On the Internal Structure of Bacteriophage Lambda

PubMed Central

Kaiser, A. D.

1966-01-01

The structure of bacteriophage lambda has been studied by electron microscopy of negatively stained particles. The phage particles will eject their DNA if they are heated or dialyzed against a chelating agent. The ghost particles, so formed, have a channel running down their tails. Since the channel is not visible in normal particles, the channel may be filled with part of the DNA molecule. Up to 30% of the ghosts contain round objects about half the internal diameter of the head. The round objects, called "cores," have the same buoyant density as the coat protein. The core may be a protein spool about which the phage DNA is wound. PMID:5967429

A gene cassette for adapting Escherichia coli strains as hosts for att-Int-mediated rearrangement and pL expression vectors.

PubMed

Balakrishnan, R; Bolten, B; Backman, K C

1994-01-28

A cassette of genes from bacteriophage lambda, when carried on a derivative of bacteriophage Mu, renders strains of Escherichia coli (and in principle other Mu-sensitive bacteria) capable of supporting lambda-based expression vectors, such as rearrangement vectors and pL vectors. The gene cassette contains a temperature-sensitive allele of the repressor gene, cIts857, and a shortened leftward operon comprising, oLpL, N, xis and int. Transfection and lysogenization of this cassette into various host bacteria is mediated by phage Mu functions. Examples of regulated expression of the gene encoding T4 DNA ligase are presented.

Physical interactions between bacteriophage and Escherichia coli proteins required for initiation of lambda DNA replication.

PubMed

Liberek, K; Osipiuk, J; Zylicz, M; Ang, D; Skorko, J; Georgopoulos, C

1990-02-25

The process of initiation of lambda DNA replication requires the assembly of the proper nucleoprotein complex at the origin of replication, ori lambda. The complex is composed of both phage and host-coded proteins. The lambda O initiator protein binds specifically to ori lambda. The lambda P initiator protein binds to both lambda O and the host-coded dnaB helicase, giving rise to an ori lambda DNA.lambda O.lambda P.dnaB structure. The dnaK and dnaJ heat shock proteins have been shown capable of dissociating this complex. The thus freed dnaB helicase unwinds the duplex DNA template at the replication fork. In this report, through cross-linking, size chromatography, and protein affinity chromatography, we document some of the protein-protein interactions occurring at ori lambda. Our results show that the dnaK protein specifically interacts with both lambda O and lambda P, and that the dnaJ protein specifically interacts with the dnaB helicase.

Enhanced detection and identification of Shiga toxin 1 and 2 from pathogenic bacteria by MALDI-TOF-TOF-MS/MS-PSD and top-down proteomic analysis

USDA-ARS?s Scientific Manuscript database

Shiga toxin producing Escherichia coli (STEC) represent a continuing threat to the Nation’s food supply and public health. Shiga toxin genes (stx) are encoded in lambda-like bacteriophages whose genome is inserted into the bacterial DNA. Environmental stress can trigger bacteriophage replication a...

Bacteriophage T5 DNA ejection under pressure.

PubMed

Leforestier, A; Brasilès, S; de Frutos, M; Raspaud, E; Letellier, L; Tavares, P; Livolant, F

2008-12-19

The transfer of the bacteriophage genome from the capsid into the host cell is a key step of the infectious process. In bacteriophage T5, DNA ejection can be triggered in vitro by simple binding of the phage to its purified Escherichia coli receptor FhuA. Using electrophoresis and cryo-electron microscopy, we measure the extent of DNA ejection as a function of the external osmotic pressure. In the high pressure range (7-16 atm), the amount of DNA ejected decreases with increasing pressure, as theoretically predicted and observed for lambda and SPP1 bacteriophages. In the low and moderate pressure range (2-7 atm), T5 exhibits an unexpected behavior. Instead of a unique ejected length, multiple populations coexist. Some phages eject their complete genome, whereas others stop at some nonrandom states that do not depend on the applied pressure. We show that contrarily to what is observed for the phages SPP1 and lambda, T5 ejection cannot be explained as resulting from a simple pressure equilibrium between the inside and outside of the capsid. Kinetics parameters and/or structural characteristics of the ejection machinery could play a determinant role in T5 DNA ejection.

Evidence of translation efficiency adaptation of the coding regions of the bacteriophage lambda.

PubMed

Goz, Eli; Mioduser, Oriah; Diament, Alon; Tuller, Tamir

2017-08-01

Deciphering the way gene expression regulatory aspects are encoded in viral genomes is a challenging mission with ramifications related to all biomedical disciplines. Here, we aimed to understand how the evolution shapes the bacteriophage lambda genes by performing a high resolution analysis of ribosomal profiling data and gene expression related synonymous/silent information encoded in bacteriophage coding regions.We demonstrated evidence of selection for distinct compositions of synonymous codons in early and late viral genes related to the adaptation of translation efficiency to different bacteriophage developmental stages. Specifically, we showed that evolution of viral coding regions is driven, among others, by selection for codons with higher decoding rates; during the initial/progressive stages of infection the decoding rates in early/late genes were found to be superior to those in late/early genes, respectively. Moreover, we argued that selection for translation efficiency could be partially explained by adaptation to Escherichia coli tRNA pool and the fact that it can change during the bacteriophage life cycle.An analysis of additional aspects related to the expression of viral genes, such as mRNA folding and more complex/longer regulatory signals in the coding regions, is also reported. The reported conclusions are likely to be relevant also to additional viruses. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Specialized nucleoprotein structures at the origin of replication of bacteriophage lambda: localized unwinding of duplex DNA by a six-protein reaction.

PubMed Central

Dodson, M; Echols, H; Wickner, S; Alfano, C; Mensa-Wilmot, K; Gomes, B; LeBowitz, J; Roberts, J D; McMacken, R

1986-01-01

The O protein of bacteriophage lambda localizes the initiation of DNA replication to a unique site on the lambda genome, ori lambda. By means of electron microscopy, we infer that the binding of O to ori lambda initiates a series of protein addition and transfer reactions that culminate in localized unwinding of the origin DNA, generating a prepriming structure for the initiation of DNA replication. We can define three stages of this prepriming reaction, the first two of which we have characterized previously. First, dimeric O protein binds to multiple DNA binding sites and self-associates to form a nucleoprotein structure, the O-some. Second, lambda P and host DnaB proteins interact with the O-some to generate a larger complex that includes additional DNA from an A + T-rich region adjacent to the O binding sites. Third, the addition of the DnaJ, DnaK, and Ssb proteins and ATP results in an origin-specific unwinding reaction, probably catalyzed by the helicase activity of DnaB. The unwinding reaction is unidirectional, proceeding "rightward" from the origin. The minimal DNA sequence competent for unwinding consists of two O binding sites and the adjacent A + T-rich region to the right of the binding sites. We conclude that the lambda O protein localizes and initiates a six-protein sequential reaction responsible for but preceding the precise initiation of DNA replication. Specialized nucleoprotein structures similar to the O-some may be a general feature of DNA transactions requiring extraordinary precision in localization and control. Images PMID:3020552

Multiple factors and processes involved in host cell killing by bacteriophage Mu: characterization and mapping.

PubMed

Waggoner, B T; Marrs, C F; Howe, M M; Pato, M L

1984-07-15

The regions of bacteriophage Mu involved in host cell killing were determined by infection of a lambda-immune host with 12 lambda pMu-transducing phages carrying different amounts of Mu DNA beginning at the left end. Infecting lambda pMu phages containing 5.0 (+/- 0.2) kb or less of the left end of Mu DNA did not kill the lambda-immune host, whereas lambda pMu containing 5.1 kb did kill, thus locating the right end of the kil gene between approximately 5.0 and 5.1 kb. For the Kil+ phages the extent of killing increased as the multiplicity of infection (m.o.i.) increased. In addition, killing was also affected by the presence of at least two other regions of Mu DNA: one, located between 5.1 and 5.8 kb, decreased the extent of killing; the other, located between 6.3 and 7.9 kb, greatly increased host cell killing. Killing was also assayed after lambda pMu infection of a lambda-immune host carrying a mini-Mu deleted for most of the B gene and the middle region of Mu DNA. Complementation of mini-Mu replication by infecting B+ lambda pMu phages resulted in killing of the lambda-immune, mini-Mu-containing host, regardless of the presence or absence of the Mu kil gene. The extent of host cell killing increased as the m.o.i. of the infecting lambda pMu increased, and was further enhanced by both the presence of the kil gene and the region located between 6.3 and 7.9 kb. These distinct processes of kil-mediated killing in the absence of replication and non-kil-mediated killing in the presence of replication were also observed after induction of replication-deficient and kil mutant prophages, respectively.

Cloning and Characterization of the P-l Promoter of Bacteriophage Lambda.

ERIC Educational Resources Information Center

Andino, Raul H.; And Others

1986-01-01

Background information, experimental approach, materials needed, procedures used, and typical results obtained are provided for genetic engineering experiments. The course in which these experiments are performed is also described. (JN)

Evaluation of humoral and cellular immune responses against HSV-1 using genetic immunization by filamentous phage particles: a comparative approach to conventional DNA vaccine.

PubMed

Hashemi, Hamidreza; Bamdad, Taravat; Jamali, Abbas; Pouyanfard, Somayeh; Mohammadi, Masoumeh Gorgian

2010-02-01

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 for vaccination of mice. BALB/c mice were inoculated with filamentous phage particles containing expression cassette of Herpes simplex virus 1 (HSV-1) glycoprotein D that has essential roles in the virus attachment and entry. Both humoral and cellular immune responses were measured in the immunized mice and compared to conventional DNA vaccination. A dose-response relationship was observed in both arms of immune responses induced by recombinant filamentous phage inoculation. The results were similar to those from DNA vaccination. Filamentous phages can be considered as suitable alternative candidate vaccines because of easier and more cost-effective production and purification over plasmid DNA or bacteriophage lambda particles. 2009 Elsevier B.V. All rights reserved.

Salt-Dependent DNA-DNA Spacings in Intact Bacteriophage lambda Reflect Relative Importance of DNA Self-Repulsion and Bending Energies

DOE Office of Scientific and Technical Information (OSTI.GOV)

X Qiu; D Rau; V Parsegian

2011-12-31

Using solution synchrotron x-ray scattering, we measure the variation of DNA-DNA d spacings in bacteriophage {lambda} with mono-, di-, and polyvalent salt concentrations, for wild-type [48.5 x 10{sup 3} base pairs (bp)] and short-genome-mutant (37.8 kbp) strains. From the decrease in d spacings with increasing salt, we deduce the relative contributions of DNA self-repulsion and bending to the energetics of packaged phage genomes. We quantify the DNA-DNA interaction energies within the intact phage by combining the measured d spacings in the capsid with measurements of osmotic pressure in DNA assemblies under the same salt conditions in bulk solution. In themore » commonly used Tris-Mg buffer, the DNA-DNA interaction energies inside the phage capsids are shown to be about 1 kT/bp, an order of magnitude larger than the bending energies.« less

Two-stage continuous operation of recombinant Escherichia coli using the bacteriophage lambda Q- vector.

PubMed

Oh, Jeong Seok; Cho, Daechul; Park, Tai Hyun

2005-11-01

A two-stage continuous culture of Escherichia coli in combination with a bacteriophage lambda system was performed in order to overcome the intrinsic plasmid instability that is frequently observed in recombinant fermentation. A phage lambda vector with a Q(-) mutation was used to enhance the expression of the lambda system. The optimal values of the important operational variables such as the substrate concentration, the dilution rate, and the mean residence time on the expression of the cloned gene were determined in both batch and continuous cultures. For all culturing modes, the full induction of the cloned gene was observed 4 h after the temperature shift. In the two stage continuous culture, the overproduction reached their maxima at D=0.25 h(-1) with 1.5 S(0) of the medium supply. The maximum productivity of the total beta-galactosidase was 16.3x10(6) U l(-1) h(-1), which was approximately seven times higher than that in the single-copy lysogenic stage. The recombinant cells were stable in the lysogenic state for more than 260 h, while they were stable for 40 h in the lytic state. The instability that developed rapidly in the second tank is believed to be due to the accumulation of lysis proteins as a result of vector leakage during the operation.

Role of DNA-DNA Interactions on the Structure and Thermodynamics of Bacteriophages Lambda and P4

PubMed Central

Petrov, Anton S.; Harvey, Stephen C.

2010-01-01

Electrostatic interactions play an important role in both packaging of DNA inside bacteriophages and its release into bacterial cells. While at physiological conditions DNA strands repel each other, the presence of polyvalent cations such as spermine and spermidine in solutions leads to the formation of DNA condensates. In this study, we discuss packaging of DNA into bacteriophages P4 and Lambda under repulsive and attractive conditions using a coarse-grained model of DNA and capsids. Packaging under repulsive conditions leads to the appearance of the coaxial spooling conformations; DNA occupies all available space inside the capsid. Under the attractive potential both packed systems reveal toroidal conformations, leaving the central part of the capsids empty. We also present a detailed thermodynamic analysis of packaging and show that the forces required to pack the genomes in the presence of polyamines are significantly lower than those observed under repulsive conditions. The analysis reveals that in both the repulsive and attractive regimes the entropic penalty of DNA confinement has a significant non-negligible contribution into the total energy of packaging. Additionally we report the results of simulations of DNA condensation inside partially packed Lambda. We found that at low densities DNA behaves as free unconfined polymer and condenses into the toroidal structures; at higher densities rearrangement of the genome into toroids becomes hindered, and condensation results in the formation of non-equilibrium structures. In all cases packaging in a specific conformation occurs as a result of interplay between bending stresses experienced by the confined polymer and interactions between the strands. PMID:21074621

Recombination between bacteriophage lambda and plasmid pBR322 in Escherichia coli.

PubMed Central

Pogue-Geile, K L; Dassarma, S; King, S R; Jaskunas, S R

1980-01-01

Recombinant lambda phages were isolated that resulted from recombination between the lambda genome and plasmid pBR322 in Escherichia coli, even though these deoxyribonucleic acids (DNAs) did not share extensive regions of homology. The characterization of these recombinant DNAs by heteroduplex analysis and restriction endonucleases is described. All but one of the recombinants appeared to have resulted from reciprocal recombination between a site on lambda DNA and a site on the plasmid. In general, there were two classes of recombinants. One class appeared to have resulted from recombination at the phage attachment site that probably resulted from lambda integration into secondary attachment sites on the plasmid. Seven different secondary attachment sites on pBR322 were found. The other class resulted from plasmid integration at other sites that were widely scattered on the lambda genome. For this second class of recombinants, more than one site on the plasmid could recombine with lambda DNA. Thus, the recombination did not appear to be site specific with respect to lambda or the plasmid. Possible mechanisms for generating these recombinants are discussed. Images PMID:6247334

Stabilization of T4 bacteriophage at acidic and basic pH by adsorption on paper.

PubMed

Meyer, Abigail; Greene, Melissa; Kimmelshue, Chad; Cademartiri, Rebecca

2017-12-01

Bacteriophages find applications in agriculture, medicine, and food safety. Many of these applications can expose bacteriophages to stresses that inactivate them including acidic and basic pH. Bacteriophages can be stabilized against these stresses by materials including paper, a common material in packaging and consumer products. Combining paper and bacteriophages creates antibacterial materials, which can reduce the use of antibiotics. Here we show that adsorption on paper protects T4, T5, and T7 bacteriophage from acidic and basic pH. We added bacteriophages to filter paper functionalized with carboxylic acid (carboxyl methyl cellulose) or amine (chitosan) groups, and exposed them to pH from 5.6 to 14. We determined the number of infective bacteriophages after exposure directly on the paper. All papers extended the lifetime of infective bacteriophage by at least a factor of four with some papers stabilizing bacteriophages for up to one week. The degree of stabilization depended on five main factors (i) the family of the bacteriophage, (ii) the charge of the paper and bacteriophages, (iii) the location of the bacteriophages within the paper, (iv) the ability of the paper to prevent bacteriophage-bacteriophage aggregation, and (v) the sensitivity of the bacteriophage proteins to the tested pH. Even when adsorbed on paper the bacteriophages were able to remove E. coli in milk. Choosing the right paper modification or material will protect bacteriophages adsorbed on that material against detrimental pH and other environmental challenges increasing the range of applications of bacteriophages on materials. Copyright © 2017 Elsevier B.V. All rights reserved.

An unexpected twist in viral capsid maturation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gertsman, Ilya; Gan, Lu; Guttman, Miklos

2009-04-14

Lambda-like double-stranded (ds) DNA bacteriophage undergo massive conformational changes in their capsid shell during the packaging of their viral genomes. Capsid shells are complex organizations of hundreds of protein subunits that assemble into intricate quaternary complexes that ultimately are able to withstand over 50 atm of pressure during genome packaging. The extensive integration between subunits in capsids requires the formation of an intermediate complex, termed a procapsid, from which individual subunits can undergo the necessary refolding and structural rearrangements needed to transition to the more stable capsid. Although various mature capsids have been characterized at atomic resolution, no such procapsidmore » structure is available for a dsDNA virus or bacteriophage. Here we present a procapsid X-ray structure at 3.65 {angstrom} resolution, termed prohead II, of the lambda-like bacteriophage HK97, the mature capsid structure of which was previously solved to 3.44 {angstrom}. A comparison of the two largely different capsid forms has unveiled an unprecedented expansion mechanism that describes the transition. Crystallographic and hydrogen/deuterium exchange data presented here demonstrate that the subunit tertiary structures are significantly different between the two states, with twisting and bending motions occurring in both helical and -sheet regions. We also identified subunit interactions at each three-fold axis of the capsid that are maintained throughout maturation. The interactions sustain capsid integrity during subunit refolding and provide a fixed hinge from which subunits undergo rotational and translational motions during maturation. Previously published calorimetric data of a closely related bacteriophage, P22, showed that capsid maturation was an exothermic process that resulted in a release of 90 kJ mol{sup -1} of energy. We propose that the major tertiary changes presented in this study reveal a structural basis for an exothermic maturation process probably present in many dsDNA bacteriophage and possibly viruses such as herpesvirus, which share the HK97 subunit fold.« less

Analysis of Endonuclease R·EcoRI Fragments of DNA from Lambdoid Bacteriophages and Other Viruses by Agarose-Gel Electrophoresis

PubMed Central

Helling, Robert B.; Goodman, Howard M.; Boyer, Herbert W.

1974-01-01

By means of agarose-gel electrophoresis, endonuclease R·EcoRI-generated fragments of DNA from various viruses were separated, their molecular weights were determined, and complete or partial fragment maps for lambda, φ80, and hybrid phages were constructed. Images PMID:4372397

PCR amplification of up to 35-kb DNA with high fidelity and high yield from lambda bacteriophage templates.

PubMed Central

Barnes, W M

1994-01-01

A target length limitation to PCR amplification of DNA has been identified and addressed. Concomitantly, the base-pair fidelity, the ability to use PCR products as primers, and the maximum yield of target fragment were increased. These improvements were achieved by the combination of a high level of an exonuclease-free, N-terminal deletion mutant of Taq DNA polymerase, Klentaq1, with a very low level of a thermostable DNA polymerase exhibiting a 3'-exonuclease activity (Pfu, Vent, or Deep Vent). At least 35 kb can be amplified to high yields from 1 ng of lambda DNA template. Images PMID:8134376

A 1-kb bacteriophage lambda fragment functions as an insulator to effectively block enhancer-promoter interactions in Arabidopsis thaliana

USDA-ARS?s Scientific Manuscript database

The 35S cauliflower mosaic virus (CaMV) promoter contains an enhancer element that is able to override the tissue-, organ- and developmental-stage specificity of nearby promoters. Consequently, the precise control of transgene expression in transgenic plants, which often contain the 35S CaMV promot...

A kinetic analysis of DNA ejection from tailed phages revealing the prerequisite activation energy.

PubMed

Raspaud, Eric; Forth, Thomas; São-José, Carlos; Tavares, Paulo; de Frutos, Marta

2007-12-01

All tailed bacteriophages follow the same general scheme of infection: they bind to their specific host receptor and then transfer their genome into the bacterium. DNA translocation is thought to be initiated by the strong pressure due to DNA packing inside the capsid. However, the exact mechanism by which each phage controls its DNA ejection remains unknown. Using light scattering, we analyzed the kinetics of in vitro DNA release from phages SPP1 and lambda (Siphoviridae family) and found a simple exponential decay. The ejection characteristic time was studied as a function of the temperature and found to follow an Arrhenius law, allowing us to determine the activation energy that governs DNA ejection. A value of 25-30 kcal/mol is obtained for SPP1 and lambda, comparable to the one measured in vitro for T5 (Siphoviridae) and in vivo for T7 (Podoviridae). This suggests similar mechanisms of DNA ejection control. In all tailed phages, the opening of the connector-tail channel is needed for DNA release and could constitute the limiting step. The common value of the activation energy likely reflects the existence for all phages of an optimum value, ensuring a compromise between efficient DNA delivery and high stability of the virus.

Family values in the age of genomics: comparative analyses of temperate bacteriophage HK022.

PubMed

Weisberg, R A; Gottesmann, M E; Hendrix, R W; Little, J W

1999-01-01

HK022 is a temperate coliphage related to phage lambda. Its chromosome has been completely sequenced, and several aspects of its life cycle have been intensively studied. In the overall arrangement, expression, and function of most of its genes, HK022 broadly resembles lambda and other members of the lambda family. Upon closer view, significant differences emerge. The differences reveal alternative strategies used by related phages to cope with similar problems and illuminate previously unknown regulatory and structural motifs. HK022 prophages protect lysogens from superinfection by producing a sequence-specific RNA binding protein that prematurely terminates nascent transcripts of infecting phage. It uses a novel RNA-based mechanism to antiterminate its own early transcription. The HK022 protein shell is strengthened by a complex pattern of covalent subunit interlinking to form a unitary structure that resembles chain-mail armour. Its integrase and repressor proteins are similar to those of lambda, but the differences provide insights into the evolution of biological specificity and the elements needed for construction of a stable genetic switch.

The Lambda Select cII Mutation Detection System.

PubMed

Besaratinia, Ahmad; Tommasi, Stella

2018-04-26

A number of transgenic animal models and mutation detection systems have been developed for mutagenicity testing of carcinogens in mammalian cells. Of these, transgenic mice and the Lambda (λ) Select cII Mutation Detection System have been employed for mutagenicity experiments by many research groups worldwide. Here, we describe a detailed protocol for the Lambda Select cII mutation assay, which can be applied to cultured cells of transgenic mice/rats or the corresponding animals treated with a chemical/physical agent of interest. The protocol consists of the following steps: (1) isolation of genomic DNA from the cells or organs/tissues of transgenic animals treated in vitro or in vivo, respectively, with a test compound; (2) recovery of the lambda shuttle vector carrying a mutational reporter gene (i.e., cII transgene) from the genomic DNA; (3) packaging of the rescued vectors into infectious bacteriophages; (4) infecting a host bacteria and culturing under selective conditions to allow propagation of the induced cII mutations; and (5) scoring the cII-mutants and DNA sequence analysis to determine the cII mutant frequency and mutation spectrum, respectively.

A Single Molecule Study of Two Bacteriophage Epigenetic Switches

NASA Astrophysics Data System (ADS)

Wang, Haowei

Epigenetic switches allow organisms to evolve into different states by activating/repressing different sets of genes without mutations of the underlying DNA sequence. The study of epigenetic switches is very important to understand the mechanism of human development, the origin of cancer, mental illness and fundamental processes such as gene regulation. The coliphage lambda epigenetic switch, which allows switching from lysogeny to lysis, has been studied for more than 50 years as a paradigm, and has recently received renewed attention. Atomic force microscopy (AFM) was used here to show that the lambda repressor oligomerizes on DNA, primarily as a dodecamer, to secure a DNA loop, which is the basis of the lambda switch. This study also provides support for the idea that specifically bound repressor stabilizes adjacent, non-specifically bound repressor molecules, which confers robustness to the switch. 186 is a member of a different coliphage family. One of the major differences between the two coliphage families is that lambda phages can be induced to switch from the lysogenic to the lytic state by UV radiation, but most coliphages of P2 family, to which 186 belongs, cannot. Interaction between coliphage 186 repressor and DNA is characterized by AFM and tethered particle motion (TPM). To expedite analysis of the AFM data, MatLab codes were written to automate the laborious, manual tracing procedures. The programs automatically recognize DNA segments and protein particles in an image, in order to measure the DNA length and position of bound particles as well as their height, diameter and volume. Application of these algorithms greatly improved the efficiency of AFM analysis. It was showed that 186 CI dimers form heptameric wheels, which induce DNA wrapping and different kinds of DNA looping producing various conformations of nucleoprotein complexes. Information about the dynamics of DNA wrapping and looping on 186 CI particles was also obtained by TPM.

Genome, Integration, and Transduction of a Novel Temperate Phage of Helicobacter pylori

PubMed Central

Luo, Cheng-Hung; Chiou, Pei-Yu; Yang, Chiou-Ying

2012-01-01

Helicobacter pylori is a common human pathogen that has been identified to be carcinogenic. This study isolated the temperate bacteriophage 1961P from the lysate of a clinical strain of H. pylori isolated in Taiwan. The bacteriophage has an icosahedral head and a short tail, typical of the Podoviridae family. Its double-stranded DNA genome is 26,836 bp long and has 33 open reading frames. Only 9 of the predicted proteins have homologs of known functions, while the remaining 24 are only similar to unknown proteins encoded by Helicobacter prophages and remnants. Analysis of sequences proximal to the phage-host junctions suggests that 1961P may integrate into the host chromosome via a mechanism similar to that of bacteriophage lambda. In addition, 1961P is capable of generalized transduction. To the best of our knowledge, this is the first report of the isolation, characterization, genome analysis, integration, and transduction of a Helicobacter pylori phage. PMID:22696647

Enhanced expression of cro-beta-galactosidase fusion proteins under the control of the PR promoter of bacteriophage lambda.

PubMed Central

Zabeau, M; Stanley, K K

1982-01-01

Hybrid plasmids carrying cro-lacZ gene fusions have been constructed by joining DNA segments carrying the PR promoter and the start of the cro gene of bacteriophage lambda to the lacZ gene fragment carried by plasmid pLG400 . Plasmids in which the translational reading frames of the cro and lacZ genes are joined in-register (type I) direct the synthesis of elevated levels of cro-beta-galactosidase fusion protein amounting to 30% of the total cellular protein, while plasmids in which the genes are fused out-of-register (type II) produce a low level of beta-galactosidase protein. Sequence rearrangements downstream of the cro initiator AUG were found to influence the efficiency of translation, and have been correlated with alterations in the RNA secondary structure of the ribosome-binding site. Plasmids which direct the synthesis of high levels of beta-galactosidase are conditionally lethal and can only be propagated when the PR promoter is repressed. Deletion of sequences downstream of the lacZ gene restored viability, indicating that this region of the plasmid encodes a function which inhibits the growth of the cells. The different applications of these plasmids for expression of cloned genes are discussed. Images Fig. 6. PMID:6327257

Isolation and characterization of glacier VMY22, a novel lytic cold-active bacteriophage of Bacillus cereus.

PubMed

Ji, Xiuling; Zhang, Chunjing; Fang, Yuan; Zhang, Qi; Lin, Lianbing; Tang, Bing; Wei, Yunlin

2015-02-01

As a unique ecological system with low temperature and low nutrient levels, glaciers are considered a "living fossil" for the research of evolution. In this work, a lytic cold-active bacteriophage designated VMY22 against Bacillus cereus MYB41-22 was isolated from Mingyong Glacier in China, and its characteristics were studied. Electron microscopy revealed that VMY22 has an icosahedral head (59.2 nm in length, 31.9 nm in width) and a tail (43.2 nm in length). Bacteriophage VMY22 was classified as a Podoviridae with an approximate genome size of 18 to 20 kb. A one-step growth curve revealed that the latent and the burst periods were 70 and 70 min, respectively, with an average burst size of 78 bacteriophage particles per infected cell. The pH and thermal stability of bacteriophage VMY22 were also investigated. The maximum stability of the bacteriophage was observed to be at pH 8.0 and it was comparatively stable at pH 5.0-9.0. As VMY22 is a cold-active bacteriophage with low production temperature, its characterization and the relationship between MYB41-22 and Bacillus cereus bacteriophage deserve further study.

Hexagonally packed DNA within bacteriophage T7 stabilized by curvature stress.

PubMed Central

Odijk, T

1998-01-01

A continuum computation is proposed for the bending stress stabilizing DNA that is hexagonally packed within bacteriophage T7. Because the inner radius of the DNA spool is rather small, the stress of the curved DNA genome is strong enough to balance its electrostatic self-repulsion so as to form a stable hexagonal phase. The theory is in accord with the microscopically determined structure of bacteriophage T7 filled with DNA within the experimental margin of error. PMID:9726924

Discovery of a protein phosphatase activity encoded in the genome of bacteriophage lambda. Probable identity with open reading frame 221.

PubMed

Cohen, P T; Cohen, P

1989-06-15

Infection of Escherichia coli with phage lambda gt10 resulted in the appearance of a protein phosphatase with activity towards 32P-labelled casein. Activity reached a maximum near the point of cell lysis and declined thereafter. The phosphatase was stimulated 30-fold by Mn2+, while Mg2+ and Ca2+ were much less effective. Activity was unaffected by inhibitors 1 and 2, okadaic acid, calmodulin and trifluoperazine, distinguishing it from the major serine/threonine-specific protein phosphatases of eukaryotic cells. The lambda phosphatase was also capable of dephosphorylating other substrates in the presence of Mn2+, although activity towards 32P-labelled phosphorylase was 10-fold lower, and activity towards phosphorylase kinase and glycogen synthase 25 50-fold lower than with casein. No casein phosphatase activity was present in either uninfected cells, or in E. coli infected with phage lambda gt11. Since lambda gt11 lacks part of the open reading frame (orf) 221, previously shown to encode a protein with sequence similarity to protein phosphatase-1 and protein phosphatase-2A of mammalian cells [Cohen, Collins, Coulson, Berndt & da Cruz e Silva (1988) Gene 69, 131-134], the results indicate that ORF221 is the protein phosphatase detected in cells infected with lambda gt10. Comparison of the sequence of ORF221 with other mammalian protein phosphatases defines three highly conserved regions which are likely to be essential for function. The first of these is deleted in lambda gt11.

Stability of monomeric Cro variants: Isoenergetic transformation of a type I' to a type II' beta-hairpin by single amino acid replacements.

PubMed

Mollah, A K M M; Stennis, Rhonda L; Mossing, Michael C

2003-05-01

The thermodynamic stabilities of three monomeric variants of the bacteriophage lambda Cro repressor that differ only in the sequence of two amino acids at the apex of an engineered beta-hairpin have been determined. The sequences of the turns are EVK-XX-EVK, where the two central residues are DG, GG, and GT, respectively. Standard-state unfolding free energies, determined from circular dichroism measurements as a function of urea concentration, range from 2.4 to 2.7 kcal/mole, while those determined from guanidine hydrochloride range from 2.8 to 3.3 kcal/mole for the three proteins. Thermal denaturation yields van't Hoff unfolding enthalpies of 36 to 40 kcal /mole at midpoint temperatures in the range of 53 to 58 degrees C. Extrapolation of the thermal denaturation free energies with heat capacities of 400 to 600 cal/mole deg gives good agreement with the parameters determined in denaturant titrations. As predicted from statistical surveys of amino acid replacements in beta-hairpins, energetic barriers to transformation from a type I' turn (DG) to a type II' turn (GT) can be quite small.

Newly Isolated Bacteriophages from the Podoviridae, Siphoviridae, and Myoviridae Families Have Variable Effects on Putative Novel Dickeya spp.

PubMed

Alič, Špela; Naglič, Tina; Tušek-Žnidarič, Magda; Ravnikar, Maja; Rački, Nejc; Peterka, Matjaž; Dreo, Tanja

2017-01-01

Soft rot pathogenic bacteria from the genus Dickeya cause severe economic losses in orchid nurseries worldwide, and there is no effective control currently available. In the last decade, the genus Dickeya has undergone multiple changes as multiple new taxa have been described, and just recently a new putative Dickeya species was reported. This study reports the isolation of three bacteriophages active against putative novel Dickeya spp. isolates from commercially produced infected orchids that show variable host-range profiles. Bacteriophages were isolated through enrichment from Dickeya -infected orchid tissue. Convective interaction media monolith chromatography was used to isolate bacteriophages from wastewaters, demonstrating its suitability for the isolation of infective bacteriophages from natural sources. Based on bacteriophage morphology, all isolated bacteriophages were classified as being in the order Caudovirales , belonging to three different families, Podoviridae , Myoviridae , and Siphoviridae . The presence of three different groups of bacteriophages was confirmed by analyzing the bacteriophage specificity of bacterial hosts, restriction fragment length polymorphism and plaque morphology. Bacteriophage BF25/12, the first reported Podoviridae bacteriophage effective against Dickeya spp., was selected for further characterization. Its genome sequence determined by next-generation sequencing showed limited similarity to other characterized Podoviridae bacteriophages. Interactions among the bacteriophages and Dickeya spp. were examined using transmission electron microscopy, which revealed degradation of electron-dense granules in response to bacteriophage infection in some Dickeya strains. The temperature stability of the chosen Podoviridae bacteriophage monitored over 1 year showed a substantial decrease in the survival of bacteriophages stored at -20°C over longer periods. It showed susceptibility to low pH and UV radiation but was stable in neutral and alkaline pH. Furthermore, the stability of the tested bacteriophage was also connected to the incubation medium and bacteriophage concentration at certain pH values. Finally, the emergence of bacteriophage-resistant bacterial colonies is highly connected to the concentration of bacteriophages in the bacterial environment. This is the first report on bacteriophages against Dickeya from the Podoviridae family to expand on potential bacteriophages to include in bacteriophage cocktails as biocontrol agents. Some of these bacteriophage isolates also showed activity against Dickeya solani , an aggressive strain that causes the soft rot of potatoes, which indicates their broad potential as biocontrol agents.

Newly Isolated Bacteriophages from the Podoviridae, Siphoviridae, and Myoviridae Families Have Variable Effects on Putative Novel Dickeya spp.

PubMed Central

Alič, Špela; Naglič, Tina; Tušek-Žnidarič, Magda; Ravnikar, Maja; Rački, Nejc; Peterka, Matjaž; Dreo, Tanja

2017-01-01

Soft rot pathogenic bacteria from the genus Dickeya cause severe economic losses in orchid nurseries worldwide, and there is no effective control currently available. In the last decade, the genus Dickeya has undergone multiple changes as multiple new taxa have been described, and just recently a new putative Dickeya species was reported. This study reports the isolation of three bacteriophages active against putative novel Dickeya spp. isolates from commercially produced infected orchids that show variable host-range profiles. Bacteriophages were isolated through enrichment from Dickeya-infected orchid tissue. Convective interaction media monolith chromatography was used to isolate bacteriophages from wastewaters, demonstrating its suitability for the isolation of infective bacteriophages from natural sources. Based on bacteriophage morphology, all isolated bacteriophages were classified as being in the order Caudovirales, belonging to three different families, Podoviridae, Myoviridae, and Siphoviridae. The presence of three different groups of bacteriophages was confirmed by analyzing the bacteriophage specificity of bacterial hosts, restriction fragment length polymorphism and plaque morphology. Bacteriophage BF25/12, the first reported Podoviridae bacteriophage effective against Dickeya spp., was selected for further characterization. Its genome sequence determined by next-generation sequencing showed limited similarity to other characterized Podoviridae bacteriophages. Interactions among the bacteriophages and Dickeya spp. were examined using transmission electron microscopy, which revealed degradation of electron-dense granules in response to bacteriophage infection in some Dickeya strains. The temperature stability of the chosen Podoviridae bacteriophage monitored over 1 year showed a substantial decrease in the survival of bacteriophages stored at -20°C over longer periods. It showed susceptibility to low pH and UV radiation but was stable in neutral and alkaline pH. Furthermore, the stability of the tested bacteriophage was also connected to the incubation medium and bacteriophage concentration at certain pH values. Finally, the emergence of bacteriophage-resistant bacterial colonies is highly connected to the concentration of bacteriophages in the bacterial environment. This is the first report on bacteriophages against Dickeya from the Podoviridae family to expand on potential bacteriophages to include in bacteriophage cocktails as biocontrol agents. Some of these bacteriophage isolates also showed activity against Dickeya solani, an aggressive strain that causes the soft rot of potatoes, which indicates their broad potential as biocontrol agents. PMID:29033917

Evidence for a lineage of virulent bacteriophages that target Campylobacter.

PubMed

Timms, Andrew R; Cambray-Young, Joanna; Scott, Andrew E; Petty, Nicola K; Connerton, Phillippa L; Clarke, Louise; Seeger, Kathy; Quail, Mike; Cummings, Nicola; Maskell, Duncan J; Thomson, Nicholas R; Connerton, Ian F

2010-03-30

Our understanding of the dynamics of genome stability versus gene flux within bacteriophage lineages is limited. Recently, there has been a renewed interest in the use of bacteriophages as 'therapeutic' agents; a prerequisite for their use in such therapies is a thorough understanding of their genetic complement, genome stability and their ecology to avoid the dissemination or mobilisation of phage or bacterial virulence and toxin genes. Campylobacter, a food-borne pathogen, is one of the organisms for which the use of bacteriophage is being considered to reduce human exposure to this organism. Sequencing and genome analysis was performed for two Campylobacter bacteriophages. The genomes were extremely similar at the nucleotide level (> or = 96%) with most differences accounted for by novel insertion sequences, DNA methylases and an approximately 10 kb contiguous region of metabolic genes that were dissimilar at the sequence level but similar in gene function between the two phages. Both bacteriophages contained a large number of radical S-adenosylmethionine (SAM) genes, presumably involved in boosting host metabolism during infection, as well as evidence that many genes had been acquired from a wide range of bacterial species. Further bacteriophages, from the UK Campylobacter typing set, were screened for the presence of bacteriophage structural genes, DNA methylases, mobile genetic elements and regulatory genes identified from the genome sequences. The results indicate that many of these bacteriophages are related, with 10 out of 15 showing some relationship to the sequenced genomes. Two large virulent Campylobacter bacteriophages were found to show very high levels of sequence conservation despite separation in time and place of isolation. The bacteriophages show adaptations to their host and possess genes that may enhance Campylobacter metabolism, potentially advantaging both the bacteriophage and its host. Genetic conservation has been shown to extend to other Campylobacter bacteriophages, forming a highly conserved lineage of bacteriophages that predate upon campylobacters and indicating that highly adapted bacteriophage genomes can be stable over prolonged periods of time.

Biomechanical stability analysis of the lambda-model controlling one joint.

PubMed

Lan, L; Zhu, K Y

2007-06-01

Computer modeling and control of the human motor system might be helpful for understanding the mechanism of human motor system and for the diagnosis and treatment of neuromuscular disorders. In this paper, a brief view of the equilibrium point hypothesis for human motor system modeling is given, and the lambda-model derived from this hypothesis is studied. The stability of the lambda-model based on equilibrium and Jacobian matrix is investigated. The results obtained in this paper suggest that the lambda-model is stable and has a unique equilibrium point under certain conditions.

Understanding the enormous diversity of bacteriophages: the tailed phages that infect the bacterial family Enterobacteriaceae.

PubMed

Grose, Julianne H; Casjens, Sherwood R

2014-11-01

Bacteriophages are the predominant biological entity on the planet. The recent explosion of sequence information has made estimates of their diversity possible. We describe the genomic comparison of 337 fully sequenced tailed phages isolated on 18 genera and 31 species of bacteria in the Enterobacteriaceae. These phages were largely unambiguously grouped into 56 diverse clusters (32 lytic and 24 temperate) that have syntenic similarity over >50% of the genomes within each cluster, but substantially less sequence similarity between clusters. Most clusters naturally break into sets of more closely related subclusters, 78% of which are correlated with their host genera. The largest groups of related phages are superclusters united by genome synteny to lambda (81 phages) and T7 (51 phages). This study forms a robust framework for understanding diversity and evolutionary relationships of existing tailed phages, for relating newly discovered phages and for determining host/phage relationships.

Understanding the enormous diversity of bacteriophages: the tailed phages that infect the bacterial family Enterobacteriaceae

PubMed Central

Grose, Julianne H.; Casjens, Sherwood R.

2014-01-01

Bacteriophages are the predominant biological entity on the planet. The recent explosion of sequence information has made estimates of their diversity possible. We describe the genomic comparison of 337 fully sequenced tailed phages isolated on 18 genera and 31 species of bacteria in the Enterobacteriaceae. These phages were largely unambiguously grouped into 56 diverse clusters (32 lytic and 24 temperate) that have syntenic similarity over >50% of the genomes within each cluster, but substantially less sequence similarity between clusters. Most clusters naturally break into sets of more closely related subclusters, 78% of which are correlated with their host genera. The largest groups of related phages are superclusters united by genome synteny to lambda (81 phages) and T7 (51 phages). This study forms a robust framework for understanding diversity and evolutionary relationships of existing tailed phages, for relating newly discovered phages and for determining host/phage relationships. PMID:25240328

Isolation and Characterization of the Lytic Cold-Active Bacteriophage MYSP06 from the Mingyong Glacier in China.

PubMed

Li, Mingyuan; Wang, Jilian; Zhang, Qi; Lin, Lianbing; Kuang, Anxin; Materon, Luis Alberto; Ji, Xiuling; Wei, Yunlin

2016-02-01

As unique ecological systems, glaciers are characterized by low temperatures and low nutrient levels, which allow them to be considered as “living fossils” for the purpose of researching the evolution of life and the environmental evolution of the earth. Glaciers are also natural microbial “reservoirs”. In this work, a lytic cold-active bacteriophage designated MYSP06 was isolated from Janthinobacterium sp. MYB06 from the Mingyong Glacier in China, and its major characteristics were determined. Electron microscopy revealed that bacteriophage MYSP06 had an isometric head (74 nm) and a long tail (10 nm in width, 210 nm in length). It was classified as a Siphoviridae with an approximate genome size of 65–70 kb. A one-step growth curve revealed that the latent and burst periods were 95 and 65 min, respectively, with an average burst size of 16 bacteriophage particles per infected cell. The bacteriophage particles (100 %) adsorbed to the host cells within 10 min after infection. Moreover, the pH value and thermal stability of bacteriophage MYSP06 were also investigated. The maximum stability of the bacteriophage was observed at the optimal pH 7.0, and the bacteriophage became completely unstable at the extremely alkaline pH 11.0; however, it was comparatively stable at the acidic alkaline pH 6.0. As MYSP06 is a cold-active bacteriophage with a lower production temperature, its characterization and its relationship with its host Janthinobacterium sp. MYB06 deserve further study.

Novel DNA packaging recognition in the unusual bacteriophage N15

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feiss, Michael; Geyer, Henriette, E-mail: henriettegeyer@gmail.com; Division of Viral Infections, Robert Koch Institute, Berlin

Phage lambda's cosB packaging recognition site is tripartite, consisting of 3 TerS binding sites, called R sequences. TerS binding to the critical R3 site positions the TerL endonuclease for nicking cosN to generate cohesive ends. The N15 cos (cos{sup N15}) is closely related to cos{sup λ}, but whereas the cosB{sup N15} subsite has R3, it lacks the R2 and R1 sites and the IHF binding site of cosB{sup λ}. A bioinformatic study of N15-like phages indicates that cosB{sup N15} also has an accessory, remote rR2 site, which is proposed to increase packaging efficiency, like R2 and R1 of lambda. N15more » plus five prophages all have the rR2 sequence, which is located in the TerS-encoding 1 gene, approximately 200 bp distal to R3. An additional set of four highly related prophages, exemplified by Monarch, has R3 sequence, but also has R2 and R1 sequences characteristic of cosB–λ. The DNA binding domain of TerS-N15 is a dimer. - Highlights: • There are two classes of DNA packaging signals in N15-related phages. • Phage N15's TerS binding site: a critical site and a possible remote accessory site. • Viral DNA recognition signals by the λ-like bacteriophages: the odd case of N15.« less

Enhancement of the antimicrobial properties of bacteriophage-K via stabilization using oil-in-water nano-emulsions.

PubMed

Esteban, Patricia Perez; Alves, Diana R; Enright, Mark C; Bean, Jessica E; Gaudion, Alison; Jenkins, A T A; Young, Amber E R; Arnot, Tom C

2014-01-01

Bacteriophage therapy is a promising new treatment that may help overcome the threat posed by antibiotic-resistant pathogenic bacteria, which are increasingly identified in hospitalized patients. The development of biocompatible and sustainable vehicles for incorporation of viable bacterial viruses into a wound dressing is a promising alternative. This article evaluates the antimicrobial efficacy of Bacteriophage K against Staphylococcus aureus over time, when stabilized and delivered via an oil-in-water nano-emulsion. Nano-emulsions were formulated via thermal phase inversion emulsification, and then bacterial growth was challenged with either native emulsion, or emulsion combined with Bacteriophage K. Bacteriophage infectivity, and the influence of storage time of the preparation, were assessed by turbidity measurements of bacterial samples. Newly prepared Bacteriophage K/nano-emulsion formulations have greater antimicrobial activity than freely suspended bacteriophage. The phage-loaded emulsions caused rapid and complete bacterial death of three different strains of S. aureus. The same effect was observed for preparations that were either stored at room temperature (18-20°C), or chilled at 4°C, for up to 10 days of storage. A response surface design of experiments was used to gain insight on the relative effects of the emulsion formulation on bacterial growth and phage lytic activity. More diluted emulsions had a less significant effect on bacterial growth, and diluted bacteriophage-emulsion preparations yielded greater antibacterial activity. The enhancement of bacteriophage activity when delivered via nano-emulsions is yet to be reported. This prompts further investigation into the use of these formulations for the development of novel anti-microbial wound management strategies. © 2014 American Institute of Chemical Engineers.

Homologous recombination between overlapping thymidine kinase gene fragments stably inserted into a mouse cell genome.

PubMed

Lin, F L; Sternberg, N

1984-05-01

We have constructed a substrate to study homologous recombination between adjacent segments of chromosomal DNA. This substrate, designated lambda tk2 , consists of one completely defective and one partially defective herpes simplex virus thymidine kinase (tk) gene cloned in bacteriophage lambda DNA. The two genes have homologous 984-base-pair sequences and are separated by 3 kilobases of largely vector DNA. When lambda tk2 DNA was transferred into mouse LMtk- cells by the calcium phosphate method, rare TK+ transformants were obtained that contained many (greater than 40) copies of the unrecombined DNA. Tk- revertants, which had lost most of the copies of unrecombined DNA, were isolated from these TK+-transformed lines. Two of these Tk- lines were further studied by analysis of their reversion back to the Tk+ phenotype. They generated ca. 200 Tk+ revertants per 10(8) cells after growth in nonselecting medium for 5 days. All of these Tk+ revertants have an intact tk gene reconstructed by homologous recombination; they also retain various amounts of unrecombined lambda tk2 DNA. Southern blot analysis suggested that at least some of the recombination events involve unequal sister chromatid exchanges. We also tested three agents, mitomycin C, 12-O-tetradecanoyl-phorbol-13-acetate, and mezerein, that are thought to stimulate recombination to determine whether they affect the reversion from Tk- to Tk+. Only mitomycin C increased the number of Tk+ revertants.

Structure of the Small Outer Capsid Protein, Soc: A Clamp for Stabilizing Capsids of T4-like Phages

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qin, Li; Fokine, Andrei; O'Donnell, Erin

2010-07-22

Many viruses need to stabilize their capsid structure against DNA pressure and for survival in hostile environments. The 9-kDa outer capsid protein (Soc) of bacteriophage T4, which stabilizes the virus, attaches to the capsid during the final stage of maturation. There are 870 Soc molecules that act as a 'glue' between neighboring hexameric capsomers, forming a 'cage' that stabilizes the T4 capsid against extremes of pH and temperature. Here we report a 1.9 {angstrom} resolution crystal structure of Soc from the bacteriophage RB69, a close relative of T4. The RB69 crystal structure and a homology model of T4 Soc weremore » fitted into the cryoelectron microscopy reconstruction of the T4 capsid. This established the region of Soc that interacts with the major capsid protein and suggested a mechanism, verified by extensive mutational and biochemical studies, for stabilization of the capsid in which the Soc trimers act as clamps between neighboring capsomers. The results demonstrate the factors involved in stabilizing not only the capsids of T4-like bacteriophages but also many other virus capsids.« less

A bacteriophage T7 RNA polymerase/promoter system for controlled exclusive expression of specific genes.

PubMed Central

Tabor, S; Richardson, C C

1985-01-01

The RNA polymerase gene of bacteriophage T7 has been cloned into the plasmid pBR322 under the inducible control of the lambda PL promoter. After induction, T7 RNA polymerase constitutes 20% of the soluble protein of Escherichia coli, a 200-fold increase over levels found in T7-infected cells. The overproduced enzyme has been purified to homogeneity. During extraction the enzyme is sensitive to a specific proteolysis, a reaction that can be prevented by a modification of lysis conditions. The specificity of T7 RNA polymerase for its own promoters, combined with the ability to inhibit selectively the host RNA polymerase with rifampicin, permits the exclusive expression of genes under the control of a T7 RNA polymerase promoter. We describe such a coupled system and its use to express high levels of phage T7 gene 5 protein, a subunit of T7 DNA polymerase. Images PMID:3156376

Simulation experiments of the effect of space environment on bacteriophage and DNA thin films

NASA Technical Reports Server (NTRS)

Fekete, A.; Ronto, Gy; Hegedus, M.; Modos, K.; Berces, A.; Kovacs, G.; Lammer, H.; Panitz, C.

2004-01-01

The main goal of PUR experiment (phage and uracil response) is to examine and quantify the effect of specific space conditions on nucleic acid models. To achieve this an improved method was elaborated for the preparation of DNA and bacteriophage thin films. The homogeneity of the films was controlled by UV spectroscopy and microscopy. To provide experimental evidence for the hypothesis that interplanetary transfer of the genetic material is possible, phage T7 and isolated T7 DNA thin films have been exposed to selected space conditions: intense UVC radiation (lambda=254 nm) and high vacuum (10(-4) Pa). The effects of DNA hydration, conformation and packing on UV radiation damage were examined. Characteristic changes in the absorption spectrum, in the electrophoretic pattern of DNA and the decrease of the amount of PCR products have been detected indicating the photodamage of isolated and intraphage DNA. c2004 COSPAR. Published by Elsevier Ltd. All rights reserved.

Homologous recombination between overlapping thymidine kinase gene fragments stably inserted into a mouse cell genome.

PubMed Central

Lin, F L; Sternberg, N

1984-01-01

We have constructed a substrate to study homologous recombination between adjacent segments of chromosomal DNA. This substrate, designated lambda tk2 , consists of one completely defective and one partially defective herpes simplex virus thymidine kinase (tk) gene cloned in bacteriophage lambda DNA. The two genes have homologous 984-base-pair sequences and are separated by 3 kilobases of largely vector DNA. When lambda tk2 DNA was transferred into mouse LMtk- cells by the calcium phosphate method, rare TK+ transformants were obtained that contained many (greater than 40) copies of the unrecombined DNA. Tk- revertants, which had lost most of the copies of unrecombined DNA, were isolated from these TK+-transformed lines. Two of these Tk- lines were further studied by analysis of their reversion back to the Tk+ phenotype. They generated ca. 200 Tk+ revertants per 10(8) cells after growth in nonselecting medium for 5 days. All of these Tk+ revertants have an intact tk gene reconstructed by homologous recombination; they also retain various amounts of unrecombined lambda tk2 DNA. Southern blot analysis suggested that at least some of the recombination events involve unequal sister chromatid exchanges. We also tested three agents, mitomycin C, 12-O-tetradecanoyl-phorbol-13-acetate, and mezerein, that are thought to stimulate recombination to determine whether they affect the reversion from Tk- to Tk+. Only mitomycin C increased the number of Tk+ revertants. Images PMID:6328272

Architecture of the 99 bp DNA-six-protein regulatory complex of the lambda att site.

PubMed

Sun, Xingmin; Mierke, Dale F; Biswas, Tapan; Lee, Sang Yeol; Landy, Arthur; Radman-Livaja, Marta

2006-11-17

The highly directional and tightly regulated recombination reaction used to site-specifically excise the bacteriophage lambda chromosome out of its E. coli host chromosome requires the binding of six sequence-specific proteins to a 99 bp segment of the phage att site. To gain structural insights into this recombination pathway, we measured 27 FRET distances between eight points on the 99 bp regulatory DNA bound with all six proteins. Triangulation of these distances using a metric matrix distance-geometry algorithm provided coordinates for these eight points. The resulting path for the protein-bound regulatory DNA, which fits well with the genetics, biochemistry, and X-ray crystal structures describing the individual proteins and their interactions with DNA, provides a new structural perspective into the molecular mechanism and regulation of the recombination reaction and illustrates a design by which different families of higher-order complexes can be assembled from different numbers and combinations of the same few proteins.

Highly repressible expression system for cloning genes that specify potentially toxic proteins.

PubMed Central

O'Connor, C D; Timmis, K N

1987-01-01

A highly repressible expression vector system that allows the cloning of potentially deleterious genes has been constructed. Undesired expression of a cloned gene was prevented (i) at the level of initiation of transcription, by the presence of the strong but highly repressible leftward promoter of bacteriophage lambda, lambda pL, and (ii) at the level of transcript elongation or translation, through synthesis of antisense RNA complementary to the mRNA of the cloned gene. The system was tested by measuring the inhibition of expression of traT, the gene for the TraT major outer membrane lipoprotein. Direct detection and functional assays indicated that an essentially complete inhibition of traT expression was obtained. As a further test of the system, the gene encoding the EcoRI restriction endonuclease was cloned in the absence of the gene of the corresponding protective EcoRI modification methylase. Transformants harboring this construct were only viable when both repression controls were operational. Images PMID:2443481

A CI-Independent Form of Replicative Inhibition: Turn Off of Early Replication of Bacteriophage Lambda

PubMed Central

Hayes, Sidney; Horbay, Monique A.; Hayes, Connie

2012-01-01

Several earlier studies have described an unusual exclusion phenotype exhibited by cells with plasmids carrying a portion of the replication region of phage lambda. Cells exhibiting this inhibition phenotype (IP) prevent the plating of homo-immune and hybrid hetero-immune lambdoid phages. We have attempted to define aspects of IP, and show that it is directed to repλ phages. IP was observed in cells with plasmids containing a λ DNA fragment including oop, encoding a short OOP micro RNA, and part of the lambda origin of replication, oriλ, defined by iteron sequences ITN1-4 and an adjacent high AT-rich sequence. Transcription of the intact oop sequence from its promoter, pO is required for IP, as are iterons ITN3–4, but not the high AT-rich portion of oriλ. The results suggest that IP silencing is directed to theta mode replication initiation from an infecting repλ genome, or an induced repλ prophage. Phage mutations suppressing IP, i.e., Sip, map within, or adjacent to cro or in O, or both. Our results for plasmid based IP suggest the hypothesis that there is a natural mechanism for silencing early theta-mode replication initiation, i.e. the buildup of λ genomes with oop + oriλ+ sequence. PMID:22590552

A minimal kinetic model for a viral DNA packaging machine.

PubMed

Yang, Qin; Catalano, Carlos Enrique

2004-01-20

Terminase enzymes are common to both eukaryotic and prokaryotic double-stranded DNA viruses. These enzymes possess ATPase and nuclease activities that work in concert to "package" a viral genome into an empty procapsid, and it is likely that terminase enzymes from disparate viruses utilize a common packaging mechanism. Bacteriophage lambda terminase possesses a site-specific nuclease activity, a so-called helicase activity, a DNA translocase activity, and multiple ATPase catalytic sites that function to package viral DNA. Allosteric interactions between the multiple catalytic sites have been reported. This study probes these catalytic interactions using enzyme kinetic, photoaffinity labeling, and vanadate inhibition studies. The ensemble of data forms the basis for a minimal kinetic model for lambda terminase. The model incorporates an ADP-driven conformational reorganization of the terminase subunits assembled on viral DNA, which is central to the activation of a catalytically competent packaging machine. The proposed model provides a unifying mechanism for allosteric interaction between the multiple catalytic sites of the holoenzyme and explains much of the kinetic data in the literature. Given that similar packaging mechanisms have been proposed for viruses as dissimilar as lambda and the herpes viruses, the model may find general utility in our global understanding of the enzymology of virus assembly.

[SOS-repair--60 years].

PubMed

Zavil'gel'skiĭ, G B

2013-01-01

This review integrates 60 years of research on SOS-repair and SOS-mutagenesis in procaryotes and eucaryotes, from Jean Weigle experiment in 1953 year (mutagenesis of lambda bacteriophage in UV-irradiated bacteria) to the latest achievements in studying SOS-mutagenesis on all living organisms--Eukarya, Archaea and Bacteria. A key role in establishing of a biochemical basis for SOS-mutagenesis belonges to the finding in 1998-1999 years that specific error-prone DNA polymerases (PolV and others) catalysed translesion synthesis on damaged DNA. This review focuses on recent studies addressing the new models for SOS-induced mutagenesis in Escherichia coli and Home sapiens cells.

Bacteriophage formulated into a range of semisolid and solid dosage forms maintain lytic capacity against isolated cutaneous and opportunistic oral bacteria.

PubMed

Brown, Teagan L; Thomas, Tereen; Odgers, Jessica; Petrovski, Steve; Spark, Marion Joy; Tucci, Joseph

2017-03-01

Resistance of bacteria to antimicrobial agents is of grave concern. Further research into the development of bacteriophage as therapeutic agents against bacterial infections may help alleviate this problem. To formulate bacteriophage into a range of semisolid and solid dosage forms and investigate the capacity of these preparations to kill bacteria under laboratory conditions. Bacteriophage suspensions were incorporated into dosage forms such as creams, ointments, pastes, pessaries and troches. These were applied to bacterial lawns in order to ascertain lytic capacity. Stability of these formulations containing phage was tested under various storage conditions. A range of creams and ointments were able to support phage lytic activity against Propionibacterium acnes. Assessment of the stability of these formulations showed that storage at 4 °C in light-protected containers resulted in optimal phage viability after 90 days. Pessaries/suppositories and troches were able to support phage lytic activity against Rhodococcus equi. We report here the in-vitro testing of semisolid and solid formulations of bacteriophage lytic against a range of bacteria known to contribute to infections of the epithelia. This study provides a basis for the future formulation of diverse phage against a range of bacteria that infect epithelial tissues. © 2016 Royal Pharmaceutical Society.

Identification and Characterization of T5-Like Bacteriophages Representing Two Novel Subgroups from Food Products

PubMed Central

Sváb, Domonkos; Falgenhauer, Linda; Rohde, Manfred; Szabó, Judit; Chakraborty, Trinad; Tóth, István

2018-01-01

During recent years, interest in the use of bacteriophages as biocontrol agents against foodborne pathogens has increased, particularly for members of the family Enterobacteriaceae, with pathogenic Escherichia coli, Shigella, and Salmonella strains among them. Here, we report the isolation and characterisation of 12 novel T5-like bacteriophages from confiscated food samples. All bacterophages effectively lysed E. coli K-12 strains and were able to infect pathogenic E. coli strains representing enterohaemorrhagic (EHEC), enteropathogenic (EPEC), enterotoxigenic (ETEC), and enteroinvasive (EIEC) pathotypes, Shigella dysenteriae, S. sonnei strains, as well as multidrug-resistant (MDR) E. coli and multiple strains representing different Salmonella enterica serovars. All the bacteriophages exhibited Siphoviridae morphology. Whole genome sequencing of the novel T5-like bacteriophages showed that they represent two distinct groups, with the genome-based grouping correlating to the different host spectra. As these bacteriophages are of food origin, their stability and lack of any virulence genes, as well as their broad and mutually complementary host spectrum makes these new T5-like bacteriophages valuable candidates for use as biocontrol agents against foodborne pathogenic enterobacteria. PMID:29487585

Multiple buoyancy driven flows in a vertical cylinder heated from below

NASA Technical Reports Server (NTRS)

Yamaguchi, Y.; Chang, C. J.; Brown, R. A.

1983-01-01

The structure of axisymmetric buoyancy-driven convection in a vertical cylinder heated from below is probed by finite element solution of the Boussinesq equations coupled with computed-implemented perturbation techniques for detecting and tracking multiple flows and for determining flow stability. Results are reported for fluids with Prandtl number of one and for cylinders with aspect ratio (Lambda) (defined as the height to radius of the cylinder) between 0.5 and 2.25. Extensive calculations of the neutral stability curve for the static solution and of the nonlinear motions along the bifurcating flow families show a continuous evolution of the primary cellular motion from a single toroidal cell to two and three cells nested radially in the cylinder, instead of the sharp transitions found for a cylinder with shear-free sidewalls. The smooth transitions in flow structure with Rayleigh number and lambda are explained by nonlinear connectivity between the first two bifurcating flow families formed either by a secondary bifurcation point for Lambda or = Lambda * approximately 0.80 or by a limit point for Lambda Lambda *. The transition between these two modes may be described by the theory of multiple limit point bifurcation.

The DNA Maturation Domain of gpA, the DNA Packaging Motor Protein of Bacteriophage Lambda, Contains an ATPase Site Associated with Endonuclease Activity

PubMed Central

Ortega, Marcos E.; Gaussier, Helene; Catalano, Carlos E.

2007-01-01

Summary Terminase enzymes are common to double-stranded DNA (dsDNA) viruses and are responsible for packaging viral DNA into the confines of an empty capsid shell. In bacteriophage lambda the catalytic terminase subunit is gpA, which is responsible for maturation of the genome end prior to packaging and subsequent translocation of the matured DNA into the capsid. DNA packaging requires an ATPase catalytic site situated in the N-terminus of the protein. A second ATPase catalytic site associated with the DNA maturation activities of the protein has been proposed; however, direct demonstration of this putative second site is lacking. Here we describe biochemical studies that define protease-resistant peptides of gpA and expression of these putative domains in E. coli. Biochemical characterization of gpA-ΔN179, a construct in which the N-terminal 179 residues of gpA have been deleted, indicates that this protein encompasses the DNA maturation domain of gpA. The construct is folded, soluble and possesses an ATP-dependent nuclease activity. Moreover, the construct binds and hydrolyzes ATP despite the fact that the DNA packaging ATPase site in the N-terminus of gpA has been deleted. Mutation of lysine 497, which alters the conserved lysine in a predicted Walker A “P-loop” sequence, does not affect ATP binding but severely impairs ATP hydrolysis. Further, this mutation abrogates the ATP-dependent nuclease activity of the protein. These studies provide direct evidence for the elusive nucleotide-binding site in gpA that is directly associated with the DNA maturation activity of the protein. The implications of these results with respect to the two roles of the terminase holoenzyme – DNA maturation and DNA packaging – are discussed. PMID:17870092

Phage-Encoded Colanic Acid-Degrading Enzyme Permits Lytic Phage Infection of a Capsule-Forming Resistant Mutant Escherichia coli Strain

PubMed Central

Kim, Min Soo; Kim, Young Deuk; Hong, Sung Sik; Park, Kwangseo; Ko, Kwan Soo

2014-01-01

In this study, we isolated a bacteriophage T7-resistant mutant strain of Escherichia coli (named S3) and then proceeded to characterize it. The mutant bacterial colonies appeared to be mucoid. Microarray analysis revealed that genes related to colanic acid production were upregulated in the mutant. Increases in colanic acid production by the mutant bacteria were observed when l-fucose was measured biochemically, and protective capsule formation was observed under an electron microscope. We found a point mutation in the lon gene promoter in S3, the mutant bacterium. Overproduction of colanic acid was observed in some phage-resistant mutant bacteria after infection with other bacteriophages, T4 and lambda. Colanic acid overproduction was also observed in clinical isolates of E. coli upon phage infection. The overproduction of colanic acid resulted in the inhibition of bacteriophage adsorption to the host. Biofilm formation initially decreased shortly after infection but eventually increased after 48 h of incubation due to the emergence of the mutant bacteria. Bacteriophage PBECO4 was shown to infect the colanic acid-overproducing mutant strains of E. coli. We confirmed that the gene product of open reading frame 547 (ORF547) of PBECO4 harbored colanic acid-degrading enzymatic (CAE) activity. Treatment of the T7-resistant bacteria with both T7 and PBECO4 or its purified enzyme (CAE) led to successful T7 infection. Biofilm formation decreased with the mixed infection, too. This procedure, using a phage cocktail different from those exploiting solely receptor differences, represents a novel strategy for overcoming phage resistance in mutant bacteria. PMID:25416767

MOF-Bacteriophage Biosensor for Highly Sensitive and Specific Detection of Staphylococcus aureus.

PubMed

Bhardwaj, Neha; Bhardwaj, Sanjeev K; Mehta, Jyotsana; Kim, Ki-Hyun; Deep, Akash

2017-10-04

To produce a sensitive and specific biosensor for Staphylococcus aureus, bacteriophages have been interfaced with a water-dispersible and environmentally stable metal-organic framework (MOF), NH 2 -MIL-53(Fe). The conjugation of the MOF with bacteriophages has been achieved through the use of glutaraldehyde as cross-linker. Highly sensitive detection of S. aureus in both synthetic and real samples was realized by the proposed MOF-bacteriophage biosensor based on the photoluminescence quenching phenomena: limit of detection (31 CFU/mL) and range of detection (40 to 4 × 10 8 CFU/mL). This is the first report exploiting the use of an MOF-bacteriophage complex for the biosensing of S. aureus. The results of our study highlight that the proposed biosensor is more sensitive than most of the previous methods while exhibiting some advanced features like specificity, regenerability, extended range of linear detection, and stability for long-term storage (even at room temperature).

Screening by imaging: scaling up single-DNA-molecule analysis with a novel parabolic VA-TIRF reflector and noise-reduction techniques.

PubMed

van 't Hoff, Marcel; Reuter, Marcel; Dryden, David T F; Oheim, Martin

2009-09-21

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 internal reflection fluorescence (VA-TIRF) reflector composed of a minimal set of optical reflective elements, and secondly, using single value decomposition (SVD) to improve the signal-to-noise ratio prior to analysing time-lapse image stacks. As an example, we visualize under identical optical conditions hundreds of surface-tethered single lambda-DNA molecules, stained with the intercalating dye YOYO-1 iodide, and stretched out in a microcapillary flow. Another novelty of our approach is that we arrange on a mechanically driven stage several capillaries containing saline, calibration buffer and lambda-DNA, respectively, thus extending the approach to high-content, high-throughput screening of single molecules. Our length measurements of individual DNA molecules from noise-reduced kymograph images using SVD display a 6-fold enhanced precision compared to raw-data analysis, reaching approximately 1 kbp resolution. Combining these two methods, our approach provides a straightforward yet powerful way of collecting statistically relevant amounts of data in a semi-automated manner. We believe that our conceptually simple technique should be of interest for a broader range of single-molecule studies, well beyond the specific example of lambda-DNA shown here.

Quality-Controlled Small-Scale Production of a Well-Defined Bacteriophage Cocktail for Use in Human Clinical Trials

PubMed Central

Merabishvili, Maya; Pirnay, Jean-Paul; Verbeken, Gilbert; Chanishvili, Nina; Tediashvili, Marina; Lashkhi, Nino; Glonti, Thea; Krylov, Victor; Mast, Jan; Van Parys, Luc; Lavigne, Rob; Volckaert, Guido; Mattheus, Wesley; Verween, Gunther; De Corte, Peter; Rose, Thomas; Jennes, Serge; Zizi, Martin; De Vos, Daniel; Vaneechoutte, Mario

2009-01-01

We describe the small-scale, laboratory-based, production and quality control of a cocktail, consisting of exclusively lytic bacteriophages, designed for the treatment of Pseudomonas aeruginosa and Staphylococcus aureus infections in burn wound patients. Based on succesive selection rounds three bacteriophages were retained from an initial pool of 82 P. aeruginosa and 8 S. aureus bacteriophages, specific for prevalent P. aeruginosa and S. aureus strains in the Burn Centre of the Queen Astrid Military Hospital in Brussels, Belgium. This cocktail, consisting of P. aeruginosa phages 14/1 (Myoviridae) and PNM (Podoviridae) and S. aureus phage ISP (Myoviridae) was produced and purified of endotoxin. Quality control included Stability (shelf life), determination of pyrogenicity, sterility and cytotoxicity, confirmation of the absence of temperate bacteriophages and transmission electron microscopy-based confirmation of the presence of the expected virion morphologic particles as well as of their specific interaction with the target bacteria. Bacteriophage genome and proteome analysis confirmed the lytic nature of the bacteriophages, the absence of toxin-coding genes and showed that the selected phages 14/1, PNM and ISP are close relatives of respectively F8, φKMV and phage G1. The bacteriophage cocktail is currently being evaluated in a pilot clinical study cleared by a leading Medical Ethical Committee. PMID:19300511

Interaction of packaging motor with the polymerase complex of dsRNA bacteriophage

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lisal, Jiri; Kainov, Denis E.; Lam, TuKiet T.

2006-07-20

Many viruses employ molecular motors to package their genomes into preformed empty capsids (procapsids). In dsRNA bacteriophages the packaging motor is a hexameric ATPase P4, which is an integral part of the multisubunit procapsid. Structural and biochemical studies revealed a plausible RNA-translocation mechanism for the isolated hexamer. However, little is known about the structure and regulation of the hexamer within the procapsid. Here we use hydrogen-deuterium exchange and mass spectrometry to delineate the interactions of the P4 hexamer with the bacteriophage phi12 procapsid. P4 associates with the procapsid via its C-terminal face. The interactions also stabilize subunit interfaces within themore » hexamer. The conformation of the virus-bound hexamer is more stable than the hexamer in solution, which is prone to spontaneous ring openings. We propose that the stabilization within the viral capsid increases the packaging processivity and confers selectivity during RNA loading.« less

Bacteriophage immobilized graphene electrodes for impedimetric sensing of bacteria (Staphylococcus arlettae).

PubMed

Bhardwaj, Neha; Bhardwaj, Sanjeev K; Mehta, Jyotsana; Mohanta, Girish C; Deep, Akash

2016-07-15

Bacteriophages are a class of viruses that specifically infect and replicate within a bacterium. They possess inherent affinity and specificity to the particular bacterial cells. This property of bacteriophages makes them an attractive biorecognition element in the field of biosensor development. In this work, we report the use of an immobilized bacteriophage for the development of a highly sensitive electrochemical sensor for Staphylococcus arlettae, bacteria from the pathogenic family of coagulase-negative staphylococci (CNS). The specific bacteriophages were covalently immobilized on the screen-printed graphene electrodes. Thus, the fabricated bacteriophage biosensor displayed quantitative response for the target bacteria (S. arlettae) for a broad detection range (2.0-2.0 × 10(6) cfu). A fast response time (2 min), low limit of detection (2 cfu), specificity, and stability over a prolonged period (3 months) are some of the important highlights of the proposed sensor. The practical utility of the developed sensor has been demonstrated by the analysis of S. arlettae in spiked water and apple juice samples. Copyright © 2016 Elsevier Inc. All rights reserved.

Isolation and characterization of two bacteriophages with strong in vitro antimicrobial activity against Pseudomonas aeruginosa isolated from dogs with ocular infections.

PubMed

Santos, Thiago M A; Ledbetter, Eric C; Caixeta, Luciano S; Bicalho, Marcela L S; Bicalho, Rodrigo C

2011-08-01

To isolate and characterize bacteriophages with strong in vitro lytic activity against various pathogenic Pseudomonas aeruginosa strains isolated from dogs with ocular infections. 26 genetically distinct P aeruginosa isolates. P aeruginosa strains were derived from dogs with naturally acquired ulcerative keratitis. From a large-scale screening for bacteriophages with potential therapeutic benefit against canine ocular infections, 2 bacteriophages (P2S2 and P5U5) were selected; host ranges were determined, and phage nucleic acid type and genetic profile were identified via enzymatic digestion. Electron microscopy was used to characterize bacteriophage ultrastructure. Bacteriophage temperature and pH stabilities were assessed by use of double-layer agar overlay titration. A cocultivation assay was used to evaluate the effect of the bacteriophages on bacterial host growth. P5U5 was active against all P aeruginosa isolates, whereas P2S2 formed lytic plaques on plates of 21 (80.8%) isolates. For each bacteriophage, the genomic nucleic acid was DNA; each was genetically distinct. Ultrastructurally, P2S2 and P5U5 appeared likely to belong to the Podoviridae and Siphoviridae families, respectively. The bacteriophages were stable within a pH range of 4 to 12; however, titers of both bacteriophages decreased following heating for 10 to 50 minutes at 45° or 60°C. Growth of each P aeruginosa isolate was significantly inhibited in coculture with P2S2 or P5U5; the dose response was related to the plaque-forming unit-to-CFU ratios. Bacteriophages P2S2 and P5U5 appear to be good candidates for phage treatment of infection caused by pathogenic P aeruginosa in dogs.

Ultrastructure and Viral Metagenome of Bacteriophages from an Anaerobic Methane Oxidizing Methylomirabilis Bioreactor Enrichment Culture

PubMed Central

Gambelli, Lavinia; Cremers, Geert; Mesman, Rob; Guerrero, Simon; Dutilh, Bas E.; Jetten, Mike S. M.; Op den Camp, Huub J. M.; van Niftrik, Laura

2016-01-01

With its capacity for anaerobic methane oxidation and denitrification, the bacterium Methylomirabilis oxyfera plays an important role in natural ecosystems. Its unique physiology can be exploited for more sustainable wastewater treatment technologies. However, operational stability of full-scale bioreactors can experience setbacks due to, for example, bacteriophage blooms. By shaping microbial communities through mortality, horizontal gene transfer, and metabolic reprogramming, bacteriophages are important players in most ecosystems. Here, we analyzed an infected Methylomirabilis sp. bioreactor enrichment culture using (advanced) electron microscopy, viral metagenomics and bioinformatics. Electron micrographs revealed four different viral morphotypes, one of which was observed to infect Methylomirabilis cells. The infected cells contained densely packed ~55 nm icosahedral bacteriophage particles with a putative internal membrane. Various stages of virion assembly were observed. Moreover, during the bacteriophage replication, the host cytoplasmic membrane appeared extremely patchy, which suggests that the bacteriophages may use host bacterial lipids to build their own putative internal membrane. The viral metagenome contained 1.87 million base pairs of assembled viral sequences, from which five putative complete viral genomes were assembled and manually annotated. Using bioinformatics analyses, we could not identify which viral genome belonged to the Methylomirabilis- infecting bacteriophage, in part because the obtained viral genome sequences were novel and unique to this reactor system. Taken together these results show that new bacteriophages can be detected in anaerobic cultivation systems and that the effect of bacteriophages on the microbial community in these systems is a topic for further study. PMID:27877158

Identification of human antibody fragment clones specific for tetanus toxoid in a bacteriophage. lambda. immunoexpression library

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mullinax, R.L.; Gross, E.A.; Amberg, J.R.

1990-10-01

The authors have applied a molecular biology approach to the identification of human monoclonal antibodies. Human peripheral blood lymphocyte mRNA was converted to cDNA and a select subset was amplified by the polymerase chain reaction. These products, containing coding sequences for numerous immunoglobulin heavy- and {kappa} light-chain variable and constant region domains, were inserted into modified bacteriophase {lambda} expression vectors and introduced into Escherichia coli by infection to yield a combinatorial immunoexpression library. Clones with binding activity to tetanus toxoid were identified by filter hybridization with radiolabeled antigen and appeared at a frequency of 0.2{percent} in the library. These humanmore » antigen binding fragments, consisting of a heavy-chain fragment covalently linked to a light chain, displayed high affinity of binding to tetanus toxoid with equilibrium constants in the nanomolar range but did not cross-react with other proteins tested. They estimate that this human immunoexpression library contains 20,000 clones with high affinity and specificity to our chosen antigen.« less

Bacterial genes mutL, mutS, and dcm participate in repair of mismatches at 5-methylcytosine sites.

PubMed Central

Lieb, M

1987-01-01

Certain amber mutations in the cI gene of bacteriophage lambda appear to recombine very frequently with nearby mutations. The aberrant mutations included C-to-T transitions at the second cytosine in 5'CC(A/T)GG sequences (which are subject to methylation by bacterial cytosine methylase) and in 5'CCAG and 5'CAGG sequences. Excess cI+ recombinants arising in crosses that utilize these mutations are attributable to the correction of mismatches by a bacterial very-short-patch (VSP) mismatch repair system. In the present study I found that two genes required for methyladenine-directed (long-patch) mismatch repair, mutL and mutS, also functioned in VSP mismatch repair; mutH and mutU (uvrD) were dispensable. VSP mismatch repair was greatly reduced in a dcm Escherichia coli mutant, in which 5-methylcytosine was not methylated. However, mismatches in heteroduplexes prepared from lambda DNA lacking 5-methylcytosine were repaired in dcm+ bacteria. These results indicate that the product of gene dcm has a repair function in addition to its methylase activity. PMID:2959653

The control of lambda DNA terminase synthesis.

PubMed Central

Murialdo, H; Davidson, A; Chow, S; Gold, M

1987-01-01

Nu1 and A, the genes coding for bacteriophage lambda DNA terminase, rank among the most poorly translated genes expressed in E. coli. To understand the reason for this low level of translation the genes were cloned into plasmids and their expression measured. In addition, the wild type DNA sequences immediately preceding the genes were reduced and modified. It was found that the elements that control translation are contained in the 100 base pairs upstream from the initiation codon. Interchanging these upstream sequences with those of an efficiently translated gene dramatically increased the translation of terminase subunits. It seems unlikely that the rare codons present in the genes, and any feature of their mRNA secondary structure play a role in the control of their translation. The elimination of cos from plasmids containing Nu1 and A also resulted in an increase in terminase production. This result suggests a role for cos in the control of late gene expression. The terminase subunit overproducer strains are potentially very useful for the design of improved DNA packaging and cosmid mapping techniques. Images PMID:3029667

The Probiotic Escherichia coli Strain Nissle 1917 Combats Lambdoid Bacteriophages stx and λ.

PubMed

Bury, Susanne; Soundararajan, Manonmani; Bharti, Richa; von Bünau, Rudolf; Förstner, Konrad U; Oelschlaeger, Tobias A

2018-01-01

Shiga toxin (Stx) producing E. coli (STEC) such as Enterohemorrhagic E. coli (EHEC) are the major cause of foodborne illness in humans. In vitro studies showed the probiotic Escherichia coli strain Nissle 1917 (EcN) to efficiently inhibit the production of Stx. Life threatening EHEC strains as for example the serotype O104:H4, responsible for the great outbreak in 2011 in Germany, evolutionary developed from certain E. coli strains which got infected by stx2 -encoding lambdoid phages turning the E. coli into lysogenic and subsequently Stx producing strains. Since antibiotics induce stx genes and Stx production, EHEC infected persons are not recommended to be treated with antibiotics. Therefore, EcN might be an alternative medication. However, because even commensal E. coli strains might be converted into Stx-producers after becoming host to a stx encoding prophage, we tested EcN for stx -phage genome integration. Our experiments revealed the resistance of EcN toward not only stx -phages but also against lambda-phages. This resistance was not based on the lack of or by mutated phage receptors. Rather it involved the expression of a phage repressor ( pr ) gene of a defective prophage in EcN which was able to partially protect E. coli K-12 strain MG1655 against stx and lambda phage infection. Furthermore, we observed EcN to inactivate phages and thereby to protect E. coli K-12 strains against infection by stx - as well as lambda-phages. Inactivation of lambda-phages was due to binding of lambda-phages to LamB of EcN whereas inactivation of stx -phages was caused by a thermostable protein of EcN. These properties together with its ability to inhibit Stx production make EcN a good candidate for the prevention of illness caused by EHEC and probably for the treatment of already infected people.

D = 5 Einstein-Maxwell-Chern-Simons black holes.

PubMed

Kunz, Jutta; Navarro-Lérida, Francisco

2006-03-03

Five-dimensional Einstein-Maxwell-Chern-Simons theory with a Chern-Simons coefficient lambda = 1 has supersymmetric black holes with a vanishing horizon angular velocity but finite angular momentum. Here supersymmetry is associated with a borderline between stability and instability, since for lambda > 1 a rotational instability arises, where counterrotating black holes appear, whose horizon rotates in the opposite sense to the angular momentum. For lambda > 2 black holes are no longer uniquely characterized by their global charges, and rotating black holes with vanishing angular momentum appear.

Genotoxicity of wastewaters used for irrigation of food crops.

PubMed

Ansari, Mohd Ikram; Malik, Abdul

2009-04-01

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 showed the presence of certain OC (DDE, DDT, Dieldrin, Aldrin, and Endosulfan) and OP (Dimethoate, Malathion, Methlyparathion, and Chlorpyrifos) pesticides in both the sampling sites. Wastewater samples were concentrated using XAD resins (XAD-4 and XAD-8) and liquid-liquid extraction procedures, and the extracts were assayed for genotoxic potential by Ames Salmonella/microsome test, DNA repair defective mutants, and bacteriophage lambda systems. The test samples exhibited significant mutagenicity with TA98, TA97a, and TA100 strains with the probable role of contaminating pesticides in the wastewater. However, XAD-concentrated samples were more mutagenic in both sites as compared to liquid-liquid-extracted samples. The damage in the DNA repair defective mutants in the presence of XAD-concentrated water samples were also found to be higher to that of liquid-liquid-extracted water samples at the dose level of 20 muL/mL culture. All the mutants invariably exhibited significant decline in their colony-forming units as compared to their isogenic wild-type counterparts. The survival was decreased by 81.7 and 75.5% in polA(-) strain in site I, and 76.0 and 73.5% in site II in polA(-) under the same experimental conditions after 6 h of treatment with XAD-concentrated and liquid-liquid-extracted samples, respectively. A significant decrease in the survival of bacteriophage lambda was also observed when treated with the test samples. Copyright 2008 Wiley Periodicals, Inc.

Incorporating Phage Therapy into WPI Dip Coatings for Applications on Fresh Whole and Cut Fruit and Vegetable Surfaces.

