A New Method for Assessing the Microbiome of the Human Gut

A technique called 'bead beating.'
Photo Credit: Courtesy of California Institute of Technology

The gut microbiome—the population and variety of bacteria within the intestine—is thought to influence a number of behavioral and disease traits in humans. Most obviously, it affects intestinal health. Cancer, inflammatory bowel disease, and celiac disease, for example, are all affected by the gut microbiome. But recent research at Caltech and other research centers has identified connections between the gut microbiome and diseases such as Parkinson's disease and multiple sclerosis as well as links between the gut microbiome and the presence of autistic behaviors, anxious behaviors, and a propensity to binge-eat sweets. (Most of this work has been done in the laboratory of Sarkis Mazmanian, Caltech's Luis B. and Nelly Soux Professor of Microbiology, who works mainly on mouse models.)

Looking directly at the human gut and the bacteria that make this space their home is often performed with sequencing—a process that analyzes the DNA sequences that make up each organism. However, this process is difficult in the intestine largely because the amount of microbial DNA in the gut is miniscule in comparison to the amount of host DNA. In intestinal tissue, roughly 99.99 percent of the DNA present is from the host organism; only 0.01 percent is microbial DNA.

However powerful the effects of these microbes, it is hard to understand their role without knowing their composition. Microbiome studies often rely on studies of feces and saliva, but these are quite different from the ecosystem of the gut itself.

Targeting a coronavirus ion channel could yield new Covid-19 drugs

MIT chemists found that the SARS-CoV-2 E protein, which acts as an ion channel, has a broad opening at the bottom when in the closed state and a narrower opening in the open state.
Image Credits: Courtesy of the researchers, MIT News, and iStock
(CC BY-NC-ND 3.0 DEED)

The genome of the SARS-CoV-2 virus encodes 29 proteins, one of which is an ion channel called E. This channel, which transports protons and calcium ions, induces infected cells to launch an inflammatory response that damages tissues and contributes to the symptoms of Covid-19.

MIT chemists have now discovered the structure of the “open” state of this channel, which allows ions to flow through. This structure, combined with the “closed” state structure that was reported by the same lab in 2020, could help scientists figure out what triggers the channel to open and close. These structures could also guide researchers in developing antiviral drugs that block the channel and help prevent inflammation.

“The E channel is an antiviral drug target. If you can stop the channel from sending calcium into the cytoplasm, then you have a way to reduce the cytotoxic effects of the virus,” says Mei Hong, an MIT professor of chemistry and the senior author of the study.

MIT postdoc Joao Medeiros-Silva is the lead author of the study, which appears today in Science Advances. MIT postdocs Aurelio Dregni and Pu Duan and graduate student Noah Somberg are also authors of the paper.

An electrical switch to control chemical reactions

The device takes the form of a small box in which the reaction medium circulates between two electrodes producing the electric field.
Photo Credit: © Stefan Matile

New pharmaceuticals, cleaner fuels, biodegradable plastics: in order to meet society’s needs, chemists have to develop new synthesis methods to obtain new products that do not exist in their natural state. A research group at the University of Geneva (UNIGE), in collaboration with Cardiff University, has discovered how to use an external electric field to control and accelerate a chemical reaction, like a "switch". This work, to be read in Science Advances, could have a considerable impact on the development of new molecules, enabling not only more environmentally friendly synthesis, but also very simple external control of a chemical reaction.

In chemistry, creating complex organic chemical compounds from simpler reagents is denoted "organic synthesis". Through successive reactions, chemists assemble small molecules to ultimately form the desired products. Organic synthesis is crucial to the manufacture of drugs, polymers, agrochemicals, pigments and fragrances. These successive steps are extremely precise and delicate to control. To limit the required resources, the yield of each reaction step should be optimal. Achieving better control and simpler operation of these reactions remains a major research challenge.

