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.     

A simple, practical and complete O-time Algorithm for RNA folding using the Four-Russians Speedup

Background  

The problem of computationally predicting the secondary structure (or folding) of RNA molecules was first introduced more than thirty years ago and yet continues to be an area of active research and development. The basic RNA-folding problem of finding a maximum cardinality, non-crossing, matching of complimentary nucleotides in an RNA sequence of length n, has an O(n ³)-time dynamic programming solution that is widely applied. It is known that an o(n ³) worst-case time solution is possible, but the published and suggested methods are complex and have not been established to be practical. Significant practical improvements to the original dynamic programming method have been introduced, but they retain the O(n ³) worst-case time bound when n is the only problem-parameter used in the bound. Surprisingly, the most widely-used, general technique to achieve a worst-case (and often practical) speed up of dynamic programming, the Four-Russians technique, has not been previously applied to the RNA-folding problem. This is perhaps due to technical issues in adapting the technique to RNA-folding.     

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.     

Listing all sorting reversals in quadratic time

We describe an average-case O(n ²) algorithm to list all reversals on a signed permutation π that, when applied to π, produce a permutation that is closer to the identity. This algorithm is optimal in the sense that, the time it takes to write the list is Ω(n ²) in the worst case.     

Design,implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics

Background  

The general problem of RNA secondary structure prediction under the widely used thermodynamic model is known to be NP-complete when the structures considered include arbitrary pseudoknots. For restricted classes of pseudoknots, several polynomial time algorithms have been designed, where the O(n ⁶)time and O(n ⁴) space algorithm by Rivas and Eddy is currently the best available program.     

Synthesis of (E)-5-(2-cIOdovinyl)-3′-0-(1-Methyl-1,4-Dihydropyridyl-3 -Carbonyl)-2′-Fluoro-2′-Deoxyuridine (Ivfru-Cds) for Brain Targetted Delivery of Ivfru,an Antiviral Nucleoside

Abstract

(E)-5-(2-lodovinyl)-2′-fluoro-3′-0-(1-methyl-1,4-dihydropyridyl-3-carbonyl)-2′-deoxyuridine (11) was synthesized for future evaluation as a lipophilic, brain-selective, pyrimidine phosphorylase-resistant, antiviral agent for the treatment of Herpes simplex encephalitis (HSE). Treatment of (E)-5-(2-iodovinyl)-2′-fluoro-2′-deoxyuridine (6) with TBDMSCI in the presence of imidazole in DMF yielded the protected 5′-O-t-butyldimethylsilyl derivative (7). Subsequent reaction with nicotinoyl chloride hydrochloride in pyridine afforded (E)-5-(-2-iodovinyl)-2′-fluoro-3′-O-(3-pyridylcarbonyl)-5′-O-t-butyldimethylsily-2′-deoxyuridine (8). Deprotection of the silyl ether moiety of 8 with n-Bu₄N⁺F^? and quaternization of the resulting 3′-O-(3-pyridylcarbonyl) derivative 9 using iodomethane afforded the corresponding 1-methylpyridinium salt 10. The latter was reduced with sodium dithionite to yield (E)-5-(2-iodovinyl)-2′-fluoro-3′-O-(1-methyl-1,4-dihydropyridyl-3-carbonyl)-2′-deoxyuridine (11).     

Synthesis of N-Arylinosines

Abstract

2′,3′,5′-Tri-O(tetrahydropyran-2-yl)inosine 1 was treated with iodobenzene or 2-bromopyridine in the presence of cuprous oxide in pyridines to give the N¹ -aryl derivatives 2a, b. Deprotection of the products afforded N¹ -arylinosines 3a, b.     

Octanuclear iron(III) complexes supported by Kemp’s tricarboxylate ligands

Reactions of FeCl₂·4H₂O and diimino ligand (L) with H₃kta (cis,cis-1,3,5-trimethylcyclohexane-1,3,5-tricarboxylic acid) in the presence of [ⁿBu₄N][OH] afforded a series of octanuclear iron(III) complexes formulated as [Fe₈O₅(kta)₂(Hkta)₄(L)₂] (L = bpy (1), 5,5′-Me₂bpy (2), 4,4′-Me₂bpy (3), phen (4), 4-Mephen (5), 4,7-Me₂phen (6), and 3,4,7,8-Me₄phen (7)). The structure of 4 was determined by X-ray crystallography to consist of a planar {Fe₈(μ₄-O)(μ₃-O)₄}¹⁴⁺ core supported by two kta³⁻ tricarboxylates, where the inner four Fe^III ions form a {Fe₄O₅} square plane, of which apex μ-oxo atoms are further connected to the outer four Fe^III ions. The peripheral part of the Fe₈ core is bridged by four Hkta²⁻ ligands and chelated by two phen ligands. ⁵⁷Fe Mössbauer spectra of 2 at 290 K and 77 K indicated the presence of high-spin octahedral Fe(III) ions, and the temperature dependent dc magnetic susceptibility data for 1, 2, and 4 showed strong antiferromagnetic exchange in the {Fe₈O₅} moiety.     

