An improved algorithm for statistical alignment of sequences related by a star tree

The insertion-deletion model developed by Thorne, Kishino and Felsenstein (1991, J. Mol. Evol., 33, 114–124; the TKF91 model) provides a statistical framework of two sequences. The statistical alignment of a set of sequences related by a star tree is a generalization of this model. The known algorithm computes the probability of a set of such sequences in O(l ^2k ) time, where l is the geometric mean of the sequence lengths and k is the number of sequences. An improved algorithm is presented whose running time is only O(2^2k l ^k).     

An optimal algorithm to reconstruct trees from additive distance data

In this article the question of reconstructing a phylogeny from additive distance data is addressed. Previous algorithms used the complete distance matrix of then OTUs (Operational Taxonomic Unit), that corresponds to the tips of the tree. This usedO(n ²) computing time. It is shown that this is wasteful for biologically reasonable trees. If the tree has internal nodes with degrees that are bounded onO(n*log(n)) algorithm is possible. It is also shown if the nodes can have unbounded degrees the problem hasn ² as lower bound.     

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.     

Assessing good operating conditions for intraoperative imaging of melanoma sentinel nodes by a portable gamma camera

ObjectiveTo provide guidance for reliable identification of low-activity sentinel nodes in the setting of melanoma surgery using a commercial hand-held gamma camera.MethodsThe average uptake of ^99mTc nanocolloid by sentinel nodes was evaluated in 95 excised nodes using a Sentinella 102^® (Oncovision, Valencia, Spain) portable gamma camera. The device sensitivity was assessed for different source depths and collimator distances, imaging an 8-mm sphere filled with a known-activity solution of ^99mTc. Five nuclear medicine physicians were asked to identify the source at different activity levels and positions within the field of view. For each image the number of signal counts inside a circular region of interest (ROI) was measured, while the variability of ROI counts among operators was assessed. The number of counts providing a minimal, near-constant inter-operator variability was determined as a criterion for a consistent identification of the source. Either the minimum activity or the acquisition time needed to collect the appropriate statistics were then calculated.ResultsThe median SN uptake (0.5%) turned out to be compatible with values reported in the literature. The sensitivity of the compact gamma camera ranged from ∼25 cpm/kBq to ∼1 cpm/kBq. A total of 50 counts in the ROI circumscribing the lymph node-simulating sphere appeared to be a robust criterion for identification of the source.ConclusionsTen megabecquerels of injected activity at the time of surgery and one minute of acquisition allows reliable identification of sentinel nodes for collimator-to-source distances up to 10 cm.     

Kinetic study of DNA binding of cisplatin and of a bicycloalkyl-substituted (ethylenediamine)dichloroplatinum(II) complex

 Salmon sperm DNA platination has been conducted under strictly pseudo-first-order conditions with cisplatin (1) and rac-{(1S,2S,4S)-exo-2-(aminomethyl)-2-amino-7-bicyclo[2.2.1]heptane}dichloroplatinum(II) (2). An aquation step first occurs for both complexes, with the rate constants k ₁ = 1.12(0.02)×10^–4 s^–1 and 1.47(0.02)×10^–4 s^–1 respectively for 1 and 2 at 37  °C, values in agreement with those previously reported. It is followed by the actual platination step whose second-order rate constant has been determined for the first time by physicochemical techniques. The values for 1 and 2 respectively are: k ₂ = 2.08(0.07) M^–1 s^–1 and 3.9(0.4) M^–1 s^–1. These kinetic data are discussed in the context of a comparison of several biological properties of the two complexes. Received: 15 May 1998 / Accepted: 26 June 1998     