PubMed

Vonasek, Erica L; Choi, Angela H; Sanchez, Juan; Nitin, Nitin

2018-06-15

There is a significant unmet need to develop antimicrobial solutions to reduce the risk of contamination in fresh produce. Bacteriophages have been proposed as a potential approach for controlling foodborne pathogens. This study evaluated the combination of edible dip coatings with T7 bacteriophages on whole and cut produce. The evaluation includes an assessment of phage loading, phage storage stability, antimicrobial activity, and phage stability during simulated gastric digestion on sliced cucumbers, sliced apples, and whole cherry tomatoes. In this evaluation, phages coated on fresh produce using edible whey protein isolate (WPI) were compared with phages coated from an aqueous suspension (control coating). The results demonstrated that WPI coatings load more phages than the control and enhanced phage stability during cold storage (4 °C) for cut apples and whole cherry tomatoes. Phage stability decreased by 1 to 3 log(PFU) in a simulated gastric environment. Phage antimicrobial activity against Escherichia coli BL21 decreased 2 to 4 log(CFU) of bacteria on cut apples and whole cherry tomatoes, while no significant bacterial reduction was observed for sliced cucumbers. Overall, the results show that WPI dip coating provides phage loading, stability, and antimicrobial activity to produce surfaces compared to the control coating, and thus may be considered an effective approach for extending phage therapy on fresh produce. The practical application is to prevent bacterial cross contamination of fresh produce by using a combination of edible coating with bacteriophages. The results demonstrate enhanced loading and stability of phages on fresh produce when used in combination with an edible coating. © 2018 Institute of Food Technologists®.

Structural energetics of the adenine tract from an intrinsic transcription terminator.

PubMed

Huang, Yuegao; Weng, Xiaoli; Russu, Irina M

2010-04-02

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 adenine tract 5'-dATAAAAA-3'. This duplex is present at the tR2 site when the DNA is not transcribed. The opening and the stability of each rU-dA/dT-dA base pair in the two structures are characterized by imino proton exchange and nuclear magnetic resonance spectroscopy. The results reveal concerted opening of the central rU-dA base pairs in the RNA-DNA hybrid. Furthermore, the stability profile of the adenine tract in the RNA-DNA hybrid is very different from that of the tract in the template DNA-DNA duplex. In the RNA-DNA hybrid, the stabilities of rU-dA base pairs range from 4.3 to 6.5 kcal/mol (at 10 degrees C). The sites of lowest stability are identified at the central positions of the tract. In the template DNA-DNA duplex, the dT-dA base pairs are more stable than the corresponding rU-dA base pairs in the hybrid by 0.9 to 4.6 kcal/mol and, in contrast to the RNA-DNA hybrid, the central base pairs have the highest stability. These results suggest that the central rU-dA/dT-dA base pairs in the adenine tract make the largest energetic contributions to transcription termination by promoting both the dissociation of the RNA transcript and the closing of the transcription bubble. The results also suggest that the high stability of dT-dA base pairs in the DNA provides a signal for the pausing of RNA polymerase at the termination site. Copyright 2010 Elsevier Ltd. All rights reserved.

Absorption Kinetics of Phage Lambda on Its Host Under Shear Flow

NASA Astrophysics Data System (ADS)

Yip, C. W.; Wu, X. L.

2000-03-01

Classical blender experiment by Hershey and Chase played a seminal role in illustrating the infectious process of bacteriophage to its host, and showed unequivocally that DNA is responsible for the transmission of heredity. Subsequent works by others have established that interaction between phage particles and bacterial cells is a diffusion-limited process in that, statistically speaking, each collision results in an irreversible infection. However, such a result is hard to reconcile with the fact that the infection appears to be independent of the density of phage receptors on the bacterial cell membrane. Thus, quantitative experiments showing how a phage finds its receptor and how long does it take would be valuable to this paradoxical view. Simple calculations based on Brownian motion of the phage particles show that the interaction time between the receptor and the phage is given by tau=b^2/(5D), where b is the length of the phage and D is its diffusion coefficient. Using a shear flow apparatus we study absorption kinetics of lambda phage on E. Coli (strain YMEL) under different flow conditions, and the results are compared with a simple diffusion model taking into account the hydrodynamic convection and the interaction time tau.

Biological trait analysis and stability of lambda-cyhalothrin resistance in the house fly, Musca domestica L. (Diptera: Muscidae).

PubMed

Abbas, Naeem; Shah, Rizwan Mustafa; Shad, Sarfraz Ali; Iqbal, Naeem; Razaq, Muhammad

2016-05-01

House flies, Musca domestica L., (Diptera: Muscidae), are pests of poultry and have the ability to develop resistance to insecticides. To design a strategy for resistance management, life history traits based on laboratory observations were established for lambda-cyhalothrin-resistant, susceptible and reciprocal crosses of M. domestica strains. Bioassay results showed that the lambda-cyhalothrin-selected strain developed a resistance ratio of 98.34 compared to its susceptible strain. The lambda-cyhalothrin-selected strain had a relative fitness of 0.26 and lower fecundity, hatchability, lower number of next generation larvae, and net reproductive rate compared with its susceptible strain. Mean population growth rates, such as intrinsic rate of population increase, and biotic potential were lower for the lambda-cyhalothrin-selected strain compared to its susceptible strain. Resistance to lambda-cyhalothrin, indoxacarb, and abamectin was unstable while resistance to bifenthrin and methomyl was stable in the lambda-cyhalothrin-selected strain of M. domestica. Development of resistance can cost considerable fitness for the lambda-cyhalothrin-selected strain. The present study provided useful information for making potential management strategies to delay resistance development in M. domestica.

Stability, ghost, and strong coupling in nonrelativistic general covariant theory of gravity with {lambda}{ne}1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang Yongqing; Wang Anzhong

2011-05-15

In this paper, we investigate three important issues: stability, ghost, and strong coupling, in the Horava-Melby-Thompson setup of the Horava-Lifshitz theory with {lambda}{ne}1, generalized recently by da Silva. We first develop the general linear scalar perturbations of the Friedmann-Robertson-Walker (FRW) universe with arbitrary spatial curvature and find that an immediate by-product of the setup is that, in all the inflationary models described by a scalar field, the FRW universe is necessarily flat. Applying them to the case of the Minkowski background, we find that it is stable, and, similar to the case {lambda}=1, the spin-0 graviton is eliminated. The vectormore » perturbations vanish identically in the Minkowski background. Thus, similar to general relativity, a free gravitational field in this setup is completely described by a spin-2 massless graviton, even with {lambda}{ne}1. We also study the ghost problem in the FRW background and find explicitly the ghost-free conditions. To study the strong coupling problem, we consider two different kinds of spacetimes, all with the presence of matter: one is cosmological, and the other is static. We find that the coupling becomes strong for a process with energy higher than M{sub pl}|c{sub {psi}|}{sup 5/2} in the flat FRW background and M{sub pl}|c{sub {psi}|}{sup 3} in a static weak gravitational field, where |c{sub {psi}|{identical_to}}|(1-{lambda})/(3{lambda}-1)|{sup 1/2}.« less

The molecular dynamics simulation of ion-induced ripple growth

DOE Office of Scientific and Technical Information (OSTI.GOV)

Suele, P.; Heinig, K.-H.

The wavelength-dependence of ion-sputtering induced growth of repetitive nanostructures, such as ripples has been studied by molecular dynamics (MD) simulations in Si. The early stage of the ion erosion driven development of ripples has been simulated on prepatterned Si stripes with a wavy surface. The time evolution of the height function and amplitude of the sinusoidal surface profile has been followed by simulated ion-sputtering. According to Bradley-Harper (BH) theory, we expect correlation between the wavelength of ripples and the stability of them. However, we find that in the small ripple wavelength ({lambda}) regime BH theory fails to reproduce the resultsmore » obtained by molecular dynamics. We find that at short wavelengths ({lambda}<35 nm) the adatom yield drops hence no surface diffusion takes place which is sufficient for ripple growth. The MD simulations predict that the growth of ripples with {lambda}>35 nm is stabilized in accordance with the available experimental results. According to the simulations, few hundreds of ion impacts in {lambda} long and few nanometers wide Si ripples are sufficient for reaching saturation in surface growth for for {lambda}>35 nm ripples. In another words, ripples in the long wavelength limit seems to be stable against ion-sputtering. A qualitative comparison of our simulation results with recent experimental data on nanopatterning under irradiation is attempted.« less

Bacteriophages as vehicles for gene delivery into mammalian cells: prospects and problems.

PubMed

Bakhshinejad, Babak; Sadeghizadeh, Majid

2014-10-01

The identification of more efficient gene delivery vehicles (GDVs) is essential to fulfill the expectations of clinical gene therapy. Bacteriophages, due to their excellent safety profile, extreme stability under a variety of harsh environmental conditions and the capability for being genetically manipulated, have drawn a flurry of interest to be applied as a newly arisen category of gene delivery platforms. The incessant evolutionary interaction of bacteriophages with human cells has turned them into a part of our body's natural ecosystem. However, these carriers represent several barriers to gene transduction of mammalian cells. The lack of evolvement of specialized machinery for targeted cellular internalization, endosomal, lysosomal and proteasomal escape, cytoplasmic entry, nuclear localization and intranuclear transcription poses major challenges to the expression of the phage-carried gene. In this review, we describe pros and cons of bacteriophages as GDVs, provide an insight into numerous barriers that bacteriophages face for entry into and subsequent trafficking inside mammalian cells and elaborate on the strategies used to bypass these barriers. Tremendous genetic flexibility of bacteriophages to undergo numerous surface modifications through phage display technology has proven to be a turning point in the uncompromising efforts to surmount the limitations of phage-mediated gene expression. The revelatory outcomes of the studies undertaken within the recent years have been promising for phage-mediated gene delivery to move from concept to reality.

An Evolutionarily Conserved Family of Virion Tail Needles Related to Bacteriophage P22 gp26: Correlation between Structural Stability and Length of the -Helical Trimeric Coiled Coil

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhardwaj, A.; Walker-Kopp, N; Casjens, S

2009-01-01

Bacteriophages of the Podoviridae family use short noncontractile tails to inject their genetic material into Gram-negative bacteria. In phage P22, the tail contains a thin needle, encoded by the phage gene 26, which is essential both for stabilization and for ejection of the packaged viral genome. Bioinformatic analysis of the N-terminal domain of gp26 (residues 1-60) led us to identify a family of genes encoding putative homologues of the tail needle gp26. To validate this idea experimentally and to explore their diversity, we cloned the gp26-like gene from phages HK620, Sf6 and HS1, and characterized these gene products in solution.more » All gp26-like factors contain an elongated {alpha}-helical coiled-coil core consisting of repeating, adjacent trimerization heptads and form trimeric fibers with length ranging between about 240 to 300 {angstrom}. gp26 tail needles display a high level of structural stability in solution, with Tm (temperature of melting) between 85 and 95 C. To determine how the structural stability of these phage fibers correlates with the length of the {alpha}-helical core, we investigated the effect of insertions and deletions in the helical core. In the P22 tail needle, we identified an 85-residue-long helical domain, termed MiCRU (minimal coiled-coil repeat unit), that can be inserted in-frame inside the gp26 helical core, preserving the straight morphology of the fiber. Likewise, we were able to remove three quarters of the helical core of the HS1 tail needle, minimally decreasing the stability of the fiber. We conclude that in the gp26 family of tail needles, structural stability increases nonlinearly with the length of the {alpha}-helical core. Thus, the overall stability of these bacteriophage fibers is not solely dependent on the number of trimerization repeats in the {alpha}-helical core.« less

Location of the unique integration site on an Escherichia coli chromosome by bacteriophage lambda DNA in vivo.

PubMed

Tal, Asaf; Arbel-Goren, Rinat; Costantino, Nina; Court, Donald L; Stavans, Joel

2014-05-20

The search for specific sequences on long genomes is a key process in many biological contexts. How can specific target sequences be located with high efficiency, within physiologically relevant times? We addressed this question for viral integration, a fundamental mechanism of horizontal gene transfer driving prokaryotic evolution, using the infection of Escherichia coli bacteria with bacteriophage λ and following the establishment of a lysogenic state. Following the targeting process in individual live E. coli cells in real time revealed that λ DNA remains confined near the entry point of a cell following infection. The encounter between the 15-bp-long target sequence on the chromosome and the recombination site on the viral genome is facilitated by the directed motion of bacterial DNA generated during chromosome replication, in conjunction with constrained diffusion of phage DNA. Moving the native bacterial integration site to different locations on the genome and measuring the integration frequency in these strains reveals that the frequencies of the native site and a site symmetric to it relative to the origin are similar, whereas both are significantly higher than when the integration site is moved near the terminus, consistent with the replication-driven mechanism we propose. This novel search mechanism is yet another example of the exquisite coevolution of λ with its host.

In vivo mutagenicity of conazole fungicides correlates with tumorigenicity.

PubMed

Ross, Jeffrey A; Moore, Tanya; Leavitt, Sharon A

2009-03-01

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 2000 p.p.m. myclobutanil. After 4 days of feeding, mice were immediately euthanized, livers were removed, DNA isolated and lacI genes recovered into infectious bacteriophage lambda particles by in vitro packaging. Bacteriophage with mutations in the lacI gene was detected by infecting into Escherichia coli, and mutant frequencies were determined using a colorimetric plaque assay. Propiconazole induced a 1.97-fold increase in mutant frequency compared to concurrent controls (P = 0.018) and triadimefon induced a 1.94-fold increase compared to concurrent controls (P = 0.009). Myclobutanil did not induce any change in mutant frequency (P = 0.548). These results provide the first evidence that the hepatotumorigenic conazoles are capable of inducing mutations in liver in vivo while the non-tumorigen myclobutanil is not, suggesting that mutagenicity may represent a key event in conazoles tumorigenic mode of action.

Characterization of the relationship between integrase, excisionase and antirepressor activities associated with a superinfecting Shiga toxin encoding bacteriophage

PubMed Central

Fogg, P. C. M.; Rigden, D. J.; Saunders, J. R.; McCarthy, A. J.; Allison, H. E.

2011-01-01

Shigatoxigenic Escherichia coli emerged as new food borne pathogens in the early 1980s, primarily driven by the dispersal of Shiga toxin-encoding lambdoid bacteriophages. At least some of these Stx phages display superinfection phenotypes, which differ significantly from lambda phage itself, driving through in situ recombination further phage evolution, increasing host range and potentially increasing the host's pathogenic profile. Here, increasing levels of Stx phage Φ24B integrase expression in multiple lysogen cultures are demonstrated along with apparently negligible repression of integrase expression by the cognate CI repressor. The Φ24B int transcription start site and promoter region were identified and found to differ from in silico predictions. The unidirectional activity of this integrase was determined in an in situ, inducible tri-partite reaction. This indicated that Φ24B must encode a novel directionality factor that is controlling excision events during prophage induction. This excisionase was subsequently identified and characterized through complementation experiments. In addition, the previous proposal that a putative antirepressor was responsible for the lack of immunity to superinfection through inactivation of CI has been revisited and a new hypothesis involving the role of this protein in promoting efficient induction of the Φ24B prophage is proposed. PMID:21062824

Mapping the stability region of the 3:2 Neptune-Pluto resonance

NASA Technical Reports Server (NTRS)

Levison, H. F.; Stern, S. A.

1993-01-01

Pluto and Charon are most likely the remnants of a large number of objects that existed in the Uranus-Neptune region at early epochs of the solar system. Numerical integrations have shown that, in general, such objects were ejected from the planetary region on timescales of approximately 10(exp 7) years after Neptune and Uranus reached their current masses. It is thought that the Pluto-Charon system survived to current times without being dynamically removed in this way because it is trapped in a set of secular and mean motion resonances with Neptune. The best-known Pluto-Neptune orbit coupling is the 3:2 mean motion resonance discovered almost 30 years ago by C. Cohen and E. Hubbard. These workers showed that the resonance angle, delta is equivalent to 3(lambda(sub P)) - 2(lambda(sub N)) - omega-bar(sub P) where omega-bar(sub P) is the longitude of perihelion of the Pluto-Charon system, and lambda(sub N) and lambda(sub P) are the mean longitude of Neptune and Pluto-Charon respectively, librates about 180 deg with an amplitude, A(sub delta), of 76 deg. A numerical simulation project to map out the stability region of the 3:2 resonance is reported. The results of these simulations are important to understanding whether Pluto's long-term heliocentric stability requires only the 3:2 resonance, or whether it instead requires one or more of the other Pluto-Neptune resonances. Our study also has another important application. By investigating stability timescales as a function of orbital elements, we gain insight into the fraction of orbital phase space which the stable 3:2 resonance occupies. This fraction is directly related to the probability that the Pluto-Charon system (and possibly other small bodies) could have been captured into this resonance.

pH-Induced Stability Switching of the Bacteriophage HK97 Maturation Pathway

PubMed Central

2015-01-01

Many viruses undergo large-scale conformational changes during their life cycles. Blocking the transition from one stage of the life cycle to the next is an attractive strategy for the development of antiviral compounds. In this work, we have constructed an icosahedrally symmetric, low-energy pathway for the maturation transition of bacteriophage HK97. By conducting constant-pH molecular dynamics simulations on this pathway, we identify which residues are contributing most significantly to shifting the stability between the states along the pathway under differing pH conditions. We further analyze these data to establish the connection between critical residues and important structural motifs which undergo reorganization during maturation. We go on to show how DNA packaging can induce spontaneous reorganization of the capsid during maturation. PMID:24495192

Spatiotemporal chaos near the onset of cellular growth during thin-film solidification of a binary alloy

NASA Technical Reports Server (NTRS)

Lee, J. T. C.; Tsiveriotis, K.; Brown, R. A.

1992-01-01

Thin-film solidification experiments with a succinonitrile-acetone alloy are used to observe the long time-scale dynamics of cellular crystal growth at growth rates only slightly above the critical value VC = Vc(lambda sub c) for the onset of morphological instability. Under these conditions only very small amplitude cells are observed with wavelengths near the value predicted by linear stability theory lambda = lambda sub c. At long times, microstructures with wavelengths significantly finer than lambda suc c form by nucleation at defects across the interface. These interfaces do not have a unique microstructure, but seem to exhibit spatiotemporal chaos on a long time scale caused by the continual birth and death of cells by tip splitting and cell annihilation in grooves.

The possible use of V. parahaemolyticus - specific bacteriophages for prevention and therapy of infections caused by V. parahaemolyticus.

PubMed

Tskhvediani, A; Khukhunashvili, T; Eliashvili, T; Tsertsvadze, G; Gachechiladze, N; Tediashvili, M

2014-06-01

Vibrio parahaemolyticus is the most common halophilic Vibrio species causing serious gastroenteritis in humans. The main source of infection is consumption of undercooked or raw seafood or exposure to contaminated water. The monitoring conducted in 2006-2008 demonstrated that warm, subtropical climate and low- to moderate salinity of water in the Black Sea coastal zone provides a favorable environment for growth and spread of V. parahaemolyticus bacteria. Antibiotics are commonly applied for control V.parahaemolyticus infections in humans. However, with the growing problem with bacterial antibiotic-resistance search for alternative biological anti-infectives, such as bacteriophages, becomes more actual. The aim of the presented work was characterization of V. parahamolyticus- specific bacteriophages in relation with their possible use for treatment and prevention of food and waterborne gastroenteritis in humans infected with V.parahaemolyticus. 69 bacteriophages specific to V.parahaemolyticus were isolated from different water sources and 5 of them were characterized according to their virion morphology, host-range, temperature and pH dependence. Stability of phages in different media and solutions, also susceptibility to action of a number of protolithic enzymes was studied as well. Obtained results showed that studied bacteriophages can be used for preparation of phage mixture as a potential therapeutic preparation against V.parahaemolyticus associated infections.

Induction of lambda prophage by 213 nm laser radiation: a quantitative comparison with 193 nm excimer radiation using image analysis.

PubMed

Matchette, L S; Grossman, L W; Hahn, D W; Cooney, C

1996-03-01

We compared the DNA damage produced by radiation from two UV laser wavelengths, 213 nm and 193 nm, with that produced by noncoherent 254 nm radiation. Following irradiation of Escherichia coli BR339, a bacteriophage lambda lysogen containing the lacZ gene, pro-phage induction was measured by assaying for beta-galactosidase. Because of the limited penetration by UV laser wavelengths an agar overlay of the lysogen was used as the irradiation target. Irradiation of 254 nm was performed in buffer suspension followed by transfer of 5 microL spots onto assay plants. Computer image analysis was used to monitor the rate of product formation, observed as an increase in optical density of the irradiated zones on assay plates. We found that the rate of product formation was a more reproducible unit of comparison than the optical density present at the end of the reaction. Although the rate of product formation was not linearly related to enzyme concentration, the data could be fit to a simple logarithmic function. Using this method, we concluded that the DNA damaging ability of 213 nm radiation was 10 times more efficient than 193 nm radiation and about 100 times less efficient than 254 nm noncoherent radiation.

Structure parameters in rotating Couette-Poiseuille channel flow

NASA Technical Reports Server (NTRS)

Knightly, George H.; Sather, D.

1986-01-01

It is well-known that a number of steady state problems in fluid mechanics involving systems of nonlinear partial differential equations can be reduced to the problem of solving a single operator equation of the form: v + lambda Av + lambda B(v) = 0, v is the summation of H, lambda is the summation of one-dimensional Euclid space, where H is an appropriate (real or complex) Hilbert space. Here lambda is a typical load parameter, e.g., the Reynolds number, A is a linear operator, and B is a quadratic operator generated by a bilinear form. In this setting many bifurcation and stability results for problems were obtained. A rotating Couette-Poiseuille channel flow was studied, and it showed that, in general, the superposition of a Poiseuille flow on a rotating Couette channel flow is destabilizing.

Stability engineering of anti-EGFR scFv antibodies by rational design of a lambda-to-kappa swap of the VL framework using a structure-guided approach.

PubMed

Lehmann, Andreas; Wixted, Josephine H F; Shapovalov, Maxim V; Roder, Heinrich; Dunbrack, Roland L; Robinson, Matthew K

2015-01-01

Phage-display technology facilitates rapid selection of antigen-specific single-chain variable fragment (scFv) antibodies from large recombinant libraries. ScFv antibodies, composed of a VH and VL domain, are readily engineered into multimeric formats for the development of diagnostics and targeted therapies. However, the recombinant nature of the selection strategy can result in VH and VL domains with sub-optimal biophysical properties, such as reduced thermodynamic stability and enhanced aggregation propensity, which lead to poor production and limited application. We found that the C10 anti-epidermal growth factor receptor (EGFR) scFv, and its affinity mutant, P2224, exhibit weak production from E. coli. Interestingly, these scFv contain a fusion of lambda3 and lambda1 V-region (LV3 and LV1) genes, most likely the result of a PCR aberration during library construction. To enhance the biophysical properties of these scFvs, we utilized a structure-based approach to replace and redesign the pre-existing framework of the VL domain to one that best pairs with the existing VH. We describe a method to exchange lambda sequences with a more stable kappa3 framework (KV3) within the VL domain that incorporates the original lambda DE-loop. The resulting scFvs, C10KV3_LV1DE and P2224KV3_LV1DE, are more thermodynamically stable and easier to produce from bacterial culture. Additionally, C10KV3_LV1DE and P2224KV3_LV1DE retain binding affinity to EGFR, suggesting that such a dramatic framework swap does not significantly affect scFv binding. We provide here a novel strategy for redesigning the light chain of problematic scFvs to enhance their stability and therapeutic applicability.

Production and Purification of Recombinant Filamentous Bacteriophages Displaying Immunogenic Heterologous Epitopes.

PubMed

Deng, Lei; Linero, Florencia; Saelens, Xavier

2016-01-01

Viruslike particles often combine high physical stability with robust immunogenicity. Furthermore, when such particles are based on bacteriophages, they can be produced in high amounts at minimal cost and typically will require only standard biologically contained facilities. We provide protocols for the characterization and purification of recombinant viruslike particles derived from filamentous bacteriophages. As an example, we focus on filamentous Escherichia coli fd phage displaying a conserved influenza A virus epitope that is fused genetically to the N-terminus of the major coat protein of this phage. A step-by-step procedure to obtain a high-titer, pure recombinant phage preparation is provided. We also describe a quality control experiment based on a biological readout of the purified fd phage preparation. These protocols together with the highlighted critical steps may facilitate generic implementation of the provided procedures for the display of other epitopes by recombinant fd phages.

Fine wavelength id for tunable laser local oscillators. [sensing the absorption emission spectra of atmospheric gases

NASA Technical Reports Server (NTRS)

Savage, M. G.; Augeri, R. C.

1980-01-01

A wavelength ID device which consists of an electronic show that the etalon has a finesse F 30 which is maintainable for several days. These tests also demonstrate that the etalon system is capable of resonance frequency stability during similar time periods. With currently available coatings, this level of performance is achievable over an optical bandwidth delta lambda = 3 micrometers centered at lambda = 10 micrometers.

Isolation and characterization of a bacteriophage for Vibrio fetus.

PubMed

Bryner, J H; Ritchie, A E; Foley, J W; Berman, D T

1970-07-01

Bacteriophages were isolated from 22 of 38 strains of Vibrio fetus by an enrichment process, utilizing the donor and host strains growing together in fluid thioglycollate medium. One phage, V-45, isolated by the conventional lawn-spot method, was characterized by stability in broth, growth kinetics, and morphology. It was sensitive to rapid thermal inactivation, chloroform, and pH values above 6.5. Calcium was required for phage replication and stability in broth. Magnesium provided the best protection against thermal inactivation at 50 C in the pH range of 6.5 to 7.5. The minimum latent period was 135 min, rise time was 75 min, and average burst size was 35 plaque-forming units per infected cell. Phage V-45 resembled Bradley's morphological group B, having a long tail without contractile sheath. Dimensions were: head, about 50 nm; tail, about 7 by 240 nm; and tail lumen, 2 to 3 nm.

Optimization and application of influence function in abrasive jet polishing.

PubMed

Li, Zhaoze; Li, Shengyi; Dai, Yifan; Peng, Xiaoqiang

2010-05-20

We analyze the material removal mechanism of abrasive jet polishing (AJP) technology, based on the fluid impact dynamics theory. Combined with the computational fluid dynamics simulation and process experiments, influence functions at different impingement angles are obtained, which are not of a regular Gaussian shape and are unfit for the corrective figuring of optics. The influence function is then optimized to obtain an ideal Gaussian shape by rotating the oblique nozzle, and its stability is validated through a line scanning experiment. The fluctuation of the influence function can be controlled within +/-5%. Based on this, we build a computed numerically controlled experimental system for AJP, and one flat BK7 optical glass with a diameter of 20mm is polished. After two iterations of polishing, the peak-to-valley value decreases from 1.43lambda (lambda=632.8nm in this paper) to 0.294lambda, and the rms value decreases from 0.195lambda to 0.029lambda. The roughness of this polished surface is within 2nm. The experimental result indicates that the optimized influence function is suitable for precision optics figuring and polishing.

Tertiary structure of human {Lambda}6 light chains.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pokkuluri, P. R.; Solomon, A.; Weiss, D. T.

1999-01-01

AL amyloidosis is a disease process characterized by the pathologic deposition of monoclonal light chains in tissue. To date, only limited information has been obtained on the molecular features that render such light chains amyloidogenic. Although protein products of the major human V kappa and V lambda gene families have been identified in AL deposits, one particular subgroup--lambda 6--has been found to be preferentially associated with this disease. Notably, the variable region of lambda 6 proteins (V lambda 6) has distinctive primary structural features including the presence in the third framework region (FR3) of two additional amino acid residues thatmore » distinguish members of this subgroup from other types of light chains. However, the structural consequences of these alterations have not been elucidated. To determine if lambda 6 proteins possess unique tertiary structural features, as compared to light chains of other V lambda subgroups, we have obtained x-ray diffraction data on crystals prepared from two recombinant V lambda 6 molecules. These components, isolated from a bacterial expression system, were generated from lambda 6-related cDNAs cloned from bone marrow-derived plasma cells from a patient (Wil) who had documented AL amyloidosis and another (Jto) with multiple myeloma and tubular cast nephropathy, but no evident fibrillar deposits. The x-ray crystallographic analyses revealed that the two-residue insertion located between positions 68 and 69 (not between 66 and 67 as previously surmised) extended an existing loop region that effectively increased the surface area adjacent to the first complementarity determining region (CDR1). Further, an unusual interaction between the Arg 25 and Phe 2 residues commonly found in lambda 6 molecules was noted. However, the structures of V lambda 6 Wil and Jto also differed from each other, as evidenced by the presence in the latter of certain ionic and hydrophobic interactions that we posit increased protein stability and thus prevented amyloid formation.« less

Validated near-atomic resolution structure of bacteriophage epsilon15 derived from cryo-EM and modeling

PubMed Central

Baker, Matthew L.; Hryc, Corey F.; Zhang, Qinfen; Wu, Weimin; Jakana, Joanita; Haase-Pettingell, Cameron; Afonine, Pavel V.; Adams, Paul D.; King, Jonathan A.; Jiang, Wen; Chiu, Wah

2013-01-01

High-resolution structures of viruses have made important contributions to modern structural biology. Bacteriophages, the most diverse and abundant organisms on earth, replicate and infect all bacteria and archaea, making them excellent potential alternatives to antibiotics and therapies for multidrug-resistant bacteria. Here, we improved upon our previous electron cryomicroscopy structure of Salmonella bacteriophage epsilon15, achieving a resolution sufficient to determine the tertiary structures of both gp7 and gp10 protein subunits that form the T = 7 icosahedral lattice. This study utilizes recently established best practice for near-atomic to high-resolution (3–5 Å) electron cryomicroscopy data evaluation. The resolution and reliability of the density map were cross-validated by multiple reconstructions from truly independent data sets, whereas the models of the individual protein subunits were validated adopting the best practices from X-ray crystallography. Some sidechain densities are clearly resolved and show the subunit–subunit interactions within and across the capsomeres that are required to stabilize the virus. The presence of the canonical phage and jellyroll viral protein folds, gp7 and gp10, respectively, in the same virus suggests that epsilon15 may have emerged more recently relative to other bacteriophages. PMID:23840063

Laser-induced damage threshold measurements of optical dielectric coatings at lambda = 1.06 micron

NASA Astrophysics Data System (ADS)

Milev, I. Ia.; Dimov, S. S.; Terziev, D. V.; Iordanova, J. I.; Todorova, L. B.; Gelkova, A. B.

1991-10-01

The laser-induced damage thresholds for lambda = 1.06 micron of commercially available dielectric optical coatings, both antireflective and high reflectance, have been determined. The dependence of the optical coatings stability on design and selection of materials has been investigated. An improvement of the coatings durability by using nonquarterwave layers in addition to the basic design of the mirrors has been obtained. The choice of the coating materials is also discussed.

Evaluation of Stability and Biological Activity of Solid Nanodispersion of Lambda-Cyhalothrin.

PubMed

Cui, Bo; Feng, Lei; Pan, Zhenzhong; Yu, Manli; Zeng, Zhanghua; Sun, Changjiao; Zhao, Xiang; Wang, Yan; Cui, Haixin

2015-01-01

Pesticides are essential agrochemicals used to protect plants from diseases, pests and weeds. However, the formulation defects of conventional pesticides cause food toxicity and ecological environmental problems. In this study, a novel, efficient and environmentally friendly formulation of lambda-cyhalothrin, a solid nanodispersion, was successfully developed based on melt-emulsification and high-speed shearing methods. The solid nanodispersion presented excellent advantages over conventional pesticide formulations in such formulation functions as dispersibility, stability and bioavailability. The formulation is free of organic solvents, and the use of surfactant is reduced. Therefore, the application of the solid nanodispersion in crop production will improve efficacy and reduce the occurrence of both pesticide residues in food and environmental pollution from pesticides.

Evaluation of Stability and Biological Activity of Solid Nanodispersion of Lambda-Cyhalothrin

PubMed Central

Cui, Bo; Feng, Lei; Pan, Zhenzhong; Yu, Manli; Zeng, Zhanghua; Sun, Changjiao; Zhao, Xiang; Wang, Yan; Cui, Haixin

2015-01-01

Pesticides are essential agrochemicals used to protect plants from diseases, pests and weeds. However, the formulation defects of conventional pesticides cause food toxicity and ecological environmental problems. In this study, a novel, efficient and environmentally friendly formulation of lambda-cyhalothrin, a solid nanodispersion, was successfully developed based on melt-emulsification and high-speed shearing methods. The solid nanodispersion presented excellent advantages over conventional pesticide formulations in such formulation functions as dispersibility, stability and bioavailability. The formulation is free of organic solvents, and the use of surfactant is reduced. Therefore, the application of the solid nanodispersion in crop production will improve efficacy and reduce the occurrence of both pesticide residues in food and environmental pollution from pesticides. PMID:26281043

Bacteriophage enzymes for the prevention and treatment of bacterial infections: Stability and stabilization of the enzyme lysing Streptococcus pyogenes cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klyachko, N. L.; Dmitrieva, N. F.; Eshchina, A. S.

2008-06-01

Recombinant, phage associated lytic enzyme Ply C capable to lyse streptococci of groups A and C was stabilized in the variety of the micelles containing compositions to improve the stability of the enzyme for further application in medicine. It was shown that, in the micellar polyelectrolyte composition M16, the enzyme retained its activity for 2 months; while in a buffer solution under the same conditions ((pH 6.3, room temperature), it completely lost its activity in 2 days

Nanopore DNA Sequencing and Genome Assembly on the International Space Station.

PubMed

Castro-Wallace, Sarah L; Chiu, Charles Y; John, Kristen K; Stahl, Sarah E; Rubins, Kathleen H; McIntyre, Alexa B R; Dworkin, Jason P; Lupisella, Mark L; Smith, David J; Botkin, Douglas J; Stephenson, Timothy A; Juul, Sissel; Turner, Daniel J; Izquierdo, Fernando; Federman, Scot; Stryke, Doug; Somasekar, Sneha; Alexander, Noah; Yu, Guixia; Mason, Christopher E; Burton, Aaron S

2017-12-21

We evaluated the performance of the MinION DNA sequencer in-flight on the International Space Station (ISS), and benchmarked its performance off-Earth against the MinION, Illumina MiSeq, and PacBio RS II sequencing platforms in terrestrial laboratories. Samples contained equimolar mixtures of genomic DNA from lambda bacteriophage, Escherichia coli (strain K12, MG1655) and Mus musculus (female BALB/c mouse). Nine sequencing runs were performed aboard the ISS over a 6-month period, yielding a total of 276,882 reads with no apparent decrease in performance over time. From sequence data collected aboard the ISS, we constructed directed assemblies of the ~4.6 Mb E. coli genome, ~48.5 kb lambda genome, and a representative M. musculus sequence (the ~16.3 kb mitochondrial genome), at 100%, 100%, and 96.7% consensus pairwise identity, respectively; de novo assembly of the E. coli genome from raw reads yielded a single contig comprising 99.9% of the genome at 98.6% consensus pairwise identity. Simulated real-time analyses of in-flight sequence data using an automated bioinformatic pipeline and laptop-based genomic assembly demonstrated the feasibility of sequencing analysis and microbial identification aboard the ISS. These findings illustrate the potential for sequencing applications including disease diagnosis, environmental monitoring, and elucidating the molecular basis for how organisms respond to spaceflight.

T7 RNA polymerase-driven inducible cell lysis for DNA transfer from Escherichia coli to Bacillus subtilis.

PubMed

Juhas, Mario; Ajioka, James W

2017-11-01

The majority of the good DNA editing techniques have been developed in Escherichia coli; however, Bacillus subtilis is better host for a plethora of synthetic biology and biotechnology applications. Reliable and efficient systems for the transfer of synthetic DNA between E. coli and B. subtilis are therefore of the highest importance. Using synthetic biology approaches, such as streamlined lambda Red recombineering and Gibson Isothermal Assembly, we integrated genetic circuits pT7L123, Repr-ts-1 and pLT7pol encoding the lysis genes of bacteriophages MS2, ΦX174 and lambda, the thermosensitive repressor and the T7 RNA polymerase into the E. coli chromosome. In this system, T7 RNA polymerase regulated by the thermosensitive repressor drives the expression of the phage lysis genes. We showed that T7 RNA polymerase significantly increases efficiency of cell lysis and transfer of the plasmid and bacterial artificial chromosome-encoded DNA from the lysed E. coli into B. subtilis. The T7 RNA polymerase-driven inducible cell lysis system is suitable for the efficient cell lysis and transfer of the DNA engineered in E. coli to other naturally competent hosts, such as B. subtilis. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Display of HIV-1 Envelope Protein on Lambda Phage Scaffold as a Vaccine Platform.

PubMed

Mattiacio, Jonelle L; Brewer, Matt; Dewhurst, Stephen

2017-01-01

The generation of a strong antibody response to target antigens is a major goal for vaccine development. Here we describe the display of the human immunodeficiency virus (HIV) envelope spike protein (Env) on a virus-like scaffold provided by the lambda phage capsid. Phage vectors, in general, have advantages over mammalian virus vectors due to their genetic tractability, inexpensive production, suitability for scale-up, as well as their physical stability, making them an attractive vaccine platform.

Evaluation of the lambda model for human postural control during ankle strategy.

PubMed

Micheau, Philippe; Kron, Aymeric; Bourassa, Paul

2003-09-01

An accurate modeling of human stance might be helpful in assessing postural deficit. The objective of this article is to validate a mathematical postural control model for quiet standing posture. The postural dynamics is modeled in the sagittal plane as an inverted pendulum with torque applied at the ankle joint. The torque control system is represented by the physiological lambda model. Two neurophysiological command variables of the central nervous system, designated lambda and micro, establish the dynamic threshold muscle at which motoneuron recruitment begins. Kinematic data and electromyographic signals were collected on four young males in order to measure small voluntary sway and quiet standing posture. Validation of the mathematical model was achieved through comparison of the experimental and simulated results. The mathematical model allows computation of the unmeasurable neurophysiological commands lambda and micro that control the equilibrium position and stability. Furthermore, with the model it is possible to conclude that low-amplitude body sway during quiet stance is commanded by the central nervous system.

A Bacteriophage-Encoded J-Domain Protein Interacts with the DnaK/Hsp70 Chaperone and Stabilizes the Heat-Shock Factor σ32 of Escherichia coli

PubMed Central

Perrody, Elsa; Cirinesi, Anne-Marie; Desplats, Carine; Keppel, France; Schwager, Françoise; Tranier, Samuel; Georgopoulos, Costa; Genevaux, Pierre

2012-01-01

The universally conserved J-domain proteins (JDPs) are obligate cochaperone partners of the Hsp70 (DnaK) chaperone. They stimulate Hsp70's ATPase activity, facilitate substrate delivery, and confer specific cellular localization to Hsp70. In this work, we have identified and characterized the first functional JDP protein encoded by a bacteriophage. Specifically, we show that the ORFan gene 057w of the T4-related enterobacteriophage RB43 encodes a bona fide JDP protein, named Rki, which specifically interacts with the Escherichia coli host multifunctional DnaK chaperone. However, in sharp contrast with the three known host JDP cochaperones of DnaK encoded by E. coli, Rki does not act as a generic cochaperone in vivo or in vitro. Expression of Rki alone is highly toxic for wild-type E. coli, but toxicity is abolished in the absence of endogenous DnaK or when the conserved J-domain of Rki is mutated. Further in vivo analyses revealed that Rki is expressed early after infection by RB43 and that deletion of the rki gene significantly impairs RB43 proliferation. Furthermore, we show that mutations in the host dnaK gene efficiently suppress the growth phenotype of the RB43 rki deletion mutant, thus indicating that Rki specifically interferes with DnaK cellular function. Finally, we show that the interaction of Rki with the host DnaK chaperone rapidly results in the stabilization of the heat-shock factor σ32, which is normally targeted for degradation by DnaK. The mechanism by which the Rki-dependent stabilization of σ32 facilitates RB43 bacteriophage proliferation is discussed. PMID:23133404

Stability Error Budget for an Aggressive Coronagraph on a 3.8 m Telescope

NASA Technical Reports Server (NTRS)

Shaklan, Stuart B.; Marchen, Luis; Krist, John; Rud, Mayer

2011-01-01

We evaluate in detail the stability requirements for a band-limited coronagraph with an inner working angle as small as 2 lambda/D coupled to an off-axis, 3.8-m diameter telescope. We have updated our methodologies since presenting a stability error budget for the Terrestrial Planet Finder Coronagraph mission that worked at 4 lambda/D and employed an 8th-order mask to reduce aberration sensitives. In the previous work, we determined the tolerances relative to the total light leaking through the coronagraph. Now, we separate the light into a radial component, which is readily separable from a planet signal, and an azimuthal component, which is easily confused with a planet signal. In the current study, throughput considerations require a 4th-order coronagraph. This, combined with the more aggressive working angle, places extraordinarily tight requirements on wavefront stability and opto-mechanical stability. We find that the requirements are driven mainly by coma that leaks around the coronagraph mask and mimics the localized signal of a planet, and pointing errors that scatter light into the background, decreasing SNR. We also show how the requirements would be relaxed if a low-order aberration detection system could be employed.

Systematic cloning of an ORFeome using the Gateway system.

PubMed

Matsuyama, Akihisa; Yoshida, Minoru

2009-01-01

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. However, recent advances in techniques for DNA cloning using site-specific recombination and for high-throughput experimental techniques have made it feasible to clone an ORFeome with the minimum of exertion. The Gateway system is one of such the approaches, employing the recombination reaction of the bacteriophage lambda. Combining traditional DNA manipulation methods with modern technique of the recombination-based cloning system, it is possible to clone an ORFeome of an organism on an individual level.

Fluctuation Pressure Assisted Ejection of DNA From Bacteriophage

NASA Astrophysics Data System (ADS)

Harrison, Michael J.

2011-03-01

The role of thermal pressure fluctuations excited within tightly packaged DNA while it is ejected from protein capsid shells is discussed in a model calculation. At equilibrium before ejection we assume the DNA is folded many times into a bundle of parallel segments that forms an equilibrium conformation at minimum free energy, which presses tightly against capsid walls. Using a canonical ensemble at temperature T we calculate internal pressure fluctuations against a slowly moving or static capsid mantle for an elastic continuum model of the folded DNA bundle. It is found that fluctuating pressures on the capsid from thermal excitation of longitudinal acoustic vibrations in the bundle whose wavelengths are exceeded by the bend persistence length may have root-mean-square values that are several tens of atmospheres for typically small phage dimensions. Comparisons are given with measured data on three mutants of lambda phage with different base pair lengths and total genome ejection pressures.

Compilation of DNA sequences of Escherichia coli (update 1991)

PubMed Central

Kröger, Manfred; Wahl, Ralf; Rice, Peter

1991-01-01

We have compiled the DNA sequence data for E.coli available from the GENBANK and EMBL data libraries and over a period of several years independently from the literature. This is the third listing replacing and increasing the former listing roughly by one fifth. However, in order to save space this printed version contains DNA sequence information only. The complete compilation is now available in machine readable form from the EMBL data library (ECD release 6). After deletion of all detected overlaps a total of 1 492 282 individual bp is found to be determined till the beginning of 1991. This corresponds to a total of 31.62% of the entire E.coli chromosome consisting of about 4,720 kbp. This number may actually be higher by some extra 2,5% derived from lysogenic bacteriophage lambda and various DNA sequences already received for statistical purposes only. PMID:2041799

Elucidating the pH-Dependent Structural Transition of T7 Bacteriophage Endolysin.

PubMed

Sharma, Meenakshi; Kumar, Dinesh; Poluri, Krishna Mohan

2016-08-23

Bacteriophages are the most abundant and diverse biological entities on earth. Bacteriophage endolysins are unique peptidoglycan hydrolases and have huge potential as effective enzybiotics in various infectious models. T7 bacteriophage endolysin (T7L), also known as N-acetylmuramoyl-l-alanine amidase or T7 lysozyme, is a 17 kDa protein that lyses a range of Gram-negative bacteria by hydrolyzing the amide bond between N-acetylmuramoyl residues and the l-alanine of the peptidoglycan layer. Although the activity profiles of several of the T7 family members have been known for many years, the molecular basis for their pH-dependent differential activity is not clear. In this study, we explored the pH-induced structural, stability, and activity characteristics of T7L by applying a variety of biophysical techniques and protein nuclear magnetic resonance (NMR) spectroscopy. Our studies established a reversible structural transition of T7L below pH 6 and the formation of a partially denatured conformation at pH 3. This low-pH conformation is thermally stable and exposed its hydrophobic pockets. Further, NMR relaxation measurements and structural analysis unraveled that T7L is highly dynamic in its native state and a network of His residues are responsible for the observed pH-dependent conformational dynamics and transitions. As bacteriophage chimeric and engineered endolysins are being developed as novel therapeutics against multiple drug resistance pathogens, we believe that our results are of great help in designing these entities as broadband antimicrobial and/or antibacterial agents.

Experimental transport studies of yttrium barium copper oxide and lambda-DNA

NASA Astrophysics Data System (ADS)

Zhang, Yuexing

This dissertation consists of two parts. In Part I, we focus on the quasi-particle transport properties in the high temperature superconductor YBa2Cu3O7-delta (YBCO), probed by the thermal Hall conductivity (kappa xy). The thermal Hall conductivity selectively reflects the transport behaviors of the charge carriers. By measuring kappaxy in the normal state YBCO, we established a new method to determine the Wiedemann-Franz (WF) ratio in cuprates. We determined the Hall-channel WF ratio kappa xy/sigmaxyT in Cu and YBCO. In the latter, we uncovered a T-linear dependence and suppression of the Hallchannel WF ratio. The suppression of the Hall-channel WF ratio in systems with predominant electron-electron scattering will be discussed. Thermal transport behaviors of the quasi-particles in the mixed state were studied by measuring kappaxx and kappa xy in a high-purity YBCO crystal. From the field-dependence of the thermal conductivity kappaxx, we separated the quasi particle contribution (kappae) from the phonon background. In the Hall channel, we observed that the (weak-field) kappa xy increased 103-fold between T c (90 K) and 30 K, implying a 100-fold enhancement of the quasi-particle lifetime. We found that kappaxy exhibited a specific scaling behavior below ˜30 K. The implication of the scaling behavior will be discussed. In Part II, we describe an experiment on determining the electrical conductivity of the bacteriophage lambda-DNA, an issue currently under intense debate. We covalently bonded the DNA to Au electrodes by incorporating thiol modified dTTP into the 'sticky' ends of the lambda-DNA. Two-probe measurements on such molecules provided a lower bound for the resistivity rho > 10 6 mum at bias potentials up to 20 V, in conflict with recent claims of moderate to high conductivity. We stress the importance of eliminating salt residues in these measurements.

What should be impossible: resolution of the mononuclear gallium coordination complex, Tris(benzohydroxamato)gallium(III).

PubMed

Brumaghim, Julia L; Raymond, Kenneth N

2003-10-08

Complexes of Ga3+, a d10 metal ion which lacks ligand-field-stabilization energy, are considered labile. In fact, hexaaquagallium(III) has a ligand exchange rate of 403 s-1, 2.5 times that of the analagous Fe3+ complex (Hugi-Cleary, D.; Helm, L.; Merbach, A. E. J. Am. Chem. Soc. 1987, 109, 4444-4450). Given this lability, resolution of Ga3+ complexes should be impossible. Despite this, we report the resolution of the Lambda and Delta isomers of tris(benzohydroxamate)gallium (III) (1), the first resolution of a mononuclear gallium complex. Not only is resolution possible, but these resolved complexes show remarkable resistance to racemization in aprotic solvents. The unprecedented stability of Lambda- and Delta-1 is a surprise, and as such, alters our understanding of classical coordination chemistry.

About Some Regge-Like Relations for (stable) Black Holes

NASA Astrophysics Data System (ADS)

Recami, E.; Tonin-Zanchin, V.; del Popolo, A.; Gambera, M.

1997-08-01

We associated, in a classical formulation of "strong gravity", hadron constituents with suitable stationary, axisymmetric solutions of some new Einstein-type equations supposed to describe the strong field inside hadrons. These new equations can be obtained by the Einstein equations with cosmological term Lambda. As a consequence, Lambda and the masses M result in our theory to be scaled up, and transformed into a "hadronic constant" and into "strong masses", respectively. Due to the unusual range of Lambda and M values considered, we met a series of solutions of the Kerr-Newman-de Sitter (hereafter KNdS) type with rather interesting properties. The requirement that those solutions be stable, i.e., that their temperature (or surface gravity) be vanishingly small, implies the coincidence of at least two of their (in general, three) horizons. Imposing the stability condition of a certain horizon does yield (once chosen the values of J, q and Lambda) mass and radius of the associated black-hole (hereafter BH). In the case of ordinary Einstein equations and for stable BHs of the KNdS type, we get in particular Regge-like (hereafter RL) relations among mass M, angular momentum J, charge q and cosmological constant Lambda; which did not receive enough attention in the previous literature. Besides, we show some particular and interesting cases of these relations. Another interesting point is that, with few exceptions, all such relations (among M, J, q, Lambda) lead to solutions that can be regarded as (stable) cosmological models.

Evolution of the iss gene in Escherichia coli.

PubMed

Johnson, Timothy J; Wannemuehler, Yvonne M; Nolan, Lisa K

2008-04-01

The increased serum survival gene iss has long been recognized for its role in extraintestinal pathogenic Escherichia coli (ExPEC) virulence. iss has been identified as a distinguishing trait of avian ExPEC but not of human ExPEC. This gene has been localized to large virulence plasmids and shares strong similarities with the bor gene from bacteriophage lambda. Here, we demonstrate that three alleles of iss occur among E. coli isolates that appear to have evolved from a common lambda bor precursor. In addition to the occurrence of iss on the ColV/BM virulence plasmids, at least two iss alleles occur within the E. coli chromosome. One of these alleles (designated type 3) was found to occur in the genomes of all currently sequenced ExPEC strains on a similar prophage element that also harbors the Sit iron and manganese transport system. When the prevalence of the three iss types was examined among 487 E. coli isolates, the iss type 3 gene was found to occur at a high frequency among ExPEC isolates, irrespective of the host source. The plasmid-borne iss allele (designated type 1) was highly prevalent among avian pathogenic E. coli and neonatal meningitis-associated E. coli isolates but not among uropathogenic E. coli isolates. This study demonstrates the evolution of iss in E. coli and provides an additional tool for discriminating among E. coli pathotypes through the differentiation of the three iss allele types and bor.

Bacteriophages infecting Bacteroides as a marker for microbial source tracking.

PubMed

Jofre, Joan; Blanch, Anicet R; Lucena, Francisco; Muniesa, Maite

2014-05-15

Bacteriophages infecting certain strains of Bacteroides are amid the numerous procedures proposed for tracking the source of faecal pollution. These bacteriophages fulfil reasonably well most of the requirements identified as appropriate for a suitable marker of faecal sources. Thus, different host strains are available that detect bacteriophages preferably in water contaminated with faecal wastes corresponding to different animal species. For phages found preferably in human faecal wastes, which are the ones that have been more extensively studied, the amounts of phages found in waters contaminated with human fecal samples is reasonably high; these amounts are invariable through the time; their resistance to natural and anthropogenic stressors is comparable to that of other relatively resistant indicator of faecal pollution such us coliphages; the abundance ratios of somatic coliphages and bacteriophages infecting Bacteroides thetaiotaomicron GA17 are unvarying in recent and aged contamination; and standardised detection methods exist. These methods are easy, cost effective and provide data susceptible of numerical analysis. In contrast, there are some uncertainties regarding their geographical stability, and consequently suitable hosts need to be isolated for different geographical areas. However, a feasible method has been described to isolate suitable hosts in a given geographical area. In summary, phages infecting Bacteroides are a marker of faecal sources that in our opinion merits being included in the "toolbox" for microbial source tracking. However, further research is still needed in order to make clear some uncertainties regarding some of their characteristics and behaviour, to compare their suitability to the one of emerging methods such us targeting Bacteroidetes by qPCR assays; or settling molecular methods for their determination. Copyright © 2014 Elsevier Ltd. All rights reserved.

Flexible body stability analysis of Space Shuttle ascent flight control system by using lambda matrix solution techniques

NASA Technical Reports Server (NTRS)

Bown, R. L.; Christofferson, A.; Lardas, M.; Flanders, H.

1980-01-01

A lambda matrix solution technique is being developed to perform an open loop frequency analysis of a high order dynamic system. The procedure evaluates the right and left latent vectors corresponding to the respective latent roots. The latent vectors are used to evaluate the partial fraction expansion formulation required to compute the flexible body open loop feedback gains for the Space Shuttle Digital Ascent Flight Control System. The algorithm is in the final stages of development and will be used to insure that the feedback gains meet the design specification.

Marine Transducing Bacteriophage Attacking a Luminous Bacterium

PubMed Central

Keynan, Alex; Nealson, Kenneth; Sideropoulos, Henry; Hastings, J. W.

1974-01-01

The isolation and partial characterization of a marine bacteriophage attacking a strain of luminous bacteria is described, including some physical, biological, and genetic properties. It is a DNA phage of density of 1.52 with a long flexible tail and an apparently icosohedral head. With respect to stability in suspension, it has a rather specific requirement for the sodium ion in high concentration; it is further stabilized by the addition of calcium and magnesium ions. These same ions are likewise all required for both good plating efficiency and plaque uniformity. Although it goes through a typical lytic growth cycle (about 45 min), with a burst size of 100, and no stable lysogens have been isolated, it is nevertheless a transducing phage specifically for the tryptophan region, transducing several, but not all, independently isolated Trp− auxotrophs to protrophy. No other auxotrophs of a variety of amino acids were transduced by this phage to prototrophy. Phage infection does not change the normal expression of the luminescent system, and light remains at near normal levels until cell lysis occurs. Images PMID:16789143

Genetic recombination induced by DNA double-strand break in bacteriophage T4: nature of the left/right bias.

PubMed

Shcherbakov, Victor P; Shcherbakova, Tamara; Plugina, Lidiya; Sizova, Svetlana; Kudryashova, Elena; Granovsky, Igor

2008-06-01

The experimental system combining double-strand breaks (DSBs), produced site-specifically by SegC endonuclease, with the famous advantages of the bacteriophage T4 rII mutant recombination analysis was used here to elucidate the origin of the recombination bias on two sides of the DSB, especially pronounced in gene 39 (topoisomerase II) and gene 59 (41-helicase loader) mutants. Three sources were found to contribute to the bias: (1) the SegC endonuclease may remain bound to the end of the broken DNA and thus protect it from exonuclease degradation; (2) in heteroduplex heterozygotes (HHs), arising as the recombinant products in the left-hand crosses, the transcribed strands are of rII mutant phenotype, so they, in contrast to the right-hand HHs, do not produce plaques on the lawn of the lambda-lysogenic host; and (3) the intrinsic polarity of T4 chromosome, reflected in transcription, may be a cause for discrimination of promoter-proximal and promoter-distal DNA sequences. It is shown that the apparent recombination bias does not imply one-sidedness of the DSB repair but just reflects a different depth of the end processing. It is inferred that the cause, underlying the "intrinsic" bias, might be interference between strand exchange and transcription. Topoisomerase and helicase functions are necessary to turn the process in favor of strand exchange. The idea is substantiated that the double-stranded to single-stranded DNA transition edge (not ss-DNA tip) serves as an actual recombinogenic element.

Influence of adaptive mutations, from thermal adaptation experiments, on the infection cycle of RNA bacteriophage Qβ.

PubMed

Kashiwagi, Akiko; Kadoya, Tamami; Kumasaka, Naoya; Kumagai, Tomofumi; Tsushima, Fumie Sano; Yomo, Tetsuya

2018-06-04

A population's growth rate is determined by multiple 'life history traits'. To quantitatively determine which life history traits should be improved to allow a living organism to adapt to an inhibitory environment is an important issue. Previously, we conducted thermal adaptation experiments on the RNA bacteriophage Qβ using three independent replicates and reported that all three end-point populations could grow at a temperature (43.6°C) that inhibited the growth of the ancestral strain. Even though the fitness values of the endpoint populations were almost the same, their genome sequence was not, indicating that the three thermally adapted populations may have different life history traits. In this study, we introduced each mutation observed in these three end-point populations into the cDNA of the Qβ genome and prepared three different mutants. Quantitative analysis showed that they tended to increase their fitness by increasing the adsorption rate to their host, shortening their latent period (i.e., the duration between phage infection and progeny release), and increasing the burst size (i.e., the number of progeny phages per infected cell), but all three mutants decreased their thermal stability. However, the degree to which these traits changed differed. The mutant with the least mutations showed a smaller decrease in thermal stability, the largest adsorption rate to the host, and the shortest latent period. These results indicated that several different adaptive routes exist by which Qβ can adapt to higher temperatures, even though Qβ is a simple RNA bacteriophage with a small genome size, encoding only four genes.

Induction of the heat shock regulon of Escherichia coli markedly increases production of bacterial viruses at high temperatures.

PubMed Central

Wiberg, J S; Mowrey-McKee, M F; Stevens, E J

1988-01-01

Production of bacteriophages T2, T4, and T6 at 42.8 to 44 degrees C was increased from 8- to 260-fold by adapting the Escherichia coli host (grown at 30 degrees C) to growth at the high temperature for 8 min before infection; this increase was abolished if the host htpR (rpoH) gene was inactive. Others have shown that the htpR protein increases or activates the synthesis of at least 17 E. coli heat shock proteins upon raising the growth temperature above a certain level. At 43.8 to 44 degrees C in T4-infected, unadapted cells, the rates of RNA, DNA, and protein synthesis were about 100, 70, and 70%, respectively, of those in T4-infected, adapted cells. Production of the major processed capsid protein, gp23, was reduced significantly more than that of most other T4 proteins in unadapted cells relative to adapted cells. Only 4.6% of the T4 DNA made in unadapted cells was resistant to micrococcal nuclease, versus 50% in adapted cells. Thus, defective maturation of T4 heads appears to explain the failure of phage production in unadapted cells. Overproduction of the heat shock protein GroEL from plasmids restored T4 production in unadapted cells to about 50% of that seen in adapted cells. T4-infected, adapted E. coli B at around 44 degrees C exhibited a partial tryptophan deficiency; this correlated with reduced uptake of uracil that is probably caused by partial induction of stringency. Production of bacteriophage T7 at 44 degrees C was increased two- to fourfold by adapting the host to 44 degrees C before infection; evidence against involvement of the htpR (rpoH) gene is presented. This work and recent work with bacteriophage lambda (C. Waghorne and C.R. Fuerst, Virology 141:51-64, 1985) appear to represent the first demonstrations for any virus that expression of the heat shock regulon of a host is necessary for virus production at high temperature. Images PMID:2446014

Analysis of capsid portal protein and terminase functional domains: interaction sites required for DNA packaging in bacteriophage T4.

PubMed

Lin, H; Rao, V B; Black, L W

1999-06-04

Bacteriophage DNA packaging results from an ATP-driven translocation of concatemeric DNA into the prohead by the phage terminase complexed with the portal vertex dodecamer of the prohead. Functional domains of the bacteriophage T4 terminase and portal gene 20 product (gp20) were determined by mutant analysis and sequence localization within the structural genes. Interaction regions of the portal vertex and large terminase subunit (gp17) were determined by genetic (terminase-portal intergenic suppressor mutations), biochemical (column retention of gp17 and inhibition of in vitro DNA packaging by gp20 peptides), and immunological (co-immunoprecipitation of polymerized gp20 peptide and gp17) studies. The specificity of the interaction was tested by means of a phage T4 HOC (highly antigenicoutercapsid protein) display system in which wild-type, cs20, and scrambled portal peptide sequences were displayed on the HOC protein of phage T4. Binding affinities of these recombinant phages as determined by the retention of these phages by a His-tag immobilized gp17 column, and by co-immunoprecipitation with purified terminase supported the specific nature of the portal protein and terminase interaction sites. In further support of specificity, a gp20 peptide corresponding to a portion of the identified site inhibited packaging whereas the scrambled sequence peptide did not block DNA packaging in vitro. The portal interaction site is localized to 28 residues in the central portion of the linear sequence of gp20 (524 residues). As judged by two pairs of intergenic portal-terminase suppressor mutations, two separate regions of the terminase large subunit gp17 (central and COOH-terminal) interact through hydrophobic contacts at the portal site. Although the terminase apparently interacts with this gp20 portal peptide, polyclonal antibody against the portal peptide appears unable to access it in the native structure, suggesting intimate association of gp20 and gp17 possibly internalizes terminase regions within the portal in the packasome complex. Both similarities and differences are seen in comparison to analogous sites which have been identified in phages T3 and lambda. Copyright 1999 Academic Press.

A Single Mutation at the Sheet Switch Region Results in Conformational Changes Favoring 6 Light-Chain Fibrillogenesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hernández-Santoyo, A.; Del Pozo Yauner, L; Fuentes-Silva, D

Systemic amyloid light-chain (LC) amyloidosis is a disease process characterized by the pathological deposition of monoclonal LCs in tissue. All LC subtypes are capable of fibril formation although {lambda} chains, particularly those belonging to the {lambda}6 type, are overrepresented. Here, we report the thermodynamic and in vitro fibrillogenic properties of several mutants of the {lambda}6 protein 6aJL2 in which Pro7 and/or His8 was substituted by Ser or Pro. The H8P and H8S mutants were almost as stable as the wild-type protein and were poorly fibrillogenic. In contrast, the P7S mutation decreased the thermodynamic stability of 6aJL2 and greatly enhanced itsmore » capacity to form amyloid-like fibrils in vitro. The crystal structure of the P7S mutant showed that the substitution induced both local and long-distance effects, such as the rearrangement of the VL (variable region of the light chain)-VL interface. This mutant crystallized in two orthorhombic polymorphs, P2{sub 1}2{sub 1}2{sub 1} and C222{sub 1}. In the latter, a monomer that was not arranged in the typical Bence-Jones dimer was observed for the first time. Crystal-packing analysis of the C222{sub 1} lattice showed the establishment of intermolecular {beta}-{beta} interactions that involved the N-terminus and {beta}-strand B and that these could be relevant in the mechanism of LC fibril formation. Our results strongly suggest that Pro7 is a key residue in the conformation of the N-terminal sheet switch motif and, through long-distance interactions, is also critically involved in the contacts that stabilized the VL interface in {lambda}6 LCs.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pletneva, Nadya V.; Pletnev, Vladimir Z.; Shemiakina, Irina I.

The wild type red fluorescent protein eqFP578 (from sea anemone Entacmaea quadricolor, {lambda}{sub ex} = 552 nm, {lambda}{sub em} = 578 nm) and its bright far-red fluorescent variant Katushka ({lambda}{sub ex} = 588 nm, {lambda}{sub em} = 635 nm) are characterized by the pronounced pH dependence of their fluorescence. The crystal structures of eqFP578f (eqFP578 with two point mutations improving the protein folding) and Katushka have been determined at the resolution ranging from 1.15 to 1.85 {angstrom} at two pH values, corresponding to low and high level of fluorescence. The observed extinguishing of fluorescence upon reducing pH in eqFP578f andmore » Katushka has been shown to be accompanied by the opposite trans-cis and cis-trans chromophore isomerization, respectively. Asn143, Ser158, His197 and Ser143, Leu174, and Arg197 have been shown to stabilize the respective trans and cis fluorescent states of the chromophores in eqFP578f and Katushka at higher pH. The cis state has been suggested as being primarily responsible for the observed far-red shift of the emission maximum of Katushka relative to that of eqFP578f.« less

Class B Alkaline Stabilization to Achieve Pathogen Inactivation

PubMed Central

Bean, Christine L.; Hansen, Jacqueline J.; Margolin, Aaron B.; Balkin, Helene; Batzer, Glenda; Widmer, Giovanni

2007-01-01

Liming is a cost-effective treatment currently employed in many Class B biosolids production plants in the United States. A bench scale model of lime stabilization was designed to evaluate the persistence of viral, bacterial and parasitic pathogens. The survival of fecal coliforms, Salmonella, adenovirus type 5, rotavirus Wa, bacteriophage MS-2, Cryptosporidium parvum oocysts, Giardia lamblia cysts, and Ascaris lumbricoides ova was evaluated under lime stabilization conditions in a water matrix. Fecal coliforms and Salmonella were undetectable following 2 hours of lime stabilization, demonstrating a 7-log reduction. Adenovirus, MS-2 and rotavirus were below detectable levels following 2 h of liming, demonstrating a 4-log reduction. G. lamblia cysts were also inactivated. A. lumbricoides ova remained viable following 72 hours of liming as did C. parvum oocysts. While this study confirmed that Ascaris ova are resistant to liming, their scarcity in sludge and low recovery efficiencies limit their use as indicator. The persistence of C. parvum oocysts after exposure to lime, suggests that this parasite would be a better choice as indicator for evaluating biosolids intended for land application. The studies done with adenovirus Type 5, rotavirus Wa and male specific bacteriophage provided preliminary data demonstrating similar inactivation rates. Monitoring anthropogenic viruses is a time consuming, labor intensive and expensive process. If further studies could demonstrate that phage could be used as an indicator of other enteric viruses, enhanced monitoring could result in greater acceptance of land application of biosolids while demonstrating no increased public health threat. PMID:17431316

Directional mechanical stability of Bacteriophage φ29 motor’s 3WJ-pRNA: Extraordinary robustness along portal axis

PubMed Central

Xu, Zhonghe; Sun, Yang; Weber, Jeffrey K.; Cao, Yi; Wang, Wei; Jasinski, Daniel; Guo, Peixuan; Zhou, Ruhong; Li, Jingyuan

2017-01-01

The molecular motor exploited by bacteriophage φ29 to pack DNA into its capsid is regarded as one of the most powerful mechanical devices present in viral, bacterial, and eukaryotic systems alike. Acting as a linker element, a prohead RNA (pRNA) effectively joins the connector and ATPase (adenosine triphosphatase) components of the φ29 motor. During DNA packing, this pRNA needs to withstand enormous strain along the capsid’s portal axis—how this remarkable stability is achieved remains to be elucidated. We investigate the mechanical properties of the φ29 motor’s three-way junction (3WJ)–pRNA using a combined steered molecular dynamics and atomic force spectroscopy approach. The 3WJ exhibits strong resistance to stretching along its coaxial helices, demonstrating its super structural robustness. This resistance disappears, however, when external forces are applied to the transverse directions. From a molecular standpoint, we demonstrate that this direction-dependent stability can be attributed to two Mg clamps that cooperate and generate mechanical resistance in the pRNA’s coaxial direction. Our results suggest that the asymmetric nature of the 3WJ’s mechanical stability is entwined with its biological function: Enhanced rigidity along the portal axis is likely essential to withstand the strain caused by DNA condensation, and flexibility in other directions should aid in the assembly of the pRNA and its association with other motor components. PMID:28560321

Immobilization of proteins onto microbeads using a DNA binding tag for enzymatic assays.

PubMed

Kojima, Takaaki; Mizoguchi, Takuro; Ota, Eri; Hata, Jumpei; Homma, Keisuke; Zhu, Bo; Hitomi, Kiyotaka; Nakano, Hideo

2016-02-01

A novel DNA-binding protein tag, scCro-tag, which is a single-chain derivative of the bacteriophage lambda Cro repressor, has been developed to immobilize proteins of interest (POI) on a solid support through binding OR consensus DNA (ORC) that is tightly bound by the scCro protein. The scCro-tag successfully bound a transglutaminase 2 (TGase 2) substrate and manganese peroxidase (MnP) to microbeads via scaffolding DNA. The resulting protein-coated microbeads can be utilized for functional analysis of the enzymatic activity using flow cytometry. The quantity of bead-bound proteins can be enhanced by increasing the number of ORCs. In addition, proteins with the scCro-tag that were synthesized using a cell-free protein synthesis system were also immobilized onto the beads, thus indicating that this bead-based system would be applicable to high-throughput analysis of various enzymatic activities. Copyright © 2015 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Design and characterization of a three-terminal transcriptional device through polymerase per second.

PubMed

Varadarajan, Prasanna Amur; Del Vecchio, Domitilla

2009-09-01

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 a bipolar junction transistor (BJT). In particular, as it occurs in a BJT, the device can be tuned to operate either as a linear amplifier or as a switch. When the device operates as a linear amplifier, gains of twofolds can be obtained, which are considerably smaller than those obtained in a BJT (in which 100-fold amplification gains can be reached). This fact suggests that the parts extracted from natural transcriptional systems may be naturally designed mostly to process and store information as opposed to amplify signals.

Novel self-organization mechanism in ultrathin liquid films: theory and experiment.

PubMed

Trice, Justin; Favazza, Christopher; Thomas, Dennis; Garcia, Hernando; Kalyanaraman, Ramki; Sureshkumar, Radhakrishna

2008-07-04

When an ultrathin metal film of thickness h (<20 nm) is melted by a nanosecond pulsed laser, the film temperature is a nonmonotonic function of h and achieves its maximum at a certain thickness h*. This is a consequence of the h and time dependence of energy absorption and heat flow. Linear stability analysis and nonlinear dynamical simulations that incorporate such intrinsic interfacial thermal gradients predict a characteristic pattern length scale Lambda that decreases for h>h*, in contrast to the classical spinodal dewetting behavior where Lambda increases monotonically as h2. These predictions agree well with experimental observations for Co and Fe films on SiO2.

Bacteriophage phi11 lysin: physicochemical characterization and comparison with phage phi80a lysin

USDA-ARS?s Scientific Manuscript database

Phage lytic enzymes are promising antimicrobial agents. Lysins of phage phi11 (LysPhi11) and phi80a (LysPhi80a) can lyse (destroy) biofilms and cells of antibiotic-resistant strains of Staphylococcus aureus. Stability of enzymes is one of the parameters making their practical use possible. The obj...

Protein chainmail variants in dsDNA viruses

PubMed Central

Zhou, Z. Hong; Chiou, Joshua

2017-01-01

First discovered in bacteriophage HK97, biological chainmail is a highly stable system formed by concatenated protein rings. Each subunit of the ring contains the HK97-like fold, which is characterized by its submarine-like shape with a 5-stranded β sheet in the axial (A) domain, spine helix in the peripheral (P) domain, and an extended (E) loop. HK97 capsid consists of covalently-linked copies of just one HK97-like fold protein and represents the most effective strategy to form highly stable chainmail needed for dsDNA genome encapsidation. Recently, near-atomic resolution structures enabled by cryo electron microscopy (cryoEM) have revealed a range of other, more complex variants of this strategy for constructing dsDNA viruses. The first strategy, exemplified by P22-like phages, is the attachment of an insertional (I) domain to the core 5-stranded β sheet of the HK97-like fold. The atomic models of the Bordetella phage BPP-1 showcases an alternative topology of the classic HK97 topology of the HK97-like fold, as well as the second strategy for constructing stable capsids, where an auxiliary jellyroll protein dimer serves to cement the non-covalent chainmail formed by capsid protein subunits. The third strategy, found in lambda-like phages, uses auxiliary protein trimers to stabilize the underlying non-covalent chainmail near the 3-fold axis. Herpesviruses represent highly complex viruses that use a combination of these strategies, resulting in four-level hierarchical organization including a non-covalent chainmail formed by the HK97-like fold domain found in the floor region. A thorough understanding of these structures should help unlock the enigma of the emergence and evolution of dsDNA viruses and inform bioengineering efforts based on these viruses. PMID:29177192

Combining Comprehensive Analysis of Off-Site Lambda Phage Integration with a CRISPR-Based Means of Characterizing Downstream Physiology.

PubMed

Tanouchi, Yu; Covert, Markus W

2017-09-19

During its lysogenic life cycle, the phage genome is integrated into the host chromosome by site-specific recombination. In this report, we analyze lambda phage integration into noncanonical sites using next-generation sequencing and show that it generates significant genetic diversity by targeting over 300 unique sites in the host Escherichia coli genome. Moreover, these integration events can have important phenotypic consequences for the host, including changes in cell motility and increased antibiotic resistance. Importantly, the new technologies that we developed to enable this study-sequencing secondary sites using next-generation sequencing and then selecting relevant lysogens using clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9-based selection-are broadly applicable to other phage-bacterium systems. IMPORTANCE Bacteriophages play an important role in bacterial evolution through lysogeny, where the phage genome is integrated into the host chromosome. While phage integration generally occurs at a specific site in the host chromosome, it is also known to occur at other, so-called secondary sites. In this study, we developed a new experimental technology to comprehensively study secondary integration sites and discovered that phage can integrate into over 300 unique sites in the host genome, resulting in significant genetic diversity in bacteria. We further developed an assay to examine the phenotypic consequence of such diverse integration events and found that phage integration can cause changes in evolutionarily relevant traits such as bacterial motility and increases in antibiotic resistance. Importantly, our method is readily applicable to other phage-bacterium systems. Copyright © 2017 Tanouchi and Covert.

About some Regge-like relations for (stable) black holes

NASA Astrophysics Data System (ADS)

Recami, E.; Tonin-Zanchin, Vilson

1991-08-01

Within a purely classical formulation of 'strong gravity', we associated hadron constituents (and even hadrons themselves) with suitable stationary, axisymmetric solutions of certain new Einstein-type equations supposed to describe the strong field inside hadrons. Such equations are nothing but Einstein equations - with cosmological term - suitably scaled down. As a consequence, the cosmological constant (lambda) and the masses M result in our theory to be scaled up and transformed into a 'hadronic constant' and into 'strong masses', respectively. Due to the unusual range of lambda and M values considered, we met a series of solutions of the Kerr-Newman-de Sitter (KNdS) type with such interesting properties that it is worth studying them - from our particular point of view - also in the case of ordinary gravity. This is the aim of the present work. The requirement that those solutions be stable, i.e., that their temperature (or surface gravity) be vanishingly small, implies the coincidence of at least two of their (in general, three) horizons. Imposing the stability condition of a certain horizon does yield (once chosen the values of J, q, and lambda) mass and radius of the associated black-hole. In the case of ordinary Einstein equations and for stable black-holes of the KNdS type, we get in particular Regge-like relations among mass M, angular momentum J, charge q, and cosmological constant (lambda). For instance, with the standard definitions Q2 is identical to Gq2 /(4(pi)(epsilon)0c4); a is identical to J/(Mc); m is identical to GM/c2, in the case lambda = 0 in which m2 = a2 + Q2 and if q is negligible we find m2 = J. When considering, for simplicity, lambda greater than 0 and J = 0 (and q still negligible), then we obtain m2 = 1/(9(lambda)).

[Strategies to prevent bacteriophage infection in industrial fermentation].

PubMed

Shen, Juntao; Xiu, Zhilong

2017-12-25

During the development of bacteria-based biotechnology, bacteriophage infection is one of the constant threats and troublesome problems in industrial fermentation. The core of puzzled bacteriophage infection is a complex arm race of coevolution between bacteriophages and their hosts where bacteriophage has evolved lots of escaped ways against bacterial resistance mechanisms. The strategies of rationally designing factories and rotation of starter strains could reduce the risk of bacteriophage infection, but often fail to avoid. Genetic engineering to increase bacterial resistance is one of the strategies to prevent bacteriophage infection and more knowledge about bacteriophage and its host is needed. Recently, there are some new findings on bacterial resistance mechanisms which provide new solutions for bacteriophage infection. For example, it is possible for a rational design of resistant strains to use CRISPR-Cas based technologies just based on the sequences of bacteriophages. Moreover, it is also possible to avoid the escape of bacteriophage by iteratively building up resistance levels to generate robust industrial starter cultures. Quorum-sensing signal molecules have recently been proved to be involved in the interactions between bacteria and bacteriophages, which provides a possible way to solve bacteriophage infection from a population level. Finally, the rapid development of bacteriophage genome editing and synthetic biology will bring some new cues for preventing bacteriophage infection in industrial fermentation.

Influence of membrane thickness and ion concentration on the properties of the gramicidin a channel. Autocorrelation, spectral power density, relaxation and single-channel studies.

PubMed

Kolb, H A; Bamberg, E

1977-01-04

The properties of the gramicidin A channel in membranes made from a series of monoglycerides have been studied. In agreement with previous studies, the dissociation rate constant kD of the dimeric channel was found to increase strongly with increasing chain length of the monoglyceride, corresponding to a decrease of the mean life-time of the channel. The value of kD, however, was not strictly correlated with the membrane thickness, as seen from a comparison of membranes with different solvent content. Furthermore, the life-time of the channel increased with the concentration of the permeable ion. This effect was tentatively explained by an electrostatic stabilization of the channel. The single-channel conductance lambda was found to decrease with increasing membrane thickness d, if d was varied by increasing the chain length of the lipid. On the other hand, if d was changed by varying the solvent content of the membranes formed from one and the same lipid, lambda remained constant. These observations were explained by the assumption of local inhomogeneities in the membrane thickness. A striking difference between the lambda values obtained from autocorrelation analysis in the presence of many presence of many channels (lambda a) and those obtained from single-channel experiments (lambda sc) occurred with membranes from longer chain-length monoglycerides. This difference disappeared at low ion concentrations. Electrostatic interactions between channels in local clusters were proposed for an interpretation of these findings.

Hyperexpansion of RNA Bacteriophage Diversity

PubMed Central

Krishnamurthy, Siddharth R.; Janowski, Andrew B.; Zhao, Guoyan; Barouch, Dan; Wang, David

2016-01-01

Bacteriophage modulation of microbial populations impacts critical processes in ocean, soil, and animal ecosystems. However, the role of bacteriophages with RNA genomes (RNA bacteriophages) in these processes is poorly understood, in part because of the limited number of known RNA bacteriophage species. Here, we identify partial genome sequences of 122 RNA bacteriophage phylotypes that are highly divergent from each other and from previously described RNA bacteriophages. These novel RNA bacteriophage sequences were present in samples collected from a range of ecological niches worldwide, including invertebrates and extreme microbial sediment, demonstrating that they are more widely distributed than previously recognized. Genomic analyses of these novel bacteriophages yielded multiple novel genome organizations. Furthermore, one RNA bacteriophage was detected in the transcriptome of a pure culture of Streptomyces avermitilis, suggesting for the first time that the known tropism of RNA bacteriophages may include gram-positive bacteria. Finally, reverse transcription PCR (RT-PCR)-based screening for two specific RNA bacteriophages in stool samples from a longitudinal cohort of macaques suggested that they are generally acutely present rather than persistent. PMID:27010970

Methods for Bacteriophage Preservation.

PubMed

Łobocka, Małgorzata B; Głowacka, Aleksandra; Golec, Piotr

2018-01-01

In a view of growing interest in bacteriophages as the most abundant members of microbial communities and as antibacterial agents, reliable methods for bacteriophage long-term preservation, that warrant the access to original or mutant stocks of unchanged properties, have become of crucial importance. A storage method that retains the infectivity of any kind of bacteriophage virions, either in a cell lysate or in a purified suspension, does not exist, due to the enormous diversity of bacteriophages and hence the differentiation of their sensitivity to various storage conditions. Here, we describe a method of long-term bacteriophage preservation, which is based on freezing of freshly infected susceptible bacteria at early stages of bacteriophage development. The infected bacteria release mature bacteriophages upon melting enabling the recovery of bacteriophage virions with high efficiency. The only limitation of this method is the sensitivity of bacteriophage host to deep-freezing, and thus it can be used for the long-term preservation of the vast majority of bacteriophages.

Heat capacity and thermal relaxation of bulk helium very near the lambda point

NASA Technical Reports Server (NTRS)

Lipa, John A.; Swanson, D. R.; Nissen, J. A.; Chui, T. C. P.

1994-01-01

In October 1992 a low temperature experiment was flown on the Space Shuttle in low Earth orbit. The objective of the mission was to measure the heat capacity and thermal conductivity of helium very close to the lambda point with the smearing effect of gravity removed. We report preliminary results from the experiment, and compare them with related measurements performed on the ground. The sample was s sphere of helium 3.5 cm in diameter contained within a copper calorimeter of vey high thermal conductivity. The calorimeter was attached to a pair of high resolution paramagnetic salt thermometers with noise levels in the 10(exp -10) K range and suspended from a high stability thermal isolation system. During the mission we found that the resolution of the thermometers was degraded somewhat due to the impact of charged particles. This effect limited the useful resolution of the measurements to about two nanokelvins from the lambda point. The results reported here are limited to about ten nanokelvins from the transition.

Mgm101 is a Rad52-related protein required for mitochondrial DNA recombination.

PubMed

Mbantenkhu, MacMillan; Wang, Xiaowen; Nardozzi, Jonathan D; Wilkens, Stephan; Hoffman, Elizabeth; Patel, Anamika; Cosgrove, Michael S; Chen, Xin Jie

2011-12-09

Homologous recombination is a conserved molecular process that has primarily evolved for the repair of double-stranded DNA breaks and stalled replication forks. However, the recombination machinery in mitochondria is poorly understood. Here, we show that the yeast mitochondrial nucleoid protein, Mgm101, is related to the Rad52-type recombination proteins that are widespread in organisms from bacteriophage to humans. Mgm101 is required for repeat-mediated recombination and suppression of mtDNA fragmentation in vivo. It preferentially binds to single-stranded DNA and catalyzes the annealing of ssDNA precomplexed with the mitochondrial ssDNA-binding protein, Rim1. Transmission electron microscopy showed that Mgm101 forms large oligomeric rings of ∼14-fold symmetry and highly compressed helical filaments. Specific mutations affecting ring formation reduce protein stability in vitro. The data suggest that the ring structure may provide a scaffold for stabilization of Mgm101 by preventing the aggregation of the otherwise unstable monomeric conformation. Upon binding to ssDNA, Mgm101 is remobilized from the rings to form distinct nucleoprotein filaments. These studies reveal a recombination protein of likely bacteriophage origin in mitochondria and support the notion that recombination is indispensable for mtDNA integrity.

Multiple functional roles of the accessory I-domain of bacteriophage P22 coat protein revealed by NMR structure and cryoEM modeling

PubMed Central

Rizzo, Alessandro A.; Suhanovsky, Margaret M.; Baker, Matthew L.; Fraser, LaTasha C.R.; Jones, Lisa M.; Rempel, Don L.; Gross, Michael L.; Chiu, Wah; Alexandrescu, Andrei T.; Teschke, Carolyn M.

