Phylogenetic analysis and homology modelling of <Emphasis Type="Italic">Paracentrotus lividus</Emphasis> nectin

The extracellular matrix protein Pl-nectin, a 210-kDa homodimer originally purified from sea urchin eggs, plays a crucial role in cell adhesion and embryonic morphogenesis. The compiled cDNA sequence, obtained by RT-PCR primer walking and 3′ RACE, identified a 984aa product containing a 23aa signal peptide and including all six internal peptides identified by protein microsequencing. The protein is a new member of the galactose-binding protein superfamily as it consists of six 151–156aa-long tandemly repeated domains (D1–D6), homologous to the discoidin-like domains, also known as F5/8-type C domains. Based on homology modelling, we present a three-dimensional structure (3D) for D5, identified as the prototype domain. The molecular modelling of the assembled Pl-nectin homodimer accounts for a Pl-nectin quaternary structure composed of two 105-kDa C-shaped monomers linked by a S–S bridge. The presence of an LDT motif between the first and the second exposed loops of the D2 domain suggests the binding of Pl-nectin to an integrin receptor. Altogether, the in silico analysis described here is consistent with previous biochemical reports and offers a basis for predictions to be experimentally tested.     

Stereoregular Polymerization of Alkyl Propiolate Catalyzed by Rh Complex

Abstract

The polymerizations of alkyl esters of propiolic acid by Rh complex catalysts were investigated. [Rh(norbornadiene)Cl]₂, which was the most active among the catalysts examined, gave rise to poly(alkyl propiolate) in a fairly high yield (～80%) in the presence of alcohol as the polymerization solvent. The polymers formed were a pale yellow powder soluble in common organic solvents except for poly(methyl propiolate). The structures of the polymers obtained were investigated by IR, ₁₃C-NMR, CP MAS ₁₃C-NMR, and laser Raman spectroscopies, together with the x-ray diffraction method. Based on these spectroscopic data, it was concluded that this Rh complex can be called a stereoregular polymerization catalyst of alkyl propiolate because the poly(alkyl propiolate) obtained has a cis-transoidal structure.     

Synthesis and Cation-Binding Properties of (1→6)-2,5-Anhydro-D-glucitol with 3,4-Di-O-Pentyl and Decyl Groups by Cyclopolymerization of 1,2:5,6-Dianhydro-D-mannitols

Abstract

The cyclopolymerizations of 1,2:5,6-dianhydro-3,4-di-O-pentyl-D-mannitol (1b) and 1,2:5,6-dianhydro-3,4-di-O-decyl-D-mannitol (1c) were carried out using BF₃OEt₂ and t-BuOK. All the resulting polymers consisted of cyclic constitutional units, i.e., the extent of cyclization was 100%. The polymer structures for the polymerization with t-BuOK were (1→6)-2,5-anhydro-3,4-di-O-pentyl-D-glucitol (2b) and (1→6)-2,5-anhydro-3,4-di-O-decyl-D-glucitol (2c), whereas those with BF₃O-decyl₂ comprised 2,5-anhydro-D-glucitols as major units along with other cyclic ones. These polymers were soluble in n-hexane, CHCl₃, and THF, but insoluble in water, which differs from the amphiphilic solubility of (1→6)-2,5-anhydro-3,4-di-O-methyl-D-glucitol (2a). The cation-binding properties of 2b and 2c were examined using alkali-metal picrates in order to compare them with those of 2a. The extraction yields for each cation decreased in the order of 2c < 2b < 2a. Every polymer exhibited a similar cation-binding selectivity in the order Cs⁺ > Rb⁺ > K⁺ ? Na⁺ > Li⁺. The ratio of K⁺ and Na⁺, K⁺/Na⁺, was 4.6 for 2a, 5.1 for 2b, and 7.1 for 2c in the increasing order 2a < 2b > 2c.     

2′,4′-BNA/LNA with 9-(2-Aminoethoxy)-1,3-diaza-2-oxophenoxazine Efficiently Forms Duplexes and Has Enhanced Enzymatic Resistance**

Artificial nucleic acids are widely used in various technologies, such as nucleic acid therapeutics and DNA nanotechnologies requiring excellent duplex-forming abilities and enhanced nuclease resistance. 2′-O,4′-C-Methylene-bridged nucleic acid/locked nucleic acid (2′,4′-BNA/LNA) with 1,3-diaza-2-oxophenoxazine (BNAP ( B^H )) was previously reported. Herein, a novel B^H analogue, 2′,4′-BNA/LNA with 9-(2-aminoethoxy)-1,3-diaza-2-oxophenoxazine (G-clamp), named BNAP-AEO ( B^AEO ), was designed. The B^AEO nucleoside was successfully synthesized and incorporated into oligodeoxynucleotides (ODNs). ODNs containing B^AEO possessed up to 10⁴-, 152-, and 11-fold higher binding affinities for complementary (c) RNA than those of ODNs containing 2′-deoxycytidine ( C ), 2′,4′-BNA/LNA with 5-methylcytosine ( L ), or 2′-deoxyribonucleoside with G-clamp ( P^AEO ), respectively. Moreover, duplexes formed by ODN bearing B^AEO with cDNA and cRNA were thermally stable, even under molecular crowding conditions induced by the addition of polyethylene glycol. Furthermore, ODN bearing B^AEO was more resistant to 3′-exonuclease than ODNs with phosphorothioate linkages.     

Determination of ammonium in river water and sewage samples by capillary zone electrophoresis with direct UV detection

We developed capillary zone electrophoresis (CZE) with direct UV detection for determination of ammonium in environmental water samples. Ammonium in the samples was partly converted into ammonia in the alkaline background electrolyte (BGE) during migration and was detected by molecular absorption of ammonia at 190 nm in approximately 7 min. The limit of detection (LOD) for ammonium was 0.24 mg/l (as nitrogen) at a signal-to-noise ratio of three. The respective values of the relative standard deviation (RSD) of peak area, peak height, and migration time for ammonium were 2.1, 1.8, and 0.46%. Major alkali and alkaline earth metal ions coexisting in the samples did not interfere with ammonium determination by the proposed method. The proposed method determined ammonium in surface water and sewage samples. The results were compared to those obtained using ion chromatography (IC).     

Chilling resistances of isolates of Pythium ultimum var. ultimum from the Arctic and Temperate Zones

Chilling resistances in moss pathogenic fungi, Pythium ultimum var. ultimum, from Longyearbyen, Svalbard (78 degree N, 15 degree E), located in the Arctic Zone and in the same isolates from Temperate Zone, were determined. Both strains had similar optimum growth temperatures. However, the strains from Svalbard could grow and survive at 0 - 5 degrees C. In addition, chilling treatment induced irregular mycelial morphology in the Arctic isolates. On the other hand, the isolates from Japan did not grow at temperatures below 5C and were destroyed after chilling stress (0 degree C for 3 days or at 4 degrees C for 1 week). The results suggested that isolates from Svalbard highly adapted to the severe spring condition in Polar environments.