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https://www.readbyqxmd.com/read/28431251/tunable-expression-tools-enable-single-cell-strain-distinction-in-the-gut-microbiome
#1
Weston R Whitaker, Elizabeth Stanley Shepherd, Justin L Sonnenburg
Applying synthetic biology to engineer gut-resident microbes provides new avenues to investigate microbe-host interactions, perform diagnostics, and deliver therapeutics. Here, we describe a platform for engineering Bacteroides, the most abundant genus in the Western microbiota, which includes a process for high-throughput strain modification. We have identified a novel phage promoter and translational tuning strategy and achieved an unprecedented level of expression that enables imaging of fluorescent-protein-expressing Bacteroides stably colonizing the mouse gut...
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28430166/-french-phage-network-second-meeting-report
#2
Clara Torres-Barceló, Oliver Kaltz, Rémy Froissart, Sylvain Gandon, Nicolas Ginet, Mireille Ansaldi
The study of bacteriophages (viruses of bacteria) includes a variety of approaches, such as structural biology, genetics, ecology, and evolution, with increasingly important implications for therapeutic and industrial uses. Researchers working with phages in France have recently established a network to facilitate the exchange on complementary approaches, but also to engage new collaborations. Here, we provide a summary of the topics presented during the second meeting of the French Phage Network that took place in Marseille in November 2016...
April 21, 2017: Viruses
https://www.readbyqxmd.com/read/28429059/a-novel-method-to-recover-inclusion-body-protein-from-recombinant-e-coli-fed-batch-processes-based-on-phage-%C3%AE-x174-derived-lysis-protein-e
#3
Daniela Ehgartner, Patrick Sagmeister, Timo Langemann, Andrea Meitz, Werner Lubitz, Christoph Herwig
Production of recombinant proteins as inclusion bodies is an important strategy in the production of technical enzymes and biopharmaceutical products. So far, protein from inclusion bodies has been recovered from the cell factory through mechanical or chemical disruption methods, requiring additional cost-intensive unit operations. We describe a novel method that is using a bacteriophage-derived lysis protein to directly recover inclusion body protein from Escherichia coli from high cell density fermentation process: The recombinant inclusion body product is expressed by using a mixed feed fed-batch process which allows expression tuning via adjusting the specific uptake rate of the inducing substrate...
April 20, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28428342/lysibodies-are-igg-fc-fusions-with-lysin-binding-domains-targeting-staphylococcus-aureus-wall-carbohydrates-for-effective-phagocytosis
#4
Assaf Raz, Anna Serrano, Christine Lawson, Maneesha Thaker, Tricia Alston, Stylianos Bournazos, Jeffrey V Ravetch, Vincent A Fischetti
The cell wall of Gram-positive bacteria contains abundant surface-exposed carbohydrate molecules that are highly conserved within and often across species. The potential therapeutic usefulness of high-affinity antibodies to cell wall carbohydrates is unquestioned, however obtaining such antibodies is challenging due to the poor overall immunogenicity of these bacterial targets. Autolysins and phage lysins are peptidoglycan hydrolases, enzymes that have evolved over a billion years to degrade bacterial cell wall...
April 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28428153/development-of-polyol-responsive-antibody-mimetics-for-single-step-protein-purification
#5
Richard J Suderman, Daren A Rice, Shane D Gibson, Eric J Strick, David M Chao
The purification of functional proteins is a critical pre-requisite for many experimental assays. Immunoaffinity chromatography, one of the fastest and most efficient purification procedures available, is often limited by elution conditions that disrupt structure and destroy enzymatic activity. To address this limitation, we developed polyol-responsive antibody mimetics, termed nanoCLAMPs, based on a 16 kDa carbohydrate binding module domain from Clostridium perfringens hyaluronidase. nanoCLAMPs bind targets with nanomolar affinity and high selectivity yet release their targets when exposed to a neutral polyol-containing buffer, a composition others have shown to preserve quaternary structure and enzymatic activity...
