Comment

Comment by Dr. Krishna Kumari Challa on Friday

To next see how cells can reconfigure themselves internally in response to change, the team exposed the cells to OC43, a coronavirus that causes the common cold, then repeated the Organelle Profiling analysis. This revealed two distinct shifts: 633 kinds of proteins relocated, meaning that their relationships with other proteins in the cellular map changed significantly. Meanwhile, the overall abundance of 429 kinds of proteins increased or decreased. But, to the team's surprise, only 54 underwent both types of changes.
The shifts in location after OC43 infection provided new clues to the underlying biology. In particular, the relocation of proteins involved in a form of programmed cell death called ferroptosis led the researchers to show that increasing ferroptosis promoted infection, while decreasing it inhibited the virus. This shows that ferroptosis plays a central role in controlling infection, and could be a target for the development of new antiviral therapies.

The researchers are continuing to look for other examples of telltale protein shuffling, both in other viral infections and in Alzheimer's disease.
The group has made the data they have generated via Organelle Profiling freely available to other scientists. The team at CZ Biohub SF is also planning to offer the tools they used, including cells and reagents, to the scientific community. A streamlined software program they are developing will allow other researchers to more readily map the compartmentalization of proteins in the scenarios they study. In return, the team hopes others will contribute their data openly to build better models of how our cells are internally organized.

 Marco Y. Hein et al, Global organelle profiling reveals subcellular localization and remodeling at proteome scale, Cell (2024). DOI: 10.1016/j.cell.2024.11.028

Part 3

Comment by Dr. Krishna Kumari Challa on Friday

Earlier the researchers developed a platform called OpenCell that used microscopy to map the precise cellular location of more than 1,300 kinds of proteins under baseline conditions.
Now rather than focus on precisely pinpointing the location of particular proteins one at a time, their new approach, Organelle Profiling, considers them as constituents of a cell's organelles, its liquid interior (the cytosol), and other internal structures. In the new study, they attached unique molecular tags to 19 such compartments that collectively account for the entire cell.

After tagging, they forced cells through a narrow syringe, gently breaking them open while keeping internal structures intact. Using antibodies designed to recognize the tags, they extracted the individual compartments before determining their protein composition with mass spectrometry, an analytical technique that identifies compounds based on their electrical charge and mass.
From within these compartments, they identified and analyzed the relative location of more than 8,000 unique kinds of proteins.
The same kind of protein could appear in multiple compartments, in some cases showing up faintly when a bit of an organelle was extracted along with a neighboring compartment. The team then looked for proteins with similar profiles. In their analysis, they built a network that treats similar proteins as connected, leading to the appearance of well-delineated clusters of proteins that define individual compartments — endoplasmic reticulum, cytosol, mitochondria, and so on.

Some proteins had significant connections that straddled compartments. These proteins, which the researchers interpreted as being located at compartment boundaries, help the compartments work together to support the cell.

In the end, the team generated a map that organizes proteins according to their relationships with one another — a high-resolution view that spans the entire cell. When they compared this map to previously collected data about the proteins, they found it matched up very well.
Part 2

Comment by Dr. Krishna Kumari Challa on Friday

Scientists create comprehensive map of protein locations within human cells

 Each of our cells is built from a collection of about 10,000 kinds of proteins. Researchers have long had the ability to track the positions of small numbers of these proteins under the lens of a microscope. However, capturing the full scope of their locations in the cell has remained more challenging, let alone following how they change locations as a cell adapts to different conditions.

Proteins in a cell must be in the right department to do their jobs. Scientists  are trying to fully map the cell's organization and  determine how these cellular proteins may be reassigned in a time of crisis or change. A hostile takeover by a virus, for example, can send a cell's proteins to new stations, from which they may either serve the pathogen's aims or help the cell as it attempts to resist the infection.

A new method, described Dec. 31 in Cell and devised by a multidisciplinary team captures spatial organization across the entire cell at an unprecedented level of detail. Their approach maps the majority of a human cell's roughly 10,000 kinds of proteins according to the organelles and other compartments containing them, providing a crucial reference to understand how our cells are built. The team also applied their method to characterize how a portion of these proteins relocate during viral infection.

The new work is an example of "spatial proteomics," a burgeoning field that was named the 2024 "Method of the Year" by the journal Nature Methods. Spatial proteomics aims to increase our understanding of how proteins function by building detailed maps of their locations in cells and tissues.

