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https://www.readbyqxmd.com/read/28819114/isothermal-amplification-of-long-discrete-dna-fragments-facilitated-by-single-stranded-binding-protein
#1
Yinhua Zhang, Nathan A Tanner
Isothermal amplification methods for detection of DNA and RNA targets have expanded significantly in recent years, promising a new wave of simple and rapid molecular diagnostics. Current isothermal methods result in the generation of short fragments (<150 base pairs) or highly branched long DNA products. Here we report the amplification of discrete target fragments of several kilobases at 37 °C from both double- and single-stranded circular template DNA using specific primer pairs. In contrast to existing methods, this amplification requires only the single-stranded DNA-binding protein gp32 from bacteriophage T4 and a strand-displacing DNA polymerase...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28818949/in-situ-architecture-function-and-evolution-of-a-contractile-injection-system
#2
Désirée Böck, João M Medeiros, Han-Fei Tsao, Thomas Penz, Gregor L Weiss, Karin Aistleitner, Matthias Horn, Martin Pilhofer
Contractile injection systems mediate bacterial cell-cell interactions by a bacteriophage tail-like structure. In contrast to extracellular systems, the type 6 secretion system (T6SS) is defined by intracellular localization and attachment to the cytoplasmic membrane. Here we used cryo-focused ion beam milling, electron cryotomography, and functional assays to study a T6SS in Amoebophilus asiaticus The in situ architecture revealed three modules, including a contractile sheath-tube, a baseplate, and an anchor...
August 18, 2017: Science
https://www.readbyqxmd.com/read/28818800/the-step-wise-framework-to-design-a-chromatography-based-hydrophobicity-assay-for-viral-particles
#3
Sarah A Johnson, Alison Walsh, Matthew R Brown, Scott C Lute, David J Roush, Michael S Burnham, Kurt A Brorson
A high-salt, hydrophobic interaction chromatography (HIC) method was developed to measure the relative hydrophobicity of a diverse set of solutes. Through the careful control of buffer pH and salt concentration, this assay was then used to ascertain for the first time the relative hydrophobicity values of three different bacteriophage, four mammalian viruses, and a range of biotech medicinal proteins as benchmarked to protein standards previously characterized for hydrophobicity.
August 9, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28817689/characterization-and-formulation-into-solid-dosage-forms-of-a-novel-bacteriophage-lytic-against-klebsiella-oxytoca
#4
Teagan L Brown, Steve Petrovski, Dannielle Hoyle, Hiu Tat Chan, Peter Lock, Joseph Tucci
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...
2017: PloS One
https://www.readbyqxmd.com/read/28817192/tssa-the-cap-protein-of-the-type-vi-secretion-system-tail
#5
REVIEW
Abdelrahim Zoued, Eric Durand, Yoann G Santin, Laure Journet, Alain Roussel, Christian Cambillau, Eric Cascales
The Type VI secretion system (T6SS) is a multiprotein and mosaic apparatus that delivers protein effectors into prokaryotic or eukaryotic cells. Recent data on the enteroaggregative Escherichia coli (EAEC) T6SS have provided evidence that the TssA protein is a key component during T6SS biogenesis. The T6SS comprises a trans-envelope complex that docks the baseplate, a cytoplasmic complex that represents the assembly platform for the tail. The T6SS tail is structurally, evolutionarily and functionally similar to the contractile tails of bacteriophages...
August 17, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28815907/t7-rna-polymerase-driven-inducible-cell-lysis-for-dna-transfer-from-escherichia-coli-to-bacillus-subtilis
#6
Mario Juhas, James W Ajioka
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...
