Bacteriophage phi 1 as a gene-cloning vector in Bacillus subtilis

Summary We attempted to use Bacillus subtilis phage 1 as a gene-cloning vector since the 1 genome was found to have few cleavage sites upon digestion with several kinds of restriction endonucleases. A 1 stock supplied by J. Ito (University of Arizona, Tucson, USA) consisted of two phages, 1E1 and 1E2, having one and two EcoRI-cleavage sites in their genomes respectively. From the latter isolate a deletion mutant 1E21 was induced to increase the size range of DNA segments to be cloned. It was demonstrated, by in vitro recombination experiments with phage 11 DNA, that 1E21 can be used for cloning EcoRI fragments of various sizes. We analyzed the DNAs of ten 1 clones isolated from independent transfectants and found that six of them carried 11 DNA fragments inserted at either of the two EcoRI-cleavage sites. Some of the hybrid phage DNAs were found to be cleaved with BamHI and HaeIII endonucleases at the 11 DNA portion, whereas the parental 1E21 DNA was insensitive to any of these enzymes. These hybrid phages would therefore be useful vectors for cloning foreign DNA fragments generated by cleavage with BamHI or HaeIII endonucleases.     

Bacillus subtilis bacteriophages SP beta c1 is a deletion mutant of SP beta

Summary The restriction fragment patterns of two mutant forms of the temperate Bacillus subtilis bacteriophage SP have been examined. The DNA of a heat-inducible mutant, SPc2, which has a molecular size of 128 kilobases (kb), yields the same restriction pattern as the wild type SPc⁺ DNA. The DNA of a clear-plaque mutant, SPc1, has a molecular size of 117 kb, and is deleted for an 11 kb region of phage DNA. Neither SPc1 nor SPc2 DNA is cleaved by the endonuclease HaeIII.     

Alternative pathway activities in aged potato tuber slices measured by three methods

To find a simple and reliable oxygen electrode-based method to estimate the values of alternative pathway activity (V _alt) and its contribution to total respiration V _alt/V _t) in aged potato (Solanum tuberosum L.) tuber slices, we compared conventional hydroxamate-inhibiting method, improved hydroxamate-inhibiting method with 2,6-dichlorophenol indophenol (DCPIP), and the oxygen isotope discrimination (OID) method. The values of V _alt and V _alt/V _t obtained with an improved hydroxamate-inhibiting method with DCPIP in 12-h- and 24-h-aged slices were about twice higher than those with the conventional hydroxamate-inhibiting method. Only a relatively small difference in the values of V _alt and V _alt/V _t obtained by the OID method and the improved hydroxamate-inhibiting method with DCPIP in 12-h and 24-h-aged slices was observed. These results indicated that the improved hydroxamate-inhibiting method with DCPIP could be considered as a new, simple, and reliable technique for the noninvasive assay of the AP activity.From Fiziologiya Rastenii, Vol. 52, No. 2, 2005, pp. 311–315.Original English Text Copyright © 2005 by Hou, Zhou, Kong, Liang, Zhang.This article was submitted by the authors in English.This revised version was published online in April 2005 with a corrected cover date.     

Detection of specific DNA sequences in yeast by colony hybridization

Summary A procedure is described for the detection of specific DNA sequences in Saccharomyces cerevisiae. This method allows a rapid screening of a large number of yeast colonies. The yeast cells of each colony, grown on nitrocellulose filters, are converted, in situ, to protoplasts by snail enzyme, and are then lysed and their DNAs are denatured and fixed on the filter. The presence of the specific DNA sequence is detected directly on the filter by hybridization with a radioactive cRNA.We have used successfully this technique to detect the presence or the absence of specific mt DNA sequences, in ⁺, ^- and ⁰ strains, and to detect the presence or the absence of the 2 m DNA sequences in different strains.     