Researchers typically study cellular responses by looking for increases or decreases in the quantity of particular proteins or their precursor mRNA molecules, as the cell "hires" or "fires" proteins to adapt to changing circumstances. In the experiments reported in the article, however, changes in proteins' location occurred largely independently from changes in their abundance — suggesting this conventional approach captures only a portion of a cell's response.

If we want to get the full picture of what's going on in cells during disease, we need to think not only about measuring abundance, but also changes in spatial organization.

Part 1

Comment by Dr. Krishna Kumari Challa on Friday

Mining dust is suffocating nearby forests in India, study shows

Dust from open cast mining suffocates surrounding forests and inhibits trees' ability to capture carbon from the atmosphere more than previously thought, according to new research by scientists in India and the UK.

Researchers  have assessed the impact of mining dust on forests in Eastern India, which is home to some of the world's major open-pit coal mines. The work is published in the Journal of Geophysical Research: Biogeosciences.

Focusing on the coal mining region of Eastern India, the research team studied detailed satellite images to inform its findings. They also collected 300 leaf samples from 30 different sites in Jharsuguda, and found dust deposits containing aluminum, silica and iron on them.

"Pollution from open cast mines creates a layer of dust that settles on the leaves of trees, making them increasingly less productive and less healthy. We knew this was the case, but we have learned that it is unfortunately worse—and more far spread—than we thought", say the scientists.

The dust affects trees' complex physiological processes, hindering their ability to capture carbon dioxide and damaging their overall health.

Dust from mines that settles on leaves impacts their function, impeding photosynthesis, light interception, nutrient availability, gas-energy exchange, plant-pathogen interactions, and causing physical damage.

Dust particles obstruct the leaves' stomata, the tiny openings through which plants exchange gases with the atmosphere. This reduces the plant's ability to capture carbon and release oxygen.

Mining dust is also impacting trees in a wide geographical area, reaching far beyond the immediate vicinity of the mines—up to 30km away from the mines. The highest concentration of negative impact is along transportation routes to and from the mines.

 This research should provide a solid foundation to inform future environmental management, as well as demonstrate the need for ongoing research to fully understand and mitigate the negative impact of mining on the delicate surrounding ecosystems.

Avinash Kumar Ranjan et al, A New Approach for Prediction of Foliar Dust in a Coal Mining Region and Its Impacts on Vegetation Physiological Processes Using Multi‐Source Satellite Data Sets, Journal of Geophysical Research: Biogeosciences (2024). DOI: 10.1029/2024JG008298

Comment by Dr. Krishna Kumari Challa on Friday

Scientists drill nearly 2 miles down to pull 1.2 million-year-old ice core from Antarctic

An international team of scientists announced this week they've successfully drilled one of the oldest ice cores yet, penetrating nearly 2 miles (2.8 kilometers) to Antarctic bedrock to reach ice they say is at least 1.2 million years old.

Analysis of the ancient ice is expected to show how Earth's atmosphere and climate have evolved. That should provide insight into how Ice Age cycles have changed, and may help in understanding how atmospheric carbon  changed climate, they said.

The same team previously drilled a core about 800,000 years old. The latest drilling went 2.8 kilometers (about 1.7 miles) deep, with a team of 16 scientists and support personnel drilling each summer over four years in average temperatures of about minus-35 Celsius (minus-25.6 Fahrenheit).

Thanks to the analysis of the ice core of the previous Epica campaign they have assessed that concentrations of greenhouse gases, such as carbon dioxide and methane, even during the warmest periods of the last 800,000 years, have never exceeded the levels seen since the Industrial Revolution began.

Today we are seeing carbon dioxide levels that are 50% above the highest levels we've had over the last 800,000 years, the scientists say.

Source: News Agencies

Comment by Dr. Krishna Kumari Challa on Friday

What we eat not only affects our health—but can also alter how our genes function

Fiber is well known to be an important part of a healthy diet, yet not many take it as 'food'.

 A study from  Medical field might finally convince us to fill our plates with beans, nuts, cruciferous veggies, avocados and other fiber-rich foods.

The research, published in Nature Metabolism on Jan. 9 identified the direct epigenetic effects of two common byproducts of fiber digestion and found that some of the alterations in gene expression had anti-cancer actions.

When we eat fiber, the gut microbiome produces short-chain fatty acids. These compounds are more than just an energy source for us: they have long been suspected to indirectly affect gene function. The researchers traced how the two most common short-chain fatty acids in our gut, propionate and butyrate, altered gene expression in healthy human cells, in treated and untreated human colon cancer cells, and in mouse intestines.