August 16, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28815508/multipart-dna-assembly-using-site-specific-recombinases-from-the-large-serine-integrase-family
#7
Femi J Olorunniji, Christine Merrick, Susan J Rosser, Margaret C M Smith, W Marshall Stark, Sean D Colloms
Assembling multiple DNA fragments into functional plasmids is an important and often rate-limiting step in engineering new functions in living systems. Bacteriophage integrases are enzymes that carry out efficient recombination reactions between short, defined DNA sequences known as att sites. These DNA splicing reactions can be used to assemble large numbers of DNA fragments into a functional circular plasmid in a method termed serine integrase recombinational assembly (SIRA). The resulting DNA assemblies can easily be modified by further recombination reactions catalyzed by the same integrase in the presence of its recombination directionality factor (RDF)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28815499/marker-removal-in-transgenic-plants-using-cre-recombinase-delivered-with-potato-virus-x
#8
Lilya Kopertekh, Joachim Schiemann
In this chapter we present an alternative method to develop marker-free transgenic plants. It makes use of the Cre/loxP recombination system from bacteriophage P1 and consists of two essential components. The first component is the transgenic plant containing a loxP-flanked marker gene. The second component is a cre transient expression vector based on potato virus X. The great benefit of this transient delivery method consists in the avoidance of stable integration of the cre recombinase gene into the plant genome...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28814344/microbial-phylogeny-determines-transcriptional-response-of-resistome-to-dynamic-composting-processes
#9
Cheng Wang, Da Dong, P J Strong, Weijing Zhu, Zhuang Ma, Yong Qin, Weixiang Wu
BACKGROUND: Animal manure is a reservoir of antibiotic resistance genes (ARGs) that pose a potential health risk globally, especially for resistance to the antibiotics commonly used in livestock production (such as tetracycline, sulfonamide, and fluoroquinolone). Currently, the effects of biological treatment (composting) on the transcriptional response of manure ARGs and their microbial hosts are not well characterized. Composting is a dynamic process that consists of four distinct phases that are distinguished by the temperature resulting from microbial activity, namely the mesophilic, thermophilic, cooling, and maturing phases...
August 16, 2017: Microbiome
https://www.readbyqxmd.com/read/28813669/the-phage-nucleus-and-tubulin-spindle-are-conserved-among-large-pseudomonas-phages
#10
Vorrapon Chaikeeratisak, Katrina Nguyen, MacKennon E Egan, Marcella L Erb, Anastasia Vavilina, Joe Pogliano
We recently demonstrated that the large Pseudomonas chlororaphis bacteriophage 201φ2-1 assembles a nucleus-like structure that encloses phage DNA and segregates proteins according to function, with DNA processing proteins inside and metabolic enzymes and ribosomes outside the nucleus. Here, we investigate the replication pathway of the Pseudomonas aeruginosa bacteriophages φKZ and φPA3. Bacteriophages φKZ and φPA3 encode a proteinaceous shell that assembles a nucleus-like structure that compartmentalizes proteins and DNA during viral infection...
August 15, 2017: Cell Reports
https://www.readbyqxmd.com/read/28812171/complete-genome-sequence-of-a-novel-virulent-ahjdlikevirus-bacteriophage-that-infects-enterococcus-faecium
#11
Shaozhen Xing, Xianglilan Zhang, Qiang Sun, Jian Wang, Zhiqiang Mi, Guangqian Pei, Yong Huang, Xiaoping An, Kaifei Fu, Lijun Zhou, Baohua Zhao, Yigang Tong
A novel virulent bacteriophage named vB_EfaP_IME199 that specifically infects Enterococcus faecium was isolated and characterized. Its optimal multiplicity of infection was 0.01, and it had a 30 minute outbreak period. High-throughput sequencing revealed that the phage has a dsDNA genome of 18,838 bp with 22 open reading frames. The genome has very low homology to all other bacteriophage sequences in the GenBank database. Run-off sequencing experiments confirmed that vB_EfaP_IME199 has short inverted terminal repeats...
