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News Article | May 9, 2017
Site: www.biosciencetechnology.com

Just four letters -- A, C, T, and G -- make up an organism's genetic code. Changing a single letter, or base, can lead to changes in protein structures and functions, impacting an organism's traits. In addition, though, subtler changes can and do happen, involving modifications of the DNA bases themselves. The best-known example of this kind of change is a methylation of the base cytosine at the 5th position on its carbon ring (5mC). In eukaryotes, a less-well known modification involves adding a methyl group to base 6 of adenine (6mA). In the May 8, 2017 issue of Nature Genetics, a team led by scientists at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, report the prevalence of 6mA modifications in the earliest branches of the fungal kingdom. Though fungi have been around for a billion years and collectively are capable of degrading nearly all naturally-occurring polymers and even some human-made ones, most of the species that have been studied belong to just two phyla, the Ascomycota and Basidiomycota. The remaining 6 groups of fungi are classified as "early diverging lineages," the earliest branches in fungal genealogy. They comprise a little-explored realm of fungi, providing a repertoire of important and valuable gene products for DOE missions in bioenergy and environment. "By and large, early-diverging fungi are very poorly understood compared to other lineages. However, many of these fungi turn out to be important in a variety of ways," said study first author and DOE JGI analyst Stephen Mondo. "Consider the Neocallimastigomycetes -- these fungi are one of the most powerful degraders of plant biomass currently known and have a tremendous arsenal of plant cell wall degrading enzymes which may be useful for bioenergy production. They are a good example of how exploring these understudied lineages leads to valuable biological and technological insights." Many of the fungal genomes used in the study were sequenced as part of the DOE JGI's 1000 Fungal Genomes initiative aimed at producing at least one reference genome for every family of fungi. For the study, the team used 16 fungal genomes sequenced at the DOE JGI using the Pacific Biosciences sequencing platform. While the technology was used with the goal of attaining very high quality genome assemblies, DOE JGI scientists have now additionally taken advantage of this sequencing platform to explore epigenetic (5mC, 6mA) modifications. They discovered very high levels of 6mA in fungi, where up to 2.8% of all adenines were methylated, confirming these findings using multiple independent methods. The previous record holder for genomic 6mA, noted Mondo, is the alga Chlamydomonas reinhardtii (sequenced and annotated by the DOE JGI), in which just 0.4% of adenines were methylated. "This is one of the first direct comparisons of 6mA and 5mC in eukaryotes, and the first 6mA study across the fungal kingdom," said DOE JGI Fungal Genomics head and senior author Igor Grigoriev. "6mA has been shown to have different functions depending on the organism. For example, in animals it is involved in suppressing transposon activity, while in algae it is positively associated with gene expression. Our analysis has shown that 6mA modifications are associated with expressed genes and is preferentially deposited based on gene function and conservation, revealing 6mA as a marker of expression for important functionally-relevant genes." In addition to 6mA performing what seems to be the opposite role of 5mC (which suppresses expression), the team found that the presence of 5mC and 6mA are inversely correlated. Specifically, while 5mC is found at repetitive regions of the genome, the methylated adenines were clustered into dense "methylated adenine clusters" (MACs) at gene promoters. 6mA was also found consistently on both strands of DNA, which may enable propagation of methylation through cell division. "Using genomics, we explore the diversity of fungi to develop catalogs of genes, enzymes, and pathways -- parts lists for bio-based economy and bioenergy applications," said Grigoriev. "A lot of this is encoded in early diverging fungi. In these fungi, we found that majority of expressed genes have 6mA MACs. Thus, the discovery of DNA methylation in early diverging fungi helps the research community better understand regulation of genes that encode the parts for bio-based economy and bioenergy applications."


