Publications

crystal structure of bacteriophage lambda cii and its dna complex.	the tetrameric cii protein from bacteriophage lambda activates transcription from the phage promoters p(re), p(i), and p(aq) by binding to two direct repeats that flank the promoter -35 element. here, we present the x-ray crystal structure of cii alone (2.8 a resolution) and in complex with its dna operator from p(re) (1.7 a resolution). the structures provide a basis for modeling of the activation complex with the rna polymerase holoenzyme, and point to the key role for the rna polymerase alpha ...	2005	16039594
fungal antigens expressed during invasive aspergillosis.	rabbits that had been infected intravenously with conidiospores of aspergillus fumigatus were used as sources of antibody for screening a lambda phage cdna expression library. the cdna was derived from a. fumigatus mrna that had been extracted from newly formed, germling hyphae. thirty-six antigens were identified using antisera from six rabbits. though many of these antigens were expected to be intracellular proteins because their genes did not encode a signal sequence, the antisera showed cons ...	2005	16040983
receipt of the c-terminal tail from a neighboring lambda int protomer allosterically stimulates holliday junction resolution.	bacteriophage lambda integrase (int) catalyzes the integration and excision of the phage lambda chromosome into and out of the esherichia coli host chromosome. the seven carboxy-terminal residues (c-terminal tail) of int comprise a context-sensitive regulatory element that links catalytic function with protein multimerization and also coordinates int functions within the multimeric recombinogenic complex. the experiments reported here show that the beta5-strand of int is not simply a placeholder ...	2005	16054645
an amino acid substitution in a capsid protein enhances phage survival in mouse circulatory system more than a 1000-fold.	in experiments with germ free mice, free from adaptive antibodies to the bacterial virus lambda phage, titers of the virus in the circulatory system have been reported to decrease by more than 10(9)pfu within 48 h of intraperitoneal intravenous or oral administration. based on these observations, serial passage techniques have been used to select lambda phage mutants, with 13,000-16,000-fold greater capacity to remain in the mouse circulatory system 24h after intraperitoneal injection. in these ...	2005	16055223
structure of lambda cii: implications for recognition of direct-repeat dna by an unusual tetrameric organization.	the temperate coliphage lambda, after infecting its host bacterium escherichia coli, can develop either along the lytic or the lysogenic pathway. crucial to the lysis/lysogeny decision is the homotetrameric transcription-activator protein cii (4 x 11 kda) of the phage that binds to a unique direct-repeat sequence t-t-g-c-n6-t-t-g-c at each of the three phage promoters it activates: p(e), p(i), and p(aq). several regions of cii have been identified for its various functions (dna binding, oligomer ...	2005	16061804
amplification and cloning of near full-length hiv-2 genomes.	the genomes of human immunodeficiency virus type 2 (hiv-2), like those of hiv-1, are not only extremely variable but are also highly recombinogenic. determination of subtypes based on partial genomes cannot predict the subtype classification of other regions of the genome owing to the frequent occurrence of recombinant genomes among subtypes. to fully understand the genetic variation and evolution of hiv-2s, full-length viral genomes need to be obtained for genetic analysis. full-length hiv-2 ge ...	2005	16061992
regulatory functions of the lambda repressor reside in the amino-terminal domain.	the repressor of bacteriophage lambda is a protein containing two domains of approximately equal size. fragments containing the amino-terminal domain of repressor bind specifically to lambda operator dna and mediate positive and negative control of lambda transcription both in vitro and in vivo.	1979	16068162
functional similarities between phage lambda orf and escherichia coli recfor in initiation of genetic exchange.	genetic recombination in bacteriophage lambda relies on dna end processing by exo to expose 3'-tailed strands for annealing and exchange by beta protein. phage lambda encodes an additional recombinase, orf, which participates in the early stages of recombination by supplying a function equivalent to the escherichia coli recfor complex. these host enzymes assist loading of the reca strand exchange protein onto ssdna coated with ssdna-binding protein. in this study, we purified the orf protein, an ...	2005	16076958
the bacteriophage 434 repressor dimer preferentially undergoes autoproteolysis by an intramolecular mechanism.	inactivation of the lambdoid phage repressor protein is necessary to induce lytic growth of a lambdoid prophage. activated reca, the mediator of the host sos response to dna damage, causes inactivation of the repressor by stimulating the repressor's nascent autocleavage activity. the repressor of bacteriophage lambda and its homolog, lexa, preferentially undergo reca-stimulated autocleavage as free monomers, which requires that each monomer mediates its own (intramolecular) cleavage. the ci repr ...	2005	16077107
dna-templated photoinduced silver deposition.	we are presenting a photography-derived methodology to achieve the photoreduction of ag+-dna complexes. lambda-phage dna was first loaded with silver ions, then irradiated with uv light at 254 nm. the dna bases acted as light sensitizers, promoting the in situ reduction of ag+ and the formation of metallic silver clusters. three different approaches will illustrate this procedure, and silver nanoparticle chains will be grown along a dna template in a rapid and specific way.	2005	16089430
partly melted dna conformations obtained with a probability peak finding method.	peaks in the probabilities of loops or bubbles, helical segments, and unzipping ends in melting dna are found in this article using a peak finding method that maps the hierarchical structure of certain energy landscapes. the peaks indicate the alternative conformations that coexist in equilibrium and the range of their fluctuations. this yields a representation of the conformational ensemble at a given temperature, which is illustrated in a single diagram called a stitch profile. this article de ...	2005	16089780
retrotransposable elements on the w chromosome of the silkworm, bombyx mori.	the sex chromosomes of the silkworm, bombyxmori, are designated zw(xy) for females and zz(xx) for males. the w chromosome of b. mori does not recombine with the z chromosome and autosomes and no genes for morphological characters have been mapped to the w chromosome as yet. furthermore, femaleness is determined by the presence of a single w chromosome, regardless of the number of autosomes or z chromosomes. to understand these interesting features of the w chromosome, it is necessary to analyze ...	2005	16093666