Adsorption Mechanism of Cr(VI) onto Coir Pith

Reductive adsorption of Cr(VI) on coir pith (hereafter CP) was examined as a function of pH, ionic strength, and temperature. The CP contains 1.33 meq g^{? 1} phenolic, 0.43 meq g^{? 1} of lactonic, and 0.35 meq g^{? 1} carboxylic sites. Thus the CP surface is enriched with electron-donating oxygen functionalities. As evidenced by infrared (IR) spectroscopy, the Cr(VI) → Cr(III) conversion is facilitated by CP sites that are enriched with O─ O functional groups. The adsorption of reduced Cr(VI) was found to occur via C─ O─ functional groups first forming innersphere complexes with the CP surface, yielding keto (> C═ O) groups on the CP surface. The reductive adsorption of Cr(VI) was almost completed within 3 to 4 h, and it was dependent on pH and background ionic strength, yielding the highest monolayer coverage (9.56E-7 mol m^{? 2}) at pH 3.7 in 0.1 M NaNO₃. The Γ_Cr(III) followed the order with respect to the ionic strength: Γ_{0.1 M} > Γ_{0.01 M} > Γ_{0.001 M}. The initial rate constant, k _i , increased with temperature as k _i ^{313 K} > k _i ^{303 K} > k _i ^{293 K} > k _i ^{283 K}.     

Spin Trapping by Use of N-Tert-Butylhydroxylamine. Involvement of Fenton Reactions

Spin trapping of short-lived R. radicals is done by use of N-tert-butylhydroxylamine (1) and H²O². The hydroxylamine is oxidized to the radical t-BuN(O)H (2) which is converted into the spin trap 2-methyl-2-nitrosopropane (3). Simultaneously, hydroxyl radicals. OH are formed from H²O². The latter radical species abstracts hydrogen atoms from suitable molecules HR to give R. radicals, which are trapped with the formation of aminooxyl radicals, i. e., t-BuN(O)R (4) detectable by EPR spectroscopy. The reaction is enhanced by the presence of iron ions. The cleavage of H²O² into. OH radicals is considered to involve both a radical-driven (t-BuN(O)H 2) and an iron-driven Fenton reaction.     

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     

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.     

Design,synthesis and in vitro biological evaluation of quinazolinone derivatives as EGFR inhibitors for antitumor treatment

Abstract

In this paper, a series of novel 3-methyl-quinazolinone derivatives was designed, synthesised and evaluated for antitumor activity in vitro on wild type epidermal growth factor receptor tyrosine kinase (EGFR^wt-TK) and three human cancer cell lines including A549, PC-3, and SMMC-7721. The results displayed that some of the compounds had good activities, especially 2-{4-[(3-Fluoro-phenylimino)-methyl]-phenoxymethyl}-3-methyl-3H-quinazolin-4-one (5?g), 2-{4-[(3,4-Difluoro-phenylimino)-methyl]-phenoxymethyl}-3-methyl-3H-quinazolin-4-one (5k) and 2-{4-[(3,5-Difluoro-phenylimino)-methyl]-phenoxymethyl}-3-methyl-3H-quinazolin-4-one (5?l) showed high antitumor activities against three cancer cell lines. Moreover, compound 5k could induce late apoptosis of A549 cells at high concentrations and arrest cell cycle of A549 cells in the G2/M phase at tested concentrations. Also, compound 5k could inhibit the EGFR^wt-TK with IC₅₀ value of 10?nM. Molecular docking data indicates that the compound 5k may exert inhibitory activity by forming stable hydrogen bonds with the R817, T830 amino acid residues and cation-Π interaction with the K72 residue of EGFR^wt-TK.     

Kinetic studies on the reactions of Fusarium galactose oxidase with five different substrates in the presence of dioxygen

