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Comment by Dr. Krishna Kumari Challa on August 25, 2023 at 12:38pm

Science and non-English-speaking scientists

Most journals offer minimal support for scientists who don't speak fluent English. An analysis of 736 biological-science journals found that only 2 stated that manuscripts would not be rejected solely on the .... A survey of the editors-in-chief of 262 of these journals found that only 6% instructed reviewers not to base their assessments solely on language proficiency. Less than 10% of journals offered author guidelines in at least one language other than English or allowed authors to publish articles in other languages.

Abstract

Scientific knowledge is produced in multiple languages but is predominantly published in English. This academic publishing practice creates a language barrier to the generation and transfer of scientific knowledge between communities with diverse linguistic backgrounds, hindering the ability of scholars and communities to address global challenges and achieve diversity and equity in science, technology, engineering, and mathematics (STEM). To overcome those barriers, publishers and journals should provide a fair system that supports non-native English speakers and disseminates knowledge across the globe. Researchers surveyed policies of 736 journals in biological sciences to assess their linguistic inclusivity, identify predictors of inclusivity, and propose actions to overcome language barriers in academic publishing. Their assessment revealed a grim landscape where most journals were making minimal efforts to overcome language barriers in academic publishing. The Impact Factor of journals was negatively associated with the adoption of a number of inclusive policies whereas the ownership by a scientific society tended to have a positive association. Counter to their expectations, the linguistic diversity of editorial boards and the Open Access model did not have a major positive association with the adoption of linguistically inclusive policies. The researchers proposed a set of actions to overcome language barriers in academic publishing, including the revision of exclusionary practices, clear communication of linguistic policies in author guidelines, and renegotiation of power dynamics between publishers and editorial boards. Academic publishing requires a change to support scholars and communities with limited English proficiency and scientific societies are well positioned to lead this cultural shift.

Nature 
Reference: EcoEvoRxiv preprint (not peer reviewed)

https://ecoevorxiv.org/repository/view/5475/

Comment by Dr. Krishna Kumari Challa on August 25, 2023 at 11:57am

How the 'treadmill conveyor belt' ensures proper cell division

Researchers at the Center for Genomic Regulation (CRG) have discovered how proteins work in tandem to regulate "treadmilling," a mechanism used by the network of microtubules inside cells to ensure proper cell division. The findings are published in the Journal of Cell Biology.

Microtubules are long tubes made of proteins that serve as infrastructure to connect different regions inside of a cell. Microtubules are also critical for cell division, where they are key components of the spindle, the structure which attaches itself to chromosomes and pulls them apart into each new cell.

For the spindle to function properly, cells rely on microtubules to "treadmill." This involves one end of the microtubule (known as the minus end) to lose components while the other (the plus end) adds components. The effect is like that of a treadmill conveyor belt, where the microtubules appear to be moving continuously without changing their overall length.

Treadmilling is crucial for cell division. The most likely theory is that treadmilling helps the cell regulate its attachments to chromosomes by maintaining tension. Because microtubules are often growing from their plus ends, this tension can be provided by constant shrinking from the minus end.

The authors of the study used various isolated proteins known to play a central role in microtubule biology, putting them together in a test tube and visualizing them using a microscope.

Three proteins were found to be critical for regulating treadmilling: KIF2A, a protein belonging to a larger family of proteins that dismantles microtubules, the γ-tubulin ring complex (γ-TuRC), a scaffold for microtubules to grow from, and spastin, an enzyme that acts like a scissor cutting microtubules.

The researchers found that the correct control of treadmilling requires the coordinated action of all three proteins. 

Gil Henkin et al, The minus end depolymerase KIF2A drives flux-like treadmilling of γTuRC-uncapped microtubules, Journal of Cell Biology (2023). DOI: 10.1083/jcb.202304020

Comment by Dr. Krishna Kumari Challa on August 25, 2023 at 11:53am

 Unlocking the secrets to brain diseases: When proteins get stuck at the solid phase

Many diseases affecting the brain and nervous system are linked to the formation of protein aggregates, or solid condensates, in cells from their liquid form condensate, but little is known about this process.

This liquid-to-solid transition can trigger the formation of what are called amyloid fibrils. These can further form plaques in neurons causing neurodegenerative diseases such as Alzheimer's.

Biomedical Engineers have now developed sophisticated optical techniques to monitor at close range the process by which these protein aggregates form.

By testing a protein associated with amyotrophic lateral sclerosis—ALS disease, which affected astrophysicist Professor Stephen Hawking—the Sydney engineers closely monitored the transition of this protein from its liquid to solid phase.

Proteins regularly form condensates during liquid-to-liquid phase separation in a wide range of critical and healthy biological functions, such as the formation of human embryos. This process assists biochemical reactions where protein concentrations are critical and also promotes healthy protein–protein interactions. However, this process also increases the risk of dysfunctional aggregation, where unhealthy aggregates of solid proteins form in human cells.

This can lead to aberrant structures associated with neurodegenerative diseases because the proteins no longer exhibit rapid reversibility back to liquid form.  It is therefore crucial to monitor condensate dynamics, as they directly affect pathological states.