August 16, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28811841/bacteriophages-in-the-gastrointestinal-tract-and-their-implications
#12
Marzanna Łusiak-Szelachowska, Beata Weber-Dąbrowska, Ewa Jończyk-Matysiak, Renata Wojciechowska, Andrzej Górski
The gut microbiota plays an essential role in health and disease of humans. Bacteriophages are the most abundant members of the gut virobiota and display great diversity. Phages can translocate through the mucosa to lymph and internal organs and play a role as regulators of the bacterial population in the gut. Increasing abundance of phages in the gut mucosa may reduce colonization by bacteria. Moreover, phages may have an immunomodulatory role in the immune response in the human gut. The role of phages in inflammatory bowel disease (IBD) remains unknown...
2017: Gut Pathogens
https://www.readbyqxmd.com/read/28811656/phageterm-a-tool-for-fast-and-accurate-determination-of-phage-termini-and-packaging-mechanism-using-next-generation-sequencing-data
#13
Julian R Garneau, Florence Depardieu, Louis-Charles Fortier, David Bikard, Marc Monot
The worrying rise of antibiotic resistance in pathogenic bacteria is leading to a renewed interest in bacteriophages as a treatment option. Novel sequencing technologies enable description of an increasing number of phage genomes, a critical piece of information to understand their life cycle, phage-host interactions, and evolution. In this work, we demonstrate how it is possible to recover more information from sequencing data than just the phage genome. We developed a theoretical and statistical framework to determine DNA termini and phage packaging mechanisms using NGS data...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811342/bacteriophages-of-gordonia-spp-display-a-spectrum-of-diversity-and-genetic-relationships
#14
Welkin H Pope, Travis N Mavrich, Rebecca A Garlena, Carlos A Guerrero-Bustamante, Deborah Jacobs-Sera, Matthew T Montgomery, Daniel A Russell, Marcie H Warner, Graham F Hatfull
The global bacteriophage population is large, dynamic, old, and highly diverse genetically. Many phages are tailed and contain double-stranded DNA, but these remain poorly characterized genomically. A collection of over 1,000 phages infecting Mycobacterium smegmatis reveals the diversity of phages of a common bacterial host, but their relationships to phages of phylogenetically proximal hosts are not known. Comparative sequence analysis of 79 phages isolated on Gordonia shows these also to be diverse and that the phages can be grouped into 14 clusters of related genomes, with an additional 14 phages that are "singletons" with no closely related genomes...
August 15, 2017: MBio
https://www.readbyqxmd.com/read/28811265/molecular-cloning-heterologous-expression-and-functional-characterization-of-gamma-tocopherol-methyl-transferase-%C3%AE-tmt-from-glycine-max
#15
Kalpana Tewari, Anil Dahuja, Archana Sachdev, Kishwar Ali, Vaibhav Kumar, Amresh Kumar, Sweta Kumari
γ-Tocopherol methyltransferase (γ-TMT) (EC 2.1.1.95) is the last enzyme in the tocopherol biosynthetic pathway and it catalyzes the conversion of γ-tocopherol into α-tocopherol, the nutritionally significant and most bioactive form of vitamin E. Although the γ-TMT gene has been successfully overexpressed in many crops to enhance their α-tocopherol content but still only few attempts have been made to uncover its structural, functional and regulation aspects at protein level. In this study, we have cloned the complete 909bp coding sequence of Glycine max γ-TMT (Gm γ-TMT) gene that encodes the corresponding protein comprising of 302 amino acid residues...
August 12, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28808331/pro-and-anti-inflammatory-responses-of-peripheral-blood-mononuclear-cells-induced-by-staphylococcus-aureus-and-pseudomonas-aeruginosa-phages
#16
Jonas D Van Belleghem, Frédéric Clement, Maya Merabishvili, Rob Lavigne, Mario Vaneechoutte
The ability of bacteriophages to kill bacteria is well known, as is their potential use as alternatives to antibiotics. As such, bacteriophages reach high doses locally through infection of their bacterial host in the human body. In this study we assessed the gene expression profile of peripheral blood monocytes from six donors for twelve immunity-related genes (i.e. CD14, CXCL1, CXCL5, IL1A, IL1B, IL1RN, IL6, IL10, LYZ, SOCS3, TGFBI and TNFA) induced by Staphylococcus aureus phage ISP and four Pseudomonas aeruginosa phages (i...
