research.

The idea that vaquitas could sustain themselves in low numbers is not new. Some scientists suspected that more than 20 years ago. Now advanced genetic tools that have emerged with the rapidly increasing power of new computer technology helped them prove the point.

“They’ve survived like this for at least 250,000 years,” said Barbara Taylor, research scientist at the Southwest Fisheries Science Center. “Knowing that gives us a lot more confidence that, in the immediate future, genetic issues are the least of our concerns.”

Sequencing the Vaquita Genome

The new analysis examined living tissue from a vaquita captured as part of a last-ditch international 2017 effort to save the fast-disappearing species. The female vaquita tragically died, but its living cells revealed the most complete and high-quality genome sequence of any dolphin, porpoise, or whale to date, generated in collaboration with the Vertebrate Genomes Project. Sequencing was led by Olivier Fedrigo, Jacquelyn Mountcastle, and Erich Jarvis at the Rockefeller University. “We felt it our moral duty to generate a high-quality reference of this species on the brink of extinction”, said Jarvis. Only in recent years have advances in sequencing technologies and high-powered computers made such detailed reconstruction possible.

While the vaquita genome is not diverse, the animals are healthy. The most recent field effort in fall 2019 spotted about nine individuals, including three calves, within their core habitat. The robust calves suggest that inbreeding depression is not harming the health of these last vaquita. “These examples and others indicate that, contrary to the paradigm of an ‘extinction vortex’ that may doom species with low diversity, some species have persisted with low genomic diversity and small population size,” scientists wrote in the new study.

The genetic data suggest that the vaquita’s isolated habitat in the far northern Gulf of California has sustained roughly 5,000 vaquitas for around 250,000 years. The advent of gillnetting for fish and shrimp only a few decades ago drove vaquitas towards extinction, as they are incidentally caught in the nets.

More recently, Illegal gillnetting for totoaba, a fish about the same size and found in the same habitat as the vaquita, has compounded the losses. The practice has caused a catastrophic decline that is estimated as cutting the remaining population in half each year.

“Small numbers do not necessarily mean the end of a species, if they have the protection they need,” Taylor said. “In conservation biology, we’re always looking for risk. We shouldn’t be so pessimistic. The sight of those three healthy calves in the water with their survivor mothers should inspire the protection they need to truly recover.”

Moving around in the half-light is difficult but not impossible. To help us in this undertaking we have the rods, a type of light-sensitive cells (photoreceptors) present in the retina of vertebrates, capable of detecting very low lights which allow to move about even in poorly lit cellars or caves. They are biological wonders capable of detecting even a single quantum of light, but they need continuous maintenance. They are the protagonists of the new study published in PNAS by a team of researchers of SISSA - Scuola Internazionale Superiore di Studi Avanzati and the Istituto officina dei materiali of the National research council CNR-Iom which reveals new and essential details of how the retina works and in particular photoreceptors.

These consist of two segments: the outer segment (OS) and the inner segment (IS). The OS of the rods is the one where the biological machine capable of capturing the light is located, while the IS is responsible for the information to be transferred to the brain. "We have understood that the outer segment is more fragile than what was thought", comments Vincent Torre, neuroscientist of SISSA leading the team that conducted the research, adding "The OS consists of a stack of lipid discs containing the proteins responsible for phototransduction. New discs are generated at the base of the OS while used discs are removed at the tip of the OS. Traditionally, it was thought that in a stack of about 1000 discs there was almost perfect uniformity. However, our work shows that only the first 200 or 300 discs at the base of the OS are those effectively capable of detecting the single photon of light, characteristic from which comes the great sensitivity of the rods. The other discs positioned close to the tip gradually lose effectiveness and sensitivity and for this reason they must be disposed of and replaced with new discs in perfect condition".