bacterial mutants able to partly suppress the effect of n mutations in bacteriophage lambda.	a method is described whereby bacterial mutants (sun) may be selected which are able to specifically suppress mutations in the n gene of bacteriophage lambda. the sun mutations seem to be allelic to sua mutations, which suppress the polarity of nonsense codons, since sua mutants have all of the properties of sun mutants and both are genetically linked to the ilv gene. in the light of these experiments and recent data by others, models originally suggested to explain polarity in bacterial operons ...	1975	16094982
e. coli k12 inf: a mutant deficient in prophage lambda induction and cell filamentation.	the bacterial mutant inf-3 (lambda) is not inducible and does not form filaments following thymine starvation. lysogenic induction is neither produced by ultraviolet light (uv) nor promoted by tif-1. this phenotype is due to a mutation infa3 located between 60 and 73 min on the e. coli k12 map. the inf mutant is resistant to x-ray and uv irradiation, in contrast to all other known non-inducible bacterial mutants. it is rec+ and able to perform host cell reactivation as well as uv-reactivation of ...	1975	16094997
unaltered stability of newly synthesized rna in strains of escherichia coli missing a ribonuclease specific for double-stranded rna.	pairs of very closely related escherichia coli strains were prepared, one having the wild-type allele for ribonuclease iii, an enzyme which specifically degrades double-stranded rna, and the other having a mutant rnase iii allele. growth and phage plating efficiency were compared in these strains. the rnase iii+ strains grow better than the rnase iii- strains and plate t7 and lambda phage better, but t4 plates with the same efficiency on both strains. on the other hand, the half lives of newly s ...	1975	16094999
genetic switches during bacteriophage lambda development.		2005	16096026
two-stage continuous operation of recombinant escherichia coli using the bacteriophage lambda q- vector.	a two-stage continuous culture of escherichia coli in combination with a bacteriophage lambda system was performed in order to overcome the intrinsic plasmid instability that is frequently observed in recombinant fermentation. a phage lambda vector with a q(-) mutation was used to enhance the expression of the lambda system. the optimal values of the important operational variables such as the substrate concentration, the dilution rate, and the mean residence time on the expression of the cloned ...	2005	16096763
characterization of an antisense transcript spanning the ul81-82 locus of human cytomegalovirus.	in this study we present the characterization of a novel transcript, ul81-82ast, ul81-82 antisense transcript, and its protein product. the transcript was initially found in a cdna library of monocytes from a seropositive donor. mrna was obtained from monocytes isolated from a healthy donor with a high antibody titer against human cytomegalovirus (hcmv). the mrnas were cloned into a lambda phage-derived vector to create the cdna library. using pcr, ul81-82ast was amplified from the library. the ...	2005	16103153
[red/et recombination and its biomedical applications].	red/et recombination, a powerful homologous recombination system based on the red operon of lambda phage or rece/ rect from rac phage, provides an innovative approach for dna engineering. deletion, insertion and mutation can be quickly and precisely performed on the target gene mediated by red/et recombination with pcr derived dna fragments or oligonucleotides. this technical platform has extensive applications in biomedical field including bacterial artificial chromosome modification, gene knoc ...	2005	16108384
rna-protein recognition: single-residue ultrafast dynamical control of structural specificity and function.	the transcription antiterminator n protein from bacteriophage lambda uses its arginine-rich motif to specifically bind a stem-loop rna hairpin (boxb) as a bent alpha-helix. a single stacking interaction between a tryptophan (trp-18) and an adenosine (a7) in the rna loop is robust and necessary for antitermination activity in vivo. previously, femtosecond fluorescence up-conversion experiments from this laboratory indicated that the n/boxb complex exists in a dynamical two-state equilibrium betwe ...	2005	16129822
analysis of the genome of azotobacter vinelandii revealed the presence of two genetically distinct group ii introns on the chromosome.	azotobacter vinelandii belongs to the y subdivision of eubacteria and has one of the highest respiratory rates. it is considered to be among the probable progenitors of mitochondria. group ii introns were originally identified on organelle genomes. analysis of the a. vinelandii genome for the presence of group ii introns using a deduced group ii intron consensus sequence identified two putative introns. the first intron (avi) which was found to be inserted in the groel, an essential gene, was al ...	2005	16134325
lambda integrase: armed for recombination.	bacteriophage lambda moves its viral genome into and out of the bacterial chromosome using site-specific recombination. crystal structures of reaction intermediates in this recombination pathway provide exciting new snapshots of full length lambda integrase interacting with both core and regulatory dna elements.	2005	16139195
structural analysis of chloroplast dna in prunus (rosaceae): evolution, genetic diversity and unequal mutations.	in order to understand the evolutionary aspects of the chloroplast dna (cpdna) structures in rosaceous plants, a physical map of peach (prunus persica cv. hakuhou) cpdna was constructed. fourteen lambda phage clones which covered the entire sequence of the peach cpdna were digested by restriction enzymes (sali, xhoi, bamhi, saci, and psti) used singly or in combination. the molecular size of peach cpdna was estimated to be about 152 kb. the gene order and contents were revealed to be equivalent ...	2005	16142464
reduced pcr sensitivity due to impaired dna recovery with the magna pure lc total nucleic acid isolation kit.	the increasing demand for molecular diagnostics in clinical microbiology laboratories necessitates automated sample processing. in the present study, we evaluated the performance of the magna pure lc total nucleic acid isolation kit (m extraction) in comparison with the manual method (si extraction) according to boom et al. (r. boom, c. j. a. sol, m. m. m. salimans, c. l. jansen, p. m. wertheim-van dillen, and j. van der noordaa, j. clin. microbiol. 28:495-503, 1990) for the detection of viral d ...	2005	16145116
[construction of cdna library from human colorectal cancer cell hrt-18].	to construct a cdna library from human colorectal cancer cell hrt-18.	2004	16145893
repetitive sequences in the its1 region of ribosomal dna in congeneric microphallid species (trematoda: digenea).	in searching for species-specific dna sequences of microphallid species (digenea, trematoda) we examined the ribosomal internal transcribed spacer regions (its) of three closely related species (levinseniella group) hosted by mud snails (first intermediate host) and marine crustaceans (second intermediate host). in the its1 region we found consistent patterns of repeating sequences of 130 bp. within each main repeat there was a varying number of subrepeats specific for each of the species. all r ...	2005	16151738
