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https://www.readbyqxmd.com/read/29792678/combinatorially-screened-peptide-as-targeted-covalent-binder-alteration-of-bait-conjugated-peptide-to-reactive-modifier
#1
Shuta Uematsu, Yudai Tabuchi, Yuji Ito, Masumi Taki
A peptide-type covalent binder for a target protein was obtained by combinatorial screening of fluoroprobe-conjugated peptide libraries on bacteriophage T7. The solvatochromic fluoroprobe works as a bait during the affinity selection process of phage display. To obtain the targeted covalent binder, the bait in the selected consensus peptide was altered into a reactive warhead possessing a sulfonyl fluoride. The reaction efficiency and site / position specificity of the covalent conjugation between the binder and the target protein were evaluated by liquid chromatography-tandem mass spectrometry (LC-MS/MS), and rationalized by a protein-ligand docking simulation...
May 24, 2018: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/29792526/phages-antibiotic-resistance-are-the-most-abundant-entities-on-earth-ready-for-a-comeback
#2
Colin Hill, Susan Mills, Reynolds P Ross
Bacteriophages, which lost out to antibiotic therapy in the past, may be poised to make a comeback. Once discarded because of their narrow activity spectrum, it can now be viewed as a major advantage that these intracellular, self-replicating entities can exert their killing effect with minimal damage to the commensal microbiome. In eastern Europe, phages continue to be used both prophylactically and therapeutically to treat infections. More recently, much needed regulated clinical trials are underway with a view to restoring phage therapy as a tool for mainstream medicine, although current regulations may impede their full potential...
May 24, 2018: Future Microbiology
https://www.readbyqxmd.com/read/29792517/is-phage-therapy-suitable-for-treating-chronic-sinusitis-staphylococcus-aureus-infection
#3
Peter G Speck, Peter-John Wormald
No abstract text is available yet for this article.
May 24, 2018: Future Microbiology
https://www.readbyqxmd.com/read/29792401/synthetic-single-domain-antibodies-for-the-conformational-trapping-of-membrane-proteins
#4
Iwan Zimmermann, Pascal Egloff, Cedric Aj Hutter, Fabian M Arnold, Peter Stohler, Nicolas Bocquet, Melanie N Hug, Sylwia Huber, Martin Siegrist, Lisa Hetemann, Jennifer Gera, Samira Gmür, Peter Spies, Daniel Gygax, Eric R Geertsma, Roger Jp Dawson, Markus A Seeger
Mechanistic and structural studies of membrane proteins require their stabilization in specific conformations. Single domain antibodies are potent reagents for this purpose, but their generation relies on immunizations, which impedes selections in the presence of ligands typically needed to populate defined conformational states. To overcome this key limitation, we developed an in vitro selection platform based on synthetic single domain antibodies named sybodies. To target the limited hydrophilic surfaces of membrane proteins, we designed three sybody libraries that exhibit different shapes and moderate hydrophobicity of the randomized surface...
May 24, 2018: ELife
https://www.readbyqxmd.com/read/29791797/modulating-macrophage-polarization-through-ccr2-inhibition-and-multivalent-engagement
#5
Michael B Deci, Scott W Ferguson, Sydney L Scatigno, Juliane Nguyen
Excessive or prolonged recruitment of inflammatory monocytes to damaged tissue can significantly worsen patient outcomes. Monocytes migrate to sites of tissue inflammation in response to high local concentrations of CCL2, a chemokine that binds to and signals through the CCR2 receptor. While the role of CCR2 in cellular migration is well studied, it is unclear how CCR2 inhibition affects macrophage polarization and if multivalency can increase downstream signaling effects. Using affinity selection with a phage library, we identified a novel scFv (58C) that binds specifically and with high affinity to the N-terminal domain of CCR2 (KD = 59...
