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Experimental Approach for Bacterial Strains Characterization [chapter]

Fabien Chhel, Adrien Goëffon, Frédéric Lardeux, Frédéric Saubion, Gilles Hunault, Tristan Boureau
2011 Lecture Notes in Computer Science  
These experiments have allowed us to characterize specific strains and diagnosis tests have been produced and used.  ...  In this work, we are particularly interested by the characterization of strains of phytopathogenic bacterias, which is an important issue in the study of plant diseases.  ... 
doi:10.1007/978-3-642-20389-3_13 fatcat:bqbpnmzacfa6vfenksmhkjorya

Double-Blind Characterization of Non-Genome-Sequenced Bacteria by Mass Spectrometry-Based Proteomics

R. E. Jabbour, S. V. Deshpande, M. M. Wade, M. F. Stanford, C. H. Wick, A. W. Zulich, E. W. Skowronski, A. P. Snyder
2010 Applied and Environmental Microbiology  
The approach also characterized doubleblind bacterial samples to the respective genus, species, and strain levels when the experimental organism was not in the database due to its genome not having been  ...  The MS proteomic approach showed strain-level discrimination for the various bacteria employed.  ...  Blind sample 17 was investigated for BACid characterization.  ... 
doi:10.1128/aem.00055-10 pmid:20363779 pmcid:PMC2876470 fatcat:nc5hyzg3nrf5rbentjxnn3tqzq

Novel Rate-Area-Shape Modeling Approach To Quantify Bacterial Killing and Regrowth forIn VitroStatic Time-Kill Studies

Soon-Ee Cheah, Jian Li, Roger L. Nation, Jürgen B. Bulitta
2014 Antimicrobial Agents and Chemotherapy  
Our aims were to develop a novel rate-area-shape modeling approach and to compare, against model-free metrics, its relative ability to characterize the rate, extent, and timing of bacterial killing and  ...  However, bacterial regrowth was more extensive (by 2 log10) and occurred approximately 3 h earlier for colistin than for doripenem.  ...  Despite the ubiquity of SCTK studies, modeling approaches that efficiently characterize the rate, extent, and timing of bacterial killing and regrowth are scarce (15, 16) .  ... 
doi:10.1128/aac.04182-14 pmid:25367905 pmcid:PMC4291376 fatcat:nil7zl4yavec3oa5rlpqjdpvkm

Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields

Luz K Medina-Cordoba, Aroon T Chande, Lavanya Rishishwar, Leonard W Mayer, Lina C Valderrama-Aguirre, Augusto Valderrama-Aguirre, John Christian Gaby, Joel E Kostka, I King Jordan
2021 Scientific Reports  
Six strains with the highest overall genotype scores were experimentally evaluated for nitrogen fixation, phosphate solubilization, and the production of siderophores, gibberellic acid, and indole acetic  ...  A genotypic and phenotypic threshold was observed that separated strains by their potential for PGP versus predicted pathogenicity.  ...  We thank the Kostka laboratory technicians Patrick Steck and Michael Blejwas for their support with laboratory analysis of sugarcane-associated bacteria at Georgia Tech.  ... 
doi:10.1038/s41598-021-88380-8 pmid:33911103 fatcat:ruspohwuobfwbg67ntvmqsrlce

Using Mass Spectrometry To Identify and Characterize Bacteria

Todd R. Sandrin, Plamen A. Demirev
2014 Microbe Magazine  
, and analytic algorithms are the basis for extending MS beyond the species level. ➤ Bioinformatics/proteomics-based MS approaches complement librarybased approaches for differentiating bacterial strains  ...  from one another. ➤ MS-based functional assays can differentiate drug-resistant from drugsusceptible strains of bacterial pathogens.  ...  In particular, we are interested in using MS to characterize bacteria beyond the species level, including for strain-typing and characterizing isolates.  ... 
doi:10.1128/microbe.9.23.1 fatcat:qkp6e26lhnhdxi2tloknmyzs4q

Comparative Proteomics of Tandem Mass Spectrometry Analyses for Bacterial Strains Identification and Differentiation [chapter]

