Publications

an action spectrum of the riboflavin-photosensitized inactivation of lambda phage.	the action spectrum of riboflavin (rb) sensitized inactivation of lambda phage was determined between 266 and 575 nm. below 304 nm, rb depresses the phage reduction by screening phage from radiation that it would otherwise absorb directly. between 308 and 525 nm, rb sensitizes the inactivation of phage. enhanced phage reduction is observed at 320 and 500 nm because of binding of rb to the phage and the shifting of the absorption curve of the phage-bound flavin relative to free flavin in phosphat ...	2005	15623353
[preparation of anti-red antisera and its subcellular localization].	to prepare rabbit anti-red antisera.	2005	15862146
targeted modification of the complete chicken lysozyme gene by poxvirus-mediated recombination.	we have developed a novel ex vivo system for the rapid one-step targeted modification of large eucaryotic dna sequences. the highly recombinant environment resulting from infection of rabbit cornea cells with the shope fibroma virus was exploited to mediate precise modifications of the complete chicken lysozyme gene domain (21.5 kb). homologous recombination was designed to occur between target dna (containing the complete lysozyme gene domain) maintained in a lambda bacteriophage vector and mod ...	2005	15864331
role of c-terminal residues in oligomerization and stability of lambda cii: implications for lysis-lysogeny decision of the phage.	a crucial element in the lysis-lysogeny decision of the temperate coliphage lambda is the phage protein cii, which has several interesting properties. it promotes lysogeny through activation of three phage promoters p(e), p(i) and p(aq), recognizing a direct repeat sequence ttgcn6ttgc at each. the three-dimensional structure of cii, a homo-tetramer of 97 residue subunits, is unknown. it is an unstable protein in vivo, being rapidly degraded by the host protease hflb (ftsh). this instability is e ...	2005	15571724
frequency of sox group b (sox1, 2, 3) and zic2 antibodies in turkish patients with small cell lung carcinoma and their correlation with clinical parameters.	expression of neuroectodermal markers is a key feature of small cell lung carcinoma (sclc). although immune responses against a number of these proteins have been associated with paraneoplastic neuronal disease (pnd), most patients with sclc have anti-neuroectodermal antibodies in the absence of pnd. whether these immune responses affect the clinical outcome in sclc is critical in understanding the potential value of these proteins as cancer vaccine targets as well as in the pathogenesis of pnd.	2005	15880380
optimization of nuclear localization signal for nuclear transport of dna-encapsulating particles.	the nuclear membrane is a tight barrier against the delivery of therapeutic genes into non-dividing tissue cells. overcoming this barrier with the aid of peptidic nuclear localization signals (nls) is crucial for improving the performance of synthetic gene-delivery vehicles. in this article, we examine the nuclear transport of lambda phage particles displaying various peptides containing the minimum nls of sv40 t antigen on their surface. as the minimum nls (pkkkrkv) is a binding domain to impor ...	2005	15911050
genotoxicity of the yamuna river water at okhla (delhi), india.	water samples from the yamuna river at okhla (delhi), india, were concentrated using xad resins (xad-4 and xad-8) and liquid-liquid extraction procedures. gas chromatographic analysis of liquid-liquid extracted water samples revealed the presence of the pesticides ddt, bhc, dieldrin, endosulfan, aldrin, 2,4-d, dimethoate, methyl parathion, and malathion at concentrations of 14, 25, 2.1, 114, 0.9, 0.6, 0.9, 1.7, and 1.9 ng/l, respectively. the genotoxicity of the extracted water samples was evalu ...	2005	15922807
nmr solution structure of the monomeric form of the bacteriophage lambda capsid stabilizing protein gpd.		2005	15929002
investigating dna adduct-targeted mutagenicity of tamoxifen: preferential formation of tamoxifen-dna adducts in the human p53 gene in sv40 immortalized hepatocytes but not endometrial carcinoma cells.	tamoxifen is a widely used drug for chemotherapy and chemoprevention of breast cancer worldwide. tamoxifen therapy is, however, associated with an increased incidence of endometrial cancer. the carcinogenicity of tamoxifen is ascribed to its genotoxic and estrogen agonist effects. we investigated dna adduct-targeted mutagenicity of tamoxifen as a function of its genotoxicity in the cii transgene in big blue mouse embryonic fibroblasts and mapped the formation of tamoxifen-induced dna adducts in ...	2005	15938631
comparative analysis of sequence-specific dna recombination systems in human embryonic stem cells.	the great potential of human embryonic stem cells (hescs) in basic research, regenerative medicine, and gene therapy is widely recognized. controlled manipulation of hesc genomes through sequence-specific dna recombination (ssr) may play a significant role in future hesc applications. however, very little is known about the functionality of ssr systems in hescs. we demonstrate here that mutant phage lambda integrase, phage p1 cre recombinase, and mutant gammadelta resolvase displayed distinct ac ...	2005	15955832
nanopores: maltoporin channel as a sensor for maltodextrin and lambda-phage.	background: to harvest nutrition from the outside bacteria e.g. e. coli developed in the outer cell wall a number of sophisticated channels called porins. one of them, maltoporin, is a passive specific channel for the maltodextrin uptake. this channel was also named lamb as the bacterial virus phage lambda mis-uses this channel to recognise the bacteria. the first step is a reversible binding followed after a lag phase by dna injection. to date little is known about the binding capacity and less ...	2005	15743521
functional analysis of the lysis genes of staphylococcus aureus phage p68 in escherichia coli.	double-stranded dna phages of both gram-positive and gram-negative bacteria typically use a holin-endolysin system to achieve lysis of their host. in this study, the lysis genes of staphylococcus aureus phage p68 were characterized. p68 gene lys16 was shown to encode a cell-wall-degrading enzyme, which causes cell lysis when externally added to clinical isolates of s. aureus. another gene, hol15, was identified embedded in the -1 reading frame at the 3' end of lys16. the deduced hol15 protein ha ...	2005	16000723
asymmetric binding of membrane proteins to groel.	the interaction of groel with non-native soluble proteins has been studied intensively and structure-function relationships have been established in considerable detail. recently, we found that groel is also able to bind membrane proteins in the absence of detergents and deliver them to liposomes in a biologically active state. here, we report that three well-studied membrane proteins (bacteriorhodopsin, lacy, and the bacteriophage lambda holin) bind asymmetrically to tetradecameric groel. each ...	2005	15639236