positive autoregulation of ci is a dispensable feature of the phage lambda gene regulatory circuitry.	complex gene regulatory circuits contain many features that are likely to contribute to their operation. it is unclear, however, whether all these features are necessary for proper circuit behavior or whether certain ones are refinements that make the circuit work better but are dispensable for qualitatively normal behavior. we have addressed this question using the phage lambda regulatory circuit, which can persist in two stable states, the lytic state and the lysogenic state. in the lysogenic ...	2005	16159777
the cytotoxic activity of the bacteriophage lambda-holin protein reduces tumour growth rates in mammary cancer cell xenograft models.	the potential use of gene therapy for cancer treatment is being intensively studied. one approach utilises the expression of genes encoding cytotoxic proteins. such proteins can affect cellular viability, for example by inhibiting the translation machinery or disturbing membrane integrity. the bacteriophage lambda (lambda)-holin protein is known to form a lesion in the cytoplasmic membrane of e. coli, triggering bacterial cell lysis and thereby enabling the release of new bacteriophage particles ...	2006	16170834
display libraries on bacteriophage lambda capsid.	phage display is an established technology that has been successfully applied, in the last fifteen years, to projects aimed at deciphering biological processes and/or at the isolation of molecules of practical value in several diverse applications. bacteriophage lambda, representing a molecular cloning and expression tool widely utilized since decades, has also been exploited to develop vectors for the display of libraries on its capsid. in the last few years, lambda display approach has been co ...	2005	16216777
a trial of somatic gene targeting in vivo with an adenovirus vector.	gene targeting in vivo provides a potentially powerful method for gene analysis and gene therapy. in order to sensitively detect and accurately measure designed sequence changes, we have used a transgenic mouse system, mutamouse, which has been developed for detection of mutation in vivo. it carries bacteriophage lambda genome with lacz+ gene, whose change to lacz-negative allele is detected after in vitro packaging into bacteriophage particles. we have also demonstrated that gene transfer with ...	2005	16219108
lysis timing and bacteriophage fitness.	the effect of lysis timing on bacteriophage (phage) fitness has received little theoretical or experimental attention. previously, the impact of lysis timing on phage fitness was studied using a theoretical model based on the marginal value theorem from the optimal foraging theory. an implicit conclusion of the model is that, for any combination of host quantity and quality, an optimal time to lyse the host would exist so that the phage fitness would be the highest. to test the prediction, an ar ...	2006	16219778
a simple method for displaying recalcitrant proteins on the surface of bacteriophage lambda.	bacteriophage lambda (lambda) permits the display of many foreign peptides and proteins on the gpd major coat protein. however, some recombinant derivatives of gpd are incompatible with the assembly of stable phage particles. this presents a limitation to current lambda display systems. here we describe a novel, plasmid-based expression system in which gpd deficient lambda lysogens can be co-complemented with both wild-type and recombinant forms of gpd. this dual expression system permits the ge ...	2005	16224099
switching dna-binding specificity by unnatural amino acid substitution.	the specificity of protein-nucleic acid recognition is believed to originate largely from hydrogen bonding between protein polar atoms, primarily side-chain and polar atoms of nucleic acid bases. one way to design new nucleic acid binding proteins of novel specificity is by structure-guided alterations of the hydrogen bonding patterns of a nucleic acid-protein complex. we have used ci repressor of bacteriophage lambda as a model system. in the lambda-repressor-dna complex, the epsilon-nh(2) grou ...	2005	16224104
construction and selection of the novel recombinant escherichia coli strain for poly(beta-hydroxybutyrate) production.	heterogeneous cloning of vitreoscilla hemoglobin gene (vgb), lytic genes of phage lambda with s amber mutation (s(-)rrz) and phb biosynthetic genes (phbcab) in the same host strain e. coli jm105 was carried out for production of poly(beta-hydroxybutyrate) (phb). a superior novel strain, vg1 (ptu14), was constructed and selected, which contained the vgb gene in the chromosomal dna and the plasmid ptu14 containing s(-)rrz and phbcab genes. when cultured in 100 ml of lbg medium in a 300-ml flask, a ...	2000	16232750
the processing of high-molecular-weight xylanase (xyne, 110 kda) from aeromonas caviae me-1 to 60-kda xylanase (xyne60) in escherichia coli and purification and characterization of xyne60.	a xylanase gene (xyne) encoding xyne (110 kda) was cloned from a lambda phage genomic library of aeromonas caviae me-1 which is a multiple-xylanase-producing bacterium. upon nucleotide sequence analysis, we found that xyne comprises 2823 by and encodes a protein of 941 amino acid residues (104,153 da), which was similar to endo-beta-1,4-xylanases which are categorized to glycosyl hydrolase family 10. an escherichia coli transformant that harbored pxed30 carrying xyne produced 110-, 84-, 72-, and ...	2003	16233373
simultaneous sequence transfer into two independent locations of a reporter vector using multisite gateway technology.	the bacteriophage lambda recombination system is increasingly used for recombinant dna applications that involve the frequent transfer of sequences into and between shuttle and reporter vectors. this approach bypasses the need for restriction endonucleases or ligases and, as such, is easily scalable and automated. however this system has not yet been tested for the ability to support the simultaneous introduction of donor fragments into two separate target sites of a single reporter plasmid. thi ...	2005	16235567
mutation spectrum in uvb-exposed skin epidermis of a mildly-affected xpg-deficient mouse.	a c-terminal 183 amino acid-truncated mutation of the mouse xpg gene (xpgdeltaex15) gives rise to a partial deficiency in nucleotide excision repair in homozygously affected cells. we studied the effect of this mutation on uvb-induced mutagenesis in mouse skin, using transgenic mice harboring lambda-phage-based bacterial lacz genes as a mutational reporter. uvb increased the lacz mutant frequency in the epidermis moderately in the homozygous mutant mice, but significantly higher than in the wild ...	2006	16247763
