Poly[3-(3,4-Dihydroxyphenyl)glyceric Acid]: A New Biologically Active Polymer from Two Comfrey Species Symphytum asperumand S. caucasicum(Boraginaceae)

Two high-molecular water-soluble preparations with high anticomplementary and antioxidant activity were isolated from the roots of Symphytum asperum and S. caucasicum. Their main chemical constituent was found to be poly[oxy-1-carboxy-2-(3,4-dihydroxyphenyl)ethylene] according to IR and NMR spectroscopy.     

Mrakia curviuscula sp. nov.: A New Psychrophilic Yeast from Forest Substrates

Seven strains with similar characteristics from the laboratory collection of yeasts isolated from forest substrates collected in the central part of European Russia corresponded to none of the known yeast species. Based on the study of their life cycle, physiological characteristics, and the nucleotide composition of their DNA and taking into account the data of PCR analysis with universal primers, the strains were ascribed to a new psychrophilic yeast species, Mrakia curviuscula sp. nov.     

Biologically Active Oligosaccharides from Pectins of Pisum sativum L. Seedlings Affecting Root Generation

Two physiologically active oligosaccharide fractions were isolated from pectin of Pisum sativum L. cell wall after its partial acid hydrolysis. These fractions displayed stimulating and inhibiting effects on root formation in thin-layer explants. The subsequent separation of these fractions by gel permeation and anion-exchange chromatography resulted in fractions with effective concentrations two orders of magnitude lower than the concentrations of the initial fractions. The resulting oligosaccharides displayed their effect on the earliest stage of the rhizogenesis associated with formation of root primordias. The rhizogenesis-inhibiting fraction suppressed cell division by 30-50%. The stimulating fraction mainly contained fragments of xyloglucan and galactan, and the inhibiting fraction contained fragments of xyloglucan, galactan, and arabinan. The polymerization degrees of the stimulating and of the inhibiting oligosaccharides were 10-11 and 5-6, respectively.     

EFOLD,a New Program Complex for Molecular Modeling: The Use of a Flexible Weighting Coefficient Scheme and the Standard Valence Geometry in Modeling the Enzyme Active Sites

An algorithm was proposed for the representation of biopolymer structures in an internal coordinate system (so-called structure regularization) by minimizing the target function using a flexible weighting coefficient scheme with three components that determine the reliability of deviations of each atom. For the structure regularization, an algorithm for taking into account the temperature factor was suggested for the first time. It was shown by the example of the aspartyl protease rhizopuspepsin that the representation in the internal coordinate system may result in an accurate reproduction of the structural details of separate molecule fragments, such as the enzyme active site region. This algorithm was implemented as one of the modules of EFOLD.     

Genetics of selection-induced mutations: I. uvrA,uvrB, uvrC,and uvrD are selection-induced specific mutator loci

Selection-induced mutations, sometimes called directed, adaptive, or Cairnsian mutations, are spontaneous mutations that occur as specific responses to environmental challenges, usually during periods of prolonged stress, and that occur more often when they are selectively advantageous than when they are selectively neutral. In this study I show that lesions in uvrA, uvrB, uvrC, or uvrD increase the mutation rate from trpA46 to trpA ⁺ by 10²– to 10⁴–fold during tryptophan starvation, but those same lesions do not affect random mutation rates in growing cells when tryptophan is present. The increased selection-induced mutation rates remain specific to the gene that is under selection in that no increase in the mutation rate from trpA46 to trpA ⁺ is detected during proline starvation.Evidence is presented showing that proline starvation produces a state of cellular stress which results in a burst of mutations from trpA46 to trpA ⁺ when proline-starved cells are plated onto medium lacking tryptophan but containing proline.These results are consistent with the hypermutable state model for selection-induced mutagenesis.     

Capnocytophaga: New genus of gram-negative gliding bacteria I. General characteristics,taxonomic considerations and significance

The characteristics of gliding bacteria isolated from both healthy and diseased sites in the oral cavity are, summarized and the taxonomic position of the bacteria discussed. Uniform attributes of the fusiform isolates include gliding motility, strictly fermentative metabolism dependent on the presence of CO₂ (or HCO ₃ ^- ), under either anaerobic or aerobic conditions, presence of benzidine-reactive components, and the production of acetic and succinic acids as the major or sole, acidic, metabolic and products. Given the guanine and cytosine content of DNA, their gliding motility, and the ability of many strains to attack polysaccharide a relationship to the cytophagas is suggested. This relationship, along with the CO₂-dependent growth is recognized by the generic name Capnocytophaga given them. Many of the isolates are grouped into three species C. ochracea, C. Sputigena, and C. gingivalis, separated on the basis of morphological and physiological traits.     