Heterometallic coordination polymers constructed by linear ligands

Eight lanthanide–copper coordination polymers of linear rigid 4-(4-pyridyl)benzoate(L¹) and isonicotinate(L²), [LnCuI(L¹)₂(OAc) (H₂O)]_n (Ln = Pr, 1; Nd, 2; Sm, 3; Eu, 4; Gd, 5), [Ln₂Cu₄I₃(L²)₇ (H₂O)]_n (Ln = La, 6; Pr, 7), and [Nd₂Cu₇I₆(L²)₇ (H₂O)₆]_n·2.5nH₂O (8), were hydrothermally synthesized and structurally characterized by single-crystal X-ray diffraction. The three-dimensional frameworks of 1–5 can be described as wave-like layer modules of [Ln(L¹)₂(OAc)(H₂O)]_n linking with each other through dimeric units of Cu₂I₂, whereas that of compounds 6 and 7 are constructed by layer modules of and Cu₄I₃ clusters. As for 8, dimeric units of Nd₂(L²)₇(H₂O)₆ connect layered polymeric forming a 3D framework.     

Synthesis, crystal structure and surface photo-electric property of a series of Co(II) coordination polymers and supramolecules

Four new Co(II) coordination complexes, [Co(o-phta)(pz)₂]_n1, [Co(PTA)₂(Imh)₂]·(HPTA)·H₂O 2, {[Co(pdc)₂(H₂O)]·(ppz)·2H₂O}_n3, [K₂Co₂(ox)(btec)(CH₃OH)₂]_n4, (H₂phta = o-phthalic acid, pz = pyrazole, HPTA = p-toluic acid, ppz = piperazine, Imh = imidazole, H₂pdc = pyridine-2,5-dicarboxylic acid, H₂(ox) = oxalic acid, H₄btec = 1,2,4,5-benzenetetracarboxylic acid), were hydrothermally synthesized and characterized by X-ray single crystal diffraction, IR, UV–Vis absorption spectrum, TG analysis and elemental analysis. The surface photovoltage properties of the four Co(II) complexes were investigated by the surface photovoltage spectroscopy (SPS). The structural analyses indicate that complexes 1 and 3 are 1D coordination polymers and complex 2 is a mononuclear molecular complex. Complexes 1, 2 and 3 are connected into 2D supramolecules by hydrogen bonds, respectively. Complex 4 is a coordination polymer with 3D structure, exhibiting a 4-nodal(4,5,6,12)-connected topology with a Schläfli symbol of (4¹⁰)₂(4²⁴·6³²·8¹⁰)(4⁵·6)₂(4⁹·6⁵·8). The results of SPS show the four complexes exhibit obvious photovoltaic responses in 300–800 nm, which indicates they all possess photo-electric conversion properties. By the comparative analysis of the SPS, it is found that structure of the complex, species of ligand and coordination micro-environment of the Co(II) ion affect the SPS. The relationships between SPS and UV–Vis absorption spectra are discussed.     

On the maximal cliques in c-max-tolerance graphs and their application in clustering molecular sequences

Given a set S of n locally aligned sequences, it is a needed prerequisite to partition it into groups of very similar sequences to facilitate subsequent computations, such as the generation of a phylogenetic tree. This article introduces a new method of clustering which partitions S into subsets such that the overlap of each pair of sequences within a subset is at least a given percentage c of the lengths of the two sequences. We show that this problem can be reduced to finding all maximal cliques in a special kind of max-tolerance graph which we call a c-max-tolerance graph. Previously we have shown that finding all maximal cliques in general max-tolerance graphs can be done efficiently in O(n ³ + out). Here, using a new kind of sweep-line algorithm, we show that the restriction to c-max-tolerance graphs yields a better runtime of O(n ² log n + out). Furthermore, we present another algorithm which is much easier to implement, and though theoretically slower than the first one, is still running in polynomial time. We then experimentally analyze the number and structure of all maximal cliques in a c-max-tolerance graph, depending on the chosen c-value. We apply our simple algorithm to artificial and biological data and we show that this implementation is much faster than the well-known application Cliquer. By introducing a new heuristic that uses the set of all maximal cliques to partition S, we finally show that the computed partition gives a reasonable clustering for biological data sets.     

