Lambda encodes an outer membrane protein: the lom gene.

Summary infected minicells synthesize a polypeptide (M _r=20,500) which is incorporated almost exclusively into the outer membrane of the minicell envelope. The gene (lom=lambda outer membrane) encoding this polypeptide has been mapped in the nonessential region of the genome between coordinates 39.4% and 40.7% of .     

On the phytochrome phototransformation kinetics in mustard seedlings

Summary The in vivo phototransformation kinetics of mustard hook and cotyledon phytochrome exhibit a deviation from a single first order curve, quite similar to that for pumpkin hooks as reported in a previous paper (Boisard, Marmé and Schäfer, 1971). The P _frP_rkinetics can be characterized by the ratios _fr, ^I · P _fr ^I / _fr, ^II · P _fr, ^II and where P _fr ^I and P _fr ^II are two populations of phytochrome molecules which convert to P _rwith a first order half-life of and . These ratios depend on the length of time of etiolation. The ratio _fr, ^I · P _fr ^I / _fr, ^II · P _fr, ^II is independent of the amount of total P _frpresent at the beginning of the P _frP_rphototransformation after a non-saturating dose of red light. The half-lives of the two populations, however, depend on the concentration of total P _frinitially present. P _frP_rphototransformation kinetics with different light intensities show that reciprocity holds.     

Phytochrome modulation of ATPase activity in a membrane fraction from Phaseolus

Membrane-bound phytochrome and ATPase (ATP phosphohydrolase EC 3.6.1.3.) activity extracted from hypocotyl hooks of etiolated Phaseolus aureus Roxb. were both separated from solute proteins by gel filtration on Sepharose C1-2B. The amount of phytochrome detected in the membrane fraction was very small and was not significantly increased by red irradiation (in vivo or in vitro). Membrane-bound ATPase activity was modulated in vitro by the phytochrome in the membrane fraction, being lower after red light than after far-red light. This effect was potentiated by a preliminary light reaction which occurred only in vivo and, in continuous red light, required 60 to 90 s at 25°C. Thus a two minute, in vivo, red irradiation reduced membrane-bound ATPase activity to about half that of the etiolated state. Subsequently bound-ATPase activity was determined by the form of phytochrome (P_r or P_fr) irrespective of whether established in vivo or in vitro. These results indicate that binding or release (of enzyme, cofactors or inhibitors) is not involved in phytochrome modulation of enzyme activity in the membrane fraction.Abbreviations R red light - F far red light - P_r inactive form of phytochrome (_max=660 nm) - P_fr active form of phytochrome (_max=730 nm) - MOPS N-morpholino-3-propansulphonic acid     

Assessment of survival during starvation ofEscherichia coli andKlebsiella pneumoniae in artificial urine: analysis of the kinetics of colony formation

A kinetic model of colony formation was proposed by Hattori, based on a count of the colonies that appear on a plate in successive short intervals of time. In this model, three parameters (,t _r and N) are defined, which reflect the ability of a bacterium to yield colonies and allow us to described the dynamics of bacterial populations in soil and ofE. coli at different growth phases. In this paper we report a reparametrization of the kinetic model of colony formation, with the aim of facilitating more accurate calculation of andt _r. Moreover, we observed that during the starvation ofE. coli andK. pneumoniae in urine, can be used to assess survival, since this parameter clearly decreases during starvation. Retardation time values (t _r) were similar inE. coli andK. pneumoniae throughout the starvation experimental period.     

Human λ light chain locus: Organization and DNA sequences of three genomicJ regions

Evidence for the genomic organization of human lambda light chain joining (J) region gene segments is presented. A mouse J probe was used in Southern hybridizations to localize joining region sequences in a cosmid clone containing the genomic cluster of six human lambda constant (C) region gene segments. The results of these hybridizations suggest the presence of at least one J gene segment upstream from each constant region gene segment. The DNA sequences indicate that the human JI, J2, and J3 gene segments have consensus nonamer and heptamer sequences, proposed to be involved in V-J joining, are capable of encoding the known amino acid sequences for the respective J peptides, and have a sequence which could give functional RNA splice site at the end of their coding regions. Our data show that a single functional J is located 1.3 or 1.6 kb upstream of each of the C gene segments known to encode the Mcg, Kern^– Oz^–, and Kern^–Oz⁺ isotypes. Therefore, the gene organization of this region of the human lambda locus is J1 CI -J2C2-J3C3. The DNA sequences ofJ 1,J 2, andJ 3 presented in this paper establish that a singleJ gene segment precedes each expressed C gene segment, and support a model for the evolution of the human JC clusters where JICI andJ2C2-J3C3. arose from different ancestral JC units.     

