Publications
| Title | Abstract | Year Filter | PMID(sorted ascending) Filter |
|---|
| a bridge crosses the active-site canyon of the epstein-barr virus nuclease with dnase and rnase activities. | epstein-barr virus, a double-stranded dna (dsdna) virus, is a major human pathogen from the herpesvirus family. the nuclease is one of the lytic cycle proteins required for successful viral replication. in addition to the previously described endonuclease and exonuclease activities on single-stranded dna and dsdna substrates, we observed an rnase activity for epstein-barr virus nuclease in the presence of mn(2+), giving a possible explanation for its role in host mrna degradation. its crystal st ... | 2009 | 19538972 |
| 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 |
| optimizing bayes error for protein structure model selection by stability mutagenesis. | site-directed mutagenesis affects protein stability in a manner dependent on the local structural environment of the mutated residue; e.g., a hydrophobic to polar substitution would behave differently in the core vs. on the surface of the protein. thus site-directed mutagenesis followed by stability measurement enables evaluation of and selection among predicted structure models, based on consistency between predicted and experimental stability changes (deltadeltago values). this paper develops ... | 2008 | 19642272 |
| profiling the autoantibody repertoire by screening phage-displayed human cdna libraries. | the advent of the serological identification of antigens by procedures such as cdna cloning and recombinant protein expression has allowed the direct molecular definition of immunogenic proteins. the phage-display technology provides several advantages over conventional immunoscreening procedures based on plasmid or lambda-phage cdna libraries. so far, attempts to display open reading frames, such as those encoded by cdna fragments, on filamentous phages have not been very successful. we managed ... | 2009 | 19649606 |
| the structure of dna overstretched from the 5'5' ends differs from the structure of dna overstretched from the 3'3' ends. | it has been suggested that the structure that results when double-stranded dna (dsdna) is pulled from the 3'3' ends differs from that which results when it is pulled from the 5'5' ends. in this work, we demonstrate, using lambda phage dsdna, that the overstretched states do indeed show different properties, suggesting that they correspond to different structures. for 3'3' pulling versus 5'5' pulling, the following differences are observed: (i) the forces at which half of the molecules in the ens ... | 2009 | 19666582 |
| the q motif of a viral packaging motor governs its force generation and communicates atp recognition to dna interaction. | a key step in the assembly of many viruses is the packaging of dna into preformed procapsids by an atp-powered molecular motor. to shed light on the motor mechanism we used single-molecule optical tweezers measurements to study the effect of mutations in the large terminase subunit in bacteriophage lambda on packaging motor dynamics. a mutation, k84a, in the putative atpase domain driving dna translocation was found to decrease motor velocity by approximately 40% but did not change the force dep ... | 2009 | 19706522 |
| replacement of the lambda boxb rna-n peptide with heterologous rna-peptide interactions relaxes the strict spatial requirements for the formation of a transcription anti-termination complex. | in bacteriophage lambda, formation of a transcriptional anti-termination complex involving the elongating rna polymerase is mediated by the interaction of boxb rna with the rna-binding domain of the n protein (n peptide). in an attempt to understand the spatial requirements for boxb/n peptide interaction within the anti-termination complex, the effects of changes in the distance between boxa and boxb rna, the length of the boxb stem, and the distance between the n peptide and remainder of the n ... | 2009 | 19708917 |
| recombinogenic engineering of conjugative plasmids with fluorescent marker cassettes. | an efficient approach for the insertion of fluorescent marker genes with sequence specificity into conjugative plasmids in escherichia coli is described. for this purpose, homologous recombination of linear double-stranded targeting dna was mediated by the bacteriophage lambda recombination functions using very short regions of homology. initial manipulation of the incfii target plasmids r1 and r1drd19 indicated that the linear targeting dna should be devoid of all extraneous homologies to the t ... | 2002 | 19709285 |
