An algorithm to equiprobably generate all directed trees withk labeled terminal nodes and unlabeled interior nodes

A computer algorithm is presented which equiprobably generates any member of the set of all directed trees withk labeled terminal nodes and unlabeled interior nodes. The algorithm requires roughlyk ² /2 storage locations. The one-time initialization requiresO(k ² ) time, while generating each tree requiresO(k) time. Contribution No. 477 in Ecology and Evolution, State University of New York at Stony Brook. This research was supported by Grant No. DEB8003508 from the National Science Foundation to Robert R. Sokal.     

The impact of different chelating leaving groups on the substitution kinetics of mononuclear PtII(1,2- trans - R , R -diaminocyclohexane)(X–Y) complexes

A set of three oxaliplatin derivatives containing 1,2-trans-R,R-diaminocyclohexane (dach) as a spectator ligand and different chelating leaving groups X–Y, viz., [Pt(dach)(O,O-cyclobutane-1,1-dicarboxylate)], or Pt(dach)(CBDCA), [Pt(dach)(N,O-glycine)]⁺, or Pt(dach)(gly), and [Pt(dach)(N,S-methionine)]⁺, or Pt(dach)(l-Met), where l-Met is l-methionine, were synthesized and the crystal structure of Pt(dach)(gly) was determined by X-ray diffraction. The effect of the leaving group on the reactivity of the resulting Pt(II) complexes was studied for the nucleophiles thiourea, glutathione (GSH) and l-Met under pseudo-first-order conditions as a function of nucleophile concentration and temperature, using UV–vis spectrophotometric techniques. ¹H NMR spectroscopy was used to follow the substitution of the leaving group by guanosine 5′-monophosphate (5′-GMP²⁻) under second-order conditions. The rate constants indicate for all reactions a direct substitution of the X–Y chelate by the selected nucleophiles, thereby showing that the nature of the chelate, viz., O–O (CBDCA²⁻), N–O (glycine) or S–N (l-Met), respectively, plays an important role in the kinetic and mechanistic behavior of the Pt(II) complex. The k ₁ values for the reaction with thiourea, l-Met, GSH and 5′-GMP²⁻ were found to be as follows (10³ k ₁, 37.5 °C, M⁻¹ s⁻¹): Pt(dach)(CBDCA) 61 ± 2, 21.6 ± 0.1, 23 ± 1, 0.352 ± 0.002; Pt(dach)(gly) 82 ± 3, 6.2 ± 0.2, 37 ± 1, 1.77 ± 0.01; Pt(dach)(l-Met) (thiourea, GSH) 62 ± 2, 24 ± 1. The activation parameters for all reactions studied suggest an associative substitution mechanism. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Direct assessment of water exchange on a Gd(III) chelate bound to a protein

 The Gd(III) complex of 4-pentylbicyclo[2.2.2]octane-1-carboxyl-di-l-aspartyl-lysine-derived DTPA, [GdL(H₂O)]^2–, binds to serum albumin in vivo, through hydrophobic interaction. A variable temperature ¹⁷O NMR, EPR, and Nuclear Magnetic Relaxation Dispersion (NMRD) study resulted in a water exchange rate of k ²⁹⁸ _ex=4.2×10⁶ s^–1, and let us conclude that the GdL complex is identical to [Gd(DTPA)(H₂O)]^2– in respect to water exchange and electronic relaxation. The effect of albumin binding on the water exchange rate has been directly evaluated by ¹⁷O NMR. Contrary to expectations, the water exchange rate on GdL does not decrease considerably when bound to bovine serum albumin (BSA); the lowest limit can be given as k _{ex, GdL-BSA}=k _ex, GdL / 2. In the knowledge of the water exchange rate for the BSA-bound GdL complex, the analysis of its NMRD profile at 35  °C yielded a rotational correlation time of 1.0 ns, one order of magnitude shorter than that of the whole protein. This value is supported by the longitudinal ¹⁷O relaxation rates. This indicates a remarkable internal flexibility, probably due to the relatively large distance between the protein- and metal-binding moieties of the ligand. Received: 25 June 1998 / Accepted: 11 August 1998     

Inhibitory effects on mushroom tyrosinase by flavones from the stem barks of Morus lhou (S.) Koidz

