Culture

In human cells, the nucleus is enclosed by a structure called the nuclear pore complex (NPC). It acts as a 'gatekeeper' controlling the transport of molecules between the nucleus and the surrounding cytoplasm (the protein-containing solution in the inside of a cell). The NPC consists of proteins known as nucleoporins; some of these, the so-called FG-NUPs, belong to the class of intrinsically disordered proteins (IDPs) and capable of forming liquid-?liquid phase separation (LLPS), lacking a well-defined tertiary structure (that is, a particular 3D shape). Although a lot is known about FG-NUPs, a thorough understanding of how their structure varies in time and space has been missing. But now, by applying high-speed atomic force microscopy (HS-AFM), Richard Wong from Kanazawa University and colleagues provide much-needed insights into the spatiotemporal structure of FG-NUPs.

The technique used by the researchers, HS-AFM, is typically used for imaging surfaces. A tiny cantilever is made to move over the surface; at any given time, the force experienced by the cantilever probe can be converted into a height measure. A scan of the whole surface then results in a height map of the sample. By repeatedly scanning the surface rapidly, a video of its evolving structure is obtained. Applying HS-AFM to FG-NUPs, Wong and colleagues were able to measure several of the molecules' properties, including the extension velocity of FG-NUP filaments (thread-like protruding structures), their bending angles and how they form knots.

The scientists studied FG-NUPs in normal colon cells and in colorectal cancer cells and organoids. They found that the former displayed less conformational dynamics. A particularly interesting conclusion is that in colon cancer cells, the structure of the so-called central plug is smaller, and cannot develop filamentous features as easily as in normal cells, a finding with high clinical relevance.

The results of Wong and colleagues regarding the central plug are very important and timely, as its morphology and function have been the subject of debate. The researchers now provide strong evidence that the central plug at least partially consists of FG-NUPs.

Apart from demonstrating that HS-AFM is a tool capable of visualizing FG-NUP filament motion in real time, another implication of the work of the scientists is "that bio-recycled nanomaterials [like NPC nanopores] ... have biocompatible advantages ... directly derived from cells and organoids, rather than other engineered nanomaterials [like e.g. carbon nanotubes, which may induce tumors and related pathologies] opening a new avenue for nano-tissue engineering."

[Background]

Nuclear pore complex

The nucleus of a cell is of key importance to any organism. It stores and organizes genetic information (DNA) in a way separating it from other cellular components in the surrounding cytoplasm. The nuclear pore complex (NPC), a very large protein complex dressed around the nucleus, is the 'gatekeeper' in the exchange of molecules between the nucleus and the cytoplasm; it lets material pass that should reach the nucleus and blocks material that should not. This communication can happen because of pores in the NPC, structures built from proteins known as FG-NUPs. FG-NUPs do not have well-defined shapes; instead, they vary in time and space. By applying a technique called high-speed atomic force microscopy, Richard Wong from Kanazawa University and colleagues have now provided new, valuable insights into the spatiotemporal structure of FG-NUPs of both normal and cancer cells.

Atomic force microscopy

Atomic force microscopy (AFM) is an imaging technique in which the image is formed by scanning a surface with a very small tip. Horizontal scanning motion of the tip is controlled via piezoelectric elements, while vertical motion is converted into a height profile, resulting in a height distribution of the sample's surface. As the technique does not involve lenses, its resolution is not restricted by the so-called diffraction limit. In a high-speed setup (HS-AFM), the method can be used to produce movies of a sample's structural evolution in real time. Wong and colleagues have successfully used HS-AFM to study the dynamics of FG-NUPs, proteins playing a key role in the transport-regulating function of the nuclear pore complex situated between a cell's nucleus and the surrounding cytoplasm.

Vortex is ubiquitous in nature including spiral arms of galaxy, planet rotation, hurricane (tornado). A vortex is a typical and well-known magnetic domain structure in dimensionally confined nanostructures with a symmetry determined by its polarity and circulation. Reversible control of low-dimensional spin structures at nanoscale with low energy consumption is highly desirable for future applications of spintronic devices. Especially, magnetic vortex at nanoscale has been explored for the next-generation data-storage devices.

For the past decades, magnetic field and spin-polarized current have been employed to flip the core and/or reverse circulation of vortex. However, the electric-field deterministic control of a magnetic vortex, which offers much higher storage density and much lower power consumption, is challenging due to the absence of planar magnetic anisotropy of the spin structure.

Chinese researchers discover a deterministic reversal of magnetic vortex circulation in a Ni79Fe21 (NiFe) island on top of a layered-perovskite Bi2WO6 (BWO) thin film using an electric field. The space-varying strain from BWO film under a bi-axial planar electric field drives the magnetic vortex circulation reversal in this magnetoelectric device. Phase-field simulation directly reveals the mesoscale dynamic reversal mechanism: the traveling strain drags the vortex core from its center to the edge of the NiFe island, then a new core emerges with opposing vortex circulation, leading to the vortex circulation reversal.

This study provides a new framework to deterministically manipulate nanoscale chiral spin texture (vortex, skyrmions etc.) with ultralow-energy consumption. Especially in physical mechanism research, it revealed new magnetoelectric coupling mechanism for more efforts to realize the electric-field control of order parameters (charge, spin and orbital) in functional thin film devices in future.

