Hexbyte Glen Cove Plants rely on the CLASSY gene family to diversify their epigenomes

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The plant Arabidopsis thaliana. Credit: Salk Institute

What determines how a cell’s genome is regulated to ensure proper growth and development? Turns out, the parts of the genome that are turned on or off in each cell-type or tissue play a major role in this process. Now, a team at Salk has shown that the CLASSY gene family regulates which parts of the genome are turned off in a tissue-specific manner. The CLASSYs essentially control where the genome is marked by DNA methylation—the addition of methyl chemical groups to the DNA that act like tags saying, “turn off.” Because DNA methylation exists across diverse organisms, including plants and animals, this research has broad implications for both agriculture and medicine. The work, published in Nature Communications on January 11, 2022, identifies the CLSY genes as major factors underlying epigenetic diversity in plant tissues.

“There have been many observations that one cell or tissue type has a different DNA methylation pattern than another, but how the methylation pathways are modulated to end up with different outcomes in different tissues has remained poorly understood,” says senior author Julie Law, associate professor in Salk’s Plant Molecular and Cellular Biology Laboratory. “We found that which CLSYs are expressed in a given tissue is the mechanism controlling how the core DNA methylation machinery is directed to different genomic locations in different tissues.”

The study of DNA methylation falls under the field of epigenetics—molecular modifications that change how the DNA functions without changing the DNA sequence itself. It’s both a necessary process and a dangerous one. For instance, it helps establish cell identity in a developing embryo but can cause cancer later in life. In plants, defects in DNA methylation can cause developmental defects and negatively impact .

DNA methylation is regulated by many factors, including certain types of small RNAs. Working with the model plant Arabidopsis thaliana, the Salk team discovered that the CLASSY gene family (CLSY 1–4) acts at different locations depending on the tissue, revealing how diverse patterns of methylation are generated during plant development.

The current work expands on a previous study by Law and her team in which they found that in Arabidopsis, the CLSY genes determine which sites in the genome are methylated, via small RNAs. The current study addresses the larger question of whether this process can result in different methylation patterns in different Arabidopsis tissues: leaf, flower bud, ovule, and rosette.

The researchers found that CLSY genes were expressed differently depending on the plant tissue type. For example, all four CLSY genes were expressed in flower buds, while CLSY3 was strongly expressed in ovules and CLSY1 was expressed in leaf and rosette tissues.

The researchers then compared plants with mutant CLSY genes against wild-type plants. They found that depending on the tissue, different combinations of CLSY family members, or even individual CLSY proteins, controlled small RNA and DNA methylation patterns at thousands of sites throughout the genome. These findings demonstrate the CLSY genes’ role in shaping the tissues’ epigenetic landscape.

The team’s findings may open the door to advances in many areas, from boosting crop yields in to informing precision medicine in humans. “Before knowing how a diversity of DNA methylation patterns was generated during development, we didn’t have the ability to manipulate that system. Finding that the CLSYs control methylation in a -specific manner represents a major advance as it provides scientists a way to alter DNA methylation patterns with much higher precision,” says Law.

Other authors included Ceyda Coruh, Guanghui Xu, Laura M. Martins, Clara Bourbousse and Alice Lambolez of Salk; and Ming Zhou of Zhejiang University in China.

More information:
The CLASSY family controls tissue-specific DNA methylation patterns in Arabidopsis, Nature Communications (2022). DOI: 10.1038/s41467-021-27690-x

Plants rely on the CLASSY gene family to diversify their epigenomes (2022, January 11)
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Hexbyte Glen Cove Researchers discover fossil of new species of pangolin in Europe

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The newly described specimen for the fossil pangolin species Smutsia olteniensis. Credit: Claire Terhune, University of Arkansas.

Deeper analysis of fossils from one of Eastern Europe’s most significant paleontological sites has led to the discovery of a new species of pangolin, previously thought to have existed in Europe during the early Pleistocene but not confirmed until now.

“It’s not a fancy fossil,” said Claire Terhune, associate professor of anthropology at the University of Arkansas. “It’s just a single bone, but it is a new species of a kind of a weird animal. We’re proud of it because the for pangolins is extremely sparse. This one happens to be the youngest pangolin ever discovered from Europe and the only pangolin fossil from Pleistocene Europe.”

The bone, a humerus—or upper arm bone—came from Grăunceanu, a rich fossil deposit in the Olteţ River Valley of Romania. For nearly a decade, Terhune and an international team of researchers have focused their attention on Grăunceanu and other sites of the Olteţ. These sites, initially discovered because of landslides during the 1960s, have produced fossils from a wide variety of animal species, including a large terrestrial monkey, short-necked giraffe, rhinos and saber-toothed cats, in addition to the new pangolin species.

