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Comment by Dr. Krishna Kumari Challa on January 26, 2023 at 11:35am

Using running to escape everyday stresses may lead to exercise dependence instead of mental well-being

Recreational running offers a lot of physical and mental health benefits—but some people can develop exercise dependence, a form of addiction to physical activity which can cause health issues. Shockingly, signs of exercise dependence are common even in recreational runners. A study published in Frontiers in Psychology investigated whether the concept of escapism can help us understand the relationship between running, well-being, and exercise dependence.

Escapism is an everyday phenomenon among humans, but little is known regarding its motivational underpinnings, how it affects experiences, and the  psychological outcomes from it.

Escapism is often defined as 'an activity, a form of entertainment, etc. that helps you avoid or forget unpleasant or boring things. In other words, many of our everyday activities may be interpreted as escapism. The psychological reward from escapism is reduced self-awareness, less rumination, and a relief from one's most pressing, or stressing, thoughts and emotions.

Escapism can restore perspective, or it can act as a distraction from problems that need to be tackled. Escapism which is adaptive, seeking out positive experiences, is referred to as self-expansion. Meanwhile maladaptive escapism, avoiding negative experiences, is called self-suppression. Effectively, running as exploration or as evasion.

These two forms of escapism are stemming from two different mindsets, to promote a positive mood, or prevent a negative mood.

Escapist activities used for self-expansion have more positive effects but also more long-term benefits. Self-suppression, by contrast, tends to suppress positive feelings as well as negative ones and lead to avoidance.

Part 1

Comment by Dr. Krishna Kumari Challa on January 26, 2023 at 8:30am

Expert analysis refutes claims that humans are colonized by bacteria before birth

Scientific claims that babies harbor live bacteria while still in the womb are inaccurate, and may have impeded research progress, according to University College Cork (UCC) researchers at APC Microbiome Ireland, a world-leading Science Foundation Ireland (SFI) Research Center, which led a perspective published today in the journal Nature.

Prior claims that the human placenta and amniotic fluid are normally colonized by bacteria would, if true, have serious implications for clinical medicine and pediatrics and would undermine established principles in immunology and reproductive biology.

To examine these claims, UCC & APC Principal Investigator Prof. Jens Walter assembled a trans-disciplinary team of 46 leading experts in reproductive biology, microbiome science, and immunology from around the world to evaluate the evidence for microbes in human fetuses.

A healthy human fetus is sterile

The team unanimously refuted the concept of a fetal microbiome and concluded that the detection of microbiomes in fetal tissues was due to contamination of samples drawn from the womb. Contamination occurred during vaginal delivery, clinical procedures or during laboratory analysis.

In the report in Nature, the international experts encourage researchers to focus their studies on the microbiomes of mothers and their newborn infnats and on the microbial metabolites crossing the placenta that prepare the fetus for post-natal life in a microbial world.

The expert international authors also provide guidance on how scientists in the future can avoid pitfalls of contamination in the analysis of other samples where microbes are expected to be absent or present at low levels, such as internal organs and tissues within the human body.

Jens Walter, Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies, Nature (2023). DOI: 10.1038/s41586-022-05546-8. www.nature.com/articles/s41586-022-05546-8

Comment by Dr. Krishna Kumari Challa on January 25, 2023 at 9:38am

Study shows how cells prevent harmful extra copies of DNA

A protein that prepares DNA for replication also prevents the replication process from running out of control, according to a new study.

 The cells of humans and all other higher organisms use a complex system of checkpoints and "licensing" proteins to ensure that they replicate their genomes precisely once before dividing. In preparation for cell division, the licensing proteins attach to specific regions in the DNA, designating them as replication origins. When the DNA synthesis phase of the cell cycle begins, replication begins only at those licensed sites, and only initiates, or "fires" once, according to the current model.

That model was missing a crucial point, though. The same factor that is allowing for this licensing to happen is only degraded after these replication origins have fired. In principle, the cell could load these licensing machines onto DNA that's already replicated, so, instead of two copies, you're getting three or four copies of that segment of the DNA, and these cells would be expected to lose genome integrity and die or become cancerous.