Five flavones displaying tyrosinase inhibitory activity were isolated from the stem barks of Morus lhou (S.) Koidz., a cultivated edible plant. The isolated compounds were identified as mormin (1), cyclomorusin (2), morusin (3), kuwanon C (4), and norartocarpetin (5). Mormin (1) was characterized as a new flavone possesing a 3-hydroxymethyl-2-butenyl at C-3. The inhibitory potencies of these flavonoids toward monophenolase activity of mushroom tyrosinase were investigated. The IC₅₀ values of compounds 1–5 for monophenolase activity were determined to be 0.088, 0.092, 0.250, 0.135 mM, and 1.2 μM, respectively. Mormin (1), cyclomorusin (2), kuwanon C (4) and norartocarpetin (5) exhibited competitive inhibition characteristics. Interestingly norartocarpetin (5) showed a time–dependent inhibition against oxidation of l–tyrosine: it also operated under the enzyme isomerization model (k₅ = 0.8424 min^{? 1}, k₆ = 0.0576 min^{? 1}, = 1.354 μM).     

Oxygen mass-transfer performance of low viscosity gas-liquid-solid system in a split-cylinder airlift bioreactor

The O₂ mass-transfer coefficient, k _L a, decreased by 20% when the viscosity of a simulated broth increased from 1.38 × 10^–3 to 3.43 × 10^–3 Pa s in a split-cylinder airlift bioreactor with a broth volume of 41 l. When the paper pulp concentration was below 10 g l^–1, k _L a hardly changed. While at 30 g l^–1, k _L a decreased by 56%. C₂O₄ ^2– and Na⁺ were found to have some effect on the k _L a value.     

2,4,5-Triphenylisothiazol-3(2H)-one 1,1-dioxides as inhibitors of human leukocyte elastase

A series of substituted 2,4,5-triphenylisothiazol-3(2H)-one 1,1-dioxides 9 was synthesized and investigated as inhibitors of human leukocyte elastase (HLE). All compounds were found to inhibit HLE in a time-dependent manner and most of them exhibited k_obs/[I] values > 300 M^{? 1}s^{? 1}. The most potent 3-oxosultam of this series was 9l (k_obs/[I] = 2440 M^{? 1}s^{? 1}). Kinetic investigations performed with 9g and different substrate concentrations did not allow to clearly distinguish between a competitive or noncompetitive mode of inhibition. A more complex interaction is supported by the failure of a linear dependency of k_obs values on the inhibitor concentration.     

Comparative genetic analysis of the Aegilops longissima and Ae. sharonensis genomes with common wheat

Aegilops longissima Schw. et Musch. (2n= 2x=14, S^lS^l) and Aegilops sharonensis Eig. (2n=2x=14, S^lS^l) are diploid species belonging to the section Sitopsis in the tribe Triticeae and potential donors of useful genes for wheat breeding. A comparative genetic map was constructed of the Ae. longissima genome, using RFLP probes with known location in wheat. A high degree of conserved colinearity was observed between the wild diploid and basic wheat genome, represented by the D genome of cultivated wheat. Chromosomes 1S^l, 2S^l, 3S^l, 5S^l and 6S^l are colinear with wheat chromosomes 1D, 2D, 3D, 5D and 6D, respectively. The analysis confirmed that chromosomes 4S^l and 7S^l are translocated relative to wheat. The short arms and major part of the long arms are homoeologous to most of wheat chromosomes 4D and 7D respectively, but the region corresponding to the distal segment of 7D was translocated from 7S^lL to the distal region of 4S^lL. The map and RFLP markers were then used to analyse the genomes and added chromosomes in a set of ’Chinese Spring’ (CS)/Ae. longissima chromosome additions. The study confirmed the availability of disomic CS/Ae. longissima addition lines for chromosomes 1S^l, 2S^l, 3S^l, 4S^l and 5S^l. An as yet unpublished set of Ae. sharonensis chromosome addition lines were also available for analysis. Due to the gametocidal nature of Ae. sharonensis chromosomes 2S^l and 4S^l, additions 1S^l, 3S^l, 5S^l, 6S^l and 7S^l were produced in a (4D)4S^l background, and 2S^l and 4S^l in a euploid wheat background. The analysis also confirmed that the 4/7 translocation found in Ae. longissima was not present in Ae. sharonensis although the two wild relatives of wheat are considered to be closely related. The phenotypes of the Ae. sharonensis addition lines are described in an Appendix. Received: 28 September 2000 / Accepted: 19 January 2001     

