FROM: NATIONAL SCIENCE FOUNDATION
No limit to life in deep sediment of ocean's "deadest" region
Marine scientists find microbes from seafloor to igneous basement below
"Who in his wildest dreams could have imagined that, beneath the crust of our Earth, there could exist a real ocean...a sea that has given shelter to species unknown?"
So wrote Jules Verne almost 150 years ago in A Journey to the Center of the Earth.
He was correct: Ocean deeps are anything but dead.
Now, scientists have found oxygen and oxygen-breathing microbes all the way through the sediment from the seafloor to the igneous basement at seven sites in the South Pacific gyre, considered the "deadest" location in the ocean.
Findings contrast with previous studies
Their findings contrast with previous discoveries that oxygen was absent from all but the top few millimeters to decimeters of sediment in biologically productive regions of the ocean.
The results are published today in a paper in the journal Nature Geoscience.
"Our objective was to understand the microbial community and microbial habitability of sediment in the deadest part of the ocean," said scientist Steven D'Hondt of the University of Rhode Island Graduate School of Oceanography, lead author of the paper.
"Our results overturn a 60-year-old conclusion that the depth limit to life is in the sediment just meters below the seafloor in such regions.
"We found that there is no limit to life in this sediment. Oxygen and aerobic microbes hang in there all the way to the igneous basement, to at least 75 meters below the seafloor."
Under the seafloor, life all the way down
Based on the researchers' predictive model and core samples they collected in 2010 from the research drillship JOIDES Resolution, they believe that oxygen and aerobic microbes occur throughout the sediment in up to 37 percent of the world's oceans and 44 percent of the Pacific Ocean.
They found that the best indicators of oxygen penetration to the igneous basement are a low sedimentation accumulation rate and a relatively thin sediment layer.
Sediment accumulates at just a few decimeters to meters per million years in the regions where the core samples were collected.
In the remaining 63 percent of the ocean, most of the sediment beneath the seafloor is expected to lack dissolved oxygen and to contain anaerobic communities.
While the researchers found evidence of life throughout the sediment, they did not detect a great deal of it.
Life in the slow lane
The team found extremely slow rates of respiration and approximately 1,000 cells per cubic centimeter of subseafloor sediment in the South Pacific gyre--rates and quantities that had been nearly undetectable.
"It's really hard to find life when it's not very active and is in extremely low concentrations," said D'Hondt.
According to D'Hondt and co-author Fumio Inagaki of the Japan Agency for Marine-Earth Science and Technology, the discovery of oxygen throughout the sediment may have significant implications for Earth's chemical evolution.
The oxidized sediment is likely carried into the mantle at subduction zones, regions of the seafloor where tectonic plates collide, forcing one plate beneath the other.
"Subduction of these big regions where oxygen penetrates through the sediment and into the igneous basement introduces oxidized minerals to the mantle, which may affect the chemistry of the upper mantle and the long-term evolution of Earth's surface oxidation," D'Hondt said.
Holistic approach to study of subseafloor biosphere
The principal research funders were the U.S. National Science Foundation (NSF) and Japan's Ministry of Education, Culture, Sports, Science and Technology.
"We take a holistic approach to the subseafloor biosphere," said Rick Murray, co-author of the paper. Murray is on leave from Boston University, currently serving as director of the NSF Division of Ocean Sciences.
"Our team includes microbiologists, geochemists, sedimentologists, physical properties specialists and others--a hallmark of interdisciplinary research."
The research involved 35 scientists from 12 countries.
The project is part of the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI), which explores life beneath the seafloor.
The research is also part of the Deep Carbon Observatory, a decade-long international science initiative to investigate the 90 percent of Earth's carbon located deep inside the planet.
The Nature Geoscience paper is available online.
-NSF-
Showing posts with label BIOLOGY. Show all posts
Showing posts with label BIOLOGY. Show all posts
Thursday, March 19, 2015
Sunday, March 1, 2015
Saturday, February 28, 2015
GENE EDITITING AND REGULATION TO IMPROVE IMMUNE SYSTEM
FROM: NATIONAL SCIENCE FOUNDATION
Rewriting genetic information to prevent disease
Breakthrough Prize winner harnesses CRISPR to improve immune system
For the last few years, scientists have been studying an ancient but only recently understood mechanism of bacterial immunity that has the potential to provide immeasurable benefits to plant and animal health.
The phenomenon known as CRISPR (for Clustered Regularly Interspaced Short Palindromic Repeats) is a natural immune system found in many bacteria with the ability to identify and destroy the genomes of invading viruses and plasmids.
Researchers are trying to harness this system for gene editing and regulation, a process that could transform "the genome of plants or animals in ways that will improve their health, or introduce genetic changes that will resist disease of climate change," says Jennifer Doudna, a Howard Hughes Medical Institute investigator and professor of biochemistry, biophysics and structural biology at the University of California, Berkeley. "The explosion of research using this technique has been amazing."
Doudna, collaborating with Emmanuelle Charpentier of Sweden's Helmholtz Center for Infection Research and Umeå University, identified how the system works and engineered it in new ways that broadened its scope. The two researchers, who described their work in a 2012 paper in the journal Science, developed a technique that enables the rewriting of genetic information and the correction of mutations that otherwise can cause disease, and also can knock out the cell's ability to make harmful proteins, she says.
"Many labs have shown in principle that this can be used to correct such mutations as those that occur in cystic fibrosis, or sickle cell disease," she says. "They are showing it in cell lines and lab animals. We're still some period of time away from using this in humans, but the pace in the field has been truly remarkable, and really exciting to see."
Many bacteria have this CRISPR-based immune system capable of identifying and destroying hostile invaders. Doudna and Charpentier showed that, in doing so, CRISPR produces the protein Cas9, a DNA-cutting enzyme guided by RNA, which relies on two short RNA guide sequences to find foreign DNA, then cleaves, or cuts, the target sequences, thereby muting the genes of the invaders.
Cas9 has evolved to provide protection against viruses that could infect the bacterium, and uses pieces of RNA derived from CRISPRS to direct its activity. The system is specific and efficient enough to stave off viral infections in bacteria.
Doudna and her colleagues programmed the process so that it can be directed by a single short RNA molecule; researchers who use it to edit genomes can customize the RNA so that it sends Cas9 to cleave, like "scissors," at their chosen location in the genome.
"When we figured out how it worked, we realized we could alter the design of RNA and program Cas9 to recognize any DNA sequence," she says. "One can therefore target Cas9 to any region of a genome simply by providing a short guide RNA that can pair with the region of interest. Once targeted, different versions of Cas9 can be used to activate or inhibit genes, as well as make target cuts within the genome. Depending on the experimental design, research can use these latter cuts to either disrupt genes or replace them with newly engineered versions."
Recently Douda and Charpentier and four other scientists received the Breakthrough Prize in life sciences, which honors transformative advances toward understanding living systems and extending human life. The prizes recognize pioneering work in physics, genetics, cosmology, neurology and mathematics, and carry a $3 million award for each researcher. The Breakthrough committee specifically cited Doudna and Charpentier for their advances in understanding the CRISPR mechanism.
Doudna has been the recipient of several National Science Foundation (NSF) grants to support her research in recent years totaling more than $1.5 million. In 2000, she received NSF's prestigious $500,000 Alan T. Waterman Award, which recognizes an outstanding young researcher in any field of science or engineering supported by NSF.
She also was a founder of the Innovative Genomics Initiative, established in 2014 at the Li Ka Shing Center for Genomic Engineering at UC Berkeley. Its goal is to promote and support genome editing research and technology in both academic and commercial research communities.
"We have a team of scientists working with various collaborative partners," she says. "We want to ensure that the technology gets into as many hands as possible, and explore ways to make it even better. We are trying to bring about fundamental change in biological and biomedical research by enabling scientists to read and write in genomes with equal ease. It's a bold new effort that embraces a new era in genomic engineering."
-- Marlene Cimons, National Science Foundation
Investigators
Jennifer Doudna
Related Institutions/Organizations
University of California-Berkeley
Rewriting genetic information to prevent disease
Breakthrough Prize winner harnesses CRISPR to improve immune system
For the last few years, scientists have been studying an ancient but only recently understood mechanism of bacterial immunity that has the potential to provide immeasurable benefits to plant and animal health.
The phenomenon known as CRISPR (for Clustered Regularly Interspaced Short Palindromic Repeats) is a natural immune system found in many bacteria with the ability to identify and destroy the genomes of invading viruses and plasmids.
Researchers are trying to harness this system for gene editing and regulation, a process that could transform "the genome of plants or animals in ways that will improve their health, or introduce genetic changes that will resist disease of climate change," says Jennifer Doudna, a Howard Hughes Medical Institute investigator and professor of biochemistry, biophysics and structural biology at the University of California, Berkeley. "The explosion of research using this technique has been amazing."
Doudna, collaborating with Emmanuelle Charpentier of Sweden's Helmholtz Center for Infection Research and Umeå University, identified how the system works and engineered it in new ways that broadened its scope. The two researchers, who described their work in a 2012 paper in the journal Science, developed a technique that enables the rewriting of genetic information and the correction of mutations that otherwise can cause disease, and also can knock out the cell's ability to make harmful proteins, she says.
"Many labs have shown in principle that this can be used to correct such mutations as those that occur in cystic fibrosis, or sickle cell disease," she says. "They are showing it in cell lines and lab animals. We're still some period of time away from using this in humans, but the pace in the field has been truly remarkable, and really exciting to see."
Many bacteria have this CRISPR-based immune system capable of identifying and destroying hostile invaders. Doudna and Charpentier showed that, in doing so, CRISPR produces the protein Cas9, a DNA-cutting enzyme guided by RNA, which relies on two short RNA guide sequences to find foreign DNA, then cleaves, or cuts, the target sequences, thereby muting the genes of the invaders.
Cas9 has evolved to provide protection against viruses that could infect the bacterium, and uses pieces of RNA derived from CRISPRS to direct its activity. The system is specific and efficient enough to stave off viral infections in bacteria.
Doudna and her colleagues programmed the process so that it can be directed by a single short RNA molecule; researchers who use it to edit genomes can customize the RNA so that it sends Cas9 to cleave, like "scissors," at their chosen location in the genome.
"When we figured out how it worked, we realized we could alter the design of RNA and program Cas9 to recognize any DNA sequence," she says. "One can therefore target Cas9 to any region of a genome simply by providing a short guide RNA that can pair with the region of interest. Once targeted, different versions of Cas9 can be used to activate or inhibit genes, as well as make target cuts within the genome. Depending on the experimental design, research can use these latter cuts to either disrupt genes or replace them with newly engineered versions."
Recently Douda and Charpentier and four other scientists received the Breakthrough Prize in life sciences, which honors transformative advances toward understanding living systems and extending human life. The prizes recognize pioneering work in physics, genetics, cosmology, neurology and mathematics, and carry a $3 million award for each researcher. The Breakthrough committee specifically cited Doudna and Charpentier for their advances in understanding the CRISPR mechanism.
Doudna has been the recipient of several National Science Foundation (NSF) grants to support her research in recent years totaling more than $1.5 million. In 2000, she received NSF's prestigious $500,000 Alan T. Waterman Award, which recognizes an outstanding young researcher in any field of science or engineering supported by NSF.
She also was a founder of the Innovative Genomics Initiative, established in 2014 at the Li Ka Shing Center for Genomic Engineering at UC Berkeley. Its goal is to promote and support genome editing research and technology in both academic and commercial research communities.
"We have a team of scientists working with various collaborative partners," she says. "We want to ensure that the technology gets into as many hands as possible, and explore ways to make it even better. We are trying to bring about fundamental change in biological and biomedical research by enabling scientists to read and write in genomes with equal ease. It's a bold new effort that embraces a new era in genomic engineering."