Study of the Solute Flows of Multicomponent and Heterogeneous Non-Ionic Solutions in Double-Membrane System

The solute flows were studied in a double-membrane osmotic-diffusive cell, in which two membranes mounted in horizontal planes separate three compartments (l,m,r) containing the non-homogeneous, non-electrolytic binary and ternary solutions. The volume of inter-membrane compartment (m), which is the infinitesimally layer of solution, and volume of external compartments (l and r) fulfill the conditions V _m 0 and V _l =V _r , respectively. In an initial moment, the solution concentrations satisfy the condition (C ^o _s ) _l < (C ^o _s ) _m >(C ^o _s ) _r. The double-membrane osmotic-diffusive cell is composed of two complexes: boundary layer/membrane/boundary layer, mounted in horizontal planes. In the cell, solute flux was measured as a function of concentration and gravitational configuration. The linear dependencies of the solute flux on concentration difference in binary solutions and nonlinear – in ternary solutions were obtained. It was shown that the double-membrane osmotic-diffusive cell has rectifying and amplifying properties of solute flows.     

The R gene product of bacteriophage lambda is the murein transglycosylase

Summary The radioactively labeled proteins synthesised in Escherichia coli minicells infected by bacteriophage R and R ⁺ were compared by polyacrylamide gel electrophoresis. R mutants, which have lost the ability to lyse host cells, lack a polypeptide of molecular weight 17.5 kD corresponding to the molecular weight of murein transglycosylase — a bacteriolytic enzyme from lysates which we have described previously. It has been shown by direct comparison using radio-labeled enzyme that transglycosylase comigrates with the R gene product. The enzyme was endetectable in induced cultures of E. coli W3350 su ^o (cI857 Ram5) and C600 (cI857 acR301), while it was present in a R _– ⁺ mutant lysate. We conclude that the transglycosylase is the R gene product.Abbreviations Muropeptide CA GlcNac-1-4-1,6-anhydro-MurNac-L-Ala-D-Glu-msA₂pm-D-Ala - muropeptide CB GlcNac-MurNac-GlcNac-1,6-anhydro-MurNac in which the carboxyl groups of MurNac and 1,6-anhydro-MurNac are substituted by the tetrapeptide L-Ala-D-Glu-msA₂pm-D-Ala - muropeptide C3 dimer of the two units GlcNac-MurNac-L-Ala-D-Glu-msA₂pm-D-Ala which are connected by D-D peptide bond between D-Ala and msA₂pm - GlcNac N-acetyl-D-glucosamine - MurNac N-acetylmuramic acid - msA₂pm meso-diaminopimelic acid - rivanol 6,9-diamino-2-ethoxyacridine lactate - SDS sodium dodecyl sulfate     

Light-controlled inhibition of hypocotyl growth inSinapis alba L. seedlings

Fluence rate-response curves were determined for the inhibition of hypocotyl growth in 54 h old dark-grownSinapis alba L. seedlings by continuous or hourly 5 min red light irradiation (24 h). In both cases a fluence rate-dependence was observed. More than 90% of the continuous light effect could be substituted for by hourly light pulses if the total fluence of the two different light regimes was the same. Measurements of the far red absorbing form of phytochrome ([P _fr]) and [P _fr]/[P tot] (total phytochrome) showed a strong fluence rate-dependence under continuous and pulsed light which partially paralleled the fluence rate-response curves for the inhibition of the hypocotyl growth.Abbreviations R red - HIR high irradiance response - P _rfr phytochrome in its red, far-red absorbing form - [P _tot]=[P _r]+[P _fr] =k ₁/(k ₁+k ₂): photoequilibrium of phytochrome at wavelength , wherebyk _1,2 rate constants ofP _rP _fr,P _frP _r photoconversion - [P _fr]/[P _tot]     

Analysis of light-controlled accumulation of carotenoids in mustard (Sinapis alba L.) seedlings

