Hydrogen bonding in nucleosides and nucleotides

An analysis of the hydrogen bonding in 76 nucleoside and 11 nucleotide crystal structures shows that the hydrogen bond lengths fall into well-defined categories according to the nature of the donor or acceptor groups. The shortest bonds are those involving P---OH or O=P groups. For donor groups, the sequence in bond lengths is

P—OH<C—OH< N−H<O_w(H)—H<N(H)—H<C−H

There are ten examples of two centre

H—H…O

bonds, which are comparable in length with P---OH …O bonds. The acceptor seqeunce is

O=P<OH₂<OH₂<O=CO(H)C<N N(H₂)C<Cl^…<O<S=C

The number of three-centre bonds, about 24%, is comparable to that observed in the carbohydrates and the amino acids. Most hydrogen bonds are involved in short finite chains. Only in the nucleotides are cyclic hydrogen bonding schemes observed.     

Seagrass depth limits

Examination of the depth limit of seagrass communities distributed worldwide showed that sea-grasses may extend from mean sea level down to a depth of 90 m, and that differences in seagrass depth limit (Z_c) are largely attributable to differences in light attenuation underwater (K). This relationship is best described by the equation

log Z_c (m) = 0.26 − 1.07 log K (m⁻)

that holds for a large number of marine angiosperm species, although differences in seagrass growth strategy and architecture also appear to contribute to explain differences in their depth limits. The equation relating seagrass depth limit and light attenuation coefficient is qualitatively similar to previous equations developed for freshwater angiosperms, but predicts that seagrasses will colonize greater depths than freshwater angiosperms in clear (transparency greater than 10 m) waters. Further, the reduction in seagrass biomass from the depth of maximum biomass towards the depth limit is also closely related to the light attenuation coefficient. The finding that seagrasses can extend to depths receiving, on average, about 11% of the irradiance at the surface, together with the use of the equation described, may prove useful in the identification of seagrass meadows that have not reached their potential extension.     

NMR studies of succinoglycan repeating-unit octasaccharides from Rhizobium meliloti and Agrobacterium radiobacter

Complete ¹H and ¹³C-nuclear magnetic resonance assignments have been obtained for the octasaccharide repeating units of the bacterial polysaccharide succinoglycan from Rhizobium meliloti Rm1021 and Agrobacterium radiobacter NCIB 11883. The assignments were used to determine the locations of the O-succinyl and O-acetyl substituents. The O-acetyl substituent in Rm1021 was attached to the 3rd residue from the reducing end, and the O-succinyl group was attached to the 7th residue in both octasaccharides. The structure of the Rm1021 octasaccharide is as shown below:

A small amount of succinate was also attached to C6 of the 6th residue in both octasaccharides.     

Spectrophotometric detection of methyl cellulose–manganate(VI) intermediate complex in the oxidation of methyl cellulose by alkaline permanganate

The formation of (methyl cellulose (MC)–Mn^(VI)O²⁻₄)

where C₂ is a metastable state that interconverts into the [MC–Mn^(VI)O₄⁻] ester intermediate, during the oxidation of methyl cellulose polysaccharide at pH≥12, was followed kinetically by spectrophotometric methods. The reaction was found to be first-order kinetics in [MnO⁻₄] and a fractional order in [MC]. Kinetic and spectrophotometric data confirmed the base-catalysed formation of Mn(VI) intermediate complex. A mechanism in agreement with the experimental data was assumed and discussed.     

Stress relaxation function of bone and bone collagen

Relaxation Young's and shear moduli of bovine bone and bone collagen were investigated. It was found that each relaxation process observed had two stages, which were referred to as process I and process II in order of time. Process II was described by a simple exponential decay while process I was not. The Kohlrausch-Williams-Watts (KWW) function, ψ(t) = exp[t/τ₁)^B] (0 < B < 1), was found to be suitable to describe process I. The normalized relaxation modulus, M_r(t), was expressed by the combination of the simple exponential type relaxation function and the KWW function

M_r=A₁exp[−(t/τ₁)^B]+A₂exp[(t/τ₁)](0<B1)

On the basis of this equation, the relaxation mechanism in bone and bone collagen was identified. According to the model proposed for the KWW relaxation function, the stress relaxation process in bone was considered to be governed by viscoelastic properties of matrix collagen fiber. The model for the KWW relaxation function requires the disordered glassy structure of collagen fiber, which is consistent with the results of the structural investigations.     

