Genome of Longest-Living Cancer: 11,000-Year-Old Living Dog Cancer Reveals Its Origin, Evolution

Genome of Longest-Living Cancer: 11,000-Year-Old Living Dog Cancer Reveals Its Origin, Evolution

A cancer normally lives and dies with a person, however this is not the case with a sexually transmitted cancer in dogs. In a study published in Science, researchers have described the genome and evolution of this cancer that has continued living within the dog population for the past 11,000 years.

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Scientists have sequenced the genome of the world's oldest continuously surviving cancer, a transmissible genital cancer that affects dogs. This cancer, which causes grotesque genital tumors in dogs around the world, first arose in a single dog that lived about 11,000 years ago. The cancer survived after the death of this dog by the transfer of its cancer cells to other dogs during mating.

The genome of this 11,000-year-old cancer carries about two million mutations -- many more mutations than are found in most human cancers, the majority of which have between 1,000 and 5,000 mutations. The team used one type of mutation, known to accumulate steadily over time as a "molecular clock," to estimate that the cancer first arose 11,000 years ago.

"The genome of this remarkable long-lived cancer has demonstrated that, given the right conditions, cancers can continue to survive for more than 10,000 years despite the accumulation of millions of mutations," says Dr Elizabeth Murchison, first author from the Wellcome Trust Sanger Institute and the University of Cambridge.

The genome of the transmissible dog cancer still harbors the genetic variants of the individual dog that first gave rise to the cancer 11,000 years ago. Analysis of these genetic variants revealed that this dog may have resembled an Alaskan Malamute or Husky. It probably had a short, straight coat that was colored either grey/brown or black. Its genetic sequence could not determine if this dog was a male or a female, but did indicate that it was a relatively inbred individual.

"We do not know why this particular individual gave rise to a transmissible cancer," says Dr Murchison, "But it is fascinating to look back in time and reconstruct the identity of this ancient dog whose genome is still alive today in the cells of the cancer that it spawned."

Transmissible dog cancer is a common disease found in dogs around the world today. The genome sequence has helped scientists to further understand how this disease has spread.

"The patterns of genetic variants in tumors from different continents suggested that the cancer existed in one isolated population of dogs for most of its history," says Dr Murchison. "It spread around the world within the last 500 years, possibly carried by dogs accompanying seafarers on their global explorations during the dawn of the age of exploration."

Transmissible cancers are extremely rare in nature. Cancers, in humans and animals, arise when a single cell in the body acquires mutations that cause it to produce more copies of itself. Cancer cells often spread to different parts of the body in a process known as metastasis. However, it is very rare for cancer cells to leave the bodies of their original hosts and to spread to other individuals. Apart from the dog transmissible cancer, the only other known naturally occurring transmissible cancer is an aggressive transmissible facial cancer in Tasmanian devils that is spread by biting.

"The genome of the transmissible dog cancer will help us to understand the processes that allow cancers to become transmissible," says Professor Sir Mike Stratton, senior author and Director of the Sanger Institute. "Although transmissible cancers are very rare, we should be prepared in case such a disease emerged in humans or other animals. Furthermore, studying the evolution of this ancient cancer can help us to understand factors driving cancer evolution more generally."

One Quarter of the World's Cartilaginous Fish, Namely Sharks and Rays, Face Imminent Extinction

One Quarter of the World's Cartilaginous Fish, Namely Sharks and Rays, Face Imminent Extinction

One quarter of the world's cartilaginous fish, namely sharks and rays, face extinction within the next few decades, according to the first study to systematically and globally assess their fate.

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The International Union for Conservation of Nature's (IUCN's) Shark Specialist Group (SSG), co-chaired by Nick Dulvy, a Simon Fraser University (SFU) Canada Research Chair in Marine Biodiversity and Conservation in British Columbia, conducted the study.

It was published ineLife journal today.Previous studies have documented local overfishing of some populations of sharks and rays. But this is the first one to survey their status through out coastal seas and oceans. It reveals that one-quarter (249) of 1,041 known shark, ray and chimaera species globally fall under three threatened categories on the IUCN Red List.

"We now know that many species of sharks and rays, not just the charismatic white sharks, face extinction across the ice-free seas of the world," says Dulvy. "There are no real sanctuaries for sharks where they are safe from overfishing."

