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https://www.readbyqxmd.com/read/29151205/filamentous-bacteriophage-viruses-preparation-magic-angle-spinning-solid-state-nmr-experiments-and-structure-determination
#1
Omry Morag, Nikolaos G Sgourakis, Gili Abramov, Amir Goldbourt
Filamentous bacteriophages are elongated semi-flexible viruses that infect bacteria. They consist of a circular single-stranded DNA (ssDNA) wrapped by a capsid consisting of thousands of copies of a major coat protein subunit. Given the increasing number of discovered phages and the existence of only a handful of structures, the development of methods for phage structure determination is valuable for biophysics and structural virology. In recent years, we developed and applied techniques to elucidate the 3D atomic-resolution structures of intact bacteriophages using experimental magic-angle spinning (MAS) solid-state NMR data...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29151202/nmr-of-macromolecular-assemblies-and-machines-at-1-ghz-and-beyond-new-transformative-opportunities-for-molecular-structural-biology
#2
Caitlin M Quinn, Mingzhang Wang, Tatyana Polenova
As a result of profound gains in sensitivity and resolution afforded by ultrahigh magnetic fields, transformative applications in the fields of structural biology and materials science are being realized. The development of dual low temperature superconducting (LTS)/high-temperature superconducting (HTS) magnets has enabled the achievement of magnetic fields above 1 GHz (23.5 T), which will open doors to an unprecedented new range of applications. In this contribution, we discuss the promise of ultrahigh field magnetic resonance...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29150707/a-guard-killer-phage-cocktail-effectively-lyses-the-host-and-inhibits-the-development-of-phage-resistant-strains-of-escherichia-coli
#3
Ling Yu, Shuang Wang, Zhimin Guo, Hongtao Liu, Diangang Sun, Guangmou Yan, Dongliang Hu, Chongtao Du, Xin Feng, Wenyu Han, Jingmin Gu, Changjiang Sun, Liancheng Lei
In recent years, after the emergence of a large number of multidrug-resistant bacteria, phages and phage-associated products for the prevention and control of bacterial disease have revealed prominent advantages as compared with antibiotics. However, bacteria are susceptible to becoming phage-resistant, thus severely limiting the application of phage therapy. In this study, Escherichia coli cells were incubated with lytic bacteriophages to obtain mutants that were resistant to the lytic phages. Then, bacteriophages against the phage-resistant variants were isolated and subsequently mixed with the original lytic phage to prepare a novel phage cocktail for bactericidal use...
November 17, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29149672/the-application-of-bacteriophages-as-novel-indicators-of-viral-pathogens-in-wastewater-treatment-systems
#4
Edgard Dias, James Ebdon, Huw Taylor
Many wastewater treatment technologies have been shown to remove bacterial pathogens more effectively than viral pathogens and, in aquatic environments, levels of traditional faecal indicator bacteria (FIB) do not appear to correlate consistently with levels of human viral pathogens. There is, therefore, a need for novel viral indicators of faecal pollution and surrogates of viral pathogens, especially given the increasing importance of indirect and direct wastewater reuse. Potential candidates include bacteriophages (phages) and the study described here sought to elucidate the relationship between three groups of phages (somatic coliphages (SOMPH), F-RNA coliphages (F-RNAPH) and human-specific phages infecting B...
November 9, 2017: Water Research
https://www.readbyqxmd.com/read/29149603/structural-basis-of-mitochondrial-transcription-initiation
#5
Hauke S Hillen, Yaroslav I Morozov, Azadeh Sarfallah, Dmitry Temiakov, Patrick Cramer
Transcription in human mitochondria is driven by a single-subunit, factor-dependent RNA polymerase (mtRNAP). Despite its critical role in both expression and replication of the mitochondrial genome, transcription initiation by mtRNAP remains poorly understood. Here, we report crystal structures of human mitochondrial transcription initiation complexes assembled on both light and heavy strand promoters. The structures reveal how transcription factors TFAM and TFB2M assist mtRNAP to achieve promoter-dependent initiation...