Response surface methodology for optimization of medium components in submerged culture of Aspergillus flavus for enhanced heparinase production

Aims: Aim of the study was to develop a medium for optimal heparinase production with a strain of Aspergillus flavus (MTCC‐8654) by using a multidimensional statistical approach. Methods and Results: Statistical optimization of intracellular heparinase production by A. flavus, a new isolate, was investigated. Plackett–Burman design was used to evaluate the affect of medium constituents on heparinase yield. The experimental results showed that the production of heparinase was dependent upon heparin, the inducer; chitin, structurally similar to heparin and NH₄NO_3, the nitrogen source. A central composite design was applied to derive a statistical model for optimizing the composition of the fermentation medium for the production of heparinase enzyme. The optimum fermentation medium consisted of (g l^?1) Mannitol, 8·0; NH₄NO₃, 2·5; K₂HPO₄, 2·5; Na₂HPO₄, 2·5; MgSO₄.7H₂O, 0·5; Chitin, 17·1; Heparin, 0·6; trace salt solution (NaMoO₄.2H₂O, CoCl₂.6H₂O, CuSO₄.5H₂O, FeSO₄.7H₂O, CaCl₂), 10^?4 mol l^?1. Conclusions: A 2·37‐fold increase in heparinase production was achieved in economic and effective manner by the application of statistical designs in medium optimization. Significance and Impact of the Study: Heparinase production was doubled by statistical optimization in a cost‐effective manner. This heparinase can find application in pharmaceutical industry and for the generation of low‐molecular‐weight heparins, active as antithrombotic and antitumour agents.     

Anticholinesterase activity of some major intermediates in carbacylamidophosphate synthesis: Preparation,spectral characterization and inhibitory potency determination

Carbacylamidophosphates with the general formula RC(O)NHP(O)R₁R₂ constitute organophosphorus compounds that are used as insecticides, pesticides and ureas inhibitors. In this work, we studied the inhibition potency of CCl₃C(O)NHP(O)Cl₂1, CHCl₂C(O)NHP(O)Cl₂2, CH₂ClC(O)NHP(O)Cl₂3 and CF₃C(O)NHP(O)Cl₂4, which are the major intermediates for carbacylamidophosphates synthesis towards human erythrocyte acetylcholinesterase (hAChe) activity using Ellman's modified kinetic method. Unexpectedly, it was observed that they were not only hydrolytically unstable but also inhibited hAChE in a similar manner to that produced by organophosphorus insecticides. Enzymatic data, bimolecular inhibition rate constants (k_i) and IC₅₀ values for inhibition of hAChE demonstrated that they are irreversible inhibitors and the inhibition potency of compound 2 (IC₅₀ = 88 μM) was the greatest in comparison with compounds 1, 3 and 4. Also the electropositivity of the phosphorus atom and the hydrophobicity of the compounds demonstrated that these two factors play an additional effect and different role in the inhibitory activity of these compounds. Hydrolytic stability of the compounds was determined by ³¹P NMR monitoring of the loss of the parent molecules with D₂O as a function of time. This study considers antiacetylcholinesterase activity according to the structural and the electronic aspects of compounds 1–4, according to IR, ¹H, ¹³C and ³¹P NMR spectral data.     

Use of glucose oxidase system in measuring aeration capacity of fermentors. Comparison of the dynamic and steady-state methods of kla measurement

A steady-state method for k_la determination has been presented using the Michaelis–Menten two-substrate kinetic equation for oxidation of glucose in the presence of the enzymes glucose oxidase and excess catalase. The conditions have been specified where spontaneous hydrolysis of lactone is sufficiently rapid, thus eliminating inhibitory action of lactone on the oxidation. In glucose oxidase-free batches, the k_la values were determined using various modification of the dynamic method. The dynamic methods in which gas interchange was effected without interrupting aeration and agitation of the batch yielded erroneously lower k_la values as compared to the results of steady-state methods if the measured k_la value was higher than 0.03 s^?1. The values yielded by the dynamic method in which the gas interchange was effected at the same time with turning on aeration and agitation of the batch agreed with values resulting from the steady-state method provided that the measured k_la values were lower than 0.08^?1 and the simultaneous interfacial transport of nitrogen and oxygen had been taken into account in the evaluation. At k_la values higher than 0.08 ^?1, this modification of the dynamic method also yielded lower k_la values as compared with the outcome of the steady-state method. The experiments performed do not, however, allow one to decide unambiguously on the whether these lower k_la values are due to failure of the adopted model to describe adequately the dynamic behavior of the system or whether they are true values differing from those yielded by the steady-state method on account of different physical properties of compared batches.     