A new study of prospective teachers finds that they are more likely to interpret the facial expressions of Black boys and girls as being angry, even when they are not. This is significantly different than how the prospective teachers interpreted the facial expressions of white children.

The authors coined the term "racialized anger bias" after an earlier study found similar results in prospective teachers' judgments of Black and white adults. These new results indicate there is also racialized anger bias against Black children.

"Racialized anger bias means that people are seeing anger where none exists," says Amy Halberstadt, corresponding author of the study and a professor of psychology at North Carolina State University. "We saw this happening to Black adults in earlier research. Now this finding highlights the urgent need to address conscious and unconscious bias in educators.

"The level of bias we found here could have significant adverse effects on children in classrooms. We already know that Black students experience many more suspensions, expulsions and disciplinary actions than white students, often for the same behavior. And this study suggests that misperceiving anger - even at an unconscious level - could play a significant role in that disparity."

For the study, the researchers surveyed 178 prospective teachers from three teacher training programs in the Southeast. Eighty-nine percent of the study participants were women, and 70% of the participants were white. The overall composition of the group was consistent with the composition of public school teachers in the United States.

The prospective teachers were shown 72 short video clips of child actors' facial expressions, with each one displaying a different emotion. The video clips were divided equally between Black and white students and between boys and girls. The prospective teachers were asked to identify the emotion being displayed in each clip. The researchers were interested in the errors that were made, especially about perceiving anger when there was none.

Each video clip was carefully examined to ensure it included only the requested emotional expression and to be certain that no anger expression was slipping into other expressions being made. The prospective teachers were also asked to answer a series of questions designed to assess each participant's explicit racial biases and implicit - or subconscious - biases.

The study found that participants were 1.36 times more likely to exhibit racialized anger bias against Black children than against white children, meaning that they were that much more likely to incorrectly view a Black child as angry when the child was not actually making an angry facial expression. For boys, participants were 1.16 times more likely to mistake a Black boy's facial expressions for anger than a white boy's. Participants were 1.74 times more likely to mistake a Black girl's facial expression for anger than a white girl's.

"Although never statistically examined before, the misperceptions of Black girls' anger verifies qualitative research of Black girls' and women's experiences, that they too are seen as angry when they are not," Halberstadt says.

The researchers found that higher levels of explicit or implicit bias did not increase the likelihood of a prospective teacher exhibiting racial anger bias against Black children. However, higher levels of explicit or implicit bias did make it less likely that study participants would view White children as being angry.

"Essentially, we found that prospective teachers are more likely to view Black children as being angry, even when they're not," Halberstadt says. "And the more biased prospective teachers were, the more likely those prospective teachers were to give White children the benefit of the doubt. In other words, if the teacher had higher levels of explicit or implicit racial bias, they were a bit more likely to give white kids a 'free pass.'

"This study suggests anger bias against Black children is alive and well among future teachers, and might play a role in the disciplinary discrepancies we see in schools. As this seems to be another form of systemic racism, we need to find meaningful ways to address this type of bias. Otherwise we are doing a disservice to our kids."

New Orleans, LA - Researchers at LSU Health New Orleans Neuroscience Center of Excellence and colleagues have discovered a new class of pipeline drugs to relieve pain and reduce fever without the danger of addiction or damage to the liver or kidneys. The research is published online in the European Journal of Medicinal Chemistry.
Current drugs have unwanted side effects. Opioids can not only cause addiction; recent studies have shown they can be no more effective at relieving pain than non-narcotic drugs. Non-steroidal anti-inflammatories (NSAIDs) can cause kidney damage. Acetaminophen is an effective drug, but overuse can result in liver damage.

The research team, led by Drs. Hernan A. Bazan, a professor in the Department of Surgery and Program Director of the Vascular Surgery Fellowship at Ochsner Clinic, and Surjyadipta Bhattacharjee, a post-doctoral researcher at the LSU Health New Orleans Neuroscience Center of Excellence, set out to discover what causes the liver damage associated with acetaminophen and then create a drug structurally similar to acetaminophen -- as effective, but without liver toxicity. Along with the chemistry team led by Professor Julio Alvarez-Builla, Department of Organic Chemistry at the University of Alcala in Madrid, they tested 21 different compounds as acetaminophen analogs.

Senior author Nicolas Bazan, MD, PhD, Boyd Professor and Director of LSU Health New Orleans Neuroscience Center of Excellence says, "The new chemical entities reduced pain in two in models without the liver and kidney toxicity associated with current over-the-counter analgesics that are commonly used to treat pain -- acetaminophen and NSAIDs. They also reduced fever in a pyretic model. This is particularly important in the search for an antipyretic with a safer profile in the COVID-19 pandemic and its associated kidney and liver disease in critically ill SARS-CoV-2 patients."

Acute and chronic pain management is one of the most prevalent and costly public health issues worldwide. According to the Centers for Disease Control and Prevention, an estimated 50 million -- 20.4% of U.S. adults had chronic pain and 8.0% of U.S. adults had high-impact chronic pain in 2016.

"Given the widespread use of acetaminophen, the risk of hepatotoxicity with overuse, and the ongoing opioid epidemic, these new chemical entities represent novel, non-narcotic analgesics that exclude hepatotoxicity, for which development may lead to safer treatment of acute and chronic pain and fever," adds Dr. Nicolas Bazan.