News Article | May 26, 2017
Site: www.eurekalert.org

One of the biggest barriers in the commercial production of sustainable biofuels is to cost-effectively break down the bioenergy crops into sugars that can then be converted into fuel. To reduce this barrier, bioenergy researchers are looking to nature and the estimated 1.5 million species of fungi that, collectively, can break down almost any substance on earth, including plant biomass. As reported May 26, 2017 in Nature Microbiology, a team led by researchers at the University of California (UC), Santa Barbara has found for the first time that early lineages of fungi can form complexes of enzymes capable of degrading plant biomass. By consolidating these enzymes, in effect into protein assembly lines, they can team up to work more efficiently than they would as individuals. The work was enabled by harnessing the capabilities of two U.S. Department of Energy (DOE) Office of Science User Facilities, the DOE Joint Genome Institute (JGI) at Lawrence Berkeley National Laboratory (Berkeley Lab) and the Environmental Molecular Sciences Laboratory (EMSL) at Pacific Northwest National Laboratory (PNNL). "There are protein complexes in bacteria called cellulosomes that pack together the enzymes to break down plant biomass," said study senior author Michelle O'Malley of UC Santa Barbara. "The idea is that these clusters are better at attacking biomass because they are keeping the different enzymes in place with plugs called dockerins so they work more efficiently. This has been detailed in bacteria for more than 20 years, but now seen for the first time in fungi." With help from both the DOE JGI and EMSL, the team has now found protein complexes in anaerobic gut fungi that O'Malley said in principle do the same thing--attack plant biomass as a cluster of enzymes. While they found that many of enzymes in these complexes resulted from horizontal gene transfers with gut bacteria, they also noted differences in the composition compared to the bacterial cellulosomes. For one thing, both dockerins and scaffoldin are not similar between fungi and bacteria. Also, the bacterial cellulosomes are species-specific. Think of them as the high school clique that does everything together. In contrast, the fungal structures that appear analogous to the bacterial cellulosomes are like the high school kids who could easily move among various social groups and are comprised of clusters of enzymes that can "dock" and work in other fungi. The study involved a comparative genomics analyses of five fungi that belong to the Neocallimastigomycetes, a clade of the early-diverging lineages that are not well-studied. Three of the fungi were isolated from animal gut samples collected by the UC Santa Barbara team and sequenced and annotated by the DOE JGI. "Proteomics data and genomics data enabled us to figure out what these complexes are and go hunting for them in other genomes," O'Malley said. "The three genomes are really well resolved to the point where you can start looking at what's there, what's regulating enzyme production, and how enzymes have evolved." Study co-senior author and DOE JGI Fungal Genomics Program head Igor Grigoriev noted that a multi-omics approach that harnessed the genomics and molecular characterization capabilities through a collaborative science initiative allowing researchers to access multiple user facilities in one proposed project known as Facilities Integrating Collaborations for User Science (FICUS), was critical for the research. "It's the first time we've seen parts of the fungal cellulosome," Grigoriev said. "Through the JGI-EMSL FICUS initiative, proteomics allowed us to find the first of these really large ~700 kiloDaltons (kDa) fungal proteins that hold all enzymes together (compared to the molecular weight of 34 kDa of an average protein). Then the high quality of genome assemblies enabled identification of multiple copies of this protein in each of the gut fungi genomes. Just having proteomics or sequencing tools isn't enough since these proteins are not similar to anything else outside of Neocallimastigomycetes. Though the fungal cellulosome was discovered through proteomics, we needed genomics and transcriptomics to decode all its parts." The work is an extension of O'Malley's studies of anaerobic gut fungi, which appeared in Science last year (watch her talk from the 2016 DOE JGI Genomics of Energy & Environment Meeting at bit.ly/JGI2016OMalley). It's a lot of the same players, but we're digging deeper now because we have high-resolution genomes, and we didn't have them then," she said. "We're able to conduct more comparative genetics and now we're trying to figure out the ecological roles in their microbiome." Understanding in greater detail the protein mechanisms of biomass degradation is crucial to advancing DOE's agenda to develop sustainable biofuels from plant feedstocks. High throughput sequencing, combined with sophisticated proteomics, illuminates not just the diversity and complexity of fungal biomass degradation capacities but also furnishes a knowledge basis for exploitation of these abilities with synthetic biology and metabolic engineering approaches. Support for this work was provided by the DOE Office of Science, including an Early Career Research Program award, as well as the National Science Foundation, the U.S. Department of Agriculture, the U.S. Army Research Office, and the University of California. The U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup. DOE JGI, headquartered in Walnut Creek, Calif., provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Follow @doe_jgi on Twitter. EMSL, the Environmental Molecular Sciences Laboratory, is a DOE Office of Science User Facility. Located at Pacific Northwest National Laboratory in Richland, Wash., EMSL offers an open, collaborative environment for scientific discovery to researchers around the world. Its integrated computational and experimental resources enable researchers to realize important scientific insights and create new technologies. Follow EMSL on Facebook, LinkedIn and Twitter. Interdisciplinary teams at Pacific Northwest National Laboratory address many of America's most pressing issues in energy, the environment and national security through advances in basic and applied science. Founded in 1965, PNNL employs 4,400 staff and has an annual budget of nearly $1 billion. It is managed by Battelle for the U.S. Department of Energy's Office of Science. As the single largest supporter of basic research in the physical sciences in the United States, the Office of Science is working to address some of the most pressing challenges of our time. For more information on PNNL, visit the PNNL News Center, or follow PNNL on Facebook, Google+, LinkedIn and Twitter. DOE's Office of Science is the largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.


