New Study Sheds Light on Boric Acid Transport and Excretion in Marine Fish

Seawater is known to contain a significant concentration of boric acid, which can be toxic and deadly to living systems. As such, fish living in marine habitats need to be able to excrete boric acid in order to maintain a healthy boron balance. Tokyo Tech researchers have now identified the gene and mechanism of boric acid transport in seawater fish and contrasted it to freshwater species.

Marine fishes live in highly saline environments with ionic concentrations that are vastly different from their blood plasma. Seawater contains a variety of toxic ion species that can build up in the body if the fish does not excrete them. One example of this is boric acid, which—in small amounts—is a vital micronutrient for animals but can prove toxic in excess. Hence, marine fish must develop physiologic means to excrete boric acid. However, how they do this is, as yet, unknown. Now, an international team led by researchers from Tokyo Institute of Technology (Tokyo Tech) has unveiled and demonstrated the molecular mechanisms underlying boric acid secretion in marine pufferfish.

Associate Professor Akira Kato of Tokyo Tech is the principal author of the study, which was published in the Journal of Biological Chemistry. He tells us more about it. "We compared euryhaline pufferfish (which are pufferfish that can survive in varying levels of salinity) accustomed to saltwater, brackish water, and freshwater. On comparing fish from these three habitats, we found that the urine of a seawater pufferfish (Takifugu pufferfish) contained 300 times more boric acid than pufferfish blood, and 60 times more boric acid than seawater." The urine of freshwater fish contained almost 1000 times less boric acid than that of seawater pufferfish. These findings established that Takifugu pufferfish living in seawater excrete boric acid in their urine. Just like in humans, the process of excretion via urine in pufferfish is mediated by the kidneys.

UH lab produces building blocks to DNA and RNA in deep space

Conceptualization of the role of methanediamine in the galactic cosmic ray mediated synthesis of DNA and RNA bases in deep space.
Illustration Credit: University of Hawaiʻi

The synthetic production of a critical building block called methanediamine for the first time by researchers in University of Hawaiʻi at Mānoa’s Department of Chemistry could lead to key insights into the origins of life. The researchers have discovered a method to produce it in a lab under conditions that mimic icy interstellar nanoparticles in cold molecular clouds in space.

Nitrogen is the most abundant element in Earth’s atmosphere. It is also incorporated into nearly one-third of some 300 molecules identified in the interstellar medium, which is the material that exists in the space between the stars in a galaxy.

Most nitrogen-containing molecules in deep space carry exclusively the nitrile moiety (organic compound that has a carbon, nitrogen functional group), while amines (a member of a family of nitrogen-containing organic compounds that is derived from ammonia) and imines (compounds containing a carbon-nitrogen double bond) are relatively rare. According to experts, an understanding of the origin of these less common molecule parts in deep space is central to the hypothesis for the origin of life because all nucleobases (nitrogen-containing compounds) found in contemporary RNA and DNA contain amines and imines.

Princeton chemists create quantum dots at room temp using lab-designed protein

Nature uses 20 canonical amino acids as building blocks to make proteins, combining their sequences to create complex molecules that perform biological functions.

But what happens with the sequences not selected by nature? And what possibilities lie in constructing entirely new sequences to make novel, or de novo, proteins bearing little resemblance to anything in nature?

That’s the terrain where Michael Hecht, professor of chemistry, works with his research group. And recently, their curiosity for designing their own sequences paid off.

They discovered the first known de novo (newly created) protein that catalyzes, or drives, the synthesis of quantum dots. Quantum dots are fluorescent nanocrystals used in electronic applications from LED screens to solar panels.

Their work opens the door to making nanomaterials in a more sustainable way by demonstrating that protein sequences not derived from nature can be used to synthesize functional materials — with pronounced benefits to the environment.