The world-first nanoscale optical observation of this process has allowed the team to determine that the transition from liquid to solid protein starts at the interface of the protein condensates. This window onto the phase transition also revealed that the internal structures of these protein agglomerates are heterogenous, where previously they were thought to be homogeneous.

Yi Shen et al, The liquid-to-solid transition of FUS is promoted by the condensate surface, Proceedings of the National Academy of Sciences (2023). DOI: 10.1073/pnas.2301366120

Comment by Dr. Krishna Kumari Challa on August 25, 2023 at 11:41am

Comment by Dr. Krishna Kumari Challa on August 25, 2023 at 11:00am

Study shows that astrocytes in the cortex modulate the dominant behavior of male mice

The social behavior of animals has been the key focus of extensive neuroscience and biomedical studies, as it is often aligned with behaviors observed in humans. Better understanding these behaviors and the neural processes underpinning them could ultimately also have implications for the treatment of different psychiatric disorders that affect how humans socialize with others.

Researchers recently conducted a study specifically exploring male dominance behavior among male mice. These behaviours naturally lead to the formation of social hierarchies among groups of mice, with some males accessing more food and water than others. 

A recent paper, published in Nature Neuroscience, highlights the role of astrocytes in the outer layer of the brain (i.e., the cortex), in modulating the dominance behavior of male mice. In addition, it sheds some light on the specific neural processes through which astrocytes modulate these behaviours.

The results gathered by the researchers hint at the involvement of communication between dmPFC astrocytes and neurons in the dominant behaviour of male mice. 

This work implies that astrocytes also play critical role in computing and processing high-order brain functions. It also suggests that such intercellular interplay may decipher the etiology of many psychiatric disorders.

 Kyungchul Noh et al, Cortical astrocytes modulate dominance behavior in male mice by regulating synaptic excitatory and inhibitory balance, Nature Neuroscience (2023). DOI: 10.1038/s41593-023-01406-4

Nguyen T. Phi et al, Control of social hierarchy beyond neurons, Nature Neuroscience (2023). DOI: 10.1038/s41593-023-01392-7

Comment by Dr. Krishna Kumari Challa on August 25, 2023 at 9:59am

Scientists discover a previously unknown way cells break down proteins

Short-lived proteins control gene expression in cells to carry out a number of vital tasks, from helping the brain form connections to helping the body mount an immune defense. These proteins are made in the nucleus and are quickly destroyed once they've done their job.

Despite their importance, the process by which these proteins get broken down and removed from cells once they are no longer needed has eluded scientists for decades—until now.

It is well established that cells can break down proteins by tagging them with a small molecule called ubiquitin. The tag tells the proteasome that the proteins are no longer needed, and it destroys them. 

However, sometimes the proteasome breaks down proteins without the help of ubiquitin tags, leading researchers to suspect that there was another, ubiquitin-independent mechanism of protein degradation.

Researchers now  identified a protein called midnolin that plays a key role in degrading many short-lived nuclear proteins. The study shows that midnolin does so by directly grabbing the proteins and pulling them into the cellular waste-disposal system, called the proteasome, where they are destroyed.

Because the proteins broken down by this process modulate genes with important functions related to the brain, the immune system, and development, scientists may eventually be able to target the process as a way of controlling protein levels to alter these functions and correct any dysfunction.

Xin Gu et al, The midnolin-proteasome pathway catches proteins for ubiquitination-independent degradation, Science (2023). DOI: 10.1126/science.adh5021.

Comment by Dr. Krishna Kumari Challa on August 24, 2023 at 1:08pm

Spectroscopy, Explained

Comment by Dr. Krishna Kumari Challa on August 24, 2023 at 1:00pm

Evidence of carbonic acid found in interstellar space for the first time

An international team of astrophysicists, astronomers and chemists has found evidence of carbonic acid (HOCOOH) in interstellar space, marking the first time it has been detected in such a setting. In their paper published in The Astrophysical Journal, the group describes their discovery, where it was found, and what it might mean for research into the origins of life.

Prior research has led to the discovery of acetic and formic acid in interstellar space; both are carboxylic acids, as is carbonic acid. All three are believed to be building blocks of life. Finding them in such distant places gives credence to theories that suggest that they were delivered to Earth via comets or meteorites. In this new effort, the researchers were studying the molecular cloud G+0.693-0.027 near the center of the Milky Way when they found evidence of HOCOOH.

Carboxylic acids have a carbon atom and are doubly bonded to an oxygen atom. They are also singly bonded to a hydroxyl group. Carbonic acid is formed here on Earth when CO2 mixes and dissolves in water. It produces the acidic effect in soft drinks. It is also responsible for the increasing acidity of the oceans due to increased amounts of atmospheric CO2. The research team notes that carbonic acid has been observed on several of Jupiter's moons, on comets and on Mercury and Mars—but this is the first time it has been detected in interstellar space. They also note that the presence of carbonic acid in an interstellar molecular cloud suggests a high degree of complexity in the interstellar medium, which means it may also harbor amino-acid-related compounds.