Fast computation of distance estimators

Background  

Some distance methods are among the most commonly used methods for reconstructing phylogenetic trees from sequence data. The input to a distance method is a distance matrix, containing estimated pairwise distances between all pairs of taxa. Distance methods themselves are often fast, e.g., the famous and popular Neighbor Joining (NJ) algorithm reconstructs a phylogeny of n taxa in time O(n ³). Unfortunately, the fastest practical algorithms known for Computing the distance matrix, from n sequences of length l, takes time proportional to l·n ². Since the sequence length typically is much larger than the number of taxa, the distance estimation is the bottleneck in phylogeny reconstruction. This bottleneck is especially apparent in reconstruction of large phylogenies or in applications where many trees have to be reconstructed, e.g., bootstrapping and genome wide applications.     

Structure and Hypotensive Effect of Flavonoid Glycosides in Kinkan (Fortunella japonica) Peelings

An attempt was made to isolate the hypotensive substances from a hot water extract of kinkan. Eight flavonoid glycosides were isolated by repeated chromatography and by gel filtration after extracting with n-butanol and treating with lead subacetate. Their structures were established to be 6,8-di-C-glucosylapigenin (1), 3,6-di-C-glucosylacacetin (2), 2″-O-α-l-rhamnosyl-4′-O-methyl-vitexin (3), 2″-O-α-l-rhamnosyl-4′-O-methylisovitexin (4), 2″-O-α-l-rhamnosylvitexin (5), 2″-O-α-l-rhamnosylorientin (6), 2″-O-α-l-rhamnosyl-4′-O-methylorientin (7) and ponicilin (8) by UV. MS, ¹-NMR and ¹³C-NMR spectroscopy, and by sugar analysis. Each component was intravenously injected in SHR-SP (0.5 ~ 1.0 mg/100 g of body weight), 1, 2, 5 and 6 were found to lower the rat blood pressure.

Among these compounds, 2, 3, 4, 6 and 7 were new flavone glycosides.     

The role of interphase nitrogen transport in the dynamic measurement of the overall volumetric mass transfer cefficient in air-sparged systems

It has been shown both theoretically and experimentally that interphase nitrogen transport may have a significant influence on the rate of interphase oxygen transport, and thereby also on the value of the volumetric mass transfer coefficient of oxygen, k_la, determined in mechanically agitated bubble fermentors using the variants of dynamic method presented in the literature. The experiments were carried out in 1M KCI solution at five stirrer frequencies and two gas inlet levels. The gas interchanges were performed either without interrupting the aeration and agitation of the charge (A) or with the aeration and agitation of the charge turned on at the same time (B). The applied variants of the interchange were N₂→ O₂→, O₂→ N₂, N₂→ air, air→ N₂, O→ O₂, and O→ air. In the two last variants the oxygen dissolved in the charge was removed by reacting with sulfite ions. The k_la values calculated by allowing for the nitrogen transport for procedure A were approximately equal to the values obtained by disregarding the nitrogen transport, whereas those for procedure B were higher (up to 40%), than the values obtained disregarding the nitrogen transport.     

Synthesis and biological evaluation of some new N4-substituted isatin-3-thiosemicarbazones

A new series of 12 N⁴-substituted isatin-3-thiosemicarbazones 2a-l has been synthesized, characterized and screened for in vitro cytotoxic, phytotoxic and urease inhibitory effects. All the compounds proved to be active in the brine shrimp bioassay; 2a, 2b, 2d, 2f and 2h-l exhibited a high degree of cytotoxic activity (LD₅₀ = 1.10 × 10^{? 5} M–3.10 × 10^{? 5} M). In urease-inhibition assay, compounds 2a, 2b, 2e, 2f, 2h-j and 2l proved to be potent inhibitors displaying relatively much greater inhibition of the enzyme with IC₅₀ values ranging from 20.6 μM to 50.6 μM. Amongst these, 2a and 2f were found to be the most potent ones exhibiting pronounced inhibition with IC₅₀ value 20.6 μM. All the synthetic compounds showed weak to moderate (10–40%) phytotoxicity at the highest tested concentration (500 μg/mL) indicating their usefulness as inhibitors of soil ureases.     

