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Comment by Dr. Krishna Kumari Challa on September 22, 2022 at 8:17am

Scientists unveil new system for naming majority of the world's microorganisms

What's in a name? For microorganisms, apparently a lot.

Prokaryotes are single-celled microorganisms—bacteria are an example—that are abundant the world over. They exist in the oceans, in soils, in extreme environments like hot springs, and even alongside and inside other organisms including humans. In short, they're everywhere, and scientists worldwide are working to both categorize and communicate about them. But here's the rub: Most don't have a name. Less than 0.2% of known prokaryotes have been formally named because current regulations—described in the International Code of Nomenclature of Prokaryotes (ICNP)—require new species to be grown in a lab and freely distributed as pure and viable cultures in collections. Essentially, to name it you have to have multiple physical specimens to prove it.

In an article published Sept. 19 in the journal Nature Microbiology, a team of scientists present a new system, the SeqCode, and a corresponding registration portal that could help microbiologists effectively categorize and communicate about the massive number of identified yet uncultivated prokaryotes.

Nearly 850 scientists representing multiple disciplines from more than 40 countries participated in a series of NSF-funded online workshops in 2021 to develop the new SeqCode, which uses genome sequence data for both cultivated and uncultivated prokaryotes as the basis for naming them.

Brian P. Hedlund et al, SeqCode: a nomenclatural code for prokaryotes described from sequence data, Nature Microbiology (2022). DOI: 10.1038/s41564-022-01214-9

Learn more about the SeqCode at https://seqco.de/

The SeqCode , the scientists think, serve the community by promoting high genome quality standards, good naming practice, and a well-ordered database.

Comment by Dr. Krishna Kumari Challa on September 21, 2022 at 12:31pm

Immune System for Your Mind Against Disinformation 

Comment by Dr. Krishna Kumari Challa on September 21, 2022 at 12:16pm

Plastic degradation in the ocean contributes to its acidification

A new study led by the Institut de Ciències del Mar (ICM-CSIC) in Barcelona has revealed that plastic degradation contributes to ocean acidification via the release of dissolved organic carbon compounds from both the plastic itself and its additives.

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Here's the real reason to turn on airplane mode when you fly

We all know the routine by heart: "Please ensure your seats are in the upright position, tray tables stowed, window shades are up, laptops are stored in the overhead bins and electronic devices are set to flight mode."

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New chemistry happens when dust meets pollution It is a new chemistry found to take place in a cloud droplet, a wet aerosol, or on the surface of a dust particle. All that it takes to get started is natural events like dust storms, ocean wave action, volcanic eruptions, and wildfires, which increase the amount of aerosols in the atmosphere.

Comment by Dr. Krishna Kumari Challa on September 21, 2022 at 12:02pm

'Night owls' could have greater risk of type 2 diabetes and heart disease than those who are 'early birds'

Are you an early bird or a night owl? Our activity patterns and sleep cycles could influence our risk of diseases, such as type 2 diabetes and heart disease. New research published in Experimental Physiology has found that wake/sleep cycles cause metabolic differences and alter our body's preference for energy sources. The researchers found that those who stay up later have a reduced ability to use fat for energy, meaning fats may build up in the body and increase risk for type 2 diabetes and cardiovascular disease.

The metabolic differences relate to how well each group can use insulin to promote glucose uptake by the cells for storage and energy use. People who are "early birds" (individuals who prefer to be active in the morning) rely more on fat as an energy source and are more active during the day with higher levels of aerobic fitness than "night owls" (people who prefer to be active later in the day and night). On the other hand, night owls use less fat for energy at rest and during exercise.

Researchers found that early birds use more fat for energy at both rest and during exercise than night owls. Early birds were also more insulin-sensitive. Night owls, on the other hand, are insulin resistant, meaning their bodies require more insulin to lower blood glucose levels, and their bodies favored carbohydrates as an energy source over fats. This group's impaired ability to respond to insulin to promote fuel use can be harmful as it indicates a greater risk of type2diabetes and/or heart disease. The cause for this shift in metabolic preference between early birds and night owls is yet unknown and needs further investigation.

Researchers also found that early birds are more physically active and have higher fitness levels than night owls who are more sedentary throughout the day.

 Early Chronotype with Metabolic Syndrome favors Resting and Exercise Fat Oxidation in Relation to Insulin-stimulated Non-Oxidative Glucose Disposal, Experimental Physiology (2022). DOI: 10.1113/EP090613

Comment by Dr. Krishna Kumari Challa on September 20, 2022 at 11:14am

Scientists Created 'Living' Synthetic Cells by Harvesting Bacteria For Parts

Researchers  have taken a major step forward in synthetic biology by designing a system that performs several key functions of a living cell, including generating energy and expressing genes.

