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Category: chemistry

Impressionist sea slugs create their patterns by arranging colorful photonic crystals

Nudibranchs are often referred to as the butterflies of the sea. Nudibranchs live worldwide, primarily in warm, shallow marine regions, and stand out for their flamboyant colors and diverse shapes. A team from the Max Planck Institute of Colloids and Interfaces in Potsdam and the University of Cambridge has now discovered how they create their colorful patterns. According to their findings, published in the Proceedings of the National Academy of Sciences, the color is produced by nanostructures, each of which creates a specific color impression.

“We were surprised to find that nudibranchs use structural colors,” says Samuel Humphrey, who conducted the research at the Max Planck Institute of Colloids and Interfaces. “Biologists had previously assumed that the colors were produced by pigments.” Pigments are chemical compounds and differently colored pigments have different chemical compositions.

In contrast, in structural colors, color is not a chemical property of the material, but it depends on the length scale of nanostructures composing the material. Such nanostructures, also called photonic crystals, are responsible for the coloration of chameleons, as well as many birds and butterflies. In such structures, color is produced by the regular arrangement of materials with different refractive indices.

Introduction to Quantum Electrodynamics (QED)

It’s now time to dig into quantum field theories with considerably more rigor than earlier in the series. First up is quantum electrodynamics, or QED. This was the first successful QFT, combining quantum mechanics and special relativity. Let’s learn what this model is all about, and how to do math with Feynman diagrams.

Script by andrew mattson, physics phd student at johns hopkins university.

Watch the whole Modern Physics playlist: http://bit.ly/ProfDavePhysics2

Classical Physics Tutorials: http://bit.ly/ProfDavePhysics1
Mathematics Tutorials: http://bit.ly/ProfDaveMaths.
General Chemistry Tutorials: http://bit.ly/ProfDaveGenChem.
Organic Chemistry Tutorials: http://bit.ly/ProfDaveOrgChem.
Biochemistry Tutorials: http://bit.ly/ProfDaveBiochem.
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Building a better, more precise droplet

A humble droplet can be an immensely useful tool for a number of fields, from medicine to manufacturing. Controlling the size of the droplet, though, is an important—and very tricky—task. With unprecedented precision, a team of researchers determined how droplets break up into smaller ones, at what size, and under what conditions. The results of this study are published in Soft Matter.

“Droplets can be used as microcontainers that encapsulate small amounts of fluid and other components,” said Prof. Corey O’Hern, who led the study. Because of that, he said, they can be used to deliver drugs to the body, or to find the genomic signatures of a single cell.

“Another cool application involves microreactors. You can put different concentrations of chemical species into the droplet, allow them to mix, and determine how they react.”

Fluorescent dye that works in superacidic conditions expands possibilities for imaging in extreme environments

Since the 1960s, boron–dipyrromethene dyes, commonly called BODIPY dyes, have been widely used for their strong fluorescence, especially in bioimaging, molecular and ion sensing, and as photosensitizers. Researchers especially like how, with simple modifications to BODIPY molecules, their emission color can be tuned—an indispensable quality for multicolor imaging applications.

However, conventional BODIPY dyes are unstable in acidic environments. Strong acids can disrupt their structure by removing the boron atom and causing the dye to lose its fluorescence. This has limited their use in highly acidic conditions.

In a new breakthrough, researchers from Hokkaido University have developed a superacid-resistant BODIPY dye. The research team, led by Professor Yasuhide Inokuma at the Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), reports the findings in Nature Communications.

Milkweed evolves ‘mind-blowing’ tactic to fight monarchs

Milkweed has found a new strategy in its epic evolutionary battle with monarch butterflies: upgrading its toxins to outmaneuver the monarch’s resistance. In a new study, published in the Proceedings of the National Academy of Sciences, researchers find that adding a small structural element containing nitrogen and sulfur to milkweed’s toxins circumvents monarchs’ ability to block them. The research sheds light on an underappreciated evolutionary tactic for plants: that not only can they increase their levels of toxicity, they can also structurally innovate to create new classes or subclasses of toxins.

“This structural innovation is a new axis for defining chemical toxins in the natural world,” said co-author Christophe Duplais, associate professor of entomology at Cornell AgriTech, in the College of Agriculture and Life Sciences (CALS). “This very simple modification makes a huge difference in terms of its ecological effect, because now this molecule is toxic to the monarch.”