pause point spectra in dna constant-force unzipping.	under constant applied force, the separation of double-stranded dna into two single strands is known to proceed through a series of pauses and jumps. given experimental traces of constant-force unzipping, we present a method whereby the locations of pause points can be extracted in the form of a pause point spectrum. a simple theoretical model of dna constant-force unzipping is presented, which generates theoretical pause point spectra through monte carlo simulation of the unzipping process. the ...	2005	15695634
the mutation that makes escherichia coli resistant to lambda p gene-mediated host lethality is located within the dna initiator gene dnaa of the bacterium.	earlier, we reported that the bacteriophage lambda p gene product is lethal to escherichia coli, and the e. coli rpl mutants are resistant to this lambda p gene-mediated lethality. in this paper, we show that under the lambda p gene-mediated lethal condition, the host dna synthesis is inhibited at the initiation step. the rpl8 mutation maps around the 83 min position in the e. coli chromosome and is 94 % linked with the dnaa gene. the rpl8 mutant gene has been cloned in a plasmid. this plasmid c ...	2005	15715952
[cloning and structural analysis of mouse genomic nucleophosmin gene].	nucleophosmin (npm) is an abundant nucleolar phosphoprotein. npm gene involved chromosomal translocations were found in the patients with anaplastic large cell lymphomas (alcl), myelodysplastic syndrome (mds), acute myeloid leukemia (aml) and acute promyelocytic leukemia (apl). to generate npm gene knockout mice and study its biological function in vivo, we screened the lambda phage genomic library derived from 129s1 mice with mouse npm cdna probe. a positive phage clone which contained the full ...	2005	16018192
[development of a new recombineering system by gap repair].	using lambda phage red recombinase mediated in vivo homologous recombination system, a 6.7 kb lambda pl operon sequence including the red encoding genes was subcloned into pbr322 by gap repair technique, and generated a pbr322-red recombinant plasmid that can provide the red recombination function and can be transferred into many kinds of bacteria. to confirm the recombination functions of pbr322-red, a single-stranded 70-bases oligo was introduced into w3110 by electroporation to create a singl ...	2005	16018266
the bacteriophage lambda dna replication protein p inhibits the oric dna- and atp-binding functions of the dna replication initiator protein dnaa of escherichia coli.	under the condition of expression of lambda p protein at lethal level, the oric dna-binding activity is significantly affected in wild-type e. coli but not in the rpl mutant. in purified system, the lambda p protein inhibits the binding of both oric dna and atp to the wild-type dnaa protein but not to the rpl dnaa protein. we conclude that the lambda p protein inhibits the binding of oric dna and atp to the wild-type dnaa protein, which causes the inhibition of host dna synthesis initiation that ...	2005	15715953
[comparison of two amine-modified chemical platforms for dna microarray preparation].	to study two amine modification procedures for dna microarray preparation based on polymeric coatings.	2005	16027070
coevolutionary arms races between bacteria and bacteriophage.	we propose a computational and theoretical framework for analyzing rapid coevolutionary dynamics of bacteriophage and bacteria in their ecological context. bacteriophage enter host cells via membrane-bound surface receptors often responsible for nutrient uptake. as such, a selective pressure will exist for the bacteria to modify its receptor configuration and, in turn, for the phage to modify its tail fiber. a mathematical model of these trait adaptations is developed by using the framework of a ...	2005	15976021
slow assembly and disassembly of lambda cro repressor dimers.	dimers of cro are required to recognize operator dna and repress transcription, but dimerization is weak compared to dna binding. fluorophore-conjugated, single-cysteine variants of cro have been used to investigate the equilibria and kinetics of dimer assembly. equilibrium distributions of mixed dimers, monitored by fluorescence resonance energy transfer (fret), confirm that labeled variants have equilibrium dimer dissociation constants in the micromolar concentration range. subunit exchange ex ...	2005	15982668
an end-healing enzyme from clostridium thermocellum with 5' kinase, 2',3' phosphatase, and adenylyltransferase activities.	we identify and characterize an end-healing enzyme, cthpnkp, from clostridium thermocellum that catalyzes the phosphorylation of 5'-oh termini of dna or rna polynucleotides and the dephosphorylation of 2',3' cyclic phosphate, 2'-phosphate, and 3'-phosphate ribonucleotides. cthpnkp also catalyzes an autoadenylylation reaction via a polynucleotide ligase-type mechanism. these characteristics are consistent with a role in end-healing during rna or dna repair. cthpnkp is a homodimer of an 870-amino- ...	2005	15987807
the structure of the excisionase (xis) protein from conjugative transposon tn916 provides insights into the regulation of heterobivalent tyrosine recombinases.	heterobivalent tyrosine recombinases play a prominent role in numerous bacteriophage and transposon recombination systems. their enzymatic activities are frequently regulated at a structural level by excisionase factors, which alter the ability of the recombinase to assemble into higher-order recombinogenic nucleoprotein structures. the tn916 conjugative transposon spreads antibiotic resistance in pathogenic bacteria and is mobilized by a heterobivalent recombinase (tn916int), whose activity is ...	2005	15733914
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
bacteriophage lambda terminase: alterations of the high-affinity atpase affect viral dna packaging.	dna packaging by large dna viruses such as the tailed bacteriophages and the herpesviruses involves dna translocation into a preformed protein shell, called the prohead. translocation is driven by an atp hydrolysis-powered dna packaging motor. the bacteriophages encode a heterodimeric viral dna packaging protein, called terminase. the terminases have an atpase center located in the n terminus of the large subunit implicated in dna translocation. in previous work with phage lambda, lethal mutatio ...	2005	15733918
polarity within pm and pe promoted phage lambda ci-rexa-rexb transcription and its suppression.	the ci-rexa-rexb operon of bacteriophage lambda confers 2 phenotypes, imm and rex, to lysogenic cells. immunity to homoimmune infecting lambda phage depends upon the ci repressor. rex exclusion of t4rii mutants requires rexa and rexb proteins. both imm and rex share temperature-sensitive conditional phenotypes when expressed from ci[ts]857 but not from ci+ lambda prophage. plasmids were made in which ci-rexa-rexb was transcribed from a non-lambda promoter, ptet. the ci857-rexa-rexb plasmid exhib ...	2005	15782233
