How the gut creates a cozy home for beneficial microbiome species

Image Credit: Courtesy of Carnegie Institution for Science

The digestive tract of fruit flies remodels itself to accommodate beneficial microbiome species and maintain long-term stability of the gut environment, according to new research led by Carnegie’s William Ludington and Allan Spradling. Their findings are published in Nature Communications.

The gut microbiome is an ecosystem of hundreds to thousands of microbial species living within the human body. These populations affect our health, fertility, and longevity. But there is still so much to learn about how these microbial species interact with our bodies and with each other.

“Every day, we encounter, and even ingest, a diverse array of bacterial species,” explained Ludington, who has been probing microbiome acquisition and composition for several years at Carnegie. “Despite this, the gut microbiome remains relatively stable over time—a phenomenon that is maintained across many species ranging from mammals to insects.”

He, Spradling, and their collaborators wanted to determine how our guts can maintain such remarkably consistent microbiome compositions. Because the human microbiome is so complex, they studied fruit flies, which are only colonized by a handful of microbial species.

Birth of a very distant cluster of galaxies from the early Universe

This image shows the protocluster around the Spiderweb galaxy (formally known as MRC 1138-262), seen at a time when the Universe was only 3 billion years old. Most of the mass in the protocluster does not reside in the galaxies that can be seen in the centre of the image, but in the gas known as the intracluster medium (ICM). The hot gas in the ICM is shown as an overlaid blue cloud.   The hot gas was detected with the Atacama Large Millimeter/submillimeter Array (ALMA), of which ESO is a partner. As light from the cosmic microwave background –– the relic radiation from the Big Bang –– travels through the ICM, it gains energy when it interacts with the electrons in the hot gas. This is known as the Sunyaev-Zeldovich effect. By studying this effect, astronomers can infer how much hot gas resides in the ICM, and show that the Spiderweb protocluster is in the process of becoming a massive cluster held together by its own gravity. 
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Image Credit: ESO/Di Mascolo et al.; HST: H. Ford

Using the Atacama Large Millimeter/submillimeter Array (ALMA), of which ESO is a partner, astronomers have discovered a large reservoir of hot gas in the still-forming galaxy cluster around the Spiderweb galaxy — the most distant detection of such hot gas yet. Galaxy clusters are some of the largest objects known in the Universe and this result, published today in Nature, further reveals just how early these structures begin to form.

Galaxy clusters, as the name suggests, host a large number of galaxies — sometimes even thousands. They also contain a vast “intracluster medium” (ICM) of gas that permeates the space between the galaxies in the cluster. This gas in fact considerably outweighs the galaxies themselves. Much of the physics of galaxy clusters is well understood; however, observations of the earliest phases of formation of the ICM remain scarce.

Previously, the ICM had only been studied in fully-formed nearby galaxy clusters. Detecting the ICM in distant protoclusters — that is, still-forming galaxy clusters – would allow astronomers to catch these clusters in the early stages of formation. A team led by Luca Di Mascolo, first author of the study and researcher at the University of Trieste, Italy, were keen to detect the ICM in a protocluster from the early stages of the Universe. 

Retinoic Acid Could Be Key to Preventing Gut Infections

Brian Sheridan conducts research on CD8 T cells to investigate immune responses with the hope of laying groundwork for new therapies and vaccines. 
Photo Credit: John Griffin, Stony Brook University

A team of scientists from the Renaissance School of Medicine (RSOM) at Stony Brook University have identified a distinct role of retinoic acid, a metabolite of vitamin A, during the immune response of the gut. This finding, detailed in a paper published in the Journal of Experimental Medicine, and highlighted in a broader piece in the journal, could help lead to ways to control the retinoic acid response and therefore could be used as a therapy or for vaccine development against infection or even to treat GI tumors.

Led by Brian Sheridan, associate professor in the Department of Microbiology and Immunology and the Center for Infectious Diseases, the study involves basic research that centers on unraveling the factors that control the generation of cytotoxic memory CD8 T cells, which are an important arm of the body’s anti-pathogen immune response as they kill pathogen-infected cells and produce anti-pathogen cytokines. In fact, memory CD8 T cells provide long-lived and frontline protection at barrier tissues, highlighting their importance in vaccine design.

To date, scientists have known that retinoic acid in the gut-draining lymph nodes promotes effector CD8 T cell migration to the intestines, enhancing the immune response. Additionally, vitamin A deficiency is associated with increased infections and poor vaccine efficiency.