May 23, 2018: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/29790974/crisprcasfinder-an-update-of-crisrfinder-includes-a-portable-version-enhanced-performance-and-integrates-search-for-cas-proteins
#6
David Couvin, Aude Bernheim, Claire Toffano-Nioche, Marie Touchon, Juraj Michalik, Bertrand Néron, Eduardo P C Rocha, Gilles Vergnaud, Daniel Gautheret, Christine Pourcel
CRISPR (clustered regularly interspaced short palindromic repeats) arrays and their associated (Cas) proteins confer bacteria and archaea adaptive immunity against exogenous mobile genetic elements, such as phages or plasmids. CRISPRCasFinder allows the identification of both CRISPR arrays and Cas proteins. The program includes: (i) an improved CRISPR array detection tool facilitating expert validation based on a rating system, (ii) prediction of CRISPR orientation and (iii) a Cas protein detection and typing tool updated to match the latest classification scheme of these systems...
May 22, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29790189/the-identification-of-a-novel-antibody-for-cd133-using-human-antibody-phage-display
#7
Paige M Glumac, Colleen L Forster, Hong Zhou, Paari Murugan, Shilpa Gupta, Aaron M LeBeau
BACKGROUND: The transmembrane glycoprotein CD133 is believed to be a marker of adult prostate stem cells and cancer stem/initiating cells. Investigating the role of CD133 in the normal biology of the prostate and in cancer is complicated by the lack of a sensitive and accurate antibody for its detection. Here, we describe the characterization of a unique antibody identified using human antibody phage display that can recognize CD133 in both formalin-fixed tissues and cell lines. METHODS: A human single-chain variable fragment (scFv) antibody phage display library possessing a diversity of 8 × 109 was screened against fully glycosylated recombinant CD133...
May 22, 2018: Prostate
https://www.readbyqxmd.com/read/29789681/genomic-and-ecological-study-of-two-distinctive-freshwater-bacteriophages-infecting-a-comamonadaceae-bacterium
#8
Kira Moon, Ilnam Kang, Suhyun Kim, Sang-Jong Kim, Jang-Cheon Cho
Bacteriophages of freshwater environments have not been well studied despite their numerical dominance and ecological importance. Currently, very few phages have been isolated for many abundant freshwater bacterial groups, especially for the family Comamonadaceae that is found ubiquitously in freshwater habitats. In this study, we report two novel phages, P26059A and P26059B, that were isolated from Lake Soyang in South Korea, and lytically infected bacterial strain IMCC26059, a member of the family Comamonadaceae...
May 22, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29789383/t7-phage-factor-required-for-managing-rpos-in-escherichia-coli
#9
Aline Tabib-Salazar, Bing Liu, Declan Barker, Lynn Burchell, Udi Qimron, Steve J Matthews, Sivaramesh Wigneshweraraj
T7 development in Escherichia coli requires the inhibition of the housekeeping form of the bacterial RNA polymerase (RNAP), Eσ70 , by two T7 proteins: Gp2 and Gp5.7. Although the biological role of Gp2 is well understood, that of Gp5.7 remains to be fully deciphered. Here, we present results from functional and structural analyses to reveal that Gp5.7 primarily serves to inhibit EσS , the predominant form of the RNAP in the stationary phase of growth, which accumulates in exponentially growing E. coli as a consequence of the buildup of guanosine pentaphosphate [(p)ppGpp] during T7 development...
May 22, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29788909/whole-genome-analysis-reveals-the-diversity-and-evolutionary-relationships-between-necrotic-enteritis-causing-strains-of-clostridium-perfringens
#10
Jake A Lacey, Theodore R Allnutt, Ben Vezina, Thi Thu Hao Van, Thomas Stent, Xiaoyan Han, Julian I Rood, Ben Wade, Anthony L Keyburn, Torsten Seemann, Honglei Chen, Volker Haring, Priscilla A Johanesen, Dena Lyras, Robert J Moore
BACKGROUND: Clostridium perfringens causes a range of diseases in animals and humans including necrotic enteritis in chickens and food poisoning and gas gangrene in humans. Necrotic enteritis is of concern in commercial chicken production due to the cost of the implementation of infection control measures and to productivity losses. This study has focused on the genomic analysis of a range of chicken-derived C. perfringens isolates, from around the world and from different years. The genomes were sequenced and compared with 20 genomes available from public databases, which were from a diverse collection of isolates from chickens, other animals, and humans...
