Publications

sequential peptide affinity purification system for the systematic isolation and identification of protein complexes from escherichia coli.	biochemical purification of affinity-tagged proteins in combination with mass spectrometry methods is increasingly seen as a cornerstone of systems biology, as it allows for the systematic genome-scale characterization of macromolecular protein complexes, representing demarcated sets of stably interacting protein partners. accurate and sensitive identification of both the specific and shared polypeptide components of distinct complexes requires purification to near homogeneity. to this end, a se ...	2009	19544035
stochastic gene expression as a molecular switch for viral latency.	stochastic 'noise' arises from random thermal fluctuations in the concentration of protein, rna, or other molecules within the cell and is an unavoidable aspect of life at the single-cell level. evidence is accumulating that this biochemical noise crucially influences cellular auto-regulatory circuits and can 'flip' genetic switches to drive probabilistic fate decisions in bacteria, viruses, cancer, and stem cells. here, we review how stochastic gene expression in key auto-regulatory proteins ca ...	2009	19595626
epistasis among deleterious mutations in the hiv-1 protease.	a central goal in molecular evolution is to understand how genetic interactions between protein mutations shape protein function and fitness. while intergenic epistasis has been extensively explored in eukaryotes, bacteria, and viruses, intragenic epistatic interactions have been insufficiently studied. here, we employ a model system in which lambda phage fitness correlates with the enzymatic activity of human immunodeficiency virus type 1 (hiv-1) protease to systematically determine the epistat ...	2009	19607838
quantitative characterization of quantum dot-labeled lambda phage for escherichia coli detection.	we characterize cdse/zns quantum dot (qd) binding to genetically modified bacteriophage as a model for bacterial detection. interactions among qds, lambda (lambda) phage, and escherichia coli are examined by several cross-validated methods. flow and image-based cytometry clarify fluorescent labeling of bacteria, with image-based cytometry additionally reporting the number of decorated phage bound to cells. transmission electron microscopy, image-based cytometry, and electrospray differential mob ...	2009	19634184
dynamics of individual polymers using microfluidic based microcurvilinear flow.	polymer dynamics play an important role in a diversity of fields including materials science, physics, biology and medicine. the spatiotemporal responses of individual molecules such as biopolymers have been critical to the development of new materials, the expanded understanding of cell structures including cytoskeletal dynamics, and dna replication. the ability to probe single molecule dynamics however is often limited by the availability of small-scale technologies that can manipulate these s ...	2009	19636465
staphylococcus aureus sara is a regulatory protein responsive to redox and ph that can support bacteriophage lambda integrase-mediated excision/recombination.	staphylococcus aureus produces a wide array of virulence factors and causes a correspondingly diverse array of infections. production of these virulence factors is under the control of a complex network of global regulatory elements, one of which is sara. sara encodes a dna binding protein that is considered to function as a transcription factor capable of acting as either a repressor or an activator. using competitive elisa assays, we demonstrate that sara is present at approximately 50 000 cop ...	2009	19919677
screening by imaging: scaling up single-dna-molecule analysis with a novel parabolic va-tirf reflector and noise-reduction techniques.	bacteriophage lambda-dna molecules are frequently used as a scaffold to characterize the action of single proteins unwinding, translocating, digesting or repairing dna. however, scaling up such single-dna-molecule experiments under identical conditions to attain statistically relevant sample sizes remains challenging. additionally the movies obtained are frequently noisy and difficult to analyse with any precision. we address these two problems here using, firstly, a novel variable-angle total i ...	2009	19950511
mobile antibiotic resistance encoding elements promote their own diversity.	integrating conjugative elements (ices) are a class of bacterial mobile genetic elements that disseminate via conjugation and then integrate into the host cell genome. the sxt/r391 family of ices consists of more than 30 different elements that all share the same integration site in the host chromosome but often encode distinct properties. these elements contribute to the spread of antibiotic resistance genes in several gram-negative bacteria including vibrio cholerae, the agent of cholera. here ...	2009	20019796
nuclease-resistant double-stranded dna controls or standards for hepatitis b virus nucleic acid amplification assays.	identical blood samples tested using different kits can give markedly different hepatitis b virus (hbv) dna levels, which can cause difficulty in the interpretation of viral load. a universal double-stranded dna control or standard that can be used in all commercial hbv dna nucleic acid amplification assay kits is urgently needed. by aligning all hbv genotypes (a-h), we found that the surface antigen gene and precore-core gene regions of hbv are the most conserved regions among the different hbv ...	2009	20025781
design and characterization of a three-terminal transcriptional device through polymerase per second.	in this paper, we provide an in silico input-output characterization of a three-terminal transcriptional device employing polymerase per second (pops) as input and output. the device is assembled from well-characterized parts of the bacteriophage lambda switch transcriptional circuit. we draw the analogy between voltage and protein concentration and between current and pops to demonstrate that the characteristics of the three-terminal transcriptional device are qualitatively similar to those of ...	2009	20051340
enzymatic synthesis of multi-milligram quantities of large, linear dna molecules for structural studies.	structural analyses of large protein-dna complexes (such as those associated with replication initiation, eukaryotic transcription activation or chromatin remodeling, among others) remain a challenge because of difficulties in obtaining multi-milligram quantities of high-quality preparations of large, linear dna molecules. this protocol describes a three-stage dna amplification procedure for making such molecules in amounts that are suitable for structural studies. in the first step, conventiona ...	2009	20147140
quantitative transcription factor binding kinetics at the single-molecule level.	we investigated the binding interaction between the bacteriophage lambda-repressor ci and its target dna using total internal reflection fluorescence microscopy. large stepwise changes in the intensity of the red fluorescent protein fused to ci were observed as it associated with and dissociated from individually labeled single-molecule dna targets. the stochastic association and dissociation were characterized by poisson statistics. dark and bright intervals were measured for thousands of indiv ...	2009	19167308
genotoxicity of agricultural soils in the vicinity of industrial area.	soil samples from agricultural fields (cultivated) in the vicinity of industrial area of ghaziabad city (india) were collected. in this city, wastewater coming from both industrial and domestic sources and without any treatment is used to irrigate the food crops. this practice has been polluting the soil and pollutants might reach the food chain. gas chromatographic analysis show the presence of certain organochlorine (dde, ddt, dieldrin, aldrin and endosulfan) and organophosphorus (dimethoate, ...	2009	19167512