The nature of driving forces for passive water transport through arthropod cuticle

1. 1.|We demonstrate using thermodynamic arguments that water loss through arthropod epicuticle is well described by a linear law relating water flux to transmembrane vapour pressure drop.

2. 2.|The relationship applies equally to systems where the liquid or vapour exist on either side of a membrane.

3. 3.|An earlier claim by some workers that water diffusion through arthropod epicuticle is proportional to chemical potential drop across the membrane is found to be theoretically unjustified.

4. 4.|Recent measurements with Periplaneta cuticle support the prediction that flux at a given temperature is proportional to the difference in vapour pressure.

The structure of a polysaccharide isolated from Inonotus levis P. Karst. mushroom (Heterobasidiomycetes)

Inonotus levis biomass was extracted with 5% NaOH containing NaBH₄, the insoluble material was discarded and the solution dialyzed. It was further treated with proteinase and the polymeric fraction isolated by gel chromatography. It contained mostly a polysaccharide of the following structure:

β-GlcA-(1→2)--Gal-(1→6)--Gal3OMe-(1→[→6)--Gal-(1→6)--Gal3OMe-(1→]_5–10

where a non-reducing terminal glucuronic acid residue was present in about half of the molecules, making thus some of the chains acidic and others neutral. Methyl groups were present at about half of the galactose residues, however, no direct proof of the presence of defined repeating units was obtained due to NMR signals overlap. We believe that these short polymeric chains might be originally attached to a protein via serine or threonine residues and were cleaved off due to the alkaline conditions of extraction. Another polymer, co-extracted with this galactan, was a branched phosphorylated mannan with a structure similar to that of the mannan from Saccharomyces cerevisiae yeast.     

Ultrastructure and histochemistry of the digestive tract of juvenile Paramphistomum epiclitum (Paramphistomidae: Digenea) during migration in Indian ruminants.

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and 1992. Ultrastructure and histochemistry of the digestive tract of juvenile Paramphistomum epiclitum (Paramphistomidae: Digenea) during migration in Indian ruminants. International Journal for Parasitology 22: 1089–1101. The digestive tract of juvenile Paramphistomum epiclitum consists of a foregut with a highly muscular terminal pharynx and an oesophagus, which leads to a pair of unbranched and blind-ending intestinal caeca. A syncytium lining the foregut is continuous with the external tegument and displays similar sensory papillae and secretory bodies (T1 and T2). A third type of secretory body (T3) is confined to the oesophageal cytons of newly excysted juveniles and is first evident in the syncytium by day 14 of migration. An epithelium lining the caeca is composed of a single layer of morphologically uniform cells whose apical surface is amplified by microvilli. Dense secretions synthesized in the caecal epithelium of mature cercariae are released during migration by a mechanism resembling modified apocrine discharge. The caecal epithelium of migrating juveniles undergoes a 10-fold increase in surface amplification (irrespective of growth) during its transition from a primarily secretory tissue to one apparently specialized for absorption.     

Structure of a rhamnan from the surface-layer glyco-protein of Bacillus stearothermophilus strain NRS 2004/3a

The structure of a glycan from the surface-layer glycoprotein of Bacillus stearothermophilus strain NRS 2004/3a has been studied by ¹H- and ¹³C-n.m.r. spectroscopy. The results indicate the glycan to be a polymer of the trisaccharide repeating-unit

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Extracellular polysaccharide of Erwinia chrysanthemi Ech6

Many strains of Erwinia chrysanthemi, which are Gram-negative bacterial phytopathogens, produce copious amounts of extracellular polysaccharides. The extracellular polysaccharide from E. chrysanthemi pv. zeae strain SR 260, a phytopathogen of corn, is a branched-chain glucomannorhamnan of proven structure (Gray et al., Carbohydr. Res. 1993, 245, 271–287). The extracellular polysaccharide from E. chrysanthemi Ech6 is different, containing no rhamnose or mannose. It is composed of -fucose, -galactose, -glucose and -glucuronic acid in the ratio 2:2:1:1. The structure of the polysaccharide is as follows:

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The exopolysaccharides produced by Streptococcus thermophilus Rs and Sts have the same repeating unit but differ in viscosity of their milk cultures

