The Molecular Mechanisms of Fringe Modification on Drosophila Notch: Examining the Structure and Function of Notch EGF Repeats
This conference paper is only provided as a long abstract in the Glycobiology journal.
59 BASIC BIOLOGICAL SCIENCES↗
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Results for “MODIFICATIONS”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Structure and cleavage activity of the tetrameric MspJI DNA modification-dependent restriction endonuclease
Abstract not provided
Horton, John R.↗
Rapid metabolic pathway assembly and modification using serine integrase site-specific recombination
Synthetic biology requires effective methods to assemble DNA parts into devices and to modify these devices once made. Here we demonstrate a convenient rapid procedure for DNA fragment assembly using site-specific recombination by ΦC31 integrase. Using six orthogonal attP/attB recombination site pairs with different overlap sequences, we can assemble up to five DNA fragments in a defined order and insert them into a plasmid vector in a single recombination reaction. ΦC31 integrase-mediated assembly is highly efficient, allowing production of large libraries suitable for combinatorial gene assembly strategies. The resultant assemblies contain arrays of DNA cassettes separated by recombination sites, which can be used to manipulate the assembly by further recombination. We illustrate the utility of these procedures to (i) assemble functional metabolic pathways containing three, four or five genes; (ii) optimize productivity of two model metabolic pathways by combinatorial assembly with randomization of gene order or ribosome binding site strength; and (iii) modify an assembled metabolic pathway by gene replacement or addition.
59 BASIC BIOLOGICAL SCIENCES↗
Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice
The type II CRISPR/Cas system from Streptococcus pyogenes and its simplified derivative, the Cas9/single guide RNA (sgRNA) system, have emerged as potent new tools for targeted gene knockout in bacteria, yeast, fruit fly, zebrafish and human cells. Here, we describe adaptations of these systems leading to successful expression of the Cas9/sgRNA system in two dicot plant species, Arabidopsis and tobacco, and two monocot crop species, rice and sorghum. Agrobacterium tumefaciens was used for delivery of genes encoding Cas9, sgRNA and a non-functional, mutant green fluorescence protein (GFP) to Arabidopsis and tobacco. The mutant GFP gene contained target sites in its 5' coding regions that were successfully cleaved by a CAS9/sgRNA complex that, along with error-prone DNA repair, resulted in creation of functional GFP genes. DNA sequencing confirmed Cas9/sgRNA-mediated mutagenesis at the target site. Rice protoplast cells transformed with Cas9/sgRNA constructs targeting the promoter region of the bacterial blight susceptibility genes, OsSWEET14 and OsSWEET11, were confirmed by DNA sequencing to contain mutated DNA sequences at the target sites. Successful demonstration of the Cas9/sgRNA system in model plant and crop species bodes well for its near-term use as a facile and powerful means of plant genetic engineering for scientific and agricultural applications.
59 BASIC BIOLOGICAL SCIENCES↗
Modification-dependent restriction endonuclease, MspJI, flips 5-methylcytosine out of the DNA helix
MspJI belongs to a family of restriction enzymes that cleave DNA containing 5-methylcytosine (5mC) or 5-hydroxymethylcytosine (5hmC). MspJI is specific for the sequence 5(h)mC-N-N-G or A and cleaves with some variability 9/13 nucleotides downstream. Earlier, we reported the crystal structure of MspJI without DNA and proposed how it might recognize this sequence and catalyze cleavage. Here we report its co-crystal structure with a 27-base pair oligonucleotide containing 5mC. This structure confirms that MspJI acts as a homotetramer and that the modified cytosine is flipped from the DNA helix into an SRA-like-binding pocket. We expected the structure to reveal two DNA molecules bound specifically to the tetramer and engaged with the enzyme's two DNA-cleavage sites. A coincidence of crystal packing precluded this organization, however. We found that each DNA molecule interacted with two adjacent tetramers, binding one specifically and the other non-specifically. The latter interaction, which prevented cleavage-site engagement, also involved base flipping and might represent the sequence-interrogation phase that precedes specific recognition. MspJI is unusual in that DNA molecules are recognized and cleaved by different subunits. Such interchange of function might explain how other complex multimeric restriction enzymes act.