Isolation of viable deletion mutants of Streptomyces actinophage (Pal 6) and their molecular characterization

Summary Deletion mutants of bacteriophage Pal 6 were isolated by successive treatments of either heat (60° C) or pyrophosphate (10 mM). These mutants were characterized by restriction enzyme cleavage analysis. The pyrophosphate resistant clones lost the whole Eco R1 fragment in which the Sal I site is located, as well as an unrelated Hind III fragment. These results show that the region containing the Sal I site in the phage genome is not essential for phage viability. This single Sal I site is therefore suitable as a potential insertion site for DNA cloning. On the other hand, the heat resistant clones that were isolated and characterized do not appear to have detectable deletions as indicated by their Eco R1 DNA digestion pattern.     

Upper limit for DNA packaging by Bacillus subtilis bacteriophage phi 105: isolation of phage deletion mutants by induction of oversized prophages

Summary We have determined the upper size limit for DNA packaging in Bacillus subtilis bacteriophage 105 by examining the plaque-forming and transducing capabilities of lysates made from strains containing prophages of various sizes. The upper size limit for efficient packaging of the phage genome appears to be about 40.2 kb, which is about 1 kb larger than the wild-type genome. This places an upper limit of about 5 kb on the size of insertions that can be accommodated in 105 transfection cloning vectors, such as 105J27. Induction of prophages that exceed the upper limit, followed by selection for plaque formation or transduction, provides a powerful means of isolating phage deletion mutants. A comparison of the location of each deletion with the resultant phenotype has enabled us to identify non-essential regions of the phage genome, and regions that are required for tail biosynthesis and for host cell lysis.     

Isolation and rapid screening of deletion mutants of temperateBacillus subtilis molecular cloning vehicle ρ14

Four deletion mutants ofBacillus subtilis temperate bacteriophage ρ14 have been isolated by selection with the chelating agent tetrasodium pyrophosphate. The presence of deletions in the genome are readily detected by restriction endonuclease digestion patterns on agarose gels. The deletion mutants have been characterized as to their resistance to the killing effect of tetrasodium pyrophosphate and their buoyant densitiese have been determined in cesium chloride density gradients. Three of the deletion mutants, designated Φdoc26, Φdoc36 and Φdoc39, are defective in the establishment of stable lysogens and form clear plaques on a sensitive host. The fourth delection mutant, designated Φdo7, still retains the ability to establish lysogeny.     

