Studies, with a luminogenic peptide substrate, on blood coagulation Factor X/Xa produced by mouse peritoneal macrophages

The formation and secretion of coagulation Factor X/Xa by mouse peritoneal macrophages was studied with a luminogenic peptide substrate (S-2613; t-butyloxycarbonylisoleucylglutamyl-γ-piperidylglycylarginylisoluminol). Amidolysis was quantified by measuring the light emitted during oxidation of isoluminol, released by Factor Xa. A lower detection limit of about 0.5ng of Factor Xa was established; the assay was linear with enzyme concentration up to at least 100ng/ml. Factor X was determined after treatment with the Factor X-activating component of Russell's-viper (Vipera russelli) venom. Macrophages, cultured in the absence of serum, released Factor X/Xa into the culture medium. The concentration of coagulation enzyme in the medium increased in an essentially linear fashion over a period of at least 3 days, at a rate corresponding to 6–8ng produced/24h per 10⁶ cells. The ratio of Factor Xa/X+Xa varied from about 60 to 100%, showing that activation of Factor X to Xa is not prerequisite to release of the enzyme from the cells. Factor Xa activity was suppressed in the presence of warfarin [3-(α-acetonylbenzyl)-4-hydroxycoumarin; 12.5μg/ml of medium], but could be restored by adding vitamin K (0.1μg/ml) along with the warfarin. Cultures to which Sepharose beads containing covalently bound anti-(Factor X) antibodies had been added showed decreased amounts of free Factor X/Xa in the culture medium. The missing activity could be demonstrated by incubating the recovered conjugate with the substrate peptide S-2613. Factor Xa produced by the macrophages was efficiently inactivated by heparin in the presence of antithrombin, heparin with high affinity for antithrombin being more effective than the corresponding low-affinity species.     

Methods development for diffraction and spectroscopy studies of metalloenzymes at X-ray free-electron lasers

X-ray free-electron lasers (XFELs) open up new possibilities for X-ray crystallographic and spectroscopic studies of radiation-sensitive biological samples under close to physiological conditions. To facilitate these new X-ray sources, tailored experimental methods and data-processing protocols have to be developed. The highly radiation-sensitive photosystem II (PSII) protein complex is a prime target for XFEL experiments aiming to study the mechanism of light-induced water oxidation taking place at a Mn cluster in this complex. We developed a set of tools for the study of PSII at XFELs, including a new liquid jet based on electrofocusing, an energy dispersive von Hamos X-ray emission spectrometer for the hard X-ray range and a high-throughput soft X-ray spectrometer based on a reflection zone plate. While our immediate focus is on PSII, the methods we describe here are applicable to a wide range of metalloenzymes. These experimental developments were complemented by a new software suite, cctbx.xfel. This software suite allows for near-real-time monitoring of the experimental parameters and detector signals and the detailed analysis of the diffraction and spectroscopy data collected by us at the Linac Coherent Light Source, taking into account the specific characteristics of data measured at an XFEL.     

Life based on phosphite: a genome-guided analysis of Desulfotignum phosphitoxidans

Background

The Delta-Proteobacterium Desulfotignum phosphitoxidans is a type strain of the genus Desulfotignum, which comprises to date only three species together with D. balticum and D. toluenicum. D. phosphitoxidans oxidizes phosphite to phosphate as its only source of electrons, with either sulfate or CO₂ as electron acceptor to gain its metabolic energy, which is of exclusive interest. Sequencing of the genome of this bacterium was undertaken to elucidate the genomic basis of this so far unique type of energy metabolism.

Results

The genome contains 4,998,761 base pairs and 4646 genes of which 3609 were assigned to a function, and 1037 are without function prediction. Metabolic reconstruction revealed that most biosynthetic pathways of Gram negative, autotrophic sulfate reducers were present. Autotrophic CO₂ assimilation proceeds through the Wood-Ljungdahl pathway. Additionally, we have found and confirmed the ability of the strain to couple phosphite oxidation to dissimilatory nitrate reduction to ammonia, which in itself is a new type of energy metabolism. Surprisingly, only two pathways for uptake, assimilation and utilization of inorganic and organic phosphonates were found in the genome. The unique for D. phosphitoxidans Ptx-Ptd cluster is involved in inorganic phosphite oxidation and an atypical C-P lyase-coding cluster (Phn) is involved in utilization of organophosphonates.