cdna library construction from a small amount of rna: adaptor-ligation approach for two-round crna amplification using t7 and sp6 rna polymerases.	in this study, we developed a method that allows cdna library construction from a small amount of rna without causing serious size bias in the resulting cdna population. for this purpose, we adopted two-round crna amplification by t7 and sp6 rna polymerases. the first-round cdnas, flanked by the promoter sequences of t7 and sp6 rna polymerases, were synthesized from 1 microg total rna and then subjected to two rounds of crna amplification. comparison of the sizes of the first-round and the secon ...	2005	15786810
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
non-equivalent interactions between amino-terminal domains of neighboring lambda integrase protomers direct holliday junction resolution.	the bacteriophage lambda site-specific recombinase (int), in contrast to other family members such as cre and flp, has an amino-terminal domain that binds "arm-type" dna sequences different and distant from those involved in strand exchange. this defining feature of the heterobivalent recombinases confers a directionality and regulation that is unique among all recombination pathways. we show that the amino-terminal domain is not a simple "accessory" element, as originally thought, but rather is ...	2005	15581892
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
quantitative kinetic analysis of the bacteriophage lambda genetic network.	the lysis-lysogeny decision of bacteriophage lambda has been a paradigm for a developmental genetic network, which is composed of interlocked positive and negative feedback loops. this genetic network is capable of responding to environmental signals and to the number of infecting phages. an interplay between ci and cro functions suggested a bistable switch model for the lysis-lysogeny decision. here, we present a real-time picture of the execution of lytic and lysogenic pathways with unpreceden ...	2005	15728384
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
self-association properties of the bacteriophage lambda terminase holoenzyme: implications for the dna packaging motor.	terminases are enzymes common to complex double-stranded dna viruses and are required for packaging of viral dna into a protective capsid. bacteriophage lambda terminase holoenzyme is a hetero-oligomer composed of the a and nu1 lambda gene products; however, the self-association properties of the holoenzyme have not been investigated systematically. here, we report the results of sedimentation velocity, sedimentation equilibrium, and gel-filtration experiments studying the self-association prope ...	2005	15755448
gene regulation at the single-cell level.	the quantitative relation between transcription factor concentrations and the rate of protein production from downstream genes is central to the function of genetic networks. here we show that this relation, which we call the gene regulation function (grf), fluctuates dynamically in individual living cells, thereby limiting the accuracy with which transcriptional genetic circuits can transfer signals. using fluorescent reporter genes and fusion proteins, we characterized the bacteriophage lambda ...	2005	15790856
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
revisited gene regulation in bacteriophage lambda.	the contribution of bacteriophage lambda to gene control research is far from over. a revised model of the lambda genetic switch includes extra cooperativity through octamerization of the ci repressor protein, mediated by long-range dna looping. structural analysis reveals remarkably subtle transcriptional activation by ci. the action of ci, activation by cii, and aspects of antitermination by n and q all confirm the utility and versatility of simple, weak adhesive interactions mediated by nucle ...	2005	15797197
transcriptional activation mechanisms of the prm promoter of lambda phage.	we investigate the transcriptional activity associated with the p(rm) promoter of lambda phage. the probability for formation of a transcriptionally active (open) rna polymerase-dna complex is calculated by means of an equilibrium statistical-mechanical model. in particular, we study two different models of the transcriptional activation mechanism when the o(r)2 site is occupied by a ci dimer (typical for a lysogen) compared to the situation when o(r)2 is vacant: (1) transcription rate increases ...	2004	15829357
robustness, stability and efficiency of phage lambda genetic switch: dynamical structure analysis.	based on the dynamical structure theory for complex networks recently developed by one of us and on the physical-chemical models for gene regulation, developed by shea and ackers in the 1980's, we formulate a direct and concise mathematical framework for the genetic switch controlling phage lambda life cycles, which naturally includes the stochastic effect. the dynamical structure theory states that the dynamics of a complex network is determined by its four elementary components: the dissipatio ...	2004	15617166
single-chain integration host factors as probes for high-precision nucleoprotein complex formation.	integration host factor (ihf) is a heterodimeric, site-specific dna-binding and dna-bending protein from escherichia coli. it is involved in high-precision dna transactions where it serves as a key architectural component of specialized nucleoprotein structures (snups). we described recently a novel approach for protein engineering using a single polypeptide chain ihf, termed scihf2, as a first example. scihf2 is made up of the alpha subunit of ihf which was inserted into the beta subunit at pep ...	2004	15563835
rapid construction of capsid-modified adenoviral vectors through bacteriophage lambda red recombination.	there are extensive efforts to develop cell-targeting adenoviral vectors for gene therapy wherein endogenous cell-binding ligands are ablated and exogenous ligands are introduced by genetic means. although current approaches can genetically manipulate the capsid genes of adenoviral vectors, these approaches can be time-consuming and require multiple steps to produce a modified viral genome. we present here the use of the bacteriophage lambda red recombination system as a valuable tool for the ea ...	2004	15610612
[progress on phage antibody library technology].	the exterior protein gene and the specific protein gene coded on the surface of phage can be fusedly expressed on the surface of phage with the recently developed technology-phage display technique. through the pcr technique, the whole light chain genes and heavy chain genes can be amplified. cloning these genes into lambda phage expression vectors and constructing phage antibody library through antigen adsorption-elution-proliferation, many targeting clones could be selected and the responding ...	2004	15727199
