Publications

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
selection-subtraction approach (ssa): a universal genetic screening technique that enables negative selection.	screening of expression libraries for bioactive clones that modulate the growth of mammalian cells has been limited largely to positive selections incapable of revealing growth suppressive or lethal genetic elements. we have developed a technique, selection-subtraction approach (ssa), that allows growth-modulating clones to be isolated based on alterations in their relative abundance in growing cell populations that have been transduced with an expression library. ssa utilizes tagged retroviral ...	2004	15187233
identification and characterization of outer membrane proteins g1a and g1b of moraxella catarrhalis.	moraxella catarrhalis is an important cause of otitis media, sinusitis, and lower respiratory tract infections in patients with chronic obstructive pulmonary disease. the purified outer membrane of m. catarrhalis contains a 29 kda band, previously named outer membrane protein g1 (omp g1). polyclonal antiserum to the omp g1 band was used to screen a genomic lambda phage library and the gene for omp g1a was cloned and sequenced. analysis of outer membrane by isoelectric focusing and amino-terminal ...	2004	15193378
bacteriophage lambda is a highly stable dna vaccine delivery vehicle.	the stability of whole bacteriophage lambda particles, used as a dna vaccine delivery system has been examined. phage were found to be highly stable under normal storage conditions. in liquid suspension, no decrease in titre was observed over a 6-month period at 4 and -70 degrees c, and phage stability was unaffected by freeze/thawing. the measured half life of phage in suspension was 36 days at 20 degrees c, 3.4 days at 37 degrees c and 2.3 days at 42 degrees c. freeze drying of a phage suspens ...	2004	15193403
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
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
holliday junction binding and resolution by the rap structure-specific endonuclease of phage lambda.	rap endonuclease targets recombinant joint molecules arising from phage lambda red-mediated genetic exchange. previous studies revealed that rap nicks dna at the branch point of synthetic holliday junctions and other dna structures with a branched component. however, on x junctions incorporating a three base-pair core of homology or with a fixed crossover, rap failed to make the bilateral strand cleavages characteristic of a holliday junction resolvase. here, we demonstrate that rap can mediate ...	2004	15223317
quantitative microfluidic separation of dna in self-assembled magnetic matrixes.	we present an experimental study of the microfluidic electrophoresis of long dna in self-assembling matrixes of magnetic bead columns. results are presented for the rapid separation of lambda-phage, 2lambda-dna, and bacteriophage t4 dna, where separation resolutions greater than 2 between lambda and t4 are achieved in times as short as 150 s. the use of a computer-piloted flow control system and injection results in high reproducibility between separations. we compare the experimentally measured ...	2004	15228353
p2 growth restriction on an rpoc mutant is suppressed by alleles of the rz1 homolog lysc.	escherichia coli strain 397c carries a temperature-sensitive mutation, rpoc397, that removes the last 50 amino acids of the rna polymerase beta' subunit and is nonpermissive for plating of bacteriophage p2. p2 gor mutants productively infect 397c and define a new gene, lysc, encoded by a reading frame that extensively overlaps the p2 lysis accessory gene, lysb. the unusual location of lysc with respect to lysb is reminiscent of the rz/rz1 lysis gene pair of phage lambda. indeed, coexpression of ...	2004	15231796
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
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
genotoxicity of acrylamide and glycidamide.	acrylamide, a known rodent carcinogen, is found in the human diet. however, the mechanism by which acrylamide exerts its carcinogenic effects remains unclear.	2004	15240786
translation repression by an rna polymerase elongation complex.	bacteriophage lambda n and bacterial nus proteins together with a unique site nut in the leader of the early viral n gene transcript bind rna polymerase (rnap) and form a highly processive antitermination complex; n bound at nut also represses n translation. in this study, we investigate whether n and nut cause n translation repression as part of the antitermination complex by testing conditions that inhibit the formation of the n-modified transcription complex for their effect on n-mediated tra ...	2004	15255895
a fragile lattice: replacing bacteriophage lambda's head stability gene d with the shp gene of phage 21 generates the mg2+-dependent virus, lambda shp.	phage lambda dna packaging is accompanied by prohead expansion, due to structural changes in gpe, the major capsid protein. rearrangement of the gpe lattice creates binding sites for trimers of gpd, the head stabilization protein. lambda-like phage 21's shp gene is homologous to lambda's d gene. gpd and gpshp share 49% amino acid identity. to ask whether gpshp could stabilize the lambda head shell, we replaced lambda's d gene with shp, creating lambda shp. unlike lambda or 21, lambda shp was str ...	2004	15262493
