Saturday, November 05, 2022

IceCube neutrinos provide new view of active galaxy

Peer-Reviewed Publication

UNIVERSITY OF ADELAIDE

Neutrino 

IMAGE: WHEN A NEUTRINO INTERACTS WITH MOLECULES IN THE CLEAR ANTARCTIC ICE, IT PRODUCES SECONDARY PARTICLES THAT LEAVE A TRACE OF BLUE LIGHT AS THEY TRAVEL THROUGH THE ICECUBE DETECTOR. view more 

CREDIT: IMAGE: NICOLLE R. FULLER, ICECUBE/NSF

An international team of scientists, including researchers at the University of Adelaide, have gathered new evidence about the energetic core of an active galaxy millions of lights years away by detecting neutrino particles emitted by it.

The scientists have found that NGC 1068, also known as Messier 77, in the constellation of Cetus, is a high-energy neutrino emitter. They have observed the particles using the IceCube Neutrino Observatory in Antarctica.

“We are peering inside active regions of the NGC 1068 galaxy 47 million light years away,” says Associate Professor Gary Hill, from the University of Adelaide’s Department of Physics, School of Physical Sciences and member of the international IceCube Collaboration.

“As we observe neutrinos emitted by it we will be able to learn more about the extreme particle acceleration and production processes occurring inside the galaxy, which hasn’t been possible up to now as other high energy emissions can’t escape from it.”

Neutrinos are subatomic particles that normally pass, by the trillion, through our bodies and every part of the Earth every second, but they rarely interact with matter – a fact that makes them difficult to detect.

The observations were made by the IceCube Neutrino Observatory at the Amundsen-Scott South Pole Station, which was completed in late 2010. NGC 1068 is visible with large binoculars and has been the subject of many astronomical observations.

In 2018, IceCube found the first ever source of neutrinos emitted by TXS 0506+056, a very distant blazar, from which super-massive black hole-powered particle jets, pointing straight at Earth, emit neutrinos. This led to the joint observations over a short time period of neutrinos and gamma-rays.

The NGC 1068 galaxy is about 100 times closer and around 80 neutrino events have so far been identified from the active galaxy. In contrast to the TXS 0506+056 blazar, NGC 1068 is oriented relative to Earth in such a way that a direct view of the central emitting region is obscured by dust. Gamma-rays are absorbed but the neutrinos can escape uninhibited from these regions.

“After the excitement in 2018 of the discovery of neutrinos from TXS 0506+056, it’s even more thrilling to find a source producing a steady stream of neutrinos that we can see with IceCube,” says Associate Professor Hill.

“The fact that neutrinos can escape from within these otherwise-obscured regions of the universe means they are also hard to detect. This requires large detectors like IceCube, which is the current leader in the field with an instrumented volume of a cubic kilometre of deep South Pole ice.”

Many neutrinos pass clear through the Earth, but some interact in the ice near the detector and create muons, which emit flashes of light that are picked up by IceCube’s more than 5000 basketball-sized optical sensors spread over 86 strings, deployed into holes drilled to nearly 2500 metres depth and now permanently frozen into the deep ice. The patterns of light are used to infer the arrival directions and energies of the particles.

“One of the best aspects of my research journey so far has been the time I have spent at the South Pole over many summer seasons working on the installation teams deploying the detector strings into the ice” says Associate Professor Hill.

“The enormous size of IceCube required many years of effort from hundreds of people around the world to complete construction and understand the response to high energy particles. In a few years we’ll be back to the South Pole to put more instruments into the ice, as part of an effort to further improve the detector.”

A future expansion of the detector, dubbed IceCube-Gen2, would be able to detect many more neutrinos, resolve more of these sources and make observations at even higher energies.

The IceCube Neutrino Observatory is operated by the IceCube Collaboration, consisting of over 350 scientists at 58 institutions around the world: https://icecube.wisc.edu/collaboration/institutions

Major funding comes from the US National Science Foundation, and from funding agencies in all other participating countries. The University of Adelaide IceCube research is supported by the Australian Research Council.

The team’s results are published in the journal Science.