Figuring out how cells avoid that fate has been tricky.  Scientists needed to be studying events in the first minutes of the DNA synthesis phase of the cell cycle, so it's a very transient period. 

 To solve this difficult experimental problem, researchers used computer-aided microscopy to monitor thousands of growing cells simultaneously, catching the replicating cells in the act and analyzing the activities of their licensing and replication factors.

The work revealed that a well-known licensing factor, CDT1, not only licenses a segment of DNA to become a replication origin, but also acts as a brake for DNA replication, preventing an essential replication enzyme called CMG helicase from functioning. To start synthesizing DNA, the cell's enzymes must first break down CDT1.

Nalin Ratnayeke et al, CDT1 inhibits CMG helicase in early S phase to separate origin licensing from DNA synthesis, Molecular Cell (2023). DOI: 10.1016/j.molcel.2022.12.004

Comment by Dr. Krishna Kumari Challa on January 25, 2023 at 9:32am

Earth's inner core may have started spinning other way: Study

Earth's inner core, a hot iron ball the size of Pluto, has stopped spinning in the same direction as the rest of the planet and might even be rotating the other way, recent research suggested.

 

Roughly 5,000 kilometers (3,100 miles) below the surface we live on, this "planet within the planet" can spin independently because it floats in the liquid metal outer core.

Exactly how the inner core rotates has been a matter of debate between scientists—and the latest research is expected to prove controversial.

What little is known about the inner core comes from measuring the tiny differences in seismic waves—created by earthquakes or sometimes nuclear explosions—as they pass through the middle of the Earth.

Seeking to track the inner core's movements, new research published in the journal Nature Geoscience analyzed seismic waves from repeating earthquakes over the last six decades.

The study's authors said they found that the inner core's rotation "came to near halt around 2009 and then turned in an opposite direction".

Researchers think the inner core rotates, relative to the Earth's surface, back and forth, like a swing.

One cycle of the swing is about seven decades", meaning it changes direction roughly every 35 years, they added.

They said it previously changed direction in the early 1970s, and predicted the next about-face would be in the mid-2040s.

The researchers said this rotation roughly lines up with changes in what is called the "length of day"—small variations in the exact time it takes Earth to rotate on its axis.

So far there is little to indicate that what the inner core does has much effect on surface dwellers.

But the researchers said they think there were physical links between all Earth's layers, from the inner core to the surface.

However, experts not involved in the study expressed caution about its findings, pointing to several other theories and warning that many mysteries remain about the center of the Earth. None of the models made so far explain all the data very well, according to them.

Other researchers published research last year suggesting that the inner core oscillates far more quickly, changing direction every six years or so. Their work was based on seismic waves from two nuclear explosions in the late 1960s and early 1970s.

Another theory has some good evidence supporting it—is that the inner core only moved significantly between 2001 to 2013 and has stayed put since.

These mathematical models are most likely all incorrect because they explain the observed data but are not required by the data.

So scientists keep guessing and make more efforts to gather more data till evidence becomes more convincing.

Yi Yang et al, Multidecadal variation of the Earth's inner-core rotation, Nature Geoscience (2023). DOI: 10.1038/s41561-022-01112-z

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Comment by Dr. Krishna Kumari Challa on January 25, 2023 at 9:15am

Study shows that the lateral orbitofrontal cortex 'writes' cognitive maps in the brain

The orbitofrontal cortex (OFC) is a region in the frontal lobe of the brain known to be involved in decision-making and information processing. The lateral part of this brain region, known as the lOFC, has been identified as a particularly salient region for the creation of so-called "cognitive maps."

Cognitive maps are mental representations of the world that are thought to guide human behaviour. While past studies have linked the lOFC to the brain's use of these maps, it is still unclear whether it creates these maps or merely deploys them when necessary.

Researchers have recently carried out a study exploring these two hypotheses, with the hope of better understanding the functions of the lOFC. Their findings, published in Nature Neuroscience, suggest that the lateral OFC is directly involved in the writing of cognitive maps.