2014-01-01

SUMMARY Some capsid proteins built on the ubiquitous HK97-fold have accessory domains that impart specific functions. Bacteriophage P22 coat protein has a unique inserted I-domain. Two prior I-domain models from sub-nanometer cryoEM reconstructions differed substantially. Therefore, the NMR structure of the I-domain was determined, which also was used to improve cryoEM models of coat protein. The I-domain has an anti-parallel 6-stranded β-barrel fold, previously not observed in HK97-fold accessory domains. The D-loop, which is dynamic both in the isolated I-domain and intact monomeric coat protein, forms stabilizing salt bridges between adjacent capsomers in procapsids. A newly described S-loop is important for capsid size determination, likely through intra-subunit interactions. Ten of eighteen coat protein temperature-sensitive-folding substitutions are in the I-domain, indicating its importance in folding and stability. Several are found on a positively charged face of the β-barrel that anchors the I-domain to a negatively charged surface of the coat protein HK97-core. PMID:24836025

Multiple functional roles of the accessory I-domain of bacteriophage P22 coat protein revealed by NMR structure and CryoEM modeling.

PubMed

Rizzo, Alessandro A; Suhanovsky, Margaret M; Baker, Matthew L; Fraser, LaTasha C R; Jones, Lisa M; Rempel, Don L; Gross, Michael L; Chiu, Wah; Alexandrescu, Andrei T; Teschke, Carolyn M

2014-06-10

Some capsid proteins built on the ubiquitous HK97-fold have accessory domains imparting specific functions. Bacteriophage P22 coat protein has a unique insertion domain (I-domain). Two prior I-domain models from subnanometer cryoelectron microscopy (cryoEM) reconstructions differed substantially. Therefore, the I-domain's nuclear magnetic resonance structure was determined and also used to improve cryoEM models of coat protein. The I-domain has an antiparallel six-stranded β-barrel fold, not previously observed in HK97-fold accessory domains. The D-loop, which is dynamic in the isolated I-domain and intact monomeric coat protein, forms stabilizing salt bridges between adjacent capsomers in procapsids. The S-loop is important for capsid size determination, likely through intrasubunit interactions. Ten of 18 coat protein temperature-sensitive-folding substitutions are in the I-domain, indicating its importance in folding and stability. Several are found on a positively charged face of the β-barrel that anchors the I-domain to a negatively charged surface of the coat protein HK97-core. Copyright © 2014 Elsevier Ltd. All rights reserved.

Incorporation of T4 bacteriophage in electrospun fibres.

PubMed

Korehei, R; Kadla, J

2013-05-01

Antibacterial food packaging materials, such as bacteriophage-activated electrospun fibrous mats, may address concerns triggered by waves of bacterial food contamination. To address this, we investigated several efficient methods for incorporating T4 bacteriophage into electrospun fibrous mats. The incorporation of T4 bacteriophage using simple suspension electrospinning led to more than five orders of magnitude decrease in bacteriophage activity. To better maintain bacteriophage viability, emulsion electrospinning was developed where the T4 bacteriophage was pre-encapsulated in an alginate reservoir via an emulsification process and subsequently electrospun into fibres. This resulted in an increase in bacteriophage viability, but there was still two orders of magnitude drop in activity. Using a coaxial electrospinning process, full bacteriophage activity could be maintained. In this process, a core/shell fibre structure was formed with the T4 bacteriophage being directly incorporated into the fibre core. The core/shell fibre encapsulated bacteriophage exhibited full bacteriophage viability after storing for several weeks at +4°C. Coaxial electrospinning was shown to be capable of encapsulating bacteriophages with high loading capacity, high viability and long storage time. These results are significant in the context of controlling and preventing bacterial infections in perishable foods during storage. © 2013 The Society for Applied Microbiology.

Evaluation of aerosol spray and intramuscular injection of bacteriophage to treat an Escherichia coli respiratory infection.

PubMed

Huff, W E; Huff, G R; Rath, N C; Balog, J M; Donoghue, A M

2003-07-01

Two studies were conducted to determine the efficacy of either aerosol or i.m. injection of bacteriophage to treat an Escherichia coli respiratory infection in broiler chickens. An additional two studies were conducted to enumerate the bacteriophage in the blood of birds at 1, 2, 3, 4, 5, 6, 24, and 48 h after being sprayed or injected i.m. with bacteriophage. Five birds were bled at each period. In study 1, there were 10 treatments with three replicate pens of 10 birds. The treatments consisted of an untreated control, heat-killed bacteriophage spray, active bacteriophage spray, E. coli challenge at 7 d of age, and E. coli challenge followed by spraying the birds with heat-killed bacteriophage or active bacteriophage at 2, 24, or 48 h after challenge. In study 2 there were 11 treatments with three replicate pens of 10 birds per pen. The treatments were untreated controls, birds injected i.m. in the thigh with heat-killed or active bacteriophage, E. coli challenge at 7 d of age, PBS challenge, E. coli challenge followed by injection of heat-killed or active bacteriophage immediately after challenge or at 24 or 48 h after challenge. In both studies the E. coli challenge consisted of injecting 10(4) cfu into the thoracic air sac. Treatment of this severe E. coli infection with the bacteriophage aerosol spray significantly reduced mortality from 50 to 20% when given immediately after the challenge but had little treatment efficacy when administered 24 or 48 h after challenge. The i.m. injection of bacteriophage significantly reduced mortality from 53 to 17%, 46 to 10%, and 44 to 20% when given immediately, 24, or 48 h after challenge, respectively. Only a few birds sprayed with bacteriophage had detectable bacteriophage in their blood with an average of 96 pfu/mL 1 h after bacteriophage administration, and no bacteriophage was detected 24 and 48 h after bacteriophage administration. All birds injected i.m. with bacteriophage had detectable levels of bacteriophage in their blood at levels of 10(4) pfu/mL of blood up to 6 h after bacteriophage administration, and four of the five birds had detectable bacteriophage in their blood at an average level of 70 pfu/mL of blood 24 h after bacteriophage administration. The relative inefficiency of the spray treatment to the i.m. injection treatment may be due to the inability to get bacteriophage into the blood at high concentrations when the birds are sprayed versus the consistent high titers achieved with the i.m. injection of bacteriophage. These data provide support to the concept that bacteriophage may be an effective alternative to antibiotics in animal production when they are administered in a way that delivers high titers of the bacteriophage to the critical site of the bacterial infection.

Bacteriophages as Potential Treatment for Urinary Tract Infections.

PubMed

Sybesma, Wilbert; Zbinden, Reinhard; Chanishvili, Nino; Kutateladze, Mzia; Chkhotua, Archil; Ujmajuridze, Aleksandre; Mehnert, Ulrich; Kessler, Thomas M

2016-01-01

Urinary tract infections (UTIs) are among the most prevalent microbial diseases and their financial burden on society is substantial. The continuing increase of antibiotic resistance worldwide is alarming so that well-tolerated, highly effective therapeutic alternatives are urgently needed. To investigate the effect of bacteriophages on Escherichia coli and Klebsiella pneumoniae strains isolated from the urine of patients suffering from UTIs. Forty-one E. coli and 9 K. pneumoniae strains, isolated from the urine of patients suffering from UTIs, were tested in vitro for their susceptibility toward bacteriophages. The bacteriophages originated from either commercially available bacteriophage cocktails registered in Georgia or from the bacteriophage collection of the George Eliava Institute of Bacteriophage, Microbiology and Virology. In vitro screening of bacterial strains was performed by use of the spot-test method. The experiments were implemented three times by different groups of scientists. The lytic activity of the commercial bacteriophage cocktails on the 41 E. coli strains varied between 66% (Pyo bacteriophage) and 93% (Enko bacteriophage). After bacteriophage adaptation of the Pyo bacteriophage cocktail, its lytic activity was increased from 66 to 93% and only one E. coli strain remained resistant. One bacteriophage of the Eliava collection could lyse all 9 K. pneumoniae strains. Based on the high lytic activity and the potential of resistance optimization by direct adaption of bacteriophages as reported in this study, and in view of the continuing increase of antibiotic resistance worldwide, bacteriophage therapy is a promising treatment option for UTIs highly warranting randomized controlled trials.

Genotoxicity assessments of alluvial soil irrigated with wastewater from a pesticide manufacturing industry.

PubMed

Anjum, Reshma; Krakat, Niclas

2015-10-01

In this study, organochlorine pesticides (OCP) and heavy metals were analyzed from wastewater- and groundwater- irrigated soils (control samples) by gas chromatography (GC) and atomic absorption spectrophotometry (AAS), respectively. Gas chromatographic analysis revealed the presence of high concentration of pesticides in soil irrigated with wastewater (WWS). These concentrations were far above the maximum residue permissible limits indicating that alluvial soils have high binding capacity of OCP. AAS analyses revealed higher concentration of heavy metals in WWS as compared to groundwater (GWS). Also, the DNA repair (SOS)-defective Escherichia coli K-12 mutant assay and the bacteriophage lambda system were employed to estimate the genotoxicity of soils. Therefore, soil samples were extracted by hexane, acetonitrile, methanol, chloroform, and acetone. Both bioassays revealed that hexane-extracted soils from WWS were most genotoxic. A maximum survival of 15.2% and decline of colony-forming units (CFUs) was observed in polA mutants of DNA repair-defective E. coli K-12 strains when hexane was used as solvent. However, the damage of polA (-) mutants triggered by acetonitrile, methanol, chloroform, and acetone extracts was 80.0, 69.8, 65.0, and 60.7%, respectively. These results were also confirmed by the bacteriophage λ test system as hexane extracts of WWS exhibited a maximum decline of plaque-forming units for lexA mutants of E. coli K-12 pointing to an elevated genotoxic potential. The lowest survival was observed for lexA (12%) treated with hexane extracts while the percentage of survival was 25, 49.2, 55, and 78% with acetonitrile, methanol, chloroform, and acetone, respectively, after 6 h of treatment. Thus, our results suggest that agricultural soils irrigated with wastewater from pesticide industries have a notably high genotoxic potential.

The structure of intense vorticity in homogeneous isotropic turbulence

NASA Technical Reports Server (NTRS)

Jimenez, J.; Wray, A. A.; Saffman, P. G.; Rogallo, R. S.

1992-01-01

The structure of the intense vorticity regions is studied in numerically simulated homogeneous, isotropic, equilibrium turbulent flow fields at four different Reynolds numbers in the range Re(sub lambda) = 36-171. In accordance with previous investigators, this vorticity is found to be organized in coherent, cylindrical or ribbon-like, vortices ('worms'). A statistical study suggests that they are just especially intense features of the background, O(omega'), vorticity. Their radii scale with the Kolmogorov microscale and their lengths with the integral scale of the flow. An interesting observation is that the Reynolds number based on the circulation of the intense vortices, gamma/nu, increases monotonically with Re(sub lambda), raising the question of the stability of the structures in the limit of Re(sub lambda) approaching infinity. One and two-dimensional statistics of vorticity and strain are presented; they are non-gaussian, and the behavior of their tails depends strongly on the Reynolds number. There is no evidence of convergence to a limiting distribution in our range of Re(sub lambda), even though the energy spectra and the energy dissipation rate show good asymptotic properties in the higher Reynolds number cases. Evidence is presented to show that worms are natural features of the flow and that they do not depend on the particular forcing scheme.

Evaluation of the broad-spectrum lytic capability of bacteriophage cocktails against various Salmonella serovars and their effects on weaned pigs infected with Salmonella Typhimurium.

PubMed

Seo, Byoung-Joo; Song, Eu-Tteum; Lee, Kichan; Kim, Jong-Won; Jeong, Chang-Gi; Moon, Sung-Hyun; Son, Jee Soo; Kang, Sang Hyeon; Cho, Ho-Seong; Jung, Byeong Yeal; Kim, Won-Il

2018-06-06

The broad-spectrum lytic capability of Salmonella bacteriophages against various Salmonella species was evaluated to determine their potential as an alternative for antibiotics, and the safety and preventive effects of the bacteriophages were assessed on mice and pigs. Four bacteriophage cocktails were prepared using 13 bacteriophages, and the lytic capability of the four bacteriophage cocktails was tested using Salmonella reference strains and field isolates. Bacteriophage cocktail C (SEP-1, SGP-1, STP-1, SS3eP-1, STP-2, SChP-1, SAP-1, SAP-2; ≥10 9 pfu/ml) showed the best lytic activity against the Salmonella reference strains (100% of 34) and field isolates (92.5% of 107). Fifty mice were then orally inoculated with bacteriophage cocktail C to determine the distribution of bacteriophages in various organs, blood and feces. The effects of bacteriophages on Salmonella infection in weaned pigs (n=15) were also evaluated through an experimental challenge with Salmonella Typhimurium after treatment with bacteriophage cocktail C. All mice exhibited distribution of the bacteriophages in all organs, blood and feces until 15 days post infection (dpi). After 35 dpi, bacteriophages were not detected in any of these specimens. As demonstrated in a pig challenge study, treatment with bacteriophage cocktail C reduced the level of Salmonella shedding in feces. The metagenomic analyses of these pig feces also revealed that bacteriophage treatment decreased the number of species of the Enterobacteriaceae family without significant disturbance to the normal fecal flora. This study showed that bacteriophages effectively controlled Salmonella in a pig challenge model and could be a good alternative for antibiotics to control Salmonella infection.

Bacteriophages as Potential Treatment for Urinary Tract Infections

PubMed Central

Sybesma, Wilbert; Zbinden, Reinhard; Chanishvili, Nino; Kutateladze, Mzia; Chkhotua, Archil; Ujmajuridze, Aleksandre; Mehnert, Ulrich; Kessler, Thomas M.

2016-01-01

Background: Urinary tract infections (UTIs) are among the most prevalent microbial diseases and their financial burden on society is substantial. The continuing increase of antibiotic resistance worldwide is alarming so that well-tolerated, highly effective therapeutic alternatives are urgently needed. Objective: To investigate the effect of bacteriophages on Escherichia coli and Klebsiella pneumoniae strains isolated from the urine of patients suffering from UTIs. Material and methods: Forty-one E. coli and 9 K. pneumoniae strains, isolated from the urine of patients suffering from UTIs, were tested in vitro for their susceptibility toward bacteriophages. The bacteriophages originated from either commercially available bacteriophage cocktails registered in Georgia or from the bacteriophage collection of the George Eliava Institute of Bacteriophage, Microbiology and Virology. In vitro screening of bacterial strains was performed by use of the spot-test method. The experiments were implemented three times by different groups of scientists. Results: The lytic activity of the commercial bacteriophage cocktails on the 41 E. coli strains varied between 66% (Pyo bacteriophage) and 93% (Enko bacteriophage). After bacteriophage adaptation of the Pyo bacteriophage cocktail, its lytic activity was increased from 66 to 93% and only one E. coli strain remained resistant. One bacteriophage of the Eliava collection could lyse all 9 K. pneumoniae strains. Conclusions: Based on the high lytic activity and the potential of resistance optimization by direct adaption of bacteriophages as reported in this study, and in view of the continuing increase of antibiotic resistance worldwide, bacteriophage therapy is a promising treatment option for UTIs highly warranting randomized controlled trials. PMID:27148173

Differential bacteriophage mortality on exposure to copper.

PubMed

Li, Jinyu; Dennehy, John J

2011-10-01

Many studies report that copper can be used to control microbial growth, including that of viruses. We determined the rates of copper-mediated inactivation for a wide range of bacteriophages. We used two methods to test the effect of copper on bacteriophage survival. One method involved placing small volumes of bacteriophage lysate on copper and stainless steel coupons. Following exposure, metal coupons were rinsed with lysogeny broth, and the resulting fluid was serially diluted and plated on agar with the corresponding bacterial host. The second method involved adding copper sulfate (CuSO(4)) to bacteriophage lysates to a final concentration of 5 mM. Aliquots were removed from the mixture, serially diluted, and plated with the appropriate bacterial host. Significant mortality was observed among the double-stranded RNA (dsRNA) bacteriophages Φ6 and Φ8, the single-stranded RNA (ssRNA) bacteriophage PP7, the ssDNA bacteriophage ΦX174, and the dsDNA bacteriophage PM2. However, the dsDNA bacteriophages PRD1, T4, and λ were relatively unaffected by copper. Interestingly, lipid-containing bacteriophages were most susceptible to copper toxicity. In addition, in the first experimental method, the pattern of bacteriophage Φ6 survival over time showed a plateau in mortality after lysates dried out. This finding suggests that copper's effect on bacteriophage is mediated by the presence of water.

The rational design of a 'type 88' genetically stable peptide display vector in the filamentous bacteriophage fd.

PubMed

Enshell-Seijffers, D; Smelyanski, L; Gershoni, J M

2001-05-15

Filamentous bacteriophages are particularly efficient for the expression and display of combinatorial random peptides. Two phage proteins are often employed for peptide display: the infectivity protein, PIII, and the major coat protein, PVIII. The use of PVIII typically requires the expression of two pVIII genes: the wild-type and the recombinant pVIII gene, to generate mosaic phages. 'Type 88' vectors contain two pVIII genes in one phage genome. In this study a novel 'type 88' expression vector has been rationally designed and constructed. Two factors were taken into account: the insertion site and the genetic stability of the second pVIII gene. It was found that selective deletion of recombinant genes was encountered when inserts were cloned into either of the two non-coding regions of the phage genome. The deletions were independent of recA yet required a functional F-episome. Transcription was also found to be a positive factor for deletion. Taking the above into account led to the generation of a novel vector, designated fth1, which can be used to express recombinant peptides as pVIII chimeric proteins in mosaic bacteriophages. The fth1 vector is not only genetically stable but also of high copy number and produces high titers of recombinant phages.

Isolation and characterization of wetland VSW-3, a novel lytic cold-active bacteriophage of Pseudomonas fluorescens.

PubMed

Qin, Kunhao; Ji, Xiuling; Zhang, Chunjing; Ding, Yafang; Kuang, Anxiu; Zhang, Shengting; Zhang, Qi; Lin, Lianbing; Wei, Yunlin

2017-02-01

Wetlands are often called the "kidneys of the Earth" and contribute substantially to environmental improvement. Pseudomonas fluorescens is a major contaminant of milk products and causes the spoilage of refrigerated foods and fresh poultry. In this study, we isolated and characterized a lytic cold-active bacteriophage named VSW-3 together with P. fluorescens SW-3 cells from the Napahai wetland in China. Electron microscopy showed that VSW-3 had an icosahedral head (56 nm) and a tapering tail (20 nm × 12 nm) and a genome size of approximate 40 kb. On the basis of the top-scoring hits in the BLASTP analysis, VSW-3 showed a high degree of module similarity to the Pseudomonas phages Andromeda and Bf7. The latent and burst periods were 45 and 20 min, respectively, with an average burst size of 90 phage particles per infected cell. The pH and thermal stability of VSW-3 were also explored. The optimal pH was found to be 7.0 and the activity decreased rapidly when the temperature exceeded 60 °C. VSW-3 is a cold-active bacteriophage, hence, it is important to research its ability to prevent product contamination caused by P. fluorescens and to characterize its relationship with its host P. fluorescens in the future.

A first step toward liposome-mediated intracellular bacteriophage therapy.

PubMed

Nieth, Anita; Verseux, Cyprien; Barnert, Sabine; Süss, Regine; Römer, Winfried

2015-01-01

The emergence of antibiotic-resistant bacteria presents a severe challenge to medicine and public health. While bacteriophage therapy is a promising alternative to traditional antibiotics, the general inability of bacteriophages to penetrate eukaryotic cells limits their use against resistant bacteria, causing intracellular diseases like tuberculosis. Bacterial vectors show some promise in carrying therapeutic bacteriophages into cells, but also bring a number of risks like an overload of bacterial antigens or the acquisition of virulence genes from the pathogen. As a first step in the development of a non-bacterial vector for bacteriophage delivery into pathogen-infected cells, we attempted to encapsulate bacteriophages into liposomes. Here we report effective encapsulation of the model bacteriophage λeyfp and the mycobacteriophage TM4 into giant liposomes. Furthermore, we show that liposome-associated bacteriophages are taken up into eukaryotic cells more efficiently than free bacteriophages. These are important milestones in the development of an intracellular bacteriophage therapy that might be useful in the fight against multi-drug-resistant intracellular pathogens like Mycobacterium tuberculosis.

Use of PRD1 bacteriophage in groundwater viral transport, inactivation, and attachment studies

USGS Publications Warehouse

Harvey, Ronald W.; Ryan, Joseph N.

2004-01-01

PRD1, an icosahedra-shaped, 62 nm (diameter), double-stranded DNA bacteriophage with an internal membrane, has emerged as an important model virus for studying the manner in which microorganisms are transported through a variety of groundwater environments. The popularity of this phage for use in transport studies involving geologic media is due, in part, to its relative stability over a range of temperatures and low degree of attachment in aquifer sediments. Laboratory and field investigations employing PRD1 are leading to a better understanding of viral attachment and transport behaviors in saturated geologic media and to improved methods for describing mathematically subsurface microbial transport at environmentally significant field scales. Radioisotopic labeling of PRD1 is facilitating additional information about the nature of viral interactions with solid surfaces in geologic media, the importance of iron oxide surfaces, and allowing differentiation between inactivation and attachment in field-scale tracer tests.

Healthy human gut phageome

PubMed Central

Manrique, Pilar; Bolduc, Benjamin; Walk, Seth T.; van der Oost, John; de Vos, Willem M.; Young, Mark J.

2016-01-01

The role of bacteriophages in influencing the structure and function of the healthy human gut microbiome is unknown. With few exceptions, previous studies have found a high level of heterogeneity in bacteriophages from healthy individuals. To better estimate and identify the shared phageome of humans, we analyzed a deep DNA sequence dataset of active bacteriophages and available metagenomic datasets of the gut bacteriophage community from healthy individuals. We found 23 shared bacteriophages in more than one-half of 64 healthy individuals from around the world. These shared bacteriophages were found in a significantly smaller percentage of individuals with gastrointestinal/irritable bowel disease. A network analysis identified 44 bacteriophage groups of which 9 (20%) were shared in more than one-half of all 64 individuals. These results provide strong evidence of a healthy gut phageome (HGP) in humans. The bacteriophage community in the human gut is a mixture of three classes: a set of core bacteriophages shared among more than one-half of all people, a common set of bacteriophages found in 20–50% of individuals, and a set of bacteriophages that are either rarely shared or unique to a person. We propose that the core and common bacteriophage communities are globally distributed and comprise the HGP, which plays an important role in maintaining gut microbiome structure/function and thereby contributes significantly to human health. PMID:27573828

Healthy human gut phageome.

PubMed

Manrique, Pilar; Bolduc, Benjamin; Walk, Seth T; van der Oost, John; de Vos, Willem M; Young, Mark J

2016-09-13

The role of bacteriophages in influencing the structure and function of the healthy human gut microbiome is unknown. With few exceptions, previous studies have found a high level of heterogeneity in bacteriophages from healthy individuals. To better estimate and identify the shared phageome of humans, we analyzed a deep DNA sequence dataset of active bacteriophages and available metagenomic datasets of the gut bacteriophage community from healthy individuals. We found 23 shared bacteriophages in more than one-half of 64 healthy individuals from around the world. These shared bacteriophages were found in a significantly smaller percentage of individuals with gastrointestinal/irritable bowel disease. A network analysis identified 44 bacteriophage groups of which 9 (20%) were shared in more than one-half of all 64 individuals. These results provide strong evidence of a healthy gut phageome (HGP) in humans. The bacteriophage community in the human gut is a mixture of three classes: a set of core bacteriophages shared among more than one-half of all people, a common set of bacteriophages found in 20-50% of individuals, and a set of bacteriophages that are either rarely shared or unique to a person. We propose that the core and common bacteriophage communities are globally distributed and comprise the HGP, which plays an important role in maintaining gut microbiome structure/function and thereby contributes significantly to human health.

Biophysics and bioinformatics of transcription regulation in bacteria and bacteriophages

NASA Astrophysics Data System (ADS)

Djordjevic, Marko

2005-11-01

Due to rapid accumulation of biological data, bioinformatics has become a very important branch of biological research. In this thesis, we develop novel bioinformatic approaches and aid design of biological experiments by using ideas and methods from statistical physics. Identification of transcription factor binding sites within the regulatory segments of genomic DNA is an important step towards understanding of the regulatory circuits that control expression of genes. We propose a novel, biophysics based algorithm, for the supervised detection of transcription factor (TF) binding sites. The method classifies potential binding sites by explicitly estimating the sequence-specific binding energy and the chemical potential of a given TF. In contrast with the widely used information theory based weight matrix method, our approach correctly incorporates saturation in the transcription factor/DNA binding probability. This results in a significant reduction in the number of expected false positives, and in the explicit appearance---and determination---of a binding threshold. The new method was used to identify likely genomic binding sites for the Escherichia coli TFs, and to examine the relationship between TF binding specificity and degree of pleiotropy (number of regulatory targets). We next address how parameters of protein-DNA interactions can be obtained from data on protein binding to random oligos under controlled conditions (SELEX experiment data). We show that 'robust' generation of an appropriate data set is achieved by a suitable modification of the standard SELEX procedure, and propose a novel bioinformatic algorithm for analysis of such data. Finally, we use quantitative data analysis, bioinformatic methods and kinetic modeling to analyze gene expression strategies of bacterial viruses. We study bacteriophage Xp10 that infects rice pathogen Xanthomonas oryzae. Xp10 is an unusual bacteriophage, which has morphology and genome organization that most closely resembles temperate phages, such as lambda. It, however, encodes its own T7-like RNA polymerase (characteristic of virulent phages), whose role in gene expression was unclear. Our analysis resulted in quantitative understanding of the role of both host and phage RNA polymerase, and in the identification of the previously unknown promoter sequence for Xp10 RNA polymerase. More generally, an increasing number of phage genomes are being sequenced every year, and we expect that methods of quantitative data analysis that we introduced will provide an efficient way to study gene expression strategies of novel bacterial viruses.

Five-Body Cluster Structure of the Double-{Lambda} Hypernucleus {sub {Lambda}{Lambda}}{sup 11}Be

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hiyama, E.; Kamimura, M.; Yamamoto, Y.

2010-05-28

Energy levels of the double {Lambda} hypernucleus, {sub {Lambda}{Lambda}}{sup 11}Be are calculated within the framework of a {alpha}{alpha}n{Lambda}{Lambda} five-body model. Interactions between constituent particles are determined so as to reproduce reasonably the observed low-energy properties of the {alpha}{alpha}, {alpha}{alpha}n nuclei and the existing data for {Lambda}-binding energies of the {alpha}{Lambda}, {alpha}{alpha}{Lambda}, {alpha}n{Lambda}, and {alpha}{alpha}n{Lambda} systems. An effective {Lambda}{Lambda} interaction is constructed so as to reproduce, within the {alpha}{Lambda}{Lambda} three-body model, the B{sub {Lambda}{Lambda}}of {sub {Lambda}{Lambda}}{sup 6}He, which was extracted from the emulsion experiment, the NAGARA event. With no adjustable parameters for the {alpha}{alpha}n{Lambda}{Lambda} system, B{sub {Lambda}{Lambda}}of the ground and boundmore » excited states of {sub {Lambda}{Lambda}}{sup 11}Be are calculated with the Gaussian expansion method. The Hida event, recently observed at KEK-E373 experiment, is interpreted as an observation of the ground state of the {sub {Lambda}{Lambda}}{sup 11}Be.« less

A bacteriophage for Myxococcus xanthus: isolation, characterization and relation of infectivity to host morphogenesis.

PubMed

Burchard, R P; Dworkin, M

1966-03-01

Burchard, Robert P. (University of Minnesota, Minneapolis), and M. Dworkin. A bacteriophage for Myxococcus xanthus: isolation, characterization and relation of infectivity to host morphogenesis. J. Bacteriol. 91:1305-1313. 1966.-A bacteriophage (MX-1) infecting Myxococcus xanthus FB(t) has been isolated from cow dung. The bacteriophage particle is approximately 175 mmu long. A tail about 100 mmu in length is encased in a contractile sheath and terminates in a tail plate. The head is polyhedral with a width of about 75 mmu. The nucleic acid of the bacteriophage is deoxyribonucleic acid and has a guanine plus cytosine content of 55.5%. The bacteriophage requires 10(-3)m Ca(++) and 10(-2)m monovalent cation for optimal adsorption. Grown on vegetative cells of M. xanthus FB(t) at 30 C in 2% Casitone medium, the bacteriophage has a latent period of 120 min and a burst size of approximately 100. Host range studies indicate that three strains of M. xanthus including a morphogenetic mutant are sensitive to the bacteriophage, whereas M. fulvus, Cytophaga, Sporocytophaga myxococcoides, and a fourth strain of M. xanthus are not. Of the two cellular forms characteristic of the Myxococcus life cycle, the bacteriophage infect only the vegetative cells; they do not adsorb to microcysts. Ability to adsorb bacteriophage is lost between 65 and 75 min after initiation of the relatively synchronous conversion of vegetative cells to microcysts. The bacteriophage does not adsorb to spheroplasts. After the appearance of visible morphogenesis and before the loss of bacteriophage receptor sites, addition of bacteriophage results in the formation of microcysts which give rise to infective centers only upon germination. The possibility that the infected microcysts are harboring intact bacteriophages has been eliminated.

Organic light-emitting diodes from homoleptic square planar complexes

DOEpatents

Omary, Mohammad A

2013-11-12

Homoleptic square planar complexes [M(N.LAMBDA.N).sub.2], wherein two identical N.LAMBDA.N bidentate anionic ligands are coordinated to the M(II) metal center, including bidentate square planar complexes of triazolates, possess optical and electrical properties that make them useful for a wide variety of optical and electrical devices and applications. In particular, the complexes are useful for obtaining white or monochromatic organic light-emitting diodes ("OLEDs"). Improved white organic light emitting diode ("WOLED") designs have improved efficacy and/or color stability at high brightness in single- or two-emitter white or monochrome OLEDs that utilize homoleptic square planar complexes, including bis[3,5-bis(2-pyridyl)-1,2,4-triazolato]platinum(II) ("Pt(ptp).sub.2").

Unusual Structure of the attB Site of the Site-Specific Recombination System of Lactobacillus delbrueckii Bacteriophage mv4

PubMed Central

Auvray, Frédéric; Coddeville, Michèle; Ordonez, Romy Catoira; Ritzenthaler, Paul

1999-01-01

The temperate phage mv4 integrates its genome into the chromosome of Lactobacillus delbrueckii subsp. bulgaricus by site-specific recombination within the 3′ end of a tRNASer gene. Recombination is catalyzed by the phage-encoded integrase and occurs between the phage attP site and the bacterial attB site. In this study, we show that the mv4 integrase functions in vivo in Escherichia coli and we characterize the bacterial attB site with a site-specific recombination test involving compatible plasmids carrying the recombination sites. The importance of particular nucleotides within the attB sequence was determined by site-directed mutagenesis. The structure of the attB site was found to be simple but rather unusual. A 16-bp DNA fragment was sufficient for function. Unlike most genetic elements that integrate their DNA into tRNA genes, none of the dyad symmetry elements of the tRNASer gene were present within the minimal attB site. No inverted repeats were detected within this site either, in contrast to the lambda site-specific recombination model. PMID:10572145

Linear nicking endonuclease-mediated strand-displacement DNA amplification.

PubMed

Joneja, Aric; Huang, Xiaohua

2011-07-01

We describe a method for linear isothermal DNA amplification using nicking endonuclease-mediated strand displacement by a DNA polymerase. The nicking of one strand of a DNA target by the endonuclease produces a primer for the polymerase to initiate synthesis. As the polymerization proceeds, the downstream strand is displaced into a single-stranded form while the nicking site is also regenerated. The combined continuous repetitive action of nicking by the endonuclease and strand-displacement synthesis by the polymerase results in linear amplification of one strand of the DNA molecule. We demonstrate that DNA templates up to 5000 nucleotides can be linearly amplified using a nicking endonuclease with 7-bp recognition sequence and Sequenase version 2.0 in the presence of single-stranded DNA binding proteins. We also show that a mixture of three templates of 500, 1000, and 5000 nucleotides in length is linearly amplified with the original molar ratios of the templates preserved. Moreover, we demonstrate that a complex library of hydrodynamically sheared genomic DNA from bacteriophage lambda can be amplified linearly. Copyright © 2011 Elsevier Inc. All rights reserved.

GWIPS-viz: development of a ribo-seq genome browser

PubMed Central

Michel, Audrey M.; Fox, Gearoid; M. Kiran, Anmol; De Bo, Christof; O’Connor, Patrick B. F.; Heaphy, Stephen M.; Mullan, James P. A.; Donohue, Claire A.; Higgins, Desmond G.; Baranov, Pavel V.

2014-01-01

We describe the development of GWIPS-viz (http://gwips.ucc.ie), an online genome browser for viewing ribosome profiling data. Ribosome profiling (ribo-seq) is a recently developed technique that provides genome-wide information on protein synthesis (GWIPS) in vivo. It is based on the deep sequencing of ribosome-protected messenger RNA (mRNA) fragments, which allows the ribosome density along all mRNA transcripts present in the cell to be quantified. Since its inception, ribo-seq has been carried out in a number of eukaryotic and prokaryotic organisms. Owing to the increasing interest in ribo-seq, there is a pertinent demand for a dedicated ribo-seq genome browser. GWIPS-viz is based on The University of California Santa Cruz (UCSC) Genome Browser. Ribo-seq tracks, coupled with mRNA-seq tracks, are currently available for several genomes: human, mouse, zebrafish, nematode, yeast, bacteria (Escherichia coli K12, Bacillus subtilis), human cytomegalovirus and bacteriophage lambda. Our objective is to continue incorporating published ribo-seq data sets so that the wider community can readily view ribosome profiling information from multiple studies without the need to carry out computational processing. PMID:24185699

Denoising of genetic switches based on Parrondo's paradox

NASA Astrophysics Data System (ADS)

Fotoohinasab, Atiyeh; Fatemizadeh, Emad; Pezeshk, Hamid; Sadeghi, Mehdi

2018-03-01

Random decision making in genetic switches can be modeled as tossing a biased coin. In other word, each genetic switch can be considered as a game in which the reactive elements compete with each other to increase their molecular concentrations. The existence of a very small number of reactive element molecules has caused the neglect of effects of noise to be inevitable. Noise can lead to undesirable cell fate in cellular differentiation processes. In this paper, we study the robustness to noise in genetic switches by considering another switch to have a new gene regulatory network (GRN) in which both switches have been affected by the same noise and for this purpose, we will use Parrondo's paradox. We introduce two networks of games based on possible regulatory relations between genes. Our results show that the robustness to noise can increase by combining these noisy switches. We also describe how one of the switches in network II can model lysis/lysogeny decision making of bacteriophage lambda in Escherichia coli and we change its fate by another switch.

Linear nicking endonuclease-mediated strand displacement DNA amplification

PubMed Central

Joneja, Aric; Huang, Xiaohua

2011-01-01

We describe a method for linear isothermal DNA amplification using nicking endonuclease-mediated strand displacement by a DNA polymerase. The nicking of one strand of a DNA target by the endonuclease produces a primer for the polymerase to initiate synthesis. As the polymerization proceeds, the downstream strand is displaced into a single-stranded form while the nicking site is also regenerated. The combined continuous repetitive action of nicking by the endonuclease and strand displacement synthesis by the polymerase results in linear amplification of one strand of the DNA molecule. We demonstrate that DNA templates up to five thousand nucleotides can be linearly amplified using a nicking endonuclease with seven base-pair recognition sequence and Sequenase version 2.0 in the presence of single-stranded DNA binding proteins. We also show that a mixture of three templates of 500, 1000, and 5000 nucleotides in length are linearly amplified with the original molar ratios of the templates preserved. Moreover, we demonstrate that a complex library of hydrodynamically sheared genomic DNA from bacteriophage lambda can be amplified linearly. PMID:21342654

Characterization of a novel lytic bacteriophage from an industrial Escherichia coli fermentation process and elimination of virulence using a heterologous CRISPR-Cas9 system.

PubMed

Halter, Mathew C; Zahn, James A

2018-03-01

Bacterial-bacteriophage interactions are a well-studied and ecologically-important aspect of microbiology. Many commercial fermentation processes are susceptible to bacteriophage infections due to the use of high-density, clonal cell populations. Lytic infections of bacterial cells in these fermentations are especially problematic due to their negative impacts on product quality, asset utilization, and fouling of downstream equipment. Here, we report the isolation and characterization of a novel lytic bacteriophage, referred to as bacteriophage DTL that is capable of rapid lytic infections of an Escherichia coli K12 strain used for commercial production of 1,3-propanediol (PDO). The bacteriophage genome was sequenced and annotated, which identified 67 potential open-reading frames (ORF). The tail fiber ORF, the largest in the genome, was most closely related to bacteriophage RTP, a T1-like bacteriophage reported from a commercial E. coli fermentation process in Germany. To eliminate virulence, both a fully functional Streptococcus thermophilus CRISPR3 plasmid and a customized S. thermophilus CRISPR3 plasmid with disabled spacer acquisition elements and seven spacers targeting the bacteriophage DTL genome were constructed. Both plasmids were separately integrated into a PDO production strain, which was subsequently infected with bacteriophage DTL. The native S. thermophilus CRISPR3 operon was shown to decrease phage susceptibility by approximately 96%, while the customized CRISPR3 operon provided complete resistance to bacteriophage DTL. The results indicate that the heterologous bacteriophage-resistance system described herein is useful in eliminating lytic infections of bacteriophage DTL, which was prevalent in environment surrounding the manufacturing facility.

Study of {Lambda}-{Lambda} oscillation in quantum coherent {Lambda}{Lambda} by using J/{psi}{yields}{Lambda}{Lambda} decay

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kang Xianwei; Department of Physics, Henan Normal University, Xinxiang 453007; Li Haibo

2010-03-01

We discuss the possibility of searching for the {Lambda}-{Lambda} oscillations for coherent {Lambda}{Lambda} production in the J/{psi}{yields}{Lambda}{Lambda} decay process. The sensitivity of measurement of {Lambda}-{Lambda} oscillation in the external field at BES-III experiment is considered. These considerations indicate an alternative way to probe the {Delta}B=2 amplitude in addition to neutron oscillation experiments. Both coherent and time-dependent information can be used to extract the {Lambda}-{Lambda} oscillation parameter. With one year's luminosity at BES-III, we can set an upper limit of {delta}m{sub {Lambda}{Lambda}<}10{sup -15} MeV at 90% confidence level, corresponding to about 10{sup -6} s of {Lambda}-{Lambda} oscillation time.

Interaction of Bacteriophages with the Immune System: Induction of Bacteriophage-Specific Antibodies.

PubMed

Dąbrowska, Krystyna

2018-01-01

In all cases when a bacteriophage makes direct contact with a mammalian organism, it may challenge the mammalian immunological system. Its major consequence is production of antibodies specific to the bacteriophage. Here we present protocols applicable in studies of bacteriophage ability to induce specific antibodies. The protocols have been divided into three parts: purification, immunization, and detection (ELISA).

Computational Determination of the Effects of Bacteriophage Bacteriophage Interactions in Human body.

PubMed

Mostafa, Marwa Mostafa; Nassef, Mohammad; Badr, Amr

2017-10-19

Chronic diseases are becoming more serious and widely spreading and this carries a heavy burden on doctors to deal with such patients. Although many of these diseases can be treated by bacteriophages, the situation is significantly dangerous in patients having concomitant more than one chronic disease, where conflicts between phages used in treating these diseases are very closer to happen. This research paper presents a method to detecting the Bacteriophage-Bacteriophage Interaction. This method is implemented based on Domain-Domain Interactions model and it was used to infer Domain-Domain Interactions between the bacteriophages injected in the human body at the same time. By testing the method over bacteriophages that are used to treat tuberculosis, salmonella and virulent E.coli, many interactions have been inferred and detected between these bacteriophages. Several effects were detected for the resulted interactions such as: playing a role in DNA repair such as non-homologous end joining, playing a role in DNA replication, playing a role in the interaction between the immune system and the tumor cells and playing a role in the stiff man syndrome. We revised all patents relating to bacteriophage bacteriophage interactions and phage therapy. The proposed method is developed to help doctors to realize the effect of simultaneously injecting different bacteriophages into the human body to treat different diseases. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Isolation and characterization of bacteriophages of Salmonella enterica serovar Pullorum.

PubMed

Bao, H; Zhang, H; Wang, R

2011-10-01

In this study, 2 bacteriophages of Salmonella Pullorum were isolated using an enrichment protocol and the double agar layer method. They were named PSPu-95 and PSPu-4-116, respectively, against clinical isolates of Salmonella Pullorum SPu-95 and SPu-116. The host ranges of the 2 bacteriophages were determined by performing spot tests with 20 bacteria strains. Both bacteriophages had wide host ranges. Bacteriophage PSPu-95 had a lytic effect on 17 of the 20 isolates (85%), and PSPu-4-116 produced a lytic effect on 14 isolates (70%) and was the only bacteriophage that produced a clear plaque on enterotoxigenic Escherichia coli K88. Transmission electron microscopy revealed the bacteriophages belonged to the order Caudovirales. Bacteriophage PSPu-95 was a member of the family Siphoviridae, but bacteriophage PSPu-4-116 belonged to the family Myoviridae. Both had a double-stranded DNA, which was digested with HindIII or EcoRI, that was estimated to be 58.3 kbp (PSPu-95) and 45.2 kbp (PSPu-4-116) by 1% agar electrophoresis. One-step growth kinetics showed that the latent periods were all less than 20 min, and the burst size was 77.5 pfu/cell for PSPu-95 and 86 pfu/cell for PSPu-4-116. The bacteriophages were able to survive in a pH range between 4 and 10, and they were able to survive in a treatment of 70°C for 60 min. The characterizations of these 2 bacteriophages were helpful in establishing a basis for adopting the most effective bacteriophage to control bacteria in the poultry industry.

Call for a dedicated European legal framework for bacteriophage therapy.

PubMed

Verbeken, Gilbert; Pirnay, Jean-Paul; Lavigne, Rob; Jennes, Serge; De Vos, Daniel; Casteels, Minne; Huys, Isabelle

2014-04-01

The worldwide emergence of antibiotic resistances and the drying up of the antibiotic pipeline have spurred a search for alternative or complementary antibacterial therapies. Bacteriophages are bacterial viruses that have been used for almost a century to combat bacterial infections, particularly in Poland and the former Soviet Union. The antibiotic crisis has triggered a renewed clinical and agricultural interest in bacteriophages. This, combined with new scientific insights, has pushed bacteriophages to the forefront of the search for new approaches to fighting bacterial infections. But before bacteriophage therapy can be introduced into clinical practice in the European Union, several challenges must be overcome. One of these is the conceptualization and classification of bacteriophage therapy itself and the extent to which it constitutes a human medicinal product regulated under the European Human Code for Medicines (Directive 2001/83/EC). Can therapeutic products containing natural bacteriophages be categorized under the current European regulatory framework, or should this framework be adapted? Various actors in the field have discussed the need for an adapted (or entirely new) regulatory framework for the reintroduction of bacteriophage therapy in Europe. This led to the identification of several characteristics specific to natural bacteriophages that should be taken into consideration by regulators when evaluating bacteriophage therapy. One important consideration is whether bacteriophage therapy development occurs on an industrial scale or a hospital-based, patient-specific scale. More suitable regulatory standards may create opportunities to improve insights into this promising therapeutic approach. In light of this, we argue for the creation of a new, dedicated European regulatory framework for bacteriophage therapy.

Intestinal colonization by enteroaggregative Escherichia coli supports long-term bacteriophage replication in mice.

PubMed

Maura, Damien; Morello, Eric; du Merle, Laurence; Bomme, Perrine; Le Bouguénec, Chantal; Debarbieux, Laurent

2012-08-01

Bacteriophages have been known to be present in the gut for many years, but studies of relationships between these viruses and their hosts in the intestine are still in their infancy. We isolated three bacteriophages specific for an enteroaggregative O104:H4 Escherichia coli (EAEC) strain responsible for diarrhoeal diseases in humans. We studied the replication of these bacteriophages in vitro and in vivo in a mouse model of gut colonization. Each bacteriophage was able to replicate in vitro in both aerobic and anaerobic conditions. Each bacteriophage individually reduced biofilms formed on plastic pegs and a cocktail of the three bacteriophages was found to be more efficient. The cocktail was also able to infect bacterial aggregates formed on the surface of epithelial cells. In the mouse intestine, bacteriophages replicated for at least 3 weeks, provided the host was present, with no change in host levels in the faeces. This model of stable and continuous viral replication provides opportunities for studying the long-term coevolution of virulent bacteriophages with their hosts within a mammalian polymicrobial ecosystem. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Nanoscale bacteriophage biosensors beyond phage display.

PubMed

Lee, Jong-Wook; Song, Jangwon; Hwang, Mintai P; Lee, Kwan Hyi

2013-01-01

Bacteriophages are traditionally used for the development of phage display technology. Recently, their nanosized dimensions and ease with which genetic modifications can be made to their structure and function have put them in the spotlight towards their use in a variety of biosensors. In particular, the expression of any protein or peptide on the extraluminal surface of bacteriophages is possible by genetically engineering the genome. In addition, the relatively short replication time of bacteriophages offers researchers the ability to generate mass quantities of any given bacteriophage-based biosensor. Coupled with the emergence of various biomarkers in the clinic as a means to determine pathophysiological states, the development of current and novel technologies for their detection and quantification is imperative. In this review, we categorize bacteriophages by their morphology into M13-based filamentous bacteriophages and T4- or T7-based icosahedral bacteriophages, and examine how such advantages are utilized across a variety of biosensors. In essence, we take a comprehensive approach towards recent trends in bacteriophage-based biosensor applications and discuss their outlook with regards to the field of biotechnology.

Nanoscale bacteriophage biosensors beyond phage display

PubMed Central

Lee, Jong-Wook; Song, Jangwon; Hwang, Mintai P; Lee, Kwan Hyi

2013-01-01

Bacteriophages are traditionally used for the development of phage display technology. Recently, their nanosized dimensions and ease with which genetic modifications can be made to their structure and function have put them in the spotlight towards their use in a variety of biosensors. In particular, the expression of any protein or peptide on the extraluminal surface of bacteriophages is possible by genetically engineering the genome. In addition, the relatively short replication time of bacteriophages offers researchers the ability to generate mass quantities of any given bacteriophage-based biosensor. Coupled with the emergence of various biomarkers in the clinic as a means to determine pathophysiological states, the development of current and novel technologies for their detection and quantification is imperative. In this review, we categorize bacteriophages by their morphology into M13-based filamentous bacteriophages and T4- or T7-based icosahedral bacteriophages, and examine how such advantages are utilized across a variety of biosensors. In essence, we take a comprehensive approach towards recent trends in bacteriophage-based biosensor applications and discuss their outlook with regards to the field of biotechnology. PMID:24143096

Shell-model predictions for Lambda Lambda hypernuclei

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gal, A.; Millener, D.

2011-06-02

It is shown how the recent shell-model determination of {Lambda}N spin-dependent interaction terms in {Lambda} hypernuclei allows for a reliable deduction of {Lambda}{Lambda} separation energies in {Lambda}{Lambda} hypernuclei across the nuclear p shell. Comparison is made with the available data, highlighting {sub {Lambda}{Lambda}}{sup 11}Be and {sub {Lambda}{Lambda}}{sup 12}Be which have been suggested as possible candidates for the KEK-E373 HIDA event.

[RATIONAL ASPECTS OF BACTERIOPHAGES USE].

PubMed

Vakarina, A A; Kataeva, L V; Karpukhina, N F

2015-01-01

Analysis of existing aspects of bacteriophage use and study features of their lytic activity by using various techniques. Effect of monophages and associated bacteriophages (staphylococci, piopolyvalent and piocombined, intestiphage, pneumonia klebsiella and polyvalent klebsiella produced by "Microgen") was studied with 380 strains of Staphylococcus aureus and 279 cultures of Klebsiella pneumoniae in liquid and solid nutrient media. From patients with intestinal disorder, sensitivity was analyzed to 184 strains of Salmonella genus bacteria 18 serological variants to salmonella bacteriophages, 137 strains of Escherichia coli (lactose-negative, hemolytic), as well as some members of OKA groups (21 serovars) to coli-proteic and piopolyvalent bacteriophages. Lytic ability of the piobacteriophage against Klebsiella and Proteus genus bacteria was determined. Staphylococcus aureus was sensitive to staphylococcus bacteriophage in 71.6% of cases and to piobacteriophage--in 86.15% of cases. A 100% lytic ability of salmonella bacteriophage against Salmonella spp. was established. Sensitivity of E. coli of various serogroups to coli-proteic and piobacteriophage was 66 - 100%. Klebsiella, Proteus genus bacteria were sensitive to piobacteriophage in only 35% and 43.15% of cases, respectively. A more rational use of bacteriophages is necessary: development of a technique, evaluation of sensitivity of bacteria to bacteriophage, introduction of corrections into their production (expansion of bacteriophage spectra, determination and indication of their concentration in accompanying documents).

Isolation and characterisation of lytic bacteriophages of Klebsiella pneumoniae and Klebsiella oxytoca.

PubMed

Karumidze, Natia; Kusradze, Ia; Rigvava, Sophio; Goderdzishvili, Marine; Rajakumar, Kumar; Alavidze, Zemphira

2013-03-01

Klebsiella bacteria have emerged as an increasingly important cause of community-acquired nosocomial infections. Extensive use of broad-spectrum antibiotics in hospitalised patients has led to both increased carriage of Klebsiella and the development of multidrug-resistant strains that frequently produce extended-spectrum β-lactamases and/or other defences against antibiotics. Many of these strains are highly virulent and exhibit a strong propensity to spread. In this study, six lytic Klebsiella bacteriophages were isolated from sewage-contaminated river water in Georgia and characterised as phage therapy candidates. Two of the phages were investigated in greater detail. Biological properties, including phage morphology, nucleic acid composition, host range, growth phenotype, and thermal and pH stability were studied for all six phages. Limited sample sequencing was performed to define the phylogeny of the K. pneumoniae- and K. oxytoca-specific bacteriophages vB_Klp_5 and vB_Klox_2, respectively. Both of the latter phages had large burst sizes, efficient rates of adsorption and were stable under different adverse conditions. Phages reported in this study are double-stranded DNA bacterial viruses belonging to the families Podoviridae and Siphoviridae. One or more of the six phages was capable of efficiently lysing ~63 % of Klebsiella strains comprising a collection of 123 clinical isolates from Georgia and the United Kingdom. These phages exhibit a number of properties indicative of potential utility in phage therapy cocktails.

Changes in the stability and biomechanics of P22 bacteriophage capsid during maturation.

PubMed

Kant, Ravi; Llauró, Aida; Rayaprolu, Vamseedhar; Qazi, Shefah; de Pablo, Pedro J; Douglas, Trevor; Bothner, Brian

2018-03-15

The capsid of P22 bacteriophage undergoes a series of structural transitions during maturation that guide it from spherical to icosahedral morphology. The transitions include the release of scaffold proteins and capsid expansion. Although P22 maturation has been investigated for decades, a unified model that incorporates thermodynamic and biophysical analyses is not available. A general and specific model of icosahedral capsid maturation is of significant interest to theoreticians searching for fundamental principles as well as virologists and material scientists seeking to alter maturation to their advantage. To address this challenge, we have combined the results from orthogonal biophysical techniques including differential scanning fluorimetry, atomic force microscopy, circular dichroism, and hydrogen-deuterium exchange mass spectrometry. By integrating these results from single particle and population measurements, an energy landscape of P22 maturation from procapsid through expanded shell to wiffle ball emerged, highlighting the role of metastable structures and the thermodynamics guiding maturation. The propagation of weak quaternary interactions across symmetric elements of the capsid is a key component for stability in P22. A surprising finding is that the progression to wiffle ball, which lacks pentamers, shows that chemical and thermal stability can be uncoupled from mechanical rigidity, elegantly demonstrating the complexity inherent in capsid protein interactions and the emergent properties that can arise from icosahedral symmetry. On a broader scale, this work demonstrates the power of applying orthogonal biophysical techniques to elucidate assembly mechanisms for supramolecular complexes and provides a framework within which other viral systems can be compared. Copyright © 2018 Elsevier B.V. All rights reserved.

Measurement of the forward-backward asymmetry of $$\\Lambda$$ and $$\\bar{\\Lambda}$$ production in $$p \\bar{p}$$ collisions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abazov, Victor Mukhamedovich

Here, we studymore » $$\\Lambda$$ and $$\\bar{\\Lambda}$$ production asymmetries in $$p \\bar{p} \\rightarrow \\Lambda (\\bar{\\Lambda}) X$$, $$p \\bar{p} \\rightarrow J/\\psi \\Lambda (\\bar{\\Lambda}) X$$, and $$p \\bar{p} \\rightarrow \\mu^\\pm \\Lambda (\\bar{\\Lambda}) X$$ events recorded by the D0 detector at the Fermilab Tevatron collider at $$\\sqrt{s} = 1.96$$ TeV. We find an excess of $$\\Lambda$$'s ($$\\bar{\\Lambda}$$'s) produced in the proton (antiproton) direction. This forward-backward asymmetry is measured as a function of rapidity. We confirm that the $$\\bar{\\Lambda}/\\Lambda$$ production ratio, measured by several experiments with various targets and a wide range of energies, is a universal function of "rapidity loss", i.e., the rapidity difference of the beam proton and the lambda.« less

Measurement of the forward-backward asymmetry of $$\\Lambda$$ and $$\\bar{\\Lambda}$$ production in $$p \\bar{p}$$ collisions

DOE PAGES

Abazov, Victor Mukhamedovich

2016-02-09

Here, we studymore » $$\\Lambda$$ and $$\\bar{\\Lambda}$$ production asymmetries in $$p \\bar{p} \\rightarrow \\Lambda (\\bar{\\Lambda}) X$$, $$p \\bar{p} \\rightarrow J/\\psi \\Lambda (\\bar{\\Lambda}) X$$, and $$p \\bar{p} \\rightarrow \\mu^\\pm \\Lambda (\\bar{\\Lambda}) X$$ events recorded by the D0 detector at the Fermilab Tevatron collider at $$\\sqrt{s} = 1.96$$ TeV. We find an excess of $$\\Lambda$$'s ($$\\bar{\\Lambda}$$'s) produced in the proton (antiproton) direction. This forward-backward asymmetry is measured as a function of rapidity. We confirm that the $$\\bar{\\Lambda}/\\Lambda$$ production ratio, measured by several experiments with various targets and a wide range of energies, is a universal function of "rapidity loss", i.e., the rapidity difference of the beam proton and the lambda.« less

RNA polymerase gene, microorganism having said gene and the production of RNA polymerase by the use of said microorganism

DOEpatents

Kotani, Hirokazu; Hiraoka, Nobutsugu; Obayashi, Akira

1991-01-01

SP6 bacteriophage RNA polymerase is produced by cultivating a new microorganism (particularly new strains of Escherichia coli) harboring a plasmid that carries SP6 bacteriophage RNA polymerase gene and recovering SP6 bacteriophage RNA polymerase from the culture broth. SP6 bacteriophage RNA polymerase gene is provided as are new microorganisms harboring a plasmid that carries SP6 bacteriophage RNA polymerase gene.

Interaction of colicin E7 with the major coat protein (g8p) may confer limited protection on colicinogenic Escherichia coli against M13 bacteriophage infection.

PubMed

Chen, Yuh-Ren; Yang, Tsung-Yeh; Lei, Guang-Sheng; Liao, Chen-Chung; Chak, Kin-Fu

2010-11-01

Colicin release provides producer strains with a competitive advantage under certain circumstances. We found that propagation of M13 bacteriophage in cells producing colicin E7 is impaired, without alteration in the efficiency of bacteriophage adsorption, as compared with non-producing cells. In contrast to the protective effect of the colicin against M13 bacteriophage infection, the endogenously expressed colicin does not confer limited protection against transfection with M13 bacteriophage DNA. Furthermore, it was found that the translocation-receptor-binding domain and toxicity domain of the colicin are able to interact with the M13 major coat protein, g8p, during bacteriophage infection. Based on these observations, we propose that interaction between colicin E7 and g8p during infection interferes with g8p depolymerizing into the cytoplasmic membrane during bacteriophage DNA penetration, thus resulting in the limited protection against M13 bacteriophage infection.

Polymer-based delivery systems for support and delivery of bacteriophages

NASA Astrophysics Data System (ADS)

Brown, Alyssa Marie

One of the most urgent problems in the fields of medicine and agriculture is the decreasing effectiveness of antibiotics. Once a miracle drug, antibiotics have recently become associated with the creation of antibiotic-resistant bacteria. The main limitations of these treatments include lack of both adaptability and specificity. To overcome these shortcomings of current antibiotic treatments, there has been a renewed interest in bacteriophage research. Bacteriophages are naturally-occurring viruses that lyse bacteria. They are highly specific, with each bacteriophage type lysing a narrow range of bacteria strains. Bacteriophages are also ubiquitous biological entities, populating environments where bacterial growth is supported. Just as humans are exposed to bacteria in their daily lives, we are exposed to bacteriophages as well. To use bacteriophages in practical applications, they must be delivered to the site of an infection in a controlled-release system. Two systems were studied to observe their support of bacteriophage lytic activity, as well as investigate the possibility of controlling bacteriophage release rates. First, hydrogels were studied, using crosslinking and blending techniques to achieve a range of release profiles. Second, polyanhydride microparticles were studied, evaluating release rates as a function of monomer chemistries.

Susceptibility of Escherichia coli isolated from uteri of postpartum dairy cows to antibiotic and environmental bacteriophages. Part I: Isolation and lytic activity estimation of bacteriophages.

PubMed

Bicalho, R C; Santos, T M A; Gilbert, R O; Caixeta, L S; Teixeira, L M; Bicalho, M L S; Machado, V S

2010-01-01

The objective of this study was to isolate bacteriophages from environmental samples of 2 large commercial dairy farms using Escherichia coli isolated from the uteri of postpartum Holstein dairy cows as hosts. A total of 11 bacteriophage preparations were isolated from manure systems of commercial dairy farms and characterized for in vitro antimicrobial activity. In addition, a total of 57 E. coli uterine isolates from 5 dairy cows were phylogenetically grouped by triplex PCR. Each E. coli bacterial host from the uterus was inoculated with their respective bacteriophage preparation at several different multiplicities of infections (MOI) to determine minimum inhibitory MOI. The effect of a single dose (MOI=10(2)) of bacteriophage on the growth curve of all 57 E. coli isolates was assessed using a microplate technique. Furthermore, genetic diversity within and between the different bacteriophage preparations was assessed by bacteriophage purification followed by DNA extraction, restriction, and agarose gel electrophoresis. Phylogenetic grouping based on triplex PCR showed that all isolates of E. coli belonged to phylogroup B1. Bacterial growth was completely inhibited at considerably low MOI, and the effect of a single dose (MOI=10(2)) of bacteriophage preparations on the growth curve of all 57 E. coli isolates showed that all bacteriophage preparations significantly decreased the growth rate of the isolates. Bacteriophage preparation 1230-10 had the greatest antimicrobial activity and completely inhibited the growth of 71.7% (n=57) of the isolates. The combined action of bacteriophage preparations 1230-10, 6375-10, 2540-4, and 6547-2, each at MOI=10(2), had the broadest spectrum of action and completely inhibited the growth (final optical density at 600 nm

Complete Nucleotide Sequence Analysis of a Novel Bacillus subtilis-Infecting Bacteriophage BSP10 and Its Effect on Poly-Gamma-Glutamic Acid Degradation

PubMed Central

Ghosh, Kuntal; Senevirathne, Amal; Kang, Hai Seong; Hyun, Woo Bin; Kim, Ji Eun; Kim, Kwang-Pyo

2018-01-01

While the harmful effects of lactic acid bacterial bacteriophages in the dairy industry are well-established, the importance of Bacillus subtilis-infecting bacteriophages on soybean fermentation is poorly-studied. In this study, we isolated a B. subtilis-infecting bacteriophage BSP10 from Meju (a brick of dried fermented soybean) and further characterized it. This Myoviridae family bacteriophage exhibited a narrow host range against B. subtilis strains (17/52, 32.7%). The genome of bacteriophage BSP10 is 153,767 bp long with 236 open reading frames and 5 tRNAs. Comparative genomics (using dot plot, progressiveMauve alignment, heat-plot, and BLASTN) and phylogenetic analysis strongly suggest its incorporation as a new species in the Nit1virus genus. Furthermore, bacteriophage BSP10 was efficient in the growth inhibition of B. subtilis ATCC 15245 in liquid culture and in Cheonggukjang (a soybean fermented food) fermentation. Artificial contamination of as low as 102 PFU/g of bacteriophage BSP10 during Cheonggukjang fermentation significantly reduced bacterial numbers by up to 112 fold in comparison to the control (no bacteriophage). Moreover, for the first time, we experimentally proved that B. subtilis-infecting bacteriophage greatly enhanced poly-γ-glutamic acid degradation during soybean fermentation, which is likely to negatively affect the functionalities of Cheonggukjang. PMID:29734701

Cationic antimicrobial peptides inactivate Shiga toxin-encoding bacteriophages

NASA Astrophysics Data System (ADS)

Del Cogliano, Manuel E.; Hollmann, Axel; Martinez, Melina; Semorile, Liliana; Ghiringhelli, Pablo D.; Maffía, Paulo C.; Bentancor, Leticia V.

2017-12-01

Shiga toxin (Stx) is the principal virulence factor during Shiga toxin-producing Escherichia coli (STEC) infections. We have previously reported the inactivation of bacteriophage encoding Stx after treatment with chitosan, a linear polysaccharide polymer with cationic properties. Cationic antimicrobial peptides (cAMPs) are short linear aminoacidic sequences, with a positive net charge, which display bactericidal or bacteriostatic activity against a wide range of bacterial species. They are promising novel antibiotics since they have shown bactericidal effects against multiresistant bacteria. To evaluate whether cationic properties are responsible for bacteriophage inactivation, we tested seven cationic peptides with proven antimicrobial activity as anti-bacteriophage agents, and one random sequence cationic peptide with no antimicrobial activity as a control. We observed bacteriophage inactivation after incubation with five cAMPs, but no inactivating activity was observed with the random sequence cationic peptide or with the non alpha helical cAMP Omiganan. Finally, to confirm peptide-bacteriophage interaction, zeta potential was analyzed by following changes on bacteriophage surface charges after peptide incubation. According to our results we could propose that: 1) direct interaction of peptides with phage is a necessary step for bacteriophage inactivation, 2) cationic properties are necessary but not sufficient for bacteriophage inactivation, and 3) inactivation by cationic peptides could be sequence (or structure) specific. Overall our data suggest that these peptides could be considered a new family of molecules potentially useful to decrease bacteriophage replication and Stx expression.

Preparation and Storage of High-Titer Lactic Streptococcus Bacteriophages1

PubMed Central

Nyiendo, J.; Seidler, Ramon J.; Sandine, W. E.; Elliker, P. R.

1974-01-01

Various techniques were employed for preparation of high-titer bacteriophage lysates of Streptococcus lactis, S. cremoris, and S. diacetilactis strains. Infection of a 4-h host culture in litmus milk at 30 C yielded the highest titers (2 × 109 to 4 × 1011 plaque-forming units/ml) for most phages. Host infection in lactose-containing broth produced similar virus numbers only when 0.1 M tris(hydroxymethyl)aminomethane buffer stabilized the pH. The pH at the time of infection as well as the inoculum phage titer were critical in obtaining high titers. Optimum conditions for infection in broth were coupled with a polyethylene glycol concentration procedure to routinely produce milligram quantities of phage from 1 liter of lysate. Neutralization of whey lysates, as a means of storage, offered no survival advantage over unneutralized samples. Storage of phage lysates in a 15% glycerol whey solution at -22 C yielded a high rate of survival in most cases, even with repeated freezing and thawing, over a period of 24 months. PMID:16349981

Use of PRD1 bacteriophage in groundwater viral transport, inactivation, and attachment studies

USGS Publications Warehouse

Harvey, R.W.; Ryan, J.N.

2004-01-01

PRD1, an icosahedra-shaped, 62 nm (diameter), double-stranded DNA bacteriophage with an internal membrane, has emerged as an important model virus for studying the manner in which microorganisms are transported through a variety of groundwater environments. The popularity of this phage for use in transport studies involving geologic media is due, in part, to its relative stability over a range of temperatures and low degree of attachment in aquifer sediments. Laboratory and field investigations employing PRD1 are leading to a better understanding of viral attachment and transport behaviors in saturated geologic media and to improved methods for describing mathematically subsurface microbial transport at environmentally significant field scales. Radioisotopic labeling of PRD1 is facilitating additional information about the nature of viral interactions with solid surfaces in geologic media, the importance of iron oxide surfaces, and allowing differentiation between inactivation and attachment in field-scale tracer tests. ?? 2004 Published by Elsevier B.V. on behalf of the Federation of European Microbiological Societies.

Bacterial detection using bacteriophages and gold nanorods by following time-dependent changes in Raman spectral signals.

PubMed

Moghtader, Farzaneh; Tomak, Aysel; Zareie, Hadi M; Piskin, Erhan

2018-03-27

This study attemps to develop bacterial detection strategies using bacteriophages and gold nanorods (GNRs) by Raman spectral analysis. Escherichia coli was selected as the target and its specific phage was used as the bioprobe. Target bacteria and phages were propagated/purified by traditional techniques. GNRs were synthesized by using hexadecyltrimethyl ammonium bromide (CTAB) as stabilizer. A two-step detection strategy was applied: Firstly, the target bacteria were interacted with GNRs in suspensions, and then they were dropped onto silica substrates for detection. It was possible to obtain clear surface-enchanced Raman spectroscopy (SERS) peaks of the target bacteria, even without using phages. In the second step, the phage nanoemulsions were droped onto the bacterial-GNRs complexes on those surfaces and time-dependent changes in the Raman spectra were monitored at different time intervals upto 40 min. These results demonstrated that how one can apply phages with plasmonic nanoparticles for detection of pathogenic bacteria very effectively in a quite simple test.

40 CFR 180.1307 - Bacteriophage of Clavibacter michiganensis subspecies michiganensis; exemption from the...

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 25 2012-07-01 2012-07-01 false Bacteriophage of Clavibacter... EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Exemptions From Tolerances § 180.1307 Bacteriophage of... exemption from the requirement of a tolerance is established for residues of lytic bacteriophage of...

40 CFR 180.1307 - Bacteriophage of Clavibacter michiganensis subspecies michiganensis; exemption from the...

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 24 2014-07-01 2014-07-01 false Bacteriophage of Clavibacter... EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Exemptions From Tolerances § 180.1307 Bacteriophage of... exemption from the requirement of a tolerance is established for residues of lytic bacteriophage of...

40 CFR 180.1307 - Bacteriophage of Clavibacter michiganensis subspecies michiganensis; exemption from the...

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 25 2013-07-01 2013-07-01 false Bacteriophage of Clavibacter... EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Exemptions From Tolerances § 180.1307 Bacteriophage of... exemption from the requirement of a tolerance is established for residues of lytic bacteriophage of...

Measurements of J/{psi} and {psi}(2S) decays into {lambda}{lambda}{pi}{sup 0} and {lambda}{lambda}{eta}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ablikim, M.; Bai, J. Z.; Cai, X.

2007-11-01

Using 58x10{sup 6} J/{psi} and 14x10{sup 6} {psi}(2S) events collected by the BESII detector at the BEPC, branching fractions or upper limits for the decays J/{psi} and {psi}(2S){yields}{lambda}{lambda}{pi}{sup 0} and {lambda}{lambda}{eta} are measured. For the isospin violating decays, the upper limits are determined to be B(J/{psi}{yields}{lambda}{lambda}{pi}{sup 0})<6.4x10{sup -5} and B[{psi}(2S){yields}{lambda}{lambda}{pi}{sup 0}]<4.9x10{sup -5} at the 90% confidence level. The isospin conserving process J/{psi}{yields}{lambda}{lambda}{eta} is observed for the first time, and its branching fraction is measured to be B(J/{psi}{yields}{lambda}{lambda}{eta})=(2.62{+-}0.60{+-}0.44)x10{sup -4}, where the first error is statistical and the second one is systematic. No {lambda}{lambda}{eta} signal is observed in {psi}(2S) decays, and B[{psi}(2S){yields}{lambda}{lambda}{eta}]<1.2x10{supmore » -4} is set at the 90% confidence level. Branching fractions of J/{psi} decays into {sigma}{sup +}{pi}{sup -}{lambda} and {sigma}{sup -}{pi}{sup +}{lambda} are also reported, and the sum of these branching fractions is determined to be B(J/{psi}{yields}{sigma}{sup +}{pi}{sup -}{lambda}+c.c.)=(1.52{+-}0.08{+-}0.16)x10{sup -3}.« less

Measurement of the branching fraction $${\\mathcal{B}}(\\Lambda^0_b\\rightarrow \\Lambda^+_c\\pi^-\\pi^+\\pi^-)$$ at CDF

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aaltonen, T.; /Helsinki Inst. of Phys.; Alvarez Gonzalez, B.

We report an analysis of the {Lambda}{sub b}{sup 0} {yields} {Lambda}{sub c}{sup +}{pi}{sup -}{pi}{sup +}{pi}{sup -} decay in a data sample collected by the CDF II detector at the Fermilab Tevatron corresponding to 2.4 fb{sup -1} of integrated luminosity. We reconstruct the currently largest samples of the decay modes {Lambda}{sub b}{sup 0} {yields} {Lambda}{sub c}(2595){sup +}{pi}{sup -} (with {Lambda}{sub c}(2595){sup +} {yields} {Lambda}{sub c}{sup +}{pi}{sup +}{pi}{sup -}), {Lambda}{sub b}{sup 0} {yields} {Lambda}{sub c}(2625){sup +}{pi}{sup -} (with {Lambda}{sub c}(2625){sup +} {yields} {Lambda}{sub c}{sup +}{pi}{sup +}{pi}{sup -}), {Lambda}{sub b}{sup 0} {yields} {Sigma}{sub c}(2455){sup ++}{pi}{sup -}{pi}{sup -} (with {Sigma}{sub c}(2455){sup ++} {yields} {Lambda}{submore » c}{sup +}{pi}{sup +}), and {Lambda}{sub b}{sup 0} {yields} {Sigma}{sub c}(2455)0{pi}{sup +}{pi}{sup -} (with {Sigma}{sub c}(2455)0 {yields} {Lambda}{sub c}{sup +}{pi}{sup -}) and measure the branching fractions relative to the {Lambda}{sub b}{sup 0} {yields} {Lambda}{sub c}{sup +}{pi}{sup -} branching fraction. We measure the ratio {Beta}({Lambda}{sub b}{sup 0} {yields} {Lambda}{sub c}{sup +}{pi}{sup -}{pi}{sup +}{pi}{sup -})/ {Beta}({Lambda}{sub b}{sup 0} {yields} {Lambda}{sub c}{sup +}{pi}{sup -})=3.04 {+-} 0.33(stat){sub -0.55}{sup +0.70}(syst) which is used to derive {Beta}({Lambda}{sub b}{sup 0} {yields} {Lambda}{sub c}{sup +}{pi}{sup -}{pi}{sup +}{pi}{sup -})=(26.8{sub -11.2}{sup +11.9}) x 10{sup -3}.« less

Study of B{yields}{lambda}{sub c}{lambda}{sub c} and B{yields}{lambda}{sub c}{lambda}{sub c}K

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, H.-Y.; Hsiao, Y.-K.; Chua, C.-K.

2009-06-01

We study the doubly charmful two-body and three-body baryonic B decays B{yields}{lambda}{sub c}{sup +}{lambda}{sub c}{sup -} and B{yields}{lambda}{sub c}{sup +}{lambda}{sub c}{sup -}K. As pointed out before, a naive estimate of the branching ratio O(10{sup -8}) for the latter decay is too small by 3 to 4 orders of magnitude compared to experiment. Previously, it has been shown that a large enhancement for the {lambda}{sub c}{sup +}{lambda}{sub c}{sup -}K production can occur due to a charmoniumlike resonance (e.g. X(4630) discovered by Belle) with a mass near the {lambda}{sub c}{lambda}{sub c} threshold. Motivated by the BABAR's observation of a resonance in themore » {lambda}{sub c}K system with a mass of order 2930 MeV, we study in this work the contribution to B{yields}{lambda}{sub c}{sup +}{lambda}{sub c}{sup -}K from the intermediate state {xi}{sub c}(2980) which is postulated to be a first positive-parity excited D-wave charmed baryon state. Assuming that a soft qq quark pair is produced through the {sigma} and {pi} meson exchanges in the configuration for B{yields}{xi}{sub c}(2980){lambda}{sub c} and {lambda}{sub c}{lambda}{sub c}, it is found that branching ratios of B{yields}{lambda}{sub c}{sup +}{lambda}{sub c}{sup -}K and B{yields}{lambda}{sub c}{sup +}{lambda}{sub c}{sup -} are of order 3.5x10{sup -4} and 5x10{sup -5}, respectively, in agreement with experiment except that the prediction for the {lambda}{sub c}{lambda}{sub c}K{sup -} is slightly smaller. In conjunction with our previous analysis, we conclude that the enormously large rate of B{yields}{lambda}{sub c}{sup +}{lambda}{sub c}{sup -}K arises from the resonances {xi}{sub c}(2980) and X(4630)« less

Convergent mechanisms favor fast amyloid formation in two lambda 6a Ig light chain mutants.

PubMed

Valdés-García, Gilberto; Millán-Pacheco, César; Pastor, Nina

2017-08-01

Extracellular deposition as amyloids of immunoglobulin light chains causes light chain amyloidosis. Among the light chain families, lambda 6a is one of the most frequent in light chain amyloidosis patients. Its germline protein, 6aJL2, and point mutants, R24G and P7S, are good models to study fibrillogenesis, because their stability and fibril formation characteristics have been described. Both mutations make the germline protein unstable and speed up its ability to aggregate. To date, there is no molecular mechanism that explains how these differences in amyloidogenesis can arise from a single mutation. To look into the structural and dynamical differences in the native state of these proteins, we carried out molecular dynamics simulations at room temperature. Despite the structural similarity of the germline protein and the mutants, we found differences in their dynamical signatures that explain the mutants' increased tendency to form amyloids. The contact network alterations caused by the mutations, though different, converge in affecting two anti-aggregation motifs present in light chain variable domains, suggesting a different starting point for aggregation in lambda chains compared to kappa chains. © 2017 Wiley Periodicals, Inc.

Measurement of the $$\\Lambda_b$$ cross section and the $$_{\\bar{\\Lambda}_b}$$ to $$\\Lambda_b$$ ratio with $$J/\\Psi \\Lambda$$ decays in $pp$ collisions at $$\\sqrt{s}=7$$ TeV

DOE PAGES

Chatrchyan, Serguei; et al.

2013-07-16

The Lambda(b) differential production cross section and the cross section ratio anti-Lambda(b)/Lambda(b) are measured as functions of transverse momentum pt(Lambda(b)) and rapidity abs(y(Lambda(b))) in pp collisions at sqrt(s) = 7 TeV using data collected by the CMS experiment at the LHC. The measurements are based on Lambda(b) decays reconstructed in the exclusive final state J/Psi Lambda, with the subsequent decays J/Psi to an opposite-sign muon pair and Lambda to proton pion, using a data sample corresponding to an integrated luminosity of 1.9 inverse femtobarns. The product of the cross section times the branching ratio for Lambda(b) to J/Psi Lambda versusmore » pt(Lambda(b)) falls faster than that of b mesons. The measured value of the cross section times the branching ratio for pt(Lambda(b)) > 10 GeV and abs(y(Lambda(b))) < 2.0 is 1.06 +/- 0.06 +/- 0.12 nb, and the integrated cross section ratio for anti-Lambda(b)/Lambda(b) is 1.02 +/- 0.07 +/- 0.09, where the uncertainties are statistical and systematic, respectively.« less

Bacteriophages and bacteriophage-derived endolysins as potential therapeutics to combat Gram-positive spore forming bacteria.

PubMed

Nakonieczna, A; Cooper, C J; Gryko, R

2015-09-01

Since their discovery in 1915, bacteriophages have been routinely used within Eastern Europe to treat a variety of bacterial infections. Although initially ignored by the West due to the success of antibiotics, increasing levels and diversity of antibiotic resistance is driving a renaissance for bacteriophage-derived therapy, which is in part due to the highly specific nature of bacteriophages as well as their relative abundance. This review focuses on the bacteriophages and derived lysins of relevant Gram-positive spore formers within the Bacillus cereus group and Clostridium genus that could have applications within the medical, food and environmental sectors. © 2015 The Society for Applied Microbiology.

Potential of a lytic bacteriophage to disrupt Acinetobacter baumannii biofilms in vitro.

PubMed

Liu, Yannan; Mi, Zhiqiang; Niu, Wenkai; An, Xiaoping; Yuan, Xin; Liu, Huiying; Wang, Yong; Feng, Yuzhong; Huang, Yong; Zhang, Xianglilan; Zhang, Zhiyi; Fan, Hang; Peng, Fan; Li, Puyuan; Tong, Yigang; Bai, Changqing

2016-10-01

The ability of Acinetobacter baumannii to form biofilms and develop antibiotic resistance makes it difficult to control infections caused by this bacterium. In this study, we explored the potential of a lytic bacteriophage to disrupt A. baumannii biofilms. The potential of the lytic bacteriophage to disrupt A. baumannii biofilms was assessed by performing electron microscopy, live/dead bacterial staining, crystal violet staining and by determining adenosine triphosphate release. The bacteriophage inhibited the formation of and disrupted preformed A. baumannii biofilms. Results of disinfection assay showed that the lytic bacteriophage lysed A. baumannii cells suspended in blood or grown on metal surfaces. These results suggest the potential of the lytic bacteriophage to disrupt A. baumannii biofilms.

Application of zinc chloride precipitation method for rapid isolation and concentration of infectious Pectobacterium spp. and Dickeya spp. lytic bacteriophages from surface water and plant and soil extracts.

PubMed

Czajkowski, Robert; Ozymko, Zofia; Lojkowska, Ewa

2016-01-01

This is the first report describing precipitation of bacteriophage particles with zinc chloride as a method of choice to isolate infectious lytic bacteriophages against Pectobacterium spp. and Dickeya spp. from environmental samples. The isolated bacteriophages are ready to use to study various (ecological) aspects of bacteria-bacteriophage interactions. The method comprises the well-known precipitation of phages from aqueous extracts of the test material by addition of ZnCl2, resuscitation of bacteriophage particles in Ringer's buffer to remove the ZnCl2 excess and a soft agar overlay assay with the host bacterium to isolate infectious individual phage plaques. The method requires neither an enrichment step nor other steps (e. g., PEG precipitation, ultrafiltration, or ultracentrifugation) commonly used in other procedures and results in isolation of active viable bacteriophage particles.

40 CFR 180.1261 - Xanthomonas campestris pv. vesicatoria and Pseudomonas syringae pv. tomato specific Bacteriophages.

Code of Federal Regulations, 2014 CFR

2014-07-01

... and Pseudomonas syringae pv. tomato specific Bacteriophages. 180.1261 Section 180.1261 Protection of.... vesicatoria and Pseudomonas syringae pv. tomato specific Bacteriophages. An exemption from the requirement of... syringae pv. tomato specific bacteriophages in or on pepper and tomato. [74 FR 26536, June 3, 2009] ...

40 CFR 180.1261 - Xanthomonas campestris pv. vesicatoria and Pseudomonas syringae pv. tomato specific Bacteriophages.

Code of Federal Regulations, 2012 CFR

2012-07-01

... and Pseudomonas syringae pv. tomato specific Bacteriophages. 180.1261 Section 180.1261 Protection of.... vesicatoria and Pseudomonas syringae pv. tomato specific Bacteriophages. An exemption from the requirement of... syringae pv. tomato specific bacteriophages in or on pepper and tomato. [74 FR 26536, June 3, 2009] ...

40 CFR 180.1261 - Xanthomonas campestris pv. vesicatoria and Pseudomonas syringae pv. tomato specific Bacteriophages.

Code of Federal Regulations, 2011 CFR

2011-07-01

... and Pseudomonas syringae pv. tomato specific Bacteriophages. 180.1261 Section 180.1261 Protection of.... vesicatoria and Pseudomonas syringae pv. tomato specific Bacteriophages. An exemption from the requirement of... syringae pv. tomato specific bacteriophages in or on pepper and tomato. [74 FR 26536, June 3, 2009] ...

40 CFR 180.1261 - Xanthomonas campestris pv. vesicatoria and Pseudomonas syringae pv. tomato specific Bacteriophages.

Code of Federal Regulations, 2013 CFR

2013-07-01

... and Pseudomonas syringae pv. tomato specific Bacteriophages. 180.1261 Section 180.1261 Protection of.... vesicatoria and Pseudomonas syringae pv. tomato specific Bacteriophages. An exemption from the requirement of... syringae pv. tomato specific bacteriophages in or on pepper and tomato. [74 FR 26536, June 3, 2009] ...

Bacteriophage therapy for refractory Pseudomonas aeruginosa urinary tract infection.

PubMed

Khawaldeh, A; Morales, S; Dillon, B; Alavidze, Z; Ginn, A N; Thomas, L; Chapman, S J; Dublanchet, A; Smithyman, A; Iredell, J R

2011-11-01

We describe the success of adjunctive bacteriophage therapy for refractory Pseudomonas aeruginosa urinary tract infection in the context of bilateral ureteric stents and bladder ulceration, after repeated failure of antibiotics alone. No bacteriophage-resistant bacteria arose, and the kinetics of bacteriophage and bacteria in urine suggest self-sustaining and self-limiting infection.

40 CFR 180.1261 - Xanthomonas campestris pv. vesicatoria and Pseudomonas syringae pv. tomato specific Bacteriophages.

Code of Federal Regulations, 2010 CFR

2010-07-01

... and Pseudomonas syringae pv. tomato specific Bacteriophages. 180.1261 Section 180.1261 Protection of.... vesicatoria and Pseudomonas syringae pv. tomato specific Bacteriophages. An exemption from the requirement of... syringae pv. tomato specific bacteriophages in or on pepper and tomato. [74 FR 26536, June 3, 2009] ...

Solving ODE Initial Value Problems With Implicit Taylor Series Methods

NASA Technical Reports Server (NTRS)

Scott, James R.

