Extinct fish is alive and well

‘Extinct’ houting from the collection of the Natural History Museum London.
Photo Credit: Ymke Winkel

The houting, a fish species that lived in North Sea estuaries and is officially extinct, turns out to be alive and well. Researchers from the University of Amsterdam and the Natural History Museum London extracted DNA from multiple houtings conserved in the museum, up to 250+ years old. Next they compared the DNA of these museum fish with DNA from various currently occurring sibling species. The biologists found hardly any genetic difference between houting and a species called European whitefish. Since this species is still common, houting also isn’t extinct.

In a recent publication in the journal BMC Ecology and Evolution, the researchers describe how they isolated mitochondrial DNA from the fish. They even managed to obtain a small piece of DNA from a dried North Sea houting from 1754 that was used by Linnaeus for the official species description. Next, they used the DNA to create a phylogenetic tree, in which all examined houting (Coregonus oxyrinchus) ended up in the same group as the European whitefish (Coregonus lavaretus).

Thousands of programmable DNA-cutters found in algae, snails, and other organisms

Amoeba proteus with pseudopodia, cytoplasm often with truncated bipyramidal crystals
Image Credit: SmallRex
(CC BY-SA 4.0 DEED)

A diverse set of species, from snails to algae to amoebas, make programmable DNA-cutting enzymes called Fanzors — and a new study from scientists at MIT’s McGovern Institute for Brain Research has identified thousands of them. Fanzors are RNA-guided enzymes that can be programmed to cut DNA at specific sites, much like the bacterial enzymes that power the widely used gene-editing system known as CRISPR. The newly recognized diversity of natural Fanzor enzymes, reported in the journal Science Advances, gives scientists an extensive set of programmable enzymes that might be adapted into new tools for research or medicine.

“RNA-guided biology is what lets you make programmable tools that are really easy to use. So, the more we can find, the better,” says McGovern Fellow Omar Abudayyeh, who led the research with McGovern Fellow Jonathan Gootenberg.

CRISPR, an ancient bacterial defense system, has made it clear how useful RNA-guided enzymes can be when they are adapted for use in the lab. CRISPR-based genome editing tools developed by MIT professor and McGovern investigator Feng Zhang, Abudayyeh, Gootenberg, and others have changed the way scientists modify DNA, accelerating research and enabling the development of many experimental gene therapies.

Females less likely to heal from ACL injuries than males

An analysis of genes expressed by healing rabbit ligaments may lead to a better understanding of ACL injury prevention and treatment in humans, according to Penn State researchers.
Photo Credit: Nicolas Hoizey

Injuries of the anterior cruciate ligament (ACL), located in the knee, are typically thought to be caused by acute traumatic events, such as sudden twists. Led by Penn State researchers, new work analyzing an animal model of ACLs suggests that such injuries can also occur as a result of chronic overuse, specifically due to a reduced ability to repair microtraumas associated with overuse. Importantly, the team said, females also are less able to heal from these microtraumas than males, which may explain why females are two to eight times more likely to tear their ACL ligaments than males.

“ACL tears are one of the most common injuries, affecting more than 200,000 people in the U.S. each year, and women are known to be particularly susceptible,” said principal investigator Spencer Szczesny, associate professor of biomedical engineering and of orthopedics and rehabilitation at Penn State. “While recent research suggests that chronic overuse can lead to ACL injuries, until now, no one had investigated the differential biological response of female and male ACLs to applied force.”

A New Method for Assessing the Microbiome of the Human Gut

A technique called 'bead beating.'
Photo Credit: Courtesy of California Institute of Technology

The gut microbiome—the population and variety of bacteria within the intestine—is thought to influence a number of behavioral and disease traits in humans. Most obviously, it affects intestinal health. Cancer, inflammatory bowel disease, and celiac disease, for example, are all affected by the gut microbiome. But recent research at Caltech and other research centers has identified connections between the gut microbiome and diseases such as Parkinson's disease and multiple sclerosis as well as links between the gut microbiome and the presence of autistic behaviors, anxious behaviors, and a propensity to binge-eat sweets. (Most of this work has been done in the laboratory of Sarkis Mazmanian, Caltech's Luis B. and Nelly Soux Professor of Microbiology, who works mainly on mouse models.)

Looking directly at the human gut and the bacteria that make this space their home is often performed with sequencing—a process that analyzes the DNA sequences that make up each organism. However, this process is difficult in the intestine largely because the amount of microbial DNA in the gut is miniscule in comparison to the amount of host DNA. In intestinal tissue, roughly 99.99 percent of the DNA present is from the host organism; only 0.01 percent is microbial DNA.

However powerful the effects of these microbes, it is hard to understand their role without knowing their composition. Microbiome studies often rely on studies of feces and saliva, but these are quite different from the ecosystem of the gut itself.

New invasive, weedy grasses discovered across Hawaiʻi, some pose major fire risk

Enneapogon cenchroides is the most flammable grass species that Faccenda discovered. It was found in Mākaha.
Photo Credit: Courtesy of University of Hawaiʻi

New species of flammable invasive grasses have been discovered and identified across most Hawaiian islands by a University of Hawaiʻi at Mānoa School of Life Sciences PhD student.

Kevin Faccenda discovered 34 invasive and/or weedy species never before reported in Hawaiʻi during more than 50 days of fieldwork conducted across Kauaʻi, Oʻahu, Maui, Molokaʻi and Hawaiʻi Island over the past year. Six of these species have never been found outside of their native range before, making Hawaiʻi the first place worldwide to experience naturalizations by these species. Faccenda says controlling the spread of these grass species and others is critical to avoid future wildfires, like the one that devastated Lahaina on August 8.