It was the Calcium, an ion present in large numbers in biological processes that allowed the understanding of this mechanism. Its concentration in the OS is an excellent indicator of the functionality and integrity of phototransduction, the process with which the photoreceptors convert light into nerve signals. "With new optical probes we measured the concentration and the distribution of calcium in the OS. Using advanced optical microscopy instruments, we were able to study the distribution of this metal with unprecedented resolution and accuracy." Dan Cojoc of Cnr-Iom explains "what has emerged from the analyses is that there is greater concentration of calcium at the base of the outer segment with respect to the tip, which helps to understand the structure of the rod showing its non-homogeneity, as was thought until now.

A second and no less important result is the discovery of spontaneous calcium flares, i.e. rapid increases in calcium. These flares are not evenly distributed but located in the tips of the OS, which shows the existence of a functional gradient along the OS, a fundamental property for photoreceptor transduction of all vertebrates." Cojoc concludes. Like a warning light, the Calcium flares indicate that the discs start to stop working at their best and need turnover. The article was also recommended to Faculty Opinions by the editor of PNAS -something reserved only for the most important contributions - for the following reasons: "This interesting article uses a new Calcium measurement method to show that light-dependent changes of Calcium in the outer segment of the rods are greater at the base than at the tip".

Neuroscientist Gordon Fain of the University of California continues, "These differences can reflect an energy gradient that originates from the mitochondria of the inner segment. The authors of the study also make the amazing observation that Calcium increases spontaneously both at the tip and at the base (but more often at the tip), as well as more rarely in the inner segment. These increases produce sudden flares, i.e. peaks of Calcium concentration, which decrease slowly for several seconds and which remain local without propagating inside the outer segment or between the inner and outer segment."

URBANA, Ill. - Extrusion is the norm in the pet and aqua feed industries, yet it remains unusual for swine feed in the United States. But the technology can improve energy and protein digestibility in pigs, according to research from the University of Illinois.

"We're not doing this much in the U.S., partly because the extrusion equipment typically is not installed in feed mills producing pig feeds. If a feed company decided they wanted to extrude diets or extrude grain by itself, as we did in this case, it would add cost. So the only way it would be economical would be if the pigs performed better with extruded grains," says Hans H. Stein, professor in the Department of Animal Sciences and the Division of Nutritional Sciences at Illinois and co-author on a study in Animal Feed Science and Technology.

Stein and his research team compared pig diets containing either extruded or unprocessed corn, wheat, and sorghum to determine ileal starch and amino acid digestibility, as well as total tract digestibility of energy and fiber. One source of each grain was ground and then divided in two batches, with one batch left as is and the other extruded in a single-screw extruder with an exit temperature of 100 degrees Celsius. Grains were ground and extruded at Kansas State University, but extrusion equipment at the new Feed Technology Center at Illinois will facilitate future research to help meet the growing global demand for animal protein.

"In extruded corn and wheat, we saw a nice improvement in amino acid digestibility. Corn in particular," Stein says. "And we observed increases for energy in extruded corn and sorghum, but not in wheat."

Starch digestibility also increased in extruded grains, compared with unprocessed grains.

"Starch is already well digested by pigs, but by extruding it, we increase its digestibility even more. And we have seen in quite a few other experiments, every time we increase starch digestibility, we increase energy digestibility," Stein says. "There's a very, very close relationship between the two."

The mechanical process of extrusion, which involves heat, pressure, and steam, leads to gelatinization of starch, which explains the link between starch and energy digestibility.

"In the extruded grains, 90% of the starch was gelatinized," Stein says. "Gelatinization opens the starch molecule, making it easier for enzymes to break down every bond within the starch. That leads to greater energy digestibility and absorption."

Fiber digestibility didn't change markedly in extruded grains versus unprocessed grains, but more of the fiber content became soluble with extrusion. "That means some of the insoluble fibers were solubilized. But because fiber digestibility didn't increase overall, that didn't have as much of an impact as we had expected," Stein says.

With pigs extracting more energy and protein from extruded grains, Stein sees a potential economic benefit that could justify the cost of adding extruding equipment to feed mills.