increasing pcr fragment stability and protein yields in a cell-free system with genetically modified escherichia coli extracts.	escherichia coli cell-free protein synthesis is a highly productive system that can be applied to high throughput expression from polymerase chain reaction (pcr) products in 96-well plates for proteomic studies as well as protein evolution. however, linear dna instability appears to be a major limitation of the system. we modified the genome of the e. coli strain a19 by removing the enda gene encoding the endonuclease i and replacing the reccbd operon (in which recd encodes the exonuclease v) by ...	2005	16254443
investigation of cc and cxc chemokine quaternary state mutants.	the chemokine family forms two different types of homodimer despite members sharing nearly identical folds. to study the formation of quaternary structure in this family, rational mutagenesis was employed on a representative member of each subfamily (mip-1beta and il-8). the variants were studied by analytical ultracentrifugation and nmr, and it was determined that formation of a folded monomer from a natural chemokine dimer is reasonably facile, while conversion between dimer types is not. mono ...	2005	16256937
characterisation of the mating-type locus in the genus xanthoria (lichen-forming ascomycetes, lecanoromycetes).	conserved regions of mating-type genes were amplified in four representatives of the genus xanthoria (x. parietina, x. polycarpa, x. flammea, and x. elegans) using pcr-based methods. the complete mat locus, containing one orf (mat1-2-1) coding for a truncated hmg-box protein, and two partial flanking genes, were cloned by screening a genomic lambda phage library of the homothallic x. parietina. the flanking genes, a homologue of sla2 of saccharomyces cerevisiae and a dna lyase gene, served to am ...	2005	16266815
exo-taq-based detection of dna-binding protein for homogeneous and microarray format.	the study of dna-protein interactions is of great importance to understand basic cellular processes such as transcription, replication and recombination. in this research, we developed a novel detection system for dna-binding proteins (dbps) involving the exonuclease (exo) iii and taq dna polymerase reactions. the system consists of three steps, as follows: the target dbp in the sample solution is incubated with probe dna, and the probe is digested with exo iii and then extended with taq using f ...	2005	16272142
human, rhesus macaque, and feline sequences highly similar to mouse mammary tumor virus sequences.	sequences highly similar (>95%) to the mouse mammary tumor virus (mmtv) env gene have been amplified from human dna samples, including dna samples from patients with breast cancer (bc) and persons who did not have bc. the sequences from human dna were distinct from the mmtv sequences used as controls in these pcr reactions, indicating that these results are not simply due to contamination. in addition to both, mouse and human-related sequences were also amplified from some monkey and cat genomic ...	2005	16276510
switches in bacteriophage lambda development.	the lysis-lysogeny decision of bacteriophage lambda (lambda) is a paradigm for developmental genetic networks. there are three key features, which characterize the network. first, after infection of the host bacterium, a decision between lytic or lysogenic development is made that is dependent upon environmental signals and the number of infecting phages per cell. second, the lysogenic prophage state is very stable. third, the prophage enters lytic development in response to dna-damaging agents. ...	2005	16285866
design of lambda cro fold: solution structure of a monomeric variant of the de novo protein.	one of the classical dna-binding proteins, bacteriophage lambda cro, forms a homodimer with a unique fold of alpha-helices and beta-sheets. we have computationally designed an artificial sequence of 60 amino acid residues to stabilize the backbone tertiary structure of the lambda cro dimer by simulated annealing using knowledge-based structure-sequence compatibility functions. the designed amino acid sequence has 25% identity with that of natural lambda cro and preserves phe58, which is importan ...	2005	16289118
mechanism of the phosphatase component of clostridium thermocellum polynucleotide kinase-phosphatase.	polynucleotide kinase-phosphatase (pnkp) from clostridium thermocellum catalyzes atp-dependent phosphorylation of 5'-oh termini of dna or rna polynucleotides and ni(2+)/mn(2+)-dependent dephosphorylation of 2',3' cyclic phosphate, 2'-phosphate, and 3'-phosphate ribonucleotides. cthpnkp is an 870-amino-acid polypeptide composed of three domains: an n-terminal module similar to bacteriophage t4 polynucleotide kinase, a central module that resembles the dinuclear metallo-phosphoesterase superfamily ...	2006	16301605
novel hydrolase diversity retrieved from a metagenome library of bovine rumen microflora.	a metagenome expression library of bulk dna extracted from the rumen content of a dairy cow was established in a phage lambda vector and activity-based screening employed to explore the functional diversity of the microbial flora. twenty-two clones specifying distinct hydrolytic activities (12 esterases, nine endo-beta-1,4-glucanases and one cyclodextrinase) were identified in the library and characterized. sequence analysis of the retrieved enzymes revealed that eight (36%) were entirely new an ...	2005	16309396
properties of a clostridium thermocellum endoglucanase produced in escherichia coli.	a cellulase gene of clostridium thermocellum was transferred to escherichia coli by molecular cloning with bacteriophage lambda and plasmid vectors and shown to be indentical with the cela gene. the cela gene product was purified from extracts of plasmid-bearing e. coli cells by heat treatment and chromatography on deae-trisacryl. it was characterized as a thermophilic endo-beta-1,4-glucanase, the properties of which closely resemble those of endoglucanase a previously isolated from c. thermocel ...	1986	16347088
isolation of a dna probe for lactobacillus curvatus.	a genomic library of lactobacillus curvatus dsm 20019 was constructed in bacteriophage lambda gt11. a 1.2-kilobase dna probe specific for l. curvatus was isolated from this library. when this probe was hybridized to dna from lactobacillus isolates from different sources classified by conventional techniques, differing degrees of hybridization were obtained. this could imply that these isolates may have been incorrectly classified.	1988	16347554
molecular cloning and expression of cellulase genes from ruminococcus albus 8 in escherichia coli bacteriophage lambda.	a genomic library of ruminococcus albus 8 dna was constructed by using the escherichia coli bacteriophage lambdadash. recombinants were screened for cellulolytic activity by plating in soft agar (0.7%) overlays containing either 1% (wt/vol) carboxymethyl cellulose (cmc), 4-methylumbelliferyl-beta-d-cellobioside (muc, 1 mg/ml), or 1% (wt/vol) ostazin brilliant red-hydroxyethyl cellulose (obr-hec). one hundred and three recombinant phage exhibiting activity against obr-hec were found, and these fe ...	1988	16347685