Carotenoid accumulation in the cotyledons of the mustard seedling (Sinapis alba L.) is controlled by light. Besides the stimulatory function of phytochrome in carotenogenesis the experiments reveal the significance of chlorophyll accumulation for the accumulation of larger amounts of acrotenoids. A specific blue light effect was not found. The data suggest that light exerts its control over carotenoid biogenesis through two separate mechanisms: A phytochrome regulation of enzyme levels before a postulated pool of free carotenoids, and a regulation by chlorophyll draining the pool by complex-formation.Abbreviations Chl chlorophyll(s) - PChl protochlorophyll(ide) - HIR high irradiance reaction (of phytochrome) - P_fr far-red absorbing, physiologically active form of phytochrome - P_r red absorbing, physiologically inactive form of phytochrome - P_fof total phytochrome, i.e. [P_r]+[P_fr] - [P_fr]/[P_fof], wavelength dependent photoequilibrium of the phytochrome system - red red light - fr far-red light     

Simple diagnostic statistical tests of models for DNA substitution

The accuracy of models for DNA substitution used in phylogenetic analyses is becoming more important with the increasing availability and analysis of molecular sequence data. It is natural to look for ways of improving these models, and to do this in a planned manner it is useful to be able to identify features of sequences that may not be described adequately. In this paper, I describe three statistics which may give useful diagnostic information on departures from models' predictions. The statistical distributions of these statistics are discussed and simple significance tests are derived. These tests are based on the (estimated) phylogeny of the sequences and so have the advantage of using the information contained in this tree. Examples are given of the application of the new tests to Markov chain models describing the evolution of primate pseudogene sequences and small-subunit RNA sequences.Abbreviations b(N,p) binomial distribution of N trials, each with probability p of success - m(N,p ₁,p ₂, ..., p _r ) multinomial distribution of N trials, with r possible outcomes having probabilities p ₁, p ₂, ..., p_r, respectively - N(, ²) Normal distribution with mean and variance ² - p() Poisson distribution with mean - bp base pairs - cdf cumulative distribution function - i.i.d. independent, identical distribution     

Purification and characterization of acid urease from Lactobacillus fermentum

Summary Acid urease was purified to an electrophoretically homogeneous state, and the molecular weight was estimated to be 220 000. The enzyme consisted of three kinds of subunits, designated , and , with molecular weights of 67 000, 16 800 and 8600, respectively, in a (₁ \₂₁)₂ structure. The isoelectric point of the enzyme was 4.8. The nickel content was found to be 1.9 atoms of nickel per ₁₂₁ unit. The amino acid profile was different from those of known bacterial neutral ureases. The enzyme was most active at pH 2 and around 65° C. It was stable between pH 3 and 9, and below 50° C. The K _m for urea was 2.7 mM at pH 2. The enzyme activity was inhibited by Ag⁺, Hg²⁺, Cu²⁺, p-chloromercuribenzoate and acetohydroxamate. The enzyme was separated into three subunits by reverse phase HPLC. The amino terminal amino acid sequences of the subunits , and were Ser-Phe-Asp-Met-, Met-Val-Pro-Gly- and Met-Arg-Leu-Thr-, respectively.Offprint requests to: S. Kakimoto     