Other LSU Health New Orleans members of the research team included William C. Gordon, PhD, Professor of Neuroscience and Ophthalmology; Dennis Paul, PhD, Professor of Pharmacology; Scott Edwards, PhD, Associate Professor of Physiology and Neuroscience; Bokkyoo Jun, PhD, Research Instructor; and Amanda R. Pahng, PhD, a post-doctoral fellow in Dr. Edwards' lab. The research team also included Drs. Carolina Burgos, Javier Recio, and Valentina Abet, at the University of Alcala in Madrid; Jessica Heap, a third-year medical student at the Tulane University School of Medicine and Alexander Ledet, a first-year MD/PhD candidate at the Albert Einstein College of Medicine in New York.

The intellectual property behind these new technologies, which are part of this discovery, have been licensed from LSU Health Sciences Center New Orleans to the life science startup South Rampart Pharma, LLC that is currently developing this new drug in late pre-clinical stages. Drs. Hernan A. Bazan, Carolina Burgos, Dennis Paul, Julio Alvarez-Builla, and Nicolas G. Bazan are named inventors on a patent assigned to LSU Health Sciences Center describing the synthesis and characterization of the novel non-hepatotoxic acetaminophen analogs (PCT/US2018/022029). The company expects to file the first FDA IND (Investigational New Drug) application by early third quarter 2020.

"Our primary goal is to develop and commercialize new alternative pain medications that lack abuse potential and have fewer associated safety concerns than current treatment options, and this peer-reviewed paper describes the discovery of the initial library of compounds as well as several proof of concept animal and molecular studies," says Dr. Hernan Bazan.

Tiny eye movements can be used as an index of humans' ability to anticipate relevant information in the environment independent of the information's sensory modality, a team of scientists has found. The work reveals a connection between eye movements and the sense of touch.

"The fact that tiny eye movements can hinder our ability to discriminate tactile stimuli, and that the suppression of those eye movements before an anticipated tactile stimulus can enhance that same ability, may reflect that common brain areas, as well as common neural and cognitive resources, underlie both eye movements and the processing of tactile stimuli," explains Marisa Carrasco, a professor of psychology and neural science at New York University and the senior author of the paper, which appears in the latest issue of the journal Nature Communications.

"This connection between the eyes and touch reveals a surprising link across perception, cognition, and action," adds Stephanie Badde, an NYU post-doctoral researcher and first author of the paper.

The study asked human participants to distinguish between two kinds of vibrations ("fast" - high frequency vs. "slow" - low frequency) that were produced by a device connected to their finger. The researchers then tracked even the tiniest of their involuntary eye movements, known as micro-saccades. These small, rapid eye-movements are known to occur even when we try to fixate our gaze on one spot. Here, participants were instructed to focus their vision on a fixation spot on a computer screen. A cue--a tap elicited by the device at their finger--would announce the next imminent vibration. What the participants did not know is that the time interval between that cue and the tactile vibration was a central part of the experimental design.

The manipulation of that interval allowed participants in some blocks to predict with more accuracy precisely when the vibration would happen. Notably, when they had that precise information, the researchers could see not only how the participants' microsaccade rates would decrease just before the vibration stimulus, but also how their ability to distinguish between fast and slow vibrations was enhanced by the suppression of micro-saccades.

The microbial composition of the intestines is complex and varies widely from one individual to another. Many factors such as environmental factors, lifestyle, genetics or illnesses affect the intestinal ecosystem of helpful gut bacteria.

Dirk Haller, Professor for Nutrition and Immunology at TUM, and his team have examined the importance of daytime-dependent fluctuations of the gut microbiome in relation to type 2 diabetes; they present their study encompassing more than 4000 people and it is the first study in this field based on a large prospective human cohort.

The relationship between gut bacteria and medical conditions

"In order to see whether changes in the gut microbiome allow conclusions about medical conditions, so-called prospective cohort studies are required," explained Prof. Haller.

In these prospective cohort studies, a cross section of the population is being observed; however, none of the participants showed any signs of disease. This population is being re-examined over time. This way, researchers can find out whether a certain observation may be typical for future occurrences of diseases.

Diagnosis and outlook of type 2 diabetes may be improved

"When certain gut bacteria do not follow a day-night rhythm, so if their number and function does not change over the course of the day, this can be an indicator for a potential type 2 diabetes disease. Knowing this can improve diagnosis and outlook of type 2 diabetes," said Chronobiologist Dr. Silke Kiessling, another contributor to the study.

These arrhythmic bacteria - those that are not changing between day and night - are a marker for potential disease. Researchers refer to this as a risk signature. "Mathematical models also show that this microbial risk signature consisting of arrhythmic bacteria helps diagnosing diabetes," explained Sandra Reitmeier, first author on the study.

Primarily, the scientists analyzed data from an existing independent cohort by Helmholtz Zentrum München. The diabetes-related results were validated using additional cohorts from Germany. "By comparing our data to cohorts in England, we could confirm that there is - among other things - a strong regional factor affecting the microbial ecosystem. Therefore, there is a demand for finding locally specified arrhythmic risk signatures," elaborated Haller.

Nutritionist Haller emphasizes that "apart from bacteria and their variations over the course of the day, other parameters such as the body mass index play a role in being able to better predict a person's future medical conditions."