Rabih E., Mary M., Samir V., Michael F., Alan W., A. Peter
2012 Tandem Mass Spectrometry - Applications and Principles  
Experimental methods Bacterial strains growth and culture conditions Pathogenic strains employed in the present study were E. coli O157:H7 and Y. pestis Colorado 92 (CO92).  ...  Overall, the protein content of the cell represents the majority of the cell dry weight, which makes it an ideal cellular component to be utilized for bacterial characterization (Loferer-Krobacher et  ... 
doi:10.5772/30864 fatcat:gg4psdpgonh53ig24swgbpbnwy

Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: a new direction for bacteriology

Timothy D Read, Ruth C Massey
2014 Genome Medicine  
Massey, R. (2014) Characterizing the genetic basis of bacterial phenotypes using genome-wide association studies: a new direction for bacteriology. Genome Medicine, 6 (11).  ...  The experimental designs have been diverse, taking advantage of different processes in bacteria for generating variation.  ...  Thanks to Jesse Shapiro and Sandeep Joseph for reading and commenting on draft versions.  ... 
doi:10.1186/s13073-014-0109-z pmid:25593593 pmcid:PMC4295408 fatcat:u6q3ksulfbgp3i5wrnen73meka

MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands

H.-Y. Ou, X. He, E. M. Harrison, B. R. Kulasekara, A. B. Thani, A. Kadioglu, S. Lory, J. C. D. Hinton, M. R. Barer, Z. Deng, K. Rajakumar
2007 Nucleic Acids Research  
the use in this study of unpublished genome data corresponding to K. pneumoniae strain Kp342 and MGH 78578, respectively.  ...  ACKNOWLEDGEMENTS We are grateful to James Lonnen, Mansi Mukesh Patel and Jon van Aartsen for support in developing this resource, and to many other colleagues for testing and suggesting enhancements to  ...  Many in silico approaches for detecting mobile genetic elements in sequenced bacterial genomes have been developed recently.  ... 
doi:10.1093/nar/gkm380 pmid:17537813 pmcid:PMC1933208 fatcat:hhp6fesaunh2vc4pcug34xjgbi

Synthesis and antimicrobial effects of colloidal gold nanoparticles against prevalent waterborne bacterial pathogens

Rajesh Kumar, Shashi Kant Shukla, Madhu Pandey, Anand Pandey, Ashutosh Pathak, Anupam Dikshit, John Spencer
2016 Cogent Chemistry  
Subsequently, a novel phylogenetic approach for reducing the cost of experimentation was also carried out. In future, Au NPs can be used in making a water purifier system or kit.  ...  The present research describes a more reliable method for assaying growth inhibition of some waterborne bacterial pathogens by gold nanoparticles.  ...  Acknowledgements The authors are thankful to Head, Department of Botany, University of Allahabad for providing the research facilities;  ... 
doi:10.1080/23312009.2016.1192522 fatcat:he2jipzbubfifd5vm4t4we2isu

Using bacterial genomes and essential genes for the development of new antibiotics

Francisco R. Fields, Shaun W. Lee, Michael J. McConnell
2017 Biochemical Pharmacology  
In addition, transcriptomic and proteomic approaches can be used to characterize RNA and protein levels on a cellular scale, providing information on bacterial physiology that can be applied to antibiotic  ...  Whole genome mutagenesis studies can also identify genes necessary for bacterial growth and survival under different environmental conditions, making them attractive targets for the development of novel  ...  This work was funded by the Ministerio de Economía y Competitividad, Instituto de Salud Carlos III -co-financed by European's Development Regional Fund "A way to achieve Europe" ERDF, Spanish Network for  ... 
doi:10.1016/j.bcp.2016.12.002 pmid:27940263 pmcid:PMC5411290 fatcat:uxo2repznbhfrmaqatr3hpkdzy

Generating robust and informative nonclinical in vitro and in vivo bacterial infection model efficacy data to support translation to humans

