The Koyal Group Info Mag Articles: 30,000 year-old giant virus found in Siberia

A new type of giant virus called “Pithovirus” has been discovered in the frozen ground of extreme north-eastern Siberia by researchers from the Information Génomique et Structurale laboratory (CNRS/AMU), in association with teams from the Biologie à Grande Echelle laboratory (CEA/INSERM/Université Joseph Fourier), Génoscope (CEA/CNRS) and the Russian Academy of Sciences. Buried underground, this giant virus, which is harmless to humans and animals, has survived being frozen for more than 30,000 years. Although its size and amphora shape are reminiscent of Pandoravirus, analysis of its genome and replication mechanism proves that Pithovirus is very different. This work brings to three the number of distinct families of giant viruses.

In the families Megaviridae (represented in particular by Mimivirus, discovered in 2003) and Pandoraviridae, researchers thought they had classified the diversity of giant viruses (the only viruses visible under optical microscopy, since their diameter exceeds 0.5 microns). These viruses, which infect amoebae such as Acanthamoeba, contain a very large number of genes compared to common viruses (like influenza or AIDS, which only contain about ten genes). Their genome is about the same size or even larger than that of many bacteria.

By studying a sample from the frozen ground of extreme north-eastern Siberia, in the Chukotka autonomous region, researchers were surprised to discover a new giant virus more than 30,000 years old (contemporaneous with the extinction of Neanderthal man), which they have named Pithovirus sibericum. Because of its amphora shape, similar to Pandoravirus, the scientists initially thought that this was a new member — albeit certainly ancient — of this family. Yet genome analysis on Pithovirus showed that this is not the case: there is no genetic relationship between Pithovirus and Pandoravirus. Though it is large for a virus, the Pithovirus genome contains much fewer genes (about 500) than the Pandoravirus genome (up to 2,500). Researchers also analyzed the protein composition (proteome) of the Pithovirus particle (1..5 microns long and 0.5 microns wide) and found that out of the hundreds of proteins that make it up, only one or two are common to the Pandoravirus particle.

Another primordial difference between the two viruses is how they replicate inside amoeba cells. While Pandoravirus requires the participation of many functions in the amoeba cell nucleus to replicate, the Pithovirus multiplication process mostly occurs in the cytoplasm (outside the nucleus) of the infected cell, in a similar fashion to the behavior of large DNA viruses, such as those of the Megaviridae family. Paradoxically, in spite of having a smaller genome than Pandoravirus, Pithovirus seems to be less reliant on the amoeba’s cellular machinery to propagate. The degree of autonomy from the host cell of giant viruses does not therefore appear to correlate with the size of their genome — itself not related to the size of the particle that transports them.

In-depth analysis of Pithovirus showed that it has almost nothing in common with the giant viruses that have previously been characterized. This makes it the first member of a new virus family, bringing to three the number of distinct families of giant viruses known to date. This discovery, coming soon after that of Pandoravirus, suggests that amphora-shaped viruses are perhaps as diverse as icosahedral viruses, which are among the most widespread today. This shows how incomplete our understanding of microscopic biodiversity is when it comes to exploring new environments.

Finally, this study demonstrates that viruses can survive in permafrost (the permanently frozen layer of soil found in the Arctic regions) almost over geological time periods, i.e. for more than 30,000 years (corresponding to the Late Pleistocene). These findings have important implications in terms of public health risks related to the exploitation of mining and energy resources in circumpolar regions, which may arise as a result of global warming. The re-emergence of viruses considered to be eradicated, such as smallpox, whose replication process is similar to Pithovirus, is no longer the domain of science fiction. The probability of this type of scenario needs to be estimated realistically. With the support of the France-Génomique infrastructure, set up as part of the national Investments for the Future program, the “Information Génomique et Structurale” laboratory is already working on the issue via a metagenomic study of the permafrost.

While there is a collective fear for microorganisms for causing human diseases in particular, many of them are actually beneficiel in the field of food, vehicle and antibiotic production. Koyal Info Mag prides itself in its wide coverage of scientific news, discoveries and resources that caters to researchers, scientists, students, scholars, healthcare practitioners and various institutions.

The above article is a repost from ScienceDaily

Zircon discovery offers clues to Earth’s formation

The Koyal Group Info Mag articles - A zircon crystal embedded in sandstone found on a sheep ranch in Australia is the oldest piece of the Earth’s crust to be discovered, shedding new light on our planet’s formation.

The zircon, described in the journal Nature Geoscience, is about 4.4 billion years old and much smaller than a single grain of rice. But the tiny crystal carries an outsize significance: It is evidence that by that point in its history, Earth had gone from a superheated ball of molten rock to a congealed surface eventually capable of supporting life.

“One of the main goals of the space program is to understand if there’s life elsewhere in the universe,” said John Valley, a University of Wisconsin professor who led the study, collaborating with scientists in Australia, Canada and Puerto Rico.