mutational analysis and homology-based modeling of the intdot core-binding domain.	tyrosine recombinases mediate a wide range of important genetic rearrangement reactions. models for tyrosine recombinases have been based largely on work done on the integrase of phage lambda and recombinases like cre, flp, and xerc/d. all of these recombinases share a common amino acid signature that is important for catalysis. several conjugative transposons (ctns) encode recombinases that are also members of the tyrosine recombinase family, but the reaction that they catalyze differs in that ...	2009	19168607
effect of late promoter activity on bacteriophage lambda fitness.	for many bacteriophages (phages), the proteins responsible for host lysis and virion morphogenesis are expressed from the same polycistronic transcript. such an expression pattern can potentially have a pleiotropic effect on the assembly rate and lysis time, thus affecting phage fitness. to study the effects of late promoter activity on phage life history traits and fitness, we constructed a series of isogenic phage lambda strains that differ only in their late promoter pr' sequences. the result ...	2009	19171945
the bacteriophage lambda ci protein finds an asymmetric solution.	the ci protein of bacteriophage lambda (lambdaci) is both a repressor and activator of transcription that has served as a model for understanding how gene regulatory proteins work. a dimeric dna-binding protein, lambdaci also forms higher-order oligomers that allow it to bind cooperatively to both adjacent and nonadjacent operator sites within the phage genome. the ability of phage lambda to transition efficiently from one program of gene expression to another depends upon the formation of these ...	2009	19181516
peptide wrwycr inhibits the excision of several prophages and traps holliday junctions inside bacteria.	peptide inhibitors of phage lambda site-specific recombination were previously isolated by screening synthetic combinatorial peptide libraries. these inhibitors cause the accumulation of complexes between the recombinase and the holliday junction intermediate of several highly divergent tyrosine recombinases. peptide wrwycr and its d-amino acid derivative bind to the center of protein-free junctions and prevent their resolution either by site-specific recombinases or by junction resolvases or he ...	2009	19181810
properties of hflx, an enigmatic protein from escherichia coli.	the escherichia coli gene hflx was first identified as part of the hfla operon, mutations in which led to an increased frequency of lysogenization upon infection of the bacterium by the temperate coliphage lambda. independent mutational studies have also indicated that the hflx protein has a role in transposition. based on the sequence of its gene, hflx is predicted to be a gtp-binding protein, very likely a gtpase. we report here purification and characterization of the hflx protein. we also sp ...	2009	19181811
generation of vibrio anguillarum ghost by coexpression of phix 174 lysis e gene and staphylococcal nuclease a gene.	vibrio anguillarum ghosts (vag) were generated, for the first time, using a conjugation vector containing a ghost bacteria inducing cassette, prk-lambdap(r)-ci-elysis, in which the expression of phix174 lysis gene e was controlled by the p ( r )/ci regulatory system of lambda phage. by scanning electron microscopy, holes ranging 80-200 nm in diameter were observed in the vag. to avoid the presence of bacterial genomic dna and an antibiotic resistance gene in the final vag product, we constructed ...	2009	19191038
naturally occurring and disease-associated auto-antibodies against topoisomerase i: a fine epitope mapping study in systemic sclerosis and systemic lupus erythematosus.	auto-antibodies against topoisomerase i (topo i) are frequently detected in sera of systemic sclerosis (ssc) patients. anti-topo i auto-antibodies are considered to be associated with the diffuse cutaneous form of systemic sclerosis (dcssc). however, anti-topo i auto-antibodies are also detected in limited cutaneous systemic sclerosis (lcssc) and systemic lupus erythematosus (sle). in this study, we compared the epitope specificity of anti-topo i auto-antibodies present in sera of dcssc, lcssc a ...	2009	19211583
molecular cloning of the phospholipase d gene from streptomyces sp. yu100 and its expression in escherichia coli.	the gene for phospholipase d (pld) of streptomyces sp. yu100 was cloned from lambda phage library and heterologously expressed in escherichia coli. using an amplified gene fragment based on the consensus sequences of streptomycetes plds, lambda phage library of streptomyces sp. yu100 chromosomal dna was screened. the sequencing result of bamhi-digested 3.8 kb fragment in a positive phage clone revealed the presence of an open reading frame of a full sequence of pld gene encoding a 540-amino acid ...	2009	19229499
global view of bionetwork dynamics: adaptive landscape.	based on recent work, i will give a nontechnical brief review of a powerful quantitative concept in biology, adaptive landscape, initially proposed by s. wright over 70 years ago, reintroduced by one of the founders of molecular biology and by others in different biological contexts, but apparently forgotten by modern biologists for many years. nevertheless, this concept finds an increasingly important role in the development of systems biology and bionetwork dynamics modeling, from phage lambda ...	2009	19232305
expansion of a chromosomal repeat in escherichia coli: roles of replication, repair, and recombination functions.	previous studies of gene amplification in escherichia coli have suggested that it occurs in two steps: duplication and expansion. expansion is thought to result from homologous recombination between the repeated segments created by duplication. to explore the mechanism of expansion, a 7 kbp duplication in the chromosome containing a leaky mutant version of the lac operon was constructed, and its expansion into an amplified array was studied.	2009	19236706
the phage lambda major tail protein structure reveals a common evolution for long-tailed phages and the type vi bacterial secretion system.	most bacteriophages possess long tails, which serve as the conduit for genome delivery. we report the solution structure of the n-terminal domain of gpv, the protein comprising the major portion of the noncontractile phage lambda tail tube. this structure is very similar to a previously solved tail tube protein from a contractile-tailed phage, providing the first direct evidence of an evolutionary connection between these 2 distinct types of phage tails. a remarkable structural similarity is als ...	2009	19251647
h1 histone modulates dna hydrolysis with wen1 and wen2 endonucleases from wheat coleoptiles.	we show that total h1 histone from wheat seedlings or rat liver enhances hydrolysis of lambda phage dna with plant endonucleases wen1 and wen2 isolated from wheat coleoptiles. optimal dna/protein weight ratio in the hydrolysis reaction is 1 : 1. the action of fractions i and iv (obtained from total wheat h1 histone by electrophoresis) on dna hydrolysis with wen1 and wen2 enzymes depends on the dna methylation status. fraction iv of wheat histone h1 stimulates hydrolysis of unmethylated lambda ph ...	2009	19267669