Intestinal bacteria's day and night rhythm as starting point for further research

Registering the time of day when taking human fecal samples for research purposes can heavily influence disease diagnostics. "Documenting these timestamps is essential for improving risk markers," Prof. Haller emphasizes.

This research substantiates the hypothesis that changes in the microbiome have an effect of nutrition-related diseases. How gut bacteria changing (or not changing) during the day affect other microbiome-associated diseases such as Crohn's disease or intestinal cancer may be subject to further scientific examination.

The results of this study are of particular importance for further work in the Collaborative Research Center of "Microbiome Signatures" (https://www.sfb1371.tum.de/), as cohort studies offer valuable possibilities of comparing data of healthy and ill subjects, particularly in the context of clinical studies.

A team of Skoltech researchers from the Severinov laboratory and their colleagues have identified the way in which a component of a two-part bacterial self-defense system from the toxin-antitoxin family works, leading to cell dormancy that helps fight off bacterial viruses, antibiotics and other insults.

Toxin-antitoxin systems are a class of multipurpose mechanisms that bacteria can use, among other things, against phage infections. Two adjacent genes encode two proteins, a toxin disrupting various cellular processes and an antitoxin that inhibits the toxin's activity. Much like Fluffy the three-headed dog from the Harry Potter series, the toxin is "dormant" while the music is playing (i.e. while the antitoxin is present), but under stress conditions -- say, when a bacteriophage attacks -- the antitoxin is no longer produced and the toxin is "unleashed", disrupting protein synthesis needed for viral replication.

"Toxin-antitoxin systems are very widespread in bacteria, and many people tried to answer what their raison d'être is, why they exist. The answer appears to be elusive, and the story of assigning biological function to these systems is full of drama, retraction of papers and the like. The answer may be the childish "just because": they may be selfish elements concerned with their own propagation more than with the well-being of the cell, which, however, does not make these systems less interesting to study or reduce the knowledge about their function to practice," says Konstantin Severinov, Skoltech professor and a coauthor of the paper.

There are various types of toxin-antitoxin systems, which are classified depending on how exactly the antitoxin blocks the toxin. Though thousands of these pairs have been predicted with the help of bioinformatics, only a handful has been thoroughly characterized. Many toxins are ribonucleases that degrade RNA, but some have different activities.

A team of researchers led by Severinov and Svetlana Dubiley of Skoltech Centre for Life Sciences studied AtaT2, a representative of a rare class of toxins called GNAT (for Gcn5-related N-acetyltransferase). They show that this toxin disrupts translation, or the synthesis of proteins by the ribosome, by targeting transfer RNAs for glycine, a common protein-building amino acid.

The scientists modified E. coli to express the toxin-antitoxin system genes on demand and then conducted in vivo tests to determine how the toxin works by observing the behavior of intoxicated cells. They also performed in vitro analysis and, by combining the two, found that the toxin interferes with translation by stalling ribosomes at the glycine codons in the protein encoding sequence, so that most of them are unable to complete the process and build a protein.

Interestingly, the antitoxin counterpart of AtaT2 does not have any glycyl residues for the toxin to target, so its synthesis is unaffected by the toxin. The researchers speculate that this might be a built-in feedback loop preventing too much AtaT2 from being produced and helping cells recover from its toxic action.

If the hypothesis about the essentially selfish nature of toxin-antitoxin systems is correct, one can imagine that different systems compete with each other for their hosts, the bacteria they inhabit. If so, the targets of related toxins should diverge with time. The Severinov team hypothesizes that GNAT toxins may thus diversify to target transfer RNAs specific for each of the 20 genetically encoded amino acids.

"If that is true, a panel of such toxins, whatever their biological function may be, can provide a powerful tool to control each of the elemental steps of protein synthesis inside the cell and may lead to development of powerful new antibiotics," Severinov notes.

Liquid droplets formed from DNA display a peculiar response to enzymes. An international collaboration between Ludwig-Maximilians-Universitaet (LMU) in Munich and UCSB has now been able to explain the mechanisms behind bubble formation.

A watched pot never boils ... but researchers from Ludwig-Maximilians University (LMU), Munich, and University of California in Santa Barbara (UCSB) and found that's not the case when watching liquids formed from DNA. Recent advances in cellular biology have found that the molecular components of living cells (such as DNA and proteins) can bind each other and form liquid droplets that appear similar to oil droplets in shaken salad dressing. These cellular droplets interact with other components to carry out basic processes critical to life, yet little is known about how those interactions function. To gain insight into this fundamental process, the LMU/UCSB team used modern methods of nanotechnology to engineer a model system, a liquid droplet formed from particles of DNA, and watched those droplets as they interacted with a DNA-cleaving enzyme.

Surprisingly, they found, in certain cases, addition of the enzyme would cause the DNA droplets to suddenly start bubbling, appearing just like boiling water. „The bizarre thing about the bubbling DNA is that we didn't heat the system--it's as if a pot of water started boiling even though you forgot to turn on the stove," says Professor Omar Saleh from UCSB, co-leader of the project. However, the bubbling behavior didn't always occur--sometimes adding the enzyme would cause the droplets to smoothly shrink away, and it was unclear why one response or the other would occur.