conversion of glucose to 2-keto-l-gulonate, an intermediate in l-ascorbate synthesis, by a recombinant strain of erwinia citreus.	a gene for 2,5-diketo-d-gluconate (25dkg) reductase, which encodes an enzyme composed of 277 amino acid residues catalyzing the reduction of 25dkg to 2-keto-l-gulonate (2klg), was cloned from corynebacterium sp. strain shs752001 and expressed in erwinia citreus shs2003, a strain which oxidizes glucose to 25dkg. the recombinant microorganism converted glucose to 2klg, a compound which can be readily converted to l-ascorbate (vitamin c). improvements in the yield of 2klg were obtained by changing ...	1988	16347687
the mode of replication is a major factor in segregational plasmid instability in lactococcus lactis.	the effects of the rolling-circle and theta modes of replication on the maintenance of recombinant plasmids in lactococcus lactis were studied. heterologous escherichia coli or bacteriophage lambda dna fragments of various sizes were inserted into vectors based on either the rolling-circle-type plasmid pwv01 or the theta-type plasmid pambeta1. all pambeta1 derivatives were stably maintained. pwv01 derivatives, however, showed size-dependent segregational instability, in particular when large dna ...	1993	16348863
bacteriophage lambda as a delivery vector for tn10-derived transposons in xenorhabdus bovienii.	xenorhabdus bovienii wild-type strains lack a functional receptor protein (lamb) in the outer membrane and as a result are unable to adsorb coliphage lambda (lambda). introduction of plasmids encoding lamb into x. bovienii t228 results in constitutive expression of lamb in the outer membrane of this organism. lamb-expressing strains of x. bovienii adsorb lambda bacteriophage particles and can be used as hosts for lambda::tn constructs. a tn10-derived transposon, element 9 (j. c. way, d. davis, d ...	1993	16349047
bacteriophage lambda as a cloning vector.	[this corrects the article on p. 582 in vol. 56.].	1993	16350252
gene-specific random mutagenesis of escherichia coli in vivo: isolation of temperature-sensitive mutations in the acyl carrier protein of fatty acid synthesis.	acyl carrier proteins (acps) are very small acidic proteins that play a key role in fatty acid and complex lipid synthesis. moreover, recent data indicate that the acyl carrier protein of escherichia coli has a large protein interaction network that extends beyond lipid synthesis. despite extensive efforts over many years, no temperature-sensitive mutants with mutations in the structural gene (acpp) that encodes acp have been isolated. we report the isolation of three such mutants by a new appro ...	2006	16352845
display of aggregation-prone ligand binding domain of human ppar gamma on surface of bacteriophage lambda.	to display the aggregation-prone ligand binding domain (lbd) of the human peroxisome proliferator-activated receptor gamma (ppargamma) on the surface of bacteriophages to establish an easy screening assay for the identification of ppargamma ligands.	2006	16364215
dna arms do the legwork to ensure the directionality of lambda site-specific recombination.	the integrase protein of bacteriophage lambda (int) catalyzes site-specific recombination between lambda phage and escherichia coli genomes. int is a tyrosine recombinase that binds to dna core sites via a c-terminal catalytic domain and to a collection of arm dna sites, distant from the site of recombination, via its n-terminal domain. the arm sites, in conjunction with accessory dna-bending proteins, provide a means of regulating the efficiency and directionality of int-catalyzed recombination ...	2006	16368232
phage library screening for the rapid identification and in vivo testing of candidate genes for a dna vaccine against mycoplasma mycoides subsp. mycoides small colony biotype.	a new strategy for rapidly selecting and testing genetic vaccines has been developed, in which a whole genome library is cloned into a bacteriophage lambda zap express vector which contains both prokaryotic (p(lac)) and eukaryotic (p(cmv)) promoters upstream of the insertion site. the phage library is plated on escherichia coli cells, immunoblotted, and probed with hyperimmune and/or convalescent-phase antiserum to rapidly identify vaccine candidates. these are then plaque purified and grown as ...	2006	16368970
determination of the termination efficiency of the transcription terminator using different fluorescent profiles in green fluorescent protein mutants.	an approach in determining the intrinsic termination efficiency (%t) of transcription termination using green fluorescent protein (gfp) mutants was developed. this approach utilizes a cassette vector in which the tested terminator is introduced between two gfp mutant genes: an ultraviolet-optimized mutant (gfpuv: f99s, m153t, v163a) and a blue-shifted mutant (bfp: f64l, s65t, t145f). the ratio of the fluorescence intensity of bfp to gfpuv after transcription and translation represents the termin ...	2005	16379390
an improved recombineering approach by adding reca to lambda red recombination.	recombineering is the use of homologous recombination in escherichia coli for dna engineering. of several approaches, use of the lambda phage red operon is emerging as the most reliable and flexible. the red operon includes three components: redalpha, a 5' to 3' exonuclease, redbeta, an annealing protein, and redgamma, an inhibitor of the major e. coli exonuclease and recombination complex, recbcd. most e. coli cloning hosts are reca deficient to eliminate recombination and therefore enhance the ...	2006	16382181
the monoclonal antibody sm5-1 recognizes a fibronectin variant which is widely expressed in melanoma.	previously we have generated the monoclonal antibody sm5-1 by using a subtractive immunization protocol of human melanoma. this antibody exhibits a high sensitivity for primary melanomas of 99% (248/250 tested) and for metastatic melanoma of 96% (146/151 tested) in paraffin embedded sections. this reactivity is superior to the one obtained by hmb-45, anti-melana or anti-tyrosinase and is comparable to anti-s100. however, as compared to anti-s100, the antibody sm5-1 is highly specific for melanoc ...	2006	16405722
overexpression of the dna mismatch repair factor, pms2, confers hypermutability and dna damage tolerance.	inherited defects in genes associated with dna mismatch repair (mmr) have been linked to familial colorectal cancer. cells deficient in mmr are genetically unstable and demonstrate a tolerance phenotype in response to certain classes of dna damage. some sporadic human cancers also show abnormalities in mmr gene function, typically due to diminished expression of one of the mutl homologs, mlh1. here, we report that overexpression of the mutl homolog, human pms2, can also cause a disruption of the ...	2006	16426742
construction of a positive selection marker by a lethal gene with the amber stop codon(s) regulator.	a novel positive selection marker for escherichia coli transformation was developed. the marker consisted of a dna fragment encoding the c-terminal ribonuclease domain (crd) of colicin e3 (cole3) and one or more amber stop codons between the initiation codon and the e3-crd coding sequence. the toxicity of the marker was controlled by the suppressor activity the host cells possessed. this allowed both effective selection and propagation of the vector possessing the maker by selecting appropriate ...	2006	16428829