-- Marlene Cimons, National Science Foundation
Investigators
Jennifer Doudna
Related Institutions/Organizations
University of California-Berkeley
Saturday, January 17, 2015
PLANT FOSSILS AND OUR WORLD'S PAST
FROM: NATIONAL SCIENCE FOUNDATION
Tiny plant fossils offer window into Earth's landscape millions of years ago
Fossilized plant pieces tell a detailed story of our planet 50 million years ago
Minuscule, fossilized pieces of plants tell a detailed story of what Earth looked like 50 million years ago.
Researchers have discovered a way of determining density of trees, shrubs and bushes in locations over time--based on clues in the cells of plant fossils preserved in rocks and soil.
Tree density directly affects precipitation, erosion, animal behavior and a host of other factors in the natural world. Quantifying vegetation structure throughout time could shed light on how Earth's ecosystems have changed over millions of years.
"Knowing an area's vegetation structure and the arrangement of leaves on the Earth's surface is key to understanding the terrestrial ecosystem," says Regan Dunn, a paleontologist at the University of Washington's Burke Museum of Natural History and Culture. "It's the context in which all land-based organisms live, but we didn't have a way to measure it until now."
The findings are published in this week's issue of the journal Science.
New method offers window into distant past
"The new methodology provides a high-resolution lens for viewing the structure of ecosystems over the deep history of our planet," says Alan Tessier, acting director of the National Science Foundation's (NSF) Division of Environmental Biology, which funded the research along with NSF's Division of Earth Sciences.
"This capability will advance the field of paleoecology and greatly improve our understanding of how future climate change will reshape ecosystems."
The team focused its fieldwork on several sites in Patagonia, which have some of the best preserved fossils in the world.
For years, paleontologists have painstakingly collected fossils from these sites and worked to precisely determine their ages using radiometric dating. The new study builds on this growing body of knowledge.
In Patagonia and other places, scientists have some idea based on records of fossilized pollen and leaves what species of plants were alive at given periods in history.
For example, the team's previous work documented vegetation composition for this area.
But there hasn't been a way to precisely quantify vegetation openness, aside from general speculations of open or bare habitats, as opposed to closed or tree-covered habitats.
"These researchers have developed a new method for reconstructing paleo-vegetation structure in open versus dense forests using plant biosilica, likely to be widely found in the fossil record," says Chris Liu, program director in NSF's Division of Earth Sciences.
"Now we have a tool to look at a lot of important intervals in our history where we don't know what happened to the structure of vegetation," adds Dunn, such as the period just after the mass extinction that killed the dinosaurs.
"Vegetation structure links all aspects of modern ecosystems, from soil moisture to primary productivity to global climate," says paper co-author Caroline Stromberg, a curator of paleobotany at the Burke Museum.
"Using this method, we can finally quantify in detail how Earth's plant and animal communities have responded to climate change over millions of years, vital for forecasting how ecosystems will change under predicted future climate scenarios."
Plant cell patterns change with sun exposure
Work by other scientists has shown that the cells found in a plant's outermost layer, called the epidermis, change in size and shape depending on how much sun it's exposed to while its leaves develop.
For example, the cells of a leaf that grow in deeper shade will be larger and curvier than the cells of leaves that develop in less covered areas.
Dunn and collaborators found that these cell patterns, indicating growth in shade or sun, similarly show up in some plant fossils.
When a plant's leaves fall to the ground and decompose, tiny silica particles inside the plants, called phytoliths, remain as part of the soil layer.
The phytoliths were found to represent epidermal cell shapes and sizes, indicating whether the plant grew in a shady or open area.
The researchers decided to check their hypothesis by testing it in a modern setting: Costa Rica.
Dunn took soil samples from sites in Costa Rica that varied from covered rainforests to open savannas to woody shrublands.
She also took photos looking directly up at the tree canopy (or lack thereof) at each site, noting the total vegetation coverage.
Back in the lab, she extracted the phytoliths from each soil sample and measured them under the microscope.
When compared with tree coverage estimated from the corresponding photos, Dunn and co-authors found that the curves and sizes of the cells directly related to how shady their environment was.
"Leaf area index" and plant cell structures compared
The researchers characterized the amount of shade as "leaf area index," a standard way of measuring vegetation over a specific area.
Testing this relationship between leaf area index and plant cell structures in modern environments allowed the scientists to develop an equation that can be used to predict vegetation openness at any time in the past, provided there are preserved plant fossils.
"Leaf area index is a well-known variable for ecologists, climate scientists and modelers, but no one's ever been able to imagine how you could reconstruct tree coverage in the past--and now we can," says co-author Richard Madden of the University of Chicago.
"We should be able to reconstruct leaf area index by using all kinds of fossil plant preservation, not just phytoliths. Once that is demonstrated, then the places in the world where we can reconstruct this will increase."
When Dunn and co-authors applied their method to 40-million-year-old phytoliths from Patagonia, they found something surprising--vegetation was extremely open, similar to a shrubland today. The appearance of these very open habitats coincided with major changes in fauna.
The paleobiologists plan to test the relationship between vegetation coverage and plant cell structure in other regions around the world.
They also hope to find other types of plant fossils that hold the same information at the cellular level as do phytoliths.
Paper co-authors are Matthew Kohn of Boise State University and Alfredo Carlini of Universidad Nacional de La Plata in Argentina.
In addition to NSF, the research was funded by the Geological Society of America, the University of Washington Biology Department and the Burke Museum.
-NSF-
Media Contacts
Cheryl Dybas, NSF
Tiny plant fossils offer window into Earth's landscape millions of years ago
Fossilized plant pieces tell a detailed story of our planet 50 million years ago
Minuscule, fossilized pieces of plants tell a detailed story of what Earth looked like 50 million years ago.
Researchers have discovered a way of determining density of trees, shrubs and bushes in locations over time--based on clues in the cells of plant fossils preserved in rocks and soil.
Tree density directly affects precipitation, erosion, animal behavior and a host of other factors in the natural world. Quantifying vegetation structure throughout time could shed light on how Earth's ecosystems have changed over millions of years.
"Knowing an area's vegetation structure and the arrangement of leaves on the Earth's surface is key to understanding the terrestrial ecosystem," says Regan Dunn, a paleontologist at the University of Washington's Burke Museum of Natural History and Culture. "It's the context in which all land-based organisms live, but we didn't have a way to measure it until now."
The findings are published in this week's issue of the journal Science.
New method offers window into distant past
"The new methodology provides a high-resolution lens for viewing the structure of ecosystems over the deep history of our planet," says Alan Tessier, acting director of the National Science Foundation's (NSF) Division of Environmental Biology, which funded the research along with NSF's Division of Earth Sciences.
"This capability will advance the field of paleoecology and greatly improve our understanding of how future climate change will reshape ecosystems."
The team focused its fieldwork on several sites in Patagonia, which have some of the best preserved fossils in the world.
For years, paleontologists have painstakingly collected fossils from these sites and worked to precisely determine their ages using radiometric dating. The new study builds on this growing body of knowledge.
In Patagonia and other places, scientists have some idea based on records of fossilized pollen and leaves what species of plants were alive at given periods in history.
For example, the team's previous work documented vegetation composition for this area.
But there hasn't been a way to precisely quantify vegetation openness, aside from general speculations of open or bare habitats, as opposed to closed or tree-covered habitats.
"These researchers have developed a new method for reconstructing paleo-vegetation structure in open versus dense forests using plant biosilica, likely to be widely found in the fossil record," says Chris Liu, program director in NSF's Division of Earth Sciences.
"Now we have a tool to look at a lot of important intervals in our history where we don't know what happened to the structure of vegetation," adds Dunn, such as the period just after the mass extinction that killed the dinosaurs.
"Vegetation structure links all aspects of modern ecosystems, from soil moisture to primary productivity to global climate," says paper co-author Caroline Stromberg, a curator of paleobotany at the Burke Museum.
"Using this method, we can finally quantify in detail how Earth's plant and animal communities have responded to climate change over millions of years, vital for forecasting how ecosystems will change under predicted future climate scenarios."
Plant cell patterns change with sun exposure
Work by other scientists has shown that the cells found in a plant's outermost layer, called the epidermis, change in size and shape depending on how much sun it's exposed to while its leaves develop.
For example, the cells of a leaf that grow in deeper shade will be larger and curvier than the cells of leaves that develop in less covered areas.
Dunn and collaborators found that these cell patterns, indicating growth in shade or sun, similarly show up in some plant fossils.
When a plant's leaves fall to the ground and decompose, tiny silica particles inside the plants, called phytoliths, remain as part of the soil layer.
The phytoliths were found to represent epidermal cell shapes and sizes, indicating whether the plant grew in a shady or open area.
The researchers decided to check their hypothesis by testing it in a modern setting: Costa Rica.
Dunn took soil samples from sites in Costa Rica that varied from covered rainforests to open savannas to woody shrublands.
She also took photos looking directly up at the tree canopy (or lack thereof) at each site, noting the total vegetation coverage.
Back in the lab, she extracted the phytoliths from each soil sample and measured them under the microscope.
When compared with tree coverage estimated from the corresponding photos, Dunn and co-authors found that the curves and sizes of the cells directly related to how shady their environment was.
"Leaf area index" and plant cell structures compared
The researchers characterized the amount of shade as "leaf area index," a standard way of measuring vegetation over a specific area.
Testing this relationship between leaf area index and plant cell structures in modern environments allowed the scientists to develop an equation that can be used to predict vegetation openness at any time in the past, provided there are preserved plant fossils.
"Leaf area index is a well-known variable for ecologists, climate scientists and modelers, but no one's ever been able to imagine how you could reconstruct tree coverage in the past--and now we can," says co-author Richard Madden of the University of Chicago.
"We should be able to reconstruct leaf area index by using all kinds of fossil plant preservation, not just phytoliths. Once that is demonstrated, then the places in the world where we can reconstruct this will increase."
When Dunn and co-authors applied their method to 40-million-year-old phytoliths from Patagonia, they found something surprising--vegetation was extremely open, similar to a shrubland today. The appearance of these very open habitats coincided with major changes in fauna.
The paleobiologists plan to test the relationship between vegetation coverage and plant cell structure in other regions around the world.
They also hope to find other types of plant fossils that hold the same information at the cellular level as do phytoliths.
Paper co-authors are Matthew Kohn of Boise State University and Alfredo Carlini of Universidad Nacional de La Plata in Argentina.
In addition to NSF, the research was funded by the Geological Society of America, the University of Washington Biology Department and the Burke Museum.
-NSF-
Media Contacts
Cheryl Dybas, NSF
Thursday, December 11, 2014
SCIENTISTS WORK TO PRESERVE BIODIVERSITY
FROM: NATIONAL SCIENCE FOUNDATION
Protecting biodiversity
In one of the world's richest biological hotspots, an international group of scientists works to preserve biodiversity amid climate change
The Congo Basin is an unruly ribbon of tropical forest: Over a million square miles spanning six countries in Central Africa, running inward along the equator from the continent's western coast. It is the second-largest contiguous tropical forest in the world. The basin is home to the classics of African wildlife--chimpanzees, elephants, gorillas--along with thousands of other less well-known species: pale, long-legged Golden Puddle Frogs, hook-beaked Olive Sunbirds, and squat Blue Duikers, which look like shrunken antelopes.
This wealth of flora and fauna, much of it native to the region, is enough to qualify the Congo Basin as a biodiversity hotspot: a biologically rich area threatened by outside forces. In Central Africa, those forces include deforestation, climate change, hunting and more.
The region is "so enriched with life," says Mary "Katy" Gonder, a Drexel University biologist and one of the lead researchers on the Central African Biodiversity Alliance (CABA). "And that life is precarious right now."