New Study Points to New Possibilities for Treating Lung Cancer Patients

Illustration Credit: Rawpixel

Currently, researchers from different institutions in the world are testing a drug against obesity and diabetes, and now a Danish research team reports that the same substance has had a beneficial effect on mice with experimental lung cancer.

The substance is the short-chain fatty acid propionate, which is naturally produced by bacteria in our gut. From there, it is distributed throughout the body, and this new research study shows that treating mice with lung cancer with propionate can reduce the occurrence of metastases.

The study also demonstrates a role for propionate in increasing the effectiveness of Cisplatin, a commonly used drug for lung cancer patients. This was shown by lab experiments carried out in cancer cells derived from patients.

Red Algae Could Be Used to Create a Drug for Coronavirus

Chemical research on Laurencia red algae began in 1965.
Photo Credit: 🇸🇮 Janko Ferlič

Laurencia red algae can be used as a basis for new drugs against the SARS-CoV-2 virus, biochemists have found. A team of scientists from the Ural Federal University, the Institute of Organic Synthesis of the Ural Branch of the Russian Academy of Sciences, together with colleagues from Australia and Germany, carried out molecular docking of 300 bioactive components (ligands) of red algae and found seven compounds with the required activity. The scientists published a description of the experiments and results in the journal Microbiology Research. 

"Laurencia belongs to the family Rhodomelaceae, which is considered one of the largest families of marine red algae, with an estimated 125 genera and 700 species worldwide. Laurencia has recently been the subject of active research. Since 2015, a total of 1,047 secondary metabolites with various useful properties have been isolated from Laurencia species alone," explains Grigory Zyryanov, Chief Researcher of the UrFU Laboratory of Advanced Materials, Green Methods and Biotechnology.

Researchers catch protons in the act of dissociation with SLAC’s ultrafast 'electron camera'

Irradiating ammonia – which is made up of one nitrogen and three hydrogens – with ultraviolet light causes one hydrogen to dissociate from the ammonia. SLAC researchers used an ultrafast “electron camera” to watch exactly what that hydrogen was doing as it dissociated. The technique had been proposed, but never proven to work, until now. In the future, researchers could use the technique to study hydrogen transfers – critical chemical reactions that drive many biological processes.
Illustration Credit: Nanna H. List/KTH Royal Institute of Technology

Scientists have caught fast-moving hydrogen atoms – the keys to countless biological and chemical reactions – in action.

A team led by researchers at the Department of Energy’s SLAC National Accelerator Laboratory and Stanford University used ultrafast electron diffraction (UED) to record the motion of hydrogen atoms within ammonia molecules. Others had theorized they could track hydrogen atoms with electron diffraction, but until now nobody had done the experiment successfully.

The results, published in Physical Review Letters, leverage the strengths of high-energy Megaelectronvolt (MeV) electrons for studying hydrogen atoms and proton transfers, in which the singular proton that makes up the nucleus of a hydrogen atom moves from one molecule to another.  

Proton transfers drive countless reactions in biology and chemistry – think enzymes, which help catalyze biochemical reactions, and proton pumps, which are essential to mitochondria, the powerhouses of cells – so it would be helpful to know exactly how its structure evolves during those reactions. But proton transfers happen super-fast – within a few femtoseconds, one millionth of one billionth of one second. It’s challenging to catch them in action.

Strep Molecule Illuminates Cancer Immune Therapies

Colorized electron microscopy shows a chain of Streptococcus pyogenes bacteria between two immune cells.
Image Credit: National Institute of Allergy and Infectious Diseases

Researchers at Harvard Medical School have discovered that a molecule made by Streptococcus pyogenes — the bacterium that causes strep throat and other infections — could help explain several long-standing medical mysteries:

• Why strep sometimes leads to serious immune complications, including rheumatic fever.
• How the immune system's recognition of the molecule may contribute to diseases like lupus.
• Why one of the first cancer immunotherapies showed promise more than 100 years ago.
• How current immune therapies for cancer could be more effective.