They also found an upper limit to the abundance of HOCOOH with respect to diatomic hydrogen in the molecular cloud, which they suggest hints at the possibility that carbonic acid may be abundant in interstellar space. They note that one of the reasons carbonic acid has not been spotted in interstellar space until now, despite its apparent abundance, is that it is undetectable by radio astronomical observations.

 Miguel Sanz-Novo et al, Discovery of the Elusive Carbonic Acid (HOCOOH) in Space, The Astrophysical Journal (2023). DOI: 10.3847/1538-4357/ace523

Comment by Dr. Krishna Kumari Challa on August 24, 2023 at 12:55pm

How a cup of water can unlock the secrets of our universe

Researchers have made a discovery that could change our understanding of the universe. In their study published in Science Advances, they reveal, for the first time, that there is a range in which fundamental constants can vary, allowing for the viscosity needed for life processes to occur within and between living cells. This is an important piece of the puzzle in determining where these constants come from and how they impact life as we know it.

In 2020, the same scientists found that the viscosity  of liquids is determined by fundamental physical constants, setting a limit on how runny a liquid can be. Now this result is taken into the realm of life sciences.

Fundamental physical constants shape the fabric of the universe we live in. Physical constants are quantities with a value that is generally believed to be both universal in nature and to remain unchanged over time—for example the mass of the electron. They govern nuclear reactions and can lead to the formation of molecular structures essential to life, but their origin is unknown. This research might bring scientists one step closer to determining where these constants come from.

Understanding how water flows in a cup turns out to be closely related to the grand challenge to figure out fundamental constants. Life processes in and between living cells require motion and it is viscosity that sets the properties of this motion. If fundamental constants change, viscosity would change too impacting life as we know it. For example, if water was as viscous as tar life would not exist in its current form or not exist at all. This applies beyond water, so all life forms using the liquid state to function would be affected.

Any change in fundamental constants including an increase or decrease would be equally bad news for flow and for liquid-based life. We expect the window to be quite narrow: for example, viscosity of our blood would become too thick or too thin for body functioning with only a few percent change of some fundamental constants such as the Planck constant or electron charge.

Surprisingly, the fundamental constants were thought to be tuned billions of years ago to produce heavy nuclei in stars and back then life as we know it today didn't exist. There was no need for these constants to be fine-tuned at that point to also enable cellular life billions of years later, and yet these constants turn out to be bio-friendly to flow in and between living cells. An accompanying conjecture is that multiple tunings may have been involved and this then suggests a similarity to biological evolution where traits were acquired independently. Through evolutionary mechanisms, fundamental constants may be the result of nature arriving at sustainable physical structures. It remains to be seen how the principles of evolution can be helpful to understand the origin of fundamental constants.

Kostya Trachenko, Constraints on fundamental physical constants from bio-friendly viscosity and diffusion, Science Advances (2023). DOI: 10.1126/sciadv.adh9024. www.science.org/doi/10.1126/sciadv.adh9024

Comment by Dr. Krishna Kumari Challa on August 24, 2023 at 12:49pm

First complete sequence of a human Y chromosome

For decades, the Y chromosome—one of the two human sex chromosomes—has been notoriously challenging for the genomics community to sequence due to the complexity of its structure.

Now, this elusive area of the genome has been fully sequenced, a feat that finally completes the set of end-to-end human chromosomes and adds 30 million new bases to the human genome reference, mostly from challenging-to-sequence satellite DNA. These bases reveal 41 additional protein-coding genes, and provide crucial insight for those studying important questions related to reproduction, evolution, and population change.

The complete, annotated Y chromosome reference is available for use on the UCSC Genome Browser and can be accessed via Github.

When scientists and clinicians study an individual's genome, they compare the individuals' DNA to that of a standard reference to determine where there is variation. Until now, the Y chromosome portion of the human genome has contained large gaps which made it difficult to understand variation and associated disease.

The structure of the Y chromosome has been challenging to decode because some of the DNA is organized in palindromes—long sequences that are the same forward and backward—spanning up to more than a million base pairs. Moreover, a very large part of the Y chromosome that was missing from the previous version of the Y reference is satellite DNA—large, highly repetitive regions of non-protein-coding DNA. On the Y chromosome, two satellites are interlinked with each other, further complicating the sequencing process.

The researchers were able to achieve a gapless read of the Y chromosome due to advances in long-read sequencing technology and new, innovative computational assembly methods that could deal with the repetitive sequences and transform the raw data from sequencing into a usable resource.

These new method assemblies allowed the team to tackle some of the particularly challenging aspects of the Y chromosome, such as pinpointing precisely where an inversion occurs in a palindromic sequence—a technique that can be used to find other inversions. The methods established in the paper will allow scientists to complete more end-to-end reads of human Y chromosomes to get a better understanding of how this genetic material affects the diverse human population.

The complete Y chromosome reference will allow scientists to better study a myriad of features about this part of the human genome in a way that has never before been possible.

The complete sequence of a human Y chromosome, Nature (2023). DOI: 10.1038/s41586-023-06457-y. www.nature.com/articles/s41586-023-06425-6. On bioRxiv: DOI: 10.1101/2022.12.01.518724

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