DKxanthene biosynthesis--understanding the basis for diversity-oriented synthesis in myxobacterial secondary metabolism

The DKxanthenes are a family of yellow pigments which play a critical role in myxobacterial development. Thirteen unique structures from Myxococcus xanthus DK1622 differ in the length of their characteristic polyene functionality, as well as the extent of methyl branching. We aimed to understand the mechanistic basis for this "molecular promiscuity" by analyzing the gene cluster in DK1622, and comparing it to the DKxanthene biosynthetic locus in a second myxobacterium, Stigmatella aurantiaca DW4/3-1, which produces a more limited range of compounds. While the core biosynthetic machinery is highly conserved, M. xanthus contains a putative asparagine hydroxylase function which is not present in S. aurantiaca. This observation accounts, in part, for the significantly larger metabolite family in M. xanthus. Detailed analysis of the encoded hybrid polyketide synthase (PKS)-nonribosomal peptide synthetase (NRPS) assembly line provides direct evidence for the mechanism underlying the variable polyene length and the observed pattern of methyl functionalities.     

Oligo(p-phenylenevinylene)-peptide conjugates: synthesis and self-assembly in solution and at the solid-liquid interface

Two oligo(p-phenylenevinylene)-peptide hybrid amphiphiles have been synthesized using solid- and liquid-phase strategies. The amphiliphiles are composed of a pi-conjugated oligo(p-phenylenevinylene) trimer (OPV) which is coupled at either a glycinyl-alanyl-glycinyl-alanyl-glycine (GAGAG) silk-inspired beta-sheet or a glycinyl-alanyl-asparagyl-prolyl-asparagy-alanyl-alanyl-glycine (GANPNAAG) beta-turn forming oligopeptide sequence. The solid-phase strategy enables one to use longer peptides if strong acidic conditions are avoided, whereas the solution-phase coupling gives better yields. The study of the two-dimensional (2D) self-assembly of OPV-GAGAG by scanning tunneling microscopy (STM) at the submolecular level demonstrated the formation of bilayers in which the molecules are lying antiparallel in a beta-sheet conformation. In the case of OPV-GANPNAAG self-assembled monolayers could not be observed. Absorption, fluorescence, and circular dichroism studies showed that OPV-GAGAG and OPV-GANPNAAG are aggregated in a variety of organic solvents. In water cryogenic temperature transmission electron microscopy (cryo-TEM), atomic force microscopy (AFM), light scattering, and optical studies reveal that self-assembled nanofibers are formed in which the helical organization of the OPV segments is dictated by the peptide sequence.     

Micro–macro multilevel latent class models with multiple discrete individual-level variables

An existing micro–macro method for a single individual-level variable is extended to the multivariate situation by presenting two multilevel latent class models in which multiple discrete individual-level variables are used to explain a group-level outcome. As in the univariate case, the individual-level data are summarized at the group-level by constructing a discrete latent variable at the group level and this group-level latent variable is used as a predictor for the group-level outcome. In the first extension, that is referred to as the Direct model, the multiple individual-level variables are directly used as indicators for the group-level latent variable. In the second extension, referred to as the Indirect model, the multiple individual-level variables are used to construct an individual-level latent variable that is used as an indicator for the group-level latent variable. This implies that the individual-level variables are used indirectly at the group-level. The within- and between components of the (co)varn the individual-level variables are independent in the Direct model, but dependent in the Indirect model. Both models are discussed and illustrated with an empirical data example.     

Isothermal Cyclic Conversion of Methane into Methanol over Copper‐Exchanged Zeolite at Low Temperature

Direct partial oxidation of methane into methanol is a cornerstone of catalysis. The stepped conversion of methane into methanol currently involves activation at high temperature and reaction with methane at decreased temperature, which limits applicability of the technique. The first implementation of copper‐containing zeolites in the production of methanol directly from methane is reported, using molecular oxygen under isothermal conditions at 200 °C. Copper‐exchanged zeolite is activated with oxygen, reacts with methane, and is subsequently extracted with steam in a repeated cyclic process. Methanol yield increases with methane pressure, enabling reactivity with less reactive oxidized copper species. It is possible to produce methanol over catalysts that were inactive in prior state of the art systems. Characterization of the activated catalyst at low temperature revealed that the active sites are small clusters of copper, and not necessarily di‐ or tricopper sites, indicating that catalysts can be designed with greater flexibility than formerly proposed.     

Mechanistic Characterisation of Two Sesquiterpene Cyclases from the Plant Pathogenic Fungus Fusarium fujikuroi

Two sesquiterpene cyclases from Fusarium fujikuroi were expressed in Escherichia coli and purified. The first enzyme was inactive because of a critical mutation, but activity was restored by sequence correction through site‐directed mutagenesis. The mutated enzyme and two naturally functional homologues from other fusaria converted farnesyl diphosphate into guaia‐6,10(14)‐diene. The second enzyme produced eremophilene. The absolute configuration of guaia‐6,10(14)‐diene was elucidated by enantioselective synthesis, while that of eremophilene was evident from the sign of its optical rotation and is opposite to that in plants but the same as in Sorangium cellulosum. The mechanisms of both terpene cyclases were studied with various ¹³C‐ and ²H‐labelled FPP isotopomers.     

Reverse mathematics,well-quasi-orders,and Noetherian spaces

A quasi-order Q induces two natural quasi-orders on \({\mathcal{P}(Q)}\), but if Q is a well-quasi-order, then these quasi-orders need not necessarily be well-quasi-orders. Nevertheless, Goubault-Larrecq (Proceedings of the 22nd Annual IEEE Symposium 4 on Logic in Computer Science (LICS’07), pp. 453–462, 2007) showed that moving from a well-quasi-order Q to the quasi-orders on \({\mathcal{P}(Q)}\) preserves well-quasi-orderedness in a topological sense. Specifically, Goubault-Larrecq proved that the upper topologies of the induced quasi-orders on \({\mathcal{P}(Q)}\) are Noetherian, which means that they contain no infinite strictly descending sequences of closed sets. We analyze various theorems of the form “if Q is a well-quasi-order then a certain topology on (a subset of) \({\mathcal{P}(Q)}\) is Noetherian” in the style of reverse mathematics, proving that these theorems are equivalent to ACA₀ over RCA₀. To state these theorems in RCA₀ we introduce a new framework for dealing with second-countable topological spaces.     

Hydrogen chemisorption on supported platinum, gold, and platinum-gold-alloy catalysts

Alloyed catalysts receive considerable attention, because of their unique catalytic properties; they often show higher selectivity, activity, and stability compared to the pure metal particles. To provide insights in the origins of these features, we report the structure and the interaction of hydrogen with each of the metals in an intimately mixed platinum-gold catalyst and compare these characteristics to those in the single metal particles. X-Ray absorption spectroscopy (XAS) and electron microscopy analysis showed that the structure of the mixed particle differed from the single metal particles. The interaction of platinum with hydrogen is stronger than the H-Au interaction and the adsorption sites were different. EXAFS analysis showed that the structure of the platinum clusters changes with increasing hydrogen coverage, observed as a relaxation of the contracted Pt-Pt distance and an increase in the Pt-Pt coordination number. No such changes were observed for gold clusters. Well-mixed PtAu-alloy clusters, with a bulk Au-to-Pt ratio of two, supported on SiO(2), adsorb hydrogen on both platinum and gold atoms, which indicates that gold cannot be regarded as an inert metal. The heat of adsorption on the platinum ensembles does not decrease upon alloying; the weakening of the overall hydrogen adsorption strength when alloying platinum with gold is an ensemble-size effect.