Human expansion 1,000 years ago linked to Madagascar’s loss of large vertebrates

Peer-Reviewed Publication

CELL PRESS

Current anthropized landscape of Madagascar 

IMAGE: CURRENT ANTHROPIZED LANDSCAPE OF MADAGASCAR view more 

CREDIT: MAGE CONSORTIUM

The island of Madagascar—one of the last large land masses colonized by humans—sits about 250 miles (400 kilometers) off the coast of East Africa. While it’s still regarded as a place of unique biodiversity, Madagascar long ago lost all its large-bodied vertebrates, including giant lemurs, elephant birds, turtles, and hippopotami. A human genetic study reported in the journal Current Biology on November 4 links these losses in time with the first major expansion of humans on the island, around 1,000 years ago.

“This human demographic expansion was simultaneous with a cultural and ecological transition on the island,” says Denis Pierron, French National Centre for Scientific Research (CNRS) researcher in Toulouse, France. “Around the same period, cities appeared in Madagascar and all the vertebrates of more than 10 kilograms disappeared.”

The origins of humans in Madagascar has long been an enigma, Pierron explained. Madagascar is home to 25 million people who speak an Asian language despite the island’s proximity to East Africa. Other groups who speak similar languages live more than 4,000 miles away. The people that live on Madagascar are known to trace their roots back to two small populations: one Bantu-speaking from Africa and another Austronesian-speaking from Asia. But, beyond that, the history remained rather murky.

To retrace the history and understand more about the origin of Malagasy people, a multi-disciplinary consortium launched in 2007 a project known as Madagascar Genetic and Ethnolinguistic (MAGE). Over a 10-year period, Malagasy and international researchers visited more than 250 villages across the country to sample the cultural and genetic human diversity.

In the new study, Pierron and his colleagues took a close look at the human genetic evidence. More specifically, they closely studied how various segments of human chromosomes were shared together with local ancestry information and computer-simulated genetic data. Together, they’ve inferred that the Malagasy ancestral Asian population was isolated on the island for more than 1,000 years with an effective population size of just a few hundred individuals.

Their isolation ended about 1,000 years ago when a small group of Bantu-speaking African people came to Madagascar. Afterwards, the population continued to expand rapidly over generations. The growing human population led to extensive changes to the Madagascar landscape and the loss of all large-bodied vertebrates that once lived there, they suggest.

The findings have important implications that may now be applied to studies of other human populations. For instance, it shows it’s possible to untangle the demographic history of ancient populations even well after two or more groups have mixed, by using genetic data and computer simulations to test the likelihood of different scenarios. The findings also offer new insights into how past changes in human populations led to changes in whole ecosystems.

“Our study supports the theory that it was not directly the arrival of humans on the island that caused the disappearance of the megafauna, but rather a change in lifestyle that caused both a human population expansion and a reduction in biodiversity in Madagascar,” Pierron says.

While these efforts have led to much better understanding of Madagascar’s history, many intriguing questions remain. For instance, Pierron asks, “If the ancestral Asian population was isolated for more than a millennium before mixing with the African population, where was this population? Already in Madagascar or in Asia? Why did the Asian population isolate itself over 2,000 years ago? Around 1,000 years ago, what triggered the observed cultural and demographic transition?” 

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This work was supported by the Région Aquitaine “Project MAGE” (Madagascar Genétique et Ethnolinguistique) and the French National Research Agency (ANR) Grants “MADEOGEN.”

Current Biology, Alva et al. “The loss of biodiversity in Madagascar is contemporaneous with major demographic events.” https://www.cell.com/current-biology/fulltext/S0960-9822(22)01602-5

Current Biology (@CurrentBiology), published by Cell Press, is a bimonthly journal that features papers across all areas of biology. Current Biology strives to foster communication across fields of biology, both by publishing important findings of general interest and through highly accessible front matter for non-specialists. Visit http://www.cell.com/current-biology. To receive Cell Press media alerts, contact press@cell.com.

Monkeypox mutations cause virus to spread rapidly, evade drugs and vaccines, MU study finds

Researchers show how monkeypox mutations cause virus to replicate, spread faster.

