keyword
MENU ▼
Read by QxMD icon Read
search

Phage

keyword
https://www.readbyqxmd.com/read/29141129/recent-trends-in-salmonella-outbreaks-and-emerging-technology-for-biocontrol-of-salmonella-using-phages-in-foods-a-review
#1
REVIEW
Jun-Hyun Oh, Mi-Kyung Park
Salmonella is one of the principal causes of foodborne outbreaks. As traditional control methods have shown efficacy against emerging Salmonella serotypes or antimicrobial-resistant Salmonella, new approaches have been attempted. The use of lytic phages for the biocontrol of Salmonella in food industry has become an attractive method owing to the many advantages offered by the use of phages as biocontrol agents. Phages are natural alternatives to traditional antimicrobial agents; they have proven effective in the control of bacterial pathogens in food industry, which has led to the development of different phage products...
November 15, 2017: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29138562/dual-uv-irradiation-based-metal-oxide-nanoparticles-for-enhanced-antimicrobial-activity-in-escherichia-coli-and-m13-bacteriophage
#2
Su-Eon Jin, Woochul Hwang, Hyo Jung Lee, Hyo-Eon Jin
Metal oxide (MO) nanoparticles have been studied as nano-antibiotics due to their antimicrobial activities even in antibiotic-resistant microorganisms. We hypothesized that a hybrid system of dual UV irradiation and MO nanoparticles would have enhanced antimicrobial activities compared with UV or MO nanoparticles alone. In this study, nanoparticles of ZnO, ZnTiO3, MgO, and CuO were selected as model nanoparticles. A dual UV collimated beam device of UV-A and UV-C was developed depending upon the lamp divided by coating...
2017: International Journal of Nanomedicine
https://www.readbyqxmd.com/read/29138440/structural-basis-for-dna-recognition-of-a-single-stranded-dna-binding-protein-from-enterobacter-phage-enc34
#3
Elina Cernooka, Janis Rumnieks, Kaspars Tars, Andris Kazaks
Modern DNA sequencing capabilities have led to the discovery of a large number of new bacteriophage genomes, which are a rich source of novel proteins with an unidentified biological role. The genome of Enterobacter cancerogenus bacteriophage Enc34 contains several proteins of unknown function that are nevertheless conserved among distantly related phages. Here, we report the crystal structure of a conserved Enc34 replication protein ORF6 which contains a domain of unknown function DUF2815. Despite the low (~15%) sequence identity, the Enc34 ORF6 structurally resembles the gene 2...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29138389/phage-display-and-selection-of-lanthipeptides-on-the-carboxy-terminus-of-the-gene-3-minor-coat-protein
#4
Johannes H Urban, Markus A Moosmeier, Tobias Aumüller, Marcus Thein, Tjibbe Bosma, Rick Rink, Katharina Groth, Moritz Zulley, Katja Siegers, Kathrin Tissot, Gert N Moll, Josef Prassler
Ribosomally synthesized and post-translationally modified peptides (RiPPs) are an emerging class of natural products with drug-like properties. To fully exploit the potential of RiPPs as peptide drug candidates, tools for their systematic engineering are required. Here we report the engineering of lanthipeptides, a subclass of RiPPs characterized by multiple thioether cycles that are enzymatically introduced in a regio- and stereospecific manner, by phage display. This was achieved by heterologous co-expression of linear lanthipeptide precursors fused to the widely neglected C-terminus of the bacteriophage M13 minor coat protein pIII, rather than the conventionally used N-terminus, along with the modifying enzymes from distantly related bacteria...
November 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/29138294/isolation-of-isoform-specific-binding-proteins-affimers-by-phage-display-using-negative-selection
#5
Anna Ah-San Tang, Christian Tiede, David J Hughes, Michael J McPherson, Darren C Tomlinson
Some 30 years after its discovery, phage display remains one of the most widely used methods of in vitro selection. Initially developed to revolutionize the generation of therapeutic antibodies, phage display is now the first choice for screening artificial binding proteins. Artificial binding proteins can be used as reagents to study protein-protein interactions, target posttranslational modifications, and distinguish between homologous proteins. They can also be used as research and affinity reagents, for diagnostic purposes, and as therapeutics...
November 14, 2017: Science Signaling
https://www.readbyqxmd.com/read/29136890/electro-acoustic-sensor-for-the-real-time-identification-of-the-bacteriophages
#6
О I Guliy, B D Zaitsev, I A Borodina, А М Shikhabudinov, S А Staroverov, L A Dykman, A S Fomin
The electro-acoustical sensor for the real-time identification of the bacteriophage FAl-SR65 is described. The polyclonal antibodies specific to the bacteriophage FAl-SR65 were for the first time obtained, and the possibility of their application to the bacteriophage detection by using the electro-acoustical method of analysis was also studied for the first time. The electro-acoustical sensor was based on the lateral electric field excited piezoelectric resonator. The frequency dependences of the real and imaginary parts of the electrical impedance of such a resonator, loaded with the virus-antibody suspension, significantly differed from those measured for the same resonator with the same virus suspension but without antibodies (control)...
