A morphological study of flower initiation and development in strawberry (Fragaria x ananassa) using cryo-scanning electron microscopy

The morphological changes in the apex of strawberry (Fragaria x ananassa) cv. Elsanta during flower initiation and early development were studied by means of apical dissections and cryo-scanning electron microscopy. Characteristic stages of development were recorded from the earliest discernible evidence of floral initiation until anthesis. The results are discussed in relation to previous studies of floral development in strawberry.     

The effect of 6-deoxy-D-fructose on flavour bioformation from strawberry (Fragaria x ananassa, cv. Elsanta) callus cultures

The biosynthesis of 2,5-dimethyl-4-hydroxy-2H-furan-3-one has been investigated in order to improve the flavour of cultivated strawberries. Callus cultures of strawberries have been established. The probable immediate precursor of 2,5-dimethyl-4-hydroxy-2H-furan-3-one (6-deoxy-D-fructose) has been fed to callus cultures and the levels of the product are compared in cultures fed with precursor and control tissues. The increased levels of 2,5-dimethyl-4-hydroxy-2H-furan-3-one-glucoside in the precursor fed cultures suggests that methylpentoses are key compounds for the biosynthesis of this specific furanone.     

Molecular identification of bacteria associated with filaments of Nodularia spumigena and their effect on the cyanobacterial growth

Colonial and filamentous cyanobacteria frequently have bacteria associated with their extracellular mucus zone or more tightly attached to their cells surface. The toxin-producing cyanobacterium Nodularia spumigena is an important component of the Baltic Sea plankton community, and its filaments are likely to provide a microenvironment suitable for the development of a particular bacteria flora. In the present work, 13 bacterial strains associated with filaments of N. spumigena from the Baltic Sea were isolated and identified by sequencing the 16S rRNA gene. Different bacterial lineages were found associated with the cyanobacterial filaments, including the alpha, beta, and gamma subdivisions of the class Proteobacter and the division Firmicutes (Gram-positive bacteria). Several 16S rRNA gene sequences were not closely related to previously reported sequences of cultured bacteria from the Baltic Sea or to any other reported sequence. Conversely, sequences related to the gamma Proteobacter genus Shewanella, a group previously described in the Baltic Sea, were found among the isolates. The bacterial isolates were grown and added to cultures of exponentially growing N. spumigena. Five isolates, related to the alpha and gamma Proteobacter and Firmicutes, affected negatively the cyanobacterial growth, leading to a lower biomass yield up to 38% relative to controls with no bacteria addition. Five gamma Proteobacter-related strains had no effect on the cyanobacterial growth, while three strains related to Shewanella baltica had a positive effect. Although none of the bacterial isolates showed strong algicidal effect, the observed stimulatory and retarding effects on N. spumigena growth under culture conditions denotes the importance of the associated bacterial community for the dynamics of these cyanobacterial populations in nature. Moreover, several new taxa recovered in this study probably belong to species not yet described.     

Molecular phylogeny of the family Tephritidae (Insecta: Diptera): New insight from combined analysis of the mitochondrial 12S, 16S,and COII genes

The phylogeny of the family Tephritidae (Diptera: Tephritidae) was reconstructed from mitochondrial 12S, 16S, and COII gene fragments using 87 species, including 79 tephritid and 8 outgroup species. Minimum evolution and Bayesian trees suggested the following phylogenetic relationships: (1) A sister group relationship between Ortalotrypeta and Tachinisca, and their basal phylogenetic position within Tephritidae; (2) a sister group relationship between the tribe Acanthonevrini and Phytalmiini; (3) monophyly of Plioreocepta, Taomyia and an undescribed new genus, and their sister group relationship with the subfamily Tephritinae; (4) a possible sister group relationship of Cephalophysa and Adramini; and (5) reconfirmation of monophyly for Trypetini, Carpomyini, Tephritinae, and Dacinae. The combination of 12S, 16S, and COII data enabled resolution of phylogenetic relationships among the higher taxa of Tephritidae.     