Peer-Reviewed Publication

UNIVERSITY OF MISSOURI-COLUMBI

virus 

IMAGE: VIRUS view more 

CREDIT: UNIVERSITY OF MISSOURI

COLUMBIA, Mo. – Monkeypox has infected more than 77,000 people in more than 100 countries worldwide, and — similar to COVID-19 — mutations have enabled the virus to grow stronger and smarter, evading antiviral drugs and vaccines in its mission to infect more people.

Now, a team of researchers at the University of Missouri have identified the specific mutations in the monkeypox virus that contribute to its continued infectiousness. The findings could lead to several outcomes: modified versions of existing drugs used to treat people suffering from monkeypox or the development of new drugs that account for the current mutations to increase their effectiveness at reducing symptoms and the spread of the virus.

Kamlendra Singh, a professor in the MU College of Veterinary Medicine and Christopher S. Bond Life Sciences Center principal investigator, collaborated with Shrikesh Sachdev, Shree Lekha Kandasamy and Hickman High School student Saathvik Kannan, to analyze the DNA sequences of more 200 strains of monkeypox virus spanning multiple decades, from 1965, when the virus first started spreading, to outbreaks in the early 2000s and again in 2022.

“By doing a temporal analysis, we were able to see how the virus has evolved over time, and a key finding was the virus is now accumulating mutations specifically where drugs and antibodies from vaccines are supposed to bind,” Sachdev said. “So, the virus is getting smarter, it is able to avoid being targeted by drugs or antibodies from our body’s immune response and continue to spread to more people.”

 

Needles in a haystack


Singh has been studying virology and DNA genome replication for nearly 30 years. He said the homology, or structure, of the monkeypox virus is very similar to the vaccinia virus, which has been used as a vaccine to treat smallpox. This enabled Singh and his collaborators to create an accurate, 3D computer model of the monkeypox virus proteins and identify both where the specific mutations are located and what their functions are in contributing to the virus becoming so infectious recently.

 

“Our focus is on looking at the specific genes involved in copying the virus genome, and monkeypox is a huge virus with approximately 200,000 DNA bases in the genome,” Singh said. “The DNA genome for monkeypox is converted into nearly 200 proteins, so it comes with all the ‘armor’ it needs to replicate, divide and continue to infect others. Viruses will make billions of copies of itself and only the fittest will survive, as the mutations help them adapt and continue to spread.”

Kannan and Kandasamy examined five specific proteins while analyzing the monkeypox virus strains: DNA polymerase, DNA helicase, bridging protein A22R, DNA glycosylase and G9R.

“When they sent me the data, I saw that the mutations were occurring at critical points impacting DNA genome binding, as well as where drugs and vaccine-induced antibodies are supposed to bind,” Singh said. “These factors are surely contributing to the virus’ increased infectivity. This work is important because the first step toward solving a problem is identifying where the problem is specifically occurring in the first place, and it is a team effort.”

 

The evolution of viruses

 

Researchers continue to question how the monkeypox virus has evolved over time. The efficacy of current CDC-approved drugs to treat monkeypox have been suboptimal, likely because they were originally developed to treat HIV and herpes but have since received emergency use authorization in an attempt to control the recent monkeypox outbreak.

 

“One hypothesis is when patients were being treated for HIV and herpes with these drugs, they may have also been infected with monkeypox without knowing, and the monkeypox virus got smarter and mutated to evade the drugs,” Singh said. “Another hypothesis is the monkeypox virus may be hijacking proteins we have in our bodies and using them to become more infectious and pathogenic.”

Singh and Kannan have been collaborating since the COVID-19 pandemic began in 2020, identifying the specific mutations causing COVID-19 variants, including Delta and Omicron. Kannan was recently recognized by the United Nations for supporting their ‘Sustainable Development Goals,’ which help tackle the world’s greatest challenges.

 

“I could not have done this research without my team members, and our efforts have helped scientists and drug developers assist with these virus outbreaks, so it is rewarding to be a part of it,” Singh said.

“Mutations in the monkeypox virus replication complex: Potential contributing factors to the 2022 outbreak” was recently published in Journal of Autoimmunity. Co-authors on the study include Shrikesh Sachdev, Athreya Reddy, Shree Lekha Kandasamy, Siddappa Byrareddy, Saathvik Kannan and Christian Lorson.

