Scientists look to past to help identify fish threatened with local extinction

Scientists look to past to help identify fish threatened with local extinction

Wildlife Conservation Society. “Scientists look to past to help identify fish threatened with local extinction.” ScienceDaily. ScienceDaily, 13 February 2019. .

Wildlife Conservation Society. (2019, February 13). Scientists look to past to help identify fish threatened with local extinction. ScienceDaily. Retrieved February 13, 2019 from www.sciencedaily.com/releases/2019/02/190213142718.htm

Wildlife Conservation Society. “Scientists look to past to help identify fish threatened with local extinction.” ScienceDaily. www.sciencedaily.com/releases/2019/02/190213142718.htm (accessed February 13, 2019).

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Scientists design ‘decoy platelets’ that reduce risk of blood clots

Scientists design ‘decoy platelets’ that reduce risk of blood clots


Wyss Institute at Harvard University

Heart disease, stroke, sepsis and cancer are incredibly serious conditions which together cause the greatest number of deaths around the world. They’re unique illnesses, but they have something in common — they’re all associated with activated platelets, which play an important role in healing, but for some can also contribute to dangerous blood clots and tumors. Now, scientists think they’ve found a way to mitigate the risks associated with these platelets, thereby “outsmarting” the catalyst for these diseases.

There are already a number of antiplatelet drugs on the market, but their effects are not easily reversible, which means patients are at risk of uncontrolled bleeding if injured. And if they need to undergo surgery for their condition, they have to stop treatment up to a week before their operation, which increases their risk of developing blood clots. But researchers at Harvard University have created a drug-free, reversible antiplatelet therapy that uses deactivated “decoy” platelets, which can be initiated and reversed immediately.

The decoys are made from existing human platelets which have been stripped clean via centrifugation and detergent, while retaining adhesive proteins on their surfaces. They bind to other cells that naturally occur in the bloodstream, but because they’ve been deactivated are unable to initiate the clotting process. So when they’re added to normal human blood, the overall clotting process is essentially diluted, allowing normal healing processes to take place without the risk of excessive clotting.

As Anne-Laure Papa, the paper’s first author, explains, “The decoys, unlike normal intact platelets, are unable to bind to the vessel wall and likely hinder the normal platelets’ ability to bind as well. A way to imagine this would be that the decoys are fast-moving skaters skating along the wall of an ice rink, and their high speed prevents other skaters from getting to the wall, thus limiting them from slowing down and grabbing onto it.”

The team also believes the therapy could play an important role in treatment for tumors. Platelets are known to bind to cancer cells, protecting them from the body’s immune system and thereby helping them form new tumors. But the researchers found that by adding decoys along with normal platelets in microfluidic channels, the platelets were almost completely prevented from helping the cancer cells invade the channel wall, suggesting that they could prevent the formation of new tumors. Papa says it’s possible that one day these decoys could be deployed during chemotherapy to prevent existing tumors from spreading, or new ones from forming.

So far, the therapy has only been tested on rabbits and mice, but the team is confident the results could be replicated in humans. Papa’s lab is now working on ensuring the decoys can last longer in the bloodstream for enhanced effectiveness, and studying whether they can be loaded with drugs to help deliver therapies directly to the sites of blood clots and tumors, or possibly even kill circulating tumor cells in the bloodstream altogether.

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Scientists developed a method that allows removal of antibiotic residue from waste water

Scientists developed a method that allows removal of antibiotic residue from waste water

In February the article “Metal-doped organic aerogels for photocatalytic degradation of trimethoprim” written by the researchers of two research groups (nanoporous materials and environmental technology research groups) of Tallinn University of Technology was published in the peer-reviewed professional journal Chemical Engineering Journal.

The head of the nanoporous materials research group, Lead Research Scientist Mihkel Koel, has, as a chemist, focused his research in particular on the implementation of the principles of waste-free chemistry, i.e. green chemistry. This article is also about development of new and effective methods for improving our living environment. Mihkel Koel said, “In modern materials science, the creation and application of materials with extreme properties is continuously of great practical interest. These materials include also the aerogels (highly porous material with extremely low density and low thermal and electrical conductivity) developed by our research group. Novel materials enable also new and effective applications in technology.”

The article is focused in particular on organic aerogels produced from phenolic compounds obtained upon processing Estonian oil shale, i.e. from local raw material. In order to produce highly porous aerogel from gel, supercritical extraction with carbon dioxide is used, in the process of which liquid is replaced by gas resulting in aerogel — a very light and porous material.

It is crucial that this aerogel is produced from local raw material, i.e. Estonian oil shale phenolic compounds,” Koel says. Due to the specificity of the compounds obtained from Estonian raw material, the reaction takes place quickly and at room temperature (earlier the production of aerogel required heating at a temperature as high as 100°C for a longer period of time). By doping these aerogels with metals, an excellent catalyst carrier is produced that can be used e.g. for waste water treatment. Mihkel Koel said, “The study of the photocatalytic activity of organic aerogels doped with metals (Fe, Cu, Co, and Ni) produced novel and surprising results. The best results were obtained by using nickel (Ni). Since aerogel is a highly porous material with large specific surface area, it is well-known for its excellent adsorbent properties, which is particularly important when acting as a catalyst. The article analyses photocatalytic degradation of substances in waste water. It appeared that this method can be successfully used e.g. for removal of the antibiotic trimethoprim, which is used to treat kidney infections, from waste water. Until now, cleaning water from pharmaceutical waste has been extremely complicated and not very effective.”