Funded in part by the National Science Foundation (NSF), the Alliance is an international partnership of scientists, students and policy makers working to build a framework to conserve biodiversity in Central Africa. The partnership spans three continents, and includes researchers from the U.S., Cameroon, Equatorial Guinea, Gabon, Germany and the United Kingdom.
NSF funding for CABA comes through the Partnerships in International Research and Education (PIRE) program, which supports innovative, international research and education collaborations. PIRE projects stimulate scientific discovery and strengthen U.S. universities; the projects forge worldwide partnerships and help train a globally engaged scientific and engineering workforce.
CABA also receives funding from the Arcus Foundation and the Exxon Mobil Foundation.
To build a conservation framework, they are using genomic tools and environmental modeling to identify areas worth conserving: sweet spots that both maximize the pattern of biodiversity and the processes that produce and maintain it.
All research is rooted in the region's socioeconomic realities. From the start, CABA members have met with government officials in the region, to ensure that policy makers are both informed about the research and play a role shaping it. Training future scientists and engineers is also a big piece of the project. They've held professional development workshops for students and scientists--both American and African--to discuss everything from experiment design and statistics to grant writing and leadership. CABA members have also helped facilitate workshops for women in science, through COACh (Committee on the Advancement of Women Chemists) International.
Exposing American students to globally focused research, partnerships and--for most of the them--a completely foreign part of the world is another "great benefit" of the project, says Nicola Anthony, a biologist at the University of New Orleans and another lead CABA scientist. "Even if they don't end up in science for a career, they'll be much better global citizens as a result of this."
CABA's "breadth and effectiveness are very impressive," says Lara Campbell, a program manager in NSF's International Science and Engineering section, which funds PIRE. "They are producing a strong cadre of American and African scientists prepared to address the many future challenges of climate change impacts on ecosystems."
-- Jessica Arriens
Investigators
Thomas Smith
Nicola Anthony
Mary Katherine Gonder
Related Institutions/Organizations
University of California-Los Angeles
University of New Orleans
Drexel University
Protecting biodiversity
In one of the world's richest biological hotspots, an international group of scientists works to preserve biodiversity amid climate change
The Congo Basin is an unruly ribbon of tropical forest: Over a million square miles spanning six countries in Central Africa, running inward along the equator from the continent's western coast. It is the second-largest contiguous tropical forest in the world. The basin is home to the classics of African wildlife--chimpanzees, elephants, gorillas--along with thousands of other less well-known species: pale, long-legged Golden Puddle Frogs, hook-beaked Olive Sunbirds, and squat Blue Duikers, which look like shrunken antelopes.
This wealth of flora and fauna, much of it native to the region, is enough to qualify the Congo Basin as a biodiversity hotspot: a biologically rich area threatened by outside forces. In Central Africa, those forces include deforestation, climate change, hunting and more.
The region is "so enriched with life," says Mary "Katy" Gonder, a Drexel University biologist and one of the lead researchers on the Central African Biodiversity Alliance (CABA). "And that life is precarious right now."
Funded in part by the National Science Foundation (NSF), the Alliance is an international partnership of scientists, students and policy makers working to build a framework to conserve biodiversity in Central Africa. The partnership spans three continents, and includes researchers from the U.S., Cameroon, Equatorial Guinea, Gabon, Germany and the United Kingdom.
NSF funding for CABA comes through the Partnerships in International Research and Education (PIRE) program, which supports innovative, international research and education collaborations. PIRE projects stimulate scientific discovery and strengthen U.S. universities; the projects forge worldwide partnerships and help train a globally engaged scientific and engineering workforce.
CABA also receives funding from the Arcus Foundation and the Exxon Mobil Foundation.
To build a conservation framework, they are using genomic tools and environmental modeling to identify areas worth conserving: sweet spots that both maximize the pattern of biodiversity and the processes that produce and maintain it.
All research is rooted in the region's socioeconomic realities. From the start, CABA members have met with government officials in the region, to ensure that policy makers are both informed about the research and play a role shaping it. Training future scientists and engineers is also a big piece of the project. They've held professional development workshops for students and scientists--both American and African--to discuss everything from experiment design and statistics to grant writing and leadership. CABA members have also helped facilitate workshops for women in science, through COACh (Committee on the Advancement of Women Chemists) International.
Exposing American students to globally focused research, partnerships and--for most of the them--a completely foreign part of the world is another "great benefit" of the project, says Nicola Anthony, a biologist at the University of New Orleans and another lead CABA scientist. "Even if they don't end up in science for a career, they'll be much better global citizens as a result of this."
CABA's "breadth and effectiveness are very impressive," says Lara Campbell, a program manager in NSF's International Science and Engineering section, which funds PIRE. "They are producing a strong cadre of American and African scientists prepared to address the many future challenges of climate change impacts on ecosystems."
-- Jessica Arriens
Investigators
Thomas Smith
Nicola Anthony
Mary Katherine Gonder
Related Institutions/Organizations
University of California-Los Angeles
University of New Orleans
Drexel University
Friday, December 5, 2014
TECH AND NEW IDEAS SOUGHT BY DOD FOR RESEARCH DEVELOPMENT PLAN
FROM: U.S. DEFENSE DEPARTMENT
DoD Seeks Future Technology Via Development Plan
By Amaani Lyle
DoD News, Defense Media Activity
WASHINGTON, Dec. 3, 2014 – The Defense Department seeks technology and innovative ideas as part of its Long Range Research Development Plan within the Defense Innovation Initiative, a broad effort that examines future capabilities, dominance and strategy, a senior DoD official said Nov. 24.
The newly-released LRRDP Request for Information will provide a way for DoD technology scouts to collaborate with industry, academia, and the general public to explore topics and ideas to better identify the “art of the possible,” said Deputy Assistant Secretary of Defense for Systems Engineering Stephen P. Welby.
“We’re interested in getting the broadest set of folks, the brightest minds we can find, to come help us on this effort,” Welby said. “We’re hoping that by casting this wide net, we’ll be able to harness the creativity and innovation going on in the broader ecosystem and help us think about the future department in a new way.”
Domains of Interest
Specific military domains of interest, he said, include space, undersea technologies, affordable protective systems against precision-guided munitions threats, air dominance and strike capability possibilities, ecologically and biologically inspired ideas and human-computer interaction.
“We expect the topics and ideas that come back will inform our science and technology planning and we’re mining that whole space,” Welby said.
He described a “small, agile team” of bright government officials who’ve been charged to engage industry, academia, not-for-profits, small businesses and the general public to help the department explore future possibilities. Inputs will also be accepted from allies and international partners who may have unique perspectives or contributions to the effort.
Officials expect the seven-month study to yield results in time to brief the defense secretary by mid-2015 and influence future budget and offset technology decisions, Welby said.
DoD’s Future
“The key opportunity out of this whole effort is to start a discussion,” he said. “We’re asking questions about people, business practices, but particularly … about technology, what we need to drive the future of the department.”
Deputy Secretary of Defense Robert O. Work will oversee the program as part of the overall effort to explore how technology can be incorporated with future DoD strategy and capabilities.
Pentagon officials noted a justified urgency in reviewing the future systems and architectures to maintain dominance over competing investments around the globe.
“There is no better time to look at the long-range strategy we’re taking to invest in technologies that will make a difference,” Welby said.
Capability Breakthrough in the 1980s
During the 1980s, Welby said, DoD found itself facing the Soviets and recognized there was a better way to confront the issue rather than a “tank-versus-tank” military buildup.
“The big breakthrough in that time period was introduction of precision weapons … and technology that allowed us to replace quantity with very precise technology-driven capabilities,” Welby said.
That, he said, has been the key driver in the way the nation has conducted itself in the national security environment for more than 40 years.
“People have understood our playbook,” Welby said. “Adversaries are now building systems that look to blunt particular United States’ advantages and we’d like to revisit that.”
Efforts in 1973 included the original Long-Range Research and Development Plan, which ushered in nascent digital technologies, early iterations of global positioning systems and the beginnings of the future Internet.
Today, he said, DoD faces challenges posed by globalization and technologies driven by both the military and commercial sectors.
“We’re now asking broader questions like, ‘How does the United States maintain its … lead against the entire path of technology and innovation going on globally?’” Welby said.
Maintaining a compelling U.S. advantage in technology is critical, he said.
DoD’s long-range plan, Welby said, will focus on “near-peer competitors,” state actors and a broader scope of conventional deterrence, namely key technologies that will enable the protection of U.S. interests and freedom of movement, and deter future aggression into the 2025 timeframe.
DoD Seeks Future Technology Via Development Plan
By Amaani Lyle
DoD News, Defense Media Activity
WASHINGTON, Dec. 3, 2014 – The Defense Department seeks technology and innovative ideas as part of its Long Range Research Development Plan within the Defense Innovation Initiative, a broad effort that examines future capabilities, dominance and strategy, a senior DoD official said Nov. 24.
The newly-released LRRDP Request for Information will provide a way for DoD technology scouts to collaborate with industry, academia, and the general public to explore topics and ideas to better identify the “art of the possible,” said Deputy Assistant Secretary of Defense for Systems Engineering Stephen P. Welby.
“We’re interested in getting the broadest set of folks, the brightest minds we can find, to come help us on this effort,” Welby said. “We’re hoping that by casting this wide net, we’ll be able to harness the creativity and innovation going on in the broader ecosystem and help us think about the future department in a new way.”
Domains of Interest
Specific military domains of interest, he said, include space, undersea technologies, affordable protective systems against precision-guided munitions threats, air dominance and strike capability possibilities, ecologically and biologically inspired ideas and human-computer interaction.
“We expect the topics and ideas that come back will inform our science and technology planning and we’re mining that whole space,” Welby said.
He described a “small, agile team” of bright government officials who’ve been charged to engage industry, academia, not-for-profits, small businesses and the general public to help the department explore future possibilities. Inputs will also be accepted from allies and international partners who may have unique perspectives or contributions to the effort.
Officials expect the seven-month study to yield results in time to brief the defense secretary by mid-2015 and influence future budget and offset technology decisions, Welby said.
DoD’s Future
“The key opportunity out of this whole effort is to start a discussion,” he said. “We’re asking questions about people, business practices, but particularly … about technology, what we need to drive the future of the department.”
Deputy Secretary of Defense Robert O. Work will oversee the program as part of the overall effort to explore how technology can be incorporated with future DoD strategy and capabilities.
Pentagon officials noted a justified urgency in reviewing the future systems and architectures to maintain dominance over competing investments around the globe.
“There is no better time to look at the long-range strategy we’re taking to invest in technologies that will make a difference,” Welby said.
Capability Breakthrough in the 1980s
During the 1980s, Welby said, DoD found itself facing the Soviets and recognized there was a better way to confront the issue rather than a “tank-versus-tank” military buildup.
“The big breakthrough in that time period was introduction of precision weapons … and technology that allowed us to replace quantity with very precise technology-driven capabilities,” Welby said.
That, he said, has been the key driver in the way the nation has conducted itself in the national security environment for more than 40 years.
“People have understood our playbook,” Welby said. “Adversaries are now building systems that look to blunt particular United States’ advantages and we’d like to revisit that.”
Efforts in 1973 included the original Long-Range Research and Development Plan, which ushered in nascent digital technologies, early iterations of global positioning systems and the beginnings of the future Internet.
Today, he said, DoD faces challenges posed by globalization and technologies driven by both the military and commercial sectors.
“We’re now asking broader questions like, ‘How does the United States maintain its … lead against the entire path of technology and innovation going on globally?’” Welby said.
Maintaining a compelling U.S. advantage in technology is critical, he said.
DoD’s long-range plan, Welby said, will focus on “near-peer competitors,” state actors and a broader scope of conventional deterrence, namely key technologies that will enable the protection of U.S. interests and freedom of movement, and deter future aggression into the 2025 timeframe.