Over two decades, the authors applied the IUCN's Red List categories and criteria to the 1,041 species at 17 workshops involving more than 300 experts. They incorporated all available information on distribution, catch, abundance, population trends, habitat use, life histories, threats and conservation measures.

Sharks and rays are at substantially higher risk of extinction than many other animals and have the lowest percentage of species considered safe. Using the IUCN Red List, the authors classified 107 species of rays (including skates) and 74 species of sharks as threatened. Just 23 percent of species were labeled as being Least Concern.

The authors identified two main hotspots for shark and ray depletion -- the Indo-Pacific (particularly the Gulf of Thailand), the Red Sea and the Mediterranean Sea.

"In the most peril are the largest species of rays and sharks, especially those living in relatively shallow water that is accessible to fisheries. The combined effects of overexploitation -- especially for the lucrative shark fin soup market -- and habit degradation are most severe for the 90 species found in freshwater.

"A whole bunch of wildly charismatic species is at risk. Rays, including the majestic manta and devil rays, are generally worse off than sharks. Unless binding commitments to protect these fish are made now, there is a real risk that our grandchildren won't see sharks and rays in the wild."

Losing these fish will be like losing whole chapters of our evolutionary history says Dulvy. "They are the only living representatives of the first lineage to have jaws, brains, placentas and the modern immune system of vertebrates."

The potential loss of the largest species is frightening for many reasons, says Dulvy. "The biggest species tend to have the greatest predatory role. The loss of top or apex predators cascades throughout marine ecosystems."

The IUCN SSG is calling on governments to safeguard sharks, rays and chimaeras through a variety of measures, including the following: prohibition on catching the most threatened species, science-based fisheries quotas, protection of key habitats and improved enforcement.

Gold Nanoparticles Help to Develop a New Method for Tracking Viruses

Gold Nanoparticles Help to Develop a New Method for Tracking Viruses

Researchers at the Nanoscience Center (NSC) of University of Jyväskylä in Finland have developed a novel method to study enterovirus structures and their functions. The method will help to obtain new information on trafficking of viruses in cells and tissues as well as on the mechanisms of virus opening inside cells. This new information is important for example for developing new antiviral drugs and vaccines. The study was published in the journalProceedings of the National Academy of Science.

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Enteroviruses are pathogenic viruses infecting humans. This group consists of polioviruses, coxsackieviruses, echoviruses and rhinoviruses. Enteroviruses are the most common causes of flu, but they also cause serious symptoms such as heart muscle infections and paralysis. Recently, enteroviruses have been linked with chronic diseases such as diabetes.

The infection mechanisms and infectious pathways of enteroviruses are still rather poorly known. Previous studies in the group of Dr. Varpu Marjomäki at the NSC have focused on the cellular factors that are important for the infection caused by selected enteroviruses. The mechanistic understanding of virus opening and the release of the viral genome in cellular structures for starting new virus production is still largely lacking. Furthermore, the knowledge of infectious processes in tissues is hampered by the lack of reliable tools for detecting virus infection.

The newly developed method involves a chemical modification of a known thiol-stabilized gold nanoparticle, the so-called Au102 cluster that was first synthesized and structurally solved by the group of Roger D Kornberg in 2007 and later characterized at NSC by the groups of prof. Hannu Häkkinen and prof. Mika Pettersson in collaboration with Kornberg. The organic thiol surface of the Au102 particles is modified by attaching linker molecules that make a chemical bond to sulfur-containing cysteine residues that are part of the surface structure of the virus. Several tens of gold particles can bind to a single virus, and the binding pattern shows up as dark tags reflecting the overall shape and structure of the virus. The gold particles allow for studies on the structural changes of the viruses during their lifespan.

The study showed also that the infectivity of the viruses is not compromised by the attached gold particles which indicates that the labeling method does not interfere with the normal biological functions of viruses inside cells. This facilitates new investigations on the virus structures from samples taken from inside cells during the various phases of the virus infection, and gives possibilities to obtain new information on the mechanisms of virus uncoating (opening and release of the genome). The new method allows also for tracking studies of virus pathways in tissues. This is important for further understanding of acute and chronic symptoms caused by viruses. Finally, the method is expected to be useful for developing of new antiviral vaccines that are based on virus-like particles.