"If feed manufacturers can increase the energy as much as we did in our study, then there certainly is value in extruding grain for pig diets," he says.

Researchers at the University of Illinois Urbana-Champaign have studied a population of women in rural Poland for the past four years to understand how their lifestyle affects their bone density. The age group and lifestyle of these women are often overlooked in such studies.

The study "Bone density and frame size in adult women: effects of body size, habitual use, and life history" was published in the American Journal of Human Biology.

"My work focuses on understanding how our activities shape our skeleton and what it means for the modern population," said Katharine Lee, a recent graduate of the Clancy group, which is affiliated with the Beckman Institute for Advanced Science and Technology.

The study focused on a population of farmers whose lifestyles involve substantial farm and domestic labor, such as growing fruits and vegetables, churning butter, beating rugs, washing windows, and caring for children. "We made some basic body measurements and looked at the physical activity patterns of these women," Lee said. "We also used a bone sonometer, which was provided through Beckman's Biomedical Imaging Center. It is a portable device that can be conveniently used to carry out bone density measurements."

Previous studies in the field have looked at bone density measurements in menopausal women. The researchers wanted to focus on women between the ages of 18 and 46, an age group that is not often looked at in bone density studies. "We wondered why there was so little research on premenopausal women, since presumably their bone density and activity predicts postmenopausal osteoporosis," said Kathryn Clancy, an associate professor of anthropology at Illinois and a part-time Beckman faculty member.

"We saw that measures such as grip strength and lean mass are associated with the bone density and frame size of these premenopausal women. We also saw that the bone density of the radius, which is the bone at the base of your thumb, is very high compared to an average white woman of European descent," Lee said. "Interestingly, we don't see this increased bone density in Polish American women. We don't fully understand what factors are causing it."

The researchers believe that this study sheds light on the specific contexts of this lifestyle. "A lot of these measures have looked at large populations and averaged, so they have missed many of these details," Lee said. "It is also important to think about which populations are not represented in the literature and look at lifestyles that are different to the modern, sedentary lifestyle that most people in the U.S. have."

Moving forward, the researchers are interested in understanding whether the childhood environment has helped shape the bone health of the women. "We have interviewed them about the different types of work they did when they were growing up. We asked whether they grew up on a farm, whether they had farm animals, or whether they tended a garden. Those activities, rather than the ones they are doing now, might be associated with the bone health measures," Lee said.

Water tainted with even a small concentration of human hormones can have profound effects on fish, according to a University of Cincinnati biologist.

UC assistant professor Latonya Jackson conducted experiments with North American freshwater fish called least killifish. She found that fish exposed to estrogen in concentrations of 5 nanograms per liter in controlled lab conditions had fewer males and produced fewer offspring.

Scientists have found estrogen at as much as 16 times that concentration in streams adjacent to sewage treatment plants.

The study suggests that even this small dose of estrogen could have significant consequences for wild fish populations living downstream from sewage treatment plants.

The study was published this week in the journal Aquatic Toxicology.

What's special about least killifish is they have a placenta and give birth to live young, Jackson said. It's uncommon among fish, who more typically lay eggs.

Jackson studied a synthetic estrogen called 17α-ethinylestradiol, an active ingredient in oral contraceptives also used in hormone replacement therapy. Estrogen been found in streams adjacent to sewage treatment plants in concentrations of as high as 60 nanograms or more per liter.

"Anything you flush down the toilet or put in the sink will get in the water supply," she said. 

This includes not only medicine people flush (never do that) but also unmetabolized chemicals that get flushed when people use the bathroom.

"Our wastewater treatment systems are good at removing a lot of things, but they weren't designed to remove pharmaceuticals," Jackson said. "So when women on birth control or hormone therapy go to the bathroom, it gets flushed into wastewater treatment plants."

Chronic exposure of fish to estrogen led to smaller populations and a gender ratio imbalance with more females than males.

Now Jackson wants to know how the exposure to hormones such as estrogen and androgen in a female fish affects her offspring. She is collaborating with the U.S. Environmental Protection Agency to examine local waters in southwestern Ohio.