The effect of three rootstocks on water use, canopy conductance and hydraulic parameters of apple trees and predicting canopy from hydraulic conductance

This study investigated the effect of the dwarfing M9, semi‐dwarfing MM106 and local Hashabi rootstocks on the water use, canopy conductance (G_c) and hydraulic conductance (k) of apple orchards with the same scion, Golden Delicious. The average summer leaf area index (LAI) was 2·4, 2·7 and 1·7 for M9, MM106 and Hashabi, respectively. Irrigation in 1997 was less than water use until June, and excessive afterwards. In 1998, irrigation was doubled, and was excessive throughout the season. Sap flow (J) in June–August 1998 totalled 476, 682 and 606 mm (or 0·60, 0·86 and 0·76 of class A pan evaporation) for M9, MM106 and Hashabi, respectively. Maximum sap velocity in the three rootstocks (approximately 70 cm h^?1) occurred in the outer 30–60% of the stem, and its decrease with depth was greater in M9 than in the other rootstocks. Midday G_c during both summers was least for M9, intermediate for Hashabi and greatest for MM106. The k value of M9 and MM106 for the soil to stem, stem to leaves and soil to leaves pathways were determined from daily courses of water potential of leaves, Ψ_l, stem, Ψ_stem and J. Specific k (k_s, i.e. relative to stem sapwood area) did not significantly differ between the two rootstocks for soil to stem and soil to leaf pathways, but leaf specific k (k_l) was greater for MM106 soil to stem (71% greater) and soil to leaf (63%) pathways, respectively. The inverse slopes of the relationships between midday canopy resistance (R_c) and vapour pressure deficit (D) for MM106 was 1·75 of that for M9, and the ratio of their Huber values, i.e. the ratio of sapwood to leaf area, was 1·6. These findings indicate that differences in water use are attributable to differences in k_l, and not to differences in wood properties (k_s). Application of a model relating R_c to orchard area specific k (k_g) showed that the slope of the relationships between midday R_c and D for the 1998 data could be predicted using common values of k_s (0·134 kg m^?2 s^?1 MPa^?1) and midday Ψ_l (?1·34 MPa) for the three rootstocks. The implications of these findings, and the similarities in the differences between rootstocks of G_c, k_l, k_g and Huber values, are discussed with respect to rootstock water use and irrigation.     

In vitro cytotoxic,antibacterial, antifungal and urease inhibitory activities of some N4- substituted isatin-3-thiosemicarbazones

A series of 15 previously reported N⁴-substituted isatin-3-thiosemicarbazones 3a-o has been screened for cytotoxic, antibacterial, antifungal and urease inhibitory activities. Compounds 3b, 3e and 3n proved to be active in cytotoxicity assay; 3e exhibited a high degree of cytotoxic activity (LD₅₀ = 1.10 × 10^{? 5} M). Compound 3h exhibited significant antibacterial activity against B. subtilis, whereas compounds 3a, 3k and 3l displayed significant antifungal activity against one or more fungal strains i.e. T. longifusus, A. flavus and M. canis. In human urease enzyme inhibition assay, compounds 3g, 3k and 3m proved to be the most potent inhibitors, exhibiting relatively pronounced inhibition of the enzyme. These compounds, being non-toxic, could be potential candidates for orally effective therapeutic agents to treat certain clinical conditions induced by bacterial ureases like H. pylori urease. This study presents the first example of inhibition of urease by isatin-thiosemicarbazones and as such provides a solid basis for further research on such compounds to develop more potent inhibitors.     