To get to the bottom of this mystery, the team carried out a rigorous set of precision experiments quantifying the shrinking and bubbling behaviors. They found that there were two types of shrinking behavior, the first cause by enzymes cutting the DNA only on the droplet surface, and the second caused by enzymes penetrating inside the droplet. "This observation was critical to unraveling the behavior, as it put it into our heads that the enzyme could start nibbling away at the droplets from the inside", notes co-leader Tim Liedl, Professor at the LMU, where the experiments were conducted.

By comparing the droplet response to the DNA particle design, the team cracked the case: they found that bubbling and penetration-based shrinking occurred together, and only happened when the DNA particles were only lightly bound together, whereas strongly-bound DNA particles would keep the enzyme on the outside. Saleh notes: „It's like trying to walk through a crowd--if the crowd is tightly holding hands, you wouldn't be able to get through."

The bubbles, then, happen only in the lightly-bound systems, when the enzyme can get through the crowded DNA particles to the interior of the droplet, and begin to eat away at the droplet from the inside. The chemical fragments created by the enzyme lead to an osmotic effect, where water is drawn in from the outside, causing a swelling phenomenon that produces the bubbles. The bubbles grow, reach the droplet surface, then release the fragments in a burp-like gaseous outburst. „It is quite striking to watch, as the bubbles swell and pop over and over", says Liedl.

The work demonstrates a complex relationship between the basic material properties of a biomolecular liquid, and its interactions with external components. The team believes the insight gained from studying the bubbling process will lead to both better models of living processes, and enhanced abilities to engineer liquid droplets for use as synthetic bioreactors.

The research was enabled by an award to Professor Saleh from the Alexander von Humboldt Foundation, which enabled him to visit Munich and work directly with Tim Liedl on this project. „These types of international collaborations are extremely productive", says Saleh.

The brain has a high energy demand and reacts very sensitively to oxygen deficiency. Ludwig-Maximilians-Universitaet (LMU) in Munich neurobiologists have now succeeded for the first time in directly correlating oxygen consumption with the activity of certain nerve cells.

The brain requires a disproportionate amount of energy compared to its body mass. This energy is mainly generated by aerobic metabolic processes that consume considerable amounts of oxygen. Therefore, the oxygen concentrations in the brain are an important parameter that influences the function of nerve cells and glial cells. However, how much oxygen is consumed in the brain and how this is related to neuronal activity was so far largely unknown. LMU neurobiologists Hans Straka, Suzan Özugur and Lars Kunz have now succeeded for the first time in directly measuring this in the intact brain and correlating it with nerve cell activity. The scientists report on their results in the journal BMC Biology.

In an already established animal model - tadpoles of the clawed frog Xenopus laevis - the scientists used electrochemical sensors to determine the concentration of oxygen in the brain and in one of the brain ventricles. They were able to specifically control the amount of oxygen available to the brain as well as inhibit nerve cell activity with the help of pharmacological substances. Using the example of nerve cells that control eye movements, the scientists succeeded in directly recording the relationship between oxygen consumption and nerve cell activity. "We have found that the brain is anoxic in a normal air-saturated environment, which means that no oxygen can be measured," says Straka. The complete oxygen was therefore immediately used by the cells to synthesize energy-rich substances. If more than twice the atmospheric oxygen concentration was available, the energy metabolism was saturated and oxygen was abundantly present in the brain. "We were also able to show that during normal operation only about 50 percent of the oxygen is used for nerve cell activity," says Straka. "So the other 50 percent are required for glial cells and for maintaining the basic metabolic rate of nerve cells. However, nerve cells with increased activity consume more oxygen."

In order to better understand how information is processed in the brain, knowledge of the relationship between oxygen availability and brain activity is essential. The scientists' results provide initial insight into this and are an important basis for further investigations of the brain's energy balance in future experiments and for measuring oxygen consumption for various nerve cell functions. This could also be relevant from a medical point of view, for example to better understand the consequences of oxygen deficiency in the brain or to better interpret the information on brain activity obtained with imaging techniques.

The active agents of many drugs are natural products, so called because often only microorganisms are able to produce the complex structures. Similar to the production line in a factory, large enzyme complexes put these active agent molecules together. A team of the Technical University of Munich (TUM) and the Goethe University Frankfurt has now succeeded in investigating the basic mechanisms of one of these molecular factories.

Many important drugs such as antibiotics or active agents against cancer are natural products which are built up by microorganisms for example bacteria or fungi. In the laboratory, these natural products can often be not produced at all or only with great effort. The starting point of a large number of such compounds are polyketides, which are carbon chains where every second atom has a double bound to an oxygen atom.

In a microbial cell such as in the Photorhabdus luminescens bacterium, they are produced with the help of polyketide synthases (PKS). In order to build up the desired molecules step by step, in the first stage of PKS type II systems, four proteins work together in changing "teams".

In a second stage, they are then modified to the desired natural product by further enzymes. Examples of bacterial natural products which are produced that way are, inter alia, the clinically used Tetracyclin antibiotics or Doxorubicin, an anti-cancer drug.

Interdisciplinary cooperation

While the modified steps of the second stage are well studied for many active agents, there have up to now hardly been any insights into the general functioning of the first stage of these molecular factories where the highly reactive polyketide intermediate product is bound to the enzyme complex and protected so that it cannot react spontaneously.

This gap is now closed by the results of the cooperation between the working groups of Michael Groll, professor of biochemistry at the Technical University of Munich, and Helge Bode, professor of molecular biotechnology at Goethe University Frankfurt, which are published in the renowned scientific journal Nature Chemistry.