Microbial hydroxylation. I. Hydroxylation of aniline byAspergillus alliaceus,A. albertensis andA. terreus

Summary Six hundred and seventy microorganisms were screened for the ability to perform stereoselective aromatic hydroxylation reactions of industrial significance, using aniline as a model substrate. TLC and HPLC analyses with diode array detection were used to identify and characterize hydroxylase activities. Of 79 cultures belonging to the speciesAspergillus alliaceus, A. albertensis, andA. terreus, 26 strains produced 2-aminophenol. Thirty strains were able to hydroxylate aniline in thepara position. Five strains ofA. terreus produced an unidentified phenolic compound in high yield.The mention of firm names or trade products does not imply that they are endorsed or recommended by the US Department of Agriculture over other firms or similar products not mentioned.     

N-acetylglucosaminyltransferase substrates prepared from glycoproteins by hydrazinolysis of the asparagine-N-acetylglucosamine linkage. Purification and structural determination of oligosaccharides with mannose andN-acetylglucosamine at the non-reducing termini

Sixteen asparagine-linked oligosaccharides ranging in size from (Man)₂(GlcNAc)₂ (Fuc)₁ to (GlcNAc)₆(Man)₃(GlcNAc)₂ were obtained from human ₁-acid glycoprotein and fibrinogen, hen ovomucoid and ovalbumin, and bovine fetuin, fibrin and thyroglobulin by hydrazinolysis, mild acid hydrolysis and glycosidase treatment. The oligosaccharides hadN-acetylglucosamine at the reducing termini and mannose andN-acetylglucosamine residues at the non-reducing termini and were prepared for use asN-acetylglucosaminyltransferase substrates. Purification of the oligosaccharides involved gel filtration and high performance liquid chromatography on reverse phase and amine-bonded silica columns. Structures were determined by 360 MHz and 500 MHz proton nuclear magnetic resonance spectroscopy, fast atom bombardment-mass spectrometry and methylation analysis. Several of these oligosaccharides have not previously been well characterized.Abbreviations bis bisecting GlcNAc - DMSO dimethylsulfoxide - FAB fast atom bombardment - Fuc l-fucose - Gal d-galactose - GLC gas-liquid chromatography - GlcNAc or Gn N-acetyl-d-glucosamine - HPLC high performance liquid chromatography - Man or M d-mannose - MES 2-(N-morpholino)ethanesulfonate - MS mass spectrometry - NMR nuclear magnetic resonance - PIPES piperazine-N,N-bis(2-ethane sulfonic acid) the nomenclature of the oligosaccharides is shown in Table 1.     

Anticapsin, a New Biologically Active Metabolite: Screening and Assay Procedures

In addition to its implication in the virulence of Streptococcus pyogenes, the hyaluronic acid capsule produced by this bacterium renders it resistant to infection by bacteriophage. A method employing S. pyogenes and a bacteriophage incorporated into an agar plate was devised as a screen to detect compounds that inhibit the formation of the hyaluronic acid capsule. Filter-paper discs saturated with experimental compounds were applied to the surface of test plates containing host plus phage and control plates of host only. After incubation, inhibition of capsule synthesis was indicated by the presence of clear zones where phage infection and lysis had occurred. Zones of growth inhibition on control plates represented classical antibacterial activity. During the testing of over 6,000 fermentation samples, anticapsin, a unique metabolite, was discovered. Modification of incubation temperature, thickness of agar layers, and host-phage input ratios resulted in a quantitative assay method having a dose-response range of 4 to 160 μg of anticapsin.     

The Synthesis and Characterization of a Helical Miniature Protein Mimicking the OGT Active Domain

The dynamic modification of many nuclear and cytoplasmic proteins with O-linked beta-N-acetylglucosamine (O-GlcNAc) on serine or threonine is catalyzed by O-GlcNAc transferase (OGT). The conserved GPGTF (glycogen phosphorylase/glycosyl transferase) motif, one of the α-helices of the second domain in OGT, was identified as a putative UDP-GlcNAc binding site. A miniature protein was designed which contains all of the conserved residues of GPGTF motif in the O-GlcNAc transferase, and was shown to adopt an alpha helix in 10% trifluoroethanol. It was anticipated that the miniature protein could shed light on the mechanism of dynamic O-GlcNAc modification and provide a potential drug for the diabetes and neurodegenerative diseases.     

