Carnegie Institution of Washington | Date: 2016-02-18
Intramolecular biosensors are disclosed, including PBP-based biosensors, comprising a ligand binding domain fused to donor and fluorescent moieties that permit detection and measurement of Fluorescence Resonance Energy Transfer upon binding ligand. At least one of the donor and fluorescent moieties may be internally fused to the biosensor such that both ends of the internally fused fluorophore are fixed. In addition, methods of improving the sensitivity of terminally fused biosensors are provided. The biosensors of the invention are useful for the detection and quantification of ligands in vivo and in culture.
Carnegie Institution of Washington and University of Massachusetts Amherst | Date: 2016-01-22
A process is provided of introducing an RNA into a living cell to inhibit gene expression of a target gene in that cell. The process may be practiced ex vivo or in vivo. The RNA has a region with double-stranded structure. Inhibition is sequence-specific in that the nucleotide sequences of the duplex region of the RNA and of a portion of the target gene are identical. The present invention is distinguished from prior art interference in gene expression by antisense or triple-strand methods.
Boss A.P.,Carnegie Institution of Washington
Astrophysical Journal | Year: 2011
Doppler surveys have shown that more massive stars have significantly higher frequencies of giant planets inside ∼3AU than lower mass stars, consistent with giant planet formation by core accretion. Direct imaging searches have begun to discover significant numbers of giant planet candidates around stars with masses of ∼1 M ⊙ to ∼2 M ⊙ at orbital distances of ∼20AU to ∼120AU. Given the inability of core accretion to form giant planets at such large distances, gravitational instabilities of the gas disk leading to clump formation have been suggested as the more likely formation mechanism. Here, we present five new models of the evolution of disks with inner radii of 20AU and outer radii of 60AU, for central protostars with masses of 0.1, 0.5, 1.0, 1.5, and 2.0 M ⊙, in order to assess the likelihood of planet formation on wide orbits around stars with varied masses. The disk masses range from 0.028 M ⊙ to 0.21 M ⊙, with initial Toomre Q stability values ranging from 1.1 in the inner disks to ∼1.6 in the outer disks. These five models show that disk instability is capable of forming clumps on timescales of ∼103yr that, if they survive for longer times, could form giant planets initially on orbits with semimajor axes of 30AU to ∼70AU and eccentricities of ∼0 to ∼0.35, with initial masses of ∼1 M Jup to ∼5 M Jup, around solar-type stars, with more protoplanets forming as the mass of the protostar (and protoplanetary disk) is increased. In particular, disk instability appears to be a likely formation mechanism for the HR 8799 gas giant planetary system. © 2011. The American Astronomical Society. All rights reserved.
Boss A.P.,Carnegie Institution of Washington
Annual Review of Earth and Planetary Sciences | Year: 2012
Isotopic abundances of short-lived radioisotopes such as 26Al appear to provide precise chronometers of events in the early Solar System, assuming that they were initially homogeneously distributed. However, both 60Fe and 26Al were likely formed in a supernova and then injected into the solar nebula in a highly heterogeneous manner. Conversely, the abundances in primitive meteorites of the three stable oxygen isotopes exhibit mass-independent fractionations that somehow survived homogenization in the solar nebula. Both the presence of refractory particles in Comet 81PWild 2 and the anomalously high crystallinity observed in protoplanetary disks may require large-scale outward radial transport from the hotter inner disk regions, even as disk gas accretes onto the central protostar. We examine here theoretical efforts to solve these seemingly disparate cosmochemical puzzles and conclude that the mixing and transport produced by a phase of marginal gravitational instability appears to meet all of these constraints. © 2012 by Annual Reviews. All rights reserved.
Elkins-Tanton L.T.,Carnegie Institution of Washington
Annual Review of Earth and Planetary Sciences | Year: 2012
Theory and observations point to the occurrence of magma ponds or oceans in the early evolution of terrestrial planets and in many early-accreting planetesimals. The apparent ubiquity of melting during giant accretionary impacts suggests that silicate and metallic material may be processed through multiple magma oceans before reaching solidity in a planet. The processes of magma ocean formation and solidification, therefore, strongly influence the earliest compositional differentiation and volatile content of the terrestrial planets, and they form the starting point for cooling to clement, habitable conditions and for the onset of thermally driven mantle convection and plate tectonics. This review focuses on evidence for magma oceans on planetesimals and planets and on research concerning the processes of compositional differentiation in the silicate magma ocean, distribution and degassing of volatiles, and cooling. © 2012 by Annual Reviews. All rights reserved.
Agency: NSF | Branch: Standard Grant | Program: | Phase: MAJOR RESEARCH INSTRUMENTATION | Award Amount: 334.27K | Year: 2015
This award provides funding for the acquisition of a shared-use, state-of-the-art combined Raman and optical spectroscopy system at the Advanced Photon Source (APS), Argonne National Laboratory (Chicago, IL). This new system will enable study of materials with unique physical and chemical properties, as well as novel technological materials, with advanced state-of-the-art techniques combined in a single instrument. This work has important implications to societal quality-of-life issues such as carbon sequestration, environmental remediation, properties of nanomaterials and earthquake generation. This work will also advance discovery and understanding by students as participants in the proposed research.