News Article | May 26, 2017
Site: phys.org

As reported May 26, 2017 in Nature Microbiology, a team led by researchers at the University of California (UC), Santa Barbara has found for the first time that early lineages of fungi can form complexes of enzymes capable of degrading plant biomass. By consolidating these enzymes, in effect into protein assembly lines, they can team up to work more efficiently than they would as individuals. The work was enabled by harnessing the capabilities of two U.S. Department of Energy (DOE) Office of Science User Facilities, the DOE Joint Genome Institute (JGI) at Lawrence Berkeley National Laboratory (Berkeley Lab) and the Environmental Molecular Sciences Laboratory (EMSL) at Pacific Northwest National Laboratory (PNNL). "There are protein complexes in bacteria called cellulosomes that pack together the enzymes to break down plant biomass," said study senior author Michelle O'Malley of UC Santa Barbara. "The idea is that these clusters are better at attacking biomass because they are keeping the different enzymes in place with plugs called dockerins so they work more efficiently. This has been detailed in bacteria for more than 20 years, but now seen for the first time in fungi." With help from both the DOE JGI and EMSL, the team has now found protein complexes in anaerobic gut fungi that O'Malley said in principle do the same thing—attack plant biomass as a cluster of enzymes. While they found that many of enzymes in these complexes resulted from horizontal gene transfers with gut bacteria, they also noted differences in the composition compared to the bacterial cellulosomes. For one thing, both dockerins and scaffoldin are not similar between fungi and bacteria. Also, the bacterial cellulosomes are species-specific. Think of them as the high school clique that does everything together. In contrast, the fungal structures that appear analogous to the bacterial cellulosomes are like the high school kids who could easily move among various social groups and are comprised of clusters of enzymes that can "dock" and work in other fungi. The study involved a comparative genomics analyses of five fungi that belong to the Neocallimastigomycetes, a clade of the early-diverging lineages that are not well-studied. Three of the fungi were isolated from animal gut samples collected by the UC Santa Barbara team and sequenced and annotated by the DOE JGI. "Proteomics data and genomics data enabled us to figure out what these complexes are and go hunting for them in other genomes," O'Malley said. "The three genomes are really well resolved to the point where you can start looking at what's there, what's regulating enzyme production, and how enzymes have evolved." Study co-senior author and DOE JGI Fungal Genomics Program head Igor Grigoriev noted that a multi-omics approach that harnessed the genomics and molecular characterization capabilities through a collaborative science initiative allowing researchers to access multiple user facilities in one proposed project known as Facilities Integrating Collaborations for User Science (FICUS), was critical for the research. "It's the first time we've seen parts of the fungal cellulosome," Grigoriev said. "Through the JGI-EMSL FICUS initiative, proteomics allowed us to find the first of these really large ~700 kiloDaltons (kDa) fungal proteins that hold all enzymes together (compared to the molecular weight of 34 kDa of an average protein). Then the high quality of genome assemblies enabled identification of multiple copies of this protein in each of the gut fungi genomes. Just having proteomics or sequencing tools isn't enough since these proteins are not similar to anything else outside of Neocallimastigomycetes. Though the fungal cellulosome was discovered through proteomics, we needed genomics and transcriptomics to decode all its parts." The work is an extension of O'Malley's studies of anaerobic gut fungi, which appeared in Science last year (watch her talk from the 2016 DOE JGI Genomics of Energy & Environment Meeting at bit.ly/JGI2016OMalley). It's a lot of the same players, but we're digging deeper now because we have high-resolution genomes, and we didn't have them then," she said. "We're able to conduct more comparative genetics and now we're trying to figure out the ecological roles in their microbiome." Understanding in greater detail the protein mechanisms of biomass degradation is crucial to advancing DOE's agenda to develop sustainable biofuels from plant feedstocks. High throughput sequencing, combined with sophisticated proteomics, illuminates not just the diversity and complexity of fungal biomass degradation capacities but also furnishes a knowledge basis for exploitation of these abilities with synthetic biology and metabolic engineering approaches. Explore further: Finding a new major gene expression regulator in fungi More information: Charles H. Haitjema et al, A parts list for fungal cellulosomes revealed by comparative genomics, Nature Microbiology (2017). DOI: 10.1038/nmicrobiol.2017.87