restoration of gene function by homologous recombination: from pcr to gene expression in one step.	we have developed a simple method for single-step cloning of any pcr product into a plasmid. a novel selection principle has been applied, in which activation of a drug selection marker is achieved following homologous recombination. in this method a dna fragment is amplified by pcr with standard oligonucleotides that contain flanking tails derived from the host plasmid and the complete lambdapr or rrna1 promoter regions. the resulting pcr product is then electroporated into an escherichia coli ...	2004	15574912
evidence of bar minigene expression and trna2ile sequestration as peptidyl-trna2ile during lambda bacteriophage development.	lambda bacteriophage development is impaired in escherichia coli cells defective for peptidyl (pep)-trna hydrolase (pth). single-base-pair mutations (bar(-)) that affect translatable two-codon open reading frames named bar minigenes (bari or barii) in the lambda phage genome promote the development of this phage in pth-defective cells (rap cells). when the bari minigene is cloned and overexpressed from a plasmid, it inhibits protein synthesis and cell growth in rap cells by sequestering trna(2)( ...	2004	15292158
structural basis for the interaction of escherichia coli nusa with protein n of phage lambda.	the c terminus of transcription factor nusa from escherichia coli comprises two repeat units, which bind during antitermination to protein n from phage lambda. to delineate the structural basis of the nusa-lambdan interaction, we attempted to crystallize the nusa c-terminal repeats in complex with a lambdan peptide (residues 34-47). the two nusa domains became proteolytically separated during crystallization, and crystals contained two copies of the first repeat unit in contact with a single lam ...	2004	15365170
ten new temperate bacteriophages of citrobacter youngae.	in a cross-test, we examined 55 strains of citrobacter youngae against each other as potential producers of temperate bacteriophages and as potential sensitive indicators for them. ten strains (18.2 %) showed the production of phages. seven different strain-specific spectra of activity (from 1 to 11 strains each) were found. phage production by 6 strains was inducible with mitomycin c, in 4 strains it was not inducible. the plaques of the phages were more or less turbid, without a lytic halo, ti ...	2004	15881402
[estimation of potential mutagenic activity of 24-epibrassinolide].	genotoxic effect of synthetic phytohormone analogue of steroid origin epibrassinolide was studied in in vitro- and in vivo-tests. epibrassinolide did not display mutagenic properties in ames' test (s. typhimurium, ta100) and dna damaging activity test (dna of phage lambda). the rise in the level of polichromatophilous erythrocytes with micronuclei was observed in the micronuclear test at intraperitoneal epibrassinolide injection at the dose of 500 mg/kg that seems to be associated with disturban ...	2004	15882035
bacterial sensitivity to bacteriophage in the aquatic environment.	there are several unusual features about phage when you first encounter them as a biologist. they are small, but conform to one of a few morphological types. next their genomes can be composed of dna or rna and be single or double stranded. finally they are numerically more abundant than prokaryotes and a significant proportion of them form an association in their microbial host populations termed lysogeny. the latter findings indicate that they are numerically significant in microbial populatio ...	2004	15884658
electrokinetic bioprocessor for concentrating cells and molecules.	bioprocessors for concentrating bioparticles, such as cells and molecules, are commonly needed in bioanalysis systems. in this microfluidic processor, a global flow field generated by ac electroosmosis transports the embedded particles to the regions near the electrode surface. the processor then utilizes electrophoretic and dielectrophoretic forces, which are effective in short range, to trap the target cells and molecules on the electrode surface. by optimizing the operating parameters, we hav ...	2004	15571340
first-time isolation and characterization of a bacteriophage encoding the shiga toxin 2c variant, which is globally spread in strains of escherichia coli o157.	a bacteriophage encoding the shiga toxin 2c variant (stx2c) was isolated from the human escherichia coli o157 strain cb2851 and shown to form lysogens on the e. coli k-12 laboratory strains c600 and mg1655. production of stx2c was found in the wild-type e. coli o157 strain and the k-12 lysogens and was inducible by growing bacteria in the presence of ciprofloxacin. phage 2851 is the first reported viable bacteriophage which carries an stx(2c) gene. electron micrographs of phage 2851 showed parti ...	2004	15557626
geometric and dynamic requirements for dna looping, wrapping and unwrapping in the activation of e.coli glnap2 transcription by ntrc.	transcriptional activation by the e.coli ntrc protein can occur via dna looping between a dna-bound activator and the target sigma(54) rna polymerase. ntrc forms an octamer on dna that is capable of binding two dna molecules. its atpase activity is required for open complex formation. geometric requirements for activation were assessed using a library of dna bending sequences created by random ligation of a-tract oligonucleotides, as well as several designed sequences. thirty random or designed ...	2004	15327947
aminoglycoside antibiotics aggregate to form starch-like fibers on negatively charged surfaces and on phage lambda-dna.	the water-soluble (> 200 mg/ml) antibiotics tobramycin, kanamycin, and neomycin spontaneously produce rigid fibers on negatively charged surfaces (mica, graphite, dna). atomic force microscopy showed single strands of tobramycin on mica at ph 7 with a length of several hundred nanometers and a diameter of 0.5 nm and double helices with a diameter of 1.0 nm and a helical pitch of 7 nm. at ph 13 (naoh) up to 15 microm long, rigid fibers with a uniform height of 2.4 nm and an apparent helical pitch ...	2004	15461517
efficient isolation of cdna clones encoding rheumatoid arthritis autoantigens by lambda phage surface display.	bacteriophage lambda surface display was used to isolate cdna clones encoding autoantigens recognized by synovial fluid (sf) or sera from patients with rheumatoid arthritis (ra). we constructed cdna libraries from human synovial sarcoma cells and synovial tissue, using the surface display vector lambdafoo. the cdna libraries were screened by affinity selection using 40 sf and 44 sera as probes separately immobilized in microtiter wells. phage clones isolated encode 13 different autoantigens; an ...	2004	15464598