cloning and sequence analysis of the glyceraldehyde-3-phosphate dehydrogenase gene from the zygomycetes fungus rhizomucor miehei.	rhizomucor miehei is important from a biotechnological aspect in consequence of its content of aspartic proteinase, which has high milk-clotting activity. a genomic library of r. miehei nrrl 5901 has been constructed in a phage (lambda fix ii) vector. the glyceraldehyde-3-phosphate dehydrogenase (gpd) gene was isolated from this library by hybridization of the recombinant phage clones with a gpd-specific gene probe generated by polymerase chain reaction. the complete nucleotide sequence encodes ...	2004	15280645
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
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
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
on the role of cro in lambda prophage induction.	the lysogenic state of bacteriophage lambda is exceptionally stable yet the prophage is readily induced in response to dna damage. this delicate epigenetic switch is believed to be regulated by two proteins; the lysogenic maintenance promoting protein ci and the early lytic protein cro. first, we confirm, in the native configuration, the previous observation that the dna loop mediated by oligomerization of ci bound to two distinct operator regions (o(l) and o(r)), increases repression of the ear ...	2005	15728734
rapid method for the construction of salmonella enterica serovar typhimurium vaccine carrier strains.	salmonella enterica serovar typhimurium is a versatile organism for the generation of live recombinant vaccines for mucosal immunization. various strategies have been devised for the stable and efficient expression of heterologous antigens by attenuated s. enterica strains, but these methods often require complex manipulations. use of phage lambda red recombinase has recently been devised for gene replacements in escherichia coli and s. enterica after introduction of pcr products. based on this ...	2005	15731059
a multipurpose vector system for the screening of libraries in bacteria, insect and mammalian cells and expression in vivo.	we have constructed a novel tetra-promoter vector (pbvboostfg) system that enables screening of gene/cdna libraries for functional genomic studies. the vector enables an all-in-one strategy for gene expression in mammalian, bacterial and insect cells and is also suitable for direct use in vivo. virus preparation is based on an improved mini tn7 transpositional system allowing easy and fast production of recombinant baculoviruses with high diversity and negligible background. cloning of the desir ...	2005	15731335
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
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
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
comparative analysis of selected genes from diachasmimorpha longicaudata entomopoxvirus and other poxviruses.	the diachasmimorpha longicaudata entomopoxvirus (dlepv) is the first symbiotic epv described from a parasitic wasp. the dlepv is introduced into the tephritid fruit fly larval host along with the wasp egg at oviposition. we sequenced a shotgun genomic library of the dlepv dna and analyzed and compared the predicted protein sequences of eight orfs with those of selected poxviruses and other organisms. blastp searches showed that five of these are homologous to poxvirus putative proteins such as m ...	2005	15749105
high-resolution physical mapping of the secalin-1 locus of rye on extended dna fibers.	high-resolution mapping of secalin-1 (sec-1) locus has been performed by fluorescence in situ hybridization to extended dna fibers of rye (secale cereale, 2n = 14), employing dna probes of lambda phage clones containing the omega-secalin gene. the fluorescent signals to rye extended dna fibers revealed continuous strings of 45 microm, corresponding to the size of 147 kb dna. to determine the copy number of sec-1 locus on dna fibers, a 1.2-kb fragment including the entire coding region of the ome ...	2005	15753562
construction and characterization of a cdna library from human liver tissue with chronic hepatitis b.	to construct a cdna library from human liver tissue with chronic hepatitis b and check its quality for investigating the expression level of liver tissue infected by hepatitis b virus. this will then be used to find the relevant genes and interesting proteins associated with the development of hepatitis b.	2005	15754427
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
engineering of a vaccinia virus bacterial artificial chromosome in escherichia coli by bacteriophage lambda-based recombination.	the large capacity of vaccinia virus (vac) for added dna, cytoplasmic expression and broad host range make it a popular choice for gene delivery, despite the burdensome need for multiple plaque purifications to isolate recombinants. here we describe how a bacterial artificial chromosome (bac) containing the entire vac genome can be engineered in escherichia coli by homologous recombination using bacteriophage lambda-encoded enzymes. the engineered vac genomes can then be used to produce clonally ...	2005	15782205