Smells influence metabolism and ageing in mice

Photo Credit: Nick Fewings

Exposure to female odors and pheromones causes weight loss and extend the life spans of mice, which may have implications for humans, University of Otago researchers have found.

Lead researcher Dr Michael Garratt, of the Department of Anatomy, says while it was already known that sensory cues in humans and animals influence the release of sex hormones, this study shows that these cues could have more wide-spread physiological effects on metabolism and ageing.

“Our studies show that female odors slow the sexual development of female mice, but consequently extends their lifespan. And we also show that the smell of females can increase male mouse energy expenditure, which subsequently influences their body weight and body fat levels,” he says.

Newborn mice were exposed to odors from adult females until they were 60 days old. Those females exposed to the odors reached sexual maturity later and lived an average 8 per cent longer than those not exposed.

There was no effect of male odors on female mouse lifespan, or changes in lifespan in males in response to odors from either sex.

ORNL-led team designs molecule to disrupt SARS-CoV-2 infection

Oak Ridge National Laboratory led a team of scientists to design a molecule that disrupts the infection mechanism of the SARS-CoV-2 coronavirus and could be used to develop new treatments for COVID-19 and future virus outbreaks.
Video Credit: Michelle Lehman/ORNL, U.S. Dept. of Energy

A team of scientists led by the Department of Energy’s Oak Ridge National Laboratory designed a molecule that disrupts the infection mechanism of the SARS-CoV-2 coronavirus and could be used to develop new treatments for COVID-19 and other viral diseases.

The molecule targets a lesser-studied enzyme in COVID-19 research, PLpro, that helps the coronavirus multiply and hampers the host body’s immune response. The molecule, called a covalent inhibitor, is effective as an antiviral treatment because it forms a strong chemical bond with its intended protein target.

“We’re attacking the virus from a different front, which is a good strategy in infectious disease research,” said Jerry Parks, who led the project and leads the Molecular Biophysics group at ORNL.

The research, detailed in Nature Communications, turned a previously identified noncovalent inhibitor of PLpro into a covalent one with higher potency, Parks said. Using mammalian cells, the team showed that the inhibitor molecule limits replication of the original SARS-CoV-2 virus strain as well as the Delta and Omicron variants.

Extinction of steam locomotives derails assumptions about biological evolution

The Union Pacific Big Boy Steam Engine (one of the largest steam engines ever built and still functioning) visited Lawrence on Sept. 2, 2021.
Photo Credit: Bruce Lieberman

When the Kinks’ Ray Davies penned the tune “Last of the Steam-Powered Trains,” the vanishing locomotives stood as nostalgic symbols of a simpler English life. But for a paleontologist at the University of Kansas, the replacement of steam-powered trains with diesel and electric engines, as well as cars and trucks, might be a model of how some species in the fossil record died out.

Bruce Lieberman, professor of ecology & evolutionary biology and senior curator of invertebrate paleontology at the KU Biodiversity Institute & Natural History Museum, sought to use steam-engine history to test the merits of “competitive exclusion,” a long-held idea in paleontology that species can drive other species to extinction through competition.

Working with former KU postdoctoral researcher Luke Strotz, now of Northwest University in Xi’an, China, Lieberman found the fossil record largely lacks the detailed data verifying competitive exclusion found in the history of steam engines: “It's really hard to actually see any evidence that competition does play a big role in evolution,” Lieberman said.

Their findings have just been published in the paper “The end of the line: competitive exclusion and the extinction of historical entities2” in the peer-reviewed journal Royal Society Open Science.

Tur­bu­lence: Decades-old the­ory gets a major remake

Ivana Stiperski and the students from the Field Course in Alpine Meteorology setting up the instruments at the “Hochhäuser” i-Box station in the Inn Valley.
Photo Credit: Tobias Posch

Turbulence plays an essential role in weather and climate, and correctly representing its effects in numerical models is crucial for accurate weather forecasts and climate projections. However, the theory describing the effect of turbulence has not changed since its conception in 1950s, despite the fact that it is not representative for the majority of the Earth’s land surface, especially over mountains and polar regions. The Innsbruck meteorologist Ivana Stiperski has now extended the turbulence theory to complex atmospheric conditions. The researcher thus paves the way for the first generalized turbulence theory over complex terrain.