Jackson said the impacts on streams are not limited to fish. Hormones and other chemicals that are not removed during treatment can bioaccumulate in the food chain or end up in our drinking water.

"Our drinking water is not a renewable resource. When we run out of clean drinking water, it's gone," Jackson said. "It's very important that we keep this resource clean."

HOUSTON - (Oct. 23, 2020) - Researchers at Rice University and Baylor College of Medicine have developed a new method to isolate specific cells, and in the process found a more robust fluorescent protein.

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."

Stress is present everywhere, even bacteria and plant cells have to cope with it. They express various specific stress proteins, but how exactly this line of defense works is often not clear. A group of scientists headed by Professor Dirk Schneider of Johannes Gutenberg University Mainz (JGU) has now discovered a protective mechanism in cyanobacteria as well as in chloroplasts of plant cells: Complex ring structures formed by a protein attach to cell membranes and dissociate. Thereafter, the individual proteins spread out on the membrane surface and form a carpet structure. "Via formation of such a shield, bacteria and chloroplasts protect their membranes under certain stress conditions," stated Professor Dirk Schneider, head of the Membrane Biochemistry section at the JGU Department of Chemistry.

The biochemist and his team have examined the protein IM30, i.e., the inner membrane-associated protein having a mass of approximately 30 kilodaltons. Previous studies have already shown that the IM30 protein is involved in the formation and preservation of membranes in photosynthetic cells. Without IM30, the amount of thylakoid membranes, in which the photosynthetic light reaction occurs, decreases, ultimately resulting in cell death. The hitherto unknown molecular mechanism of membrane stabilization has now been observed and revealed in detail. The results of this collaborative research project have recently been published in the Nature journal Communications Biology.

Atomic Force Microscopy (AFM) reveals ring disassembly and carpet formation

"For quite some time now, we were well aware that IM30 is somehow related to stress. However, we did not know how exactly these proteins manage to protect the cells on a molecular level", explained Schneider. Employing biochemical and biophysical methods in cooperation especially with Professor Stefan Weber of the Max Planck Institute of Polymer Research in Mainz and Professor Eva Wolf of the Institute of Molecular Biology (IMB), the mystery was finally solved. Using atomic force microscopy, the scientists were able to observe how the ring structures disassemble and form carpets on membrane surfaces. "For the very first time we were able to visualize the neat IM30 structure on the surface of membranes," said Schneider.

Intrinsically disordered proteins have important functions

IM30 belongs to the group of intrinsically disordered proteins, which have shifted into the focus of science in recent years. When IM30 binds to the membrane, it unfolds in half - which makes it particularly complicated to study. The traditional understanding of proteins has been based on the assumption that their function is associated with its structure and that disordered structures more or less take over no function. "It is now becoming increasingly clear that disordered protein regions can be involved in defined interactions", stated Schneider as to the classification of the results in a large-scale context.

The study defines the thus far enigmatic structural basis for the physiological function of IM30 and related proteins, including the phage shock protein A (PspA), the main representative of the protein family to which IM30 belongs. It also "highlights a hitherto unrecognized concept of membrane stabilization by intrinsically disordered proteins," stated the authors in the Communications Biology paper. In fact, self-organization of proteins on membrane surfaces, resulting in membrane-covering protein structures, has already been observed before, for example in Alzheimer's or Parkinson's disease. In these cases, however, the result is membrane destabilization. In contrast, the protective protein carpet formed by IM30 results in membrane stabilization.

"Our discovery now answers the long-standing question as to how exactly the protein protects the membrane. This, however, raises new questions, for example how the individual proteins exactly interact on the membrane surface and form the carpet," said Schneider about the research now planned.