February 1, 2018: Talanta
https://www.readbyqxmd.com/read/29136863/the-biological-acoustic-sensor-to-record-the-interactions-of-the-microbial-cells-with-the-phage-antibodies-in-conducting-suspensions
#7
О I Guliy, B D Zaitsev, I A Borodina, А М Shikhabudinov, A A Teplykh, S A Staroverov, A S Fomin
The acoustic biological sensor for the analysis of the bacterial cells in conducting suspension was developed. The sensor represented the two channel delay line based on the piezoelectric plate of Y-X lithium niobate thick of 0.2mm. Two pairs of the interdigital transducers (IDT) for the excitation and reception of shear horizontal acoustic wave of zero order (SH0) in each channel were deposited by the method of photolithography. One channel of the delay line was electrically shorted by the deposition of thin aluminum film between IDTs...
February 1, 2018: Talanta
https://www.readbyqxmd.com/read/29134604/muprints-and-whole-genome-insertion-scans-methods-for-investigating-chromosome-accessibility-and-dna-dynamics-using-bacteriophage-mu
#8
N Patrick Higgins
Bacteriophage Mu infects a broad range of gram-negative bacteria. After infection, Mu amplifies its DNA through a coupled transposition/replication cycle that inserts copies of Mu throughout all domains of the folded chromosome. Mu has the most relaxed target specificity of the known transposons (Manna et al., J Bacteriol 187: 3586-3588, 2005) and the Mu DNA packaging process, called "headful packaging", incorporates 50-150 bp of host sequences covalently bound to its left end and 2 kb of host DNA linked to its right end into a viral capsid...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29134601/transposable-bacteriophages-as-genetic-tools
#9
Ariane Toussaint
Phage Mu is the paradigm of a growing family of bacteriophages that infect a wide range of bacterial species and replicate their genome by replicative transposition. This molecular process, which is used by other mobile genetic elements to move within genomes, involves the profound rearrangement of the host genome [chromosome(s) and plasmid(s)] and can be exploited for the genetic analysis of the host bacteria and the in vivo cloning of host genes. In this chapter we review Mu-derived constructs that optimize the phage as a series of genetic tools that could inspire the development of similarly efficient tools from other transposable phages for a large spectrum of bacteria...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29134600/visualization-of-phage-genomic-data-comparative-genomics-and-publication-quality-diagrams
#10
Dann Turner, J Mark Sutton, Darren M Reynolds, Eby M Sim, Nicola K Petty
The presentation of bacteriophage genomes as diagrams allows the location and organization of features to be communicated in a clear and effective manner. A wide range of software applications are available for the clear and accurate visualization of genomic data. Several of these applications incorporate comparative analysis tools, allowing for insertions, deletions, rearrangements and variations in syntenic regions to be visualized. In this chapter, freely available software and resources for the generation of high-quality graphical maps of bacteriophage genomes are listed and discussed...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29134599/phage-genome-annotation-using-the-rast-pipeline
#11
Katelyn McNair, Ramy Karam Aziz, Gordon D Pusch, Ross Overbeek, Bas E Dutilh, Robert Edwards
Phages are complex biomolecular machineries that have to survive in a bacterial world. Phage genomes show many adaptations to their lifestyle such as shorter genes, reduced capacity for redundant DNA sequences, and the inclusion of tRNAs in their genomes. In addition, phages are not free-living, they require a host for replication and survival. These unique adaptations provide challenges for the bioinformatics analysis of phage genomes. In particular, ORF calling, genome annotation, noncoding RNA (ncRNA) identification, and the identification of transposons and insertions are all complicated in phage genome analysis...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29134597/essential-steps-in-characterizing-bacteriophages-biology-taxonomy-and-genome-analysis
#12
Ramy Karam Aziz, Hans-Wolfgang Ackermann, Nicola K Petty, Andrew M Kropinski
Because of the rise in antimicrobial resistance there has been a significant increase in interest in phages for therapeutic use. Furthermore, the cost of sequencing phage genomes has decreased to the point where it is being used as a teaching tool for genomics. Unfortunately, the quality of the descriptions of the phage and its annotation frequently are substandard. The following chapter is designed to help people working on phages, particularly those new to the field, to accurately describe their newly isolated viruses...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29134596/preparing-cdna-libraries-from-lytic-phage-infected-cells-for-whole-transcriptome-analysis-by-rna-seq
#13
Bob Blasdel, Pieter-Jan Ceyssens, Rob Lavigne