| immunogenicity of bacteriophage lambda particles displaying porcine circovirus 2 (pcv2) capsid protein epitopes. | phage lambda particles displaying four immunodominant regions of porcine circovirus 2 (pcv2) capsid protein (ldp-d-cap) was shown to be immunogenic in pigs. the immunodominant regions were fused to the carboxyl-terminal of lambda head protein d. expression of d-cap on lambda display particles was demonstrated by elisa and western blots. pigs receiving ldp-d-cap, without incorporating adjuvant, showed significant anti-pcv2 immune response following the primary vaccination. the ldp-d-cap preparati ... | 2009 | 19712770 |
| systematic cloning of an orfeome using the gateway system. | with the completion of the genome projects, there are increasing demands on the experimental systems that enable to exploit the entire set of protein-coding open reading frames (orfs), viz. orfeome, en masse. systematic proteomic studies based on cloned orfeomes are called "reverse proteomics," and have been launched in many organisms in recent years. cloning of an orfeome is such an attractive way for comprehensive understanding of biological phenomena, but is a challenging and daunting task. h ... | 2009 | 19718505 |
| high-throughput production of the recombinant proteins expressed in escherichia coli utilizing cdna resources. | conventionally, expression plasmids in escherichia coli have generally been constructed using ligation reaction-assisted cloning followed by the generation of inserts. in such cases, the insert was generated by polymerase chain reaction (pcr), digestion using restriction enzymes, or oligonucleotide synthesis. to overcome the restrictions of these conventional methods, we improved them by utilizing an in vitro site-specific recombination reaction, based on the integrase-excisionase system of bact ... | 2009 | 19718510 |
| sequence-specific recognition of dna by the c-terminal domain of nucleoid-associated protein h-ns. | the molecular determinants necessary and sufficient for recognition of its specific dna target are contained in the c-terminal domain (h-nsctd) of nucleoid-associated protein h-ns. h-nsctd protects from dnasei cleavage a few short dna segments of the h-ns-sensitive hns promoter whose sequences closely match the recently identified h-ns consensus motif (tcg(t/a)t(a/t)aatt) and, alone or fused to the protein oligomerization domain of phage lambda ci repressor, inhibits transcription from the hns p ... | 2009 | 19740756 |
| why do phage play dice? | phage lambda is among the simplest organisms that make a developmental decision. an infected bacterium goes either into the lytic state, where the phage particles rapidly replicate and eventually lyse the cell, or into a lysogenic state, where the phage goes dormant and replicates along with the cell. experimental observations by p. kourilsky are consistent with a single phage infection deterministically choosing lysis and double infection resulting in a stochastic choice. we argue that the phag ... | 2009 | 19740995 |
| modeling of the genetic switch of bacteriophage tp901-1: a heteromer of ci and mor ensures robust bistability. | the lytic-lysogenic switch of the temperate lactococcal phage tp901-1 is fundamentally different from that of phage lambda. in phage tp901-1, the lytic promoter p(l) is repressed by ci, whereas repression of the lysogenic promoter p(r) requires the presence of both of the antagonistic regulator proteins, mor and ci. we model the central part of the switch and compare the two cases for p(r) repression: the one where the two regulators interact only on the dna and the other where the two regulator ... | 2009 | 19747486 |
| analysis of the spacial requirements for rna-protein interactions within the n antitermination complex of bacteriophage lambda. | in bacteriophage lambda, formation of a transcriptional antitermination complex consisting of the lambda n protein, nut rna transcript (boxa-boxb), host factors, and rna polymerase is mediated by the interaction of the boxb rna with the rna-binding domain of n. in order to understand the spacial requirements of this boxb/n interaction within the complex, the effects of changes in the length of the nut site linker, the boxb stem, and the peptide spacer connecting the rna-binding domain and activa ... | 2009 | 19749275 |
| influence of internal capsid pressure on viral infection by phage lambda. | ejection of the genome from the virus, phage lambda, is the initial step in the infection of its host bacterium. in vitro, the ejection depends sensitively on internal pressure within the virus capsid; however, the in vivo effect of internal pressure on infection of bacteria is unknown. here, we use microfluidics to monitor individual cells and determine the temporal distribution of lysis due to infection as the capsid pressure is varied. the lysis probability decreases markedly with decreased c ... | 2009 | 19751656 |