The polysaccharides produced by Streptococcus thermophilus Rs and Sts in skimmed milk consist of -Gal and -Rha in a molar ratio of 5:2. Linkage analysis and 1D/2D NMR (¹H and ¹³C) studies revealed that both polysaccharides have the same branched heptasaccharide repeating unit:

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Remarkably, the two strains differ in their effects on the viscosity of stirred milk cultures. The milk culture of S. thermophilus Rs is non-ropy and affords 135 mg/L polysaccharide with an average molecular mass of 2.6×10³ kDa. In contrast, the milk culture of S. thermophilus Sts is ropy and produces 127 mg/L polysaccharide with an average molecular mass of 3.7×10³ kDa. Permeability measurements of non-stirred milk cultures of both strains suggest that both strains have a similar effect on the protein–polysaccharide network. Therefore, the only clear difference between both strains, which may cause the difference in ropiness of the milk cultures, is the difference in molecular mass of the polysaccharide.     

The structure of the exopolysaccharide of Pseudomonas fluorescens strain H13

An acidic exopolysaccharide was isolated from P. fluorescens strain H13. The structure of the polysaccharide repeating unit was determined using chemical methods and 1D and 2D NMR techniques. The repeating unit was characterized as a trisaccharide composed of -glucose, 2-acetamido-2-deoxy- -glucose and

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acid.     

Transition behavior and phase structure of chitin/ poly(2-hydroxyethyl methacrylate) composites synthesized by a solution coagulation/bulk polymerization method

Chitin/poly(2-hydroxyethyl methacrylate) (PHEMA) composites were synthesized via photo-polymerization in a gel state of chitin swollen with HEMA monomer as reactive impregnant. The transition behavior and phase structure of the chitin/PHEMA composites were characterized by differential scanning calorimetry, dynamic viscoelastic analysis, and solid-state ¹³C NMR spectroscopy. For compositions containing 20wt% chitin, it was reasonably assumed that an original network structure of chitin gels was sufficiently perpetuated into the cross-linked PHEMA matrix, resulting in the formation of an interpenetrating polymer network (IPN) type organization. Owing to this IPN effect, the lowering of the dynamic modulus É of the composites in the glass transition temperature region was extremely suppressed, compared with the corresponding

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E" height="15" width="11">-drop observed for plain PHEMA samples. From measurements of the proton spin-lattice relaxation times t_1ρ^h in the NMR study, the IPN-like composites were estimated to be homogeneous on a scale of less than ˜2.4nm.     

Structural studies of the O-antigen from Vibrio cholerae O:21

The O-antigen from Vibrio cholerae O:21 has been investigated, using n.m.r. spectroscopy, methylation analysis, and Smith degradation as the main methods. It is concluded that the O-antigen is composed of tetrasaccharide repeating-units having the following structure (in which Hep = -glycero- -manno-heptose).

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An efficient synthesis of methyl tetra-o-hexyl gentiooctaoside, an octaosyl analogue of ANP receptor antagonist HS-142-1

Methyl

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, a 3-O hexyl analogue of the octaosyl component of fungal lipooligosaccharide HS-142-1, was stereo- and regioselectively synthesized as a potent antagonist for the tetrameric atrial natriuretic peptide (ANP) receptors.     

Electrophoretic studies on the Anisakis simplex complex (Ascaridida:Anisakidae) from the Mediterranean and North-East Atlantic

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and 1986. Electrophoretic studies on the Anisakis simplex complex (Ascaridida: Anisakidae) from the Mediterranean and North-East Atlantic. International Journal for Parasitology 16: 633–640. The genetic variation of the sibling species Anisakis simplex A and A. simplex B was investigated by electrophoretic analysis of 22 gene-enzyme systems. The two species are reproductively isolated and no gene flow takes place between them. Three loci, Sod, Adk-2 and Lap-1, show distinct alleles in A. simplex A and A. simplex B, allowing their reliable identification both at the larval and adult stages. A fourth locus, Got, appears to be diagnostic at the 95% level. The value of Nei's genetic distance found between A. simplex A and A. simplex B is 0.28. Parameters of genetic variability (He, P, A) are given for both species. The geographic distribution of A. simplex A and A. simplex B appears to be mainly Mediterranean for the former, and mainly North Atlantic for the latter. Several paratenic hosts (fish and squid) and one cetacean definitive host are identified for each of the two species. The names A. pegreffii and A. simplex are tentatively proposed for A. simplex A and A. simplex B respectively.     