The findings also contradict a long-standing belief that the immune system ignores this bacterial molecule and could propel efforts to tame or activate the immune system to treat a range of diseases.

The team, led by the lab of HMS biochemist Jon Clardy, published its findings in the Journal of the American Chemical Society.

“We were very surprised by the results, but the data were compelling,” said Clardy, the Christopher T. Walsh PhD Professor of Biological Chemistry and Molecular Pharmacology in the Blavatnik Institute at HMS.

Scientists illuminate the mechanics of solid-state batteries

The image conceptualizes the processing, structure and mechanical behavior of glassy ion conductors for solid state lithium batteries.
Illustration Credit: Adam Malin/ORNL, U.S. Dept. of Energy

As current courses through a battery, its materials erode over time. Mechanical influences such as stress and strain affect this trajectory, although their impacts on battery efficacy and longevity are not fully understood.

A team led by researchers at the Department of Energy’s Oak Ridge National Laboratory developed a framework for designing solid-state batteries, or SSBs, with mechanics in mind. Their paper, published in Science, reviewed how these factors change SSBs during their cycling.

“Our goal is to highlight the importance of mechanics in battery performance,” said Sergiy Kalnaus, a scientist in ORNL’s Multiphysics Modeling and Flows group. “A lot of studies have focused on chemical or electric properties but have neglected to show the underlying mechanics.”

The team spans several ORNL research areas including computation, chemistry and materials science. Together, their review painted a more cohesive picture of the conditions that affect SSBs by using perspectives from across the scientific spectrum. “We’re trying to bridge the divide between disciplines,” said Kalnaus.

New material discovery could revolutionize rollout of global vaccinations

Photo Credit: RF._.studio

New raw vaccine materials that could make vaccines more accessible, sustainable, and ethical have been discovered.

Adjuvants are vaccine ingredients that boost a person’s immune response to a vaccine, providing greater protection against disease. One of the most prevalent adjuvant materials used in vaccines is squalene, which is typically sourced from shark livers.

Researchers at the University of Nottingham collaborated with the Access to Advanced Health Institute (AAHI) to identify synthetic alternatives to squalene that ensure sustainable, reliable, and ethical sourcing of adjuvant raw materials for vaccines moving forward.

New synthetic adjuvant materials were developed from commercially available methacrylate monomers, ensuring that a reliable supply of the material is continually available.

The combination of these adjuvant materials is scalable through catalytic chain transfer polymerization, a process that allows high levels of control over the molecular weight of the product polymer. Controlling the molecular weight is key to the use of adjuvant material in formulations for vaccines as it allows for purification in the manufacturing process and optimizes biological responses following immunization.

Giant molecular rotors operate in solid crystal

Artistic depiction of a giant rotor molecule rotating in the solid state.
Illustration Credit: Rempei Ando, et al. Angewandte Chemie International Edition.

Concave, umbrella-like metal complexes provide space to enable the largest molecular rotor operational in the solid-state.

Solid materials are generally known to be rigid and unmoving, but scientists are turning this idea on its head by exploring ways to incorporate moving parts into solids. This can enable the development of exotic new materials such as amphidynamic crystals—crystals which contain both rigid and mobile components—whose properties can be altered by controlling molecular rotation within the material. 

A major challenge to achieving motion in crystals—and in solids in general—is the tightly packed nature of their structure. This restricts dynamic motion to molecules of a limited size. However, a team led by Associate Professor Mingoo Jin from the Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University has set a size record for such dynamic motion, demonstrating the largest molecular rotor shown to be operational in the solid-state.

A molecular rotor consists of a central rotating molecule that is connected by axis molecules to stationary stator molecules, similar to the way that a wheel and axle are connected to a car frame. Such systems have been previously reported, but the crystalline material in this study features an operational rotor consisting of the molecule pentiptycene, which is nearly 40% larger in diameter than previous rotors in the solid-state, marking a significant advancement. 