 Reactions (25  °C) of galactose oxidase, GOase_ox from Fusarium NRRL 2903 with five different primary-alcohol-containing substrates RCH₂OH:- D-galactose (I) and 2-deoxy-d-galactose (II) (monosaccharides); methyl-β-d-galactopyranoside (III) (glycoside);d-raffinose (IV) (trisaccharide); and dihydroxyacetone (V) have been studied in the presence of O₂. The GOase_ox state has a tyrosyl radical coordinated at a square-pyramidal Cu^II active site, and is a two-equivalent oxidant. Reactant concentrations were [GOase_ox] (0.8–10 μM), RCH₂OH (1.0–6.0 mM), and O₂ (0.14–0.29 mM), with I=0.100 M (NaCl). The reactions, monitored at 450 nm by stopped-flow spectrophotometry, terminated with depletion of the O₂. Each trace was fitted to the competing reactions GOase_ox+RCH₂ OH → GOase_redH₂+RCHO (k ₁), and GOase_redH₂+O₂→ GOase_ox+H₂O₂ (k ₂), with GOase_redH₂ written as the doubly protonated two-electron-reduced Cu^I product. It was necessary to avoid auto-redox interconversion of GOase_ox and GOase_semi . Information obtained at pH 7.5 indicates a 5 : 95 (ox : semi) "native" mix equilibration complete in ∼3 h. At pH >7.5, rate constants 10^–4 k ₁ / M^–1 s^–1 for the reactions of GOase_ox with (I) (1.19), (II) (1.07), (III) (1.29), (IV) (1.81), (V) (2.94) were determined. On decreasing the pH to 5.5, k ₁ values decreased by factors of up to a half, and acid dissociation pK _as in the range 6.6–6.9 were obtained. UV-Vis spectrophotometric studies on GOase_ox gave an independently determined pK _a of 6.7. No corresponding reactions of the Tyr495Phe variant were observed, and there are no similar UV-Vis absorbance changes for this variant. The pK _a is therefore assigned to protonation of Tyr-495 which is a ligand to the Cu. The rate constant k ₂ (1.01×10⁷ M^–1 s^–1) is independent of pH in the range 5.5–9.0 investigated, suggesting that H⁺ (or H-atoms) for the O₂ → H₂O₂ change are provided by the active site of GOase_red . The Cu^I of GOase_red is less extensively complexed, and a coordination number of three is likely. Received: 4 February 1997 / Accepted: 16 May 1997     

Kinetic study of aroxyl radical-scavenging action of vitamin E in membranes of egg yolk phosphatidylcholine vesicles

Vitamin E is localized in membranes and functions as an efficient inhibitor of lipid peroxidation in biological systems. In this study, we measured the reaction rates of vitamin E (α-, β-, γ-, δ-tocopherols, TocH) and tocol with aroxyl radical (ArO) as model lipid peroxyl radicals in membranes by stopped-flow spectrophotometry. Egg yolk phosphatidylcholine (EYPC) vesicles were used as a membrane model. EYPC vesicles were prepared in the aqueous methanol solution (MeOH:H₂O = 7:3, v/v) that gave the lowest turbidity in samples. The second-order rate constants (k_s) for α-TocH in MeOH/H₂O solution with EYPC vesicles were apparently 3.45 × 10⁵ M⁻¹ s⁻¹, which was about 8 times higher than that (4.50 × 10⁴ M⁻¹ s⁻¹) in MeOH/H₂O solution without EYPC vesicles. The corrected k_s of α-TocH in vesicles, which was calculated assuming that the concentration of α-TocH was 133 times higher in membranes of 10 mM EYPC vesicles than in the bulk MeOH/H₂O solution, was 2.60 × 10³ M⁻¹ s⁻¹, which was one-seventeenth that in MeOH/H₂O solution because of the lower mobility of α-TocH in membranes. Similar analyses were performed for other vitamin E analogues. The k_s of vitamin E in membranes increased in the order of tocol < δ-TocH < γ-TocH ∼ β-TocH < α-TocH. There was not much difference in the ratios of reaction rates in vesicles and MeOH/H₂O solution among vitamin E analogues [k_s(vesicle)/k_s (MeOH/H₂O) = 7.7, 10.0, 9.5, 7.4, and 5.1 for α-, β-, γ-, δ-TocH, and tocol, respectively], but their reported ratios in solutions of micelles and ethanol were quite different [k_s(micelle)/k_s(EtOH) = 100, 47, 41, 15, and 6.3 for α-, β-, γ-, δ-TocH, and tocol, respectively]. These results indicate that the reaction sites of vitamin E analogues were similar in vesicle membranes but depended on hydrophobicity in micelle membranes, which increased in the order of tocol < δ-TocH < γ-TocH ∼ β-TocH < α-TocH.     