Residents of U.S. counties with more social connections (measured as Facebook friends) to China or Italy - the first countries to report major COVID-19 outbreaks - were more likely to adhere to social distancing restrictions at the onset of the pandemic, according to a new study. The findings suggest that social networks supplied pandemic-related information that significantly influenced individual behavior. However, social ties also could have negative effects on pandemic-related behavior. For instance, areas within the U.S. with more connections to counties with low education levels, high proportions of 2016 Trump voters, and high fractions of people who deny the existence of climate change experienced less adherence to mobility restrictions during the early pandemic. Previous research suggests online social connections may act as warning systems during natural disasters and can impact personal health decisions by spreading both facts and misinformation. To explore the role of these connections in the context of COVID-19-era social distancing, Ben Charoenwong and colleagues measured social connectedness between U.S. counties and foreign countries using aggregated, anonymized data from Facebook's Social Connectedness Index. The researchers combined this data with anonymized, county-level mobile phone location data that served as a proxy for adherence to social distancing measures between February 1 and March 30, 2020. They found that a one-standard-deviation increase in social connections with China or Italy correlated with a nearly 50% increase in the effectiveness of mobility restrictions. The authors also conclude that differences in how effectively Democrats and Republicans adhere to social distancing arise from discrepancies in the information they receive (facilitated by their social connections) rather than due to biases in how they interpret that information. "This finding has important policy implications, as it suggests changes in the information environment can boost the effectiveness of non-pharmaceutical interventions," the authors write.

LA JOLLA, CA--Through intricate experiments designed to account for sex-specific differences, scientists at Scripps Research have collaborated to zero in on certain changes in the brain that may be responsible for driving alcohol abuse among people with post-traumatic stress disorder, or PTSD.

In studies with rodents, researchers found that males and females exhibit their own distinct symptoms and brain features of PTSD and alcohol use disorder. Such differences are not typically accounted for in laboratory-based studies yet could lead to more successful clinical treatments.

The findings, published in Molecular Psychiatry, also present a new model for identifying biomarkers that may indicate a person with PTSD is more likely to develop alcohol use disorder.

"Having PTSD significantly increases the risk of developing alcohol use disorder, as individuals use alcohol to cope with stress and anxiety. Yet the underlying biology of comorbid disorders is generally not well understood," says Dean Kirson, PhD, a postdoctoral fellow in neurophysiology in the lab of professor Marisa Roberto, PhD, and a co-lead author with Michael Steinman, PhD. "We hope our new knowledge of sex-specific changes in the brain will help propel the development of more targeted treatments."

About 7 percent to 8 percent of the country's population will have PTSD at some point in their life, according to the U.S. Department of Veterans Affairs. Causes include combat exposure, physical abuse, an accident or other forms of trauma. Alcohol abuse disorder is also common, affecting some 15 million people in the United States. Those with stress and anxiety disorders such as PTSD are not only more likely to abuse alcohol, but also have increased alcohol withdrawal symptoms and relapse risk.

"Most people know or will know someone struggling with one or both of these disorders and may try to help them. However, there are very few effective treatments currently," Roberto says. "Both are complex disorders that affect similar brain circuitry. My lab has been studying addiction and stress separately, so here we teamed up with the Zorrilla lab to apply a novel translationally-relevant behavioral model to examine what changes occur when these disorders are comorbid."

The joint study between Roberto and Eric Zorrilla, PhD--who are co-senior authors--examined behavior, sleep patterns, inflammatory immune responses and levels of a neurotransmitter known as GABA (short for gamma-Aminobutyric acid), which lowers anxiety and increases feelings of relaxation and is a common feature of alcohol dependence.

For both male and female rats, traumatic stress and alcohol exacerbated other behaviors common in PTSD, such as social avoidance startle reactions and defensive behavior. Those who were identified as "drinking-vulnerable" prior to trauma most strongly showed avoidance of trauma-reminiscent places.

However, the scientists noted key differences in how males and females behave following trauma and saw markedly different patterns of GABA signaling. For example, males showed increased GABA receptor function, while females showed increased GABA release.

"This may be important because there is growing awareness that medicines could potentially have different levels of effectiveness in male and female patients and understanding the biology that explains why these differences exist could improve outcomes," Steinman says.

