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.     

ISL1: a new transposable element in Lactobacillus casei

Summary The genome structures of a temperate Lactobacillus phage, FSW, and its virulent mutants, FSVs, were examined by restriction, heteroduplex and nucleotide-sequence analyses. The results showed that two out of three FSVs had the same 1.3 kbp insertion (designated as ISL1) at different positions in the FSW sequence. ISL1 was 1,256 bp long and contained at least two long open reading frames of 279 and 822 bases on one strand. Inverted repeats were found at the termini of the ISL1 which was bracketed by 3 bp direct repeats of the FSW sequence. From this evidence, we concluded that ISL1 was a transposable element in Lactobacillus casei.     

Yeast ribosomal proteins

Summary Homology maps between bacteriophages 81, 80 and were constructed on the basis of electron microscope observation of DNA heteroduplexes. In 81/80 heteroduplex, the left half and the right terminal region of 13% the total molecular length were highly homologous, while the remaining region covering the early gene cluster was entirely nonhomologous. In 81/ heteroduplex, high-degree homologies were detected at the left 14% terminal region covering the head gene cluster, the central 3.8% region covering the att-int-xis region and the 1.3% Q homology region. Low-degree homologies of shorter length were scattered at the tail gene cluster, b2 region, cIII region, PQ region and SR region. Comparing our results with the homology maps of other lambdoid phages reported by Simon et al. (1971) and Fiandt et al. (1971), a phylogenic relation of 81 to other lambdoid phages and the role of recombination in the course of divergence of lambdoid phages are discussed.     

Characterization of the effectors required for stable inheritance of Streptococcus pyogenes pSM19035-derived plasmids in Bacillus subtilis

The low-copy-number and broad-host-range pSM19035-derived plasmid pBT233 is stably inherited in Bacillus subtilis cells. Two distinct regions, segA and segB, enhance the segregational stability of the plasmid. Both regions function in a replicon-independent manner. The maximization of random plasmid segregation is accomplished by the recombination proficiency of the host or the presence of the pBT233 segA region. The segA region contains two open reading frames (or) [ and ]. Inactivation or deletion of or results in SegA^– plasmids. Better than random segregation requires an active segB region. The segB region contains two ors (or and or). Inactivation of either of the orfs does not lead to an increase in cell death, but or^– plasmids are randomly segregated. These results suggest that pBT233 stabilization relies on a complex system involving resolution of plasmid oligomers (segA) and on the function(s) encoded by the segB region.     

Exploration and exploitation of soil by apple,kiwifruit, peach,Asian pear and grape roots

Measurements of root-length density (RLD) in a range of 31 apple, kiwifruit, peach, Asian pear and grape orchards were used to derive indices to describe the exploration and exploitation of rooting volumes. Orchards were of various ages and located on a range of soil types, geographic regions, management systems etc. Data were obtained from core samples of volume 1.66×10^-4 m³ randomly taken within a standard volume, determined by average planting grids, of 2 m radius centred on tree stems, and 1 m depth. Root systems were described using an exploitation index, E(), and an exploration index, E(0). E() is defined as the proportion of the soil volume which contains roots at RLD greater than or equal to some specified value, . E(0) is defined as the proportion of the soil volume which contains roots at any RLD greater than zero. These indices are dependent on sample size, as are all volumetric or soil-coring data.Estimates of E(0) for each orchard were obtained as the proportions of cores containing any RLD>O and assessed for dependence on species. Peach trees had a significantly higher value of E(0), equal to almost 1.0, compared to the other four species where E(0) was approximately 0.8 (p0.01) or less. There was also some variation with age. E(0) was lower for very young plants which had not fully occupied the sampled soil volume. Exploration indices for woody roots increased with rootstock age but otherwise did not explain large differences in E() between species for given values.For example at =0.05×10⁴ m.m^-3, E() was approximately 0.45 for peach and kiwifruit, and 0.05 for apple, Asian pear and grape, whereas at =0.5×10⁴ m.m^-3 the corresponding values were 0.1 and almost zero. Negative exponential curves relating E(), scaled by dividing by E(0), to were fitted for each of the 31 orchards. Exponents for these curves, k, were significantly smaller for kiwifruit and peaches than apples, grapes and Asian pears (p0.05), and smaller for apples than grapes and Asian pears (p0.05). A larger k implies a rapid fall-off in E() as increases. Although all five species contained zero and low RLD samples, only kiwifruit and peaches contained higher RLD values and consequently have higher mean RLD. This trend was consistent across all soils, regions, sampling dates, and plant ages.The analyses demonstrate that core sampling can give useful insights into macro-scale root-system distribution, such as the proportion of a soil volume explored and how it is exploited. If positions of core samples are noted during sampling using angular direction, depth and radial distance as spatial coordinates the method can be used to describe root-system structures.     