Scientists Have Created New Substance to Treat Neurological Disorders

Scientists used a set of 1,2,3-triazole derivatives and modeled the structure of the putative inhibitor.
 Photo Credit: Andrey Fomin

The international team of scientists, including chemists from the Ural Federal University, has developed a substance that may become the basis for drugs that suppress or alleviate a number of neurological disorders. These include, for example, psychosis, schizophrenia, Parkinson's and Huntington's diseases, etc. The scientists reported the development and first results of the study in the Journal of Biomolecular Structure and Dynamics. The study was supported by a grant from the Ministry of Science and Higher Education of the Russian Federation (Project No. 075-15-2020-777).

"We found that the enzyme Phosphodiesterase 10A, which is produced in the body, is directly linked to neurological disorders. If you inhibit this enzyme, you can significantly slow down or even suppress the disease. For this purpose, we used a set of derivatives of 1,2,3-triazole, a pharmacophore whose fragments are contained in many drugs, and modeled the structure of the putative TP-10 inhibitor. We hypothesize that it would have a positive effect on conditions associated with brain dysfunction by reducing the activity of the Phosphodiesterase 10A enzyme. Other inhibitors developed by foreign companies still have no reliable antipsychotic efficacy so far," notes Dhananjay Bhattacherjee, senior researcher at the Department of Organic and Biomolecular Chemistry at UrFU.

Intricate ‘snowflakes’ created in liquid metal

A snowflake-like zinc crystal synthesized in liquid gallium by researchers at UNSW Sydney.
Image Credit: Dr Jianbo Tang

Researchers, including those from UNSW Sydney, have synthesized complex symmetrical zinc crystals in liquid gallium which can potentially be used in a range of catalysis applications.

It’s beginning to look a lot like Christmas at UNSW Sydney’s School of Chemical Engineering where researchers have grown crystals made of zinc that look like snowflakes - inside a liquid metal.

The team predominantly used zinc metal dissolved in liquid gallium as the solvent, creating distinctive structures that often resembled those of six-branched snowflake crystals.

Apart from their structural beauty, these liquid metal-grown crystals can enable future processes for making catalytic materials for producing hydrogen from organic fuels. The metallic crystals can also be specially formulated, during their synthesis and extraction, to make semiconductors for electronic and optical devices of computers, mobile phones and solar cells of the future.

Why synonymous mutations are not always silent

New modeling shows how synonymous mutations that change the DNA sequence of a gene, but not the sequence of the encoded protein can impact protein production and function by changing the rate of protein synthesis. Top: illustration of a new class of protein misfolding called a non-covalent lasso entanglement that can result from changes to the rate of protein synthesis caused by synonymous mutations. Bottom: structure of a protein showing its native state and misfolded state with non-covalent lasso entanglement.
Illustration Credit: Yang Jiang | Pennsylvania State University

New modeling shows how synonymous mutations — those that change the DNA sequence of a gene but not the sequence of the encoded protein — can still impact protein production and function. A team of researchers led by Penn State chemists modeled how genetic changes that alter the speed of protein synthesis, but not the sequence of amino acids that comprise the protein, can lead to misfolding that changes the protein’s activity level, and then corroborated their models experimentally. The results demonstrate the importance of kinetics — the rate of protein synthesis — in addition to sequence for determining protein structure and function and could have implications in fields such as biopharmaceutics for fine tuning the activity of synthesized proteins.

Proteins are composed of long strings of amino acids that then fold up into three-dimensional functional structures. Each amino acid is encoded by a triplet of letters in the DNA alphabet of A, T, C and G called a codon, but there is redundancy built in to the system such that more than one codon can correspond to the same amino acid. Therefore, a mutation that changes the DNA sequence of a gene won’t necessarily change the sequence of the encoded protein if the mutation results in a "synonymous codon." To make a protein, DNA in the nucleus of a cell is first transcribed into a messenger RNA (mRNA). The mRNA is then transported out of the nucleus where it is translated into a nascent protein by a cellular organelle called a ribosome. After translation the protein is folded into its final functional form.

Scientists invent pioneering technique to construct rare molecules

Bahamaolide A is a polyketide natural product with potent antifungal activity, which was isolated from bacteria cultured from a sediment sample collected at North Cat Cay in the Bahamas and has now been synthesized in the chemical laboratory for the first time.
Image Credit: University of Bristol and Wikimedia Commons

Scientists have created a much faster way to make certain complex molecules, which are widely used by pharmaceuticals for antibiotics and anti-fungal medicines.