The team also found that males exhibited an immune-based biomarker--small proteins known as cytokines, which are secreted by immune cells--that determined vulnerability to alcohol use disorder. The females did not.

"We identified profiles of specific cytokines, many not previously linked to stress behaviors, that strongly related to poor drinking outcomes," says Zorilla, associate professor

In the Department of Molecular Medicine. "These may be important clinically or even mechanistically, but they were unique to males, so we have work ahead of us to find similar biomarkers for females."

The Roberto and Zorrilla labs plan to conduct additional research into the mechanisms behind the biological changes they observed and test which brain systems can be targeted to treat both PTSD and alcohol abuse.

"We also plan to further investigate the role of the immune system in these disorders," Roberto says. "These distinct biomarkers may aid in targeted treatment."

LA JOLLA, CA--A team led by scientists at Scripps Research has developed a theoretical approach that could ease the process of making highly complex, compact molecules.

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.

BOSTON - For the first time, researchers have successfully created airway basal stem cells in vitro from induced pluripotent stem cells by reprogramming blood cells taken from patients. Given that airway basal cells are defined as stem cells of the airways because they can regenerate the airway epithelium in response to injury, this study may help accelerate research on diseases impacting the airway, including COVID-19, influenza, asthma and cystic fibrosis. Led by researchers at the Center for Regenerative Medicine at Boston Medical Center and Boston University (CReM), in collaboration with The University of Texas Health Science Center at Houston (UTHealth), these findings represent a critical first step towards airway regeneration, which will advance the field of regenerative medicine as it relates to airway and lung diseases.

Published in Cell Stem Cell, the novel study outlines how to efficiently generate and purify large quantities of airway basal stem cells using patient samples. This allows for the development of individual, disease-specific airway basal stem cells in a lab that can be used to develop disease models, which may ultimately lead to drug development and a platform in which targeted drug approaches can be tested. The study's findings and cells will be shared freely given the CReM's "Open Source Biology" philosophy, or sharing of information and findings that will help advance science across the globe.

"Simply put, we have developed a way to reproduce patient-specific airway basal cells in the lab, with the ultimate goal of being able to regenerate the airway for patients with airway diseases," said Finn Hawkins, MB, BCh, a pulmonologist and physician-scientist at Boston Medical Center, principal investigator in the CReM and the Pulmonary Center and the study's first author.

"These results could lead to a better understanding, and therefore treatments for, a variety of airway diseases," said Shingo Suzuki, PhD, co-first author and post-doctoral researcher at UTHealth. For example, cystic fibrosis is caused by a genetic mutation that is present in all of the airway cells. "If we could make pluripotent stem cells using a sample from a patient who has cystic fibrosis, correct the mutation and replace the defective airway cells with corrected airway basal cells that are otherwise genetically identical, we might eventually be able to cure the disease, and other diseases in the future using this same technology," added Hawkins.

Induced pluripotent stem cells are the master stem cells that can produce any cell or tissue in the human body. They are created by reprogramming a human sample, such as a drop of blood, into a population of cells that are similar to embryonic stem cells, including the ability to form different cell types within organs. For this study, the researchers established methods to generate an airway stem cell population, basal cells in the laboratory. These are an important cell type in human airways that maintain the lining of cells in the airway, including the cells the make mucus and those that propel the mucus upwards and out of the lungs.

The researchers first engineered induced pluripotent stem cells with a genetic sequence encoding a fluorescent protein that would allow them to visualize, track and purify basal cells if present. Then, the researchers turned to studies of the embryo and prior work in this field to determine how basal form as the lungs develop. By manipulating induced pluripotent stem cells with a series of steps aimed to simulate what happens during lung development the researchers successfully generated cells that were highly similar to human airway basal cells in terms of their appearance, the genes they expressed and most importantly, their ability to both proliferate and form the other cell types of the airway. The cells, termed ibasal cells, were able to regenerate an airway in vivo using a rodent trachea model.