Ultrasound may rid groundwater of toxic ‘forever chemicals’

PFAS is notoriously difficult to clean from the environment, but ultrasound may offer a more effective solution compared to past efforts.
Photo Credit: Edward Jenner

New research suggests that ultrasound may have potential in treating a group of harmful chemicals known as PFAS to eliminate them from contaminated groundwater.

Invented nearly a century ago, per- and poly-fluoroalkyl substances, also known as “forever chemicals,” were once widely used to create products such as cookware, waterproof clothing and personal care items. Today, scientists understand that exposure to PFAS can cause a number of human health issues such as birth defects and cancer. But because the bonds inside these chemicals don’t break down easily, they’re notoriously difficult to remove from the environment.

Such difficulties have led researchers at The Ohio State University to study how ultrasonic degradation, a process that uses sound to degrade substances by cleaving apart the molecules that make them up, might work against different types and concentrations of these chemicals.

By conducting experiments on lab-made mixtures containing three differently sized compounds of fluorotelomer sulfonates – PFAS compounds typically found in firefighting foams – their results showed that over a period of three hours, the smaller compounds degraded much faster than the larger ones. This is in contrast to many other PFAS treatment methods in which smaller PFAS are actually more challenging to treat.

Topological Insulator Catalysts for High-Yield Room-Temperature Synthesis of Organoureas

The unique quantum properties of bismuth selenide make it a promising catalyst for the synthesis of organic ureas, as demonstrated by scientists at Tokyo Tech. Thanks to its topological surface states, the proposed catalyst exhibits remarkably high catalytic activity and durability when used for the synthesis of various urea derivatives, which are widely utilized as nitrogen fertilizers.

Synthetic fertilizers, one the most important developments in modern agriculture, have enabled many countries to secure a stable food supply. Among them, organic ureas (or organoureas) have become prominent sources of nitrogen for crops. Since these compounds do not dissolve immediately in water, but instead are slowly decomposed by soil microorganisms, they provide a stable and controlled supply of nitrogen, which is crucial for plant growth and function.

However, traditional methods to synthesize organoureas are environmentally harmful due to their use of toxic substances, such as phosgene. Although alternative synthesis strategies have been demonstrated, these either rely on expensive and scarce noble metals or employ catalysts that cannot be reused easily.

Could RNA folding play a role in the origin of life?

New research in membaneless compartments that model protocells reveals that naturally occurring chemical modifications to RNA molecules help them fold better into functional structures. Image of the structures of tRNA molecules from protocells determined by high-throughput sequencing using tRNA structure-seq are overlaid on and image of the membraneless compartments made through liquid-liquid phase separation.
(CC BY-NC-ND 4.0)
Image Credit: Bevilacqua and Keating Labs / Penn State.

New research in model protocells reveals naturally occurring chemical modifications to RNA molecules help them properly fold into functional structures

To investigate potential early steps taken by the first life to develop on Earth, researchers have been studying a model of pre-life protocells comprising membraneless compartments. Now, a team of Penn State scientists have found that RNA molecules within these compartments fold better when they have naturally occurring chemical modifications. These modifications that allow for better folding in RNAs may offer a hint into how the molecules evolved from arbitrary chemical compounds to the dynamic, organized building blocks of life. The new study, published by a team of Penn State scientists in the journal Science Advances, used high-throughput genetic sequencing to determine the structure of the RNAs, which also has implications for the design of delivery methods for RNA-based therapeutics that rely on properly folded RNAs to function.

Clean, sustainable fuels made ‘from thin air’ and plastic waste

Carbon capture from air and its photoelectrochemical conversion into fuel with simultaneous waste plastic conversion into chemicals. 
Photo Credit: Ariffin Mohamad Annuar

Researchers have demonstrated how carbon dioxide can be captured from industrial processes – or even directly from the air – and transformed into clean, sustainable fuels using just the energy from the sun.