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Study investigates male and female travellers’ ‘transformations’

Peer-Reviewed Publication

UNIVERSITY OF OTAGO

Dr Jessica Mei Pung 

IMAGE: DR JESSICA MEI PUNG view more 

CREDIT: UNIVERSITY OF OTAGO

A new University of Otago-led study has revealed men and women experience change while travelling in similar ways.

Consumers are increasingly seeking activities that help them achieve new levels of enrichment and since the lift of COVID-19 travel restrictions, they are more conscious of the value they want to gain from their holidays.

The study, published in the international journal Tourism Recreation Research, examines male and female travellers’ subjective travel experiences and identifies nine types of tourist transformation, a process people undergo when they experience change during a trip.

Lead author Dr Jessica Mei Pung, of the Department of Marketing, says of the types identified, there was a significant difference between men and women’s experiences in just two - reflection and transformative learning outcomes.

“Female travellers have a greater engagement in consciousness and self-examination compared with males,” Dr Pung says.

“Secondly, female travellers show a greater achievement of self-efficacy as a result of facing challenges and solving problems during their trips.

“Holiday experiences are an opportunity for female travellers to reflect more on their personal relationships, while males might have a less reflective approach to change and be more oriented towards mastering a specific activity.”

The study provides useful knowledge for the design of transformative tourism products and services. Research comparing female tourists’ transformations with males’ is limited and is reflected in the tourism experiences on offer.

For women, there are getaway packages and wellbeing retreats, while men are targeted with more general offerings, especially within sports tourism.

“There is an untapped market for transformative trips that are not necessarily portrayed as feminine or masculine but that can deliver different types of experiences and benefits. As a result, tourism operators need to rethink how they communicate the offering to their male customers as effectively as they do to their female customers.”

Interestingly, the study, which surveyed 514 people, reveals men and women experience the other seven types of tourist transformation in similar ways.

“For example, there are no differences in how they experience the distance from their everyday lives, or in their levels of immersion in nature and in the social dynamics of the holiday activities.

“Independence, freedom and self-confidence are equally perceived by both sets of respondents, showing that feelings of empowerment do not represent an outcome exclusive to women travellers.”

Morning blue light treatment improves sleep in patients with PTSD

University of Arizona Health Sciences researchers explore a noninvasive, drug-free treatment that offers hope for healing from the severe symptoms of post-traumatic stress disorder.

Peer-Reviewed Publication

UNIVERSITY OF ARIZONA HEALTH SCIENCES

TUCSON, Arizona — People with post-traumatic stress disorder (PTSD) experienced better sleep, a reduction in the severity of PTSD symptoms and more effective treatments after exposure to blue light therapy, according to a new study conducted by researchers in the University of Arizona College of Medicine – Tucson’s Department of Psychiatry and recently published in Frontiers in Behavioral Neuroscience.

Sleep is crucial for maintaining physical and mental health, and inadequate sleep over time can impact all aspects of life with serious implications for long-term health, relationships, cognitive abilities such as learning, and healing.

The influence of sleep disruption on PTSD symptom severity is well established. Those who seek treatment to allay their PTSD symptoms often face a vicious cycle where poor sleep interferes with the effectiveness of treatments, negating any lessening of symptoms, which in turn contributes to sleep disruptions. To reduce and eliminate the emotional impact of traumatic memories, the patient needs quality sleep to integrate healing mechanisms achieved through cognitive or exposure therapy treatments. 

“This research is exciting and unique because it points to an easy-to-use method for helping those with PTSD to retain the benefits of therapy long after the treatment ends,” said psychiatry professor William “Scott” Killgore, PhD, director of the Social, Cognitive and Affective Neuroscience (SCAN) Lab and senior author on the paper, “Morning blue light treatment improves sleep complaints, symptom severity, and retention of fear extinction memory in post-traumatic stress disorder.”

Dr. Killgore and the SCAN Lab team conducted a comprehensive assessment of daily morning blue-wavelength light exposure on individuals with clinically significant levels of PTSD. The goal was to ascertain if blue light therapy would help improve sleep and PTSD symptoms and sustain learned fear extinction memories, an analog of therapeutic treatment for trauma.