Theoretical Study of Antagonists and Inhibitors of Mammalian Adenosine Deaminase: I. Adenosine and Its Aza- and Deazaanalogues

Aza- and deazaanalogues of adenosine, including their 1-protonated forms (except for that of 1-deazaadenosine), were studied by computer computation to find a relationship between their molecular structures and substrate properties for the mammalian adenosine deaminase. The atomic charge distribution and maps of the electrostatic potential around their van der Waals molecular surface were calculated for these compounds using the ab initio STO-3G method. The conformational studies are carried out by the MM⁺ method of molecular mechanics. The mechanism that determines the substrate selectivity of mammalian adenosine deaminase is discussed.     

Systematics and distribution of the New Zealand onychoteuthid fauna (Cephalopoda: Oegopsida), including a new species, Notonykia nesisi sp. nov.

Onychoteuthid squids are among the most common cephalopods found in New Zealand waters, and comprise a major portion of the regional diets of teuthophagous marine mammals. Although several recent publications have addressed aspects of various species’ biology and reproduction, the systematics of the group remains poorly understood. Herein the ontogenetic and adult morphologies of regionally occurring known species of the genera Moroteuthis, Onychoteuthis, and Notonykia are redescribed, and Notonykia nesisi sp. nov. is described for the first time. Ontogenetic and sexually dimorphic variation in characters and character states associated with body proportions, and beak, radula, tentacular hook, palatine tooth and gladius morphologies are also described and compared between local onychoteuthid taxa for the first time.     

New fungal genera, Tectonidula gen. nov. for Calosphaeria-like fungi with holoblastic-denticulate conidiogenesis and Natantiella gen. nov. for three species segregated from Ceratostomella

Two morphologically similar groups of ascomycetes with globose to subglobose perithecia, elongate necks, unitunicate asci floating freely at maturity, and hyaline ascospores currently placed in Calosphaeria s. lat. and Ceratostomella s. lat., respectively, are studied. The Calosphaeria-like fungi have groups of perithecia growing between cortex and wood, arranged in circular groups with converging necks and piercing the cortex in a common point; the asci with a shallow apical ring and U- to horseshoe-shaped hyaline ascospores are compared with Calosphaeria pulchella, the type species of the genus. Conidiogenesis of the investigated Calosphaeria-like fungi is holoblastic-denticulate; ramichloridium-like and sporothrix-like conidiophores and conidia were formed in vitro. Ascospore and ascus morphology, structure of the ascal apex, ascogenous system, mode of conidiogenesis and the large subunit rRNA sequences of this group differ considerably from C. pulchella and both groups are unrelated. Thus a new genus, Tectonidula, is described with two accepted species, T. hippocrepida and T. fagi; they are separated by ascospore and ascus morphology and holoblastic-denticulate conidiogenesis from the core species of Calosphaeria. The placement of Tectonidula among perithecial ascomycetes is discussed. The relationship of Tectonidula with Barbatosphaeria and two ramichloridium-like hyphomycetous genera Rhodoveronaea and Myrmecridium is investigated. Three species formerly attributed to Ceratostomella are studied. The revision of the herbarium type specimen and fresh material of Ceratostomella ligneola revealed that it is conspecific with Ceratostomella ampullasca and Ceratostomella similis. The LSU phylogeny clearly separated C. ligneola from Ceratostomella s. str. and morphologically similar Lentomitella. On the basis of molecular sequence data and detailed comparison of morphology of asci, ascospores and ascogenous system the genus Natantiella is described for C. ligneola with C. ampullasca and C. similis as its synonyms. Natantiella produced sterile mycelium in vitro.     