Interaction of (2′ -5′) and (3′ -5′) Linked 2-Aminoadenylyl-3-aminoadenosines with Polyuridylic Acid

Abstract

2′-5′ and 3′-5′ linked 2-aminoadenylyl-2-aminoadenosines [(2′-5′)n²Apn²A (1) and (3′-5′)n²Apn²A (2)] were synthesized by condensation of 5′-O-monomethoxytrityl-N ² N ⁶-dibenzoyl-2-aminoadenosine and N ²,N ⁶,2′,3′-O-tetrabenzoyl-2-aminoadenosine 5′-phosphate using dicyclohexylcarbodiimide (DCC). The conformational properties of these dimers 1 and 2 were examined by UV, NMR and CD spectroscopy. The results reveal that the 2′-5′-isomer 1 takes a stacked conformation, which contains a larger base-base overlap and is more stable against thermal perturbation with respect to the 3′-5′-isomer 2. Interactions of 1 and 2 with polyuridylic acid (Poly (U)) were also examined by Tm, mixing curves, UV and CD spectra. Both the dinucleoside isomers 1 and 2 formed a complex of 1 : 2 stoichiometry with poly(U), which was much more stable than that of the corresponding ApA isomer     

DNA sequence-specific ligands: XIV. Synthesis of fluorescent biologically active dimeric bisbenzimidazoles DB(3, 4, 5, 7, 11)

Five fluorescent symmetrical dimeric bisbenzimidazoles DB(n) containing four 2,6-substituted benzimidazole cores and differing in the length of the oligomethylene linker between two bisbenzimidazole rings (n = 3, 4, 5, 7, 11) have been synthesized. The ability of the dimeric bisbenzimidazoles to form complexes with the double-stranded DNA has been shown by spectral methods. Upon binding to the double-stranded DNA, DB(n) are localized in the narrow groove. The data on the inhibition of the DNA methyltransferase Dnmt3a by DB(n) indicate that dimeric bisbenzimidazoles DB(3) and DB(11) site-specifically bind to the oligonucleotide duplex.     

Genomic dispersion of 28S rDNA during karyotypic evolution in the ant genusMyrmecia (formicidae)

Figure 2a–r of the above article is reprinted here at the request of the author because the print quality was not up to standard in the issue. Fig. 2a–r. Localization of 28S rDNA (white arrowheads) by fluorescence in situ hybridization of preparations from various Myrmecia species with different chromosome numbers. a–d, i–m Hybridized in situ and propidium iodide-stained chromosomes. e–h, n–r 4’,6-diamidino-2-phenylindole-stained chromosomes. a, e M. croslandi (2n=4). b, f M. pilosula (2n=22); the inset in b shows repeated layers of rDNA-positive signals in C-band. c, g M. pilosula (2n=23). d, h M. gulosa (2n=38). i, n M. forficata (2n=52). j, o M. mandibularis (2n=56). k, p Myrmecia sp. cf. M. arnoldi (2n=60) i, q M. occidentalis (2n=64) m, r M. simillima (2n=70). Bars represent 10 μm. The long bar in h applies also to d; the short bar in r to all other panels Chromosoma (1996) 105:190–196 Received: 22 March 1996; in revised form: 3 June 1996 / Accepted: 4 June 1996     

Efficient maximum likelihood pedigree reconstruction

A simple and efficient algorithm is presented for finding a maximum likelihood pedigree using microsatellite (STR) genotype information on a complete sample of related individuals. The computational complexity of the algorithm is at worst (O(n³2ⁿ)), where n is the number of individuals. Thus it is possible to exhaustively search the space of all pedigrees of up to thirty individuals for one that maximizes the likelihood. A priori age and sex information can be used if available, but is not essential. The algorithm is applied in a simulation study, and to some real data on humans.     

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.     