The researchers from the University of Cambridge developed a solar-powered reactor that converts captured CO2 and plastic waste into sustainable fuels and other valuable chemical products. In tests, CO2 was converted into syngas, a key building block for sustainable liquid fuels, and plastic bottles were converted into glycolic acid, which is widely used in the cosmetics industry.

Unlike earlier tests of their solar fuels technology however, the team took CO2 from real-world sources – such as industrial exhaust or the air itself. The researchers were able to capture and concentrate the CO2 and convert it into sustainable fuel.

Although improvements are needed before this technology can be used at an industrial scale, the results, reported in the journal Joule, represent another important step toward the production of clean fuels to power the economy, without the need for environmentally destructive oil and gas extraction.

Chemistry without detours: TUD researchers introduce a two-step process for producing phosphorus-containing chemicals

Example of a complex biomolecule from the group of functionalized nucleotides, achieved through the method developed by the Weigand Research Group using conventional phosphoric acid.
Image Credit: © Weigand Group

Professor Jan J. Weigand and his team from the TUD Dresden University of Technology have achieved a ground breaking advancement in the production of phosphorus-containing chemicals. In a recent publication in the renowned scientific journal Nature Synthesis, they present an innovative synthesis method that requires only two process steps for the previously complex production of functionalized phosphates. This promising innovation not only contributes to environmental protection but also saves significant time and costs. Furthermore, it offers the industry the opportunity to become less dependent on third countries. The research team has already filed two patents for this new process.

Phosphorus and its compounds are essential components of life and indispensable in our daily lives. In the human body, this element plays a crucial role in energy transfer and numerous cellular functions. Phosphorus compounds are used in fertilizers, detergents, medications, and many other products. Additionally, phosphorus is an essential ingredient in flame retardants, battery electrolytes, and catalysts. On Earth, phosphorus exists exclusively in the form of phosphates. The production of phosphorus-containing chemicals typically involves a complex and energy-intensive multi-step process. Initially, highly toxic white phosphorus (P4) is produced via a redox pathway and then further processed into phosphorus trichloride (PCl3) and other problematic and sometimes highly toxic intermediate products. Phosphorus chemistry based on P4 is associated with significant challenges but plays an indispensable role in the chemical industry due to its great importance.

UC Irvine scientists create long-lasting, cobalt-free, lithium-ion batteries

“We are basically the first group that started thinking about the supply chain, or the pain point, that nickel will bring to the EV industry in a matter of, I would say, three to five years,” says Huolin Xin, UCI professor of physics & astronomy, lead author of a paper in Nature Energy on a new way to use nickel in lithium-ion batteries.
Photo Credit: Steve Zylius / UCI

In a discovery that could reduce or even eliminate the use of cobalt – which is often mined using child labor – in the batteries that power electric cars and other products, scientists at the University of California, Irvine have developed a long-lasting alternative made with nickel.

“Nickel doesn’t have child labor issues,” said Huolin Xin, the UCI professor of physics & astronomy whose team devised the method, which could usher in a new, less controversial generation of lithium-ion batteries. Until now, nickel wasn’t a practical substitute because large amounts of it were required to create lithium batteries, he said. And the metal’s cost keeps climbing.

To become an economically viable alternative to cobalt, nickel-based batteries needed to use as little nickel as possible.

“We’re the first group to start going in a low-nickel direction,” said Xin, whose team published its findings in the journal Nature Energy. “In a previous study by my group, we came up with a novel solution to fully eliminate cobalt. But that formulation still relied on a lot of nickel.”

A Novel Technique to Observe Colloidal Particle Degradation in Real Time

Height images of nanoplastics degrading in real time, captured using high-speed atomic force microscopy. The left side shows a particle containing water, and the right side shows a water-free particle.
Image Credit: Daisuke Suzuki from Shinshu University

Researchers develop an innovative approach using atomic force microscopy to shed light on the degradation of colloidal particles

Degradation of colloidal particles is a common occurrence in nature, be it removal of waste products from cells or the natural degradation of polymers, such as plastics, in the environment. Nanoplastics are a major environmental concern, but little is known about how they are created from plastics over time. Researchers from Shinshu University have now developed a novel approach that utilizes high-speed atomic force microscopy to observe, in real time, the course of degradation of colloidal particles.