Neutrons see stress in 3D-printed parts, advancing additive manufacturing

The OpeN-AM experimental platform, installed at the VULCAN instrument at ORNL’s Spallation Neutron Source, features a robotic arm that prints layers of molten metal to create complex shapes. This allows scientists to study 3D printed welds microscopically.
Photo Credit: Jill Hemman, ORNL/U.S. Dept. Of Energy

Using neutrons to see the additive manufacturing process at the atomic level, scientists have shown that they can measure strain in a material as it evolves and track how atoms move in response to stress.

“The automotive, aerospace, clean energy and tool-and-die industries — any industry that needs complex and high-performance parts — could use additive manufacturing,” said Alex Plotkowski, materials scientist in ORNL’s Materials Science and Technology Division and the lead scientist of the experiment. Plotkowski and his colleagues reported their findings in Nature Communications.

ORNL scientists have developed OpeN-AM, a 3D printing platform that can measure evolving residual stress during manufacturing using the VULCAN beamline at ORNL’s Spallation Neutron Source, or SNS, a Department of Energy Office of Science user facility. When combined with infrared imaging and computer modeling, this system enables unprecedented insight into material behavior during manufacturing.

Targeting a coronavirus ion channel could yield new Covid-19 drugs

MIT chemists found that the SARS-CoV-2 E protein, which acts as an ion channel, has a broad opening at the bottom when in the closed state and a narrower opening in the open state.
Image Credits: Courtesy of the researchers, MIT News, and iStock
(CC BY-NC-ND 3.0 DEED)

The genome of the SARS-CoV-2 virus encodes 29 proteins, one of which is an ion channel called E. This channel, which transports protons and calcium ions, induces infected cells to launch an inflammatory response that damages tissues and contributes to the symptoms of Covid-19.

MIT chemists have now discovered the structure of the “open” state of this channel, which allows ions to flow through. This structure, combined with the “closed” state structure that was reported by the same lab in 2020, could help scientists figure out what triggers the channel to open and close. These structures could also guide researchers in developing antiviral drugs that block the channel and help prevent inflammation.

“The E channel is an antiviral drug target. If you can stop the channel from sending calcium into the cytoplasm, then you have a way to reduce the cytotoxic effects of the virus,” says Mei Hong, an MIT professor of chemistry and the senior author of the study.

MIT postdoc Joao Medeiros-Silva is the lead author of the study, which appears today in Science Advances. MIT postdocs Aurelio Dregni and Pu Duan and graduate student Noah Somberg are also authors of the paper.

Calorie restriction in humans builds strong muscle and stimulates healthy aging genes

NIH study suggests a small reduction in daily calories is beneficial for wellness.
Photo Credit: rawpixel

Reducing overall calorie intake may rejuvenate your muscles and activate biological pathways important for good health, according to researchers at the National Institutes of Health and their colleagues. Decreasing calories without depriving the body of essential vitamins and minerals, known as calorie restriction, has long been known to delay the progression of age-related diseases in animal models. This new study, published in Aging Cell, suggests the same biological mechanisms may also apply to humans.

Researchers analyzed data from participants in the Comprehensive Assessment of Long-Term Effects of Reducing Intake of Energy (CALERIE), a study supported by the National Institute on Aging (NIA) that examined whether moderate calorie restriction conveys the same health benefits seen in animal studies. They found that during a two-year span, the goal for participants was to reduce their daily caloric intake by 25%, but the highest the group was able to reach was a 12% reduction. Even so, this slight reduction in calories was enough to activate most of the biological pathways that are important in healthy aging.

Negative attitudes towards breastfeeding in public still an issue

Photo Credit: seeseehundhund

International law supports women’s right to breastfeed in public. However, women report having been subjected to negative responses and judgmental looks when breastfeeding outside the home. This is according to a new study from Lund University in Sweden, based on surveys answered by women living in Sweden, Ireland and Australia.

The researchers behind the study say that societies everywhere need to give clearer, explicit support for breastfeeding in public – and that society needs to welcome breastfeeding, regardless of the setting.

“Women and children lack access to public spaces. This affects opportunities to breastfeed when children need it, which in turn has a negative effect on both women and children,” says Charlotta Dykes, doctoral student and pediatric nurse.

She illustrates that point with one of many similar statements from women in their study: “Just how hungry is my child, will they be okay until I get home? Is there a better spot close by? Can I easily turn to face the other direction?”

Over 40 percent of Antarctica’s ice shelves are smaller

Photo Credit: Derek Oyen

71 of the 162 ice shelves that surround Antarctica have reduced in volume over 25 years from 1997 to 2021, with a net release of 7.5 trillion tons of meltwater into the oceans, say scientists.

They found that almost all the ice shelves on the western side of Antarctica experienced ice loss. In contrast, most of the ice shelves on the eastern side stayed the same or increased in volume. 

Over the 25 years, the scientists calculated almost 67 trillion tons of ice was exported to the ocean, which was offset by 59 trillion tons of ice being added to the ice shelves, giving a net loss of 7.5 trillion tons. 

Dr Benjamin Davison, a research fellow at the University of Leeds who led the study, said: “There is a mixed picture of ice-shelf deterioration, and this is to do with the ocean temperature and ocean currents around Antarctica. 

“The western half is exposed to warm water, which can rapidly erode the ice shelves from below, whereas much of East Antarctica is currently protected from nearby warm water by a band of cold water at the coast.”