dna repair, a novel antibacterial target: holliday junction-trapping peptides induce dna damage and chromosome segregation defects.	holliday junction intermediates arise in several central pathways of dna repair, replication fork restart, and site-specific recombination catalysed by tyrosine recombinases. previously identified hexapeptide inhibitors of phage lambda integrase-mediated recombination block the resolution of holliday junction intermediates in vitro and thereby inhibit recombination, but have no dna cleavage activity themselves. the most potent peptides are specific for the branched dna structure itself, as oppos ...	2006	16430689
gateway-compatible vectors for plant functional genomics and proteomics.	gateway cloning technology facilitates high-throughput cloning of target sequences by making use of the bacteriophage lambda site-specific recombination system. target sequences are first captured in a commercially available "entry vector" and are then recombined into various "destination vectors" for expression in different experimental organisms. gateway technology has been embraced by a number of plant laboratories that have engineered destination vectors for promoter specificity analyses, pr ...	2006	16441352
direct selection of antibodies from complex libraries with the protein fragment complementation assay.	the aim of the present study was to develop the protein fragment complementation assay (pca) for the intracellular selection of specific binding molecules from the fully synthetic hucal antibody library. here, we describe the first successful selections of specific antibodies by pca, and we discuss the opportunities and limitations of this approach. first, we enriched an antibody specific for the capsid protein d of bacteriophage lambda (gpd) by ten successive rounds of competitive liquid cultur ...	2006	16442560
charge reduced electrospray size spectrometry of mega- and gigadalton complexes: whole viruses and virus fragments.	the ability to analyze and identify large macromolecular complexes whose molecular weight is beyond the analyzable range of mass spectrometry is of great interest. the size of such complexes makes them suitable for analysis via mobility size spectrometry. in this work, charge reduced electrospray size spectrometry was used for the analysis of bacteriophage viruses with total molecular masses ranging from 3.6 mda up to the gigadalton range. the electrospray source used was operated in "cone jet" ...	2006	16448059
functional expression of individual plasmid-coded rna bacteriophage ms2 genes.	the genes of the rna-containing bacteriophage ms2 were individually inserted into thermoinducible expression plasmids under control of the phage lambda p(l) promoter. three phage-coded proteins (a-protein, coat protein, and replicase) were expressed at high efficiency. induced cultures specifically complemented superinfecting amber mutants of phage ms2. regulatory mechanisms operative during the natural infection cycle of the phage were reproduced by the plasmid expression system.	1982	16453413
cloning of a gene localized and expressed at the ecdysteroid regulated puff 74ef in salivary glands of drosophila larvae.	the puffing cycle of salivary gland chromosomes of drosophila larvae, which initiates the developmental path to pupariation, is induced by ecdysteroid hormone. its action leads to prominent puffs at loci 2b5, 74ef and 75b. fragments of the 74ef puff of the d. melanogaster 3l chromosome were microdissected from salivary gland squashes. ecori-digested dna of these fragments was cloned into lambda phage. clones were screened with puff stage-specific cdna probes. thirteen out of 650 clones hybridize ...	1984	16453498
new cloning vehicles for transformation of higher plants.	we have constructed a set of small vectors based on the tumor-inducing (ti) plasmid of agrobacterium tumefaciens which allow the transfer of exogenous dna into plant chromosomes. these vectors contain: (i) a chimeric gene containing the transcriptional control signals from the nopaline synthase gene and the coding sequence for neomycin phosphotransferase; (ii) the cole1 replicon; (iii) the cos site of bacteriophage lambda; (iv) the border sequences from the ends of the t-dna region of the ti pla ...	1985	16453603
functional characterization of visual opsin repertoire in medaka (oryzias latipes).	a variety of visual pigment repertoires present in fish species is believed due to the great variation under the water of light environment. a complete set of visual opsin genes has been isolated and characterized for absorption spectra and expression in the retina only in zebrafish. medaka (oryzias latipes) is a fish species phylogenetically distant from zebrafish and has served as an important vertebrate model system in molecular and developmental genetics. we previously isolated a medaka rod ...	2006	16460888
the effect of genome length on ejection forces in bacteriophage lambda.	a variety of viruses tightly pack their genetic material into protein capsids that are barely large enough to enclose the genome. in particular, in bacteriophages, forces as high as 60 pn are encountered during packaging and ejection, produced by dna bending elasticity and self-interactions. the high forces are believed to be important for the ejection process, though the extent of their involvement is not yet clear. as a result, there is a need for quantitative models and experiments that revea ...	2006	16469346
functional alignment of regulatory networks: a study of temperate phages.	the relationship between the design and functionality of molecular networks is now a key issue in biology. comparison of regulatory networks performing similar tasks can provide insights into how network architecture is constrained by the functions it directs. here, we discuss methods of network comparison based on network architecture and signaling logic. introducing local and global signaling scores for the difference between two networks, we quantify similarities between evolutionarily closel ...	2005	16477325
linking bacteriophage infection to quorum sensing signalling and bioluminescent bioreporter monitoring for direct detection of bacterial agents.	to incorporate into the lambda phage genome, a luxi-based acyl-homoserine lactone (ahl) synthase genetic construct and exploit the autoamplified power of quorum sensing to translate a phage infection event into a chemical signature detectable by a lux-based bioluminescent bioreporter, with focus towards facile detection of microbial pathogens.	2006	16478488
frequent immune response to a melanocyte specific protein ku-mel-1 in patients with vogt-koyanagi-harada disease.	to isolate autoantigens possibly involved in the pathogenesis of vogt-koyanagi-harada (vkh) disease.	2006	16481377