The method was developed at the NSC as a wide cross-disciplinary collaboration between chemists, physicists and biologists. Researchers involved in the work are Tanja Lahtinen, Kirsi Salorinne, Jaakko Koivisto and Mika Pettersson from the Department of Chemistry, Sami Malola from the Department of Physics and Mari Martikainen and Varpu Marjomäki from the Department of Biology and Environmental Science. The research was coordinated by Docent Varpu Marjomäki and the Scientific Director of NSC, professor Hannu Häkkinen.

The research was funded by the Academy of Finland and the TEKES FiDiPro -project NOVAC (Novel methods for vaccination and virus detection).

New Evidence of 'Nordic Grog' Discovered in Scandinavia

New Evidence of 'Nordic Grog' Discovered in Scandinavia

A blazing fire was not the only thing to keep Bronze and Iron Age Scandinavians warm through long cold winters. From northwest Denmark, circa 1500-1300 BC, to the Swedish island of Gotland as late as the first century AD, Nordic peoples were imbibing an alcoholic "grog" or extreme hybrid beverage rich in local ingredients, including honey, bog cranberry, lingonberry, bog myrtle, yarrow, juniper, birch tree resin, and cereals including wheat, barley and/or rye -- and sometimes, grape wine imported from southern or central Europe.

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New research published in the Danish Journal of Archaeology examines evidence derived from samples inside pottery and bronze drinking vessels and strainers from four sites in Demark and Sweden. The research proves the existence of an early, widespread, and long-lived Nordic grog tradition, one with distinctive flavors and probable medicinal purposes  and the first chemically attested evidence for the importation of grape wine from southern or central Europe as early as 1100 BC, demonstrating both the social and cultural prestige attached to wine, and the presence of an active trading network across Europe  more than 3,000 years ago.

"Far from being the barbarians so vividly described by ancient Greeks and Romans, the early Scandinavians, northern inhabitants of so-called Proxima Thule, emerge with this new evidence as a people with an innovative flair for using available natural products in the making of distinctive fermented beverages," notes Dr. Patrick E. McGovern, lead author of the paper. "They were not averse to adopting the accoutrements of southern or central Europeans, drinking their preferred beverages out of imported and often ostentatiously grand vessels. They were also not averse to importing and drinking the southern beverage of preference, grape wine, though sometimes mixed with local ingredients."

To reach their conclusions the researchers, based at the University of Pennsylvania Museum of Archaeology and Anthropology, obtained ancient residue samples from four sites in a 150-mile radius of southern Sweden and encompassing Denmark. The oldest, dated 1500 -- 1300 BC, was from Nandrup in northwestern Denmark, where a warrior prince had been buried in an oak coffin with a massively hafted bronze sword, battle-ax, and pottery jar whose interior was covered with a dark residue that was sampled. A second Danish sample, dated to a later phase of the Nordic Bronze Age from about 1100 -- 500 BC, came from a pit hoard at Kostræde, southwest of Copenhagen. A brownish residue filling a perforation of a bronze strainer, the earliest strainer yet recovered in the region, was sampled. A third Danish sample was a dark residue on the interior base of a large bronze bucket from inside a wooden coffin of a 30-year-old woman, dating to the Early Roman Iron Age, about 200 BC, at Juellinge on the island of Lolland, southwest of Kostræde. The bucket was part of a standard, imported Roman wine-set, and the woman held the strainer-cup in her right hand. A reddish-brown residue filling the holes and interior of a strainer-cup, again part of imported Roman wine-set, provided the fourth sample. Dating to the first century AD, the strainer-cup was excavated from a hoard, which also included a large gold torque or neck ring and a pair of bronze bells, at Havor on the Swedish island of Gotland in the Baltic Sea.

According to Dr. McGovern, the importation of southern wine grew apace in the Bronze and Iron Ages, and eventually eclipsed the grog tradition -- but never completely. Many of the ingredients in Nordic grog went on to be consumed in birch beer and as the principal bittering agents (so-called gruit) of medieval beers, before hops gained popularity, and the German purity law (Reinheitsgebot) which limited ingredients of beer to barley, hops and water was enacted in Bavaria in 1516 and eventually became the norm in northern Europe.