Comparative analysis of fecal DNA extraction methods with phylogenetic microarray: Effective recovery of bacterial and archaeal DNA using mechanical cell lysis

Several different protocols are used for fecal DNA extraction, which is an integral step in all phylogenetic and metagenomic approaches to characterize the highly diverse intestinal ecosystem. We compared four widely used methods, and found their DNA yields to vary up to 35-fold. Bacterial, archaeal and human DNA was quantified by real-time PCR, and a compositional analysis of different extracts was carried out using the Human Intestinal Tract Chip, a 16S rRNA gene-based phylogenetic microarray. The overall microbiota composition was highly similar between the methods in contrast to the profound differences between the subjects (Pearson correlations > 0.899 and 0.735, respectively). A detailed comparative analysis of mechanical and enzymatic methods showed that despite their overall similarity, the mechanical cell disruption by repeated bead beating showed the highest bacterial diversity and resulted in significantly improved DNA extraction efficiency of archaea and some bacteria, including Clostridium cluster IV. By applying the mechanical disruption method a high prevalence (67%) of methanogenic archaea was detected in healthy subjects (n = 24), exceeding the typical values reported previously. The assessment of performance differences between different methodologies serves as a concrete step towards the comparison and reliable meta-analysis of the results obtained in different laboratories.     

Molecular identification and phylogenetic relationships of seven Indian Sciaenids (Pisces: Perciformes,Sciaenidae) based on 16S rRNA and cytochrome c oxidase subunit I mitochondrial genes

The partial sequences of 16S rRNA and cytochrome c oxidase subunit I (COI) mitochondrial genes were analyzed for species identification and phylogenetic relationships among the commercially important Indian sciaenids (Otolithes cuvieri, Otolithes ruber, Johnius dussumieri, Johnius elongatus, Johnieops vogleri, Otolithoides biauritus and Protonibea diacanthus). Sequence analysis of both genes revealed that the seven species fell into three distinct groups, which were genetically distant from each other and exhibited identical phylogenetic resolution. Partial sequences of both the genes provided sufficient phylogenetic information to distinguish the seven sciaenids indicating the usefulness of mtDNA-based approach in species identification.     

The importance of the ratio UV-B/photosynthetic active radiation (PAR) during leaf development as determining factor of plant sensitivity to increased UV-B irradiance: effects on growth, gas exchange and pigmentation of bean plants (Phaseolus vulgaris cv. Label)

To evaluate the effect of different naturally occurring irradiation conditions on the sensitivity of bean (Phaseolus vulgaris cv. Label) to increased UV-B levels, plants were grown under six different light treatments. In the control series (at ambient levels of UV-B), UV-B and visible light were decreased in parallel, resulting in three different total irradiation treatments with the same UV-B/PAR ratio. A second series with a 15% increase in UV-B irradiation at each PAR level was used to investigate the effect of UV-B under the varying total irradiance levels. The different total irradiance levels resulted in large differences in total dry weight, specific leaf weight, photosynthesis-light response and pigment concentrations. Nevertheless, the 15% increase in UV-B resulted in equal reductions in total dry weight (from 24.5 to 34.3%) and effective photosynthesis for all light levels. The accumulation of protective pigments in the primary bean leaves was strongly correlated to the total irradiance level (200% increase from the lowest to the highest light level), but was not influenced by increasing UV-B levels. As the UV-B/PAR ratio outside increases with decreasing total irradiance (when induced by cloud cover) this implies that low radiation levels are potentially dangerous to some plants, even though the UV-B levels may seem negligible.     

Molecular analysis of the bacterial communities in the live Pacific oyster (Crassostrea gigas) and the influence of postharvest temperature on its structure

Aims: To evaluate the effect of postharvest temperature on bacterial communities in live Pacific oysters (Crassostrea gigas) using nonculture‐based methods. Methods and Results: Live oysters were compared before and after storage at 4, 6, 15, 20 and 30°C using terminal restriction fragment length polymorphism (T‐RFLP). Bacterial communities in freshly harvested (control) vs stored oysters were significantly different. Changes in bacterial communities at 4, 15 and 30°C observed by T‐RFLP were further investigated by clone library analysis. Members of the Proteobacteria predominated (43·0–57·0% of clones) in control oysters, while storage altered the bacterial profile. At 4°C, Psychrilyobacter spp. (phylum Fusobacteria) predominated (43·8% of clones), while at 15 and 30°C, members of the phylum Bacteroidetes represented 63·0 and 60·2% of clones, respectively. High microbial diversity in oysters was observed, with at least 73 different genera‐related clones among all samples. Conclusions: Changes in the overall bacterial community of Pacific oysters were influenced by storage temperature and would likely not be detected by standard culture‐based methods currently used to assess oyster quality. Certain dominant genera, such as Psychrilyobacter, Polynucleobacter and a bacterial group related to Alkaliflexus, should be further studied as possible indicators for postharvest temperature control. Significance and Impact of the Study: This work is the first report describing the effect of different storage temperatures on bacterial diversity in postharvest live Pacific oysters using molecular‐based methods.     