Mihkel Koel adds that the nanoporous materials research group studies also silica and cellulose aerogels and carbon aerogel produced at high temperature pyrolysis of organic aerogel (by heating up to 700-800 °C without air supply). When carbon aerogels are doped with metals, a material is produced that exhibits the best catalytic properties for electrolysis. In collaboration with the research group of a researcher from the Institute of Chemistry, University of Tartu, Kaido Tammeveski, a goal has been set for the future to use these catalysts in the development of low-temperature fuel cells.

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Neanderthal footprints found in Gibraltar

Neanderthal footprints found in Gibraltar

The  international journal Quaternary Science Reviews has just published a paper which has involved the participation of Gibraltarian scientists from The Gibraltar National Museum alongside colleagues from Spain, Portugal and Japan. The results which have been published come from an area of the Catalan Bay Sand Dune.

This work started ten years ago, when the first dates using the OSL method were obtained. It is then that the first traces of footprints left by vertebrates were found. In subsequent years the successive natural collapse of sand has revealed further material and has permitted a detailed study including new dates.

The sand sheets in the rampant dunes above Catalan Bay are a relic of the last glaciation, when sea level was up to 120 metres below present levels and a great field of dunes extended eastwards from the base of the Rock. The identified footprints correspond to species which are known, from fossil material, to have inhabited Gibraltar. The identified footprints correspond to Red Deer, Ibex, Aurochs, Leopard and Straight-tusked Elephant. In addition the scientists have found the footprint of a young human (106-126 cm in height), possibly Neanderthal, which dates to around 29 thousand years ago. It would coincide with late Neanderthal dates from Gorham’s Cave.

If confirmed to be Neanderthal, these dunes would become only the second site in the world with footprints attributed to these humans, the other being Vartop Cave in Romania. These findings add further international importance to the Gibraltar Pleistocene heritage, declared of World Heritage Value in 2016.

The research was supported by HM Government of Gibraltar under the Gibraltar Caves Project and the annual excavations in the Gibraltar Caves, with additional support to the external scientists from the Spanish EU project MICINN-FEDER: CGL2010-15810/BTE.

Minister for Heritage John Cortes MP commented, “This is extraordinary research and gives us an incredible insight into the wildlife community of Gibraltar’s past. We should all take a moment to imagine the scene when these animals walked across our landscape. It helps us understand the importance of looking after our heritage. I congratulate the research team on uncovering this fascinating, hidden evidence of our Rock’s past.”

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New clue in curious case of cassowary casque: 200-year-old mystery surrounding iconic Australian bird

New clue in curious case of cassowary casque: 200-year-old mystery surrounding iconic Australian bird

A team of Australian scientists has completed research that could help solve a 200-year-old mystery surrounding an iconic Australian bird.

The La Trobe University researchers have published new evidence in Scientific Reports on the southern cassowary and its distinctive helmet — known as a casque.

Danielle Eastick, from La Trobe’s Department of Ecology, Environment and Evolution and her team have shown the cranial structure acts like a radiator or “thermal window” to help the large, flightless birds keep cool in hot weather.

“Our results are quite compelling and it’s highly probable this is what the casque is actually used for,” Ms Eastick said.

“It’s really exciting to think we may have solved a mystery that has baffled scientists for so long.”

Using a handheld thermal imaging device, Ms Eastick obtained readings from 20 captive cassowaries, from Victoria through to northern Queensland and in different weather conditions.

The images showed that the birds released minimal heat from their casque when the weather was just five degrees and the greatest levels when the mercury reached 36 degrees.

Ms Eastick explained that as a large bodied, dark feathered creature, which is native to northern Queensland and Papua New Guinea, cassowaries face a thermal challenge in high temperatures.

“Just as humans sweat and dogs pant in hot weather or following exercise, cassowaries offload heat from their casque in order to survive. The hotter the ambient temperature, the more heat they release.”

“The casque has caused considerable curiosity and speculation for nearly two centuries and animal experts have proposed various theories, including that it’s a protective weapon used for fighting other animals or a means of attracting the opposite sex, but all are inconclusive.”

The “thermal window” explanation may provide a rare glimpse into the physiology of dinosaurs.

“Many dinosaurs also had casques, so it’s possible they too helped keep cool this way.”

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Uncovering the evolution of the brain: Scientists compare the development of brain cells between humans and nonhuman primates in a novel way

Uncovering the evolution of the brain: Scientists compare the development of brain cells between humans and nonhuman primates in a novel way

What makes us human, and where does this mysterious property of “humanness” come from? Humans are genetically similar to chimpanzees and bonobos, yet there exist obvious behavioral and cognitive differences. Now, researchers from the Salk Institute, in collaboration with researchers from the anthropology department at UC San Diego, have developed a strategy to more easily study the early development of human neurons compared with the neurons of nonhuman primates. The study, which appeared in eLife on February 7, 2019, offers scientists a novel tool for fundamental brain research.

“This study provides insights into the developmental organization of the brain and lays the groundwork for further comparative analyses between humans and nonhuman primates,” says one of the senior authors of the study, Salk President and Professor Rusty Gage, who holds the Vi and John Adler Chair for Research on Age-Related Neurodegenerative Disease.