Scientists reasoned that if the lOFC is needed for updating maps, then it would also be critical for the creation of new maps during the initial learning of a new association, i.e., the creation of a new cognitive map.

They conducted experiments using rats and the findings gathered by them provide additional evidence for the cartographer hypothesis, suggesting that the lOFC plays a key role in writing cognitive maps. However, they also show that blocking activity in the lOFC does not fully disrupt model-based behavior, but rather prevents the rats from incorporating all aspects of the task they are learning to complete into cognitive maps.

Overall, it now seems that the lOFC is most important for incorporating, or updating, information that is related to the specific identity of predicted outcomes. This represents a new and more nuanced hypothesis for lOFC function, and really of how the brain parses information when learning about the structure of reality.

Kauê Machado Costa et al, The role of the lateral orbitofrontal cortex in creating cognitive maps, Nature Neuroscience (2022). DOI: 10.1038/s41593-022-01216-0

Comment by Dr. Krishna Kumari Challa on January 25, 2023 at 8:34am

In addition to their role in cancer-cell death via pyroptosis, pore-forming gasdermins are a family of proteins also implicated in the immune response. One of these proteins, gasdermin D, has held sway in cancer-cell death when induced by the formation of caspase-1–activating inflammasomes. But the story of pyroptosis apparently doesn't begin and end with gasdermin D or or its close cousin, gasdermin E. It is a molecular saga that is far more complex than other studies have reported, scientists say.

Caspase-1 activates gasdermin D under inflammatory conditions, whereas caspase-3 activates gasdermin E under apoptotic conditions, such as those induced by chemotherapy, scientists asserted. These pathways are thought to be separate.

However, researchers found that they are part of an integrated network of gatekeepers that enables pyroptotic cell death. They observed that gasdermin D was the primary pyroptotic mediator in cultured blood cells in response to doxorubicin and etoposide, two common chemotherapies for hematopoietic malignancies.

 just to illustrate how complex gasdermins are in health and disease, another gasdermin protein, gasdermin A, along with gasdermin D, additionally have been implicated in autoimmune diseases and certain cancers. Yet, as reported in intricate detail in the Case Western study, gasdermin proteins are noteworthy for their pore-forming capabilities, particularly under the influence of chemotherapy.

 offers fresh insight into pyroptotic pathways by uncovering multiple routes to cancer-cell death—a contrarian stance to prevailing scientific wisdom. Even though a high abundance of gasdermin E had a dominant effect, the conversion to pyroptosis in human myeloid cells could be independently mediated via the transmembrane protein pannexin-1, a channel also known as PANX1. This occurred either through the induction of an alternate pyroptotic pathway dependent on gasdermin D or independent entirely of gasdermins.

In blood and bone marrow biopsies from 15 leukemia patients, the relative abundance of gasdermin E, gasdermin D, and PANX1 predicted which pathway would mediate pyroptotic cell death in response to chemotherapy exposure.

The take home message from the study is multifocal: Cancer cells don't simply die just because they've been exposed to chemo. They die through a programmed mechanism that can proceed through any one of several signaling pathways. 

They also have soundly demonstrated that pyroptosis during chemotherapy doesn't rely solely on gasdermin E. Studying human myeloid cells exposed to chemo, the scientists found that pyroptosis can also proceed through PANX1. And even in the face of dogma-challenging research, there may be other pore-forming pathways that have yet to be found.

 Bowen Zhou et al, Gasdermins and pannexin-1 mediate pathways of chemotherapy-induced cell lysis in hematopoietic malignancies, Science Signaling (2022). DOI: 10.1126/scisignal.abl6781

Part 2

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Comment by Dr. Krishna Kumari Challa on January 25, 2023 at 8:29am

How cancer cells die: Scientists explore new pathways of pyroptosis, killer kin of apoptosis

You can't understand the life cycle of a cell without learning how they die. That is why the concept of apoptosis—programmed cell death—is taught in schools.