“What’s especially exciting is that although some work in the 1930s suggested the presence of pangolins in Europe during the Pleistocene, those fossils had been lost, and other researchers doubted their validity,” Terhune said. “Now we know for sure that pangolins were present in Europe around at least 2 million years ago.”

Modern-day pangolins exist in Asia and Africa. Often referred to as scaly anteaters, they look somewhat like the armadillos that roam the southern United States. With scales from head to tail, they are sometimes mistaken as reptiles, but modern pangolins are actually mammals and are most closely related to carnivores. They are also among the most illegally trafficked animals in the world. According to the World Wildlife Fund, the eight species of living pangolins on two continents range from “vulnerable” to “critically endangered.”

The new pangolin fossil is between about 1.9 to 2.2 million years old, placing it within the range of the Pleistocene Epoch, which ran from roughly 2.6 million years ago to about 11,700 years ago. The identification of this fossil as a pangolin is significant because previous research suggested that pangolins disappeared from the European paleontological record during the middle-Miocene, closer to 10 million years ago. Previous work hypothesized that pangolins were pushed toward more tropical and sub-tropical equatorial environments due to global cooling trends.

As the youngest and best documented fossil pangolin from Europe and the only fossil from Pleistocene Europe, the new species revises an earlier understanding of evolution and bio-geography. Smutsia olteniensis, as the new is called, shares several unique traits with other living members of the genus Smutsia, which are currently found only in Africa.

This work was published in the Journal of Vertebrate Paleontology.

Terhune’s collaborators were Sabrina Curran at Ohio University, Timothy Gaudin the University of Tennessee at Chattanooga, and Alexandru Petculescu at Emil Racoviţă Institute of Speleology in Bucharest.

More information:
Claire E. Terhune et al, The youngest pangolin (Mammalia, Pholidota) from Europe, Journal of Vertebrate Paleontology (2021). DOI: 10.1080/02724634.2021.1990075

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Hexbyte Glen Cove Researchers find low oxygen and sulfide in the oceans played greater role in ancient mass exteinction

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Seth Young’s research group collecting and describing limestone samples from a field site in the Roberts Mountains, Nevada. Credit: Anders Lindskog/Florida State University

Florida State University researchers have new insight into the complicated puzzle of environmental conditions that characterized the Late Ordovician Mass Extinction (LOME), which killed about 85% of the species in the ocean.

Their work on the 445-million-year-old mass event was published online in the journal AGU Advances on Monday.

“We found that reducing conditions—with low to no and little to no hydrogen sulfide levels—are probably playing a much more important role than we previously thought,” said lead author Nevin Kozik, a doctoral candidate in the Department of Earth, Ocean and Atmospheric Science and researcher at the FSU-headquartered National High Magnetic Field Laboratory. “If you imagine a pie chart of the causes of this extinction, we’re increasing that wedge that signifies , which is happening in concert with a cooling climate and widespread habitat loss due to .”

The research is the first study to use measurements of multiple elements from several sites to examine the conditions that led to the LOME, the second-largest extinction event in the Earth’s history and the only mass extinction to occur during what are called icehouse conditions, when Earth’s climate is cold enough at the poles to support ice sheets year-round.

To measure oxygen and sulfide concentrations from millions of years ago, scientists use geochemical proxies that correspond to ancient marine conditions. Iodine concentrations and sulfur isotopes from three sites provided information on the oxygen and sulfide levels in the ancient ocean.

The extinction happened in two distinct pulses. Using these geochemical measurements as environmental proxies, the researchers found that decreased ahead of the first pulse and remained low. Levels of hydrogen sulfide in the oceans decreased initially leading into the first pulse of the extinction event, but then these levels increased afterward coinciding with the second and final pulse of the extinction.

At the same time the Earth’s climate was cooling, glaciers were growing at the ancient South Pole (modern-day North Africa), which led to decreasing sea levels and habitat loss for marine organisms in shallow seaways in the tropics.

“The geological record indicates that many environmental factors were at play leading to this extinction event,” Kozik said. “The processes we are linking together here are like several punches that beat down life during this time.”

Even while conditions were becoming inhospitable for many organisms around the planet, the environment in some places remained oxygen-rich and able to support a diversity of life. The researchers found evidence of higher oxygen levels at a site near present-day Quebec that was home to a shallow reef on the continental shelf 445 million years ago.

“We know that life had to survive and persist after this mass extinction, and we now have an indication that at least this location had enough oxygen to support life,” said co-author Seth Young, associate professor in the Department of Earth, Ocean and Atmospheric Science and researcher at the FSU-headquartered National High Magnetic Field Laboratory. “That’s consistent with what you find in the rock and , which are that reefs are persisting through this extinction event. The fossils are suggesting that, at least there, life was OK.”

