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Comment by Dr. Krishna Kumari Challa on November 18, 2021 at 9:03am

Understanding how proteins are broken down in cells using advanced microscopes

How do organisms break down proteins when they are finished doing their job?

Protein degradation is a carefully orchestrated process. Proteins are marked for disposal with a molecular label called ubiquitin, and then fed into proteasomes, a kind of cellular paper shredder that chops up the proteins into small pieces. This process of ubiquitination, or labeling proteins with ubiquitin, is involved in a wide range of cellular processes, including cell division, DNA repair, and immune responses.

In a new study published in Nature on November 17, 2021, researchers used advanced electron microscopes to delve deeper into the process of protein degradation. They described the structure of a key enzyme that helps mediate ubiquitination in yeast, part of a cellular process called the N-degron pathway that may be responsible for determining the rate of degradation for up to 80% of equivalent proteins in humans. Malfunctions in this pathway can lead to accumulation of damaged or misfolded proteins, which underlies the aging process, neurodegeneration, and some rare autosomal recessive disorders, so understanding it better provides an opportunity to develop treatments.

Researchers were able to describe the structure of several intermediate enzyme complexes involved in the pathway, which will help researchers looking for ways to target proteins with drugs or intervene in a malfunctioning protein degradation process.

 Minglei Zhao, Structural insights into Ubr1-mediated N-degron polyubiquitination, Nature (2021). DOI: 10.1038/s41586-021-04097-8. www.nature.com/articles/s41586-021-04097-8

https://phys.org/news/2021-11-advanced-microscopes-scientists-cells...

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Comment by Dr. Krishna Kumari Challa on November 18, 2021 at 8:39am

Researchers find the finger snap to have the highest acceleration the human body produces

Snapping of fingers: Using an intermediate amount of friction, not too high and not too low, a snap of the finger produces the highest rotational accelerations observed in humans, even faster than the arm of a professional baseball pitcher. The results were published Nov. 17 in the Journal of the Royal Society Interface.

 In earlier work researc

hers had developed a general framework for explaining the surprisingly powerful and ultrafast motions observed in living organisms. The framework seemed to naturally apply to the snap. It posits that organisms depend on the use of a spring and latching mechanism to store up energy, which they can then quickly release.

Using high-speed imaging, automated image processing, and dynamic force sensors, the researchers analyzed a variety of finger snaps. They explored the role of friction by covering fingers with different materials, including metallic thimbles to simulate the effects of trying to snap while wearing a metallic gauntlet, much like Thanos.

For an ordinary snap with bare fingers, the researchers measured maximal rotational velocities of 7,800 degrees per second and rotational accelerations of 1.6 million degrees per second squared. The rotational velocity is less than that measured for the fastest rotational motions observed in humans, which come from the arms of professional baseball players during the act of pitching. However, the snap acceleration is the fastest human angular acceleration yet measured, almost three times faster than the rotational acceleration of a professional baseball pitcher's arm.

The finger snap occurs in only seven milliseconds, more than twenty times faster than the blink of an eye, which takes more than 150 milliseconds.

When the fingertips of the subjects were covered with metal thimbles, their maximal rotational velocities decreased dramatically, confirming the researchers' imaginations.

Reducing both the compressibility and friction of the skin by using things like metal armours make it a lot harder to build up enough force in your fingers to actually snap.

Surprisingly, increasing the friction of the fingertips with rubber coverings also reduce speed and acceleration. The researchers concluded that a Goldilocks zone of friction was necessary—too little friction and not enough energy was stored to power the snap, and too much friction led to energy dissipation as the fingers took longer to slide past each other, wasting the stored energy into heat.

The ultrafast snap of a finger is mediated by skin friction, Journal of the Royal Society Interface (2021). DOI: 10.1098/rsif.2021.0672. rsif.royalsocietypublishing.or … .1098/rsif.2021.0672

https://phys.org/news/2021-11-art-finger-snap-highest-human.html?ut...

Comment by Dr. Krishna Kumari Challa on November 17, 2021 at 10:29am

The results : The most striking result is the very high estimated probability of winning when batting second in Dubai (where Australia triumphed in the tournament’s final). Even when the batting-second team was ranked lower than its opponent, there still was a high estimated probability of victory.

The analysis revealed some evidence that it was beneficial to bat second in this world cup, but this is likely to depend greatly on the conditions. If we assume a match is played on a randomly selected pitch from the four venues used, and there is a 50% chance the higher-ranked team bats second, my model estimates the probability of winning when batting second is around 0.6, with a 95% confidence interval of 0.48 to 0.71.

So there is a likely benefit to batting second, but it’s far from a foregone conclusion.

https://theconversation.com/does-batting-second-in-t20-world-cup-cr...

Part 4

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Comment by Dr. Krishna Kumari Challa on November 17, 2021 at 10:06am

 analysis found that the timing of the match did not statistically influence the winning probability of the team batting second. In other words, the advantage of batting first or second did not depend on whether the match was staged during the afternoon or the evening.

That leaves two variables that might conceivably influence the situation: the venue hosting the match, and whether the team batting second has a higher or lower ranking than its opponent. That gives eight possible combinations (four venues times two possibilities for batting order) for which the statistical model can generate results.

Because there is just a handful of matches in each category, we can strengthen our statistical analysis using a concept called the “95% confidence interval”. Rather than generating only a single probability estimate, we can also calculate an upper and lower limit to our estimate, between which we can be 95% confident that the true probability is found.

Part 3

Comment by Dr. Krishna Kumari Challa on November 17, 2021 at 10:05am

The first question to ask is whether the pattern of results seen during the world cup could have arisen purely by chance. We do this by using statistical tests to calculate the “p-value”, which tells us the probability of obtaining 29 or more “batting second” wins out of 45 matches if the true winning chance were 50-50.