2000-01-01

In this paper we introduce a new class of numerical methods for integrating ODE initial value problems. Specifically, we propose an extension of the Taylor series method which significantly improves its accuracy and stability while also increasing its range of applicability. To advance the solution from t (sub n) to t (sub n+1), we expand a series about the intermediate point t (sub n+mu):=t (sub n) + mu h, where h is the stepsize and mu is an arbitrary parameter called an expansion coefficient. We show that, in general, a Taylor series of degree k has exactly k expansion coefficients which raise its order of accuracy. The accuracy is raised by one order if k is odd, and by two orders if k is even. In addition, if k is three or greater, local extrapolation can be used to raise the accuracy two additional orders. We also examine stability for the problem y'= lambda y, Re (lambda) less than 0, and identify several A-stable schemes. Numerical results are presented for both fixed and variable stepsizes. It is shown that implicit Taylor series methods provide an effective integration tool for most problems, including stiff systems and ODE's with a singular point.

Bounds on area and charge for marginally trapped surfaces with a cosmological constant

NASA Astrophysics Data System (ADS)

Simon, Walter

2012-03-01

We sharpen the known inequalities AΛ ⩽ 4π(1 - g) (Hayward et al 1994 Phys. Rev. D 49 5080, Woolgar 1999 Class. Quantum Grav. 16 3005) and A ⩾ 4πQ2 (Dain et al 2012 Class. Quantum Grav. 29 035013) between the area A and the electric charge Q of a stable marginally outer-trapped surface (MOTS) of genus g in the presence of a cosmological constant Λ. In particular, instead of requiring stability we include the principal eigenvalue λ of the stability operator. For Λ* = Λ + λ > 0, we obtain a lower and an upper bound for Λ*A in terms of Λ*Q2, as well as the upper bound Q \\le 1/(2\\sqrt{\\Lambda ^{*}}) for the charge, which reduces to Q \\le 1/(2\\sqrt{\\Lambda }) in the stable case λ ⩾ 0. For Λ* < 0, there only remains a lower bound on A. In the spherically symmetric, static, stable case, one of our area inequalities is saturated iff the surface gravity vanishes. We also discuss implications of our inequalities for ‘jumps’ and mergers of charged MOTS.

Predicting bacteriophage proteins located in host cell with feature selection technique.

PubMed

Ding, Hui; Liang, Zhi-Yong; Guo, Feng-Biao; Huang, Jian; Chen, Wei; Lin, Hao

2016-04-01

A bacteriophage is a virus that can infect a bacterium. The fate of an infected bacterium is determined by the bacteriophage proteins located in the host cell. Thus, reliably identifying bacteriophage proteins located in the host cell is extremely important to understand their functions and discover potential anti-bacterial drugs. Thus, in this paper, a computational method was developed to recognize bacteriophage proteins located in host cells based only on their amino acid sequences. The analysis of variance (ANOVA) combined with incremental feature selection (IFS) was proposed to optimize the feature set. Using a jackknife cross-validation, our method can discriminate between bacteriophage proteins located in a host cell and the bacteriophage proteins not located in a host cell with a maximum overall accuracy of 84.2%, and can further classify bacteriophage proteins located in host cell cytoplasm and in host cell membranes with a maximum overall accuracy of 92.4%. To enhance the value of the practical applications of the method, we built a web server called PHPred (〈http://lin.uestc.edu.cn/server/PHPred〉). We believe that the PHPred will become a powerful tool to study bacteriophage proteins located in host cells and to guide related drug discovery. Copyright © 2016 Elsevier Ltd. All rights reserved.

Genomic diversity of bacteriophages infecting the fish pathogen Flavobacterium psychrophilum.

PubMed

Castillo, Daniel; Middelboe, Mathias

2016-12-01

Bacteriophages infecting the fish pathogen Flavobacterium psychrophilum can potentially be used to prevent and control outbreaks of this bacterium in salmonid aquaculture. However, the application of bacteriophages in disease control requires detailed knowledge on their genetic composition. To explore the diversity of F. pyschrophilum bacteriophages, we have analyzed the complete genome sequences of 17 phages isolated from two distant geographic areas (Denmark and Chile), including the previously characterized temperate bacteriophage 6H. Phage genome size ranged from 39 302 to 89 010 bp with a G+C content of 27%-32%. None of the bacteriophages isolated in Denmark contained genes associated with lysogeny, whereas the Chilean isolates were all putative temperate phages and similar to bacteriophage 6H. Comparative genome analysis showed that phages grouped in three different genetic clusters based on genetic composition and gene content, indicating a limited genetic diversity of F. psychrophilum-specific bacteriophages. However, amino acid sequence dissimilarity (25%) was found in putative structural proteins, which could be related to the host specificity determinants. This study represents the first analysis of genomic diversity and composition among bacteriophages infecting the fish pathogen F. psychrophilum and discusses the implications for the application of phages in disease control. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Occurrence of bacteriophages infecting Aeromonas, Enterobacter, and Klebsiella in water and association with contamination sources in Thailand.

PubMed

Wangkahad, Bencharong; Bosup, Suchada; Mongkolsuk, Skorn; Sirikanchana, Kwanrawee

2015-06-01

The co-residence of bacteriophages and their bacterial hosts in humans, animals, and environmental sources directed the use of bacteriophages to track the origins of the pathogenic bacteria that can be found in contaminated water. The objective of this study was to enumerate bacteriophages of Aeromonas caviae (AecaKS148), Enterobacter sp. (EnspKS513), and Klebsiella pneumoniae (KlpnKS648) in water and evaluate their association with contamination sources (human vs. animals). Bacterial host strains were isolated from untreated wastewater in Bangkok, Thailand. A double-layer agar technique was used to detect bacteriophages. All three bacteriophages were detected in polluted canal samples, with likely contamination from human wastewater, whereas none was found in non-polluted river samples. AecaKS148 was found to be associated with human fecal sources, while EnspKS513 and KlpnKS648 seemed to be equally prevalent in both human and animal fecal sources. Both bacteriophages were also present in polluted canals that could receive contamination from other fecal sources or the environment. In conclusion, all three bacteriophages were successfully monitored in Bangkok, Thailand. This study provided an example of bacteriophages for potential use as source identifiers of pathogen contamination. The results from this study will assist in controlling sources of pathogen contamination, especially in developing countries.

Development of a novel and highly efficient method of isolating bacteriophages from water.

PubMed

Liu, Weili; Li, Chao; Qiu, Zhi-Gang; Jin, Min; Wang, Jing-Feng; Yang, Dong; Xiao, Zhong-Hai; Yuan, Zhao-Kang; Li, Jun-Wen; Xu, Qun-Ying; Shen, Zhi-Qiang

2017-08-01

Bacteriophages are widely used to the treatment of drug-resistant bacteria and the improvement of food safety through bacterial lysis. However, the limited investigations on bacteriophage restrict their further application. In this study, a novel and highly efficient method was developed for isolating bacteriophage from water based on the electropositive silica gel particles (ESPs) method. To optimize the ESPs method, we evaluated the eluent type, flow rate, pH, temperature, and inoculation concentration of bacteriophage using bacteriophage f2. The quantitative detection reported that the recovery of the ESPs method reached over 90%. The qualitative detection demonstrated that the ESPs method effectively isolated 70% of extremely low-concentration bacteriophage (10 0 PFU/100L). Based on the host bacteria composed of 33 standard strains and 10 isolated strains, the bacteriophages in 18 water samples collected from the three sites in the Tianjin Haihe River Basin were isolated by the ESPs and traditional methods. Results showed that the ESPs method was significantly superior to the traditional method. The ESPs method isolated 32 strains of bacteriophage, whereas the traditional method isolated 15 strains. The sample isolation efficiency and bacteriophage isolation efficiency of the ESPs method were 3.28 and 2.13 times higher than those of the traditional method. The developed ESPs method was characterized by high isolation efficiency, efficient handling of large water sample size and low requirement on water quality. Copyright © 2017. Published by Elsevier B.V.

Elucidation of the mechanisms of action of Bacteriophage K/nano-emulsion formulations against S. aureus via measurement of particle size and zeta potential.

PubMed

Esteban, Patricia Perez; Jenkins, A Toby A; Arnot, Tom C

2016-03-01

In earlier work we have demonstrated the effect that nano-emulsions have on bacterial growth, and most importantly the enhanced bacteriophage infectivity against Staphylococcus aureus in planktonic culture when phage are carried in nano-emulsions. However, the mechanisms of enhancement of the bacteriophage killing effect are not specifically understood. This work focuses on the investigation of the possible interactions between emulsion droplets and bacterial cells, between emulsion droplets and bacteriophages, and finally interactions between all three components: nano-emulsion droplets, bacteria, and bacteriophages. The first approach consists of simple calculations to determine the spatial distribution of the components, based on measurements of particle size. It was found that nano-emulsion droplets are much more numerous than bacteria or bacteriophage, and due to their size and surface area they must be covering the surface of both cells and bacteriophage particles. Stabilisation of bacteriophages due to electrostatic forces and interaction with nano-emulsion droplets is suspected, since bacteriophages may be protected against inactivation due to 'charge shielding'. Zeta potential was measured for the individual components in the system, and for all of them combined. It was concluded that the presence of nano-emulsions could be reducing electrostatic repulsion between bacterial cells and bacteriophage, both of which are very negatively 'charged'. Moreover, nano-emulsions lead to more favourable interaction between bacteriophages and bacteria, enhancing the anti-microbial or killing effect. These findings are relevant since the physicochemical properties of nano-emulsions (i.e. particle size distribution and zeta potential) are key in determining the efficacy of the formulation against infection in the context of responsive burn wound dressings-which is the main target for this work. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Membrane filtration immobilization technique-a simple and novel method for primary isolation and enrichment of bacteriophages.

PubMed

Ghugare, G S; Nair, A; Nimkande, V; Sarode, P; Rangari, P; Khairnar, K

2017-02-01

To develop a method for the isolation and enrichment of bacteriophages selectively against specific bacteria coupled with a membrane filtration technique. Rapid isolation and concentration of host-specific bacteriophages was achieved by exposure of the sample suspected to contain bacteriophages to a specific host immobilized on a 0·45 μm membrane in a membrane filtration unit. The principle behind this method is the exploitation of host-specific interaction of bacteriophages with their host and maximizing this interaction using a classic membrane filtration method. This provides a chance for each bacteriophage in the sample to interact with the specific host on the membrane filter fitted with a vacuum pump. Specific bacteriophages of the host are retained on the membrane along with its host cells due to the effect of adsorption and these adsorbed bacteriophages (along with their hosts) on the filter disc are then amplified and enriched in regular nutritive broth tryptose soya broth by incubation. With the help of the plaque assay method, host-specific phages of various bacterial species were isolated, segregated and enriched. The phage concentration method coupled with membrane filtration immobilization of host bacteria was able to isolate and enrich the host-specific bacteriophages by several fold using a lower quantity of an environmental water sample, or other phage suspensions. Enrichment of phages from single plaques was also achieved. The isolation and detection of host-specific bacteriophages from a low density bacteriophage water sample in a single step by the use of a simple and basic microbiological technique can be achieved. Enrichment of phages from low phage titre suspensions is also achieved very effectively. © 2016 The Society for Applied Microbiology.

Metavirome Sequencing of the Termite Gut Reveals the Presence of an Unexplored Bacteriophage Community

PubMed Central

Tikhe, Chinmay V.; Husseneder, Claudia

2018-01-01

The Formosan subterranean termite; Coptotermes formosanus is nutritionally dependent on the complex and diverse community of bacteria and protozoa in their gut. Although, there have been many studies to decipher the taxonomic and functional diversity of bacterial communities in the guts of termites, their bacteriophages remain unstudied. We sequenced the metavirome of the guts of Formosan subterranean termite workers to study the diversity of bacteriophages and other associated viruses. Results showed that the termites harbor a virome in their gut comprised of varied and previously unknown bacteriophages. Between 87–90% of the predicted dsDNA virus genes by Metavir showed similarity to the tailed bacteriophages (Caudovirales). Many predicted genes from the virome matched to bacterial prophage regions. These data are suggestive of a virome dominated by temperate bacteriophages. We predicted the genomes of seven novel Caudovirales bacteriophages from the termite gut. Three of these predicted bacteriophage genomes were found in high proportions in all the three termite colonies tested. Two bacteriophages are predicted to infect endosymbiotic bacteria of the gut protozoa. The presence of these putative bacteriophages infecting endosymbionts of the gut protozoa, suggests a quadripartite relationship between the termites their symbiotic protozoa, endosymbiotic bacteria of the protozoa and their bacteriophages. Other than Caudovirales, ss-DNA virus related genes were also present in the termite gut. We predicted the genomes of 12 novel Microviridae phages from the termite gut and seven of those possibly represent a new proposed subfamily. Circovirus like genomes were also assembled from the termite gut at lower relative abundance. We predicted 10 novel circovirus genomes in this study. Whether these circoviruses infect the termites remains elusive at the moment. The functional and taxonomical annotations suggest that the termites may harbor a core virome comprised of the bacteriophages infecting endosymbionts of the gut protozoa. PMID:29354098

[The expression of interferon-lambda1 in CHO cell].

PubMed

Yuan, Wu-Mei; Ma, Fen-Lian; Zhang, Qian; Zheng, Wen-Zhi; Zheng, Li-Shu

2013-06-01

To construct the eukaryotic expression vector PCI-dhfr-lambda1 and PCI-dhfr-SP163-lambda1 which linked the enhancer SP163 with interferon lambda1. Then express the interferon lambda1 in CHO (dhfr-) cells. Using PCR method to introduce the restriction enzyme sites and through the fusion PCR binding the enhancer with the interferon Lambda1. After sequenced, lambda1 and SP163-lambda1 was inserted into PCI-dhfr forming the expression vector PCI-dhfr-lambda1 and PCI-dhfr-SP163-lambda1 which was constructed successfully confirming by sequencing. Then the expressing vectors were transfected into CHO (dhfr-) cells using liposome transfection method and interferon lambda1 protein was assayed with indirect immunofluorescence and Western Blot. Using cytopathic effect inhibition evaluated the antiviral activity of interferon lambda1. Successfully constructing the eukaryotic expression vectors of interferon lambda and the vectors could express interferon lambda1. The result of immunofluorescence showed the enhancer developed the expression of interferon lambda1. Detecting the interferon lambda1 in CHO (dhfr-) cells after transfecting 48 hour using Western Blot. The cytopathic effect inhibition showed the expressed interferon lambda1 has the antiviral activity. Successfully expressed the interferon lambda1 in CHO (dhfr-) cells and the protein possesses antiviral activity, which may supply a valuable basis for building the stable cell line of interferon lambda1.

Energy of the ground and 2{sup +} excited states of {sub {lambda}}{sub {lambda}}{sup 10}Be: A partial ten-body model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shoeb, Mohammad; Sonika

2009-08-15

The energies of the ground and excited 2{sup +} states of {sub {lambda}}{sub {lambda}}{sup 10}Be have been calculated variationally in the Monte Carlo framework. The hypernucleus is treated as a partial ten-body problem in the {lambda}{lambda}+{alpha}{alpha} model where nucleonic degrees of freedom of {alpha}'s are taken into consideration ignoring the antisymmetrization between two {alpha}'s. The central two-body {lambda}N and {lambda}{lambda} and the three-body dispersive and two-pion exchange {lambda}NN forces, constrained by the {lambda}p scattering data and the observed ground state energies of {sub {lambda}}{sup 5}He and {sub {lambda}}{sub {lambda}}{sup 6}He, are employed. The product-type trial wave function predicts binding energymore » for the ground state considerably less than for the event reported by Danysz et al.; however, it is consistent with the value deduced assuming a {gamma} ray of 3.04 MeV must have escaped undetected in the decay of the product {sub {lambda}}{sup 9}Be* {yields} {sub {lambda}}{sup 9}Be+{gamma} of the emulsion event {sub {lambda}}{sub {lambda}}{sup 10}Be{yields} {pi}{sup -}+p+{sub {lambda}}{sup 9}Be* and for the excited 2{sup +} state closer to the value measured in the Demachi-Yanagi event. The hypernucleus {sub {lambda}}{sub {lambda}}{sup 10}Be has an oblate shape in the excited state. These results are consistent with the earlier four-body {alpha} cluster model approach where {alpha}'s are assumed to be structureless entities.« less

Photochemistry and reactivity of the phenyl radical-water system: a matrix isolation and computational study.

PubMed

Mardyukov, Artur; Crespo-Otero, Rachel; Sanchez-Garcia, Elsa; Sander, Wolfram

2010-08-02

The reaction of the phenyl radical 1 with water has been investigated by using matrix isolation spectroscopy and quantum chemical calculations. The primary thermal product of the reaction between 1 and water is a weakly bound complex stabilized by an OH...pi interaction. This complex is photolabile, and visible-light irradiation (lambda>420 nm) results in hydrogen atom transfer from water to radical 1 and the formation of a highly labile complex between benzene and the OH radical. This complex is stable under the conditions of matrix isolation, however, continuous irradiation with lambda>420 nm light results in the complete destruction of the aromatic system and formation of an acylic unsaturated ketene. The mechanisms of all reaction steps are discussed in the light of ab initio and DFT calculations.

Optical fiber sensor having an active core

NASA Technical Reports Server (NTRS)

Egalon, Claudio Oliveira (Inventor); Rogowski, Robert S. (Inventor)

1993-01-01

An optical fiber is provided. The fiber is comprised of an active fiber core which produces waves of light upon excitation. A factor ka is identified and increased until a desired improvement in power efficiency is obtained. The variable a is the radius of the active fiber core and k is defined as 2 pi/lambda wherein lambda is the wavelength of the light produced by the active fiber core. In one embodiment, the factor ka is increased until the power efficiency stabilizes. In addition to a bare fiber core embodiment, a two-stage fluorescent fiber is provided wherein an active cladding surrounds a portion of the active fiber core having an improved ka factor. The power efficiency of the embodiment is further improved by increasing a difference between the respective indices of refraction of the active cladding and the active fiber core.

40 CFR 180.1301 - Escherichia coli O157:H7 specific bacteriophages; temporary exemption from the requirement of a...

Code of Federal Regulations, 2011 CFR

2011-07-01

... bacteriophages; temporary exemption from the requirement of a tolerance. 180.1301 Section 180.1301 Protection of... bacteriophages; temporary exemption from the requirement of a tolerance. A temporary exemption from the requirement of a tolerance is established for residues of lytic bacteriophages that are specific to...

40 CFR 180.1301 - Escherichia coli O157:H7 specific bacteriophages; temporary exemption from the requirement of a...

Code of Federal Regulations, 2014 CFR

2014-07-01

... bacteriophages; temporary exemption from the requirement of a tolerance. 180.1301 Section 180.1301 Protection of... bacteriophages; temporary exemption from the requirement of a tolerance. A temporary exemption from the requirement of a tolerance is established for residues of lytic bacteriophages that are specific to...

40 CFR 180.1301 - Escherichia coli O157:H7 specific bacteriophages; temporary exemption from the requirement of a...

Code of Federal Regulations, 2013 CFR

2013-07-01

... bacteriophages; temporary exemption from the requirement of a tolerance. 180.1301 Section 180.1301 Protection of... bacteriophages; temporary exemption from the requirement of a tolerance. A temporary exemption from the requirement of a tolerance is established for residues of lytic bacteriophages that are specific to...

40 CFR 180.1301 - Escherichia coli O157:H7 specific bacteriophages; temporary exemption from the requirement of a...

Code of Federal Regulations, 2012 CFR

2012-07-01

... bacteriophages; temporary exemption from the requirement of a tolerance. 180.1301 Section 180.1301 Protection of... bacteriophages; temporary exemption from the requirement of a tolerance. A temporary exemption from the requirement of a tolerance is established for residues of lytic bacteriophages that are specific to...

Beauty Baryons at CDF and DO

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kryemadhi, Abaz

The results from Tevatron in the baryonic sector are presented. The lifetime of {lambda}b {yields} J/{psi}{lambda}, the observation of hadronic decay of {lambda}b {yields} {lambda}c{pi}, the semileptonic decays of {lambda}b {yields} {lambda}c{mu}{nu}, the hadronization of the b-baryons, and the {lambda}b decays to {lambda}b {yields} p{pi} and {lambda}b {yields} pK are discussed. These measurements paint a nice picture of our understanding of the beauty baryons.

Improved measurement of the form factors in the decay lambda+c-->lambda + nue.

PubMed

Hinson, J W; Huang, G S; Lee, J; Miller, D H; Pavlunin, V; Rangarajan, R; Sanghi, B; Shibata, E I; Shipsey, I P J; Cronin-Hennessy, D; Park, C S; Park, W; Thayer, J B; Thorndike, E H; Coan, T E; Gao, Y S; Liu, F; Stroynowski, R; Artuso, M; Boulahouache, C; Blusk, S; Dambasuren, E; Dorjkhaidav, O; Mountain, R; Muramatsu, H; Nandakumar, R; Skwarnicki, T; Stone, S; Wang, J C; Csorna, S E; Danko, I; Bonvicini, G; Cinabro, D; Dubrovin, M; McGee, S; Bornheim, A; Lipeles, E; Pappas, S P; Shapiro, A; Sun, W M; Weinstein, A J; Briere, R A; Chen, G P; Ferguson, T; Tatishvili, G; Vogel, H; Watkins, M E; Adam, N E; Alexander, J P; Berkelman, K; Boisvert, V; Cassel, D G; Duboscq, J E; Ecklund, K M; Ehrlich, R; Galik, R S; Gibbons, L; Gittelman, B; Gray, S W; Hartill, D L; Heltsley, B K; Hsu, L; Jones, C D; Kandaswamy, J; Kreinick, D L; Magerkurth, A; Mahlke-Krüger, H; Meyer, T O; Mistry, N B; Patterson, J R; Peterson, D; Pivarski, J; Richichi, S J; Riley, D; Sadoff, A J; Schwarthoff, H; Shepherd, M R; Thayer, J G; Urner, D; Wilksen, T; Warburton, A; Weinberger, M; Athar, S B; Avery, P; Breva-Newell, L; Potlia, V; Stoeck, H; Yelton, J; Benslama, K; Cawlfield, C; Eisenstein, B I; Gollin, G D; Karliner, I; Lowrey, N; Plager, C; Sedlack, C; Selen, M; Thaler, J J; Williams, J; Edwards, K W; Besson, D; Anderson, S; Frolov, V V; Gong, D T; Kubota, Y; Li, S Z; Poling, R; Smith, A; Stepaniak, C J; Urheim, J; Metreveli, Z; Seth, K K; Tomaradze, A; Zweber, P; Ahmed, S; Alam, M S; Ernst, J; Jian, L; Saleem, M; Wappler, F; Arms, K; Eckhart, E; Gan, K K; Gwon, C; Honscheid, K; Kagan, H; Kass, R; Pedlar, T K; von Toerne, E; Severini, H; Skubic, P; Dytman, S A; Mueller, J A; Nam, S; Savinov, V

2005-05-20

Using the CLEO detector at the Cornell Electron Storage Ring, we have studied the distribution of kinematic variables in the decay lambda(+)(c)lambda--> e(+)nu(e). By performing a four-dimensional maximum likelihood fit, we determine the form factor ratio, R= f(2)/f(1) = -0.31 +/- 0.05(stat) +/- 0.04(syst), the pole mass, M(pole) = [2.21 +/- 0.08(stat) +/- 0.14(syst)] GeV/c(2), and the decay asymmetry parameter of the lambda(+)(c), alpha (lambda(c)) = -0.86 +/-0.03(stat) +/- 0.02(syst), for q(2) = 0.67 (GeV/c(2))(2). We compare the angular distributions of the lambda(+)(c) and lambda(-)(c) and find no evidence for CP violation: A(lambda(c)) = (alpha(lambda(c)) + alpha (lambda(c)))/(alpha(lambda(c))-alpha(lambda(c))) = 0.00 +/- 0.03(stat) +/- 0.01(syst) +/- 0.02, where the third error is from the uncertainty in the world average of the CP-violating parameter, A(lambda), for ppi(-).

Optimizing the European regulatory framework for sustainable bacteriophage therapy in human medicine.

PubMed

Verbeken, Gilbert; Pirnay, Jean-Paul; De Vos, Daniel; Jennes, Serge; Zizi, Martin; Lavigne, Rob; Casteels, Minne; Huys, Isabelle

2012-06-01

For practitioners at hospitals seeking to use natural (not genetically modified, as appearing in nature) bacteriophages for treatment of antibiotic-resistant bacterial infections (bacteriophage therapy), Europe's current regulatory framework for medicinal products hinders more than it facilitates. Although many experts consider bacteriophage therapy to be a promising complementary (or alternative) treatment to antibiotic therapy, no bacteriophage-specific framework for documentation exists to date. Decades worth of historical clinical data on bacteriophage therapy (from Eastern Europe, particularly Poland, and the former Soviet republics, particularly Georgia and Russia, as well as from today's 27 EU member states and the US) have not been taken into account by European regulators because these data have not been validated under current Western regulatory standards. Consequently, applicants carrying out standard clinical trials on bacteriophages in Europe are obliged to initiate clinical work from scratch. This paper argues for a reduced documentation threshold for Phase 1 clinical trials of bacteriophages and maintains that bacteriophages should not be categorized as classical medicinal products for at least two reasons: (1) such a categorization is scientifically inappropriate for this specific therapy and (2) such a categorization limits the marketing authorization process to industry, the only stakeholder with sufficient financial resources to prepare a complete dossier for the competent authorities. This paper reflects on the current regulatory framework for medicines in Europe and assesses possible regulatory pathways for the (re-)introduction of bacteriophage therapy in a way that maintains its effectiveness and safety as well as its inherent characteristics of sustainability and in situ self-amplification and limitation.

Dehydration of bacteriophages in electrospun nanofibers: effect of excipients in polymeric solutions

NASA Astrophysics Data System (ADS)

Koo, Charmaine K. W.; Senecal, Kris; Senecal, Andre; Nugen, Sam R.

2016-12-01

Bacteriophages are viruses capable of infecting and lysing target bacterial cells; as such they have potential applications in agriculture for decontamination of foods, food contact surfaces and food rinse water. Although bacteriophages can retain infectivity long-term using lyophilized storage, the process of freeze-drying can be time consuming and expensive. In this study, electrospinning was used for dehydrating bacteriophages in polyvinylpyrrolidone polymer solutions with addition of excipients (sodium chloride, magnesium sulfate, Tris-HCl, sucrose) in deionized water. The high voltage dehydration reduced the infectivity of bacteriophages following electrospinning, with the damaging effect abated with addition of storage media (SM) buffer and sucrose. SM buffer and sucrose also provided the most protection over extended storage (8 weeks; 20 °C 1% relative humidity) by mitigating environmental effects on the dried bacteriophages. Magnesium sulfate however provided the least protection due to coagulation effects of the ion, which can disrupt the native conformation of the bacteriophage protein coat. Storage temperatures (20 °C, 4 °C and -20 °C 1% relative humidity) had a minimal effect while relative humidity had substantial effect on the infectivity of bacteriophages. Nanofibers stored in higher relative humidity (33% and 75%) underwent considerable damage due to extensive water absorption and disruption of the fibers. Overall, following storage of nanofiber mats for eight weeks at ambient temperatures, high infective phage concentrations (106-107 PFU ml-1) were retained. Therefore, this study provided valuable insights on preservation and dehydration of bacteriophages by electrospinning in comparison to freeze drying and liquid storage, and the influence of excipients on the viability of bacteriophages.

Wavefront Tilt And Beam Walk Correction For A Pulsed Laser System

NASA Astrophysics Data System (ADS)

Bartosewcz, Mike; Tyburski, Joe

1986-05-01

The Lockheed Beam Alignment Assembly (BAA) is designed to be a space qualifiable, long life, low bandwidth beam stabilization system. The BAA will stabilize a wandering pulsed laser beam with an input beam tilt of ±750 microradians and translation of ±2.5 mm by two orders of magnitude at the bandwidth of interest. A bandwidth of three hertz was selected to remove laser and optical train thermal drifts and launch induced strain effects. The lambda over twenty RMS wavefront will be maintained in the optics at full power under vacuum test, to demonstrate space qualifiability and optical performance.

[TL, the new bacteriophage of Pseudomonas aeruginosa and its application for the search of halo-producing bacteriophages].

PubMed

Pleteneva, E A; Burkal'tseva, M V; Shaburova, O V; Krylov, S V; Pechnikova, E V; Sokolova, O S; Krylov, V N

2011-01-01

The properties of new virulent bacteriophage TL of Pseudomonas aeruginosa belonging to the family Podoviridae (genome size of 46 kb) were investigated. This bacteriophage is capable of lysogenizing the bacterial lawn in halo zones around negative colonies (NC) of other bacteriophages. TL forms large NC, that are hardly distinguishable on the lawn of P. aeruginisa PAO1. At the same time, on the lawns of some phage-resistant PAO1 mutants, as well as on those produced by a number of clinical isolates, TL forms more transparent NC. It is suggested that more effective growth of the bacteriophage TL NC is associated with the differences in outer lipopolysaccharide (LPS) layer of the cell walls of different bacterial strains, as well as of the bacteria inside and outside of the halos. This TL property was used to optimize selection of bacteriophages producing halos around NC on the lawn of P. aeruginosa PAO1. As a result, a group of bacteriophages differing in the patterns of interaction between their halos and TL bacteriophage, as well as in some characters was identified. Taking into consideration the importance of cell-surfaced structures of P. aeruginosa in manifestation of virulence and pathogenicity, possible utilization of specific phage enzymes, polysacchadide depolymerases, for more effective treatment of P. aeruginosa infections is discussed.

Observation of B{sup 0}{yields}{lambda}{lambda}K{sup 0} and B{sup 0}{yields}{lambda}{lambda}K*{sup 0} at Belle

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chang, Y.-W.; Wang, M.-Z.; Chao, Y.

2009-03-01

We study the charmless decays B{yields}{lambda}{lambda}h, where h stands for {pi}{sup +}, K{sup +}, K{sup 0},K*{sup +}, or K*{sup 0}, using a 605 fb{sup -1} data sample collected at the {upsilon}(4S) resonance with the Belle detector at the KEKB asymmetric energy e{sup +}e{sup -} collider. We observe B{sup 0}{yields}{lambda}{lambda}K{sup 0} and B{sup 0}{yields}{lambda}{lambda}K*{sup 0} with branching fractions of (4.76{sub -0.68}{sup +0.84}(stat){+-}0.61(syst))x10{sup -6} and (2.46{sub -0.72}{sup +0.87}{+-}0.34)x10{sup -6}, respectively. The significances of these signals in the threshold-mass enhanced mass region, M{sub {lambda}}{sub {lambda}}<2.85 GeV/c{sup 2}, are 12.4{sigma} and 9.3{sigma}, respectively. We also update the branching fraction B(B{sup +}{yields}{lambda}{lambda}K{sup +})=(3.38{sub -0.36}{sup +0.41}{+-}0.41)x10{supmore » -6} with better accuracy, and report the following measurement or 90% confidence level upper limit in the threshold-mass-enhanced region: B(B{sup +}{yields}{lambda}{lambda}K*{sup +})=(2.19{sub -0.88}{sup +1.13}{+-}0.33)x10{sup -6} with 3.7{sigma} significance; B(B{sup +}{yields}{lambda}{lambda}{pi}{sup +})<0.94x10{sup -6}. A related search for B{sup 0}{yields}{lambda}{lambda}D{sup 0} yields a branching fraction B(B{sup 0}{yields}{lambda}{lambda}D{sup 0})=(1.05{sub -0.44}{sup +0.57}{+-}0.14)x10{sup -5}. This may be compared with the large, {approx}10{sup -4}, branching fraction observed for B{sup 0}{yields}ppD{sup 0}. The M{sub {lambda}}{sub {lambda}} enhancements near threshold and related angular distributions for the observed modes are also reported.« less

Application of bacteriophages in post-harvest control of human pathogenic and food spoiling bacteria.

PubMed

Pérez Pulido, Rubén; Grande Burgos, Maria José; Gálvez, Antonio; Lucas López, Rosario

2016-10-01

Bacteriophages have attracted great attention for application in food biopreservation. Lytic bacteriophages specific for human pathogenic bacteria can be isolated from natural sources such as animal feces or industrial wastes where the target bacteria inhabit. Lytic bacteriophages have been tested in different food systems for inactivation of main food-borne pathogens including Listeria monocytogenes, Staphylococcus aureus, Escherichia coli O157:H7, Salmonella enterica, Shigella spp., Campylobacter jejuni and Cronobacter sakazkii, and also for control of spoilage bacteria. Application of lytic bacteriophages could selectively control host populations of concern without interfering with the remaining food microbiota. Bacteriophages could also be applied for inactivation of bacteria attached to food contact surfaces or grown as biofilms. Bacteriophages may receive a generally recognized as safe status based on their lack of toxicity and other detrimental effects to human health. Phage preparations specific for L. monocytogenes, E. coli O157:H7 and S. enterica serotypes have been commercialized and approved for application in foods or as part of surface decontamination protocols. Phage endolysins have a broader host specificity compared to lytic bacteriophages. Cloned endolysins could be used as natural preservatives, singly or in combination with other antimicrobials such as bacteriocins.

Genomic Diversity of Type B3 Bacteriophages of Caulobacter crescentus.

PubMed

Ash, Kurt T; Drake, Kristina M; Gibbs, Whitney S; Ely, Bert

2017-07-01

The genomes of the type B3 bacteriophages that infect Caulobacter crescentus are among the largest phage genomes thus far deposited into GenBank with sizes over 200 kb. In this study, we introduce six new bacteriophage genomes which were obtained from phage collected from various water systems in the southeastern United States and from tropical locations across the globe. A comparative analysis of the 12 available genomes revealed a "core genome" which accounts for roughly 1/3 of these bacteriophage genomes and is predominately localized to the head, tail, and lysis gene regions. Despite being isolated from geographically distinct locations, the genomes of these bacteriophages are highly conserved in both genome sequence and gene order. We also identified the insertions, deletions, translocations, and horizontal gene transfer events which are responsible for the genomic diversity of this group of bacteriophages and demonstrated that these changes are not consistent with the idea that modular reassortment of genomes occurs in this group of bacteriophages.

Bacteriophage in polar inland waters

USGS Publications Warehouse

Säwström, Christin; Lisle, John; Anesio, A.M.; Priscu, John C.; Laybourn-Parry, J.

2008-01-01

Bacteriophages are found wherever microbial life is present and play a significant role in aquatic ecosystems. They mediate microbial abundance, production, respiration, diversity, genetic transfer, nutrient cycling and particle size distribution. Most studies of bacteriophage ecology have been undertaken at temperate latitudes. Data on bacteriophages in polar inland waters are scant but the indications are that they play an active and dynamic role in these microbially dominated polar ecosystems. This review summarises what is presently known about polar inland bacteriophages, ranging from subglacial Antarctic lakes to glacial ecosystems in the Arctic. The review examines interactions between bacteriophages and their hosts and the abiotic and biotic variables that influence these interactions in polar inland waters. In addition, we consider the proportion of the bacteria in Arctic and Antarctic lake and glacial waters that are lysogenic and visibly infected with viruses. We assess the relevance of bacteriophages in the microbial loop in the extreme environments of Antarctic and Arctic inland waters with an emphasis on carbon cycling.

Inactivation of Adenovirus Type 5, Rotavirus WA and Male Specific Coliphage (MS2) in Biosolids by Lime Stabilization

PubMed Central

Hansen, Jacqueline J.; Warden, Paul S.; Margolin, Aaron B.

2007-01-01

The use of lime to reduce or eliminate pathogen content is a cost-effective treatment currently employed in many Class B biosolids production plants in the United States. A bench scale model of lime stabilization was designed to evaluate the survival of adenovirus type 5, rotavirus Wa, and the male specific bacteriophage, MS2, in various matrices. Each virus was initially evaluated independently in a reverse osmosis treated water matrix limed with an aqueous solution of calcium hydroxide for 24-hr at 22 ± 5°C. In all R/O water trials, adenovirus type 5, rotavirus Wa and MS2 were below detectable levels (<100.5 TCID50/mL and <1 PFU/mL respectively) following 0.1-hr of liming. Adenovirus type 5, rotavirus Wa, and MS2, were inoculated into composted, raw and previously limed matrices, representative of sludge and biosolids, to achieve a final concentration of approximately 104 PFU or TCID50/mL. Each matrix was limed for 24-hr at 22 ± 5°C and 4 ± 2°C. In all trials virus was below detectable levels following a 24-hr incubation. The time required for viral inactivation varied depending on the temperature and sample matrix. This research demonstrates reduction of adenovirus type 5, rotavirus Wa, and male-specific bacteriophage, in water, sludge and biosolids matrices following addition of an 8% calcium hydroxide slurry to achieve a pH of 12 for 2-hr reduced to 11.5 for 22-hr by addition of 0.1 N HCl. In these trials, MS2 was a conservative indicator of the efficacy of lime stabilization of adenovirus Type 5 and rotavirus Wa and therefore is proposed as a useful indicator organism. PMID:17431317

Solution structure of the antitermination protein NusB of Escherichia coli: a novel all-helical fold for an RNA-binding protein.

PubMed Central

Huenges, M; Rölz, C; Gschwind, R; Peteranderl, R; Berglechner, F; Richter, G; Bacher, A; Kessler, H; Gemmecker, G

1998-01-01

The NusB protein of Escherichia coli is involved in the regulation of rRNA biosynthesis by transcriptional antitermination. In cooperation with several other proteins, it binds to a dodecamer motif designated rrn boxA on the nascent rRNA. The antitermination proteins of E.coli are recruited in the replication cycle of bacteriophage lambda, where they play an important role in switching from the lysogenic to the lytic cycle. Multidimensional heteronuclear NMR experiments were performed with recombinant NusB protein labelled with 13C, 15N and 2H. The three-dimensional structure of the protein was solved from 1926 NMR-derived distances and 80 torsion angle restraints. The protein folds into an alpha/alpha-helical topology consisting of six helices; the arginine-rich N-terminus appears to be disordered. Complexation of the protein with an RNA dodecamer equivalent to the rrn boxA site results in chemical shift changes of numerous amide signals. The overall packing of the protein appears to be conserved, but the flexible N-terminus adopts a more rigid structure upon RNA binding, indicating that the N-terminus functions as an arginine-rich RNA-binding motif (ARM). PMID:9670024

Expression of chimeric ras protein with OmpF signal peptide in Escherichia coli: localization of OmpF fusion protein in the inner membrane.

PubMed

Yamamoto, T; Okawa, N; Endo, T; Kaji, A

1991-08-01

The ras gene was fused with the DNA sequence of OmpF signal peptide or with the DNA sequence of OmpF signal peptide plus the amino terminal portion of the OmpF gene. They were placed in plasmids together with the bacteriophage lambda PL promoter. These plasmids were introduced into Escherichia coli strain K-12 and the OmpF signal peptide fusion proteins were expressed. These fusion proteins were identified as 29.0 and 30.0 kDa proteins. However, processed products of these proteins were not found in the extract. The fusion proteins were localized mostly in the cytoplasm and the inner membrane, but none of them was secreted into the periplasmic space. On the other hand, the ras protein alone was found in the cytoplasm and not in the inner membrane. Viable counts of E. coli harbouring these plasmids decreased when these fused proteins were induced. Induction of the ras protein alone did not harm cells. These observations suggest that insertion of the heterologous proteins into the inner membrane may cause the bactericidal effect.

Real-time multiplex PCR assay for detection of Yersinia pestis and Yersinia pseudotuberculosis.

PubMed

Matero, Pirjo; Pasanen, Tanja; Laukkanen, Riikka; Tissari, Päivi; Tarkka, Eveliina; Vaara, Martti; Skurnik, Mikael

2009-01-01

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 the plasminogen activator. In addition, the wzz gene was used as a target to specifically identify both Y. pestis and the closely related Y. pseudotuberculosis group. The primer and probe sets described for the different genes can be used either in single or in multiplex PCR assays because the individual probes were designed with different fluorochromes. The assays were found to be both sensitive and specific; the lower limit of the detection was 10-100 fg of extracted Y. pestis or Y. pseudotuberculosis total DNA. The sensitivity of the tetraplex assay was determined to be 1 cfu for the ypo2088 and pla probe labelled with FAM and JOE fluorescent dyes, respectively.

Occurrence and numbers of bacteriophages and bacterial indicators in faeces of yellow-legged seagull (Larus cachinnans).

PubMed

Muniesa, M; Jofre, J; Lucena, F

1999-12-01

Faeces from feral populations of yellow-legged seagulls from the northern coastal area of Catalonia (North-eastern Spain) contained variable amounts of faecal coliforms, faecal streptococci, somatic coliphages, F-specific bacteriophages and Bacteroides fragilis bacteriophages. Occurrence and numbers of bacterial indicators and bacteriophages in the faeces of yellow-legged seagulls are in the ranges described in the faeces of different animals. The ratios between numbers of bacterial indicators and numbers of bacteriophages are much higher in faeces of seagulls than in treated or raw sewage contributed by out-falls of the same area.

Bacteriophages in dairy products: pros and cons.

PubMed

Mc Grath, Stephen; Fitzgerald, Gerald F; van Sinderen, Douwe

2007-04-01

Since the time bacteriophages were first identified as a major cause of fermentation failure in the dairy industry, researchers have been struggling to develop strategies to exclude them from the dairy environment. Over 70 years of research has led to huge improvements in the consistency and quality of fermented dairy products, while also facilitating an appreciation of the beneficial properties of bacteriophages with respect to dairy product development. With specific reference to Lactococcus lactis and cheese production, this review outlines some recently reported novel methods aimed at limiting the bacteriophage infection as well as highlighting some beneficial aspects of bacteriophage activity.

Removal of MS2, Qβ and GA bacteriophages during drinking water treatment at pilot scale.

PubMed

Boudaud, Nicolas; Machinal, Claire; David, Fabienne; Fréval-Le Bourdonnec, Armelle; Jossent, Jérôme; Bakanga, Fanny; Arnal, Charlotte; Jaffrezic, Marie Pierre; Oberti, Sandrine; Gantzer, Christophe

2012-05-15

The removal of MS2, Qβ and GA, F-specific RNA bacteriophages, potential surrogates for pathogenic waterborne viruses, was investigated during a conventional drinking water treatment at pilot scale by using river water, artificially and independently spiked with these bacteriophages. The objective of this work is to develop a standard system for assessing the effectiveness of drinking water plants with respect to the removal of MS2, Qβ and GA bacteriophages by a conventional pre-treatment process (coagulation-flocculation-settling-sand filtration) followed or not by an ultrafiltration (UF) membrane (complete treatment process). The specific performances of three UF membranes alone were assessed by using (i) pre-treated water and (ii) 0.1 mM sterile phosphate buffer solution (PBS), spiked with bacteriophages. These UF membranes tested in this work were designed for drinking water treatment market and were also selected for research purpose. The hypothesis serving as base for this study was that the interfacial properties for these three bacteriophages, in terms of electrostatic charge and the degree of hydrophobicity, could induce variations in the removal performances achieved by drinking water treatments. The comparison of the results showed a similar behaviour for both MS2 and Qβ surrogates whereas it was particularly atypical for the GA surrogate. The infectious character of MS2 and Qβ bacteriophages was mostly removed after clarification followed by sand filtration processes (more than a 4.8-log reduction) while genomic copies were removed at more than a 4.0-log after the complete treatment process. On the contrary, GA bacteriophage was only slightly removed by clarification followed by sand filtration, with less than 1.7-log and 1.2-log reduction, respectively. After the complete treatment process achieved, GA bacteriophage was removed with less than 2.2-log and 1.6-log reduction, respectively. The effectiveness of the three UF membranes tested in terms of bacteriophages removal showed significant differences, especially for GA bacteriophage. These results could provide recommendations for drinking water suppliers in terms of selection criteria for membranes. MS2 bacteriophage is widely used as a surrogate for pathogenic waterborne viruses in Europe and the United States. In this study, the choice of MS2 bacteriophage as the best surrogate to be used for assessment of the effectiveness of drinking water treatment in removal of pathogenic waterborne viruses in worst conditions is clearly challenged. It was shown that GA bacteriophage is potentially a better surrogate as a worst case than MS2. Considering GA bacteriophage as the best surrogate in this study, a chlorine disinfection step could guaranteed a complete removal of this model and ensure the safety character of drinking water plants. Copyright © 2012 Elsevier Ltd. All rights reserved.

Productive performance of weanling piglets was improved by administration of a mixture of bacteriophages, targeted to control Coliforms and Clostridium spp. shedding in a challenging environment.

PubMed

Hosseindoust, A R; Lee, S H; Kim, J S; Choi, Y H; Kwon, I K; Chae, B J

2017-10-01

This study was conducted to investigate the effects of bacteriophages in different environments on growth performance, digestibility, ileal and caecal microbiota, gut morphology and immunity of weanling pigs. Two hundred piglets were randomly assigned to four treatment groups with five replicate pens with 10 pigs per pen. A 2 × 2 factorial arrangement of treatments was used to investigate the response of weanling pigs to supplemental bacteriophages (0 and 1.0 g/kg of diet) in contaminated or hygienic environments. Bacteriophages supplementation did not affect average daily gain (ADG), average daily feed intake (ADFI) and gain:feed in phases I and III; however, there was a significant improvement in ADG and gain:feed in phase II. The supplementation of bacteriophages increased the overall gain:feed of pigs. The overall result showed a greater ADG and ADFI in hygienic room. There were reductions in population of both ileal (p < 0.05) and caecal (p < 0.01) Clostridium spp. and ileal coliforms (p < 0.01) with the inclusion of bacteriophages in the diet. Bacteriophages increased ileal Lactobacillus and caecal Bifidobacterium and tended to increase ileal Bifidobacterium (p = 0.08). Contaminated environment decreased ileal Lactobacillus and caecal Bifidobacterium and tended to increase ileal Clostridium (p = 0.08) and coliforms (p = 0.08). Total anaerobic bacteria was tended to decrease (p = 0.06) in contaminated environment. Jejunal villus height increased in pigs received bacteriophages, but they did not affect other morphological items. The interaction between bacteriophages and environment tended to be significant (p = 0.06) for ileal villus height and ileal villus height to crypt depth ratio. The overall faecal score was significantly greater in hygienic environment and bacteriophages groups. The present findings indicate that there is an interactive effect on feed efficiency between bacteriophages and contaminated environment. In addition, bacteriophages improve jejunum morphology, and intestinal microbiota of pigs. Journal of Animal Physiology and Animal Nutrition © 2016 Blackwell Verlag GmbH.

Convection-enhanced delivery of M13 bacteriophage to the brain

PubMed Central

Ksendzovsky, Alexander; Walbridge, Stuart; Saunders, Richard C.; Asthagiri, Ashok R.; Heiss, John D.; Lonser, Russell R.

2013-01-01

Object Recent studies indicate that M13 bacteriophage, a very large nanoparticle, binds to β-amyloid and α-synuclein proteins, leading to plaque disaggregation in models of Alzheimer and Parkinson disease. To determine the feasibility, safety, and characteristics of convection-enhanced delivery (CED) of M13 bacteriophage to the brain, the authors perfused primate brains with bacteriophage. Methods Four nonhuman primates underwent CED of M13 bacteriophage (900 nm) to thalamic gray matter (4 infusions) and frontal white matter (3 infusions). Bacteriophage was coinfused with Gd-DTPA (1 mM), and serial MRI studies were performed during infusion. Animals were monitored for neurological deficits and were killed 3 days after infusion. Tissues were analyzed for bacteriophage distribution. Results Real-time T1-weighted MRI studies of coinfused Gd-DTPA during infusion demonstrated a discrete region of perfusion in both thalamic gray and frontal white matter. An MRI-volumetric analysis revealed that the mean volume of distribution (Vd) to volume of infusion (Vi) ratio of M13 bacteriophage was 2.3 ± 0.2 in gray matter and 1.9 ± 0.3 in white matter. The mean values are expressed ± SD. Immunohistochemical analysis demonstrated mean Vd:Vi ratios of 2.9 ± 0.2 in gray matter and 2.1 ± 0.3 in white matter. The Gd-DTPA accurately tracked M13 bacteriophage distribution (the mean difference between imaging and actual bacteriophage Vd was insignificant [p > 0.05], and was −2.2% ± 9.9% in thalamic gray matter and 9.1% ± 9.5% in frontal white matter). Immunohistochemical analysis revealed evidence of additional spread from the initial delivery site in white matter (mean Vd:Vi, 16.1 ± 9.1). All animals remained neurologically intact after infusion during the observation period, and histological studies revealed no evidence of toxicity. Conclusions The CED method can be used successfully and safely to distribute M13 bacteriophage in the brain. Furthermore, additional white matter spread after infusion cessation enhances distribution of this large nanoparticle. Real-time MRI studies of coinfused Gd-DTPA (1 mM) can be used for accurate tracking of distribution during infusion of M13 bacteriophage. PMID:22606981

Convection-enhanced delivery of M13 bacteriophage to the brain.

PubMed

Ksendzovsky, Alexander; Walbridge, Stuart; Saunders, Richard C; Asthagiri, Ashok R; Heiss, John D; Lonser, Russell R

2012-08-01

Recent studies indicate that M13 bacteriophage, a very large nanoparticle, binds to β-amyloid and α-synuclein proteins, leading to plaque disaggregation in models of Alzheimer and Parkinson disease. To determine the feasibility, safety, and characteristics of convection-enhanced delivery (CED) of M13 bacteriophage to the brain, the authors perfused primate brains with bacteriophage. Four nonhuman primates underwent CED of M13 bacteriophage (900 nm) to thalamic gray matter (4 infusions) and frontal white matter (3 infusions). Bacteriophage was coinfused with Gd-DTPA (1 mM), and serial MRI studies were performed during infusion. Animals were monitored for neurological deficits and were killed 3 days after infusion. Tissues were analyzed for bacteriophage distribution. Real-time T1-weighted MRI studies of coinfused Gd-DTPA during infusion demonstrated a discrete region of perfusion in both thalamic gray and frontal white matter. An MRI-volumetric analysis revealed that the mean volume of distribution (Vd) to volume of infusion (Vi) ratio of M13 bacteriophage was 2.3 ± 0.2 in gray matter and 1.9 ± 0.3 in white matter. The mean values are expressed ± SD. Immunohistochemical analysis demonstrated mean Vd:Vi ratios of 2.9 ± 0.2 in gray matter and 2.1 ± 0.3 in white matter. The Gd-DTPA accurately tracked M13 bacteriophage distribution (the mean difference between imaging and actual bacteriophage Vd was insignificant [p > 0.05], and was -2.2% ± 9.9% in thalamic gray matter and 9.1% ± 9.5% in frontal white matter). Immunohistochemical analysis revealed evidence of additional spread from the initial delivery site in white matter (mean Vd:Vi, 16.1 ± 9.1). All animals remained neurologically intact after infusion during the observation period, and histological studies revealed no evidence of toxicity. The CED method can be used successfully and safely to distribute M13 bacteriophage in the brain. Furthermore, additional white matter spread after infusion cessation enhances distribution of this large nanoparticle. Real-time MRI studies of coinfused Gd-DTPA (1 mM) can be used for accurate tracking of distribution during infusion of M13 bacteriophage.

An Ensemble Method to Distinguish Bacteriophage Virion from Non-Virion Proteins Based on Protein Sequence Characteristics.

PubMed

Zhang, Lina; Zhang, Chengjin; Gao, Rui; Yang, Runtao

2015-09-09

Bacteriophage virion proteins and non-virion proteins have distinct functions in biological processes, such as specificity determination for host bacteria, bacteriophage replication and transcription. Accurate identification of bacteriophage virion proteins from bacteriophage protein sequences is significant to understand the complex virulence mechanism in host bacteria and the influence of bacteriophages on the development of antibacterial drugs. In this study, an ensemble method for bacteriophage virion protein prediction from bacteriophage protein sequences is put forward with hybrid feature spaces incorporating CTD (composition, transition and distribution), bi-profile Bayes, PseAAC (pseudo-amino acid composition) and PSSM (position-specific scoring matrix). When performing on the training dataset 10-fold cross-validation, the presented method achieves a satisfactory prediction result with a sensitivity of 0.870, a specificity of 0.830, an accuracy of 0.850 and Matthew's correlation coefficient (MCC) of 0.701, respectively. To evaluate the prediction performance objectively, an independent testing dataset is used to evaluate the proposed method. Encouragingly, our proposed method performs better than previous studies with a sensitivity of 0.853, a specificity of 0.815, an accuracy of 0.831 and MCC of 0.662 on the independent testing dataset. These results suggest that the proposed method can be a potential candidate for bacteriophage virion protein prediction, which may provide a useful tool to find novel antibacterial drugs and to understand the relationship between bacteriophage and host bacteria. For the convenience of the vast majority of experimental Int. J. Mol. Sci. 2015, 16,21735 scientists, a user-friendly and publicly-accessible web-server for the proposed ensemble method is established.

Application of bacteriophages to reduce Salmonella contamination on workers' boots in rendering-processing environment.

PubMed

Gong, C; Jiang, X; Wang, J

2017-10-01

Workers' boots are considered one of the re-contamination routes of Salmonella for rendered meals in the rendering-processing environment. This study was conducted to evaluate the efficacy of a bacteriophage cocktail for reducing Salmonella on workers' boots and ultimately for preventing Salmonella re-contamination of rendered meals. Under laboratory conditions, biofilms of Salmonella Typhimurium avirulent strain 8243 formed on rubber templates or boots were treated with a bacteriophage cocktail of 6 strains (ca. 9 log PFU/mL) for 6 h at room temperature. Bacteriophage treatments combined with sodium hypochlorite (400 ppm) or 30-second brush scrubbing also were investigated for a synergistic effect on reducing Salmonella biofilms. Sodium magnesium (SM) buffer and sodium hypochlorite (400 ppm) were used as controls. To reduce indigenous Salmonella on workers' boots, a field study was conducted to apply a bacteriophage cocktail and other combined treatments 3 times within one wk in a rendering-processing environment. Prior to and after bacteriophage treatments, Salmonella populations on the soles of rubber boots were swabbed and enumerated on XLT-4, Miller-Mallinson or CHROMagar™ plates. Under laboratory conditions, Salmonella biofilms formed on rubber templates and boots were reduced by 95.1 to 99.999% and 91.5 to 99.2%, respectively. In a rendering-processing environment (ave. temperature: 19.3°C; ave. relative humidity: 48%), indigenous Salmonella populations on workers' boots were reduced by 84.2, 92.9, and 93.2% after being treated with bacteriophages alone, bacteriophages + sodium hypochlorite, and bacteriophages + scrubbing for one wk, respectively. Our results demonstrated the effectiveness of bacteriophage treatments in reducing Salmonella contamination on the boots in both laboratory and the rendering-processing environment. © 2017 Poultry Science Association Inc.

Bacteriophage cocktail and multi-strain probiotics in the feed for weanling pigs: effects on intestine morphology and targeted intestinal coliforms and Clostridium.

PubMed

Kim, J S; Hosseindoust, A; Lee, S H; Choi, Y H; Kim, M J; Lee, J H; Kwon, I K; Chae, B J

2017-01-01

Two experiments were conducted to investigate the effects of dietary supplementation of bacteriophage cocktail, probiotics and a combination of these two supplements on performance and gut health of weanling pigs. In Experiment 1, 150 weaned piglets were randomly allotted to three treatments on the basis of BW. The dietary treatments included a basal diet supplemented with 0 (control), 1.0 and 1.5 g/kg bacteriophage cocktail. Pigs fed 1.0 and 1.5 g/kg bacteriophage product had greater (P<0.05) average daily gain (ADG), apparent total tract digestibility of dry matter from day 22 to 35, ileal Lactobacillus spp., villus height (duodenum and jejunum), and fewer coliforms (ileum) and Clostridium spp. (ileum). In Experiment 2, 200 weaned piglets were randomly allotted to four treatments. Dietary treatments included basal diet, basal diet supplemented with 3.0 g/kg fermented probiotic product (P), 1.0 g/kg bacteriophage cocktail (B) and combination of 1.0 g/kg bacteriophage cocktail and 3.0 g/kg fermented probiotic product. Pigs fed bacteriophage cocktail diets had greater (P<0.05) overall ADG, gain to feed ratio (G : F), fecal score from day 8 to day 21, and pigs fed bacteriophage cocktail diets had fewer coliforms (ileum) Clostridium spp. (ileum and cecum). Probiotics significantly increased G : F, colonization of Lactobacillus spp. in ileum. At day 35, bacteriophage treatment group showed greater (P<0.05) villus height of the duodenum, but a deeper crypt in duodenum. The present results indicate that the bacteriophage cocktail had a potential to enhance the performance and gut health of weanling pigs, however their combination with probiotics did not show an interaction.

Bacteriophages Infecting Propionibacterium acnes

PubMed Central

2013-01-01

Viruses specifically infecting bacteria, or bacteriophages, are the most common biological entity in the biosphere. As such, they greatly influence bacteria, both in terms of enhancing their virulence and in terms of killing them. Since the first identification of bacteriophages in the beginning of the 20th century, researchers have been fascinated by these microorganisms and their ability to eradicate bacteria. In this review, we will cover the history of the Propionibacterium acnes bacteriophage research and point out how bacteriophage research has been an important part of the research on P. acnes itself. We will further discuss recent findings from phage genome sequencing and the identification of phage sequence signatures in clustered regularly interspaced short palindromic repeats (CRISPRs). Finally, the potential to use P. acnes bacteriophages as a therapeutic strategy to combat P. acnes-associated diseases will be discussed. PMID:23691509

Bacteriophages as indicators of faecal pollution and enteric virus removal.

PubMed

McMinn, B R; Ashbolt, N J; Korajkic, A

2017-07-01

Bacteriophages are an attractive alternative to faecal indicator bacteria (FIB), particularly as surrogates of enteric virus fate and transport, due to their closer morphological and biological properties. Based on a review of published data, we summarize densities of coliphages (F+ and somatic), Bacteroides spp. and enterococci bacteriophages (phages) in individual human waste, raw wastewater, ambient fresh and marine waters and removal through wastewater treatment processes utilizing traditional treatments. We also provide comparisons with FIB and enteric viruses whenever possible. Lastly, we examine fate and transport characteristics in the aquatic environment and provide an overview of the environmental factors affecting their survival. In summary, concentrations of bacteriophages in various sources were consistently lower than FIB, but more reflective of infectious enteric virus levels. Overall, our investigation indicates that bacteriophages may be adequate viral surrogates, especially in built systems, such as wastewater treatment plants. Bacteriophage are alternative fecal indicators that may be better surrogates for viral pathogens than fecal indicator bacteria (FIB). This report offers a summary of the existing literature concerning the utility of bacteriophage as indicators of viral presence (fecal sources and surface waters) and persistence (in built infrastructure and aquatic environments). Our findings indicate that bacteriophage levels in all matrices examined are consistently lower than FIB, but similar to viral pathogens. Furthermore, in built infrastructure (e.g. wastewater treatment systems) bacteriophage closely mimic viral pathogen persistence suggesting they may be adequate sentinels of enteric virus removal. © 2017 The Society for Applied Microbiology.

Tables of Transition Probabilities and Branching Ratios for Electric Dipole Transitions Between Arbitrary Levels of Hydrogen-Like Atoms

NASA Technical Reports Server (NTRS)

Omidvar, K.

1980-01-01

Branching ratios in hydrogen-like atoms due to electric-dipole transitions are tabulated for the initial principal and angular momentum quantum number n, lambda, and final principal and angular momentum quantum numbers n, lambda. In table 1, transition probabilities are given for transitions n, lambda, yields n, where sums have been made with respect to lambda. In this table, 2 or = n' or = 10, o or = lambda' or = n'-1, and 1 or = n or = n'-1. In addition, averages with respect to lambda' and sums with respect to n, and lifetimes are given. In table 2, branching ratios are given for transitions n' lambda' yields ni, where sums have been made with respect to lambda. In these tables, 2 or = n' or = 10, 0 or = lambda', n'-1, and 1 or = n or = n'-1. Averages with respect to lambda' are also given. In table 3, branching ratios are given for transitions n' lambda' yields in lambda, where 1 or = n or = 5, 0 or = lambda or = n-1, n n' or = 15, and 0 or = lambda' or = n(s), where n(s), is the smaller of the two numbers n'-1 and 6. Averages with respect to lambda' are given.

Measurement of the Λ b cross section and the Λ ¯ b to Λ b ratio with J / ψ Λ decays in pp collisions at s = 7 TeV

DOE PAGES

Chatrchyan, S.; Khachatryan, V.; Sirunyan, A. M.; ...

2012-05-31

The Lambda(b) differential production cross section and the cross section ratio anti-Lambda(b)/Lambda(b) are measured as functions of transverse momentum pt(Lambda(b)) and rapidity abs(y(Lambda(b))) in pp collisions at sqrt(s) = 7 TeV using data collected by the CMS experiment at the LHC. The measurements are based on Lambda(b) decays reconstructed in the exclusive final state J/Psi Lambda, with the subsequent decays J/Psi to an opposite-sign muon pair and Lambda to proton pion, using a data sample corresponding to an integrated luminosity of 1.9 inverse femtobarns. The product of the cross section times the branching ratio for Lambda(b) to J/Psi Lambda versusmore » pt(Lambda(b)) falls faster than that of b mesons. The measured value of the cross section times the branching ratio for pt(Lambda(b)) > 10 GeV and abs(y(Lambda(b))) < 2.0 is 1.06 +/- 0.06 +/- 0.12 nb, and the integrated cross section ratio for anti-Lambda(b)/Lambda(b) is 1.02 +/- 0.07 +/- 0.09, where the uncertainties are statistical and systematic, respectively.« less

{lambda}{sub b}{yields}p, {lambda} transition form factors from QCD light-cone sum rules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang Yuming; Lue Caidian; Shen Yuelong

2009-10-01

Light-cone sum rules for the {lambda}{sub b}{yields}p, {lambda} transition form factors are derived from the correlation functions expanded by the twist of the distribution amplitudes of the {lambda}{sub b} baryon. In terms of the {lambda}{sub b} three-quark distribution amplitude models constrained by the QCD theory, we calculate the form factors at small momentum transfers and compare the results with those estimated in the conventional light-cone sum rules (LCSR) and perturbative QCD approaches. Our results indicate that the two different versions of sum rules can lead to the consistent numbers of form factors responsible for {lambda}{sub b}{yields}p transition. The {lambda}{sub b}{yields}{lambda}more » transition form factors from LCSR with the asymptotic {lambda} baryon distribution amplitudes are found to be almost 1 order larger than those obtained in the {lambda}{sub b}-baryon LCSR, implying that the preasymptotic corrections to the baryonic distribution amplitudes are of great importance. Moreover, the SU(3) symmetry breaking effects between the form factors f{sub 1}{sup {lambda}{sub b}}{sup {yields}}{sup p} and f{sub 1}{sup {lambda}{sub b}}{sup {yields}}{sup {lambda}} are computed as 28{sub -8}{sup +14}% in the framework of {lambda}{sub b}-baryon LCSR.« less

First observation and measurement of the resonant structure of the lambda_b->lambda_c pi-pi+pi- decay mode

DOE Office of Scientific and Technical Information (OSTI.GOV)

Azzurri, P.; Barria, P.; Ciocci, M.A.

The authors present the first observation of the {Lambda}{sub b}{sup 0} {yields} {Lambda}{sub c}{sup +}{pi}{sup -}{pi}{sup +}{pi}{sup -} decay using data from an integrated luminosity of approximately 2.4 fb{sup -1} of p{bar p} collisions at {radical}s = 1.96 TeV, collected with the CDF II detector at the Fermilab Tevatron. They also present the first observation of the resonant decays {Lambda}{sub b}{sup 0} {yields} {Sigma}{sub c}(2455){sup 0} {pi}{sup +}{pi}{sup -} {yields} {Lambda}{sub c}{sup +}{pi}{sup -}{pi}{sup +}{pi}{sup -}, {Lambda}{sub b}{sup 0} {yields} {Sigma}{sub c}(2455){sup ++}{pi}{sup -}{pi}{sup -} {yields} {Lambda}{sub c}{sup +}{pi}{sup -}{pi}{sup +}{pi}{sup -}, {Lambda}{sub b}{sup 0} {yields} {Lambda}{sub c}(2595){sup +}{pi}{sup -}more » {yields} {Lambda}{sub c}{sup +}{pi}{sup -}{pi}{sup +}{pi}{sup -} and {Lambda}{sub b}{sup 0} {yields} {Lambda}{sub c}(2625){sup +}{pi}{sup -} {yields} {Lambda}{sub c}{sup +}{pi}{sup -}{pi}{sup +}{pi}{sup -}, and measure their relative branching ratios.« less

Spin correlations in the {Lambda}{Lambda} and {Lambda}{Lambda}-bar systems generated in relativistic heavy-ion collisions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lyuboshitz, V. L.; Lyuboshitz, V. V., E-mail: Valery.Lyuboshitz@jinr.r

2010-05-15

Spin correlations for the {Lambda}{Lambda} and {Lambda}{Lambda}-bar pairs, generated in relativistic heavy-ion collisions, and related angular correlations at the joint registration of hadronic decays of two hyperons, in which space parity is not conserved, are analyzed. The correlation tensor components can be derived from the double angular distribution of products of two decays by the method of 'moments'. The properties of the 'trace' of the correlation tensor (a sum of three diagonal components), determining the relative fractions of the triplet states and singlet state of respective pairs, are discussed. Spin correlations for two identical particles ({Lambda}{Lambda}) and two nonidentical particlesmore » ({Lambda}{Lambda}-bar) are considered from the viewpoint of the conventional model of one-particle sources. In the framework of this model, correlations vanish at sufficiently large relative momenta. However, under these conditions, in the case of two nonidentical particles ({Lambda}{Lambda}-bar) a noticeable role is played by two-particle annihilation (two-quark, two-gluon) sources, which lead to the difference of the correlation tensor from zero. In particular, such a situation may arise when the system passes through the 'mixed phase.'« less

A review of current methods using bacteriophages in live animals, food and animal products intended for human consumption.

PubMed

Cooper, Ian R

2016-11-01

Bacteriophages are utilised in the food industry as biocontrol agents to reduce the load of bacteria, and thus reduce potential for human infection. This review focuses on current methods using bacteriophages within the food chain. Limitations of research will be discussed, and the potential for future food-based bacteriophage research. Copyright © 2016 Elsevier B.V. All rights reserved.

Toward modern inhalational bacteriophage therapy: nebulization of bacteriophages of Burkholderia cepacia complex.

PubMed

Golshahi, Laleh; Seed, Kimberley D; Dennis, Jonathan J; Finlay, Warren H

2008-12-01

Antibiotic-resistant bacterial infections have renewed interest in finding substitute methods of treatment. The purpose of the present in vitro study was to investigate the possibility of respiratory delivery of a Burkholderia cepacia complex (BCC) bacteriophage by nebulized aerosol administration. Bacteriophages in isotonic saline were aerosolized with Pari LC star and eFlow nebulizers, at titers with mean value (standard deviation) of 2.15 x 10(8) (1.63 x 10(8)) plaque-forming unit (PFU)/mL in 2.5-mL nebulizer fills. The breathing pattern of an adult was simulated using a pulmonary waveform generator. During breath simulation, the size distributions of the nebulized aerosol were measured using phase doppler anemometry (PDA). Efficiency of nebulizer delivery was subsequently determined by collection of aerosol on low resistance filters and measurement of bacteriophage titers. These filter titers were used as input data to a mathematical lung deposition model to predict regional deposition of bacteriophages in the lung and initial bacteriophage titers in the liquid surface layer of each conducting airway generation. The results suggest that BCC bacteriophages can be nebulized successfully within a reasonable delivery time and predicted titers in the lung indicate that this method may hold potential for treatment of bacterial lung infections common among cystic fibrosis patients.

Campylobacter bacteriophages and bacteriophage therapy.

PubMed

Connerton, P L; Timms, A R; Connerton, I F

2011-08-01

Members of the genus Campylobacter are frequently responsible for human enteric disease with occasionally very serious outcomes. Much of this disease burden is thought to arise from consumption of contaminated poultry products. More than 80% of poultry in the UK harbour Campylobacter as a part of their intestinal flora. To address this unacceptably high prevalence, various interventions have been suggested and evaluated. Among these is the novel approach of using Campylobacter-specific bacteriophages, which are natural predators of the pathogen. To optimize their use as therapeutic agents, it is important to have a comprehensive understanding of the bacteriophages that infect Campylobacter, and how they can affect their host bacteria. This review will focus on many aspects of Campylobacter-specific bacteriophages including: their first isolation in the 1960s, their use in bacteriophage typing schemes, their isolation from the different biological sources and genomic characterization. As well as their use as therapeutic agents to reduce Campylobacter in poultry their future potential, including their use in bio-sanitization of food, will be explored. The evolutionary consequences of naturally occurring bacteriophage infection that have come to light through investigations of bacteriophages in the poultry ecosystem will also be discussed. © 2011 The Authors. Journal of Applied Microbiology © 2011 The Society for Applied Microbiology.

Predicting In Vivo Efficacy of Therapeutic Bacteriophages Used To Treat Pulmonary Infections

PubMed Central

Henry, Marine; Lavigne, Rob

2013-01-01

The potential of bacteriophage therapy to treat infections caused by antibiotic-resistant bacteria has now been well established using various animal models. While numerous newly isolated bacteriophages have been claimed to be potential therapeutic candidates on the basis of in vitro observations, the parameters used to guide their choice among billions of available bacteriophages are still not clearly defined. We made use of a mouse lung infection model and a bioluminescent strain of Pseudomonas aeruginosa to compare the activities in vitro and in vivo of a set of nine different bacteriophages (PAK_P1, PAK_P2, PAK_P3, PAK_P4, PAK_P5, CHA_P1, LBL3, LUZ19, and PhiKZ). For seven bacteriophages, a good correlation was found between in vitro and in vivo activity. While the remaining two bacteriophages were active in vitro, they were not sufficiently active in vivo under similar conditions to rescue infected animals. Based on the bioluminescence recorded at 2 and 8 h postinfection, we also define for the first time a reliable index to predict treatment efficacy. Our results showed that the bacteriophages isolated directly on the targeted host were the most efficient in vivo, supporting a personalized approach favoring an optimal treatment. PMID:24041900

Virulent Bacteriophages Can Target O104:H4 Enteroaggregative Escherichia coli in the Mouse Intestine

PubMed Central

Maura, Damien; Galtier, Matthieu; Le Bouguénec, Chantal

2012-01-01

In vivo bacteriophage targeting of enteroaggregative Escherichia coli (EAEC) was assessed using a mouse intestinal model of colonization with the O104:H4 55989Str strain and a cocktail of three virulent bacteriophages. The colonization model was shown to mimic asymptomatic intestinal carriage found in humans. The addition of the cocktail to drinking water for 24 h strongly decreased ileal and weakly decreased fecal 55989Str concentrations in a dose-dependent manner. These decreases in ileal and fecal bacterial concentrations were only transient, since 55989Str concentrations returned to their original levels 3 days later. These transient decreases were independent of the mouse microbiota, as similar results were obtained with axenic mice. We studied the infectivity of each bacteriophage in the ileal and fecal environments and found that 55989Str bacteria in the mouse ileum were permissive to all three bacteriophages, whereas those in the feces were permissive to only one bacteriophage. Our results provide the first demonstration that bacterial permissivity to infection with virulent bacteriophages is not uniform throughout the gut; this highlights the need for a detailed characterization of the interactions between bacteria and bacteriophages in vivo for the further development of phage therapy targeting intestinal pathogens found in the gut of asymptomatic human carriers. PMID:23006754

Streptococcus mutans genes that code for extracellular proteins in Escherichia coli K-12.

PubMed

Holt, R G; Abiko, Y; Saito, S; Smorawinska, M; Hansen, J B; Curtiss, R

1982-10-01

Chromosomal DNA from Streptococcus mutans 6715 (serotype g) was cloned into Escherichia coli K-12 by using the cosmid pJC74 cloning vector and a bacteriophage lambda in vitro packaging system. Rabbit antiserum against S. mutans extracellular proteins was used for immunological screening of the clone bank. Twenty-one clones produced weak to strong precipitin bands around the colonies, but only after the lambda c1857 prophage was induced by being heated to lyse the E. coli cells. None of the clones expressed enzyme activity for several known S. mutans extracellular enzymes. One of these clones contained a 45-kilobase recombinant plasmid designated pYA721. An 8.5-kilobase fragment of S. mutans DNA from pYA721 was isolated and recloned into the BamHI restriction site of the plasmid vector pACYC184 to construct pYA726. pYA726 contained all, or nearly all, of the gene for a surface protein antigen (the spaA protein) of S. mutans 6715. This was deduced from immunological studies in which extracts of cells harboring pYA726 reacted with antisera against both purified 6715 spaA protein (about 210,000 daltons) and the immunologically similar antigen I/II of serotype c strains of S. mutans. In addition, the S. mutans spaA protein was found to possess at least one antigenic determinant not present on the protein specified by pYA726. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of E. coli clone extracts revealed that pYA726 produced a polypeptide with a molecular mass of about 180,000 daltons which was predominantly found in the periplasmic space of E. coli cells. Antisera to the spaA protein of S. mutans reacted with extracellular protein from representative strains of S. mutans serotypes a, c, d, e, f, and g, but not b.

How does gravity save or kill Q-balls?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tamaki, Takashi; Sakai, Nobuyuki; Department of Education, Yamagata University, Yamagata 990-8560

2011-02-15

We explore stability of gravitating Q-balls with potential V{sub 4}({phi})=(m{sup 2}/2){phi}{sup 2}-{lambda}{phi}{sup 4}+({phi}{sup 6}/M{sup 2}) via catastrophe theory, as an extension of our previous work on Q-balls with potential V{sub 3}({phi})=(m{sup 2}/2){phi}{sup 2}-{mu}{phi}{sup 3}+{lambda}{phi}{sup 4}. In flat spacetime Q-balls with V{sub 4} in the thick-wall limit are unstable and there is a minimum charge Q{sub min}, where Q-balls with Q

Bacteriophage-based synthetic biology for the study of infectious diseases

PubMed Central

Lu, Timothy K.

2014-01-01

Since their discovery, bacteriophages have contributed enormously to our understanding of molecular biology as model systems. Furthermore, bacteriophages have provided many tools that have advanced the fields of genetic engineering and synthetic biology. Here, we discuss bacteriophage-based technologies and their application to the study of infectious diseases. New strategies for engineering genomes have the potential to accelerate the design of novel phages as therapies, diagnostics, and tools. Though almost a century has elapsed since their discovery, bacteriophages continue to have a major impact on modern biological sciences, especially with the growth of multidrug-resistant bacteria and interest in the microbiome. PMID:24997401

UTILIZING SYNTHETIC UV SPECTRA TO EXPLORE THE PHYSICAL BASIS FOR THE CLASSIFICATION OF LAMBDA BOÖTIS STARS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, Kwang-Ping; Johnson, Dustin M.; Tarbell, Erik S.

2016-04-15

Lambda Boo-type stars are a group of late B to early F-type Population I dwarfs that show mild to extreme deficiencies of iron-peak elements (up to 2 dex), but their C, N, O, and S abundances are near solar. This intriguing stellar class has recently regained the spotlight because of the directly imaged planets around a confirmed Lambda Boo star, HR 8799, and a suggested Lambda Boo star, Beta Pictoris. The discovery of a giant asteroid belt around Vega, another possible Lambda Boo star, also suggests hidden planets. The possible link between Lambda Boo stars and planet-bearing stars motivates usmore » to study Lambda Boo stars systematically. Since the peculiar nature of the prototype Lambda Boötis was first noticed in 1943, Lambda Boo candidates published in the literature have been selected using widely different criteria. In order to determine the origin of Lambda Boo stars’ unique abundance pattern and to better discriminate between theories explaining the Lambda Boo phenomenon, a consistent working definition of Lambda Boo stars is needed. We have re-evaluated all published Lambda Boo candidates and their available ultraviolet and visible spectra. In this paper, using observed and synthetic spectra, we explore the physical basis for the classification of Lambda Boo stars, and develop quantitative criteria that discriminate metal-poor stars from bona fide Lambda Boo stars. Based on these stricter Lambda Boo classification criteria, we conclude that neither Beta Pictoris nor Vega should be classified as Lambda Boo stars.« less

Simulated hatchery system to assess bacteriophage efficacy against Vibrio harveyi.

PubMed

Raghu Patil, J; Desai, Srividya Narayanamurthy; Roy, Panchali; Durgaiah, Murali; Saravanan, R Sanjeev; Vipra, Aradhana

2014-12-02

Vibriosis caused by luminous Vibrio harveyi commonly contributes to poor survival in shrimp hatcheries and aquaculture ponds. Lytic bacteriophages pathogenic for V. harveyi are currently being investigated as an alternative to antibiotics to prevent vibriosis. Here, 8 bacteriophages were isolated from oysters and clams using V. harveyi strains as baiting hosts. Among these bacteriophages, 1 strain (VHP6b) identified as broadly pathogenic for 27 V. harveyi strains examined was further characterized by electron microscopy and genome sequence analysis. Phage VHP6b possessed a tail and morphology consistent with it being a member of the family Siphoviridae, and its genome and proteome were most closely related to the Vibrio phages SSP02 and MAR10. An integrase gene essential for lysogeny was not evident. The ability of bacteriophage VHP6b to protect shrimp postlarvae against vibriosis caused by V. harveyi strain VH6 was demonstrated in a model system designed to simulate typical hatchery conditions. Bacteriophage treatment improved survival of postlarvae by 40 to 60% under these conditions, so therapies based on this or other bacteriophages may be useful in shrimp hatcheries.

Taking Bacteriophage Therapy Seriously: A Moral Argument

PubMed Central

Verbeken, Gilbert; Huys, Isabelle; Jennes, Serge; Chanishvili, Nina; Górski, Andrzej; De Vos, Daniel

2014-01-01

The excessive and improper use of antibiotics has led to an increasing incidence of bacterial resistance. In Europe the yearly number of infections caused by multidrug resistant bacteria is more than 400.000, each year resulting in 25.000 attributable deaths. Few new antibiotics are in the pipeline of the pharmaceutical industry. Early in the 20th century, bacteriophages were described as entities that can control bacterial populations. Although bacteriophage therapy was developed and practiced in Europe and the former Soviet republics, the use of bacteriophages in clinical setting was neglected in Western Europe since the introduction of traditional antibiotics. Given the worldwide antibiotic crisis there is now a growing interest in making bacteriophage therapy available for use in modern western medicine. Despite the growing interest, access to bacteriophage therapy remains highly problematic. In this paper, we argue that the current state of affairs is morally unacceptable and that all stakeholders (pharmaceutical industry, competent authorities, lawmakers, regulators, and politicians) have the moral duty and the shared responsibility towards making bacteriophage therapy urgently available for all patients in need. PMID:24868534

Bacteriophages and Biofilms

PubMed Central

Harper, David R.; Parracho, Helena M. R. T.; Walker, James; Sharp, Richard; Hughes, Gavin; Werthén, Maria; Lehman, Susan; Morales, Sandra

2014-01-01

Biofilms are an extremely common adaptation, allowing bacteria to colonize hostile environments. They present unique problems for antibiotics and biocides, both due to the nature of the extracellular matrix and to the presence within the biofilm of metabolically inactive persister cells. Such chemicals can be highly effective against planktonic bacterial cells, while being essentially ineffective against biofilms. By contrast, bacteriophages seem to have a greater ability to target this common form of bacterial growth. The high numbers of bacteria present within biofilms actually facilitate the action of bacteriophages by allowing rapid and efficient infection of the host and consequent amplification of the bacteriophage. Bacteriophages also have a number of properties that make biofilms susceptible to their action. They are known to produce (or to be able to induce) enzymes that degrade the extracellular matrix. They are also able to infect persister cells, remaining dormant within them, but re-activating when they become metabolically active. Some cultured biofilms also seem better able to support the replication of bacteriophages than comparable planktonic systems. It is perhaps unsurprising that bacteriophages, as the natural predators of bacteria, have the ability to target this common form of bacterial life.

Bacteriophages as indicators of faecal pollution and enteric ...

EPA Pesticide Factsheets

Bacteriophages are an attractive alternative to fecal indicator bacteria (FIB), particularly as surrogates of enteric virus fate and transport due to their closer morphological and biological properties compared to FIB. Based on a meta-analysis of published data, we summarize concentrations of coliphages (F+ and somatic), Bacteroides spp. and enterococci bacteriophages (phages) in human waste, non-human waste, fresh and marine waters as well as removal through wastewater treatment processes. We also provide comparisons with FIB and enteric viruses whenever possible. Lastly, we examine fate and transport characteristics in the environment and provide an overview of the methods available for detection and enumeration of bacteriophages. In summary, concentrations of FIB bacteriophages in various sources were consistently lower than FIB, but more reflective of infectious enteric virus levels. Our investigation supports use of bacteriophages as viral surrogates especially for wastewater treatment processes, while additional research is needed to clarify their utility as indicators of viral fate and transport in the ambient water. Describes concentrations and removal through environmental and engineered systems of bacteriophages, fecal indicator bacteria and viral pathogens.

Bivariate- distribution for transition matrix elements in Breit-Wigner to Gaussian domains of interacting particle systems.

PubMed

Kota, V K B; Chavda, N D; Sahu, R

2006-04-01

Interacting many-particle systems with a mean-field one-body part plus a chaos generating random two-body interaction having strength lambda exhibit Poisson to Gaussian orthogonal ensemble and Breit-Wigner (BW) to Gaussian transitions in level fluctuations and strength functions with transition points marked by lambda = lambda c and lambda = lambda F, respectively; lambda F > lambda c. For these systems a theory for the matrix elements of one-body transition operators is available, as valid in the Gaussian domain, with lambda > lambda F, in terms of orbital occupation numbers, level densities, and an integral involving a bivariate Gaussian in the initial and final energies. Here we show that, using a bivariate-t distribution, the theory extends below from the Gaussian regime to the BW regime up to lambda = lambda c. This is well tested in numerical calculations for 6 spinless fermions in 12 single-particle states.

Genetic evolution of bacteriophage. I. Hybrids between unrelated bacteriophages P22 and Fels 2.