The extinction event is an ancient analogue to what’s happening on Earth today. Earth today, as in the Late Ordovician, is in an icehouse period and is experiencing a major loss in biodiversity, a warming climate and a decrease in oceanic oxygen.

“All of those things are really important and provide a modern perspective on this mass extinction event,” Young said. “It’s important to not only understand what caused this extinction event, but also how did the Earth system get out of this and continue on. That’s the impetus for studying many of these things, not only to understand why this happened, but what was the survival period like and what led to the reemergence and rediversification of life.”

Researchers from Virginia Polytechnic Institute and State University and University of California, Riverside contributed to this study.

More information:
Nevin P. Kozik et al, Geochemical Records Reveal Protracted and Differential Marine Redox Change Associated With Late Ordovician Climate and Mass Extinctions, AGU Advances (2022). DOI: 10.1029/2021AV000563

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Hexbyte Glen Cove Research on magnetite in salmon noses illuminates understanding of sensory mechanisms enabling magnetic perception

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Credit: CC0 Public Domain

It’s widely understood that animals such as salmon, butterflies and birds have an innate magnetic sense, allowing them to use the Earth’s magnetic field for navigation to places such as feeding and breeding grounds.

But scientists have struggled to determine exactly how the underlying sensory mechanism for magnetic perception actually works.

In a paper published this week in the Proceedings of the National Academy of Sciences, an international team of researchers, including scientists from Oregon State University, outlines a new theory. Magnetite crystals that form inside specialized receptor cells of and other animals may have roots in ancient genetic systems that were developed by bacteria and passed to animals long ago through evolutionary genetics.

The theory is based on new evidence from nanoscopic magnetic material found within cells in the noses of salmon. The paper’s lead author is Renee Bellinger, who began the research as a doctoral student at Oregon State, completing her Ph.D. in fisheries science in 2014.

“The cells that contain magnetic material are very scarce,” said Bellinger, who now works as a research geneticist at the U.S. Geological Survey and is affiliated with the University of Hawaii, Hilo. “We weren’t able to definitively prove magnetite as the underlying key to magnetic perception in animals, but our study revealed associated genes as an important tool to find new evidence of how potential magnetic sensors may function.”

“Finding magnetic receptors is like trying to find a needle in haystack. This work paves the way to make the ‘needle’ glow really bright so we can find and understand receptor cells more easily,” Bellinger said.

The findings have the potential for widespread application, from improving salmon management through better understanding of how they use the ocean to targeted medical treatments based on magnetism, said coauthor Michael Banks, a genomics, conservation and behavior professor at Oregon State.

“Salmon live a hard and fast life, going out to the ocean to specific areas to feed and then coming back to their original spawning grounds where they die. They don’t have the opportunity to teach their offspring where to go, yet the still somehow know where to go,” Banks said. “If we can figure out the way animals such as salmon and orient, there’s a lot of potential applications for helping to preserve the species, but also for human applications such as medicine or other orientation technology.”

Bellinger’s work built on research from more than 20 years ago by Michael Walker of the University of Auckland in New Zealand, who initially traced magnetic sensing to tissue in the noses of trout.

“He narrowed it down to magnetite in the olfactory rosette,” Bellinger said. “We were expecting to see chains of crystals in the noses of salmon, similar to how magnetite-producing bacteria grow chains of crystals and use them as a compass needle. But it turns out the individual crystals are organized in compact clusters, like little eggs. The configuration was different than the original hypothesis.”

The form in which magnetite appears, as tiny crystals inside specialized receptor cells, represents biomineralization, or the process by which living organisms produce minerals. The similarity between magnetite crystals of bacteria and fish suggests that they share a common evolutionary genetic history, Bellinger said.

The mechanism for developing magnets was developed by bacteria more than two billion years ago and then passed on to animals. Today, these tools to perceive magnetism continue to be present across a broad array of animal species, said Banks, who is affiliated with OSU’s Department of Fisheries, Wildlife, and Conservation Sciences in OSU’s College of Agricultural Sciences and the Coastal Oregon Marine Experiment Station at OSU’s Hatfield Marine Science Center.

The process for sharing them across animal life may have been similar to the evolution of , which control how animals release energy. Mitochondria originated in bacteria and were then transferred to other organisms, he said.

Understanding the evolutionary history of is a step toward further pinpointing the underlying process, the researchers said. Banks, Bellinger and colleagues would next like to test their new understanding and associated markers to further address the mystery of why and how some life forms have well-tuned tools for long and precise migratory strategies.