the efficiency of mispaired ligations by lambda integrase is extremely sensitive to context.	the integrase protein (int) of phage lambda is a well-studied representative of the tyrosine recombinase family, whose defining features are two sequential pairs of dna cleavage/ligation reactions that proceed via a 3' phosphotyrosine covalent intermediate to first form and then resolve a holliday junction recombination intermediate. we devised an assay that takes advantage of dna hairpin formation at one int target site to trap int cleavages at a different target site, and thereby reveal iterat ...	2004	15364588
dna microarray probe preparation by gel isolation nested pcr.	to develop a simplified method that can rapidly prepare dna microarray probes in a massive scale, a lambda phage genomic dna-fragments library was constructed for the microarray-probes collection. four methods of dna band recovery from the first pcr products were tested and compared. the dna microarray probes were collected by a novel method of nested pcr that was mediated by gel isolation of the first pcr products. this method was named gin-pcr. the probes that were prepared by this gin-pcr tec ...	2004	15469719
nonspecific binding of the or repressors ci and cro of bacteriophage lambda.	we estimate the gibbs free energy for nonspecific binding (deltagnsb) to the escherichia coli dna for two regulatory proteins of the lambda phage, ci and cro. by means of a statistical-mechanical approach, we calculate the ci and cro activities associated with the operator or of an introduced lambda phage genome (prophage). in this statistical model we apply in vitro-measured binding free energies to fit in vivo experimental data for ci and cro activities, respectively, where deltagnsb is introd ...	2004	15488529
absence of intrinsic electric conductivity in single dsdna molecules.	the intrinsic dc conductivity of long, individual lambda phage dsdna molecules has been investigated by ultrasensitive low current-voltage-spectroscopy (iv) under ambient conditions and controlled low humidity inert gas atmosphere on microfabricated metal-insulator-metal gap structures. we found a strong dependence of the measured conductivity on the apparent humidity, which we attribute to capillary condensation of water to the immobilized dna molecules, giving rise to additional ionic currents ...	2004	15288944
the complete map of the ig heavy chain constant gene region reveals evidence for seven igg isotypes and for igd in the horse.	this report contains the first map of the complete ig h chain constant (ighc) gene region of the horse (equus caballus), represented by 34 overlapping clones from a new bacterial artificial chromosome library. the different bacterial artificial chromosome inserts containing ighc genes were identified and arranged by hybridization using overgo probes specific for individual equine ighc genes. the analysis of these ighc clones identified two previously undetected ighc genes of the horse. the newly ...	2004	15322185
the recognition and modification sites for the bacterial type i restriction systems kpnai, styseai, styseni and stysgi.	using an in vivo plasmid transformation method, we have determined the dna sequences recognized by the kpnai, styseai, styseni and stysgi r-m systems from klebsiella oxytoca strain m5a1, salmonella eastbourne, salmonella enteritidis and salmonella gelsenkirchen, respectively. these type i restriction-modification systems were originally identified using traditional phage assay, and described here is the plasmid transformation test and computer program used to determine their dna recognition sequ ...	2004	15199175
complex spatial distribution and dynamics of an abundant escherichia coli outer membrane protein, lamb.	advanced techniques for observing protein localization in live bacteria show that the distributions are dynamic. for technical reasons, most such techniques have not been applied to outer membrane proteins in gram-negative bacteria. we have developed two novel live-cell imaging techniques to observe the surface distribution of lamb, an abundant integral outer membrane protein in escherichia coli responsible for maltose uptake and for attachment of bacteriophage lambda. using fluorescently labell ...	2004	15341654
regulatory circuit design and evolution using phage lambda.	bistable gene regulatory circuits can adopt more than one stable epigenetic state. to understand how natural circuits have this and other systems properties, several groups have designed regulatory circuits de novo. here we describe an alternative approach. we have modified an existing bistable circuit, that of phage lambda. with this approach, we used powerful genetic selections to identify functional circuits and selected for variants with altered behavior. the lambda circuit involves two anta ...	2004	15342489
little lambda, who made thee?	the study of the bacteriophage lambda has been critical to the discipline of molecular biology. it was the source of key discoveries in the mechanisms of, among other processes, gene regulation, recombination, and transcription initiation and termination. we trace here the events surrounding these findings and draw on the recollections of the participants. we show how a particular atmosphere of interactions among creative scientists yielded spectacular insights into how living things work.	2004	15590784
chromosomal duplications and cointegrates generated by the bacteriophage lamdba red system in escherichia coli k-12.	an escherichia coli strain in which recbcd has been genetically replaced by the bacteriophage lambda red system engages in efficient recombination between its chromosome and linear double-stranded dna species sharing sequences with the chromosome. previous studies of this experimental system have focused on a gene replacement-type event, in which a 3.5 kbp dsdna consisting of the cat gene and flanking lac operon sequences recombines with the e. coli chromosome to generate a chloramphenicol-resis ...	2004	15596011
cold-active dnak of an antarctic psychrotroph shewanella sp. ac10 supporting the growth of dnak-null mutant of escherichia coli at cold temperatures.	shewanella sp. ac10 is a psychrotrophic bacterium isolated from the antarctica that actively grows at such low temperatures as 0 degrees c. immunoblot analyses showed that a heat-shock protein dnak is inducibly formed by the bacterium at 24 degrees c, which is much lower than the temperatures causing heat shock in mesophiles such as escherichia coli. we found that the shewanella dnak (shednak) shows much higher atpase activity at low temperatures than the dnak of e. coli (ecodnak): a characteris ...	2004	15599780
solubilization and delivery by groel of megadalton complexes of the lambda holin.	groel can solubilize membrane proteins by binding them in its hydrophobic cavity when detergent is removed by dialysis. the best-studied example is bacteriorhodopsin, which can bind in the groel chaperonin at two molecules per tetradecamer. applying this approach to the holin and antiholin proteins of phage lambda, we find that both proteins are solubilized by groel, in an atp-sensitive mode, but to vastly different extents. the antiholin product, s107, saturates the chaperonin at six molecules ...	2004	15215521