August 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28807909/development-and-use-of-personalized-bacteriophage-based-therapeutic-cocktails-to-treat-a-patient-with-a-disseminated-resistant-acinetobacter-baumannii-infection
#17
Robert T Schooley, Biswajit Biswas, Jason J Gill, Adriana Hernandez-Morales, Jacob Lancaster, Lauren Lessor, Jeremy J Barr, Sharon L Reed, Forest Rohwer, Sean Benler, Anca M Segall, Randy Taplitz, Davey M Smith, Kim Kerr, Monika Kumaraswamy, Victor Nizet, Leo Lin, Melanie D McCauley, Steffanie A Strathdee, Constance A Benson, Robert K Pope, Brian M Leroux, Andrew C Picel, Alfred J Mateczun, Katherine E Cilwa, James M Regeimbal, Luis A Estrella, David M Wolfe, Matthew S Henry, Javier Quinones, Scott Salka, Kimberly A Bishop-Lilly, Ry Young, Theron Hamilton
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 a MDR A. baumannii infection. Despite multiple antibiotic courses and efforts at percutaneous drainage of a pancreatic pseudocyst, the patient deteriorated over a four-month period...
August 14, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28807826/structural-plasticity-of-t4-transcription-co-activator-gp33-revealed-by-a-protease-resistant-unfolded-state
#18
Radhakrishnan Mahalakshmi, Svetlana Rajkumar Maurya, Bhawna Burdak, Parini Surti, Manoj S Patel, Vikas Jain
Gene 33 protein (gp33) is a transcriptional coactivator for late genes of the T4 bacteriophage. gp33 possesses a 5-helix bundle core, with unstructured N- and C-terminal regions that account for >50% of the protein sequence. It plays a unique role of interacting with host RNA polymerase, couples transcription with DNA replication, and plays the dual function as repressor and co-activator in phage transcription. Here, we identify protein structural plasticity as the molecular basis of the dual nature in gp33...
August 12, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28805554/apitherapeutics-and-phage-loaded-nanofibers-as-wound-dressings-with-enhanced-wound-healing-and-antibacterial-activity
#19
Wessam A Sarhan, Hassan Me Azzazy
AIM: Develop green wound dressings which exhibit enhanced wound-healing ability and potent antibacterial effects. METHODS: Honey, polyvinyl alcohol, chitosan nanofibers were electrospun and loaded with bee venom, propolis and/or bacteriophage against the multidrug-resistant Pseudomonas aeruginosa and examined for their antibacterial, wound-healing ability and cytotoxicity. RESULTS: Among different formulations of nanofibers, honey, polyvinyl alcohol, chitosan-bee venom/bacteriophage exhibited the most potent antibacterial activity against all tested bacterial strains (Gram-positive and -negative strains) and achieved nearly complete killing of multidrug-resistant P...
September 2017: Nanomedicine
https://www.readbyqxmd.com/read/28804739/selection-of-genetically-modified-bacteriophages-using-the-crispr-cas-system
#20
Miriam Manor, Udi Qimron
We present a CRISPR-Cas based technique for deleting genes from the T7 bacteriophage genome. A DNA fragment encoding homologous arms to the target gene to be deleted is first cloned into a plasmid. The T7 phage is then propagated in Escherichia coli harboring this plasmid. During this propagation, some phage genomes undergo homologous recombination with the plasmid, thus deleting the targeted gene. To select for these genomes, the CRISPR-Cas system is used to cleave non-edited genomes, enabling isolation of the desired recombinant phages...
August 5, 2017: Bio-protocol
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