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
copper increases the damage to dna and proteins caused by reactive oxygen species.	copper [cu(ii)] is an ubiquitous transition and trace element in living organisms. it increases reactive oxygen species (ros) and free-radical generation that might damage biomolecules like dna, proteins, and lipids. furthermore, ability of cu(ii) greatly increases in the presence of oxidants. ros, like hydroxyl (.oh) and superoxide (.o(2)) radicals, alter both the structure of the dna double helix and the nitrogen bases, resulting in mutations like the at-->gc and gc-->at transitions. proteins, ...	2005	15784956
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
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
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
[construction and characterization of a cdna library from human liver tissue of cirrhosis].	to construct a cdna library from human liver tissue of cirrhosis.	2005	15812880
effective breakage of phage lambda dna by shearing with ceramic-coated needle of syringe.	the loss of biological activity of phage lambda dna was much greater when the dna was sheared using a ceramic-coated needle attached to a syringe compared with a conventional stainless steel needle. inactivation of the biological activity was due to breakage at the middle of the molecule. the thickness of the ceramic-coating was a crucial factor for the breakage. because approximately the same level of inactivation was observed with a non-coated needle as with thin glass and quartz tubes, it was ...	2005	15824459
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
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
single-particle visualization of assembly: i. dimerization in a planar zone.	summary single-particle fluorescence microscopy of association/dissociation is required for analysis of biological assembly reactions. toward achieving this goal, wang et al. (j. microsc., 2004, 213, 101-109) used molten agarose to concentrate thermally diffusing particles in a thin zone of solution next to the surface of a coverglass (plane of concentration). the present study details the first real-time, single-particle analysis of the association/dissociation of thermally diffusing particles ...	2005	15655066
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
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
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
identification of tumor-associated autoantigens with serex.	serological analysis of tumor antigens by recombinant cdna expression cloning (serex) allows the systematic cloning of tumor antigens recognized by the spontaneous autoantibody repertoire of cancer patients. for serex, cdna expression libraries are constructed from fresh tumor specimens, packaged into lambda-phage vectors, and expressed recombinantly in escherichia coli. recombinant proteins expressed during the lytic infection of bacteria are transferred onto nitrocellulose membranes to be prob ...	2005	15585919
purification, cloning, and properties of alpha-galactosidase from saccharopolyspora erythraea and its use as a reporter system.	an alpha-galactosidase from the erythromycin-producing bacterium saccharopolyspora erythraea was purified to near homogeneity. the enzyme has an apparent molecular mass of 45 kda as determined by sds-page. the ph optimum, k(m) for p-nitrophenyl-alpha-d: -glucopyranoside (pnpalphag), k(m) for melibiose and the v(max) are similar to those of other studied alpha-galactosidase enzymes. the n-terminal amino-acid sequence of this protein was determined. pcr amplification was used to generate a 640-bp ...	2005	15538554
measurements of dna lengths remaining in a viral capsid after osmotically suppressed partial ejection.	the effect of external osmotic pressure on the extent of dna ejection from bacteriophage-lambda was recently investigated (evilevitch et al., 2003). the total length of dna ejected was measured via the 260-nm absorption by free nucleotides, after opening of the capsids in the presence of varying amounts of polyethylene glycol 8000 and dnase i. as a function of osmolyte concentration, this absorption was shown to decrease progressively, ultimately vanishing completely for a sufficiently high exte ...	2005	15489301
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
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
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
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
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
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
