Construction of a bacterial artificial chromosome library containing large Eco RI and Hin dIII genomic fragments of lettuce

 Existing bacterial artificial chromosome (BAC) vectors were modified to have unique EcoRI cloning sites. This provided an additional site for generating representative libraries from genomic DNA digested with a variety of enzymes. A BAC library of lettuce was constructed following the partial digestion of genomic DNA with HindIII or EcoRI. Several experimental parameters were investigated and optimized. The BAC library of over 50,000 clones, representing one to two genome equivalents, was constructed from six ligations; average insert sizes for each ligation varied between 92.5 and 142 kb with a combined average insert size of 111 kb. The library was screened with markers linked to disease resistance genes; this identified 134 BAC clones from four regions containing resistance genes. Hybridization with low-copy genomic sequences linked to resistance genes detected fewer clones than expected from previous estimates of genome size. The lack of hybridization to chloroplast and mitochondrial sequences demonstrated that the library was predominantly composed of nuclear DNA. The unique EcoRI site in the BAC vector should allow the integration of BAC cloning with other technologies that utilize EcoRI digestion, such as AFLP^TM markers and RecA-assisted restriction endonuclease (RARE) cleavage, to clone specific large EcoRI fragments from genomic DNA. Received: 5 August 1996 / Accepted: 23 August 1996     

Construction of a bacterial artificial chromosome (BAC) library and identification of overlapping BAC clones with chromosome 4-specific RFLP markers in rice

 To facilitate construction of physical map of the rice genome, a bacterial artificial chromosome (BAC) library of IR64 genomic DNA was constructed. It consists of 18 432 clones and contains 3.28 rice genomic equivalents. The insert size ranged from 37 to 364 kb with an average of 107 kb. We used 31 RFLP markers on chromosome 4 to screen the library by colony hybridization. Sixty eight positive clones were identified with 2.2 positive clones per RFLP marker. The positive clones were analyzed to generate 29 contigs whose sizes ranged from 50 to 384 kb with an average of 145.6 kb. Chromosome walking was initiated for ten contigs linked to resistance genes. Thirty eight BAC clones were obtained and two contigs were integrated. Altogether, they covered 5.65 Mb (15.1%) of chromosome 4. These contigs may be used as landmarks for physical mapping of chromosome 4, and as starting points for chromosome walking towards the map-based cloning of disease resistance genes which were located nearby. Received: 15 November 1996 / Accepted: 24 January 1997     

Calcium-induced protein phosphorylation and changes in levels of calmodulin and calreticulin in maize sperm cells

 To examine possible calcium (Ca²⁺)-mediated prefertilization events in male gametes of higher plants, we studied protein phosphorylation and the Ca²⁺-binding proteins, calmodulin and calreticulin, in sperm cells isolated from maize (Zea mays L.) pollen in the presence and absence of Ca²⁺. Using immunoblotting, we detected calmodulin and calreticulin and Ca²⁺-induced variations. Exposure of sperm cells to 1 mM Ca²⁺ for 1 h increased calmodulin content by 136% compared with the control. Ca²⁺ had little effect on calreticulin at 1 h, but induced a 34% increase after 3 h. Phosphorylation of proteins was low in 1 h-control and Ca²⁺-treated cells. However, a 13-fold increase in phosphorylation of a 18-kDa protein was found at 12 h in the presence of Ca²⁺. Ca²⁺-induced changes in calmodulin, calreticulin and protein phosphorylation observed in maize sperm cells may reflect prefertilization changes in vivo that facilitate sperm cell fusion with egg and central cells. Received: 26 July 1996 / Revision accepted: 7 February 1997     

Glial cells phagocytose neuronal debris during the metamorphosis of the central nervous system in Drosophila melanogaster