April 17, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28428053/discrimination-between-ulcerative-colitis-and-crohn-s-disease-using-phage-display-identified-peptides-and-virus-mimicking-synthetic-nanoparticles
#6
Sonia Facchin, Liboria Digiglio, Renata D'Incà, Elisabetta Casarin, Elisa Dassie, Monica Dettin, Annj Zamuner, Andrea Buda, Michele De Boni, Duilio Della Libera, Alessandra D'Urso, Giacomo Carlo Sturniolo, Margherita Morpurgo
Discrimination between Crohn Disease (CD) and Ulcerative Colitis (UC) is an unsolved clinical issue in up to 10-15% of inflammatory bowel disease (IBD) patients. We developed a method capable to discriminate between the two clinical conditions by combining random peptide phage display screenings and nanoparticle (NP) based assays. We identified two peptides able to recognize selectively biopsies of inflamed mucosa of either CD or UC patients. The peptides were integrated into synthetic virus-mimicking nanoassemblies using a poly-avidin NP platform...
April 17, 2017: Nanomedicine: Nanotechnology, Biology, and Medicine
https://www.readbyqxmd.com/read/28426329/mathematical-modelling-of-crispr-cas-system-effects-on-biofilm-formation
#7
Qasim Ali, Lindi M Wahl
Clustered regularly interspaced short palindromic repeats (CRISPR), linked with CRISPR associated (Cas) genes, can confer adaptive immunity to bacteria, against bacteriophage infections. Thus from a therapeutic standpoint, CRISPR immunity increases biofilm resistance to phage therapy. Recently, however, CRISPR-Cas genes have been implicated in reducing biofilm formation in lysogenized cells. Thus CRISPR immunity can have complex effects on phage-host-lysogen interactions, particularly in a biofilm. In this contribution, we develop and analyse a series of dynamical systems to elucidate and disentangle these interactions...
April 20, 2017: Journal of Biological Dynamics
https://www.readbyqxmd.com/read/28426191/genome-wide-abolishment-of-mobile-genetic-elements-using-genome-shuffling-and-crispr-cas-assisted-mage-allows-the-efficient-stabilization-of-a-bacterial-chassis
#8
Kinga Umenhoffer, Gábor Draskovits, Ákos Nyerges, Ildikó Karcagi, Balázs Bogos, Edit Tímár, Bálint Csörgő, Róbert Herczeg, István Nagy, Tamás Fehér, Csaba Pal, Gyorgy Posfai
The ideal bacterial chassis provides a simplified, stable and predictable host environment for synthetic biological circuits. Mutability and evolution can, however, compromise stability, leading to deterioration of artificial genetic constructs. By eliminating certain sources of instability, these undesired genetic changes can be mitigated. Specifically, deletion of prophages and insertion sequences, non-essential constituents of bacterial genomes, has been shown to be beneficial in cellular and genetic stabilization...
April 20, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28424941/isolation-and-complete-genome-sequence-of-a-novel-pseudoalteromonas-phage-ph357-from-the-yangtze-river-estuary
#9
Zheng Gong, Min Wang, Qingwei Yang, Zhongshi Li, Jun Xia, Yu Gao, Yong Jiang, Xue Meng, Zhaoyang Liu, Ding Yang, Fangfei Zhang, Hongbing Shao, Duobing Wang
Phage PH357, a novel lytic Pseudoalteromonas lipolytica phage belonging to the Myoviridae family was isolated from the Yangtze River estuary. The microbiological characterization demonstrated that phage PH357 is stable from -20 to 60 °C and the optimal pH 7. The one-step growth curve showed a latent period of 20 min, a rise period of 20 min, and the average burst size was about 85 virions per cell. Complete genome of phage PH357 was determined. Genome of phage PH357 consisted of a linear, double-stranded 136,203 bp DNA molecule with 34...
April 20, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28424939/characterization-and-complete-genome-sequence-of-a-novel-siphoviridae-bacteriophage-bs5
#10
Xue Meng, Min Wang, Siyuan You, Duobing Wang, Yan Li, Zhaoyang Liu, Yu Gao, Lu Liu, Yaoyuan Zhang, Zhenghao Yan, Chunyan Liu, Yong Jiang, Hongbing Shao
A novel Siphoviridae family Phage BS5, which infects Pseudoalteromonas atlantica, was isolated from the surface waters of the Yellow Sea. Morphological study by transmission electron microscopy revealed that the novel phage belongs to Siphoviridae. The complete genome sequence of PBS5 contained a linear, double-strand 39949-bp DNA molecule with a G + C content of 40.6% and 65 putative open reading frames. Twelve conserved domains were detected by BLASTP in NCBI, and of these the functions of 5 were known...