Biosynthesis of novel daidzein derivatives using Bacillus amyloliquefaciens whole cells

Abstract

Biotransformation of daidzein was performed by using Bacillus amyloliquefaciens KCTC 13588, Lactococcus lactis subsp. lactis KCTC 3769, Leuconostoc citreum KCTC 13186, Kluyveromyces lactis var. lactis KCTC 17704, Pediococcus pentosaceus KCTC 3116, and Lactobacillus sakei KCTC 13416 cells as a biocatalyst. Four derivatives of daidzein such as daidzein-7-O-phosphate, daidzein-7-O-β-D-glucoside, daidzein-7-O-β-(6′′-O-succinyl)-D-glucoside, and 4′-Ethoxy-daidzein-7-O-β-(6′′-O-succinyl)-D-glucoside were isolated from the biotransformation reaction mixture. The structures of the molecules were elucidated by HPLC, HR-QTOF-ESI/MS and ¹H-NMR analyses. Among them 4′-Ethoxy-daidzein-7-O-β-(6′′-O-succinyl)-D-glucoside derivative is novel compound and not reported elsewhere till now.     

Determination of tannic acid in industrial wastewater based on chemiluminescence system of KIO4–H2O2–Tween40

The oxidation reaction of H₂O₂ with KIO₄ can produce chemiluminescence (CL) in the presence of the surfactant Tween40 and the CL intensity of the CL system KIO₄–H₂O₂–Tween40 can be strikingly enhanced after injection of tannic acid. On this basis, a flow injection method with CL detection was established for the determination of tannic acid. The method is simple, rapid and effective to determine tannic acid in the range of 7.0 × 10^?9 to 1.0 × 10^?5 mol/L with a determination limit of 2.3 × 10^?9 mol/L. The relative standard deviation is 2.6% for the determination of 5.0 × 10^?6 mol/L tannic acid (n = 11). The method has been applied to determine the content of tannic acid in industrial wastewater with satisfactory results. It is believed that the CL reaction formed singlet oxygen ¹O₂* and the emission was from an excited oxygen molecular pair O₂(¹Δ_g)O₂(¹∑^?_g) in the KIO₄–H₂O₂–Tween40 reaction. Tween40 played an important role in enhancing stabilization of the excited oxygen molecular pair O₂(¹Δ_g)O₂(¹∑^?_g) and in increasing CL intensity. Copyright © 2010 John Wiley & Sons, Ltd.     

Density functional theory molecular modelling,DNA interactions,antioxidant, antimicrobial,anticancer and biothermodynamic studies of bioactive water soluble mixed ligand complexes

A novel series of bioactive water soluble mixed ligand complexes (1–5) [M^II(L)(phen)AcO]. nH₂O {where M?=?Cu (1) n?=?2; Co (2), Mn (3), Ni (4), n?=?4 and Zn (5) n?=?2} were synthesized from 2-(2-Morpholinoethylimino) methyl)phenol Schiff base ligand (LH), 1, 10-phenanthroline and metal(II) acetate salt in a 1:1:1 stoichiometric ratio and characterized by several spectral techniques. The obtained analytical and spectral data suggest the octahedral geometry around the central metal ion. Density functional theory calculations have been further supportive to explore the optimized structure and chemical reactivity of these complexes from their frontier molecular orbitals. Gel electrophoresis result indicates that complex (1) manifested an excellent DNA cleavage property than others. The observed binding constants with free energy changes by electronic absorption technique and DNA binding affinity values by viscosity measurements for all compounds were found in the following order (1)?>?(2)?>?(4)?>?(5)?>?(3) > (LH). The binding results and thermodynamic parameters are described the intercalation mode. In vitro antioxidant properties disclose that complex (1) divulges high scavenging activity against DPPH^?, ^?OH, O₂^?? NO^?, and Fe³⁺. The antimicrobial reports illustrate that the complexes (1–5) were exhibited well defined inhibitory effect than ligand (LH) against the selected different pathogenic species. The observed percentage growth inhibition against A549, HepG2, MCF-7, and NHDF cell lines suggest that complex (1) has exhibited superior anticancer potency than others. Thus, the complex (1) may contribute as potential anticancer agent due to its unique interaction mode with DNA.GRAPHICAL ABSTRACT

Communicated by Ramaswamy H. Sarma     

Optimized ancestral state reconstruction using Sankoff parsimony

Background  

Parsimony methods are widely used in molecular evolution to estimate the most plausible phylogeny for a set of characters. Sankoff parsimony determines the minimum number of changes required in a given phylogeny when a cost is associated to transitions between character states. Although optimizations exist to reduce the computations in the number of taxa, the original algorithm takes time O(n ²) in the number of states, making it impractical for large values of n.