| characterization of the ngoaxp: phase-variable type iii restriction-modification system in neisseria gonorrhoeae. | methyltransferases associated with type iii restriction-modification (rm) systems are phase-variably expressed in a variety of pathogenic bacteria. ngoaxp, the type iii rm system encoded by neisseria gonorrhoeae, was characterized in this study. the cloned resngoaxp and ngoaxpmod genes were expressed in escherichia coli strains. the restriction and modification activities of ngoaxp were confirmed in vivo by the lambda phage restriction and modification test and in vitro by the methylation of dna ... | 2009 | 19758331 |
| transcription from bacteriophage lambda pr promoter is regulated independently and antagonistically by dksa and ppgpp. | the stringent response effector, guanosine tetraphosphate (ppgpp), adjust gene expression and physiology in bacteria, by affecting the activity of various promoters. rna polymerase-interacting protein, dksa, was proposed to be the co-factor of ppgpp effects; however, there are reports suggesting independent roles of these regulators. bacteriophage lambda major lytic promoter, pr, is down-regulated by the stringent response and ppgpp. here, we present evidence that dksa significantly stimulates p ... | 2009 | 19759216 |
| differential efficiency of induction of various lambdoid prophages responsible for production of shiga toxins in response to different induction agents. | shiga toxin-producing escherichia coli (stec) is a group of pathogenic strains responsible for bloody diarrhea and hemorrhagic colitis, with often severe complications. shiga toxins are the main factors causing the phathogenicity of stec. production of these toxins depends on the presence of stx1 and stx2 genes, which are located on lambdoid prophages, and their expression is stimulated upon prophage induction. therefore, a transition of the phage genome from the prophage state to an extrachromo ... | 2009 | 19761828 |
| the appearance of circular dna after lysogenic induction in escherichia coli cr34(lambda). | a circular (non-ended) form of dna is synthesized both after ultraviolet light and after thymineless induction of the lysogen escherichia coli cr34(lambda). this new dna species is shown to have characteristics identical to the circular dna formed from lambda phage dna immediatelyafter infection. thus, the formation of a circular lambda dna isnot limited to that derived directly from an infecting phage dna but is also formed during the normal replication of the lambda dna after lysogenic inducti ... | 1966 | 19768868 |
| 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 |
| polk mutant mice have a spontaneous mutator phenotype. | mice defective for the polk gene, which encodes dna polymerase kappa, are viable and do not manifest obvious phenotypes. the present studies document a spontaneous mutator phenotype in polk(-/-) mice. the initial indication of enhanced spontaneous mutations in these mice came from the serendipitous observation of a postulated founder mutation that manifested in multiple disease states among a cohort of mice comprising all three possible polk genotypes. polk(-/-) and isogenic wild-type controls c ... | 2009 | 19783230 |
| kinetic analysis of the genome packaging reaction in bacteriophage lambda. | bacteriophage lambda is a double-stranded dna virus that infects the escherichia coli bacterium. lambda genomic dna is replicated via rolling circle replication, resulting in multiple genomes linked head to tail at the cos site. to insert a single lambda genome into the viral capsid, the lambda terminase enzyme introduces symmetric nicks, 12 bp apart, at the cos site, and then promotes a strand separation reaction, releasing the tail end of the previous genome and leaving a binary complex consis ... | 2009 | 19788336 |
| [statistical fluctuations of the filling level of operator by repressor determine the level of noise of reporter gene expression]. | the regulation of the reporter gene activity in a single bacterial cell by means of lambda-phage c1 repressor has been described by the methods of statistical thermodynamics. the equations for the calculation of the mean production rate of the reporter protein and its standard deviation as a function of c1 repressor concentration in the cell have been obtained. the stochastic nature of c1 repressor binding with or1 and or2 operator sites becomes apparent when both repressor molecules and operato ... | 2009 | 19795776 |
| minimal gene regulatory circuits that can count like bacteriophage lambda. | the behavior of living systems is dependent on large dynamical gene regulatory networks (grns). however, the functioning of even the smallest grns is difficult to predict. the bistable grn of bacteriophage lambda is able to count to make a decision between lysis and lysogeny on the basis of the number of phages infecting the cell, even though replication of the phage genome eliminates this initial difference. by simulating the behavior of a large number of random transcriptional grns, we show th ... | 2009 | 19796646 |