News Article | April 19, 2017
Site: phys.org

In a paper published April 18, 2017, in Nature Plants, a team led by Thomas Brutnell, Ph.D. Director of the Enterprise Institute for Renewable Fuels at the Danforth Center and researchers at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, conducted genetic screens to identify genes that may play a role in flower development on the panicle of green foxtail. Green foxtail is a wild relative of the common crop foxtail millet. These Setaria species are related to several candidate bioenergy grasses including switchgrass and Miscanthus and serve as grass model systems to study grasses that photosynthetically fix carbon from CO2 through a water-conserving (C4) pathway. The genomes of both green foxtail and foxtail millet have been sequenced and annotated through the DOE JGI's Community Science Program. "We have identified four recessive mutants that lead to reduced and uneven flower clusters," said Pu Huang, Ph.D., the lead author of the paper. "By ultimately identifying the gene in green foxtail we identified a new determinant in the control of grain yield that could be crucial to improving food crops like maize." The grass Setaria has been proposed as a model for food and bioenergy crops for its short stature and rapid life cycle, compared to most bioenergy grasses. After constructing a mutant population resource for the grass, the Brutnell lab screened 2,700 M2 families, deep sequenced a mutant pool to identify the causative mutation and confirmed a homologous gene in maize played a similar role. "Identifying this new player in panicle architecture may enable the design of plants with either enhanced or reduced panicle structures," stated Brutnell. "For instance, maize breeding has selected for reduced male panicles, also known as tassels, to reduce shading in the field while still producing sufficient pollen.  However, grain yields in sorghum are directly related to the architecture of the panicle. By showing that this gene influences panicle architecture in Setaria and maize, we have expanded the tool box for breeders." At the Danforth Center, plants hold the key to discoveries and products that will enrich and restore both the environment and the lives of people around the globe. Brutnell's lab research includes the search for the next generation of biofuels: alternative sources of energy that are affordable, sustainable and ecologically sound. The research develops novel computational tools and model systems to identify genes that will improve yield in crops through enhanced photosynthesis. Explore further: New discovery will enhance yield and quality of cereal and bioenergy crops More information: Pu Huang et al. Sparse panicle1 is required for inflorescence development in Setaria viridis and maize, Nature Plants (2017). DOI: 10.1038/nplants.2017.54


News Article | May 3, 2017
Site: globenewswire.com

Vienna, Vir., May 03, 2017 (GLOBE NEWSWIRE) -- Today, the Jane Goodall Institute’s board of directors announced that as of March 21, 2017, Carlos Drews, who has a doctorate in zoology, joined the Jane Goodall Institute as the organization’s executive director. In this role, Drews is responsible for advancing the mission of the Institute building on the legacy of Dr. Jane Goodall, the organization's founder and UN Messenger of Peace. This mission includes promoting understanding and protection of great apes and their habitat, and inspiring individual action by young people of all ages to help animals, other people and to protect the world we all share. As he joins the Institute, Drews will be responsible for leading the organization’s staff of more than 200 conservation professionals in Democratic Republic of Congo, Republic of Congo, Uganda, Tanzania and the United States. On his new post Drews comments, “Having worked all my life with passion in the field of conservation stewardship, the position as JGI’s executive director is the most rewarding role I can play — allowing me to continue to work with African great apes specifically, and to build on my convictions about community-based conservation and the power of the young generation to shape a better world.” Prior to taking on his current role at the Institute, Drews spent 13 years working for the World Wildlife Fund. Most recently, Drews served as the global director of species conservation at WWF International in Switzerland where he was responsible for engaging governments, NGOs, corporations and donors to rally behind a joint marine & terrestrial species conservation agenda. Previously at WWF, Latin-America & the Caribbean, Drews headed the regional species and fisheries team where he was instrumental in reducing the amount of sea turtles injured by long-line fishing in the Eastern Pacific. As a child, Drews dreamed of studying animals in Africa. He realized this dream years later when he arrived in Tanzania as a graduate student researching psychological warfare in baboon communities – a study that earned him the John Napier Medal of the Primate Society of Great Britain. “Great apes are exposed to habitat loss, disease, poaching and other threats," Drews remarks on threats to great apes. "They are a sensitive litmus test for our relationship with fellow creatures on Earth, given their close proximity to us: if we do not fix the way we treat and respect our closest living relatives, what chance may other animals have, I wonder?" A native of Colombia, Drews earned his doctorate from the University of Cambridge and has carried out research into wildlife behavioral ecology in Africa and Latin America, which includes research on the behavioral ecology of primates as well as caimans. He also holds a masters in biology from Munich’s Ludwig-Maximilians as well as a masters in applied biology from the University of Cambridge. A longtime admirer of Jane Goodall and her work, Drews works to preserve and build on Goodall’s legacy at the helm her namesake Institute. Working with a talented staff located all over the world, Drews unites the Institute's team and positions it to ensure long-term success of their conservation efforts. Reflecting on his new work with Goodall, Drews shares, “Remarkably for me, this position gives me the opportunity to be mentored by an outstanding conservation leader that I have very much admired for at least three decades. I feel strongly committed and determined to equip JGI to move sustainably towards Jane Goodall´s vision.” The Jane Goodall Institute is a global community conservation organization that advances the vision and work of Dr. Jane Goodall. By protecting chimpanzees and inspiring action to conserve the natural world we all share, we improve the lives of people, animals and the environment. Founded in 1977 by Dr. Goodall, JGI makes a difference through community-centered conservation and the innovative use of science and technology. We work closely with local communities around the world, inspiring hope through the collective power of individual action. Through Roots & Shoots, our youth-led community action and learning program, young people in nearly 100 countries are acquiring the knowledge and skills to become compassionate conservation leaders in their own backyards. A photo accompanying this announcement is available at http://www.globenewswire.com/NewsRoom/AttachmentNg/2200ee70-f2ac-4b1f-bc26-c6ba39814739 A photo accompanying this announcement is available at http://www.globenewswire.com/NewsRoom/AttachmentNg/f06504b5-3a3c-4684-b56b-08f823769d97 A photo accompanying this announcement is available at http://www.globenewswire.com/NewsRoom/AttachmentNg/fda04319-5edf-421c-82d6-e0abadb9623b