dynamics and stability of individual base pairs in two homologous rna-dna hybrids.	nuclear magnetic resonance spectroscopy and proton exchange have been used to characterize two rna-dna hybrids from the tr2 intrinsic transcription terminator site of phage lambda. the hybrids have the same base sequence [5'-ggcgcaggcc(t/u)(t/u)cc-3'/5'-ggaaggcc(t/u)gcgcc-3'] but differ from each other by an interchange of dna and rna strands. the opening of single base pairs in the two hybrids is characterized by measuring the rates of exchange of imino protons with solvent protons as a functio ...	2009	19296713
simply and reliably integrating micro heaters/sensors in a monolithic pcr-ce microfluidic genetic analysis system.	a novel fabrication process was presented to construct a monolithic integrated pcr-ce microfluidic dna analysis system as a step toward building a total genetic analysis microsystem. microfabricated titanium/platinum (ti/pt) heaters and resistance temperature detectors (rtds) were integrated on the backside of a bonded glass chip to provide good thermal transfer and precise temperature detection for the drilled pcr-wells. this heater/rtd integration procedure was simple and reliable, and the res ...	2009	19319907
reversible transformation between rings and coils in a dynamic hydrogen-bonded self-assembly.	several proteins, such as tobacco mosaic virus coat protein and the beta protein of the bacteriophage lambda, are known to exhibit unique dynamic self-organization processes involving ring-shaped and extended helical nanostructures triggered by chemical stimuli. however, transformation of rings into coils as observed in biological assemblies has never been realized with synthetic molecular building blocks. oligo(p-phenylenevinylene) functionalized on one end with barbituric acid and on the other ...	2009	19323464
nmr structure of the amino-terminal domain of the lambda integrase protein in complex with dna: immobilization of a flexible tail facilitates beta-sheet recognition of the major groove.	the integrase protein (int) from bacteriophage lambda is the archetypal member of the tyrosine recombinase family, a large group of enzymes that rearrange dna in all domains of life. int catalyzes the insertion and excision of the viral genome into and out of the escherichia coli chromosome. recombination transpires within higher-order nucleoprotein complexes that form when its amino-terminal domain binds to arm-type dna sequences that are located distal to the site of strand exchange. arm-site ...	2009	19324050
production of double-stranded rna for interference with tmv infection utilizing a bacterial prokaryotic expression system.	in many species, the introduction of double-stranded rna (dsrna) induces potent and specific gene silencing, a phenomenon called rna interference (rnai). rnai is the process of sequence-specific, posttranscriptional gene silencing (ptgs) in animals and plants, mediated by dsrna homologous to the silenced genes. in plants, ptgs is part of a defense mechanism against virus infection, and dsrna is the pivotal factor that induces gene silencing. here, we report an efficient method that can produce d ...	2009	19330324
inefficient quality control of thermosensitive proteins on the plasma membrane.	misfolded proteins are generally recognised by cellular quality control machinery, which typically results in their ubiquitination and degradation. for soluble cytoplasmic proteins, degradation is mediated by the proteasome. membrane proteins that fail to fold correctly are subject to er associated degradation (erad), which involves their extraction from the membrane and subsequent proteasome-dependent destruction. proteins with abnormal transmembrane domains can also be recognised in the golgi ...	2009	19337370
gene and epigene networks: two levels in organizing the hereditary system.	intracellular governing gene networks consisting of genes and regulatory bonds among them are considered as the first level in organizing the hereditary system. we give examples of both prokaryotic gene network that controls the development of the lambda-phage and eukaryotic gene network that controls the early drosophila ontogenesis. using the method of generalized threshold models kinetic curves are shown for some gene products of these networks. gene networks that govern ontogenetic processes ...	2009	19358855
guidance for data collection and computational modelling of regulatory networks.	many model regulatory networks are approaching the depth of characterisation of bacteriophage lambda, wherein the vast majority of individual components and interactions are identified, and research can focus on understanding whole network function and the role of interactions within that broader context. in recent years, the study of the system-wide behaviour of phage lambda's genetic regulatory network has been greatly assisted by the combination of quantitative measurements with theoretical a ...	2009	19381541
dna looping provides stability and robustness to the bacteriophage lambda switch.	the bistable gene regulatory switch controlling the transition from lysogeny to lysis in bacteriophage lambda presents a unique challenge to quantitative modeling. despite extensive characterization of this regulatory network, the origin of the extreme stability of the lysogenic state remains unclear. we have constructed a stochastic model for this switch. using forward flux sampling simulations, we show that this model predicts an extremely low rate of spontaneous prophage induction in a reca m ...	2009	19416825
the x-ray crystal structure of the phage lambda tail terminator protein reveals the biologically relevant hexameric ring structure and demonstrates a conserved mechanism of tail termination among diverse long-tailed phages.	the tail terminator protein (trp) plays an essential role in phage tail assembly by capping the rapidly polymerizing tail once it has reached its requisite length and serving as the interaction surface for phage heads. here, we present the 2.7-a crystal structure of a hexameric ring of gpu, the trp of phage lambda. using sequence alignment analysis and site-directed mutagenesis, we have shown that this multimeric structure is biologically relevant and we have delineated its functional surfaces. ...	2009	19426744
regulation of clpqy (hslvu) gene expression in escherichia coli.	the escherichia coli clpyq (hsluv) complex is an atp-dependent protease, and the clpq(+)y(+) (hslv(+)u(+)) operon encodes two heat shock proteins, clpq and clpy, respectively. the transcriptional (op) or translational (pr) clpq(+)::lacz fusion gene was constructed, with the clpq(+)y(+) promoter fused to a lacz reporter gene. the clpq(+)::lacz (op or pr) fusion gene was each crossed into lambda phage. the lambdaclpq(+)::lacz(+) (op), a transcriptional fusion gene, was used to form lysogens in the ...	2009	19440251
host-parasite relations of bacteria and phages can be unveiled by oligostickiness, a measure of relaxed sequence similarity.	motivation: the recent metagenome analysis has been producing a large number of host-unassigned viruses. although assigning viruses to their hosts is basically important not only for virology but also for prevention of epidemic, it has been a laborious and difficult task to date. the only effective method for this purpose has been to find them in a same microscopic view. now, we tried a computational approach based on genome sequences of bacteria and phages, introducing a physicochemical paramet ...	2009	19126576
microbial conversion of glycerol to 1,3-propanediol by an engineered strain of escherichia coli.	in an effort to improve industrial production of 1,3-propanediol (1,3-pd), we engineered a novel polycistronic operon under the control of the temperature-sensitive lambda phage p(l)p(r) promoter regulated by the cits857 repressor and expressed it in escherichia coli k-12 er2925. the genes for the production of 1,3-pd in clostridium butyricum, dhab1 and dhab2, which encode the vitamin b(12)-independent glycerol dehydratase dhab1 and its activating factor, dhab2, respectively, were tandemly array ...	2009	19139229