What's usually not taught is another way that cells die, a process called pyroptosis, an inflammatory and necrotic form of cell death that primarily involves cancer cells. During chemotherapy, apoptosis can morph into pyroptosis. For patients receiving chemo, apoptosis not only turns into pyroptosis, the process can help activate the immune system. Both the initiation of pyroptosis and activation of the immune system are mediated through specific protein pathways.

To date, most studies have connected chemotherapy-induced pyroptosis to a mediator protein called gasdermin E, which is typically thought of as the sole executioner in this process. Yet, an intriguing round of research has taken a deep dive into the process of pyroptosis, uncovering new molecular pathways that trigger this form of programmed cell death.

New discoveries have emerged from a novel series of investigations that challenge prevailing scientific wisdom about the way cells die under the influence of chemotherapy. The research sheds new light on pyroptosis in chemo-based cancer treatment by expanding the possible number of protein pathways involved in this form of cell death, and hinting that still other pathways may be found in the future.

In response to chemotherapy, the induction of apoptotic cell death can be converted to a form of lytic cell death called pyroptosis.

The term "lytic cell death," or "cell lysis," refers to the breakdown of a cell caused by irrevocable damage to its outermost membrane. A cell can't survive when its contents are spilling out through holes, and that's what pyroptosis is all about. It's bruising and violent—and aimed at cell death. During pyroptosis, a cascade of molecular reactions punch large pores in cell membranes, irrevocably destabilizing, and ultimately, destroying the cells.

For chemo to have an impact, it must trigger biological pathways that lead to cell death. The scientists' elegant recent research, which includes analyses of blood and bone marrow biopsies from patients with acute myeloid leukemia, open a new window of understanding into the multiple pathways that pyroptosis can be triggered under the influence of chemo.

Pyroptosis is a mechanism of programmed, necrotic cell death mediated by the gasdermins, a family of pore-forming proteins. The new research, published in the journal Science Signaling, highlights several pore-forming pathways that can lead to cell death under the influence of widely used chemotherapeutic agents.

Part 1

Comment by Dr. Krishna Kumari Challa on January 24, 2023 at 11:19am

Researchers use bacterial communication as a target for new drugs

The pathogen Pseudomonas aeruginosa is the cause of a large number of serious infections and places a particular burden on immunocompromised patients. The increasing spread of antimicrobial resistance makes it even more difficult to combat the dreaded hospital pathogen.

A research team  has now discovered a new class of active compounds that disrupt the bacterium's chemical communication pathways. This not only reduces the pathogen's disease-causing properties, but also simultaneously enhances the effectiveness of antibiotics. 

Although bacteria are among the simplest life forms on our planet, in the course of evolution they have developed ways to communicate efficiently with one another. Unlike humans, their communication is not mediated with words but with chemical signals. This interaction also plays a fundamental role in infection processes of pathogenic bacteria in humans. For example, bacteria communicate to their swarm when it is time to produce substances that counteract the human immune system. Interfering with these communication pathways is a promising starting point for the development of new therapies.

The researchers  did not focus now on the communication messengers themselves, but on their receptors—i.e., the parts of the bacterium that are responsible for signal processing. In this specific case, the researchers targeted the receptor PqsR.

When this receptor is activated, inflammation-promoting substances and biofilms are formed, in which P. aeruginosa is largely protected from antibiotics. The drug class now described was chemically designed and optimized by the researchers so that it can attack its target PqsR as efficiently as possible. This was based on structural data obtained by X-ray crystallography. 

In further laboratory experiments, the scientists were able to show that the optimized substances reliably prevent the formation of the pro-inflammatory molecule pyocyanin in a large number of clinical isolates of P. aeruginosa. Furthermore, they were able to show that the new active ingredient is capable of impairing biofilm formation and can even further enhance the effect of the antibiotic tobramycin. Finally, the researchers were able to transfer the promising properties of their active substance to a mouse model. Here, the combined administration of tobramycin and the new PqsR inhibitor was able to combat the P. aeruginosa infection significantly better than either substance alone.

The authors see great potential in the new compound class for future application in humans. 