Conclusions

We present the whole genome sequence of the first bacterium able to gain metabolic energy via phosphite oxidation. The data obtained provide initial information on the composition and architecture of the phosphite–utilizing and energy-transducing systems needed to live with phosphite as an unusual electron donor.     

Photochemical properties of a riboflavins/cytochrome P450 2B4 complex

The present study demonstrates the possible use of a non-covalent complex of riboflavins with cytochrome P450 2B4 (artificial flavocytochrome P450 2B4) for photo-induced intermolecular electron transfer between the isoalloxazine cycle of flavins and the ferric heme group of cytochrome P450 2B4. Riboflavin was used as a light-induced electron donor for the transfer of electrons to cytochrome P450. The quantitative measurement of the photocurrent, generated by photoreduction of non-covalent flavocytochrome P450 2B4, was carried out. In the presence of typical substrates for cytochrome P450 2B4 the decrease of cathodic photocurrent occurred, generated not only by riboflavin itself but also by a riboflavin/cytochrome P450 complex. It was demonstrated that flavocytochromes might serve as molecular amplifiers of a photocurrent, generated upon flavins' reduction. Introduction of flavin residues into the cytochrome P450 molecule transformed this haemoprotein into a photoreceptor and a photodiode and, in addition, into a photosensitive and photo-activated enzyme.     

Chemical composition of aquatic dissolved organic matter in five boreal forest catchments sampled in spring and fall seasons

The chemical composition and carbon isotope signature of aquatic dissolved organic matter (DOM) in five boreal forest catchments in Scandinavia were investigated. The DOM was isolated during spring and fall seasons using a reverse osmosis technique. The DOM samples were analyzed by elemental analysis, FT-IR, solid-state CP-MAS ¹³C-NMR, and C-1s NEXAFS spectroscopy. In addition, the relative abundance of carbon isotopes (¹²C, ¹³C, ¹⁴C) in the samples was measured. There were no significant differences in the chemical composition or carbon isotope signature of the DOM sampled in spring and fall seasons. Also, differences in DOM composition between the five catchments were minor. Compared to reference peat fulvic and humic acids, all DOM samples were richer in O-alkyl carbon and contained less aromatic and phenolic carbon, as shown by FT-IR, ¹³C-NMR, and C-1s NEXAFS spectroscopy. The DOM was clearly enriched in ¹⁴C relative to the NBS oxalic acid standard of 1950, indicating that the aquatic DOM contained considerable amounts of organic carbon younger than about 50 years. The weight-based C:N ratios of 31 ± 6 and the values of indicate that the isolated DOM is of terrestrial rather than aquatic origin. We conclude that young, hydrophilic carbon compounds of terrestrial origin are predominant in the samples investigated, and that the composition of the aquatic DOM in the studied boreal forest catchments is rather stable during low to intermediate flow conditions.     

Atypical human liver alcohol dehydrogenase: the beta 2-Bern subunit has an amino acid exchange that is identical to the one in the beta 2-Oriental chain

The "atypical' human liver alcohol dehydrogenase dimer, homogeneous for beta 2-Bern chains, was isolated from human liver of Caucasian individuals. It is derived from an allelic variant at the ADH2 gene locus and exhibits a considerably higher specific activity and lower pH optimum than its "typical' counterpart (isoenzyme beta 1 beta 1) from the beta 1-chain predominant in Caucasians. Peptides were prepared by trypsin or CNBr cleavage, and were purified by exclusion chromatography and reverse-phase high-performance liquid chromatography (RP-HPLC). Structural analysis of the peptides showed that beta 2-Bern differs at one position from beta 1. Thus, Arg-47 in beta 1 is substituted by His in beta 2-Bern. This exchange, compatible with a one-base mutation, explains all functional differences by altered interactions with the pyrophosphate moiety of the coenzyme. The difference is also structurally identical to that found for another atypical beta 2-subunit, the beta 2-Oriental type of major Asian occurrence, linking these two atypical forms of human alcohol dehydrogenase.     