Existence and uniqueness of a sharp travelling wave in degenerate non-linear diffusion Fisher-KPP equations

In this paper we use a dynamical systems approach to prove the existence of a unique critical value c ^* of the speed c for which the degenerate density-dependent diffusion equation u _ct = [D(u)u _x ] _x + g(u) has: 1. no travelling wave solutions for 0 < c < c ^*, 2. a travelling wave solution u(x, t) = (x - c ^* t) of sharp type satisfying (– ) = 1, () = 0 ^*; '(^*–) = – c ^*/D'(0), '(^*+) = 0 and 3. a continuum of travelling wave solutions of monotone decreasing front type for each c > c ^*. These fronts satisfy the boundary conditions (– ) = 1, '(– ) = (+ ) = '(+ ) = 0. We illustrate our analytical results with some numerical solutions.     

Transductional mapping of nine linked chromosomal genes in Bacillus thuringiensis

Summary We have previously described a phage (63) for generalized transduction in Bacillus thuringiensis and used it for mapping of four chromosomal antibiotic resistance markers, namely nalA-rifA-strA-spcA (Landén et al. 1981). From 63 we have now isolated a host range mutant called 64 which contains 52–56 megadalton of DNA. Phage 64 was found to be a more efficient transducing vector than 63. The host range of 64 is wide, with good growth on subspecies gelechiae, kurstaki, galleriae, thuringiensis and thompsoni, restriction on some derivatives of finitimus and ostrinae and no growth on alesti, israelensis and aizawai.Using 64 and a series of new mutants of subspecies gelechiae we have no added five new genes to the antibiotic resistance group described before. The gene order found was guaB-purB-metA-novA-(purA-nalA)-rifA-strA-spcA. Linkage was also demonstrated between hisA and lysA.     

Modulation of formation of tumor metastases by peritoneal macrophages elicited by various agents

Summary We have studied the formation of experimental B16 melanoma metastases in the lungs of mice inoculated IV with tumoricidal or nontumoricidal peritoneal macrophages elicited by various agents. IV inoculation of peritoneal M elicited by Brewer's thioglycollate medium (TG-M) 1 day before the injection of B16 melanoma cells dramatically increased the number of metastatic foci in the lungs. NIH thioglycollate broth and proteose peptone each elicited a relatively low number of M, which were morphologically distinguishable from TG-M and did not influence the yield of B16 melanoma colonies in the lungs. Resident or C. pravum-elicited M also did not augment metastatis formation. TG-M became highly tumoricidal after IP stimulation with poly I: C. However, tumoricidal TG-M inoculated IV 1 day before IV inoculation of B16 melanoma cells did not have an antimetastatic effect. On the contrary, both tumoricidal and nontumoricidal TG-M augmented metastasis formation. Poly I: C treatment had a substantial antimetastatic effect in the normal mice, but not in mice with adoptively transferred TG-M. Histological analysis revealed that IV-inoculated TG-M (tumoricidal or nontumoricidal, either viable or disrupted) induced severe intravascular reaction in the lungs, but not in the liver or kidney. This reaction manifested in the aggregation of the various blood cells, preferentially neutrophils. These reactions were not observed after IV inoculation of PM or NIH TG-M.Intravascular inflammatory reactions induced by TG-M may be responsible for the augmentation of metastasis formation, partly by suppression of NK reactivity and mostly by the acceleration of the processes of tumor cell extravasation. These data may provide some insight into the failure to achieve systemic adoptive immunotherapy using activated peritoneal TG-M. Abbreviations used in this paper are: TG-M, thioglycollate-elicited macrophages; PM, proteose-peptone-elicited macrophages; NIH TG-M, macrophages elicited with NIH thioglycollate broth; CP-M, macrophages; elicited with C. parvum; poly I: C, polyinosinic: polycytidylic acid; TGM, thioglycollate medium; NIHTGB, NIH thioglycollate broth     

Intracellular effects of phage phi W-14 DNA on transformation of Bacillus subtilis