 Using electron microscopy we demonstrate that degenerating neurons and cellular debris resulting from neuronal reorganization are phagocytosed by glial cells in the brain and nerve cord of the fruitfly Drosophila melanogaster during the first few hours following pupariation. At this stage several classes of glial cells appear to be engaged in intense phagocytosis. In the cell body rind, neuronal cell bodies are engulfed and phagocytosed by the same glial cells that enwrap healthy neurons in this region. In the neuropil, cellular debris in tracts and synaptic centres resulting from metamorphic re-differentiation of larval neurons is phagocytosed by neuropil-associated glial cells. Phagocytic glial cells are hypertrophied, produce large amounts of lysosome-like bodies and contain a large number of mitochondria, condensed chromatin bodies, membranes and other remains from neuronal degeneration in phagosomes. Received: 23 January 1996 / Accepted in revised form: 21 May 1996     

Stability of Hor1-specific YAC-clones and physical mapping of Hor1-loci in barley

 The hordeins are the major class of storage proteins in barley and are encoded by multigene families. Two YAC-clones specific for the C-hordein-coding Hor1-locus of barley (Hordeum vulgare L.) were selected. The clones were constructed with DNA from the cultivars ‘Franka’ and ‘Hockey’ and have insert sizes of 330 kb and 350 kb, respectively. Performing partial digestions and hybridizations with vector-specific probes, a restriction analysis was conducted using restriction enzymes with a 8-bp recognition sequence. Both clones cover the complete region of the Hor1-locus, but exhibit a different pattern of restriction sites reflecting the polymorphic nature of the locus on the scale of long-range restriction mapping. The maximal extent of the regions homologous to the Hor1-specific probe, pBSC5, was 105 kb in the ‘Hockey’-derived YAC and 190 kb in the yeast artificial chromosome constructed with ‘Franka’-DNA. Furthermore the high degree of instability observed with the Hor1-specific YAC-clones is discussed in conjunction with the structure of the Hor1-locus. Received: 19 December 1996 / Accepted: 31 January 1997     

Genetic variation for in vitro sesame pollen germination and tube growth

  In vitro pollen germination and tube length studies are valuable in elucidating mechanisms (germination capacity and rate, tube growth rate) possibly associated with genetic differences in male transmission. On each of two collection dates, the percentage germination and tube length of the binucleate pollen grains from five diverse sesame (Sesamum indicum L.) genotypes were determined at eight times (30, 60, 90, 120, 150, 180, 240, 300 min) after inoculation on a semisolid medium containing 10% (100 g l^-1) sucrose (C₁₂H₂₂O₁₁), 0.4% (4 g l^-1) purified agar (Fisher Lot 914409), 0.1% (1 g l^-1) calcium nitrate [Ca(NO₃)₂ ⋅ 4H₂O] and 0.01% (100 mg l^-1) boric acid (H₃BO₃). Before heating, the pH of the medium was adjusted to 7.0 with a 0.1 N potassium hydroxide (KOH) solution. Over the five genotypes, 5% germination was found 30 min after inoculation and a maximum of 37% germination 120 min after inoculation with no significant changes thereafter. As indicated by the highly significant genotype×time after inoculation interaction, the genotypes differed in the time at which germination was initiated and maximum germination attained. Over all five genotypes, the tube length was 91 μm 30 min after inoculation, reaching a maximum of 1000 μm 300 min after inoculation. As shown by the highly significant genotype×time after inoculation interaction, the genotypes differed in the time at which tube length was observed and the maximum tube length was attained. Little or no relationship between percent germination and tube length was observed among the genotypes. For both percent germination and tube length, the statistical significance of collection date and its interactions with genotype and time after inoculation indicated that environment in the form of collection date was also an influencing factor. These results indicated that genetic differences among genotypes were present for in vitro germination capacity, germination rate and tube growth rate and that these factors singly or in combination could alter male transmission of genetic elements. Received: 5 February 1997 / Accepted: 23 June 1997     

The α-gliadin gene family. II. DNA and protein sequence variation, subfamily structure, and origins of pseudogenes

