The DOE/Genomes To Life program now is called MAGGIE......just to keep us off track. but, it appears they are working full force with geo and bio engineers to re-specie-ize the environment.
So, we have a good idea of just who is behind this construction of archaean and other species to infect the wildlife. So, that would take how many years? but, if directed/forced it would not take very long.
MAGGIE:Molecular Assemblies, Genes and Genomics Integrated Efficiently.
MAGGIE integrates an interdisciplinary team at Lawrence Berkeley National Lab with researchers at The Scripps Research Institute, the University of Georgia, the University of California Berkeley[/color],(which is where AN KING works in the genetics and genomics division~remember we found AN KING etched on a crystal hexagon?)and the Institute for Systems Biology into a unified Genomics GTL program. Major overall goals are 1) to facilitate instrument and technology development and optimizations though cross-disciplinary collaborations, 2) to comprehensively characterize complex molecular machines including protein complexes (PCs) and modified proteins (MPs) and 3) to provide critical enabling technologies and a prototypical map of PCs and MPs for the GTL Program.
MAGGIE focuses on providing an integrated, multidisciplinary program and synchrotron facilities at the Advanced Light Source (ALS)
to achieve efficient key technologies and databases for the molecular-level understanding of the dynamic macromolecular machines that underlie all of microbial cell biology.
Together the six MAGGIE Component Subprojects have complementary and synergistic capabilities that unite and leverage the biophysical strengths at LBNL and the ALS with those of top university and research institutes. The Program management and data sharing is promoting synergistic investigator interactions to provide interdisciplinary expertise and scientific critical mass to meet the emerging experimental challenges. Although a new program, we have already had substantial progress as shown on our website: masspec.scripps.edu/MAGGIE/index.php and in our publications (see below).
MAGGIE is moving to meet the challenges posed by comprehensive characterizations of molecular machines by combining the advantages of specific microbial systems with those of advanced technologies. We highlight 7 initial accomplishments for the overall program: 1) the Pyrococcus system is providing PCs and MPs from native biomass, 2) the Sulfolobus system is providing genetics for tagged complexes, 3) the Halobacterium system is providing extensive system biology results and capabilities, 4) novel developments in high throughput mass spectrometry promise to make large impacts on the research community, 5) the SIBLYS beamline and SAXS facilities are now working as unique and productive world class facilities to visualize PCs and MPs in solution, 6) graph theory is providing characterizations of protein module interactions using cliques, and 7) GAGGLE software is providing a superb technology for communications across multiple databases.
Peroxisome proliferator activated receptor (PPAR) ã coactivator-1á (PGC-1á) is a potent transcriptional coactivator of oxidative metabolism and is induced in response to a variety of environmental cues. It regulates a broad array of target genes by coactivating a whole host of transcription factors. The estrogen-related receptor (ERR) family of nuclear receptors are key PGC-1á partners in the regulation of mitochondrial and tissue-specific oxidative metabolic pathways; these receptors also demonstrate strong physical and functional interactions with this coactivator. Here we perform comprehensive biochemical, biophysical, and structural analyses of the complex formed between PGC-1á and ERRã. PGC-1á activation domain (PGC-1á2–220) is intrinsically disordered with limited secondary and no defined tertiary structure. Complex formation with ERRã induces significant changes in the conformational mobility of both partners, highlighted by significant stabilization of the ligand binding domain (ERRãLBD) as determined by HDX (hydrogen/deuterium exchange) and an observed disorder-to-order transition in PGC-1á2–220. Small-angle X-ray scattering studies allow for modeling of the solution structure of the activation domain in the absence and presence of ERRãLBD, revealing a stable and compact binary complex. These data show that PGC-1á2–220 undergoes a large-scale conformational change when binding to the ERRãLBD, leading to substantial compaction of the activation domain. This change results in stable positioning of the N-terminal part of the activation domain of PGC-1á, favorable for assembly of an active transcriptional complex. These data also provide structural insight into the versatile coactivation profile of PGC-1á and can readily be extended to understand other transcriptional coregulators.
notice it's name.....ERRy...eeeeeeeeerie......
PGC-1á is unusual or even unique in its ability to respond to a wide variety of physiological signals, coactivate a broad range of transcription factors, and coordinate the regulation of oxidative metabolic gene programs in a tissue-specific manner
Disorder-to-order transition underlies the structural basis for the assembly of a transcriptionally active PGC-1á/ERRã complex
MAGIC provides robust GTL technologies and comprehensive characterizations to efficiently couple gene sequences and genomic analyses with protein interactions: thereby elucidating functional relationships and pathways within organisms and between ecosystem community members.