recombineering reveals a diverse collection of ribosomal proteins l4 and l22 that confer resistance to macrolide antibiotics.	mutations in ribosomal proteins l4 and l22 confer resistance to erythromycin and other macrolide antibiotics in a variety of bacteria. l4 and l22 have elongated loops whose tips converge in the peptide exit tunnel near the macrolide-binding site, and resistance mutations typically affect residues within these loops. here, we used bacteriophage lambda red-mediated recombination, or "recombineering," to uncover new l4 and l22 alleles that confer macrolide resistance in escherichia coli. we randomi ...	2009	19150357
real-time multiplex pcr assay for detection of yersinia pestis and yersinia pseudotuberculosis.	a multiplex real-time polymerase chain reaction (pcr) assay was developed for the detection of yersinia pestis and yersinia pseudotuberculosis. the assay includes four primer pairs, two of which are specific for y. pestis, one for y. pestis and y. pseudotuberculosis and one for bacteriophage lambda; the latter was used as an internal amplification control. the y. pestis-specific target genes in the assay were ypo2088, a gene coding for a putative methyltransferase, and the pla gene coding for th ...	2009	19161535
real-time pcr microfluidic devices with concurrent electrochemical detection.	electrochemistry-based detection methods hold great potential towards development of hand-held nucleic-acid analyses instruments. in this work, we demonstrate the implementation of in situ electrochemical (ec) detection method in a microfluidic flow-through ec-qpcr (ftec-qpcr) device, where both the amplification of the target nucleic-acid sequence and subsequent ec detection of the pcr amplicon are realized simultaneously at selected pcr cycles in the same device. the ftec-qpcr device utilizes ...	2009	19162460
sequence-dependent upstream dna-rna polymerase interactions in the open complex with lambdapr and lambdaprm promoters and implications for the mechanism of promoter interference.	upstream interactions of escherichia coli rna polymerase (rnap) in an open promoter complex (rpo) formed at the p(r) and p(rm) promoters of bacteriophage lambda have been studied by atomic force microscopy. we demonstrate that the previously described 30-nm dna compaction observed upon rpo formation at p(r) [rivetti, c., guthold, m. & bustamante, c. (1999). wrapping of dna around the e. coli rna polymerase open promoter complex. embo j., 18, 4464-4475.] is a consequence of the specific interacti ...	2009	19061900
proteasome inhibitors enhance bacteriophage lambda (lambda) mediated gene transfer in mammalian cells.	bacteriophage lambda vectors can transfer their genomes into mammalian cells, resulting in expression of phage-encoded genes. however, this process is inefficient. experiments were therefore conducted to delineate the rate limiting step(s) involved, using a phage vector that contains a mammalian luciferase reporter gene cassette. the efficiency of phage-mediated gene transfer in mammalian cells was quantitated, in the presence or absence of pharmacologic inhibitors of cell uptake and degradation ...	2009	19064273
modifying bacteriophage lambda with recombineering.	recombineering is a recently developed method of in vivo genetic engineering used in escherichia coli and other gram-negative bacteria. recombineering can be used to create single-base changes, small and large deletions, and small insertions in phage lambda as well as in bacterial chromosomes, plasmids, and bacterial artificial chromosomes (bacs). this technique uses the bacteriophage lambda generalized recombination system, red, to catalyze homologous recombination between linear dna and a repl ...	2009	19066825
the igf2/h19 imprinting control region exhibits sequence-specific and cell-type-dependent dna methylation-mediated repression.	methylation of cpgs is generally thought to repress transcription without significant influence from the sequence surrounding the methylated dinucleotides. using the mouse igf2/h19 imprinting control region (icr), igf2r differentially methylated region 2 (dmr2) and bacterial sequences, we addressed how methylation-dependent repression (mdr) from a distance varies with cpg number, density and surrounding sequence. in stably transfected f9 cells, the methylated icr repressed expression from a cpg- ...	2009	19074953
in vivo mutagenicity of conazole fungicides correlates with tumorigenicity.	triadimefon, propiconazole and myclobutanil are conazoles, an important class of agricultural and therapeutic fungicides. triadimefon and propiconazole are mouse liver tumorigens, while myclobutanil is not. all three conazoles are generally inactive in short-term genotoxicity tests. we studied the in vivo mutagenicity of these three conazoles using the big blue mouse assay system. groups of mice were fed either control diet or diet containing 1800 p.p.m. triadimefon, 2500 p.p.m. propiconazole or ...	2009	19028983
cleavage of bacteriophage lambda ci repressor involves the reca c-terminal domain.	the sos response to dna damage in escherichia coli involves at least 43 genes, all under the control of the lexa repressor. activation of these genes occurs when the lexa repressor cleaves itself, a reaction catalyzed by an active, extended reca filament formed on dna. it has been shown that the lexa repressor binds within the deep groove of this nucleoprotein filament, and presumably, cleavage occurs in this groove. bacteriophages, such as lambda, have repressors (ci) that are structural homolo ...	2009	19013467
genotoxicity of wastewaters used for irrigation of food crops.	in most towns of india, wastewater coming from both industrial and domestic sources and without any treatment is used to irrigate the agricultural crops. this practice has been polluting the soil, and pollutants could possibly reach the food chain. for the above reasons, the wastewaters of ghaziabad city (india), which is used for irrigation, were sampled (at two different sites) and monitored for the presence of genotoxic agents from january 2005 to june 2007. gas chromatographic analysis showe ...	2009	18442071
a gateway recombination herpesvirus cloning system with negative selection that produces vectorless progeny.	crossover recombination based on the lambda phage integration/excision functions enables insertion of a gene of interest into a specific locus by a simple one-step in vitro recombination reaction. recently, a highly efficient recombination system for targeted mutagenesis, which utilizes lambda phage crossover recombination cloning, has been described for a human herpesvirus 2 bacterial artificial chromosome (bac). the disadvantages of the system are that it allows only neutral selection (loss of ...	2009	18948138
high-cell density shake-flask expression and rapid purification of the large fragment of thermus aquaticus dna polymerase i using a new chemically and temperature inducible expression plasmid in escherichia coli.	we have developed a new expression vector, pci(ts) ind(+), based upon the powerful rightward promoter of bacteriophage lambda, which is controlled by a temperature-sensitive and chemically-inducible version of the lambda repressor on the same plasmid. locating the repressor gene on the plasmid makes this vector "portable" in that it can be used to transform any strain of escherichia coli. hence, control over strains, induction conditions, and harvest times can be used to optimize yields of heter ...	2009	18952180