Cell recycling studies for α-amylase production by Bacillus amyloliquefaciens

Production of -amylase by a strain of Bacillus amyloliquefaciens was investigated in a cell recycle bioreactor incorporating a membrane filtration module for cell separation. Experimental fermentation studies with the B. amyloliquefaciens strain WA-4 clearly showed that incorporating cell recycling increased -amylase yield and volumetric productivity as compared to conventional continuous fermentation. The effect of operating conditions on -amylase production was difficult to demonstrate experimentally due to the problems of keeping the permeate and bleed rates constant over an extended period of time. Computer simulations were therefore undertaken to support the experimental data, as well as to elucidate the dynamics of -amylase production in the cell recycle bioreactor as compared to conventional chemostat and batch fermentations. Taken together, the simulations and experiments clearly showed that low bleed rate (high recycling ratio) various a high level of -amylase activity. The simulated fermentations revealed that this was especially pronounced at high recycling ratios. Volumetric productivity was maximum at a dilution rate of around 0.4 h^–1 and a high recycling ratio. The latter had to exceed 0.75 before volumetric productivity was significantly greater than with conventional chemostat fermentation.List of Symbols a proportionality constant relating the specific growth rate to the logarithm of G (h) - a ₁ reaction order with respect to starch concentration - a ₂ reaction order with respect to glucose concentration - B bleed rate (h^–1) - C starch concentration (g/l) - C ₀ starch concentration in the feed (g/l) - D dilution rate (h^–1) - D _E volumetric productivity (KNU/(mlh)) - e intracellular -amylase concentration (g/g cell mass) - E extracellular -amylase concentration (KNU/ml) - F volumetric flow rate (l/h) - G average number of genome equivalents of DNA per cell - k _l intracellular equilibrium constant - k ₂ intracellular equilibrium constant - k _s Monod saturation constant (g/l) - k ₃ excretion rate constant (h^–1) - k _d first order decay constant (h^–1) - k _gl rate constant for glucose production - k _st rate constant for starch hydrolysis - k _t1 proportionality constant for -amylase production (gmRNA/g substrate) - k ₁ translation constant (g/(g mRNAh)) - KNU kilo Novo unit - m maintenance coefficient (g substrate/(g cell massh)) - n number of binding sites for the co-repressor on the cytoplasmic repressor - Q repression function K₁/K₂Q1.0 - R ratio of recycling - R _s rate of glucose production (g/lh) - r _c rate of starch hydrolysis (g/(lh)) - R _eX retention by the filter of the compounds X: starch or -amylase - r intracellular -amylase mRNA concentration (g/g cell mass) - r _C volumetric productivity of starch (g/lh) - r _E volumetric productivity of intracellular -amylase (KNU/(g cell massh)) - r _r volumetric productivity of intracellular mRNA (g/(g cell massh)) - r _e volumetric productivity of extracellular -amylase (KNU/(mlh)) - r _s volumetric productivity of glucose (g/(lh)) - r _X volumetric productivity of cell mass (g/(lh)) - S ₀ free reducing sugar concentration in the feed (g/l) - S extracellular concentration of reducing sugar (g/1) - t time (h) - V volume (l) - X cell mass concentration (g/l) - Y yield coefficient (g cell mass/g substrate) - Y _E/S yield coefficient (KNU -amylase/g substrate) - Y _E total amount of -amylase produced (KNU) - substrate uptake (g substrate/(g cell massh)) - specific growth rate of cell mass (h^–1) - _d specific death rate of cells (h^–1) - _m maximum specific growth rate of cell mass (h^–1) This study was supported by Bioprocess Engineering Programme of the Nordic Industrial Foundation and the Center for Process Biotechnology, the Technical University of Denmark.     

Na/H exchange in cultured epithelial cells from fish gills

Using primary cultures of gill pavement cells from freshwater rainbow trout, a method is described for achieving confluent monolayers of the cells on glass coverslips. A continuous record of intracellular pH was obtained by loading the cells with the pH-sensitive flourescent dye 2,7-bis(2-carboxyethyl)-5(6)-carboxyfluorescein and mounting the coverslips in the flowthrough cuvette of a spectrofluorimeter. Experiments were performed in HEPES-buffered media nominally free of HCO₃. Resting intracellular pH (7.43 at extracellular pH=7.70) was insensitive to the removal of Cl^– or the application of 4-acetamido-4-isothiocyanatostilbene-2,2-disulfonic acid (0.1 mmol·l^–1), but fell by about 0.3 units when Na⁺ was removed or in the presence of amiloride (0.2 mmol·l^–1). Exposure to elevated ammonia (ammonia prepulse; 30 mmol·l^–1 as NH₄Cl for 6–9 min) produced an increase in intracellular pH (to about 8.1) followed by a slow decay, and washout of the pulse caused intracellular pH to fall to about 6.5. Intracellular non-HCO ₃ ^– buffer capacity was about 13.4 slykes. Rapid recovery of intracellular pH from intracellular acidosis induced by ammonia prepulse was inhibited more than 80% in Na⁺-free conditions or in the presence of amiloride (0.2 mmol·l^–1). Neither bafilomycin A₁ (3 mol·l^–1) nor Cl removal altered the intracellular pH recovery rate. The K _m for Na⁺ of the intracellular pH recovery mechanism was 8.3 mmol·l^–1, and the rate constant at V _max was 0.008·s^–1 (equivalent to 5.60 mmol H⁺·l^–1 cell water·min^–1), which was achieved at external Na⁺ levels from 25 to 140 mmol·l^–1. We conclude that intracellular pH in cultured gill pavement cells in HEPES-buffered, HCO ₃ ^– -free media, both at rest and during acidosis, is regulated by a Na⁺/H⁺ antiport and not by anion-dependent mechanisms or a vacuolar H⁺-ATPase.Abbreviations BCECF 2,7-bis(2-carboxyethyl)-5(6)-carboxy-fluorescein - BCECF/AM 2,7-bis(2-carboxyethyl)-5(6)-carboxy-fluorescein, acetoxymethylester - Cholin-Cl choline chloride - DMSO dimethyl sulfoxide - EDTA ethylene diamine tetra-acetic acid - FBS foetal bovine serum - H ⁺ -ATPase Proton-dependent adenosine triphosphatase - HEPES N-[2-hydroxyethyl]piperazine-N[2-ethanesulfonic acid] - pH _i intracellular pH - pH _e extracellular pH - PBS phosphate-buffered saline - SITS 4-acetamido-4-isothiocyanatostilbene-2,2-disulfonic acid     