lambda-repressor oligomerization kinetics at high concentrations using fluorescence correlation spectroscopy in zero-mode waveguides.	fluorescence correlation spectroscopy (fcs) has demonstrated its utility for measuring transport properties and kinetics at low fluorophore concentrations. in this article, we demonstrate that simple optical nanostructures, known as zero-mode waveguides, can be used to significantly reduce the fcs observation volume. this, in turn, allows fcs to be applied to solutions with significantly higher fluorophore concentrations. we derive an empirical fcs model accounting for one-dimensional diffusion ...	2004	15613638
male mouse meiotic chromosome cores deficient in structural proteins sycp3 and sycp2 align by homology but fail to synapse and have possible impaired specificity of chromatin loop attachment.	the targeted deletion of the meiotic chromosome core component mmsycp3 results in chromosome synaptic failure at male meiotic prophase, extended meiotic chromosomes, male sterility, oocyte aneuploidy and absence of the mmsycp2 chromosome core component. to test the functions of sycp2 and sycp3 proteins in the cores, we determined the effect of their deletion on homology recognition by whole chromosome painting and the effect on chromatin loop attachment to the cores with endogenous and exogenous ...	2004	15237206
sequence-specific rho-rna interactions in transcription termination.	the bacteriophage lambda tr1 terminator encodes a region of the nascent cro transcript containing rna residues recognized by termination factor rho. to identify ribonucleotide-protein interactions contributing to termination, a library of reporter gene plasmids was constructed containing predominantly single-nucleotide substitutions in a 24 nt region previously shown to be critical for efficient termination. screening 16 822 bacterial transformants identified 110 terminator mutants, most of whic ...	2004	15181174
polymorphic cytochrome p450 2d6: humanized mouse model and endogenous substrates.	cytochrome p450 2d6 (cyp2d6) is the first well-characterized polymorphic phase i drug-metabolizing enzyme, and more than 80 allelic variants have been identified for the cyp2d6 gene, located on human chromosome 22q13.1. human debrisoquine and sparteine metabolism is subdivided into two principal phenotypes--extensive metabolizer and poor metabolizer--that arise from variant cyp2d6 genotypes. it has been estimated that cyp2d6 is involved in the metabolism and disposition of more than 20% of presc ...	2004	15237854
identification of a panel of tumor-associated antigens from breast carcinoma cell lines, solid tumors and testis cdna libraries displayed on lambda phage.	tumor-associated antigens recognized by humoral effectors of the immune system are a very attractive target for human cancer diagnostics and therapy. recent advances in molecular techniques have led to molecular definition of immunogenic tumor proteins based on their reactivity with autologous patient sera (serex).	2004	15541172
sequence tolerance of the phage lambda prm promoter: implications for evolution of gene regulatory circuitry.	much of the gene regulatory circuitry of phage lambda centers on a complex region called the o(r) region. this approximately 100-bp region is densely packed with regulatory sites, including two promoters and three repressor-binding sites. the dense packing of this region is likely to impose severe constraints on its ability to change during evolution, raising the question of how the specific arrangement of sites and their exact sequences could evolve to their present form. here we ask whether th ...	2004	15547271
probabilistic cross-link analysis and experiment planning for high-throughput elucidation of protein structure.	emerging high-throughput techniques for the characterization of protein and protein-complex structures yield noisy data with sparse information content, placing a significant burden on computation to properly interpret the experimental data. one such technique uses cross-linking (chemical or by cysteine oxidation) to confirm or select among proposed structural models (e.g., from fold recognition, ab initio prediction, or docking) by testing the consistency between cross-linking data and model ge ...	2004	15557270
dual role of boxb rna motif in the mechanisms of termination/antitermination at the lambda tr1 terminator revealed in vivo.	rho-dependent transcription termination at the phage lambda tr1 terminator is governed primarily by the upstream rut element that encodes two rna regions ruta and rutb. the two regions are separated by the boxb rna motif, which is believed to be dispensable for rho activity but serves as a binding site for lambda n protein in the antitermination process. by using a minimal in vivo termination system, we show that the intervening boxb rna motif has a double function in the mechanisms of terminati ...	2004	15178249
a minimal kinetic model for a viral dna packaging machine.	terminase enzymes are common to both eukaryotic and prokaryotic double-stranded dna viruses. these enzymes possess atpase and nuclease activities that work in concert to "package" a viral genome into an empty procapsid, and it is likely that terminase enzymes from disparate viruses utilize a common packaging mechanism. bacteriophage lambda terminase possesses a site-specific nuclease activity, a so-called helicase activity, a dna translocase activity, and multiple atpase catalytic sites that fun ...	2004	14717582
genetic screen for monitoring severe acute respiratory syndrome coronavirus 3c-like protease.	a novel coronavirus (scov) is the etiological agent of severe acute respiratory syndrome. site-specific proteolysis plays a critical role in regulating a number of cellular and viral processes. since the main protease of scov, also termed 3c-like protease, is an attractive target for drug therapy, we have developed a safe, simple, and rapid genetic screen assay to monitor the activity of the scov 3c-like protease. this genetic system is based on the bacteriophage lambda regulatory circuit, in wh ...	2004	15564515
mammalian cell transduction and internalization properties of lambda phages displaying the full-length adenoviral penton base or its central domain.	in recent years a strong effort has been devoted to the search for new, safe and efficient gene therapy vectors. phage lambda is a promising backbone for the development of new vectors: its genome can host large inserts, dna is protected from degradation by the capsid and the ligand-exposed d and v proteins can be extensively modified. current phage-based vectors are inefficient and/or receptor-independent transducers. to produce new, receptor-selective and transduction-efficient vectors for mam ...	2004	15150649
