Rainbow Trout Subspecies Newly Named

The McCloud River Redband Trout is known as “cali sulat” in the Winnemem Wintu language, with “cali” meaning good or beautiful and “sulat” the term for trout.
Photo Credit: Steve MacMillan

The McCloud River redband trout, or O. mykiss calisulat, is newly identified as its own distinct subspecies of rainbow trout in a study from the University of California, Davis. It is the first newly identified subspecies of Pacific trout since 2008 and the youngest rainbow trout subspecies by more than 100 years.

The study, published in the journal Zootaxa, notes that fish biologists have suspected the McCloud River redband trout was its own subspecies since at least the 1970s, but only newer genetics techniques — including genomewide DNA sequencing — allowed the UC Davis-led team to tease the puzzle apart and confirm it as a subspecies.

Northern California’s McCloud River originates from spring-fed streams near Mount Shasta before passing over a series of waterfalls, the McCloud Falls. The waterfalls are impassable to upstream movement of fishes and divide the Upper McCloud River from the Lower McCloud River.

The McCloud River redband trout is the only known native fish found in the Upper McCloud Basin.

“It’s persisted so long in isolation,” said lead author Matthew “Mac” Campbell, a research affiliate with the Department of Animal Science’s Genomic Variation Laboratory. “They’ve survived in glacial refugia during the Pleistocene era and have been above those waterfalls for at least 10,000 years.”

Cell mapping and ‘mini placentas’ give new insights into human pregnancy

Cells of the placenta 
Image Credit: Kenny Roberts, Wellcome Sanger Institute

Researchers from the University of Cambridge, the Wellcome Sanger Institute, the Friedrich Miescher Institute for Biomedical Research (FMI), Switzerland, EMBL’s European Bioinformatics Institute (EMBL-EBI), and collaborators, have created an in-depth picture of how the placenta develops and communicates with the uterus.

The study, published today in the journal Nature, is part of the Human Cell Atlas initiative to map every cell type in the human body. It informs and enables the development of experimental models of the human placenta.

"For the first time, we have been able to draw the full picture of how the placenta develops and describe in detail the cells involved in each of the crucial steps. This new level of insight can help us improve laboratory models to continue investigating pregnancy disorders, which cause illness and death worldwide,” said Anna Arutyunyan, co-first author at the University of Cambridge and Wellcome Sanger Institute.

The placenta is a temporary organ built by the fetus that facilitates vital functions such as fetal nutrition, oxygen and gas exchange, and protects against infections. The formation and embedding of the placenta into the uterus, known as placentation, is crucial for a successful pregnancy.

Three newly discovered sea worms that glow in the dark

 Polycirrus onibi, a newly discovered marine worm that glows in the dark was named after a creature from Japanese folklore.
Photo Credit: Naoto Jimi / Nagoya University

A research group from Nagoya University in central Japan has discovered three new species of bioluminescent polycirrus worms from different parts of Japan. Usually found in shallow water, polycirrus are small worms, known for their bioluminescence. The researchers named one of their discoveries after a ghostly yokai, a creature in Japanese folklore; another after a lantern yokai; and the other after an influential Japanese marine biologist. They published their findings in the journal Royal Society Open Science. 

Scientists have studied only a small fraction of the more than 7,000 species of luminescent organisms in the world. Research remains limited to certain species because of the existence of specimens that are difficult to classify into species. Without correct identification of the species, comparisons of different results are of limited use.  

Naoto Jimi (he/him) and Special Assistant Professor Manabu Bessho-Uehara (he/him) at Nagoya University’s Graduate School of Science, led a research group with members from AIST, Olympus Corporation, and Japan Underwater Films Corporation, that organized Polycirrus according to their diversity. They discovered three new species, all of which emit blue-violet light.   

Ancient DNA reveals entwined African and Asian ancestry along the Swahili coast of eastern Africa

Rice researchers Mary Prendergast and Jeffrey Fleisher.
Photo Credit: Brandon Martin.

A new genetic study of medieval people who lived along the Indian Ocean coast of eastern Africa — an area often called the “Swahili coast” for its language and culture — revealed that they had both African and Persian ancestry.

The results suggest that maritime trade connections long recognized by archaeologists based on imported goods and architectural influences fostered relationships between Asian merchants and African traders and their families.

“Entwined African and Asian genetic roots of medieval peoples of the Swahili coast” was published today in Nature. It examines genetic ancestry and cultural influences in eastern Africa by using DNA from the skeletal remains of 80 individuals who were buried in six medieval and early modern coastal towns in Kenya and Tanzania dating to the years 1250-1800 and an inland town in Kenya dating to after 1650.

Analysis of the genetic data enabled scientists to estimate that people of African and Persian ancestry began to have children together around the year 1000, centuries before the burials themselves.

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. 
Full Size Image
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.