Findings inspire to new syntheses of active agents

"In the context of this work, we were for the first time able to analyze complexes of the different partner proteins of type II polyketide synthase with the help of X-ray structure analysis and now understand the complete catalytic cycle in detail," Michael Groll explains.

"Based on these findings, it will be possible in the future to manipulate the central biochemical processes in a targeted manner and thus change the basic structures instead of being restricted to the decorating enzymes," Helge Bode adds.

Although it is a long way to develop improved antibiotics and other drugs, both groups are optimistic that now also the structure and the mechanism of the missing parts of the molecular factory can be explained. "We already have promising data of the further protein complexes," says Maximilian Schmalhofer, who was involved in the study as a doctoral candidate in Munich.

Abu Dhabi, UAE, July 6, 2020: As many diseases, including neurodegenerative diseases such as Alzheimer's, have been linked to the defective functioning of motor proteins in cell transport systems, understanding the intricacies of how motor proteins work in their native crowded cell environments is essential to understanding what goes wrong when they function incorrectly. Molecular motors are specialized proteins that bind to a variety of organelles, referred to as cell cargo, and transport them along microtubule filaments (structural proteins commonly referred to as the highway of the cell). Motor proteins often work in groups, binding to one cargo and inching together along the filament's path in the cell.

In the recent study Macromolecular crowding acts as a physical regular of intracellular transport, published in the journal Nature Physics, lead researcher and Assistant Professor of Physics at NYU Abu Dhabi George Shubeita and his team present the findings that in a native cell environment, which is crowded with a high concentration of macromolecules, the crowding significantly impacts the speed of groups of motor proteins, but not singular motor proteins. Motor proteins have been isolated from cells and studied in a laboratory setting, but this is the first time that cargo carried by motor proteins have been studied both in their native cell and in a setting that imitates the crowded cellular environment.

To simulate the crowded nature of cells, bovine serum albumin (a serum concentrated with proteins) was applied to glass slides, in addition to the kinesin motor proteins and microtubule filaments. Utilizing the laser light of optical tweezers to probe the movement of single motors and groups of motors, it was found that in more crowded environments, motors were more likely to fall off the filament when opposed. A group of motors would therefore be set-back each time a singular motor fell from the guideway. Even though groups of motors are shown to slow down in native cell environments, they are commonly used to carry cargo over long distances and overcome hindrances they face in a crowded cell by sharing the load, which singular motors cannot do.

"Our work highlights the balance that regulates the function of motors to achieve a robust transport system within the complex cell," said Shubeita. "Transporting cargoes to where they are needed within the living cell is important for its survival. Molecular motors act as nano-machines that achieve this task with utmost precision, despite the extremely crowded inner works of the cell. By modeling the cell's environment, we have unraveled the details about the behavior of motors in the human body which is essential to understand what goes wrong when motors seize to behave properly in disease."

As dying stars take their final few breaths of life, they gently sprinkle their ashes into the cosmos through the magnificent planetary nebulae. These ashes, spread via stellar winds, are enriched with many different chemical elements, including carbon.

Findings from a study published today in Nature Astronomy show that the final breaths of these dying stars, called white dwarfs, shed light on carbon's origin in the Milky Way.

"The findings pose new, stringent constraints on how and when carbon was produced by stars of our galaxy, ending up within the raw material from which the Sun and its planetary system were formed 4.6 billion years ago," says Jeffrey Cummings, an Associate Research Scientist in the Johns Hopkins University's Department of Physics & Astronomy and an author on the paper.

The origin of carbon, an element essential to life on Earth, in the Milky Way galaxy is still debated among astrophysicists: some are in favor of low-mass stars that blew off their carbon-rich envelopes by stellar winds became white dwarfs, and others place the major site of carbon's synthesis in the winds of massive stars that eventually exploded as supernovae.

Using data from the Keck Observatory near the summit of Mauna Kea volcano in Hawaii collected between August and September 2018, the researchers analyzed white dwarfs belonging to the Milky Way's open star clusters. Open star clusters are groups of up to a few thousand stars held together by mutual gravitational attraction.

From this analysis, the research team measured the white dwarfs' masses, and using the theory of stellar evolution, also calculated their masses at birth.

The connection between the birth masses to the final white dwarf masses is called the initial-final mass relation, a fundamental diagnostic in astrophysics that contains the entire life cycles of stars. Previous research always found an increasing linear relationship: the more massive the star at birth, the more massive the white dwarf left at its death.

But when Cummings and his colleagues calculated the initial-final mass relation, they were shocked to find that the white dwarfs from this group of open clusters had larger masses than astrophysicists previously believed. This discovery, they realized, broke the linear trend other studies always found. In other words, stars born roughly 1 billion years ago in the Milky Way didn't produce white dwarfs of about 0.60-0.65 solar masses, as it was commonly thought, but they died leaving behind more massive remnants of about 0.7 - 0.75 solar masses.

The researchers say that this kink in the trend explains how carbon from low-mass stars made its way into the Milky Way. In the last phases of their lives, stars twice as massive as the Milky Way's Sun produced new carbon atoms in their hot interiors, transported them to the surface and finally spread them into the surrounding interstellar environment through gentle stellar winds. The research team's stellar models indicate that the stripping of the carbon-rich outer mantle occurred slowly enough to allow the central cores of these stars, the future white dwarfs, to grow considerably in mass.