In this case, we arrive at a “p-value” of around 0.04, or 4%. This probability is reasonably small, suggesting there is indeed some evidence that batting second was beneficial at this world cup, and that the pattern of results may not have arisen by chance.

But given our data set contains only 45 matches, our test does not have much statistical power, which means this evidence is far from overwhelming.

In other words, there is a non-negligible probability (4%) that this pattern of results arose by chance, and that batting second doesn’t confer a crucial advantage after all.

part 2

Comment by Dr. Krishna Kumari Challa on November 17, 2021 at 10:04am

Does batting second in T20 world cup cricket offer a crucial advantage? A statistics professor explains

2021 ICC Men’s T20 World Cup, the tournament’s results: Of the 45 matches played at the tournament, 29 (around 64%) were won by the team batting second. Put another way, teams batting second won almost twice as many matches as teams batting first.

Some critics have gone as far as to suggest teams can “win on a coin toss” when deciding which side will bat first.

There are a range of suggested advantages to batting second, particularly in shorter forms of cricket. Perhaps chief among them is knowing exactly what score will win the game, and being able to plan the innings accordingly. As the afternoon or evening progresses, dew can also form on the ground, making it harder for bowlers to grip the ball and for fielders to retrieve it, and easier for batters to hit balls that “skid onto the bat” rather than changing direction.

But what do the stats actually say? Does the coin toss really confer a crucial advantage? 

Part 1

Comment by Dr. Krishna Kumari Challa on November 17, 2021 at 9:58am

A personalized exosuit for real-world walking

Comment by Dr. Krishna Kumari Challa on November 17, 2021 at 9:48am

Synthetic biology yields easy-to-use underwater adhesives

Several marine organisms, such as mussels, secrete adhesive proteins that allow them to stick to different surfaces under sea water. This attractive underwater adhesion property has inspired decades of research to create biomimetic glues for underwater repair or biological tissue repair. However, existing glues often do not have the desirable adhesion, are hard to use underwater, or are not biocompatible for medical applications. Now, there is a solution from synthetic biology.

Researchers  have developed a method that uses engineered microbes to produce the necessary ingredients for a biocompatible adhesive hydrogel that is as strong as spider silk and as adhesive as mussel foot protein (Mfp), which means it can stick to a myriad of surfaces underwater.

The team integrated the silk-amyloid protein with Mfp and, using a synthetic biology approach, synthesized a tri-hybrid protein that has the benefits of both the strong adhesion of Mfp and the high strength of spider silk. Using the tri-hybrid protein, they prepared adhesive hydrogels.

Because the protein-based adhesive can be biocompatible and biodegradable, the lab is particularly excited about its potential applications in tissue repair. This protein, they write in the paper, is particularly attractive for tendon-bone repair, which suffers from a high failure rate from current suture-based strategies.

Eugene Kim et al, A Biosynthetic Hybrid Spidroin-Amyloid-Mussel Foot Protein for Underwater Adhesion on Diverse Surfaces, ACS Applied Materials & Interfaces (2021). DOI: 10.1021/acsami.1c14182

https://phys.org/news/2021-11-synthetic-biology-yields-easy-to-use-...

Comment by Dr. Krishna Kumari Challa on November 17, 2021 at 9:23am

Killing bacteria with nanoparticles

Researchers  have developed a new technology based on nanoparticles to kill dangerous bacteria that hide inside human cells.

Burkholderia is a genus of bacterium that causes a deadly disease called melioidosis. This disease kills tens of thousands of people each year, particularly in southeast Asia. Antibiotics administered orally or intravenously often don't work very well against it as the bacteria hide away and grow in white blood cells called macrophages.

New research has shown that tiny capsules called polymersomes—which are about 1000th the diameter of a human hair—could be used to carry bug-killing antibiotics right to the site where the bacteria grow inside the cells. Their findings have been published in the journal ACS Nano.

Macrophages are cells of the immune system that have evolved to take up particles from the blood which is crucial to their role in preventing infection, but it also means that they can be exploited by some bacteria which infect and grow inside them.

In this study, the research team added polymersomes to macrophages which were infected with bacteria. Their results showed that the polymersomes were readily taken up by the macrophages and associated with the bacteria inside the cells. This means they could be an effective way to get a high concentration of antibiotics to the site of infection. The team hope this could eventually lead to patients being treated by injection or inhalation of antibiotic-laden capsules, saving many lives each year.

Eleanor Porges et al, Antibiotic-Loaded Polymersomes for Clearance of Intracellular Burkholderia thailandensis, ACS Nano (2021). DOI: 10.1021/acsnano.1c05309

https://phys.org/news/2021-11-bacteria-nanoparticles.html?utm_sourc...

Comment by Dr. Krishna Kumari Challa on November 17, 2021 at 9:10am

To understand how the brain enables navigation with and without visual cues, the researchers recorded from neurons across all layers in the retrosplenial cortex as the animals were free to roam around a large arena. This enabled the neuroscientists to identify neurons in the brain called angular head velocity (AHV) cells, which track the speed and direction of the head.

This work  showed that a single cell can see both kinds of signals: vestibular and visual. What was also critically important was the development of a behavioral task that enabled the scientists to determine that mice improve their estimation of their own head angular speed when a visual cue is present. It's pretty compelling that both the coding of head motion and the mouse's estimates of their motion speed both significantly improve when visual cues are available.

 Troy W Margrie, Multi-sensory coding of angular head velocity in the retrosplenial cortex, Neuron (2021). DOI: 10.1016/j.neuron.2021.10.031. www.cell.com/neuron/fulltext/S0896-6273(21)00846-1

https://medicalxpress.com/news/2021-11-neuroscientists-illuminate-b...

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