Quantitative and time-course analysis of microbial degradation of 1H,1H,2H,2H,8H,8H–perfluorododecanol in activated sludge

A methylene group in the fluorinated carbon backbone of 1H,1H,2H,2H,8H,8H–perfluorododecanol (degradable telomer fluoroalcohol, DTFA) renders the molecule cleavable by microbial degradation into two fluorinated carboxylic acids. Several biodegradation products of DTFA are known, but their rates of conversion and fates in the environment have not been determined. We used liquid chromatography coupled with tandem mass spectrometry (LC/MS/MS) to quantitatively investigate DTFA biodegradation by the microbial community in activated sludge in polyethylene terephthalate (PET) flasks, which we also determined here showed least adsorption of DTFA. A reduction in DTFA concentration in the medium was accompanied by rapid increases in the concentrations of 2H,2H,8H,8H–perfluorododecanoic acid (2H,2H,8H,8H–PFDoA), 2H,8H,8H-2-perfluorododecenoic acid (2H,8H,8H-2-PFUDoA), and 2H,2H,8H-7-perfluorododecenoic acid and 2H,2H,8H-8-perfluorododecenoic acid (2H,2H,8H-7-PFUDoA/2H,2H,8H-8-PFUDoA), which were in turn followed by an increase in 6H,6H–perfluorodecanoic acid (6H,6H–PFDeA) concentration, and decreases in 2H,2H,8H,8H–PFDoA, 2H,8H,8H-2-PFUDoA, and 2H,2H,8H-7-PFUDoA/2H,2H,8H-8-PFUDoA concentrations. Accumulation of perfluorobutanoic acid (PFBA), a presumed end product of DTFA degradation, was also detected. Our quantitative and time-course study of the concentrations of these compounds reveals main routes of DTFA biodegradation, and the presence of new biodegradation pathways.

     

Determination of Hα,Hβ and Hβ,C′ coupling constants in13C-labeled proteins

Summary A sensitive method to assign H protons stereospecifically as well as to determine rotamer populations about ₁, in two 3D experiments is presented. The SOFT-HCCH-COSY experiment allowed us to measure the³J(H,C) couplings, using constant time evolution of C in t₂ and C_aliphatic-selective decoupling during t₃. The SOFT-HCCH-E.COSY experiment allowed us to measure the³J(H,H) couplings, using constant time evolution of C in t₂, a small flip angle¹H excitation pulse in the second mixing time, and double-band-selective decoupling (aliphatic and carbonyl carbons) during t₃. The method was applied to ribonuclease T₁.     

The vertebrate linker histones H10, H5, and H1M are descendants of invertebrate “orphon” histone H1 genes

We investigated the evolutionary history of the divergent vertebrate linker histones H1⁰, H5, and HIM. We observed that the sequence of the central conserved domain of these vertebrate proteins shares characteristic features with histone H1 proteins of plants and invertebrate animals which otherwise never appear in any vertebrate histone H1 protein. A quantitative analysis of 58 linker histone sequences also reveals that these proteins are more similar to invertebrate and plant histone H1 than to histone H1 of vertebrates. A phylogenetic tree deduced from an alignment of the central domain of all known linker histones places H1⁰, H5, and HIM in close vicinity to invertebrate sperm histone H1 proteins and to invertebrate histone H1 proteins encoded by polyadenylated mRNAs. We therefore conclude that the ancestors of the vertebrate linker histones H1⁰, H5, and HIM diverged from the main group of histone H1 proteins before the vertebrate type of histone H1 was established in evolution. We discuss this observation in the general context of linker histone evolution. Correspondence to: B. and E. Schulze     

Origin, functions and chemistry of H‐2 regulated odorants

Genes located within the major histocompatibility complex (MHC) of mice are responsible for individual differences in body odor (odortypes). In this review we suggest that the MHC genes themselves are responsible for odor differences among MHC‐congenic mice. Recent studies indicating that volatile carboxylic acids are at least in part responsible for the individual odors and what this finding implies about the pathway from gene to odorant are also reviewed. We suggest that odorants or their precursors are bound directly by MHC products and are released into serum and concentrated in urine. Finally, possible functions of MHC odortypes in mice are enumerated and important future research questions are raised. This revised version was published online in July 2006 with corrections to the Cover Date.     