Rearrangements between the operators in the bacteriophage lambda

Summary The left operator mutant v2s develops poorly during infection as a result of constitutive expression of the left operon. A revertant of v2s, designated iri, was found to contain an inversion of the cI region with the inversion endpoints to be within the lambda operators o _L and o _R. Formation of the inversion is facilitated by a translocation of right operator o _R ^c mutant sequence to the left operator in v2s. The inversion in iri positions wild-type o _R sequence at o _L returning control of the left operon to repression by the lambda cro repressor.     

Control by light of hypocotyl growth in de-etiolated mustard seedlings

After sowing, mustard (Sinapis alba L.) seedlings were grown for 48 h in white light (25°C). These fully de-etiolated, green seedlings were used as experimental material between 48 and 72 (84) h after sowing. The question researched was to what extent control by light of hypocotyl elongation is due to phytochrome in these seedlings. It was found that the light effect on hypocotyl growth is very probably exerted through phytochrome only. In particular, we found no indication for the involvement of a specific blue light photoreceptor pigment.Abbreviations HIR high irradiance reaction - P_fr far-red absorbing, physiologically active form of phytochrome - P_r red absorbing, physiologically inactive form of phytochrome - Pot total phytochrome, i.e. [P_r]+[P_fr] - [P_fr]/[P_tot] - red red light - fr far-red light - wl white light - bl blue light - di dichromatic irradiation - l hypocotyl length     

Mutations of coliphage lambda affecting the expression of replicative functions O and P

Summary A selection technique, using the thermoinducible prophage CI857Nsus7 Nsus53, has lead to the characterization of a new class of prophage mutations (called r), which prevent host killing upon thermal induction.N-defective r mutants efficiently complement i⁴³⁴ or O and P mutants, but not the corresponding mutants of i²¹. Complementation data suggest that the i²¹ hybrid fails to provide the positive regulatory mechanism dependent on the N-gene product, since it cannot activate the Q gene of a N-defective mutant. Thus, it seems possible that r mutants cannot express genes O and P unless the N-gene product is present in the cell. This interpretation is supported by the fact that r mutants are not defective and form plaques when their N-gene is functional. r mutation confer a clear phenotype, and map in the y-CII region. Results of a density gradient analysis suggest that they result from small insertions of DNA. Induced N-defective r prophages appear to be only poorly transcribed on strand H.Complementation tests performed in a strain lysogenic for indicate that the C17 mutation can suppress a r mutation in a cis position, even in the absence of the N-gene product.These results suggest that the expression of genes O and P, in addition to gene Q, is under the positive regulation of the N-gene product.     