| plasmids derived from lambdoid bacteriophages as models for studying replication of mobile genetic elements responsible for the production of shiga toxins by pathogenic escherichia coli strains. | genes encoding shiga toxins in pathogenic escherichia coli strains (shiga toxin-producing e. coli, stec) are located on lambdoid prophages. however, studies on the replication of these phages were not reported to date. | 2009 | 19797917 |
| high adsorption rate is detrimental to bacteriophage fitness in a biofilm-like environment. | bacterial biofilm is ubiquitous in nature. however, it is not clear how this crowded habitat would impact the evolution of bacteriophage (phage) life history traits. in this study, we constructed isogenic lambda phage strains that only differed in their adsorption rates, because of the presence/absence of extra side tail fibers or improved tail fiber j, and maker states. the high cell density and viscosity of the biofilm environment was approximated by the standard double-layer agar plate. the p ... | 2009 | 19804637 |
| a computational study of lambda-lac mutants. | we present a comprehensive, computational study of the properties of bacteriophage lambda mutants designed by atsumi and little (2006 proc. natl. acad. sci. 103 4558-63). these phages underwent a genetic reconstruction where cro was replaced by a dimeric form of the lac repressor. to clarify the theoretical characteristics of these mutants, we built a detailed thermodynamic model. the mutants all have a different genetic wiring than the wild-type lambda. one group lacks regulation of p(rm) by th ... | 2009 | 19809101 |
| 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 |
| lambda-prophage induction modeled as a cooperative failure mode of lytic repression. | we analyze a system-level model for lytic repression of lambda phage in e. coli using reliability theory, showing that the repressor circuit comprises four redundant components whose failure mode is prophage induction. our model reflects the specific biochemical mechanisms involved in regulation, including long-range cooperative binding, and its detailed predictions for prophage induction in e. coli under ultraviolet radiation are in good agreement with experimental data. | 2009 | 19905052 |
| nanomechanical fingerprints of gamma radiation damage to dna. | the exposure of cancer cells to ionizing radiation results in potentially lethal dna lesions. for this reason, identification and quantification of various lesions have intensively been investigated. it has also been anticipated that dna lesions may affect not only the chemical but also the mechanical integrity of the double helix. however, the relationship between dna damage and mechanics has not been studied. here, the mechanical properties of dna damaged by ionizing radiation are examined at ... | 2009 | 19908788 |
| precise characterization of the conformation fluctuations of freely diffusing dna: beyond rouse and zimm. | we studied the dynamics of single freely diffusing fluorescence-labeled double-stranded lambda-phage dna molecules using dual-color 3-dimensional feedback tracking microscopy and intramolecular fluorescence correlation spectroscopy. our technique is independently sensitive to the molecule's diffusion coefficient d and radius of gyration r(g) and is concentration insensitive, providing greater precision for characterizing the molecule's intramolecular motion than other methods. we measured d = 0. ... | 2009 | 19911791 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| amino-acid sequence of lambda phage endolysin. | 1971 | 20480992 | |
| enhancement of bacteriophage λ stability using a λq-s- mutant in the continuous culture of escherichia coli. | in this study, we used a bacteriophage λq⁻s⁻ mutant that increased the stability of recombinant escherichia coli during continuous culture. the operation was conducted in two stages: the first stage was carried out to promote cell growth, and the second stage was performed for product formation. the productivity of recombinant proteins depends on the substrate concentration of the fresh medium supplied to the second stage (s₃) and dilution rate of the second stage (d₂). with the optimal value of ... | 2010 | 20499104 |
| mutations altering a structurally conserved loop-helix-loop region of a viral packaging motor change dna translocation velocity and processivity. | many double-stranded dna viruses employ atp-driven motors to translocate their genomes into small, preformed viral capsids against large forces resisting confinement. here, we show via direct single-molecule measurements that a mutation t194m downstream of the walker b motif in the phage lambda gpa packaging motor causes an 8-fold reduction in translocation velocity without substantially changing processivity or force dependence, whereas the mutation g212s in the putative c (coupling) motif caus ... | 2010 | 20525695 |