Two important processes in brain development include neuron maturation and migration. Maturation involves neuron growth as the neurons increase their connections between each other for better communication. Migration is the physical movement of neurons into different parts of the developing brain. The authors sought to compare neuron maturation and migration between humans and nonhuman primates.

To accomplish this task, the Gage lab devised a new method utilizing stem cell technology to take skin cells from primates and coax them, via a virus and chemical cocktails, to develop into neural progenitor cells, a cell type that has the ability to become multiple types of cells in the brain, including neurons. These new primate cell lines can then be perpetually propagated, allowing researchers new avenues to study aspects of neuronal development of live neurons without tissue samples from endangered primates such as chimpanzees and bonobos.

“This is a novel strategy to study human evolution,” says Carol Marchetto, a Salk senior staff scientist in the Laboratory of Genetics, co-first author and one of the study’s senior authors. “We are happy to share these primate cell lines with the scientific community, so that researchers from around the world can examine primate brain development without the use of tissue samples. We anticipate this will lead to numerous new findings over the next few years about the brain’s evolution.”

The researchers first explored the differences in gene expression related to neuronal movement, comparing human, chimpanzee and bonobo cells. They also investigated the migration properties of the neurons inherent to each species. They found 52 genes related to migration, and, interestingly, chimpanzee and bonobo neurons had periods of rapid migration, while human neurons were slow to move.

In order to compare neuron movement and maturation outside of a dish, the scientists transplanted the neural progenitor cells from both humans and chimpanzees into the brains of rodents, enabling the neurons to thrive and providing additional developmental cues for the neurons to develop.

The researchers then analyzed the differences in migration distance, shape and size of the neurons for up to 19 weeks after transplantation. They observed the length, density and quantity of extensions of the neurons called dendrites, as well as the size of the cell bodies, which house the nucleus and DNA.

The chimpanzee neurons migrated a greater distance and covered a 76 percent greater area than the human neurons after two weeks. Human neurons were slower to develop but reached longer lengths than the chimpanzee neurons. This slower growth pattern may allow humans to reach more developmental milestones than nonhuman primates, which could account for differences in behavior and cognitive abilities.

In the future, the authors hope to construct an evolutionary tree of multiple primate species, utilizing induced pluripotent stem cell lines, to better understand of the evolution of the human brain. In addition, the authors plan to use this platform to study gene regulation differences between primate species that underlie the differences in neuronal maturation and can potentially impact brain organization in humans.

“We have limited knowledge about the evolution of the brain, especially when it comes to differences in cellular development between species,” says Marchetto. “We’re excited about the tremendous possibilities this work opens up for the field of neuroscience and brain evolution.”

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Uncovering the evolution of the brain: Scientists compare the development of brain cells between humans and nonhuman primates in a novel way

Uncovering the evolution of the brain: Scientists compare the development of brain cells between humans and nonhuman primates in a novel way

What makes us human, and where does this mysterious property of “humanness” come from? Humans are genetically similar to chimpanzees and bonobos, yet there exist obvious behavioral and cognitive differences. Now, researchers from the Salk Institute, in collaboration with researchers from the anthropology department at UC San Diego, have developed a strategy to more easily study the early development of human neurons compared with the neurons of nonhuman primates. The study, which appeared in eLife on February 7, 2019, offers scientists a novel tool for fundamental brain research.

“This study provides insights into the developmental organization of the brain and lays the groundwork for further comparative analyses between humans and nonhuman primates,” says one of the senior authors of the study, Salk President and Professor Rusty Gage, who holds the Vi and John Adler Chair for Research on Age-Related Neurodegenerative Disease.

Two important processes in brain development include neuron maturation and migration. Maturation involves neuron growth as the neurons increase their connections between each other for better communication. Migration is the physical movement of neurons into different parts of the developing brain. The authors sought to compare neuron maturation and migration between humans and nonhuman primates.

To accomplish this task, the Gage lab devised a new method utilizing stem cell technology to take skin cells from primates and coax them, via a virus and chemical cocktails, to develop into neural progenitor cells, a cell type that has the ability to become multiple types of cells in the brain, including neurons. These new primate cell lines can then be perpetually propagated, allowing researchers new avenues to study aspects of neuronal development of live neurons without tissue samples from endangered primates such as chimpanzees and bonobos.

“This is a novel strategy to study human evolution,” says Carol Marchetto, a Salk senior staff scientist in the Laboratory of Genetics, co-first author and one of the study’s senior authors. “We are happy to share these primate cell lines with the scientific community, so that researchers from around the world can examine primate brain development without the use of tissue samples. We anticipate this will lead to numerous new findings over the next few years about the brain’s evolution.”

The researchers first explored the differences in gene expression related to neuronal movement, comparing human, chimpanzee and bonobo cells. They also investigated the migration properties of the neurons inherent to each species. They found 52 genes related to migration, and, interestingly, chimpanzee and bonobo neurons had periods of rapid migration, while human neurons were slow to move.

In order to compare neuron movement and maturation outside of a dish, the scientists transplanted the neural progenitor cells from both humans and chimpanzees into the brains of rodents, enabling the neurons to thrive and providing additional developmental cues for the neurons to develop.