Effet de la longueur d'onde de préillumination sur la désactivation des formes oxydées du donneur d'électrons du Photosystème II

Effect of preillumination wavelength on the deactivation of oxidized forms of the Photosystem II electron donor

Deactivation was studied using chlorella cells or spinach chloroplasts after an illumination of different wavelengths (light I = 710 nm, light II = 650 or 480 nm). The measurements concerned mainly the third oxidized state S₃ of the System II electron donor, according to the scheme proposed by

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, (Photochem. Photobiol., 11 (1970)457). The time course of deactivation was followed during the dark after each preillumination. Different results were obtained with algae in state 1 or state 2 as defined by

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, (Biochim. Biophys. Acta, 189 (1969) 366). In state 1 the deactivation of S₃ is faster after light 11 than after light 1; in state 2, except at the beginning of the decay, the deactivation of S₃ is almost the same after the two kinds of preillumination. With chloroplasts the deactivation is slower, but always faster after light II than after light I, no transition between state 1 and state 2 was observed. The results are discussed with reference to the possible reducing substrates of the reaction.     

The structure of the O-antigenic chain of the lipopolysaccharide of Rhizobium trifolii 4s

The structure of the O-antigen chain of the lipopolysaccharide (LPS) of Rhizobium trifolii 4s has been determined by a combination of chemical and spectroscopic methods. The glycosyl components were found to be -rhamnose, N-acetyl- -glucosamine, and N-acetyl- -mannosamine in 3:1:1 molar proportion, as determined by gas chromatography and gas chromatography-mass spectrometry of alditol acetate and persilylated (R)-2-hydroxybutyl glycoside derivatives. The linkage positions and configurations of the glycosyl residues were obtained by 1D and 2D NMR spectroscopy. The polymer has a pentasaccharide repeating-unit containing rhammose and N-acetylglucosamine in the main chain and N-acetylmannosamine as the sole-side chain component. This latter residue is linked to a main-chain rhamnose residue. This result was suggested by NMR spectroscopy and confirmed by periodate oxidation. The sequence was deduced by 1D and 2D NMR NOE experiments and by partial hydrolysis studies. The repeating unit of the polysaccharide is shown. This constitutes the first complete structure of an O-antigenic chain of the lipopolysaccharide of any strain of Rhizobium trifolii.

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Ultrastructure and histochemistry of the protonephridial system of juvenile Paramphistomum epiclitum and Fischoederius elongatus (Paramphistomidae: Digenea) during migration in Indian ruminants.

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and 1992. Ultrastructure and histochemistry of the protonephridial system of juvenile Paramphistomum epiclitum and Fischoederius elongatus (Paramphistomidae: Digenea) during migration in Indian ruminants. International Journal for Parasitology 22: 1103–1115. The protonephridial system of juvenile Paramphistomum epiclitum and Fischoederius elongatus consists of a bilaterally symmetrical arrangement of primary, secondary and tertiary ducts which connect individual flame cells with a simple common bladder. Primary and secondary ducts are formed from columns of adjoining cells which provide an epithelial lining, whose luminal surface is elaborated with either short tubercles or lamellae. Groups of cilia project from the luminal surface at frequent intervals along secondary ducts. By contrast, the tertiary ducts and bladder are lined with a nucleated syncytium which ends at a junctional complex formed with the terminal canal. The latter is continuous with the tegumental syncytium and opens at a nephridiopore on the postero-dorsal surface. Tertiary ducts of mature cercariae contain concretions which are voided by migrating juveniles in whose tertiary ducts lipids are progressively accumulated. Evidence for the role of protonephridia in excretion and possibly in osmoregulation and ionic balance is currently examined.     

Electrophoretic variation among the five polish populations of the bank vole

Electrophoretic variation in proteins encoded by 21 loci was analysed in five populations of the bank vole (Clethrionomys glareolus) from southern and eastern Poland. Intrapopulation variation is high

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; the average Nei's distance among populations equals 0.193. Comparatively high F_IS (0.306) values suggest high levels of differentiation. Variation in allele frequencies (F_ST is high (ranging from 0.137 to 0.572) and reflects considerable geographic genetic heterogeneity. Genetic and geographic distances are not consistently associated.