strand invasion promoted by recombination protein beta of coliphage lambda.	studies of phage lambda in vivo have indicated that its own recombination enzymes, beta protein and lambda exonuclease, are capable of catalyzing two dissimilar pathways of homologous recombination that are widely distributed in nature: single-strand annealing and strand invasion. the former is an enzymatic splicing of overlapping ends of broken homologous dna molecules, whereas the latter is characterized by the formation of a three-stranded synaptic intermediate and subsequent strand exchange. ...	2004	15574500
a novel cell-free protein synthesis system.	an efficient cell-free protein synthesis system has been developed using a novel energy-regenerating source. using the new energy source, 3-phosphoglycerate (3-pga), protein synthesis continues beyond 2 h. in contrast, the reaction rate slowed down considerably within 30-45 min using a conventional energy source, phosphoenol pyruvate (pep) under identical reaction conditions. this improvement results in the production of twice the amount of protein obtained with pep as an energy source. we have ...	2004	15163516
unequal access of chromosomal regions to each other in salmonella: probing chromosome structure with phage lambda integrase-mediated long-range rearrangements.	we have investigated the fluidity of the salmonella chromosome architecture using the phage lambda site-specific recombination system as a probe. we determined how chromosome position affects the extent of integrase-mediated recombination between pairs of inversely oriented att sites at various loci. we also investigated the accessibility of each chromosomal att site to an extrachromosomal partner carried on a low-copy plasmid. recombination events were assayed by semi-quantitative polymerase ch ...	2004	15066024
crystal structure of a truncated version of the phage lambda protein gpd.		2004	15317025
internal control dna for pcr assays introduced into lambda phage particles exhibits nuclease resistance.		2004	15319317
expression, purification, crystallization, and nmr studies of the helicase interaction domain of escherichia coli dnag primase.	in escherichia coli, the dnag primase is the rna polymerase that synthesizes rna primers at replication forks. it is composed of three domains, a small n-terminal zinc-binding domain, a larger central domain responsible for rna synthesis, and a c-terminal domain comprising residues 434-581 [dnag(434-581)] that interact with the hexameric dnab helicase. presumably because of this interaction, it had not been possible previously to express the c-terminal domain in a stably transformed e. coli stra ...	2004	14711519
measurement of the phase diagram of dna unzipping in the temperature-force plane.	we separate double stranded lambda phage dna by applying a fixed force at a constant temperature ranging from 15 to 50 degrees c, and measure the minimum force required to separate the two strands. the measurements also offer information on the free energy of double stranded dna (dsdna) at temperatures where dsdna does not thermally denature in the absence of force. while parts of the phase diagram can be explained using existing models and free energy parameters, others deviate significantly. p ...	2004	15324279
inhibition of pcr amplification by phytic acid, and treatment of bovine fecal specimens with phytase to reduce inhibition.	development of effective polymerase chain reaction (pcr)-based diagnostic tests using ruminant fecal specimens has been thwarted by excessive inhibition. a pcr system based on amplification of 1000 copies of bacteriophage lambda-dna was used as a model to evaluate inhibition levels in bovine feces. dilution experiments using a bovine fecal specimen suggested that as little as 40 microg of feces (in a 100-microl pcr) affected the efficiency of amplification. it was discovered that phytic acid (th ...	2004	15325752
the sigma 70 subunit of rna polymerase mediates a promoter-proximal pause at the lac promoter.	the sigma(70) subunit of rna polymerase plays an essential role in transcription initiation. in addition, sigma(70) has a critical regulatory role during transcription elongation at the bacteriophage lambda late promoter, lambda p(r'). at this promoter, sigma(70) mediates a pause in early elongation through contact with a dna sequence element in the initially transcribed region that resembles a promoter -10 element. here we provide evidence that sigma(70) also mediates a pause in early elongatio ...	2004	15122345
riboflavin and uv-light based pathogen reduction: extent and consequence of dna damage at the molecular level.	we are developing a technology based on the combined application of riboflavin (rb) and light for inactivating pathogens in blood products while retaining the biological functions of the treated cells and proteins. virus and bacteria reduction measured by tissue culture infectivity or colony formation with uv light alone and in combination with rb yield equivalent results. the effects of rb as a sensitizing agent on dna in white cells, bacteria and viruses in combination with uv light exposure h ...	2004	15339215
a bayesian approach to dna sequence segmentation.	many deoxyribonucleic acid (dna) sequences display compositional heterogeneity in the form of segments of similar structure. this article describes a bayesian method that identifies such segments by using a markov chain governed by a hidden markov model. markov chain monte carlo (mcmc) techniques are employed to compute all posterior quantities of interest and, in particular, allow inferences to be made regarding the number of segment types and the order of markov dependence in the dna sequence. ...	2004	15339274
involvement of colicin in the limited protection of the colicin producing cells against bacteriophage.	the restriction/modification system is considered to be the most common machinery of microorganisms for protection against bacteriophage infection. however, we found that mitomycin c induced escherichia coli containing cole7-k317 can confer limited protection against bacteriophage m13k07 and lambda infection. our study showed that degree of protection is correlated with the expression level of the cole7 operon, indicating that colicin e7 alone or the colicin e7-immunity protein complex is direct ...	2004	15110756
pap: detection of ultra rare mutations depends on p* oligonucleotides: "sleeping beauties" awakened by the kiss of pyrophosphorolysis.	pyrophosphorolysis-activated polymerization (pap) was initially developed to enhance the specificity of allele-specific pcr for detection of known mutations in the presence of a great excess of wild-type allele. the high specificity of pap derives from the serial coupling of activation of a 3' blocked pyrophosphorolysis-activable oligonucleotide (p()) with extension of the unblocked, activated p(). in theory, pap can detect a copy of a single base mutation present in 3x10(11) copies of the wil ...	2004	15108273