A Tropical Freshwater Wetland: I. Structure,Growth, and Regeneration

Forested wetlands dominated by Terminalia carolinensis are endemic to Micronesia but common only on the island of Kosrae, Federated States of Micronesia. On Kosrae, these forests occur on Nansepsep, Inkosr, and Sonahnpil soil types, which differ in degree of flooding and soil saturation. We compared forest structure, growth, nutrition, and regeneration on two sites each on Nansepsep and Inkosr soils and one site on the much less common Sonahnpil soil type. Terminalia tree sizes were similar on all three soil types, but forests differed in total basal area, species of smaller trees, and total plant species diversity. Terminalia regeneration was found only on the Inkosr soil type, which had the highest water table levels. Other Terminalia species are relatively light demanding, and T. carolinensis exhibited similar characteristics. It is therefore likely that Terminalia requires periodic, but perhaps naturally rare, stand-replacing disturbances (e.g., typhoons) in order to maintain its dominance, except on the wettest sites, where competition from other species is reduced. Terminalia swamps in the Nansepsep soil type appeared to be at the greatest risk of conversion to other uses, but swamps on all three types may face greater pressure as Kosrae's population increases and the island's infrastructure becomes more developed.     

A New Family,Alteromonadaceae fam. nov., Including Marine Proteobacteria of the Genera Alteromonas,Pseudoalteromonas, Idiomarina,and Colwellia

The taxonomic positions of the marine genera Alteromonas, Pseudoalteromonas, Idiomarina, and Colwellia within the gamma subclass of the class Proteobacteria were specified on the basis of their phenotypic, genotypic, and phylogenetic characteristics. Gram-negative aerobic bacteria of the genera Alteromonas, Pseudoalteromonas, and Idiomarina and facultatively anaerobic bacteria of the genus Colwellia were found to form a phylogenetic cluster with a 16S rRNA sequence homology of 90% or higher. The characteristics of these genera presented in this paper allow their reliable taxonomic identification. Based on the analysis of our experimental data and analyses available in the literature, we propose to combine the genera Alteromonas, Pseudoalteromonas, Idiomarina, and Colwellia into a new family, Alteromonadaceae fam. nov., with the type genus Alteromonas.     

The primary structure of a cDNA for PsaN,encoding an extrinsic lumenal polypeptide of barley photosystem I

A cDNA clone encoding a 15.501 Da photosystem I (PSI) subunit of barley was isolated using an oligonucleotide based on the NH₂-terminal amino acid sequence of the isolated protein. The polypeptide, which migrates with an apparent molecular mass of 9.5 kDa on denaturing SDS-PAGE, has been designated PSI-N, and the corresponding gene is PsaN. Analysis of the deduced protein sequence indicates a mature protein of 85 amino acid residues and a molecular mass of 9818 Da. PSI-N is a hydrophilic, extrinsic protein with no predicted membrane-spanning regions. The transit peptide of 60 residues (5683 Da) contains a predicted hydrophobic -helix, suggesting that the protein is routed into the thylakoid lumen. Thus, PSI-N is the second known lumenal protein component associated with PSI, together with PSI-F.     

New Noncleavable Analogs of 8-Oxoguanine-DNA Glycosylase Substrates

8-Oxoguanine-DNA glycosylases play a key role in repairing oxidatively damaged DNA. Excision repair enzymes Escherichia coli formamidopyrimidine-DNA glycosylase (Fpg protein) and human 8-oxoguanine-DNA glycosylase (hOGG1) catalyze excision of 7,8-dihydro-8-oxoguanine (oxoG) from DNA and subsequent cleavage of the sugar–phosphate backbone. Contacts between DNA phosphate groups and amino acid residues of the active centers of the enzymes are of importance for specific binding and catalysis. To construct noncleavable analogs of Fpg protein and hOGG1 substrates, modifications of phosphate groups bound to a damaged nucleotide were tested for their effect on the substrate properties of modified DNA duplexes. New oxoG-containing analogs of Fpg protein and hOGG1 substrates were synthetic DNA duplexes that contained a pyrophosphate or a substituted pyrophosphate group bound with the 5- or 3-OH of 8-oxoguanosine. The duplexes proved to be recognized and specifically bound by Fpg protein and hOGG1. Analysis of the mechanism of their interaction with Fpg protein and hOGG1 showed that modification of the internucleotide phosphate bound with 3-OH of 8-oxoguanosine prevents oxoG excision from DNA. Yet both enzymes efficiently cleaved the DNA duplexes when the modified phosphate was bound with the 5-OH of 8-oxoguanosine. DNA duplexes with a pyrophosphate or substituted pyrophosphate group at 3-OH of 8-oxoguanosine are noncleavable analogs of 8-oxoguanine-DNA glycosylase substrates and can be used to study the structures of catalytically active forms of Fpg protein and hOGG1 and their prokaryotic or eukaryotic homologs in complex with oxoG-containing DNA.     