PubMed

Yamamoto, N

1969-01-01

A new bacteriophage species, designated F22, was isolated from phage P22 stocks grown on Salmonella typhimurium Q1 lysogenic for Fels 2 at a frequency of less than 10(-11). P22 has a very short tail with a hexagonal base plate and six spikes. Phage Fels 2 is morphologically similar to E. coli T-even phages, having a long tail with a contractile sheath and carrying no genetic region related to P22. Phage F22 is morphologically and serologically indistinguishable from Fels 2, but carries the c(c(1), c(2), and c(3)) markers of P22. The color markers h(21), g, and m(3) of P22 do not appear in F22. Thus, F22 is evidently a recombinant between the unrelated bacteriophages P22 and Fels 2. The recombination between unrelated bacteriophages could play an important role in the evolution of bacteriophages.

The effects of bacteriophage and nanoparticles on microbial processes

NASA Astrophysics Data System (ADS)

Moody, Austin L.

There are approximately 1031 tailed phages in the biosphere, making them the most abundant organism. Bacteriophages are viruses that infect bacteria. Due to the large diversity and abundance, no two bacteriophages that have been isolated are genetically the same. Phage products have potential in disease therapy to solve bacteria-related problems, such as infections resulting from resistant strains of Staphylococcus aureus. A bacteriophage capable of infecting methicillin-resistant S. aureus (MRSA) was isolated from bovine hair. The bacteriophage, named JB phage, was characterized using purification, amplification, cesium chloride banding, scanning electron microscopy, and transmission electron microscopy. JB phage and nanoparticles were used in various in vitro and in vivo models to test their effects on microbial processes. Scanning and transmission electron microscopy studies revealed strong interactions between JB phage and nanoparticles, which resulted in increased bacteriophage infectivity. JB phage and nanoparticle cocktails were used as a therapeutic to treat skin and systemic infections in mice caused by MRSA.

Anticancer activity of bacteriophage T4 and its mutant HAP1 in mouse experimental tumour models.

PubMed

Dabrowska, Krystyna; Opolski, Adam; Wietrzyk, Joanna; Switala-Jelen, Kinga; Godlewska, Joanna; Boratynski, Janusz; Syper, Danuta; Weber-Dabrowska, Beata; Gorski, Andrzej

2004-01-01

Previously, we have shown the ability of the bacteriophage T4 and its substrain HAP1 (selected for a higher affinity to melanoma cells) to reveal antimetastatic activity in a mouse melanoma model. Here, we investigated the potential phage anticancer activity in primary tumour models. Mice were inoculated subcutaneously with B16 or LLC cells (collected from in vitro culture). Bacteriophages T4 and HAP1 were injected intraperitoneally daily (8 x 10(8)pfu/mouse, except the experiment concerning the dose-dependence). Treatment with purified preparations of bacteriophage T4 resulted in significant reduction of tumour size, the effect being dose-dependent. HAP1 was more effective than T4 and its activity was also dose-dependent. Parallel experiments with non-purified bacteriophage lysates resulted in significant stimulation of tumour growth. These data suggest that purified bacteriophages may inhibit tumour growth, a phenomenon with potentially important clinical implications in oncology.

Isolation of bacteriophages from air using vacuum filtration technique: an improved and novel method.

PubMed

Magare, B; Nair, A; Khairnar, K

2017-10-01

Development of a simple and economical air sampler for isolation and enrichment of bacteriophages from air samples. A vacuum filtration unit with simple modifications was used for isolation of bacteriophages from air sampled in the lavatory. Air was sampled at the rate of 62 l min -1 by bubbling into Mcllvaine buffer for 30 min, which was used as bacteriophage solution for enrichment and plaque assessment against individual hosts. Alternatively, the aforementioned phage solution was enriched using a host consortium before plaque assessment. Phages were isolated in the range of 1-12 PFU per ml by the first method, whereas enrichment with host consortium gave phages around 10- to 1000-folds higher in number. Combining with established enrichment method, an improvement of about 10 times in phage isolation efficiency was attained. The method is very useful for studying the natural bacteriophages of air, requiring only a basic microbiological laboratory setup making it simple and economical. This study brings out a simple, economical air sampler for assessing air bacteriophages that can be employed by any microbial laboratory. Although various methods are available for studying bacteriophages in water and soil, very limited are available for air. To the best of our knowledge, the method developed in this study is unique in its design and concept for studying bacteriophages in air. The sampler is sterilizable by autoclaving and maintains a healthy rate of airflow provided by conventional vacuum pumps. The use of a nonspecific 'trapping solution' allows for the qualitative and quantitative study of air bacteriophages. © 2017 The Society for Applied Microbiology.

In vitro Effectiveness of Commercial Bacteriophage Cocktails on Diverse Extended-Spectrum Beta-Lactamase Producing Escherichia coli Strains.

PubMed

Gundogdu, Aycan; Bolkvadze, Darajen; Kilic, Huseyin

2016-01-01

The objective of this study is to determine the in vitro susceptibility of Georgian bacteriophage cocktails on multidrug resistant (MDR) extended-spectrum beta-lactamase producing Escherichia coli (ESBL-EC) isolated from patients' blood and urine cultures. A total of 615 E. coli isolates were included in this study. Phene Plate (PhP)-typing and phylogenetic grouping were used for the typing. Antimicrobial resistance profiles and ESBL production of all isolates were confirmed according to Clinical and Laboratory Standards Institute (CLSI) criteria. The activities of four bacteriophage cocktails (Enko-phage, SES-bacteriophage, Pyo-bacteriophage, and Intesti-bacteriophage) were determined against 142 ESBL-EC using in vitro spot tests. According to this, Enko-phage were active against 87.3% of the tested strains while that ratio was 81.7% for Intesti-bacteriophage, 81.7% for Pyo-bacteriophage, and 59.2% for SES-bacteriophage cocktails. Based on the contingency tests, the phage cocktails were observed to be statistically significantly ( p < 0.001) more effective on ESBL-EC strains belonging to phylogenetic groups D and B2. The employed phage cocktails were found to be affective against all tested resistant types. These results are promising especially for the infections that are caused by MDR pathogens that are difficult to treat. As this is a preliminary step to the potential clinical trials to be designed for the country, in vitro confirmation of their success on a MDR ESBL-EC collection should be accepted as an initial action, which is encouraging to consider clinical trials of phage therapy especially in countries which are not introduce phage therapy.

Preparation and evaluation of MS2 bacteriophage-like particles packaging hepatitis E virus RNA.

PubMed

Wang, Shen; Liu, Ying; Li, Dandan; Zhou, Tiezhong; Gao, Shenyang; Zha, Enhui; Yue, Xiqing

2016-10-01

Hepatitis E virus (HEV) is the pathogen causing hepatitis E (HE). It arouses global public health concern since it is a zoonotic disease. The objective of this letter is to report a cost-effective internal control prepared for monitoring procedures of HEV reverse transcriptase (RT)-PCR detection. A selected conserved HEV RNA fragment was integrated into the downstream of the truncated MS2 bacteriophage genome based on Armored RNA technology. The resulting MS2-HEV gene harbored by the pET-28b-MS2-HEV plasmid was transformed into E. coli BL21(DE3) for expression analysis by SDS-PAGE. The expression products were purified and concentrated by ultrasonication and ultrafiltration separation. The morphology and stability properties of the virus-like particles (VLPs) were evaluated by electron microscopy scanning and nuclease challenges, respectively. SDS-PAGE results showed that the constructed MS2-HEV gene expressed efficiently and the purity of the VLPs was highly consistent with the result in electron microscopy. Stability evaluation results demonstrated that the prepared VLPs exhibited strong resistance to DNase I and RNase A attacks and also performed long-lasting protection of coated HEV RNA for at least 4 months at -20°C. These data revealed that the prepared VLPs meet the basic requirements of use as internal control material in the HEV RNA amplification assay. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Stability and infectivity of cytolethal distending toxin type V gene-carrying bacteriophages in a water mesocosm and under different inactivation conditions.

PubMed

Allué-Guardia, Anna; Jofre, Juan; Muniesa, Maite

2012-08-01

Two cytolethal distending toxin (Cdt) type V-encoding bacteriophages (Φ62 and Φ125) were induced spontaneously from their wild-type Escherichia coli strains and from the lysogens generated in Shigella sonnei. The stability of Cdt phages was determined at various temperatures and pH values after 1 month of storage by means of infectivity tests using a plaque blot assay and analysis of phage genomes using real-time quantitative PCR (qPCR): both were highly stable. We assessed the inactivation of Cdt phages by thermal treatment, chlorination, UV radiation, and in a mesocosm in both summer and winter. The results for the two Cdt phages showed similar trends and were also similar to the phage SOM23 used for reference, but they showed a much higher persistence than Cdt-producing E. coli. Cdt phages showed maximal inactivation after 1 h at 70°C, 30 min of UV radiation, and 30 min of contact with a 10-ppm chlorine treatment. Inactivation in a mesocosm was higher in summer than in winter, probably because of solar radiation. The treatments reduced the number of infectious phages but did not have a significant effect on the Cdt phage particles detected by qPCR. Cdt phages were quantified by qPCR in 73% of river samples, and these results suggest that Cdt phages are a genetic vehicle and the natural reservoir for cdt in the environment.

Correlation Measurement of Lambda-anti-Lambda, Lambda-Lambda and anti-Lambda-anti-Lambda with the ATLAS detector at s=7 TeV

NASA Astrophysics Data System (ADS)

Cheng, Hok-Chuen

This thesis summaries the measurements of correlations between Lambda 0Lambda0, Lambda0Lambda 0, and Lambda0Lambda 0 hyperon pairs produced inclusively at the LHC, which are useful for a better understanding of the quark-antiquark pair production and jet fragmentation and hadronization processes. The analysis is based on hyperon pairs selected using the muon and minimum bias data samples collected at the ATLAS experiment from proton-proton collisions at a center-of-mass energy of 7 TeV in 2010. Excess Lambda0Lambda 0 are observed near the production threshold and are identified to be originated from the parton system in the string model in the MC sample, decaying either directly or through heavy strange resonances such as Sigma0 and Sigma*(1385). Dynamical correlations have been explored through a correlation function defined as the ratio of two-particle to single-particle densities. Positive correlation is observed for Lambda0Lambda0 and anticorrelation is observed for Lambda0Lambda 0 and Lambda0Lambda 0 for Q in [0,2] GeV. The structure replicates similar correlations in pp, pp, and pppp events in PYTHIA generator as predicted by the Lund string fragmentation model. Parameters of the "popcorn" mechanism implemented in the PYTHIA generator are tuned and are found to have little impact on the structure observed. The spin composition of the sample is extracted using a data-driven reference sample built by event mixing. Appropriate corrections have been made to the kinematic distributions in the reference sample by kinematic weighting to make sure that the detector effects are well modeled. A modified Pearson's chi2 test statistics is calculated for the costheta* distribution to determine the best-fitted A-value for data. The results are consistent with zero for both like-type and unlike-type hyperon pairs in Q ∈ [0,10] GeV and Q ∈ [1,10] GeV respectively. The data statistics in the range of Q ∈ [0, 1] GeV is currently too low for the estimation of the emitter size for Fermi-Dirac correlation.

Accurate model annotation of a near-atomic resolution cryo-EM map

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hryc, Corey F.; Chen, Dong-Hua; Afonine, Pavel V.

Electron cryomicroscopy (cryo-EM) has been used to determine the atomic coordinates (models) from density maps of biological assemblies. These models can be assessed by their overall fit to the experimental data and stereochemical information. However, these models do not annotate the actual density values of the atoms nor their positional uncertainty. Here, we introduce a computational procedure to derive an atomic model from a cryo- EM map with annotated metadata. The accuracy of such a model is validated by a faithful replication of the experimental cryo-EM map computed using the coordinates and associated metadata. The functional interpretation of any structuralmore » features in the model and its utilization for future studies can be made in the context of its measure of uncertainty. We applied this protocol to the 3.3-Å map of the mature P22 bacteriophage capsid, a large and complex macromolecular assembly. With this protocol, we identify and annotate previously undescribed molecular interactions between capsid subunits that are crucial to maintain stability in the absence of cementing proteins or cross-linking, as occur in other bacteriophages.« less

Whey powders are a rich source and excellent storage matrix for dairy bacteriophages.

PubMed

Wagner, Natalia; Brinks, Erik; Samtlebe, Meike; Hinrichs, Jörg; Atamer, Zeynep; Kot, Witold; Franz, Charles M A P; Neve, Horst; Heller, Knut J

2017-01-16

Thirteen whey powders and 5 whey powder formulations were screened for the presence of dairy bacteriophages using a representative set of 8 acid-producing Lactococcus lactis and 5 Streptococcus thermophilus, and 8 flavour-producing Leuconostoc pseudomesenteroides and Leuconostoc mesenteroides strains. Lytic L. lactis phages were detected in all samples, while S. thermophilus and Leuconostoc phages were present in 50% or 40% of the samples, respectively. Maximal phage titers were 6×10 7 plaque-forming units (pfu)/g of whey powder for L. lactis phages, 1×10 7 pfu/g for Leuconostoc phages and 1×10 5 pfu/g for S. thermophilus phages. In total, 55 phages were isolated and characterized. Thirty one of the 33 lactococcal phages tested belonged to the wide-spread 936 phage group. In the course of this study, a PCR detection method for Leuconostoc phages (Ali et al., 2013) was adapted to new phage isolates. Furthermore, a remarkably high stability of phages in whey powder samples was documented during a long-term storage period of 4 years. Copyright © 2016 Elsevier B.V. All rights reserved.

Accurate model annotation of a near-atomic resolution cryo-EM map.

PubMed

Hryc, Corey F; Chen, Dong-Hua; Afonine, Pavel V; Jakana, Joanita; Wang, Zhao; Haase-Pettingell, Cameron; Jiang, Wen; Adams, Paul D; King, Jonathan A; Schmid, Michael F; Chiu, Wah

2017-03-21

Electron cryomicroscopy (cryo-EM) has been used to determine the atomic coordinates (models) from density maps of biological assemblies. These models can be assessed by their overall fit to the experimental data and stereochemical information. However, these models do not annotate the actual density values of the atoms nor their positional uncertainty. Here, we introduce a computational procedure to derive an atomic model from a cryo-EM map with annotated metadata. The accuracy of such a model is validated by a faithful replication of the experimental cryo-EM map computed using the coordinates and associated metadata. The functional interpretation of any structural features in the model and its utilization for future studies can be made in the context of its measure of uncertainty. We applied this protocol to the 3.3-Å map of the mature P22 bacteriophage capsid, a large and complex macromolecular assembly. With this protocol, we identify and annotate previously undescribed molecular interactions between capsid subunits that are crucial to maintain stability in the absence of cementing proteins or cross-linking, as occur in other bacteriophages.

Accurate model annotation of a near-atomic resolution cryo-EM map

PubMed Central

Hryc, Corey F.; Chen, Dong-Hua; Afonine, Pavel V.; Jakana, Joanita; Wang, Zhao; Haase-Pettingell, Cameron; Jiang, Wen; Adams, Paul D.; King, Jonathan A.; Schmid, Michael F.; Chiu, Wah

2017-01-01

Electron cryomicroscopy (cryo-EM) has been used to determine the atomic coordinates (models) from density maps of biological assemblies. These models can be assessed by their overall fit to the experimental data and stereochemical information. However, these models do not annotate the actual density values of the atoms nor their positional uncertainty. Here, we introduce a computational procedure to derive an atomic model from a cryo-EM map with annotated metadata. The accuracy of such a model is validated by a faithful replication of the experimental cryo-EM map computed using the coordinates and associated metadata. The functional interpretation of any structural features in the model and its utilization for future studies can be made in the context of its measure of uncertainty. We applied this protocol to the 3.3-Å map of the mature P22 bacteriophage capsid, a large and complex macromolecular assembly. With this protocol, we identify and annotate previously undescribed molecular interactions between capsid subunits that are crucial to maintain stability in the absence of cementing proteins or cross-linking, as occur in other bacteriophages. PMID:28270620

Stability of bacteriophages in burn wound care products

PubMed Central

Monserez, Riet; van Belleghem, Jonas; Rose, Thomas; Jennes, Serge; De Vos, Daniel; Verbeken, Gilbert; Vaneechoutte, Mario; Pirnay, Jean-Paul

2017-01-01

Bacteriophages could be used along with burn wound care products to enhance antimicrobial pressure during treatment. However, some of the components of the topical antimicrobials that are traditionally used for the prevention and treatment of burn wound infection might affect the activity of phages. Therefore, it is imperative to determine the counteraction of therapeutic phage preparations by burn wound care products before application in patients. Five phages, representatives of two morphological families (Myoviridae and Podoviridae) and active against 3 common bacterial burn wound pathogens (Acinetobacter baumannii, Pseudomonas aeruginosa and Staphylococcus aureus) were tested against 13 different products commonly used in the treatment of burn wounds. The inactivation of the phages was quite variable for different phages and different products. Majority of the anti-infective products affected phage activity negatively either immediately or in the course of time, although impact was not always significant. Products with high acidity had the most adverse effect on phages. Our findings demonstrate that during combined treatment the choice of phages and wound care products must be carefully defined in advance. PMID:28750102

Peering down the barrel of a bacteriophage portal: the genome packaging and release valve in p22.

PubMed

Tang, Jinghua; Lander, Gabriel C; Olia, Adam S; Olia, Adam; Li, Rui; Casjens, Sherwood; Prevelige, Peter; Cingolani, Gino; Baker, Timothy S; Johnson, John E

2011-04-13

The encapsidated genome in all double-strand DNA bacteriophages is packaged to liquid crystalline density through a unique vertex in the procapsid assembly intermediate, which has a portal protein dodecamer in place of five coat protein subunits. The portal orchestrates DNA packaging and exit, through a series of varying interactions with the scaffolding, terminase, and closure proteins. Here, we report an asymmetric cryoEM reconstruction of the entire P22 virion at 7.8 Å resolution. X-ray crystal structure models of the full-length portal and of the portal lacking 123 residues at the C terminus in complex with gene product 4 (Δ123portal-gp4) obtained by Olia et al. (2011) were fitted into this reconstruction. The interpreted density map revealed that the 150 Å, coiled-coil, barrel portion of the portal entraps the last DNA to be packaged and suggests a mechanism for head-full DNA signaling and transient stabilization of the genome during addition of closure proteins. Copyright © 2011 Elsevier Ltd. All rights reserved.

Accurate model annotation of a near-atomic resolution cryo-EM map

DOE PAGES

Hryc, Corey F.; Chen, Dong-Hua; Afonine, Pavel V.; ...

2017-03-07

Electron cryomicroscopy (cryo-EM) has been used to determine the atomic coordinates (models) from density maps of biological assemblies. These models can be assessed by their overall fit to the experimental data and stereochemical information. However, these models do not annotate the actual density values of the atoms nor their positional uncertainty. Here, we introduce a computational procedure to derive an atomic model from a cryo- EM map with annotated metadata. The accuracy of such a model is validated by a faithful replication of the experimental cryo-EM map computed using the coordinates and associated metadata. The functional interpretation of any structuralmore » features in the model and its utilization for future studies can be made in the context of its measure of uncertainty. We applied this protocol to the 3.3-Å map of the mature P22 bacteriophage capsid, a large and complex macromolecular assembly. With this protocol, we identify and annotate previously undescribed molecular interactions between capsid subunits that are crucial to maintain stability in the absence of cementing proteins or cross-linking, as occur in other bacteriophages.« less

Methods for generation of reporter phages and immobilization of active bacteriophages on a polymer surface

NASA Technical Reports Server (NTRS)

Morgan, Mark Thomas (Inventor); Kothapalli, Aparna (Inventor); Applegate, Bruce Michael (Inventor); Perry, Lynda Louise (Inventor)

2012-01-01

Novel reporter bacteriophages are provided. Provided are compositions and methods that allow bacteriophages that are used for specific detection or killing of E. coli 0157:H7 to be propagated in nonpathogenic E. coli, thereby eliminating the safety and security risks of propagation in E. coli 0157:H7. Provided are compositions and methods for attaching active bacteriophages to the surface of a polymer in order to kill target bacteria with which the phage comes into contact. Provided are modified bacteriophages immobilized to a surface, which capture E. coli 0157:H7 and cause the captured cells to emit light or fluorescence, allowing detection of the bacteria in a sample.

Template reporter bacteriophage platform and multiple bacterial detection assays based thereon

NASA Technical Reports Server (NTRS)

Goodridge, Lawrence (Inventor)

2007-01-01

The invention is a method for the development of assays for the simultaneous detection of multiple bacteria. A bacteria of interest is selected. A host bacteria containing plasmid DNA from a T even bacteriophage that infects the bacteria of interest is infected with T4 reporter bacteriophage. After infection, the progeny bacteriophage are plating onto the bacteria of interest. The invention also includes single-tube, fast and sensitive assays which utilize the novel method.

Effects of bacteriophage on the quality and shelf life of Paralichthys olivaceus during chilled storage.

PubMed

Li, Meng; Lin, Hong; Khan, Muhammad Naseem; Wang, Jingxue; Kong, Linghong

2014-06-01

The microbiological spoilage of fishery foods is mainly due to specific spoilage organisms (SSOs), with Shewanella putrefaciens being the SSO of most chilled marine fish. Bacteriophages have shown excellent capability to control micro-organisms. The aim of this study was to determine a specific bacteriophage to prevent spoilage by reducing SSO (S. putrefaciens) levels in the marine fish Paralichthys olivaceus (olive flounder) under chilled storage. Chilled flounder fillets were inoculated with S. putrefaciens and treated with different concentrations of bacteriophage Spp001 ranging from 10(4) to 10(8) plaque-forming units (pfu) mL(-1) . Bacterial growth (including total viable count and SSO) of the bacteriophage-treated groups was significantly inhibited compared with that of the negative control group (P < 0.05). Sensory evaluation and biochemical parameters revealed that the bacteriophage could extend the shelf life of chilled flounder fillets (from <4 to 14 days) with good esthetic quality, even at low temperature (4 °C). Furthermore, bacteriophage concentrations of 10(6) and 10(8) pfu mL(-1) were more effective than the chemical preservative potassium sorbate (5 g L(-1) ). The bacteriophage Spp001 offered effective biocontrol of S. putrefaciens under chilled conditions, retaining the quality characteristics of spiked fish fillets, and thus could be a potential candidate for use in chilled fish fillet biopreservation. © 2013 Society of Chemical Industry.

Pulmonary Bacteriophage Therapy on Pseudomonas aeruginosa Cystic Fibrosis Strains: First Steps Towards Treatment and Prevention

PubMed Central

Morello, Eric; Saussereau, Emilie; Maura, Damien; Huerre, Michel; Touqui, Lhousseine; Debarbieux, Laurent

2011-01-01

Multidrug-resistant bacteria are the cause of an increasing number of deadly pulmonary infections. Because there is currently a paucity of novel antibiotics, phage therapy—the use of specific viruses that infect bacteria—is now more frequently being considered as a potential treatment for bacterial infections. Using a mouse lung-infection model caused by a multidrug resistant Pseudomonas aeruginosa mucoid strain isolated from a cystic fibrosis patient, we evaluated bacteriophage treatments. New bacteriophages were isolated from environmental samples and characterized. Bacteria and bacteriophages were applied intranasally to the immunocompetent mice. Survival was monitored and bronchoalveolar fluids were analysed. Quantification of bacteria, bacteriophages, pro-inflammatory and cytotoxicity markers, as well as histology and immunohistochemistry analyses were performed. A curative treatment (one single dose) administrated 2 h after the onset of the infection allowed over 95% survival. A four-day preventive treatment (one single dose) resulted in a 100% survival. All of the parameters measured correlated with the efficacy of both curative and preventive bacteriophage treatments. We also showed that in vitro optimization of a bacteriophage towards a clinical strain improved both its efficacy on in vivo treatments and its host range on a panel of 20 P. aeruginosa cystic fibrosis strains. This work provides an incentive to develop clinical studies on pulmonary bacteriophage therapy to combat multidrug-resistant lung infections. PMID:21347240

In vitro design of a novel lytic bacteriophage cocktail with therapeutic potential against organisms causing diabetic foot infections.

PubMed

Mendes, João J; Leandro, Clara; Mottola, Carla; Barbosa, Raquel; Silva, Filipa A; Oliveira, Manuela; Vilela, Cristina L; Melo-Cristino, José; Górski, Andrzej; Pimentel, Madalena; São-José, Carlos; Cavaco-Silva, Patrícia; Garcia, Miguel

2014-08-01

In patients with diabetes mellitus, foot infections pose a significant risk. These are complex infections commonly caused by Staphylococcus aureus, Pseudomonas aeruginosa and Acinetobacter baumannii, all of which are potentially susceptible to bacteriophages. Here, we characterized five bacteriophages that we had determined previously to have antimicrobial and wound-healing potential in chronic S. aureus, P. aeruginosa and A. baumannii infections. Morphological and genetic features indicated that the bacteriophages were lytic members of the family Myoviridae or Podoviridae and did not harbour any known bacterial virulence genes. Combinations of the bacteriophages had broad host ranges for the different target bacterial species. The activity of the bacteriophages against planktonic cells revealed effective, early killing at 4 h, followed by bacterial regrowth to pre-treatment levels by 24 h. Using metabolic activity as a measure of cell viability within established biofilms, we found significant cell impairment following bacteriophage exposure. Repeated treatment every 4 h caused a further decrease in cell activity. The greatest effects on both planktonic and biofilm cells occurred at a bacteriophage : bacterium input multiplicity of 10. These studies on both planktonic cells and established biofilms allowed us to better evaluate the effects of a high input multiplicity and a multiple-dose treatment protocol, and the findings support further clinical development of bacteriophage therapy. © 2014 The Authors.

Abundance of Antibiotic Resistance Genes in Bacteriophage following Soil Fertilization with Dairy Manure or Municipal Biosolids, and Evidence for Potential Transduction.

PubMed

Ross, Joseph; Topp, Edward

2015-11-01

Animal manures and municipal biosolids recycled onto crop production land carry antibiotic-resistant bacteria that can influence the antibiotic resistome of agricultural soils, but little is known about the contribution of bacteriophage to the dissemination of antibiotic resistance genes (ARGs) in this context. In this work, we quantified a set of ARGs in the bacterial and bacteriophage fractions of agricultural soil by quantitative PCR. All tested ARGs were present in both the bacterial and phage fractions. We demonstrate that fertilization of soil with dairy manure or human biosolids increases ARG abundance in the bacterial fraction but not the bacteriophage fraction and further show that pretreatment of dairy manure can impact ARG abundance in the bacterial fraction. Finally, we show that purified bacteriophage can confer increased antibiotic resistance to soil bacteria when combined with selective pressure. The results indicate that soilborne bacteriophage represents a substantial reservoir of antibiotic resistance and that bacteriophage could play a significant role in the horizontal transfer of resistance genes in the context of an agricultural soil microbiome. Overall, our work reinforces the advisability of composting or digesting fecal material prior to field application and suggests that application of some antibiotics at subclinical concentrations can promote bacteriophage-mediated horizontal transfer of ARGs in agricultural soil microbiomes. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Abundance of Antibiotic Resistance Genes in Bacteriophage following Soil Fertilization with Dairy Manure or Municipal Biosolids, and Evidence for Potential Transduction

PubMed Central

Ross, Joseph

2015-01-01

Animal manures and municipal biosolids recycled onto crop production land carry antibiotic-resistant bacteria that can influence the antibiotic resistome of agricultural soils, but little is known about the contribution of bacteriophage to the dissemination of antibiotic resistance genes (ARGs) in this context. In this work, we quantified a set of ARGs in the bacterial and bacteriophage fractions of agricultural soil by quantitative PCR. All tested ARGs were present in both the bacterial and phage fractions. We demonstrate that fertilization of soil with dairy manure or human biosolids increases ARG abundance in the bacterial fraction but not the bacteriophage fraction and further show that pretreatment of dairy manure can impact ARG abundance in the bacterial fraction. Finally, we show that purified bacteriophage can confer increased antibiotic resistance to soil bacteria when combined with selective pressure. The results indicate that soilborne bacteriophage represents a substantial reservoir of antibiotic resistance and that bacteriophage could play a significant role in the horizontal transfer of resistance genes in the context of an agricultural soil microbiome. Overall, our work reinforces the advisability of composting or digesting fecal material prior to field application and suggests that application of some antibiotics at subclinical concentrations can promote bacteriophage-mediated horizontal transfer of ARGs in agricultural soil microbiomes. PMID:26341211

Reduction of Salmonella in ground chicken using a bacteriophage.

PubMed

Grant, Ar'Quette; Parveen, Salina; Schwarz, Jurgen; Hashem, Fawzy; Vimini, Bob

2017-08-01

This study's goal was to ascertain the effectiveness of a commercially available Salmonella bacteriophage during ground chicken production focusing on: water source, different Salmonella serovars, and time. Salmonella-free boneless, skinless chicken meat was inoculated with 4.0 Log CFU/cm2 of either a cocktail of 3 Salmonella isolates derived from ground chicken (GC) or a cocktail of 3 Salmonella strains not isolated from ground chicken (non-GC). Bacteriophages were spread onto the chicken using sterile tap or filtered water for 30 min or 8 h. Salmonella was recovered using standard plating method. Greater Salmonella reduction was observed when the bacteriophage was diluted in sterile tap water than in sterile filtered water: 0.39 Log CFU/cm2 and 0.23 Log CFU/cm2 reduction after 30 min, respectively (P < 0.05). The non-GC isolates showed reductions of 0.71 Log CFU/cm2 and 0.90 Log CFU/cm2 after 30 min and 8 h, respectively (P < 0.05). The GC isolates were less sensitive to the bacteriophage: 0.39 Log CFU/cm2 and 0.67 Log CFU/cm2 reductions after 30 min and 8 h, respectively (P < 0.05). In conclusion, bacteriophage reduction was dependent on water used to dilute the bacteriophage, Salmonella's susceptibility to the bacteriophage, and treatment time. © 2017 Poultry Science Association Inc.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Akaishi, Yoshinori; College of Science and Technology, Nihon University, Funabashi 274-8501; Myint, Khin Swe

The overbinding problem of {sub {lambda}}{sup 5}He is solved by introducing a concept of coherent {lambda}-{sigma} coupling which is equivalent to a {lambda}NN three-body force. This three-body force is coherently enhanced in the 0{sup +} states of {sub {lambda}}{sup 4}H and {sub {lambda}}{sup 4}He. The 0{sup +}-1{sup +} splitting in these hypernuclei is mainly due to coherent {lambda}-{sigma} coupling and partly due to the {lambda}N spin-spin interaction. A {lambda}NN three-body potential is derived from the coupled-channel treatment. The origin of the repulsive and attractive nature of the three-body force is discussed. Coherent {lambda}-{sigma} coupling becomes more important in neutron-rich hypernucleimore » and especially in neutron-star matter at high densities. The possible existence of ''hyperheavy hydrogen'', {sub {lambda}}{sup 6}H, is suggested.« less

PARASITIC INTERFERENCE IN LONG BASELINE OPTICAL INTERFEROMETRY: REQUIREMENTS FOR HOT JUPITER-LIKE PLANET DETECTION

DOE Office of Scientific and Technical Information (OSTI.GOV)

Matter, A.; Lopez, B.; Lagarde, S.

2009-12-01

The observable quantities in optical interferometry, which are the modulus and the phase of the complex visibility, may be corrupted by parasitic fringes superimposed on the genuine fringe pattern. These fringes are due to an interference phenomenon occurring from stray light effects inside an interferometric instrument. We developed an analytical approach to better understand this phenomenon when stray light causes cross talk between beams. We deduced that the parasitic interference significantly affects the interferometric phase and thus the associated observables including the differential phase and the closure phase. The amount of parasitic flux coupled to the piston between beams appearsmore » to be very influential in this degradation. For instance, considering a point-like source and a piston ranging from lambda/500 to lambda/5 in the L band (lambda = 3.5 mum), a parasitic flux of about 1% of the total flux produces a parasitic phase reaching at most one-third of the intrinsic phase. The piston, which can have different origins (instrumental stability, atmospheric perturbations, etc.), thus amplifies the effect of parasitic interference. According to the specifications of piston correction in space or at ground level (respectively lambda/500 approx 2 nm and lambda/30 approx 100 nm), the detection of hot Jupiter-like planets, one of the most challenging aims for current ground-based interferometers, limits parasitic radiation to about 5% of the incident intensity. This was evaluated by considering different types of hot Jupiter synthetic spectra. Otherwise, if no fringe tracking is used, the detection of a typical hot Jupiter-like system with a solar-like star would admit a maximum level of parasitic intensity of 0.01% for piston errors equal to lambda/15. If the fringe tracking specifications are not precisely observed, it thus appears that the allowed level of parasitic intensity dramatically decreases and may prevent the detection. In parallel, the calibration of the parasitic phase by a reference star, at this accuracy level, seems very difficult. Moreover, since parasitic phase is an object-dependent quantity, the use of a hypothetical phase abacus, directly giving the parasitic phase from a given parasitic flux level, is also impossible. Some instrumental solutions, implemented at the instrument design stage for limiting or preventing this parasitic interference, appear to be crucial and are presented in this paper.« less

Investigation of prevalence of free Shiga toxin-producing Escherichia coli (STEC)-specific bacteriophages and its correlation with STEC bacterial hosts in a produce-growing area in Salinas, California.

PubMed

Liao, Yen-Te; Quintela, Irwin A; Nguyen, Kimberly; Salvador, Alexandra; Cooley, Michael B; Wu, Vivian C H

2018-01-01

Shiga toxin-producing E. coli (STEC) causes approximately 265,000 illnesses and 3,600 hospitalizations annually and is highly associated with animal contamination due to the natural reservoir of ruminant gastrointestinal tracts. Free STEC-specific bacteriophages against STEC strains are also commonly isolated from fecal-contaminated environment. Previous studies have evaluated the correlation between the prevalence of STEC-specific bacteriophages and STEC strains to improve animal-associated environment. However, the similar information regarding free STEC-specific bacteriophages prevalence in produce growing area is lacking. Thus, the objectives of this research were to determine the prevalence of STEC-specific phages, analyze potential effects of environmental factors on the prevalence of the phages, and study correlations between STEC-specific bacteriophages and the bacterial hosts in pre-harvest produce environment. Surface water from 20 samples sites was subjected to free bacteriophage isolation using host strains of both generic E. coli and STEC (O157, six non-O157 and one O179 strains) cocktails, and isolation of O157 and non-O157 STEC strains by use of culture methods combined with PCR-based confirmation. The weather data were obtained from weather station website. Free O145- and O179-specific bacteriophages were the two most frequently isolated bacteriophages among all (O45, O145, O157 and O179) in this study. The results showed June and July had relatively high prevalence of overall STEC-specific bacteriophages with minimum isolation of STEC strains. In addition, the bacteriophages were likely isolated in the area-around or within city-with predominant human impact, whereas the STEC bacterial isolates were commonly found in agriculture impact environment. Furthermore, there was a trend that the sample sites with positive of free STEC bacteriophage did not have the specific STEC bacterial hosts. The findings of the study enable us to understand the ecology between free STEC-specific phages and STEC bacteria for further pre-harvest food safety management in produce environment.

The Effectiveness of Bacteriophages against Methicillin-Resistant Staphylococcus aureus ST398 Nasal Colonization in Pigs.

PubMed

Verstappen, Koen M; Tulinski, Pawel; Duim, Birgitta; Fluit, Ad C; Carney, Jennifer; van Nes, Arie; Wagenaar, Jaap A

2016-01-01

Methicillin-resistant Staphylococcus aureus (MRSA) is an important colonizer in animals and an opportunistic pathogen in humans. In humans, MRSA can cause infections that might be difficult to treat because of antimicrobial resistance. The use of bacteriophages has been suggested as a potential approach for the control of MRSA colonization to minimize the-often occupational-exposure of humans. The aim of this study was to assess the efficacy of bacteriophage treatment on porcine nasal colonization with MRSA in vitro, in vivo, and ex vivo. The effectiveness of a bacteriophage combination of phage K*710 and P68 was assessed in vitro by incubating them with MRSA V0608892/1 (ST398) measuring the OD600 hourly. To study the in vivo effect, bacteriophages were administered in a gel developed for human application, which contain 109 plaque-forming units (pfu)/mL (K and P68 in a 19.25:1 ratio) for 5 days to piglets (N = 8) that were experimentally colonized with the MRSA strain. Eight piglets experimentally colonized were used as a negative control. The MRSA strain was also used to colonize porcine nasal mucosa explants and bacteriophages were applied to assess the ex vivo efficacy of treatment. Bacteriophages were effective in vitro. In vivo, sixteen piglets were colonized with MRSA but the number of CFU recovered after the application of the bacteriophages in 8 piglets was not reduced compared to the control animals (approx. 105 CFU/swab). In the ex vivo model, 108 CFU were used to establish colonization with MRSA; a reduction of colonization was not observed after application of bacteriophages. However, application of mupirocin both in vivo and ex vivo resulted in a near eradication of MRSA. i) The MRSA strain was killed in the presence of the bacteriophages phage K*710 and P68 in vitro. ii) Bacteriophages did not reduce porcine nasal colonization in vivo or ex vivo. Physiological in vivo and ex vivo conditions may explain these observations. Efficacy in the ex vivo model matched that of the in vivo system.

Isolation and Characterization of Lytic Properties of Bacteriophages Specific for M. haemolytica Strains.

PubMed

Urban-Chmiel, Renata; Wernicki, Andrzej; Stęgierska, Diana; Dec, Marta; Dudzic, Anna; Puchalski, Andrzej

2015-01-01

The objective of this study was isolation and morphological characterization of temperate bacteriophages obtained from M. haemolytica strains and evaluation of their lytic properties in vitro against M. haemolytica isolated from the respiratory tract of calves. The material for the study consisted of the reference strain M. haemolytica serotype 1 (ATCC®) BAA-410™, reference serotypes A1, A2, A5, A6, A7, A9 and A11, and wild-type isolates of M. haemolytica. Bacteriophages were induced from an overnight bacterial starter culture of all examined M. haemolytica strains treated with mitomycin C. The lytic properties and host ranges were determined by plaque assays. The morphology of the bacteriophages was examined in negative-stained smears with 5% uranyl acetate solution using a transmission electron microscope. The genetic analysis of the bacteriophages was followed by restriction analysis of bacteriophage DNA. This was followed by analysis of genetic material by polymerase chain reaction (PCR). Eight bacteriophages were obtained, like typical of the families Myoviridae, Siphoviridae and Podoviridae. Most of the bacteriophages exhibited lytic properties against the M. haemolytica strains. Restriction analysis revealed similarities to the P2-like phage obtained from the strain M. haemolytica BAA-410. The most similar profiles were observed in the case of bacteriophages φA1 and φA5. All of the bacteriophages obtained were characterized by the presence of additional fragments in the restriction profiles with respect to the P2-like reference phage. In the analysis of PCR products for the P2-like reference phage phi-MhaA1-PHL101 (DQ426904) and the phages of the M. haemolytica serotypes, a 734-bp phage PCR product was obtained. The primers were programmed in Primer-Blast software using the structure of the sequence DQ426904 of reference phage PHL101. The results obtained indicate the need for further research aimed at isolating and characterizing bacteriophages, including sequence analysis of selected fragments. Moreover, standardization of methods for obtaining them in order to eliminate M. haemolytica bacteria involved in the etiopathogenesis of BRDC is essential.

Two New Lytic Bacteriophages of the Myoviridae Family Against Carbapenem-Resistant Acinetobacter baumannii

PubMed Central

Zhou, Weilong; Feng, Yu; Zong, Zhiyong

2018-01-01

Two lytic bacteriophages, WCHABP1 and WCHABP12, were recovered from hospital sewage and were able to infect 9 and 12 out of 18 carbapenem-resistant Acinetobacter baumannii clinical strains, which belonged to different clones. Electron microscopy scan showed that both bacteriophages had the similar morphology as those of the Myoviridae family. Whole genomic sequencing revealed 45.4- or 45.8-kb genome with a 37.6% GC content for WCHABP1 and WCHABP12, both of which showed significant DNA sequence similarity with bacteriophages of the Ap22virus genus within the Myoviridae family. Taxonomic analysis was therefore performed following the proposal approved by the International Committee on Taxonomy of Viruses, which confirmed that WCHABP1 and WCHABP12 represented two new species of the Ap22virus genus. No tRNAs but 88 and 89 open reading frames (ORFs) were predicted for the two bacteriophages, among which 22 and 21 had known function and encoded proteins for morphogenesis, packaging, lysis, and nucleiotide metabolism. The C-terminal amino acids of the large unit of fiber tail proteins varied between the bacteriophages, which may explain their different host ranges. For most lytic bacteriophages, a set of holin and endolysin are required for lysis. However, no known holin-encoding genes were identified in WCHABP1 and WCHABP12, suggesting that they may use alternative, yet-to-be-identified, novel holins for host cell membrane lysis. To test the efficacy of the bacteriophages in protecting against A. baumannii infection, a Galleria mellonella larva model was used. Only <20% G. mellonella larvae survived at 96 h after being infected by carbapenem-resistant A. baumannii strains, from which the two bacteriophages were recovered. With the administration of WCHABP1 and WCHABP12, the survival of larvae increased to 75%, while the treatment of polymyxin B only slightly increased the survival rate to 25%. The isolation of two new lytic bacteriophages in this study could expand our sight on Acinetobacter bacteriophages and may offer new potential therapeutic alternatives against A. baumannii. PMID:29760690

Shigella Phages Isolated during a Dysentery Outbreak Reveal Uncommon Structures and Broad Species Diversity.

PubMed

Doore, Sarah M; Schrad, Jason R; Dean, William F; Dover, John A; Parent, Kristin N

2018-04-15

In 2016, Michigan experienced the largest outbreak of shigellosis, a type of bacillary dysentery caused by Shigella spp., since 1988. Following this outbreak, we isolated 16 novel Shigella -infecting bacteriophages (viruses that infect bacteria) from environmental water sources. Most well-known bacteriophages infect the common laboratory species Escherichia coli and Salmonella enterica , and these phages have built the foundation of molecular and bacteriophage biology. Until now, comparatively few bacteriophages were known to infect Shigella spp., which are close relatives of E. coli We present a comprehensive analysis of these phages' host ranges, genomes, and structures, revealing genome sizes and capsid properties that are shared by very few previously described phages. After sequencing, a majority of the Shigella phages were found to have genomes of an uncommon size, shared by only 2% of all reported phage genomes. To investigate the structural implications of this unusual genome size, we used cryo-electron microscopy to resolve their capsid structures. We determined that these bacteriophage capsids have similarly uncommon geometry. Only two other viruses with this capsid structure have been described. Since most well-known bacteriophages infect Escherichia or Salmonella , our understanding of bacteriophages has been limited to a subset of well-described systems. Continuing to isolate phages using nontraditional strains of bacteria can fill gaps that currently exist in bacteriophage biology. In addition, the prevalence of Shigella phages during a shigellosis outbreak may suggest a potential impact of human health epidemics on local microbial communities. IMPORTANCE Shigella spp. bacteria are causative agents of dysentery and affect more than 164 million people worldwide every year. Despite the need to combat antibiotic-resistant Shigella strains, relatively few Shigella -infecting bacteriophages have been described. By specifically looking for Shigella -infecting phages, this work has identified new isolates that (i) may be useful to combat Shigella infections and (ii) fill gaps in our knowledge of bacteriophage biology. The rare qualities of these new isolates emphasize the importance of isolating phages on "nontraditional" laboratory strains of bacteria to more fully understand both the basic biology and diversity of bacteriophages. Copyright © 2018 American Society for Microbiology.

The Effectiveness of Bacteriophages against Methicillin-Resistant Staphylococcus aureus ST398 Nasal Colonization in Pigs

PubMed Central

Duim, Birgitta; Fluit, Ad C; Carney, Jennifer; van Nes, Arie; Wagenaar, Jaap A

2016-01-01

Methicillin-resistant Staphylococcus aureus (MRSA) is an important colonizer in animals and an opportunistic pathogen in humans. In humans, MRSA can cause infections that might be difficult to treat because of antimicrobial resistance. The use of bacteriophages has been suggested as a potential approach for the control of MRSA colonization to minimize the—often occupational—exposure of humans. The aim of this study was to assess the efficacy of bacteriophage treatment on porcine nasal colonization with MRSA in vitro, in vivo, and ex vivo. The effectiveness of a bacteriophage combination of phage K*710 and P68 was assessed in vitro by incubating them with MRSA V0608892/1 (ST398) measuring the OD600 hourly. To study the in vivo effect, bacteriophages were administered in a gel developed for human application, which contain 109 plaque-forming units (pfu)/mL (K and P68 in a 19.25:1 ratio) for 5 days to piglets (N = 8) that were experimentally colonized with the MRSA strain. Eight piglets experimentally colonized were used as a negative control. The MRSA strain was also used to colonize porcine nasal mucosa explants and bacteriophages were applied to assess the ex vivo efficacy of treatment. Bacteriophages were effective in vitro. In vivo, sixteen piglets were colonized with MRSA but the number of CFU recovered after the application of the bacteriophages in 8 piglets was not reduced compared to the control animals (approx. 105 CFU/swab). In the ex vivo model, 108 CFU were used to establish colonization with MRSA; a reduction of colonization was not observed after application of bacteriophages. However, application of mupirocin both in vivo and ex vivo resulted in a near eradication of MRSA. In conclusion: i) The MRSA strain was killed in the presence of the bacteriophages phage K*710 and P68 in vitro. ii) Bacteriophages did not reduce porcine nasal colonization in vivo or ex vivo. Physiological in vivo and ex vivo conditions may explain these observations. Efficacy in the ex vivo model matched that of the in vivo system. PMID:27487020

Properties of nearly perfect crystals at very low temperatures

NASA Technical Reports Server (NTRS)

Weber, J.; Hamilton, J. J.

1994-01-01

Data shows that the frequency stability of 5 MHz AT-cut quartz crystal oscillators is improved by lowering the temperature to 4.3 K. The resultant level of stability is apparently not, at this point, sufficient for a clock accurate to 1 part in 10(exp 17). However, many improvements are possible in the scheme presented here. These would involve better temperature regulation, better crystal mounting and vibration isolation, and lower temperatures. Below the lambda-transition at 2.17 K the residual bubbling of the bath would be eliminated. Thus, the prospect of a successful clock built on this scheme is not ruled out.

Measurement of sigma Lambda b0/sigma B0 x B(Lambda b0-->Lambda c+pi-)/B(B0-->D+pi-) in pp collisions at square root s=1.96 TeV.

PubMed

Abulencia, A; Adelman, J; Affolder, T; Akimoto, T; Albrow, M G; Ambrose, D; Amerio, S; Amidei, D; Anastassov, A; Anikeev, K; Annovi, A; Antos, J; Aoki, M; Apollinari, G; Arguin, J-F; Arisawa, T; Artikov, A; Ashmanskas, W; Attal, A; Azfar, F; Azzi-Bacchetta, P; Azzurri, P; Bacchetta, N; Badgett, W; Barbaro-Galtieri, A; Barnes, V E; Barnett, B A; Baroiant, S; Bartsch, V; Bauer, G; Bedeschi, F; Behari, S; Belforte, S; Bellettini, G; Bellinger, J; Belloni, A; Benjamin, D; Beretvas, A; Beringer, J; Berry, T; Bhatti, A; Binkley, M; Bisello, D; Blair, R E; Blocker, C; Blumenfeld, B; Bocci, A; Bodek, A; Boisvert, V; Bolla, G; Bolshov, A; Bortoletto, D; Boudreau, J; Boveia, A; Brau, B; Brigliadori, L; Bromberg, C; Brubaker, E; Budagov, J; Budd, H S; Budd, S; Budroni, S; Burkett, K; Busetto, G; Bussey, P; Byrum, K L; Cabrera, S; Campanelli, M; Campbell, M; Canelli, F; Canepa, A; Carillo, S; Carlsmith, D; Carosi, R; Casarsa, M; Castro, A; Catastini, P; Cauz, D; Cavalli-Sforza, M; Cerri, A; Cerrito, L; Chang, S H; Chen, Y C; Chertok, M; Chiarelli, G; Chlachidze, G; Chlebana, F; Cho, I; Cho, K; Chokheli, D; Chou, J P; Choudalakis, G; Chuang, S H; Chung, K; Chung, W H; Chung, Y S; Ciljak, M; Ciobanu, C I; Ciocci, M A; Clark, A; Clark, D; Coca, M; Compostella, G; Convery, M E; Conway, J; Cooper, B; Copic, K; Cordelli, M; Cortiana, G; Crescioli, F; Cuenca Almenar, C; Cuevas, J; Culbertson, R; Cully, J C; Cyr, D; DaRonco, S; D'Auria, S; Davies, T; D'Onofrio, M; Dagenhart, D; de Barbaro, P; De Cecco, S; Deisher, A; De Lentdecker, G; Dell'Orso, M; Delli Paoli, F; Demortier, L; Deng, J; Deninno, M; De Pedis, D; Derwent, P F; Di Giovanni, G P; Dionisi, C; Di Ruzza, B; Dittmann, J R; DiTuro, P; Dörr, C; Donati, S; Donega, M; Dong, P; Donini, J; Dorigo, T; Dube, S; Efron, J; Erbacher, R; Errede, D; Errede, S; Eusebi, R; Fang, H C; Farrington, S; Fedorko, I; Fedorko, W T; Feild, R G; Feindt, M; Fernandez, J P; Field, R; Flanagan, G; Foland, A; Forrester, S; Foster, G W; Franklin, M; Freeman, J C; Furic, I; Gallinaro, M; Galyardt, J; Garcia, J E; Garberson, F; Garfinkel, A F; Gay, C; Gerberich, H; Gerdes, D; Giagu, S; Giannetti, P; Gibson, A; Gibson, K; Gimmell, J L; Ginsburg, C; Giokaris, N; Giordani, M; Giromini, P; Giunta, M; Giurgiu, G; Glagolev, V; Glenzinski, D; Gold, M; Goldschmidt, N; Goldstein, J; Gomez, G; Gomez-Ceballos, G; Goncharov, M; González, O; Gorelov, I; Goshaw, A T; Goulianos, K; Gresele, A; Griffiths, M; Grinstein, S; Grosso-Pilcher, C; Group, R C; Grundler, U; Guimaraes da Costa, J; Gunay-Unalan, Z; Haber, C; Hahn, K; Hahn, S R; Halkiadakis, E; Hamilton, A; Han, B-Y; Han, J Y; Handler, R; Happacher, F; Hara, K; Hare, M; Harper, S; Harr, R F; Harris, R M; Hartz, M; Hatakeyama, K; Hauser, J; Heijboer, A; Heinemann, B; Heinrich, J; Henderson, C; Herndon, M; Heuser, J; Hidas, D; Hill, C S; Hirschbuehl, D; Hocker, A; Holloway, A; Hou, S; Houlden, M; Hsu, S-C; Huffman, B T; Hughes, R E; Husemann, U; Huston, J; Incandela, J; Introzzi, G; Iori, M; Ishizawa, Y; Ivanov, A; Iyutin, B; James, E; Jang, D; Jayatilaka, B; Jeans, D; Jensen, H; Jeon, E J; Jindariani, S; Jones, M; Joo, K K; Jun, S Y; Jung, J E; Junk, T R; Kamon, T; Karchin, P E; Kato, Y; Kemp, Y; Kephart, R; Kerzel, U; Khotilovich, V; Kilminster, B; Kim, D H; Kim, H S; Kim, J E; Kim, M J; Kim, S B; Kim, S H; Kim, Y K; Kimura, N; Kirsch, L; Klimenko, S; Klute, M; Knuteson, B; Ko, B R; Kondo, K; Kong, D J; Konigsberg, J; Korytov, A; Kotwal, A V; Kovalev, A; Kraan, A C; Kraus, J; Kravchenko, I; Kreps, M; Kroll, J; Krumnack, N; Kruse, M; Krutelyov, V; Kubo, T; Kuhlmann, S E; Kuhr, T; Kusakabe, Y; Kwang, S; Laasanen, A T; Lai, S; Lami, S; Lammel, S; Lancaster, M; Lander, R L; Lannon, K; Lath, A; Latino, G; Lazzizzera, I; Le, Y; LeCompte, T; Lee, J; Lee, J; Lee, Y J; Lee, S W; Lefèvre, R; Leonardo, N; Leone, S; Levy, S; Lewis, J D; Lin, C; Lin, C S; Lindgren, M; Lipeles, E; Lister, A; Litvintsev, D O; Liu, T; Lockyer, N S; Loginov, A; Loreti, M; Loverre, P; Lu, R-S; Lucchesi, D; Lujan, P; Lukens, P; Lungu, G; Lyons, L; Lys, J; Lysak, R; Lytken, E; Mack, P; MacQueen, D; Madrak, R; Maeshima, K; Makhoul, K; Maki, T; Maksimovic, P; Malde, S; Manca, G; Margaroli, F; Marginean, R; Marino, C; Marino, C P; Martin, A; Martin, M; Martin, V; Martínez, M; Maruyama, T; Mastrandrea, P; Masubuchi, T; Matsunaga, H; Mattson, M E; Mazini, R; Mazzanti, P; McFarland, K S; McIntyre, P; McNulty, R; Mehta, A; Mehtala, P; Menzemer, S; Menzione, A; Merkel, P; Mesropian, C; Messina, A; Miao, T; Miladinovic, N; Miles, J; Miller, R; Mills, C; Milnik, M; Mitra, A; Mitselmakher, G; Miyamoto, A; Moed, S; Moggi, N; Mohr, B; Moore, R; Morello, M; Movilla Fernandez, P; Mülmenstädt, J; Mukherjee, A; Muller, Th; Mumford, R; Murat, P; Nachtman, J; Nagano, A; Naganoma, J; Nakano, I; Napier, A; Necula, V; Neu, C; Neubauer, M S; Nielsen, J; Nigmanov, T; Nodulman, L; Norniella, O; Nurse, E; Oh, S H; Oh, Y D; Oksuzian, I; Okusawa, T; Oldeman, R; Orava, R; Osterberg, K; Pagliarone, C; Palencia, E; Papadimitriou, V; Paramonov, A A; Parks, B; Pashapour, S; Patrick, J; Pauletta, G; Paulini, M; Paus, C; Pellett, D E; Penzo, A; Phillips, T J; Piacentino, G; Piedra, J; Pinera, L; Pitts, K; Plager, C; Pondrom, L; Portell, X; Poukhov, O; Pounder, N; Prakoshyn, F; Pronko, A; Proudfoot, J; Ptohos, F; Punzi, G; Pursley, J; Rademacker, J; Rahaman, A; Ranjan, N; Rappoccio, S; Reisert, B; Rekovic, V; Renton, P; Rescigno, M; Richter, S; Rimondi, F; Ristori, L; Robson, A; Rodrigo, T; Rogers, E; Rolli, S; Roser, R; Rossi, M; Rossin, R; Ruiz, A; Russ, J; Rusu, V; Saarikko, H; Sabik, S; Safonov, A; Sakumoto, W K; Salamanna, G; Saltó, O; Saltzberg, D; Sánchez, C; Santi, L; Sarkar, S; Sartori, L; Sato, K; Savard, P; Savoy-Navarro, A; Scheidle, T; Schlabach, P; Schmidt, E E; Schmidt, M P; Schmitt, M; Schwarz, T; Scodellaro, L; Scott, A L; Scribano, A; Scuri, F; Sedov, A; Seidel, S; Seiya, Y; Semenov, A; Sexton-Kennedy, L; Sfyrla, A; Shapiro, M D; Shears, T; Shepard, P F; Sherman, D; Shimojima, M; Shochet, M; Shon, Y; Shreyber, I; Sidoti, A; Sinervo, P; Sisakyan, A; Sjolin, J; Slaughter, A J; Slaunwhite, J; Sliwa, K; Smith, J R; Snider, F D; Snihur, R; Soderberg, M; Soha, A; Somalwar, S; Sorin, V; Spalding, J; Spinella, F; Spreitzer, T; Squillacioti, P; Stanitzki, M; Staveris-Polykalas, A; St Denis, R; Stelzer, B; Stelzer-Chilton, O; Stentz, D; Strologas, J; Stuart, D; Suh, J S; Sukhanov, A; Sun, H; Suzuki, T; Taffard, A; Takashima, R; Takeuchi, Y; Takikawa, K; Tanaka, M; Tanaka, R; Tecchio, M; Teng, P K; Terashi, K; Thom, J; Thompson, A S; Thomson, E; Tipton, P; Tiwari, V; Tkaczyk, S; Toback, D; Tokar, S; Tollefson, K; Tomura, T; Tonelli, D; Torre, S; Torretta, D; Tourneur, S; Trischuk, W; Tseng, J; Tsuchiya, R; Tsuno, S; Turini, N; Ukegawa, F; Unverhau, T; Uozumi, S; Usynin, D; Vallecorsa, S; van Remortel, N; Varganov, A; Vataga, E; Vázquez, F; Velev, G; Veramendi, G; Veszpremi, V; Vidal, R; Vila, I; Vilar, R; Vine, T; Vollrath, I; Volobouev, I; Volpi, G; Würthwein, F; Wagner, P; Wagner, R G; Wagner, R L; Wagner, J; Wagner, W; Wallny, R; Wang, S M; Warburton, A; Waschke, S; Waters, D; Wester, W C; Whitehouse, B; Whiteson, D; Wicklund, A B; Wicklund, E; Williams, G; Williams, H H; Wilson, P; Winer, B L; Wittich, P; Wolbers, S; Wolfe, C; Wright, T; Wu, X; Wynne, S M; Yagil, A; Yamamoto, K; Yamaoka, J; Yamashita, T; Yang, C; Yang, U K; Yang, Y C; Yao, W M; Yeh, G P; Yoh, J; Yorita, K; Yoshida, T; Yu, G B; Yu, I; Yu, S S; Yun, J C; Zanello, L; Zanetti, A; Zaw, I; Zhang, X; Zhou, J; Zucchelli, S

2007-03-23

We present the first observation of the baryon decay Lambda b0-->Lambda c+pi- followed by Lambda c+-->pK-pi+ in 106 pb-1 pp collisions at square root s=1.96 TeV in the CDF experiment. In order to reduce systematic error, the measured rate for Lambda b0 decay is normalized to the kinematically similar meson decay B0-->D+pi- followed by D+-->pi+K-pi+. We report the ratio of production cross sections (sigma) times the ratio of branching fractions (B) for the momentum region integrated above pT>6 GeV/c and pseudorapidity range |eta|<1.3: sigma(pp-->Lambda b0X)/sigma(pp-->B0X)xB(Lambda b0-->Lambda c+pi-)/B(B0-->D+pi-)=0.82+/-0.08(stat)+/-0.11(syst)+/-0.22[B(Lambda c+-->pK-pi+)].

Bacteriophage-based therapy in cystic fibrosis-associated Pseudomonas aeruginosa infections: rationale and current status

PubMed Central

Hraiech, Sami; Brégeon, Fabienne; Rolain, Jean-Marc

2015-01-01

Pulmonary infections involving Pseudomonas aeruginosa are among the leading causes of the deterioration of the respiratory status of cystic fibrosis (CF) patients. The emergence of multidrug-resistant strains in such populations, favored by iterative antibiotic cures, has led to the urgent need for new therapies. Among them, bacteriophage-based therapies deserve a focus. One century of empiric use in the ex-USSR countries suggests that bacteriophages may have beneficial effects against a large range of bacterial infections. Interest in bacteriophages has recently renewed in Western countries, and the in vitro data available suggest that bacteriophage-based therapy may be of significant interest for the treatment of pulmonary infections in CF patients. Although the clinical data concerning this specific population are relatively scarce, the beginning of the first large randomized study evaluating bacteriophage-based therapy in burn infections suggests that the time has come to assess the effectiveness of this new therapy in CF P. aeruginosa pneumonia. Consequently, the aim of this review is, after a brief history, to summarize the evidence concerning bacteriophage efficacy against P. aeruginosa and, more specifically, the in vitro studies, animal models, and clinical trials targeting CF. PMID:26213462

[Determination of Azospirillum Brasilense Cells With Bacteriophages via Electrooptical Analysis of Microbial Suspensions].

PubMed

Gulii, O I; Karavayeva, O A; Pavlii, S A; Sokolov, O I; Bunin, V D; Ignatov, O V

2015-01-01

The dependence-of changes in the electrooptical properties of Azospirillum brasilense cell suspension Sp7 during interaction with bacteriophage ΦAb-Sp7 on the number and time of interactions was studied. Incubation of cells with bacteriophage significantly changed the electrooptical signal within one minute. The selective effect of bacteriophage ΦAb on 18 strains of bacteria of the genus Azospirillum was studied: A. amazonense Ami4, A. brasilense Sp7, Cd, Sp107, Sp245, Jm6B2, Brl4, KR77, S17, S27, SR55, SR75, A. halopraeferans Au4, A. irakense KBC1, K A3, A. lipoferum Sp59b, SR65 and RG20a. We determined the limit of reliable determination of microbial cells infected with bacteriophage: - 10(4) cells/mL. The presence of foreign cell cultures of E. coli B-878 and E. coli XL-1 did not complicate the detection of A brasilense Sp7 cells with the use of bacteriophage ΦAb-Sp7. The results demonstrated that bacteriophage (ΦAb-Sp7 can be used for the detection of Azospirillum microbial cells via t electrooptical analysis of cell suspensions.

Bacteriophages as indicators of human and animal faecal contamination in raw and treated wastewaters from Tunisia.

PubMed

Yahya, M; Hmaied, F; Jebri, S; Jofre, J; Hamdi, M

2015-05-01

We aimed at quantifying bacteriophages in raw and treated wastewaters of human and animal origin in Tunisia to assess their usefulness for tracking the origin of faecal pollution and in the follow-up of effectiveness of water treatments process. The concentrations of bacteriophages in wastewater samples were determined by double layer agar technique. Somatic coliphages and F-specific RNA bacteriophages were present in all types of samples in high concentrations. The values of Escherichia coli were variable depending on geographical location. On the other hand, bacteriophages infecting strain GA17 were detected preferably when human faecal contamination was occurred. Bacteriophages appear as a feasible and widely applicable manner to detect faecal contamination in Tunisia. On the other hand, phages infecting GA17 could be good markers for tracking the origin of faecal pollution in the area studied. The reuse of treated wastewaters can be a solution to meet the needs of water in the geographical area of study. Bacteriophages seem to predict differently the presence of faecal contamination in water than bacterial indicators. Consequently, they can be a valuable additional tool to improve water resources management for minimizing health risks. © 2015 The Society for Applied Microbiology.

Biocontrol of Listeria monocytogenes and Escherichia coli O157:H7 in Meat by Using Phages Immobilized on Modified Cellulose Membranes ▿

PubMed Central

Anany, H.; Chen, W.; Pelton, R.; Griffiths, M. W.

2011-01-01

The ability of phages to specifically interact with and lyse their host bacteria makes them ideal antibacterial agents. The range of applications of bacteriophage can be extended by their immobilization on inert surfaces. A novel method for the oriented immobilization of bacteriophage has been developed. The method was based on charge differences between the bacteriophage head, which exhibits an overall net negative charge, and the tail fibers, which possess an overall net positive charge. Hence, the head would be more likely to attach to positively charged surfaces, leaving the tails free to capture and lyse bacteria. Cellulose membranes modified so that they had a positive surface charge were used as the support for phage immobilization. It was established that the number of infective phages immobilized on the positively charged cellulose membranes was significantly higher than that on unmodified membranes. Cocktails of phages active against Listeria or Escherichia coli immobilized on these membranes were shown to effectively control the growth of L. monocytogenes and E. coli O157:H7 in ready-to-eat and raw meat, respectively, under different storage temperatures and packaging conditions. The phage storage stability was investigated to further extend their industrial applications. It was shown that lyophilization can be used as a phage-drying method to maintain their infectivity on the newly developed bioactive materials. In conclusion, utilizing the charge difference between phage heads and tails provided a simple technique for oriented immobilization applicable to a wide range of phages and allowed the retention of infectivity. PMID:21803890

Expression of a bioactive bacteriophage endolysin in Nicotiana benthamiana plants

USDA-ARS?s Scientific Manuscript database

The emergence and spread of antibiotic-resistant pathogens has led to an increased interest in alternative antimicrobial treatments, such as bacteriophage, bacteriophage-encoded peptidoglycan hydrolases (endolysins) and antimicrobial peptides. In our study, the antimicrobial activity of the CP933 en...

Characterization of the endolysin from the Enterococcus faecalis bacteriophage VD13

USDA-ARS?s Scientific Manuscript database

Bacteriophage infecting bacteria produce endolysins (peptidoglycan hydrolases) to lyse the host cell from within and release nascent bacteriophage particles. Recombinant endolysins can also lyse Gram-positive bacteria when added exogenously. As a potential alternative to antibiotics, we cloned and...

A filamentous bacteriophage targeted to carcinoembryonic antigen induces tumor regression in mouse models of colorectal cancer.

PubMed

Murgas, Paola; Bustamante, Nicolás; Araya, Nicole; Cruz-Gómez, Sebastián; Durán, Eduardo; Gaete, Diana; Oyarce, César; López, Ernesto; Herrada, Andrés Alonso; Ferreira, Nicolás; Pieringer, Hans; Lladser, Alvaro

2018-02-01

Colorectal cancer is a deadly disease, which is frequently diagnosed at advanced stages, where conventional treatments are no longer effective. Cancer immunotherapy has emerged as a new form to treat different malignancies by turning-on the immune system against tumors. However, tumors are able to evade antitumor immune responses by promoting an immunosuppressive microenvironment. Single-stranded DNA containing M13 bacteriophages are highly immunogenic and can be specifically targeted to the surface of tumor cells to trigger inflammation and infiltration of activated innate immune cells, overcoming tumor-associated immunosuppression and promoting antitumor immunity. Carcinoembryonic antigen (CEA) is highly expressed in colorectal cancers and has been shown to promote several malignant features of colorectal cancer cells. In this work, we targeted M13 bacteriophage to CEA, a tumor-associated antigen over-expressed in a high proportion of colorectal cancers but largely absent in normal cells. The CEA-targeted M13 bacteriophage was shown to specifically bind to purified CEA and CEA-expressing tumor cells in vitro. Both intratumoral and systemic administration of CEA-specific bacteriophages significantly reduced tumor growth of mouse models of colorectal cancer, as compared to PBS and control bacteriophage administration. CEA-specific bacteriophages promoted tumor infiltration of neutrophils and macrophages, as well as maturation dendritic cells in tumor-draining lymph nodes, suggesting that antitumor T-cell responses were elicited. Finally, we demonstrated that tumor protection provided by CEA-specific bacteriophage particles is mediated by CD8 + T cells, as depletion of circulating CD8 + T cells completely abrogated antitumor protection. In summary, we demonstrated that CEA-specific M13 bacteriophages represent a potential immunotherapy against colorectal cancer.

In vitro Effectiveness of Commercial Bacteriophage Cocktails on Diverse Extended-Spectrum Beta-Lactamase Producing Escherichia coli Strains

PubMed Central

Gundogdu, Aycan; Bolkvadze, Darajen; Kilic, Huseyin

2016-01-01

The objective of this study is to determine the in vitro susceptibility of Georgian bacteriophage cocktails on multidrug resistant (MDR) extended-spectrum beta-lactamase producing Escherichia coli (ESBL-EC) isolated from patients’ blood and urine cultures. A total of 615 E. coli isolates were included in this study. Phene Plate (PhP)-typing and phylogenetic grouping were used for the typing. Antimicrobial resistance profiles and ESBL production of all isolates were confirmed according to Clinical and Laboratory Standards Institute (CLSI) criteria. The activities of four bacteriophage cocktails (Enko-phage, SES-bacteriophage, Pyo-bacteriophage, and Intesti-bacteriophage) were determined against 142 ESBL-EC using in vitro spot tests. According to this, Enko-phage were active against 87.3% of the tested strains while that ratio was 81.7% for Intesti-bacteriophage, 81.7% for Pyo-bacteriophage, and 59.2% for SES-bacteriophage cocktails. Based on the contingency tests, the phage cocktails were observed to be statistically significantly (p < 0.001) more effective on ESBL-EC strains belonging to phylogenetic groups D and B2. The employed phage cocktails were found to be affective against all tested resistant types. These results are promising especially for the infections that are caused by MDR pathogens that are difficult to treat. As this is a preliminary step to the potential clinical trials to be designed for the country, in vitro confirmation of their success on a MDR ESBL-EC collection should be accepted as an initial action, which is encouraging to consider clinical trials of phage therapy especially in countries which are not introduce phage therapy. PMID:27857711

Stable carbon isotope fractionation during the biodegradation of lambda-cyhalothrin.

PubMed

Shen, Xiaoli; Xu, Zemin; Zhang, Xichang; Yang, Fangxing

2015-11-01

In this study, the microbial degradation of lambda-cyhalothrin in soil was investigated using compound-specific stable isotope analysis. The results revealed that lambda-cyhalothrin was biodegraded in soil under laboratory conditions. The half-lives of lambda-cyhalothrin were determined to be 49 and 161 days in non-sterile and sterile soils spiked with 2mg/kg lambda-cyhalothrin and 84 and 154 days in non-sterile and sterile soils spiked with 10mg/kg lambda-cyhalothrin, respectively. The biodegradation of lambda-cyhalothrin resulted in carbon isotope fractionation, which shifted from -29.0‰ to -26.5‰ in soil spiked with 2mg/kg lambda-cyhalothrin, and to -27.5‰ with 10mg/kg lambda-cyhalothrin. A relationship was established between the stable carbon isotope fraction and the residual concentrations of lambda-cyhalothrin by the Rayleigh equation in which the carbon isotope enrichment factor ε of the microbial degradation of lambda-cyhalothrin in the soil was calculated as -2.53‰. This study provides an approach to quantitatively evaluate the biodegradation of lambda-cyhalothrin in soil in field studies. Copyright © 2015 Elsevier B.V. All rights reserved.

Comparative genomic analysis of novel bacteriophages infecting Vibrio parahaemolyticus isolated from western and southern coastal areas of Korea.

PubMed

Yu, Junhyeok; Lim, Jeong-A; Kwak, Su-Jin; Park, Jong-Hyun; Chang, Hyun-Joo

2018-05-01

Vibrio parahaemolyticus, a foodborne pathogen, has become resistant to antibiotics. Therefore, alternative bio-control agents such bacteriophage are urgently needed for its control. Six novel bacteriophages specific to V. parahaemolyticus (vB_VpaP_KF1~2, vB_VpaS_KF3~6) were characterized at the molecular level in this study. Genomic similarity analysis revealed that these six bacteriophages could be divided into two groups with different genomic features, phylogenetic grouping, and morphologies. Two groups of bacteriophages had their own genes with different mechanisms for infection, assembly, and metabolism. Our results could be used as a future reference to study phage genomics or apply phages in future bio-control studies.

Occurrence of Propionibacterium freudenreichii bacteriophages in swiss cheese.

PubMed Central

Gautier, M; Rouault, A; Sommer, P; Briandet, R

1995-01-01

We isolated bacteriophages active against Propionibacterium freudenreichii from 16 of 32 swiss cheese samples. Bacteriophage concentrations ranged from 14 to 7 x 10(5) PFU/g, depending on the sample and the sensitive strain used for detection. Only a few strains, 8 of the 44 strains of P. freudenreichii in our collection, were sensitive. We observed that multiplication of bacteriophages occurred in the cheese loaf during multiplication of propionibacteria in a warm curing room, but it seems that these bacteriophages have no adverse effect on the development of the propionic flora. We also found that sensitive cells, originating from either the starter or the cheese-making milk, were present at a high level (10(9) CFU/g) in the cheese. PMID:7618869

A novel approach for separating bacteriophages from other bacteriophages using affinity chromatography and phage display.

PubMed

Ceglarek, Izabela; Piotrowicz, Agnieszka; Lecion, Dorota; Miernikiewicz, Paulina; Owczarek, Barbara; Hodyra, Katarzyna; Harhala, Marek; Górski, Andrzej; Dąbrowska, Krystyna

2013-11-14

Practical applications of bacteriophages in medicine and biotechnology induce a great need for technologies of phage purification. None of the popular methods offer solutions for separation of a phage from another similar phage. We used affinity chromatography combined with competitive phage display (i) to purify T4 bacteriophage from bacterial debris and (ii) to separate T4 from other contaminating bacteriophages. In 'competitive phage display' bacterial cells produced both wild types of the proteins (expression from the phage genome) and the protein fusions with affinity tags (expression from the expression vectors). Fusion proteins were competitively incorporated into the phage capsid. It allowed effective separation of T4 from a contaminating phage on standard affinity resins.

A novel approach for separating bacteriophages from other bacteriophages using affinity chromatography and phage display

PubMed Central

Ceglarek, Izabela; Piotrowicz, Agnieszka; Lecion, Dorota; Miernikiewicz, Paulina; Owczarek, Barbara; Hodyra, Katarzyna; Harhala, Marek; Górski, Andrzej; Dąbrowska, Krystyna

2013-01-01

Practical applications of bacteriophages in medicine and biotechnology induce a great need for technologies of phage purification. None of the popular methods offer solutions for separation of a phage from another similar phage. We used affinity chromatography combined with competitive phage display (i) to purify T4 bacteriophage from bacterial debris and (ii) to separate T4 from other contaminating bacteriophages. In ‘competitive phage display’ bacterial cells produced both wild types of the proteins (expression from the phage genome) and the protein fusions with affinity tags (expression from the expression vectors). Fusion proteins were competitively incorporated into the phage capsid. It allowed effective separation of T4 from a contaminating phage on standard affinity resins. PMID:24225840

Improved bacteriophage genome data is necessary for integrating viral and bacterial ecology.

PubMed

Bibby, Kyle

2014-02-01

The recent rise in "omics"-enabled approaches has lead to improved understanding in many areas of microbial ecology. However, despite the importance that viruses play in a broad microbial ecology context, viral ecology remains largely not integrated into high-throughput microbial ecology studies. A fundamental hindrance to the integration of viral ecology into omics-enabled microbial ecology studies is the lack of suitable reference bacteriophage genomes in reference databases-currently, only 0.001% of bacteriophage diversity is represented in genome sequence databases. This commentary serves to highlight this issue and to promote bacteriophage genome sequencing as a valuable scientific undertaking to both better understand bacteriophage diversity and move towards a more holistic view of microbial ecology.

Dynamics of a family of transcendental meromorphic functions having rational Schwarzian derivative

NASA Astrophysics Data System (ADS)

Sajid, M.; Kapoor, G. P.

2007-02-01

In the present paper, a class of critically finite transcendental meromorphic functions having rational Schwarzian derivative is introduced and the dynamics of functions in one parameter family is investigated. It is found that there exist two parameter values [lambda]*=[phi](0)>0 and , where and is the real root of [phi]'(x)=0, such that the Fatou sets of f[lambda](z) for [lambda]=[lambda]* and [lambda]=[lambda]** contain parabolic domains. A computationally useful characterization of the Julia set of the function f[lambda](z) as the complement of the basin of attraction of an attracting real fixed point of f[lambda](z) is established and applied for the generation of the images of the Julia sets of f[lambda](z). Further, it is observed that the Julia set of explodes to whole complex plane for [lambda]>[lambda]**. Finally, our results found in the present paper are compared with the recent results on dynamics of one parameter families [lambda]tanz, [R.L. Devaney, L. Keen, Dynamics of meromorphic maps: Maps with polynomial Schwarzian derivative, Ann. Sci. Ecole Norm. Sup. 22 (4) (1989) 55-79; L. Keen, J. Kotus, Dynamics of the family [lambda]tan(z), Conform. Geom. Dynam. 1 (1997) 28-57; G.M. Stallard, The Hausdorff dimension of Julia sets of meromorphic functions, J. London Math. Soc. 49 (1994) 281-295] and , [lambda]>0 [G.P. Kapoor, M. Guru Prem Prasad, Dynamics of : The Julia set and bifurcation, Ergodic Theory Dynam. Systems 18 (1998) 1363-1383].

The Genome Sequence of Bacteriophage CPV1 Virulent for Clostridium perfringens

USDA-ARS?s Scientific Manuscript database

Application of bacteriophages and their lytic enzymes to control Clostridium perfringens is one potential approach to reduce the pathogen on poultry farms and in poultry-processing facilities. Bacteriophages lytic for C. perfringens were isolated from sewage, feces and broiler intestinal contents. P...

Alternative bacteriophage life cycles: the carrier state of Campylobacter jejuni

PubMed Central

Siringan, Patcharin; Connerton, Phillippa L.; Cummings, Nicola J.; Connerton, Ian F.

2014-01-01

Members of the genus Campylobacter are frequently responsible for human enteric disease, often through consumption of contaminated poultry products. Bacteriophages are viruses that have the potential to control pathogenic bacteria, but understanding their complex life cycles is key to their successful exploitation. Treatment of Campylobacter jejuni biofilms with bacteriophages led to the discovery that phages had established a relationship with their hosts typical of the carrier state life cycle (CSLC), where bacteria and bacteriophages remain associated in equilibrium. Significant phenotypic changes include improved aerotolerance under nutrient-limited conditions that would confer an advantage to survive in extra-intestinal environments, but a lack in motility eliminated their ability to colonize chickens. Under these circumstances, phages can remain associated with a compatible host and continue to produce free virions to prospect for new hosts. Moreover, we demonstrate that CSLC host bacteria can act as expendable vehicles for the delivery of bacteriophages to new host bacteria within pre-colonized chickens. The CSLC represents an important phase in the ecology of Campylobacter bacteriophage. PMID:24671947

Alternative bacteriophage life cycles: the carrier state of Campylobacter jejuni.

PubMed

Siringan, Patcharin; Connerton, Phillippa L; Cummings, Nicola J; Connerton, Ian F

2014-03-26

Members of the genus Campylobacter are frequently responsible for human enteric disease, often through consumption of contaminated poultry products. Bacteriophages are viruses that have the potential to control pathogenic bacteria, but understanding their complex life cycles is key to their successful exploitation. Treatment of Campylobacter jejuni biofilms with bacteriophages led to the discovery that phages had established a relationship with their hosts typical of the carrier state life cycle (CSLC), where bacteria and bacteriophages remain associated in equilibrium. Significant phenotypic changes include improved aerotolerance under nutrient-limited conditions that would confer an advantage to survive in extra-intestinal environments, but a lack in motility eliminated their ability to colonize chickens. Under these circumstances, phages can remain associated with a compatible host and continue to produce free virions to prospect for new hosts. Moreover, we demonstrate that CSLC host bacteria can act as expendable vehicles for the delivery of bacteriophages to new host bacteria within pre-colonized chickens. The CSLC represents an important phase in the ecology of Campylobacter bacteriophage.

GENETIC EVOLUTION OF BACTERIOPHAGE, I. HYBRIDS BETWEEN UNRELATED BACTERIOPHAGES P22 AND FELS 2*

PubMed Central

Yamamoto, Nobuto

1969-01-01

A new bacteriophage species, designated F22, was isolated from phage P22 stocks grown on Salmonella typhimurium Q1 lysogenic for Fels 2 at a frequency of less than 10-11. P22 has a very short tail with a hexagonal base plate and six spikes. Phage Fels 2 is morphologically similar to E. coli T-even phages, having a long tail with a contractile sheath and carrying no genetic region related to P22. Phage F22 is morphologically and serologically indistinguishable from Fels 2, but carries the c(c1, c2, and c3) markers of P22. The color markers h21, g, and m3 of P22 do not appear in F22. Thus, F22 is evidently a recombinant between the unrelated bacteriophages P22 and Fels 2. The recombination between unrelated bacteriophages could play an important role in the evolution of bacteriophages. Images PMID:4890254

Comparative Genomics of Bacteriophage of the Genus Seuratvirus

PubMed Central

Sazinas, Pavelas; Redgwell, Tamsin; Rihtman, Branko; Grigonyte, Aurelija; Michniewski, Slawomir; Scanlan, David J; Hobman, Jon

2018-01-01

Abstract Despite being more abundant and having smaller genomes than their bacterial host, relatively few bacteriophages have had their genomes sequenced. Here, we isolated 14 bacteriophages from cattle slurry and performed de novo genome sequencing, assembly, and annotation. The commonly used marker genes polB and terL showed these bacteriophages to be closely related to members of the genus Seuratvirus. We performed a core-gene analysis using the 14 new and four closely related genomes. A total of 58 core genes were identified, the majority of which has no known function. These genes were used to construct a core-gene phylogeny, the results of which confirmed the new isolates to be part of the genus Seuratvirus and expanded the number of species within this genus to four. All bacteriophages within the genus contained the genes queCDE encoding enzymes involved in queuosine biosynthesis. We suggest these genes are carried as a mechanism to modify DNA in order to protect these bacteriophages against host endonucleases. PMID:29272407

Growing Bacteriophage M13 in Liquid Culture.

PubMed

Green, Michael R; Sambrook, Joseph

2017-11-01

Stocks of bacteriophage M13 are usually grown in liquid culture. The infected bacteria do not lyse but, instead, grow at a slower than normal rate to form a dilute suspension. The inoculum of bacteriophage is almost always a freshly picked plaque or a suspension of bacteriophage particles obtained from a single plaque, as described here. Infected cells contain up to 200 copies of double-stranded, replicative-form DNA and extrude several hundred bacteriophage particles per generation. Thus, a 1-mL culture of infected cells can produce enough double-stranded viral DNA (1-2 mg) for restriction mapping and recovery of cloned DNA inserts and sufficient single-stranded DNA (∼5-10 mg) for site-directed mutagenesis, DNA sequencing, or synthesis of radiolabeled probes. The titer of bacteriophages in the supernatant from infected cells is so high (∼10 12 pfu/mL) that a small aliquot serves as a permanent stock of the starting plaque. © 2017 Cold Spring Harbor Laboratory Press.

Characterization and formulation into solid dosage forms of a novel bacteriophage lytic against Klebsiella oxytoca.