Processing raw DNA sequence data is an especially challenging task for relatively small laboratories and core facilities that produce as many as 5000 or more DNA sequences per week from multiple projects in widely differing species. To meet this challenge, we have developed the flexible, scalable, and automated sequence processing package described here.
MAGIC-SPP is a DNA sequence processing package consisting of an Oracle 9i relational database, a Perl pipeline, and user interfaces implemented either as JavaServer Pages (JSP) or as a Java graphical user interface (GUI). The database not only serves as a data repository, but also controls processing of trace files. MAGIC-SPP includes an administrative interface, a laboratory information management system, and interfaces for exploring sequences, monitoring quality control, and troubleshooting problems related to sequencing activities. In the sequence trimming algorithm it employs new features designed to improve performance with respect to concerns such as concatenated linkers, identification of the expected start position of a vector insert, and extending the useful length of trimmed sequences by bridging short regions of low quality when the following high quality segment is sufficiently long to justify doing so.
MAGIC-SPP has been designed to minimize human error, while simultaneously being robust, versatile, flexible and automated. It offers a unique combination of features that permit administration by a biologist with little or no informatics background. It is well suited to both individual research programs and core facilities.
Energy Department awards $92 million WASHINGTON, D.C. -- The Department of Energy today announced research awards totaling $92 million for six projects to better understand microbes and microbial communities. The microbial world and biotechnology promise solutions to major Energy Department challenges in: energy, including the production of ethanol and hydrogen; cleanup of pollution at former nuclear weapons production sites; and minimizing global warming by controlling the cycling of atmospheric carbon dioxide.
"Unique microbial biochemistries amassed over eons in every niche on the planet now offer a virtually limitless resource that can be applied to develop biology-based solutions to these challenges," said Dr. Raymond L. Orbach, Director of DOE's Office of Science.
The six projects involve 75 senior scientists at 21 institutions: four DOE national laboratories, 15 universities or research institutes, one federal laboratory and one private company.
The grants are part of the Office of Science's Genomics: GTL research program. "The GTL program's goal is to understand microbes so well that their diverse capabilities can be harnessed for DOE and other national energy and environmental needs," Orbach said.
DOE investments in genomics research over the past 20 years now help allow scientists rapidly decode and interpret the complete DNA sequence of any organism. Because genomics reveals the blueprint for life, it is the starting point to understand biological functions as well as a link between biological research and the development of biotechnology solutions. With genomics data as a starting point, the GTL program uses a "systems biology" approach to transform the way scientists conduct biological investigations and describe living systems.
Over the next five years, the six new research projects will: help scientists understand how microbial communities function in their natural habitats and respond to changes in their environments. This information is essential to be able to take advantage of the diverse capabilities of microbes and microbial communities;
develop new approaches to identify and characterize the proteins being produced within a complex microbial community;
develop new strategies to look inside microbes at the molecular machines they use to carry out their functions, to isolate those machines and to understand their functions. These capabilities are needed to be able to use or modify microbial molecular machines to address DOE energy and environmental mission needs; and
develop new computational tools to allow scientists to better find, organize and use the complex and rapidly growing types and amounts of information generated in the GTL program.
The six projects, their funding, lead institutions, lead investigators and collaborating institutions are:
Genome-Based Models to Optimize In Situ Bioremediation of Uranium and Harvesting Electrical Energy from Waste Organic Matter ($21.8 million over five years). University of Massachussetts, Amherst. Derek Lovley, Principal Investigator. Collaborating institutions: The Institute for Genomic Research, Rockville, Md.; University of Tennessee, Memphis, Tenn.; University of Indiana, Bloomington, Ind.; University of California at San Diego; Genomatica, San Diego, Calif.; Argonne National Laboratory, Argonne, Ill.
Proteogenomic Approaches for the Molecular Characterization of Natural Microbial Communities ($10.5 million over five years). University of California, Berkeley. Jillian Banfield, Principal Investigator. Collaborating institutions: Oak Ridge National Laboratory, Oak Ridge, Tenn.; Lawrence Livermore National Laboratory, Livermore, Calif.; U.S. Geological Survey, Boulder, Colo.