News Article | May 3, 2017
Site: globenewswire.com

Vienna, Vir., May 03, 2017 (GLOBE NEWSWIRE) -- Today, the Jane Goodall Institute’s board of directors announced that as of March 21, 2017, Carlos Drews, who has a doctorate in zoology, joined the Jane Goodall Institute as the organization’s executive director. In this role, Drews is responsible for advancing the mission of the Institute building on the legacy of Dr. Jane Goodall, the organization's founder and UN Messenger of Peace. This mission includes promoting understanding and protection of great apes and their habitat, and inspiring individual action by young people of all ages to help animals, other people and to protect the world we all share. As he joins the Institute, Drews will be responsible for leading the organization’s staff of more than 200 conservation professionals in Democratic Republic of Congo, Republic of Congo, Uganda, Tanzania and the United States. On his new post Drews comments, “Having worked all my life with passion in the field of conservation stewardship, the position as JGI’s executive director is the most rewarding role I can play — allowing me to continue to work with African great apes specifically, and to build on my convictions about community-based conservation and the power of the young generation to shape a better world.” Prior to taking on his current role at the Institute, Drews spent 13 years working for the World Wildlife Fund. Most recently, Drews served as the global director of species conservation at WWF International in Switzerland where he was responsible for engaging governments, NGOs, corporations and donors to rally behind a joint marine & terrestrial species conservation agenda. Previously at WWF, Latin-America & the Caribbean, Drews headed the regional species and fisheries team where he was instrumental in reducing the amount of sea turtles injured by long-line fishing in the Eastern Pacific. As a child, Drews dreamed of studying animals in Africa. He realized this dream years later when he arrived in Tanzania as a graduate student researching psychological warfare in baboon communities – a study that earned him the John Napier Medal of the Primate Society of Great Britain. “Great apes are exposed to habitat loss, disease, poaching and other threats," Drews remarks on threats to great apes. "They are a sensitive litmus test for our relationship with fellow creatures on Earth, given their close proximity to us: if we do not fix the way we treat and respect our closest living relatives, what chance may other animals have, I wonder?" A native of Colombia, Drews earned his doctorate from the University of Cambridge and has carried out research into wildlife behavioral ecology in Africa and Latin America, which includes research on the behavioral ecology of primates as well as caimans. He also holds a masters in biology from Munich’s Ludwig-Maximilians as well as a masters in applied biology from the University of Cambridge. A longtime admirer of Jane Goodall and her work, Drews works to preserve and build on Goodall’s legacy at the helm her namesake Institute. Working with a talented staff located all over the world, Drews unites the Institute's team and positions it to ensure long-term success of their conservation efforts. Reflecting on his new work with Goodall, Drews shares, “Remarkably for me, this position gives me the opportunity to be mentored by an outstanding conservation leader that I have very much admired for at least three decades. I feel strongly committed and determined to equip JGI to move sustainably towards Jane Goodall´s vision.” The Jane Goodall Institute is a global community conservation organization that advances the vision and work of Dr. Jane Goodall. By protecting chimpanzees and inspiring action to conserve the natural world we all share, we improve the lives of people, animals and the environment. Founded in 1977 by Dr. Goodall, JGI makes a difference through community-centered conservation and the innovative use of science and technology. We work closely with local communities around the world, inspiring hope through the collective power of individual action. Through Roots & Shoots, our youth-led community action and learning program, young people in nearly 100 countries are acquiring the knowledge and skills to become compassionate conservation leaders in their own backyards. A photo accompanying this announcement is available at http://www.globenewswire.com/NewsRoom/AttachmentNg/2200ee70-f2ac-4b1f-bc26-c6ba39814739 A photo accompanying this announcement is available at http://www.globenewswire.com/NewsRoom/AttachmentNg/f06504b5-3a3c-4684-b56b-08f823769d97 A photo accompanying this announcement is available at http://www.globenewswire.com/NewsRoom/AttachmentNg/fda04319-5edf-421c-82d6-e0abadb9623b