The first-of-its-kind discovery by chemists at the University of Bristol has the potential to speed up the production of such drugs, making them cheaper and more accessible.

The breakthrough, published in Nature Chemistry, marks the culmination of a five-year research project which has finally cracked how to reconstruct in a laboratory a particularly complex molecule, from the family of molecules known as polyketides.

Lead author Sheenagh Aiken, a PhD student at the university’s School of Chemistry when the work was completed, said: “It’s an exciting discovery, which could bring important benefits for the pharmaceutical industry and public health.

Ural Chemists Improved Material for Fuel Cells

Scientists were able to identify the optimal amount of iron administered.
Photo Credit: Ilya Safarov

Chemists at Ural Federal University and the Institute of High-Temperature Electrochemistry, Ural Branch of the Russian Academy of Sciences have improved a material for high-performance electrochemical devices. Such materials are used as electrodes in solid oxide fuel cells (SOFC) or proton-ceramic fuel cells (PCFC). Scientists proposed the infiltration method as a simple and affordable way to improve electrochemical performance. Their method increased the conductivity of this material, consequently improving the performance (increased power) of fuel cells. The change now makes the reaction go faster. The material and method are described in the journal Catalysts.

In the course of their research, chemists introduced iron into the basic barium cerate-zirconate, which means that they added iron ions to the complex oxide perovskites. In this way they were able to obtain a high level of mixed ion-electron conductivity, which is necessary for good electrodes. Similar materials exist today, but scientists around the world are trying to optimize them-improving their properties to increase efficiency.

Automated chemical reaction prediction: now in stereo

The AFIR method traces back the reaction of endiandric acid C methyl ester, a 52-atom natural product, to its starting materials using only quantum chemical calculations.
Illustration Credit: Tsuyoshi Mita et al. JACS. November 30, 2022

Automated reaction path search method predicts accurate stereochemistry of pericyclic reactions using only target molecule structure.

Researchers at the Institute for Chemical Reaction Design and Discovery (WPI-ICReDD) have demonstrated the expanded use of a computational method called the Artificial Force Induced Reaction (AFIR) method, predicting pericyclic reactions with accurate stereoselectivity based only on information about the target product molecule. The accurate prediction of a molecule’s stereochemistry—i.e., the 3D arrangement of its constituent atoms—is unprecedented for such an automated reaction path search method. This study serves as proof of concept that the AFIR method has the potential to discover novel reactions with specific stereochemistry.

In this study, AFIR is used to calculate retrosynthetic, or reverse, reactions going from product molecules to starting materials. Previously, AFIR has been used to predict small, simple reactions, but accurate stereochemistry predictions were out of reach, limiting the technique’s applicability. In this study, researchers overcome this hurdle by using the AFIR method on a major class of chemical reactions called pericyclic reactions, which are commonly found in biological processes, including the synthesis of Vitamin D.

Lychee Peel Powder Can Remove Persistent Dye from Wastewater

The peel of the lychee makes up about 15% of the weight of the fruit.
Photo Credit: Jamie Trinh

The international team of scientists, which includes chemists from the Ural Federal University, found out that chemically modified lychee peel eliminates a very persistent red dye from wastewater. The researchers have developed a new method that can be used to clean wastewater near textile production facilities in an environmentally friendly and cheap way. By doing so, it can prevent disease in humans and save animals, fish and birds that interact with dyed water. It will also help make the world's dirtiest rivers cleaner: the Buringanga River in Bangladesh, the Ganges in India, and the Chintarum in Indonesia, for example. A description of the new method and the results of the experiments were published in the Journal of Molecular Liquids.

"Red dyes emitted in various industries such as textiles, cosmetics, leather, food and plastic are dangerous environmental pollutants. From 20 to 40% of persistent dyes remain in wastewater and cause a critical increase in its acidity and alkalinity. The key factor here is the nature of these dyes. They contribute to increased deposition of calcium salts in organs, are considered highly toxic and pose a serious threat to humans, causing various cancers and mutagenic phenomena at cellular and molecular levels," explains Grigory Zyryanov, Professor of the Department of Organic and Biomolecular Chemistry at the Ural Federal University.