complementation of an escherichia coli dnak defect by hsc70-dnak chimeric proteins.	escherichia coli dnak and rat hsc70 are members of the highly conserved 70-kda heat shock protein (hsp70) family that show strong sequence and structure similarities and comparable functional properties in terms of interactions with peptides and unfolded proteins and cooperation with cochaperones. we show here that, while the dnak protein is, as expected, able to complement an e. coli dnak mutant strain for growth at high temperatures and lambda phage propagation, hsc70 protein is not. however, ...	2004	15342595
modulation of dna repair and recombination by the bacteriophage lambda orf function in escherichia coli k-12.	the orf gene of bacteriophage lambda, fused to a promoter, was placed in the galk locus of escherichia coli k-12. orf was found to suppress the recombination deficiency and sensitivity to uv radiation of mutants, in a delta(recc ptr recb recd)::p(tac) gam bet exo pae ci deltarecg background, lacking recf, reco, recr, ruvab, and ruvc functions. it also suppressed defects of these mutants in establishing replication of a psc101-related plasmid. compared to orf, the reca803 allele had only small ef ...	2004	15090511
genetic immunisation against hepatitis b using whole bacteriophage lambda particles.	mice and rabbits have been vaccinated with whole bacteriophage lambda particles containing a dna vaccine expression cassette under the control of the cmv promoter (enhanced green fluorescent protein [lambda-egfp] or hepatitis b surface antigen [lambda-hbsag]). mice were vaccinated twice intramuscularly (i.m.) with 5x10(9) of lambda-egfp phage (containing 250 ng dna) and exhibited specific anti-egfp responses 28 days post-vaccination. rabbits were vaccinated i.m. with 4x10(10) of lambda-hbsag pha ...	2004	15068849
a lentiviral cdna library employing lambda recombination used to clone an inhibitor of human immunodeficiency virus type 1-induced cell death.	expression cloning technology of cdnas is a suitable tool for identifying novel functional properties of genes. here, we generated a lentiviral cdna library-expressing system for human t cells based on a site-specific recombination system of phage lambda for transferring cdna libraries with a minimum loss of its complexity. the library-transduced cd4(+) t cells were challenged with wild-type human immunodeficiency virus type 1 (hiv-1), and the cells that acquired resistance to hiv-1-induced cyto ...	2004	15452256
somatic gene targeting with rna/dna chimeric oligonucleotides: an analysis with a sensitive reporter mouse system.	targeted gene correction provides a potentially powerful method for gene therapy. rna/dna chimeric oligonucleotides were reported to be able to correct a point mutation with a high efficiency in cultured rodent cells, in the body of mice and rats, and in plants. the efficiency of correction in the liver of rats was claimed to be as high as 20% after tail-vein injection. however, several laboratories have failed to reproduce the high efficiency.	2004	15459966
crystal structure of the excisionase-dna complex from bacteriophage lambda.	the excisionase (xis) protein from bacteriophage lambda is the best characterized member of a large family of recombination directionality factors that control integrase-mediated dna rearrangements. it triggers phage excision by cooperatively binding to sites x1 and x2 within the phage, bending dna significantly and recruiting the phage-encoded integrase (int) protein to site p2. we have determined the co-crystal structure of xis with its x2 dna-binding site at 1.7a resolution. xis forms a uniqu ...	2004	15066428
initial cos cleavage of bacteriophage lambda concatemers requires proheads and gpfi in vivo.	the development of bacteriophage lambda and double-stranded dna viruses in general involves the convergence of two separate pathways: dna replication and head assembly. clearly, packaging will proceed only if an empty capsid shell, the prohead, is present to receive the dna, but genetic evidence suggests that proheads play another role in the packaging process. for example, lambda phages with an amber mutation in any head gene or in fi, the gene encoding the accessory packaging protein gpfi, are ...	2004	15066036
pressure inactivation kinetics of phage lambda ci 857.	inactivation curves of phage lambda ci 857 inactivated by high hydrostatic pressure were obtained at three pressure levels (300, 350, and 400 mpa) in buffered media and ultrahigh-temperature 2% reduced fat milk. pressurization of phage lambda in buffered media at 300 mpa for 300 min, 350 mpa for 36 min, and 400 mpa for 8 min reduced the titer of phage lambda by 7.5, 6.7, and 7.7 log, respectively. pressurization of phage lambda in milk at 300 mpa for 400 min, 350 mpa for 80 min, and 400 mpa for ...	2004	15035365
conserved translational frameshift in dsdna bacteriophage tail assembly genes.	a programmed translational frameshift similar to frameshifts in retroviral gag-pol genes and bacterial insertion elements was found to be strongly conserved in tail assembly genes of dsdna phages and to be independent of sequence similarities. in bacteriophage lambda, this frameshift controls production of two proteins with overlapping sequences, gpg and gpgt, that are required for tail assembly. we developed bioinformatic approaches to identify analogous -1 frameshifting sites and experimentall ...	2004	15469818
bistability and switching in the lysis/lysogeny genetic regulatory network of bacteriophage lambda.	bistability and switching are two important aspects of the genetic regulatory network of lambda phage. positive and negative feedbacks are key regulatory mechanisms in this network. by the introduction of threshold values, the developmental pathway of lambda phage is divided into different stages. if the protein level reaches a threshold value, positive or negative feedback will be effective and regulate the process of development. using this regulatory mechanism, we present a quantitative model ...	2004	14990387
identification and mapping of self-assembling protein domains encoded by the escherichia coli k-12 genome by use of lambda repressor fusions.	self-assembling proteins and protein fragments encoded by the escherichia coli genome were identified from e. coli k-12 strain mg1655. libraries of random dna fragments cloned into a series of lambda repressor fusion vectors were subjected to selection for immunity to infection by phage lambda. survivors were identified by sequencing the ends of the inserts, and the fused protein sequence was inferred from the known genomic sequence. four hundred sixty-three nonredundant open reading frame-encod ...	2004	14973045
gene order and dynamic domains.	when considering the daunting complexity of eukaryotic genomes, some comfort can be found in the fact that the human genome may contain only 30,000 to 40,000 genes. moreover, growing evidence suggests that genomes may be organized in such a way as to take advantage of space. a gene's location in the linear dna sequence and its position in the three-dimensional nucleus can both be important in its regulation. contrary to prevailing notions in this postgenomic era, the bacteriophage lambda, a para ...	2004	15499009