dna molecule dynamics in converging-diverging microchannels.	the conformation and dynamics of double-stranded dna molecules in a pressure-driven flow-through sharp/gradual converging (contraction half)-diverging (expansion half) square microchannels with a contraction/expansion ratio of 4:1/1:4 were examined using fluorescently labelled lambda-phage dna at 2.2< or =de< or =30.7 (de is deborah number, a dimensionless number used in rheology to characterize how fluid a material is). both the diffusion and stretching of individual dna molecules and their loc ...	2009	18251714
expression, purification, and characterization of a novel ca(2+)- and phospholipid-binding protein annexin b2.	annexin b2 (anxb2) is a novel member of the annexin family of ca(2+)- and phospholipid-binding proteins from cysticercus cellulosae. to obtain highly pure anxb2 with an easy and inexpensive purification approach, its cdna was cloned into the prokaryotic expression vector pjla503 and the translation initiation codon was immediately under the control of the inducible bacteriophage lambda promoters p(r) and p(l). after induction by shifting temperature, large amounts of non-fusion protein were prod ...	2010	19455404
generation of a recombinant full-length human antibody binding to botulinum neurotoxin a.	in order to develop a recombinant full-length human anti-botulinum neurotoxin a (bont/a) antibody, human peripheral blood mononuclear cells (pbmc) were collected from three healthy volunteers and induced for bont/a-specific immune response by in vitro immunization. the genes encoding human fd fragment, consisting of antibody heavy chain variable region and constant region 1 with the genes encoding antibody light chain, were cloned from the immunized pbmc. afterwards, one combinatory human antige ...	2010	19466383
identification of antisense rna stem-loops that inhibit rna-protein interactions using a bacterial reporter system.	many well-characterized examples of antisense rnas from prokaryotic systems involve hybridization of the looped regions of stem-loop rnas, presumably due to the high thermodynamic stability of the resulting loop-loop and loop-linear interactions. in this study, the identification of rna stem-loops that inhibit u1a protein binding to the hpii rna through rna-rna interactions was attempted using a bacterial reporter system based on phage lambda n-mediated antitermination. as a result, loop sequenc ...	2010	20156995
microfluidic assays for dna manipulation based on a block copolymer immobilization strategy.	methods to manipulate and visualize isolated dna and oligonucleotide strands are important for investigation of their biophysics as well as their interactions with proteins. herein, we report such a method by combining a block copolymer surface functionalization strategy with microfluidics. the copolymer poly(l-lysine-graft-polyethylene glycol) (pll-g-peg) coated one surface of the microfluidic channels, rendering it passive to adsorption and thus minimizing any noise arising from nontargeted ad ...	2010	20158193
an antimicrobial peptide that targets dna repair intermediates in vitro inhibits salmonella growth within murine macrophages.	the hexapeptide wrwycr was previously identified on the basis of its ability to inhibit bacteriophage lambda integrase-mediated recombination by trapping and preventing resolution of the holliday junction intermediate. this peptide inhibits several unrelated dna repair enzymes that bind to and process holliday junctions and branched dna substrates. wrwycr and its d stereoisomer, wrwycr, are bactericidal against both gram-positive and gram-negative bacteria, causing the accumulation of dna breaks ...	2010	20176906
emergence of acrab-mediated tigecycline resistance in a clinical isolate of enterobacter cloacae during ciprofloxacin treatment.	tigecycline resistance remains rare amongst enterobacteriaceae in the uk, as elsewhere, but has been associated with upregulation of the acrab efflux system. using isolates of an enterobacter cloacae strain that developed tigecycline resistance in vivo during ciprofloxacin therapy as well as laboratory-selected mutants, we investigated the role of this pump and the global regulator rama in tigecycline resistance. laboratory mutants were selected from a susceptible clinical isolate in vitro by ex ...	2010	20189357
missa is a highly efficient in vivo dna assembly method for plant multiple-gene transformation.	we describe a highly efficient in vivo dna assembly method, multiple-round in vivo site-specific assembly (missa), which facilitates plant multiple-gene transformation. missa is based on conjugational transfer, which is driven by donor strains, and two in vivo site-specific recombination events, which are mediated by inducible cre recombinase and phage lambda site-specific recombination proteins in recipient strains, to enable in vivo transfer and in vivo assembly of multiple transgenic dna. the ...	2010	20200068
cbf gene copy number variation at frost resistance-2 is associated with levels of freezing tolerance in temperate-climate cereals.	frost resistance-1 (fr-1) and fr-2 are two loci affecting freezing tolerance and winter hardiness of the temperate-climate cereals. fr-1 is hypothesized to be due to the pleiotropic effects of vrn-1. fr-2 spans a cluster of c-repeat binding factor (cbf) genes. these loci are genetically and functionally linked. recent studies indicate cbf transcripts are downregulated by the vrn-1 encoded mads-box protein or a factor in the vrn-1 pathway. here, we report that barley genotypes 'dicktoo' and 'nure ...	2010	20213518
the 2009 lindau nobel laureate meeting: werner arber, physiology or medicine 1978.	swiss microbial geneticist, werner arber shared the 1978 nobel prize in physiology or medicine with hamilton smith and daniel nathans for their discovery of restriction endonucleases. werner arber was born in granichen, switzerland in 1929. following a public school education, he entered the swiss polytechnical school in zurich in 1949, working toward a diploma in natural sciences. there, his first research experience involved isolating and characterizing an isomer of chlorine. following graduat ...	2010	20220745
production of recombinant proteins in e. coli by the heat inducible expression system based on the phage lambda pl and/or pr promoters.	the temperature inducible expression system, based on the pl and/or pr phage lambda promoters regulated by the thermolabile ci857 repressor has been widely use to produce recombinant proteins in prokaryotic cells. in this expression system, induction of heterologous protein is achieved by increasing the culture temperature, generally above 37 degrees c. concomitant to the overexpression of heterologous protein, the increase in temperature also causes a variety of complex stress responses. many s ...	2010	20298615
backbone 1h, 13c, and 15n resonance assignments for lysozyme from bacteriophage lambda.	lysozyme from lambda bacteriophage (lambda lysozyme) is an 18 kda globular protein displaying some of the structural features common to all lysozymes; in particular, lambda lysozyme consists of two structural domains connected by a helix, and has its catalytic residues located at the interface between these two domains. an interesting feature of lambda lysozyme, when compared to the well-characterised hen egg-white lysozyme, is its lack of disulfide bridges; this makes lambda lysozyme an interes ...	2010	20300891