April 20, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28424938/characterization-and-genome-sequence-of-marine-alteromonas-gracilis-phage-pb15-isolated-from-the-yellow-sea-china
#11
Yu Gao, Qian Liu, Min Wang, Guihua Zhao, Yong Jiang, Gill Malin, Zheng Gong, Xue Meng, Zhaoyang Liu, Tongtong Lin, Yutong Li, Hongbing Shao
A novel marine Alteromonas gracilis siphovirus, phage PB15, was isolated from the surface water of the Yellow Sea in August 2015. It has a head diameter of 58 ± 5 nm head and a contractile tail approximately 105 ± 10 nm in length, and overall, the morphology suggests that PB15 belongs to the family Siphoviridae. PB15 phage is stable at over the temperature range 0-60 °C. The best MOI of these phage was 0.1, and infectivity decreased above 60 °C. The results suggest that phage is stable at pH value ranging between 3...
April 20, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28421059/phages-in-the-human-body
#12
REVIEW
Ferran Navarro, Maite Muniesa
Bacteriophages, viruses that infect bacteria, have re-emerged as powerful regulators of bacterial populations in natural ecosystems. Phages invade the human body, just as they do other natural environments, to such an extent that they are the most numerous group in the human virome. This was only revealed in recent metagenomic studies, despite the fact that the presence of phages in the human body was reported decades ago. The influence of the presence of phages in humans has yet to be evaluated; but as in marine environments, a clear role in the regulation of bacterial populations could be envisaged, that might have an impact on human health...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28421049/transcriptomic-and-metabolomics-profiling-of-phage-host-interactions-between-phage-pap1-and-pseudomonas-aeruginosa
#13
Xia Zhao, Mengyu Shen, Xingyu Jiang, Wei Shen, Qiu Zhong, Yuhui Yang, Yinling Tan, Melissa Agnello, Xuesong He, Fuquan Hu, Shuai Le
The basic biology of bacteriophage-host interactions has attracted increasing attention due to a renewed interest in the therapeutic potential of bacteriophages. In addition, knowledge of the host pathways inhibited by phage may provide clues to novel drug targets. However, the effect of phage on bacterial gene expression and metabolism is still poorly understood. In this study, we tracked phage-host interactions by combining transcriptomic and metabolomic analyses in Pseudomonas aeruginosa infected with a lytic bacteriophage, PaP1...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28421038/bacteriophages-against-serratia-as-fish-spoilage-control-technology
#14
Igor Hernández
Bacteria of the genus Serratia, mainly S. proteamaculans and S. fonticola, are important spoilage agents in Atlantic horse mackerel (Trachurus trachurus). In order to evaluate whether bacteriophages against Serratia could delay the spoilage process, 11 viral strains active against this genus were isolated from food and best candidate was applied to fresh mackerel filets. All the phages belong to the Siphoviridae and Podoviridae families and were active at multiplicity of infection (MOI) levels below 1:1 in Long & Hammer broth...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28418081/assessment-of-biofilm-removal-capacity-of-a-broad-host-range-bacteriophage-jhp-against-pseudomonas-aeruginosa
#15
Muafia Shafique, Iqbal Ahmad Alvi, Zaigham Abbas, Shafiq Ur Rehman
Pseudomonas aeruginosa is an efficient biofilm-dwelling microbial pathogen, associated with nosocomial infections. These biofilm-associated infections are resistant to antibiotics and immune defenses, therefore pose major problem against their treatment. This scenario demands alternative therapeutic regimens, and bacteriophage therapy is one among potential strategies for clinical management of multiple drug resistance. In this investigation, the efficacy of a bacteriophage, JHP, is evaluated to eradicate P...