Summary Uptake of transforming DNA by competent Bacillus subtilis cells in the presence of phage W-14 DNA (in which half the thymine residues are replaced by -putrescinyl-thymine) is accompanied by a decrease in the amount of trichloracetic acid-precipitable label of the former retained by recipient cells during subsequent incubation. Fractionation of lysates of cells incubated for 0.5 min at 37°C after DNA uptake at 30°C in the presence of low concentrations of W-14 DNA (0.1 g/ml) demonstrated the presence of single-stranded transforming DNA molecules, typical for DNA taken up by B. subtilis. The intracellular effect of W-14 DNA was enhanced by an increase in its concentration (to 0.5–1 g/ml), or by increasing the temperature of uptake (to 37°C). With either of these treatments transforming DNA taken up was found in the form of a broad asymmetric band, indicative of degradation, and partially located at the density characteristic for single-stranded molecules. Fractionation of lysates of cells treated (0.1 g/ml) or untreated with W-14 DNA, and incubated for 20 min at 37°C after DNA uptake, showed disappearance of the single-stranded band. Donor DNA label was then found exclusively in the recipient DNA band, its amount being lower in samples treated with W-14 DNA. The influence of a high concentration of W-14 DNA on retention of transforming DNA label was correlated with its effect on transformation. On exposure to low concentrations of phage DNA, such a correlation was observed only after longer periods of incubation, due to slower intracellular degradation of homologous DNA taken up. The results are consistent with the proposal that W-14 DNA-induced reduction in efficiency of transformation is due to intracellular stimulation of transforming DNA degradation, leading to a decrease in the number of donor molecules available for recombination with the recipient chromosome.     

Comparative study of the thiourea carrier in erythrocytes

Summary A densimeter technique was used to measure the rate of exit of thiourea from erythrocytes of various species of mammals. The cells were first equilibrated with a 200mm thiourea solution in 1% NaCl. An aliquot of these cells was added to 1% NaCl containing 4.6–23.1mm thiourea. Facilitated diffusion was demonstrated in each case. Using exit times or initial rates, calculations of half-saturation constants () inmm and maximum transport rates (K) in isotones per min were made by three different methods. The following values were obtained: human –=60, 42, 35;K=1.2, 2.9, 0.9; rabbit –=46, 33, 32;K=0.8, 2.1, 0.8; mouse –=46,40, 30;K=3.4, 8.5, 3.2; rat –=65, 42, 23;K=6.1, 15.3, 3.7; ox –=107, 63, 88;K=0.6, 1.4, 0.4; sheep –=56, 38, 56;K=0.9, 2.2, 0.6; and pig –=110, 64, 49;K=1.6, 3.6, 1.1.     

Photocontrol of hypocotyl elongation in light-grown Cucumis sativus L.

The control by phytochrome of hypocotyl elongation of light-grown Cucumis sativus L. after a white-light period was examined. The farred-absorbing form of phytochrome inhibits hypocotyl elongation. The response to phytochrome photostationary state () is not linear; all values of from 0.004 to 0.13 promote growth maximally, in the range of values of from 0.13 to 0.22 there is a linear growth response, between values of of 0.22 and 0.35 there is again no differential effect, and for values above 0.35 there is a strong (near linear) effect of on elongation. A kinetic examination of events following the white-light period shows that the major recovery from the photoperiod requires 8.5 h of darkness. End-of-day far-red treatment produces a very different response pattern, with a minor growth stimulation within 28 min of treatment followed by a major effect after 80 to 90 min. Three hours after far-red treatment there is a transient decline in growth rate which persists for about 2 h. Over the whole time course there is a great stimulation of growth rate compared with the controls. A similar growth-rate pattern also occurs if the end-of-day is 0.48, although the magnitude of the growth stimulation is less. Two components are affected by end-of-day , namely the time at which growth recovers and the subsequent growth rate. In the long term, the latter accounts for most of the differences in elongation growth. The dark recovery when only the hypocotyl is irradiated requires 4 h, but end-of-day far-red treatment reduces this to about 1.5 h. The persistence of the far-red-absorbing form of phytochrome for many hours in darkness in these light-grown plants is also demonstrated.Abbreviations and symbols D darkness - FR far-red light - Pfr far-red-absorbing form of phytochrome - R red light - WL white light (from fluorescent lamps) - photostationary state of phytochrome - _c calculated      

"Nick translation" in Escherichia coli rep strains deficient in DNA polymerase I activities.

