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Comment by Dr. Krishna Kumari Challa on November 16, 2021 at 9:46am

Prions may channel RNA's messages

Prions get mostly bad press, but they may be the keys to controlling protein synthesis in cells.

Prions, proteins that can misfold and aggregate, have been implicated in many neurodegenerative diseases. Yet some prions are involved in storing long term memories. New models by  scientists describe how they can regulate the translation of RNA messages into new proteins by forming organized protein synthesis factories.

Vectorial channeling as a mechanism for translational control by functional prions and condensates, Proceedings of the National Academy of Sciences (2021). DOI: 10.1073/pnas.2115904118.

Comment by Dr. Krishna Kumari Challa on November 16, 2021 at 9:39am

In wild populations, diet and geography did influence microbiome composition and diversity.

Diet contributed to natural microbiome structure. The authors collected feces from each rodent at the time of capture to get a snapshot of their diet. Using these samples, they found that animals with more diverse diets had more diverse microbiomes, and animals that fed on similar plants also showed similarities in their microbial communities.

Geography also played a role. The authors found that individuals at the same site had more similar microbiomes, and these communities became more dissimilar as animals were sampled at more distant locations.

However, host relatedness was still the most important factor predicting the microbial makeup of these wild mammals. And these effects only increased when animals were in captivity.

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While every individual experienced a large shift, each individual's microbiome was still closer to its wild self than it would be to any other woodrat species. Researchers didn't see microbiomes merging into the same makeup; species retained distinct bacterial communities. With the differences of diet and habitat removed, they saw even more clearly the extent to which host relatedness influences microbiome structure.

The research team also found that microbiome responses to captivity were species specific, suggesting that host evolutionary history influences not only microbiome structure, but also stability.

Part 2

Comment by Dr. Krishna Kumari Challa on November 16, 2021 at 9:39am

Microbiomes: It's who you are that matters most

Every mammal hosts a hidden community of other organisms—the microbiome. Their intestines teem with complex microbial populations that are critical for nutrition, fighting disease and degrading harmful toxins. Throughout their lives, mammals are exposed to countless microbes through their food and environment, but only a small subset take up permanent residence in the host. Although scientists agree that diet, geography and evolutionary history structure the microbiome, the relative influence of each factor is a mystery. No rigorous study has investigated all three at once in wild mammal populations. Until now.

A team of University of Utah biologists analyzed the bacteria in the gut microbiome of woodrats (Neotoma species), a group of closely related herbivorous rodents abundant in the southwestern United States. The animals offered a unique opportunity to test how diet, geography and evolutionary history influence microbiome structure. The many woodrat species are morphologically similar, but populations live in a variety of habitats and have distinct diets. Woodrats are famous for eating extremely toxic plants and do so with support from specialized gut bacteria.

Woodrats are amazing—they have incredibly diverse diets. Individuals from the same species eat different foods at different locations, so it creates a natural experiment. It's hard to say what's driving their different microbiomes—is it what they're eating? Is it where they're living? Or is it who they are?

The researchers used DNA barcoding techniques to characterize the diet and gut bacteria of seven woodrat species from 25 populations at 19 locations across the southwestern U.S. The biologists then brought the rodents into captivity, fed them a diet of rabbit chow for one month and then resampled their microbiome. The results show that in both wild and captive individuals, evolutionary history was the biggest predictor of microbiome structure—more than diet and geography.

Microbiome stability and structure is governed by host phylogeny over diet and geography in woodrats (Neotoma spp.), Proceedings of the National Academy of Sciences (2021). DOI: 10.1073/pnas.2108787118.

https://phys.org/news/2021-11-woodrat-microbiomes.html?utm_source=n...

Part1

Comment by Dr. Krishna Kumari Challa on November 14, 2021 at 1:22pm

Experiment flooded calcium channels with 'decoys'
The experiment that revealed the function of the neuronal clusters was designed by Nicholas C. Vierra, a postdoctoral researcher in Trimmer's lab and lead author for the study.

"We developed an approach that let us uncouple the calcium channel from the potassium channel clusters in neurons. A key finding was that this treatment blocked calcium-triggered gene expression. This suggests that the calcium channel-potassium channel partnership at these clusters is important for neuronal function," Vierra said.

For their experiment, the researchers essentially "tricked" the calcium channels at these clusters by flooding the neurons with decoy potassium channel fragments. When the calcium channels grabbed onto the decoys instead of the real potassium channels, they fell away from the clusters.

As a result, the process known as excitation-transcription coupling, which links changes in neuronal electrical activity to changes in gene expression, was inactivated.

"There are a lot of different calcium channels, but the particular type of calcium channel found at these clusters is necessary for converting changes in electrical activity to changes in gene expression," Trimmer said. "We found that if you interfere with the calcium-signaling proteins located at these unusual clusters, you basically eliminate excitation-transcription coupling, which is critical for learning, memory, and other forms of neuronal plasticity."