Researchers take first step towards controlling photosynthesis using mirrors

The researchers used ultrafast laser spectroscopy
Photo Credit: Pavel Chabera

With the help of mirrors, placed only a few hundred nanometers apart, a research team has managed to use light more efficiently. The finding could eventually be useful for controlling solar energy conversion during photosynthesis, or other reactions driven by light. For example, one application could be converting carbon dioxide into fuel.

The sunlight that hits Earth for one hour is almost equivalent to the total energy consumption of mankind for an entire year. At the same time, our global emissions of carbon dioxide are increasing. Harnessing the sun's energy to capture greenhouse gas and then convert it into fuel is a hot research field.

A research team at Lund University in Sweden was previously able to show that with ultrafast laser spectroscopy, and the help of advanced materials, it would be possible to reduce the levels of greenhouse gases in the atmosphere in the long term. In their latest study in Nature Communications, the team has made new progress when it comes to taking advantage of light.

Rice lab’s catalyst could be key for hydrogen economy

Rice University researchers have engineered a key light-activated nanomaterial for the hydrogen economy. Using only inexpensive raw materials, a team from Rice’s Laboratory for Nanophotonics, Syzygy Plasmonics Inc. and Princeton University’s Andlinger Center for Energy and the Environment created a scalable catalyst that needs only the power of light to convert ammonia into clean-burning hydrogen fuel.

The research is published in the journal Science.

The research follows government and industry investment to create infrastructure and markets for carbon-free liquid ammonia fuel that will not contribute to greenhouse warming. Liquid ammonia is easy to transport and packs a lot of energy, with one nitrogen and three hydrogen atoms per molecule. The new catalyst breaks those molecules into hydrogen gas, a clean-burning fuel, and nitrogen gas, the largest component of Earth’s atmosphere. And unlike traditional catalysts, it doesn’t require heat. Instead, it harvests energy from light, either sunlight or energy-stingy LEDs.

The pace of chemical reactions typically increases with temperature, and chemical producers have capitalized on this for more than a century by applying heat on an industrial scale. The burning of fossil fuels to raise the temperature of large reaction vessels by hundreds or thousands of degrees results in an enormous carbon footprint. Chemical producers also spend billions of dollars each year on thermocatalysts — materials that don’t react but further speed reactions under intense heating.

A Radical New Approach in Synthetic Chemistry

The Laser Electron Accelerator Facility (LEAF) generates intense high-energy electron pulses that allow scientists to add or subtract electrons from molecules to make chemically reactive species and monitor what happens as a reaction proceeds.
Full Size Original
Photo Credit: Courtesy of Brookhaven National Laboratory

Scientists at the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory helped measure how unpaired electrons in atoms at one end of a molecule can drive chemical reactivity on the molecule’s opposite side. As described in a paper recently published in the Journal of the American Chemical Society, this work, done in collaboration with Princeton University, shows how molecules containing these so-called free radicals could be used in a whole new class of reactions.

“Most reactions involving free radicals take place at the site of the unpaired electron,” explained Brookhaven Lab chemist Matthew Bird, one of the co-corresponding authors on the paper. The Princeton team had become experts in using free radicals for a range of synthetic applications, such as polymer upcycling. But they’ve wondered whether free radicals might influence reactivity on other parts of the molecule as well, by pulling electrons away from those more distant locations.

“Our measurements show that these radicals can exert powerful ‘electron-withdrawing’ effects that make other parts of the molecule more reactive,” Bird said.

The Princeton team demonstrated how that long-distance pull can overcome energy barriers and bring together otherwise unreactive molecules, potentially leading to a new approach to organic molecule synthesis.

Major discovery about mammalian brains surprises researchers

Illustration shows vacuolar-type adenosine triphosphatases (V-ATPases, large blue structures) on a synaptic vesicle from a nerve cell in the mammalian brain.
Illustration Image: C. Kutzner, H. Grubmüller and R. Jahn/Max Planck Institute for Multidisciplinary Sciences.

