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.     

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.     

Isolation and characterization of ?80dgal transducing phages that carry gal operator-promoter insertion mutations

Summary 80dgal transducing bacteriophages have been isolated by the F-fusion technique of Press et al. (1971) and gal-operator-promoter insertion mutations have been introduced by homogenote formation.Five different 80dgal isolates have been studied in more detail. One of the 80 phages transduces the gal operon and gene aroG as well as at least part of the trp-operon; the gal operon of another 80dgal transducing phage is inverted with respect to the 80dgal sequences. Heteroduplex DNA mapping indicates that one of the 80dgal isolates in addition to the gal operon and a portion of the adjacent chromosomal region carries an IS2-element which is derived from the F'gal episome.The isolated 80dgal phages may be utilized for preparing pure gal mRNA and insertion-RNA as well as pure gal operon DNA.     

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.     

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.     

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.     

Vertical distribution and diurnal migrations of krill — Euphausia superba Dana — from hydroacoustical observations,SIBEX, December 1983/January 1984

Summary The depth distributions of krill density with the resolution of 0.435 m has been obtained on the basis of SIBEX hydroacoustic data. Krill was observed to be mainly in a layer from 20 to 100 m with the maximum of biomass migrating from the near surface area at night to greater depths during day. The krill migration pattern can be described by the function: H(t)=A+Bcos (2t/T+), where H is depth of the mass center of biomass, t-time, A-mean depth of krill occurrence, B-amplitude of diurnal changes, T=24 h and -phase of migration process. The parameters of migration pattern: A, B, T and depend on the body length of krill.     

Die optischen Übertragungseigenschaften der Komplexaugen von Drosophila

Summary The transfer properties of the optical system in the arthropod compound eye are determined by the interommatidial angle , influencing the resolving power, and by the width of the visual fields of single ommatidia , influencing the response at high spatial frequencies of brightness distributions in the object space. The energy transfer/ receptor is proportional to ( )² and decreases with in-inreasing approximation of the perfect-imaging condition: gD 0; 0. However, a value > 0 has to be maintained in order to overcome the threshold of nervous excitation at a certain minimum-brightness level. Theoretical treatment yields /=0.62 to 0.88 as the corresponding optimum-imaging relation. The actual ratio can be derived from measurements of the optomotor reactions to the movement of periodic brightness patterns. The approximate value 0.76 is obtained from the fruitfly Drosophila with normal and mutant eye pigmentation. As a result, the parameters of this imaging system are found to be established in a way that enables optimum performance at sufficient illumination. An dieser Stelle möchte ich Dr. W. Reichardt für sein eingehendes Interesse und manche anregende Diskussion über die Sehvorgänge im Komplexauge meinen Dank sagen. Dr. K. Kirschfeld verdanke ich ebenfalls wertvolle Hinweise. Herrn E. Freiberg bin ich für die Anfertigung der Abbildungen sehr verbunden.     

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.     

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     

Comparisons of the Genomes of New Giant Phages Isolated from Environmental Pseudomonas aeruginosa Strains of Different Regions

To study the genome diversity of bacteriophages from geographically distant natural populations, new giant KZ-like Pseudomonas aeruginosa phages isolated in two different regions were compared with earlier known phages of three species (KZ, Lin68, EL). A broad spectrum of lytic activity was demonstrated for all KZ-like phages. Phages of the KZ species proved to be common in natural populations of various regions, while EL- and Lin68-related phages were extremely rare. Most KZ-related phages had unique DNA restriction patterns, but the differences between these were only minor, and the genomes did not contain nonhomologous fragments. The spectrum of capsid polypeptides proved to be conserved in each species, and was proposed as a character necessary and sufficient for express classification of phages with an accuracy of species. Phages isolated in different geographical regions showed no substantial difference. Some phages only slightly differing in DNA restriction pattern from KZ may be used to study the origin of KZ genes coding for orthologs of proteins of unrelated species (other phages, pathogenic bacteria, eukaryotes).     

Patterns and conformations of commonly occurring supersecondary structures (basic motifs) in protein data bank

Short peptides connecting-helices and-strands have been analyzed in 240 proteins refined at resolutions of 0.25 nm or better. Connecting peptides of lengths between one and five residues have been classified as part of supersecondary motifs of four types:, , , and. Careful consideration has been given to the definition of secondary structures on the basis of hydrogen bonds and main-chain conformational angles. Using five classes of residue conformation—a, b, e, l, t—in the nonregular structure regions of, space, 34 classes of supersecondary motifs occurring at least five times have been identified. Among these 34 classes, 11 classes that occur more than 25 times are commonly occurring supersecondary structure motifs. The patterns and conformations of the 11 commonly occurring supersecondary structure motifs have been characterized, demonstrating that patterns and conformations adopted by supersecondary structure motifs are limited. The results have relevance to structure prediction, comparative modeling, and protein folding.     

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.     

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.     