May 22, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29786121/genome-sequence-of-the-novel-virulent-bacteriophage-pmbt14-with-lytic-activity-against-pseudomonas-fluorescens-dsm-50090-r
#11
Sabrina Koberg, Stefanie Gieschler, Erik Brinks, Mareike Wenning, Horst Neve, Charles M A P Franz
Psychrotrophic gram-negative Pseudomonas spp. represent a serious problem in the dairy industry as they can cause spoilage of milk and dairy products. Bacteriophages have moved into focus as promising biocontrol agents for such food spoilage bacteria. The virulent Siphoviridae phage PMBT14 was isolated on a mutant variant of P. fluorescens DSM 50090 challenged with an unrelated virulent P. fluorescens DSM 50090 Podoviridae phage (i.e., mutant strain DSM 50090R ). PMBT14 has a 47,820-bp dsDNA genome with 76 predicted open reading frames (ORFs)...
May 21, 2018: Archives of Virology
https://www.readbyqxmd.com/read/29785946/-crispr-cas-systems-in-genome-engineering-of-bacteriophages
#12
Cai Jiao Liang, Fan Mei Meng, Yun Can Ai
Researches on CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated genes) systems, that are adaptive immunity systems encoded by prokaryotes, have promoted the development of new genome-editing tools. Bacteriophages are not only the driving elements for the evolution of prokaryotes' CRISPR arrays, but also the targets of the CRISPR/Cas systems. Studies on functional genomics of bacteriophages have been lagging behind the discovery of new phage strains and the sequencing of their genomes...
May 20, 2018: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/29785502/comparative-persistence-of-human-sewage-specific-enterococcal-bacteriophages-in-freshwater-and-seawater
#13
Namfon Booncharoen, Skorn Mongkolsuk, Kwanrawee Sirikanchana
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...
May 21, 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29782009/construction-of-synthetic-phage-displayed-fab-library-with-tailored-diversity
#14
Ganggang Huang, Zhenwei Zhong, Shane Miersch, Sachdev S Sidhu, Shin-Chen Hou, Donghui Wu
Demand for monoclonal antibodies (mAbs) in basic research and medicine is increasing yearly. Hybridoma technology has been the dominant method for mAb development since its first report in 1975. As an alternative technology, phage display methods for mAb development are increasingly attractive since Humira, the first phage-derived antibody and one of the best-selling mAbs, was approved for clinical treatment of rheumatoid arthritis in 2002. As a non-animal based mAb development technology, phage display bypasses antigen immunogenicity, humanization, and animal maintenance that are required from traditional hybridoma technology based antibody development...
May 1, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29781609/enhancement-and-analysis-of-human-anti-aflatoxin-b1-afb1-scfv-antibody-ligand-interaction-using-chain-shuffling
#15
Kuntalee Rangnoi, Kiattawee Choowongkomon, Richard O'Kennedy, Florian Rüker, Montarop Yamabhai
A human anti-aflatoxin B1 (AFB1) scFv antibody (yAFB1-c3), selected from a naïve human phage-displayed scFv library, was used as a template for improving and analysis of antibody-ligand interactions using the chain-shuffling technique. The variable heavy and variable light (VH/VL) shuffled library was constructed from the VH of 25 pre-selected clones recombined with the VL of yAFB1-c3 and vice versa. Affinity selection from these library demonstrated that the VH domain played an important role in the binding of scFv to free AFB1...