Jürgen B. Bulitta, William Hope, Ann E. Eakin, Tina Guina, Vincent H. Tam, Arnold Louie, George L. Drusano, Jennifer L. Hoover
2019 Antimicrobial Agents and Chemotherapy  
of Therapeutics against Bacterial Pathogens".  ...  Despite these robust tools and published guidance, characterizing nonclinical PK/PD relationships may not be straightforward, especially for a new drug or new class.  ...  Some studies and bacterial strains may not perform the same as others, even in 675 well-characterized animal models; between strain variability is expected, and can 676 complicate the establishment of  ... 
doi:10.1128/aac.02307-18 fatcat:wwzgxeqvofd57fpwyhyxmao454

Teraherz vibrational spectroscopy of E. coli and molecular constituents: Computational modeling and experiment

Tatiana Globus, Igor Sizov, Boris Gelmont
2013 Advances in Bioscience and Biotechnology  
to examine, detect, and identify bacterial cells with high accuracy and selectivity to the level of strains.  ...  Simplified models of DNA macromolecules with a short sequencing have been constructed for several E. coli strains with the goal to predict their absorption spectra.  ...  Simultaneously with experimental characterization, computational modeling techniques have been developed using the energy minimization, normal mode analysis and MD approaches to understand and predict  ... 
doi:10.4236/abb.2013.43a065 fatcat:lihi4ow7erazvkf2su7pw35lbe

Immunization with Lipopolysaccharide-Deficient Whole Cells Provides Protective Immunity in an Experimental Mouse Model of Acinetobacter baumannii Infection

Meritxell García-Quintanilla, Marina R. Pulido, Jerónimo Pachón, Michael J. McConnell, Gunnar F. Kaufmann
2014 PLoS ONE  
The increasing clinical importance of infections caused by multidrug resistant Acinetobacter baumannii warrants the development of novel approaches for prevention and treatment.  ...  Discussion The development of a vaccine against A. baumannii for use in humans represents a novel approach for combating the increasing number of infections caused by multidrug and pandrug resistant strains  ...  group for the characterization of vaccine for preventing infection by A. baumannii [16] [17] [18] .  ... 
doi:10.1371/journal.pone.0114410 pmid:25485716 pmcid:PMC4259314 fatcat:agubfk73bfa6jnx6d2cnn3oqjm

Quantitative, image-based phenotyping methods provide insight into spatial and temporal dimensions of plant disease

Andrew M. Mutka, Sarah J. Fentress, Joel W. Sher, Jeffrey C. Berry, Chelsea Pretz, Dmitri A. Nusinow, Rebecca Bart
2016 Plant Physiology  
Specifically, we quantified bacterial populations, water-soaking disease symptoms, and pathogen spread from the site of inoculation over time for strains with mutations in avrBs2, xopX, and xopK as compared  ...  We generated Xam strains in which individual predicted type III effector (T3E) genes were mutated and applied multiple imaging approaches to investigate the role of these proteins in bacterial virulence  ...  In a laboratory context, fine-scale imaging of disease symptoms on a single leaf may be the optimal approach for investigating certain experimental questions, while whole-plant or fieldscale imaging would  ... 
doi:10.1104/pp.16.00984 pmid:27443602 pmcid:PMC5047107 fatcat:ghq4y4qfajdh7ar2zhcg3f3txe

Deciphering the bacterial glycocode: recent advances in bacterial glycoproteomics

Scott A Longwell, Danielle H Dube
2013 Current Opinion in Chemical Biology  
This review focuses on recent advances in deciphering the bacterial glycocode, including metabolic glycan labeling to discover and characterize bacterial glycoproteins, lectinbased microarrays to monitor  ...  bacterial glycoprotein dynamics, crosslinking sugars to assess the roles of bacterial glycoproteins, and harnessing bacterial glycosylation systems for the efficient production of industrially important  ...  SL thanks the Arnold and Mabel Beckman Foundation for an undergraduate research fellowship and the Idea Network for Biological Research Excellence for a post baccalaureate research fellowship.  ... 
doi:10.1016/j.cbpa.2012.12.006 pmid:23276734 pmcid:PMC3594442 fatcat:4ls27ryem5fkziqd2xanjgvslu
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