NMR Study on The Tuning of North ⇆ South Equilibrium in Nucleos(t)ides by Metal Ion Interactions

Abstract

The NMR study on the interactions of dGpMe (1), MepdG (2) and dG (3) with Mg²⁺, Zn²⁺ and Hg²⁺ ions in D₂O solution has shown that binding of softer metal ions to N7 shifts N ? S pseudorotational equilibrium towards N-type conformations. At the same time the population of the anti conformers is slightly increased.     

Essai d'interprétation des cinétiques d'échange isotopique entre C18O2 et eau d'une feuille: Expériences à l'obscurité

Summary The interpretation of photosynthesis experiments using ¹⁸O as a tracer becomes very difficult on account of the exchange rate between oxygen atoms of carbon dioxide and water. The mathematical analysis of the kinetics of isotope exchange between CO₂ highly enriched with ¹⁸O and the water of an aerial leaf kept in darkness allows the determination of two velocity coefficients, k _e and k. k _e, related to the gaseous CO₂ diffusion, makes it possible to evaluate the CO₂ flow between the gaseous phase and the leaf, as well as the diffusion resistance of the boundary layer and the leaf stomata. k, related to the CO₂ hydration, gives the in situ enzymic activity of carbonic anhydrase. Measurements carried out on a great number of leaves show that k _e and k vary in the same direction.In addition, a simple relation exists between the isotopic composition of the gaseous phase and the corresponding values of the C¹⁸O₂ inside the leaf. Thus it is possible to determine the conditions for a leaf that may be favourable for light experiments designed to ascertain the origin of photosynthetic oxygen by use of ¹⁸O.     

Fast computing betweenness centrality with virtual nodes on large sparse networks

Betweenness centrality is an essential index for analysis of complex networks. However, the calculation of betweenness centrality is quite time-consuming and the fastest known algorithm uses O(N(M + N log N)) time and O(N + M) space for weighted networks, where N and M are the number of nodes and edges in the network, respectively. By inserting virtual nodes into the weighted edges and transforming the shortest path problem into a breadth-first search (BFS) problem, we propose an algorithm that can compute the betweenness centrality in O(wDN2) time for integer-weighted networks, where w is the average weight of edges and D is the average degree in the network. Considerable time can be saved with the proposed algorithm when w < log N/D + 1, indicating that it is suitable for lightly weighted large sparse networks. A similar concept of virtual node transformation can be used to calculate other shortest path based indices such as closeness centrality, graph centrality, stress centrality, and so on. Numerical simulations on various randomly generated networks reveal that it is feasible to use the proposed algorithm in large network analysis.     

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).     

34S/32S and 18O/16O Fractionation During Sulfur Disproportionation by Desulfobulbus propionicus

In the present study, coupled stable sulfur and oxygen isotope fractionation during elemental sulfur disproportionation according to the overall reaction: 4H₂O + 4S^? → 3H₂S + SO₄ ^{2 ?} + 2H⁺, was experimentally investigated for the first time using a pure culture of the sulfate reducer Desulfobulbus propionicus at 35^?C. Bacterial disproportionation of elemental sulfur is an important process in the sulfur cycle of natural surface sediments and leads to the simultaneous formation of sulfide and sulfate. A dual-isotope approach considering both sulfur and oxygen isotope discrimination has been shown to be most effective in evaluating specific microbial reactions. The influence of iron- and manganese bearing-solids (Fe(II)CO₃, Fe(III)OOH, Mn(IV)O₂) acting in natural sediments as scavengers for hydrogen sulfide, was considered, too. Disproportionation of elemental sulfur was observed in the presence of iron solids at a cell-specific sulfur disproportionation rate of about 10^{? 9.5± 0.4} μ mol S^? cell^{? 1} h^{? 1}. No disproportionation, however, was observed with MnO₂. In the presence of iron solids, newly formed sulfate was enriched in ¹⁸ O compared to water by about +21‰ (≡ ? _H2O ), in agreement with a suggested oxygen isotope exchange via traces of intra- or extracellular sulfite that is formed as a disproportionation intermediate. Dissolved sulfate was also enriched in ³⁴S compared to elemental sulfur by up to +35%. Isotope fractionation by Desulfobulbus propionicusis highest for all disproportionating bacteria investigated, so far, and may impact on the development of isotope signals at the redox boundary of surface sediments.     