April 18, 2017: APMIS: Acta Pathologica, Microbiologica, et Immunologica Scandinavica
https://www.readbyqxmd.com/read/28416599/characterization-of-t-dependent-and-t-independent-b-cell-responses-to-a-virus-like-particle
#16
Wenhua Liao, Zhaolin Hua, Can Liu, Lin Lin, Rui Chen, Baidong Hou
Natural pathogens, such as viruses, often induce T-dependent and T-independent Ab responses. However, the activation and differentiation of Ag-specific B cells under these conditions had not been examined in detail. In this study, we used bacterial phage Qβ-derived virus-like particles (Qβ-VLPs) as an immunogen to examine the T-independent and T-dependent phases of the response in mice. Using Qβ-specific cell labeling and enrichment methods developed in this study, we were able to characterize the rare Ag-specific B cells in detail...
April 17, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28415614/connexin40-controls-endothelial-activation-by-dampening-nfkb-activation
#17
Jean-Francois Denis, Ke Ludwig Scheckenbach, Anna Pfenniger, Merlijn J Meens, Rob Krams, Lucile Miquerol, Steven Taffet, Marc Chanson, Mario Delmar, Brenda R Kwak
Connexins are proteins forming gap junction channels for intercellular communication. Connexin40 (Cx40) is highly expressed by endothelial cells (ECs) of healthy arteries but this expression is lost in ECs overlying atherosclerotic plaques. Low/oscillatory shear stress observed in bends and bifurcations of arteries is atherogenic partly through activation of the pro-inflammatory NFκB pathway in ECs. In this study, we investigated the relation between shear stress, Cx40 and NFκB. Shear stress-modifying casts were placed around carotid arteries of mice expressing eGFP under the Cx40 promoter (Cx40+/eGFP)...
March 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28414716/dynamics-of-adaptive-immunity-against-phage-in-bacterial-populations
#18
Serena Bradde, Marija Vucelja, Tiberiu Teşileanu, Vijay Balasubramanian
The CRISPR (clustered regularly interspaced short palindromic repeats) mechanism allows bacteria to adaptively defend against phages by acquiring short genomic sequences (spacers) that target specific sequences in the viral genome. We propose a population dynamical model where immunity can be both acquired and lost. The model predicts regimes where bacterial and phage populations can co-exist, others where the populations exhibit damped oscillations, and still others where one population is driven to extinction...
April 17, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28414460/analysis-of-novel-interactions-between-components-of-the-selenocysteine-biosynthesis-pathway-sephs1-sephs2-sepsecs-and-secp43
#19
Flore Oudouhou, Bastien Casu, Arnold Steve Dopgwa Puemi, Jurgen Sygusch, Christian Baron
In mammalian cells, the incorporation of the 21st amino acid, selenocysteine, into proteins is guided by the Sec machinery. The function of this protein complex requires several protein-protein and protein-RNA interactions, leading to the incorporation of selenocysteine at UGA codons. It is guided by stem-loop structures localized in the 3' untranslated regions of the selenoprotein-encoding genes. Here, we conducted a global analysis of interactions between the Sec biosynthesis and incorporation components using a bioluminescence resonance energy transfer assay in mammalian cells that showed that selenocysteine synthase (SEPSECS), SECp43, and selenophosphate synthetases SEPHS1 and SEPHS2 form oligomers in eukaryotic cells...
April 20, 2017: Biochemistry
https://www.readbyqxmd.com/read/28414441/suppression-of-enteric-bacteria-by-bacteriophages-importance-of-phage-polyvalence-in-the-presence-of-soil-bacteria
#20
Pingfeng Yu, Jacques Mathieu, Yu Yang, Pedro J J Alvarez
Bacteriophages are widely recognized for their importance in microbial ecology and bacterial control. However, little is known about how phage polyvalence (i.e., broad host range) affects bacterial suppression and interspecies competition in environments harboring enteric pathogens and soil bacteria. Here we compare the efficacy of polyvalent phage PEf1 versus coliphage T4 in suppressing a model enteric bacterium (E. coli K-12) in mixtures with soil bacteria (Pseudomonas putida F1 and Bacillus subtilis 168)...
April 21, 2017: Environmental Science & Technology
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