Horton, J. R.↗
Denys-Drash syndrome associated WT1 glutamine 369 mutants have altered sequence-preferences and altered responses to epigenetic modifications
Mutations in human zinc-finger transcription factor WT1 result in abnormal development of the kidneys and genitalia and an array of pediatric problems including nephropathy, blastoma, gonadal dysgenesis and genital discordance. Several overlapping phenotypes are associated with WT1 mutations, including Wilms tumors, Denys-Drash syndrome (DDS), Frasier syndrome (FS) and WAGR syndrome (Wilms tumor, aniridia, genitourinary malformations, and mental retardation). These conditions vary in severity from individual to individual; they can be fatal in early childhood, or relatively benign into adulthood. DDS mutations cluster predominantly in zinc fingers (ZF) 2 and 3 at the C-terminus of WT1, which together with ZF4 determine the sequence-specificity of DNA binding. We examined three DDS associated mutations in ZF2 of human WT1 where the normal glutamine at position 369 is replaced by arginine (Q369R), lysine (Q369K) or histidine (Q369H). These mutations alter the sequence-specificity of ZF2, we find, changing its affinity for certain bases and certain epigenetic forms of cytosine. X-ray crystallography of the DNA binding domains of normal WT1, Q369R and Q369H in complex with preferred sequences revealed the molecular interactions responsible for these affinity changes. DDS is inherited in an autosomal dominant fashion, implying a gain of function by mutant WT1 proteins. This gain, we speculate, might derive from the ability of the mutant proteins to sequester WT1 into unproductive oligomers, or to erroneously bind to variant target sequences.
59 BASIC BIOLOGICAL SCIENCES↗
Structural basis for the synergy of 4'- and 2'-modifications on siRNA nuclease resistance, thermal stability and RNAi activity
Abstract not provided
Harp, Joel M.↗
Modification in Applying Appendix D of 40 CFR Part 61 to Heated Solid Radionuclide Materials With High Melting and Boiling Points
Appendix D of Title 40 Part 61 of the US Code of Federal Regulations (CFR) provides a procedure that US Department of Energy (US DOE) facility owners and operators can use to estimate radionuclide emissions to the atmosphere for dose calculations instead of measuring emissions for minor sources under the 40 CFR Part 61, Subpart H, National Emission Standards for Emissions of Radionuclides Other Than Radon From Department of Energy Facilities, regulation. The procedure assumes that any radioactive material heated above 100 °C is completely vaporized and emitted to the atmosphere. In 1991, the US DOE Oak Ridge Reservation (ORR) requested approval to use different release fractions (RFs) for uranium because of its high melting and boiling points. In response to the request, the US Environmental Protection Agency (US EPA) Region IV approved the use of modified RFs for elemental uranium provided no reaction had taken place to alter its chemical form. In 2015, the ORR requested approval to use different RFs for tungsten, again because of its high melting and boiling points. EPA Region IV approved the use of modified RFs for heated radioactive tungsten metal. In accordance with the two precedents set for heating uranium and radioactive tungsten metals, in 2016, the ORR requested approval to use modified RFs in a similar fashion for other radioactive solid metals and compounds with melting and boiling points above 500 °C that might be heated above 100 °C in future research projects and experiments. EPA Region IV again granted approval to use modified RFs for the list of compounds. This note discusses the proposed modified RFs and their development.
36 MATERIALS SCIENCE↗
An evolutionary algorithm for designing microbial communities via environmental modification
Despite a growing understanding of how environmental composition affects microbial communities, it remains difficult to apply this knowledge to the rational design of synthetic multispecies consortia. This is because natural microbial communities can harbour thousands of different organisms and environmental substrates, making up a vast combinatorial space that precludes exhaustive experimental testing and computational prediction. Here, we present a method based on the combination of machine learning and metabolic modelling that selects optimal environmental compositions to produce target community phenotypes. In this framework, dynamic flux balance analysis is used to model the growth of a community in candidate environments. A genetic algorithm is then used to evaluate the behaviour of the community relative to a target phenotype, and subsequently adjust the environment to allow the organisms to approach this target. We apply this iterative process to thousands of in silico communities of varying sizes, showing how it can rapidly identify environments that yield desired taxonomic compositions and patterns of metabolic exchange. Moreover, this combination of approaches produces testable predictions for the assembly of experimental microbial communities with specific properties and can facilitate rational environmental design processes for complex microbiomes.
59 BASIC BIOLOGICAL SCIENCES↗
Magnetic field induced modification of a first-order ferromagnetic transition in Eu 2 In
Here, we present a comprehensive study of the temperature-and magnetic-field-dependent magnetization, specific heat, and local crystal structure across the first-order ferromagnetic–paramagnetic transition in Eu 2 In. Anomalies in the magnetocaloric response are observed near 𝐻 ≈ 25 kOe, including changes in field scaling of magnetic entropy, local entropy exponent, and universal master curve, which suggest an apparent weakening of the first-order character of the transition. However, quantitative analysis of the magnetocaloric parameters together with modified Arrott plots demonstrates that the transition remains first order up to at least 70 kOe. Specific-heat measurements reveal a field-induced splitting of the sharp zero-field anomaly into a doublet, providing a natural explanation for the change in the magnetocaloric response. Magnetic-field-dependent extended x-ray absorption fine structure (EXAFS) measurements show no detectable field-induced changes in the local coordination environment of Eu. We therefore attribute these observations to a magnetic-field-induced two-step transition process in Eu 2 In.