Die Aktivit?tsperiodik bei V?geln mit und ohne dunklem Schlafkasten

Zusammenfassung In 2 Versuchsserien wurden Kohlmeisen(Parus major) und japanische Möwchen(Lonchura striata var.domestica) einzeln und schallisoliert gehalten. In der ersten Versuchsserie, in der alle Vögel einen dunklen Schlafkasten hatten, wurde der Einfluß der Beleuchtungsstärke auf die Periode () der Hüpfaktivität und auf das Verhältnis von Aktivitätszeit zu Ruhezeit ( : -Verhältnis) untersucht. Sowhol Kohlmeisen als auch japanische Möwchen folgen der Regel, daß mit wachsender Beleuchtungsstärke die Periode kürzer und das : -Verhältnis größer wird.In der 2. Serie wurde der Einfluß Ruhe im dunklen Schlafkasten auf die Periodenlänge und auf das : -Verhältnis untersucht. Es wurden die Messungen aus Bedingung 1 (der Vogel hat einen dunklen Schlafkasten zur Verfügung) mit den Messungen aus Bedingung 2 (der Vogel hat keinen oder einen hellen Schlafkasten zur Verfügung) verglichen. Das Ergebnis bei Kohlmeisen entspricht den Befunden bei konstantem Licht verschiedener Intensität. Unter Bedingung 1 ist länger und das : -Verhältnis kleiner als in Bedingung 2. Das Ausmaß der Änderung von nach Fortnahme des dunklen Kastens ist unabhängig von der Periodenlänge in Bedingung 1. Das Ausmaß der änderung von : ist unabhängig von a : in Bedingung 1, jedoch schwach negativ korreliert mit der Periodenlänge in Bedingung 1.Bei japanischen Möwchen entsprechen die Ergebnisse dieser Versuchsserie nicht der Regel für tagaktive Vögel. Mit Benützen des dunklen Schlafkastens ist kürzer als ohne den Schlafkasten. Ohne den Schlafkasten ist etwa 24 Std. Das : -Verhältnis ist in Bedingung 1 unter bestimmten Voraussetzungen kleiner als in Bedingung 2. Das Ausmaß der Änderung von nach Fortnahme des Kastens ist mit der dazugehörigen Periode in Bedingung 1 hochsignifikant korreliert (Regressionskoeffizient b=-1.01, Korrelationskoeffizient r=0.89). Ebenfalls ist das Ausmaß der Änderung von : nach Fortnahme des Kastens mit : aus Bedingung 1 korreliert; es scheint, als würde ein bevorzugtes : -Verhältnis von etwa 2.0 eingeregelt.Die Ergebnisse werden im Hinblick auf 4 Punkte diskutiert: 1) Das circadiane System arbeitet innerhalb eines engen Bereiches von - und : -Werten optimal. 2) Der Optimalbereich wird bevorzugt unter ungünstigen Bedingungen angestrebt. 3) Der Entzug des dunklen Schlafkastens belastet japanische Möwchen mehr als Kohlmeisen. 4) Bei japanischen Möwchen wird in Bedingung 1 durch fortplfanzungsphysiologischen Einfluß verkürzt.

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Circadian activity rhythms of birds with and without a dark nest box

Summary Perch-hopping activity of Great tits(Parus major) and Bengales finches(Lonchura striata domestica), housed individually in soundproof boxes, was studied in two series of experiments. In the first series all birds had access to a dark nest box, in which they retired during their subjective night. In this experiment the effect of light intensity on the freerunning circadian activity rhythm was investigated. Both Great tits and Bengalese finches obey the circadian rule by responding to an increase in light intensity with shortening the circadian period () and with an increase of the ratio of activity time and rest time ( : ).In the second series of experiments the influence of sleeping in the dark nest box on both circadian period and : -ratio was studied. The results of two experimental conditions — without and with access to a dark nest box — were compared. In the Great tits, the results are in agreement with the effect of light intensity: when a dark nestbox is available, is longer and the : -ratio is smaller than in the absence of a nest box. The magnitude of the change in free-running period after removal of the nest box is independent of the original value of ; the amount of change : -ratio is likewise independent of the original : -ratio, but is weakly correlated to the original .InLonchura striata var. domestica, removal of the dark nest box leads to a lenghtening of the free-running period to about 24 hours; the : -ratio is smaller in the presence of a dark nestbox, if certain other conditions are fulfilled. The magnitude of the change in after removal of the nest box is highly correlated to the original free-running period (r=-0.89) in such a way that, without nest box, the period approaches a value of 24 hours. Also, the amount of change in : -ratio due to nest box removal is negatively correlated to the original : -ratio. A probably preferred : -ratio of 2.0 is adopted.These results are discussed in the view of 4 points: 1) The circadian system operates at its optimum within a narrow range of - and : -values. 2) This optimal range is especially adopted when conditions become adverse. 3) Removal of the dark nest box results in a more stressful situation for Bengalese finches than for Great tits. 4) In the Bengalese finches, is shortened in the presence of a nest box due to effects on reproductive physiology.

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Herrn Prof. Dr. JürgenAschoff zum 60. Geburtstag gewidemt.     