Study participants committed to 30 minutes of morning light exposure daily for six weeks, with half of the participants using blue-wavelength light and half using amber light. Researchers examined the neurobiological, autonomic and behavioral outcome changes during the study.

The 43 participants who received blue light therapy not only demonstrated significant improvements in the severity of their PTSD symptoms, but also reported improvements in sleep and showed an increased retention of fear extinction memories. In comparison, the 39 study participants who received amber light did not show the same retention of the extinction memories, but rather showed a return of the original fear memories.

“While the limitations of the research include its modest sample size and difficulties monitoring compliance, the possibilities of utilizing a treatment that is relatively simple, drug-free and inexpensive can offer hope for the large population of people living with the intense challenges of post-traumatic stress disorder,” Dr. Killgore said.

“The data are thrilling,” said Jordan Karp, MD, professor and chair of the College of Medicine – Tucson’s Department of Psychiatry. “This nonpharmacological intervention is a promising life-changing and life-saving possibility for people suffering from PTSD.”

This study was supported by the US Army Medical Research and Development Command (W81XWH-14-0570). 

Dissecting the ecology of microalgae and bacteria across time and space

A new cultivation technology called a “porous microplate” reveals how photosynthetic microalgae interact with their micro-environment.

DOE/US DEPARTMENT OF ENERGY

A schematic diagram of the porous microplate between culture wells. This allows microalgae and bacteria to be cultured in wells at different distances from one another and exchange nutrients without being in physical contact. view more

Credit: Image courtesy of Hyungseok Kim, Massachusetts Institute of Technology

The Science

Microalgae are algae too small to see with the human eye that live in both fresh and sea water. They are responsible for half of fixation of carbon that occurs on Earth through photosynthesis. Fixation is the process where carbon dioxide moves from the atmosphere into solid organic forms. This makes microalgae important in controlling climate change. Microalgae also have the potential to be a sustainable bioenergy source. The water immediately outside their cells, called the “phycosphere,” is rich with organic carbon that is secreted by the algae. The phycosphere is an ideal ecosystem for the growth of bacteria. However, detecting and measuring bacterial cell activity and population growth in the phycosphere is difficult. This is because scientists have not been able to track single bacteria and their locations in relation to algal cells over the course of an algal population growth cycle.

The Impact

This research sought new ways to study how the phycosphere structures bacterial communities across time and space. The researchers created a new co-culture method called a “porous microplate.” The microplate is made of a material with nanoscale pores, smaller than the microalgae and bacteria. Microplates sit in the walls between culture wells, which are tiny pools where microalgae and bacteria grow in a lab. The tiny pores mean the microplates can pass nutrients and molecules associated with metabolism between culture cells while blocking physical contact between algae in adjacent wells. This design enabled the researchers to stretch out the phycosphere in both space and time. As a result, they could quantify how bacteria grow and how the bacterial community changes at different distances from the algal cells. The new method will help microbiologists and other researchers understand microalgae and ultimately their role in our planet’s climate.

Summary

After sequencing the DNA of algal microbiome cultured in the microplate, the team revealed that certain bacteria responded to the algal production of organic carbon in a spatially dependent manner. Specifically, they found that bacteria associated with the algae reached higher abundances when placed closer to the algal culture well. This result fits with expectations for real phycosphere environments. The researchers also unexpectedly found that cultivation of the diatom Phaeodactylum in the microplate led to yields 20 times greater than batch cultures due to continuous supplementation of nutrients.

The new porous microplate incubation method is highly effective for algal cultivation, allowing the diatom Phaeodactylum to accumulate to its theoretical physical limit, densely packed with cell-to-cell distances equal to their cell radius. This result may be important to efforts to produce increased and more efficient algal biomass production at large scales. Moreover, the porous microplate system facilitates investigation of community-level microbial interactions in complex small-scale ecosystems mediated by metabolite exchange. The system shows that the algal phycosphere is a complex ecosystem which allows multiple microbial groups to thrive in different locations within this microscale environment.

 

Funding

The work was supported by the Department of Energy Office of Science’s Genome Sciences Program as part of the ÂµBiospheres Scientific Focus Area research program. Additional support was provided by the Kwanjeong Educational Foundation.