Decarboxylation kinetics for the carbonatotris(pyridine)cobalt(III) ion in perchloric acid solutions

The kinetics of the decomposition reactions of the CO(py)₃(CO₃)(H₂O)⁺ ion have been investigated in aqueous perchloric acid solutions over a range of hydrogen ion concentrations (0.10 to 5.0 M) and at two ionic strengths (I = 1.0 and 5.0 M). At the lower ionic strength, plots of ln (A_t–A_∞ versus time show a nonlinearity that is consistent with that expected for consecutive first-order reactions. The rates of the faster reaction are similar to those reported for the spontaneous reduction of aquopyridine-cobalt(III) cations. At the higher ionic strength, the above noted curvature is not apparent and the decarboxylation kinetics of the title complex may be described by a pseudo-first-order rate constant: k_obs = k[H₃O⁺]. At 20°C, k = (1.75−+0.09) s⁻¹ M⁻¹ with activation parameters ofΔH^‡ = (97 −+ 4) kJ mol⁻¹ and ΔS^‡ = −(54 −+ 32) J deg⁻¹ mol⁻¹. These kinetic parameters are compared with those previously reported for the similar complexes, Co(py)₄CO₃⁺ and Co(py)₂(CO₃)(H₂O)₂⁺.     

Rapid in vitro propagation of Holarrhena antidysenterica using seedling cotyledonary nodes

A rapid in vitro propagation of Holarrhena antidysenterica has been developed. Seedling cotyledonary nodes on Murashige and Skoog medium (MS) containing 2 mg dm⁻³ N⁶-benzyladenine (BA) produced highest number of multiple shoots. The shoot numbers were increased further upon subculture on MS medium supplemented with 0.5 mg dm⁻³ BA. By repeated subculture of derived shoots, a high multiplication rate was established. The excised shoots were rooted on MS basal medium without growth regulators. The in vitro formed shoots were also rooted ex vitro by dipping them in 2 mg dm⁻³ of indole-3-butyric acid (IBA) solution for 2 min before transferring them onto the hardening medium. Successful hardening and further establishment (survival 90 %) of micropropagated plants under natural conditions was observed.     

Quantitative Structure-Activity Relationships for the Pre-Steady State of <Emphasis Type="Italic">Pseudomonas Species</Emphasis> Lipase Inhibitions by <Emphasis Type="Italic">p</Emphasis>-Nirophenyl-<Emphasis Type="Italic">N</Emphasis>-Substituted Carbamates

The pre-steady states of Pseudomonas species lipase inhibitions by p-nitrophenyl-N-substituted carbamates (1–6) are composed of two steps: (1) formation of the non-covalent enzyme–inhibitor complex (E:I) from the inhibitor and the enzyme and (2) formation of the tetrahedral enzyme–inhibitor adduct (E–I) from the E:I complex. From a stopped-flow apparatus, the dissociation constant for the E:I complex, K_S, and the rate constant for formation of the tetrahedral E–I adduct from the E:I complex, k₂ are obtained from the non-linear least-squares of curve fittings of first-order rate constant (k_obs) versus inhibition concentration ([I]) plot against k_obs=k₂+k₂[I]/(K_S+[I]). Values of pK_S, and log k₂ are linearly correlated with the σ^* values with the ρ^* values of −2.0 and 0.36, respectively. Therefore, the E:I complexes are more positive charges than the inhibitors due to the ρ^* value of −2.0. The tetrahedral E–I adducts on the other hand are more negative charges than the E:I complexes due to the ρ^* value of 0.36. Formation of the E:I complex from the inhibitor and the enzyme are further divided into two steps: (1) the pre-equilibrium protonation of the inhibitor and (2) formation of the E:I complex from the protonated inhibitor and the enzyme.