The resulting ibasal cells, made from patients with a variety of lung diseases, were also able to model the airway diseases affecting those patients, including the mucus metaplasia that is characteristic of asthmatic airways, the chloride channel dysfunction that causes cystic fibrosis, and the defects in beating of the cilia that causes the disease primary ciliary dyskinesia. This approach will enable future opportunities to study these genetic changes, and how to reverse them in order to cure the disease in humans. From a practical perspective, ibasal cells grow well in special culture conditions in a lab, allowing them to be made in large numbers, and patient specific basal cells can be grown, frozen for future work, and shared with the broader research community.

"We demonstrated the potential of these ibasal cells to model both human development and disease, providing evidence of their capacity to regenerate airway epithelium," said Hawkins, who is also an assistant professor of medicine at Boston University School of Medicine. "We expect this will be a significant breakthrough and will contribute to new insights and treatment options for airway diseases, as our results have overcome several important hurdles currently limiting progress in the field."

A new method for verifying a widely held but unproven theoretical explanation of the formation of stars and planets has been proposed by researchers at the U.S. Department of Energy's (DOE) Princeton Plasma Physics Laboratory (PPPL). The method grows from simulation of the Princeton Magnetorotational Instability (MRI) Experiment, a unique laboratory device that aims to demonstrate the MRI process that is believed to have filled the cosmos with celestial bodies.

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."

The CRISPR Journal announces the publication of its October 2020 issue. The Journal is dedicated to validating and publishing outstanding research and commentary on all aspects of CRISPR and gene editing, including CRISPR biology, technology, and genome editing, and commentary and debate of key policy, regulatory, and ethical issues affecting the field. The Journal, led by Editor-in-Chief Rodolphe Barrangou, PhD (North Carolina State University) and Executive Editor Dr. Kevin Davies, is published bimonthly in print and online. Visit The CRISPR Journal website for more information.

This press release is copyright Mary Ann Liebert, Inc. Its use is granted only for journalists and news media receiving it directly from The CRISPR Journal. For full-text copies of articles or to arrange interviews with Dr. Barrangou, Dr. Davies, authors, or members of the editorial board, contact Kathryn Ryan at the Publisher.

1. Heritable Human Genome Editing: The Community Responds
In September 2020, a major report -- Heritable Human Genome Editing (HHGE) -- was published by the National Academies of Sciences and the UK's Royal Society. The report, triggered by the outrage that accompanied the news of the birth of genetically edited "CRISPR babies" in 2018 -- outlined a narrow translational pathway for the safe, responsible use of human embryo editing.

In this multi-author Perspective, The CRISPR Journal invited 50 experts from the world of genetics, CRISPR, bioethics, law and other areas to share their personal reactions to the HHGE report. Three dozen offered candid comments, which have been collated into this Perspective. Among the experts offering their reactions are Nobel laureate Jennifer Doudna, Art Caplan, George Church, Eric Topol, Bob Cook-Deegan, Laura Hercher, Kiran Musunuru, Hank Greely, David Liu, and Feng Zhang. While many applaud the findings of the HHGE commission, several recurring reservations were documented, including lack of ethical considerations, societal consensus, health disparities, and regulatory questions.

Contact: Kevin Davies (The CRISPR Journal)

2. Global Regulation and Policy Landscape of HHGE
In an original research article, Marcy Darnovsky, Francoise Baylis, and colleagues present the most comprehensive survey to date of global laws and regulations regarding hereditary human genome editing (HHGE). The authors surveyed 106 countries, gathering policy documents from 96 of them pertaining to regulations or guidelines for the use of genome editing on early-stage human embryos (or gametes).

Most countries do not have policies that specifically address the use of genetically modified in vitro embryos in laboratory research. 23 countries prohibit this research while 11 permit it. Meanwhile, the authors found that 75 of the 96 countries prohibit the use of heritable genome editing (five countries provide certain exceptions). No country explicitly permits HHGE.