The availability of a system capable of concomitant in-situ X-ray diffraction and spectroscopy studies of materials at ambient and extreme pressure and temperature conditions (static and dynamic), including high spatial resolution studies of advanced and newly synthesized materials, will greatly enhance research capabilities of APS users. This instrumentation will enhance our understanding of planetary interiors by enabling studies of synthetic samples at the relevant conditions and of naturally-occurring minerals, rocks and their inclusions. Similarly, study of materials under conditions of high pressures and variable temperatures (low to very high) will be revealing for understanding of physical and chemical phenomena in condensed matter under extreme conditions including phase transitions and chemical reactions which provide a basis for synthesis of new materials under extreme conditions. Study of materials with reduced dimensionality, such as nanomaterials, will advance our understanding of their electronic and vibrational properties, crucial information for designing new advanced technology devices.
Agency: NSF | Branch: Standard Grant | Program: | Phase: BIO Innovation Activities | Award Amount: 299.85K | Year: 2016
Phenotyping plants under real world conditions is highly challenging. The Frommer lab (Stanford) developed a suite of genetically encoded biosensors that report subcellular levels of ions or metabolites (e.g. ions, sugars) or that report the activity of particular transporters with high temporal resolution. Typically, plants expressing these sensors are analyzed using fluorescence microscopy. This project will explore whether ion levels can be quantified (here the signaling intermediate calcium as a proof of concept) in specific regions of plant leaves using a remote imaging system. The Kramer lab at MSU developed a growth chamber that can mimic and replay field conditions and simultaneously phenotype photosynthetic parameters using a fluorescence imaging system. This collaboration brings together these two innovative platforms: the dynamic environmental imaging system (DEPI), and genetically encoded ultrasensitive fluorescent biosensor technology. The project aims to develop a novel system that can monitor genetically encoded sensors in intact plants with unprecedented depth and the parallel option for high throughput phenotyping of photosynthesis. The project will lay the groundwork for establishing systems and tools as community resources with the potential to transform photosynthesis research programs around the world. This high-risk project will lay the basis for phenotyping genetic variants in Arabidopsis as well as crops and expand the usefulness of genetically encoded biosensors to large scale screening. In addition, this project will train a postdoctoral scientist with experience in physical chemistry in phenotyping. The project will also train high school students and undergraduate students, and where possible minority students will be engaged in this endeavor.
Such an imaging system would present a completely novel tool for phenotyping molecular events in intact plants and thus present a new tool for screening genetic variants and to discover new biology at the whole plant level. The project will demonstrate the potential of this technology by monitoring novel ultrasensitive calcium sensors to test long-standing hypotheses regarding the role of calcium in signaling processes and the response patterns in leaves in fluctuating environmental conditions and specific signaling processes. One of the challenges is the sensitivity of the combined plant-imaging system. The Frommer lab developed novel ultrasensitive calcium sensors that will be used here and that may enable us to observe calcium dynamics over the whole growth cycle in populations of 100s of plants simultaneously. This approach, if successful, could be expanded to other fluorescent biosensors and implemented for crop plant screening. At the same time, such a system may uncover new biology in the areas of plant cell signaling and chloroplast ion dynamics.
Agency: NSF | Branch: Continuing grant | Program: | Phase: PLANT GENOME RESEARCH PROJECT | Award Amount: 3.13M | Year: 2014
PI: Matthew M. S. Evans (Carnegie Institution of Washington)
CoPIs: Donald L. Auger (South Dakota State University), John E. Fowler (Oregon State University), R. Keith Slotkin (The Ohio State University) and Erik W. Volbrecht (Iowa State University)
Senior Collaborators: Allison Phillips (Wisconsin Lutheran College) and Jennifer Eustaquio (Stanford University)
This project comprises foundational research on epigenetics and gene expression, and thus may have broad implications for the manifestation of important plant traits, particularly in crops with large numbers of transposons in their genomes. More specifically, gametophytes are central to plant reproduction; thus this project is directly relevant to several agricultural objectives (e.g., controlling pollen fertility, limiting pollen-mediated transgene flow, inducing apomixis), particularly given the projects focus on a crucial crop plant, maize. Additionally, the project will provide a data framework for other researchers to determine how gametophytes function and how they can be manipulated to generate improved crop plants. This project will train a number of undergraduate, graduate and post-graduate scientists in an interdisciplinary fashion through frequent exchanges between the partnering laboratories. Undergraduates will gain experience in modern laboratory techniques as well as computational analysis of large-scale data sets. Undergraduate students will simultaneously be trained as researchers and educators through Stanford Universitys Science in Service Program. Undergraduates learn to be Science Mentors for high school students and develop laboratory curricula that are then performed by local high school programs under the supervision of the undergraduate mentors. As part of the project, students from the high school programs also participate in the project, getting exposure to genetics and image analysis.