Major discovery about mammalian brains surprises researchers, University of Copenhagen researchers have made an incredible discovery. Namely, a vital enzyme that enables brain signals is switching on/off at random, even taking hours-long “breaks from work”. These findings may have a major impact on our understanding of the brain and the development of pharmaceuticals. 

Millions of neurons are constantly messaging each other to shape thoughts and memories and let us move our bodies at will. When two neurons meet to exchange a message, neurotransmitters are transported from one neuron to another with the aid of a unique enzyme.

This process is crucial for neuronal communication and the survival of all complex organisms. Until now, researchers worldwide thought that these enzymes were active at all times to convey essential signals continuously. But this is far from the case.

Using a groundbreaking method, researchers from the University of Copenhagen’s Department of Chemistry have closely studied the enzyme and discovered that its activity is switching on and off at random intervals, which contradicts our previous understanding.

A Solution for Reclaiming Valuable Resources Flushed Down the Drain

A problem at sewage treatment plants - the buildup of 'brown grease' - could yield a bounty of biofuel, thanks to the work of UConn researchers
Photo Credit: kubinger

For the everyday products we use, a pattern has become numbingly familiar: Something is made, we use it, we throw it away. Yet, for a sustainable future – one where we don’t simply extract and toss resources – we need to make this linear process circular, says UConn Department of Chemical and Biomolecular Engineering Emeritus Professor Richard Parnas.

Parnas and his team research biodiesel and how to make it out of waste resources. Parnas also co-founded REA Resource Recovery Systems, which supported UConn Chemical Engineering graduate student Cong Liu Ph.D. ‘22 to develop technology to improve a critical process of removing sulfur from biodiesel made from waste materials. In this case, the materials originate from sewage, and the technology is being implemented in a project at Danbury’s John Oliver Memorial Sewer Plant scheduled to go into operation in January 2023 that will convert fats, oils, and grease into biodiesel whose lifecycle emissions are more than 74% lower than petroleum-based diesel.

Covid-19: the Spike protein is no longer the only target

Possible mechanism of action of a drug targeting Nsp1 of SARS-CoV-2. In infected cells, Nsp1 blocks the ribosome mRNA canal by acting as a "cap" that prevents the expression of the host's mRNA. Linking a ligand to the proposed cryptic pocket highlighted in purple could prevent blockage mediated by Nsp1 and, ultimately, restore the ability of the ribosome to initiate the translation of the mRNA.
Photo Credit: UNIGE Alberto Borsatto

A research team led by the UNIGE reveals a hidden cavity on a key SARS-CoV-2 protein to which drugs could bind.

With the continuous emergence of new variants and the risk of new strains of the virus, the development of innovative therapies against SARS-CoV-2 remains a major public health challenge. Currently, the proteins that are on the surface of the virus and/or are involved in its replication are the preferred therapeutic targets, like the Spike protein targeted by vaccines. One of them, the non-structural protein Nsp1, had been studied little until now. A team from the University of Geneva (UNIGE), in collaboration with University College London (UCL) and the University of Barcelona, has now revealed the existence of a hidden ''pocket’ on its surface. A potential drug target, this cavity opens the way to the development of new treatments against Covid-19 and other coronaviruses. These results can be found in the journal eLife.

Simplified process shines light on new catalyst opportunities

Members of the research team at the Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University. Top Row, Left to Right: Satoshi Maeda, Yu Harabuchi, Hiroki Hayashi, Hitomi Katsuyama. Bottom Row, left to right: Wataru Kanna, Hideaki Takano, Tsuyoshi Mita
Photo Credit: ICReDD

Theory-guided development of an easier, more versatile process for synthesizing unsymmetric ligands provides new avenues of exploration in transitional metal catalysis.

Researchers at the Institute for Chemical Reaction Design and Discovery (WPI-ICReDD) have discovered the key to synthesizing a molecular tool that could greatly expand the variety of catalytic reactions possible with transition metals. The team has taken a well-established set of compounds that can be used to make transition metal catalysts and developed a simple, radical-based reaction for creating unsymmetric variants of these molecules using mild conditions. Easier access to a wider variety of these unsymmetric compounds opens a realm of new possibilities for designing transition metal catalysts.