Monocyclic β-lactam and unexpected oxazinone formation: synthesis,crystal structure,docking studies and antibacterial evaluation

Novel monocyclic β-lactam derivatives bearing aryl, phenyl and heterocyclic rings were synthesized as possible antibacterial agents. Cyclization of imines (3h, 3t) with phenylacetic acid in the presence of phosphoryl chloride and triethyl amine did not afford the expected β-lactams. Instead, highly substituted 1,3-oxazin-4-ones (4h, 4t) were isolated as the only product and confirmed by single crystal X-ray analysis of 4t. The results of antibacterial activity showed that compound 4l exhibited considerable antibacterial activity with MIC and MBC values of 62.5?µg/mL against Klebsiella pneumoniae. Cytotoxicity assay on Chinese Hamster Ovary (CHO) cell line revealed non-cytotoxic behavior of compounds 4d, 4h, 4k and 4l up to 200?μg/mL conc. Molecular docking was performed for compound 4l with penicillin binding protein-5 to identify the nature of interactions. The results of both in silico and in vitro evaluation provide the basis for compound 4l to be carried as a potential lead molecule in the drug discovery pipeline against bacterial infections.     

Calcium‐dependent behavioural responses to acute copper exposure in Oncorhynchus mykiss

Using rainbow trout Oncorhynchus mykiss, the present study demonstrated that: (1) calcium (Ca) increased the range of copper (Cu) concentrations that O. mykiss avoided; (2) Ca conserved the maintenance of pre‐exposure swimming activity during inescapable acute (10 min) Cu exposure. Data showed that when presented with a choice of Cu‐contaminated water (ranging from 0 to 454 µg Cu l^?1) and uncontaminated water in a choice tank, O. mykiss acclimated and tested at low Ca concentration (3 mg Ca l^?1) avoided the 10 µg Cu l^?1 only. By contrast, O. mykiss acclimated and tested at high Ca concentration (158 mg Ca l^?1) avoided all the Cu concentrations ≥37 µg l^?1. The Cu avoidance was connected with increased spontaneous swimming speed in the Cu‐contaminated water. When subjected to inescapable Cu exposure (35 µg Cu l^?1), O. mykiss acclimated and tested at low Ca concentration reduced their spontaneous swimming speed, whereas no response was observed in O. mykiss acclimated and tested at high Ca concentration. Collectively, the data support the conclusion that in O. mykiss the behavioural responses to acute Cu exposure are Ca‐dependent.     

Kinetics of kojic acid fermentation by Aspergillus flavus using different types and concentrations of carbon and nitrogen sources

Kinetics of kojic acid fermentation by Aspergillus flavus Link 44-1 using various sources of carbon [glucose, xylose, sucrose, starch, maltose, lactose or fructose] and nitrogen [NH₄Cl, (NH₄)₂S₂O₈, (NH₄)₂NO₃, yeast extract or peptone] were analyzed using models based on logistic and Luedeking–Piret equations. The highest kojic acid production (39.90 g l⁻¹) in submerged batch fermentation was obtained when 100 g l⁻¹ glucose was used as a carbon source. Organic nitrogen sources such as peptone and yeast extract were favorable for kojic acid production as compared to inorganic nitrogen sources. Yeast extract at 5 g l⁻¹ was optimal. The optimal carbon to nitrogen (C/N) ratio for kojic acid fermentation was 93.3. In a resuspended cell system, the rate of glucose conversion to kojic acid by cell-bound enzymes increased with increasing glucose concentration up to 70 g l⁻¹, suggesting that the reaction followed the Michaelis–Menten enzyme kinetic model. The value of K _m and V _max for the reaction was 18.47 g l⁻¹ glucose and 0.154 g l⁻¹ h⁻¹, respectively. Journal of Industrial Microbiology & Biotechnology (2000) 25, 20–24. Received 13 October 1999/ Accepted in revised form 02 April 2000     

Stopped-flow Measurement of Reaction Rate of Triose Reductone with 2,6-Dichlorophenolindophenol and Its Application to the Determination of Triose Reductone

The reduction of 2, 6-dichlorophenolindophenol by triose reductone was studied in a wide pH range (pH 2~11), using a stopped-flow apparatus. The apparent first-order rate constant, k_app, and the second-order rate constant, k, were obtained. The k-pH profile resembles that of l-ascorbic acid, though the rate of l-ascorbic acid is considerably larger than that of triose reductone. Determination of triose reductone by stopped-flow method is possible, even in the presence of various organic substances.