Secondary structure and phylogenetic analysis of the internal transcribed spacers 1 and 2 of bush crickets (Orthoptera: Tettigoniidae: Barbitistini)

We inferred secondary structure models of the internal transcribed spacers (ITS) 1 and 2 of bush crickets using a combined comparative and thermodynamic approach. The inferred secondary structure models were used to account for interdependency of interacting nucleotides in a phylogenetic analysis of the bush cricket genus Poecilimon. Our analysis indicates that the two previously reported conformational structures (i.e., hairpin and ring) of ITS2 are likely to fold in bush crickets as well and that both predicted structures are similar to those proposed for other eukaryotes. Comparing predicted ITS1 secondary structure models proved to be difficult because of substantial variation in their nucleotide sequence length. Our study revealed that the phylogenetic signal of ITS1 and ITS2 is largely congruent with that preserved in the mitochondrial genes 16S rRNA, tRNA‐Val and 12S rRNA. The phylogenetic signal in both the nuclear and the mitochondrial genome question the monophyly of the genus Poecilimon: species of the genera Poecilimonella, Parapoecilimon, Polysarcus and Phonochorion consistently cluster within Poecilimon.     

Molecular Systematics of the Malagasy Babblers (Passeriformes: Timaliidae) and Warblers (Passeriformes: Sylviidae), Based on Cytochrome b and 16S rRNA Sequences

The phylogenetic relationships of the Timaliidae (babblers) and Sylviidae (warblers) have long challenged ornithologists. We focus here on three Malagasy genera currently assigned to the Timaliidae, Mystacornis, Oxylabes, and Neomixis, and on their relationships with other babblers and warblers using the sequences of two mitochondrial genes (cytochrome b and 16S rRNA). Maximum parsimony analyses show that the Malagasy “babblers” are not related to any of the other African and Asian babblers. The genus Mystacornis is neither a babbler nor a warbler. The other Malagasy “babblers” are members of warbler groups (the monophyly of the Sylviidae is not demonstrated). Oxylabes madagascariensis and Hartertula flavoviridis (we recognize Hartertula as a genus for the species flavoviridis, previously Neomixis flavoviridis) constitute, with two presumed sylviine taxa, Thamnornis chloropetoides and Cryptosylvicola randrianasoloi, a warbler radiation endemic to the island of Madagascar. The other Neomixis species (tenella, striatigula, and viridis) belong to another warbler group comprising cisticoline taxa. These results show that the Timaliidae did not disperse to Madagascar. Rather, the island has been colonized, independently, by at least two clades of warblers, probably originating from Africa, where the Sylviidae radiation has been the most extensive.     

Influence of Polyamines on Growth of Hairy Root Cultures of Witloof Chicory (Cichorium intybus L. cv. Lucknow Local) and Formation of Coumarins

The effect of polyamines (putrescine, spermidine, and spermine) was examined for growth and production of two coumarins, esculetin and esculin, in the hairy roots of chicory (Cichorium intybus L. cv. Lucknow local). Of the polyamines administered, 1.5 mm putrescine alone resulted in a 2.3-fold higher increase in the growth of hairy roots as well as in the production of esculetin and esculin, which was 3.37 times more than that of the control on day 21. The endogenous level of conjugated putrescine was more than fivefold that of free putrescine levels in untreated samples. The production of esculetin and esculin in hairy root cultures strictly correlated with growth in all of the treatments. Putrescine at 1.5 mm resulted in a greater length of primary root (18.29 ± 1.37 cm) compared with the control (10.96 ± 0.82 cm) and more secondary and tertiary roots. This study also provides insight into the morphogenetic changes that occur in roots in response to the external supply of polyamines. Received July 20, 1998; accepted January 19, 1999     