November 16, 2017: Cell
https://www.readbyqxmd.com/read/29149017/the-ms6-mycolyl-arabinogalactan-esterase-lysb-is-essential-for-an-efficient-mycobacteriophage-induced-lysis
#6
Adriano M Gigante, Cheri M Hampton, Rebecca S Dillard, Filipa Gil, Maria João Catalão, José Moniz-Pereira, Elizabeth R Wright, Madalena Pimentel
All dsDNA phages encode two proteins involved in host lysis, an endolysin and a holin that target the peptidoglycan and cytoplasmic membrane, respectively. Bacteriophages that infect Gram-negative bacteria encode additional proteins, the spanins, involved in disruption of the outer membrane. Recently, a gene located in the lytic cassette was identified in the genomes of mycobacteriophages, which encodes a protein (LysB) with mycolyl-arabinogalactan esterase activity. Taking in consideration the complex mycobacterial cell envelope that mycobacteriophages encounter during their life cycle, it is valuable to evaluate the role of these proteins in lysis...
November 17, 2017: Viruses
https://www.readbyqxmd.com/read/29147941/artificial-bio-nanomachines-based-on-protein-needles-derived-from-bacteriophage-t4
#7
REVIEW
Hiroshi Inaba, Takafumi Ueno
Bacteriophage T4 is a natural bio-nanomachine which achieves efficient infection of host cells via cooperative motion of specific three-dimensional protein architectures. The relationships between the protein structures and their dynamic functions have recently been clarified. In this review we summarize the design principles for fabrication of nanomachines using the component proteins of bacteriophage T4 based on these recent advances. We focus on the protein needle known as gp5, which is located at the center of the baseplate at the end of the contractile tail of bacteriophage T4...
November 16, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/29147662/effectiveness-of-a-lytic-phage-srg1-against-vancomycin-resistant-enterococcus-faecalis-in-compost-and-soil
#8
Sidra Rahmat Ullah, Saadia Andleeb, Taskeen Raza, Muhsin Jamal, Khalid Mehmood
Nosocomial infections caused by vancomycin-resistant Enterococcus have become a major problem. Bacteriophage therapy is proposed as a potential alternative therapy. Bacteriophages are viruses that infect bacteria and are ubiquitous in nature. Lytic bacteriophage was isolated from sewage water that infects VREF, the causative agent of endocarditis, bacteraemia, and urinary tract infections (UTIs). The phage produced clear plaques with unique clear morphology and well-defined boundaries. TEM results of phage revealed it to be 108 ± 0...
2017: BioMed Research International
https://www.readbyqxmd.com/read/29147114/antibiotic-resistant-bacterial-isolates-from-captive-green-turtles-and-in-vitro-sensitivity-to-bacteriophages
#9
Alessandro Delli Paoli Carini, Ellen Ariel, Jacqueline Picard, Lisa Elliott
This study aimed to test multidrug resistant isolates from hospitalised green turtles (Chelonia mydas) and their environment in North Queensland, Australia, for in vitro susceptibility to bacteriophages. Seventy-one Gram-negative bacteria were isolated from green turtle eye swabs and water samples. Broth microdilution tests were used to determine antibiotic susceptibility. All isolates were resistant to at least two antibiotics, with 24% being resistant to seven of the eight antibiotics. Highest resistance rates were detected to enrofloxacin (77%) and ampicillin (69...
2017: International Journal of Microbiology
https://www.readbyqxmd.com/read/29146843/complete-genome-sequences-of-vibrio-cholerae-specific-bacteriophages-24-and-x29
#10
Sudhakar G Bhandare, Andrew Warry, Richard D Emes, Steven P T Hooton, Paul A Barrow, Robert J Atterbury
The complete genomes of two Vibrio cholerae bacteriophages of potential interest for cholera bacteriophage (phage) therapy were sequenced and annotated. The genome size of phage 24 is 44,395 bp encoding 71 putative proteins, and that of phage X29 is 41,569 bp encoding 68 putative proteins.