Summary Using X174 replicative form (RF) DNA as an in vivo probe, we have investigated the coordinated action of the 53 exonuclease and polymerase activities of DNA polymerase I in order to understand better its physiological role. We constructed double mutants containing the rep mutation (the replication of X174 RF does not occur in rep mutants) together with a mutation affecting DNA polymerase I, either polA12 or polA546ex. Using these mutants, which are believed to be thermosensitive in the polymerase function or the 53 exonuclease function respectively, we studied the kinetics of nick translation at the permissive and non-permissive temperatures in vivo. The substrate was the X174 replicative form DNA nicked by the X174 gene A protein. E. coli rep polA546ex gave the lowest rate of nick translation, although the ability to perform nick translation, at least as measured by our assay, was still present. E. coli rep polA12 showed a similar low rate at the non-permissive temperature but a rate close to the wildtype level at the permissive temperature. Formation of the parental replicative form molecule in either strain was affected little, even at the restrictive temperature. Our results suggest that DNA polymerase I may not play a major role in ongoing DNA replication.     

DNA Replication and Cell Cycle Progression Regulatedby Long Range Interaction between Protein Complexes bound to DNA

A nonstationary interaction that controlsDNA replication and the cell cycle isderived from many-body physics in achemically open T cell. The model predictsa long range force F() =– (/2) (1 – )(2 – )between thepre-replication complexes (pre-RCs) boundby the origins in DNA, = /N being the relativedisplacement of pre-RCs, the number of pre-RCs, Nthe number of replicons to be replicated,and the compressibilitymodulus in the lattice of pre-RCs whichbehaves dynamically like an elasticallybraced string. Initiation of DNAreplication is induced at the threshold = N by a switch ofsign of F'(), fromattraction (–) and assembly in the G ₁ phase (0<<N), to repulsion (+) and partialdisassembly in the S phase (N< < 2N), withrelease of licensing factors from pre-RCs,thus explaining prevention ofre-replication. Replication is terminatedby a switch of sign of force at = 2N, from repulsion inS phase back to attraction in G ₂, when all primed replicons havebeen duplicated once. F(0) = 0corresponds to a resting cell in theabsence of driving force at = 0. The model thus ensures that the DNAcontent in G ₂ cells is exactlytwice that of G ₁ cells. The switch of interaction at the R-point, at which N pre-RCs have been assembled, starts the release of Rb protein thus also explaining the shift in the Rb phosphorylation from mitogen-dependent cyclinD to mitogen-independent cyclin E.Shape,slope and scale of the response curvesderived agree well with experimental datafrom dividing T cells and polymerising MTs,the variable length of which is due to anonlinear dependence of the growthamplitude on the initial concentrations oftubulin dimers and guanosine-tri-phosphate(GTP). The model also explains the dynamic instabilityin growing MTs.     

Catalase in salivary gland striated and excretory duct cells. II. ? Body: an ellipsoidal peroxisomal organelle with crystalloid axial projections

Synopsis A new distinctive and unique peroxisomal organelle with a spindle shape has been observed in luminal epithelial cells of striated and excretory ducts of mouse salivary glands. Light microscopic studies indicate it has an ellipsoidal centre from which catalase-positive filamentous or rod-like processes protrude along its major axis; hence, it is called a body. A role for this specialized peroxisome in the formation of nearby free filaments and rods is suggested by the frequent observation of segmentation of its axial processes. Complementary ultrastructural studies of osmium-fixed preparations show that the deformation to an oval shape results from the pressure of the extruding crystalloid coincident with the major axis of the ellipsoidal body. The size range and conformation of body axial processes are comparable to those of free catalase-positive rods and filaments observed in the same cells. The periodic substructure of the crystalloid in the body core is identical with that of nearby cytoplasmic rods. These observations are consistent with the view that the rods and filaments observed free in the cytoplasm are formed by extrusion from the crystalloid core of the body. Bodies could also be responsible for the Aver rods of leukemic leukocytes.     

Photosystem II quantum yields,off-line measured P/I parameters and carbohydrate dynamics inChlorella vulgaris grown under a fluctuating light regime and its application for optimizing mass cultures

The influence of hourly fluctuating irradiance on a continuous culture ofChlorella vulgaris on the quantum yield for stable charge separation at photosystem II (_II,E) was examined. Linear regression analysis between _II,E and Ft or Fm' showed that Ft or Fm' explained 86 and 54% of the variability in _II,E respectively. The total amount of reducible Q_A remained constant during the light period. Only pigments that are known to operate in the xanthophyll cycle were variable. Violaxanthine reversibly decreased during the day, while an opposite pattern was observed for antheraxanthine. The changes in violaxanthine significantly (P 0.001) explained 87% of Fm' and 90% of the estimated values for the rate constant for energy dissipation by non-photochemical pathways. The magnitude of the variability in _II,E was well within range of regulation by the photosynthetic processes itself. The results suggest that _II,E alone can not be used as an index for the optimal cultivation of microalgae. Guidelines are proposed to translate fluorescence-derived parameters into general strategies to optimize productivity. Estimates ofin situ rates of primary photosynthesis derived from _II,E or from P/I derived estimates were significantly different, while predicted concentrations of carbohydrate concentrations were similar.Alfred Wegener Institute for Polar and Marine Research     

