The Structure of a Transient Complex of a Nonribosomal Peptide Synthetase and a Cytochrome P450 Monooxygenase

Studying the interplay between nonribosomal peptide synthetases (NRPS), a major source of secondary metabolites, and crucial external modifying enzymes is a challenging task since the interactions involved are often transient in nature. By applying a range of synthetic inhibitor‐type compounds, a stabilized complex appropriate for structural analysis was generated for such a tailoring enzyme and an NRPS domain. The complex studied comprises an NRPS peptidyl carrier protein (PCP) domain bound to the Cytochrome P450 enzyme that is crucial for the provision of β‐hydroxylated amino acid precursors in the biosynthesis of the cyclic depsipeptide skyllamycin. The structure reveals that complex formation is governed by hydrophobic interactions, the presence of which can be controlled through minor alterations in PCP structure that enable selectivity amongst multiple highly similar PCP domains.     

Evaluation of a potential epigenetic biomarker by quantitative methyl-single nucleotide polymorphism analysis

Tumorigenesis is characterized by alterations of methylation profiles including loss and gain of 5-methylcytosine. Recently, we identified a single CpG, which seemed to be consistently hypomethylated in pilocytic astrocytomas but not in other gliomas. To evaluate its applicability as a biomarker, we examined its methylation status in a large panel of gliomas (n = 97). Methylation-dependent DNA sequence variation may be considered a kind of single nucleotide polymorphism (methylSNP). MethylSNPs can be easily converted into common SNPs of the C/T type by sodium bisulfite treatment of the DNA and afterwards subjected to conventional SNP typing. We adapted SnaPshot trade mark and Pyrosequencing trade mark to determine the methylation of our test CpG in a quantitative manner. The adapted methods, called SNaPmeth and PyroMeth, respectively, gave nearly identical results, however data obtained with PyroMeth showed less scattering. Furthermore, the integrated software for allele frequency determination from Pyrosequencing could be used directly for data analysis while SnaPmeth data had to be exported and processed manually. Although data did not confirm our previous result of a preferential hypomethylation of the tested CpG in pilocytic astrocytomas, we consider quantitative methylSNP analysis by SNaPmeth or PyroMeth a favorable alternative to existing high-throughput methylation assays. It combines single CpG analysis with accurate quantitation and is amenable to high throughput.     

Reconstruction of inclusions in an elastic body

We consider the reconstruction of elastic inclusions embedded inside of a planar region, bounded or unbounded, with isotropic inhomogeneous elastic parameters by measuring displacements and tractions at the boundary. We probe the medium with complex geometrical optics solutions having polynomial-type phase functions. Using these solutions we develop an algorithm to reconstruct the exact shape of a large class of inclusions including star-shaped domains and we implement numerically this algorithm for some examples.     

The X-Ray Transform for a Generic Family of Curves and Weights

We study the weighted integral transform on a compact manifold with boundary over a smooth family of curves Γ. We prove generic injectivity and a stability estimate under the condition that the conormal bundle of Γ covers T ^* M. Second author was partly supported by NSF Grant DMS-0400869; third author was partly supported by NSF and a Walker Family Endowed Professorship.     

Reconstructions for some coupled-physics inverse problems

This letter announces and summarizes results obtained in Bal and Uhlmann (2011) [1] and considers several natural extensions. The aforementioned paper proposes a procedure for reconstructing coefficients in a second-order, scalar, elliptic equation from knowledge of a sufficiently large number of its solutions. We present this derivation and extend it to show which parameters may or may not be reconstructed for several hybrid (also called coupled-physics) imaging modalities including photo-acoustic tomography, thermo-acoustic tomography, transient elastography, and magnetic resonance elastography. Stability estimates are also proposed.     

On Bounded-Degree Vertex Deletion parameterized by treewidth

Given an undirected graph $G$ and an integer $d\ge 0$, the NP-hard Bounded-Degree Vertex Deletion problem asks to delete as few vertices as possible from $G$ such that the resulting graph has maximum vertex degree $d$. Our main result is to prove that Bounded-Degree Vertex Deletion is W[1]-hard with respect to the parameter treewidth. As a side result, we obtain that the NP-hard Vector Dominating Set problem is W[1]-hard with respect to the parameter treewidth. On the positive side, we show that Bounded-Degree Vertex Deletion becomes fixed-parameter tractable when parameterized by the combined parameter treewidth and number of vertices to delete, and when parametrized by the feedback edge set number.     