May 21, 2018: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/29780362/characterization-and-genomic-study-of-phage-vb_ecos-b2-infecting-multidrug-resistant-escherichia-coli
#16
Yue Xu, Xinyan Yu, Yu Gu, Xu Huang, Genyan Liu, Xiaoqiu Liu
The potential of bacteriophage as an alternative antibacterial agent has been reconsidered for control of pathogenic bacteria due to the widespread occurrence of multi-drug resistance bacteria. More and more lytic phages have been isolated recently. In the present study, we isolated a lytic phage named vB_EcoS-B2 from waste water. VB_EcoS-B2 has an icosahedral symmetry head and a long tail without a contractile sheath, indicating that it belongs to the family Siphoviridae . The complete genome of vB_EcoS-B2 is composed of a circular double stranded DNA of 44,283 bp in length, with 54...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29780361/challenges-and-promises-for-planning-future-clinical-research-into-bacteriophage-therapy-against-pseudomonas-aeruginosa-in-cystic-fibrosis-an-argumentative-review
#17
REVIEW
Martina Rossitto, Ersilia V Fiscarelli, Paola Rosati
Although early aggressive and prolonged treatment with specific antibiotics can extend survival in patients with cystic fibrosis (CF) colonized by opportunistic Pseudomonas aeruginosa (PA), antibiotics fail to eradicate the infecting multidrug-resistant (MDR) PA strains in CF. Century-long research has suggested treating patients with bacteriophages (phages, prokaryotic viruses) naturally hosted by bacteria. Although the only phage types used in therapy, lytic phages, lyse PA aggregated in biofilm matrix by depolymerase degrading enzymes, how they can effectively, safely, and persistently do so in patients with CF is unclear...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29779790/a-hyperthermophilic-phage-decoration-protein-suggests-common-evolutionary-origin-with-herpesvirus-triplex-proteins-and-an-anti-crispr-protein
#18
Nicholas P Stone, Brendan J Hilbert, Daniel Hidalgo, Kevin T Halloran, Jooyoung Lee, Erik J Sontheimer, Brian A Kelch
Virus capsids are protein shells that protect the viral genome from environmental assaults, while maintaining the high internal pressure of the tightly packaged genome. To elucidate how capsids maintain stability under harsh conditions, we investigated the capsid components of the hyperthermophilic phage P74-26. We determined the structure of capsid protein gp87 and show that it has the same fold as decoration proteins in many other phages, despite lacking significant sequence homology. We also find that gp87 is significantly more stable than mesophilic homologs...
April 26, 2018: Structure
https://www.readbyqxmd.com/read/29778602/structure-guided-combinatorial-engineering-facilitates-affinity-and-specificity-optimization-of-anti-cd81-antibodies
#19
Bryce Nelson, Jarrett Adams, Andreas Kuglstatter, Zhijian Li, Seth F Harris, Yang Liu, Sandya Bohini, Han Ma, Klaus Klumpp, Junjun Gao, Sachdev S Sidhu
Hepatitis C viral infection is the major cause of chronic hepatitis that affects as many as 71 million people worldwide. Rather than target the rapidly shifting viruses and their numerous serotypes, four independent antibodies were made to target the host antigen CD81 and were shown to block Hepatitis C viral entry. The single-chain variable fragment of each antibody was crystallized in complex with the CD81 large extracellular loop (LEL) in order to guide affinity maturation of two distinct antibodies by phage display...
May 17, 2018: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29778530/exploiting-bacteriophage-proteomes-the-hidden-biotechnological-potential
#20
REVIEW
Sílvio B Santos, Ana Rita Costa, Carla Carvalho, Franklin L Nóbrega, Joana Azeredo
Bacteriophages encode many distinct proteins for the successful infection of a bacterial host. Each protein plays a specific role in the phage replication cycle, from host recognition, through takeover of the host machinery, and up to cell lysis for progeny release. As the roles of these proteins are being revealed, more biotechnological applications can be anticipated. Phage-encoded proteins are now being explored for the control, detection, and typing of bacteria; as vehicles for drug delivery; and for vaccine development...
May 16, 2018: Trends in Biotechnology
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