Influence of SOS repair on the specificity of radiation mutagenesis in bacteriophage ?X174

Summary The ochre mutant oc9 of bacteriophage X174 was irradiated with -rays and the revertants were assayed on unirradiated and UV-irradiated host bacteria carrying an amber suppressor. The yield of revertants (amber+wild type) was higher on UV-irradiated than on unirradiated bacteria, showing that -irradiated X174 was subjected to W-mutagenesis.For oc9 -irradiated in the presence of oxygen the fraction of amber mutants among the revertants was lower when mutants were scored on UV-irradiated bacteria than when assayed on unirradiated indicator cells. The same fraction of ambers was obtained when mutants were assayed on unirradiated and UV-irradiated samples of a recA indicator strain. UV-irradiated X174 showed a similar phenomenon. These results suggest that the specificity with regard to insertion of bases opposite radiation damage in X174 DNA is different for host cells in which SOS repair has been induced and cells in which SOS repair is not operative.     

Construction of stable lactose-utilizing Xanthomonas campestris by chromosomal integration of cloned lac genes using filamentous phage ϕLf DNA

Summary Previously, we constructed a lactose-utilizing strain of Xanthomonas campestris, Xc17 (pKMLT), by cloning lacZY genes with the RK2-derived vector pLAFR1. In this study, the narrow-host-range, -galactosidase expression plasmid pKM was fused with an integration vector pS19 to form pSF14. Following insertion into Xc17, pSF14 was integrated into the host chromosome. The integration function was provided by the 0.85-kb EcoRI-PstI fragment from the filamentous phage Lf. The integration caused no adverse effect to the cells and was stable for at least 66 generations without selection. The engineered strain, Xc17::pSF14, was able to grow as well and produce as much xanthan gum in lactose medium as the wild-type cells did in glucose medium, and the Xc17(pKMLT) in lactose medium. Therefore, Xc17::pSF14 is potentially useful for xanthan production by direct use of whey lactose as the fermentation substrate. This study has advanced one more step our efforts to contruct lactose-utilizing X. campestris and confirmed the feasibility of using pS19 as an integration vector.     

Host genes involved in the replication of single-stranded DNA phage ?K

Summary Using various replication mutants of E. coli, the host genes that participate in the replication of some K12-specific single-stranded DNA phages have been determined. Functional products of dnaE,-F,-G and -Z genes are required for the multiplication of K, whereas dnaA,-B,-C(D), H,-I and -P are dispensable for viral replication. In contrast with polB, recA, B, C, or xth functions, host rep activity is essential for K. At the restrictive temperature, the yield of K was markedly reduced in the ligts7 mutant and partially decreased in a polA ^ts strain. The phage K is thus less dependent on the host cells than X174 and A which require additionally the dnaB,-C(D) and -H functions. Replication of phage St-1 depends on dnaG and -Z gene products, but not on dnaP function. Although not much affected in polA ^ts host, growth of St-1 was significantly diminished in dnaF or ligts7 mutants.     

Genetic studies of the ribosomal proteins in Escherichia coli. XI. Mapping of the genes for L21, L27, S15 and S21 by using hybrid bacteria and over-production of these proteins in the merodiploid strains.

Summary Host capacity for growth of single-stranded DNA phages was investigated with several replication mutants of E. coli. In dnaL708, dnaM709 and dnaS707 mutants, multiplication of K was not restricted even at 42°C. In dnaM710 cells, however, growth of K was severely affected at 42°C but not at 33°C. Upon infection of K, parental replicative form was synthesized at the restrictive temperature, whereas subsequent step (replication of progeny replicative form) was blocked in the dnaZ strain. Growth of X174 and 3, as tested by transfection, was also thermosensitive in the dnaM710 mutant but not in the dnaL708, dnaM709 and dnaS707 strains. In contrast with , microvirid phages could grow in E. coli cells bearing the groPC259, groPC756 or seg-2 mutation.This paper is number 15 in the series entitled Sensivity of Escherichia coli to Viral Nucleic Acid