| acridine-n peptide conjugates display enhanced affinity and specificity for boxb rna targets. | arginine-rich peptides and small-molecule intercalating agents utilize distinct molecular mechanisms for rna recognition. here, we combined these distinct binding modules in an effort to create conjugate ligands with enhanced affinity and specificity using the bacteriophage lambda n peptide-boxb interaction as a model system. we first designed and synthesized a series of peptide-acridine conjugates using portions of the rna-binding domain of n protein (11- and 22- residue peptide segments) and t ... | 2010 | 20527807 |
| cylinders vs. spheres: biofluid shear thinning in driven nanoparticle transport. | increasingly, the research community applies magnetophoresis to micro and nanoscale particles for drug delivery applications and the nanoscale rheological characterization of complex biological materials. of particular interest is the design and transport of these magnetic particles through entangled polymeric fluids commonly found in biological systems. we report the magnetophoretic transport of spherical and rod-shaped particles through viscoelastic, entangled solutions using lambda-phage dna ... | 2010 | 20571853 |
| assembly and maturation of the bacteriophage lambda procapsid: gpc is the viral protease. | viral capsids are robust structures designed to protect the genome from environmental insults and deliver it to the host cell. the developmental pathway for complex double-stranded dna viruses is generally conserved in the prokaryotic and eukaryotic groups and includes a genome packaging step where viral dna is inserted into a pre-formed procapsid shell. the procapsids self-assemble from monomeric precursors to afford a mature icosahedron that contains a single "portal" structure at a unique ver ... | 2010 | 20620152 |
| transcription, processing and function of crispr cassettes in escherichia coli. | crispr/cas, bacterial and archaeal systems of interference with foreign genetic elements such as viruses or plasmids, consist of dna loci called crispr cassettes (a set of variable spacers regularly separated by palindromic repeats) and associated cas genes. when a crispr spacer sequence exactly matches a sequence in a viral genome, the cell can become resistant to the virus. the crispr/cas systems function through small rnas originating from longer crispr cassette transcripts. while laboratory ... | 2010 | 20624226 |
| a forward-genetic screen and dynamic analysis of lambda phage host-dependencies reveals an extensive interaction network and a new anti-viral strategy. | latently infecting viruses are an important class of virus that plays a key role in viral evolution and human health. here we report a genome-scale forward-genetics screen for host-dependencies of the latently-infecting bacteriophage lambda. this screen identified 57 escherichia coli (e. coli) genes--over half of which have not been previously associated with infection--that when knocked out inhibited lambda phage's ability to replicate. our results demonstrate a highly integrated network betwee ... | 2010 | 20628568 |
| intramolecular fluorescence correlation spectroscopy in a feedback tracking microscope. | we derive the statistics of the signals generated by shape fluctuations of large molecules studied by feedback tracking microscopy. we account for the influence of intramolecular dynamics on the response of the tracking system and derive a general expression for the fluorescence autocorrelation function that applies when those dynamics are linear. we show that in comparison to traditional fluorescence correlation spectroscopy, tracking provides enhanced sensitivity to translational diffusion, mo ... | 2010 | 20655860 |
| h-ns-mediated repression of crispr-based immunity in escherichia coli k12 can be relieved by the transcription activator leuo. | the recently discovered prokaryotic crispr/cas defence system provides immunity against viral infections and plasmid conjugation. it has been demonstrated that in escherichia coli transcription of the cascade genes (casabcde) and to some extent the crispr array is repressed by heat-stable nucleoid-structuring (h-ns) protein, a global transcriptional repressor. here we elaborate on the control of the e. coli crispr/cas system, and study the effect on crispr-based anti-viral immunity. transformati ... | 2010 | 20659289 |
| inhibition of superinfection and the evolution of viral latency. | latent viruses generally defend their host cell against superinfection by nonlatent virulent mutants that could destroy the host cell. superinfection inhibition thus seems to be a prerequisite for the maintenance of viral latency. yet viral latency can break down when resistance to superinfection inhibition, known as ultravirulence, occurs. to understand the evolution of viral latency, we have developed a model that analyzes the epidemiology of latent infection in the face of ultravirulence. we ... | 2010 | 20660193 |