The H50Q Mutation Enhances α-Synuclein Aggregation,Secretion, and Toxicity

Over the last two decades, the identification of missense mutations in the α-synuclein (α-Syn) gene SNCA in families with inherited Parkinson disease (PD) has reinforced the central role of α-Syn in PD pathogenesis. Recently, a new missense mutation (H50Q) in α-Syn was described in patients with a familial form of PD and dementia. Here we investigated the effects of this novel mutation on the biophysical properties of α-Syn and the consequences for its cellular function. We found that the H50Q mutation affected neither the structure of free or membrane-bound α-Syn monomer, its interaction with metals, nor its capacity to be phosphorylated in vitro. However, compared with the wild-type (WT) protein, the H50Q mutation accelerated α-Syn fibrillization in vitro. In cell-based models, H50Q mutation did not affect α-Syn subcellular localization or its ability to be phosphorylated by PLK2 and GRK6. Interestingly, H50Q increased α-Syn secretion from SHSY5Y cells into culture medium and induced more mitochondrial fragmentation in hippocampal neurons. Although the transient overexpression of WT or H50Q did not induce toxicity, both species induced significant cell death when added to the culture medium of hippocampal neurons. Strikingly, H50Q exhibited more toxicity, suggesting that the H50Q-related enhancement of α-Syn aggregation and secretion may play a role in the extracellular toxicity of this mutant. Together, our results provide novel insight into the mechanism by which this newly described PD-associated mutation may contribute to the pathogenesis of PD and related disorders.     

1H NMR Assignments and Conformational Analysis of the Oligoribonucleotides CA,CAU, CAUG,ACAUG, and UCAUG: Observation of Pyrimidine H5-H1′ Long-Range Scalar Couplings

Abstract

Conformational analysis and ¹H NMR spectral assignments have been carried out using COSY and RELAY methods for a series of related oligoribonucleotides including two pen- tamers with 5′-dangling bases. Intraresidue long-range five bond scalar coupling was observed between pyrimidine H5 and H1′ protons in the COSY-45 spectra and this feature was useful for both assignment purposes and conformational analysis. The ribose ring conformations were predominantly C3′-endo with the C2′-endo population increasing at the 3′-terminus. The 5′-dangling bases were not stacked efficiently, exhibiting lower % C3′-endo values than their 3′-nearest neighbors. Backbone torsion angle populations, β′, γ⁺, ε′, were determined using ′H-′H, ′H-³¹P, and ¹³C-³¹P coupling constants. From β′ and γ⁺ populations the U3-G4 step in CAUG was found to be less efficiently stacked than the C1-A2 and A2-U3 steps. This observation in solution is consistent with the fiber diffraction A-RNA model (S. Arnott, D.W.L. Hukins, S.D. Dover, W. Fuller and A.R. Hodgson, J. Mol. Biol. 81, 107-122, 1973) which also predicts poor stacking in a U-G dinucleotide. The ε′ populations were >65% for all C3′- O3′ bonds and consistent with a right-handed A-RNA helix.     

B30H8, B39H9 2−, B42H10, B48H10, and B72H12: polycyclic aromatic snub hydroboron clusters analogous to polycyclic aromatic hydrocarbons