integration of stable extracellular dna released from escherichia coli into the bacillus subtilis genome vector by culture mix method.	the stable cloning of giant dna is a necessary process in the production of recombinant/synthetic genomes. handling dna molecules in test tubes becomes increasingly difficult as their size increases, particularly above 100 kb. the need to prepare such large dna molecules in a regular manner has limited giant dna cloning to certain laboratories. recently, we found stable plasmid dna of up to 100 kb in escherichia coli culture medium during the infection and propagation of lambda phage. the extrac ...	2010	20308163
substrate specificity and biochemical properties of m3.bstf5i dna methyltransferase from the bstf5i restriction-modification system.	optimal conditions for dna methylation by the m3.bstf5i enzyme from bacillus stearothermophilus and kinetic parameters of lambda phage dna modification and that of a number of oligonucleotide substrates are established. comparison of m1.bstf5i and m3.bstf5i kinetic parameters revealed that with similar temperature optima and affinity for dna, m3.bstf5i has nearly fourfold lower turnover number (0.24 min(-1)) and modifies the hemimethylated recognition site with lower efficiency under optimal con ...	2010	20331425
selenomethionine or methylseleninic acid inhibits mutagenesis of a reporter gene in mouse bone marrow.	recent laboratory and clinical studies have utilized selenium in the form of pure seleno-l-methionine (semet) in combination with dna-damaging cancer chemotherapy drugs. in mice, the selenium protected bone marrow and other tissues from dose-limiting toxicity. in fact, because of the protection from dose-limiting toxicity, a doubling or even tripling of the maximum tolerated dose (mtd) was enabled. previously we showed that semet protects bone marrow by a dna repair mechanism that requires the x ...	2010	20332431
myth and reality: practical test system for the measurement of anti-dna antibodies in the diagnosis of systemic lupus erythematosus (sle).	the myth persists that only the labor intensive farr radioimmunoassay and crithidia luciliae immunofluorescence (cl-ifa) are systemic lupus erythematosus (sle)-specific tests. we compared them to elisa with bacteriophage lambda dna (el-dsdna) and denatured calf thymus dna (el-ssdna). by percentile ranking, the specificity cut-off level was set both out of clinical context (socc) on 100 blood bank donors, and in clinical context (sicc) on 100 patients with either rheumatoid arthritis or scleroder ...	2010	20333761
escherichia coli mw005: lambda red-mediated recombineering and copy-number induction of oriv-equipped constructs in a single host.	escherichia coli strain el350 contains chromosomally integrated phage lambda red recombinase genes enabling this strain to be used for modifying the sequence of resident clones via recombineering. bac and fosmid clones are highly suitable for modification by recombineering but, because they are present at low (1-2) copies per cell, the dna is difficult to isolate in high yield and purity. to overcome this limitation vectors, e.g. pcc1fos, have been constructed that contain the additional replica ...	2010	20350301
fluorogenic peptide substrates for serine and threonine phosphatases.	a new fluorescent assay for ser/thr protein phosphatases has been developed. hydrolysis of a phosphoser residue liberates the ser hydroxyl group, which induces a cyclization reaction on the n-terminal carbamate and releases a fluorescent reporter. sequence selectivity is observed using several peptide substrates against alkaline phosphatase (alp), bacteriophage lambda protein phosphatase (lambda-ppase), and vaccinia h1 related phosphatase (vhr). these studies suggest that the assay could be a us ...	2010	20359238
bacteriophage lambda: a paradigm revisited.	bacteriophage lambda has an archetypal immunity system, which prevents the superinfection of its escherichia coli lysogens. it is now known that superinfection can occur with toxigenic lambda-like phages at a high frequency, and here we demonstrate that the superinfection of a lambda lysogen can lead to the acquisition of additional lambda genomes, which was confirmed by southern hybridization and quantitative pcr. as many as eight integration events were observed but at a very low frequency (6. ...	2010	20375161
regions and residues of an asymmetric operator dna interacting with the monomeric repressor of temperate mycobacteriophage l1.	previously, the repressor protein of mycobacteriophage l1 bound to two operator dnas with dissimilar affinity. surprisingly, the putative operator consensus sequence, 5'ggtgga/ctgtcaag, lacks the dyad symmetry reported for the repressor binding operators of lambda and related phages. to gain insight into the structure of the l1 repressor-asymmetric operator dna complex, we have performed various in vitro experiments. a dimethyl sulfate protection assay revealed that five guanine bases, mostly di ...	2010	20377203
fadd-calmodulin interaction: a novel player in cell cycle regulation.	analyses of knockout and mutant transgenic mice as well as in vitro studies demonstrated a complex role of fadd in the regulation of cell fate. fadd is involved in death receptor induced apoptosis, cell cycle progression and cell proliferation. in a search for mechanisms that might regulate fadd functions, we identified, upon the screening of a lambda-phage cdna library, calmodulin (cam) as a novel fadd interacting protein. cam is a key mediator of signals by the secondary messenger calcium and ...	2010	20420860
the tripartite capsid gene of salmonella phage gifsy-2 yields a capsid assembly pathway engaging features from hk97 and lambda.	phage gifsy-2, a lambdoid phage infecting salmonella, has an unusually large composite gene coding for its major capsid protein (mcp) at the c-terminal end, a clpp-like protease at the n-terminus, and a approximately 200 residue central domain of unknown function but which may have a scaffolding role. this combination of functions on a single coding region is more extensive than those observed in other phages such as hk97 (scaffold-capsid fusion) and lambda (protease-scaffold fusion). to study t ...	2010	20427067
cloning and sequencing the first hla gene.	this perspectives article recounts the isolation and sequencing of the first human histocompatibility gene (hla) in 1980-1981. at the time, general knowledge of the molecules of the immune system was already fairly extensive, and gene rearrangements in the immunoglobulin complex (discovered in 1976) had generated much excitement: hla was quite obviously the next frontier. the author was able to use a homologous murine h-2 cdna to identify putative human hla genomic clones in a lambda-phage libra ...	2010	20457890
recombinant lambda-phage nanobioparticles for tumor therapy in mice models.	abstract: lambda phages have considerable potential as gene delivery vehicles due to their genetic tractability, low cost, safety and physical characteristics in comparison to other nanocarriers and gene porters. little is known concerning lambda phage-mediated gene transfer and expression in mammalian hosts. we therefore performed experiments to evaluate lambda-zap bacteriophage-mediated gene transfer and expression in vitro. for this purpose, we constructed recombinant lambda-phage nanobiopart ...	2010	20459865
decision making at a subcellular level determines the outcome of bacteriophage infection.	when the process of cell-fate determination is examined at single-cell resolution, it is often observed that individual cells undergo different fates even when subject to identical conditions. this "noisy" phenotype is usually attributed to the inherent stochasticity of chemical reactions in the cell. here we demonstrate how the observed single-cell heterogeneity can be explained by a cascade of decisions occurring at the subcellular level. we follow the postinfection decision in bacteriophage l ...	2010	20478257