Mostafa M. Hamed et al, Towards Translation of PqsR Inverse Agonists: From In Vitro Efficacy Optimization to In Vivo Proof‐of‐Principle, Advanced Science (2023). DOI: 10.1002/advs.202204443

Comment by Dr. Krishna Kumari Challa on January 24, 2023 at 11:12am

A sugar cane pathogen is gearing up a new era of antibiotic discovery

A potent plant toxin with a unique way of killing harmful bacteria has emerged as one of the strongest new antibiotic candidates in decades.

The antibiotic, called albicidin, is produced by the bacterial plant pathogen Xanthomonas albilineans, which causes the devastating leaf scald disease in sugar cane. Albicidin is thought to be used by the pathogen to attack the plant, enabling its spread. It has been known for some time that albicidin is highly effective at killing bacteria including E. coli and S. aureus. These superbugs, notorious for their growing resistance to existing antibiotics, have prompted a vital need for effective new drugs.

Despite its antibiotic potential and low toxicity in pre-clinical experiments, pharmaceutical development of albicidin has been hampered because scientists did not know precisely how it interacted with its target, the bacterial enzyme DNA gyrase (gyrase). This enzyme binds to DNA and, through a series of elegant movements, twists it up, a process known as supercoiling which is vital for cells to function properly.

Now researchers  have exploited advances in cryo-electron microscopy to obtain a first snapshot of albicidin bound to gyrase. It showed that albicidin forms an L-shape, enabling it to interact with both the gyrase and the DNA in a unique way.

In order for gyrase to do its job, it must momentarily cut the DNA double helix. This is dangerous, as broken DNA is lethal to the cell. Normally, gyrase quickly joints the two pieces of DNA back together again as it works, but albicidin prevents it from happening, resulting in broken DNA and bacterial death. The effect of albicidin is akin to a spanner thrown between two gears.

The way albicidin interacts with gyrase is sufficiently different from existing antibiotics that the molecule and its derivatives are likely to be effective against many of the current antibiotic resistant bacteria.

 By the nature of the interaction, albicidin targets a really essential part of the enzyme and it's hard for bacteria to evolve resistance to that. Trials have already started to use this knowledge to produce new era antibiotics.

Jonathan Heddle, Molecular mechanism of topoisomerase poisoning by the peptide antibiotic albicidin, Nature Catalysis (2023). DOI: 10.1038/s41929-022-00904-1. www.nature.com/articles/s41929-022-00904-1

Comment by Dr. Krishna Kumari Challa on January 24, 2023 at 10:52am

Novel method helps recover obscured images

A novel method that produces a clear image by using a simple cost-effective random scattering medium in real time could help overcome problems of obscured images.

When light passes through a light-scattering material, it is diffused rather than absorbed, which means a clear image of the source object is lost. Scattering media include clouds, which poses problems for Earth-based astronomy, and body tissue, which affects medical imaging.

Previous methods for reconstructing scattered light have required some initial knowledge of the object and the ability to control the wavefront of light illuminating it. This has involved complicated optical elements and high vulnerability to motion and mechanical instability. Computational algorithms are then able to post-process the detected light to generate an image.

To get more efficient ways of reconstruction, speckle-correlation imaging was proposed. This extracts information about the source from fluctuations in the intensity, or speckles, in the transmitted light.

However, many of the technologies based on speckle-correlation need time-consuming and intricately calibrated computational reconstruction. Also, still missing is some information such as the image orientation and location.

Now researchers have developed a way to directly obtain a clear image from a single shot of the speckle image.

They passed light from a small standardized test object through a thin diffusing material. By moving a camera in a direction away from the diffuser, they were able to build a three-dimensional image, taking slices through the speckles.

By looking at enlarged sections of these images, the researchers, to their surprise, could directly see reproductions of the test object; they could see through the random diffuser with the naked eye and real-time video imaging. It required no complex equipment for the active control of light nor prior knowledge of the source or diffusion medium. They could also find the lost orientation information and location of the test object.

Jietao Liu et al, Directly and instantly seeing through random diffusers by self-imaging in scattering speckles, PhotoniX (2023). DOI: 10.1186/s43074-022-00080-2

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