Calculations performed at the ab initio level using the recently reported planar concentric π-aromatic B₁₈H₆ ²⁺(1) [Chen Q et al. (2011) Phys Chem Chem Phys 13:20620] as a building block suggest the possible existence of a new class of B_3n H _m polycyclic aromatic hydroboron (PAHB) clusters—B₃₀H₈(2), B₃₉H₉ ^2?(3), B₄₂H₁₀(4/5), B₄₈H₁₀(6), and B₇₂H₁₂(7)—which appear to be the inorganic analogs of the corresponding C _n H _m polycyclic aromatic hydrocarbon (PAHC) molecules naphthalene C₁₀H₈, phenalenyl anion C₁₃H₉ ^?, phenanthrene/anthracene C₁₄H₁₀, pyrene C₁₆H₁₀, and coronene C₂₄H₁₂, respectively, in a universal atomic ratio of B:C?=?3:1. Detailed canonical molecular orbital (CMO), adaptive natural density partitioning (AdNDP), and electron localization function (ELF) analyses indicate that, as they are hydrogenated fragments of a boron snub sheet [Zope RR, Baruah T (2010) Chem Phys Lett 501:193], these PAHB clusters are aromatic in nature, and exhibit the formation of islands of both σ- and π-aromaticity. The predicted ionization potentials of PAHB neutrals and electron detachment energies of small PAHB monoanions should permit them to be characterized experimentally in the future. The results obtained in this work expand the domain of planar boron-based clusters to a region well beyond B₂₀, and experimental syntheses of these snub B_3n H _m clusters through partial hydrogenation of the corresponding bare B_3n may open up a new area of boron chemistry parallel to that of PAHCs in carbon chemistry.

Growth, Sporulation, δ-Endotoxins Synthesis, and Toxicity During Culture of Bacillus thuringiensis H14

Growth, sporulation, synthesis of δ-endotoxins, and toxicity against the larvae of Aedes aegypti and Culex pipiens were studied during fermentation of Bacillus thuringiensis H14 in a 20-L fermentor. Measurements of optical density and dielectric permittivity for biomass determination suggest a highly promising technique for on-line evaluation of sporulation. The synthesis of 65-, 25- and 130-kDa proteins started at 16, 18, and 23 h, respectively. These proteins were enriched in different ways until the end of culture (48 h). Toxicity in the course of sporulation was significantly different for the larvae of both mosquito species. Maximal activity against Ae. aegypti was obtained at the end of culture, whereas for Cx. pipiens, the sample at 38 h was the most active.     

1H, 13C, and 15N resonance assignments of human ζ-COP

The ζ-COP is one subunit of the COP I coatomer, which mediates the protein trafficking from the cis-Golgi complex to the endoplasmic reticulum and also functions in the intra-Golgi trafficking. The NMR assignments of the ζ-COP are essential for its solution structure determination.     

How relevant are S=O and P=O Double Bonds for the Description of the Acid Molecules H2SO3, H2SO4, and H3PO4, respectively?

The acid molecules H₂SO₃, H₂SO₄, and H₃PO₄ are usually drawn using "Lewis structures" which exhibit the octet extension by 3d-orbitals on sulfur and phosphorus, respectively. Thus, S=O and P=O double bonds are assumed to be formed. The natural d-orbital occupancies on S and P, however, were calculated to be as low as 0.1 e, and therefore, an octet extension can hardly be expected. After the natural bond orbitals (NBO) search procedure was forced to attempt to form different Lewis structures of bonds and lone pairs, we defined the optimal Lewis structure, if a dominant structure exists at all, by the maximum electronic charge in Lewis orbitals. Indeed, sulfur obeys the octet rule in the optimal zwitterionic Lewis structures and does not form S=O double bonds. No dominant resonance structure could be found for H₃PO₄ where polarized PO ?-bond and zwitterionic PO bond structures exhibit similar weights.     

New synonymies and combinations in Argyrostrotis Hübner (Lepidoptera, Erebidae, Erebinae, Poaphilini)

After examining the type specimens of species in the eastern North American genus Argyrostrotis the number of known species in the genus is reduced from 10 to six through synonymy. A key to species is included along with illustrations of the adults and genitalia of each species. Three Neotropical species currently included in Argyrostrotis (Argyrostrotis eurysaces Schaus, 1914; Argyrostrotis quadrata Dognin, 1910; and Celiptera surrufula Dyar, 1913) are transferred to other genera as Argyrosticta eurysaces (Schaus, 1914), comb. n. [Noctuidae: Bagisarinae], Heterochroma quadrata (Dognin, 1910), comb. n. [Noctuidae: Amphipyrinae], and Ptichodis surrufula (Dyar, 1913), comb. n. [Erebidae: Erebinae: Euclidiini].     