They found direct epigenetic changes at specific genes that regulate cell proliferation and differentiation, along with apoptosis, or pre-programmed cell death processes—all of which are important for disrupting or controlling the unchecked cell growth that underlies cancer.

A direct link between eating fiber and modulation of gene function that has anti-cancer effects is likely a global mechanism because the short-chain fatty acids that result from fiber digestion can travel all over the body. 

It is generally the case that people's diet is very fiber poor, and that means their microbiome is not being fed properly and cannot make as many short-chain fatty acids as it should. This is not doing our health any favours.

By identifying the gene targets of these important molecules, we can understand how fiber exerts its beneficial effects and what goes wrong during cancer.

Short-chain fatty acid metabolites propionate and butyrate are unique epigenetic regulatory elements linking diet, metabolism and gene expression, Nature Metabolism (2025). DOI: 10.1038/s42255-024-01191-9

Comment by Dr. Krishna Kumari Challa on Thursday

Why do birds make so many different sounds?

Birds make sounds to communicate, whether to find a potential mate, ward off predators, or just sing for pleasure.

But the conditions that contribute to the immense diversity of the sounds they make are not well understood. Researchers have conducted the first-ever global study of the factors that influence bird sounds, using more than 100,000 audio recordings from around the world. The new study, recently published in the journal Proceedings of the Royal Society B, revealed insightful patterns for why birds make certain noises and at what frequency.

Researchers analyzed audio recordings of bird sounds taken by people around the world and submitted to a bird-watching repository called xeno-canto. The analyzed recordings represented 77% of known bird species.

The study's major takeaways included:

The habitats of bird species influence the frequency of the sounds they may make in unexpected ways. For example, in ecosystems with a lot of rushing water there is a constant level of white noise occurring at a lower frequency. In such cases, researchers found that birds tend to make sounds of higher frequency, likely so they wouldn't be drowned out by the water.

Bird species living at the same latitudes make similar sounds. Observing this pattern on a global scale is an important piece of the puzzle in the evolutionary story of bird sounds. It could inspire further research into the aspects of geographic location that influence bird sounds.

A bird's beak shape and body mass are important. Generally, smaller birds create higher frequency sounds while larger birds create lower frequency sounds. The global analysis not only proved this hypothesis correct, but it also added new information about the nature of the relationship between beak shape, body mass and sound.

Smaller bird species tend to have a wider range of frequencies at which they can make sound as a protection mechanism. Smaller, more vulnerable birds can benefit from being able to make a range of sounds. Higher frequencies can help them communicate with fellow birds of the same species, while lower frequencies can serve as camouflage, tricking potential threats into thinking they are larger and less vulnerable than they actually are.

The research also contributed to the broader understanding of soundscapes—all of the sounds heard in any particular landscape.

: H. S. Sathya Chandra Sagar et al, Global analysis of acoustic frequency characteristics in birds, Proceedings of the Royal Society B: Biological Sciences (2024). DOI: 10.1098/rspb.2024.1908

Comment by Dr. Krishna Kumari Challa on Thursday

Plant cells gain immune capabilities when it's time to fight disease, scientists discover

Human bodies defend themselves using a diverse population of immune cells that circulate from one organ to another, responding to everything from cuts to colds to cancer. But plants don't have this luxury.

Because plant cells are immobile, each individual cell is forced to manage its own immunity in addition to its many other responsibilities, like turning sunlight into energy or using that energy to grow. How these multitasking cells accomplish it all—detecting threats, communicating those threats, and responding effectively?

Research by  scientists reveals how plant cells switch roles to protect themselves against pathogens. When a threat is encountered, the cells enter a specialized immune state and temporarily become PRimary IMmunE Responder (PRIMER) cells—a new cell population that acts as a hub to initiate the immune response.

The researchers also discovered that PRIMER cells are surrounded by another population of cells they call bystander cells, which seem to be important for transmitting the immune response throughout the plant.

The findings, published in Nature on January 8, 2025, bring researchers closer to understanding the plant immune system—an increasingly important task amid the growing threats of antimicrobial resistance and climate change, which both escalate the spread of infectious disease.

Plants encounter a wide range of pathogens, like bacteria that sneak in through leaf surface pores or fungi that directly invade plant "skin" cells. Since plant cells are stationary, when they encounter any of these pathogens, they become singularly responsible for responding and alerting nearby cells.

Another interesting side effect of immobile cells is the fact that different pathogens may enter a plant at different locations and times, leading to varying immune response stages occurring simultaneously across the plant.