Studies of cotyledon protoplast cultures from Brassica napus,B. campestris and B. oleracea. I: Cell wall regeneration and cell division

Protoplasts isolated from cotyledons of a number of cultivars of Brassica napus, B. campestris and B. oleracea were cultured in different media to study the characteristics of cell wall regeneration and cell division at early stages of culture. Time course analysis using Calcolfluor White staining indicated that cell wall regeneration began in some protoplasts 2–4 h following isolation in all cultivars. 30–70% of cultured cotyledon protoplasts exhibited cell wall regeneration at 24 h and about 60–90% at 72 h after the initiation of culture. Results also indicated that a low percentage (0.4–5.4%) of cultured cotyledon protoplasts entered their first cell division one day after initial culture in all twelve cultivars. The percentage of dividing cells increased linearly up to 40% from 1 to 7 day, indicating that cotyledon protoplasts of Brassica had a high capacity for cell division. Factors that influence the level of cell wall regeneration and cell division during cotyledon protoplast culture have been investigated in this study. Cotyledons from seedlings germinated in a dark/dim light regime provided a satisfactory tissue source for protoplast isolation and culture for all Brassica cultivars used. The percentages of protoplasts exhibiting cell wall regeneration and division were significantly influenced by cultivar and species examined, with protoplasts from all five cultivars of B. campestris showing much lower rates of cell wall regeneration than those of B. napus and B. oleracea over 24–120 h, and with the levels of cell division in B. napus cultivars being much higher than those in B. campestris and B. oleracea over 1–9 days. The capacity of cell wall regeneration and cell division in cotyledon protoplast culture of the Brassica species appears under strong genetic control. Cell wall regeneration in protoplast culture was not affected by the culture medium used. In contrast, the composition of the culture medium played an important role in determining the level of cell division, and the interaction between medium type and cultivars was very significant.Abbreviations BA benzylaminopurine - CPW Composition of Protoplast Washing-solution - CW Calcolfluor White - EDTA ethylenediamine-tetraacetic acid - KT Kinetin - Md MS modified Murashige and Skoog medium - 2,4-d 2,4-dichlorophenoxyacetic acid - NAA -naphthaleneacetic acid - IAA indole-3-acetic acid - PAR photosynthetically active radiation - SDS sodium dodecyl sulfate     

Photoreactive dTTP Analogues as Substrates for Thermostable DNA Polymerase from Thermus thermophilus B35

Substrate properties of several dTTP analogues bearing a photoreactive 2-nitro-5-azidobenzoyl (NAB) group attached at position 5 of uracil through linkers of various lengths, dTTP–NAB-x-dUTP (where x = 2, 4, 7–13 is the number of atoms in the linker), were studied. All the analogues are substrates for thermostable Thermus thermophilus B35 DNA polymerase in the elongation reaction of the 5-³²P-labeled primer–template complex. The kinetic parameters of some of the analogues were determined and compared with those of natural dTTP. It was shown that an increase in the linker length results in a higher efficiency of the analogue. The incorporation of NAB-x-dUP residues into the 3 primer end did not impede further elongation of the chain in the presence of natural dNTP.     

The genusAntennaria (Asteraceae: Inuleae) in western North America: Morphometric analysis ofAntennaria alborosea,A. corymbosa,A. marginata,A. microphylla,A. parvifolia,A. rosea,andA. umbrinella

Multivariate analysis of vegetative and reproductive characters was used to examine morphological relatedness amongAntennaria alborosea A. E. Porsild,A. corymbosa E. Nels.,A. marginata Greene,A. microphylla Rydb.,A. parvifolia Nutt.,A. rosea Greene, andA. umbrinella Rydb. Both pistillate and staminate plants were examined. Some of the characters examined were variable in one species, but stable in another (i.e., presence or absence of papillae on the achenes). Our analyses indicate that the seven species are morphologically distinct. It is hypothesized that theA. rosea agamic complex arose through hybridization amongA. corymbosa, A. microphylla, A. umbrinella, and possiblyA. dioica (L.)Gaertn. However, hybridization between the three former species and others, as well as their subsequent morphological responses to different environmental conditions causes confusion in recognizing the taxa.Antennaria angustifolia Rydb.,A. arida E. Nels.,A. confinis Greene,A. scariosa E. Nels.,A. foliacea humilis Rydb.,A. concinna E. Nels., andA. viscidula E. Nels. are considered to represent F 1 hybrids.