The researchers then analyzed the differences in migration distance, shape and size of the neurons for up to 19 weeks after transplantation. They observed the length, density and quantity of extensions of the neurons called dendrites, as well as the size of the cell bodies, which house the nucleus and DNA.

The chimpanzee neurons migrated a greater distance and covered a 76 percent greater area than the human neurons after two weeks. Human neurons were slower to develop but reached longer lengths than the chimpanzee neurons. This slower growth pattern may allow humans to reach more developmental milestones than nonhuman primates, which could account for differences in behavior and cognitive abilities.

In the future, the authors hope to construct an evolutionary tree of multiple primate species, utilizing induced pluripotent stem cell lines, to better understand of the evolution of the human brain. In addition, the authors plan to use this platform to study gene regulation differences between primate species that underlie the differences in neuronal maturation and can potentially impact brain organization in humans.

“We have limited knowledge about the evolution of the brain, especially when it comes to differences in cellular development between species,” says Marchetto. “We’re excited about the tremendous possibilities this work opens up for the field of neuroscience and brain evolution.”

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The physical forces of cells in action: Swiss scientists have developed probes designed to reveal the physical forces inside living cells; a world first

The physical forces of cells in action: Swiss scientists have developed probes designed to reveal the physical forces inside living cells; a world first

The detection of physical forces is one of the most complex challenges facing science. Although Newton’s apple has long solved the problem of gravity, imaging the physical forces that act in living cells remains one of the main mysteries of current biology. Considered to play a decisive role in many biological processes, the chemical tools to visualize the physical forces in action do not exist. But today, researchers from the University of Geneva (UNIGE) and the National Centre of Competence in Research (NCCR) in Chemical Biology, Switzerland, have developed probes inspired by lobster cooking, they enable to enter into cells. For the first time, physical forces can be imaged live inside the cells. These results, a turning point in the study of life sciences, can be found in the Journal of the American Chemical Society.

Since its creation in 2010, one of the central objectives of the NCCR Chemical Biology has been to solve the problem of detecting cellular physical forces. “Our approach to creating tension probes was inspired by the color change of shrimp, crabs or lobsters during cooking,” says Stefan Matile, Professor in the Department of Organic Chemistry at the Faculty of Science of the UNIGE and member of the NCCR. In live shrimp, the physical forces of the surrounding proteins flatten and polarize the carotenoid pigment, called astaxanthin, until it turns blue. “During cooking, these proteins are unfolded and the lobster pigment can regain its natural dark orange color,” continues the Geneva chemist. Intrigued by these crustaceans, the development of fluorescent probes operating on the same principle of planarization and polarization required about eight years of research.

External force probes have proven their worth

Last year, the NCCR teams finally produced the first fluorescent probe capable of imaging the forces acting on the outer membrane, called the plasma membrane, of living cells. Requests for samples from more than 50 laboratories around the world came in immediate response to the release of these results, demonstrating the importance of this breakthrough for life sciences. To meet this demand, UNIGE’s force probes were launched under the Flipper-TR® brand at the end of last year.

What about the internal forces of the cells?

The study of forces that apply outside the cells is not limited to chemical tools for fluorescence imaging. Cellular surfaces are accessible to physical tools like micropipettes, optical clamps, cantilevers of atomic force microscopes, etc. “But these physical tools are obviously not applicable to the study of forces within cells,” says Aurélien Roux, a professor in the Department of Biochemistry at the Faculty of Science of the UNIGE and a member of the NCCR. “Organelles such as mitochondria, responsible for energy production; endoplasmic reticulum, responsible for protein synthesis; endosomes, responsible for trafficking material to and within cells; or the nucleus, which stores genetic information, are simply beyond the reach of physical tools from outside.” Until today visualization of the forces that operate and control these organelles inside the cells was still impossible, although essential to understand their function!

This fundamental challenge in the life sciences is now being met. The NCCR team, led by Stefan Matile, Aurélien Roux and Suliana Manley, professor at the EPFL Institute of Physics, also member of the NCCR, succeeded in getting their force probes into the cells and selectively marking the various organelles. They are now able to show, for example, how tension rises in the mitochondria that are beginning to divide. “For the very first time, physical forces can be imaged live inside the cells,” enthuses Aurélien Roux. This new chemistry tool finally allows scientists to achieve what they have wanted to do for a very long time. “These new probes now offer us the opportunity to tackle mechanobiology and revolutionize the study of life sciences,” concludes Stefan Matile.

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The physical forces of cells in action: Swiss scientists have developed probes designed to reveal the physical forces inside living cells; a world first

The physical forces of cells in action: Swiss scientists have developed probes designed to reveal the physical forces inside living cells; a world first

The detection of physical forces is one of the most complex challenges facing science. Although Newton’s apple has long solved the problem of gravity, imaging the physical forces that act in living cells remains one of the main mysteries of current biology. Considered to play a decisive role in many biological processes, the chemical tools to visualize the physical forces in action do not exist. But today, researchers from the University of Geneva (UNIGE) and the National Centre of Competence in Research (NCCR) in Chemical Biology, Switzerland, have developed probes inspired by lobster cooking, they enable to enter into cells. For the first time, physical forces can be imaged live inside the cells. These results, a turning point in the study of life sciences, can be found in the Journal of the American Chemical Society.