Trimmer and Vierra hope their findings will open new avenues of research.

"A lot of research has focused on calcium signaling in dendrites—the sites where neurons receive signals from other neurons. Calcium signaling in the cell body of neurons has received less attention," said Vierra. "Now we understand much more about the significance of signaling at these specific sites on the cell body of the neuron."

"We are only at the beginning of understanding the significance of this signaling, but these new results may provide information that could shape new research into its role in brain function, and perhaps eventually into the development of new classes of therapeutics," said Trimmer.

Additional authors on the study include Samantha C. O'Dwyer, Collin Matsumoto and L. Fernando Santana, Department of Physiology and Membrane Biology, UC Davis School of Medicine.

https://researchnews.cc/news/9979/Researchers-may-have-unlocked-fun...

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Comment by Dr. Krishna Kumari Challa on November 14, 2021 at 1:21pm

Researchers may have unlocked function of mysterious structure found on neurons

 For 30 years, mysterious clusters of proteins found on the cell body of neurons in the hippocampus, a part of the brain, both intrigued and baffled James Trimmer.

Now, the distinguished professor of physiology and membrane biology at the UC Davis School of Medicine may finally have an answer. In a new study published in PNAS, Trimmer and his colleagues reveal these protein clusters are calcium signaling "hotspots" in the neuron that play a crucial role in activating gene transcription.

Transcription allows portions of the neuron's DNA to be "transcribed" into strands of RNA that are then used to create the proteins needed by the cell.

Structures found in many animals
Trimmer's lab studies the enigmatic clusters in mice, but they exist in invertebrates and all vertebrates—including humans. Trimmer estimates that there can be 50 to 100 of these large clusters on a single neuron.

He and his colleagues knew that the clusters are formed by a protein that passes potassium ions through membranes (a potassium channel). They also knew these clusters contain a particular type of calcium channel. Calcium channels allow calcium to enter cells, where it triggers a variety of physiological responses depending on the type of cell.

"The presence of these clusters in neurons is highly conserved," Trimmer said. Highly conserved features are relatively unchanged through evolutionary timescales, suggesting they have an important functional property in these very different types of animals.

The hippocampus, one region of the brain where the clusters are found on neurons, plays a major role in learning and memory. Researchers knew that disruption to these clusters—for example, from genetic mutations in the potassium channel—results in severe neurological disorders. But it was not clear why.

"We have known the function of other types of ion channel clusters, for example those at synapses, for a long time. However, there was no known role that these much larger structures on the cell body played in the physiology of the neuron," Trimmer said.

Comment by Dr. Krishna Kumari Challa on November 14, 2021 at 1:09pm

Achieving razor-sharp vision in the metaverse

Comment by Dr. Krishna Kumari Challa on November 14, 2021 at 1:04pm

The gene in question, proboscipedia, would plainly reveal itself since it directs the formation of strikingly different mouth parts—smooth and spongy in D. mel but more grill-like (resembling the face of the alien in Predator science fiction films) in D. mim.

Study coauthor Emily Bulger first collected the notoriously difficult-to-breed D. mim samples from Hawai'i Volcanoes National Park, along with the only native fruit (Sapindus saponaria—Hawaiian soapberry) that the insects are known to eat, in order to establish a temporary colony in Bier's laboratory. Auradkar then collaborated with coauthor Sushil Devkota to decipher the genome sequence of the D. mim proboscipedia gene, which was nearly 44,000 bases long. The researchers then deleted the D. mel proboscipedia gene and replaced it with the D. mim version of the same.

As McGinnis had predicted, the new results revealed that the graceful facial structure of D. mel emerged as the "winner" over the rough features of D. mim. One trait of D. mim, however, did surface during the experiment: Sensory organs called maxillary palps that stick out from the face in D. mel instead ran parallel to feeding mouthparts as they do in D. mim. Auradkar used sophisticated genetic tools to determine the basis for this difference and tracked it down to a change in the pattern by which the proboscipedia gene is activated (control region changes).

The experiment's results help answer longstanding questions about whether Hox genes function as "master" regulatory genes that dictate different body parts in organisms. Or, as McGinnis proposed, whether Hox genes instead provide abstract positional codes and serve as scaffolds for downstream genes that best benefit the organism. Other than the maxillary palps, the new results demonstrated that McGinnis' scaffolding idea proved to be the case.

McGinnis says that beyond the implications for evolutionary biology, the results could help explain developmental issues rooted in fundamental human genetic processes.

"These fly studies provide a window into deep evolutionary time and inform us about the mechanisms by which body plans change during evolution," said Bier. "These insights may lead to a better of understanding of processes tied to congenital birth defects in humans. With the advent of powerful new CRISPR-based genome editing systems for human therapy on the horizon, new strategies might be formulated to mitigate some of the effects of these often debilitating conditions."

https://researchnews.cc/news/9981/New-research-helps-explain-the-ge...

part 2

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Comment by Dr. Krishna Kumari Challa on November 14, 2021 at 1:04pm

New research helps explain the genetic basis for why we look the way we do

 Which genes control the defining features that make us look as we do? And how do they make it happen?