Tuesday, November 25, 2014
CROP PRODUCTION MAY CAUSE GREATER CHANGES IN SEASONS
FROM: NATIONAL SCIENCE FOUNDATION
Boosts in productivity of corn and other crops modify Northern Hemisphere carbon dioxide cycle
Croplands help drive greater seasonal change in annual cycle
Each year in the Northern Hemisphere, levels of atmospheric carbon dioxide drop in the summer as plants "inhale," then climb again as they exhale after the growing season.
During the last 50 years, the size of this seasonal swing has increased by as much as half, for reasons that aren't fully understood.
Now a team of researchers has shown that agricultural production may generate up to a quarter of the increase in this seasonal carbon cycle, with corn playing a leading role.
"This study shows the power of modeling and data mining in addressing potential sources contributing to seasonal changes in carbon dioxide," says Liz Blood, program director for the National Science Foundation's MacroSystems Biology Program, which funded the research. "It points to the role of basic research in finding answers to complex problems."
In the Northern Hemisphere, there's a strong seasonal cycle of vegetation, says scientist Mark Friedl of Boston University (BU), senior author of a paper reporting the results in this week's issue of the journal Nature.
"Something is changing about this cycle," says Friedl. "Ecosystems are becoming more productive, pulling in more atmospheric carbon during the summer and releasing more during the dormant period."
Most of this annual change is attributed to the effects of higher temperatures driven by climate change--including longer growing seasons, quicker uptake of carbon by vegetation and the "greening" of higher latitudes with more vegetation.
"But that's not the whole story," says Josh Gray of BU, lead author of the paper. "We've put humans and croplands into the story."
The scientists gathered global production statistics for four leading crops--corn, wheat, rice and soybeans--that together represent about 64 percent of all calories consumed worldwide.
They found that production of these crops in the Northern Hemisphere has more than doubled since 1961 and translates to about a billion metric tons of carbon captured and released each year.
These croplands are "ecosystems on steroids," says Gray, noting that they occupy about 6 percent of the vegetative land area in the Northern Hemisphere, but are responsible for up to a quarter of the total increase in seasonal carbon exchange of atmospheric carbon dioxide.
The growth in seasonal variation doesn't have a huge impact on global terrestrial carbon uptake and release, he says, since carbon gathered by the crops is released each year.
However, understanding the effects of agricultural production, the researchers maintain, will help improve models of global climate, particularly in discovering how well ecosystems will buffer rising levels of carbon dioxide in the future.
The BU investigators collaborated with a team of scientists, including Eric Kort of the University of Michigan, Steve Frolking of the University of New Hampshire, Christopher Kucharik of the University of Wisconsin, Navin Ramankutty of the University of British Columbia and Deepak Ray of the University of Minnesota.
The work highlights extraordinary increases in crop production in recent decades.
"These indications of increased productivity speak well for agriculture," says Tom Torgersen, program director for the National Science Foundation's Water Sustainability and Climate Program, which also funded the research. "But such enhanced agricultural productivity makes significant demands on water supplies, which will require further investigation. "
Adds Friedl, "It's a remarkable story of what we've done in agriculture in general. And in particular in corn, which is one crop that's just exploded."
Corn alone accounts for two-thirds of the crop contribution to the increased seasonal exchange in carbon, he says. Almost 90 percent is produced in the midwestern United States and China.
"Over the last 50 years, the area of croplands in the Northern Hemisphere has been relatively stable, but production has intensified enormously," Friedl says.
"The fact that this land area can affect the composition of the atmosphere is an amazing fingerprint of human activity on the planet."
-NSF-
Media Contacts
Cheryl Dybas, NSF
Boosts in productivity of corn and other crops modify Northern Hemisphere carbon dioxide cycle
Croplands help drive greater seasonal change in annual cycle
Each year in the Northern Hemisphere, levels of atmospheric carbon dioxide drop in the summer as plants "inhale," then climb again as they exhale after the growing season.
During the last 50 years, the size of this seasonal swing has increased by as much as half, for reasons that aren't fully understood.
Now a team of researchers has shown that agricultural production may generate up to a quarter of the increase in this seasonal carbon cycle, with corn playing a leading role.
"This study shows the power of modeling and data mining in addressing potential sources contributing to seasonal changes in carbon dioxide," says Liz Blood, program director for the National Science Foundation's MacroSystems Biology Program, which funded the research. "It points to the role of basic research in finding answers to complex problems."
In the Northern Hemisphere, there's a strong seasonal cycle of vegetation, says scientist Mark Friedl of Boston University (BU), senior author of a paper reporting the results in this week's issue of the journal Nature.
"Something is changing about this cycle," says Friedl. "Ecosystems are becoming more productive, pulling in more atmospheric carbon during the summer and releasing more during the dormant period."
Most of this annual change is attributed to the effects of higher temperatures driven by climate change--including longer growing seasons, quicker uptake of carbon by vegetation and the "greening" of higher latitudes with more vegetation.
"But that's not the whole story," says Josh Gray of BU, lead author of the paper. "We've put humans and croplands into the story."
The scientists gathered global production statistics for four leading crops--corn, wheat, rice and soybeans--that together represent about 64 percent of all calories consumed worldwide.
They found that production of these crops in the Northern Hemisphere has more than doubled since 1961 and translates to about a billion metric tons of carbon captured and released each year.
These croplands are "ecosystems on steroids," says Gray, noting that they occupy about 6 percent of the vegetative land area in the Northern Hemisphere, but are responsible for up to a quarter of the total increase in seasonal carbon exchange of atmospheric carbon dioxide.
The growth in seasonal variation doesn't have a huge impact on global terrestrial carbon uptake and release, he says, since carbon gathered by the crops is released each year.
However, understanding the effects of agricultural production, the researchers maintain, will help improve models of global climate, particularly in discovering how well ecosystems will buffer rising levels of carbon dioxide in the future.
The BU investigators collaborated with a team of scientists, including Eric Kort of the University of Michigan, Steve Frolking of the University of New Hampshire, Christopher Kucharik of the University of Wisconsin, Navin Ramankutty of the University of British Columbia and Deepak Ray of the University of Minnesota.
The work highlights extraordinary increases in crop production in recent decades.
"These indications of increased productivity speak well for agriculture," says Tom Torgersen, program director for the National Science Foundation's Water Sustainability and Climate Program, which also funded the research. "But such enhanced agricultural productivity makes significant demands on water supplies, which will require further investigation. "
Adds Friedl, "It's a remarkable story of what we've done in agriculture in general. And in particular in corn, which is one crop that's just exploded."
Corn alone accounts for two-thirds of the crop contribution to the increased seasonal exchange in carbon, he says. Almost 90 percent is produced in the midwestern United States and China.
"Over the last 50 years, the area of croplands in the Northern Hemisphere has been relatively stable, but production has intensified enormously," Friedl says.
"The fact that this land area can affect the composition of the atmosphere is an amazing fingerprint of human activity on the planet."
-NSF-
Media Contacts
Cheryl Dybas, NSF
Tuesday, November 18, 2014
NSF PRESENTS FINDINGS FROM PAPER ON LARGE ANIMALS AND EFFECTS ON TROPICAL FORESTS
FROM: THE NATIONAL SCIENCE FOUNDATION
Fruits of the forest gone: Overhunting of large animals has catastrophic effects on trees
As the animals go, so go tropical forests
The elephant has long been an important spiritual, cultural and national symbol in Thailand. At the beginning of the 20th century, its numbers exceeded 100,000.
Today, those numbers have plunged to 2,000. Elephants, as well as other large, charismatic animals such as tigers, monkeys and civet cats, are under attack from hunters and poachers.
Overhunting of animals affects entire forest
While the loss of these animals is concerning for species conservation, now researchers at the University of Florida have shown that overhunting can have widespread effects on the forest itself.
Overhunting leads to the extinction of a dominant tree species, Miliusa horsfieldii, or the Miliusa beech, with likely cascading effects on other forest biota.
The scientists report their results in the current issue of the journal Proceedings of the Royal Society B.
Co-authors of the paper are Trevor Caughlin and Jeremy Lichstein of the University of Florida and Doug Levey, formerly of the University of Florida and now a program director in the National Science Foundation's Division of Environmental Biology.
Other co-authors are researchers at King Mongkut's University of Technology Thonburi in Thailand, Wageningen University in the Netherlands and the Royal Thai Forest Department.
Loss of one tree species has far-reaching implications
The ecologists show how vital large animals are to maintaining the biodiversity of tropical forests in Thailand.
The team looked at how these mammals contribute to moving seeds through the forest.
"It's not surprising that seed dispersers help trees get to new places," says Levey. "The effects of hunting can extend far beyond the hunted, threatening the overall health of the trees that make up the forest."
Adds Caughlin, "On the surface, it doesn't seem that seed dispersal would be important for tree populations. But seed dispersal has an effect over the whole life of a tree."
Animals critical to seed transport through the forest
The scientists looked at the growth and survival of trees that sprouted from parent trees and grew up in crowded environs, compared to trees from seeds that were widely transported across the forest by animals.
The information was supplemented with a dataset from the Thai Royal Forest Department that contains more than 15 years of data on trees.
The researchers then created a long-term simulation and ran it on the University of Florida's supercomputer, the HiPerGator.
"Having that computing power was very important," says Caughlin, "because we had to simulate the fate of millions of seeds."
The scientists discovered that trees that grow from seeds transported by now-overhunted animals are hardier and healthier.
"Our study is the first to quantify the decades-long effects of animal seed dispersal across the entire tree life cycle, from seeds to seedlings to adult trees," says Lichstein.
Probability of tree extinction increased tenfold
The results show that loss of animal seed-dispersers increases the probability of tree extinction by more than tenfold over a 100-year period.
"The entire ecosystem is at risk," says Caughlin.
"We hope the study will provide a boost for those trying to curb overhunting," he says, "and provide incentives to stop the wildlife trade."
-- Cheryl Dybas, NSF
-- Gigi Marino, University of Florida
Tuesday, November 11, 2014
THE SPECIATION OF TREES
FROM: THE NATIONAL SCIENCE FOUNDATION
Tracing the evolution of forest trees
Evergreen tree in Hawaii offers clues into survival of tropical ecosystems
There are at least 60,000 identified tree species in the world, "but we know next to nothing about how they got here," Elizabeth Stacy says. "Trees form the backbone of our forests, and are ecologically and economically important, yet we don't know much about how speciation happens in trees."
Speciation, the evolutionary process by which new biological species arise, fascinates Stacy, an associate professor of biology at the University of Hawaii Hilo, and forms the core of her research. The National Science Foundation (NSF)-funded scientist is focusing on the origins of the many forms of Metrosideros, a diverse genus of forest trees, and on one of its species in particular--Hawaii's M. polymorpha--as a model for studying diversification.
The Hawaiian Islands were formed and continue to be formed from volcanic activity, which makes them an ideal place to study speciation. Because the islands are so isolated, their plant and animal species almost certainly colonized for the first time millions of years ago when wind, ocean currents, birds and insects carried early specimens there.
"Hawaii is a fantastic place to study evolution and the origins of species," Stacy says. "It's like its own planet, its own evolutionary experiment."
Metrosideros comprises trees and shrubs found predominantly in the Pacific Rim region. The name means "iron heartwood," and derives from the ancient Greek metra, or "heartwood," and sideron, or "iron." Stacy is trying to discern the relationships among the many forms of this genus in Hawaii and learn how reproductive barriers arise between diverging populations.
"Over time, Metrosideros has diversified into five species," she says. "M. polymorpha is by far the most abundant. It's unusual for its huge ecological breadth. You can find it in almost every habitat in Hawaii. It's everywhere."
Insights into the evolution of such long-lived trees as these could have important implications for future conservation practices in Hawaii, and possibly elsewhere.