Since its creation in 2010, one of the central objectives of the NCCR Chemical Biology has been to solve the problem of detecting cellular physical forces. “Our approach to creating tension probes was inspired by the color change of shrimp, crabs or lobsters during cooking,” says Stefan Matile, Professor in the Department of Organic Chemistry at the Faculty of Science of the UNIGE and member of the NCCR. In live shrimp, the physical forces of the surrounding proteins flatten and polarize the carotenoid pigment, called astaxanthin, until it turns blue. “During cooking, these proteins are unfolded and the lobster pigment can regain its natural dark orange color,” continues the Geneva chemist. Intrigued by these crustaceans, the development of fluorescent probes operating on the same principle of planarization and polarization required about eight years of research.

External force probes have proven their worth

Last year, the NCCR teams finally produced the first fluorescent probe capable of imaging the forces acting on the outer membrane, called the plasma membrane, of living cells. Requests for samples from more than 50 laboratories around the world came in immediate response to the release of these results, demonstrating the importance of this breakthrough for life sciences. To meet this demand, UNIGE’s force probes were launched under the Flipper-TR® brand at the end of last year.

What about the internal forces of the cells?

The study of forces that apply outside the cells is not limited to chemical tools for fluorescence imaging. Cellular surfaces are accessible to physical tools like micropipettes, optical clamps, cantilevers of atomic force microscopes, etc. “But these physical tools are obviously not applicable to the study of forces within cells,” says Aurélien Roux, a professor in the Department of Biochemistry at the Faculty of Science of the UNIGE and a member of the NCCR. “Organelles such as mitochondria, responsible for energy production; endoplasmic reticulum, responsible for protein synthesis; endosomes, responsible for trafficking material to and within cells; or the nucleus, which stores genetic information, are simply beyond the reach of physical tools from outside.” Until today visualization of the forces that operate and control these organelles inside the cells was still impossible, although essential to understand their function!

This fundamental challenge in the life sciences is now being met. The NCCR team, led by Stefan Matile, Aurélien Roux and Suliana Manley, professor at the EPFL Institute of Physics, also member of the NCCR, succeeded in getting their force probes into the cells and selectively marking the various organelles. They are now able to show, for example, how tension rises in the mitochondria that are beginning to divide. “For the very first time, physical forces can be imaged live inside the cells,” enthuses Aurélien Roux. This new chemistry tool finally allows scientists to achieve what they have wanted to do for a very long time. “These new probes now offer us the opportunity to tackle mechanobiology and revolutionize the study of life sciences,” concludes Stefan Matile.

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Scientists use machine learning to ID source of Salmonella: Quick identification of animal source key to stopping foodborne illness outbreaks

Scientists use machine learning to ID source of Salmonella: Quick identification of animal source key to stopping foodborne illness outbreaks

A team of scientists led by researchers at the University of Georgia Center for Food Safety in Griffin has developed a machine-learning approach that could lead to quicker identification of the animal source of certain Salmonella outbreaks.

In the research, published in the January 2019 issue of Emerging Infectious Diseases, Xiangyu Deng and his colleagues used more than a thousand genomes to predict the animal sources, especially livestock, of Salmonella Typhimurium.

Deng, an assistant professor of food microbiology at the center, and Shaokang Zhang, a postdoctoral associate with the center, led the project, which also included experts from the Centers for Disease Control and Prevention, the U.S. Food and Drug Administration, the Minnesota Department of Health and the Translational Genomics Research Institute.

According to the Foodborne Disease Outbreak Surveillance System, close to 3,000 outbreaks of foodborne illness were reported in the U.S. from 2009 to 2015. Of those, 900 — or 30 percent — were caused by different serotypes of Salmonella, including Typhimurium, Deng said.

“We had at least three outbreaks of Typhimuirum, or its close variant, in 2018. These outbreaks were linked to chicken, chicken salad and dried coconut,” he said. “There are more than 2,600 serotypes of Salmonella, and Typhimurium is just one of them, but since the 1960s, about a quarter of Salmonella isolates linked to outbreaks reported to U.S. national surveillance are Typhimurium.”

The researchers trained the “machine,” an algorithm called Random Forest, with more than 1,300 S. Typhimurium genomes with known sources. After the training, the “machine” learned how to predict certain animal sources of S. Typhimurium genomes.

For this study, the scientists used Salmonella Typhimurium genomes from three major surveillance and monitoring programs: the CDC’s PulseNet network; the FDA’s GenomeTrakr database of sources in the United States, Europe, South America, Asia and Africa; and retail meat isolates from the FDA arm of the National Antimicrobial Resistance Monitoring System.

“With so many genomes, machine learning is a natural choice to deal with all these data.

We used this big collection of Typhimurium genomes as the training set to build the classifier,” said Deng who was awarded the UGA Creative Research Medal in 2017 for his work in this area. “The classifier predicts the source of the Typhimurium isolate by interrogating thousands of genetic features of its genome.”

Overall, the system predicted the animal source of the S. Typhimurium with 83 percent accuracy. The classifier performed best in predicting poultry and swine sources, followed by bovine and wild bird sources. The machine also detects whether its prediction is precise or imprecise. When the prediction was precise, the machine was accurate about 92 percent of the time, Deng said.

“We retrospectively analyzed eight of the major zoonotic outbreaks that occurred in the U.S. from 1998 to 2013,” he said. “The classifier attributed seven of them to the correct livestock source.”