The temperate B. subtilis phage phi 105 genome contains at least two distinct regions encoding superinfection immunity

Summary Two different PstI fragments of temperate phage 105 DNA are shown to confer superinfection immunity upon Bacillus subtilis when inserted into the multicopy cloning vector pE194 cop-6. The 2.3 kb PstI fragment I is located almost entirely within EcoRI fragment F and encompasses a region previously known to encode a repressor. The other fragment, PstI-E (4.3 kb) maps inside the EcoRI-B fragment, and allows an explanation of the clear-plaque phenotype of the deletion mutant 105DII:6c. The two regions can be distinguished functionally, since only the PstI fragment I product interacts with a specific 105 promoter-operator site.     

Restriction and modification in Bacillus subtilis 168. Regulation of hsrM(nonB) expression in spoOA mutants and effects on permissiveness for phi15 and phi105 phages

Summary Gene hsrM (nonB) of Bacillus subtilis 168, causing non-permissiveness to phage SP10 (Saito et al. 1979) and reduced plating efficiency of unmodified phage 105, is responsible for non-permissiveness of B. subtilis 168 for phages 15 and PZA. Upon transformation to sporulation deficiency (allele spoOA) B. subtilis 168 becomes permissive for 15 and PZA and loses the ability to restrict 105. spoOA str-1 double transformants of B. subtilis 168, however, retain the restriction 168 and non-permissiveness for 15 and PZA phages, in spite of their Spo^– phenotype. Therefore it appears that a functional product of the spoOA gene is required for expression of gene hsrM in wild-type bacteria, but is not essential in streptomycin-resistant bacteria. Phage genomes (PZA) were trapped in spores of the restriction deficient strain with much higher efficiency than in the wild-type.     

On the density of intracellular water

The density of individualArtemia cysts has been determined by sedimentation velocity measurements at unit gravity. Dried cyst (< 0.02 g H₂O/g dry weight) densities, _s were obtained by successive sedimentation in two nonpenetrating organic solvents. This removes geometric terms from the equation relating density to sedimentation velocity. Hydrated cysts ( 1.68 g H₂O/g dry weight) were sedimented in 0.0750 m NaCl to obtain their density ( _c). Values of _s, _c, and their ratios were found to be independent of cyst volume; therefore, the weight fraction of water in hydrated cysts is very nearly the same in cysts of greatly different size. It can be concluded that measurement of the water content of large populations of these cysts accurately reflects the water content of individual cysts, a point which has been assumed in previous work on this system. If _s does not change appreciably when dried cysts are fully hydrated then the density of their water, _w, can be calculated to be 1.022 g/cm³ (±0.0011 ). That value is significantly higher than the density of pure water and is very close to estimates of _w in skeletal muscle and amphibian oocytes obtained by others. However, the assumption that _s is independent of hydration is open to serious criticism, for all these studies. Consequently, conclusions and interpretations derived from such measurements must be considered to be tentative and uncertain.     

Modelling of predator–prey trophic interactions. Part I: two trophic levels

A class of lumped parameter models to describe the local dynamics in a controlled environment of a two-trophic chain is considered. The class is characterized by a trophic function (functional response of predator to the abundance of prey) depending on the ratio of prey biomass x and a linear function of predator biomass y: f(qx/[(1-)k+y]), where q is the efficiency of the predation process, k is a reference biomass, and (01) specifies the predation model. The trophic function is defined only by some properties determining its shape. A stability analysis of the models has been performed by taking the parameters q and as bifurcation parameters: the regions in the (,q) plane of existence and stability of nonnegative equilibrium states and limit cycles are determined. This analysis shows that the behaviour of the models is qualitatively similar for 0<1 (in particular the null state is always a saddle point), while the value =1 gives rise to some kind of structural instability of the system (in particular the null state becomes an attractor for sufficiently high predation efficiency).     

Electron microscopic analysis of the yeast mitochondrial DNA segment conferring chloramphenicol resistance

Summary Mitochondrial DNAs from six ^- mutants carrying the genetic locus Ribl and deleted for the rest of the genome were analyzed. Distribution of circular molecules from one mutant followed exactly the frequency rule, 1/n, for multimers with discreet classes n, 2n, 3n, etc. Another, genetically unstable mutant displayed a continuous spectrum of circular molecules of various lengths. Four other mutants contained multiple series of circular molecules. Partial denaturation maps show that the mutants analyzed show a common segment ca. 1.0 m long and differ by characteristic deletions of extremites of this segment. Short terminal deletions of the right i.e. pointing towards the Rib3 locus, terminus of this segment are correlated with modifications of the recombination properties related to the locus.     