Kumar, Ajay [Ames Laboratory (AMES), Ames, IA (Uni↗
Dynamic modification of the fragmentation of autoionizing states of O{sub 2}{sup +}
The dynamic process of fragmentation of excited states of the molecular oxygen cation is investigated in a two-part study. First, using monochromatic 41.6 eV radiation and cold-target recoil-ion momentum spectroscopy detection of O{sup +} + O{sup +} ion pairs and associated electrons, we establish that this channel is populated only by an indirect process enabled by autoionization of excited oxygen atoms and identify the final active potential curves. Second, we probe the dynamics of this process using an attosecond pulse train of 35-42 eV EUV followed by an intense IR laser pulse. The results are compared with a model calculation.
74 ATOMIC AND MOLECULAR PHYSICS↗
Probing autoionizing states of molecular oxygen with XUV transient absorption: Electronic-symmetry-dependent line shapes and laser-induced modifications
In this paper, we used extreme ultraviolet (XUV) transient absorption spectroscopy to study the autoionizing Rydberg states of oxygen in an electronically- and vibrationally-resolved fashion. XUV pulse initiates molecular polarization and near-infrared pulse perturbs its evolution. Transient absorption spectra show positive optical-density (OD) change in the case of $ns{{\sigma}}_{g}$ and $nd{{\pi}}_{g}$ autoionizing states of oxygen and negative OD change for $nd{{\sigma}}_{g}$ states. Multiconfiguration time-dependent Hartree-Fock (MCTDHF) calculations are used to simulate the transient absorption and the resulting spectra and temporal evolution agree with experimental observations. We model the effect of near-infrared perturbation on molecular polarization and find that the laser-induced phase-shift model agrees with the experimental and MCTDHF results, while the laser-induced attenuation model does not. Finally, we relate the electronic-state-symmetry-dependent sign of the OD change to the Fano parameters of the static absorption line shapes.
74 ATOMIC AND MOLECULAR PHYSICS↗
Schottky signal modification as a diagnostic tool for coherent electron cooling
Not Available
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Nonvolatile Ionic Modification of the Dzyaloshinskii-Moriya Interaction
The possibility of tuning the Dzyaloshinskii-Moriya interaction (DMI) by electric (E)-field gating in ultrathin magnetic materials has opened up new perspectives in terms of controlling the stabilization of chiral spin structures. The most recent efforts have used voltage-induced charge redistribution at the interface between a metal and an oxide to modulate the DMI. This approach is attractive for active devices but tends to be volatile, making it energy-demanding, and it is limited by Coulomb screening in the metal. Here we demonstrate nonvolatile E-field manipulation of the DMI by ionic-liquid gating of Pt/Co/Hf O 2 ultrathin films. The E-field effect on the DMI scales with the E-field exposure time, and we propose that it is linked to the migration of oxygen species from the Hf O 2 layer into the Co and Pt layers and subsequent anchoring. Here, this effect permanently changes the properties of the material, showing that E fields can be used not only for local gating in devices but also as a highly scalable materials design tool for postgrowth tuning of the DMI.
Domain walls↗
Oxygen vacancy induced electronic structure modification of KTaO 3
The observation of a metallic interface between band insulators LaAlO 3 and SrTiO 3 has led to massive efforts to understand the origin of the phenomenon as well as to search for other systems hosting such two-dimensional electron gases (2-DEGs). However, the understanding of the origin of the 2-DEG is very often hindered as several possible mechanisms such as polar catastrophe, cationic intermixing, and oxygen vacancy (OV) can be operative simultaneously. The presence of a heavy element makes the KTaO 3 (KTO) based 2-DEG a potential platform to investigate spin-orbit coupling driven novel electronic and magnetic phenomena. In this work, we investigate the sole effect of OV in KTO, which makes KTO metallic. O K-edge x-ray absorption spectroscopy measurements find that OV dopes electrons in Ta t * 2g antibonding states. Photoluminescence measurements reveal the existence of a highly localized deep midgap state in oxygen-deficient KTO. Our detailed ab initio calculations demonstrate that such deep midgap state arises due to the linear clustering of OVs around Ta. Finally, our present work emphasizes that we must pay attention to the possible presence of OVs in interpreting emergent behavior of KTO-based heterostructures.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