Deng says the tool has limitations; it cannot predict seafood as a source and it has difficulty predicting Salmonella strains that “jump around among different animals.”

“I’d call this approach a proof of concept. It will get better as more genomes from various sources become available,” he said.

In tweets about the study, Frank Yiannas, deputy director of the FDA, called the machine learning of whole genome sequences project “a new era of smarter food safety and epidemiology.”

To the average person, the success of this project means strains of Salmonella Typhimurium could be traced back to the source faster. Identifying what causes a foodborne illness outbreak is key to stopping it and preventing further illnesses.

“Using our method, investigators can better link cases of the same outbreak and better match isolates from food or food processing environments to isolates from sick people,” he said. “This will give investigators more confidence to implicate a specific source that is behind the outbreak.”

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Scientists use machine learning to ID source of Salmonella: Quick identification of animal source key to stopping foodborne illness outbreaks

Scientists use machine learning to ID source of Salmonella: Quick identification of animal source key to stopping foodborne illness outbreaks

A team of scientists led by researchers at the University of Georgia Center for Food Safety in Griffin has developed a machine-learning approach that could lead to quicker identification of the animal source of certain Salmonella outbreaks.

In the research, published in the January 2019 issue of Emerging Infectious Diseases, Xiangyu Deng and his colleagues used more than a thousand genomes to predict the animal sources, especially livestock, of Salmonella Typhimurium.

Deng, an assistant professor of food microbiology at the center, and Shaokang Zhang, a postdoctoral associate with the center, led the project, which also included experts from the Centers for Disease Control and Prevention, the U.S. Food and Drug Administration, the Minnesota Department of Health and the Translational Genomics Research Institute.

According to the Foodborne Disease Outbreak Surveillance System, close to 3,000 outbreaks of foodborne illness were reported in the U.S. from 2009 to 2015. Of those, 900 — or 30 percent — were caused by different serotypes of Salmonella, including Typhimurium, Deng said.

“We had at least three outbreaks of Typhimuirum, or its close variant, in 2018. These outbreaks were linked to chicken, chicken salad and dried coconut,” he said. “There are more than 2,600 serotypes of Salmonella, and Typhimurium is just one of them, but since the 1960s, about a quarter of Salmonella isolates linked to outbreaks reported to U.S. national surveillance are Typhimurium.”

The researchers trained the “machine,” an algorithm called Random Forest, with more than 1,300 S. Typhimurium genomes with known sources. After the training, the “machine” learned how to predict certain animal sources of S. Typhimurium genomes.

For this study, the scientists used Salmonella Typhimurium genomes from three major surveillance and monitoring programs: the CDC’s PulseNet network; the FDA’s GenomeTrakr database of sources in the United States, Europe, South America, Asia and Africa; and retail meat isolates from the FDA arm of the National Antimicrobial Resistance Monitoring System.

“With so many genomes, machine learning is a natural choice to deal with all these data.

We used this big collection of Typhimurium genomes as the training set to build the classifier,” said Deng who was awarded the UGA Creative Research Medal in 2017 for his work in this area. “The classifier predicts the source of the Typhimurium isolate by interrogating thousands of genetic features of its genome.”

Overall, the system predicted the animal source of the S. Typhimurium with 83 percent accuracy. The classifier performed best in predicting poultry and swine sources, followed by bovine and wild bird sources. The machine also detects whether its prediction is precise or imprecise. When the prediction was precise, the machine was accurate about 92 percent of the time, Deng said.

“We retrospectively analyzed eight of the major zoonotic outbreaks that occurred in the U.S. from 1998 to 2013,” he said. “The classifier attributed seven of them to the correct livestock source.”

Deng says the tool has limitations; it cannot predict seafood as a source and it has difficulty predicting Salmonella strains that “jump around among different animals.”

“I’d call this approach a proof of concept. It will get better as more genomes from various sources become available,” he said.

In tweets about the study, Frank Yiannas, deputy director of the FDA, called the machine learning of whole genome sequences project “a new era of smarter food safety and epidemiology.”

To the average person, the success of this project means strains of Salmonella Typhimurium could be traced back to the source faster. Identifying what causes a foodborne illness outbreak is key to stopping it and preventing further illnesses.

“Using our method, investigators can better link cases of the same outbreak and better match isolates from food or food processing environments to isolates from sick people,” he said. “This will give investigators more confidence to implicate a specific source that is behind the outbreak.”

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A better eyeshot of the makeup of ancient meteorites: Scientists use powerful imaging techniques for an improved view of meteorite components

A better eyeshot of the makeup of ancient meteorites: Scientists use powerful imaging techniques for an improved view of meteorite components

A team of Japanese and American scientists has visualized meteorite components at resolution powers much higher than ever before. Their efforts resulted in a much better look at — and enhanced understanding of — substances inside carbonaceous chondrites, the organic-containing meteorites that land on Earth. These substances include hydrogen, carbon, nitrogen and water, all of which are needed for life.

The study was published online on January 2, 2019 in Proceedings of the National Academy of Sciences (PNAS).

Carbonaceous chondrites are made of materials such as rocks, organics, ice, and fine grain dust, most of which are formed in the Solar System. The origin of organic matter that is found in meteorites dates back to the formation of the Solar System, or approximately 4.5 billion years ago. Therefore, when found on Earth and analyzed in detail, these carbonaceous chondrites are helpful for understanding the history of the Solar System, the formation of organic compounds, the presence of water on Earth, and ultimately the origin of life.