Comparison of the directionality of the halogen,hydrogen, and lithium bonds between HOOOH and XF (X = Cl,Br, H,Li)

Detailed electrostatic potential (ESP) analyses were performed to compare the directionality of halogen bonds with those of hydrogen bonds and lithium bonds. To do this, the interactions of HOOOH with the molecules XF (X?=?Cl, Br, H, Li) were investigated. For each molecule, the percentage of the van der Waals (vdW) molecular surface that intersected with the ESP surface was used to roughly quantify the directionality of the halogen/hydrogen/lithium bond associated with the molecule. The size of the region of intersection was found to increase in the following order: ClF?<?BrF?<?HF?<?LiF. The maximum ESP in the region of intersection, V _{S, max}, was observed to become more positive according to the sequence ClF?<?BrF?<?HF?<?LiF. For ClF and BrF, the positive electrostatic potential was concentrated in a very small region of the vdW molecular surface. On the other hand, for HF and LiF, the positive electrostatic potential was more diffusely scattered across the vdW surface than for ClF and BrF. Also, the optimized geometries of the dipolymers HOOOH···?XF (X?=?Cl, Br, H, Li) indicated that halogen bonds are more directional than hydrogen bonds and lithium bonds, consistent with the results of ESP analyses.

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Graphical abstract Electrostatic potential (ESP) contour maps in the xz plane of ClF and BrF

     

Measuring protein synthesis using metabolic ²H labeling, high-resolution mass spectrometry, and an algorithm

We recently developed a method for estimating protein dynamics in vivo with heavy water ((2)H(2)O) using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) [16], and we confirmed that (2)H labeling of many hepatic free amino acids rapidly equilibrated with body water. Although this is a reliable method, it required modest sample purification and necessitated the determination of tissue-specific amino acid labeling. Another approach for quantifying protein kinetics is to measure the (2)H enrichments of body water (precursor) and protein-bound amino acid or proteolytic peptide (product) and to estimate how many copies of deuterium are incorporated into a product. In the current study, we used nanospray linear trap Fourier transform ion cyclotron resonance mass spectrometry (LTQ FT-ICR MS) to simultaneously measure the isotopic enrichment of peptides and protein-bound amino acids. A mathematical algorithm was developed to aid the data processing. The most notable improvement centers on the fact that the precursor/product labeling ratio can be obtained by measuring the labeling of water and a protein (or peptide) of interest, thereby minimizing the need to measure the amino acid labeling. As a proof of principle, we demonstrate that this approach can detect the effect of nutritional status on albumin synthesis in rats given (2)H(2)O.     

The levels of ζ, γ, and δ chains in patients with Hb H disease

Summary Details are given of a study of blood samples from 24 patients with Hb H disease from different Mediterranean countries and from the Far East. Four different types of -thal-1 (--) were observed, namely-() ( 20.5-kb deletion);--MED-I ( 17.5-kb deletion);--MED-II (>26.5-kb deletion); and--SEA ( 18-kb deletion, in Orientals only). The -thal-2 was mainly of the deletion type (16 with the 3.7-kb deletion; 1 with the 4.2-kb deletion), while 4 of the 7 patients with a nondeletional type had the five-nucleotide deletion at the donor splice site of the first intron of the 2 gene. All patients had a mild-to-moderate hemolytic anemia; no significant differences in hematology were observed between the groups. Hb A₂ was decreased to about one-third of the normal level. The Hb H formation varied considerably and its quantitation was not always satisfactory. Patients with Hb H disease due to any -thal-1 combined with a nondeletional -thal-2 had the highest Hb H levels and a more marked anemia. The chain production was small and absent in patients with the MED-II type of -thal-1 because this deletion included the and genes. The highest chain levels were present in the four patients with the SEA type of -thal-1. The chain production was increased, particularly in patients with a mutation of C T at position-158 to the ^G globin gene. This chain was primarily present as Hb Bart's (or ₄) and only about 15% was recovered as Hb F or ₂₂. The evaluation of the rate of chains produced in these patients was greatly facilitated by data from one patient who had Hb H disease and a heterozygosity for the ^A-⁺. The low levels of Hb A₂ and of Hb F (relative to Hb Bart's) can be explained by a decreased affinity of chains for and chains as compared with chains in conditions of severe chain deficiency.     