Expression in Bacillus subtilis of the gene for human urogastrone using synthetic ribosome binding sites

Summary A chemically synthesised gene coding for human urogastrone which was earlier cloned in E. coli (Smith et al. 1982) has now been cloned into expression vectors for Bacillus subtilis Two types of constructs have been made, one giving production of methionylurogastrone and the other giving rise to a methionyl-urogastrone- galactosidase fusion polypeptide facilitating quantification of expression levels.The ribosome binding sites used in the expression plasmids are synthetically made oligonucleotides residing on short restriction fragments to allow easy replacement by other ribosome binding sites.Using shuttle vectors and constitutive promoters from Bacillus phages 105 and SPP1, we were able to detect levels of expression amounting to a few thousand molecules per cell during logarithmic growth in both E. coli and B. subtilis.     

Off-resonance R1rho relaxation outside of the fast exchange limit: an experimental study of a cavity mutant of T4 lysozyme

An ¹⁵N off-resonance R ₁ spin relaxation study of an L99A point mutant of T4 lysozyme is presented. Previous CPMG-based relaxation dispersion studies of exchange in this protein have established that the molecule interconverts between a populated ground state and an excited state (3.4%) with an exchange rate constant of 1450 s^–1 at 25°C. It is shown that for the majority of residues in this protein the offset dependence of the R ₁ relaxation rates cannot be well fit using models which are only valid in the fast exchange regime. In contrast, a recently derived expression by Trott and Palmer (J. Magn. Reson., 154, 157–160, 2002) which is valid over a wider window of exchange than other relations, is shown to fit the data well. Values of (signed) chemical shift differences between exchanging sites have been extracted and are in reasonable agreement with shift differences measured using CPMG methods. A set of simulations is presented which help establish the exchange regimes that are best suited to analysis by off-resonance R ₁ techniques.     

Molecular cloning of heterologous chromosomal DNA by recombination between a plasmid vector and a homologous resident plasmid in Bacillus subtilis

Summary The difficulty experienced in the shotgun cloning of chromosomal DNA on plasmid vectors in Bacillus subtilis is analyzed and an explanation for this difficulty is offered based on an inherent property of competent cells which imposes a requirement of plasmid multimers in transformation of plasmidfree recipients (Canosi et al., 1978). A stratagem which uses cloning by recombination between the vector and a resident homologous plasmid is tested and shown to be successful. Several recombinant plasmids are obtained containing Bacillus licheniformis DNA fragments which complement aromatic amino acid mutants of Bacillus subtilis. The yield of recombinant clones ranges from 6.7 to 210 per g of chromosomal DNA, depending on the selection and the restriction endonuclease. The various trp clones obtained after cutting chromosomal DNA with BglII and BclI do not complement trpE and exhibit both orientations with respect to the vector. The location of several restriction endonuclease cleavage sites in the cloned trp fragments is presented, and their relationship to the genetic map of Bacillus licheniformis is described.Abbreviations Km kanamycin - Cm chloramphenicol - Em erythromycin - CCC covalently closed circular - OC open circular - resistant - MDal megadalton In partial fulfillment of the requirements for the doctoral degree in the Department of Microbiology at the New York University School of Medicine, for S.C.     

Host-dependent modification of bacteriophage T7 and SAMase-negative T3 derivatives affecting their adsorption ability

Summary When passaging phage T7 and SAMase-negative T3 mutants betweenE. coli strains with identical (EcoB) or without (EcoO) DNA host specificity, phenotypically a host-controlled modification and restriction is observed. This phenomenon is not due to classical modification and restriction of the bacteriophage DNA but depends on the reversibly altered adsorption capacity of the phages on the different host strains.     