News Article | April 22, 2017
Site: www.PR.com

St. Louis, MO, April 22, 2017 --( In a paper published April 18, 2017 in Nature Plants, a team led by Thomas Brutnell, Ph.D. Director of the Enterprise Institute for Renewable Fuels at the Danforth Center and researchers at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, conducted genetic screens to identify genes that may play a role in flower development on the panicle of green foxtail. Green foxtail is a wild relative of the common crop foxtail millet. These Setaria species are related to several candidate bioenergy grasses including switchgrass and Miscanthus and serve as grass model systems to study grasses that photosynthetically fix carbon from CO2 through a water-conserving (C4) pathway. The genomes of both green foxtail and foxtail millet have been sequenced and annotated through the DOE JGI’s Community Science Program. “We have identified four recessive mutants that lead to reduced and uneven flower clusters,” said Pu Huang, Ph.D., the lead author of the paper. “By ultimately identifying the gene in green foxtail we identified a new determinant in the control of grain yield that could be crucial to improving food crops like maize.” The grass Setaria has been proposed as a model for food and bioenergy crops for its short stature and rapid life cycle, compared to most bioenergy grasses. After constructing a mutant population resource for the grass, the Brutnell lab screened 2,700 M2 families, deep sequenced a mutant pool to identify the causative mutation and confirmed a homologous gene in maize played a similar role. “Identifying this new player in panicle architecture may enable the design of plants with either enhanced or reduced panicle structures,” stated Brutnell. “For instance, maize breeding has selected for reduced male panicles, also known as tassels, to reduce shading in the field while still producing sufficient pollen. However, grain yields in sorghum are directly related to the architecture of the panicle. By showing that this gene influences panicle architecture in Setaria and maize, we have expanded the tool box for breeders.” At the Danforth Center, plants hold the key to discoveries and products that will enrich and restore both the environment and the lives of people around the globe. Brutnell’s lab research includes the search for the next generation of biofuels: alternative sources of energy that are affordable, sustainable and ecologically sound. The research develops novel computational tools and model systems to identify genes that will improve yield in crops through enhanced photosynthesis. About The Donald Danforth Plant Science Center Founded in 1998, the Donald Danforth Plant Science Center is a not-for-profit research institute with a mission to improve the human condition through plant science. Research, education and outreach aim to have impact at the nexus of food security and the environment, and position the St. Louis region as a world center for plant science. The Center’s work is funded through competitive grants from many sources, including the National Institutes of Health, U.S. Department of Energy, National Science Foundation and the Bill & Melinda Gates Foundation. To keep up to date with Danforth Center’s current operations and areas of research, please visit, www.danforthcenter.org, featuring information on Center scientists, news and the “Roots & Shoots” blog. Follow us on Twitter at @DanforthCenter. St. Louis, MO, April 22, 2017 --( PR.com )-- Researchers at the Enterprise Rent-A-Car Institute for Renewable Fuels at the Donald Danforth Plant Science Center have discovered a gene that influences grain yield in grasses related to food crops. Four mutations were identified that could impact candidate crops for producing renewable and sustainable fuels.In a paper published April 18, 2017 in Nature Plants, a team led by Thomas Brutnell, Ph.D. Director of the Enterprise Institute for Renewable Fuels at the Danforth Center and researchers at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, conducted genetic screens to identify genes that may play a role in flower development on the panicle of green foxtail. Green foxtail is a wild relative of the common crop foxtail millet. These Setaria species are related to several candidate bioenergy grasses including switchgrass and Miscanthus and serve as grass model systems to study grasses that photosynthetically fix carbon from CO2 through a water-conserving (C4) pathway. The genomes of both green foxtail and foxtail millet have been sequenced and annotated through the DOE JGI’s Community Science Program.“We have identified four recessive mutants that lead to reduced and uneven flower clusters,” said Pu Huang, Ph.D., the lead author of the paper. “By ultimately identifying the gene in green foxtail we identified a new determinant in the control of grain yield that could be crucial to improving food crops like maize.”The grass Setaria has been proposed as a model for food and bioenergy crops for its short stature and rapid life cycle, compared to most bioenergy grasses. After constructing a mutant population resource for the grass, the Brutnell lab screened 2,700 M2 families, deep sequenced a mutant pool to identify the causative mutation and confirmed a homologous gene in maize played a similar role.“Identifying this new player in panicle architecture may enable the design of plants with either enhanced or reduced panicle structures,” stated Brutnell. “For instance, maize breeding has selected for reduced male panicles, also known as tassels, to reduce shading in the field while still producing sufficient pollen. However, grain yields in sorghum are directly related to the architecture of the panicle. By showing that this gene influences panicle architecture in Setaria and maize, we have expanded the tool box for breeders.”At the Danforth Center, plants hold the key to discoveries and products that will enrich and restore both the environment and the lives of people around the globe. Brutnell’s lab research includes the search for the next generation of biofuels: alternative sources of energy that are affordable, sustainable and ecologically sound. The research develops novel computational tools and model systems to identify genes that will improve yield in crops through enhanced photosynthesis.About The Donald Danforth Plant Science CenterFounded in 1998, the Donald Danforth Plant Science Center is a not-for-profit research institute with a mission to improve the human condition through plant science. Research, education and outreach aim to have impact at the nexus of food security and the environment, and position the St. Louis region as a world center for plant science. The Center’s work is funded through competitive grants from many sources, including the National Institutes of Health, U.S. Department of Energy, National Science Foundation and the Bill & Melinda Gates Foundation.To keep up to date with Danforth Center’s current operations and areas of research, please visit, www.danforthcenter.org, featuring information on Center scientists, news and the “Roots & Shoots” blog. Follow us on Twitter at @DanforthCenter. Click here to view the list of recent Press Releases from Donald Danforth Plant Science Center