The team calculated that stars had to be at least 1.5 solar masses to spread its carbon-rich ashes upon death.

The findings, according to Paola Marigo, a Professor of Physics and Astronomy at the University of Padova and the study's first author, helps scientists understand the properties of galaxies in the universe. By combining the theories of cosmology and stellar evolution, the researchers expect that bright carbon-rich stars close to their death, like the progenitors of the white dwarfs analyzed in this study, are presently contributing to the light emitted by very distant galaxies. This light, which carries the signature of newly produced carbon, is routinely collected by the large telescopes from space and Earth to probe the evolution of cosmic structures. Therefore, this new understanding of how carbon is synthesized in stars also means having a more reliable interpreter of the light from the far universe.

A new analysis of white dwarf stars supports their role as a key source of carbon, an element crucial to all life, in the Milky Way and other galaxies.

Approximately 90 percent of all stars end their lives as white dwarfs, very dense stellar remnants that gradually cool and dim over billions of years. With their final few breaths before they collapse, however, these stars leave an important legacy, spreading their ashes into the surrounding space through stellar winds enriched with chemical elements, including carbon, newly synthesized in the star's deep interior during the last stages before its death.

Every carbon atom in the universe was created by stars, through the fusion of three helium nuclei. But astrophysicists still debate which types of stars are the primary source of the carbon in our own galaxy, the Milky Way. Some studies favor low-mass stars that blew off their envelopes in stellar winds and became white dwarfs, while others favor massive stars that eventually exploded as supernovae.

In the new study, published July 6 in Nature Astronomy, an international team of astronomers discovered and analyzed white dwarfs in open star clusters in the Milky Way, and their findings help shed light on the origin of the carbon in our galaxy. Open star clusters are groups of up to a few thousand stars, formed from the same giant molecular cloud and roughly the same age, and held together by mutual gravitational attraction. The study was based on astronomical observations conducted in 2018 at the W. M. Keck Observatory in Hawaii and led by coauthor Enrico Ramirez-Ruiz, professor of astronomy and astrophysics at UC Santa Cruz.

"From the analysis of the observed Keck spectra, it was possible to measure the masses of the white dwarfs. Using the theory of stellar evolution, we were able to trace back to the progenitor stars and derive their masses at birth," Ramirez-Ruiz explained.

The relationship between the initial masses of stars and their final masses as white dwarfs is known as the initial-final mass relation, a fundamental diagnostic in astrophysics that integrates information from the entire life cycles of stars, linking birth to death. In general, the more massive the star at birth, the more massive the white dwarf left at its death, and this trend has been supported on both observational and theoretical grounds.

But analysis of the newly discovered white dwarfs in old open clusters gave a surprising result: the masses of these white dwarfs were notably larger than expected, putting a "kink" in the initial-final mass relation for stars with initial masses in a certain range.

"Our study interprets this kink in the initial-final mass relationship as the signature of the synthesis of carbon made by low-mass stars in the Milky Way," said lead author Paola Marigo at the University of Padua in Italy.

In the last phases of their lives, stars twice as massive as our Sun produced new carbon atoms in their hot interiors, transported them to the surface, and finally spread them into the interstellar medium through gentle stellar winds. The team's detailed stellar models indicate that the stripping of the carbon-rich outer mantle occurred slowly enough to allow the central cores of these stars, the future white dwarfs, to grow appreciably in mass.

Analyzing the initial-final mass relation around the kink, the researchers concluded that stars bigger than 2 solar masses also contributed to the galactic enrichment of carbon, while stars of less than 1.5 solar masses did not. In other words, 1.5 solar masses represents the minimum mass for a star to spread carbon-enriched ashes upon its death.

These findings place stringent constraints on how and when carbon, the element essential to life on Earth, was produced by the stars of our galaxy, eventually ending up trapped in the raw material from which the Sun and its planetary system were formed 4.6 billion years ago.

"Now we know that the carbon came from stars with a birth mass of not less than roughly 1.5 solar masses," said Marigo.

Coauthor Pier-Emmanuel Tremblay at University of Warwick said, "One of most exciting aspects of this research is that it impacts the age of known white dwarfs, which are essential cosmic probes to understand the formation history of the Milky Way. The initial-to-final mass relation is also what sets the lower mass limit for supernovae, the gigantic explosions seen at large distances and that are really important to understand the nature of the universe."

By combining the theories of cosmology and stellar evolution, the researchers concluded that bright carbon-rich stars close to their death, quite similar to the progenitors of the white dwarfs analyzed in this study, are presently contributing to a vast amount of the light emitted by very distant galaxies. This light, carrying the signature of newly produced carbon, is routinely collected by large telescopes to probe the evolution of cosmic structures. A reliable interpretation of this light depends on understanding the synthesis of carbon in stars.

BATON ROUGE, LOUISIANA, July 6, 2020--Puerto Rico's population of African-European hybrid honey bees (AHB) are famously known for being much gentler than their continental counterparts. Now Agricultural Research Service (ARS) scientists and their colleagues have found that this reduced defending of the nest is determined by colony-level genetics as opposed to individual bee's DNA, according to a study just published in the Proceedings of the National Academy of Sciences.

