Steady-state kinetics of the anaerobic reaction of soybean lipoxygenase-1 with linoleic acid and 13-L-hydroperoxylinoleic acid.

The steady-state kinetics of the anaerobic reaction of soybean lipoxygenase-1 with linoleic acid and 13-L-hydroperoxylinoleic acid were studied. Initial rates of the formation of oxodienoic acids**, absorbing at 285 nm, were measured at pH 10. About 50% of the consumed 13-L-hydroperoxylinoleic acid was converted into oxodienoic acids regardless of the initial ratio of the two substrates. A linear inhibition by both linoleic acid and 13-L-hydroperoxylinoleic acid was observed in the concentration range studied, which is on the upper side limited by the concentrations at which micelle- or acid-soap formation starts. A kinetic scheme is proposed based on one active site in lipoxygenase-1 which alternately binds the two substrates. Values for the kinetic constants were calculated by fitting simultaneously the complete set of data to the appropriate rate equation.     

Effect of lipid hydroperoxide on lipoxygenase kinetics.

In order to investigate the activation of lipoxygenase and to clarify the role of the oxygenation product hydroperoxide in this process, the effect of 13-hydroperoxylinoleic acid (P, 0-35 microM) on linoleic acid (S, 1-80 microM) oxygenation catalysis by 12 nM lipoxygenase-1 from soybean was studied at pH 10, 25 degrees C, and 240 microM O2 with rapid kinetic techniques. The following observations were made: (1) Iron(II) and iron(III) lipoxygenases are kinetically different: reactions started with the Fe(II) enzyme form show a lag phase, whereas iron(III) lipoxygenase induces an initial burst. (2) Oxidation of the enzyme alone is not sufficient to abolish the lag phase: at [S] greater than 50 microM, the initial burst in the iron(III) lipoxygenase curves is still followed by a lag. The lag phase disappears completely only in the presence of micromolar quantities of P. (3) The approximate dissociation constants for S and P are 15 and 24 microM, respectively, 1 order of magnitude smaller than the corresponding values in the absence of oxygen. The observed kinetics are predicted by numerical integration of the rate equations of a model based on the single lipid binding site mechanism for the anaerobic lipoxygenase reaction [Ludwig et al. (1987) Eur. J. Biochem. 168, 325-337; Verhagen et al. (1978) Biochim. Biophys. Acta 529, 369-379]. A quasi-steady-state approximation of the model suggests that a high [S]/[P] the fraction of active iron(III) lipoxygenase is small and that, therefore, a lag phase is intrinsic to the mechanism.     

Restoration of the Cirsio dissecti‐Molinietum in The Netherlands: Can we rely on soil seed banks?

Abstract. Vegetation and soil seed banks of a threatened Atlantic fen meadow community were studied using recent phytosociological records and seedling emergence from soil samples. Similarly managed but differently degraded stands that suffered different levels of species impoverishment were compared. The actual vegetation was related to a set of phytosociological references representing the subassociations of the community. DCA positions of reference relevés from the different subassociations were overlapping, suggesting that in all references many common species occur. Recent records were positioned in‐between the seed bank samples and the references. The soil seed banks of all stands were dominated by ordinary species. Most character species had at most sparse seed banks and no seedlings of locally extinct character species, mentioned in historic floristic records, were detected. In contrast species of pioneer and small‐sedge communities as well as those of heathlands were abundant in the seed banks. Based on the vertical distribution of seeds in the soil layers most fen meadow species were classified into transient or short‐term persistent seed bank types. We concluded that complete restoration of the Cirsio dissecti‐Molinietum without reintroduc‐tion is only likely in stands that were degraded only a few years ago. On the other hand, the presence of viable seeds of Nanocyperion and Parvocaricetea species is promising for the restoration of these communities even after decades. Recreation of pioneer habitats by sod cutting will preserve these species.     

Nutrient stress, host plant quality and herbivore performance of a leaf-mining fly on grass

Environmental stresses affect plant growth and performance in nature. Host plant quality in turn affects herbivore performance and population dynamics. In view of these interactions, two major hypotheses were formulated. The plant stress hypothesis proposes that physiologically stressed plants become more susceptible to herbivores. The plant vigour hypothesis proposes that plants that grow vigorously are favourable to herbivores. Here we test the plant stress/plant vigour hypotheses for a leaf miner, Agromyza nigripes (Diptera; Agromyzidae), on the grass Holcus lanatus. We assessed larval performance (survival, developmental time, pupal mass) on grasses growing under different levels of nutrients (Hoagland solution) and drought stress, under controlled field and greenhouse conditions. Plant vigour and nutrient content were high on soils with an intermediate nutrient concentration and lower under drought stress and soil nutrient shortage and overdose. Larval performance was also highest on wet soils with intermediate nutrient supply. The results of the mining flies support the plant vigour hypothesis (density, survival and development better on vigorous plants). Herbivore performance is higher on leaves with a higher protein content.     