With factors like timing, location, response state, and more all at play, an infected plant is a complicated organism to understand.

To tackle this, the research team turned to two sophisticated cell profiling techniques called time-resolved single-cell multiomics and spatial transcriptomics. By pairing the two, the team was able to capture the plant immune response in each cell with unprecedented spatiotemporal resolution.

Discovering these rare PRIMER cells and their surrounding bystander cells is a huge insight into how plant cells communicate to survive the many external threats they face day-to-day.

Joseph Ecker, A rare PRIMER cell state in plant immunity, Nature (2025). DOI: 10.1038/s41586-024-08383-z. www.nature.com/articles/s41586-024-08383-z

Comment by Dr. Krishna Kumari Challa on Thursday

The discoveries were possible thanks to the creation of Human Domainome 1, an enormous library of protein variants. The catalog includes more than half a million mutations across 522 human protein domains, the bits of a protein which determine its function. It is the largest catalog of human protein domain variants to date.

Protein domains are specific regions which can fold into a stable structure and perform a job independently of the rest of the protein. Human Domainome 1 was created by systematically changing each amino acid in these domains to every other possible amino acid, creating a catalog of all possible mutations.

The impact of these mutations on protein stability was discovered by introducing mutated protein domains into yeast cells. The transformed yeast could only produce one type of mutated protein domain, and cultures were grown in test tubes under conditions which linked the stability of the protein to the growth of the yeast. If a mutated protein was stable, the yeast cell would grow well. If the protein was unstable, the yeast cell's growth would be poor.
Using a special technique, the researchers ensured only the yeast cells producing stable proteins could survive and multiply. By comparing the frequency of each mutation before and after the yeast growth, they determined which mutations led to stable proteins and which caused instability.

Though Human Domainome 1 is around 4.5 times bigger than previous libraries of protein variants, it still only covers 2.5% of known human proteins. As researchers increase the size of the catalog, the exact contribution of disease-causing mutations to protein instability will become increasingly clear.

In the meantime, researchers can use the information from the 522 protein domains to extrapolate to proteins that are similar. This is because mutations often have similar effects on proteins that are structurally or functionally related. By analyzing a diverse set of protein domains, the researchers discovered patterns in how mutations affect protein stability that are consistent across related proteins.

Essentially, this means that data from one protein domain can help predict how mutations will impact other proteins within the same family or with similar structures. The 'rules' from these 522 domains are enough to help us make educated predictions about many more proteins than there are in the catalog.
The study has limitations. The researchers examined protein domains in isolation rather than within full-length proteins. In living organisms, proteins interact with other parts of the protein and with other molecules in the cell.

The study might not fully capture how mutations affect proteins in their natural habitat inside human cells. The researchers plan on overcoming this by studying mutations in longer protein domains, and eventually, full-length proteins.

Ben Lehner, Site saturation mutagenesis of 500 human protein domains, Nature (2025). DOI: 10.1038/s41586-024-08370-4. www.nature.com/articles/s41586-024-08370-4

Part 3

Comment by Dr. Krishna Kumari Challa on Thursday

Rett Syndrome is a neurological disorder which causes severe cognitive and physical impairments. It is caused by mutations in the MECP2 gene, which produces a protein responsible for regulating gene expression in the brain.
The study found that many mutations in MECP2 do not destabilize the protein but are instead found in regions which affect how MECP2 binds to DNA to regulate other genes. This loss of function could be disrupting brain development and function.
By distinguishing whether a mutation destabilizes a protein or alters its function without affecting stability, we can tailor more precise treatment strategies. This could mean the difference between developing drugs that stabilize a protein versus those that inhibit a harmful activity. It's a significant step toward personalized medicine.
The study also found that the way mutations cause disease often relates to whether the disease is recessive or dominant. Dominant genetic disorders occur when a single copy of a mutated gene is enough to cause the disease, even if the other copy is normal, while recessive conditions occur when an individual inherits two copies of a mutated gene, one from each parent.

Mutations causing recessive disorders were more likely to destabilize proteins, while mutations causing dominant disorders often affected other aspects of protein function, such as interactions with DNA or other proteins, rather than just stability.

For example, the study found that a recessive mutation in the CRX protein, which is important for eye function, destabilizes the protein significantly, which could be causing heritable retinal dystrophies because the lack of a stable, functional protein impairs normal vision.

However, two different types of dominant mutations meant the protein remained stable but functioned improperly anyway, causing retinal disease even though the protein's structure is intact.
Part 2

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