"About the closest thing to the grog today is produced on the island of Gotland in the Baltic Sea," Dr. McGovern noted. "You can taste Gotlandsdryka in farmhouses. It's made from barley, honey, juniper, and other herbs like those in the ancient version."

Ants Protect Acacia Plants Against Pathogens

Ants Protect Acacia Plants Against Pathogens

The biological term "symbiosis" refers to what economists and politicians usually call a win-win situation: a relationship between two partners which is beneficial to both. The mutualistic association between acacia plants and the ants that live on them is an excellent example: The plants provide food and accommodation in the form of food bodies and nectar as well as hollow thorns which can be used as nests. The ants return this favor by protecting the plants against herbivores. Researchers at the Max Planck Institute for Chemical Ecology in Jena, Germany, have now found that ants also keep harmful leaf pathogens in check. The presence of ants greatly reduces bacterial abundance on surfaces of leaves and has a visibly positive effect on plant health. Study results indicate that symbiotic bacteria colonizing the ants inhibit pathogen growth on the leaves.

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Myrmecophytes are plants which live in a symbiotic relationship with ants. The acacia species Acacia hindsii, which is native to tropical dry forests in Central America, is such a myrmecophyte. Its inhabitants are ants of the genusPseudomyrmex. The ants depend completely on their host plants for nectar and the food bodies rich in proteins and lipids which they require. The acacia also provides shelter, the so-called domatia, in the hollows of its swollen thorns. In return for room and board, mutualistic Pseudomyrmex ferrugineus ants become bodyguards, protecting their host against herbivores and competing plants. However, some ants also benefit from the plant's services without giving anything in return, such as the parasitic ant species Pseudomyrmex gracilis.

Scientists at the Max Planck Institute for Chemical Ecology have now looked more deeply into the insect-plant interaction, asking whether the tiny bodyguards also provide protection against microbial pathogens. They compared the leaves of acacia plants which were inhabited by either mutualistic or parasitic ants to leaves from which ants had been removed. Intriguingly, the leaves of acacia colonized by parasitic ants showed more leaf damage from herbivores and microbial pathogens than did the leaves that had mutualistic ants. The presence of the right symbiotic partner seemed to have a positive effect on the plant's health.

Analysis of the surfaces of the leaves revealed that the number of plant pathogens as well as of necrotic plant tissues increased considerably when mutualistic Pseudomyrmex ferrugineus ants were absent. These plants also showed strong immune responses in the form of an increased concentration of salicylic acid, a plant hormone which regulates defense against pathogens. Detailed analysis of the bacterial composition on the surfaces of the leaves suggested that the presence of mutualistic ants changed the bacterial populations and reduced harmful pathogens. Although far less pronounced, this effect could also be observed in parasitic ants.

How antimicrobial protection is transferred from ants to plant is still unclear. Chilean researcher Marcia González-Teuber, first author of the publication, suspected that microorganisms associated with the ants might play a role. Because acacia leaves are touched mainly by ants' legs, she extracted the legs of mutualistic and parasitic ants and tested the effect of the extracts on the growth of bacterial pathogens in the lab.

Plant pathogen Pseudomonas syringae was sensitive to the application of leg extracts of both ant species and its growth was inhibited. In the next step, the scientist isolated and identified bacteria from the legs of the ants.  In lab tests, bacterial strains of the genera Bacillus, Lactococcus, Pantoea and Burkholderiaeffectively inhibited the growth of Pseudomonas bacteria isolated from infected acacia leaves. Interestingly, some of the bacterial genera associated with the ants are known to produce antibiotic substances.

The Jena researchers have thus added another level of interaction to the symbiosis between ants and their host plants. "Such mutualistic relationships are much more complex than previously thought. In the future, we will have to include bacteria and other microorganisms in our considerations," says Wilhelm Boland, head of the Department of Bioorganic Chemistry at the Max Planck Institute. Studies on symbiotic relationships between ants and myrmecophytic plants should not overlook the role of bacterial partners that help the ants protect "their" plants.