News Article | May 8, 2017
Site: www.eurekalert.org

Just four letters -- A, C, T, and G -- make up an organism's genetic code. Changing a single letter, or base, can lead to changes in protein structures and functions, impacting an organism's traits. In addition, though, subtler changes can and do happen, involving modifications of the DNA bases themselves. The best-known example of this kind of change is a methylation of the base cytosine at the 5th position on its carbon ring (5mC). In eukaryotes, a less-well known modification involves adding a methyl group to base 6 of adenine (6mA). In the May 8, 2017 issue of Nature Genetics, a team led by scientists at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, report the prevalence of 6mA modifications in the earliest branches of the fungal kingdom. Though fungi have been around for a billion years and collectively are capable of degrading nearly all naturally-occurring polymers and even some human-made ones, most of the species that have been studied belong to just two phyla, the Ascomycota and Basidiomycota. The remaining 6 groups of fungi are classified as "early diverging lineages," the earliest branches in fungal genealogy. They comprise a little-explored realm of fungi, providing a repertoire of important and valuable gene products for DOE missions in bioenergy and environment. "By and large, early-diverging fungi are very poorly understood compared to other lineages. However, many of these fungi turn out to be important in a variety of ways," said study first author and DOE JGI analyst Stephen Mondo. "Consider the Neocallimastigomycetes -- these fungi are one of the most powerful degraders of plant biomass currently known and have a tremendous arsenal of plant cell wall degrading enzymes which may be useful for bioenergy production. They are a good example of how exploring these understudied lineages leads to valuable biological and technological insights." Many of the fungal genomes used in the study were sequenced as part of the DOE JGI's 1000 Fungal Genomes initiative aimed at producing at least one reference genome for every family of fungi. For the study, the team used 16 fungal genomes sequenced at the DOE JGI using the Pacific Biosciences sequencing platform. While the technology was used with the goal of attaining very high quality genome assemblies, DOE JGI scientists have now additionally taken advantage of this sequencing platform to explore epigenetic (5mC, 6mA) modifications. They discovered very high levels of 6mA in fungi, where up to 2.8% of all adenines were methylated, confirming these findings using multiple independent methods. The previous record holder for genomic 6mA, noted Mondo, is the alga Chlamydomonas reinhardtii (sequenced and annotated by the DOE JGI), in which just 0.4% of adenines were methylated. "This is one of the first direct comparisons of 6mA and 5mC in eukaryotes, and the first 6mA study across the fungal kingdom," said DOE JGI Fungal Genomics head and senior author Igor Grigoriev. "6mA has been shown to have different functions depending on the organism. For example, in animals it is involved in suppressing transposon activity, while in algae it is positively associated with gene expression. Our analysis has shown that 6mA modifications are associated with expressed genes and is preferentially deposited based on gene function and conservation, revealing 6mA as a marker of expression for important functionally-relevant genes." In addition to 6mA performing what seems to be the opposite role of 5mC (which suppresses expression), the team found that the presence of 5mC and 6mA are inversely correlated. Specifically, while 5mC is found at repetitive regions of the genome, the methylated adenines were clustered into dense "methylated adenine clusters" (MACs) at gene promoters. 6mA was also found consistently on both strands of DNA, which may enable propagation of methylation through cell division. "Using genomics, we explore the diversity of fungi to develop catalogs of genes, enzymes, and pathways -- parts lists for bio-based economy and bioenergy applications," said Grigoriev. "A lot of this is encoded in early diverging fungi. In these fungi, we found that majority of expressed genes have 6mA MACs. Thus, the discovery of DNA methylation in early diverging fungi helps the research community better understand regulation of genes that encode the parts for bio-based economy and bioenergy applications." Mondo described the identification and proposed role of 6mA in early diverging fungi at the 2017 Genomics of Energy & Environment Meeting. Watch his talk on the DOE JGI's YouTube channel at http://bit. . The U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup. DOE JGI, headquartered in Walnut Creek, Calif., provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Follow @doe_jgi on Twitter. DOE's Office of Science is the largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.