The Höglwald field experiments – aims,concept and basic data

An outline is given of the aims and the concept of the interdisciplinary research work exerted at the Höglwald, an experimental field station in Southern Germany. The Höglwald lies in the temperate suboceanic broadleaf zone. Under natural conditions beech would prevail. The soils are mostly developed as Typic Hapludalfs, weakly aquic in the argillic horizon and strongly acidified in the topsoil. The investigations performed in stands of Norway spruce (Picea abies L. Karst) and European beech (Fagus sylvatica L.) were initiated in 1982/83. The main aims are (1) to test experimentally the soil acidification hypothesis predicting root damage by aluminium toxicity, (2) to study the effects of compensatory liming with and without artificially increased acid input, (3) to investigate comprehensively nitrogen cycling and turnover including studies about (a) N-gas fluxes, (b) root reactions to excess N-supply, (c) N-assimilation in the canopy, (d) effects of experimentally increased N-input on trees, soil and seepage water chemistry, and (e) N-turnover under natural and experimentally produced drought periods. Part of these investigations were also performed in a mixed stand of spruce and beech to show possible interactions of both species.     

[15N,1H]/[13C,1H]-TROSY for simultaneous detection of backbone 15N–1H, aromatic 13C–1H and side-chain 15N–1H2 correlations in large proteins

This paper describes a [¹⁵N,¹H]/[¹³C,¹H]-TROSY experiment for the simultaneous acquisition of the heteronuclear chemical shift correlations of backbone amide ¹⁵N–¹H groups, side chain ¹⁵N–¹H₂ groups and aromatic ¹³C–¹H groups in otherwise highly deuterated proteins. The ¹⁵N–¹H and ¹³C–¹H correlations are extracted from two subspectra of the same data set, thus preventing possible spectral overlap of aromatic and amide protons in the ¹H dimension. The side-chain ¹⁵N–¹H₂ groups, which are suppressed in conventional [¹⁵N,¹H)-TROSY, are observed with high sensitivity in the ¹⁵N–¹H subspectrum. [¹⁵N,¹H]/[¹³C,¹H]-TROSY was used as the heteronuclear correlation block in a 3D [¹H,¹H]-NOESY-[¹⁵N,¹H]/[¹³C,¹H]-TROSY experiment with the membrane protein OmpA reconstituted in detergent micelles of molecular weight 80000 Da, which enabled the detection of numerous NOEs between backbone amide protons and both aromatic protons and side chain ¹⁵N–¹H₂ groups.     

Taxonomy and biogeography of the Nearctic Raphia Hübner (Lepidoptera,Noctuidae, Raphiinae)

The taxonomic status and biogeography of the North American Raphia species is reviewed using adult morphology, larval host plants, geographic phenotypic variation, and variation of mtDNA COI barcode sequences. Lack of diagnostic morphological differences, combined with relatively low mtDNA barcode divergences and clinal phenotypic variation in key geographic regions indicate that the six previously recognized species of North American Raphia are best interpreted as parapatric subspecies. Raphia frater abrupta Grote, stat. n., R. f. coloradensis Putnam-Cramer, stat. r., R. f. piazzi Hill, stat. n., and R. f. elbea Smith, stat. n., are accordingly revised to subspecies of R. frater Grote. Type locality restrictions are provided for Raphia abrupta and Raphia frater and a neotype is designated for Raphia frater var. coloradensis.