"Because it is so abundant and dominant, Metrosideros is a keystone species for many of Hawaii's terrestrial environments," Stacy says. "It is an important resource for native birds and insects. Insights into how the many forms of Metrosideros originated and how different they are from each other today can reveal insights into the same for the many animals that use Metrosideros. Understanding the ecological needs of species is an essential first step in their conservation.
"Conservation biology has gained an appreciation for evolution," she adds. "Over the last decade, people have grown to appreciate that we need to pay attention to the processes that give rise to species. Speciation is literally the origin of the biodiversity that we are concerned about saving. To really think about long-term conservation, we need to be aware of these evolutionary processes."
Stacy is conducting her research under an NSF Faculty Early Career Development (CAREER) award, which she received in 2010. The award supports junior faculty who exemplify the role of teacher-scholars through outstanding research, excellent education and the integration of education and research within the context of the mission of their organization. NSF is funding her work with about $750,000 over five years.
Her project uses molecular genetic methods to "try to unravel the very shrouded evolutionary history of Metrosideros in Hawaii," she says. "We're experimenting with novel molecular markers--previously inaccessible genes and gene regions--to get a clearer picture of how the forms of Metrosideros are related, both within and across islands."
Uncovering the evolutionary relationships among closely related trees is especially difficult because of their tendency to hybridize, and thus share the same genetic material, she adds.
Also, she and her team are conducting experiments in the field and in the greenhouse with seedlings of various forms, exposing them to different stresses to compare their differences.
"These experiments are revealing insights into how long-term exposure of tree populations to Hawaii's famous environmental gradients can lead to diversification, and they reveal which specific environmental factors, for example, water, light and wind are most important for causing the differences among the forms of the tree," she says.
"Lastly, we are looking at their reproductive barriers: can you two make 'babies' with each other, and how fit are your 'babies?"' she adds. "How well do your offspring survive, and reproduce compared to everyone else in your population? We do a lot of hand-crossing, or hand pollination, where you take pollen from one tree and pollinate another."
These crosses allow examination of the both prezygotic (before fertilization) and postzygotic (after fertilization) barriers that accumulate between diverging populations on the way to speciation.
"I posit that adaptation of this widespread tree to Hawaii's highly varied environments has led to the evolution of partial reproductive isolating barriers between forms that are adapted to different habitats," she says.
As part of the grant's educational component, she is encouraging her students to participate in research through field and lab projects. The team also has established Ho'oulu Lehua, a community-based organization that provides hands-on environmental education for youth with projects that address real conservation issues in the native forests of East Hawaii Island.
The goal of Ho'oulu Lehua, under the leadership of CAREER technician Jennifer Johansen, is to strengthen connections between Hawaii's young people and native forests through restoration activities based on scientific understanding and cultural traditions.
"This island has 11 of 13 climate zones," she says. "We have desert, and wet forests and bogs. Because we are in this amazing evolutionary laboratory, I think we excel in engaging our students with authentic research experiences outside. You can't do this stuff in a lab."
-- Marlene Cimons, National Science Foundation
Investigators
Elizabeth Stacy
Related Institutions/Organizations
University of Hawaii at Hilo
Tracing the evolution of forest trees
Evergreen tree in Hawaii offers clues into survival of tropical ecosystems
There are at least 60,000 identified tree species in the world, "but we know next to nothing about how they got here," Elizabeth Stacy says. "Trees form the backbone of our forests, and are ecologically and economically important, yet we don't know much about how speciation happens in trees."
Speciation, the evolutionary process by which new biological species arise, fascinates Stacy, an associate professor of biology at the University of Hawaii Hilo, and forms the core of her research. The National Science Foundation (NSF)-funded scientist is focusing on the origins of the many forms of Metrosideros, a diverse genus of forest trees, and on one of its species in particular--Hawaii's M. polymorpha--as a model for studying diversification.
The Hawaiian Islands were formed and continue to be formed from volcanic activity, which makes them an ideal place to study speciation. Because the islands are so isolated, their plant and animal species almost certainly colonized for the first time millions of years ago when wind, ocean currents, birds and insects carried early specimens there.
"Hawaii is a fantastic place to study evolution and the origins of species," Stacy says. "It's like its own planet, its own evolutionary experiment."
Metrosideros comprises trees and shrubs found predominantly in the Pacific Rim region. The name means "iron heartwood," and derives from the ancient Greek metra, or "heartwood," and sideron, or "iron." Stacy is trying to discern the relationships among the many forms of this genus in Hawaii and learn how reproductive barriers arise between diverging populations.
"Over time, Metrosideros has diversified into five species," she says. "M. polymorpha is by far the most abundant. It's unusual for its huge ecological breadth. You can find it in almost every habitat in Hawaii. It's everywhere."
Insights into the evolution of such long-lived trees as these could have important implications for future conservation practices in Hawaii, and possibly elsewhere.
"Because it is so abundant and dominant, Metrosideros is a keystone species for many of Hawaii's terrestrial environments," Stacy says. "It is an important resource for native birds and insects. Insights into how the many forms of Metrosideros originated and how different they are from each other today can reveal insights into the same for the many animals that use Metrosideros. Understanding the ecological needs of species is an essential first step in their conservation.
"Conservation biology has gained an appreciation for evolution," she adds. "Over the last decade, people have grown to appreciate that we need to pay attention to the processes that give rise to species. Speciation is literally the origin of the biodiversity that we are concerned about saving. To really think about long-term conservation, we need to be aware of these evolutionary processes."
Stacy is conducting her research under an NSF Faculty Early Career Development (CAREER) award, which she received in 2010. The award supports junior faculty who exemplify the role of teacher-scholars through outstanding research, excellent education and the integration of education and research within the context of the mission of their organization. NSF is funding her work with about $750,000 over five years.
Her project uses molecular genetic methods to "try to unravel the very shrouded evolutionary history of Metrosideros in Hawaii," she says. "We're experimenting with novel molecular markers--previously inaccessible genes and gene regions--to get a clearer picture of how the forms of Metrosideros are related, both within and across islands."
Uncovering the evolutionary relationships among closely related trees is especially difficult because of their tendency to hybridize, and thus share the same genetic material, she adds.
Also, she and her team are conducting experiments in the field and in the greenhouse with seedlings of various forms, exposing them to different stresses to compare their differences.
"These experiments are revealing insights into how long-term exposure of tree populations to Hawaii's famous environmental gradients can lead to diversification, and they reveal which specific environmental factors, for example, water, light and wind are most important for causing the differences among the forms of the tree," she says.
"Lastly, we are looking at their reproductive barriers: can you two make 'babies' with each other, and how fit are your 'babies?"' she adds. "How well do your offspring survive, and reproduce compared to everyone else in your population? We do a lot of hand-crossing, or hand pollination, where you take pollen from one tree and pollinate another."
These crosses allow examination of the both prezygotic (before fertilization) and postzygotic (after fertilization) barriers that accumulate between diverging populations on the way to speciation.
"I posit that adaptation of this widespread tree to Hawaii's highly varied environments has led to the evolution of partial reproductive isolating barriers between forms that are adapted to different habitats," she says.
As part of the grant's educational component, she is encouraging her students to participate in research through field and lab projects. The team also has established Ho'oulu Lehua, a community-based organization that provides hands-on environmental education for youth with projects that address real conservation issues in the native forests of East Hawaii Island.
The goal of Ho'oulu Lehua, under the leadership of CAREER technician Jennifer Johansen, is to strengthen connections between Hawaii's young people and native forests through restoration activities based on scientific understanding and cultural traditions.
"This island has 11 of 13 climate zones," she says. "We have desert, and wet forests and bogs. Because we are in this amazing evolutionary laboratory, I think we excel in engaging our students with authentic research experiences outside. You can't do this stuff in a lab."
-- Marlene Cimons, National Science Foundation
Investigators
Elizabeth Stacy
Related Institutions/Organizations
University of Hawaii at Hilo
Sunday, November 2, 2014
NSF ARTICLE: TESTING FOR PATHOGENS
FROM: NATIONAL SCIENCE FOUNDATION
Testing for pathogens
Innovation Corps researchers focus on medical applications rather than food safety in response to customer needs
When Sunny Shah and his research colleagues at the University of Notre Dame developed a new diagnostic tool for detecting the presence of bacteria, viruses and other pathogens, they assumed that the food industry would be the perfect market.
It made sense, particularly amid ongoing concerns over food safety. The test could identify, among other things, E. coli 0157, which has caused a number of deadly outbreaks in the United States, as well as the bacterium responsible for brucellosis, a disease caused by eating undercooked meat or unpasteurized dairy products.
Their test was accurate and inexpensive. It just wasn't fast enough.
"Even though we could provide a cheaper test than what is already available, they said they would be willing to pay more for a faster test," Shah says, referring to his conversations with representatives from food processing plants, health agencies and food testing labs. "They said we needed to produce results within two hours, not two days, because they wouldn't be able to ship anything out, and had to pay for refrigeration, while waiting for test results."
So the National Science Foundation (NSF)-funded scientist switched his focus--he likes to call it a "pivot"--from food safety to medical applications. In addition to food-borne bacteria, the test also can recognize the virus that causes Dengue fever, potentially valuable for surveillance activities both here and abroad, and human papillomavirus (HPV), which is linked to cervical and oral cancers.
Shah, who also is assistant director for the ESTEEM graduate program, which exposes those with STEM (science, technology, engineering, and mathematics) backgrounds to business and entrepreneurial courses, received $50,000 in 2013 from NSF's Innovation Corps (I-Corps) program. I-Corps helps scientists assess how, and whether, they can translate their promising discoveries into viable commercial products.
The award supports a set of activities and programs that prepare scientists and engineers to extend their focus beyond the laboratory into the commercial world, with the idea of providing near-term benefits for the economy and society.
It is a public-private partnership program that teaches grantees to identify valuable product opportunities that can emerge from academic research, and offers entrepreneurship training to student participants.
Although things did not turn out as originally planned in this case, Shah's experience nevertheless actually embodies the I-Corps philosophy, since one of its major goals is to mentor scientists in ways that allow them to evaluate the commercial potential of their discoveries, and send them in different directions if necessary to ensure their research ends up in the best possible place to do the most good at an affordable price.
"It doesn't matter what we, as researchers, think is the value of our technology," Shah says. "It's what the customer thinks that is important and the only way to identify this customer need is by getting out and interviewing them."
NSF also earlier supported the research that developed the test in 2011. Shah's research colleagues on this project include Hsueh-Chia Chang, professor of chemical and biomolecular engineering, Satyajyoti Senapati, research assistant professor, and Zdenek Slouka, postdoctoral associate in the Chang group. For the I-Corps grant, Kerry Wilson, managing director of Springboard Engineers, played the role of the business mentor, while Shah was the entrepreneurial lead
The test uses a biochip that can detect the DNA or RNA of a particular pathogen.
"Every pathogen has a unique biomarker, and what we do is put a probe on our biochip that captures that biomarker," Shah says. "If the sample has that particular pathogen, then its biomarker will bind to this probe and give us a signal. There are changes in the electrical properties, so it gives us a visual electrical signal that can easily be translated into a target present/absent signal."
Each chip is programmed for a specific pathogen, "but in the future we hope to develop what we call a multiplex biochip that can detect numerous pathogens all on the same device," Shah adds.
The plan now is to develop the tool for future use by dentists to test their patients during office visits for early detection of HPV-related oral cancer before there are visible signs of disease.
"Usually dentists now just examine you visually for lesions, but this would be a sample swab that could give you advance warning," he says.
The test also might be useful as a diagnostic tool for food-borne disease after infection, that is, in testing an already ill patient's blood, he says.
The team recently received a National Institutes of Health grant to study a possible future surveillance role for the test in screening mosquitoes for the presence of Dengue Fever.