The researchers found no significant correlations between individual bees' defensiveness and specific genes. By contrast, they saw strong correlations between a colony's level of defensiveness and how frequently specific genes appeared within the colony.

"It's as if your home environment is a better predictor of how belligerent your temper is than are your individual tendencies in responding to situations. In more scientific terms, for these bees, it is the frequency of the appearance of a gene in the genetic makeup of the colony that is a better predictor than is the genetic makeup of a single bee," explained ARS geneticist Arian Avalos with the Honey Bee Breeding, Genetics, and Physiology Research Unit in Baton Rouge, Louisiana, who led the study.

Defensiveness in honey bees arises from the coordinated actions of colony members, primarily nonreproductive "soldier" bees. Some soldier bees act as guards, patrolling the hive entrance and release alarm pheromones when they encounter an intruder, while other soldiers respond to the alarm by flying out of the hive to sting the intruder. Honey bees die after stinging, so the decision that stinging is called for is a serious one.

"We were also able to winnow down the differences in genetics between aggressive and gentle African-European hybrid honey bees from having to analyze the whole genome to just 256 genes" Avalos said. Honey bees have a total of about 10,000 genes in their genome.

AHB are the descendants of honey bees imported from Africa into Brazil in the 1950s in the hopes of breeding a bee better adapted to the tropics. They instead escaped, interbred with European honey bees (EHB) already present and spread south to Argentina and north into Central America and finally into the United States in only 40 years.

African honey bees, which are a separate sub-species of honey bee distinct from EHB, are best known for their strong, vigorous defense of their nests. In the United States, this behavior has been evident and predominant wherever AHB spread and interbred with EHBs.

AHB arrived to Puerto Rico in 1994 aboard ships carrying cargo like oil pipes from South America and were no gentler than other AHB. However, within a few years of arrival to Puerto Rico, AHB began to show reduced defense of their nests and today are about on par with EHB in this trait. Researchers suspect several factors could have contributed to this process all related to the challenges of surviving in a remote oceanic island with a high density of human population. The process may have also been abetted by major hurricanes such as Irma and Maria, which could have reduced the bees' overall population and genetic diversity.

The Agricultural Research Service is the U.S. Department of Agriculture's chief scientific in-house research agency. Daily, ARS focuses on solutions to agricultural problems affecting America. Each dollar invested in agricultural research results in $20 of economic impact.

PULLMAN, Wash. -- Washington State University researchers have developed an easy-to-use software program to identify drug-resistant genes in bacteria.

The program could make it easier to identify the deadly antimicrobial resistant bacteria that exist in the environment. Such microbes annually cause more than 2.8 million difficult-to-treat pneumonia, bloodstream and other infections and 35,000 deaths in the U.S. The researchers, including PhD computer science graduate Abu Sayed Chowdhury, Shira Broschat in the School of Electrical Engineering and Computer Science, and Douglas Call in the Paul G. Allen School for Global Animal Health, report on their work in the journal Scientific Reports.

Antimicrobial resistance (AMR) occurs when bacteria or other microorganisms evolve or acquire genes that encode drug-resistance mechanisms. Bacteria that cause staph or strep infections or diseases such as tuberculosis and pneumonia have developed drug-resistant strains that make them increasingly difficult and sometimes impossible to treat. The problem is expected to worsen in future decades in terms of increased infections, deaths, and health costs as bacteria evolve to "outsmart" a limited number of antibiotic treatments.

"We need to develop tools to easily and efficiently predict antimicrobial resistance that increasingly threatens health and livelihoods around the world," said Chowdhury, lead author on the paper.

As large-scale genetic sequencing has become easier, researchers are looking for AMR genes in the environment. Researchers are interested in where microbes are living in soil and water and how they might spread and affect human health. While they are able to identify genes that are similar to known AMR-resistant genes, they are probably missing genes for resistance that look very unique from a protein sequence perspective.

The WSU research team developed a machine-learning algorithm that uses features of AMR proteins rather than the similarity of gene sequences to identify AMR genes. The researchers used game theory, a tool that is used in several fields, especially economics, to model strategic interactions between game players, which in turn helps identify AMR genes. Using their machine learning algorithm and game theory approach, the researchers looked at the interactions of several features of the genetic material, including its structure and the physiochemical and composition properties of protein sequences rather than simply sequence similarity.

“Our software can be employed to analyze metagenomic data in greater depth than would be achieved by simple sequence matching algorithms,” Chowdhury said. “This can be an important tool to identify novel antimicrobial resistance genes that eventually could become clinically important.”

“The virtue of this program is that we can actually detect AMR in newly sequenced genomes,” Broschat said. “It’s a way of identifying AMR genes and their prevalence that might not otherwise have been found. That’s really important.”

The WSU team considered resistance genes found in species of Clostridium, Enterococcus, Staphylococcus, Streptococcus, and Listeria. These bacteria are the cause of many major infections and infectious diseases including staph infections, food poisoning, pneumonia, and life-threatening colitis due to C. difficile. They were able to accurately classify resistant genes with up to 90 percent accuracy.

They have developed a software package that can be easily downloaded and used by other researchers to look for AMR in large pools of genetic material. The software can also be improved over time. While it’s trained on currently available data, researchers will be able to re-train the algorithm as more data and sequences become available.

“You can bootstrap and improve the software as more positive data becomes available,”
Broschat said.