Co-authors of the paper are Jiandong Wei of Shanghai University in China; Uwe Hartmann of Saarland University in Germany; Herve Cadiou of the Institute of Cellular and Integrative Neuroscience in France; and Michael Winklhofer of the University of Oldenburg in Germany.

More information:
M. Renee Bellinger et al, Conservation of magnetite biomineralization genes in all domains of life and implications for magnetic sensing, Proceedings of the National Academy of Sciences (2022). DOI: 10.1073/pnas.2108655119

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Hexbyte Glen Cove Problematic anonymous student feedback on teachers

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by Richard Lakeman, Deb Massey, Dima Nasrawi, Jann Fielden, Marie Hutchinson, Megan Lee, Rosanne Coutts, The Conversation

Credit: Shutterstock

Student evaluations, in the form of anonymous online surveys, are ubiquitous in Australian universities. Most students in most courses are offered the opportunity to rate the “quality” of their teachers and the course they take.

The original intention of student surveys was to help improve the learning experience. But it’s now become much more. Student surveys are often the only measure of teaching quality (along with pass rates). For lecturers, positive ratings and comments are often required to ensure continued employment or promotion.

But these anonymous surveys have also become a platform for defamatory, racist, misogynistic and homophobic comments against staff.

We surveyed 791 Australian academics from different universities about their experience of anonymous . The participating academics shared verbatim some of the non-constructive feedback students gave them. We collated examples of this feedback and published these in the journal Assessment & Evaluation in Higher Education.

We grouped the feedback into five broad themes: attire, appearance and accent; allegations against character; general insults; projections of blame; and threats or calls for punishment.

1. Attire, appearance and accent

Often the comments about appearance were gendered, misogynistic or racist with variations on being “too fat,” “ugly” and “old.”

One student wrote: “You look like something the cat dragged in.”

Another said: “People who’s [sic] mother tongue is not English should not be employed as lecturers.”

2. Allegations against character

These typically accused the lecturer of incompetence, racism or having negative attitudes towards students: “She is really rude which is why everyone hates her. You are a cultural Marxist, your Wokeness undermines everything you do. Not all your students are left wing nut jobs like you. You seriously need to lose some weight.”

3. General insults

Most insults were clearly designed to wound the teacher and there was no pretense about the comments having anything to do with teaching—although the following was an exception: “What the fuck did you think you were doing to take a couple of days off for your grandmother’s funeral when we had an assignment due? “

Apart from variations on “I hate everything about you,” most insults were a combination of unimaginative adjectives or name calling including “bitch,” “bitter,” “crap,” “devil’s spawn,” “dick,” “dog,” “dinosaur,” “idiot,” “loser,” “mentally unstable,” “mole,” “Nazi,” “needs to chill,” “out of control,” “pathetic,” “psychotic,” “senile shit,” “smiling assassin,” “trash,” “unhappy” and “useless.”

4. Projections of blame

Most student evaluation surveys are done before grades are released but many students anticipated failure and blamed the teacher: “That fucking dyke bitch failed me she’s fucking useless that’s why I failed.”

5. Threats and punishment

Hand-in-hand with projection of blame were threats or calls for punishment. Most often these called for the teacher to be sacked but also included far more harsher measures:

“I’d like to shove a broom up her arse.”

“She should be stabbed with a pitchfork.”

“If I was X, I would jump off the tallest building and kill myself if I was that dumb.”

Some managed to combine themes to achieve maximum offensiveness:

“Stupid old hag needs a good fucking. “

“This bitch should be fired immediately. Why is someone this ugly allowed to teach? She better be careful I never see her in the car park. She needs to get a better fashion pick. Her clothes are hideous.”

The impacts are serious

An analysis of research on university student evaluations of teaching, published in March 2021, found they were influenced by factors that have nothing to do with teaching quality. These include student demographics, and the teaching academic’s culture and identity. It also found evaluations include increasingly abusive comments.

While much of the criticism may seem like playground-level name calling, the impacts can be serious.

As part of our survey we asked teachers how anonymous student evaluations of their teaching affected their well-being, mental health, and professional and personal relationships. From our ongoing analysis of the data (yet to be published) a profile is emerging of a highly traumatized workforce. Early career academics, casual staff, women and minorities are disproportionately affected. Many appear to be triggered by every round of evaluations.

If Australian universities persist in employing anonymous surveys, university teachers can continue to expect to receive racist, misogynistic, defamatory comments, threats of censure and even death.

Even the Australian government is taking action against anonymous hate speech by announcing an inquiry into trolling on social media. But universities still protect people who want to insult, defame and make baseless accusations about others protected by a veil of anonymity.

Perhaps it is time to unmask the anonymous online trolls in the university sector, or require students to be potentially identifiable. The risk of being identified might at least reduce exposure to hate speech and increase civility in the corridors of higher learning.

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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