 The derived amino-acid sequences of all reported α-gliadin clones are compared and analyzed, and the patterns of sequence change within the α-gliadin family are examined. The most variable sequences are two polyglutamine domains. These two domains are characteristic features of the α-gliadin storage proteins and account for most of the variation in protein size of this otherwise highly conserved protein family. In addition, their encoding DNA sequences form microsatellites. Single-base substitutions in the α-gliadin genes show a preponderance of transitions, including the C to T substitution which contributes to the generation of stop codons, and consequently to the observation that approximately 50% of the α-gliadin genes are pseudogenes. In one unusual gene, a microsatellite has expanded to 321 bp as compared to the normal 36–72 bp, and may result from similar mechanisms that produce polyglutamine-associated genetic diseases in humans. A comparison of the 27 reported sequences show several α-gliadin gene subfamilies, at least some of which are genome specific. Received: 1 October 1996/Accepted: 20 December 1996     

Continuous production of ethanol using yeast cells immobilized in preformed cellulose beads

 Saccharomyces cerevisiae cells were immobilized on preformed cellulose beads by adsorption. The fermentation capacity of the immobilized yeast cells was found to be practically independent of the hydrogen ion concentration between pH 3.1 and 6.25. The fermentation capacity was maximal at 30 °C. The immobilized yeast cells were used for continuous production of ethanol in a fluidized-bead reactor. The average values characteristic for the process were an ethanol concentration of 41.9±0.1 g l^-1, a fermentation efficiency of 82.9±2.1% and a volumetric productivity of 3.94±0.52 g l^-1 h^-1. Received: 9 October 1995/Accepted: 22 April 1996     

Growth and fermentation responses of Selenomonas ruminantium to limiting and non-limiting concentrations of ammonium chloride

 The objective of this study was to assess fermentation product, growth rate and growth yield responses of Selenomonas ruminantium HD₄ to limiting and non-limiting ammonia concentrations. The ammonia half-inhibition constant for S. ruminantium in batch culture was 296 mM. Cells were grown in continuous culture with a defined ascorbate-reduced basal medium containing either 0.5, 5, 25, 50, 100 or 200 mM NH₄Cl and dilution rates were 0.07, 0.14, 0.24 or 0.40 h^-1. Ammonia was the growth-limiting nutrient when 0.5 mM NH₄Cl was provided and the half-saturation constant was 72 μM. Specific rates of glucose utilization and fermentation acid carbon formation were highest for 0.5 mM NH₄Cl. Lactate production (moles per mole of glucose disappearing) increased at the fastest dilution rate (0.40 h^-1) for 5.0 mM NH₄Cl while acetate and propionate decreased when compared to slower dilutions (0.07 and 0.14 h^-1). Lactate production remained low while acetate and propionate remained high for all dilution rates when NH₄Cl concentrations were 25 mM or greater. Yield (Y _Glc and Y _ATP) were nearly doubled when NH₄Cl was increased from 0.5 mM (25.1 g cells/mol glucose used and 13.9 g cells/mol ATP produced respectively) to the higher concentrations. Y _Glc was highest at 25 mM and 50 mM NH₄Cl (48.2 cells/mol and 43.1 cells/mol respectively) as was Y _ATP (23.2 cells/mol and 20.8 cells/mol respectively). Y _NH3 was highest at the lowest NH₄Cl concentration. The maximal fermentation product formation rate occurred at a growth-limiting ammonia concentration, while maximal glucose and ATP bacterial yields occurred at non-growth-limiting ammonia concentrations. Given the growth response of this ruminal bacterium, it is possible that maximization of ruminal bacterial yield may necessitate sacrificing the substrate degradation rate and vice versa. Received: 5 December 1995/Received revision: 2 April 1996/Accepted: 22 April 1996     

Octanoate increases cytosolic Ca2+ concentration and membrane conductance in ovine pancreatic acinar cells