Functions of base flipping in E. coli nucleotide excision repair

UvrB is the main damage recognition protein in bacterial nucleotide excision repair and is capable of recognizing various structurally unrelated types of damage. Previously we have shown that upon binding of Escherichia coli UvrB to damaged DNA two nucleotides become extrahelical: the nucleotide directly 3' to the lesion and its base-pairing partner in the non-damaged strand. Here we demonstrate using a novel fluorescent 2-aminopurine-menthol modification that the position of the damaged nucleotide itself does not change upon UvrB binding. A co-crystal structure of B. caldotenax UvrB and DNA has revealed that one nucleotide is flipped out of the DNA helix into a pocket of the UvrB protein where it stacks on Phe249 [J.J. Truglio, E. Karakas, B. Hau, H. Wang, M.J. DellaVecchia, B. van Houten, C. Kisker, Structural basis for DNA recognition and processing by UvrB, Nat. Struct. Mol. Biol. 13 (2006) 360-364]. By mutating the equivalent of Phe249 (Tyr249) in the E. coli UvrB protein we show that on damaged DNA neither of the extrahelical nucleotides is inserted into this protein pocket. The mutant UvrB protein, however, resulted in an increased binding and incision of undamaged DNA showing that insertion of a base into the nucleotide-binding pocket is important for dissociation of UvrB from undamaged sites. Replacing the nucleotides in the non-damaged strand with a C3-linker revealed that the extruded base in the non-damaged strand is not directly involved in UvrB-binding or UvrC-mediated incision, but that its displacement is needed to allow access for residues of UvrB or UvrC to the neighboring base, which is directly opposite the DNA damage. This interaction is shown to be essential for optimal 3'-incision by UvrC. After 3'-incision base flipping in the non-damaged DNA strand is lost, indicative for a conformational change needed to prepare the UvrB-DNA complex for 5'-incision.     

The amphioxus (Branchiostoma floridae) genome contains a highly diversified set of G protein-coupled receptors

Background

When natural hybridization occurs at sites where the hybridizing species differ in abundance, the pollen load delivered to the rare species should be predominantly from the common species. Previous authors have therefore proposed a hypothesis on the direction of hybridization: interspecific hybrids are more likely to have the female parent from the rare species and the male parent from the common species. We wish to test this hypothesis using data of plant hybridizations both from our own experimentation and from the literature.

Results

By examining the maternally inherited chloroplast DNA of 6 cases of F1 hybridization from four genera of plants, we infer unidirectional hybridization in most cases. In all 5 cases where the relative abundance of the parental species deviates from parity, however, the direction is predominantly in the direction opposite of the prediction based strictly on numerical abundance.

Conclusion

Our results show that the observed direction of hybridization is almost always opposite of the predicted direction based on the relative abundance of the hybridizing species. Several alternative hypotheses, including unidirectional postmating isolation and reinforcement of premating isolation, were discussed.     

Characterization of a CRM1-dependent nuclear export signal in the C terminus of herpes simplex virus type 1 tegument protein UL47

The herpes simplex virus type 1 tegument protein known as VP13/14, or hUL47, localizes to the nucleus and binds RNA. Using fluorescence loss in photobleaching analysis, we show that hUL47 undergoes nucleocytoplasmic shuttling during infection. We identify the hUL47 nuclear export signal (NES) as a C-terminal 10-residue hydrophobic peptide and measure its efficiency relative to that of the classical human immunodeficiency virus type 1 Rev NES. Finally, we show that the hUL47 NES is sensitive to the inhibitor of CRM1-mediated nuclear export leptomycin B. Hence, hUL47 joins a growing list of virus-encoded RNA-binding proteins that use CRM1 to exit the nucleus.     

Structure-activity relationship study of human liver microsomes-catalyzed hydrolysis rate of ester prodrugs of MENT by comparative molecular field analysis (CoMFA)

A series of MENT esters (3-71) was designed, prepared and tested to study the structure-activity relationship (SAR) of the hydrolysis rate with human liver microsomes of these prodrugs. Compounds were obtained covering a wide range of metabolic stability. The results are useful for the proper selection of prodrugs for different pharmaceutical formulations to deliver the potent and prostate-sparing androgen MENT. The MENT esters can especially be administered for male hormone replacement therapy and male contraception. Comparative molecular field analysis (CoMFA) was applied to a dataset of 28 esters, for which ED50 values could be obtained. The CoMFA model where the electrostatic and H-bond molecular fields were combined turned out to be most predictive. Despite the limited size of the dataset, CoMFA can help to rationalize the SAR of the ester hydrolysis rate of ester prodrugs of MENT.     

Optimization of the mechanical performance of a two-duct semicircular duct system--part 1: dynamics and duct dimensions

The classical representation of the semicircular duct system consists of three separate duct circuits. The ducts are, however, in reality, hydrodynamically interconnected. Muller & Verhagen (1988a,b) derived equations for the mechanical behaviour of an interconnected system with three ducts (anterior, posterior and horizontal). An analytical solution of these equations would, however, be too complex to provide surveyable formulae. A system of two interconnected ducts avoids this complexity whilst keeping the essentials of the coupling of ducts intact. The solution of the equation of motion leads to expressions for time constants and maximal endolymph excursions which are functions of morphological parameters, viz. the ratios of radii (gamma) and lengths (lambda) of the common vestibular part (crus commune or utriculus) and the ducts. The system possesses two short time constants which are shown to have similar values. The maximum endolymph displacements in the two ducts after a steplike stimulus are the products of the respective initial velocities and combinations of time constants. The initial velocities depend strongly on the position of the labyrinth with respect to the excitating rotation vector. Measured data of gamma and lambda are compared with the theoretical results. For gamma, excellent agreement was found. lambda is treated elsewhere.