Their artificially constructed cell even transformed from a sphere shape to a more natural amoeba-like shape over the first 48 hours of 'life', indicating that the proto-cytoskeletal filaments were working.

Building something that comes close to what we might think of as alive is no walk in the park, not least thanks to the fact even the simplest of organisms rely on countless biochemical operations involving mind-bendingly complex machinery to grow and replicate.

Scientists have previously focused on getting artificial cells to perform a single function, such as gene expression, enzyme catalysis, or ribozyme activity.

If scientists crack the secret to custom building and programming artificial cells capable of mimicking life more closely, it could create a wealth of possibilities in everything from manufacturing to medicine.

While some engineering efforts focus on redesigning the blueprints themselves, others are investigating ways to reduce existing cells to scraps that can then be reconstructed into something relatively novel.

To perform this latest bottom-up bioengineering feat, researchers used two bacterial colonies – Escherichia coli and Pseudomonas aeruginosa – for parts.

These two bacteria were mixed with empty microdroplets in a viscous liquid. One population was captured inside the droplets and the other was trapped at the droplet surface.

The scientists then burst open the bacteria membranes by bathing the colonies in lysozyme (an enzyme) and melittin (a polypeptide which comes from honeybee venom).

The bacteria spilled their contents, which were captured by the droplets to create membrane-coated protocells.

The scientists then demonstrated that the cells were capable of complex processing, such as the production of the energy storage molecule ATP through glycolysis, and the transcription and translation of genes.

https://www.nature.com/articles/s41586-022-05223-w

Comment by Dr. Krishna Kumari Challa on September 20, 2022 at 8:46am

Researchers transplanted the RNA editing machine of moss into human cells and it worked!

If everything is to run smoothly in living cells, the genetic information must be correct. But unfortunately, errors in the DNA accumulate over time due to mutations. Land plants have developed a peculiar correction mode: They do not directly improve the errors in the genome, but rather elaborately in each individual transcript. Researchers  have transplanted this correction machinery from the moss Physcomitrium patens into human cells. Surprisingly, the corrector started working there too, but according to its own rules. The results have now been published in the journal Nucleic Acids Research.

In living cells, there is a lot of traffic, similar to a large construction site. In land plants, blueprints in the form of DNA are stored not only in the cell nucleus, but also in the cell's power plants (mitochondria) and the photosynthesis units (chloroplasts). These blueprints contain building instructions for proteins that enable metabolic processes. But how is the blueprint information passed on in mitochondria and chloroplasts? This is done by creating transcripts (RNA) of the desired parts of the blueprint. This information is then used to produce the required proteins.

However, this process does not run entirely smoothly. Over time, mutations cause within the DNA accumulating errors that must be corrected in order to obtain perfectly functioning proteins. Otherwise, the energy supply in plants would collapse. At first glance, the correction strategy seems rather bureaucratic: Instead of improving the slip-ups directly in the blueprint—the DNA—they are cleaned up in each of the many transcripts by so-called RNA editing processes.

Compared to letterpress printing, it would be like correcting each individual book by hand, rather than improving the printing plates. Why living cells make this effort we do not know yet. Presumably, these mutations increased as plants spread from water to land during evolution.

Now, researchers have gone one step further: They transferred the RNA editing machinery from the moss into standard human cell lines, including kidney and cancer cells. The results showed that the land plant correction mechanism also works in human cells   which was previously unknown.

But that's not all: the RNA editing machines PPR56 and PPR65, which only act in mitochondria in the moss, also introduce nucleotide changes in RNA transcripts of the cell nucleus in human cells.

Surprisingly for the research team, PPR56 makes changes at more than 900 points of attack in human cell targets. In the moss, on the other hand, this RNA corrector is only responsible for two correction sites.

Elena Lesch et al, Plant mitochondrial RNA editing factors can perform targeted C-to-U editing of nuclear transcripts in human cells, Nucleic Acids Research (2022). DOI: 10.1093/nar/gkac752

Comment by Dr. Krishna Kumari Challa on September 20, 2022 at 7:10am

Physicist makes new discovery about telomeres

With the aid of physics and a minuscule magnet, researchers have discovered a new structure of telomeric DNA. Telomeres are sometimes seen as the key to living longer. They protect genes from damage but get a bit shorter each time a cell divides. If they become too short, the cell dies. The new discovery will help us understand aging and disease.
In every cell of our bodies are chromosomes that carry genes that determine our characteristics (what we look like, for instance). At the ends of these chromosomes are telomeres, which protect the chromosomes from damage. They're a bit like aglets, the plastic tips at the end of a shoelace.

The DNA between the telomeres is two meters long, so it has to be folded to fit in a cell. This is achieved by wrapping the DNA is wrapped around packages of proteins; together, the DNA and proteins are called a nucleosome. These are arranged into something similar to a string of beads, with a nucleosome, a piece of free (or unbound) DNA, a nucleosome and so on.