Turbulence is the most important exchange mechanism between the Earth's surface and the overlying atmosphere. However, this mechanism remains one of the last great puzzles of classical physics and mathematics. Ivana Stiperski, head of the research group "Atmospheric Turbulence" at the Department of Atmospheric and Cryospheric Sciences at the University of Innsbruck, has dedicated her work to the study of turbulence over mountains, and since 2020 her team is working on the topic within the framework of an ERC Consolidator Grant. "Turbulence affects phenomena as diverse as climate, storm systems, air pollution and glacier melt. Accurate weather forecasts and climate predictions therefore require a precise description of turbulence, and over the complex terrain of mountainous regions this is particularly difficult as very little is known about how complex terrain modifies turbulence, and no major advance has happened over the past 70 years", Stiperski explains. Until now, the understanding of atmospheric turbulence and how it is included in weather and climate models has been based on the so-called similarity theory, more specifically the "Monin-Obukhov similarity theory " first postulated in 1954. This decades-old theory of turbulence, however, assumes that the Earth’s surface is flat and horizontally homogeneous (i.e., has uniform characteristics in the horizontal, such as for example infinite grasslands or corn fields), and therefore it is not representative for the majority of the Earth’s land surface. This incorrect representation of turbulence adds uncertainty to weather prediction and climate projections.

Wild animals stop the spread of socially transmitted misinformation

For wild animals, false alarms are the most widespread form of misinformation.
Photo Credit: Kaylee Rose Fahimipour

Despite the benefits of learning about the world through social ties, social connections also provide a conduit for misinformation that impedes effective decision-making.

For wild animals, false alarms are the most widespread form of misinformation. For example, when an individual animal in a group makes the decision to produce an alarm signal or initiate an escape maneuver in the absence of a real threat. This initial action produces sensory stimuli that can be perceived by others in the group as an indication of danger, resulting in a cascade of erroneous escape responses that can spread contagiously.

Behavioral and neurophysiological studies suggest that relatively simple behavioral strategies control decision-making in many of these settings. Yet, it is unknown whether these strategies somehow account for the possibility of exposure to misinformation.

How whale shark rhodopsin evolved to see, in the deep blue sea!

Whale shark
Photo Credit: Mitsumasa Koyanagi, OMU

A new study reveals that the photoreceptor rhodopsin of whale sharks (Rhincodon typus), pictured here, evolved to improve sight for the low-light low-temperature deep-sea environment in a unique way.

A research group including Professors Mitsumasa Koyanagi and Akihisa Terakita of the Osaka Metropolitan University Graduate School of Science has investigated both the genetic information and structure of the photoreceptor rhodopsin, responsible for detecting dim light, of whale sharks to investigate how they can see in the dim light at extreme depths. The research group compared the whale sharks to zebra sharks, which are considered their closest relative, and brown-banded bamboo sharks, which are in the same group: the order orectolobiformes—commonly known as carpet sharks.

“This research used genetic information and molecular biological techniques to achieve stunning results—without harming whale sharks’ or their biology. Our research approach is to use these techniques to provide clues that reveal the mysteries of how these organisms live,” explained Professor Koyanagi. “The beautiful part is that it even works for species where information is limited, such as large or wild animals that are difficult to observe or follow in their natural habitat.”

Coronavirus causes chaos in infected cells’ RNA

Illustration Credit: Fusion Medical Animation

Coronavirus disease (COVID-19) hijacks parts of infected cells' vital RNA machinery, thereby blocking important functions in the cells. These damaging changes in the RNA can likely be reversed, potentially leading to new drugs against COVID-19, University of Gothenburg researchers show.

Genetic material in the body's cells consists of DNA, which serves as long-term storage of genetic information. RNA carries this encoded information to the cells for transcription and translation. These processes enable them to make proteins, which perform most intracellular tasks. The cells' RNA is modifiable to allow correct transfer of the DNA information to the proteins. In recent years, scientific understanding of the complexity and importance of these RNA modifications has grown.

Drastic impact

It has been shown that RNA modifications take place in various viruses, but exactly how the viruses affect the RNA modification processes when they infect cells is unknown. This study reports that SARS-CoV-2 infection disrupts the RNA modifications, and the extent of these RNA modification changes surprised the researchers.

One of the modifications affected by SARS-CoV-2, known as m6A (a multifaceted regulator of gene expression), is highly important for RNA’s basic functions, including transportation of data to the protein-making parts of the cell, and transcription and translation into amino acids there.

“We were surprised at the extent and drastic scale of m6A RNA modification loss in SARS-CoV-2 infection. We also found that the coronavirus variants have differing effects on m6A levels,” says Tanmoy Mondal, researcher at Sahlgrenska Academy, University of Gothenburg, who led the project.