Mitochondrial DNA in yeast recombination and subsequent modification following mating between a grande and a suppressive petite

Summary The fluorinated pyrimidines 5-fluorouracil (5FU) and 5-fluorocytosine (5FC) induce the cytoplasmic petite mutation in the yeastSaccharomyces cerevisiae with high efficiency. It was found that in order to induce the mutation, 5FC must first be deaminated to 5FU. However, mutagenesis does not depend on the further conversion of 5FU to its deoxyriboside (5FUDR) and subsequent blockade of intracellular thymidine synthesis, since 5FUDR itself was found not to be mutagenic, and 5FU-induced mutagenesis was not antagonised by supplying thymidine monophosphate (dTMP) to a dTMP permeable strain. In any case, observations of the molecular changes accompanying petite induction in log phase cells ruled out the possibility that mutagenesis resulted simply from the dilution out of replication-blocked mitDNA molecules, since the appearance of mutants coincided with the synthesis of altered mitDNA molecules. In different strains, the resulting defective molecules were either maintained, giving rise to suppressive ^– petites, or completely degraded, to give pure clones of neutral ⁰ mutants. It is suggested that this degradative process was a consequence of the incorporation of 5FU into RNA.     

Critical impeller speed for solid suspension in turbine agitated contactors

The present study in solid-liquid contactors, an attempt has been made to calculate the minimum/critical impeller speed required for complete suspension of solids. A new correlation, involving Reynolds number, modified Froude number, along with the agitation characteristics is proposed. The effect of impeller geometry as well as impeller clearance are clearly established for 6-blade (flat) turbine agitated contactors.List of Symbols B Solid weight fraction (%) - c Clearance of the impeller from the tank bottom (m) - d _P Average particle size(m) - d _R Impeller diameter (m) - d _T Vessel diameter (m) - g Acceleration due to gravity m/sec₂ - N _cs Critical impeller speed (S^–1) Greek Letters Kinematic viscosity m²/sec - _L Density of liquid kg/m³ - _S Density of solid kg/m³ - Density difference between solid and liquid kg/m³     

Purification and characterization of an<Emphasis Type="Italic"> N</Emphasis>-acetylglucosaminidase produced by a<Emphasis Type="Italic"> Trichoderma harzianum</Emphasis> strain which controls<Emphasis Type="Italic"> Crinipellis perniciosa</Emphasis>

Isolate 1051 of Trichoderma harzianum, a mycoparasitic fungus, was found to impair development of the phytopathogen, Crinipellis perniciosa, in the field. This Trichoderma strain growing in liquid medium containing chitin produced substantial amounts of chitinases. The N-acetylglucosaminidase present in the culture-supernatant was purified to homogeneity by gel filtration and hydrophobic interaction chromatography, as demonstrated by SDS-PAGE analysis. The enzyme had a molecular mass of 36 kDa and hydrolyzed the synthetic substrate -nitrophenyl-N-acetylglucosaminide (NGlcNAc) with Michaelis–Menten kinetics. Maximal activities were determined at pH 4.0 and a temperature range of 50–60°C. K _m and V _max values for NGlcNAc hydrolysis were 8.06 moles ml^–1 and 3.36 moles ml^–1 min^–1, respectively, at pH 6.0 and 37°C. The enzyme was very sensitive to Fe³⁺, Mn²⁺ and Co²⁺ ions, but less sensitive to Zn²⁺, Al³⁺, Cu²⁺ and Ca²⁺. Glucose at a final concentration of 1 mM inhibited 65% of the original activity of the purified enzyme. Determination of the product (reducing sugar) of hydrolysis of C. perniciosa mycelium and scanning electron microscopic analysis revealed that the N-acetylglucosaminidase hydrolyses the C. perniciosa cell wall.