By studying how the conditions of life came together on our planet, scientists believe we will learn what to look for on other planets.

But the earliest rocks and first evidences of life have been subject to dispute over the years. Some scientists, for example, maintain that the earliest evidence of life is about 3.8 billion years old and found in Isua, Greenland. Skeptics, however, note that no fossils were found in the Greenland rock. They point instead to 3.5 billion-year-old evidence of life found in rocks in Pilbara, Australia.

That’s no small difference — 300 million years.

The age of the zircon described by the Valley team, however, does not appear to be in dispute. The Valley team used a new technique called atom-probe tomography, which allowed them to confirm the accuracy of the crystal’s age. The new instrument, made in Wisconsin, is so sensitive that researchers were able to identify the atomic number and mass of each atom in the sample.

“I think they have shown unequivocally, beyond a shadow of a doubt, that this grain is that old,” said Samuel Bowring, an expert in the early history of the Earth and a geology professor at the Massachusetts Institute of Technology. Bowring was not involved in the new study.

“It’s only one grain, mind you,” he added, “but it’s very significant.”

Jim Mattinson, a professor emeritus in the department of earth science at University of California, Santa Barbara, said zircons have been found previously that were about the same age as the one in the current paper, but the earlier discoveries were met with skepticism.

“This paper drives a nail into that coffin (of doubt),” Mattinson said. “We’re really getting back as far as we can go in the Earth’s geologic records.”

Zircon crystals are composed mainly of the elements zirconium, silicon and oxygen. Small amounts of uranium also appear in zircon.

The uranium decays at a set rate, forming lead. Because of these characteristics, scientists can use the lead and any remaining uranium in a zircon crystal to calculate the age.

Zircon is found embedded in younger rock. Valley found the zircon used for the current study in sandstone collected in the arid Jack Hills of western Australia, a region known to contain some of the oldest pieces of the planet’s crust.

“The oldest rock in Australia was collected not far from where we were working,” Valley said.

Dating of the zircon helps clarify an early chapter in the Earth’s history. Scientists have theorized that one of the crucial early events occurred when an asteroid roughly the size of Mars struck a glancing blow to the Earth, vaporizing the mantle and crust. Dust from the collision merged to form the moon.

The enormous energy from the collision transformed the surfaces of the Earth and moon into oceans of molten rock. Both subsequently cooled. Zircon was one of the minerals formed when the planet cooled.

Although minerals also were formed as far back in history, what makes zircon so valuable to geologists is its ability to endure. Zircon is a very hard mineral with stable chemistry able to survive extreme temperatures.

“We like to say that zircons are forever,” Valley said. “They really persist in the rock record.”

Scientists share discoveries at Ocean Sciences Meeting on February 24-28

The Koyal Group Info Mag Articles - Dozens of University of Hawai‘i at Mānoa (UHM) scientists and student researchers will present new research findings at the 2014 Ocean Sciences Meeting at the Hawai‘i Convention Center on February 24-28.  This 17th biennial meeting will be the largest international assembly of oceanographers and other aquatic science researchers and policy makers, with attendance expected to exceed 4,000.

For a full list of sessions and presentations, visit:  Conference registration is complimentary for members of the news media.

A selection of School of Ocean and Earth Science and Technology (SOEST) highlights includes the following:

Science Research Sessions and Presentations:

Celebrating 25 years of sustained marine observations, scientists working at the open ocean field site Station ALOHA will share biological, chemical and physical oceanography discoveries deriving from Hawai‘i’s own unique ocean science field programs.  Station ALOHA was established by the Hawaiʻi Ocean Time-series (HOT) program in 1988, and has been visited on a monthly basis since that time.  The emerging data comprise one of the only existing records of decadal-scale ecosystem change in the North Pacific Ocean. "Time series research is more important than ever before; understanding planetary change requires high quality observations and measurements,” said Matthew Church, UHM Oceanography Professor and HOT Program Principle Investigator.  “Humans are influencing the oceans in many ways, and measurements made at Station ALOHA are helping us understand and document how ocean ecosystems are responding to these changes.”  This session includes more than 25 presentations drawing from observations from present day back to 1988, including long-term changes and trends observed in ocean biology, chemistry, and physics.  Among the notable topics highlighted in this session include documenting ocean acidification, studies on time-varying changes in biodiversity, and the influence of local and regional climate on ocean ecosystem behavior around Hawai‘i.

Chip Fletcher, UHM Geology Professor and his team will describe their effort to monitor and evaluate beach erosion rates at the Royal Hawaiian Beach in Waikīkī. One year after a major sand replenishment program, the beach width appears to vary by location and by season, resulting in net erosion in eastern and western portions of beach.