丙烯对柿果实采后细胞壁物质代谢和几种生理指标的影响

丙烯处理的柿果实,其软化进程显著加快,呼吸速率和乙烯释放高峰提前,且峰值升高,细胞壁各组分的代谢速度加快,柿果实中多聚半乳糖醛酸酶（PG）和纤维素酶（Cx）活性提高,且高峰提前。     

Phylogenetic analysis of six species of pacific abalone (Haliotidae) based on DNA sequences of 16s rRNA and cytochrome c oxidase subunit I mitochondrial genes

Six species of abalones (Haliotidae) are found on the Korean coasts. Identification and characterization of these abalones are usually based on morphologic characters. In this research we compared the partial sequences of the mitochondrial 16S ribosomal RNA and cytochrome c oxidase subunit I genes to identify species using molecular data and to determine their phylogenetic relationships. Sequence alignments and phylogenetic analysis revealed that the 6 species fell into 2 distinct groups which were genetically distant from each other and exhibited little internal phylogenetic resolution. One group included Haliotis discus hannai, H. discus discus, H. madaka, and H. gigantea, while the other group contained H. diversicolor supertexta and H. diversicolor diversicolor. The 16S rRNA sequences were relatively more conserved than to the COI sequences, but both gene sequences provided sufficient phylogenetic information to distinguish among the 6 species of Pacific abalone, and thus could be valuable molecular characters for species identification.     

Classification of Streptomyces phylogroup pratensis (Doroghazi and Buckley, 2010) based on genetic and phenotypic evidence,and proposal of Streptomyces pratensis sp. nov.

The Streptomyces phylogroup pratensis (Doroghazi and Buckley, 2010) contains isolates obtained from grassy fields, as well as Streptomyces flavogriseus ATCC 33331 and strain CGMCC 4.1868. This latter strain was received as Streptomyces griseoplanus but was subsequently found to be mislabeled, and S. flavogriseus ATCC 33331 (=IAF-45-CD) was shown to be clearly distinct from the type strain S. flavogriseus ATCC 25452^T (=CGMCC 4.1884^T). In order to evaluate the taxonomic position of phylogroup pratensis further, sequences of the 16S rRNA gene and five protein-coding housekeeping genes (atpD, gyrB, recA, rpoB and trpB) were determined for six strains of the phylogroup and type strains of 19 related species, which were selected by a BLAST search based on the sequences of the phylogroup. The 16S rRNA gene sequences for the phylogroup were identical to those of eight species belonging to cluster I of the S. griseus clade. However, in all the individual protein-coding gene and MLSA phylogenies, the phylogroup strains without exception formed an obviously distinct cluster that could be equated with a new species status. The phylogenetic evidence for the new species assignment was also supported by corresponding DNA–DNA hybridization values and by phenotypic characteristics. It is therefore proposed that the phylogroup should be classified as Streptomyces pratensis sp. nov., and the type strain is ch24^T (=CGMCC 4.6829^T = NRRL B-24916^T).     

Characterization of Desulfomicrobium salsuginis sp. nov. and Desulfomicrobium aestuarii sp. nov., two new sulfate-reducing bacteria isolated from the Adour estuary (French Atlantic coast) with specific mercury methylation potentials

Three strains of sulfate-reducing bacteria (ADR21, ADR26 and ADR28) were isolated from Adour estuary sediments (French South Atlantic coast). Cells of these isolates were rod-shaped, motile and stained Gram-negative. The 16S rRNA and dsrAB genes sequence analyses indicated that these three strains belonged to the genus Desulfomicrobium within the delta Proteobacteria, with Desulfomicrobium escambiense strain DSM10707^T as their closest relative. According to phenotypic characteristics, strains ADR21 and ADR28 could be considered as members of the same species. The relatedness values, based on DNA–DNA hybridization studies, between strains ADR21/DSM10707^T, ADR26/DSM10707^T and ADR21/ADR26 ranged between 30.6–40.8%, 45.2–43.0% and 19.0–26.4%, respectively. Strains ADR21 and ADR28 grew well on lactate, fumarate, malate, formate, ethanol and H₂/acetate in the presence of sulfate as an electron acceptor. Thiosulfate, nitrate, fumarate and DMSO were alternative electron acceptors. Malate was well fermented but pyruvate and fumarate only poorly. Strain ADR26 could not grow on ethanol or fumarate and was unable to use DMSO or fumarate as electron acceptors. The three new strains exhibited differences compared to the type strain of D. escambiense, such as temperature optima, substrate utilization and mercury methylation capacities. On the basis of both genetic and phenotypic evidences, strain ADR21 is proposed as the type strain of the species Desulfomicrobium salsuginis sp. nov., and strain ADR26 as the type strain of the species Desulfomicrobium aestuarii sp. nov.     