 In order to investigate the cellular mechanisms involved in amylase release in response to stimulation with short-chain fatty acids, changes in intracellular calcium concentration ([Ca²⁺]_i), membrane current and amylase release were measured in pancreatic acinar cells of sheep. Both octanoate and acetylcholine raised [Ca²⁺]_i in acinar cells in a concentration-dependent manner. The rise in [Ca²⁺]_i in response to the stimulation with octanoate (10 mmol ⋅ l^-1) was reduced in a medium without CaCl₂, but was markedly enhanced by reintroduction of CaCl₂ into the medium up to 2.56 mmol ⋅ l^-1. Perfusion of the cells with a medium containing octanoate (5 mmol ⋅ l^-1) or acetylcholine (0.5 μmol ⋅ l^-1) immediately raised inward current across the cell membrane at a holding-membrane potential of −30 mV. The inward current became greater as the holding potential became more negative. The equilibrium potential was 1.8 mV and 3.9 mV for octanoate and acetylcholine, respectively, being consistent with that for Cl^-. Although intracellular application of octanoate through a patch-clamp pipette also raised inward current after several minutes in some cells (4 out of 12), this possibility was significantly smaller than that for extracellular application. In other cells, even though the intracellular application of octanoate did not cause an increase in current, it always caused responses immediately after introduction of the fatty acid into the medium. Stimulation with fatty acid as well as acetylcholine raised amylase release in a concentration-dependent manner in cells dispersed from tissue segments with crude collagenase and trypsin inhibitor. Without trypsin inhibitor, crude collagenase significantly and selectively reduced the octanoate (10 mmol ⋅ l^-1)-induced amylase release. Dispersion with crude collagenase and trypsin significantly reduced both responses induced by octanoate and acetylcholine (5.5 μmol ⋅ l^-1). We conclude that fatty acids and acetylcholine increase [Ca²⁺]_i, which consequently evokes a rise in transmembrane ion (Cl^-) conductance and amylase release, and that trypsin-sensitive protein(s) in the cell membrane are involved in secretory processes activated by stimulation with fatty acids in ovine pancreatic acinar cells. Accepted: 14 May 1996     

A meiosis-specific protein kinase, Ime2, is required for the correct timing of DNA replication and for spore formation in yeast meiosis

 In this report we study the regulation of premeiotic DNA synthesis in Saccharomyces cerevisiae. DNA replication was monitored by fluorescence-activated cell sorting analysis and by analyzing the pattern of expression of the DNA polymerase α-primase complex. Wild-type cells and cells lacking one of the two principal regulators of meiosis, Ime1 and Ime2, were compared. We show that premeiotic DNA synthesis does not occur in ime1Δ diploids, but does occur in ime2Δ diploids with an 8–9 h delay. At late meiotic times, ime2Δ diploids exhibit an additional round of DNA synthesis. Furthermore, we show that in wild-type cells the B-subunit of DNA polymerase α is phosphorylated during premeiotic DNA synthesis, a phenomenon that has previously been reported for the mitotic cell cycle. Moreover, the catalytic subunit and the B-subunit of DNA polymerase α are specifically degraded during spore formation. Phosphorylation of the B-subunit does not occur in ime1Δ diploids, but does occur in ime2Δ diploids with an 8–9 h delay. In addition, we show that Ime2 is not absolutely required for commitment to meiotic recombination, spindle formation and nuclear division, although it is required for spore formation. Received: 20 February 1996 / Accepted: 7 June 1996     

Effect of ferrous iron concentration on the catalytic activity of immobilized cells of Thiobacillus ferrooxidans

 The kinetics of continuous oxidation of ferrous iron by immobilized cells of Thiobacillus ferrooxidans was studied in a packed-bed bioreactor. Polyurethane foam biomass support particles were used as carriers for cell immobilization. Effects of ferrous iron concentration and its volumetric loading on the kinetics of the reaction were investigated. Media containing different concentrations of ferrous iron in the range 5–20 kg m^-3 were tested. For each medium the kinetics of the reaction at different volumetric loadings of ferrous iron, at a constant temperature of 30^°C, were determined. With media containing 5 kg m^-3 and 10 kg m^-3 Fe²⁺, the fastest oxidation rates of 34.25 kg m^-3 h^-1 and 32 kg m^-3 h^-1 were achieved at a dilution rate of around 6 h^-1, which represents a residence time of 10 min. Employing a higher concentration of ferrous iron (20 kg m^-3) in the medium resulted in lower oxidation rates, with a maximum value of 10 kg m^-3 h^-1, indicating an inhibitory effect of ferrous iron on growth and activity of T. ferrooxidans. The reliable performance of the bioreactor during the course of the experiments confirmed the suitability of polyurethane foam biomass support particles as carriers for T. ferrooxidans immobilization. Received: 5 December 1995/Received revision: 21 April 1996/Accepted: 29 April 1996     