News Article | May 8, 2017
Site: phys.org

Linderina pennispora is one of the early-diverging fungi whose genomes were sequenced, annotated and analyzed for the study led by US Department of Energy Joint Genome Institute researchers in the May 8, 2017 issue of Nature Genetics. Credit: ZyGoLife Research Consortium via Flickr, CC BY-SA 2.0 Just four letters—A, C, T, and G—make up an organism's genetic code. Changing a single letter, or base, can lead to changes in protein structures and functions, impacting an organism's traits. In addition, though, subtler changes can and do happen, involving modifications of the DNA bases themselves. The best-known example of this kind of change is a methylation of the base cytosine at the 5th position on its carbon ring (5mC). In eukaryotes, a less-well known modification involves adding a methyl group to base 6 of adenine (6mA). In the May 8, 2017 issue of Nature Genetics, a team led by scientists at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, report the prevalence of 6mA modifications in the earliest branches of the fungal kingdom. Though fungi have been around for a billion years and collectively are capable of degrading nearly all naturally-occurring polymers and even some human-made ones, most of the species that have been studied belong to just two phyla, the Ascomycota and Basidiomycota. The remaining 6 groups of fungi are classified as "early diverging lineages," the earliest branches in fungal genealogy. They comprise a little-explored realm of fungi, providing a repertoire of important and valuable gene products for DOE missions in bioenergy and environment. "By and large, early-diverging fungi are very poorly understood compared to other lineages. However, many of these fungi turn out to be important in a variety of ways," said study first author and DOE JGI analyst Stephen Mondo. "Consider the Neocallimastigomycetes—these fungi are one of the most powerful degraders of plant biomass currently known and have a tremendous arsenal of plant cell wall degrading enzymes which may be useful for bioenergy production. They are a good example of how exploring these understudied lineages leads to valuable biological and technological insights." Many of the fungal genomes used in the study were sequenced as part of the DOE JGI's 1000 Fungal Genomes initiative aimed at producing at least one reference genome for every family of fungi. For the study, the team used 16 fungal genomes sequenced at the DOE JGI using the Pacific Biosciences sequencing platform. While the technology was used with the goal of attaining very high quality genome assemblies, DOE JGI scientists have now additionally taken advantage of this sequencing platform to explore epigenetic (5mC, 6mA) modifications. They discovered very high levels of 6mA in fungi, where up to 2.8% of all adenines were methylated, confirming these findings using multiple independent methods. The previous record holder for genomic 6mA, noted Mondo, is the alga Chlamydomonas reinhardtii (sequenced and annotated by the DOE JGI), in which just 0.4% of adenines were methylated. "This is one of the first direct comparisons of 6mA and 5mC in eukaryotes, and the first 6mA study across the fungal kingdom," said DOE JGI Fungal Genomics head and senior author Igor Grigoriev. "6mA has been shown to have different functions depending on the organism. For example, in animals it is involved in suppressing transposon activity, while in algae it is positively associated with gene expression. Our analysis has shown that 6mA modifications are associated with expressed genes and is preferentially deposited based on gene function and conservation, revealing 6mA as a marker of expression for important functionally-relevant genes." In addition to 6mA performing what seems to be the opposite role of 5mC (which suppresses expression), the team found that the presence of 5mC and 6mA are inversely correlated. Specifically, while 5mC is found at repetitive regions of the genome, the methylated adenines were clustered into dense "methylated adenine clusters" (MACs) at gene promoters. 6mA was also found consistently on both strands of DNA, which may enable propagation of methylation through cell division. "Using genomics, we explore the diversity of fungi to develop catalogs of genes, enzymes, and pathways—parts lists for bio-based economy and bioenergy applications," said Grigoriev. "A lot of this is encoded in early diverging fungi. In these fungi, we found that majority of expressed genes have 6mA MACs. Thus, the discovery of DNA methylation in early diverging fungi helps the research community better understand regulation of genes that encode the parts for bio-based economy and bioenergy applications." Explore further: Genome sequences of early-diverging fungi help track origins of white rot fungi More information: Widespread adenine N6-methylation of active genes in fungi, Nature Genetics (2017). nature.com/articles/doi:10.1038/ng.3859


Onuma T.,JGI Inc. | Okada K.,JGI Inc. | Otsubo A.,Japan Petroleum Exploration Co.
Energy Procedia | Year: 2011

History of surface deformation related with CO 2 injection at In Salah Gas Project, Algeria, was analyzed using satellite-borne Synthetic Aperture Radar (SAR) data. The Project is widely known as long term CO 2 storage project, of which injection has been performed since August 2004, with injected amount of 0.75 million tons CO 2 per year. Surface deformation around three injection wells, KB-501 through KB-503, has been analyzed by Differential Interferometry SAR (DInSAR), a promising remote sensing technique to detect surface deformation at an order of millimeters, using 47 scenes of ENVISAT ASAR spanning from July 2003 to May 2010. Amongst three injection wells, CO 2 injection at KB-502 has been temporarily shut down in July 2007, due to CO 2 breakthrough at an appraisal well KB-5 located 1.3km to the northwest of KB-502. Permanent decommission of KB- 5 was completed and the injection at KB-502 was restarted in November 2009. DInSAR analysis has revealed the surface displacement pattern between July 2007 and May 2010 around KB-502, which is thought to be related with shut-down and recommencement of CO 2 injection. © 2011 Published by Elsevier Ltd.

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