comparison of bactericidal activity of six lysozymes at atmospheric pressure and under high hydrostatic pressure.	the antibacterial working range of six lysozymes was tested under ambient and high pressure, on a panel of five gram-positive (enterococcus faecalis, bacillus subtilis, listeria innocua, staphylococcus aureus and micrococcus lysodeikticus) and five gram-negative bacteria (yersinia enterocolitica, shigella flexneri, escherichia coli o157:h7, pseudomonas aeruginosa and salmonella typhimurium). the lysozymes included two that are commercially available (hen egg white lysozyme or hewl, and mutanolys ...	2006	16487612
interaction of bacteriophage lambda with its cell surface receptor: an in vitro study of binding of the viral tail protein gpj to lamb (maltoporin).	the cell surface receptor for bacteriophage lambda is lamb (maltoporin). responsible for phage binding to lamb is the c-terminal part, gpj, of phage tail protein j. to study the interaction between lamb and gpj, a chimera protein composed of maltose binding protein (mbp or male) connected to the c-terminal part of j (gpj, amino acids 684-1131) of phage tail protein j of bacteriophage lambda was expressed in escherichia coli and purified to homogeneity. the interaction of the mbp-gpj chimera prot ...	2006	16489764
efficient display of scfv antibodies on bacteriophage lambda.	in the present work we demonstrate the efficient display of functional scfv antibodies on the bacteriophage lambda capsid. a single-chain (scfv) anti-cea antibody gene was cloned in two different vectors to obtain fusion of the scfv antibody to the n- or c-terminus of the bacteriophage lambda capsid protein d (gpd). lambda bacteriophage assembly occurs in the reducing environment of the cytoplasm; despite this the lambda-displayed anti-cea antibody fragments retain the capacity to recognize the ...	2006	16497320
the structural basis of cooperative regulation at an alternate genetic switch.	bacteriophage lambda is a paradigm for understanding the role of cooperativity in gene regulation. comparison of the regulatory regions of lambda and the unrelated temperate bacteriophage 186 provides insight into alternate ways to assemble functional genetic switches. the structure of the c-terminal domain of the 186 repressor, determined at 2.7 a resolution, reveals an unusual heptamer of dimers, consistent with presented genetic studies. in addition, the structure of a cooperativity mutant of ...	2006	16507359
the upstream-activating sequences of the sigma54 promoter pu of pseudomonas putida filter transcription readthrough from upstream genes.	although the m-xylene-responsive sigma54 promoter pu of pseudomonas putida mt-2, borne by the tol plasmid pwwo, is one of the strongest known promoters in vivo, its base-line level in the absence of its aromatic inducer is below the limit of any detection procedure. this is unusual because regulatory networks (such as the one to which pu belongs) can hardly escape the noise caused by intrinsic fluctuations in background transcription, including that transmitted from upstream promoters. this stud ...	2006	16510445
evidence that the promoter can influence assembly of antitermination complexes at downstream rna sites.	the n protein of phage lambda acts with escherichia coli nus proteins at rna sites, nut, to modify rna polymerase (rnap) to a form that overrides transcription terminators. these interactions have been thought to be the primary determinants of the effectiveness of n-mediated antitermination. we present evidence that the associated promoter, in this case the lambda early p(r) promoter, can influence n-mediated modification of rnap even though modification occurs at a site (nutr) located downstrea ...	2006	16513752
role of the lytic repressor in prophage induction of phage lambda as analyzed by a module-replacement approach.	using a module exchange approach, we have tested a long-standing model for the role of cro repressor in lambda prophage induction. this epigenetic switch from lysogeny to the lytic state occurs on activation of the host sos system, which leads to specific cleavage of ci repressor. it has been proposed that cro repressor, which operates during lytic growth and which we shall term the lytic repressor, is crucial to prophage induction. in this view, cro binds to the o(r)3 operator, thereby repressi ...	2006	16537413
the impact of phage lambda: from restriction to recombineering.	experiments using phage lambda provided early insights into important molecular mechanisms, including genetic recombination and the control of gene expression. before recombinant dna technology, the use of lambda, most particularly lambda transducing phages, illustrated the importance of cloning bacterial genes, already providing some insight into how to use cloned genes to advantage. subsequently, lambda made significant contributions to recombinant dna technology, including the early generatio ...	2006	16545077
repression of lambda-associated enzyme synthesis after lambda(vir) superinfection of lysogenic hosts.	lisio, arnold l. (national institutes of health, bethesda, md.), and arthur weissbach. repression of lambda-associated enzyme synthesis after lambda(vir) superinfection of lysogenic hosts. j. bacteriol. 90:661-666. 1965.-phage lambda(vir) is a multiple mutant of lambda which is capable of overcoming the immunity of a host lysogenic for lambda, and initiating normal vegetative replication of the superinfecting phage genome. superinfection of escherichia coli k-112 (lambda(22)) with lambda(vir) re ...	1965	16562064
episome-mediated transfer of drug resistance in enterobacteriaceae x. restriction and modification of phages by fi r factors.	watanabe, tsutomu (keio university, tokyo, japan), toshiya takano, toshihiko arai, hiroshi nishida, and sachiko sato. episome-mediated transfer of drug resistance in enterobacteriaceae. x. restriction and modification of phages by fi(-) r factors. j. bacteriol. 92:477-486. 1966.-an fi(-) r factor, which restricts phages lambda, t1, and t7 without modifying them, was found to restrict and not to modify an f(-)-specific phage, w-31, in escherichia coli k-12, but not to restrict phage p-22 in salmo ...	1966	16562138
a novel method for evaluating free radical scavenging abilities of antioxidants using ultraviolet induction of bacteriophage lambda.	a novel biological method used to evaluate free radical scavenging abilities of antioxidants using ultraviolet (uv) induction of bacteriophage lambda in lysogenic escherichia coli kappa12 (lambda+) has been developed. this method is based on the induction of bacteriophage lambda from lysogenic cycle to lytic cycle by ultraviolet irradiation, and formation of free radicals during the course of induction. in the experiments, 10(8)cells/ml and 30s (39j/m2) were determined as the cell density of the ...	2006	16574238
gene expression profiles in murine hematopoietic stem cells revisited: analysis of cdna libraries reveals high levels of translational and metabolic activities.	gene expression studies from hematopoietic stem cell (hsc) populations purified to variable degrees have defined a set of stemness genes. unexpectedly, results also hinted toward a hsc chromatin poised in a wide-open state. with the aim of providing a robust tool for further studies into the molecular biology of hscs, the studies herein describe the construction and comparative molecular analysis of lambda-phage cdna libraries from highly purified hscs that retained their long-term repopulating ...	2006	16574753