Milkweed and monarchs have coevolved over millions of years, each building defenses and counter-defenses. One such defense is the monarchs’ ability to block milkweed’s toxins, called cardenolides, from binding to their target enzyme in the monarch’s cells. Monarchs have even evolved to sequester the toxins in their wings, to poison birds that peck at them.

Single-cell analysis identifies RETN+ monocyte-derived Resistin as a therapeutic target in hepatitis B virus-related acute-on-chronic liver failure

GUTImage from the paper by Xu et al entitled.

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HepatitisB HBV

Background Acute-on-chronic liver failure (ACLF) is characterised by intense systemic inflammation and high short-term mortality, yet effective targeted therapies are lacking.

Objective To explore monocyte heterogeneity in HBV-related ACLF (HBV-ACLF) to identify specific subsets and associated therapeutic targets.

Design Peripheral blood mononuclear cells from healthy controls (n=4), patients with acute decompensation (n=5), and patients with ACLF (n=9) underwent single-cell RNA sequencing (scRNA-seq). Findings were integrated with hepatic scRNA-seq, bulk transcriptomics, multiplex immunohistochemistry and in vitro functional assays. The in vivo roles of candidate targets were validated in two murine ACLF models.

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Consequences of the Novel ALS-Associated KIF5A Variant c.2993-6C

Regulation and activation of UvrD-family DNA helicases/ translocases.

For the past few decades, the active form of superfamily 1A (SF1A) UvrDfamily helicases has been controversial due to the absence of structures of the active dimeric form of these enzymes.

A key interaction in the monomeric structures is between a regulatory domain (2B) and duplex DNA that was proposed to facilitate DNA unwinding but is likely inhibitory.

However, recent cryo-EM structures show that Mycobacterium tuberculosis UvrD1 forms a covalent dimer, with dimerization occurring between the 2B domains of each subunit, resulting in major reorientations of the 2B domains that prevent the 2B–DNA interaction, thus relieving its inhibitory effect.

The same dimerization interface is used in Escherichia coli UvrD dimers, suggesting that this is a general mechanism to activate most SF1A helicases.

Due to these insights, textbook descriptions of helicase mechanisms based on the monomeric structures require re-evaluation. sciencenewshighlights ScienceMission https://sciencemission.com/conundrum-resolved

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AI rebuilds molecules from exploding fragments

Researchers at the Department of Energy’s SLAC National Accelerator Laboratory and collaborating institutions recently built a generative AI model that can recreate molecular structures from the movement of the molecule’s ions after they are blasted apart by X-rays, a technique called Coulomb explosion imaging.

The research, published in Nature Communications, is an important step toward being able to take snapshots of molecules during chemical reactions—an advance that could have important impacts in medicine and industry. The machine learning model closely predicted the geometries of a range of different molecules made of less than ten atoms, paving the way for applying the technique to larger molecules.

“We were pretty excited about this,” said Xiang Li, an associate scientist at SLAC’s Linac Coherent Light Source (LCLS) and lead author of the study. “It is the first AI model built for molecular structure reconstruction from Coulomb explosion imaging.”

Most mass spectrometers can process just a few molecules at once: Reengineered prototype does a billion simultaneously

Mass spectrometry is already a powerful tool for determining what kind and how many molecules are present in a given sample. But most instruments still analyze their molecules one or just a few at a time, an approach that is inefficient and costly, and in which rare, but significant molecules can easily fall between the cracks.

A more powerful version of the technology could one day allow scientists to read the full molecular contents of a single cell, track thousands of chemical reactions at once, and ultimately accelerate efforts like drug development.

Now, a new study describes the first big step in that direction by producing a prototype, dubbed MultiQ-IT, that’s capable of handling vast numbers of molecules at once. The findings, published in the journal Science Advances, offer a blueprint for faster, more sensitive instruments that could position mass spectrometry for the kind of transformation that reshaped genomics and computing.

New DNA base editor minimizes bystander edits while maintaining high efficiency

The trajectory of base editing has been remarkable, progressing from the laboratory to patient care, treating debilitating or terminal illnesses, in less than a decade. A type of gene editing that makes chemical changes to our DNA, base editing was developed by Alexis Komor, associate professor in the Department of Biochemistry and Molecular Biophysics at the University of California San Diego.

For all of base editing’s success, it is still a relatively new technology, and researchers like Komor are working to improve its efficiency, while lowering the incidence of unwanted edits. One type of unwanted edit is called a bystander edit. This occurs when a base editor not only edits the desired nucleobase, but also edits surrounding bases as well. Komor’s lab has developed a way to minimize bystander edits. This work appears in Nature Biotechnology.

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