In the early 2000s, scientists from the UK made a worrisome discovery that the oceans are teeming with small particles of plastic (less than one millimeter in length) due to the continuous degradation of plastic waste. These microscopic particles of plastic have become a major environmental concern. Scientists classify these small particles as either microplastics or nanoplastics based on their size; the latter term is used exclusively for particles smaller than one micrometer.

New way of identifying proteins supports drug development

The illustration shows how different areas of PRC2 protein (the one on the right side) binds to survivin. The color pixel diagram shows binding strength to survivin. The bright pink pixels are the strongest binders.
Illustration Credit: Atsarina Larasati Anindya

All living cells contain proteins with different functions, depending on the type of cell. Researchers at the University of Gothenburg have discovered a way to identify proteins without even looking at their structure. Their method is faster, easier and more reliable than previous methods.

Currently, the general view is that each protein’s structure is what controls its function in cells. The atomic sequences, meaning how the atoms are arranged in the proteins, create the protein’s structure and shape. But there are many proteins that lack a well-defined structure.

Researcher Gergely Katona has developed a new method where proteins are scanned based on the number of amino acids (or the number of different atoms) they contain in order to identify them and their function instead of identifying them based on their structure. With this scanning method, the researchers were able to predict relatively reliably which combination of amino acids is needed to bind to the protein survivin. The outcome was a reliability of about 80 per cent, which is better than when you use the protein’s primary structures for identification. The results are now published in the scientific journal iScience.

Process turns harmful pollutants into harmless substances

Conceptual image
Illustration Credit: Evan Fields/UCR

As scientists look for ways to clean up “forever chemicals” in the environment, an increasing concern is a subgroup of these pollutants that contain one or more chlorine atoms in their chemical structure.

In a recent study published in the journal Nature Water, University of California, Riverside, environmental and chemical engineering Associate Professor Jinyong Liu and UCR graduate student Jinyu Gao describe newly discovered chemical reaction pathways that destroy chlorinated forever chemicals and render them into harmless compounds.

Known formally as PFAS or poly- and per-fluoroalkyl substances, forever chemicals have been used in thousands of products ranging from potato chip bags, stain and water repellents used on fabrics, cleaning products, non-stick cookware, and fire-suppressing foams. They are so named because they persist in the environment for decades or longer due to their strong fluorine-to-carbon chemical bonds.

Chlorinated PFAS are a large group in the forever chemical family of thousands of compounds. They include a variety of non-flammable hydraulic fluids used in industry and compounds used to make chemically stable films that serve as moisture barriers in various industrial, packaging, and electronic applications.

A Baking Soda Solution for Clean Hydrogen Storage

A research team at PNNL has proposed a safe pathway to store and release clean energy based on the chemistry of baking soda.   
Image Credit: Composite image by Shannon Colson | Pacific Northwest National Laboratory

In a world of continuously warmer temperatures, a growing consensus demands that energy sources have zero, or next-to-zero, carbon emissions. That means growing beyond coal, oil, and natural gas by getting more energy from renewable sources.

One of the most promising renewable energy carriers is clean hydrogen, which is produced without fossil fuels.

It’s a promising idea because the most abundant element in the universe is hydrogen, found in 75 percent of all matter. Moreover, a hydrogen molecule has two paired atoms—Gemini twins that are both non-toxic and highly combustible.

Hydrogen’s combustive potential makes it an attractive subject for energy researchers around the world.

At Pacific Northwest National Laboratory (PNNL), a team is investigating hydrogen as a medium for storing and releasing energy, largely by cracking its chemical bonds. Much of their work is linked to the Hydrogen Materials-Advanced Research consortium (HyMARC) at the Department of Energy (DOE).