Production of poly(3-hydroxyalkanoates) by Pseudomonas putida KT2442 in continuous cultures

 The synthesis of poly(3-hydroxyalkanoates) (PHA) by Pseudomonas putida KT2442 growing on long-chain fatty acids was studied in continuous cultures. The effects of the growth rate on the biomass and polymer concentration were determined and it was found that the PHA concentrations decreased with increasing growth rates. The highest volumetric productivity was 0.13 g PHA l^-1 h^-1 at a specific growth rate (μ) of 0.1 h^-1. The molecular mass of the polymer remained constant at all growth rates but changes in the monomeric composition of the PHA synthesized were observed. Variation of the carbon to nitrogen (C/N) ratio of the substrate feed at μ=0.1 h^-1 revealed optimal PHA formation at C/N=20 mol/mol. In order to optimize PHA production P. putida KT2442 was cultivated to high cell densities in oxygen-limited continuous cultures. In this way a maximum biomass concentration of 30 g/l containing approximately 23% PHA was achieved. This corresponds to a volumetric productivity of 0.69 g  l^-1 h^-1. Received: 14 December 1995 / Received revision: 18 April 1996 / Accepted: 22 April 1996     

Overwintering populations of Mesodinium rubrum (Ciliophora: Haptorida) in lakes of the Vestfold Hills, East Antarctica

 The autotrophic ciliate Mesodinium rubrum Lohmann was observed during winter and spring in saline lakes ranging in salinity from 2 to 78‰ in the Vestfold Hills, Antarctica. The ciliate remained active during winter, and contained chlorophyll even though the level of light available for photosynthesis was minimal. No evidence of encystment as a means of survival during winter was observed. A seasonal study in one of the lakes, Ace Lake, revealed that M. rubrum was present throughout the year at abundances ranging from 1×10⁴ to 3.5×10⁵ cells l^-1. During the winter period, when little light penetrated the lake’s ice cover, cells were most common immediately under the ice at 2 m, where cell numbers were typically 8×10⁴ cells l^-1. Received: 3 January 1996/Accepted: 21 April 1996     

A generalized transport model for biased cell migration in an anisotropic environment

 A generalized transport model is derived for cell migration in an anisotropic environment and is applied to the specific cases of biased cell migration in a gradient of a stimulus (taxis; e.g., chemotaxis or haptotaxis) or along an axis of anisotropy (e.g., contact guidance). The model accounts for spatial or directional dependence of cell speed and cell turning behavior to predict a constitutive cell flux equation with drift velocity and diffusivity tensor (termed random motility tensor) that are explicit functions of the parameters of the underlying random walk model. This model provides the connection between cell locomotion and the resulting persistent random walk behavior to the observed cell migration on longer time scales, thus it provides a framework for interpreting cell migration data in terms of underlying motility mechanisms. Received: 8 April 1999     

Growth of Corynebacterium glutamicum in ammonium- and potassium-limited continuous cultures under high osmotic pressure

 In order to determine the possible effect of nutrient limitations on the response of Corynebacterium glutamicum to a saline osmotic up-shock, the bacteria were grown in continuous cultures, at osmotic pressures of 0.4 osmol/kg and 1.2 osmol/kg, under ammonia and potassium limitation. At the low osmolality of 0.4 osmol/kg, the glutamate and proline levels of 15 mg/g and 5 mg/g dry weight respectively were lower than previously reported in glucose-limited continuous cultures (50 mg/g and 10 mg/g dry weight respectively). On the other hand, the internal trehalose pool was much higher at 40 mg/g dry weight. When the medium osmolality was increased to 1.2 osmol/kg by NaCl addition, under ammonia limitation, the proline content rose from 5 mg/g to 20 mg/g dry weight and the trehalose content from 40 mg/g to 70 mg/g dry weight, whereas the intracellular pool of glutamate remained essentially constant. An increase in the internal sodium content was also observed. Similar results were found for the internal pool of glutamate, proline and trehalose when C. glutamicum was grown under potassium limitations at an osmolality of 1.2 osmol/kg. There were also higher levels of sodium ions, glutamine and alanine. According to the present results, whereas proline was previously reported to be the dominantly accumulated osmoprotectant in C. glutamicum grown under glucose limitations, under ammonia and potassium limitations trehalose represented the dominantly synthesized metabolite. Received: 19 December 1995/Received revision: 9 April 1996/Accepted: 15 April 1996     