Within the floral tissues of flowering plants, multicellular haploid female and male gametophytes produce the gametes that undergo fertilization to produce seeds. Although gametophytes are small and undergo few cell divisions, they are crucial for producing the next generation, and execute diverse biological processes. Plant seed formation and reproduction, and thus global agriculture, are dependent on gametophyte function. In spite of their critical role in plant reproduction, gametophyte function and development has largely been overlooked due to their small size and imbedded location within the parental tissue. The maize genome, like many crop plant genomes, harbors a large number of mobile DNA elements, called transposons, and control of these elements, often through regulation of epigenetic states, is critical for maintenance of gene function and genome structure. Gametophytes help set epigenetic states in the next generation, however little is known, especially in the female gametophyte, about how transposon expression is regulated, and how that control impacts the concurrent expression of protein-coding genes. This project will use tissue micro-dissection techniques and whole genome analysis to understand the mechanisms that underlie developmental regulation of epigenetic states and cellular functions in the gametophytes of both sexes in maize. This project will screen for new mutants and genes that function in gametophyte development; perform genome-wide analysis of expression of genes, transposons, and different classes of RNAs with cellular detail; generate visual reporters for transposon activity; and characterize transposon expression in developing gametophytes. This project will determine the spatial and temporal expression pattern for genes and transposons in developing gametophytes, as well as define how they function to program gametophyte development. The effect of relevant mutants on transposon expression is expected to increase understanding of the interaction between basic gametophyte development and control of transposon activity in the important crop plant, maize. The sequence gene expression data generated from this project will be widely accessible through the project website (www.maizegametophyte.org) and the National Center for Biotechnology Information Gene Expression Omnibus (www.ncbi.nlm.nih.gov/geo), and the Maize Genetics and Genomics Database (maizegdb.org). Seed stocks will be deposited with the Maize Genetics Cooperation Stock Center.
Agency: NSF | Branch: Continuing grant | Program: | Phase: PETROLOGY AND GEOCHEMISTRY | Award Amount: 346.15K | Year: 2015
The Earths core-mantle boundary (CMB) and inner core boundary (ICB) are the most important deep chemical boundaries that define the dynamics of the interior and control the generation of Earth magnetic field. The boundaries reset the element redistribution through metal-silicate differentiation and inner crystallization. The goal of this study is to understand the behavior of element partitioning at these boundaries using newly developed high-pressure and temperature techniques and state-of-the-art analytical tools that allow simulating the conditions of the boundaries and analyzing the chemical compositions of the coexisting phases in the recovered samples. The proposed work will significantly advance our knowledge of Earths deep processes and experimental techniques to investigate element redistribution at deep chemical boundaries.
The focus of the proposed research is on the silicon (Si) and oxygen (O) partitioning between mantle and core at high pressure and temperature, applicable to core-mantle differentiation and the incorporation of Si and O in the core. Specific projects include (1) determining the Si and O partitioning between liquid mantle silicate and molten core iron alloy up to CMB pressure, and (2) determining the effect of pressure on the Si, O, and S partitioning coefficients between solid and liquid iron alloy and examining their partitioning behavior at ICB conditions. The research will produce high-quality data under extreme conditions that are necessary for understanding the chemistry of Earths core and providing insight into the Earth accretion environment and the evolution of Earths interior. It will open new research opportunities at the interface of petrology, mineral physics, geochemistry, and geophysics.
Agency: NSF | Branch: Continuing grant | Program: | Phase: STELLAR ASTRONOMY & ASTROPHYSC | Award Amount: 68.85K | Year: 2016
This award funds research on an extensive dataset that will provide firm tests of the types of stars that end their life as Type Ia supernovae. The researchers will recalibrate data to higher precision and gain a better understanding of systematic errors and uncertainties. Results from this work will help provide tests of general relativity and improve our understanding of dark energy. Graduate students and postdoctoral researchers will be trained and mentored in research. Public outreach programs incorporating research results will be carried out at the home institutions of the PIs. The final reduced data will be made available to the astronomical community.
This project will be accomplished by completing data reduction of optical and near-infrared wavelength images to produce final light curves of supernova explosions. They will also complete data reduction of near-infrared spectra of supernova explosions with an emphasis on improved removal of telluric absorption. They will produce new spectral templates for the community, analyze host galaxy properties, and produce Hubble diagrams. Finally, they will compare theory with observation and look for evidence of interaction with non-degenerate companions or circumstellar material. They will also probe the explosion physics as a function of luminosity and light curve decline rate. The dataset will also be used to improve the precision of using supernova Type Ia data as distance indicators for constraining the nature of dark energy.