PubMed

Brown, Teagan L; Petrovski, Steve; Hoyle, Dannielle; Chan, Hiu Tat; Lock, Peter; Tucci, Joseph

2017-01-01

To isolate and characterize bacteriophage lytic for the opportunistic pathogen Klebsiella oxytoca and their formulation into a range of solid dosage forms for in-vitro testing. We report the isolation, genomic and functional characterization of a novel bacteriophage lytic for Klebsiella oxytoca, which does not infect the closely related Klebsiella pneumoniae. This bacteriophage was formulated into suppositories and troches and shown to be released and lyse underlying Klebsiella oxytoca bacteria in an in-vitro model. These bacteriophage formulations were stable for at least 49 days at 4°C. The successful in-vitro assay of these formulations here suggests that they could potentially be tested in-vivo to determine whether such a therapeutic approach could modulate the gut microbiome, and control Klebsiella oxytoca overgrowth, during antibiotic therapy regimes. This study reports a novel bacteriophage specific for Klebsiella oxytoca which can be formulated into solid dosage forms appropriate for potential delivery in testing as a therapy to modulate gut microbiome during antibiotic therapies.

Effectiveness of cooking to reduce norovirus and infectious F-specific RNA bacteriophage concentrations in Mytilus edulis.

PubMed

Flannery, J; Rajko-Nenow, P; Winterbourn, J B; Malham, S K; Jones, D L

2014-08-01

The aim of this study was to determine if domestic cooking practices can reduce concentrations of norovirus (NoV) and F-specific RNA (FRNA) bacteriophage in experimentally contaminated mussels. Mussels (n = 600) contaminated with NoV and FRNA bacteriophage underwent four different cooking experiments performed in triplicate at ~70°C and >90°C. Concentrations of infectious FRNA bacteriophage (using a plaque assay) were compared with concentrations of FRNA bacteriophage and NoV determined using a standardised RT-qPCR. Initial concentrations of infectious FRNA bacteriophage (7·05 log10  PFU g(-1) ) in mussels were not significantly reduced in simmering water (~70°C); however, cooking at higher temperatures (>90°C) reduced infectious FRNA bacteriophage to undetected levels within 3 min. Further investigation determined the time required for a 1-log reduction of infectious FRNA bacteriophage at 90°C to be 42 s therefore a >3-log reduction in infectious virus can be obtained by heating mussel digestive tissue to 90°C for 126 s. Domestic cooking practices based on shell opening alone do not inactivate infectious virus in mussels, however, cooking mussels at high temperatures is effective to reduce infectious virus concentrations and the risk of illness in consumers. The data will contribute towards evidence-based cooking recommendations for shellfish to provide a safe product for human consumption. © 2014 The Society for Applied Microbiology.

Jovian Chromophore Characteristics from Multispectral HST Images

NASA Technical Reports Server (NTRS)

Strycker, Paul D.; Chanover, Nancy J.; Simon-Miller, Amy A.; Banfield, Don; Gierasch, Peter J.

2011-01-01

The chromophores responsible for coloring the jovian atmosphere are embedded within Jupiter's vertical aerosol structure. Sunlight propagates through this vertical distribution of aerosol particles, whose colors are defined by omega-bar (sub 0)(lambda), and we remotely observe the culmination of the radiative transfer as I/F(lambda). In this study, we employed a radiative transfer code to retrieve omega-bar (sub 0)(lambda) for particles in Jupiter's tropospheric haze at seven wavelengths in the near-UV and visible regimes. The data consisted of images of the 2008 passage of Oval BA to the south of the Great Red Spot obtained by the Wide Field Planetary Camera 2 on-board the Hubble Space Telescope. We present derived particle colors for locations that were selected from 14 weather regions, which spanned a large range of observed colors. All omega-bar (sub 0)(lambda) curves were absorbing in the blue, and omega-bar (sub 0)(lambda) increased monotonically to approximately unity as wavelength increased. We found accurate fits to all omega-bar (sub 0)(lambda) curves using an empirically derived functional form: omega-bar (sub 0)(lambda) = 1 A exp(-B lambda). The best-fit parameters for the mean omega-bar (sub 0)(lambda) curve were A = 25.4 and B = 0.0149 for lambda in units of nm. We performed a principal component analysis (PCA) on our omega-bar (sub 0)(lambda) results and found that one or two independent chromophores were sufficient to produce the variations in omega-bar (sub 0)(lambda). A PCA of I/F(lambda) for the same jovian locations resulted in principal components (PCs) with roughly the same variances as the omega-bar (sub 0)(lambda) PCA, but they did not result in a one-to-one mapping of PC amplitudes between the omega-bar (sub 0)(lambda) PCA and I/F(lambda) PCA. We suggest that statistical analyses performed on I/ F(lambda) image cubes have limited applicability to the characterization of chromophores in the jovian atmosphere due to the sensitivity of 1/ F(lambda) to horizontal variations in the vertical aerosol distribution.

Mechanisms of Hyperbilirubinemia During Peginterferon Lambda-1a Therapy for Chronic Hepatitis C Infection: A Retrospective Investigation.

PubMed

Zwirtes, Ricardo; Narasimhan, Premkumar; Wind-Rotolo, Megan M; Xu, Dong; Hruska, Matthew W; Kishnani, Narendra; Colston, Elizabeth M; Srinivasan, Subasree

2016-11-01

The phase 2b EMERGE study compared the efficacy/safety of peginterferon lambda-1a (Lambda) and peginterferon alfa-2a (Alfa), both with ribavirin (RBV), for treatment of chronic hepatitis C virus (HCV) infection. A key safety finding was a higher frequency of hyperbilirubinemia with Lambda/RBV versus Alfa/RBV. To characterize mechanisms of hyperbilirubinemia associated with Lambda/RBV, we conducted a retrospective analysis of safety data from the HCV genotype 1 and genotype 4 cohort of the EMERGE study. Subjects were randomized to once-weekly Lambda (120/180/240 μg) or Alfa (180 μg), with daily RBV, for 48 weeks. Early-onset Lambda/RBV-related hyperbilirubinemia events (6-12 weeks) resulted mostly from RBV-induced hemolysis evidenced by sustained reticulocytosis and a predominantly unconjugated pattern of hyperbilirubinemia. The higher hyperbilirubinemia frequency with Lambda/RBV versus Alfa/RBV was attributed to bone marrow suppression known to occur with Alfa but not Lambda. Late-onset (>12 weeks) Lambda/RBV-related hyperbilirubinemia events occurred most frequently with higher Lambda doses and were associated with increased levels of hepatic transaminase and direct bilirubin fractions compared with early events. This dual pattern of hyperbilirubinemia observed while on Lambda/RBV treatment is thought to be caused by exaggerated RBV-induced hemolysis in early-onset events compared with possible direct Lambda-induced hepatocellular toxicity in late-onset events.

Rearrangement and expression of the human {Psi}C{lambda}6 gene segment results in a surface Ig receptor with a truncated light chain constant region

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stiernholm, N.B.J.; Verkoczy, L.K.; Berinstein, N.L.

1995-05-01

The constant region of the human Ig{lambda} locus consists of seven tandemly organized J-C gene segments. Although it has been established that the J-C{lambda}1, J-C{lambda}2, J-C{lambda}3, and J-C{lambda}7 gene segments are functional, and code for the four distinct Ig{lambda} isotypes found in human serum, the J-C{lambda}4, J-C{lambda}5, and J-C{lambda}6 gene segments are generally considered to be pseudogenes. Although one example of a functional J-C{lambda}6 gene segment has been documented, in the majority of cases, J-C{lambda}6 is rendered nonfunctional by virtue of a single duplication of four nucleotides, creating a premature translational arrest. We show here that rearrangements to the J-C{lambda}6more » gene segment do occur, and that such a rearrangement encodes an Ig{lambda} protein that lacks the terminal end of the constant region. We also show that this truncated protein is expressed on the surface with the IgH chain, creating an unusual surface Ig (sIg) receptor (sIg{triangle}CL). Cells that express this receptor on the surface do so at significantly reduced levels compared with clonally related variants, which express sIg receptors with conventional Ig{lambda} L chains. However, the effects of sIg cross-linking on tyrosine phosphorylation and surface expression of the CD25 and CD71 Ags are similar in cells that express conventional sIg receptors and in those that express sIg{triangle}CL receptors, suggesting that the latter could possibly function as an Ag receptor. 35 refs., 7 figs.« less

Existence and non-uniqueness of similarity solutions of a boundary-layer problem

NASA Technical Reports Server (NTRS)

Hussaini, M. Y.; Lakin, W. D.

1986-01-01

A Blasius boundary value problem with inhomogeneous lower boundary conditions f(0) = 0 and f'(0) = - lambda with lambda strictly positive was considered. The Crocco variable formulation of this problem has a key term which changes sign in the interval of interest. It is shown that solutions of the boundary value problem do not exist for values of lambda larger than a positive critical value lambda. The existence of solutions is proven for 0 lambda lambda by considering an equivalent initial value problem. It is found however that for 0 lambda lambda, solutions of the boundary value problem are nonunique. Physically, this nonuniqueness is related to multiple values of the skin friction.

Existence and non-uniqueness of similarity solutions of a boundary layer problem

NASA Technical Reports Server (NTRS)

Hussaini, M. Y.; Lakin, W. D.

1984-01-01

A Blasius boundary value problem with inhomogeneous lower boundary conditions f(0) = 0 and f'(0) = - lambda with lambda strictly positive was considered. The Crocco variable formulation of this problem has a key term which changes sign in the interval of interest. It is shown that solutions of the boundary value problem do not exist for values of lambda larger than a positive critical value lambda. The existence of solutions is proven for 0 lambda lambda by considering an equivalent initial value problem. It is found however that for 0 lambda lambda, solutions of the boundary value problem are nonunique. Physically, this nonuniqueness is related to multiple values of the skin friction.

Measurement of the Lambda b0 lifetime in Lambda b0-->J/psi Lambda 0 in pp collisions at square root s=1.96 TeV.

PubMed

Abulencia, A; Adelman, J; Affolder, T; Akimoto, T; Albrow, M G; Ambrose, D; Amerio, S; Amidei, D; Anastassov, A; Anikeev, K; Annovi, A; Antos, J; Aoki, M; Apollinari, G; Arguin, J-F; Arisawa, T; Artikov, A; Ashmanskas, W; Attal, A; Azfar, F; Azzi-Bacchetta, P; Azzurri, P; Bacchetta, N; Badgett, W; Barbaro-Galtieri, A; Barnes, V E; Barnett, B A; Baroiant, S; Bartsch, V; Bauer, G; Bedeschi, F; Behari, S; Belforte, S; Bellettini, G; Bellinger, J; Belloni, A; Benjamin, D; Beretvas, A; Beringer, J; Berry, T; Bhatti, A; Binkley, M; Bisello, D; Blair, R E; Blocker, C; Blumenfeld, B; Bocci, A; Bodek, A; Boisvert, V; Bolla, G; Bolshov, A; Bortoletto, D; Boudreau, J; Boveia, A; Brau, B; Brigliadori, L; Bromberg, C; Brubaker, E; Budagov, J; Budd, H S; Budd, S; Budroni, S; Burkett, K; Busetto, G; Bussey, P; Byrum, K L; Cabrera, S; Campanelli, M; Campbell, M; Canelli, F; Canepa, A; Carrillo, S; Carlsmith, D; Carosi, R; Carron, S; Casarsa, M; Castro, A; Catastini, P; Cauz, D; Cavalli-Sforza, M; Cerri, A; Cerrito, L; Chang, S H; Chen, Y C; Chertok, M; Chiarelli, G; Chlachidze, G; Chlebana, F; Cho, I; Cho, K; Chokheli, D; Chou, J P; Choudalakis, G; Chuang, S H; Chung, K; Chung, W H; Chung, Y S; Ciljak, M; Ciobanu, C I; Ciocci, M A; Clark, A; Clark, D; Coca, M; Compostella, G; Convery, M E; Conway, J; Cooper, B; Copic, K; Cordelli, M; Cortiana, G; Crescioli, F; Cuenca Almenar, C; Cuevas, J; Culbertson, R; Cully, J C; Cyr, D; DaRonco, S; D'Auria, S; Davies, T; D'Onofrio, M; Dagenhart, D; de Barbaro, P; De Cecco, S; Deisher, A; De Lentdecker, G; Dell'Orso, M; Delli Paoli, F; Demortier, L; Deng, J; Deninno, M; De Pedis, D; Derwent, P F; Di Giovanni, G P; Dionisi, C; Di Ruzza, B; Dittmann, J R; DiTuro, P; Dörr, C; Donati, S; Donega, M; Dong, P; Donini, J; Dorigo, T; Dube, S; Efron, J; Erbacher, R; Errede, D; Errede, S; Eusebi, R; Fang, H C; Farrington, S; Fedorko, I; Fedorko, W T; Feild, R G; Feindt, M; Fernandez, J P; Field, R; Flanagan, G; Foland, A; Forrester, S; Foster, G W; Franklin, M; Freeman, J C; Furic, I; Gallinaro, M; Galyardt, J; Garcia, J E; Garberson, F; Garfinkel, A F; Gay, C; Gerberich, H; Gerdes, D; Giagu, S; Giannetti, P; Gibson, A; Gibson, K; Gimmell, J L; Ginsburg, C; Giokaris, N; Giordani, M; Giromini, P; Giunta, M; Giurgiu, G; Glagolev, V; Glenzinski, D; Gold, M; Goldschmidt, N; Goldstein, J; Gomez, G; Gomez-Ceballos, G; Goncharov, M; González, O; Gorelov, I; Goshaw, A T; Goulianos, K; Gresele, A; Griffiths, M; Grinstein, S; Grosso-Pilcher, C; Group, R C; Grundler, U; Guimaraes da Costa, J; Gunay-Unalan, Z; Haber, C; Hahn, K; Hahn, S R; Halkiadakis, E; Hamilton, A; Han, B-Y; Han, J Y; Handler, R; Happacher, F; Hara, K; Hare, M; Harper, S; Harr, R F; Harris, R M; Hartz, M; Hatakeyama, K; Hauser, J; Heijboer, A; Heinemann, B; Heinrich, J; Henderson, C; Herndon, M; Heuser, J; Hidas, D; Hill, C S; Hirschbuehl, D; Hocker, A; Holloway, A; Hou, S; Houlden, M; Hsu, S-C; Huffman, B T; Hughes, R E; Husemann, U; Huston, J; Incandela, J; Introzzi, G; Iori, M; Ishizawa, Y; Ivanov, A; Iyutin, B; James, E; Jang, D; Jayatilaka, B; Jeans, D; Jensen, H; Jeon, E J; Jindariani, S; Jones, M; Joo, K K; Jun, S Y; Jung, J E; Junk, T R; Kamon, T; Karchin, P E; Kato, Y; Kemp, Y; Kephart, R; Kerzel, U; Khotilovich, V; Kilminster, B; Kim, D H; Kim, H S; Kim, J E; Kim, M J; Kim, S B; Kim, S H; Kim, Y K; Kimura, N; Kirsch, L; Klimenko, S; Klute, M; Knuteson, B; Ko, B R; Kondo, K; Kong, D J; Konigsberg, J; Korytov, A; Kotwal, A V; Kovalev, A; Kraan, A C; Kraus, J; Kravchenko, I; Kreps, M; Kroll, J; Krumnack, N; Kruse, M; Krutelyov, V; Kubo, T; Kuhlmann, S E; Kuhr, T; Kusakabe, Y; Kwang, S; Laasanen, A T; Labarga, L; Lai, S; Lami, S; Lammel, S; Lancaster, M; Lander, R L; Lannon, K; Lath, A; Latino, G; Lazzizzera, I; LeCompte, T; Lee, J; Lee, J; Lee, Y J; Lee, S W; Lefèvre, R; Leonardo, N; Leone, S; Levy, S; Lewis, J D; Lin, C; Lin, C S; Lindgren, M; Lipeles, E; Liss, T M; Lister, A; Litvintsev, D O; Liu, T; Lockyer, N S; Loginov, A; Loreti, M; Loverre, P; Lu, R-S; Lucchesi, D; Lujan, P; Lukens, P; Lungu, G; Lyons, L; Lys, J; Lysak, R; Lytken, E; Mack, P; MacQueen, D; Madrak, R; Maeshima, K; Makhoul, K; Maki, T; Maksimovic, P; Malde, S; Manca, G; Margaroli, F; Marginean, R; Marino, C; Marino, C P; Martin, A; Martin, M; Martin, V; Martínez, M; Maruyama, T; Mastrandrea, P; Masubuchi, T; Matsunaga, H; Mattson, M E; Mazini, R; Mazzanti, P; McFarland, K S; McIntyre, P; McNulty, R; Mehta, A; Mehtala, P; Menzemer, S; Menzione, A; Merkel, P; Mesropian, C; Messina, A; Miao, T; Miladinovic, N; Miles, J; Miller, R; Mills, C; Milnik, M; Mitra, A; Mitselmakher, G; Miyamoto, A; Moed, S; Moggi, N; Mohr, B; Moore, R; Morello, M; Movilla Fernandez, P; Mülmenstädt, J; Mukherjee, A; Muller, Th; Mumford, R; Murat, P; Nachtman, J; Nagano, A; Naganoma, J; Nahn, S; Nakano, I; Napier, A; Necula, V; Neu, C; Neubauer, M S; Nielsen, J; Nigmanov, T; Nodulman, L; Norniella, O; Nurse, E; Oh, S H; Oh, Y D; Oksuzian, I; Okusawa, T; Oldeman, R; Orava, R; Osterberg, K; Pagliarone, C; Palencia, E; Papadimitriou, V; Paramonov, A A; Parks, B; Pashapour, S; Patrick, J; Pauletta, G; Paulini, M; Paus, C; Pellett, D E; Penzo, A; Phillips, T J; Piacentino, G; Piedra, J; Pinera, L; Pitts, K; Plager, C; Pondrom, L; Portell, X; Poukhov, O; Pounder, N; Prokoshin, F; Pronko, A; Proudfoot, J; Ptochos, F; Punzi, G; Pursley, J; Rademacker, J; Rahaman, A; Ranjan, N; Rappoccio, S; Reisert, B; Rekovic, V; Renton, P; Rescigno, M; Richter, S; Rimondi, F; Ristori, L; Robson, A; Rodrigo, T; Rogers, E; Rolli, S; Roser, R; Rossi, M; Rossin, R; Ruiz, A; Russ, J; Rusu, V; Saarikko, H; Sabik, S; Safonov, A; Sakumoto, W K; Salamanna, G; Saltó, O; Saltzberg, D; Sánchez, C; Santi, L; Sarkar, S; Sartori, L; Sato, K; Savard, P; Savoy-Navarro, A; Scheidle, T; Schlabach, P; Schmidt, E E; Schmidt, M P; Schmitt, M; Schwarz, T; Scodellaro, L; Scott, A L; Scribano, A; Scuri, F; Sedov, A; Seidel, S; Seiya, Y; Semenov, A; Sexton-Kennedy, L; Sfyrla, A; Shapiro, M D; Shears, T; Shepard, P F; Sherman, D; Shimojima, M; Shochet, M; Shon, Y; Shreyber, I; Sidoti, A; Sinervo, P; Sisakyan, A; Sjolin, J; Slaughter, A J; Slaunwhite, J; Sliwa, K; Smith, J R; Snider, F D; Snihur, R; Soderberg, M; Soha, A; Somalwar, S; Sorin, V; Spalding, J; Spinella, F; Spreitzer, T; Squillacioti, P; Stanitzki, M; Staveris-Polykalas, A; St Denis, R; Stelzer, B; Stelzer-Chilton, O; Stentz, D; Strologas, J; Stuart, D; Suh, J S; Sukhanov, A; Sun, H; Suzuki, T; Taffard, A; Takashima, R; Takeuchi, Y; Takikawa, K; Tanaka, M; Tanaka, R; Tecchio, M; Teng, P K; Terashi, K; Tesarek, R J; Thom, J; Thompson, A S; Thomson, E; Tipton, P; Tiwari, V; Tkaczyk, S; Toback, D; Tokar, S; Tollefson, K; Tomura, T; Tonelli, D; Torre, S; Torretta, D; Tourneur, S; Trischuk, W; Tsuchiya, R; Tsuno, S; Turini, N; Ukegawa, F; Unverhau, T; Uozumi, S; Usynin, D; Vallecorsa, S; van Remortel, N; Varganov, A; Vataga, E; Vázquez, F; Velev, G; Veramendi, G; Veszpremi, V; Vidal, R; Vila, I; Vilar, R; Vine, T; Vollrath, I; Volobouev, I; Volpi, G; Würthwein, F; Wagner, P; Wagner, R G; Wagner, R L; Wagner, J; Wagner, W; Wallny, R; Wang, S M; Warburton, A; Waschke, S; Waters, D; Weinberger, M; Wester, W C; Whitehouse, B; Whiteson, D; Wicklund, A B; Wicklund, E; Williams, G; Williams, H H; Wilson, P; Winer, B L; Wittich, P; Wolbers, S; Wolfe, C; Wright, T; Wu, X; Wynne, S M; Yagil, A; Yamamoto, K; Yamaoka, J; Yamashita, T; Yang, C; Yang, U K; Yang, Y C; Yao, W M; Yeh, G P; Yoh, J; Yorita, K; Yoshida, T; Yu, G B; Yu, I; Yu, S S; Yun, J C; Zanello, L; Zanetti, A; Zaw, I; Zhang, X; Zhou, J; Zucchelli, S

2007-03-23

We report a measurement of the Lambda b0 lifetime in the exclusive decay Lambda b0-->J/psi Lambda 0 in pp collisions at square root s=1.96 TeV using an integrated luminosity of 1.0 fb-1 of data collected by the CDF II detector at the Fermilab Tevatron. Using fully reconstructed decays, we measure tau(Lambda b0)=1.593(-0.078)(+0.083)(stat)+/-0.033(syst) ps. This is the single most precise measurement of tau(Lambda b0) and is 3.2sigma higher than the current world average.

Observation of the baryonic B decay B{sup 0}{yields}{Lambda}{sub c}{sup +}{Lambda}K{sup -}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lees, J. P.; Poireau, V.; Tisserand, V.

2011-10-01

We report the observation of the baryonic B decay B{sup 0}{yields}{Lambda}{sub c}{sup +}{Lambda}K{sup -} with a significance larger than 7 standard deviations based on 471x10{sup 6} BB pairs collected with the BABAR detector at the PEP-II storage ring at SLAC. We measure the branching fraction for the decay B{sup 0}{yields}{Lambda}{sub c}{sup +}{Lambda}K{sup -} to be (3.8{+-}0.8{sub stat}{+-}0.2{sub sys}{+-}1.0{sub {Lambda}}{sub c}{sup +})x10{sup -5}. The uncertainties are statistical, systematic, and due to the uncertainty in the {Lambda}{sub c}{sup +} branching fraction. We find that the {Lambda}{sub c}{sup +}K{sup -} invariant-mass distribution shows an enhancement above 3.5 GeV/c{sup 2}.

Doublet-spacing enhancement caused by {Lambda}N-{Sigma}N coupling in {sub {Lambda}L}i hypernuclear isotopes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Umeya, Atsushi; Harada, Toru; Research Center for Physics and Mathematics, Osaka Electro-Communication University, Neyagawa, Osaka 572-8530

2011-03-15

We theoretically investigate energy spacings of doublets in {sub {Lambda}L}i hypernuclear isotopes with A=7-10 in shell-model calculations with a {Lambda}N-{Sigma}N coupling effect. The calculated results show that the energy shifts are {Delta}{epsilon}=0.09-0.28 MeV and the {Sigma}-mixing probabilities are P{sub {Sigma}}=0.10%-0.34% in {Lambda} ground states for the isotopes because of the {Lambda}N-{Sigma}N coupling in the first-order perturbation. It is found that the energy spacing of the doublet is enhanced as a neutron number N increases; the contribution of the {Lambda}N-{Sigma}N coupling interaction is comparable to that of the {Lambda}N interaction in the neutron-rich {Lambda} hypernuclei. The coherent mechanism of this doublet-spacingmore » enhancement is also discussed in terms of Fermi-type and Gamow-Teller-type {Lambda}N-{Sigma}N couplings.« less

Identification of novel bacteriophage peptides using a combination of gene sequence LC-MS-MS analysis and BLASTP

USDA-ARS?s Scientific Manuscript database

Introduction: In an effort to characterize novel bacteriophage with lytic activity against pathogenic E.coli associated with foodborne illness, gene sequencing and mass spectrometry have been used to identify expressed peptides which differentiate isolated bacteriophage from other known phage. Here,...

[Genetic study of bacteriophage phi81. I. Isolation, study of complementation and preliminary mapping of amber-mutants of bacteriophage phi81].

PubMed

Sineokiĭ, S P; Pogosov, V Z; Iankovskiĭ, N K; Krylov, V N

1976-01-01

123 Amber mutants of lambdoid bacteriophage phi81 are isolated and distributed into 19 complementation groups. Deletion mapping made possible to locate 5 gene groups on the genetic map of bacteriophage phi81 and to determine a region of possible location of mm' sticky ends on the prophage genetic map. A gene of phage phi81 is localized, which controls the adsorption specificity, and which functional similarity to a respective gene of phage phi80 is demonstrated.

Isolation of Dickeya dadantii strains from potato disease and biocontrol by their bacteriophages.

PubMed

Soleimani-Delfan, Abbas; Etemadifar, Zahra; Emtiazi, Giti; Bouzari, Majid

2015-01-01

One of the most economically important bacterial pathogens of plants and plant products is Dickeya dadantii. This bacterium causes soft rot disease in tubers and other parts of the potato and other plants of the Solanaceae family. The application of restricted host range bacteriophages as biocontrol agents has recently gained widespread interest. This study purposed to isolate the infectious agent of the potato and evaluate its biocontrol by bacteriophages. Two phytopathogenic strains were isolated from infected potatoes, identified based on biochemical and 16S rRNA gene sequencing, and submitted to GenBank as D. dadantii strain pis3 (accession no. HQ423668) and D. dadantii strain sip4 (accession no. HQ423669). Their bacteriophages were isolated from Caspian Sea water by enriching the water filtrate with D. dadantii strains as hosts using spot or overlay methods. On the basis of morphotypes, the isolated bacteriophages were identified as members of the Myoviridae and Siphoviridae families and could inhibit the growth of antibiotic resistant D. dadantii strains in culture medium. Moreover, in Dickeya infected plants treated with bacteriophage, no disease progression was detected. No significant difference was seen between phage-treated and control plants. Thus, isolated bacteriophages can be suggested for the biocontrol of plant disease caused by Dickeya strains.

Genomic and proteomic characterization of SuMu, a Mu-like bacteriophage infecting Haemophilus parasuis

PubMed Central

2012-01-01

Background Haemophilus parasuis, the causative agent of Glässer’s disease, is prevalent in swine herds and clinical signs associated with this disease are meningitis, polyserositis, polyarthritis, and bacterial pneumonia. Six to eight week old pigs in segregated early weaning herds are particularly susceptible to the disease. Insufficient colostral antibody at weaning or the mixing of pigs with heterologous virulent H. parasuis strains from other farm sources in the nursery or grower-finisher stage are considered to be factors for the outbreak of Glässer’s disease. Previously, a Mu-like bacteriophage portal gene was detected in a virulent swine isolate of H. parasuis by nested polymerase chain reaction. Mu-like bacteriophages are related phyologenetically to enterobacteriophage Mu and are thought to carry virulence genes or to induce host expression of virulence genes. This study characterizes the Mu-like bacteriophage, named SuMu, isolated from a virulent H. parasuis isolate. Results Characterization was done by genomic comparison to enterobacteriophage Mu and proteomic identification of various homologs by mass spectrometry. This is the first report of isolation and characterization of this bacteriophage from the Myoviridae family, a double-stranded DNA bacteriophage with a contractile tail, from a virulent field isolate of H. parasuis. The genome size of bacteriophage SuMu was 37,151 bp. DNA sequencing revealed fifty five open reading frames, including twenty five homologs to Mu-like bacteriophage proteins: Nlp, phage transposase-C-terminal, COG2842, Gam-like protein, gp16, Mor, peptidoglycan recognition protein, gp29, gp30, gpG, gp32, gp34, gp36, gp37, gpL, phage tail tube protein, DNA circulation protein, gpP, gp45, gp46, gp47, COG3778, tail fiber protein gp37-C terminal, tail fiber assembly protein, and Com. The last open reading frame was homologous to IS1414. The G + C content of bacteriophage SuMu was 41.87% while its H. parasuis host genome’s G + C content was 39.93%. Twenty protein homologs to bacteriophage proteins, including 15 structural proteins, one lysogeny-related and one lysis-related protein, and three DNA replication proteins were identified by mass spectrometry. One of the tail proteins, gp36, may be a virulence-related protein. Conclusions Bacteriophage SuMu was characterized by genomic and proteomic methods and compared to enterobacteriophage Mu. PMID:22823751

Hyperparasitism by the bacteriophage (Caudovirales) infecting Candidatus Xenohaliotis californiensis (Rickettsiales-like prokaryote) parasite of wild abalone Haliotis fulgens and Haliotis corrugata from the Peninsula of Baja California, Mexico.

PubMed

Cruz-Flores, Roberto; Cáceres-Martínez, Jorge; Muñoz-Flores, Monserrat; Vásquez-Yeomans, Rebeca; Hernández Rodriguez, Mónica; Ángel Del Río-Portilla, Miguel; Rocha-Olivares, Axayácatl; Castro-Longoria, Ernestina

2016-10-01

Candidatus Xenohaliotis californiensis (CXc) is a Rickettsiales-like prokaryote that is considered the causal agent of Withering Syndrome (WS), a chronic disease of abalone, from the west coast of North America and it is listed by the International Organization for Animal Health (OIE) as a reportable agent due to its pathogenicity. This bacterium in red abalone Haliotis rufescens, black abalone Haliotis cracherodii, and yellow abalone Haliotis corrugata from California, US and Baja California, Mexico has been found to be infected by a bacteriophage. To date, there is no information on the epizootiology of CXc and its bacteriophage in natural populations of abalone; furthermore, it is unknown if the bacteriophage was also present in CXc infecting blue abalone Haliotis fulgens. The objective of this study was to determine the distribution, prevalence and intensity of CXc, as well as to determine the distribution and prevalence of the bacteriophage and to study interactions between host sex and hyperparasitism in blue abalone and yellow abalone. Tissue samples were obtained from seven localities where the commercial capture of wild abalone is carried out. Samplings were conducted throughout the 2012-2013 capture seasons and a total of 182 blue abalone and 170 yellow abalone were obtained. The prevalence and intensity of CXc and the prevalence of the bacteriophage were determined by histology. The identity of CXc was confirmed by PCR, product sequence analysis and in situ hybridization while the identity of the bacteriophage was corroborated by TEM. The prevalence of CXc infected and uninfected by the bacteriophage was 80% in blue abalone and 62% in yellow abalone. Low infection intensities were found in 86% of blue abalone and 82% of yellow abalone. Infection intensity was significantly higher in undifferentiated yellow abalone. The bacteriophage in CXc showed a prevalence of 22% and 31% in blue abalone and yellow abalone respectively. These results show that CXc and its bacteriophage are widely distributed in the peninsula of Baja California and that they are well established in natural populations of blue abalone and yellow abalone. Additionally, this data constitutes the first record of a bacteriophage in blue abalone. Copyright © 2016 Elsevier Inc. All rights reserved.

Genomic and proteomic characterization of SuMu, a Mu-like bacteriophage infecting Haemophilus parasuis.

PubMed

Zehr, Emilie S; Tabatabai, Louisa B; Bayles, Darrell O

2012-07-23

Haemophilus parasuis, the causative agent of Glässer's disease, is prevalent in swine herds and clinical signs associated with this disease are meningitis, polyserositis, polyarthritis, and bacterial pneumonia. Six to eight week old pigs in segregated early weaning herds are particularly susceptible to the disease. Insufficient colostral antibody at weaning or the mixing of pigs with heterologous virulent H. parasuis strains from other farm sources in the nursery or grower-finisher stage are considered to be factors for the outbreak of Glässer's disease. Previously, a Mu-like bacteriophage portal gene was detected in a virulent swine isolate of H. parasuis by nested polymerase chain reaction. Mu-like bacteriophages are related phyologenetically to enterobacteriophage Mu and are thought to carry virulence genes or to induce host expression of virulence genes. This study characterizes the Mu-like bacteriophage, named SuMu, isolated from a virulent H. parasuis isolate. Characterization was done by genomic comparison to enterobacteriophage Mu and proteomic identification of various homologs by mass spectrometry. This is the first report of isolation and characterization of this bacteriophage from the Myoviridae family, a double-stranded DNA bacteriophage with a contractile tail, from a virulent field isolate of H. parasuis. The genome size of bacteriophage SuMu was 37,151 bp. DNA sequencing revealed fifty five open reading frames, including twenty five homologs to Mu-like bacteriophage proteins: Nlp, phage transposase-C-terminal, COG2842, Gam-like protein, gp16, Mor, peptidoglycan recognition protein, gp29, gp30, gpG, gp32, gp34, gp36, gp37, gpL, phage tail tube protein, DNA circulation protein, gpP, gp45, gp46, gp47, COG3778, tail fiber protein gp37-C terminal, tail fiber assembly protein, and Com. The last open reading frame was homologous to IS1414. The G + C content of bacteriophage SuMu was 41.87% while its H. parasuis host genome's G + C content was 39.93%. Twenty protein homologs to bacteriophage proteins, including 15 structural proteins, one lysogeny-related and one lysis-related protein, and three DNA replication proteins were identified by mass spectrometry. One of the tail proteins, gp36, may be a virulence-related protein. Bacteriophage SuMu was characterized by genomic and proteomic methods and compared to enterobacteriophage Mu.

Galaxy formation in Lambda greater than 0 Friedmann models: Consequences for the number counts versus redshift test

NASA Technical Reports Server (NTRS)

Martel, Hugo

1994-01-01

We study the effect of the cosmological constant Lambda on galaxy formation using a simple spherical top-hat overdensity model. We consider models with Omega(sub 0) = 0.2, lambda(sub 0) = 0, and Omega(sub 0) = 0.2, lambda(sub 0) = 0.8 (where Omega(sub 0) is the density parameter, and lambda(sub 0) identically equal Lambda/3 H(sub 0 exp 2) where H(sub 0) is the Hubble constant). We adjust the initial power spectrum amplitude so that both models reproduce the same large-scale structures. The galaxy formation era in the lambda(sub 0) = 0 model occurs early (z approximately 6) and is very short, whereas in the lambda(sub 0) = 0.8 model the galaxy formation era starts later (z approximately 4), and last much longer, possibly all the way to the present. Consequently, galaxies at low redshift (z less than 1) are significantly more evolved in the lambda(sub 0) = 0 model than in the lambda(sub 0) = 0.8 model. This result implies that previous attempts to determine Lambda using the number counts versus redshift test are probably unreliable.

Norovirus and FRNA bacteriophage determined by RT-qPCR and infectious FRNA bacteriophage in wastewater and oysters.

PubMed

Flannery, John; Keaveney, Sinéad; Rajko-Nenow, Paulina; O'Flaherty, Vincent; Doré, William

2013-09-15

Norovirus (NoV), the leading cause of adult non-bacterial gastroenteritis can be commonly detected in wastewater but the extent of NoV removal provided by wastewater treatment plants (WWTPs) is unclear. We monitored a newly commissioned WWTP with UV disinfection on a weekly basis over a six month period for NoV using RT-qPCR and for FRNA bacteriophage GA using both RT-qPCR (total concentration) and a plaque assay (infectious concentration). Mean concentrations of NoV GI and GII in influent wastewater were reduced by 0.25 and 0.41 log10 genome copies 100 ml(-1), respectively by the WWTP. The mean concentration of total FRNA bacteriophage GA was reduced by 0.35 log genome copies 100 ml(-1) compared to a reduction of infectious FRNA bacteriophage GA of 2.13 log PFU 100 ml(-1). A significant difference between concentrations of infectious and total FRNA bacteriophage GA was observed in treated, but not in untreated wastewaters. We conclude that RT-qPCR in isolation underestimates the reduction of infectious virus during wastewater treatment. We further compared the concentrations of infectious virus in combined sewer overflow (CSO) and UV treated effluents using FRNA bacteriophage GA. A greater percentage (98%) of infectious virus is released in CSO discharges than UV treated effluent (44%). Following a CSO discharge, concentrations of NoV GII and infectious FRNA bacteriophage GA in oysters from less than the limit of detection to 3150 genome copies 100 g(-1) and 1050 PFU 100 g(-1) respectively. Copyright © 2013 Elsevier Ltd. All rights reserved.

Isolation, characterization, and application of bacteriophages for Salmonella spp. biocontrol in pigs.

PubMed

Albino, Luiz A A; Rostagno, Marcos H; Húngaro, Humberto M; Mendonça, Regina C S

2014-08-01

Foodborne illness due to Salmonella-contaminated pork products is an important public health problem, causing significant economic losses worldwide. The use of bacteriophages is a potential intervention tool that has attracted interest for the control of foodborne pathogens. The objective of this study was to detect the presence of Salmonella in commercial pig farms and to isolate specific autochthonous bacteriophages against Salmonella Typhimurium, to characterize them and to evaluate their lytic capacity against Salmonella Typhimurium in vivo and in vitro. Salmonella was isolated on 50% (4/8) of the farms, with serotype Typhimurium being the most prevalent, detected in 48.2% of samples (13/27). The isolated Salmonella Typhimurium bacteriophages belong to the Podoviridae family, were active against serotypes Abony, Enteritidis, Typhi, and Typhimurium, but not against serotypes Arizonae, Cholerasuis, Gallinarum, and Pullorum. In in vitro tests, bacteriophage at 10(7) PFU/mL and 10(9) PFU/mL significantly reduced (p<0.05) Salmonella Typhimurium counts in 1.6 and 2.5 log10 colony-forming units (CFU)/mL, respectively, after 24 h. Before the in vivo treatment with bacteriophages, Salmonella was identified in 93.3% (28/30) of the fecal samples from the pigs inoculated with 10(6) CFU/mL, and only in 56.6% (17/30) after the treatment consisting of oral administration of the pool of the bacteriophages after the fasting period, simulating a common preslaughter practice. These results indicate that the pool of bacteriophages administered was capable of reducing the colonization of Salmonella in pigs.

Significance of the Bacteriophage Treatment Schedule in Reducing Salmonella Colonization of Poultry

PubMed Central

Bardina, Carlota; Spricigo, Denis A.; Cortés, Pilar

2012-01-01

Salmonella remains the major cause of food-borne diseases worldwide, with chickens known to be the main reservoir for this zoonotic pathogen. Among the many approaches to reducing Salmonella colonization of broilers, bacteriophage offers several advantages. In this study, three bacteriophages (UAB_Phi20, UAB_Phi78, and UAB_Phi87) obtained from our collection that exhibited a broad host range against Salmonella enterica serovar Enteritidis and Salmonella enterica serovar Typhimurium were characterized with respect to morphology, genome size, and restriction patterns. A cocktail composed of the three bacteriophages was more effective in promoting the lysis of S. Enteritidis and S. Typhimurium cultures than any of the three bacteriophages alone. In addition, the cocktail was able to lyse the Salmonella enterica serovars Virchow, Hadar, and Infantis. The effectiveness of the bacteriophage cocktail in reducing the concentration of S. Typhimurium was tested in two animal models using different treatment schedules. In the mouse model, 50% survival was obtained when the cocktail was administered simultaneously with bacterial infection and again at 6, 24, and 30 h postinfection. Likewise, in the White Leghorn chicken specific-pathogen-free (SPF) model, the best results, defined as a reduction of Salmonella concentration in the chicken cecum, were obtained when the bacteriophage cocktail was administered 1 day before or just after bacterial infection and then again on different days postinfection. Our results show that frequent treatment of the chickens with bacteriophage, and especially prior to colonization of the intestinal tract by Salmonella, is required to achieve effective bacterial reduction over time. PMID:22773654

Bacteriophage cocktail for biocontrol of Salmonella in dried pet food.

PubMed

Heyse, Serena; Hanna, Leigh Farris; Woolston, Joelle; Sulakvelidze, Alexander; Charbonneau, Duane

2015-01-01

Human salmonellosis has been associated with contaminated pet foods and treats. Therefore, there is interest in identifying novel approaches for reducing the risk of Salmonella contamination within pet food manufacturing environments. The use of lytic bacteriophages shows promise as a safe and effective way to mitigate Salmonella contamination in various food products. Bacteriophages are safe, natural, highly targeted antibacterial agents that specifically kill bacteria and can be targeted to kill food pathogens without affecting other microbiota. In this study, we show that a cocktail containing six bacteriophages had a broadspectrum activity in vitro against a library of 930 Salmonella enterica strains representing 44 known serovars. The cocktail was effective against 95% of the strains in this tested library. In liquid culture dose-ranging experiments, bacteriophage cocktail concentrations of ≥10(8) PFU/ml inactivated more than 90% of the Salmonella population (10(1) to 10(3) CFU/ml). Dried pet food inoculated with a mixture containing equal proportions of Salmonella serovars Enteritidis (ATCC 4931), Montevideo (ATCC 8387), Senftenberg (ATCC 8400), and Typhimurium (ATCC 13311) and then surface treated with the six-bacteriophage cocktail (≥2.5 ± 1.5 × 10(6) PFU/g) achieved a greater than 1-log (P < 0.001) reduction compared with the phosphate-buffered saline-treated control in measured viable Salmonella within 60 min. Moreover, this bacteriophage cocktail reduced natural contamination in samples taken from an undistributed lot of commercial dried dog food that tested positive for Salmonella. Our results indicate that bacteriophage biocontrol of S. enterica in dried pet food is technically feasible.

Development of in-vitro models to elucidate mechanisms of intrinsic cellular and tissue fluorescence

NASA Astrophysics Data System (ADS)

Savage, Howard E.; Kolli, Venkateswara; Saha, Sanjoy; Zhang, Jian C.; Glasgold, Mark; Sacks, Peter G.; Alfano, Robert R.; Schantz, Stimson P.

1995-04-01

In vitro cell model systems have been used to study the mechanisms of intrinsic cellular and tissue fluorescence as a potential biomarker for cancer. Phenotypic characteristics of cancer that are different from normal tissue include changes in histoarchitecture, proliferation rates and differentiation. a nitrosmethlybenzylamine (NMBA)/rat esophageal carcinogenesis model (NMBA), a transforming growth factor beta (TGF- (beta) )/normal epithelial cell model, and a retinoic acid (RA)/multicellular tumor spheroid model (RAMTS) were used to assess fluorescence changes associated respectively with changes in histoarchitecture, proliferation rates and differentiation. A xenon based fluorescence spectrophotometer (Mediscience Corp.) was used to collect excitation and emission spectra. Two excitation scans ((lambda) Ex 200-360 nm, (lambda) Em 380 nm; (lambda) Ex 240-430 nm, (lambda) Em 450 nm) and two emission scans ((lambda) Ex 300 nm, (lambda) Em 320-580 nm; (lambda) Ex 340 nm, (lambda) Em 360-660 nm) were used to analyze the three model systems. Using the NMBA model. Differences were seen in the excitation scan ((lambda) Ex 200-360 nm, (lambda) Em 380 nm) and the emission scan ((lambda) Ex 340 nm, (lambda) Em 360-660 nm) when normal rat esophageal tissue was compared to hyperplastic and tumor tissue. In the (TGF-(beta) ) model, differences were seen in the excitation scan ((lambda) Ex 240-430 nm, (lambda) Em 450 nm) when comparing proliferation slowed (TGF-(beta) treated) epithelial cells to their untreated controls. In the RAMTS model, differences were seen with all four scans when RA treated multicellular tumor spheroids (nondifferentiating) were compared to untreated control cells (differentiating). The data indicate that fluorescence changes seen in these model systems may relate to changes in histoarchitecture, proliferation rates and differentiation. Their relationship to in vivo fluorescence changes seen in cancer patients remains to be elucidated.

First measurement of the ratio of branching fractions B({lambda}{sub b}{sup 0}{yields}{lambda}{sub c}{sup +}{mu}{sup -}{nu}{sub {mu}})/B({lambda}{sub b}{sup 0}{yields}{lambda}{sub c}{sup +}{pi}{sup -})

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aaltonen, T.; Maki, T.; Mehtala, P.

2009-02-01

This article presents the first measurement of the ratio of branching fractions B({lambda}{sub b}{sup 0}{yields}{lambda}{sub c}{sup +}{mu}{sup -}{nu}{sub {mu}})/B({lambda}{sub b}{sup 0}{yields}{lambda}{sub c}{sup +}{pi}{sup -}). Measurements in two control samples using the same technique B(B{sup 0}{yields}D{sup +}{mu}{sup -}{nu}{sub {mu}})/B(B{sup 0}{yields}D{sup +}{pi}{sup -}) and B(B{sup 0}{yields}D*(2010){sup +}{mu}{sup -}{nu}{sub {mu}})/B(B{sup 0}{yields}D*(2010){sup +}{pi}{sup -}) are also reported. The analysis uses data from an integrated luminosity of approximately 172 pb{sup -1} of pp collisions at {radical}(s)=1.96 TeV, collected with the CDF II detector at the Fermilab Tevatron. The relative branching fractions are measured to be (B({lambda}{sub b}{sup 0}{yields}{lambda}{sub c}{sup +}{mu}{sup -}{nu}{sub {mu}})/B({lambda}{sub b}{sup 0}{yields}{lambda}{sub c}{supmore » +}{pi}{sup -}))=16.6{+-}3.0(stat){+-}1.0(syst)(+2.6/-3.4)(PDG){+-}0.3 (EBR), (B(B{sup 0}{yields}D{sup +}{mu}{sup -}{nu}{sub {mu}})/B(B{sup 0}{yields}D{sup +}{pi}{sup -}))9.9{+-}1.0(stat){+-}0.6(syst){+-}0.4(PDG){+-}0.5(EBR), and (B(B{sup 0}{yields}D*(2010){sup +}{mu}{sup -}{nu}{sub {mu}})/B(B{sup 0}{yields}D*(2010){sup +}{pi}{sup -}))=16.5{+-}2.3(stat){+-} 0.6(syst){+-}0.5(PDG){+-}0.8(EBR). The uncertainties are from statistics (stat), internal systematics (syst), world averages of measurements published by the Particle Data Group or subsidiary measurements in this analysis (PDG), and unmeasured branching fractions estimated from theory (EBR), respectively. This article also presents measurements of the branching fractions of four new {lambda}{sub b}{sup 0} semileptonic decays: {lambda}{sub b}{sup 0}{yields}{lambda}{sub c}(2595){sup +}{mu}{sup -}{nu}{sub {mu}}, {lambda}{sub b}{sup 0}{yields}{lambda}{sub c}(2625){sup +}{mu}{sup -}{nu}{sub {mu}}, {lambda}{sub b}{sup 0}{yields}{sigma}{sub c}(2455){sup 0}{pi}{sup +}{mu}{sup -}{nu}{sub {mu}}, and {lambda}{sub b}{sup 0}{yields}{sigma}{sub c}(2455){sup ++}{pi}{sup -}{mu}{sup -}{nu}{sub {mu}}, relative to the branching fraction of the {lambda}{sub b}{sup 0}{yields}{lambda}{sub c}{sup +}{mu}{sup -}{nu}{sub {mu}} decay. Finally, the transverse-momentum distribution of {lambda}{sub b}{sup 0} baryons produced in pp collisions is measured and found to be significantly different from that of B{sup 0} mesons, which results in a modification in the production cross-section ratio {sigma}{sub {lambda}{sub b}{sup 0}}/{sigma}{sub B{sup 0}} with respect to the CDF I measurement.« less

76 FR 66187 - Bacteriophage of Clavibacter Michiganensis Subspecies Michiganensis; Exemption From the...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-26

... bacteria, which means they attach to, infect, and reproduce in bacteria, and are host-specific for bacteria... bacteria. In addition, there is no evidence for bacteriophage infecting any other life form, including humans, except bacteria (Refs. 7, 12, and 13). Humans and other animals commonly consume bacteriophage as...

Genome Sequences of 19 Novel Erwinia amylovora Bacteriophages

PubMed Central

Esplin, Ian N. D.; Berg, Jordan A.; Sharma, Ruchira; Allen, Robert C.; Arens, Daniel K.; Ashcroft, Cody R.; Bairett, Shannon R.; Beatty, Nolan J.; Bickmore, Madeline; Bloomfield, Travis J.; Brady, T. Scott; Bybee, Rachel N.; Carter, John L.; Choi, Minsey C.; Duncan, Steven; Fajardo, Christopher P.; Foy, Brayden B.; Fuhriman, David A.; Gibby, Paul D.; Grossarth, Savannah E.; Harbaugh, Kala; Harris, Natalie; Hilton, Jared A.; Hurst, Emily; Hyde, Jonathan R.; Ingersoll, Kayleigh; Jacobson, Caitlin M.; James, Brady D.; Jarvis, Todd M.; Jaen-Anieves, Daniella; Jensen, Garrett L.; Knabe, Bradley K.; Kruger, Jared L.; Merrill, Bryan D.; Pape, Jenny A.; Payne Anderson, Ashley M.; Payne, David E.; Peck, Malia D.; Pollock, Samuel V.; Putnam, Micah J.; Ransom, Ethan K.; Ririe, Devin B.; Robinson, David M.; Rogers, Spencer L.; Russell, Kerri A.; Schoenhals, Jonathan E.; Shurtleff, Christopher A.; Simister, Austin R.; Smith, Hunter G.; Stephenson, Michael B.; Staley, Lyndsay A.; Stettler, Jason M.; Stratton, Mallorie L.; Tateoka, Olivia B.; Tatlow, P. J.; Taylor, Alexander S.; Thompson, Suzanne E.; Townsend, Michelle H.; Thurgood, Trever L.; Usher, Brittian K.; Whitley, Kiara V.; Ward, Andrew T.; Ward, Megan E. H.; Webb, Charles J.; Wienclaw, Trevor M.; Williamson, Taryn L.; Wells, Michael J.; Wright, Cole K.; Breakwell, Donald P.; Hope, Sandra

2017-01-01

ABSTRACT Erwinia amylovora is the causal agent of fire blight, a devastating disease affecting some plants of the Rosaceae family. We isolated bacteriophages from samples collected from infected apple and pear trees along the Wasatch Front in Utah. We announce 19 high-quality complete genome sequences of E. amylovora bacteriophages. PMID:29146842

Seven Bacteriophages Isolated from the Female Urinary Microbiota

PubMed Central

Malki, Kema; Sible, Emily; Cooper, Alexandria; Garretto, Andrea; Bruder, Katherine; Watkins, Siobhan C.

2016-01-01

Recent research has debunked the myth that urine is sterile, having uncovered bacteria within the bladders of healthy individuals. However, the identity, diversity, and putative roles of bacteriophages in the bladder are unknown. We report the draft genome sequences of seven bacteriophages isolated from microbial communities from adult female bladders. PMID:27881533

Biotinylation of environmentally isolated Shiga toxin-producing Escherichia coli (STEC) – specific bacteriophages for biosensor and biocontrol applications

USDA-ARS?s Scientific Manuscript database

Like common bacteriophages, Shiga toxin-producing Escherichia coli (STEC) bacteriophages are viruses that recognize and bind to specific bacterial host (STEC) for propagation. They co-exist with STEC hosts, which cause epidemic food and waterborne illnesses, but may act as host populations limiting ...

Potential impact of environmental bacteriophages in spreading antibiotic resistance genes.

PubMed

Muniesa, Maite; Colomer-Lluch, Marta; Jofre, Juan

2013-06-01

The idea that bacteriophage transduction plays a role in the horizontal transfer of antibiotic resistance genes is gaining momentum. Such transduction might be vital in horizontal transfer from environmental to human body-associated biomes and here we review many lines of evidence supporting this notion. It is well accepted that bacteriophages are the most abundant entities in most environments, where they have been shown to be quite persistent. This fact, together with the ability of many phages to infect bacteria belonging to different taxa, makes them suitable vehicles for gene transfer. Metagenomic studies confirm that substantial percentages of the bacteriophage particles present in most environments contain bacterial genes, including mobile genetic elements and antibiotic resistance genes. When specific genes of resistance to antibiotics are detected by real-time PCR in the bacteriophage populations of different environments, only tenfold lower numbers of these genes are observed, compared with those found in the corresponding bacterial populations. In addition, the antibiotic resistance genes from these bacteriophages are functional and generate resistance to the bacteria when these genes are transfected. Finally, reports about the transduction of antibiotic resistance genes are on the increase.

Development and Use of Personalized Bacteriophage-Based Therapeutic Cocktails To Treat a Patient with a Disseminated Resistant Acinetobacter baumannii Infection.

PubMed

Schooley, Robert T; Biswas, Biswajit; Gill, Jason J; Hernandez-Morales, Adriana; Lancaster, Jacob; Lessor, Lauren; Barr, Jeremy J; Reed, Sharon L; Rohwer, Forest; Benler, Sean; Segall, Anca M; Taplitz, Randy; Smith, Davey M; Kerr, Kim; Kumaraswamy, Monika; Nizet, Victor; Lin, Leo; McCauley, Melanie D; Strathdee, Steffanie A; Benson, Constance A; Pope, Robert K; Leroux, Brian M; Picel, Andrew C; Mateczun, Alfred J; Cilwa, Katherine E; Regeimbal, James M; Estrella, Luis A; Wolfe, David M; Henry, Matthew S; Quinones, Javier; Salka, Scott; Bishop-Lilly, Kimberly A; Young, Ry; Hamilton, Theron

2017-10-01

Widespread antibiotic use in clinical medicine and the livestock industry has contributed to the global spread of multidrug-resistant (MDR) bacterial pathogens, including Acinetobacter baumannii We report on a method used to produce a personalized bacteriophage-based therapeutic treatment for a 68-year-old diabetic patient with necrotizing pancreatitis complicated by an MDR A. baumannii infection. Despite multiple antibiotic courses and efforts at percutaneous drainage of a pancreatic pseudocyst, the patient deteriorated over a 4-month period. In the absence of effective antibiotics, two laboratories identified nine different bacteriophages with lytic activity for an A. baumannii isolate from the patient. Administration of these bacteriophages intravenously and percutaneously into the abscess cavities was associated with reversal of the patient's downward clinical trajectory, clearance of the A. baumannii infection, and a return to health. The outcome of this case suggests that the methods described here for the production of bacteriophage therapeutics could be applied to similar cases and that more concerted efforts to investigate the use of therapeutic bacteriophages for MDR bacterial infections are warranted.

Antigenic properties of HCMV peptides displayed by filamentous bacteriophages vs. synthetic peptides.

PubMed

Ulivieri, Cristina; Citro, Alessandra; Ivaldi, Federico; Mascolo, Dina; Ghittoni, Raffaella; Fanigliulo, Daniela; Manca, Fabrizio; Baldari, Cosima Tatiana; Li Pira, Giuseppina; Del Pozzo, Giovanna

2008-08-15

Several efforts have been invested in the identification of CTL and Th epitopes, as well as in the characterization of their immunodominance and MHC restriction, for the generation of a peptide-based HCMV vaccine. Small synthetic peptides are, however, poor antigens and carrier proteins are important for improving the efficacy of synthetic peptide vaccines. Recombinant bacteriophages appear as promising tools in the design of subunit vaccines. To investigate the antigenicity of peptides carried by recombinant bacteriophages we displayed different HCMV MHCII restricted peptides on the capsid of filamentous bacteriophage (fd) and found that hybrid bacteriophages are processed by human APC and activate HCMV-specific CD4 T-cells. Furthermore we constructed a reporter T-cell hybridoma expressing a chimeric TCR comprising murine alphabeta constant regions and human variable regions specific for the HLA-A2 restricted immunodominant NLV peptide of HCMV. Using the filamentous bacteriophage as an epitope carrier, we detected a more robust and long lasting response of the reporter T-cell hybridoma compared to peptide stimulation. Our results show a general enhancement of T-cell responses when antigenic peptides are carried by phages.

Development and Use of Personalized Bacteriophage-Based Therapeutic Cocktails To Treat a Patient with a Disseminated Resistant Acinetobacter baumannii Infection

PubMed Central

Biswas, Biswajit; Gill, Jason J.; Hernandez-Morales, Adriana; Lancaster, Jacob; Lessor, Lauren; Barr, Jeremy J.; Reed, Sharon L.; Rohwer, Forest; Benler, Sean; Segall, Anca M.; Taplitz, Randy; Smith, Davey M.; Kerr, Kim; Kumaraswamy, Monika; Nizet, Victor; Lin, Leo; McCauley, Melanie D.; Strathdee, Steffanie A.; Benson, Constance A.; Pope, Robert K.; Leroux, Brian M.; Picel, Andrew C.; Mateczun, Alfred J.; Cilwa, Katherine E.; Regeimbal, James M.; Estrella, Luis A.; Wolfe, David M.; Henry, Matthew S.; Quinones, Javier; Salka, Scott; Bishop-Lilly, Kimberly A.; Young, Ry; Hamilton, Theron

2017-01-01

ABSTRACT Widespread antibiotic use in clinical medicine and the livestock industry has contributed to the global spread of multidrug-resistant (MDR) bacterial pathogens, including Acinetobacter baumannii. We report on a method used to produce a personalized bacteriophage-based therapeutic treatment for a 68-year-old diabetic patient with necrotizing pancreatitis complicated by an MDR A. baumannii infection. Despite multiple antibiotic courses and efforts at percutaneous drainage of a pancreatic pseudocyst, the patient deteriorated over a 4-month period. In the absence of effective antibiotics, two laboratories identified nine different bacteriophages with lytic activity for an A. baumannii isolate from the patient. Administration of these bacteriophages intravenously and percutaneously into the abscess cavities was associated with reversal of the patient's downward clinical trajectory, clearance of the A. baumannii infection, and a return to health. The outcome of this case suggests that the methods described here for the production of bacteriophage therapeutics could be applied to similar cases and that more concerted efforts to investigate the use of therapeutic bacteriophages for MDR bacterial infections are warranted. PMID:28807909

Inhibiting the Growth of Escherichia coli O157:H7 in Beef, Pork, and Chicken Meat using a Bacteriophage

PubMed Central

Seo, Jina; Seo, Dong Joo; Oh, Hyejin; Jeon, Su Been; Oh, Mi-Hwa; Choi, Changsun

2016-01-01

This study aimed to inhibit Escherichia coli (E. coli) O157:H7 artificially contaminated in fresh meat using bacteriophage. Among 14 bacteriophages, the highly lytic bacteriophage BPECO19 strain was selected to inhibit E. coli O157:H7 in artificially contaminated meat samples. Bacteriophage BPECO19 significantly reduced E. coli O157:H7 bacterial load in vitro in a multiplicity of infection (MOI)-dependent manner. E. coli O157:H7 was completely inhibited only in 10 min in vitro by the treatment of 10,000 MOI BPECO19. The treatment of BPECO19 at 100,000 MOI completely reduced 5 Log CFU/cm2 E. coli O157:H7 bacterial load in beef and pork at 4 and 8h, respectively. In chicken meat, a 4.65 log reduction of E. coli O157:H7 was observed at 4 h by 100,000 MOI. The treatment of single bacteriophage BPECO19 was an effective method to control E. coli O157:H7 in meat samples. PMID:27194926

Characterization and formulation into solid dosage forms of a novel bacteriophage lytic against Klebsiella oxytoca

PubMed Central

Petrovski, Steve; Hoyle, Dannielle; Chan, Hiu Tat; Lock, Peter; Tucci, Joseph

2017-01-01

Aim To isolate and characterize bacteriophage lytic for the opportunistic pathogen Klebsiella oxytoca and their formulation into a range of solid dosage forms for in-vitro testing. Methods and results We report the isolation, genomic and functional characterization of a novel bacteriophage lytic for Klebsiella oxytoca, which does not infect the closely related Klebsiella pneumoniae. This bacteriophage was formulated into suppositories and troches and shown to be released and lyse underlying Klebsiella oxytoca bacteria in an in-vitro model. These bacteriophage formulations were stable for at least 49 days at 4°C. Conclusions The successful in-vitro assay of these formulations here suggests that they could potentially be tested in-vivo to determine whether such a therapeutic approach could modulate the gut microbiome, and control Klebsiella oxytoca overgrowth, during antibiotic therapy regimes. Significance and impact of the study This study reports a novel bacteriophage specific for Klebsiella oxytoca which can be formulated into solid dosage forms appropriate for potential delivery in testing as a therapy to modulate gut microbiome during antibiotic therapies. PMID:28817689

The fate of deleted DNA produced during programmed genomic deletion events in Tetrahymena thermophila.

PubMed Central

Saveliev, S V; Cox, M M

1994-01-01

Thousands of DNA deletion events occur during macronuclear development in the ciliate Tetrahymena thermophila. In two deleted genomic regions, designated M and R, the eliminated sequences form circles that can be detected by PCR. However, the circles are not normal products of the reaction pathway. The circular forms occur at very low levels in conjugating cells, but are stable. Sequencing analysis showed that many of the circles (as many as 50% of those examined) reflected a precise deletion in the M and R regions. The remaining circles were either smaller or larger and contained varying lengths of sequences derived from the chromosomal DNA surrounding the eliminated region. The chromosomal junctions left behind after deletion were more precise, although deletions in either the M or R regions can generate any of several alternative junctions (1). Some new chromosomal junctions were detected in the present study. The results suggest that the deleted segment is released as a linear DNA species that is degraded rapidly. The species is only rarely converted to the stable circles we detect. The deletion mechanism is different from those proposed for deletion events in hypotrichous ciliates (2-4), and does not reflect a conservative site-specific recombination process such as that promoted by the bacteriophage lambda integrase (5). Images PMID:7838724

Bacteriophage-based nanoprobes for rapid bacteria separation

NASA Astrophysics Data System (ADS)

Chen, Juhong; Duncan, Bradley; Wang, Ziyuan; Wang, Li-Sheng; Rotello, Vincent M.; Nugen, Sam R.

2015-10-01

The lack of practical methods for bacterial separation remains a hindrance for the low-cost and successful development of rapid detection methods from complex samples. Antibody-tagged magnetic particles are commonly used to pull analytes from a liquid sample. While this method is well-established, improvements in capture efficiencies would result in an increase of the overall detection assay performance. Bacteriophages represent a low-cost and more consistent biorecognition element as compared to antibodies. We have developed nanoscale bacteriophage-tagged magnetic probes, where T7 bacteriophages were bound to magnetic nanoparticles. The nanoprobe allowed the specific recognition and attachment to E. coli cells. The phage magnetic nanprobes were directly compared to antibody-conjugated magnetic nanoprobes. The capture efficiencies of bacteriophages and antibodies on nanoparticles for the separation of E. coli K12 at varying concentrations were determined. The results indicated a similar bacteria capture efficiency between the two nanoprobes.The lack of practical methods for bacterial separation remains a hindrance for the low-cost and successful development of rapid detection methods from complex samples. Antibody-tagged magnetic particles are commonly used to pull analytes from a liquid sample. While this method is well-established, improvements in capture efficiencies would result in an increase of the overall detection assay performance. Bacteriophages represent a low-cost and more consistent biorecognition element as compared to antibodies. We have developed nanoscale bacteriophage-tagged magnetic probes, where T7 bacteriophages were bound to magnetic nanoparticles. The nanoprobe allowed the specific recognition and attachment to E. coli cells. The phage magnetic nanprobes were directly compared to antibody-conjugated magnetic nanoprobes. The capture efficiencies of bacteriophages and antibodies on nanoparticles for the separation of E. coli K12 at varying concentrations were determined. The results indicated a similar bacteria capture efficiency between the two nanoprobes. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr03779d

On the nature of the nova-like variable CD-42 deg 14462

NASA Technical Reports Server (NTRS)

Guinan, E. F.; Sion, E. M.

1981-01-01

Low dispersion long and short wavelength IUE spectra of the nova like system CD-42 deg 14462 were obtained on August 24 U.T. The short wave spectrum exhibits absorption features due to C III (lambda 1175), Lalpha 1216), NV (lambda1240), HeII (lambda 1640), SiIV (lambda1394), NIV (lambda1875) with CIV (lambda1550) as a P Cygni feature with blue shifted absorption suggesting the presence of material leaving the system. Possible interpretations of this object are discussed.

Anti p and anti Lambda production in Si + Au collisions at the AGS

NASA Technical Reports Server (NTRS)

Wu, Yue-Dong

1996-01-01

(anti (ital p)) and (anti (Lambda)) production in central Si + Au collisions has been measured by E589 at the BNL-AGS. Preliminary (ital m)(sub (perpendicular)) spectra are presented for (anti (ital p))'s and (anti (Lambda))'s. The (ital dn/dy) distribution for (anti (ital p))'s is also presented. Based on the (anti (ital p)) and (anti (Lambda)) measurements, (anti (Lambda))/(anti (ital p)) ratios are calculated in the rapidity range of 1.1-1.5.

Complete genome sequence of IME15, the first T7-like bacteriophage lytic to pan-antibiotic-resistant Stenotrophomonas maltophilia.

PubMed

Huang, Yong; Fan, Huahao; Pei, Guangqian; Fan, Hang; Zhang, Zhiyi; An, Xiaoping; Mi, Zhiqiang; Shi, Taoxing; Tong, Yigang

2012-12-01

T7-like bacteriophages are a class of virulent bacteriophages which have a clearer genetic background and smaller genomes than other phages. In addition, it grows faster and is easier to culture than other phages. At present, the numbers of available T7-like bacteriophage genomes and Stenotrophomonas maltophilia genomes are small, and IME15 is the first T7-like virulent Stenotrophomonas phage whose sequence has been reported. It shows effective lysis of S. maltophilia. Here we announce its complete genome, and major findings from its annotation are described.

ASYMMETRIC ABSORPTION PROFILES OF Ly{alpha} AND Ly{beta} IN DAMPED Ly{alpha} SYSTEMS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Hee-Won, E-mail: hwlee@sejong.ac.kr

2013-08-01

Damped Ly{alpha} systems observed in the quasar spectra are characterized by a high neutral hydrogen column density, N{sub HI} > 2 x 10{sup 20} cm{sup -2}. The absorption wing profiles are often fitted using the Voigt function due to the fact that the scattering cross section near the resonant line center is approximately described by the Lorentzian function. Since a hydrogen atom has infinitely many p states that participate in the electric dipole interaction, the cross section starts to deviate from the Lorentzian in an asymmetric way in the line wing regions. We investigate this asymmetry in the absorption linemore » profiles around Ly{alpha} and Ly{beta} as a function of the neutral hydrogen column density N{sub HI}. In terms of {Delta}{lambda} {identical_to} {lambda} - {lambda}{sub {alpha}}, we expand the Kramers-Heisenberg formula around Ly{alpha} to find {sigma}({lambda}) {approx_equal} (0.5f{sub 12}){sup 2}{sigma}{sub T}({Delta}{lambda}/{lambda}{sub {alpha}}){sup -2}[1 + 3.792({Delta}{lambda}/{lambda}{sub {alpha}})], where f{sub 12} and {sigma}{sub T} are the oscillator strength of Ly{alpha} and the Thomson scattering cross section, respectively. In terms of {Delta}{lambda}{sub 2} {identical_to} {lambda} - {lambda}{sub {beta}} in the vicinity of Ly{beta}, the total scattering cross section, given as the sum of cross sections for Rayleigh and Raman scattering, is shown to be {sigma}({lambda}) {approx_equal} {sigma}{sub T}(0.5f{sub 13}){sup 2}(1 + R{sub 0})({Delta}{lambda}{sub 2}/{lambda}{sub {beta}}){sup -2}[1 - 24.68({Delta}{lambda}{sub 2}/{lambda}{sub {beta}})] with f{sub 13} and the factor R{sub 0} = 0.1342 being the oscillator strength for Ly{beta} and the ratio of the Raman cross section to Rayleigh cross section, respectively. A redward asymmetry develops around Ly{alpha}, whereas a blue asymmetry is obtained for Ly{beta}. The absorption center shifts are found to be almost proportional to the neutral hydrogen column density.« less

The interplay between mechanics and stability of viral cages

NASA Astrophysics Data System (ADS)

Hernando-Pérez, Mercedes; Pascual, Elena; Aznar, María; Ionel, Alina; Castón, José R.; Luque, Antoni; Carrascosa, José L.; Reguera, David; de Pablo, Pedro J.

2014-02-01

The stability and strength of viral nanoparticles are crucial to fulfill the functions required through the viral cycle as well as using capsids for biomedical and nanotechnological applications. The mechanical properties of viral shells obtained through Atomic Force Microscopy (AFM) and continuum elasticity theory, such as stiffness or Young's modulus, have been interpreted very often in terms of stability. However, viruses are normally subjected to chemical rather than to mechanical aggression. Thus, a correct interpretation of mechanics in terms of stability requires an adequate linkage between the ability of viral cages to support chemical and mechanical stresses. Here we study the mechanical fragility and chemical stability of bacteriophage T7 in two different maturation states: the early proheads and the final mature capsids. Using chemical stress experiments we show that proheads are less stable than final mature capsids. Still, both particles present similar anisotropic stiffness, indicating that a continuum elasticity description in terms of Young's modulus is not an adequate measure of viral stability. In combination with a computational coarse-grained model we demonstrate that mechanical anisotropy of T7 emerges out of the discrete nature of the proheads and empty capsids. Even though they present the same stiffness, proheads break earlier and have fractures ten times larger than mature capsids, in agreement with chemical stability, thus demonstrating that fragility rather than stiffness is a better indicator of viral cages' stability.The stability and strength of viral nanoparticles are crucial to fulfill the functions required through the viral cycle as well as using capsids for biomedical and nanotechnological applications. The mechanical properties of viral shells obtained through Atomic Force Microscopy (AFM) and continuum elasticity theory, such as stiffness or Young's modulus, have been interpreted very often in terms of stability. However, viruses are normally subjected to chemical rather than to mechanical aggression. Thus, a correct interpretation of mechanics in terms of stability requires an adequate linkage between the ability of viral cages to support chemical and mechanical stresses. Here we study the mechanical fragility and chemical stability of bacteriophage T7 in two different maturation states: the early proheads and the final mature capsids. Using chemical stress experiments we show that proheads are less stable than final mature capsids. Still, both particles present similar anisotropic stiffness, indicating that a continuum elasticity description in terms of Young's modulus is not an adequate measure of viral stability. In combination with a computational coarse-grained model we demonstrate that mechanical anisotropy of T7 emerges out of the discrete nature of the proheads and empty capsids. Even though they present the same stiffness, proheads break earlier and have fractures ten times larger than mature capsids, in agreement with chemical stability, thus demonstrating that fragility rather than stiffness is a better indicator of viral cages' stability. Electronic supplementary information (ESI) available: Purification of T7 proheads and capsids, coarse-grained simulations of the indentation of T7 empty capsids, Finite Element (FE) simulations, and justification of the anisotropic stiffness based on structural information. See DOI: 10.1039/c3nr05763a

Access to bacteriophage therapy: discouraging experiences from the human cell and tissue legal framework.

PubMed

Verbeken, G; Huys, I; De Vos, D; De Coninck, A; Roseeuw, D; Kets, E; Vanderkelen, A; Draye, J P; Rose, T; Jennes, S; Ceulemans, C; Pirnay, J P

2016-02-01

Cultures of human epithelial cells (keratinocytes) are used as an additional surgical tool to treat critically burnt patients. Initially, the production environment of keratinocyte grafts was regulated exclusively by national regulations. In 2004, the European Tissues and Cells Directive 2004/23/EC (transposed into Belgian Law) imposed requirements that resulted in increased production costs and no significant increase in quality and/or safety. In 2007, Europe published Regulation (EC) No. 1394/2007 on Advanced Therapy Medicinal Products. Overnight, cultured keratinocytes became (arguably) 'Advanced' Therapy Medicinal Products to be produced as human medicinal products. The practical impact of these amendments was (and still is) considerable. A similar development appears imminent in bacteriophage therapy. Bacteriophages are bacterial viruses that can be used for tackling the problem of bacterial resistance development to antibiotics. Therapeutic natural bacteriophages have been in clinical use for almost 100 years. Regulators today are framing the (re-)introduction of (natural) bacteriophage therapy into 'modern western' medicine as biological medicinal products, also subject to stringent regulatory medicinal products requirements. In this paper, we look back on a century of bacteriophage therapy to make the case that therapeutic natural bacteriophages should not be classified under the medicinal product regulatory frames as they exist today. It is our call to authorities to not repeat the mistake of the past. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Bacteriophage Infectivity Against Pseudomonas aeruginosa in Saline Conditions

PubMed Central

Scarascia, Giantommaso; Yap, Scott A.; Kaksonen, Anna H.; Hong, Pei-Ying

2018-01-01

Pseudomonas aeruginosa is a ubiquitous member of marine biofilm, and reduces thiosulfate to produce toxic hydrogen sulfide gas. In this study, lytic bacteriophages were isolated and applied to inhibit the growth of P. aeruginosa in planktonic mode at different temperature, pH, and salinity. Bacteriophages showed optimal infectivity at a multiplicity of infection of 10 in saline conditions, and demonstrated lytic abilities over all tested temperature (25, 30, 37, and 45°C) and pH 6–9. Planktonic P. aeruginosa exhibited significantly longer lag phase and lower specific growth rates upon exposure to bacteriophages. Bacteriophages were subsequently applied to P. aeruginosa-enriched biofilm and were determined to lower the relative abundance of Pseudomonas-related taxa from 0.17 to 5.58% in controls to 0.01–0.61% in treated microbial communities. The relative abundance of Alphaproteobacteria, Pseudoalteromonas, and Planococcaceae decreased, possibly due to the phage-induced disruption of the biofilm matrix. Lastly, when applied to mitigate biofouling of ultrafiltration membranes, bacteriophages were determined to reduce the transmembrane pressure increase by 18% when utilized alone, and by 49% when used in combination with citric acid. The combined treatment was more effective compared with the citric acid treatment alone, which reported ca. 30% transmembrane pressure reduction. Collectively, the findings demonstrated that bacteriophages can be used as a biocidal agent to mitigate undesirable P. aeruginosa-associated problems in seawater applications. PMID:29770130

A simple and novel modification of comet assay for determination of bacteriophage mediated bacterial cell lysis.

PubMed

Khairnar, Krishna; Sanmukh, Swapnil; Chandekar, Rajshree; Paunikar, Waman

2014-07-01

The comet assay is the widely used method for in vitro toxicity testing which is also an alternative to the use of animal models for in vivo testing. Since, its inception in 1984 by Ostling and Johansson, it is being modified frequently for a wide range of application. In spite of its wide applicability, unfortunately there is no report of its application in bacteriophages research. In this study, a novel application of comet assay for the detection of bacteriophage mediated bacterial cell lysis was described. The conventional methods in bacteriophage research for studying bacterial lysis by bacteriophages are plaque assay method. It is time consuming, laborious and costly. The lytic activity of bacteriophage devours the bacterial cell which results in the release of bacterial genomic material that gets detected by ethidium bromide staining method by the comet assay protocol. The objective of this study was to compare efficacy of comet assay with different assay used to study phage mediated bacterial lysis. The assay was performed on culture isolates (N=80 studies), modified comet assay appear to have relatively higher sensitivity and specificity than other assay. The results of the study showed that the application of comet assay can be an economical, time saving and less laborious alternative to conventional plaque assay for the detection of bacteriophage mediated bacterial cell lysis. Copyright © 2014 Elsevier B.V. All rights reserved.

Bacteriophage Applications for Food Production and Processing

PubMed Central

Moye, Zachary D.; Woolston, Joelle; Sulakvelidze, Alexander

2018-01-01

Foodborne illnesses remain a major cause of hospitalization and death worldwide despite many advances in food sanitation techniques and pathogen surveillance. Traditional antimicrobial methods, such as pasteurization, high pressure processing, irradiation, and chemical disinfectants are capable of reducing microbial populations in foods to varying degrees, but they also have considerable drawbacks, such as a large initial investment, potential damage to processing equipment due to their corrosive nature, and a deleterious impact on organoleptic qualities (and possibly the nutritional value) of foods. Perhaps most importantly, these decontamination strategies kill indiscriminately, including many—often beneficial—bacteria that are naturally present in foods. One promising technique that addresses several of these shortcomings is bacteriophage biocontrol, a green and natural method that uses lytic bacteriophages isolated from the environment to specifically target pathogenic bacteria and eliminate them from (or significantly reduce their levels in) foods. Since the initial conception of using bacteriophages on foods, a substantial number of research reports have described the use of bacteriophage biocontrol to target a variety of bacterial pathogens in various foods, ranging from ready-to-eat deli meats to fresh fruits and vegetables, and the number of commercially available products containing bacteriophages approved for use in food safety applications has also been steadily increasing. Though some challenges remain, bacteriophage biocontrol is increasingly recognized as an attractive modality in our arsenal of tools for safely and naturally eliminating pathogenic bacteria from foods. PMID:29671810

Screening of Pro-Asp Sequences Exposed on Bacteriophage M13 as an Ideal Anchor for Gold Nanocubes.

PubMed

Lee, Hwa Kyoung; Lee, Yujean; Kim, Hyori; Lee, Hye-Eun; Chang, Hyejin; Nam, Ki Tae; Jeong, Dae Hong; Chung, Junho

2017-09-15

Bacteriophages are thought to be ideal vehicles for linking antibodies to nanoparticles. Here, we define the sequence of peptides exposed as a fusion protein on M13 bacteriophages to yield optimal binding of gold nanocubes and efficient bacteriophage amplification. We generated five helper bacteriophage libraries using AE(X) 2 DP, AE(X) 3 DP, AE(X) 4 DP, AE(X) 5 DP, and AE(X) 6 DP as the exposed portion of pVIII, in which X was a randomized amino acid residue encoded by the nucleotide sequence NNK. Efficient phage amplification was achievable only in the AE(X) 2 DP, AE(X) 3 DP, and AE(X) 4 DP libraries. Through biopanning with gold nanocubes, we enriched the phage clones and selected the clone with the highest fold change after enrichment. This clone displayed Pro-Asp on the surface of the bacteriophage and had amplification yields similar to those of the wild-type helper bacteriophage (VCSM13). The clone displayed even binding of gold nanocubes along its length and minimal aggregation after binding. We conclude that, for efficient amplification, the exposed pVIII amino acid length should be limited to six residues and Ala-Glu-Pro-Asp-Asp-Pro (AEPDDP) is the ideal fusion protein sequence for guaranteeing the optimal formation of a complex with gold nanocubes.

Genome Sequences of 19 Novel Erwinia amylovora Bacteriophages.

PubMed

Esplin, Ian N D; Berg, Jordan A; Sharma, Ruchira; Allen, Robert C; Arens, Daniel K; Ashcroft, Cody R; Bairett, Shannon R; Beatty, Nolan J; Bickmore, Madeline; Bloomfield, Travis J; Brady, T Scott; Bybee, Rachel N; Carter, John L; Choi, Minsey C; Duncan, Steven; Fajardo, Christopher P; Foy, Brayden B; Fuhriman, David A; Gibby, Paul D; Grossarth, Savannah E; Harbaugh, Kala; Harris, Natalie; Hilton, Jared A; Hurst, Emily; Hyde, Jonathan R; Ingersoll, Kayleigh; Jacobson, Caitlin M; James, Brady D; Jarvis, Todd M; Jaen-Anieves, Daniella; Jensen, Garrett L; Knabe, Bradley K; Kruger, Jared L; Merrill, Bryan D; Pape, Jenny A; Payne Anderson, Ashley M; Payne, David E; Peck, Malia D; Pollock, Samuel V; Putnam, Micah J; Ransom, Ethan K; Ririe, Devin B; Robinson, David M; Rogers, Spencer L; Russell, Kerri A; Schoenhals, Jonathan E; Shurtleff, Christopher A; Simister, Austin R; Smith, Hunter G; Stephenson, Michael B; Staley, Lyndsay A; Stettler, Jason M; Stratton, Mallorie L; Tateoka, Olivia B; Tatlow, P J; Taylor, Alexander S; Thompson, Suzanne E; Townsend, Michelle H; Thurgood, Trever L; Usher, Brittian K; Whitley, Kiara V; Ward, Andrew T; Ward, Megan E H; Webb, Charles J; Wienclaw, Trevor M; Williamson, Taryn L; Wells, Michael J; Wright, Cole K; Breakwell, Donald P; Hope, Sandra; Grose, Julianne H

2017-11-16

Erwinia amylovora is the causal agent of fire blight, a devastating disease affecting some plants of the Rosaceae family. We isolated bacteriophages from samples collected from infected apple and pear trees along the Wasatch Front in Utah. We announce 19 high-quality complete genome sequences of E. amylovora bacteriophages. Copyright © 2017 Esplin et al.

Interference with propagation of typing bacteriophages by extrachromosomal elements in Salmonella typhimurium: bacteriophage type 505.

PubMed Central

van Embden, J D; van Leeuwen, W J; Guinée, P A

1976-01-01

Samonella typhimurium bacteriophage type 505 is the most frequently encountered phage type in the Netherlands and its neighboring countries. Phage type 505 was analyzed with regard o the interference with propagation of the typing phages by the prophages and plasmids, present in the type strain S. typhimurium 505... Images PMID:783145

Biological UV dosimeters in simulated space irradiation conditions

NASA Astrophysics Data System (ADS)

Rontó, G.; Bérces, A.; Fekete, A.; Kovács, G.; Lammer, H.

For the measurement of the harmful biological effect of solar UV radiation bacteriophage T7 and polycrystalline uracil dosimeters were used. For terrestrial dosimetric purposes bacteriophage T7 has been applied in solution, while uracil in the form of thin layers. For space irradiation dosimetry the uracil, phage T7-DNA and bacteriophage T7 thin layer samples were prepared in vacuum tightly closed sandwich forms covered either by calciumfluoride or quartz windows. The experimental conditions tested correspond to the conditions planned in the EXPOSE facility: the samples were surrounded by nitrogen atmosphere at various humidities, their vacuum stability was tested in the vacuum chamber of the Institute of Space Research,, Graz. All kinds of the thin film samples have been stored in an atmosphere containing Nitrogen and Hidrogen, in quality control no change in the structure of them has been found. To attenuate the high extraterrestrial irradiance neutral filters of 0.5 and 1.0 optical densities have been tested. Irradiation of the samples has been performed with various UV sources: solar simulator, low pressure Mercury lamp, Deuterium lamp. Dose-effect functions have been determined using for the evaluation spectrophotometry in the characteristic UV range, HPLC of photoproducts, PCR of two different primer sequences of phage T7-DNA. Photoproduct formation kinetics was followed by the saturation level of uracil thin layer. Attenuation ability of the neutral filters was controlled with low pressure Mercury lamp by the exposure necessary for saturation of uracil dosimeters. A three and tenfold increase in the exposure was found respectively, while the influence of spectral composition of the irradiation source was tested using Deuterium lamp supplied with Ca F2 and quartz filters respectively. A doubling of the irradiance was necessary for the saturation of uracil with quartz filter.