"This is not a huge problem for the United States, although there have been a number of cases in parts of Florida in recent years, but it is an issue in South America, Brazil and India, and other areas, " he says.
The impact of I-Corps allowed Shah to make the transition. "Knowing the market and the customer early is extremely important in the technology commercialization process," he says. The program helped him to "quickly assess a particular market to identify customer need and be ready to pivot from one market to another, if needed."
-- Marlene Cimons, National Science Foundation
Investigators
Sunny Shah
Li-Jing Cheng
Hsueh-Chia Chang
Satyajyoti Senapati
Related Institutions/Organizations
University of Notre Dame
Thursday, October 16, 2014
SCIENTISTS LOOK TO SUNFLOWERS FOR ANSWERS
FROM: NATIONAL SCIENCE FOUNDATION
Ten things to know about the flowers of fall: Sunflowers
Scientists unfurl common flowers' genetic secrets
Scientists are finding that answers to biological and environmental questions large and small may be hidden in the petals of common sunflowers.
For example, how frequently and under what conditions does evolution take the same path? When independent populations evolve the same characteristics, are the underlying genetic changes similar or different?
To peer into the world of speciation--how one species branches into another--the National Science Foundation (NSF) spoke with George Gilchrist, a program director in the agency's Division of Environmental Biology and with Ken Whitney, a plant biologist at the University of New Mexico who studies populations of experimental sunflowers in Texas.
With funding from NSF, Whitney and botanist Loren Rieseberg of Indiana University Bloomington and the University of British Columbia are learning whether sunflowers are converging or diverging in their traits.
1) Why do scientists study sunflowers?
Whitney (KW): Sunflowers represent a "recent" success story. In the past three million years, this group has diverged (or branched into new species) in some 50 species in North America. Sunflowers live in a variety of habitats, from forests to deserts to salt marshes.
Sunflowers also contain examples of many important processes, including the evolution of both annual and perennial lifestyles, hybridization (mating between species) and the phenomena of polyploidy (the doubling of chromosome sets in a lineage). All this combines in an "evolutionary cauldron."
2) Where did sunflowers originate?
(KW): The genus Helianthus, true sunflowers, is native to North America. The common sunflower, H. annuus, and its seeds are one of only three crops that were domesticated north of Mexico. The second, sumpweed, was a favorite of Native Americans, but is no longer in use; the third, Jerusalem artichoke, is actually the root of another sunflower species, H. tuberosus.
3) What are the major commercial uses of sunflowers?
(KW): Oilseed sunflower varieties are used to produce oil used in cooking. A separate set of varieties, called confectionary varieties, has been developed to produce the large seeds we eat directly--such as those that are roasted and salted.
4) How do sunflowers link North America and Russia?
(KW): Although the crop sunflower originated in North America, it had to travel to Europe to achieve its current form. Much of the breeding for large seed size and high oil content was done in Russia in the 1800s, a legacy that is still with us in the sunflower variety called "Russian Mammoth." Many of us grow this plant in home gardens.
Sunflower varieties from Russia made it back to the U.S. in the late 1880s, but it was not until the 1930s and 1940s that crop sunflowers were grown on a large commercial scale in the United States.
5) What's the difference between wild sunflowers and those that are domesticated and grown as crops?
(KW): Both wild and crop sunflowers are the same species, H. annuus. Wild sunflowers have many flowering heads on each plant, and have small seeds. A major event in the domestication of the sunflower was the creation of a "monocephalic" plant with a single large flowering head and large seeds.
6) How much diversity is there in wild sunflowers?
(KW): The 50 or so species of wild sunflowers are both ecologically and genetically diverse. The U.S. Department of Agriculture maintains seed stocks of most wild sunflower species, in part because they contain genetic material that can be used to improve cultivated sunflower varieties. For example, a pest-resistant species might provide genes that could decrease pest damage in cultivated sunflowers.
7) What ecological factors drive sunflowers' diversity?
(KW): Sunflowers live in a wide range of habitats, and are widespread across the North American continent. That geographic range means that sunflowers have adapted to very different environmental conditions during the course of their radiation.
8) Are there medical treatments derived from sunflower products?
(KW): Sunflower products, especially the oil from the seeds, have long been used in folk medicine, but I'm not aware of any uses in modern medicine.
9) Do wild sunflowers hybridize? What role has hybridization played in speciation?
(KW): Sunflowers are notorious for hybridizing: mating across species boundaries and exchanging genetic material between species. Sometimes this genetic exchange leads to improved performance, for example in the Texas sunflower our team has been studying.
We have evidence that when wild H. annuus captured genes from another species, H. debilis, it was able to expand its range southward and become a new subspecies, H. annuus texanus. In other sunflowers, hybridization may lead to entirely new species. The sunflowers H. annuus and H. petiolaris have hybridized repeatedly and have produced three new sunflower species that live on the desert floor, on sand dunes, and in salt marshes.
Gilchrist (GG): This research has been critical to understanding how hybridization can lead to rapid speciation. While many hybrids are sterile, some genetic changes create hybrids with extra sets of chromosomes that are fully fertile, but reproductively isolated from their parents.
These new hybrid sunflowers often are uniquely adapted to new habitats that neither of the parent species occupies. Speciation by hybridization is very common in plants and may play a major role in plant diversification.
10) Do insects and pathogens attack sunflowers?
(KW): Sunflowers are indeed attacked by insects, especially grasshoppers, caterpillars, aphids and their relatives, as well as by fungal and bacterial pathogens.
A sunflower's life, scientists say, is no bed of roses.
-- Cheryl Dybas,
Saturday, September 20, 2014
A MEASURE OF OCEAN PROTEINS MAY REVEAL HOW OCEAN SYSTEMS OPERATE
FROM: THE NATIONAL SCIENCE FOUNDATION
Scientists apply biomedical technique to reveal changes in body of the ocean
Researchers look at biochemical reactions happening inside ocean organisms
For decades, doctors have developed methods to diagnose how different types of cells and systems in the body are functioning. Now scientists have adapted an emerging biomedical technique to study the vast body of the ocean.
In a paper published in the journal Science, scientists demonstrate that they can identify and measure proteins in the ocean, revealing how single-celled marine organisms and ocean ecosystems operate.
The National Science Foundation (NSF) and the Gordon and Betty Moore Foundation funded the research.
"Proteins are the molecules that catalyze the biochemical reactions happening in organisms," says Woods Hole Oceanographic Institution (WHOI) biogeochemist Mak Saito, the paper's lead author.
"Instead of just measuring what species are in the ocean, now we can look inside those organisms and see what biochemical reactions they're performing in the face of various ocean conditions.
"It's a potentially powerful tool we can use to reveal the inner biochemical workings of organisms in ocean ecosystems--and to start diagnosing how the oceans are responding to pollution, climate change and other shifts."
The emerging biomedical technique of measuring proteins--a field called proteomics--builds on the more familiar field of genomics that has allowed scientists to detect and identify genes in cells.
"Proteomics is an advanced diagnostic tool that allows us to take the pulse of, for example, phytoplankton cells while they respond to environmental cues," says paper co-author Anton Post, currently on leave from the Marine Biological Laboratory in Woods Hole, Mass., and a program officer in NSF's Division of Ocean Sciences.
The new study is an initial demonstration that proteomic techniques can be applied to marine species not only to identify the presence of proteins, but for the first time, to precisely count their numbers.
"We're leveraging that biomedical technology and translating it for use in the oceans," Saito says.
"Just as you'd analyze proteins in a blood test to get information on what's happening inside your body, proteomics gives us a new way to learn what's happening in ocean ecosystems, especially under multiple stresses and over large regions.
"With that information, we can identify changes, assess their effects on society and devise strategies to adapt."
For their study, the scientists collected water samples during a research cruise along a 2,500-mile stretch of the Pacific Ocean from Hawaii to Samoa.
The transect cut across regions with widely different concentrations of nutrients, from areas rich in iron to the north to areas near the equator that are rich in phosphorus and nitrogen but devoid of iron.
Back in the lab, the scientists analyzed the samples, focusing on proteins produced by one of the ocean's most abundant microbes, Prochlorococcus.
They used mass spectrometers to separate individual proteins in the samples, identifying them by their peptide sequences.
In subsequent steps, the scientists demonstrated for the first time that they could precisely measure the amounts of specific proteins in individual species at various locations in the ocean.
The results painted a picture of what factors were controlling microbial photosynthesis and growth and how the microbes were responding to different conditions over a large geographic region of the sea.
For example, in areas where nitrogen was limited, the scientists found high levels of a protein that transports urea, a form of nitrogen, which the microbes used to maximize their ability to obtain the essential nutrient.
In areas where iron was deficient, they found an abundance of proteins that help grab and transport iron.
"The microbes have biochemical systems that are ready to turn on to deal with low-nutrient situations," Saito says.
In areas in-between, where the microbes were starved for both nutrients, proteins indicated which biochemical machinery the microbes used to negotiate multiple environmental stresses.
The protein measurements enabled the scientists to map when, where, and how ecosystem changes occurred over broad areas of the ocean.
"We measured about 20 biomarkers that indicate metabolism, but we can scale up that capacity to measure many more simultaneously," Saito says.
"We're building an oceanic proteomic capability, which includes sampling with ocean-going robots, to allow us to diagnose the inner workings of ocean ecosystems and understand how they respond to global change."
Along with Saito and Post, the research team included Matthew McIlvin, Dawn Moran, Tyler Goepfert and Carl Lamborg of WHOI and Giacomo DiTullio of the College of Charleston in South Carolina.
-NSF-
Scientists apply biomedical technique to reveal changes in body of the ocean
Researchers look at biochemical reactions happening inside ocean organisms
For decades, doctors have developed methods to diagnose how different types of cells and systems in the body are functioning. Now scientists have adapted an emerging biomedical technique to study the vast body of the ocean.
In a paper published in the journal Science, scientists demonstrate that they can identify and measure proteins in the ocean, revealing how single-celled marine organisms and ocean ecosystems operate.
The National Science Foundation (NSF) and the Gordon and Betty Moore Foundation funded the research.
"Proteins are the molecules that catalyze the biochemical reactions happening in organisms," says Woods Hole Oceanographic Institution (WHOI) biogeochemist Mak Saito, the paper's lead author.
"Instead of just measuring what species are in the ocean, now we can look inside those organisms and see what biochemical reactions they're performing in the face of various ocean conditions.
"It's a potentially powerful tool we can use to reveal the inner biochemical workings of organisms in ocean ecosystems--and to start diagnosing how the oceans are responding to pollution, climate change and other shifts."
The emerging biomedical technique of measuring proteins--a field called proteomics--builds on the more familiar field of genomics that has allowed scientists to detect and identify genes in cells.
"Proteomics is an advanced diagnostic tool that allows us to take the pulse of, for example, phytoplankton cells while they respond to environmental cues," says paper co-author Anton Post, currently on leave from the Marine Biological Laboratory in Woods Hole, Mass., and a program officer in NSF's Division of Ocean Sciences.
The new study is an initial demonstration that proteomic techniques can be applied to marine species not only to identify the presence of proteins, but for the first time, to precisely count their numbers.
"We're leveraging that biomedical technology and translating it for use in the oceans," Saito says.
"Just as you'd analyze proteins in a blood test to get information on what's happening inside your body, proteomics gives us a new way to learn what's happening in ocean ecosystems, especially under multiple stresses and over large regions.
"With that information, we can identify changes, assess their effects on society and devise strategies to adapt."
For their study, the scientists collected water samples during a research cruise along a 2,500-mile stretch of the Pacific Ocean from Hawaii to Samoa.
The transect cut across regions with widely different concentrations of nutrients, from areas rich in iron to the north to areas near the equator that are rich in phosphorus and nitrogen but devoid of iron.