Dynamic Spatial Organization of Multi-Protein Complexes Controlling Microbial Polar Organization, Chromosome Replication, and Cytokinesis ($17.9 million over five years). Stanford University. Harley McAdams, Principal Investigator. Collaborating institutions: Case Western Reserve University, Cleveland, Ohio; Princeton University, Princeton, N.J.; University of California at San Diego; University of California at San Francisco; Lawrence Berkeley National Laboratory, Berkeley, CA.
High Throughput Identification and Structural Characterization of Multi-Protein Complexes During Stress Response in Desulfovibrio vulgaris. ($25.8 million over five years). Lawrence Berkeley National Laboratory. Mark Biggin, Principal Investigator. Collaborating institutions: University of California at Berkeley; University of Missouri, Columbia, Mo.; University of California at San Francisco.
Molecular Assemblies, Genes, and Genomics Integrated Efficiently ($12.9 million over five years). Lawrence Berkeley National Laboratory. John Tainer, Principal Investigator. Collaborating institutions: The Scripps Research Institute, La Jolla, Calif.; University of California at Berkeley; The Institute for Systems Biology, Seattle, Wash.; University of Georgia, Athens, Ga.; The Burnham Institute, La Jolla, Calif. An Integrated Knowledge Resource for the Shewanella Federation ($3 million over three years). Oak Ridge National Laboratory. Edward Uberbacher, Principal Investigator.
MAGGIE will provide robust GTL technologies and comprehensive characterizations to efficiently couple gene sequences and genomic analyses with protein interactions and thereby elucidate functional relationships and pathways. The operational principle guiding MAGGIE objectives can be succinctly stated: protein functional relationships involve interaction mosaics that self-assemble from independent protein pieces that are tuned by modifications and metabolites. MAGGIE builds strong synergies among the Components to address long term and immediate GTL objectives by combining the advantages of specific microbial systems with those of advanced technologies. The objective for the proposed 5-year MAGGIE Program is therefore to comprehensively characterize the Protein Complexes (PCs) and Modified Proteins (MPs) underlying microbial cell biology. A compelling overall goal is to help reduce the immense complexity of protein interactions to interpretable patterns though an interplay among experimental efforts of MAGGIE Program members in molecular biology, biochemistry, biophysics, mathematics, computational science, and informatics. MAGGIE will address immediate GTL missions by accomplishing three specific goals: 1) provide a comprehensive, hierarchical map of prototypical microbial PCs and MPs by combining native biomass and tagged protein characterizations from hyperthermophiles (temperature-trapping otherwise reversible protein interactions) with comprehensive systems biology characterizations of a non-thermophilic model organism, 2) develop and apply advanced mass spectroscopy and SAXS technologies for high throughput characterizations of PCs and MPs, and 3) create and test powerful computational descriptions for protein functional interactions. In concert, MAGGIE investigators will characterize microbial metabolic modularity and provide the informed basis to design functional islands suitable to transform microbes for specific DOE missions.
and unanticipated metals with implications for a complete understanding of cell biology. This research was funded by the Department of Energy (DE-FG02-07ER64326) as part of the MAGGIE project.
219 Access to Shape and Assembly of Macromolecular Complexes in Pathways Using Small Angle X-Ray Scattering
220 The ENIGMA Project: Mapping Protein Assemblies and Modifications by Cellular Deconstruction and Mass Spectrometry in the Hyperthermophiles Sulfolobus solfataricus, Pyrococcus furiosus, and Halobacterium NRC-1
221 High-Pressure Cryocooling of Protein Crystals: Applications to Understanding Pressure Effects on Proteins
222 Opportunities for Structural Biology and Imaging at NSLS-II
223 Robotic Chemical Protein Synthesis for the Experimental Validation of the Functional Annotation of Microbial Genomes
The new method, which combines liquid chromatography, high-throughput tandem mass spectometry and inductively coupled plasma mass spectometry, reveals all the metalloproteins in an organism—and what the team found has been very surprising, since metals now seem to be much more important for proteins than ever before suspected. Knowledge about how metals work in proteins has given insights into such things as how proteins repair DNA damaged by cancer-causing processes, how organisms get energy for growth and how some biofuels are produced. The importance of the work may therefore go in many diverse directions and promises to lead to important discoveries and applications in many biological fields, Adams said.
tash: Hi skizit, I have watched all your videos on youtube and cant thank you enough for all you have educated me on. I cry for you alot and a bit for me. I was wanting to send you photos of what is raining down everyday here in Australia in hope you can tell me
Dec 11, 2019 23:28:22 GMT -5
tash: not sure where to send them as hush mail and rocket mail bounced back
Dec 11, 2019 23:30:03 GMT -5