Attenuation and colloidal mobilization of bacteriophages in natural sediments under anoxic as compared to oxic conditions.

PubMed

Klitzke, Sondra; Schroeder, Jendrik; Selinka, Hans-Christoph; Szewzyk, Regine; Chorus, Ingrid

2015-06-15

Redox conditions are known to affect the fate of viruses in porous media. Several studies report the relevance of colloid-facilitated virus transport in the subsurface, but detailed studies on the effect of anoxic conditions on virus retention in natural sediments are still missing. Therefore, we investigated the fate of viruses in natural flood plain sediments with different sesquioxide contents under anoxic conditions by considering sorption to the solid phase, sorption to mobilized colloids, and inactivation in the aqueous phase. Batch experiments were conducted under oxic and anoxic conditions at pH values between 5.1 and 7.6, using bacteriophages MS2 and PhiX174 as model viruses. In addition to free and colloid-associated bacteriophages, dissolved and colloidal concentrations of Fe, Al and organic C as well as dissolved Ca were determined. Results showed that regardless of redox conditions, bacteriophages did not adsorb to mobilized colloids, even under favourable charge conditions. Under anoxic conditions, attenuation of bacteriophages was dominated by sorption over inactivation, with MS2 showing a higher degree of sorption than PhiX174. Inactivation in water was low under anoxic conditions for both bacteriophages with about one log10 decrease in concentration during 16 h. Increased Fe/Al concentrations and a low organic carbon content of the sediment led to enhanced bacteriophage removal under anoxic conditions. However, even in the presence of sufficient Fe/A-(hydr)oxides on the solid phase, bacteriophage sorption was low. We presume that organic matter may limit the potential retention of sesquioxides in anoxic sediments and should thus be considered for the risk assessment of virus breakthrough in the subsurface. Copyright © 2015 Elsevier B.V. All rights reserved.

Bacteriophage-nanocomposites: an easy and reproducible method for the construction, handling, storage and transport of conjugates for deployment of bacteriophages active against Pseudomonas aeruginosa.

PubMed

Cooper, Ian R; Illsley, Matthew; Korobeinyk, Alina V; Whitby, Raymond L D

2015-04-01

The purpose of this work was proof of concept to develop a novel, cost effective protocol for the binding of bacteriophages to a surface without loss of function, after storage in various media. The technology platform involved covalently bonding bacteriophage 13 (a Pseudomonas aeruginosa bacteriophage) to two magnetised multiwalled carbon nanotube scaffolds using a series of buffers; bacteriophage-nanotube (B-N) conjugates were efficacious after storage at 20 °C for six weeks. B-N conjugates were added to human cell culture in vitro for 9 days without causing necrosis and apoptosis. B-N conjugates were frozen (-20 °C) in cell culture media for several weeks, after which recovery from the human cell culture medium was possible using a simple magnetic separation technique. The retention of viral infective potential was demonstrated by subsequent spread plating onto lawns of susceptible P. aeruginosa. Analysis of the human cell culture medium revealed the production of interleukins by the human fibroblasts upon exposure to the bacteriophage. One day after exposure, IL-8 levels transitorily increased between 60 and 100 pg/mL, but this level was not found on any subsequent days, suggesting an initial but not long lasting response. This paper outlines the development of a method to deliver antimicrobial activity to a surface that is small enough to be combined with other materials. To our knowledge at time of publication, this is the first report of magnetically coupled bacteriophages specific to human pathogens which can be recovered from test systems, and could represent a novel means to conditionally deploy antibacterial agents into living eukaryotic systems without the risks of some antibiotic therapies. Copyright © 2015. Published by Elsevier B.V.

Bacteriophage sensitivity patterns among bacteria isolated from marine waters

NASA Astrophysics Data System (ADS)

Moebus, K.; Nattkemper, H.

1981-09-01

Phage-host cross-reaction tests were performed with 774 bacterial strains and 298 bacteriophages. The bacteria (bacteriophages) were isolated at different times from water samples collected in the Atlantic Ocean between the European continental shelf and the Sargasso Sea: 733 (258) strains; in the North Sea near Helgoland: 31 (31) strains; and in the Bay of Biscay: 10 (9) strains. Of the Atlantic Ocean bacteria 326 were found to be susceptible to one or more Atlantic Ocean bacteriophage(s). The bacteriophage sensitivity patterns of these bacteria vary considerably, placing 225 of them in two large clusters of bacteriophage-host systems. Taking all into account, 250 of the 326 Atlantic Ocean bacteria are different from each other. This high degree of variation among the bacteria distinguishes microbial populations derived from widely separated eastern and western regions of the Atlantic Ocean. It also sets apart from each other the populations derived from samples collected at successive stations some 200 miles apart, although to a lesser degree. With bacterial populations found from samples collected on the way back and forth between Europe and the Sargasso Sea a gradual change was observed from "western" phage sensitivity patterns to "eastern" ones. Sixty-nine Atlantic Ocean bacteria are sensitive to bacteriophages isolated from the North Sea and the Bay of Biscay; of these only 26 strains are also susceptible to Atlantic Ocean phages. The interpretation of the results is based on the hydrographical conditions prevailing in the northern Atlantic Ocean including the North Sea, and on the assumption that the microbial populations investigated have undergone genetic changes while being transported within water masses from west to east.

Use of a bacteriophage cocktail to control Salmonella in food and the food industry.

PubMed

Spricigo, Denis Augusto; Bardina, Carlota; Cortés, Pilar; Llagostera, Montserrat

2013-07-15

The use of lytic bacteriophages for the biocontrol of food-borne pathogens in food and in the food industry is gaining increasing acceptance. In this study, the effectiveness of a bacteriophage cocktail composed of three different lytic bacteriophages (UAB_Phi 20, UAB_Phi78, and UAB_Phi87) was determined in four different food matrices (pig skin, chicken breasts, fresh eggs, and packaged lettuce) experimentally contaminated with Salmonella enterica serovar Typhimurium and S. enterica serovar Enteritidis. A significant bacterial reduction (>4 and 2 log/cm(2) for S. Typhimurium and S. Enteritidis, respectively; p≤0.005) was obtained in pig skin sprayed with the bacteriophage cocktail and then incubated at 33 °C for 6h. Significant decreases in the concentration of S. Typhimurium and S. Enteritidis were also measured in chicken breasts dipped for 5 min in a solution containing the bacteriophage cocktail and then refrigerated at 4 °C for 7 days (2.2 and 0.9 log10 cfu/g, respectively; p≤0.0001) as well as in lettuce similarly treated for 60 min at room temperature (3.9 and 2.2 log10 cfu/g, respectively; p≤0.005). However, only a minor reduction of the bacterial concentration (0.9 log10 cfu/cm(2) of S. Enteritidis and S. Typhimurium; p≤0.005) was achieved in fresh eggs sprayed with the bacteriophage cocktail and then incubated at 25 °C for 2 h. These results show the potential effectiveness of this bacteriophage cocktail as a biocontrol agent of Salmonella in several food matrices under conditions similar to those used in their production. Copyright © 2013 Elsevier B.V. All rights reserved.

Control of Salmonella on sprouting mung bean and alfalfa seeds by using a biocontrol preparation based on antagonistic bacteria and lytic bacteriophages.

PubMed

Ye, Jianxiong; Kostrzynska, Magdalaena; Dunfield, Kari; Warriner, Keith

2010-01-01

The following reports on the application of a combination of antagonistic bacteria and lytic bacteriophages to control the growth of Salmonella on sprouting mung beans and alfalfa seeds. Antagonistic bacteria were isolated from mung bean sprouts and tomatoes by using the deferred plate assay to assess anti-Salmonella activity. From the isolates screened, an Enterobacter asburiae strain (labeled "JX1") exhibited stable antagonistic activity against a broad range of Salmonella serovars (Agona, Berta, Enteritidis, Hadar, Heidelberg, Javiana, Montevideo, Muenchen, Newport, Saint Paul, and Typhimurium). Lytic bacteriophages against Salmonella were isolated from pig or cattle manure effluent. A bacteriophage cocktail prepared from six isolates was coinoculated with E. asburiae JX1 along with Salmonella in broth culture. The combination of E. asburiae JX1 and bacteriophage cocktail reduced the levels of Salmonella by 5.7 to 6.4 log CFU/ml. Mung beans inoculated with Salmonella and sprouted over a 4-day period attained levels of 6.72 + or - 0.78 log CFU/g. In contrast, levels of Salmonella were reduced to 3.31 + or - 2.48 or 1.16 + or - 2.14 log CFU/g when the pathogen was coinoculated with bacteriophages or E. asburiae JX1, respectively. However, by using a combination of E. asburiae JX1 and bacteriophages, the levels of Salmonella associated with mung bean sprouts were only detected by enrichment. The biocontrol preparation was effective at controlling the growth of Salmonella under a range of sprouting temperatures (20 to 30 degrees Celsius) and was equally effective at suppressing the growth of Salmonella on sprouting alfalfa seeds. The combination of E. asburiae JX1 and bacteriophages represents a promising, chemical-free approach for controlling the growth of Salmonella on sprouting seeds.

Bacteriophages for detection and control of bacterial pathogens in food and food-processing environment.

PubMed

Brovko, Lubov Y; Anany, Hany; Griffiths, Mansel W

2012-01-01

This chapter presents recent advances in bacteriophage research and their application in the area of food safety. Section 1 describes general facts on phage biology that are relevant to their application for control and detection of bacterial pathogens in food and environmental samples. Section 2 summarizes the recently acquired data on application of bacteriophages to control growth of bacterial pathogens and spoilage organisms in food and food-processing environment. Section 3 deals with application of bacteriophages for detection and identification of bacterial pathogens. Advantages of bacteriophage-based methods are presented and their shortcomings are discussed. The chapter is intended for food scientist and food product developers, and people in food inspection and health agencies with the ultimate goal to attract their attention to the new developing technology that has a tremendous potential in providing means for producing wholesome and safe food. Copyright © 2012 Elsevier Inc. All rights reserved.

Phage-based extraction of polyhydroxybutyrate (PHB) produced from synthetic crude glycerol.

PubMed

Hand, Steven; Gill, Jason; Chu, Kung-Hui

2016-07-01

Polyhydroxybutyrate (PHB), a biodegradable plastic, is an attractive alternative to traditional petrochemical-derived plastics. However, its production is expensive due to high feedstock and extraction costs. As bacteriophages are natural predators to bacteria and specific to their hosts, bacteriophages offer a new and unique means to release PHB from bacteria via cell lysis. This study examined the feasibility of using bacteriophages as an effective bioextractant to release PHB produced by Pseudomonas oleovorans cultured with glycerol containing common impurities which are generated from biodiesel production. While bacteria in stationary growth are known to be immune to bacteriophages, a bacteriophage Ke14 - isolated from soil - could lyse the PHB-filled cells effectively when excess nutrients were provided to trigger cell regrowth. The short-term nutrient treatment facilitated cell lysis with a little expense of PHB depolymerization, offering a new way to release PHB from cells without energy/solvent input. Copyright © 2016 Elsevier B.V. All rights reserved.

M13 Bacteriophage-Based Self-Assembly Structures and Their Functional Capabilities.

PubMed

Moon, Jong-Sik; Kim, Won-Geun; Kim, Chuntae; Park, Geun-Tae; Heo, Jeong; Yoo, So Y; Oh, Jin-Woo

2015-06-01

Controlling the assembly of basic structural building blocks in a systematic and orderly fashion is an emerging issue in various areas of science and engineering such as physics, chemistry, material science, biological engineering, and electrical engineering. The self-assembly technique, among many other kinds of ordering techniques, has several unique advantages and the M13 bacteriophage can be utilized as part of this technique. The M13 bacteriophage (Phage) can easily be modified genetically and chemically to demonstrate specific functions. This allows for its use as a template to determine the homogeneous distribution and percolated network structures of inorganic nanostructures under ambient conditions. Inexpensive and environmentally friendly synthesis can be achieved by using the M13 bacteriophage as a novel functional building block. Here, we discuss recent advances in the application of M13 bacteriophage self-assembly structures and the future of this technology.

Mutation of M13 Bacteriophage Major Coat Protein for Increased Conjugation to Exogenous Compounds.

PubMed

Tridgett, Matthew; Lloyd, James R; Kennefick, Jack; Moore-Kelly, Charles; Dafforn, Timothy R

2018-06-20

Over the past ten years there has been increasing interest in the conjugation of exogenous compounds to the surface of the M13 bacteriophage. M13 offers a convenient scaffold for the development of nanoassemblies with useful functions, such as highly specific drug delivery and pathogen detection. However, the progress of these technologies has been hindered by the limited efficiency of conjugation to the bacteriophage. Here we generate a mutant version of M13 with an additional lysine residue expressed on the outer surface of the M13 major coat protein, pVIII. We show that this mutation is accommodated by the bacteriophage and that up to an additional 520 exogenous groups can be attached to the bacteriophage surface via amine-directed conjugation. These results could aid the development of high payload drug delivery nanoassemblies and pathogen detection systems with increased sensitivity.

M13 Bacteriophage-Based Self-Assembly Structures and Their Functional Capabilities

PubMed Central

Moon, Jong-Sik; Kim, Won-Geun; Kim, Chuntae; Park, Geun-Tae; Heo, Jeong; Yoo, So Y; Oh, Jin-Woo

2015-01-01

Controlling the assembly of basic structural building blocks in a systematic and orderly fashion is an emerging issue in various areas of science and engineering such as physics, chemistry, material science, biological engineering, and electrical engineering. The self-assembly technique, among many other kinds of ordering techniques, has several unique advantages and the M13 bacteriophage can be utilized as part of this technique. The M13 bacteriophage (Phage) can easily be modified genetically and chemically to demonstrate specific functions. This allows for its use as a template to determine the homogeneous distribution and percolated network structures of inorganic nanostructures under ambient conditions. Inexpensive and environmentally friendly synthesis can be achieved by using the M13 bacteriophage as a novel functional building block. Here, we discuss recent advances in the application of M13 bacteriophage self-assembly structures and the future of this technology. PMID:26146494

The NMR-Rosetta capsid model of M13 bacteriophage reveals a quadrupled hydrophobic packing epitope.

PubMed

Morag, Omry; Sgourakis, Nikolaos G; Baker, David; Goldbourt, Amir

2015-01-27

Filamentous phage are elongated semiflexible ssDNA viruses that infect bacteria. The M13 phage, belonging to the family inoviridae, has a length of ∼1 μm and a diameter of ∼7 nm. Here we present a structural model for the capsid of intact M13 bacteriophage using Rosetta model building guided by structure restraints obtained from magic-angle spinning solid-state NMR experimental data. The C5 subunit symmetry observed in fiber diffraction studies was enforced during model building. The structure consists of stacked pentamers with largely alpha helical subunits containing an N-terminal type II β-turn; there is a rise of 16.6-16.7 Å and a tilt of 36.1-36.6° between consecutive pentamers. The packing of the subunits is stabilized by a repeating hydrophobic stacking pocket; each subunit participates in four pockets by contributing different hydrophobic residues, which are spread along the subunit sequence. Our study provides, to our knowledge, the first magic-angle spinning NMR structure of an intact filamentous virus capsid and further demonstrates the strength of this technique as a method of choice to study noncrystalline, high-molecular-weight molecular assemblies.

The NMR–Rosetta capsid model of M13 bacteriophage reveals a quadrupled hydrophobic packing epitope

PubMed Central

Morag, Omry; Sgourakis, Nikolaos G.; Baker, David; Goldbourt, Amir

2015-01-01

Filamentous phage are elongated semiflexible ssDNA viruses that infect bacteria. The M13 phage, belonging to the family inoviridae, has a length of ∼1 μm and a diameter of ∼7 nm. Here we present a structural model for the capsid of intact M13 bacteriophage using Rosetta model building guided by structure restraints obtained from magic-angle spinning solid-state NMR experimental data. The C5 subunit symmetry observed in fiber diffraction studies was enforced during model building. The structure consists of stacked pentamers with largely alpha helical subunits containing an N-terminal type II β-turn; there is a rise of 16.6–16.7 Å and a tilt of 36.1–36.6° between consecutive pentamers. The packing of the subunits is stabilized by a repeating hydrophobic stacking pocket; each subunit participates in four pockets by contributing different hydrophobic residues, which are spread along the subunit sequence. Our study provides, to our knowledge, the first magic-angle spinning NMR structure of an intact filamentous virus capsid and further demonstrates the strength of this technique as a method of choice to study noncrystalline, high-molecular-weight molecular assemblies. PMID:25587134

[Study of fusion of bacteriophage f2 double-stranded RNA, poly(A).poly(U), and poly(G).poly(C) in the presence of tetraethylammonium bromide].

PubMed

Permogorov, V I; Tiaglov, B V; Minaev, V E

1980-01-01

The data on the dependence of the melting curve parameters of double-stranded RNA (replicative form of RNA of f2 bacteriophage) poly(A) times poly(U) and poly(G) times poly(C) on the concentration of (C2H5)4NBr were obtained. The RNA melting range width is shown to pass through the minimum value T =2.1+/-0.1degrees at the point of inversion of relative stability of GC and AU pairs that corresponds to 4.0+/-0.1 M concentration of (C2H5)4NBr. Using the melting temperatures of poly(A) times poly(U) and poly(G) times poly(C) the rependence of Tgc-Tau parameter on (C2H5)4NBr concentration was shown. It was concluded from these data that the effect of the double-stranded RNA stacking heterogeneity was negligible in the 0-3 M range of (C2H5)4NBr concentration. Melting curves of RNA were obtained at various values of Tgc-Tau parameter. It was shown that the profile of fine structure of melting curves depends on the value of Tgc-Tau parameter.

Bacteriophage phi 6 RNA-dependent RNA polymerase: molecular details of initiating nucleic acid synthesis without primer.

PubMed

Laurila, Minni R L; Makeyev, Eugene V; Bamford, Dennis H

2002-05-10

Like most RNA polymerases, the polymerase of double-strand RNA bacteriophage phi6 (phi6pol) is capable of primer-independent initiation. Based on the recently solved phi6pol initiation complex structure, a four-amino acid-long loop (amino acids 630-633) has been suggested to stabilize the first two incoming NTPs through stacking interactions with tyrosine, Tyr(630). A similar loop is also present in the hepatitis C virus polymerase, another enzyme capable of de novo initiation. Here, we use a series of phi6pol mutants to address the role of this element. As predicted, mutants at the Tyr(630) position are inefficient in initiation de novo. Unexpectedly, when the loop is disordered by changing Tyr(630)-Lys(631)-Trp(632) to GSG, phi6pol becomes a primer-dependent enzyme, either extending complementary oligonucleotide or, when the template 3' terminus can adopt a hairpin-like conformation, utilizing a "copy-back" initiation mechanism. In contrast to the wild-type phi6pol, the GSG mutant does not require high GTP concentration for its optimal activity. These findings suggest a general model for the initiation of de novo RNA synthesis.

Effect of temperature and sunlight on the stability of human adenoviruses and MS2 as fecal contaminants on fresh produce surfaces.

PubMed

Carratalà, Anna; Rodriguez-Manzano, Jesús; Hundesa, Ayalkibet; Rusiñol, Marta; Fresno, Sandra; Cook, Nigel; Girones, Rosina

2013-06-17

Determining the stability, or persistence in an infectious state, of foodborne viral pathogens attached to surfaces of soft fruits and salad vegetables is essential to underpin risk assessment studies in food safety. Here, we evaluate the effect of temperature and sunlight on the stability of infectious human adenoviruses type 2 and MS2 bacteriophages on lettuce and strawberry surfaces as representative fresh products. Human adenoviruses have been selected because of their double role as viral pathogens and viral indicators of human fecal contamination. Stability assays were performed with artificially contaminated fresh samples kept in the dark or under sunlight exposure at 4 and 30°C over 24h. The results indicate that temperature is the major factor affecting HAdV stability in fresh produce surfaces, effecting decay between 3 and 4 log after 24h at 30°C. The inactivation times to achieve a reduction between 1 and 4-log are calculated for each experimental condition. This work provides useful information to be considered for improving food safety regarding the transmission of foodborne viruses through supply chains. Copyright © 2013 Elsevier B.V. All rights reserved.

Measurement of sigma(Lambda(b)0) / sigma(anti-B 0) x B(Lambda0(b) ---> Lambda+(c) pi-) / B(anti-B0 ---> D+ pi-) in p anti-p collisions at S**(1/2) = 1.96-TeV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abulencia, A.; Acosta, D.; Adelman, Jahred A.

2006-01-01

The authors present the first observation of the baryon decay {Lambda}{sub b}{sup 0} {yields} {Lambda}{sub c}{sup +} {pi}{sup -} followed by {Lambda}{sub c}{sup +} {yields} pK{sup -} {pi}{sup +} in 106 pb{sup -1} p{bar p} collisions at {radical}s = 1.96 TeV in the CDF experiment. IN order to reduce systematic error, the measured rate for {Lambda}{sub b}{sup 0} decay is normalized to the kinematically similar meson decay {bar B}{sup 0} {yields} D{sup +}{pi}{sup -} followed by D{sup +} {yields} {pi}{sup +}K{sup -}{pi}{sup +}. They report the ratio of production cross sections ({sigma}) times the ratio of branching fractions ({Beta}) formore » the momentum region integrated above p{sub T} > 6 GeV/c and pseudorapidity range |{eta}| < 1.3: {sigma}(p{bar p} {yields} {Lambda}{sub b}{sup 0}X)/{sigma}(p{bar p} {yields} {bar B}{sup 0} X) x {Beta}({Lambda}{sub b}{sup 0} {yields} {Lambda}{sub c}{sup +}{pi}{sup -})/{Beta}({bar B}{sup 0} {yields} D{sup +}{pi}{sup -}) = 0.82 {+-} 0.08(stat) {+-} 0.11(syst) {+-} 0.22 ({Beta}({Lambda}{sub c}{sup +} {yields} pK{sup -} {pi}{sup +})).« less

Inhibitory effect of tocotrienol on eukaryotic DNA polymerase {lambda} and angiogenesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mizushina, Yoshiyuki; Nakagawa, Kiyotaka; Shibata, Akira

2006-01-20

Tocotrienols, vitamin E compounds that have an unsaturated side chain with three double bonds, selectively inhibited the activity of mammalian DNA polymerase {lambda} (pol {lambda}) in vitro. These compounds did not influence the activities of replicative pols such as {alpha}, {delta}, and {epsilon}, or even the activity of pol {beta} which is thought to have a very similar three-dimensional structure to the pol {beta}-like region of pol {lambda}. Since {delta}-tocotrienol had the strongest inhibitory effect among the four ({alpha}- to {delta}-) tocotrienols, the isomer's structure might be an important factor in the inhibition of pol {lambda}. The inhibitory effect ofmore » {delta}-tocotrienol on both intact pol {lambda} (residues 1-575) and a truncated pol {lambda} lacking the N-terminal BRCA1 C-terminus (BRCT) domain (residues 133-575, del-1 pol {lambda}) was dose-dependent, with 50% inhibition observed at a concentration of 18.4 and 90.1 {mu}M, respectively. However, del-2 pol {lambda} (residues 245-575) containing the C-terminal pol {beta}-like region was unaffected. Tocotrienols also inhibited the proliferation of and formation of tubes by bovine aortic endothelial cells, with {delta}-tocotrienol having the greatest effect. These results indicated that tocotrienols targeted both pol {lambda} and angiogenesis as anti-cancer agents. The relationship between the inhibition of pol {lambda} and anti-angiogenesis by {delta}-tocotrienol was discussed.« less

The formation of low-ionization emission in the halo of NGC 891

NASA Technical Reports Server (NTRS)

Sokolowski, James; Bland-Hawthorn, Jonathan

1993-01-01

Imaging and Spectroscopic study first revealed the presence of a diffuse ionized medium (DIM), having unusual excitation, pervading the lower halo of the edge-on spiral galaxy NGC 891. Emission from this DIM is strongest northeast of the nucleus, at radii between 2 and 8 kpc (hereafter region 1). The (N2)(lambda)6583/H(alpha) and (S2)(lambda) (lambda)6716,6731/H(alpha) ratios increase dramatically with z in region 1, from 0.6 and 0.5 respectively at z is approximately equal to 500 pc to 1.1 and 1.0 at z is approximately equal to 1 kpc, while nondetections of (O1)(lambda)6300 and (O3)(lambda)5007 emission yield upper limits of (O1)(lambda)6300/H(alpha) less than or equal to 0.05 and (O3)(lambda)5007/H(alpha) less than or equal to 0.15 for z less than 1 kpc. Previous photoionization models, using the radiation field from disk O and B stars, have been successful in reproducing the elevated (N2)(lambda)6583/H(alpha) and (S2)(lambda)(lambda)6716.6731/H(alpha) ratios observed. However, these radiation bounded models also produce significant (O3)(lambda)5007 emission, in conflict with the observed upper limit. Here, we report the results of new, matter bounded models for the photoionization of the DIM in region 1 of NGC 891.

Measurement of the Lambda(0)(b) lifetime in the exclusive decay Lambda(0)(b) -> J/psi Lambda(0) in p(p)over-bar collisions at root s=1.96 TeV

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abazov V. M.; Abbott, B.; Acharya, B. S.

2012-06-07

We measure the {Lambda}{sub b}{sup 0} lifetime in the fully reconstructed decay {Lambda}{sub b}{sup 0} {yields} J/{psi}{Lambda}{sup 0} using 10.4 fb{sup -1} of p{bar p} collisions collected with the D0 detector at {radical}s = 1.96 TeV. The lifetime of the topologically similar decay channel B{sup 0} {yields} J/{psi}K{sub S}{sup 0} is also measured. We obtain {tau}({Lambda}{sub b}{sup 0}) = 1.303 {+-} 0.075(stat) {+-} 0.035(syst) ps and {tau}(B{sup 0}) = 1.508 {+-} 0.025(stat) {+-} 0.043(syst) ps. Using these measurements, we determine the lifetime ratio of {tau}({Lambda}{sub b}{sup 0})/{tau}(B{sup 0}) = 0.864 {+-} 0.052(stat) {+-} 0.033(syst).

Use of bacteriophage to prevent Pseudomonas aeruginosa contamination and fouling in Jet A aviation fuel.

PubMed

Bojanowski, Caitlin L; Crookes-Goodson, Wendy J; Robinson, Jayne B

2016-11-01

In the present study, the use of bacteriophages to prevent growth and/or biofouling by Pseudomonas aeruginosa PAO1 was investigated in microcosms containing Jet A aviation fuel as the carbon source. Bacteriophages were found to be effective at preventing biofilm formation but did not always prevent planktonic growth in the microcosms. This result was at odds with experiments conducted in nutrient-rich medium, demonstrating the necessity to test antimicrobial and antifouling strategies under conditions as near as possible to the 'real world'. The success of the bacteriophages at preventing biofilm formation makes them potential candidates as antifouling agents for fuel systems.

The role of bacteriophages in periodontal health and disease.

PubMed

Pinto, Graça; Silva, Maria Daniela; Peddey, Mark; Sillankorva, Sanna; Azeredo, Joana

2016-10-01

The human periodontium health is commonly compromised by chronic inflammatory conditions and has become a major public health concern. Dental plaque, the precursor of periodontal disease, is a complex biofilm consisting mainly of bacteria, but also archaea, protozoa, fungi and viruses. Viruses that specifically infect bacteria - bacteriophages - are most common in the oral cavity. Despite this, their role in the progression of periodontal disease remains poorly explored. This review aims to summarize how bacteriophages interact with the oral microbiota, their ability to increase bacterial virulence and mediate the transfer of resistance genes and suggests how bacteriophages can be used as an alternative to the current periodontal disease therapies.

[Biological properties of bacteriophages, active to Yersinia enterocolitica].

PubMed

Darsavelidze, M A; Kapanadze, Zh S; Chanishvili, T G

2004-01-01

The biological properties of 16 clones of Y. enterolitica bacteriophages were tested to select the most active for subsequent use. For the first time Y. enterocolitica virulent phages belonging to the family of Podoviridae were described and 7 serological groups of phages with no cross reactions were registered. The technology for the production of new therapeutic and prophylactic Y. enterocolitica polyvalent bacteriophage under laboratory conditions was developed. The effective multiplicity of contamination ensuring the maximum release of phages from bacterial cells, the optimum incubation temperature and the time of exposure were established. The experimental batches of therapeutic and prophylactic Y. enterocolitica polyvalent bacteriophage thus obtained met the requirements for antibacterial preparations.

[POSSIBILITIES OF APPLICATION OF MALDI-TOF MASS-SPECTROMETRY FOR STUDY OF CARBOHYDRATE-SPECIFIC RECEPTORS FOR DIAGNOSTIC BACTERIOPHAGE EL TOR].

PubMed

Telesmanich, N R; Goncharenko, E V; Chaika, S O; Chaika, I A; Telicheva, V O

2016-01-01

Study mechanisms of interaction of diagnostic bacteriophage El Tor with sensitive strain Vibrio cholerae El Tor 18507 using direct protein profiling, identification of constant and variable proteins, taking part in interaction of the phage and cell, as well as carbohydrate-specific phage receptors. . A commercial preparation of cholera diagnostic bacteriophage El Tor, strain V. cholerae El Tor 18507 were used. Effect of carbohydrates on bacteriophage activity was determined in experiments with phage by a classic and modified by us method. Protein profiles of the studied objects were studied using MSP-analysis method. Sucrose was shown to inhibit lytic activity of bacteriophage. Proteome profiles of El Tor bacteriophage and sensitive indicator strains were studied, identification of constant and variable proteins of the studied objects by MSP Peak-list program was carried out. Analysis of changes of profiles of phage and microbial cell during interaction with sucrose gave a basis for assuming, that sucrose in the mixture of culture-phage enters interaction namely with phage protein receptors, blocking receptors specific for cholera vibrio, that subsequently manifests in a sharp decrease of phage activity against the sensitive strain.

Modeling removal of bacteriophages MS2 and PRD1 by dune recharge at Castricum, Netherlands

NASA Astrophysics Data System (ADS)

Schijven, Jack F.; Hoogenboezem, Wim; Hassanizadeh, S. Majid; Peters, Jos H.

1999-04-01

Removal of model viruses by dune recharge was studied at a field site in the dune area of Castricum, Netherlands. Recharge water was dosed with bacteriophages MS2 and PRD1 for 11 days at a constant concentration in a 10- by 15-m compartment that was isolated in a recharge basin. Breakthrough was monitored for 120 days at six wells with their screens along a flow line. Concentrations of both phages were reduced about 3 log10 within the first 2.4 m and another 5 log10 in a linear fashion within the following 27 m. A model accounting for one-site kinetic attachment as well as first-order inactivation was employed to simulate the bacteriophage breakthrough curves. The major removal process was found to be attachment of the bacteriophages. Detachment was very slow. After passage of the pulse of dosed bacteriophages, there was a long tail whose slope corresponds to the inactivation rate coefficient of 0.07-0.09 day-1 for attached bacteriophages. The end of the rising and the start of the declining limbs of the breakthrough curves could not be simulated completely, probably because of an as yet unknown process.

Genomics of Three New Bacteriophages Useful in the Biocontrol of Salmonella

PubMed Central

Bardina, Carlota; Colom, Joan; Spricigo, Denis A.; Otero, Jennifer; Sánchez-Osuna, Miquel; Cortés, Pilar; Llagostera, Montserrat

2016-01-01

Non-typhoid Salmonella is the principal pathogen related to food-borne diseases throughout the world. Widespread antibiotic resistance has adversely affected human health and has encouraged the search for alternative antimicrobial agents. The advances in bacteriophage therapy highlight their use in controlling a broad spectrum of food-borne pathogens. One requirement for the use of bacteriophages as antibacterials is the characterization of their genomes. In this work, complete genome sequencing and molecular analyses were carried out for three new virulent Salmonella-specific bacteriophages (UAB_Phi20, UAB_Phi78, and UAB_Phi87) able to infect a broad range of Salmonella strains. Sequence analysis of the genomes of UAB_Phi20, UAB_Phi78, and UAB_Phi87 bacteriophages did not evidence the presence of known virulence-associated and antibiotic resistance genes, and potential immunoreactive food allergens. The UAB_Phi20 genome comprised 41,809 base pairs with 80 open reading frames (ORFs); 24 of them with assigned function. Genome sequence showed a high homology of UAB_Phi20 with Salmonella bacteriophage P22 and other P22likeviruses genus of the Podoviridae family, including ST64T and ST104. The DNA of UAB_Phi78 contained 44,110 bp including direct terminal repeats (DTR) of 179 bp and 58 putative ORFs were predicted and 20 were assigned function. This bacteriophage was assigned to the SP6likeviruses genus of the Podoviridae family based on its high similarity not only with SP6 but also with the K1-5, K1E, and K1F bacteriophages, all of which infect Escherichia coli. The UAB_Phi87 genome sequence consisted of 87,669 bp with terminal direct repeats of 608 bp; although 148 ORFs were identified, putative functions could be assigned to only 29 of them. Sequence comparisons revealed the mosaic structure of UAB_Phi87 and its high similarity with bacteriophages Felix O1 and wV8 of E. coli with respect to genetic content and functional organization. Phylogenetic analysis of large terminase subunits confirms their packaging strategies and grouping to the different phage genus type. All these studies are necessary for the development and the use of an efficient cocktail with commercial applications in bacteriophage therapy against Salmonella. PMID:27148229

A Randomized Study of Peginterferon Lambda-1a Compared to Peginterferon Alfa-2a in Combination with Ribavirin and Telaprevir in Patients with Genotype-1 Chronic Hepatitis C.

PubMed

Flisiak, Robert; Shiffman, Mitchell; Arenas, Juan; Cheinquer, Hugo; Nikitin, Igor; Dong, Yuping; Rana, Khurram; Srinivasan, Subasree

2016-01-01

A randomized, double-blind, multinational, phase 3 study was conducted comparing the efficacy and safety of peginterferon lambda-1a (Lambda)/ribavirin (RBV)/telaprevir (TVR) vs. peginterferon alfa-2a (Alfa)/RBV/TVR in patients with chronic hepatitis C virus (HCV) genotype-1 (GT-1) infection. Patients (treatment-naïve or relapsers on prior Alfa/RBV treatment) were randomly assigned in a 2:1 ratio to receive Lambda/RBV/TVR or Alfa/RBV/TVR. Total duration of treatment was either 24 or 48 weeks (response-guided treatment), with TVR administered for the first 12 weeks. The primary endpoint was the proportion of patients who achieved a sustained virologic response at post treatment week 12 (SVR12), which was tested for noninferiority of Lambda/RBV/TVR. A total of 838 patients were enrolled, and 617 were treated; 411 and 206 patients received Lambda/RBV/TVR and Alfa/RBV/TVR, respectively. The majority of patients were treatment-naïve, with HCV GT-1b and a high baseline viral load (≥800,000 IU/mL). Less than 10% of patients had cirrhosis (Lambda, 7.5%; Alfa, 6.8%). Lambda/RBV/TVR did not meet the criterion for noninferiority (lower bound of the treatment difference interval was -12.3%); the SVR12 in all patients (modified intent-to-treat) was 76.2% in the Lambda arm and 82.0% in the Alfa arm. Overall, the frequency of adverse events in each arm was comparable (Lambda, 91.7%; Alfa, 97.1%). As expected based on the safety profile of the 2 interferons, there were more hepatobiliary events observed in the Lambda arm and more hematologic events in the Alfa arm. In this comparison of Lambda/RBV/TVR and Alfa/RBV/TVR in patients who were treatment-naïve or had relapsed on prior Alfa/RBV treatment, Lambda failed to demonstrate noninferiority based on SVR12 results. Treatment with Lambda/RBV/TVR was associated with a higher incidence of relapse. More patients discontinued Lambda/RBV/TVR treatment during the first 4 weeks of study treatment, mainly due to hepatobiliary-related events, and more Lambda patients were lost to follow-up.

Comparison of two filtration-elution procedures to improve the standard methods ISO 10705-1 & 2 for bacteriophage detection in groundwater, surface water and finished water samples.

PubMed

Helmi, K; Jacob, P; Charni-Ben-Tabassi, N; Delabre, K; Arnal, C

2011-09-01

To select a reliable method for bacteriophage concentration prior detection by culture from surface water, groundwater and drinking water to enhance the sensitivity of the standard methods ISO 10705-1 & 2. Artificially contaminated (groundwater and drinking water) and naturally contaminated (surface water) 1-litre samples were processed for bacteriophages detection. The spiked samples were inoculated with about 150 PFU of F-specific RNA bacteriophages and somatic coliphages using wastewater. Bacteriophage detection in the water samples was achieved using the standard method without and with a concentration step (electropositive Anodisc membrane or a pretreated electronegative Micro Filtration membrane, MF). For artificially contaminated matrices (drinking and ground waters), recovery rates using the concentration step were superior to 70% whilst analyses without concentration step mainly led to false negative results. Besides, the MF membrane presented higher performances compared with the Anodisc membrane. The concentration of a large volume of water (up to one litre) on a filter membrane avoids false negative results obtained by direct analysis as it allows detecting low number of bacteriophages in water samples. The addition of concentration step before applying the standard method could be useful to enhance the reliability of bacteriophages monitoring in water samples as bio-indicators to highlight faecal pollution. © No claim to French Government works. Letters in Applied Microbiology © 2011 The Society for Applied Microbiology.

Apparatus and method for closed-loop control of reactor power in minimum time

DOEpatents

Bernard, Jr., John A.

1988-11-01

Closed-loop control law for altering the power level of nuclear reactors in a safe manner and without overshoot and in minimum time. Apparatus is provided for moving a fast-acting control element such as a control rod or a control drum for altering the nuclear reactor power level. A computer computes at short time intervals either the function: .rho.=(.beta.-.rho.).omega.-.lambda..sub.e '.rho.-.SIGMA..beta..sub.i (.lambda..sub.i -.lambda..sub.e ')+l* .omega.+l* [.omega..sup.2 +.lambda..sub.e '.omega.] or the function: .rho.=(.beta.-.rho.).omega.-.lambda..sub.e .rho.-(.lambda..sub.e /.lambda..sub.e)(.beta.-.rho.)+l* .omega.+l* [.omega..sup.2 +.lambda..sub.e .omega.-(.lambda..sub.e /.lambda..sub.e).omega.] These functions each specify the rate of change of reactivity that is necessary to achieve a specified rate of change of reactor power. The direction and speed of motion of the control element is altered so as to provide the rate of reactivity change calculated using either or both of these functions thereby resulting in the attainment of a new power level without overshoot and in minimum time. These functions are computed at intervals of approximately 0.01-1.0 seconds depending on the specific application.

Bacteriophage-based Probiotic Preparation for Managing Shigella Infections

DTIC Science & Technology

2015-04-16

for a probiotic preparation – based on naturally occurring bacteriophages – as a way to condition the GI tract’s microflora gently and favorably...10-Apr-2013 Approved for Public Release; Distribution Unlimited Final Report: Bacteriophage-based Probiotic Preparation for Managing Shigella...Research Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 Phage, Shigella, probiotics REPORT DOCUMENTATION PAGE 11. SPONSOR/MONITOR’S

On Spectral Invariance of Single Scattering Albedo for Weakly Absorbing Wavelengths

NASA Technical Reports Server (NTRS)

Marshak, Alexander; Knyazikhin, Yuri; Chiu, J. Christine; Wiscombe, Warren J.

2011-01-01

This note shows that for water droplets at weakly absorbing wavelengths, the ratio omega(sub O lambda(r))/omega(sub O lambda(r(sub O)) of two single scattering albedo spectra, omega(sub O lambda(r) and omega(sub O lambda(r (sub O)), is a linear function of omega(sub O lambda(r). The slope and intercept of the linear function are wavelength independent and sum to unity. This relationship allows for a representation of any single scattering albedo omega(sub O lambda(r) via one known spectrum omega(sub O lambda(r(sub O)). The note provides a simple physical explanation of the discovered relationship. In addition to water droplets, similar linear relationships were found for the single scattering albedo of non-spherical ice crystals.

Bacteriophages for treating urinary tract infections in patients undergoing transurethral resection of the prostate: a randomized, placebo-controlled, double-blind clinical trial.

PubMed

Leitner, Lorenz; Sybesma, Wilbert; Chanishvili, Nina; Goderdzishvili, Marina; Chkhotua, Archil; Ujmajuridze, Aleksandre; Schneider, Marc P; Sartori, Andrea; Mehnert, Ulrich; Bachmann, Lucas M; Kessler, Thomas M

2017-09-26

Urinary tract infections (UTI) are among the most prevalent microbial diseases and their financial burden on society is substantial. The continuing increase of antibiotic resistance worldwide is alarming. Thus, well-tolerated, highly effective therapeutic alternatives are urgently needed. Although there is evidence indicating that bacteriophage therapy may be effective and safe for treating UTIs, the number of investigated patients is low and there is a lack of randomized controlled trials. This study is the first randomized, placebo-controlled, double-blind trial investigating bacteriophages in UTI treatment. Patients planned for transurethral resection of the prostate are screened for UTIs and enrolled if in urine culture eligible microorganisms ≥10 4 colony forming units/mL are found. Patients are randomized in a double-blind fashion to the 3 study treatment arms in a 1:1:1 ratio to receive either: a) bacteriophage (i.e. commercially available Pyo bacteriophage) solution, b) placebo solution, or c) antibiotic treatment according to the antibiotic sensitivity pattern. All treatments are intended for 7 days. No antibiotic prophylaxes will be given to the double-blinded treatment arms a) and b). As common practice, the Pyo bacteriophage cocktail is subjected to periodic adaptation cycles during the study. Urinalysis, urine culture, bladder and pain diary, and IPSS questionnaire will be completed prior to and at the end of treatment (i.e. after 7 days) or at withdrawal/drop out from the study. Patients with persistent UTIs will undergo antibiotic treatment according to antibiotic sensitivity pattern. Based on the high lytic activity and the potential of resistance optimization by direct adaptation of bacteriophages, and considering the continuing increase of antibiotic resistance worldwide, bacteriophage therapy is a very promising treatment option for UTIs. Thus, our randomized controlled trial investigating bacteriophages for treating UTIs will provide essential insights into this potentially revolutionizing treatment option. This study has been registered at clinicaltrials.gov ( www.clinicaltrials.gov/ct2/show/NCT03140085 ). April 27, 2017.

Pegylated interferons Lambda-1a and alfa-2a display different gene induction and cytokine and chemokine release profiles in whole blood, human hepatocytes and peripheral blood mononuclear cells.

PubMed

Freeman, J; Baglino, S; Friborg, J; Kraft, Z; Gray, T; Hill, M; McPhee, F; Hillson, J; Lopez-Talavera, J C; Wind-Rotolo, M

2014-06-01

Pegylated interferon-lambda-1a (Lambda), a type III interferon (IFN) in clinical development for the treatment of chronic HCV infection, has shown comparable efficacy and an improved safety profile to a regimen based on pegylated IFN alfa-2a (alfa). To establish a mechanistic context for this improved profile, we investigated the ex vivo effects of Lambda and alfa on cytokine and chemokine release, and on expression of IFN-stimulated genes (ISGs) in primary human hepatocytes and peripheral blood mononuclear cells (PBMCs) from healthy subjects. Our findings were further compared with changes observed in blood analysed from HCV-infected patients treated with Lambda or alfa in clinical studies. mRNA transcript and protein expression of the IFN-λ-limiting receptor subunit was lower compared with IFN-α receptor subunits in all cell types. Upon stimulation, alfa and Lambda induced ISG expression in hepatocytes and PBMCs, although in PBMCs Lambda-induced ISG expression was modest. Furthermore, alfa and Lambda induced release of cytokines and chemokines from hepatocytes and PBMCs, although differences in their kinetics of induction were observed. In HCV-infected patients, alfa treatment induced ISG expression in whole blood after single and repeat dosing. Lambda treatment induced modest ISG expression after single dosing and showed no induction after repeat dosing. Alfa and Lambda treatment increased IP-10, iTAC, IL-6, MCP-1 and MIP-1β levels in serum, with alfa inducing higher levels of all mediators compared with Lambda. Overall, ex vivo and in vivo induction profiles reported in this analysis strongly correlate with clinical observations of fewer related adverse events for Lambda vs those typically associated with alfa. © 2014 John Wiley & Sons Ltd.

Environmental chemistry, ecotoxicity, and fate of lambda-cyhalothrin.

PubMed

He, Li-Ming; Troiano, John; Wang, Albert; Goh, Kean

2008-01-01

Lambda-cyhalothrin is a pyrethroid insecticide used for controlling pest insects in agriculture, public health, and in construction and households. Lambda-cyhalothrin is characterized by low vapor pressure and a low Henry's law constant but by a high octanol-water partition coefficient (K(ow)) and high water-solid-organic carbon partition coefficient (K(oc)) values. Lambda-cyhalothrin is quite stable in water at pH < 8, whereas it hydrolyzes to form HCN and aldehyde under alkaline conditions. Although lambda-cyhalothrin is relatively photostable under natural irradiation, with a half-life > 3 wk, its photolysis process is fast under UV irradiation, with a half-life < 10 min. The fate of lambda-cyhalothrin in aquatic ecosystems depends on the nature of system components such as suspended solids (mineral and organic particulates) and aquatic organisms (algae, macrophytes, or aquatic animals). Lambda-cyhalothrin residues dissolved in water decrease rapidly if suspended solids and/or aquatic organisms are present because lambda-cyhalothrin molecules are strongly adsorbed by particulates and plants. Adsorbed lambda-cyhalothrin molecules show decreased degradation rates because they are less accessible to breakdown than free molecules in the water column. On the other hand, lambda-cyhalothrin adsorbed to suspended solids or bottom sediments may provide a mechanism to mitigate its acute toxicity to aquatic organisms by reducing their short-term bioavailability in the water column. The widespread use of lambda-cyhalothrin has resulted in residues in sediment, which have been found to be toxic to aquatic organisms including fish and amphipods. Mitigation measures have been used to reduce the adverse impact of lambda-cyhalothrin contributed from agricultural or urban runoff. Mitigation may be achieved by reducing the quantity of runoff and suspended solid content in runoff through wetlands, detention ponds, or vegetated ditches.

Non-LTE radiative transfer with lambda-acceleration - Convergence properties using exact full and diagonal lambda-operators

NASA Technical Reports Server (NTRS)

Macfarlane, J. J.

1992-01-01

We investigate the convergence properties of Lambda-acceleration methods for non-LTE radiative transfer problems in planar and spherical geometry. Matrix elements of the 'exact' A-operator are used to accelerate convergence to a solution in which both the radiative transfer and atomic rate equations are simultaneously satisfied. Convergence properties of two-level and multilevel atomic systems are investigated for methods using: (1) the complete Lambda-operator, and (2) the diagonal of the Lambda-operator. We find that the convergence properties for the method utilizing the complete Lambda-operator are significantly better than those of the diagonal Lambda-operator method, often reducing the number of iterations needed for convergence by a factor of between two and seven. However, the overall computational time required for large scale calculations - that is, those with many atomic levels and spatial zones - is typically a factor of a few larger for the complete Lambda-operator method, suggesting that the approach should be best applied to problems in which convergence is especially difficult.

Mass and K{lambda} Coupling of the N*(1535)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, B.C.; Graduate School of the Chinese Academy of Sciences, Beijing 100049; Zou, B.S.

2006-02-03

Using a resonance isobar model and an effective Lagrangian approach, from recent BES results on J/{psi}{yields}pp{eta} and {psi}{yields}pK{sup +}{lambda}, we deduce the ratio between effective coupling constants of N*(1535) to K{lambda} and p{eta} to be R{identical_to}g{sub N*(1535)K{lambda}}/g{sub N*(1535)p{eta}}=1.3{+-}0.3. With the previous known value of g{sub N*(1535)p{eta}}, the obtained new value of g{sub N*(1535)K{lambda}} is shown to reproduce recent pp{yields}pK{sup +}{lambda} near-threshold cross section data as well. Taking into account this large N*K{lambda} coupling in the coupled channel Breit-Wigner formula for the N*(1535), its Breit-Wigner mass is found to be around 1400 MeV, much smaller than the previous value of aboutmore » 1535 MeV obtained without including its coupling to K{lambda}. The implication on the nature of N*(1535) is discussed.« less

Determination of protein secondary structure and solvent accessibility using site-directed fluorescence labeling. Studies of T4 lysozyme using the fluorescent probe monobromobimane.

PubMed

Mansoor, S E; McHaourab, H S; Farrens, D L

1999-12-07

We report an investigation of how much protein structural information could be obtained using a site-directed fluorescence labeling (SDFL) strategy. In our experiments, we used 21 consecutive single-cysteine substitution mutants in T4 lysozyme (residues T115-K135), located in a helix-turn-helix motif. The mutants were labeled with the fluorescent probe monobromobimane and subjected to an array of fluorescence measurements. Thermal stability measurements show that introduction of the label is substantially perturbing only when it is located at buried residue sites. At buried sites (solvent surface accessibility of <40 A(2)), the destabilizations are between 3 and 5.5 kcal/mol, whereas at more exposed sites, DeltaDeltaG values of < or = 1.5 kcal/mol are obtained. Of all the fluorescence parameters that were explored (excitation lambda(max), emission lambda(max), fluorescence lifetime, quantum yield, and steady-state anisotropy), the emission lambda(max) and the steady-state anisotropy values most accurately reflect the solvent surface accessibility at each site as calculated from the crystal structure of cysteine-less T4 lysozyme. The parameters we identify allow the classification of each site as buried, partially buried, or exposed. We find that the variations in these parameters as a function of residue number reflect the sequence-specific secondary structure, the determination of which is a key step for modeling a protein of unknown structure.

Peginterferon lambda for the treatment of HBeAg-positive chronic hepatitis B: A randomized phase 2b study (LIRA-B).

PubMed

Chan, Henry L Y; Ahn, Sang Hoon; Chang, Ting-Tsung; Peng, Cheng-Yuan; Wong, David; Coffin, Carla S; Lim, Seng Gee; Chen, Pei-Jer; Janssen, Harry L A; Marcellin, Patrick; Serfaty, Lawrence; Zeuzem, Stefan; Cohen, David; Critelli, Linda; Xu, Dong; Wind-Rotolo, Megan; Cooney, Elizabeth

2016-05-01

Peginterferon lambda-1a (lambda) is a Type-III interferon, which, like alfa interferons, has antiviral activity in vitro against hepatitis B virus (HBV) and hepatitis C virus (HCV); however, lambda has a more limited extra-hepatic receptor distribution. This phase 2b study (LIRA-B) evaluated lambda in patients with chronic HBV infection. Adult HBeAg+ interferon-naive patients were randomized (1:1) to weekly lambda (180 μg) or peginterferon alfa-2a (alfa) for 48 weeks. The primary efficacy endpoint was HBeAg seroconversion at week 24 post-treatment; lambda non-inferiority was demonstrated if the 80% confidence interval (80% CI) lower bound was >-15%. Baseline characteristics were balanced across groups (lambda N=80; alfa N=83). Early on-treatment declines in HBV-DNA and qHBsAg through week 24 were greater with lambda. HBeAg seroconversion rates were comparable for lambda and alfa at week 48 (17.5% vs. 16.9%, respectively); however lambda non-inferiority was not met at week 24 post-treatment (13.8% vs. 30.1%, respectively; lambda vs. alfa 80% CI lower bound -24%). Results for other key secondary endpoints (virologic, serologic, biochemical) and post hoc combined endpoints (HBV-DNA <2000 IU/ml plus HBeAg seroconversion or ALT normalization) mostly favored alfa. Overall adverse events (AE), serious AE, and AE-discontinuation rates were comparable between arms but AE-spectra differed (more cytopenias, flu-like, and musculoskeletal symptoms observed with alfa, more ALT flares and bilirubin elevations seen with lambda). Most on-treatment flares occurred early (weeks 4-12), associated with HBV-DNA decline; all post-treatment flares were preceded by HBV-DNA rise. On-treatment, lambda showed greater early effects on HBV-DNA and qHBsAg, and comparable serologic/virologic responses at end-of-treatment. However, post-treatment, alfa-associated HBeAg seroconversion rates were higher, and key secondary results mostly favored alfa. ClinicalTrials.gov number: NCT01204762. Copyright © 2016 European Association for the Study of the Liver. Published by Elsevier B.V. All rights reserved.

First Observation of Charmed Resonances in the $$\\Lambda^0_b \\to \\Lambda^+_c \\pi^- \\pi^+ \\pi^-$$ Inclusive Decay and Measurement of Their Relative Branching Ratios at CDF

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barria, Patrizia

2012-01-01

We present the observation of themore » $$\\Lambda^0_b$$ decay into a $$\\Lambda^+_c \\pi^- \\pi^+ \\pi^-$$ final state, in $$p\\bar{p}$$ collisions at $$\\sqrt{s}$$ = 1:96 TeV. The data analyzed were collected by the CDF II detector at the Fermilab Tevatron collider, and correspond to 2:4 $$fb^{-1}$$ of integrated luminosity. We fit the invariant mass distribution of the reconstructed candidates to extract a signal yield of 848 $$\\pm$$ 93 $$\\Lambda^0_b$$ into $$\\Lambda^+_c \\pi^- \\pi^+ \\pi^-$$....« less

Further observations of the lambda 10830 He line in stars and their significance as a measure of stellar activity

NASA Technical Reports Server (NTRS)

Zirin, H.

1975-01-01

Measurements of the lambda 1030 He line in 198 stars are given along with data on other features in that spectral range. Nearly 80% of all G and K stars show some lambda 10830; of these, half are variable and 1/4 show emission. It was confirmed that lambda 10830 is not found in M stars, is weak in F stars, and is particularly strong in close binaries. The line is found in emission in extremely late M and S stars, along with P gamma, but P gamma is not in emission in G and K stars with lambda 10830 emissions. Variable He emission and Ti I emission are found in the RV Tauri variables R Scuti and U Mon. In R Aqr the Fe XIII coronal line lambda 10747 and a line at lambda 11012 which may be singlet He or La II are found, as well as lambda 10830 and P gamma. The nature of coronas or hot chromospheres in the various stars is discussed. It was concluded that the lambda 10830 intensity must be more or less proportional to the energy deposited in the chromosphere corona by non-thermal processes.

A photon spectrometric dose-rate constant determination for the Advantage Pd-103 brachytherapy source

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Zhe Jay; Bongiorni, Paul; Nath, Ravinder

Purpose: Although several dosimetric characterizations using Monte Carlo simulation and thermoluminescent dosimetry (TLD) have been reported for the new Advantage Pd-103 source (IsoAid, LLC, Port Richey, FL), no AAPM consensus value has been established for the dosimetric parameters of the source. The aim of this work was to perform an additional dose-rate constant ({Lambda}) determination using a recently established photon spectrometry technique (PST) that is independent of the published TLD and Monte Carlo techniques. Methods: Three Model IAPD-103A Advantage Pd-103 sources were used in this study. The relative photon energy spectrum emitted by each source along the transverse axis wasmore » measured using a high-resolution germanium spectrometer designed for low-energy photons. For each source, the dose-rate constant was determined from its emitted energy spectrum. The PST-determined dose-rate constant ({sub PST}{Lambda}) was then compared to those determined by TLD ({sub TLD}{Lambda}) and Monte Carlo ({sub MC}{Lambda}) techniques. A likely consensus {Lambda} value was estimated as the arithmetic mean of the average {Lambda} values determined by each of three different techniques. Results: The average {sub PST}{Lambda} value for the three Advantage sources was found to be (0.676{+-}0.026) cGyh{sup -1} U{sup -1}. Intersource variation in {sub PST}{Lambda} was less than 0.01%. The {sub PST}{Lambda} was within 2% of the reported {sub MC}{Lambda} values determined by PTRAN, EGSnrc, and MCNP5 codes. It was 3.4% lower than the reported {sub TLD}{Lambda}. A likely consensus {Lambda} value was estimated to be (0.688{+-}0.026) cGyh{sup -1} U{sup -1}, similar to the AAPM consensus values recommended currently for the Theragenics (Buford, GA) Model 200 (0.686{+-}0.033) cGyh{sup -1} U{sup -1}, the NASI (Chatsworth, CA) Model MED3633 (0.688{+-}0.033) cGyh{sup -1} U{sup -1}, and the Best Medical (Springfield, VA) Model 2335 (0.685{+-}0.033) cGyh{sup -1} U{sup -1} {sup 103}Pd sources. Conclusions: An independent {Lambda} determination has been performed for the Advantage Pd-103 source. The {sub PST}{Lambda} obtained in this work provides additional information needed for establishing a more accurate consensus {Lambda} value for the Advantage Pd-103 source.« less

78 FR 71609 - Methiocarb, Lambda-Cyhalothrin, Permethrin and Prodiamine; Notice of Receipt of Requests To...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-29

... ENVIRONMENTAL PROTECTION AGENCY [EPA-HQ-OPP-2009-1017; FRL-9902-77] Methiocarb, Lambda-Cyhalothrin... receipt of requests by the registrants to voluntarily amend their Methiocarb, Lambda- Cyhalothrin... Willowood Lambda Cyhalothrin LLC, Gowan Company, Farnam Companies, Inc., Pyxis Regulatory Consulting, Inc...

Lytic bacteriophages

PubMed Central

Sharma, Manan

2013-01-01

Foodborne illnesses resulting from the consumption of produce commodities contaminated with enteric pathogens continue to be a significant public health issue. Lytic bacteriophages may provide an effective and natural intervention to reduce bacterial pathogens on fresh and fresh-cut produce commodities. The use of multi-phage cocktails specific for a single pathogen has been most frequently assessed on produce commodities to minimize the development of bacteriophage insensitive mutants (BIM) in target pathogen populations. Regulatory approval for the use of several lytic phage products specific for bacterial pathogens such as Escherichia coli O157:H7, Salmonella spp. and Listeria monocytogenes in foods and on food processing surfaces has been granted by various agencies in the US and other countries, possibly allowing for the more widespread use of bacteriophages in the decontamination of fresh and minimally processed produce. Research studies have shown lytic bacteriophages specific for E. coli O157:H7, Salmonella spp. and Listeria monocytogenes have been effective in reducing pathogen populations on leafy greens, sprouts and tomatoes. PMID:24228223

RGD peptide-displaying M13 bacteriophage/PLGA nanofibers as cell-adhesive matrices for smooth muscle cells

NASA Astrophysics Data System (ADS)

Shin, Yong Cheol; Lee, Jong Ho; Jin, Oh Seong; Lee, Eun Ji; Jin, Lin Hua; Kim, Chang-Seok; Hong, Suck Won; Han, Dong-Wook; Kim, Chuntae; Oh, Jin-Woo

2015-01-01

Extracellular matrices (ECMs) are network structures that play an essential role in regulating cellular growth and differentiation. In this study, novel nanofibrous matrices were fabricated by electrospinning M13 bacteriophage and poly(lactic- co-glycolic acid) (PLGA) and were shown to be structurally and functionally similar to natural ECMs. A genetically-engineered M13 bacteriophage was constructed to display Arg-Gly-Asp (RGD) peptides on its surface. The physicochemical properties of RGD peptide-displaying M13 bacteriophage (RGD-M13 phage)/PLGA nanofibers were characterized by using scanning electron microscopy and Fourier-transform infrared spectroscopy. We used immunofluorescence staining to confirm that M13 bacteriophages were homogenously distributed in RGD-M13 phage/PLGA matrices. Furthermore, RGD-M13 phage/PLGA nanofibrous matrices, having excellent biocompatibility, can enhance the behaviors of vascular smooth muscle cells. This result suggests that RGD-M13 phage/PLGA nanofibrous matrices have potentials to serve as tissue engineering scaffolds.

Evaluation of consumers’ perception and willingness to pay for bacteriophage treated fresh produce

PubMed Central

Naanwaab, Cephas; Yeboah, Osei-Agyeman; Ofori Kyei, Foster; Sulakvelidze, Alexander; Goktepe, Ipek

2014-01-01

Food-borne illnesses caused by bacteria such as enterohemorrhagic E. coli and Salmonella spp. take a significant toll on American consumers’ health; they also cost the United States an estimated $77.7 billion annually in health care and other losses.1 One novel modality for improving the safety of foods is application of lytic bacteriophages directly onto foods, in order to reduce or eliminate their contamination with specific foodborne bacterial pathogens. The main objective of this study was to assess consumers’ perception about foods treated with bacteriophages and examine their willingness to pay (WTP) an additional amount (10–30 cents/lb) for bacteriophage-treated fresh produce. The study utilized a survey questionnaire administered by telephone to consumers in 4 different states: Alabama, Georgia, North Carolina, and South Carolina. The results show that consumers are in general willing to pay extra for bacteriophage-treated fresh produce if it improves their food safety. However, income, race, and the state where a consumer lives are significant determinants in their WTP. PMID:26713224

Bacteriophage application on red meats and poultry: Effects on Salmonella population in final ground products.

PubMed

Yeh, Y; Purushothaman, P; Gupta, N; Ragnone, M; Verma, S C; de Mello, A S

2017-05-01

This research was conducted to study the effects of bacteriophage application during tumbling on Salmonella populations in ground meat and poultry. Red meat trim and poultry were inoculated with a Salmonella cocktail to result in a contamination level of 7logCFU/g in ground products. A commercial preparation containing bacteriophages S16 and Felix-O1a (FO1a) was applied during tumbling at 10 7 and 10 8 PFU/ml. Samples were held at 4°C for 6h and 18h (red meat) and 30min and 6h (poultry). Overall, bacteriophage application on trim reduced 1 and 0.8logCFU/g of Salmonella in ground beef and ground pork, respectively. For ground chicken and ground turkey, Salmonella was reduced by 1.1 and 0.9logCFU/g, respectively. This study shows that bacteriophage application during tumbling of red meat trim and poultry can provide additional Salmonella control in ground products. Copyright © 2017 Elsevier Ltd. All rights reserved.

Structural relationship of curcumin derivatives binding to the BRCT domain of human DNA polymerase lambda.

PubMed

Takeuchi, Toshifumi; Ishidoh, Tomomi; Iijima, Hiroshi; Kuriyama, Isoko; Shimazaki, Noriko; Koiwai, Osamu; Kuramochi, Kouji; Kobayashi, Susumu; Sugawara, Fumio; Sakaguchi, Kengo; Yoshida, Hiromi; Mizushina, Yoshiyuki

2006-03-01

We previously reported that phenolic compounds, petasiphenol and curcumin (diferuloylmethane), were a selective inhibitor of DNA polymerase lambda (pol lambda) in vitro. The purpose of this study was to investigate the molecular structural relationship of curcumin and 13 chemically synthesized derivatives of curcumin. The inhibitory effect on pol lambda (full-length, i.e. intact pol lambda including the BRCA1 C- terminal [BRCT] domain) by some derivatives was stronger than that by curcumin, and monoacetylcurcumin (compound 13) was the strongest pol lambda inhibitor of all the compounds tested, achieving 50% inhibition at a concentration of 3.9 microm. The compound did not influence the activities of replicative pols such as alpha, delta, and epsilon. It had no effect on pol beta activity either, although the three-dimensional structure of pol beta is thought to be highly similar to that of pol lambda. Compound 13 did not inhibit the activity of the C-terminal catalytic domain of pol lambda including the pol beta-like core, in which the BRCT motif was deleted from its N-terminal region. MALDI-TOF MS analysis demonstrated that compound 13 bound selectively to the N-terminal domain of pol lambda, but did not bind to the C-terminal region. Based on these results, the pol lambda-inhibitory mechanism of compound 13 is discussed.

[Advance on genome research of Yersinia pestis bacteriophage].

PubMed

Tan, H L; Wang, P; Li, W

2017-04-10

Completion of the genome sequences on Yersinia pestis bacteriophage offered unprecedented opportunity for researchers to carry out related genomic studies. This review was based on the genomic sequences and provided a genomic perspective in describing the essential features of genome on Yersinia pestis bacteriophage. Based on the comparative genomics, genetic evolutionary relationship was discussed. Description of functions from the gene prediction and protein annotation provided evidence for further related studies.

FRNA Bacteriophages as Viral Indicators of Faecal Contamination in Mexican Tropical Aquatic Systems.

PubMed

Arredondo-Hernandez, Luis Jose Rene; Diaz-Avalos, Carlos; Lopez-Vidal, Yolanda; Castillo-Rojas, Gonzalo; Mazari-Hiriart, Marisa

2017-01-01

A particular challenge to water safety in populous intertropical regions is the lack of reliable faecal indicators to detect microbiological contamination of water, while the numerical relationships of specific viral indicators remain largely unexplored. The aim of this study was to investigate the numerical relationships of FRNA-bacteriophage genotypes, adenovirus 41, and human adenoviruses (HADV) in Mexican surface water systems to assess sewage contamination. We studied the presence of HADV, HADV41 and FRNA bacteriophage genotypes in water samples and quantified by qPCR and RT-qPCR. Virus and water quality indicator variances, as analyzed by principal component analysis and partial least squared regression, followed along the major percentiles of water faecal enterococci. FRNA bacteriophages adequately deciphered viral and point source water contamination. The strongest correlation for HADV was with FRNA bacteriophage type II, in water samples higher than the 50th percentiles of faecal enterococci, thus indicating urban pollution. FRNA bacteriophage genotypes I and III virus indicator performances were assisted by their associations with electrical conductivity and faecal enterococci. In combination, our methods are useful for inferring water quality degradation caused by sewage contamination. The methods used have potential for determining source contamination in water and, specifically, the presence of enteric viruses where clean and contaminated water have mixed.

Quick bacteriophage-mediated bioluminescence assay for detecting Staphylococcus spp. in sonicate fluid of orthopaedic artificial joints.

PubMed

Šuster, Katja; Podgornik, Aleš; Cör, Andrej

2017-07-01

Staphylococcus spp. accounts for up to two thirds of all microorganisms causing prosthetic joint infections, with Staphylococcus aureus and Staphylococcus epidermidis being the major cause. The present study describes a diagnostic model to detect staphylococci using a specific bacteriophage and bioluminescence detection, exploring the possibility of its use on sonicate fluid of orthopaedic artificial joints. Intracellular adenosine-5'-triphosphate release by bacteriophage mediated lysis of staphylococci was assessed to determine optimal parameters for detection. With the optimized method, a limit of detection of around 103 CFU/mL was obtained after incubation with bacteriophage for 2 h. Importantly, sonicate fluid did not prevent the ability of bacteriophage to infect bacteria and all simulated infected sonicate fluid as well as 6 clinical samples with microbiologically proven staphylococcal infection were detected as positive. The total assay took approximately 4 h. Collectively, the results indicate that the developed method promises a rapid, inexpensive and specific diagnostic detection of staphylococci in sonicate fluid of infected prosthetic joints. In addition, the unlimited pool of different existing bacteriophages, with different specificity for all kind of bacteria gives the opportunity for further investigations, improvements of the current model and implementation in other medical fields for the purpose of the establishment of a rapid diagnosis.

FRNA Bacteriophages as Viral Indicators of Faecal Contamination in Mexican Tropical Aquatic Systems

PubMed Central

Diaz-Avalos, Carlos; Lopez-Vidal, Yolanda; Castillo-Rojas, Gonzalo; Mazari-Hiriart, Marisa

2017-01-01

A particular challenge to water safety in populous intertropical regions is the lack of reliable faecal indicators to detect microbiological contamination of water, while the numerical relationships of specific viral indicators remain largely unexplored. The aim of this study was to investigate the numerical relationships of FRNA-bacteriophage genotypes, adenovirus 41, and human adenoviruses (HADV) in Mexican surface water systems to assess sewage contamination. We studied the presence of HADV, HADV41 and FRNA bacteriophage genotypes in water samples and quantified by qPCR and RT-qPCR. Virus and water quality indicator variances, as analyzed by principal component analysis and partial least squared regression, followed along the major percentiles of water faecal enterococci. FRNA bacteriophages adequately deciphered viral and point source water contamination. The strongest correlation for HADV was with FRNA bacteriophage type II, in water samples higher than the 50th percentiles of faecal enterococci, thus indicating urban pollution. FRNA bacteriophage genotypes I and III virus indicator performances were assisted by their associations with electrical conductivity and faecal enterococci. In combination, our methods are useful for inferring water quality degradation caused by sewage contamination. The methods used have potential for determining source contamination in water and, specifically, the presence of enteric viruses where clean and contaminated water have mixed. PMID:28114378

Evidence of a Dominant Lineage of Vibrio cholerae-Specific Lytic Bacteriophages Shed by Cholera Patients over a 10-Year Period in Dhaka, Bangladesh

PubMed Central

Seed, Kimberley D.; Bodi, Kip L.; Kropinski, Andrew M.; Ackermann, Hans-Wolfgang; Calderwood, Stephen B.; Qadri, Firdausi; Camilli, Andrew

2011-01-01

Lytic bacteriophages are hypothesized to contribute to the seasonality and duration of cholera epidemics in Bangladesh. However, the bacteriophages contributing to this phenomenon have yet to be characterized at a molecular genetic level. In this study, we isolated and sequenced the genomes of 15 bacteriophages from stool samples from cholera patients spanning a 10-year surveillance period in Dhaka, Bangladesh. Our results indicate that a single novel bacteriophage type, designated ICP1 (for the International Centre for Diarrhoeal Disease Research, Bangladesh cholera phage 1) is present in all stool samples from cholera patients, while two other bacteriophage types, one novel (ICP2) and one T7-like (ICP3), are transient. ICP1 is a member of the Myoviridae family and has a 126-kilobase genome comprising 230 open reading frames. Comparative sequence analysis of ICP1 and related isolates from this time period indicates a high level of genetic conservation. The ubiquitous presence of ICP1 in cholera patients and the finding that the O1 antigen of lipopolysaccharide (LPS) serves as the ICP1 receptor suggest that ICP1 is extremely well adapted to predation of human-pathogenic V. cholerae O1. PMID:21304168

Serum Free Light Chains in Neoplastic Monoclonal Gammopathies: Relative Under-Detection of Lambda Dominant Kappa/Lambda Ratio, and Underproduction of Free Lambda Light Chains, as Compared to Kappa Light Chains, in Patients With Neoplastic Monoclonal Gammopathies.

PubMed

Lee, Won Sok; Singh, Gurmukh

2018-07-01

Quantitative evaluation of serum free light chains is recommended for the work up of monoclonal gammopathies. Immunoglobulin light chains are generally produced in excess of heavy chains. In patients with monoclonal gammopathy, κ/λ ratio is abnormal less frequently with lambda chain lesions. This study was undertaken to ascertain if the levels of overproduction of the two light chain types and their detection rates are different in patients with neoplastic monoclonal gammopathies. Results of serum protein electrophoresis (SPEP), serum protein immunofixation electrophoresis (SIFE), urine protein electrophoresis (UPEP), urine protein immunofixation electrophoresis (UIFE), and serum free light chain assay (SFLCA) in patients with monoclonal gammopathies were examined retrospectively. The κ/λ ratios were appropriately abnormal more often in kappa chain lesions. Ratios of κ/λ were normal in about 25% of patients with lambda chain lesions in whom free homogenous lambda light chains were detectable in urine. An illustrative case suggests underproduction of free lambda light chains, in some instances. The lower prevalence of lambda dominant κ/λ ratio in lesions with lambda light chains is estimated to be due to relative under-detection of lambda dominant κ/λ ratio in about 25% of the patients and because lambda chains are not produced in as much excess of heavy chains as are kappa chains, in about 5% of the patients. The results question the medical necessity and clinical usefulness of the serum free light chain assay. UPEP/UIFE is under-utilized.

Search for CP Violation in Hyperon Decay: $$\\Xi^- / \\bar{\\Xi}^+$$ and $$\\Lambda / \\bar{\\Lambda}$$ (in French)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leros, Nicolas

2001-06-01

The HyperCP(EB71) experiment, performed at the Fermi National Accelerator Laboratory in the United States, provides a primary search for direct OP violation in the decays ofmore » $$\\Xi^-/\\bar{\\Xi}^+$$ and $$\\Lambda/ \\bar{\\Lambda}$$ hyperons....« less

Survival studies of a temperate and lytic bacteriophage in bovine faeces and slurry.

PubMed

Nyambe, S; Burgess, C; Whyte, P; Bolton, D

2016-10-01

Cattle are the main reservoir of verocytotoxigenic Escherichia coli (VTEC), food-borne pathogens that express verocytotoxins (vtx) encoded by temperate bacteriophage. Bovine faeces and unturned manure heaps can support the survival of VTEC and may propagate and transmit VTEC. This study investigated the survival of a vtx2 bacteriophage, φ24B ::Kan, in bovine faeces and slurry. The survival of an anti-Escherichia coli O157:H7 lytic bacteriophage, e11/2, was examined in the same matrices, as a possible bio-control option for VTEC. Samples were inoculated with φ24B ::Kan and/or e11/2 bacteriophage at a concentration of 7-8 log10  PFU g(-1)  (faeces) or ml(-1) (slurry), stored at 4 and 14°C and examined every 2 days for 36 days. The ability of φ24B ::Kan to transduce E. coli cells was examined. Moreover, E. coli concentrations in the faeces and slurry were monitored throughout the experiment as were the pH and aw (faeces only). Both bacteriophages survived well in faeces and slurry. In addition, φ24B ::Kan was able to form lysogens. φ24B ::Kan and e11/2 phage can survive and remain infective in bovine faeces and slurry for at least 30 days under representative Irish temperatures. Bovine faeces and slurry may act as a reservoir for vtx bacteriophages. The survival of the anti-O157 phage suggests it may be a suitable bio-control option in these matrices. © 2016 The Society for Applied Microbiology.

Isolation and in vitro evaluation of bacteriophages against MDR-bacterial isolates from septic wound infections.

PubMed

Pallavali, Roja Rani; Degati, Vijaya Lakshmi; Lomada, Dakshayani; Reddy, Madhava C; Durbaka, Vijaya Raghava Prasad

2017-01-01

Multi-drug resistance has become a major problem for the treatment of pathogenic bacterial infections. The use of bacteriophages is an attractive approach to overcome the problem of drug resistance in several pathogens that cause fatal diseases. Our study aimed to isolate multi drug resistant bacteria from patients with septic wounds and then isolate and apply bacteriophages in vitro as alternative therapeutic agents. Pus samples were aseptically collected from Rajiv Gandhi Institute of Medical Science (RIMS), Kadapa, A.P., and samples were analyzed by gram staining, evaluating morphological characteristics, and biochemical methods. MDR-bacterial strains were collected using the Kirby-Bauer disk diffusion method against a variety of antibiotics. Bacteriophages were collected and tested in vitro for lytic activity against MDR-bacterial isolates. Analysis of the pus swab samples revealed that the most of the isolates detected had Pseudomonas aeruginosa as the predominant bacterium, followed by Staphylococcus aureus, Klebsiella pneumoniae and Escherichia coli. Our results suggested that gram-negative bacteria were more predominant than gram-positive bacteria in septic wounds; most of these isolates were resistant to ampicillin, amoxicillin, penicillin, vancomycin and tetracycline. All the gram-positive isolates (100%) were multi-drug resistant, whereas 86% of the gram-negative isolates had a drug resistant nature. Further bacteriophages isolated from sewage demonstrated perfect lytic activity against the multi-drug resistant bacteria causing septic wounds. In vitro analysis of the isolated bacteriophages demonstrated perfect lysis against the corresponding MDR-bacteria, and these isolated phages may be promising as a first choice for prophylaxis against wound sepsis, Moreover, phage therapy does not enhance multi-drug resistance in bacteria and could work simultaneously on a wide variety of MDR-bacteria when used in a bacteriophage cocktail. Hence, our results suggest that these bacteriophages could be potential therapeutic options for treating septic wounds caused by P. aeruginosa, S. aureus, K. pneumoniae and E. coli.

Construction of genetically engineered M13K07 helper phage for simultaneous phage display of gold binding peptide 1 and nuclear matrix protein 22 ScFv antibody.

PubMed

Fatemi, Farnaz; Amini, Seyed Mohammad; Kharrazi, Sharmin; Rasaee, Mohammad Javad; Mazlomi, Mohammad Ali; Asadi-Ghalehni, Majid; Rajabibazl, Masoumeh; Sadroddiny, Esmaeil

2017-11-01

The most common techniques of antibody phage display are based on the use of M13 filamentous bacteriophages. This study introduces a new genetically engineered M13K07 helper phage displaying multiple copies of a known gold binding peptide on p8 coat proteins. The recombinant helper phages were used to rescue a phagemid vector encoding the p3 coat protein fused to the nuclear matrix protein 22 (NMP22) ScFv antibody. Transmission electron microscopy (TEM), UV-vis absorbance spectroscopy, and field emission scanning electron microscopy (FE-SEM) with energy dispersive X-ray spectroscopy (EDX) analysis revealed that the expression of gold binding peptide 1 (GBP1) on major coat protein p8 significantly enhances the gold-binding affinity of M13 phages. The recombinant bacteriophages at concentrations above 5×10 4 pfu/ml red-shifted the UV-vis absorbance spectra of gold nanoparticles (AuNPs); however, the surface plasmon resonance of gold nanoparticles was not changed by the wild type bacteriophages at concentrations up to 10 12 pfu/ml. The phage ELISA assay demonstrated the high affinity binding of bifunctional bacteriophages to NMP22 antigen at concentrations of 10 5 and 10 6 pfu/ml. Thus, the p3 end of the bifunctional bacteriophages would be able to bind to specific target antigen, while the AuNPs were assembled along the coat of virus for signal generation. Our results indicated that the complex of antigen-bacteriophages lead to UV-vis spectral changes of AuNPs and NMP22 antigen in concentration range of 10-80μg/ml can be detected by bifunctional bacteriophages at concentration of 10 4 pfu/ml. The ability of bifunctional bacteriophages to bind to antigen and generate signal at the same time, makes this approach applicable for identifying different antigens in immunoassay techniques. Copyright © 2017 Elsevier B.V. All rights reserved.

Distinct Stabilities of the Structurally Homologous Heptameric Co-Chaperonins GroES and gp31

NASA Astrophysics Data System (ADS)

Dyachenko, Andrey; Tamara, Sem; Heck, Albert J. R.

2018-05-01

The GroES heptamer is the molecular co-chaperonin that partners with the tetradecamer chaperonin GroEL, which assists in the folding of various nonnative polypeptide chains in Escherichia coli. Gp31 is a structural and functional analogue of GroES encoded by the bacteriophage T4, becoming highly expressed in T4-infected E. coli, taking over the role of GroES, favoring the folding of bacteriophage proteins. Despite being slightly larger, gp31 is quite homologous to GroES in terms of its tertiary and quaternary structure, as well as in its function and mode of interaction with the chaperonin GroEL. Here, we performed a side-by-side comparison of GroES and gp31 heptamer complexes by (ion mobility) tandem mass spectrometry. Surprisingly, we observed quite distinct fragmentation mechanisms for the GroES and gp31 heptamers, whereby GroES displays a unique and unusual bimodal charge distribution in its released monomers. Not only the gas-phase dissociation but also the gas-phase unfolding of GroES and gp31 were found to be very distinct. We rationalize these observations with the similar discrepancies we observed in the thermal unfolding characteristics and surface contacts within GroES and gp31 in the solution. From our data, we propose a model that explains the observed simultaneous dissociation pathways of GroES and the differences between GroES and gp31 gas-phase dissociation and unfolding. We conclude that, although GroES and gp31 exhibit high homology in tertiary and quaternary structure, they are quite distinct in their solution and gas-phase (un)folding characteristics and stability. [Figure not available: see fulltext.

The SXT conjugative element and linear prophage N15 encode toxin-antitoxin-stabilizing systems homologous to the tad-ata module of the Paracoccus aminophilus plasmid pAMI2.

PubMed

Dziewit, Lukasz; Jazurek, Magdalena; Drewniak, Lukasz; Baj, Jadwiga; Bartosik, Dariusz

2007-03-01

A group of proteic toxin-antitoxin (TA) cassettes whose representatives are widely distributed among bacterial genomes has been identified. These cassettes occur in chromosomes, plasmids, bacteriophages, and noncomposite transposons, as well as in the SXT conjugative element of Vibrio cholerae. The following four homologous loci were subjected to detailed comparative studies: (i) tad-ata from plasmid pAMI2 of Paracoccus aminophilus (the prototype of this group), (ii) gp49-gp48 from the linear bacteriophage N15 of Escherichia coli, (iii) s045-s044 from SXT, and (iv) Z3230-Z3231 from the genomic island of enterohemorrhagic Escherichia coli O157:H7 strain EDL933. Functional analysis revealed that all but one of these loci (Z3230-Z3231) are able to stabilize heterologous replicons, although the host ranges varied. The TA cassettes analyzed have the following common features: (i) the toxins are encoded by the first gene of each operon; (ii) the antitoxins contain a predicted helix-turn-helix motif of the XRE family; and (iii) the cassettes have two promoters that are different strengths, one which is located upstream of the toxin gene and one which is located upstream of the antitoxin gene. All four toxins tested are functional in E. coli; overexpression of the toxins (in the absence of antitoxin) results in a bacteriostatic effect manifested by elongation of bacterial cells and growth arrest. The toxins have various effects on cell viability, which suggests that they may recognize different intracellular targets. Preliminary data suggest that different cellular proteases are involved in degradation of antitoxins encoded by the loci analyzed.

New SPUDT cell structures.

PubMed

Martin, Guenter; Schmidt, Hagen; Wall, Bert

2004-07-01

The present paper describes single-phase unidirectional transducers (SPUDT) cells with all fingers wider than lambda/8 while maintaining the unidirectional effect. The first solution is related to a SPUDT consisting of lambda/4 and lambda/2 wide fingers arranged in two tracks. Each track has no significant unidirectional effect. Both tracks form a waveguide, and the waveguide coupling generates the interaction of the tracks. As a result of that interaction, a unidirectional effect arises as verified by experiment. This transducer type is called double-track (DT) SPUDT. A second solution is suggested that includes, in contrast to distributed acoustic reflection transducer (DART), electrode width control (EWC), and Hunsinger cells, SPUDT cell fingers with one and the same width only. Cell types with lambda/6, lambda/5, and lambda/3 wide fingers called uniform width electrode (UWE) cells are considered. One of these cell types, including exclusively lambda/5 wide fingers, is experimentally investigated and a unidirectional effect is found. Moreover, a filter example using the lambda/5 cell type has been designed for reducing SPUDT reflections. The echo suppression expected could be verified experimentally. No waveguide coupling is required for this cell type.