The focus of this research is on a class of compounds called 1,2-bis(diphenylphosphino)ethane derivatives (DPPEs). DPPEs are bidentate — i.e., they attach to the metal center of a catalyst in two locations. However, DPPEs have typically been symmetric, with each attachment arm being the same, which limits the possible structural variety and reactivity. This study overcomes that limit, reporting on a versatile method for developing unsymmetric DPPEs using ethylene, an abundantly available feedstock chemical.

Looking at oxygen storage dynamics in three-way catalysts

Photo Credit: kalhh

In light of vehicular pollutants contributing to decreasing air quality, governments across the globe are posing stricter emission regulations for automobiles. This calls for the development of more efficient exhaust gas after-treatment systems (i.e., systems to “clean” exhaust gas before it is released into the atmosphere). The most common mode for treating exhaust emissions of gasoline-fueled internal combustion engines are three-way catalysts (TWCs) or catalytic converters. TWCs often comprise active metals such as platinum (Pt) and palladium (Pd) nanoparticles and oxygen storage materials with a high specific surface area, such as a solid solution of CeO2-ZrO2(CZ). These components can catalyze multiple oxidation and reduction reactions that can convert harmful exhaust from vehicular engines to harmless gases.

The durability, precision, and performance of a TWC is dependent on factors like the oxygen stored or removed from the bulk and surface of the oxygen storage materials. So, clearly understanding the oxygen transport and dynamics of the storage material is necessary to improve its efficiency. Unfortunately, there is a lack of techniques that can enable direct tracking of the oxygen storage process in TWCs.

Toxins force construction of ‘roads to nowhere’

This image shows the effects of the toxin VopF, depicted in green in the cell on the left, on actin filaments, depicted in magenta in both cells.
Image Credit: Elena Kudryashova

Toxins released by a type of bacteria that cause diarrheal disease hijack cell processes and force important proteins to assemble into “roads to nowhere,” redirecting the proteins away from other jobs that are key to proper cell function, a new study has found.

The affected proteins are known as actins, which are highly abundant and have multiple roles that include helping every cell unite its contents, maintain its shape, divide and migrate. Actins assemble into thread-like filaments to do certain work inside cells.

Researchers found that two toxins produced by the Vibrio genus of bacteria cause actins to start joining together into these filaments – which could be thought of as cellular highways on which cargo is delivered – at the wrong location inside cells, and headed in the wrong direction.

Understanding a cerium quirk could help advance grid-scale energy storage

When the cerium atom is short three electrons, it is surrounded by water molecules. But when it gives up a fourth electron, some water molecules shift out of the way to let in sulfates. This dance costs energy, but understanding that energy loss paves the way for more efficient cerium batteries.
Image Credit: Dylan Herrera, Goldsmith Lab, University of Michigan

It turns out cerium flow batteries lose voltage when electrolyte molecules siphon off energy to form different complexes around the metal

An explanation for why flow batteries using the metal cerium in a sulfuric acid electrolyte fall short on voltage, discovered through a study led by the University of Michigan, could pave the way for better battery chemistry.

Flow batteries are one of the methods under consideration for storing intermittent sources of renewable electricity, such as solar and wind power. They can bank large quantities of energy by keeping the chemical potential in liquid form, with two electrolytes that flow through porous electrodes to charge and discharge. The metal cerium could store energy at a relatively high voltage, meaning more energy per metal ion, and at low cost.

One of the challenges with cerium is figuring out how to make electric charges transfer to and from the electrode efficiently. On its way through the positive electrode, cerium either picks up or drops off an electron, depending on whether the battery is charging or discharging.

However, the cerium in a sulfuric acid electrolyte doesn’t pick up and drop off the electron as quickly as expected, meaning energy is wasted. It turned out that the water molecules and sulfate molecules were doing a complicated dance around the cerium, and that’s how the energy was lost.