Parendozoicomonas haliclonae gen. nov. sp. nov. isolated from a marine sponge of the genus Haliclona and description of the family Endozoicomonadaceae fam. nov. comprising the genera Endozoicomonas,Parendozoicomonas, and Kistimonas

Two Gram-stain-negative, facultative anaerobic, motile, rod-shaped strains, S-B4-1U^T and JOB-63a, forming small whitish transparent colonies on marine agar, were isolated from a sponge of the genus Haliclona. The strains shared 99.7% 16S rRNA gene sequence identity and a DNA-DNA hybridization value of 100%, but were differentiated by genomic fingerprinting using rep-PCRs. 16S rRNA gene sequence phylogeny placed the strains as a sister branch to the monophyletic genus Endozoicomonas (Oceanospirillales; Gammaproteobacteria) with 92.3–94.3% 16S rRNA gene sequence similarity to Endozoicomonas spp., 91.9 and 92.1% to Candidatus Endonucleobacter bathymodiolin, and 91.9 to 92.1% to the type strains of Kistimonas spp. Core genome based phylogeny of strain S-B4-1U^T confirmed the phylogenetic placement. Major fatty acids were summed feature 3 (C_16:1 ω7c/C_16:1 ω6c) and 8 (C_18:1 ω7c/C_18:1 ω6c) followed by C_10:0 3-OH, C_16:0, and C_18:0. The G + C content was 50.1–51.4 mol%. The peptidoglycan diamino acid of strain S-B4-1U^T was meso-diaminopimelic acid, the predominant polyamine spermidine, the major respiratory quinone ubiquinone Q-9; phosphatidylethanolamine, phosphatidylglycerol and phosphatidylserine were major polar lipids. Based on the clear phylogenetic distinction, the genus Parendozoicomonas gen. nov. is proposed, with Parendozoicomonas haliclonae sp. nov. as type species and strain S-B4-1U^T (= CCM 8713^T = DSM 103671^T = LMG 29769^T) as type strain and JOB-63a as a second strain of the species. Based on the 16S rRNA gene sequence phylogeny of the Oceanospirillales within the Gammaproteobacteria, the Endozoicomonaceae fam. nov. is proposed including the genera Endozoicomonas, Parendozoicomonas, and Kistimonas as well as the Candidatus genus Endonucleobacter.     

Nucleotide sequence of an endo-β-1,4-glucanase gene fromBacillus subtilis CK-2

The gene encoding endo--1,4-glucanase inBacillus subtilis CK-2 was cloned intoEscherichia coli DH5, and the nucleotide sequence determined. The 1500 bp gene encodes a protein of 499 amino-acid residues with a calculated molecular mass of 55 261, and is equipped with a typicalB. subtilis signal peptide. Nucleotide sequence comparison revealed only 2 basepairs deviation between this gene and the endo--1,4-glucanase gene ofB. subtilis PAP115, and 93% to 95% homology was found between the amino acid sequences of these enzymes and otherB. subtilis endo--1,4-glucanases. Regions of similarity were also observed between the carboxy-terminal part of these enzymes and the part of theB. lautus PL236celA enzyme constituting the cellulose-binding domain.     

Variants within the 5′-flanking regions of bovine milk protein genes: I. κ-casein-encoding gene

In order to identify DNA variants within the 5-flanking region of the bovine -casein (Cn)-encoding gene, this area of the gene from 13 cows belonging to seven breeds (Holstein Friesian, Brown Swiss, German Simmental, Jersey, Galloway, Scottish Highland and Ceylon Dwarf Zebu) was analysed. For each individual, about 1 kb of the 5-flanking region including exon I was amplified by polymerase chain reaction (PCR). The biotinylated PCR product was immobilized on magnetic beads followed by direct bidirectional sequencing using an automated DNA sequencer. Fifteen DNA variants were identified, some of which are located within potential regulatory sites and possibly involved in the expression of the -casein encoding gene.Abbreviations AP2 activator protein 2 - bp base pair(s) - GRE/RC glucocorticoid response element/reverse complement - HNF3 hepatocyte nuclear factor 3 Cn -casein - MGF mammary gland-specific nuclear factor - nt nucleotid(s), OCT1 octamer-binding site 1 - PA polyacrylamide - PCR polymerase chain reaction - PMF pregnancy-specific mammary nuclear factor - kb kilobase(s) or 1000 bp     

Identification and characterization of gibberellin-insensitive mutants selected from among dwarf mutants of rice