Kinetic coefficients for simultaneous reduction of sulfate and uranium by Desulfovibrio desulfuricans

 Previously it was demonstrated that bacteria are capable of transforming soluble uranyl ion, U(VI), to insoluble uraninite, U(IV); however, the rate for this transformation has not been determined. We report the kinetic coefficients for Desulfovibrio desulfuricans DSM 1924 grown in a continuous-flow chemostat where pyruvate was the electron donor and sulfate was the electron acceptor. The medium was supplemented with 1 mM uranyl nitrate, and the chemostat flow rate ranged from 1.12 ml/h to 4.75 ml/h with incubation at 28°C. The maximum rate of pyruvate utilization (k) was determined to be 4.7 days^-1, while the half-velocity constant (K _s) was 127 mg/l. The yield coefficient (Y) of cells per mole of pyruvate oxidized was calculated to be 0.021 g, while the endogenous decay coefficient (k _d) was determined to be 0.072 days^-1. More than 90% of U(VI) was transformed to U(VI) in the chemostat under the conditions employed. Received: 7 September 1995/Received last revision: 10 January 1996/Accepted: 5 February 1996     

Degradation of anthracene by laccase of Trametes versicolor in the presence of different mediator compounds

 Laccase of Trametes versicolor was generally able to oxidize anthracene in vitro. After 72 h incubation about 35% of the anthracene was transformed stoichiometrically to 9,10-anthraquinone. Transformation of anthracene increased rapidly in the presence of different mediators that readily generate stable radicals: 2,2′-azino-bis-(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS) and 1-hydroxybenzotriazole. For the reaction, the presence of both the laccase and the mediator was necessary. In the presence of 0.005 mM 1-hydroxybenzotriazole this conversion had removed 47% of the anthracene after 72 h; 75% of the substrate was oxidized during this period when ABTS (1 mM) was used as mediator. In contrast to reactions without or with only low concentrations of a mediator, there was a discrepancy between the disappearance of anthracene and the formation of 9,10-anthraquinone in mediator-forced reactions. Coupling-products of mediators with anthracene degradation products were found. Anthracene disappeared nearly completely after incubation for 72 h with laccase in a 0.1 mM solution of 1-hydroxybenzotriazole and was transformed to 9,10-anthraquinone in about 80% yield; 90% of the substrate was transformed in the presence of ABTS (2.0 mM) resulting again in 80% quinone. Phenothiazine was not effective in this system. Received: 9 April 1996/Received last revision: 7 June 1996/Accepted: 10 June 1996     

Selection of an adhesive phenotype of Streptococcus salivarius subsp. thermophilus for use in fixed-bed reactors

 Streptococcus salivarius subsp. thermophilus was cultivated in a chemostat in order to obtain an adhesive phenotype of this strain. When the system was operated at low dilution rates (D<0.2 h^-1) for about 4 weeks, the strain formed a visible film on the surface of the culture vessel. The biofilm cells were not washed out even when dilution rates were increased (D=6.9 h^-1), and this resulted in a high biomass productivity (P=4.1 g l^-1h^-1). On the other hand, when the culture was grown at dilution rates faster than 0.2 h^-1, only the free suspended cells were present in the culture broth, and were washed out at velocities of about 1.0 h^-1. The biomass productivity was consequently lower (P=1.33 g l^-1h^-1) than in the previous case. The selected adhesive phenotype was grown on different glass beads and the possibility of lactate fermentation in a continuous and semicontinuous mode was demonstrated. Received: 16 August 1995/Received revision: 18 March 1996/Accepted: 25 March 1996