interaction of the intrinsically unstructured phage lambda n protein with escherichia coli nusa.	n protein of the escherichia coli phage lambda (lambdan) is involved in antitermination, a transcription regulatory process that is essential for the expression of delayed early genes during phage lytic development. lambdan is an intrinsically unstructured protein that possesses three distinct binding sites interacting with the carboxy terminus of the e. coli host factor protein nusa, the viral nutboxb-rna, and rna polymerase, respectively. heteronuclear nmr experiments with lambdan(1-53) in com ...	2006	16584189
regulation by coliphage lambda of the expression of the capacity to synthesize a sequence of host enzymes.		1960	16590796
cohesion of dna molecules isolated from phage lambda.		1963	16591099
isolation of the lambda phage repressor.		1967	16591470
recombination between higher plant dna and the ti plasmid of agrobacterium tumefaciens.	the ti plasmid sequences (t-dna) from the octopine-producing crown gall tumor a6s/2 were isolated by molecular cloning, using the bacteriophage lambda vector charon 4a. analysis of the cloned dna segments indicates that the ti plasmid sequences are covalently joined to plant nuclear dna. these data demonstrate that genetic recombination between a eukaryote and a prokaryote can occur as a natural phenomenon.	1980	16592915
short direct repeats flank the t-dna on a nopaline ti plasmid.	crown gall disease results from the insertion of a segment of the agrobacterium ti plasmid, called t-dna, into host plant nuclear dna. we have subjected to sequence analysis the border regions of pti t37 (ends of t-dna) and one left t-dna/plant dna border fragment isolated from bt37 tobacco teratoma by molecular cloning. these sequence studies, taken together with published sequence of a right t-dna/plant dna border fragment, allowed us to identify the positions of left and right borders at the ...	1982	16593241
structure and expression of a pea nuclear gene encoding a chlorophyll a/b-binding polypeptide.	a nuclear gene ab80 has been isolated from a phage lambda charon 4 library of pea dna. the sequence of the gene has been determined and it has been shown to contain an uninterrupted reading frame of 269 amino acids, corresponding to a precursor to a constituent polypeptide of the light-harvesting chlorophyll a/b-protein complex. primer extension and s1 nuclease studies defined a cap site for ab80. the first methionine codon 3' from this site is 69 nucleotides away and is the initiating codon of ...	1984	16593461
cloning of the bronze locus in maize by a simple and generalizable procedure using the transposable controlling element activator (ac).	the bronze (bz) locus of maize has been cloned by an indirect procedure utilizing the cloned transposable controlling element activator (ac). restriction endonuclease fragments of maize dna were cloned in bacteriophage lambda and recombinant phage with homology to the center of the ac element were isolated. the cloned fragments were analyzed to determine which contained sequences that were structurally identical to a previously isolated ac element. two such fragments were identified. sequences f ...	1984	16593478
repair of defined single base-pair mismatches in escherichia coli.	heteroduplexes with single base-pair mismatches of known sequence were prepared by annealing separated strands of bacteriophage lambda dna and used to transfect escherichia coli. each of the eight possible single base-pair mismatches was constructed. genetic analysis of the progeny phages obtained from transfected bacteria indicates that the e. coli mismatch repair system does not recognize (or does not repair) all single base-pair mismatches with equal efficiency. in particular, the a.g, c.t, a ...	1985	16593539
a cosmid for selecting genes by complementation in aspergillus nidulans: selection of the developmentally regulated ya locus.	we constructed a 9.9-kilobase cloning vector, designated pkby2, for isolating genes by complementation of mutations in aspergillus nidulans. pkby2 contains the bacteriophage lambda cos site, to permit in vitro assembly of phage particles; a bacterial origin of replication and genes for resistance to ampicillin and chloramphenicol, to permit propagation in escherichia coli; the a. nidulans trpc(+) gene, to permit selection in aspergillus; and a unique bamhi restriction site, to permit insertion o ...	1985	16593541
linkage and homology analysis divides the eight genes for the small subunit of petunia ribulose 1,5-bisphosphate carboxylase into three gene families.	twenty-six lambda phage clones with homology to coding sequences of the small subunit (ssu) of ribulose 1,5-bisphosphate carboxylase have been isolated from an embl3 lambda phage bank of petunia (mitchell) dna. restriction mapping of the phage inserts shows that the clones were obtained from five nonoverlapping regions of petunia dna that carry seven ssu genes. comparison of the hindiii genomic fragments of petunia dna with the hindiii restriction fragments of the isolated phage indicates that p ...	1985	16593584
cdna cloning of the complete genome of tobacco mosaic virus and production of infectious transcripts.	the entire genome of tobacco mosaic virus (tmv) was copied into a series of subgenomic cdna clones. cdna sequences of the 5' and 3' ends of tmv were cloned separately. a synthetic oligonucleotide primer was used to generate a pst i site at the 5' terminus, whereas a different primer was used to generate an nde i site at the 3' terminus. this strategy permitted removal of non-tmv sequences from cloned cdna inserts by treatment with exonuclease vii following restriction endonuclease cleavage. pst ...	1986	16593669
nitrate reductase from squash: cdna cloning and nitrate regulation.	the assimilation of nitrate in plants involves the reduction of nitrate to ammonia in two steps. the first step requires nitrate reductase, a nitrate-inducible enzyme. when seedlings of squash (cucurbita maxima l.) were treated with nitrate, both nitrate reductase activity and protein were induced in the cotyledons. poly(a)(+) rna was prepared from cotyledons of nitrate-treated seedlings and was used to construct a lambdagt11 cdna library. using antibodies from mice immunized against purified ni ...	1986	16593773
cloning of genes developmentally regulated during plant embryogenesis.	genes specifically induced during somatic embryogenesis may play key roles in plant embryo development. an antiserum against an extract of carrot somatic embryos revealed a few rare antigens induced at the onset of embryogenesis. through differential immunoadsorption techniques, we purified antibodies against the embryo-specific antigens and probed a phage lambda gt11 library of cdna from carrot somatic embryos. this paper describes three distinct cdna clones that hybridize to embryo-specific rn ...	1987	16593822