Dependence of phytochrome dark reactions on the initial photostationary state

Summary Under conditions of continuous irradiation, the P _jr destruction rate constants (k _d ) of phytochrome in hooks and cotyledons of squash (Cucurbita pepo L.) seedlings do not depend on the photostationary state and are the same in both organs. On the other hand, the rate constants of the dark reversion and the first destruction step, plotted as a function of ⁰ , show optimum curves with maxima between ⁰ and 0.5. Similar results were obtained for dark reactions of mustard (Sinapis alba L.)-hook phytochrome in vivo. This indicates a cooperative behaviour of these phytochrome dark reactions.Abbreviations P _r red-absorbing form of phytochrome - P _fr far-red-absorbing form of phytochrome - [P _tot] [P _r ]+[P _fr ] - [P _tot] ([P _fr ]/[P _tot]), photostationary state - ⁰ at t=0, immediately after saturating irradiation     

Denitrification kinetics of simulated fish processing wastewater at different ratios of nitrate to biomass

Denitrification was studied in anoxic batch cultures of a simulated fish processing wastewater at 37 r C and pH 7.5, using a denitrifying enrichment culture from fishery wastewater. Different initial nitrate to biomass ratios (So/Xo) were used: nitrate and biomass varied from 7.5 to 94.7 mg NO₃-N l^–1, and from 20 to 4300 mg volatile suspended solids l^–1, respectively. The specific maximum denitrification rate (r _m) and the cell yield (Y _{X / S}) depended on the So/Xo ratio under anoxic conditions: r _m increased from 1.2 to 1584 mg NO₃-N g^–1 VSS h^–1 and Y _{X / S} decreased from 42 to 0.03 mg VSS mg^–1 NO₃-N when So/Xo varied from 5.5 10^{– 3} to 9.3 mg NO₃-N/mg VSS. Nomenclature C_{NO3 – N} nitrate concentration, mg NO₃-N l^–1 K _S saturation constant, mg NO₃-N l^–1 r _m specific maximum denitrification rate, mg NO₃-N g^–1 VSS h^–1 So initial substrate concentration, mg l^–1 t time, h TOC total organic carbon VSS volatile suspended solids x biomass concentration, g VSS l^–1 Xo initial biomass concentration, g VSS l^–1 Y _X/S substrate to biomass cell yield, mg VSS/mg N Greek symbols: _m maximum specific growth rate of the anoxic microbial population, 1 h^–1     

l-threonine production by l-aspartate- and l-homoserine-resistant mutant of Escherichia coli

Summary Growth and l-threonine productivity of l-threonine producer Escherichia coli H-4290 were inhibited by precursor amino acids, l-homoserine and l-aspartate. l-Threonine hyper-producers were isolated among the mutants resistant to l-homoserine and l-aspartate. Mutants H-4351 (Hom^r) and H-4578 (Hom^r, Asp^r) accumulated 22.2 g/l and 24.3 g/l of l-threonine in test tube cultures, while the parental strain H-4290 accumulated 18.2 g/l. The enzyme level of aspartokinase I (first enzyme of the threonine operon) was enhanced 2.3 times (H-4351) and 3 times (H-4578) that of H-4290. Mutant H-4578 accumulated 76 g/l of l-threonine in a 2-l jar fermentor after 75 h cultivation.Abbreviations DAP diaminopimeric acid - Met ^l poor growth in methionine-free medium - AHV -amino--hydroxyvaleric acid - Thr-N^- lack of ability to utilize l-threonine as a nitrogen source - Rif rifampicin - Lys+Met^r resistant to l-lysine and dl-methionine     

Diatom species–environment relationships and inference models from Isachsen, Ellef Ringnes Island, Canadian High Arctic

Surface sediment diatom assemblages were examined from 26 freshwater sites near Isachsen (78°47N, 103°32W), Ellef Ringnes Island, a region of diverse and atypical water chemistry for high arctic sites. One hundred and sixty eight diatom taxa were identified from these samples, over 50% of which had not previously been recorded in the Canadian High Arctic. Variations in diatom assemblages were related to changes in measured environmental variables using multivariate techniques. Canonical correspondence analysis (CCA) indicated that five variables contributed significantly to explaining patterns of diatom variation (i.e., COND, DIC, Mn, TPF, TPU). The first CCA axis (=0.44) was primarily controlled by conductivity-related variables, while CCA axis 2 (=0.21) was related to particulate concentrations. Diatom-based inference models were generated for the reconstruction of conductivity (RMSEP_jack=0.32, r²_jack=0.76) and pH (RMSEP_jack=0.40, r²_jack=0.69). The strengths of these models indicate that it will be possible to reliably infer past trends in conductivity and pH from diatom assemblages preserved in dated sediment cores from the Isachsen region.