Arthrobacter globiformis and its bacteriophage in soil

NASA Technical Reports Server (NTRS)

Casida, L. E., Jr.; Liu, K.-C.

1974-01-01

An attempt was made to correlate bacteriophages for Arthrobacter globiformis with soils containing that bacterium. The phages were not detected unless the soil was nutritionally amended (with glucose or sucrose) and incubated for several days. Phage was continuously produced after amendment without the addition of host Arthrobacter. These results indicate that the bacteriophage is present in a masked state and that the bacteria are present in an insensitive form which becomes sensitive after addition of nutrient.

A Review of Phage Therapy against Bacterial Pathogens of Aquatic and Terrestrial Organisms.

PubMed

Doss, Janis; Culbertson, Kayla; Hahn, Delilah; Camacho, Joanna; Barekzi, Nazir

2017-03-18

Since the discovery of bacteriophage in the early 1900s, there have been numerous attempts to exploit their innate ability to kill bacteria. The purpose of this report is to review current findings and new developments in phage therapy with an emphasis on bacterial diseases of marine organisms, humans, and plants. The body of evidence includes data from studies investigating bacteriophage in marine and land environments as modern antimicrobial agents against harmful bacteria. The goal of this paper is to present an overview of the topic of phage therapy, the use of phage-derived protein therapy, and the hosts that bacteriophage are currently being used against, with an emphasis on the uses of bacteriophage against marine, human, animal and plant pathogens.

Preparation of RNA from bacteria infected with bacteriophages: a case study from the marine unicellular Synechococcus sp. WH7803 infected by phage S-PM2.

PubMed

Shan, Jinyu; Clokie, Martha

2009-01-01

Bacteriophages manipulate bacterial gene expression in order to express their own genes or influence bacterial metabolism. Gene expression can be studied using real-time PCR or microarrays. Either technique requires the prior isolation of high quality RNA uncontaminated by the presence of genomic DNA. We outline the considerations necessary when working with bacteriophage infected bacterial cells. We also give an example of a protocol for extraction and quantification of high quality RNA from infected bacterial cells, using the marine cyanobacterium WH7803 and the phage S-PM2 as a case study. This protocol can be modified to extract RNA from the host/bacteriophage of interest.

Plating Bacteriophage M13.

PubMed

Green, Michael R; Sambrook, Joseph

2017-10-03

A plaque of bacteriophage M13 derives from infection of a single bacterium by a single virus particle. The progeny particles infect neighboring bacteria, which, in turn, release another generation of daughter virus particles. If the bacteria are growing in semisolid medium (e.g., containing agar or agarose), then the diffusion of the progeny particles is limited. Cells infected with bacteriophage M13 are not killed, but have a longer generation time than uninfected Escherichia coli In consequence, plaques appear as areas of slower-growing cells on a faster-growing lawn of bacterial cells. This protocol describes plating of bacteriophage M13 stocks. Plaques are readily detectable on top agar after 4-8 h of incubation at 37°C. © 2017 Cold Spring Harbor Laboratory Press.

Use of encapsulated bacteriophages to enhance farm to fork food safety.

PubMed

Hussain, Malik A; Liu, Huan; Wang, Qi; Zhong, Fang; Guo, Qian; Balamurugan, Sampathkumar

2017-09-02

Bacteriophages have been successfully applied to control the growth of pathogens in foods and to reduce the colonization and shedding of pathogens by food animals. They are set to play a dominant role in food safety in the future. However, many food-processing operations and the microenvironments in food animals' guts inactivate phages and reduce their infectivity. Encapsulation technologies have been used successfully to protect phages against extreme environments, and have been shown to preserve their activity and enable their release in targeted environments. A number of encapsulation technologies have shown potential for use with bacteriophages. This review discusses the current state of knowledge about the use of encapsulation technologies with bacteriophages to control pathogens in foods and food animals.

The risk of renal disease is increased in lambda myeloma with bone marrow amyloid deposits.

PubMed

Kozlowski, Piotr; Montgomery, Scott; Befekadu, Rahel; Hahn-Strömberg, Victoria

2017-01-01

Light chain amyloidosis (AL) is a rare deposition disease and is present in 10-15% of patients with myeloma (MM). In contrast to symptomatic AL in MM, presence of bone marrow (BM) amyloid deposits (AD) in MM is not connected to kidney damage. Renal AD but not BM-AD occur mostly in MM with lambda paraprotein (lambda MM). We investigated amyloid presence in BM clots taken at diagnosis in 84 patients with symptomatic MM and compared disease characteristics in MM with kappa paraprotein (kappa MM)/lambda MM with and without BM-AD. Lambda MM with BM-AD was compared with kappa MM without BM-AD, kappa MM with BM-AD, and lambda MM without BM-AD: lambda MM with BM-AD patients had a significantly higher mean creatinine level (4.23 mg/dL vs 1.69, 1.14, and 1.28 mg/dL, respectively) and a higher proportion presented with severe kidney failure (6/11 [55%] vs 6/32 [19%], 1/22 [5%], and 3/19 [16%], respectively). Proteinuria was more common in lambda MM with BM-AD patients compared with kappa MM without BM-AD patients (8/11 [73%] vs 5/32 [16%], respectively). Kidney damage was more common in lambda MM with BM-AD indicating presence of renal AD.

Elevated carboxylesterase activity contributes to the lambda-cyhalothrin insensitivity in quercetin fed Helicoverpa armigera (Hübner).

PubMed

Chen, Chengyu; Liu, Ying; Shi, Xueyan; Desneux, Nicolas; Han, Peng; Gao, Xiwu

2017-01-01

Quercetin as one of the key plant secondary metabolite flavonol is ubiquitous in terrestrial plants. In this study, the decrease in sensitivity to lambda-cyhalothrin was observed in quercetin-fed Helicoverpa armigera larvae. In order to figure out the mechanisms underlying the decreased sensitivity of H. armigera larvae to lambda-cyhalothrin by quercetin induction, the changes in carboxylesterase activity and in-vitro hydrolytic metabolic capacity to lambda-cyhalothrin were examined. The LC50 value of quercetin-fed H. armigera larvae to lambda-cyhalothrin showed 2.41-fold higher than that of the control. S, S, S-Tributyl phosphorotrithioate (DEF) treatment showed a synergism effect on lambda-cyhalothrin toxicity to quercetin-fed H. armigera. Moreover, the activity of carboxylesterase was significantly higher in quercetin-fed H. armigera larvae after fed on quercetin for 48 h. The in-vitro hydrolytic metabolic capacity to lambda-cyhalothrin in quercetin-fed H. armigera larvae midgut was 289.82 nmol 3-PBA/mg protein/min, which is significant higher than that in the control group (149.60 nmol 3-PBA/mg protein/min). The elevated CarE enzyme activity and corresponding increased hydrolytic metabolic capacity to lambda-cyhalothrin in quercetin-fed H. armigera contributed to the enhanced tolerance to lambda-cyhalothrin.

Elevated carboxylesterase activity contributes to the lambda-cyhalothrin insensitivity in quercetin fed Helicoverpa armigera (Hübner)

PubMed Central

Chen, Chengyu; Liu, Ying; Desneux, Nicolas; Han, Peng; Gao, Xiwu

2017-01-01

Quercetin as one of the key plant secondary metabolite flavonol is ubiquitous in terrestrial plants. In this study, the decrease in sensitivity to lambda-cyhalothrin was observed in quercetin-fed Helicoverpa armigera larvae. In order to figure out the mechanisms underlying the decreased sensitivity of H. armigera larvae to lambda-cyhalothrin by quercetin induction, the changes in carboxylesterase activity and in-vitro hydrolytic metabolic capacity to lambda-cyhalothrin were examined. The LC50 value of quercetin-fed H. armigera larvae to lambda-cyhalothrin showed 2.41-fold higher than that of the control. S, S, S-Tributyl phosphorotrithioate (DEF) treatment showed a synergism effect on lambda-cyhalothrin toxicity to quercetin-fed H. armigera. Moreover, the activity of carboxylesterase was significantly higher in quercetin-fed H. armigera larvae after fed on quercetin for 48 h. The in-vitro hydrolytic metabolic capacity to lambda-cyhalothrin in quercetin-fed H. armigera larvae midgut was 289.82 nmol 3-PBA/mg protein/min, which is significant higher than that in the control group (149.60 nmol 3-PBA/mg protein/min). The elevated CarE enzyme activity and corresponding increased hydrolytic metabolic capacity to lambda-cyhalothrin in quercetin-fed H. armigera contributed to the enhanced tolerance to lambda-cyhalothrin. PMID:28817718

Quadrupole deformation ({beta},{gamma}) of light {Lambda} hypernuclei in a constrained relativistic mean field model: Shape evolution and shape polarization effect of the {Lambda} hyperon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lu Bingnan; Zhao Enguang; Center of Theoretical Nuclear Physics, National Laboratory of Heavy Ion Accelerator, Lanzhou 730000

2011-07-15

The shapes of light normal nuclei and {Lambda} hypernuclei are investigated in the ({beta},{gamma}) deformation plane by using a newly developed constrained relativistic mean field (RMF) model. As examples, the results of some C, Mg, and Si nuclei are presented and discussed in details. We found that for normal nuclei the present RMF calculations and previous Skyrme-Hartree-Fock models predict similar trends of the shape evolution with the neutron number increasing. But some quantitative aspects from these two approaches, such as the depth of the minimum and the softness in the {gamma} direction, differ a lot for several nuclei. For {Lambda}more » hypernuclei, in most cases, the addition of a {Lambda} hyperon alters slightly the location of the ground state minimum toward the direction of smaller {beta} and softer {gamma} in the potential energy surface E{approx}({beta},{gamma}). There are three exceptions, namely, {sub {Lambda}}{sup 13}C, {sub {Lambda}}{sup 23}C, and {sub {Lambda}}{sup 31}Si in which the polarization effect of the additional {Lambda} is so strong that the shapes of these three hypernuclei are drastically different from their corresponding core nuclei.« less

Serum Free Light Chains in Neoplastic Monoclonal Gammopathies: Relative Under-Detection of Lambda Dominant Kappa/Lambda Ratio, and Underproduction of Free Lambda Light Chains, as Compared to Kappa Light Chains, in Patients With Neoplastic Monoclonal Gammopathies

PubMed Central

Lee, Won Sok; Singh, Gurmukh

2018-01-01

Background Quantitative evaluation of serum free light chains is recommended for the work up of monoclonal gammopathies. Immunoglobulin light chains are generally produced in excess of heavy chains. In patients with monoclonal gammopathy, κ/λ ratio is abnormal less frequently with lambda chain lesions. This study was undertaken to ascertain if the levels of overproduction of the two light chain types and their detection rates are different in patients with neoplastic monoclonal gammopathies. Methods Results of serum protein electrophoresis (SPEP), serum protein immunofixation electrophoresis (SIFE), urine protein electrophoresis (UPEP), urine protein immunofixation electrophoresis (UIFE), and serum free light chain assay (SFLCA) in patients with monoclonal gammopathies were examined retrospectively. Results The κ/λ ratios were appropriately abnormal more often in kappa chain lesions. Ratios of κ/λ were normal in about 25% of patients with lambda chain lesions in whom free homogenous lambda light chains were detectable in urine. An illustrative case suggests underproduction of free lambda light chains, in some instances. Conclusions The lower prevalence of lambda dominant κ/λ ratio in lesions with lambda light chains is estimated to be due to relative under-detection of lambda dominant κ/λ ratio in about 25% of the patients and because lambda chains are not produced in as much excess of heavy chains as are kappa chains, in about 5% of the patients. The results question the medical necessity and clinical usefulness of the serum free light chain assay. UPEP/UIFE is under-utilized. PMID:29904440

Antitumor activity of type I and type III interferons in BNL hepatoma model.

PubMed

Abushahba, Walid; Balan, Murugabaskar; Castaneda, Ismael; Yuan, Yao; Reuhl, Kenneth; Raveche, Elizabeth; de la Torre, Andrew; Lasfar, Ahmed; Kotenko, Sergei V

2010-07-01

Hepatocellular carcinoma (HCC) occurs most commonly secondary to cirrhosis due to chronic hepatitis C or B virus (HCV/HBV) infections. Type I interferon (IFN-alpha) treatment of chronic HCV/HBV infections reduces the incidence of HCC in cirrhotic patients. However, IFN-alpha toxicity limits its tolerability and efficacy highlighting a need for better therapeutic treatments. A recently discovered type III IFN (IFN-lambda) has been shown to possess antiviral properties against HCV and HBV in vitro. In phase I clinical trials, IFN-lambda treatment did not cause significant adverse reactions. Using a gene therapy approach, we compared the antitumor properties of IFN-alpha and IFN-lambda in a transplantable hepatoma model of HCC. BALB/c mice were inoculated with syngeneic BNL hepatoma cells, or BNL cells expressing IFN-lambda (BNL.IFN-lambda cells) or IFN-alpha (BNL.IFN-alpha cells). Despite the lack of antiproliferative activity of IFNs on BNL cells, both BNL.IFN-lambda and BNL.IFN-alpha cells displayed retarded growth kinetics in vivo. Depletion of NK cells from splenocytes inhibited splenocyte-mediated cytotoxicity, demonstrating that NK cells play a role in IFN-induced antitumor responses. However, isolated NK cells did not respond directly to IFN-lambda. There was also a marked NK cell infiltration in IFN-lambda producing tumors. In addition, IFN-lambda and, to a lesser extent, IFN-alpha enhanced immunocytotoxicity of splenocytes primed with irradiated BNL cells. Splenocyte cytotoxicity against BNL cells was dependent on IL-12 and IFN-gamma, and mediated by dendritic cells. In contrast to NK cells, isolated from spleen CD11c+ and mPDCA+ dendritic cells responded directly to IFN-lambda. The antitumor activities of IFN-lambda against hepatoma, in combination with HCV and HBV antiviral activities warrant further investigation into the clinical use of IFN-lambda to prevent HCC in HCV/HBV-infected cirrhotic patients, as well as to treat liver cancer.

A randomized, controlled study of peginterferon lambda-1a/ribavirin ± daclatasvir for hepatitis C virus genotype 2 or 3.

PubMed

Foster, Graham R; Chayama, Kazuaki; Chuang, Wan-Long; Fainboim, Hugo; Farkkila, Martti; Gadano, Adrian; Gaeta, Giovanni B; Hézode, Christophe; Inada, Yukiko; Heo, Jeong; Kumada, Hiromitsu; Lu, Sheng-Nan; Marcellin, Patrick; Moreno, Christophe; Roberts, Stuart K; Strasser, Simone I; Thompson, Alexander J; Toyota, Joji; Paik, Seung Woon; Vierling, John M; Zignego, Anna L; Cohen, David; McPhee, Fiona; Wind-Rotolo, Megan; Srinivasan, Subasree; Hruska, Matthew; Myler, Heather; Portsmouth, Simon D

2016-01-01

Peginterferon Lambda was being developed as an alternative to alfa interferon for the treatment of chronic hepatitis C virus (HCV) infection. We compared peginterferon Lambda-1a plus ribavirin (Lambda/RBV) and Lambda/RBV plus daclatasvir (DCV; pangenotypic NS5A inhibitor) with peginterferon alfa-2a plus RBV (alfa/RBV) in treatment-naive patients with HCV genotype 2 or 3 infection. In this multicenter, double-blind, phase 3 randomized controlled trial, patients were assigned 2:2:1 to receive 24 weeks of Lambda/RBV, 12 weeks of Lambda/RBV + DCV, or 24 weeks of alfa/RBV. The primary outcome measure was sustained virologic response at post-treatment Week 12 (SVR12). Overall, 874 patients were treated: Lambda/RBV, n = 353; Lambda/RBV + DCV, n = 349; alfa/RBV, n = 172. Patients were 65 % white and 33 % Asian, 57 % male, with a mean age of 47 years; 52 % were infected with genotype 2 (6 % cirrhotic) and 48 % with genotype 3 (9 % cirrhotic). In the Lambda/RBV + DCV group, 83 % (95 % confidence interval [CI] 78.5, 86.5) achieved SVR12 (90 % genotype 2, 75 % genotype 3) whereas SVR12 was achieved by 68 % (95 % CI 63.1, 72.9) with Lambda/RBV (72 % genotype 2, 64 % genotype 3) and 73 % (95 % CI 66.6, 79.9) with peginterferon alfa/RBV (74 % genotype 2, 73 % genotype 3). Lambda/RBV + DCV was associated with lower incidences of flu-like symptoms, hematological abnormalities, and discontinuations due to adverse events compared with alfa/RBV. The 12-week regimen of Lambda/RBV + DCV was superior to peginterferon alfa/RBV in the combined population of treatment-naive patients with genotype 2 or 3 infection, with an improved tolerability and safety profile compared with alfa/RBV.

Dynamic processes in Be star atmospheres. 2: He I 2P-nD line formation in lambda Eridani (outburst)

NASA Technical Reports Server (NTRS)

Smith, Myron A.; Hubeny, Ivan; Lanz, Thierry; Meylan, Thomas

1994-01-01

The He I lambda 6678 line of early Be stars generally shows violet (V) and red (R) emission whenever hydrogen alpha emission is present, but its use as a diagnostic has been handicapped by a poor understanding of the processes that drive it into emission. In an attempt to address this problem we obtained three series of eschelle spectra of the first two members of the singlet and triplet 2P-nD series of lambda Eri (B2e) during 1992 November 3-5 at Kitt Peak. During these observations lambda 6678 showed substantial emission variability in both the wings and central profile, providing an opportunity to compare its behavior with that of the lambda 4922, lambda 5876, and lambda 4471 lines. We found that the responses of the lines were different in several respects. Whereas the emissions in the V wings of all four lines scaled together, the R wing of the lambda 4922 line invariably responded with increased absorption whenever the R wing of lambda 6678 line showed increased emission. These same trends occurred within the central photospheric profiles. The R-wing behavior shows that much, but not all of the emission in lambda 6678 is caused by matter projected against the stellar disk. The excitation temperatures of the neighboring 2(sup 1) P transitions, lambda 6678 and lambda 4922 must be greater than and less than the photospheric continuum temperature, respectively. We have investigated departures from local thermodynamic equilibrium (LTE) for the He I spectrum in a variety of ad hoc, perturbed model atmospheres. We have found only one way to cause the source function of lambda 6678 to increase so strongly, namely, by increasing the atmospheric temperature in the line formation region to 30,000 - 40,000 K. This effect was discovered by Auer and Mihalas for O3-O4 atmospheric models, but it has not been applied to active B stars. Our models suggest that lambda 6678 emission in Be stars can be used as a sensitive monitor of localized hot spots on these stars' surfaces. The energies involved in heating the active portions of the atmosphere are too high to be produced by gravitational infall. This leaves magnetically induced flares among the few known processes on the surfaces of stars capable of sustaining this energy level.

[Excitation transfer between high-lying states in K2 in collisions with ground state K and H2 molecules].

PubMed

Shen, Xiao-Yan; Liu, Jing; Dai, Kang; Shen, Yi-Fan

2010-02-01

Pure potassium vapor or K-H2 mixture was irradiated in a glass fluorescence cell with pulses of 710 nm radiation from an OPO laser, populating K2 (1lambda(g)) state by two-photon absorption. Cross sections for 1lambda(g)-3lambda(g) transfer in K2 were determined using methods of molecular fluorescence. During the experiments with pure K vapor, the cell temperature was varied between 553 and 603 K. The K number density was determined spectroscopically by the white-light absorption measurement in the blue wing of the self-broadened resonance D2 line. The resulting fluorescence included a direct component emitted in the decay of the optically excitation and a sensitized component arising from the collisionally populated state. The decay signal of time-resolved fluorescence from1lambda(g) -->1 1sigma(u)+ transition was monitored. It was seen that just after the laser pulse the fluorescence of the photoexcited level decreased exponentially. The effective lifetimes of the 1lambda(g) state can be resolved. The plot of reciprocal of effective lifetimes of the 1lambda(g) state against K densities yielded the slope that indicated the total cross section for deactivation and the intercept that provided the radiative lifetime of the state. The radiative lifetime (20 +/- 2) ns was obtained. The cross section for deactivation of the K2(1lambda(g)) molecules by collisions with K is (2.5 +/- 0.3) x 10(-14) cm2. The time-resolved intensities of the K23lambda(g) --> 1 3sigma(u)+ (484 nm) line were measured. The radiative lifetime (16.0 +/- 3.2) ns and the total cross section (2.5 +/- 0.6) x 10(-14) cm2 for deactivation of the K2 (3lambda(g)) state can also be determined through the analogous procedure. The time-integrated intensities of 1lambda(g) --> 1 1sigma(u)+ and 3lambda(g) --> 1 3sigma(u)+ transitions were measured. The cross section (1.1 +/- 0.3) x10(-14) cm2 was obtained for K2 (1lambda(g))+ K --> K2 (3lambda(g)) + K collisions. During the experiments with K-H2 mixture, the cell temperature was kept constant at 553 K. The H2 pressure was varied between 40 and 400 Pa. The effects of K2-K collisions could not be neglected. These effects were subtracted out using the results of the pure K experiments. The cross section (2.7 +/- 1.1) x 10(-15) cm2 was obtained for K2 (1lambda(g)) + H2 --> K2 (3lambda(g))+H2 collisions. The cross section is (6.8 +/- 2.7) x 10(-15) cm2 for K2 (3lambda(g)) + H2 --> states out of K2 (3lambda(g)) + H2 collisions.

Transformation of Clostridium acetobutylicum Protoplasts with Bacteriophage DNA

PubMed Central

Reid, Sharon J.; Allcock, Errol R.; Jones, David T.; Woods, David R.

1983-01-01

Techniques for the transformation of Clostridium acetobutylicum protoplasts with bacteriophage DNA are described. Transformation required regeneration of protoplasts and a 2-h eclipse period. PMID:16346174

Magnetic penetration depth of YBa2Cu3O(7-delta) thin films determined by the power transmission method

NASA Technical Reports Server (NTRS)

Heinen, Vernon O.; Miranda, Felix A.; Bhasin, Kul B.

1992-01-01

A power transmission measurement technique was used to determine the magnetic penetration depth (lambda) of YBa2Cu3O(7-delta) superconducting thin films on LaAlO3 within the 26.5 to 40.0 GHz frequency range, and at temperatures from 20 to 300 K. Values of lambda ranging from 1100 to 2500 A were obtained at low temperatures. The anisotropy of lambda was determined from measurements of c-axis and a-axis oriented films. An estimate of the intrinsic value of lambda of 90 +/- 30 nm was obtained from the dependence of lambda on film thickness. The advantage of this technique is that it allows lambda to be determined nondestructively.

Measurement of the Branching Ratio Lambda_c+ -> p pi+ pi- (in Spanish)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lopez-Hinojosa, Guillermo; /San Luis Potosi U.

2008-03-01

The confirmation of the Cabibbo-suppressed charm baryon decay mode {Lambda}{sub c}{sup +} {yields} p{pi}{sup +}{pi}{sup -} is reported. All data analyzed are from SELEX, a fixed target experiment at Fermilab that took data during 1996 and 1997, mainly with a 600 GeV/c {Sigma}{sup -} beam. The branching ratio of the Cabibbo-suppressed decay mode {Lambda}{sub c}{sup +} {yields} p{pi}{sup +}{pi}{sup -} relative to the Cabibbo-favored mode {Lambda}{sub c}{sup +} {yields} pK{sup -}{pi}{sup +} is measured to be: {Gamma}({Lambda}{sub c}{sup +} {yields} p{pi}{sup +}{pi}{sup -})/{Gamma}({Lambda}{sub c}{sup +} {yields} pK{sup -}{pi}{sup +}) = 0.103 {+-} 0.022.

Treatment of Highly Virulent Extraintestinal Pathogenic Escherichia coli Pneumonia With Bacteriophages.

PubMed

Dufour, Nicolas; Debarbieux, Laurent; Fromentin, Mélanie; Ricard, Jean-Damien

2015-06-01

To study the effect of bacteriophage treatment on highly virulent extraintestinal Escherichia coli pneumonia in mice and compare it with conventional antimicrobial treatment. Animal investigation. University research laboratory. Pathogen-free 8-week-old Balb/cJRj male mice. Two bacteriophages (536_P1 and 536_P7) were isolated from sewage using strain 536, a highly virulent extraintestinal E. coli. Their in vitro and in vivo efficacy against strain 536 and a ventilator-associated pneumonia E. coli were tested. The first group of mice were infected by intranasal instillation of bioluminescent strain 536 and received 536_P1 intranasally, ceftriaxone, or control. The second group of mice was infected with the ventilator-associated pneumonia strain and received 536_P7. Adaptation of 536_P7 to this clinical isolate was also evaluated in vitro and in vivo. In vivo efficacy of bacteriophage and antibiotic treatment were assessed by recording bioluminescence for short-time periods and by recording body weight and survival of mice for longer periods. Both treatments improved survival compared with control (100% vs 0%), and in vivo bioluminescence recordings showed a similar rapid decrease of emitted light, suggesting prompt bacterial clearance. The majority of mice infected by the ventilator-associated pneumonia strain were not rescued by treatment with 536_P7; however, in vitro adaptation of this bacteriophage toward the ventilator-associated pneumonia strain led to isolate a variant which significantly improved in vivo treatment efficacy (animal survival increased from 20% to 75%). Bacteriophage treatment was as effective as antibiotherapy to provide 100% survival rate in a lethal model of highly virulent E. coli pneumonia. Adaptation of a bacteriophage is a rapid solution to improve its efficacy toward specific strains. These results suggest that phage therapy could be a promising therapeutic strategy for ventilator-associated pneumonia.

Comparative persistence of human sewage-specific enterococcal bacteriophages in freshwater and seawater.

PubMed

Booncharoen, Namfon; Mongkolsuk, Skorn; Sirikanchana, Kwanrawee

2018-07-01

Enterococcus faecalis bacteria have been recently reported for their ability to host bacteriophages that are specifically from human sewage, suggesting their application to track human fecal contamination in water resources. However, little is known about the survivability of sewage-specific enterococcal bacteriophages in various water matrices under ambient and storage conditions. In this study, bacteriophages that were derived from the Thailand-isolated E. faecalis strains AIM06 and SR14 exhibited morphologies consistent with the Siphoviridae, Podoviridae, and Myoviridae families. Four representative bacteriophages were separately spiked into environmental water samples (n = 7) comprising freshwater and seawater with low- and high-pollution (LF, HF, LS, and HS, respectively) levels, defined according to Thailand Water Quality Standards. All bacteriophages decayed fastest in HS or HF samples at 30 °C, reaching a 5-log 10 reduction in 2.2 to 9.8 days, and slowest in LS samples, requiring 8.8 to 23.5 days. The decay rates were 5 to 53 times lower at a storage temperature of 5 °C. HF samples could be stored for as little as 2.5 days to prevent the decay of 50% of the phages. Myoviridae phages decayed faster than Siphoviridae phages and Podoviridae phages in most water matrices at 30 °C. Moreover, the decay rates were 1.8 to 92 times slower in filtered samples, emphasizing a strong role for water constituents, i.e., suspended solids and natural microorganisms, in phage persistence. This study emphasized that differential enterococcal bacteriophage persistence should be considered when planning the monitoring and interpreting of fecal sources by microbial source tracking.

Top-down effects of a lytic bacteriophage and protozoa on bacteria in aqueous and biofilm phases.

PubMed

Zhang, Ji; Ormälä-Odegrip, Anni-Maria; Mappes, Johanna; Laakso, Jouni

2014-12-01

Lytic bacteriophages and protozoan predators are the major causes of bacterial mortality in natural microbial communities, which also makes them potential candidates for biological control of bacterial pathogens. However, little is known about the relative impact of bacteriophages and protozoa on the dynamics of bacterial biomass in aqueous and biofilm phases. Here, we studied the temporal and spatial dynamics of bacterial biomass in a microcosm experiment where opportunistic pathogenic bacteria Serratia marcescens was exposed to particle-feeding ciliates, surface-feeding amoebas, and lytic bacteriophages for 8 weeks, ca. 1300 generations. We found that ciliates were the most efficient enemy type in reducing bacterial biomass in the open water, but least efficient in reducing the biofilm biomass. Biofilm was rather resistant against bacterivores, but amoebae had a significant long-term negative effect on bacterial biomass both in the open-water phase and biofilm. Bacteriophages had only a minor long-term effect on bacterial biomass in open-water and biofilm phases. However, separate short-term experiments with the ancestral bacteriophages and bacteria revealed that bacteriophages crash the bacterial biomass dramatically in the open-water phase within the first 24 h. Thereafter, the bacteria evolve phage-resistance that largely prevents top-down effects. The combination of all three enemy types was most effective in reducing biofilm biomass, whereas in the open-water phase the ciliates dominated the trophic effects. Our results highlight the importance of enemy feeding mode on determining the spatial distribution and abundance of bacterial biomass. Moreover, the enemy type can be crucially important predictor of whether the rapid defense evolution can significantly affect top-down regulation of bacteria.

Isolation and characterization of bacteriophages specific to hydrogen-sulfide-producing bacteria.

PubMed

Gong, Chao; Heringa, Spencer; Singh, Randhir; Kim, Jinkyung; Jiang, Xiuping

2013-01-01

The objectives of this study were to isolate and characterize bacteriophages specific to hydrogen-sulfide-producing bacteria (SPB) from raw animal materials, and to develop a SPB-specific bacteriophage cocktail for rendering application. Meat, chicken offal, and feather samples collected from local supermarkets and rendering processing plants were used to isolate SPB (n = 142). Bacteriophages (n = 52) specific to SPB were isolated and purified from the above samples using 18 of those isolated SPB strains as hosts. The host ranges of bacteriophages against 5 selected SPB strains (Escherichia coli, Citrobacter freundii, and Hafnia alvei) were determined. Electron microscopy observation of 9 phages selected for the phage cocktail revealed that 6 phages belonged to the family of Siphoviridae and 3 belonged to the Myoviridae family. Restriction enzyme digestion analysis with endonuclease DraI detected 6 distinguished patterns among the 9 phages. Phage treatment prevented the growth of SPB for up to 10 h with multiplicity of infection ratios of 1, 10, 100, and 1000 in tryptic soy broth at 30 °C, and extended the lag phase of SPB growth for 2 h at 22 °C with multiplicities of infection of 10, 100, and 1000. These results suggest that the selected bacteriophage cocktail has a high potential for phage application to control SPB in raw animal materials destined for the rendering process.

Vibrio parahaemolyticus and its specific bacteriophages as an indicator in cockles (Anadara granosa) for the risk of V. parahaemolyticus infection in Southern Thailand.

PubMed

Yingkajorn, Mingkwan; Sermwitayawong, Natthawan; Palittapongarnpimp, Prasit; Nishibuchi, Mitsuaki; Robins, William P; Mekalanos, John J; Vuddhakul, Varaporn

2014-05-01

Correlation between the numbers of Vibrio parahaemolyticus and its specific bacteriophages in cockles was investigated from June 2009 to May 2010 in Hat Yai, Songkhla, Thailand. Cockles obtained monthly from a local market were sampled to determine the numbers of V. parahaemolyticus and bacteriophages that could form plaques on ten strains of pandemic and nonpandemic V. parahaemolyticus. In addition, V. parahaemolyticus isolates from clinical samples from Hat Yai hospital over the same period were investigated. All 139 cockles sampled were positive for V. parahaemolyticus. However, only 76 of them were positive for bacteriophages. During the testing period, the number of bacteriophages was not significantly correlated with the incidence of V. parahaemolyticus-infected patients, but the numbers of V. parahaemolyticus isolates from the cockle samples were closely related to the number of infected patients. The bacteriophages isolated from V. parahaemolyticus also infected Vibrio alginolyticus and Vibrio mimicus, suggesting that the broad host range of phages may be a factor of providing the possibility of their participation in the processes of genetic exchange between V. parahaemolyticus and closely related Vibrio spp. In conclusion, this study indicated that the number of V. parahaemolyticus in cockles may be a useful tool for predicting the relative risk of infection by V. parahaemolyticus in this area of Thailand.

Comparative analysis of the biological and physical properties of Enterococcus faecalis bacteriophage vB_EfaS_GEC-EfS_3 and Streptococcus mitis bacteriophage vB_SmM_GEC-SmitisM_2.

PubMed

Rigvava, Sophio; Tchgkonia, Irina; Jgenti, Darejan; Dvalidze, Teona; Carpino, James; Goderdzishvili, Marina

2013-01-01

Enterococcus faecalis and Streptococcus mitis are common commensal inhabitants of the human gastrointestinal and genitourinary tracts. However, both species can be opportunistic pathogens and cause disease in nosocomial settings. These infections can be difficult to treat because of the frequency of antibiotic resistance among these strains. Bacteriophages are often suggested as an alternative therapeutic agent against these infections. In this study, E. faecalis and S. mitis strains were isolated from female patients with urinary tract infections. Bacteriophages active against these strains were isolated from sewage water from the Mtkvari River. Two phages, designated vB_EfaS_GEC-EfS_3 (Syphoviridae) and vB_SmM_GEC-SmitisM_2 (Myoviridae), were specific for E. faecalis and S. mitis, respectively. Each phage's growth patterns and adsorption rates were quantified. Sensitivity to ultraviolet light and temperature was determined, as was host range and serology. The S. mitis bacteriophage was found to be more resistant to ultraviolet light and exposure to high temperatures than the E. faecalis bacteriophage, despite having a much greater rate of replication. While each phage was able to infect a broad range of strains of the same species as the host species from which they were isolated, they were unable to infect other host species tested.

[Immunodetection of bacteriophages by a piezoelectric resonator with lateral electric field].

PubMed

Gulii, O I; Zaitsev, B D; Shikhabudinov, A M; Teplykh, A A; Borodina, I A; Pavlii, S A; Larionova, O S; Fomin, A S; Staroverov, S A; Dykman, L A; Ignatov, O V

2016-01-01

It has been demonstrated that electroacoustic analysis with polyclonal antibodies can be used for bacteriophage detection. The frequency dependences of the real and imaginary parts of electrical impedance of a resonator with a viral suspension with antibodies were shown to be essentially different from the dependences of a resonator with control viral suspension without antibodies. It was shown that ΦAl-Sp59b bacteriophages were detected with the use of antibodies in the presence of foreign virus particles. The ΦAl-Sp59b bacteriophage content in the analyzed suspension was ~1010–106 phages/mL; the time of analysis was no more than 5 min. The optimally informative parameter for obtaining reliable information was the change in the real or imaginary part of electrical impedance at a fixed frequency near the resonance upon the addition of specific antibodies to the analyzed suspension. It was demonstrated that the interaction between bacteriophages and antibodies can be recorded, offering good prospects for the development of a biological sensor for liquid-phase identification and virus detection.

Antibacterial efficacy of nisin, bacteriophage P100 and sodium lactate against Listeria monocytogenes in ready-to-eat sliced pork ham.

PubMed

Figueiredo, Ana Cláudia L; Almeida, Rogeria C C

The effectiveness of bacteriophage P100, nisin and sodium lactate, individually and in combination, in inhibiting Listeria monocytogenes in ready-to-eat pork ham slices was assessed. The antimicrobials were applied to the surfaces of ready-to-eat pork ham slices, which were inoculated with a mixture of L. monocytogenes. Among the individual antimicrobial treatments, bacteriophage P100 was the most effective, decreasing L. monocytogenes to undetectable levels at zero and 72h post-infection. Sodium lactate was the least effective treatment. Treatment with nisin at zeroh significantly reduced initial cell density (p<0.05). However, this pattern was not observed at 72h of storage. A significant difference (p<0.05) existed between the results of separate bacteriophage and nisin treatments after refrigerated storage, but not immediately upon inoculation of the bacteria. The results showed that the use of bacteriophage P100 is the method of choice for the control of bacteria. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Self-Assembled Nanoporous Biofilms from Functionalized Nanofibrous M13 Bacteriophage.

PubMed

Devaraj, Vasanthan; Han, Jiye; Kim, Chuntae; Kang, Yong-Cheol; Oh, Jin-Woo

2018-06-12

Highly periodic and uniform nanostructures, based on a genetically engineered M13 bacteriophage, displayed unique properties at the nanoscale that have the potential for a variety of applications. In this work, we report a multilayer biofilm with self-assembled nanoporous surfaces involving a nanofiber-like genetically engineered 4E-type M13 bacteriophage, which was fabricated using a simple pulling method. The nanoporous surfaces were effectively formed by using the networking-like structural layers of the M13 bacteriophage during self-assembly. Therefore, an external template was not required. The actual M13 bacteriophage-based fabricated multilayered biofilm with porous nanostructures agreed well with experimental and simulation results. Pores formed in the final layer had a diameter of about 150⁻500 nm and a depth of about 15⁻30 nm. We outline a filter application for this multilayered biofilm that enables selected ions to be extracted from a sodium chloride solution. Here, we describe a simple, environmentally friendly, and inexpensive fabrication approach with large-scale production potential. The technique and the multi-layered biofilms produced may be applied to sensor, filter, plasmonics, and bio-mimetic fields.

Bacteriophage-Based Bacterial Wilt Biocontrol for an Environmentally Sustainable Agriculture

PubMed Central

Álvarez, Belén; Biosca, Elena G.

2017-01-01

Bacterial wilt diseases caused by Ralstonia solanacearum, R. pseudosolanacearum, and R. syzygii subsp. indonesiensis (former R. solanacearum species complex) are among the most important plant diseases worldwide, severely affecting a high number of crops and ornamentals. Difficulties of bacterial wilt control by non-biological methods are related to effectiveness, bacterial resistance and environmental impact. Alternatively, a great many biocontrol strategies have been carried out, with the advantage of being environmentally friendly. Advances in bacterial wilt biocontrol include an increasing interest in bacteriophage-based treatments as a promising re-emerging strategy. Bacteriophages against the bacterial wilt pathogens have been described with either lytic or lysogenic effect but, they were proved to be active against strains belonging to R. pseudosolanacearum and/or R. syzygii subsp. indonesiensis, not to the present R. solanacearum species, and only two of them demonstrated successful biocontrol potential in planta. Despite the publication of three patents on the topic, until now no bacteriophage-based product is commercially available. Therefore, there is still much to be done to incorporate valid bacteriophages in an integrated management program to effectively fight bacterial wilt in the field. PMID:28769942

Bacteriophage-Based Bacterial Wilt Biocontrol for an Environmentally Sustainable Agriculture.

PubMed

Álvarez, Belén; Biosca, Elena G

2017-01-01

Bacterial wilt diseases caused by Ralstonia solanacearum , R. pseudosolanacearum , and R. syzygii subsp. indonesiensis (former R. solanacearum species complex) are among the most important plant diseases worldwide, severely affecting a high number of crops and ornamentals. Difficulties of bacterial wilt control by non-biological methods are related to effectiveness, bacterial resistance and environmental impact. Alternatively, a great many biocontrol strategies have been carried out, with the advantage of being environmentally friendly. Advances in bacterial wilt biocontrol include an increasing interest in bacteriophage-based treatments as a promising re-emerging strategy. Bacteriophages against the bacterial wilt pathogens have been described with either lytic or lysogenic effect but, they were proved to be active against strains belonging to R. pseudosolanacearum and/or R. syzygii subsp. indonesiensis , not to the present R. solanacearum species, and only two of them demonstrated successful biocontrol potential in planta . Despite the publication of three patents on the topic, until now no bacteriophage-based product is commercially available. Therefore, there is still much to be done to incorporate valid bacteriophages in an integrated management program to effectively fight bacterial wilt in the field.

Complete genome sequence of new bacteriophage phiE142, which causes simultaneously lysis of multidrug-resistant Escherichia coli O157:H7 and Salmonella enterica.

PubMed

Amarillas, Luis; Chaidez, Cristobal; González-Robles, Arturo; León-Félix, Josefina

2016-01-01

The emergence of antibiotic-resistant foodborne bacteria is a global health problem that requires immediate attention. Bacteriophages are a promising biotechnological alternative approach against bacterial pathogens. However, a detailed analysis of phage genomes is essential to assess the safety of the phages prior to their use as biocontrol agents. Therefore, here we report the complete genome sequence of bacteriophage phiE142, which is able to lyse Salmonella and multidrug-resistant Escherichia coli O157:H7 strains. Bacteriophage phiE142 belongs to the Myoviridae family due to the presence of long non-flexible tail and icosahedral head. The genome is composed of 121,442 bp and contains 194 ORFs, and 2 tRNAs. Furthermore, the phiE142 genome does not contain any genes coding for food-borne allergens, antibiotics resistance, virulence factors, or associated with lysogenic conversion. The bacteriophage phiE142 is characterized by broad host range and compelling genetic attributes making them potential candidates as a biocontrol agent.

Experimental bacteriophage treatment of honeybees (Apis mellifera) infected with Paenibacillus larvae, the causative agent of American Foulbrood Disease

PubMed Central

Yost, Diane G.; Tsourkas, Philippos; Amy, Penny S.

2016-01-01

ABSTRACT American Foulbrood Disease (AFB) is an infection of honeybees caused by the bacterium Paenibacillus larvae. One potential remedy involves using biocontrol, such as bacteriophages (phages) to lyse P. larvae. Therefore, bacteriophages specific for P. larvae were isolated to determine their efficacy in lysing P. larvae cells. Samples from soil, beehive materials, cosmetics, and lysogenized P. larvae strains were screened; of 157 total samples, 28 were positive for at least one P. larvae bacteriophage, with a total of 30. Newly isolated bacteriophages were tested for the ability to lyse each of 11 P. larvae strains. Electron microscopy demonstrated that the phage isolates were from the family Siphoviridae. Seven phages with the broadest host ranges were combined into a cocktail for use in experimental treatments of infected bee larvae; both prophylactic and post-infection treatments were conducted. Results indicated that although both pre- and post-treatments were effective, prophylactic administration of the phages increased the survival of larvae more than post-treatment experiments. These preliminary experiments demonstrate the likelihood that phage therapy could be an effective method to control AFB. PMID:27144085

Autofluorescence spectroscopy of oral mucosa

NASA Astrophysics Data System (ADS)

Majumdar, S. K.; Uppal, A.; Gupta, P. K.

1998-06-01

We report the results of an in-vitro study on autofluorescence from pathologically characterized normal and malignant squamous tissues from the oral cavity. The study involved biopsy samples from 47 patients with oral cancer of which 11 patients had cancer of tongue, 17 of buccal mucosa and 19 of alveolus. The results of excitation and emission spectroscopy at several wavelengths (280 nm less than or equal to (lambda) exless than or equal to 460 nm; 340 nm less than or equal to (lambda) em less than or equal to 520 nm) showed that at (lambda) ex equals 337 nm and 400 nm the mean value for the spectrally integrated fluorescence intensity [(Sigma) (lambda ) IF((lambda) )] from the normal tissue sites was about a factor of 2 larger than that from the malignant tissue sites. At other excitation wavelengths the difference in (Sigma) (lambda ) IF((lambda) ) was not statistically significant. Similarly, for (lambda) em equals 390 nm and 460 nm, the intensity of the 340 nm band of the excitation spectra from normal tissues was observed to be a factor of 2 larger than that from malignant tissues. Analysis of these results suggests that NADH concentration is higher in normal oral tissues compared to the malignant. This contrasts with our earlier observation of an reduced NADH concentration in normal sites of breast tissues vis a vis malignant sites. For the 337 nm excited emission spectra a 10-variable MVLR score (using (Sigma) (lambda ) IF((lambda) ) and normalized intensities at nine wavelengths as input parameters) provided a sensitivity and specificity of 95.7% and 93.1% over the sample size investigated.

Engineering bacteriophage for a pragmatic low-resource setting bacterial diagnostic platform.

PubMed

Talbert, Joey N; Alcaine, Samuel D; Nugen, Sam R

2016-04-01

Bacteriophages represent multifaceted building blocks that can be incorporated as substitutes for, or in unison with other detection methods, to create powerful new diagnostics for the detection of bacteria. The ease of phage manipulation, production, and detection speed clearly highlights that there remains unrealized opportunities to leverage these phage-based components in diagnostics amenable to resource-limited settings. The passage of regulations like the Food Safety Modernization act, and the ever increasing extent of global trade and travel, will create further demand for these types of diagnostics. While phage-based diagnostics have begun to entering the market place, further research is needed to ensure the potential benefits of phage-based technologies for public health are fully realized. We are just beginning to explore the possibilities that phage-based detection can offer us in the future. The combination of engineered phages as well as engineered enzymes could result in ultrasensitive detection systems for low-resource settings. Because the reporter enzyme is synthesized in vivo, we need to consider the options outside of normal enzyme reporters. In this case, common enzyme issues such as purification and long-term stability are less important. Phage-based diagnostics were conceptualized from out-of-the box thinking and the evolution of these systems should be as well.

Peptide deformylases from Vibrio parahaemolyticus phage and bacteria display similar deformylase activity and inhibitor binding clefts.

PubMed

Grzela, Renata; Nusbaum, Julien; Fieulaine, Sonia; Lavecchia, Francesco; Desmadril, Michel; Nhiri, Naima; Van Dorsselaer, Alain; Cianferani, Sarah; Jacquet, Eric; Meinnel, Thierry; Giglione, Carmela

2018-02-01

Unexpected peptide deformylase (PDF) genes were recently retrieved in numerous marine phage genomes. While various hypotheses dealing with the occurrence of these intriguing sequences have been made, no further characterization and functional studies have been described thus far. In this study, we characterize the bacteriophage Vp16 PDF enzyme, as representative member of the newly identified C-terminally truncated viral PDFs. We show here that conditions classically used for bacterial PDFs lead to an enzyme exhibiting weak activity. Nonetheless, our integrated biophysical and biochemical approaches reveal specific effects of pH and metals on Vp16 PDF stability and activity. A novel purification protocol taking in account these data allowed strong improvement of Vp16 PDF specific activity to values similar to those of bacterial PDFs. We next show that Vp16 PDF is as sensitive to the natural inhibitor compound of PDFs, actinonin, as bacterial PDFs. Comparison of the 3D structures of Vp16 and E. coli PDFs bound to actinonin also reveals that both PDFs display identical substrate binding mode. We conclude that bacteriophage Vp16 PDF protein has functional peptide deformylase activity and we suggest that encoded phage PDFs might be important for viral fitness. Copyright © 2017 Elsevier B.V. All rights reserved.

Possible Use of Bacteriophages Active against Bacillus anthracis and Other B. cereus Group Members in the Face of a Bioterrorism Threat

PubMed Central

Weber-Dąbrowska, Beata; Borysowski, Jan; Górski, Andrzej

2014-01-01

Anthrax is an infectious fatal disease with epidemic potential. Nowadays, bioterrorism using Bacillus anthracis is a real possibility, and thus society needs an effective weapon to neutralize this threat. The pathogen may be easily transmitted to human populations. It is easy to store, transport, and disseminate and may survive for many decades. Recent data strongly support the effectiveness of bacteriophage in treating bacterial diseases. Moreover, it is clear that bacteriophages should be considered a potential incapacitative agent against bioterrorism using bacteria belonging to B. cereus group, especially B. anthracis. Therefore, we have reviewed the possibility of using bacteriophages active against Bacillus anthracis and other species of the B. cereus group in the face of a bioterrorism threat. PMID:25247187

Survival of microorganisms in smectite clays - Implications for Martian exobiology

NASA Technical Reports Server (NTRS)

Moll, Deborah M.; Vestal, J. R.

1992-01-01

The survival of Baccillus subtilis, Azotobacter chroococcum, and the enteric bacteriophage MS2 has been examined in clays representing terrestrial (Wyoming type montmorillonite) and Martian (Fe3+ montmorillonite) soils exposed to terrestrial and Martian environmental conditions of temperature and atmospheric composition and pressure. An important finding is that MS2 survived simulated Mars conditions better than the terrestrial environment, probably owing to stabilization of the virus caused by the cold and dry conditions of the simulated Mars environment. This finding, the first published indication that viruses may be able to survive in Mars-type soils, may have important implications for future missions to Mars.

Phage Lambda P Protein: Trans-Activation, Inhibition Phenotypes and their Suppression

PubMed Central

Hayes, Sidney; Erker, Craig; Horbay, Monique A.; Marciniuk, Kristen; Wang, Wen; Hayes, Connie

2013-01-01

The initiation of bacteriophage λ replication depends upon interactions between the oriλ DNA site, phage proteins O and P, and E. coli host replication proteins. P exhibits a high affinity for DnaB, the major replicative helicase for unwinding double stranded DNA. The concept of P-lethality relates to the hypothesis that P can sequester DnaB and in turn prevent cellular replication initiation from oriC. Alternatively, it was suggested that P-lethality does not involve an interaction between P and DnaB, but is targeted to DnaA. P-lethality is assessed by examining host cells for transformation by ColE1-type plasmids that can express P, and the absence of transformants is attributed to a lethal effect of P expression. The plasmid we employed enabled conditional expression of P, where under permissive conditions, cells were efficiently transformed. We observed that ColE1 replication and plasmid establishment upon transformation is extremely sensitive to P, and distinguish this effect from P-lethality directed to cells. We show that alleles of dnaB protect the variant cells from P expression. P-dependent cellular filamentation arose in ΔrecA or lexA[Ind-] cells, defective for SOS induction. Replication propagation and restart could represent additional targets for P interference of E. coli replication, beyond the oriC-dependent initiation step. PMID:23389467

Cloning structural genes for Treponema pallidum immunogens and characterisation of recombinant treponemal surface protein, P2 (P2 star).

PubMed Central

Peterson, K M; Baseman, J B; Alderete, J F

1987-01-01

A genomic library consisting of partially digested 10 to 20 kilobase pair fragments of Treponema pallidum deoxyribonucleic acid (DNA) was constructed using bacteriophage lambda EMBL-3 as the vector. Positive clones expressing T pallidum antigens were detected with sera from experimentally infected rabbits. Treponemal proteins ranging in molecular weight from 37,000 daltons to 120,000 daltons were identified by sodium dodecyl sulphate-polyacrylamide gel electrophoresis and immunoblotting of phage lysate proteins. One recombinant phage was examined further and contained an insert encoding a prominent treponemal 37,000 dalton protein. The recombinant protein was not recognised by antiserum directed against a fibronectin binding treponemal adhesion that contained the same electrophoretic mobility. Neither did antibody to the recombinant 37,000 dalton protein react with any treponemal proteins purified by fibronectin affinity chromatography. The recombinant protein in Escherichia coli lysates was labelled P2 (P2 star) to differentiate it from the comigrating adhesin protein called P2. Native P2 protein was present on T pallidum surfaces as shown by radioimmunoprecipitation assays with extrinsically labelled organisms. A cross reactive molecule like P2 was not synthesised by the avirulent spirochaete, T phagedenis biotype Reiter, which indicated that P2 is a protein specific to virulent T pallidum organisms. Finally, only sera of patients with primary syphilis possessed appreciable concentrations of antibody to recombinant P2 protein. Images PMID:3315959

Depolymerized products of lambda-carrageenan as a potent angiogenesis inhibitor.

PubMed

Chen, Haimin; Yan, Xiaojun; Lin, Jing; Wang, Feng; Xu, Weifeng

2007-08-22

Since angiogenesis is involved in initiating and promoting several diseases such as cancer and cardiovascular events, this study was designed to evaluate the anti-angiogenesis of low-molecular-weight (LMW), highly sulfated lambda-carrageenan oligosaccharides (lambda-CO) obtained by carrageenan depolymerization, by CAM (chick chorioallantoic membrane) model and human umbilical vein endothelial cells (HUVECs). Significant inhibition of vessel growth was observed at 200 microg/pellet. A histochemistry assay also revealed a decrease of capillary plexus and connective tissue in lambda-CO treated samples. lambda-CO inhibited the viability of cells at the high concentration of 1 mg/mL, whereas it affected the cell survival slightly (>95%) at a low concentration (<250 microg/mL), and HUVEC is the most sensitive to lambda-CO among three kinds of cells. Furthermore, the inhibitory action of lambda-CO was also observed in the endothelial cell invasion and migration at relatively low concentration (150-300 microg/mL), through down-regulation of intracellular matrix metalloproteinases (MMP-2) expression on endothelial cells. Taken together, these findings demonstrate that lambda-CO is a potential angiogenesis inhibitor with combined effects of inhibiting invasion, migration, and proliferation.

Oxidative and apoptotic effects of lambda-cyhalothrin modulated by piperonyl butoxide in the liver of Oreochromis niloticus.

PubMed

Piner, Petek; Uner, Nevin

2012-05-01

The aim of this study was to investigate the toxic effects of pyrethroid pesticide lambda-cyhalothrin in the presence of piperonyl butoxide as a modulator in the liver of juvenile Oreochromis niloticus. LC(50) (96h) value of lambda-cyhalothrin was determined as 2.901μg/L for O. niloticus. The fish were exposed to 0.48μg/L (1/6 of the 96-h LC(50)) lambda-cyhalothrin and 10μg/L piperonyl butoxide for 96-h and 15-d. tGSH, GSH, GSSG, Hsp70 and TBARS contents, GPx, GR, GST and caspase-3 enzymes activities were determined. Lambda-cyhalothrin caused increases in tGSH, GSH, TBARS contents, and GST activity. Piperonyl butoxide treatment with lambda-cyhalothrin caused significant increases in tGSH GSH, Hsp70, TBARS contents, and GPx and GST activities while caspase-3 activity was decreased. The results of the present study revealed that lambda-cyhalothrin caused oxidative stress which upregulated GSH and GSH-related enzymes. Piperonyl butoxide increased the oxidative stress potential and apoptotic effects of lambda-cyhalothrin. Copyright © 2012 Elsevier B.V. All rights reserved.

Determination of $${{\\rm{\\Lambda }}}_{\\overline{{\\rm{MS}}}}$$ at five loops from holographic QCD

DOE PAGES

Deur, Alexandre; Brodsky, Stanley J.; de Téramond, Guy F.

2017-08-25

Here, the recent determination of themore » $$\\beta$$--function of the QCD running coupling $$\\alpha_{\\overline{MS}}(Q^2)$$ to five-loops, provides a verification of the convergence of a novel method for determining the fundamental QCD parameter $$\\Lambda_s$$ based on the Light-Front Holographic approach to nonperturbative QCD. The new 5-loop analysis, together with improvements in determining the holographic QCD nonperturbative scale parameter $$\\kappa$$ from hadronic spectroscopy, leads to an improved precision of the value of $$\\Lambda_s$$ in the $${\\overline{MS}}$$ scheme close to a factor of two; we find $$\\Lambda^{(3)}_{\\overline{MS}}=0.339\\pm0.019$$ GeV for $$n_{f}=3$$, in excellent agreement with the world average, $$\\Lambda_{\\overline{MS}}^{(3)}=0.332\\pm0.017$$ GeV. Lastly, we also discuss the constraints imposed on the scale dependence of the strong coupling in the nonperturbative domain by superconformal quantum mechanics and its holographic embedding in anti-de Sitter space.« less

IUE and Einstein observations of the LINER galaxy NGC 4579

NASA Technical Reports Server (NTRS)

Reichert, G. A.; Puchnarewicz, E. M.; Mason, K. O.

1990-01-01

Results of International Ultraviolet Explorer (IUE) and Einstein observations of the LINER galaxy NGC 4579 are reported. Spatial profiles of the long wavelength IUE emission show a two component structure, with an unresolved core superimposed on broader underlying emission. The core spectrum shows strong C II lambda 2326 and broad Mg II lambda 2800 emission, and perhaps emission due to blends of Fe II multiplets (2300 to 23600 angstrom). The short wavelength emission is spatially unresolved, and shows C II lambda 1335, C III lambda 1909 broad C IV lambda 1550 emission, and a broad feature at approximately 1360 angstrom which may be due to 0.1 lambda 1356. Contrary to previous reports no evidence for He II lambda 1640 is found in the spectrum. An unresolved x ray source is detected at the location of the nucleus; its spectrum is well fitted by a power law of energy slope alpha approximately -0.5. These results further support the idea that NGC 4579 may contain a dwarf Seyfert nucleus.

Segregated tandem filter for enhanced conversion efficiency in a thermophotovoltaic energy conversion system

DOEpatents

Brown, Edward J.; Baldasaro, Paul F.; Dziendziel, Randolph J.

1997-01-01

A filter system to transmit short wavelength radiation and reflect long wavelength radiation for a thermophotovoltaic energy conversion cell comprises an optically transparent substrate segregation layer with at least one coherent wavelength in optical thickness; a dielectric interference filter deposited on one side of the substrate segregation layer, the interference filter being disposed toward the source of radiation, the interference filter including a plurality of alternating layers of high and low optical index materials adapted to change from transmitting to reflecting at a nominal wavelength .lambda..sub.IF approximately equal to the bandgap wavelength .lambda..sub.g of the thermophotovoltaic cell, the interference filter being adapted to transmit incident radiation from about 0.5.lambda..sub.IF to .lambda..sub.IF and reflect from .lambda..sub.IF to about 2.lambda..sub.IF ; and a high mobility plasma filter deposited on the opposite side of the substrate segregation layer, the plasma filter being adapted to start to become reflecting at a wavelength of about 1.5.lambda..sub.IF.

[In vitro anti-angiogenic action of lambda-carrageenan oligosaccharides].

PubMed

Chen, Hai-Min; Yan, Xiao-Jun; Wang, Feng; Lin, Jing; Xu, Wei-Feng

2007-06-01

This study was designed to evaluate the inhibition effect of lambda-carrageenan oligosaccharides on neovascularization in vitro by chick chorioallantoic membrane (CAM) model and human umbilical vein endothelial cell ( HUVEC). lambda-Carrageenan oligosaccharides caused a dose-dependent decrease of the vascular density of CAM, and adversely affected capillary plexus formation. At a high concentration of 1 mg x mL(-1), this compound inhibited the endothelial cell proliferation, while low concentration of lambda-carrageenan oligosaccharides (< 250 microg x mL(-1)) affected the cell survival slightly (> 95%). Different cytotoxic sensitivity of lambda-carrageenan oligosaccharides in three kinds of cells was observed, of which HUVEC is the most sensitive to this oligosaccharides. The inhibitory action of lambda-carrageenan oligosaccharides on the endothelial cell invasion and migration was also observed at relatively low concentration (150 - 300 microg x mL(-1)) through down-regulation of intracellular matrix metalloproteinases-2 (MMP-2) expression on endothelial cells. Current observations demonstrated that lambda-carrageenan oligosaccharides are potential angiogenesis inhibitor with combined effects of inhibiting invasion, migration and proliferation.

Effect of atmospheric extinction on laser rangefinder performance at 1.54 and 0.6 microns

NASA Technical Reports Server (NTRS)

Hutt, D. L.; Theriault, J.-M.; Larochelle, V.; Bonnier, D.

1992-01-01

Extinction of laser rangefinder (LRF) pulses by the atmosphere depends on the wavelength, weather conditions, and aerosol concentration along the optical path. In the IR, extinction is due to absorption by molecular constituents and scattering and absorption by aerosols. The total atmospheric extinction alpha(lambda) is the sum of the molecular and aerosol contributions, alpha(sub m)(lambda)and Alpha(sub a)(lambda). We present simple expressions for alpha(sub m)(lambda) and alpha(sub a)(lambda) for two LRF sources: Er:glass and CO2 which operate at 1.54 and 10.6 microns, respectively. The expressions are based on accepted models of atmospheric aerosols and molecular extinction and give an estimate of alpha(lambda) as a function of standard meteorological parameters, assuming horizontal beam propagation. Signal-to-noise ratios of LRF returns, measured from a reference target under different weather conditions are compared to predictions based on the estimate of alpha(lambda).

On Spectral Invariance of Single Scattering Albedo for Water Droplets and Ice Crystals at Weakly Absorbing Wavelengths

NASA Technical Reports Server (NTRS)

Marshak, Alexander; Knyazikhin, Yuri; Chiu, J. Christine; Wiscombe, Warren J.

2012-01-01

The single scattering albedo omega(sub O lambda) in atmospheric radiative transfer is the ratio of the scattering coefficient to the extinction coefficient. For cloud water droplets both the scattering and absorption coefficients, thus the single scattering albedo, are functions of wavelength lambda and droplet size r. This note shows that for water droplets at weakly absorbing wavelengths, the ratio omega(sub O lambda)(r)/omega(sub O lambda)(r (sub O)) of two single scattering albedo spectra is a linear function of omega(sub O lambda)(r). The slope and intercept of the linear function are wavelength independent and sum to unity. This relationship allows for a representation of any single scattering albedo spectrum omega(sub O lambda)(r) via one known spectrum omega(sub O lambda)(r (sub O)). We provide a simple physical explanation of the discovered relationship. Similar linear relationships were found for the single scattering albedo spectra of non-spherical ice crystals.

Duality symmetry and power-law fading of frustration in a quantum multiconnected superconductor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sun, S.N.; Ralston, J.P.

1991-03-01

We generalize the Alexander--de Gennes equations to a new system of superconducting-wire networks, allowing for variation of the cross-sectional area of wires. The generalized equations are solved for a square lattice of different cross-sectional-area ratios {lambda} in the {ital x} and {ital y} directions. A symmetry of {lambda}{r arrow}1/{lambda} is related to the Aubry-Andre duality and an obvious geometric property. We find that even a slight geometric asymmetry can soften the fine structure of the magnetic phase boundary considerably. We obtain a power-law dependence on the parameter {lambda} as {lambda}{r arrow}{infinity} and {lambda}{r arrow}0. For a finite-area ratio {lambda}, wemore » speculate that a simple analytic fit incorporating the dual symmetry is close to the exact nonperturbative behavior. The system is also related analytically to a recent study of Hu and Chen, which revealed a power-law behavior for a rectangular lattice.« less

Further improvements of a new model for turbulent convection in stars

NASA Technical Reports Server (NTRS)

Canuto, V. M.; Mazzitelli, I.

1992-01-01

The effects of including a variable molecular weight and of using the newest opacities of Rogers and Iglesias (1991) as inputs to a recent model by Canuto and Mazzitelli (1991) for stellar turbulent convection are studied. Solar evolutionary tracks are used to conclude that the the original model for turbulence with mixing length Lambda = z, Giuli's variable Q unequal to 1 and the new opacities yields a fit to solar T(eff) within 0.5 percent. A formulation of Lambda is proposed that extends the purely nonlocal Lambda = z expression to include local effects. A new expression for Lambda is obtained which generalizes both the mixing length theory (MLT) phenomenological expression for Lambda as well as the model Lambda = z. It is argued that the MLT should now be abandoned.

The evaluation of hollow-fiber ultrafiltration and celite concentration of enteroviruses, adenoviruses and bacteriophage from different water matrices

EPA Pesticide Factsheets

The data to support the evaluation of hollow-fiber ultrafiltration and celite concentration of enteroviruses, adenoviruses and bacteriophage from different water matricesThis dataset is associated with the following publication:Rhodes , E., E. Huff, D. Hamilton, and J. Jones. The evaluation of hollow-fiber ultrafiltration and celite concentration of enteroviruses, adenoviruses and bacteriophage from different water matrices. JOURNAL OF VIROLOGICAL METHODS. Elsevier Science Ltd, New York, NY, USA, 228(2): 31-38, (2016).

Rayleigh, the unit for light radiance.

PubMed

Baker, D J

1974-09-01

A 0.7% accurate formula is derived for the easy conversion of power spectral radiance L(lambda) in W cm(-2) sr(-1) microm(-1)to rayleigh spectral radiance R(lambda) in rayleigh/microm, R(lambda) = 2pilambdaL(lambda) x 10(13), where the wavelength lambda is in microm. The rationale for the rayleigh unit is discussed in terms of a photon rate factor and a solid angle factor. The latter is developed in terms of an equivalence theorem about optical receivers and extended sources, and the concept is extended to the computation of photon volume emission rates from altitude profiles of zenith radiance.

Susceptibility of Escherichia coli isolated from uteri of postpartum dairy cows to antibiotic and environmental bacteriophages. Part II: In vitro antimicrobial activity evaluation of a bacteriophage cocktail and several antibiotics.

PubMed

Santos, T M A; Gilbert, R O; Caixeta, L S; Machado, V S; Teixeira, L M; Bicalho, R C

2010-01-01

The use of pathogenic-specific antimicrobials, as proposed by bacteriophage therapy, is expected to reduce the incidence of resistance development. Eighty Escherichia coli isolated from uteri of Holstein dairy cows were phenotypically characterized for antimicrobial resistance to ampicillin, ceftiofur, chloramphenicol, florfenicol, spectinomycin, streptomycin, and tetracycline by broth microdilution method. The lytic activity of a bacteriophage cocktail against all isolates was performed by a similar method. Additionally, the effect of different concentrations of antimicrobials and multiplicities of infections (MOI) of the bacteriophage cocktail on E. coli growth curve was measured. Isolates exhibited resistance to ampicillin (33.7%), ceftiofur (1.2%), chloramphenicol (100%), and florfenicol (100%). All strains were resistant to at least 2 of the antimicrobial agents tested; multidrug resistance (>or=3 of 7 antimicrobials tested) was observed in 35% of E. coli isolates. The major multidrug resistance profile was found for ampicillin-chloramphenicol-florfenicol, which was observed in more than 96.4% of the multidrug-resistant isolates. The bacteriophage cocktail preparation showed strong antimicrobial activity against multidrug-resistant E. coli. Multiplicity of infection as low as 10(-4) affected the growth of the E. coli isolates. The ratio of 10 bacteriophage particles per bacterial cell (MOI=10(1)) was efficient in inhibiting at least 50% of all isolates. Higher MOI should be tested in future in vitro studies to establish ratios that completely inhibit bacterial growth during longer periods. All isolates resistant to florfenicol were resistant to chloramphenicol and, because florfenicol was recently introduced into veterinary clinics, this finding suggests that the selection pressure of chloramphenicol, as well as other antimicrobials, may still play a relevant role in the emergence and dissemination of florfenicol resistance in E. coli. The bacteriophage cocktail had a notable capacity to inhibit the in vitro growth of E. coli isolates, and it may be an attractive alternative to conventional treatment of metritis by reducing E. coli in uteri of postpartum dairy cows. Copyright 2010 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

In vitro evaluation of a novel bacteriophage cocktail as a preventative for bovine coliform mastitis.

PubMed

Porter, J; Anderson, J; Carter, L; Donjacour, E; Paros, M

2016-03-01

The objective of this study was to investigate the potential use of bacteriophage in preventing Escherichia coli mastitis on dairies. A cocktail consisting of 4 distinct bacteriophages was generated by screening against 36 E. coli isolates from dairy cows in Washington State with clinical mastitis. The bacteriophage significantly inhibited growth of 58% of the Washington State isolates and 54% of E. coli mastitis isolates from New York State, suggesting that the cocktail of phages had a relatively broad spectrum of action against relevant strains from 2 distinct geographies. The ability to suppress bacterial growth of these isolates in a liquid growth medium was not affected by the ratio of bacteriophage particles to bacterial cells (multiplicity of infection, MOI). For those E. coli that were completely inhibited by the phage cocktail, an MOI as low as 10 had the same effect as 10 µg/mL of ceftiofur on the growth rate of E. coli over a 12-h period using optical density measurements. A 3.3- to 5.6-log reduction of growth was achieved when E. coli was co-incubated with our phage cocktail in raw milk over a 12-h period at physiologic temperature. A modified gentamicin protection assay using bovine mammary epithelial cells provided a model to test whether bacteriophage could prevent cell attachment and invasion by chronic coliform mastitis strains. Pretreatment of cell cultures with the phage cocktail significantly reduced adhesion and intracellular survival of E. coli compared with controls. When combined with a bismuth-based teat sealant, the phage cocktail was able to inhibit bacterial growth when challenged with 1.6 × 10(3) cfu/mL of a clinical mastitis E. coli strain. In vitro results show bactericidal activity by our phage in raw milk and mammary tissue culture systems. Before a bacteriophage-based dry-cow treatment becomes a potential option for dairies, in vivo studies must be able to demonstrate that a specific dose of bacteriophage can protect cows from experimentally induced E. coli mastitis without inducing an inflammatory reaction. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

5' modification of duplex DNA with a ruthenium electron donor-acceptor pair using solid-phase DNA synthesis

NASA Technical Reports Server (NTRS)

Frank, Natia L.; Meade, Thomas J.

2003-01-01

Incorporation of metalated nucleosides into DNA through covalent modification is crucial to measurement of thermal electron-transfer rates and the dependence of these rates with structure, distance, and position. Here, we report the first synthesis of an electron donor-acceptor pair of 5' metallonucleosides and their subsequent incorporation into oligonucleotides using solid-phase DNA synthesis techniques. Large-scale syntheses of metal-containing oligonucleotides are achieved using 5' modified phosporamidites containing [Ru(acac)(2)(IMPy)](2+) (acac is acetylacetonato; IMPy is 2'-iminomethylpyridyl-2'-deoxyuridine) (3) and [Ru(bpy)(2)(IMPy)](2+) (bpy is 2,2'-bipyridine; IMPy is 2'-iminomethylpyridyl-2'-deoxyuridine) (4). Duplexes formed with the metal-containing oligonucleotides exhibit thermal stability comparable to the corresponding unmetalated duplexes (T(m) of modified duplex = 49 degrees C vs T(m) of unmodified duplex = 47 degrees C). Electrochemical (3, E(1/2) = -0.04 V vs NHE; 4, E(1/2) = 1.12 V vs NHE), absorption (3, lambda(max) = 568, 369 nm; 4, lambda(max) = 480 nm), and emission (4, lambda(max) = 720 nm, tau = 55 ns, Phi = 1.2 x 10(-)(4)) data for the ruthenium-modified nucleosides and oligonucleotides indicate that incorporation into an oligonucleotide does not perturb the electronic properties of the ruthenium complex or the DNA significantly. In addition, the absence of any change in the emission properties upon metalated duplex formation suggests that the [Ru(bpy)(2)(IMPy)](2+)[Ru(acac)(2)(IMPy)](2+) pair will provide a valuable probe for DNA-mediated electron-transfer studies.

A-type Stellar Abundances: A Corollary to Herschel Observations of Debris Disks

NASA Astrophysics Data System (ADS)

Draper, Zachary H.; Matthews, Brenda; Venn, Kim; Lambert, David; Kennedy, Grant; Sitnova, Tatyana

2018-04-01

In order to assess the relationship between metallicity and exoplanetary systems, we compare the abundances of AF-type main-sequence stars with debris disk properties assessed using Herschel observations of an unbiased survey of nearby stars. Hot stars are not as commonly observed, given their unique constraints in data reduction, lack of metal lines, and “astrophysical noise” from rotation speed. Here, we address that deficiency using new and archival spectra of 83 AF-type stars. We measure the abundances of a few species in addition to Fe in order to classify the stars with Ap/Am or Lambda Boo signatures. Lambda Boo stars have a chemical signature of solar-abundant volatile species and sub-solar refractory abundances that is hypothesized to be altered by the pollution of volatiles. Overall, we see no correlation between debris disks and metallicity, primarily because the sample size is cut significantly when using only reliable fits to the spectroscopic data. The abundance measured from the Mg II 4481 blend is a useful diagnostic because it can be reliably measured at large v·sin(i) and is found to be lower around stars with bright debris disks. We find that Lambda Boo stars have brighter debris disks compared to a bias-free sample of AF stars. The trend with disk brightness and Mg abundances suggests pollution effects can be significant and used as a marker for the stability of planetary systems. We explore trends with other species, such as with the C/O ratios, but are significantly limited by the low number of reliable detections.

Total enantioselectivity in the DNA binding of the dinuclear ruthenium(II) complex [[Ru(Me2bpy)2]2(mu-bpm)]4+ [bpm = 2,2'-bipyrimidine; Me2bpy = 4,4'-dimethyl-2,2'-bipyridine].

PubMed

Smith, Jayden A; Collins, J Grant; Patterson, Bradley T; Keene, F Richard

2004-05-07

The binding of the three stereoisomers (DeltaDelta-, LambdaLambda- and DeltaLambda-) of the dinuclear ruthenium(II) complex [[Ru(Me2bpy)2]2(mu-bpm)]4+ [Me2bpy = 4,4'-dimethyl-2,2'-bipyridine; bpm = 2,2'-bipyrimidine] to a tridecanucleotide containing a single adenine bulge has been studied by 1H NMR spectroscopy. The addition of the DeltaDelta-isomer to d(CCGAGAATTCCGG)2 induced significant chemical shift changes for the base and sugar resonances of the residues at the bulge site (G3A4G5/C11C10), whereas small shifts were observed upon addition of the enantiomeric LambdaLambda-form. NOESY spectra of the tridecanucleotide bound with the DeltaDelta-isomer revealed intermolecular NOE's between the metal complex and the nucleotide residues at the bulge site, while only weak NOE's were observed to terminal residues to the LambdaLambda-form. Competitive binding studies were performed where both enantiomers were simultaneously added to the tridecanucleotide, and for all ratios of the two stereoisomers the DeltaDelta-isomer remained selectively bound at the bulge site with the LambdaLambda-enantiomer localised at the terminal regions of the tridecanucleotide. The meso-diastereoisomer (DeltaLambda) was found to bind to the tridecanucleotide with characteristics intermediate between the DeltaDelta- and LambdaLambda-enantiomers of the rac form. Two distinct sets of metal complex resonances were observed, with one set having essentially the same shift as the free metal complex, whilst the other set of resonances exhibited significant shifts. The NOE data indicated that the meso-diastereoisomer does not bind as selectively as the DeltaDelta-isomer, with NOE's observed to a greater number of nucleotide residues compared to the DeltaDelta-form. This study provides a rare example of total enantioselectivity in the binding of an inert transition metal complex to DNA, produced by the shape recognition of both ruthenium(II) centres.

Somatic diversification of chicken immunoglobulin light chains by point mutations.

PubMed

Parvari, R; Ziv, E; Lantner, F; Heller, D; Schechter, I

1990-04-01

The light-chain locus of chicken has 1 functional V lambda 1 gene, 1 J gene, and 25 pseudo-V lambda-genes (where V = variable and J = joining). A major problem is which somatic mechanisms expand this extremely limited germ-line information to generate many different antibodies. Weill's group [Reynaud, C. A., Anquez, V., Grimal, H. & Weill, J. C. (1987) Cell 48, 379-388] has shown that the pseudo-V lambda-genes diversify the rearranged V lambda 1 by gene conversion. Here we demonstrate that chicken light chains are further diversified by somatic point mutations and by V lambda 1-J flexible joining. Somatic point mutations were identified in the J and 3' noncoding DNA of rearranged light-chain genes of chicken. These regions were analyzed because point mutations in V lambda 1 are obscured by gene conversion; the J and 3' noncoding DNA are presented in one copy per haploid genome and are not subject to gene conversion. In rodents point mutations occur as frequently in the V-J coding regions as in the adjacent flanking DNA. Therefore, we conclude that somatic point mutations diversify the V lambda 1 of chicken. The frequency (0-1%) and distribution of the mutations (decreasing in number with increased distance from the V lambda 1 segment) in chicken were as observed in rodents. Sequence variability at the V lambda 1-J junctions could be attributed to imprecise joining of the V lambda 1 and J genes. The modification by gene conversion of rearranged V lambda 1 genes in the bursa was similar in chicken aged 3 months (9.5%) or 3 weeks (9.1%)--i.e., gene conversion that generates the preimmune repertoire in the bursa seems to level off around 3 weeks of age. This preimmune repertoire can be further diversified by somatic point mutations that presumably lead to the formation of antibodies with increased affinity. A segment with structural features of a matrix association region [(A + T)-rich and four topoisomerase II binding sites] was identified in the middle of the J-C lambda intron (where C = constant).

FAR-ULTRAVIOLET SPECTRAL IMAGES OF THE VELA SUPERNOVA REMNANT: SUPPLEMENTS AND COMPARISONS WITH OTHER WAVELENGTH IMAGES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Il-Joong; Seon, Kwang-Il; Han, Wonyong

We present the improved far-ultraviolet (FUV) emission-line images of the entire Vela supernova remnant (SNR) using newly processed Spectroscopy of Plasma Evolution from Astrophysical Radiation/Far-Ultraviolet Imaging Spectrograph (SPEAR/FIMS) data. The incomplete C III {lambda}977 and O VI {lambda}{lambda}1032, 1038 images presented in the previous study are updated to cover the whole region. The C IV {lambda}{lambda}1548, 1551 image with a higher resolution and new images at Si IV {lambda}{lambda}1394, 1403, O IV] {lambda}1404, He II {lambda}1640.5, and O III] {lambda}{lambda}1661, 1666 are also shown. Comparison of emission-line ratios for two enhanced FUV regions reveals that the FUV emissions of themore » east-enhanced FUV region may be affected by nonradiative shocks of another very young SNR, the Vela Jr. SNR (RX J0852.0-4622, G266.6-1.2). This result is the first FUV detection that is likely associated with the Vela Jr. SNR, supporting previous arguments that the Vela Jr. SNR is close to us. The comparison of the improved FUV images with soft X-ray images shows that an FUV filamentary feature forms the boundary of the northeast-southwest asymmetrical sections of the X-ray shell. The southwest FUV features are characterized as the region where the Vela SNR is interacting with slightly denser ambient medium within the dim X-ray southwest section. From a comparison with the H{alpha} image, we identify a ring-like H{alpha} feature overlapped with an extended hot X-ray feature of similar size and two local peaks of C IV emission. Their morphologies are expected when the H{alpha} ring is in direct contact with the near or far side of the Vela SNR.« less

Limits on the Decay-Rate Difference of Neutral-B Mesons and on CP, T, and CPT Violation in B0-antiB0 Oscillations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aubert, B

2004-02-29

Using events in which one of two neutral-B mesons from the decay of an {Upsilon}(4S) resonance is fully reconstructed, we set limits on the difference between the decay rates of the two neutral-B mass eigenstates and on CP, T, and CPT violation in B{sup 0}{bar B}{sup 0} mixing. The reconstructed decays, comprising both CP and flavor eigenstates, are obtained from 88 million {Upsilon}(4S) {yields} B{bar B} decays collected with the BABAR detector at the PEP-II asymmetric-energy B Factory at SLAC. We determine six independent parameters governing oscillations ({Delta}m, {Delta}{Lambda}/{Lambda}), CPT and CP violation (Re z, Im z), and CP andmore » T violation (Im {lambda}{sub CP}, |q/p|), where {lambda}{sub cp} characterizes B{sup 0} and {bar B}{sup 0} decays to states of charmonium plus K{sub S}{sup 0} or K{sub L}{sup 0}. The results are sgn(Re {lambda}{sub CP}){Delta}{Lambda}/{Lambda} = .0.008 {+-} 0.037(stat.) {+-} 0.018(syst.) [-0.084, 0.068], |q/p| = 1.029 {+-} 0.013(stat.) {+-} 0.011(syst.) [1.001, 1.057], (Re {lambda}{sub CP}/|{lambda}{sub CP}|)Re z = 0.014 {+-} 0.035(stat.) {+-} 0.034(syst.) [-0.072, 0.101], Imz = 0.038 {+-} 0.029(stat.) {+-} 0.025(syst.) [-0.028, 0.104]. The values inside square brackets indicate the 90% confidence-level intervals. The values of Im {lambda}{sub CP} and {Delta}m are consistent with previous analyses and are used as cross-checks. These measurements are in agreement with Standard Model expectations.« less

Simple model for lambda-doublet propensities in bimolecular reactions

NASA Technical Reports Server (NTRS)

Bronikowski, Michael J.; Zare, Richard N.

1990-01-01

A simple geometric model is presented to account for lambda-doublet propensities in bimolecular reactions A + BC - AB + C. It applies to reactions in which AB is formed in a pi state, and in which the unpaired molecular orbital responsible for lambda-doubling arises from breaking the B-C bond. The lambda-doublet population ratio is predicted to be 2:1 provided that: (1) the motion of A in the transition state determines the plane of rotation of AB; (2) the unpaired pi orbital lying initially along the B-C bond may be resolved into a projection onto the AB plane of rotation and a projection perpendicular to this plane; (3) there is no preferred geometry for dissociation of ABC. The 2:1 lambda-doublet ratio is the 'unconstrained dynamics prior' lambda-doublet distribution for such reactions.

Effective screening length of isotropic liquid samples submitted to an applied voltage.

PubMed

Zola, R S; Evangelista, L R; Barbero, G

2006-05-25

A cell of isotropic liquid in the shape of a slab of thickness d and containing ionic impurities is considered. It is shown that the screening effect produced by the ionic charges on the external field is characterized by an effective surface length, lambda(S)(U), depending on the applied voltage U. The analysis indicates that lambda(S)(U)) < lambda(D) when the applied voltage is very large, and lambda(S)(U) --> lambda(D) for very small values of the applied voltage, where lambda(D) is the Debye screening length. The presence of the ions is responsible also for a counterpotential, v, that for small U is such to cancel the effective electric field in the sample, whereas in the opposite limit it is inversely proportional to the applied difference of potential.

The Legacy Archive for Microwave Background Data Analysis (LAMBDA)

NASA Astrophysics Data System (ADS)

Miller, Nathan; LAMBDA

2018-01-01

The Legacy Archive for Microwave Background Data Analysis (LAMBDA) provides CMB researchers with archival data for cosmology missions, software tools, and links to other sites of interest. LAMBDA is one-stop shopping for CMB researchers. It hosts data from WMAP along with many suborbital experiments. Over the past year, LAMBDA has acquired new data from SPTpol, SPIDER and ACTPol. In addition to the primary CMB, LAMBDA also provides foreground data.LAMBDA has several ongoing efforts to provide tools for CMB researchers. These tools include a web interface for CAMB and a web interface for a CMB survey footprint database and plotting tool. Additionally, we have recently developed a Docker container with standard CMB analysis tools and demonstrations in the form of Jupyter notebooks. These containers will be publically available through Docker's container repository and the source will be available on github.