Concentration of live pico- and nanoplankton by means of tangential flow filtration

A tangential flow filtration system for concentrating live pico-and nanoplankton was tested on natural seawater (<20 µm)from Kiel Bight. Twenty- to thirty-fold concentration of samplesranging from 79 to 152 dm³ was easily achieved, the time necessarydepending on sample volume, pumping pressure and filtrate/retentateratio. Losses of different kinds of cells in relation to theconcentration factor were quantified. Recovery rates were negativelycorrelated with the frequency of sample recirculation throughthe filtration unit.     

Why do organisms produce gametes of only two different sizes? Some theoretical aspects of the evolution of anisogamy

This paper extends the population genetic model of (the evolution of) anisogamy of Charlesworth (1978), which is based on the model of Parker, Baker & Smith (1972). The effect of parthenogenesis on the evolution of anisogamy is examined; this effect turns out to be only quantitative. Furthermore, the problem of the occurrence of only two different gamete sizes is considered. It is shown that a stable polymorphism with three different gamete sizes cannot exist. This result is robust to changes in the mating structure (random or disassortative gamete fusion) and to changes in the mode of reproduction (only sexual or partially parthenogenetic).     

Bioanalysis of aplidine, a new marine antitumoral depsipeptide, in plasma by high-performance liquid chromatography after derivatization with trans-4′-hydrazino-2-stilbazole

A sensitive bio-analytical assay in plasma of the depsipeptide aplidine is reported, based on reversed-phase liquid chromatography and fluorescence detection of the trans-4′-hydrazino-2-stilbazole (4′H2S) derivative of the analyte. At ambient temperature, two conformations of the depsipeptide are observed in solution due to cis–trans isomerism at the proline–pyruvoyl peptide bond. Aplidine is isolated from the matrix by solid-phase extraction on an octadecyl modified silica stationary phase. After evaporation of the acetone eluate, a derivatization with 4′H2S is performed in a water–acetonitrile mixture at pH 4. The reaction mixture is injected directly into the chromatograph and the analyte is quantified by fluorescence detection at 410 and 560 nm for excitation and emission, respectively. The method has been validated in the 2–100 ng/ml-range, 2 ng/ml being the lower limit of quantification. Precision and accuracy both meet the current requirements for a bioanalytical assay. The identity of the 4′H2S reaction products of aplidine have been confirmed by mass spectrometric analysis. Finally, the method has been employed for a pilot pharmacokinetic study of aplidine in mice which demonstrated its usefulness for pharmacological research.     

COMPOSITION OF VOLATILES IN RELATION TO TAXONOMY OF AMERICAN ALLIUMS

The North American species of Allium exclusive of A. schoenoprasum and A. tricoccum of Old World affinity are grouped on the basis of morphological similarity into eight discontinuous species alliances typified by A. acuminatum, A. campanulatum, A. canadense, A. cernuum, A. falcifolium, A. kunthii, A. sanbornii, and A. validum, respectively. Representatives of each of these alliances were compared with respect to volatile constituents responsible for characteristic odors by means of gas chromatography. Results indicate that these volatiles provide evidence of relationship useful in the classification of alliums. Uniformity was found in composition of volatiles in the representatives of the A. canadense, A. cernuum, A. kunthii, and A. sanbornii alliances. Variation was observed in the A. acuminatum, A. campanulatum, and A. falcifolium alliances. A. validum was the only species of its alliance studied. Vapors of A. validum contain mostly n-propyl sulfides (onion-like odor) as does the cultivated A. cepa. Methyl sulfides (cabbage-like odor) predominate in the A. sanbornii alliance. A few species of the A. acuminatum and A. falcifolium alliances contain mainly allyl sulfides (garlic-like odor).