Neurofeedback Tunes Key Brain Networks, Improving Well-Being in PTSD

Neurofeedback Tunes Key Brain Networks, Improving Well-Being in PTSD

Pioneering research conducted at Western University points to a promising avenue for the treatment of post-traumatic stress disorder (PTSD): utilising neurofeedback training to alter the plasticity of brain networks linked to the condition.

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During neurofeedback, intentional control of one's own brain activity may be learned with what's called a brain-computer interface, which is able to represent graphically a person's real-time brain activation on a computer. This can be done noninvasively with brainwave activities, for example, where the computer monitor behaves like a virtual "mirror" to real electrical oscillations produced by neurons in the cortex. These are recorded by surface sensors on the scalp, also known as an electroencephalogram (EEG).

Available online at the psychiatry journal Acta Psychiatrica Scandinavica, lead authors Rosemarie Kluetsch and Tomas Ros describe the details: "This is the first study to show that key brain networks involved in mediating affect and cognition in PTSD can be volitionally modulated via neurofeedback, with measurable outcomes on subjective well-being. It was achieved by harnessing multiple imaging techniques, including EEG and functional MRI (fMRI). In a nutshell, using fMRI we captured the patients' resting-state brain activity just before and after a 30-minute neurofeedback training session, which was carried out outside the scanner using EEG.

We then searched for any differences in connectivity within well-known brain networks. Interestingly, we discovered significant correlations between EEG and fMRI network activities as well as changes in self-reported calmness. This indicated that neurofeedback was able to directly modulate the brain bases of emotional processing in PTSD."

Senior author and principal investigator Dr. Ruth Lanius, a professor at the Department of Psychiatry at Western's Schulich School of Medicine & Dentistry and a scientist with Lawson Health Research Institute, adds "The last decade of neuroscience research has offered a deeper understanding of the key brain networks involved in cognitive and emotional functions. Connectivity in the salience and default mode networks, for example, has been found to be altered in PTSD.

We are now on the threshold of being able to use this information to understand the neural mechanisms underlying certain disorders and their treatments. Neurofeedback offers great promise as a type of brain training that is directly based on the functional activation of these brain networks. We are therefore thrilled to see the first evidence of this in action, along with significant changes in subjective well-being. Our hope and vision for the future is that this approach could improve and potentially augment PTSD treatment."

Accidental Discovery Dramatically Improves Electrical Conductivity

Accidental Discovery Dramatically Improves Electrical Conductivity

Quite by accident, Washington State University researchers have achieved a 400-fold increase in the electrical conductivity of a crystal simply by exposing it to light. The effect, which lasted for days after the light was turned off, could dramatically improve the performance of devices like computer chips.

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WSU doctoral student Marianne Tarun chanced upon the discovery when she noticed that the conductivity of some strontium titanate shot up after it was left out one day. At first, she and her fellow researchers thought the sample was contaminated, but a series of experiments showed the effect was from light.

The phenomenon they witnessed -- "persistent photoconductivity" -- is a far cry from superconductivity, the complete lack of electrical resistance pursued by other physicists, usually using temperatures near absolute zero. But the fact that they've achieved this at room temperature makes the phenomenon more immediately practical.

And while other researchers have created persistent photoconductivity in other materials, this is the most dramatic display of the phenomenon. The research, which was funded by the National Science Foundation, appears this month in the journal Physical Review Letters.

"The discovery of this effect at room temperature opens up new possibilities for practical devices," said Matthew McCluskey, co-author of the paper and chair of WSU's physics department. "In standard computer memory, information is stored on the surface of a computer chip or hard drive. A device using persistent photoconductivity, however, could store information throughout the entire volume of a crystal."

This approach, called holographic memory, "could lead to huge increases in information capacity," McCluskey said. Strontium titanate and other oxides, which contain oxygen and two or more other elements, often display a dizzying variety of electronic phenomena, from the high resistance used for insulation to superconductivity's lack of resistance.

"These diverse properties provide a fascinating playground for scientists but applications so far have been limited," said McCluskey, Tarun and physicist Farida Selim, now at Bowling Green State University, exposed a sample of strontium titanate to light for 10 minutes. Its improved conductivity lasted for days. They theorize that the light frees electrons in the material, letting it carry more current.