Whole genome wide analysis of transcription using RNA-Seq methods is a powerful way to elucidate differential expression of gene features in bacteria across different conditions as well as for discovering previously exotic RNA species. Indeed, RNA sequencing has revolutionized the study of bacterial transcription with the diversity and quantity of small noncoding RNA elements that have been found and its ability to clearly define operons, promoters , and terminators . We discuss our experience with applying RNA sequencing technology to analyzing the lytic cycle, including extraction, processing, and a guide to the customized statistical analysis necessary for analyzing differential host and phage transcription...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29134595/genome-sequencing-of-dsdna-containing-bacteriophages-directly-from-a-single-plaque
#14
Witold Kot
The sequencing of phage genomes has become a routine procedure for phage characterization. The protocol presented here allows rapid isolation of DNA from a single phage plaque followed by building ready-to-sequence Illumina-compatible library.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29134594/amplification-for-whole-genome-sequencing-of-bacteriophages-from-single-isolated-plaques-using-sispa
#15
Derick E Fouts
Genomics has greatly transformed our understanding of phage biology; however, traditional methods of DNA isolation for whole genome sequencing have required phages to be grown to high titers in large-scale preparations, potentially selecting for only those phages that can grow efficiently under laboratory conditions. This may also select for mutations or deletions that enable more efficient growth in culture. The ability to sequence a bacteriophage genome from a single isolated plaque reduces these risks while decreasing the time and complexity of bacteriophage genome sequencing...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29134592/identification-of-dna-base-modifications-by-means-of-pacific-biosciences-rs-sequencing-technology
#16
Philip Kelleher, James Murphy, Jennifer Mahony, Douwe van Sinderen
Whole phage genomes can be sequenced readily using one or a combination of next generation sequencing (NGS) technologies. One of the most recently developed NGS platforms, the so-called Single-Molecule Real-Time (SMRT) sequencing approach provided by the PacBio RS platform, is particularly useful in providing complete (i.e., un-gapped) genome sequences, but differs from other technologies in that the platform also allows for downstream analysis to identify nucleotides that have been modified by DNA methylation...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29134591/sequencing-assembling-and-finishing-complete-bacteriophage-genomes
#17
Daniel A Russell
Next-generation DNA sequencing (NGS) technologies have made generating genomic sequence for organisms of interest affordable and commonplace. However, NGS platforms and analysis software are generally tuned to be used on large and complex genomes or metagenomic samples. Determining the complete genome sequence of a single bacteriophage requires a somewhat different perspective, workflow, and sensitivity to the nature of phages. Because phage genomes consist of mostly coding regions (see Pope/Jacobs-Sera chapter), a very high standard should be adopted when completing these genomes so that the subsequent steps of annotation and analysis are not sabotaged by sequencing errors...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29134590/application-of-a-virucidal-agent-to-avoid-overestimation-of-phage-kill-during-phage-decontamination-assays-on-ready-to-eat-meats
#18
Andrew Chibeu, S Balamurugan
We describe a method for assessing the effectiveness of tea extract based virucide (TeaF) application to remove phage LISTEX™ P100 not bound to Listeria monocytogenes from stomached rinses prior to direct plating and bacterial enumeration, where the phage is being used as a decontaminant to reduce L. monocytogenes levels on ready-to-eat meat.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29134589/encapsulation-of-listeria-phage-a511-by-alginate-to-improve-its-thermal-stability
#19
Hanie Ahmadi, Qi Wang, Loong-Tak Lim, S Balamurugan
Microencapsulation is a versatile method for enhancing the stability of bacteriophages under harsh conditions, such as those which occur during thermal processing. For food applications, encapsulation in food-grade polymer matrices is desirable owing to their nontoxicity and low cost. Here, we describe the encapsulation of Listeria phage A511 using sodium alginate, gum arabic, and gelatin to maximize its viability during thermal processing.
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29134588/encapsulation-strategies-of-bacteriophage-felix-o1-for-oral-therapeutic-application
#20
Golam S Islam, Qi Wang, Parviz M Sabour
Due to emerging antibiotic-resistant strains among the pathogens, a variety of strategies, including therapeutic application of bacteriophages, have been suggested as a possible alternative to antibiotics in food animal production. As pathogen-specific biocontrol agents, bacteriophages are being studied intensively. Primarily their applications in the food industry and animal production have been recognized in the USA and Europe, for pathogens including Salmonella, Campylobacter, Escherichia coli, and Listeria...
2018: Methods in Molecular Biology
keyword
keyword
34876
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"