Effects of light, temperature, gibberellin (GA3) and their interaction on coleoptile and leaf elongation of tall, semi-dwarf and dwarf wheat

Near-isogenic wheat lines differing in height-reducing (Rht) alleles, in each of two cultivars, were used to investigate the effects of light intensity and of their interaction with temperature and GA₃ application, on the elongation of the coleoptile and the first seedling leaf. Darkness caused a conspicuous increase in the lengths of the coleoptile and of the sheath and lamina of the first leaf, in GA₃ treated and untreated seedlings of all genotypes grown at 11 and 25°C. The genotype effects and the effects of light intensity and GA₃ application on leaf length were ascribed entirely to their effects on the rate of leaf elongation since the duration of leaf elongation was not affected by these factors. Temperature elevation from 11 to 25°C caused a 55% shortening of the duration of leaf elongation and a concomitant increase in elongation rate, which diminished with increased genotypic dwarfness. Accordingly, temperature elevation resulted in a significant reduction in leaf-length of the light-grown dwarf genotypes and the dark-grown dwarf and semi-dwarf genotypes. It is suggested that this temperature × light × genotype interaction effect is due to environmental dependent upper limits of elongation rate set by the Rht alleles.Abbreviations PAR Photosynthetic Active Radiation     

Improvement of ciliate identification and quantification: a new protocol for fluorescence in situ hybridization (FISH) in combination with silver stain techniques

A new protocol for taxon specific probe based fluorescent in situ hybridization was developed for the identification and quantification of ciliates in microbial communities. Various fixatives and experimental parameters were evaluated and optimized with respect to cell permeability and morphological preservation. Optimum results were adaption by obatined of a modified fixation method using Bouin's solution. Furthermore, conventional staining procedures such as different Protargol stain techniques and a silver nitrate impregnation method were modified and can now be applied in combination with fluorescence in situ hybridization. The new protocol allows a rapid and reliable identification as well as quantification of ciliates based upon classical morphological aspects and rRNA based phylogenetic relationships performed in one experiment. Furthermore, a set of specific probes targeting different regions of the 18S rRNA was designed for Glaucoma scintillans Ehrenberg, 1830 and tested by applying this new approach of combining in situ cell hybridization with conventional staining techniques.     

Phylogenetic relationships among the microgastroid wasps (Hymenoptera: braconidae): combined analysis of 16S and 28S rDNA genes and morphological data

Relationships among the microgastroid complex of braconid wasps were investigated using sequence data from the 16S mitochondrial rDNA and 28S (D2 expansion region) nuclear rDNA genes, as well as morphological data. Parsimony analysis of these gene fragments, both separately and combined, indicated that Neoneurus (Neoneurinae) and Ichneutes (Ichneutinae) were no more closely related to the microgastroids than were a range of helconoid taxa. Combined parsimony analysis of the microgastroids indicated the relationships ((Cardiochilinae + Microgastrinae) + Miracinae) + Cheloninae, with Adeliinae falling inside the Cheloninae. Bootstrap proportions for each of these nodes were greater than 70%. Character reweighting (sensu Farris), using the rescaled consistency index, also recovered these relationships. Mapping of lifestyle traits onto this relatively well supported phylogeny indicated that solitary endoparasitism is ancestral for the microgastroids, with a single origin for egg-larval endoparasitism in the Cheloninae + Adeliinae. Mapping of the radiation of the microgastroids into lepidopteran hosts was less clear, due to the specialized biology of the most basal microgastroid clade, the Cheloninae + Adeliinae. Our data are consistent with attack of concealed lepidopteran hosts as the plesiomorphic lifestyle, at least for the Miracinae + Cardiochilinae + Microgastrinae, with radiation into more exposed hosts in the Cardiochilinae + Microgastrinae.