a quantitative description of the binding states and in vitro function of antitermination protein n of bacteriophage lambda.	the n protein of bacteriophage lambda activates transcription of genes that lie downstream of termination sequences by suppressing transcription termination. n binds to specific (boxb) and non-specific sites on the transcript rna and contacts rna polymerase via cis-rna looping, resulting in "antitermination" of transcription. to find the effect of n-boxb binding on antitermination, we quantitatively relate binding measurements made in isolation to in vitro antitermination activity. we measure bi ...	2005	15854643
[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
holliday junction-binding peptides inhibit distinct junction-processing enzymes.	holliday junctions (hj) are the central intermediates in both homologous recombination and site-specific recombination performed by tyrosine recombinases such as the bacteriophage lambda integrase (int) protein. previously, our lab identified peptide inhibitors of int-mediated recombination that prevent the resolution of hj intermediates. we now show that two of these inhibitors bind hj dna in the square-planar conformation even in the absence of int protein. the peptides prevent unwinding of br ...	2005	15867153
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
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
low energy cd of rna hairpin unveils a loop conformation required for lambdan antitermination activity.	n protein coded by phage lambda is a transcription factor that stimulates the antitermination activity of escherichia coli rna polymerase by binding specifically to the nascent rna transcript at a stemloop structure called boxb. we use a new biophysical technique, involving the monitoring of the low energy circular dichroism spectra of 2-aminopurine residues site-specifically placed in the boxb rna loop, to investigate this binding interaction. the low energy cd spectra of these 2-aminopurine pr ...	2005	16033760
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
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
a new plasmid vector for regulated gene expression in bacillus subtilis.	we have developed a novel regulated expression vector for bacillus subtilis based on the staphylococcus aureus plasmid pub110. this vector, named ppr54, carries the p(r) promoter and the ci857 gene (encoding a temperature-sensitive transcriptional repressor) from the escherichia coli phage lambda. using the gfp gene from the jellyfish aequorea victoria as a reporter, we show that ppr54 is a useful vector for controllable production of heterologous proteins in b. subtilis.	2005	15941587
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
involvement of cellular death signals in the reactivation of herpes simplex virus type 1 and lambda bacteriophage from a latent state.	herpes simplex virus (hsv) 1 has adapted to the human host through two modes of infection, the acute-transient infection that may cause diseases (such as encephalitis) and the latent state, which is a source for recurrent infection and disease. while much information has been gathered on the cellular and molecular concomitants of establishment and maintenance of hsv-1 latent state, the biological basis of viral reactivation is still unclear. despite their obvious differences, hsv-1 and the bacte ...	2005	15967186
a structural basis for allosteric control of dna recombination by lambda integrase.	site-specific dna recombination is important for basic cellular functions including viral integration, control of gene expression, production of genetic diversity and segregation of newly replicated chromosomes, and is used by bacteriophage lambda to integrate or excise its genome into and out of the host chromosome. lambda recombination is carried out by the bacteriophage-encoded integrase protein (lambda-int) together with accessory dna sites and associated bending proteins that allow regulati ...	2005	15973401
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 e. coli nusa carboxy-terminal domains are structurally similar and show specific rnap- and lambdan interaction.	the carboxy-terminal domain of the transcription factor escherichia coli nusa, nusactd, interacts with the protein n of bacteriophage lambda, lambdan, and the carboxyl terminus of the e. coli rna polymerase alpha subunit, alphactd. we solved the solution structure of the unbound nusactd with high-resolution nuclear magnetic resonance (nmr). additionally, we investigated the binding sites of lambdan and alphactd on nusactd using nmr titrations. the solution structure of nusactd shows two structur ...	2005	15987884
single-molecule studies of repressor-dna interactions show long-range interactions.	we have performed single-molecule studies of gfp-laci repressor proteins bound to bacteriophage lambda dna containing a 256 tandem lac operator insertion confined in nanochannels. an integrated photon molecular counting method was developed to determine the number of proteins bound to dna. by using this method, we determined the saturated mean occupancy of the 256 tandem lac operators to be 13, which constitutes only 2.5% of the available sites. this low occupancy level suggests that the repress ...	2005	15994229
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