In rice, many dwarf mutants have been isolated and characterized. We have investigated the relationship between dwarfism and the gibberellin (GA)-mediated control of physiological processes. Twenty-three rice cultivars and mutants (9 normal, 3 semi-dwarf, 11 dwarf) were analyzed in terms of two GA-mediated processes, namely, elongation of shoots and production of -amylase activity in the endosperm. As a result, we identified four different groups (groups N, T, D and E). Two-dimensional plotting of the extent of induction of -amylase in the endosperm versus the extent of enhancement of shoot elongation upon treatment with exogenous gibberellic acid (GA₃) provided a useful method for the rapid allocation of large numbers of dwarf mutants of rice to the various groups. Members of group N (normal type), which included all normal cultivars and semi-dwarf mutants, showed a slight increase in elongation of shoots and a remarkable increase in production of -amylase with the application of GA₃ during germination. All of the dwarf mutants were classified as being members of the other three groups. Members of group T (Tan-ginbozu type), including three dwarf mutants, were highly responsive to exogenous GA₃ in terms of elongation of shoots and production of -amylase, with associated lower levels of endogenous GA. In contrast, members of the other three groups, including group N, had normal levels of endogenous GAs. Members of group D (Daikoku type) were only slightly responsive to exogenous GA₃, an indication that they are GA-insensitive mutants. Members of group E (Ebisu type) had responses to GA₃ similar to those of group N, not only in terms of elongation of shoots but also in terms of -amylase production, an indication that they are dwarf mutants that can be considered as neither GA-deficient nor GA-insensitive mutants. We also examined a GA-insensitive mutant selected from among 19 near-isogenic dwarf lines of Shiokari, and we concluded that the d-1 gene is associated with the phenotype of GA-insensitive dwarf mutants.     

Glucanases and chitinases ofBacillus circulans WL-12

Summary Lysis of cell walls of various yeast species by -1,3- and -1,6-glucanases ofBacillus circulans WL-12 was investigated. Selective enzymolysis of cell walls ofPyricularia oryzae by single and combined actions of -1,3-, -1,6-glucanases and chitinase was followed. Chemical structure of the cell wall glucan ofP. oryzae was determined by chemical and enzymatic methods. Multiple component nature of glucanases ofB. circulans WL-12, their induction and lytic actions on cell walls of various yeasts were studied. Genes specifying glucanases and chitinases ofB. circulans WL- 12 were cloned inE. coli, and their nucleotide sequences were determined. Fibronectin type III modules were found in the chitinases. Functions of the domains of the deduced structures of the glucanases and the chitinases were studied by various methods including molecular genetic techniques.This paper is dedicated to Professor Herman Jan Phaff in honor of his 50 years of active research which still continues.     

Immunological detection of tonoplast polypeptides in the plasma membrane of pea cotyledons

The tonoplast is usually characterized by the presence of two electrogenic proton pumps: a vacuolartype H⁺-ATPase and a pyrophosphatase, as well as a putative water-channel-forming protein (γ-TIP). Using a post-embedding immunogold labelling technique, we have detected the presence of these transport-protein complexes not only in the tonoplast, but also in the plasma membrane and trans Golgi elements of maturing pea (Pisum sativum L.) cotyledons. These ultrastructural observations are supported by Western blotting with highly purified plasma-membrane fractions. In contrast to the vacuolar-type H⁺-ATPase, whose activity was not measurable, considerable pyrophosphatase activity was detected in the plasma-membrane fraction. These results are discussed in terms of a possible temporary repository for tonoplast proteins en route to the vacuole.     

An overview of Acipenseriformes

Acipenseriformes occupy a special place in the history of ideas concerning fish evolution, but in many respects, phylogenetic studies of the group remain in their infancy. Even such basic questions as the monophyly of Acipenser (the largest genus) are unanswered. We define relationships based on comparative osteology, which allows us to incorporate well-preserved fossils into analyses. Acipenseriformes has existed at least since the Lower Jurassic (approximately 200 MYBP), and all fossil and recent taxa are from the Holarctic. Phylogenetic relationships among Paleozoic and Early Mesozoic actinopterygians are problematic, but most workers agree that Acipenseriformes is monophyletic and derived from some component of paleonisciform fishes. (Paleonisciformes is a grade of primitive non-neopterygian actinopterygians, sensu Gardiner 1993.) Taxa discussed in comparison here are: Cheirolepis, Polypterus, Mimia, Moythomasia, Birgeria, Saurichthys, Lepisosteus and Amia. We review generic diversity within the four nominal families of fossil and recent Acipenseriformes (Chondrosteidae, Peipiaosteidae, Polyodontidae, and Acipenseridae), and provide a cladogram summarizing osteological characters for those four groups. Monophyly of the two extant families is well-supported, but there are no comprehensive studies of all of the known species and specimens of Chondrosteidae and Peipiaosteidae. As a result, sister-group relationships among Chondrosteidae, Peipiaosteidae, and Acipenseroidei (= Polyodontidae + Acipenseridae) are unresolved. We discuss five features fundamental to the biology of acipenseriforms that benefit from the availability of our new phylogenetic hypothesis: (1) specializations of jaws and operculum relevant to jaw protrusion, feeding, and ram ventilation; (2) anadromy or potamodromy and demersal spawning; (3) paedomorphosis and evolution of the group; (4) the bioégeography of Asian and North American polyodontids and scaphirhynchines; and (5) the great abundance of electroreceptive organs in the rostral and opercular regions. Finally, we summarize our nomenclatural recommendations.     