Glycosylidene Carbenes. Part 13. Synthesis and thermolysis of representative 1-azi-glycoses

In the context of the hypothesis postlating a heterolytic cleavage of a C? N bond during thermolysis of alkoxydiazirines (Scheme 1), we report the preparation of the diazirines 4 , 5 , 7 , and 8 , the kinetic parameters for the thermolysis in MeOH of the diazirines 1 and 4–9 , and the products of their thermolysis in an aprotic environment. The diazirines 4 , 57 , and 8 (Scheme 2–5) were prepared from the known hemiacetals 10 , 19 , 34 (prepared from 31 in an improved way), and 42 according to an established method. The oximes 11 , 20 , 35 , and 43 were obtained from the corresponding hemiacetals as (E/Z)-mixtures; 43 was formed together with the cyclic hydroxylamine 44 . Oxidation of 11 , 35 , and 43 (N-chlorosuccinimide/1,8-diazabicyclo[5.4.0]undec-7-ene (NCS/DBU) or NaIO₄) gave good yields of the (Z)-hydroximolactones 12 , 36 , and 45 , while the oxime 20 led to a mixture of the (E)- and (Z)-hydroximolactones 21 and 22 , which adopt different conformations. Their configuration was assigned, inter alia, by a comparison with the enol ethers 28 and 29 , which were obtained, together with 30 , from the reaction of the diazirine 5 with benzaldehyde and PBu₃. Treatment of the hydroximolactone O-sulfonates 13 , 23 , 37 , and 46 with NH₃/MeOH afforded the diaziridines 15 , 25 , 38 , and 47 in good yields, while the (E)-sulfonate 24 decomposed readily. Oxidation of the diaziridines gave 4 , 5 , 7 , and 8 , respectively. Thermolysis of the diazirines 1 and 4–9 in MeOH yielded the anomeric methyl glycosides 50/51 , 16/17 , 26/27 , 52/53 , 39/40 , 48/49 , and 54/55 , respectively. A comparison of the kinetic data of the thermolysis at four different temperatures shows the importance of conformational and electronic factors and is compatible with the hypothesis of a heterolytic cleavage of a C? N bond. An early transition state is evidenced by the absence of torsional strain by an annulated 1,3-dioxane ring. Thermolysis of 1 in MeCN at 23° led mostly to the diasteroisomeric (Z,Z)-, (E,E)-, and (E,Z)-lactone azines 56 , 57 , and 58 (Scheme 6), which convert to 56 under mild conditions, and to 59 (3%). The benzyloxyglucal 59 was obtained in higher yields (18%), together with 44% of 56–58 , by thermolysis of solid 1 . Similarly, thermolysis at higher temperatures of 4 in toluene, THF, or dioxane and of 9 in CH₂Cl₂ or THF yielded the (Z,Z)-lactone azines 60 and 61 , respectively, the latter being accompanied by the dihydro-oxazole 62 .     

Recovering singularities of a potential from singularities of scattering data

In this paper we show that the leading singularities of certain potentials can be determined from the leading singularities of the backscattering (as well as other determined sets of scattering data). The potentials in question are conormal with respect to smooth surfaces of arbitrary dimension; the restrictions on their orders allow for unbounded potentials in all dimension greater than or equal to three.Partially supported by NSF Grant DMS-9101298 and an Alfred P. Sloan Research FellowshipPartially supported by NSF Grant DMS-9100178     

Polyelectrolyte Adsorption on NH3-Plasma-Treated Poly(tetrafluoroethylene-co-hexafluoropropylene)

A two-step procedure for a permanently hydrophilic surface modification of poly(tetrafluoroethylene-co-hexafluoropropylene) (FEP, fluorinated ethylene propylene) was studied. In the first step a cationic polymer surface was created by low-pressure ammonia plasma treatment introducing nitrogen-containing functional groups. Afterwards, the anionic poly(sodium 4-styrenesulfonate) was adsorbed onto the plasma-treated FEP surface. The adsorption was assumed to be controlled by ionic interactions. The modification effects and their long-term behavior were evaluated by means of water contact angle goniometry. Furthermore, electrokinetic measurements and X-ray photoelectron spectroscopy were used for surface characterization.     

Interactions between silica particles and poly(2-vinylpyridine) brushes in aqueous solutions of monovalent and multivalent salts

AFM colloidal probe technique, scratch tests, and spectroscopic ellipsometry are employed to study the conformation of a poly(2-vinyl pyridine) brush grafted to a planar surface and its interaction with microsized silica spheres in solutions containing monovalent (Cl^?) and multivalent counterions (SO₄ ^2? and PO₄ ^3?) at pH 2.5. During approach of the sphere, steric repulsion is observed with all salts at any concentration. The approach force-distance curves are fitted according to the Alexander-de Gennes model in order to calculate the equilibrium brush thickness L. These data are compared to the brush thickness determined by ellipsometry and AFM scratch tests. Different values are obtained but all of them decrease with increasing salt concentration. This effect is enhanced by counterions of higher valence because they have a stronger screening effect and ion correlation due to their greater charge per unit volume. With NaCl solutions, a reswelling of diluted P2VP coils is observed at Cl^? concentrations >1 M. When the sphere is retracted, weak adhesion forces occur at Cl^? concentrations >1.3?×?10^?2 M and at all concentrations of SO₄ ^2? and PO₄ ^3?.