November 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29146842/genome-sequences-of-19-novel-erwinia-amylovora-bacteriophages
#11
Ian N D Esplin, Jordan A Berg, Ruchira Sharma, Robert C Allen, Daniel K Arens, Cody R Ashcroft, Shannon R Bairett, Nolan J Beatty, Madeline Bickmore, Travis J Bloomfield, T Scott Brady, Rachel N Bybee, John L Carter, Minsey C Choi, Steven Duncan, Christopher P Fajardo, Brayden B Foy, David A Fuhriman, Paul D Gibby, Savannah E Grossarth, Kala Harbaugh, Natalie Harris, Jared A Hilton, Emily Hurst, Jonathan R Hyde, Kayleigh Ingersoll, Caitlin M Jacobson, Brady D James, Todd M Jarvis, Daniella Jaen-Anieves, Garrett L Jensen, Bradley K Knabe, Jared L Kruger, Bryan D Merrill, Jenny A Pape, Ashley M Payne Anderson, David E Payne, Malia D Peck, Samuel V Pollock, Micah J Putnam, Ethan K Ransom, Devin B Ririe, David M Robinson, Spencer L Rogers, Kerri A Russell, Jonathan E Schoenhals, Christopher A Shurtleff, Austin R Simister, Hunter G Smith, Michael B Stephenson, Lyndsay A Staley, Jason M Stettler, Mallorie L Stratton, Olivia B Tateoka, P J Tatlow, Alexander S Taylor, Suzanne E Thompson, Michelle H Townsend, Trever L Thurgood, Brittian K Usher, Kiara V Whitley, Andrew T Ward, Megan E H Ward, Charles J Webb, Trevor M Wienclaw, Taryn L Williamson, Michael J Wells, Cole K Wright, Donald P Breakwell, Sandra Hope, Julianne H Grose
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.
November 16, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29145601/identification-and-functional-analysis-of-potential-prophage-derived-recombinases-for-genome-editing-in-lactobacillus-casei
#12
Yongping Xin, Tingting Guo, Yingli Mu, Jian Kong
Numerous LAB bacteriophage genomes have been sequenced, while the functional genes are yet to be exploited. In this study, a λ Red-like recombinase operon LCABL_13040-50-60 was identified from a prophage PLE3 in Lactobacillus casei BL23 genome, and its recombination function was confirmed by replacement of a 167 bp galK fragment with chloramphenicol-resistant gene (cat) in the L. casei BL23 genome. Further functional analysis showed that LCABL_13040 and LCABL_13060 were analogs to the host nuclease inhibitor (Redγ) and 5'-3' exonuclease (Redα/RecE), respectively...
November 14, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/29140461/a-bacterial-three-hybrid-assay-detects-escherichia-coli-hfq-srna-interactions-in-vivo
#13
Katherine E Berry, Ann Hochschild
The interaction of RNA molecules with proteins is a critical aspect of gene regulation across all domains of life. Here, we report the development of a bacterial three-hybrid (B3H) assay to genetically detect RNA-protein interactions. The basis for this three-hybrid assay is a transcription-based bacterial two-hybrid assay that has been used widely to detect and dissect protein-protein interactions. In the three-hybrid assay, a DNA-bound protein with a fused RNA-binding moiety (the coat protein of bacteriophage MS2 (MS2CP)) is used to recruit a hybrid RNA upstream of a test promoter...
November 11, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29138562/dual-uv-irradiation-based-metal-oxide-nanoparticles-for-enhanced-antimicrobial-activity-in-escherichia-coli-and-m13-bacteriophage
#14
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
#15
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
#16
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/29137115/cost-effective-and-handmade-paper-based-immunosensing-device-for-electrochemical-detection-of-influenza-virus
#17
Sivaranjani Devarakonda, Renu Singh, Jyoti Bhardwaj, Jaesung Jang
Although many studies concerning the detection of influenza virus have been published, a paper-based, label-free electrochemical immunosensor has never been reported. Here, we present a cost-effective, handmade paper-based immunosensor for label-free electrochemical detection of influenza virus H1N1. This immunosensor was prepared by modifying paper with a spray of hydrophobic silica nanoparticles, and using stencil-printed electrodes. We used a glass vaporizer to spray the hydrophobic silica nanoparticles onto the paper, rendering it super-hydrophobic...
November 11, 2017: Sensors
https://www.readbyqxmd.com/read/29136890/electro-acoustic-sensor-for-the-real-time-identification-of-the-bacteriophages
#18
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/29134604/muprints-and-whole-genome-insertion-scans-methods-for-investigating-chromosome-accessibility-and-dna-dynamics-using-bacteriophage-mu
#19
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/29134603/use-of-rp4-mini-mu-for-gene-transfer
#20
Frédérique Van Gijsegem
Gene cloning is an invaluable technique in genetic analysis and exploitation of genetic properties of a broad range of bacteria. Numerous in vitro molecular cloning protocols have been devised but the efficiency of these techniques relies on the frequency with which the recombinant DNA can be introduced in the recipient strain. Here, we describe an in vivo gene transfer and cloning technique based on transposable bacteriophage Mu property to rearrange its host genome. This technique uses the broad host range plasmid RP4 carrying a transposable mini-MuA(+) derivative and was successfully used as well in enteric as in environmental nonenteric bacteria...
2018: Methods in Molecular Biology
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