phage wo of wolbachia: lambda of the endosymbiont world.	the discovery of an extraordinarily high level of mobile elements in the genome of wolbachia, a widespread arthropod and nematode endosymbiont, suggests that this bacterium could be an excellent model for assessing the evolution and function of mobile dna in specialized bacteria. in this paper, we discuss how studies on the temperate bacteriophage wo of wolbachia have revealed unexpected levels of genomic flux and are challenging previously held views about the clonality of obligate intracellula ...	2010	20083406
icp0 antagonizes icp4-dependent silencing of the herpes simplex virus icp0 gene.	icp0 is a regulatory protein that plays a critical role in the replication-latency balance of herpes simplex virus (hsv). absence of icp0 renders hsv prone to establish quiescent infections, and thus cellular repressor(s) are believed to silence hsv mrna synthesis when icp0 fails to accumulate. to date, an icp0-antagonized repressor has not been identified that restricts hsv mrna synthesis by more than 2-fold. we report the unexpected discovery that hsv's major transcriptional regulator, icp4, m ...	2010	20098619
a novel escherichia coli-derived mutation detected with the big blue cii mutant selectable assay.	transgenic mouse mutation detection systems allow investigation of the origins and mechanisms of mutation associated with exogenous and endogenous mutagen exposures in individual tissues and cell types. in the past, selection assays for transgenic mutants have been contaminated with nonmurine-derived mutations and assay validation is critical to ensure murine in vivo origins of mutations. this is critical in studies of spontaneous mutations and extrapolation to endogenous mammalian genes. herein ...	2010	20120017
structural energetics of the adenine tract from an intrinsic transcription terminator.	intrinsic transcription termination sites generally contain a tract of adenines in the dna template that yields a tract of uracils at the 3' end of the nascent rna. to understand how this base sequence contributes to termination of transcription, we have investigated two nucleic acid structures. the first is the rna-dna hybrid that contains the uracil tract 5'-ruuuuuau-3' from the tr2 intrinsic terminator of bacteriophage lambda. the second is the homologous dna-dna duplex that contains the aden ...	2010	20132823
vaccinia virus particles mix inefficiently, and in a way that would restrict viral recombination, in coinfected cells.	it is well established that poxviruses are subjected to genetic recombination, but attempts to map vaccinia virus genes using classical genetic crosses were historically confounded by high levels of experimental noise and a poor correlation between physical and genetic map distances. these virus-by-virus crosses also never produced the 50% recombinant progeny that should be seen in experiments involving distant markers. poxviruses replicate in membrane-wrapped cytoplasmic structures called viros ...	2010	20032178
homologous overexpression of a lipase from burkholderia cepacia using the lambda red recombinase system.	red recombinase system of the lambda phage is widely used for recombination of short linear dna fragments and genome. using this system, we obtained t7 rna polymerase (rnap) substitution mutants in burkholderia cepacia. to test the expression abilities of the t7 mutants, four different lipase expression vectors were transformed and the lipase activity of these recombinants was evaluated. our results suggest that 500 nt homology between the unit and the genome is sufficient to generate mutations ...	2010	20033831
single-molecule and fret fluorescence correlation spectroscopy analyses of phage dna packaging: colocalization of packaged phage t4 dna ends within the capsid.	linear dnas of any sequence can be packaged into empty viral procapsids by the phage t4 terminase with high efficiency in vitro. packaging substrates of 5 kbp and 50 kbp, terminated by energy transfer dye pairs, were constructed from plasmid and lambda phage dnas. nuclease and fluorescence correlation spectroscopy (fcs) assays showed that approximately 20% of the substrate dna was packaged and that the dna dye ends of the packaged dna were protected from nuclease digestion. upon packaging, both ...	2010	19962991
selection of bacteriophage lambda integrases with altered recombination specificity by in vitro compartmentalization.	in vitro compartmentalization (ivc) was employed for the first time to select for novel bacteriophage lambda integrase variants displaying significantly enhanced recombination activity on a non-cognate target dna sequence. these variants displayed up to 9-fold increased recombination activity over the parental enzyme, and one mutant recombined the chosen non-cognate substrate more efficiently than the parental enzyme recombined the wild-type dna substrate. the in vitro specificity phenotype exte ...	2010	19966270
dna heats up: energetics of genome ejection from phage revealed by isothermal titration calorimetry.	most bacteriophages are known to inject their double-stranded dna into bacteria upon receptor binding in an essentially spontaneous way. this downhill thermodynamic process from the intact virion to the empty viral capsid plus released dna is made possible by the energy stored during active packaging of the genome into the capsid. only indirect measurements of this energy have been available until now, using either single-molecule or osmotic suppression techniques. in this work, we describe for ...	2010	19969001
efficacy of bacteriophage therapy in a model of burkholderia cenocepacia pulmonary infection.	the therapeutic potential of bacteriophages (phages) in a mouse model of acute burkholderia cenocepacia pulmonary infection was assessed. phage treatment was administered by either intranasal inhalation or intraperitoneal injection. bacterial density, macrophage inflammatory protein 2 (mip-2), and tumor necrosis factor alpha (tnf-alpha) levels were significantly reduced in lungs of mice treated with intraperitoneal phages (p < .05). no significant differences in lung bacterial density or mip-2 l ...	2010	20001604
identification of adamts13 peptide sequences binding to von willebrand factor.	adamts13 cleaves multimeric von willebrand factor (vwf) to regulate vwf-mediated thrombus formation. to search adamts13 peptide sequences binding to vwf, a lambda-phage library expressing various peptides of adamts13 on the surface was screened using vwf either immobilized or in solution under static condition. by the first screening, peptides sharing the c-terminus of spacer domain from arg(670) to gln(684) (epitope-a) were selected. to explore additional sites, peptide sequences from the first ...	2010	19944670
specific hydrophobic residues in the alpha4 helix of lambdacii are crucial for maintaining its tetrameric structure and directing the lysogenic choice.	the cii protein of the temperate bacteriophage lambda is the decision-making factor that determines the viral lytic/lysogenic choice. it is a homotetrameric transcription activator that recognizes and binds specific direct repeat sequences ttgcn(6)ttgc in the lambda genome. the quaternary structure of cii is held by a four-helix bundle. it is known that the tetrameric organization of cii is necessary for its activity, but the molecular mechanism behind this requirement is not known. by specific ...	2010	19776236