Contact: Marcy Darnovsky (Center for Genetics and Society, Berkeley CA) and Francoise Baylis (Dalhousie University, Nova Scotia, Canada)

3. A Pathway for HHGE: An Interview with Dame Kay Davies
Last month, the National Academies/Royal Society commission on Heritable Human Genome Editing (HHGE), co-chaired by two eminent geneticists, Rockefeller University president Rick Lifton and University of Oxford professor Dame Kay Davies, issued its long-awaited report on the path forward for HHGE.

In an exclusive interview in this issue of The CRISPR Journal, commission co-chair Dame Kay Davies offers a glimpse behind the scenes as she discusses how the commission's report was produced. She summarizes the chief recommendations and addresses some of the chief regulatory and ethical concerns that have been raised. (The full interview can be heard as Episode 17 of Guidepost, The CRISPR Journal's flagship podcast series.)

Contact: Kay E. Davies (University of Oxford)

MIAMI--As the world enters a next wave of the ongoing COVID-19 pandemic, we are aware now more than ever of the importance of a healthy immune system to protect ourselves from disease. This is not only true for humans but corals too, which are in an ongoing battle to ward off deadly diseases spreading on a reef.

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 man-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.

Plant biology researchers at the University of Illinois and computer scientists at the University of California Irvine have developed a new method of fossil pollen identification through the combination of super-resolution microscopy and machine learning. The team, led by Dr. Surangi Punyasena and Ms. Ingrid Romero (associate professor and graduate student in Plant Biology, respectively), developed and trained three convolutional neural network models to identify fossil pollen specimens from an unknown group of legumes.

"The global fossil pollen record is one of the most abundant terrestrial records that we have," said Punyasena. "It's the record that preserves the history of environmental and ecosystem change for the last 470 million years." The pollen record is crucial for understanding how plant species evolved and dispersed globally. By reconstructing how different ecosystems and species have changed through time, we can better understand current plant relationships and better inform conservation and climate mitigation efforts.

However, correctly measuring and identifying the morphological features of a pollen grain can be incredibly difficult. "Much of the palynological record doesn't have biological identifications associated with it," explained Punyasena. "Many of the types that we know from deeper time (beyond the last 100 thousand years or so) are groups for which we don't have a definitive sense of their identity. The effort needed to classify these types has just been too great."

Traditional methods such as scanning electron and transmission electron microscopy destroy the sample and are very labor- and time-intensive. Airyscan, by comparison, is a light microscopy method that can see below the diffraction limit of light and can be used to non-destructively collect cross-sectional images from inside and outside of the pollen grain. "This method is very useful for samples that are not abundant," said Romero. "You can mount the grains on a slide and image them efficiently without damaging the sample."

This new approach allows researchers to train machine classification models using pollen from living plants and then confirm their fossil relatives, iteratively learning from each identification to differentiate among specimens that closely resemble one another. This allowed the team to recognize genera within a larger morphological grouping of fossil legume pollen for the first time. The trained models classified fossil specimens from western Africa and northern South America dating back to the Paleocene (66-56 million years ago), Eocene (56-34 million years ago) and Miocene (23-5.3 million years ago). The most accurate model used a combination of images from both the exterior and interior of the pollen grain and was able to correctly identify samples with 90.3% accuracy.

These results suggest that Airyscan microscopy and machine learning methods could not only aid in identification of unknown specimens, but also help to constrain the time of a plant group's origin or extinction. With more information about the relationships and distribution of pollen samples in deep time, researchers can better pinpoint when and where evolutionary changes occurred.

"We have seen a huge improvement in imaging capabilities and the power of computer vision algorithms. We have gotten to the point where these algorithms can interpret complex images in a very efficient and intelligent way, giving us usable identifications. That is the key difference and innovation of these models - it's the ability to train a system on pristine modern taxa and then use that system to identify unknown and often physically distorted fossil types," said Punyasena. "This approach replicates and extends the abilities of the human analyst."