Being able to visualize organic and inorganic components of meteorites that have landed on Earth is important because it enables researchers to understand the effects of external factors — such as water and temperature — on them. More specifically, a method that enables researchers to better see and analyze the molecular structures ultimately helps them understand the spatial relationships between organic matter and minerals. This is vital for tracing the formation as well as the evolution of organic matter and ultimately understand the history of the formation of the Solar System. Also, understanding the origin of meteorites is crucial for determining the origins of both water and life on the planet.

However, studies to date have been limited with their methods as well as microscopy that has provided images at much lower resolutions. Therefore, formations and evolutions of extraterrestrial organic matter have thus far remained fairly unknown and have only been analyzed after extraction, which is a complicated multi-step process that is prone to many types of methodological errors.

“Researchers have recently mostly conducted analysis for organic matter to see the distributions and associations with inorganic compounds that may help us understand chemistry such as mineral catalyzed synthesis of organic matter, during alteration processes in the meteorite parent asteroids and historic dust processes in the early Solar System. However, since the components of meteorites are very fine, microscopic techniques to analyze such distributions and associations are limited,” says Yoko Kebukawa, Ph.D., an Associate Professor at the Faculty of Engineering, Yokohama National University in Japan and the corresponding author of the paper.

Specific to this research, the focus has been on visualizing components of carbonaceous chondrites via a powerful microscopy method that provides images of meteorite components at much better resolutions. This method, atomic force microscopy-based infrared spectroscopy (AFM-IR) enabled the researchers to view the components of two carbonaceous chondrites, the Murchison meteorite and the Bell meteorite at much higher resolutions. This, in turn, provided much more detailed images than those that have been obtained thus far.

“The AFM-IR technique enabled us to overcome the limitation of poor spatial resolution of infrared spectroscopy to see the fine details of organic matter as it is distributed in meteorites and associations of minerals,” Kebukawa adds.

In the future, the team plans to focus on the roles of minerals in the formations and evolution of organic matter in meteorites during external processes that affect the bodies they come from. According to Kebukawa, “This requires two things, namely analyses of meteorites that have been altered in several ways as well as proper experimental simulations of these alteration processes that will enable the aforementioned methods.”

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Self-repairing shoes may be a reality thanks to 3D-printed rubber

Self-repairing shoes may be a reality thanks to 3D-printed rubber


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Shoes will invariably wear out with enough use, but scientists might have found a way to delay the shopping trip for their replacements. A USC team has created a self-healing 3D-printed rubber that could be ideal for footwear, tires and even soft robotics. The effort involves 3D printing the material with photopolymerization (solidifying a resin with light) while introducing an oxidizer at just the right ratio to add self-healing properties without slowing down the solidifying process.

The result is a rubber that’s highly durable, but can still be made in a reasonable amount of time. An object that takes 20 minutes to make (such as a shoe sole) can survive being cut in half with a few hours of repair time. And the warmer it is, the faster the material heals. In the lab, it took two hours to fix a cut at roughly 140F.

This might not be ready for the real world in the near future. Researchers would still need to find a way to make this available for mass production. And even if it’s ready, it would be important to dial back the hype. This might prevent your shoes from cracking and minimize gouges, but it’s not going to keep your running shoes looking brand new after hundreds of trips to the gym. Nonetheless, it could still represent a breakthrough — and the USC team is working on self-healing properties for harder materials like plastic that could be used in body armor and car parts.

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Scientists study organization of life on a planetary scale

Scientists study organization of life on a planetary scale

When we think of life on Earth, we might think of individual examples ranging from animals to bacteria. When astrobiologists study life, however, they have to consider not only individual organisms, but also ecosystems, and the biosphere as a whole.

In astrobiology, there is an increasing interest in whether life as we know it is a quirk of the particular evolutionary history of the Earth or, instead, if life might be governed by more general organizing principles.

If general principles exist that can explain properties common to all life on Earth, scientists hypothesize, then they may be universal to all life, even life on other planets. If a “universal biology” exists, it would have important implications for the search for life beyond Earth, for engineering synthetic life in the lab, and for solving the origin of life, enabling scientists to predict at least some properties of alien life.

Previous research in this area has primarily focused on specific levels of organization within biology such as individual organisms or ecological communities. These levels form a hierarchy where individuals are composed of interacting molecules and ecosystems are composed of interacting individuals.

An interdisciplinary team of researchers at Arizona State University (ASU) has gone beyond focusing on individual levels in this hierarchy to study the hierarchy itself, focusing on the biosphere as a whole. The results of their study have been recently published Science Advances.

“To understand the general principles governing biology, we must understand how living systems organize across levels, not just within a given level,” says lead author Hyunju Kim of ASU’s Beyond Center and the School of Earth and Space Exploration.

Through this study, the team found that biochemistry, both at the level of organisms and ecosystems, is governed by general organizing principles. “This means there is a logic to the planetary-scale organization of biochemistry,” says co-lead author Harrison Smith of ASU’s School of Earth and Space Exploration. “Scientists have talked about this type of logic for a long time, but until now they have struggled to quantify it. Quantifying it can help us constrain the way that life arises on a planet.”