Back in the lab, the scientists analyzed the samples, focusing on proteins produced by one of the ocean's most abundant microbes, Prochlorococcus.
They used mass spectrometers to separate individual proteins in the samples, identifying them by their peptide sequences.
In subsequent steps, the scientists demonstrated for the first time that they could precisely measure the amounts of specific proteins in individual species at various locations in the ocean.
The results painted a picture of what factors were controlling microbial photosynthesis and growth and how the microbes were responding to different conditions over a large geographic region of the sea.
For example, in areas where nitrogen was limited, the scientists found high levels of a protein that transports urea, a form of nitrogen, which the microbes used to maximize their ability to obtain the essential nutrient.
In areas where iron was deficient, they found an abundance of proteins that help grab and transport iron.
"The microbes have biochemical systems that are ready to turn on to deal with low-nutrient situations," Saito says.
In areas in-between, where the microbes were starved for both nutrients, proteins indicated which biochemical machinery the microbes used to negotiate multiple environmental stresses.
The protein measurements enabled the scientists to map when, where, and how ecosystem changes occurred over broad areas of the ocean.
"We measured about 20 biomarkers that indicate metabolism, but we can scale up that capacity to measure many more simultaneously," Saito says.
"We're building an oceanic proteomic capability, which includes sampling with ocean-going robots, to allow us to diagnose the inner workings of ocean ecosystems and understand how they respond to global change."
Along with Saito and Post, the research team included Matthew McIlvin, Dawn Moran, Tyler Goepfert and Carl Lamborg of WHOI and Giacomo DiTullio of the College of Charleston in South Carolina.
-NSF-
Sunday, September 14, 2014
Tuesday, September 9, 2014
Tuesday, September 2, 2014
Tuesday, August 5, 2014
NSF: RESEARCHERS INVESTIGATE REMARKABLE APPROACH TO DESALINATION
FROM: NATIONAL SCIENCE FOUNDATION
Rice scientists reprogram protein pairs; attempt to modify bacterial decisions
Desalination has come a long way, baby.
On Aug. 3, some 330 years ago, a certain Captain Gifford of His Majesty's Ship Mermaid, was asked to conduct onboard his 24-gun Royal Naval vessel what may have been the first government-sponsored, scientific desalination experiment.
Diarist and later Secretary to the Admiralty Commission in England Samuel Pepys wrote to Gifford saying, "Whereas a Proposal has been made to Us of an Engine to be fixed in one of Our Ships for the making an Experiment of producing fresh water (at Sea) out of Salt."
We do not know whether Gifford actually conducted the experiment, but we do know desalination--the pulling of salt, minerals and other contaminants from soil and water--has become a worldwide concern. Population increases, the scarcity of fresh water in arid regions and a greater need for environmental cleanup has scientists scrambling to improve the process.
Researchers at Rice University in Houston, Texas, for example, are computationally investigating ways to rewire one of desalination's most useful tools: Bacteria.
Bacteria as an environmental cleaning agent is based on the microorganisms' ability to sense its environment, consume pollutants, break them down and excrete different, less-harmful substances than the original contaminant. But bacteria's response mechanisms can do many other things such as provide scientifically discrete information, diagnose levels of toxins in food and water, detect poisonous chemicals, report dangerous compounds in the human body and more.
That's why Jose Onuchic and Herbert Levine, co-directors of Rice's Center for Theoretical Biological Physics are working to treat bacteria like computers with the intention of reprograming them to perform specific activities.
The researchers have a plan to modify the proteins responsible for how bacteria respond to external stimuli, triggering the bacteria to predictably "decide" what actions to take when confronted with targeted environmental conditions.
Directed bacterial responses, the researchers believe, could revolutionize bacteria-based environmental cleanup, modern desalination and a host of medical and industrial applications.
The project, "Molecular Underpinnings of Bacterial Decision-Making" is one of a number of high-risk, potentially high-reward projects in the National Science Foundation's INSPIRE program. INSPIRE funds potentially transformative research that does not fit into a single scientific field, but crosses disciplinary boundaries.
"This research project by two highly respected scientists and their colleagues is an excellent example of basic research that can have tremendous societal benefits," says Kamal Shukla, program director in NSF's Division of Molecular and Cellular Biosciences.
The project is co-funded by NSF's Directorates for Biological Sciences and Mathematical and Physical Sciences.
Special molecules...
"The information encoded in the genome not only contains the blueprint for making proteins that fold into unique 3-D structures," says Onuchic explaining the basis of the research, "but also contains rich information about functional protein-protein interactions." Two-component signaling (TCS) systems, found mainly in bacteria, are an example of this idea.
TCS systems are the dominant means by which bacteria sense the environment and carry out appropriate actions. These signaling pathways, determine how bacteria respond to heat, sunlight, toxins, oxygen and other environmental stimuli.
They also regulate characteristics such as how poisonous bacteria are, their ability to produce disease, their nutrient uptake, their ability to yield secondary organic compounds, etc.
"Our research tries to understand and potentially re-engineer two-component signaling systems," says Ryan Cheng, a postdoctoral fellow at Rice working on the project. "A successful understanding of the special molecules that make up these systems would allow us to take them apart like Lego blocks and start building new blocks or circuits to achieve a specific goal."
Earlier this year in a paper published in the Proceedings of the National Academy of Sciences, the researchers revealed a scoring metric they devised to interpret how TCS proteins interact with each other and to predict how signaling modifications might affect TCS systems.
The metric, based on sequence data from the coevolution of TCS proteins, could form a framework for fine tuning TCS signals and/or mix-matching TCS proteins leading to novel bacterial responses.
"Many proteins have evolved to produce specific behaviors under the additional constraint that they physically bind to another protein," says Faruck Morcos, a postdoctoral fellow at Rice, whose research focuses on computational biology and bioinformatics.
"Random mutations that may occur to one protein over geological timescales need to occur alongside mutations to the second protein in order to maintain their ability to interact with one another."
However, when the signal between two proteins that have evolved together is modified or a protein is matched with a non-evolutionary signaling partner, directed responses can occur.
"Hence, by applying methods from statistical physics, one can quantify and extract the statistical connections associated with amino acid coevolution between families of interacting proteins," Morcos says, and determine which proteins can successfully signal each other to produce predetermined outcomes.
Practical applications...
With this operating premise, Onuchic and Levine, along with a small cadre of colleagues, plan to use the framework to engineer new, predictable behaviors in a model bacterium called Bacillus subtilis. Moreover, they plan to use B. subtilis as the prototype for changes in other protein-based systems.
"The potential applications for sanitation engineers are both numerous and profound," says Joshua Boltz, senior technologist and the biofilm technologies practice leader at CH2M HILL, a U.S. engineering company with major sewerage programs in London and Abu Dhabi, as well as clean water projects in the United States, Europe and Canada.
"Using membranes as a desalination tool to separate solids from liquids has emerged as a mature technology that is widely used globally," says Boltz zeroing in on an area where the research could benefit his industry. But, "A key concern with using membranes is their fouling, or a reduction in filtration capacity due to orifice clogging as a result of biofilms."
The researchers at Rice believe they can help reduce the buildup of biofilms in desalination equipment. Biofilms are thin layers of cells that stick to each other on a surface and have the ability to obstruct the flow of liquids in water purification systems.
"It has been shown experimentally that wrinkle formation in the biofilms of B. subtilis result from localized cell death," says Cheng. "Since cell death is regulated by two-component and related signaling systems, the potential for controlling the morphology and mechanical properties of biofilms exists."
The researchers surmise that this can perhaps be accomplished by introducing engineered bacteria to existing biofilms that can mechanically weaken existing biofilms through programmed cell death.
"While our research so far has exclusively dealt with quantifying the degree of interaction between a single pair of TCS proteins, a significant challenge will be to extend this work to make in vivo predictions," says Levine.
"Extending our methodology to complicated systems containing many potentially competing protein-protein interactions, e.g. living systems, will be a significant challenge for us in the future. We hope to extend this methodology to predictively understand how making a specific site-directed mutation affects the characteristics of an organism."
-- Bobbie Mixon,
Investigators
Jose Onuchic
Herbert Levine
Related Institutions/Organizations
William Marsh Rice University
Thursday, July 31, 2014
SKIN CANCER RATES INCREASING: SURGEON GENERAL ISSUES CALL TO ACTION
FROM: U.S. DEPARTMENT OF HEALTH AND HUMAN SERVICES
Surgeon General issues call to action to prevent skin cancer
Skin cancer rates rising: most cases are preventable
Even though most skin cancers can be prevented, rates of skin cancer, including melanoma, are increasing in the United States. Nearly 5 million people in the U.S. are treated for skin cancer every year, at an average annual cost of $8.1 billion. It is also one of the most common types of cancer among U.S. teens and young adults.
A key message in today’s report is that although people with lighter skin are at higher risk, anyone can get skin cancer—and it can be disfiguring, even deadly. Over the last three decades, the number of Americans who have had skin cancer is estimated to be higher than the number for all other cancers combined.
“While many other cancers, such as lung cancer, are decreasing, rates of melanoma -- the deadliest form of skin cancer -- are increasing,” said Assistant Secretary for Health Howard K. Koh, M.D., M.P.H. “As a skin oncologist who worked in this field for many years, I have cared for both the young and old with skin cancers. Almost all of these cancers were caused by unnecessary ultraviolet radiation exposure, usually from excessive time in the sun or from the use of indoor tanning devices.”
Melanoma is the deadliest form of skin cancer. Each year, more than 63,000 new cases are diagnosed in the U.S. and nearly 9,000 people die from this disease. Rates of melanoma increased more than 200 percent from 1973 to 2011. Melanoma is also one of the most common types of cancer among U.S. teens and young adults.
According to research cited in the Call to Action, more than 400,000 cases of skin cancer, about 6,000 of which are melanomas, are estimated to be related to indoor tanning in the U.S. each year. Currently, as many as 44 states plus the District of Columbia have some type of law or regulation related to indoor tanning, but nearly one out of every three white women aged 16 to 25 years engages in indoor tanning each year.
“Tanned skin is damaged skin, and we need to shatter the myth that tanned skin is a sign of health,” said Acting Surgeon General Boris D. Lushniak, M.D., M.P.H. “When people tan or get sunburned, they increase their risk of getting skin cancer later in life.”
The Surgeon General’s Call to Action helps to educate consumers by providing everyday steps they can take to lead healthy and active lives while being outdoors. These steps include wearing protective gear (such as a hat, sunglasses, and other protective clothing) and seeking shade along with the use of a broad-spectrum sunscreen with a sun protection factor (SPF) of 15 or higher to protect any exposed skin, especially during midday hours.
“We want all Americans to lead healthy, active lives,” Dr. Lushniak said, “We all need to take an active role to prevent skin cancer by protecting our skin while being outdoors and avoiding intentional sun exposure and indoor tanning.”
The report calls on all sectors of Americans society, including the business, health care, education, government and nonprofit sectors, as well as families and individuals, to do more. Examples include communities providing shade in outdoor settings, health care providers counseling patients on the importance of using sun protection, and educational institutions discouraging indoor tanning.
Sunday, July 27, 2014
BEETLE INSPIRES NEW MATERIALS DEVELOPED TO TRAP AND CHANNEL SMALL AMOUNTS OF FLUIDS
FROM: NATIONAL SCIENCE FOUNDATION
Quenching the world's water and energy crises, one tiny droplet at a time
In pursuit of beetle biomimicry, NSF-funded engineers develop new, textured materials to trap and channel small amounts of liquid
In the Namib Desert of Africa, the fog-filled morning wind carries the drinking water for a beetle called the Stenocara.
Tiny droplets collect on the beetle's bumpy back. The areas between the bumps are covered in a waxy substance that makes them water-repellant, or hydrophobic (water-fearing). Water accumulates on the water-loving, or hydrophilic, bumps, forming droplets that eventually grow too big to stay put, then roll down the waxy surface.