dna packaging by lambda-like bacteriophages: mutations broadening the packaging specificity of terminase, the lambda-packaging enzyme.	the dna-packaging specificities of phages lambda and 21 depend on the specific dna interactions of the small terminase subunits, which have support helix-turn-recognition helix-wing dna-binding motifs. lambda-terminase with the recognition helix of 21 preferentially packages 21 dna. this chimeric terminase's ability to package lambdadna is reduced approximately 20-fold. phage lambda with the chimeric terminase is unable to form plaques, but pseudorevertants are readily obtained. some pseudorever ...	2010	19841094
hfld, an escherichia coli protein involved in the lambda lysis-lysogeny switch, impairs transcription activation by lambdacii.	the cii protein of bacteriophage lambda is the key regulator for the lytic-lysogenic choice of the viral lifecycle. an unstable homotetrameric transcription activator of the three phage promoters p(e), p(i) and p(aq), lambdacii is stabilized by lambdaciii and destabilized by the host protease, escherichia coli hflb (ftsh). in addition, other e. coli proteins hflk, hflc and hfld also influence lysogeny by acting upon cii. among these, hfld (22.9kda), a peripheral membrane protein that is exposed ...	2010	19853572
fine tuning of the e. coli nusb:nuse complex affinity to boxa rna is required for processive antitermination.	phage lambda propagation in escherichia coli host cells requires transcription antitermination on the lambda chromosome mediated by lambdan protein and four host nus factors, nusa, b, e (ribosomal s10) and g. interaction of e. coli nusb:nuse heterodimer with the single stranded boxa motif of lambdanutl or lambdanutr rna is crucial for this reaction. similarly, binding of nusb:nuse to a boxa motif is essential to suppress transcription termination in the ribosomal rna (rrn) operons. we used fluor ...	2010	19854945
tuning a genetic switch: experimental evolution and natural variation of prophage induction.	genetic switches allow organisms to modulate their phenotype in response to environmental changes. understanding the evolutionary processes by which switches are tuned is central to understanding how phenotypic variation is realized. prophage induction by phage lambda is the classic example of a genetic switch and allows lambda to move between two different modes of transmission: as a lysogen it reproduces vertically as a component of the host genome; as a free phage it reproduces horizontally b ...	2010	19891623
phisite: database of gene regulation in bacteriophages.	we have developed phisite, database of gene regulation in bacteriophages. to date it contains detailed information about more than 700 experimentally confirmed or predicted regulatory elements (promoters, operators, terminators and attachment sites) from 32 bacteriophages belonging to siphoviridae, myoviridae and podoviridae families. the database is manually curated, the data are collected mainly form scientific papers, cross-referenced with other database resources (embl, uniprot, ncbi taxonom ...	2010	19900969
evaluation of humoral and cellular immune responses against hsv-1 using genetic immunization by filamentous phage particles: a comparative approach to conventional dna vaccine.	phage display is based on expressing peptides as a fusion to one of the phage coat proteins. to date, many vaccine researches have been conducted to display immunogenic peptides or mimotopes of various pathogens and tumors on the surface of filamentous bacteriophages. in recent years as a new approach to application of phages, recombinant bacteriophage lambda particles were used as dna delivery vehicles to mammalian cells. in this study, recombinant filamentous phage whole particles were used fo ...	2010	19903497
quantification of cyprinid herpesvirus 3 in environmental water by using an external standard virus.	cyprinid herpesvirus 3 (cyhv-3), a lethal dna virus that spreads in natural lakes and rivers, infects common carp and koi. we established a quantification method for cyhv-3 that includes a viral concentration method and quantitative pcr combined with an external standard virus. viral concentration methods were compared using the cation-coated filter and ultrafiltration methods. the recovery of virus-like particles was similar for the two methods (cation-coated filter method, 44%+/-19%, n=3; ultr ...	2010	19915032
characterisation of methacrylate monoliths for bacteriophage purification.	binding of three different bacteriophages (phages), namely t7, lambda and m13 on methacrylate monoliths was investigated. phage m13 exhibited the highest dynamic binding capacity of 4.5×10(13) pfu/ml while t7 and lambda showed capacity of 1×10(13) pfu/ml, all corresponding to values of around 1mg/ml. interestingly, capacity for lambda phage was increased 5-fold by increasing nacl concentration in a loaded sample from 0 to 0.2m while there was a constant capacity decrease for t7 and m13 phages. u ...	2010	21238969
recombinant dna-methyltransferase m1.bspaci from bacillus psychrodurans ac: purification and properties.	a restriction-modification system from bacillus psychrodurans ac (recognition sequence 5'-ccgc-3') comprises two dna methyltransferases: m1.bspaci and m2.bspaci. the bspacim1 gene was cloned in the pjw2 vector and expressed in escherichia coli cells. high-purity m1.bspaci preparation has been obtained by chromatography on different carriers. m1.bspaci has a temperature optimum of 30°c and demonstrates maximum activity at ph 8.0. m1.bspaci modifies the first cytosine in the recognition sequence 5 ...	2010	21314619
probing dna with micro- and nanocapillaries and optical tweezers.	we combine for the first time optical tweezer experiments with the resistive pulse technique based on capillaries. quartz glass capillaries are pulled into a conical shape with tip diameters as small as 27 nm. here, we discuss the translocation of λ-phage dna which is driven by an electrophoretic force through the nanocapillary. the resulting change in ionic current indicates the folding state of single λ-phage dna molecules. our flow cell design allows for the straightforward incorporation of o ...	2010	21339600
the solution structure of the c-terminal ig-like domain of the bacteriophage λ tail tube protein.	immunoglobulin (ig)-like domains are found frequently on the surface of tailed double-stranded dna bacteriophages, yet their functional role remains obscure. here, we have investigated the structure and function of the c-terminal ig-like domain of gpv (gpv(c)), the tail tube protein of phage λ. this domain has been predicted through sequence similarity to be a member of the bacterial ig-like domain 2 (big_2) family, which is composed of more than 1300 phage and bacterial sequences. using trypsin ...	2010	20826161
evolution of complex gene regulatory circuits by addition of refinements.	how do complex gene regulatory circuits evolve? these circuits involve many interacting components, which work together to specify patterns of gene expression. they typically include many subtle mechanistic features, but in most cases it is unclear whether these features are essential for the circuit to work at all, or if instead they make a functional circuit work better. in the latter case, such a feature is here termed 'dispensable', and it is plausible that the feature has been added at a la ...	2010	20833317
the shear flow processing of controlled dna tethering and stretching for organic molecular electronics.	dna has been recently explored as a powerful tool for developing molecular scaffolds for making reproducible and reliable metal contacts to single organic semiconducting molecules. a critical step in the process of exploiting dna-organic molecule-dna (dod) array structures is the controlled tethering and stretching of dna molecules. here we report the development of reproducible surface chemistry for tethering dna molecules at tunable density and demonstrate shear flow processing as a rationally ...	2010	21126082