For this research, the team constructed biochemical networks using a global database of 28,146 annotated genomes and metagenomes and 8,658 catalogued biochemical reactions. In so doing, they uncovered scaling laws governing biochemical diversity and network structure that are shared across levels of organization from individuals to ecosystems, to the biosphere as a whole.

“Quantifying general principles of life — not restricted to a domain on the tree of life, or a particular ecosystem — is a challenge,” says Smith. “We were able to do that by combining tools from network science and scaling theory, while simultaneously leveraging large genomic datasets that researchers have been cataloging.”

The research team, led by Kim and Smith under supervision of Sara Walker of the ASU School of Earth and Space Exploration and the Beyond Center, also includes Cole Mathis of the Beyond Center and the ASU Department of Physics (now at the University of Glasgow), and Jason Raymond of the School of Earth and Space Exploration.

“Understanding the organizing principles of biochemistry at a global scale better enables us to understand how life operates as a planetary process,” says Walker. “The ability to more rigorously identify universal properties of life on Earth will also provide astrobiologists with new quantitative tools to guide our search for alien life — both in the lab on other worlds.”

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Early spring rain boosts methane from thawing permafrost by 30 percent

Early spring rain boosts methane from thawing permafrost by 30 percent

Arctic permafrost is thawing as the Earth warms due to climate change. In some cases, scientists predict that this thawing soil will release increasing amounts of methane, a potent greenhouse gas, that is known to trap more heat in our planet’s atmosphere.

Now a University of Washington-led team has found a new reason behind increased methane emissions from a thawing permafrost bog in Alaska: Early spring rainfall warms up the bog and promotes the growth of plants and methane-producing microbes. The team showed that early precipitation in 2016 warmed the bog about three weeks earlier than usual, and increased the bog’s methane emissions by 30 percent compared to previous years. These results were recently published in Geophysical Research Letters.

“In general, the chance of generating methane goes up with increased rainfall because soils get waterlogged. But what we see here is different,” said corresponding author Rebecca Neumann, an associate professor in the UW Department of Civil & Environmental Engineering. “Early rainfall sent a slog of warm water moving into our bog. We believe microbes in the bog got excited because they were warmed up, so they released nutrients from the soil that allowed more plant growth. Methane production and emission are tightly linked with soil temperature and plant growth.

“Our results emphasize that these permafrost regions are sensitive to the thermal effects of rain, and because we’re anticipating that these environments are going to get wetter in the future, we could be seeing increases in methane emissions that we weren’t expecting.”

In northern latitudes, bogs form when ice-rich permafrost thaws. The thawed area sinks relative to the surrounding landscape as the ice melts, and soil becomes waterlogged, creating a wetland with grassy plants called sedges growing across the surface.

Neumann and her team studied a thawing permafrost bog located about 20 miles from Fairbanks, Alaska, from 2014 through 2016. Over the years, the researchers tracked methane emissions in and around the bog, sedge plant growth and soil temperature at 16 different depths.

In 2016 the team saw temperatures at the edge of the bog increase 20 days earlier, and cumulative methane emissions across the bog increase by 30 percent as compared to the previous years.

“We saw the plants going crazy and methane emissions going bonkers,” Neumann said. “2016 had above average rainfall, but so did 2014. So what was different about this year?”

The key turned out to be the timing of the precipitation: The spring rainfall started earlier in 2016 compared to 2014. In the spring the ground is colder than the air. So the rain, which is the same temperature as the air, warms up the ground as it enters the soil. The earlier the spring rains come, the sooner the soil in the surrounding forest gets saturated. Any surplus rain then flows down into the bog, rapidly warming the bog soils.

The warm soil aids microbes living in the bog and speeds up their metabolisms. Normally microbes use oxygen to break down organic matter, and they release carbon dioxide into the air. But in waterlogged soils, like a bog created by permafrost thaw, there’s no oxygen around. So the microbes have to use whatever is available, and they end up converting organic matter into methane.

“It’s the bottom of the barrel in terms of energy production for them,” Neumann said. “The microbes in this bog on some level are like ‘Oh man, we’re stuck making methane because that’s all this bog is allowing us to do.'”

At the same time, the sedge plants are also fueled by the warmer soil. In 2016 the team found more of these plants at the warmer edges of the bog. Sedges, like most plants, take carbon dioxide from the air to make their food, which they send to their roots to help them grow. Sometimes the food leaks out of the roots into the soil where it can become food for the microbes. So more sedges directly fuel the microbes to make more methane.

In addition, sedges contain hollow, air-filled tubes that allow oxygen to flow from the air to their roots. These tubes also allow the microbes’ methane to escape the bog and enter the atmosphere.

“The plants are really doing two things,” Neumann said. “They’re providing yummy carbon that lets the microbes make more methane than they would have otherwise. The plants also provide a conduit that allows methane to escape into the atmosphere. They’re a double whammy for methane production and emission.”

As the Earth warms, these northern latitude regions are expected to experience more rainfall. If this rain falls in spring or early summer, these areas could release more methane into the atmosphere than is currently predicted. Neumann and her team plan to examine methane emissions from other bogs to see if this pattern holds true across northern latitudes.

“In general, the ability of rain to transport thermal energy into soils has been underappreciated,” Neumann said. “Our study shows that by affecting soil temperature and methane emissions, rain can increase the ability of thawing permafrost landscapes to warm the climate.”

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