The beetle slakes its thirst by tilting its back end up and sipping from the accumulated droplets that fall into its mouth. Incredibly, the beetle gathers enough water through this method to drink 12 percent of its body weight each day.
More than a decade ago, news of this creature's efficient water collection system inspired engineers to try and reproduce these surfaces in the lab.
Small-scale advances in fluid physics, materials engineering and nanoscience since that time have brought them close to succeeding.
These tiny developments, however, have the prospect to lead to macro-scale changes. Understanding how liquids interact with different materials can lead to more efficient, inexpensive processes and products, and might even lead to airplane wings impervious to ice and self-cleaning windows.
Beetle bumps in the lab
Using various methods to create intricately patterned surfaces, engineers can make materials that closely mimic the beetle's back.
"Ten years ago no one had the ability to pattern surfaces like this at the nanoscale," says Sumanta Acharya, a National Science Foundation (NSF) program director. "We observed naturally hydrophobic surfaces like the lotus leaf for decades. But even if we understood it, what could we do about it?"
What researchers have done is create surfaces that so excel at repelling or attracting water they've added a "super" at the front of their description: superhydrophobic or superhydrophilic.
Many superhydrophobic surfaces created by chemical coatings are already in the marketplace (water-repellant shoes! shirts! iPhones!).
However, many researchers focus on materials with physical elements that make them superhydrophobic.
These materials have micro or nano-sized pillars, poles or other structures that alter the angles at which water droplets contact their surface. These contact angles determine whether a water droplet beads up like a teeny crystal ball or relaxes a bit and rests on the surface like a spilled milkshake.
By varying the layout of these surfaces, researchers can now trap, direct and repulse small amounts of water for a variety of new purposes.
"We can now do things with fluids we only imagined before," says mechanical engineer Constantine Megaridis at the University of Illinois at Chicago. Megaridis and his team have two NSF grants from the Engineering Directorate's Division of Chemical, Bioengineering, Environmental and Transport Systems.
"The developments have enabled us to create devices -- devices with the potential to help humanity -- that do things much better than have ever been done before," he says.
Megaridis has used his beetle-inspired designs to put precise, textured patterns on inexpensive materials, making microfluidic circuits.
Plastic strips with superhydrophilic centers and superhydrophobic surroundings that combine or separate fluids have the potential to serve as platforms for diagnostic tests (watch "The ride of the water droplets").
"Imagine you want to bring drops of blood or water or any liquid to a certain location," Megaridis explains. "Just like a highway, the road is the strip for the liquid to travel down, and it ends up collecting in a fluid storage tank on the surface." The storage tank could hold a reactive agent. Medical personnel could use the disposable strips to field-test water samples for E. coli, for example.
Devices such as these -- created in engineering labs -- are now working their way to the marketplace.
Water, water in the air
NBD Nanotechnologies, a Boston-based company funded by NSF's Small Business Technology Transfer program, aims to scale up the durability and functionality of surface coatings for industrial use.
One of the most impactful applications for superhydrophobic or hydrophobic research is improved condensation efficiency. When water vapor condenses to a liquid, it typically forms a film. That film is a barrier between the vapor and the surface, making it more difficult for other droplets to form. If that film can be prevented by whisking away droplets immediately after they condense--say, with a superhydrophobic surface--the rate of condensation increases.
Condensers are everywhere. They're in your refrigerator, car and air conditioner. More efficient condensation would let all this equipment function with less energy. Better efficiency is especially important in places where large-scale cooling is paramount, such as power plants.
"NBD makes more durable coatings that span large surface areas," says NBD Nanotechnologies senior scientist Sara Beaini. "Durability is an important factor, because when you're working on the micro level you depend on having a pristine surface structure. Any mechanical or chemical abrasion that distorts the surface structures can significantly reduce or eliminate the advantageous surface properties quickly."
NBD, which you might have guessed stands for Namib Beetle Design, has partnered with Megaridis and others to improve durability, the main challenge in commercializing superhydrophobic research. Power plant condensers with durable hydrophobic or superhydrophobic coatings could be more efficient. And with water and energy shortages looming, partnerships such as theirs that help to transfer this breakthrough from the lab to the outside world are increasingly valuable.
Other groups have applied hydrophobic patterning methods in clever ways.
Kripa Varanasi, mechanical engineer at MIT and NSF CAREER awardee, has applied superhydrophobic coatings to metal, ceramics and glass, including the insides of ketchup bottles. Julie Crockett and Daniel Maynes at Brigham Young University developed extreme waterproofing by etching microscopic ridges or posts onto CD-sized wafers.
With all these cross-country efforts, many are optimistic for a future where people in dry areas can harvest fresh water from a morning wind, and lower their energy needs dramatically.
"If someone comes up with a really cheap solution, then applications are waiting," said Rajesh Mehta, NSF Small Business Innovation Research/Small Business Technology Transfer program director.
-- Sarah Bates
Investigators
Constantine Megaridis
Sara Beaini
Julie Crockett
Kripa Varanasi
Brent Webb
R Daniel Maynes
Related Institutions/Organizations
University of Illinois at Chicago
Iowa State University
Brigham Young University
NBD Nanotechnologies, Inc.
Massachusetts Institute of Technology
Tuesday, July 22, 2014
RESEARCH USING SUPERCOMPUTER THAT COULD LINK GENES TO TRAITS AND DISEASES
FROM: NATIONAL SCIENCE FOUNDATION
"Bottom-up" proteomics
NSF-funded supercomputer helps researchers interpret genomes
Tandem protein mass spectrometry is one of the most widely used methods in proteomics, the large-scale study of proteins, particularly their structures and functions.
Researchers in the Marcotte group at the University of Texas at Austin are using the Stampede supercomputer to develop and test computer algorithms that let them more accurately and efficiently interpret proteomics mass spectrometry data.
The researchers are midway through a project that analyzes the largest animal proteomics dataset ever collected (data equivalent to roughly half of all currently existing shotgun proteomics data in the public domain). These samples span protein extracts from a wide variety of tissues and cell types sampled across the animal tree of life.
The analyses consume considerable computing cycles and require the use of Stampede's large memory nodes, but they allow the group to reconstruct the 'wiring diagrams' of cells by learning how all of the proteins encoded by a genome are associated into functional pathways, systems, and networks. Such models let scientists better define the functions of genes, and link genes to traits and diseases.
"Researchers would usually analyze these sorts of datasets one at a time," Edward Marcotte said. "TACC let us scale this to thousands."
Friday, July 18, 2014
CLAYS STUDIED FOR SUPERBUG KILLING PROPERTIES
FROM: NATIONAL SCIENCE FOUNDATION
New answer to MRSA, other 'superbug' infections: clay minerals?
Researchers discover natural clay deposits with antibacterial properties
Such antibiotic resistance is now a major public health concern.
"This serious threat is no longer a prediction for the future," states a 2014 World Health Organization report, "it's happening right now in every region of the world and has the potential to affect anyone, of any age, in any country."
Could the answer to this threat be hidden in clays formed in minerals deep in the Earth?
Biomedicine meets geochemistry
"As antibiotic-resistant bacterial strains emerge and pose increasing health risks," says Lynda Williams, a biogeochemist at Arizona State University (ASU), "new antibacterial agents are urgently needed."
To find answers, Williams and colleague Keith Morrison of ASU set out to identify naturally-occurring antibacterial clays effective at killing antibiotic-resistant bacteria.
The scientists headed to the field--the rock field. In a volcanic deposit near Crater Lake, Oregon, they hit pay dirt.
Back in the lab, the researchers incubated the pathogens Escherichia coli and Staphylococcus epidermidis, which breeds skin infections, with clays from different zones of the Oregon deposit.
They found that the clays' rapid uptake of iron impaired bacterial metabolism. Cells were flooded with excess iron, which overwhelmed iron storage proteins and killed the bacteria.
"The ability of antibacterial clays to buffer pH also appears key to their healing potential and viability as alternatives to conventional antibiotics," state the scientists in a paper recently published in the journal Environmental Geochemistry and Health.
"Minerals have long had a role in non-traditional medicine," says Enriqueta Barrera, a program director in the National Science Foundation's (NSF) Division of Earth Sciences, which funded the research.
"Yet there is often no understanding of the reaction between the minerals and the human body or agents that cause illness. This research explains the mechanism by which clay minerals interfere with the functioning of pathogenic bacteria. The results have the potential to lead to the wide use of clays in the pharmaceutical industry."
Ancient remedies new again
Clay minerals, says Williams, have been sought for medicinal purposes for millennia.
Studies of French clays--green clays historically used in France in mineral baths--show that the clays have antibacterial properties. French green clays have been used to treat Mycobacterium ulcerans, the pathogen that causes Buruli ulcers.
Common in Africa, Buruli ulcers start as painful skin swellings. Then infection leads to the destruction of skin and large, open ulcers on arms or legs.
Delayed treatment--or treatment that doesn't work--may cause irreversible deformities, restriction of joint movement, widespread skin lesions, and sometimes life-threatening secondary infections.
Treatment with daily applications of green clay poultices healed the infections. "These clays," says Williams, "demonstrated a unique ability to kill bacteria while promoting skin cell growth."
Unfortunately, the original French green clays were depleted. Later testing of newer samples didn't show the same results.
Research on French green clays, however, spurred testing of other clays with likely antibacterial properties.
"To date," says Williams, "the most effective antibacterial clays are those from the Oregon deposit."
Samples from an area mined by Oregon Mineral Technologies (OMT) proved active against a broad spectrum of bacteria, including methicillin-resistant S. aureus (MRSA) and extended-spectrum beta-lactamase-resistant E. coli (ESBL).
What's in those rocks?
Understanding the geologic environment that produces antibacterial minerals is important for identifying other promising locations, says Williams, "and for evaluating specific deposits with bactericidal activity."
The OMT deposit was formed near volcanoes active over tens to hundreds of thousands of years. The Crater Lake region is blanketed with ash deposits from such volcanoes.
OMT clays may be 20 to 30 million years old. They were "born" eons before deposits from volcanoes such as Mt. Mazama, which erupted 7,700 years ago to form the Crater Lake caldera.
Volcanic eruptions over the past 70,000 or so years produced silica-rich magmas and hydrothermal waters that may have contributed to the Oregon deposit's antibacterial properties.
To find out, Williams and Morrison took samples from the main OMT open pit. Four types of rocks were collected: two blue clays, and one white and one red "alteration zone" rock from the upper part of the deposit.
Blue clay to the rescue
The OMT blue samples were strongly bactericidal against E. coli and S. epidermidis. The OMT white sample reduced the population of E. coli and S. epidermidis by 56 percent and 29 percent, respectively, but the red sample didn't show an antibacterial effect.
"We can use this information to propose the medicinal application of certain natural clays, especially in wound healing," says Williams.
Chronic, non-healing wounds, adds Morrison, are usually more alkaline (vs. acidic) than healthy skin. The pH of normal skin is slightly acidic, which keeps numbers of bacteria low.
"Antibacterial clays can buffer wounds to a low [more acidic] pH," says Williams, like other accepted chronic wound treatments, such as acidified nitrate. "The clays may shift the wound environment to a pH range that favors healing, while killing invading bacteria."
The Oregon clays could lead to the discovery of new antibacterial mechanisms, she says, "which would benefit the health care industry and people in developing nations. A low-cost topical antibacterial agent is quickly needed."
Answers to Buruli ulcers, MRSA and other antibiotic-resistant infections may lie not in a high-tech lab, but in ancient rocks forged in a hot zone: Oregon's once--and perhaps future--volcanoes.
-- Cheryl Dybas, NSF
Investigators
Lynda Williams
Related Institutions/Organizations
Arizona State University
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