| protein damage and death by radiation in escherichia coli and deinococcus radiodurans. | deinococcus radiodurans is among a small number of bacterial species that are extremely resistant to ionizing radiation, uv light, toxic chemicals, and desiccation. we measured proteome oxidation (i.e., protein carbonylation, pc) in d. radiodurans as well as in standard and evolved resistant strains of escherichia coli exposed to ionizing radiation or uvc light and found a consistent correlation with cell killing. the unique quantitative relationship between incurred pc and cell death holds over ... | 2010 | 20660760 |
| phages have adapted the same protein fold to fulfill multiple functions in virion assembly. | evolutionary relationships may exist among very diverse groups of proteins even though they perform different functions and display little sequence similarity. the tailed bacteriophages present a uniquely amenable system for identifying such groups because of their huge diversity yet conserved genome structures. in this work, we used structural, functional, and genomic context comparisons to conclude that the head-tail connector protein and tail tube protein of bacteriophage lambda diverged from ... | 2010 | 20660769 |
| single-stranded heteroduplex intermediates in lambda red homologous recombination. | the red proteins of lambda phage mediate probably the simplest and most efficient homologous recombination reactions yet described. however the mechanism of dsdna recombination remains undefined. | 2010 | 20670401 |
| the polypeptide core of microcin e492 stably associates with the mannose permease and interferes with mannose metabolism. | microcin e492 (mcce492) is an antibacterial protein whose activity on target cells requires manyz, the inner membrane component of the mannose permease. we show here that mcea, the polypeptide core of mcce492, stably associates with manyz both in the presence and in the absence of mceb, the mcce492 immunity protein. the two known physiological activities of the mannose permease were assayed in cells co-expressing mcea and mceb. under these conditions, growth on mannose as the sole carbon source ... | 2010 | 20674740 |
| dual expression system for assembling phage lambda display particle (ldp) vaccine to porcine circovirus 2 (pcv2). | the bacteriophage lambda small capsid protein d forms trimers on the phage head. d-fusion polypeptides can be expressed from plasmids in e. coli and remain soluble without aggregation. we report a dual expression system for the display of four immunodominant regions of porcine circovirus 2 (pcv2) capsid protein (cap) as d-cap fusions on lambda display particles (ldp). the ldp-d-cap preparation proved an effective vaccine in pigs, eliciting both cellular and humoral immune responses and pcv2 neut ... | 2010 | 20674873 |
| mutagenesis of the repeat regions of herpesviruses cloned as bacterial artificial chromosomes. | cloning of infectious and pathogenic herpesvirus genomes in a bacterial artificial chromosome (bac) vector greatly facilitates genetic manipulation of their genomes. bac-based mutagenesis strategies of viruses can advance our understanding of the viral gene functions and determinants of pathogenicity, and can ultimately help to develop molecularly defined improved vaccines against virus diseases. unlike the virus stocks, where continuous passage in tissue culture can lead to phenotypic alteratio ... | 2010 | 20676975 |
| structural and functional views of salt-bridge interactions of λ integrase in the higher order recombinogenic complexes visualized by genetic method. | the integrase protein encoded by bacteriophage λ (int) catalyzes site a specific dna recombination by which the viral chromosome is inserted into and excised out of the host genome through the formation of higher order recombinogenic nucleoprotein complexes. genetic and biochemical studies on the int carried out by isolating "multimer-specific" mutants had revealed informative functional characteristics of specific electrostatic interactions occurring among the functional domains of int. the λ i ... | 2010 | 20708599 |
| reca-independent single-stranded dna oligonucleotide-mediated mutagenesis. | the expression of beta, the single-stranded annealing protein (ssap) of bacteriophage lambda in escherichia coli promotes high levels of oligonucleotide (oligo)-mediated mutagenesis and offers a quick way to create single or multiple base pair insertions, deletions, or substitutions in the bacterial chromosome. high rates of mutagenesis can be obtained by the use of mismatch repair (mmr)-resistant mismatches or mmr-deficient hosts, which allow for the isolation of unselected mutations. it has re ... | 2010 | 20711416 |