Isolation and characterization of a plaque-forming lac-transducing phage phi80plac with special reference to its integration and excision

Summary From a double lysogen for 80dlac type II (Beckwith and Signer, 1966) and 80, we isolated a plaque-forming lac-transducing coliphage 80plac after selecting a strain with a suitable deletion in the 80 prophage. The lac region of the phage is i ⁺ o ⁺ z ⁺ y ⁺ a ^- and supposed to be located between genes 15 (N) and imm (CI). The phage showed feckless phenotype indicating deletion of genes of the red system. The phage is also deleted for int or att function, and integrates exclusively at the host lac region, largely dependent on the host rec system. Excision of the prophage upon UV-irradiation or by mating the male lysogen with a non-lysogenic female was efficient and largely dependent on the host rec system. But a considerable amount of rec-independent excision was observed at least in the case of zygotic induction, which was not likely to be caused by int-xis, red or ter system of the phage. 80plac/o ^e phage was also isolated by incorporation of o ^e1 mutation from strain 2000o ^e.     

Secondary structural effects on protein NMR chemical shifts

For an amino acid in protein, its chemical shift, (, )_s, is expressed as a function of its backbone torsion angles ( and ) and secondary state (s): (, )_{s=, )_coil+(, )_s}, where (, )_coil represents its chemical shift at coil state (s=coil); (, )_s (s=sheet or helix) is herein defined as secondary structural effect correction factor, which are quantitatively determined from Residue-specific Secondary Structure Shielding Surface (RSS) for ¹³CO, ¹³C, ¹³C,¹H, ¹⁵N, and ¹HN nuclei. The secondary structural effect correction factors defined in this study differ from those in earlier investigations by separating out the backbone conformational effects. As a consequence, their magnitudes are significantly smaller than those earlier reported. The present (, )_sheet and (, )_helix were found varying little with backbone conformation and the 20 amino acids, specifically for ¹³CO, ¹³C, and ¹H nuclei. This study also carries out some useful investigations on other chemical shift prediction approaches – the traditional shielding surfaces, SHIFTS, SHIFTX, PROSHIFT, and identifies some unexpected shortcomings with these methods. It provides some useful insights into understanding protein chemical shifts and suggests a new route to improving chemical shifts prediction. The RSS surfaces were incorporated into the program PRSI [Wang and Jardetzky, J. Biomol. NMR, 28: 327–340 (2004)], which is available for academic users at http://www.pronmr.com or by sending email to the author (yunjunwang@yahoo.com).     

Polysaccharide and protein secretion by grass microhairs

Summary Secretory activities of bicellular microhairs from grasses belonging to the subfamilies Chloridoideae, Arundinoideae, Panicoideae, and Bambusoideae, and including the chloridoid, panicoid and Enneapogon microhair morphological types, have been investigated. Light microscopic histochemistry indicated that all microhairs studied secrete polysaccharide and protein (or glycoprotein), including those which also secrete salt. Localization of polysaccharide at ultrastructural level using periodic acid-thiocarbohydrazidesilver proteinate staining revealed that in panicoid type microhairs dictyosomes are involved in polysaccharide secretion, whereas in the chloridoid and Enneapogon types partitioning membranes seem to be involved instead.Abbreviations Ag silver precipitates representing localization of polysaccharide - BC basal cell - C cuticle - CC cap cell - CH cuticular chamber - CN system of membrane bound channels and vesicles - CP chloroplast - CW cell wall - D dictyosomes - M mitochondria - N nucleus - PTM partitioning membranes - RER rough endoplasmic reticulum - S secretory material - St starch grain - US unstained dictyosome cisternae - V vesicle     

Long Range Force between Pre-Replication Complexes (Pre-RC) in DNA Controls Replication and Cell Cycle Progression

A nonstationary interaction, that controls DNA replication and the cell cycle, is derived from a manybody physics model in a chemically open T cell. The model predicts a long range force F()=-(/2) (1-)(2-) between the pre-replication complexes (pre-RCs) bound by DNA, =/N being the relative displacement of preRCs, the number of pre-RCs, N the threshold for initiation, and the compressibility modulus in thelattice of pre-RCs which behaves like an elastically braced string. Initiation of DNA replication is induced by a switch of sign of F(), from attraction (-)and assembly in the G ₁ phase (0 < < N), to repulsion (+) and partialdisassembly in the S phase (N < < 2N), with release of licensing factors from the pre-RCs, thus explaining prevention of re-replication. Replication is terminated by a switch of sign of F at = 2N, when all primed replicons are duplicated once, and F(0)=0 corresponds to a resting cell in absence of driving force at = 0. The switch of sign of force at = N also explains the dynamic instability in growing microtubules (MTs), as well as switch in the interleukin-2 (IL2) interaction with its receptor in late G ₁, at the restriction point. Shape, slope and scale of the response curves derived agree well with experimental data from dividing T cells and polymerizing MTs, the variable length of which is due to anonlinear dependence of the growth amplitude on the initial concentrations of tubulin dimers and guanosine-tri-phosphate (GTP).