Elevated CO2 and the magnitude and seasonal dynamics of root production and loss in t Betula papyrifera

The impact of elevated atmospheric CO₂ on belowground plant growth is poorly understood relative to its effects on aboveground growth. We carried out a study of the seasonal dynamics of gross root production and death to determine how elevated CO₂ affected the dynamics of net and gross root production through a full growing season. We quantified gross root production and root loss from sequential, in situ images of fine roots of t Betula papyrifera in ambient (375 ppm.) and elevated (700 ppm) CO₂ atmospheres from 2 weeks following germination through leaf senescence. We found that elevated CO₂ led to increases in the magnitude of cumulative gross production (P) and cumulative gross loss (L) of roots. However, the effect of elevated CO₂ on these processes was seasonally dependent. Elevated CO₂ led to greater levels of enhancement in P early in the growing season, prior to maximum standing root length (NP). In contrast, elevated CO₂ led to greater levels of enhancement in L in the last half of the growing season, after maximum NP had been reached. This difference in the timing of when elevated CO₂ affects P and L led to a transitory, early enhancement in NP. By the end of the growing season, there was no significant effect of elevated CO₂ on NP, and P was 87% greater than NP for ambient CO₂ and 117% greater in elevated CO₂. We conclude that static assessments of belowground productivity may greatly underestimate gross fine root productivity and turnover and this bias can be exaggerated with elevated CO₂.     

Mutations conferring azide resistance enhance symbiotic nitrogen fixation in Rhizobium loti

Azide-resistant (AzR) mutants of Rhizobium loti strain NZP2037 were isolated. Mutations conferring azide resistance (azi) appeared at a frequency of 0.5 × 10-7. Nine AzR mutants of R. loti were characterised for their symbiotic behaviour with Lotus pedunculatus plants. In comparison to the wild type parent strain, AzR mutants exhibited either similar or higher symbiotic effectiveness. The azi mutations which enhanced nitrogen fixation as well as improving shoot dry weight of the inoculated plants also increased nodulation. Unlike several azi mutations in Escherichia coli, these azi mutations did not alter sensitivity of R. loti to phenethyl alcohol. One of the AzR mutants exhibited higher micro-aerobic, N, N, N, N-tetramethyl-p-phenylenediamine (TMPD) oxidase activity.     

Wnt/β-catenin pathway promotes acute lung injury induced by LPS through driving the Th17 response in mice

T helper cell 17 (Th17), one type of CD4⁺ T cell, plays an important role in regulating the acute lung injury (ALI) inflammatory response. Recent studies showed that Wnt/β-catenin pathway could modulate the differentiation and the function of CD4⁺ T cell. However, whether Wnt/β-catenin could regulate the differentiation and function of Th17 in the development and progress of ALI induced by lipopolysaccharide (LPS) is still unknown. To test this, we used dickkopf1 (Dkk-1) to block the Wnt/β-catenin pathway and LiCl to activate the Wnt/β-catenin pathway by instillation to the murine model of ALI. Our results revealed that activation of Wnt/β-catenin pathway significantly aggravated the LPS-induced lung inflammation. Meanwhile, we observed that activation of Wnt/β-catenin pathway promoted Th17 response by analyzing CD4⁺ T cells and the related cytokines secretions. Enhanced Th17 response was responsible for the further neutrophils infiltration and pro-inflammatory cytokines production. In addition, activation of Wnt/β-catenin pathway resulted in induced expression of retinoic acid related orphan receptor-γt (RORγt) via histone acetyltransferase p300. These data suggested that Wnt/β-catenin pathway might be a potential target to treat the LPS-induced inflammation in ALI.