This string of beads then folds up even more. How it does so depends on the length of the DNA between the nucleosomes, the beads on the string. Two structures that occur after folding were already known. In one of them, two adjacent beads stick together and free DNA hangs in between. If the piece of DNA between the beads is shorter, the adjacent beads do not manage to stick together. Then two stacks form alongside each other.

In their study physicists found another telomere structure. Here the nucleosomes are much closer together, so there is no longer any free DNA between the beads. This ultimately creates one big helix, or spiral, of DNA.

The new structure was discovered with a combination of electron microscopy and molecular force spectroscopy.  Here one end of the DNA is attached to a glass slide and a tiny magnetic ball is stuck to the other. A set of strong magnets above this ball then pull the string of pearls apart. By measuring the amount of force needed to pull the beads apart one by one, you find out more about how the string is folded. The researchers  then used an electron microscope to get a better picture of the structure.

 If we know the structure of the molecules, this will give us more insight into how genes are switched on and off and how enzymes in cells deal with telomeres: how they repair and copy DNA, for example. The discovery of the new telomeric structure will improve our understanding of the building blocks in the body. And that in turn will ultimately help us study aging and diseases such as cancer and develop drugs to fight them.

Aghil Soman et al, Columnar structure of human telomeric chromatin, Nature (2022). DOI: 10.1038/s41586-022-05236-5

Comment by Dr. Krishna Kumari Challa on September 20, 2022 at 6:59am

Warmer Earth could see smaller butterflies that struggle to fly, affecting food systems

Comment by Dr. Krishna Kumari Challa on September 17, 2022 at 12:22pm

Constipated scorpions, love at first sight inspire Ig Nobels

The sex lives of constipated scorpions, cute ducklings with an innate sense of physics, and a life-size rubber moose may not appear to have much in common, but they all inspired the winners of this year's Ig Nobels, the prize for comical scientific achievement.

The winners, honored in 10 categories, also included scientists who found that when people on a blind date are attracted to each other, their heart rates synchronize, and researchers who looked at why legal documents can be so utterly baffling, even to lawyers themselves.

You feel science is fun if you read things like these: 

Scorpions can detach a body part to escape a predator—a process called autotomy. But when they lose their tails, they also lose the last portion of the digestive tract, which leads to constipation—and, eventually, death, scientists wrote in the journal "Integrated Zoology."

The long-term decrease in the locomotor performance of autotomized males may impair mate searching.

https://arstechnica.com/science/2022/09/maya-ritual-enemas-and-cons...

Comment by Dr. Krishna Kumari Challa on September 16, 2022 at 11:52am

Researchers develop painless tattoos that can be self-administered

 Instead of sitting in a tattoo chair for hours enduring painful punctures, imagine getting tattooed by a skin patch containing microscopic needles. Researchers have developed low-cost, painless, and bloodless tattoos that can be self-administered and have many applications, from medical alerts to tracking neutered animals to cosmetics.

Researchers have miniaturized the needle so that it's painless, but still effectively deposits tattoo ink in the skin.

Tattoos are used in medicine to cover up scars, guide repeated cancer radiation treatments, or restore nipples after breast surgery. Tattoos also can be used instead of bracelets as medical alerts to communicate serious medical conditions such as diabetes, epilepsy, or allergies.

Various cosmetic products using microneedles are already on the market—mostly for anti-aging—but developing microneedle technology for tattoos is new. 

Tattoos typically use large needles to puncture repeatedly into the skin to get a good image, a time-consuming and painful process. The  Tech team has developed microneedles that are smaller than a grain of sand and are made of tattoo ink encased in a dissolvable matrix.
Because the microneedles are made of tattoo ink, they deposit the ink in the skin very efficiently.

Although most microneedle patches for pharmaceuticals or cosmetics have dozens or hundreds of microneedles arranged in a square or circle, microneedle patch tattoos imprint a design that can include letters, numbers, symbols, and images. By arranging the microneedles in a specific pattern, each microneedle acts like a pixel to create a tattoo image in any shape or pattern.

The researchers start with a mold containing microneedles in a pattern that forms an image. They fill the microneedles in the mold with tattoo ink and add a patch backing for convenient handling. The resulting patch is then applied to the skin for a few minutes, during which time the microneedles dissolve and release the tattoo ink. Tattoo inks of various colors can be incorporated into the microneedles, including black-light ink that can only be seen when illuminated with ultraviolet light.

Song Li, Youngeun Kim, Jeong Woo Lee, Mark R. Prausnitz. Microneedle patch tattoos. iScience, 2022; 105014 DOI: 10.1016/j.isci.2022.105014

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