In 1990, University of California San Diego biologist William McGinnis conducted a seminal experiment that helped scientists unravel how high-level control genes called Hox genes shape our appearance features. The "McGinnis experiment" helped pave the way for understanding the role of Hox genes in determining the uniform appearances of species, from humans to chimpanzees to flies.

McGinnis, a professor emeritus of Cell and Developmental Biology and former dean of the Division of Biological Sciences, helped discover a defining DNA region that he termed the "homeobox," a sequence within genes that directs anatomical development. Since the now-famous McGinnis experiment, evolutionary and developmental biologists have pondered how these highly influential Hox genes determine the identities of different body regions.

More than three decades later, a study published in Science Advances and led by Ankush Auradkar, a UC San Diego postdoctoral scholar mentored by coauthor McGinnis and study senior author Ethan Bier, helps answer questions about how Hox genes function.

The now-textbook McGinnis experiment tested whether the proteins produced by a human or mouse Hox gene could function in flies. Following in these footsteps, the new study leveraged modern CRISPR gene editing to investigate whether all aspects of Hox gene function, which consists of both protein coding and control regions, could be replaced in a common laboratory fruit fly (Drosophila melanogaster) with its counterpart from a rarer Hawaiian cousin (Drosophila mimica), which has a very different face.

1. Ankush Auradkar, Emily A. Bulger, Sushil Devkota, William McGinnis, Ethan Bier. Dissecting the evolutionary role of the Hox gene proboscipedia in Drosophila mouthpart diversification by full locus replacement. Science Advances, 2021; 7 (46) DOI: 10.1126/sciadv.abk1003

Part 1

Comment by Dr. Krishna Kumari Challa on November 14, 2021 at 12:13pm

Researchers discover link between dietary fat and the spread of cancer

A new study uncovers how palmitic acid alters the cancer genome, increasing the likelihood the cancer will spread. Researchers have started developing therapies that interrupt this process and say a clinical trial could start in the next couple of years.
Metastasis—or the spread—of cancer remains the main cause of death in cancer patients and the vast majority of people with metastatic cancer can only be treated, but not cured. Fatty acids are the building blocks of fat in our body and the food we eat. Metastasis is promoted by fatty acids in our diet, but it has been unclear how this works and whether all fatty acids contribute to metastasis.
Newly published findings reveal that one such fatty acid commonly found in palm oil, called palmitic acid, promotes metastasis in oral carcinomas and melanoma skin cancer in mice. Other fatty acids called oleic acid and linoleic acid—omega-9 and omega-6 fats found in foods such as olive oil and flaxseeds—did not show the same effect. Neither of the fatty acids tested increased the risk of developing cancer in the first place.
The research found that when palmitic acid was supplemented into the diet of mice, it not only contributed to metastasis, but also exerts long-term effects on the genome. Cancer cells that had only been exposed to palmitic acid in the diet for a short period of time remained highly metastatic even when the palmitic acid had been removed from the diet.
The researchers discovered that this "memory" is caused by epigenetic changes—changes to how our genes function. The epigenetic changes alter the function of metastatic cancer cells and allow them to form a neural network around the tumor to communicate with cells in their immediate environment and to spread more easily. By understanding the nature of this communication, the researchers uncovered a way to block it and are now in the process of planning a clinical trial to stop metastasis in different types of cancer.

Salvador Benitah, Dietary palmitic acid promotes a prometastatic memory via Schwann cells, Nature (2021). DOI: 10.1038/s41586-021-04075-0. www.nature.com/articles/s41586-021-04075-0

https://researchnews.cc/news/9975/Researchers-discover-link-between...

Comment by Dr. Krishna Kumari Challa on November 13, 2021 at 11:36am

For this study, the researchers compiled an exhaustive list of all bird species that have been present in nine different archipelagos* before and after human-caused extinctions occurred. This covered 1,302 bird species, including 265 globally or locally extinct, and 355 established introductions from 143 separate species. In addition, the scientists visited different museum collections, including the Natural History Museum, to measure several morphological traits in skin or skeleton specimens. With this data, the researchers were able to quantify the trait diversity before and after bird extinctions, and identify the ecological niches extinct birds once filled.

The research team found that before human arrival, island bird communities were more morphologically diverse than they are today. Their findings show how human-driven extinctions have disproportionally affected some types of birds (for example, larger birds and flightless birds are more likely to go extinct), leading to the loss of certain ecological roles.

The researchers also found that different archipelagos are becoming more and more similar in terms of trait diversity as native birds go extinct and the same kind of alien species are being newly established in many places.

https://phys.org/news/2021-11-birds-roles-human-caused-extinct-spec...

Part 2

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