In the “Story of Marine Debris from the 2011 Tsunami in Japan,” UHM International Pacific Research Center scientists Jan Hafner and Nikolai Maximenko will present the latest synthesis of modeling and observations over the 3 years tracking the debris. This synthesis has resulted in understanding the pathways of the drift from the debris. The improved ocean drift model can help locate marine debris, marine animals, and people lost at sea.

Other research presentations will focus on ocean acidification, sea-level rise and inundation, and climate change including extreme sea level variability due to El Nino events, among many other topics.

Education and Engagement:

UH Mānoa’s Center for Microbial Oceanography: Research and Education (C-MORE) and the Monterey Bay Aquarium Research Institute are hosting a Youth Science Symposium on Tuesday, February 25, from 4-6 p.m. Nearly 20 middle and high school youth scientists will present posters of their research.

SOEST will share several programs aimed at recruiting Native Hawaiian students into ocean and earth science.  Funded by C-MORE and NSF, the Ocean TECH program engages middle school, high school and community college students in the ocean and earth sciences through technology, career pathways and interaction with career professionals.  Funded by the UHM Sea Grant College Program and offered in partnership with Kapiʻolani and Leeward Community Colleges, the SOEST Maile Mentoring Bridge supports Native Hawaiian students throughout their undergraduate years through mentoring relationships that offer encouragement and the sharing of academic and non-academic knowledge.

“Marine Microbiological Mysteries” is a new UHM Outreach College program designed for grades 9-12 to help foster interest in pursuing STEM careers. The hands-on learning opportunity at the Waikīkī Aquarium places microbiology in a real-world context.  This presentation is part of an OSM session titled “Sea-ing connections: Ocean science as a catalyst to inspire the next wave of young (preK-16) scientists and keep students engaged within and outside the classroom.”

Sci-Fi Is Cool (Flying Cars! Life on Mars!)—But Real Science is Cooler

Physicist (and Star Trek expert) Lawrence Krauss talks about the unpredictability of the future.

The Koyal Group Info Mag Articles - Lawrence Krauss is a busy man. A theoretical physicist and cosmologist at Arizona State University, Krauss has studied the universe, served on the science policy committee for Barack Obama’s first presidential campaign, and crossed paths with intellectuals like Stephen Hawking and Christopher Hitchens. He has authored several books, including The Physics of Star Trek. In February 2014, Krauss took part in an American Association for the Advancement of Science symposium titled Where’s My Flying Car? Science, Science Fiction, and a Changing Vision of the Future.


So, where is my flying car?

Your flying car is still in the dreams of people 50 years ago. You can feel bad that we don’t have flying cars, that we’re not living in hotels in space, but the real world intervenes. Certain [technological innovations] are just a lot harder, a lot more expensive.

At the same time, there’s a flipside: The real things that have happened are much more interesting. The Internet is a clear example of how our lives have changed in ways we couldn’t have imagined: a distributed information source, which is invisible to everyone, where you can access anything, and it’s distributed throughout the whole world. Basically, communication is instantaneous.

When it comes to the things that people really want in science fiction—like space travel—the simplest things end up causing them not to happen. Humans are 100-pound bags of water, built to live on Earth.

We hoped for flying cars and got the Internet instead. What’s to blame for the difference between our hopes and the reality we end up with instead?

I would say [innovations] almost never come from predictable places. If innovations were predictable, they wouldn’t be discoveries. When people extrapolate into the future, they extrapolate [from] the known present. If I knew what the next big thing was, I’d be doing it now.

What have we done to the world? Climate change. Overpopulation. Global inequity. Perhaps a virus we set loose from the animal world by displacing so many exotic species, which could wipe us all out. These all either seem to be here already or looming in our near future.

The virus thing: I wouldn’t stay up overnight on it. We’re pretty robust; we’ve survived for four and a half million years.

So what does the future hold?

It looks like we’re destroying the world as we know it. We certainly are entering Earth 2.0. But where that will go is not clear.

Are you hopeful for the future?

It depends on the day. I’m not very hopeful that humanity can act en masse to address what are now truly global problems that require a new way of thinking. As Einstein said when nuclear weapons were created: “Everything’s changed save the way we think.”

I think we need to change the way we think to address these global problems. Will it happen? Maybe kicking and screaming. My friend, the writer Cormac McCarthy, told me once: “I’m a pessimist, but that’s no reason to be gloomy.” In a sense, that’s my attitude.

Five hundred years from now, will we be living on Mars?

Maybe. If we do space travel, it will tend to be one-way trips. Throughout human history, people have done these ridiculously difficult one-way voyages for one reason: because where they lived was so awful they were willing to get on a little wooden vessel that might sink and go across an ocean to some unknown place that they would probably never return from because it was so crummy where they were.

Maybe we’ll do that for ourselves. We’ll make the world so miserable that living in some harsh environment on Mars might seem attractive.