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SUBJECT INDEX [chapter]

2005 Microbial Forensics  
See International Committee on the Taxonomy of Viruses IMMS.  ...  Database, 15 National Bioforensic Information Encyclopedia, 15 National Bioforensics Analysis Center (BFAC), 11-12 National Center for Biologic Information, 103 National Institutes of Health (NIH  ... 
doi:10.1016/b978-012088483-4/50023-8 fatcat:nt5jec2u3jbstmg4zhulgt3szu

Population-Sequencing as a Biomarker for Sample Characterization

John P. Jakupciak
2013 Journal of Biomarkers  
The idea of using sequence analysis directly for sample characterization has been met with skepticism.  ...  The application of Population-Sequencing will facilitate sample characterization and genome identification strategies.  ...  Acknowledgment The author would like to thank DTRA for supporting this work under Contract W911SR-10-C-0026.  ... 
doi:10.1155/2013/861823 pmid:26317024 pmcid:PMC4437355 fatcat:fbypnn2tzjb2fjgvdu2o7s36s4

Evaluation of Oxford Nanopore's MinION Sequencing Device for Microbial Whole Genome Sequencing Applications

Andrea D. Tyler, Laura Mataseje, Chantel J. Urfano, Lisa Schmidt, Kym S. Antonation, Michael R. Mulvey, Cindi R. Corbett
2018 Scientific Reports  
Overall sequencing yield and quality improved through the course of this set of experiments.  ...  The aim of this study was to evaluate the capability of the MinION sequencer for bacterial genomic and metagenomic applications, with specific emphasis placed on the quality, yield, and accuracy of generated  ...  The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.  ... 
doi:10.1038/s41598-018-29334-5 pmid:30026559 pmcid:PMC6053456 fatcat:pfzzzdh5kreldnftmanpzjbmnu

PlasmidHawk: Alignment-based Lab-of-Origin Prediction of Synthetic Plasmids [article]

Qi Wang, Tian Rui Liu, R. A. Leo Elworth, Todd Treangen
2020 bioRxiv   pre-print
In addition, PlasmidHawk can precisely single out the signature sub-sequences that are responsible for the lab-of-origin detection.  ...  A recent study employed machine learning to identify the lab-of-origin of DNA sequences to help mitigate some of these concerns.  ...  This new technology has the promise of significantly improving the quality of human life 11 through various fields, such as increasing agricultural yields 2 , accelerating drug discovery 3 or advancing  ... 
doi:10.1101/2020.05.22.110270 fatcat:go2fx62wozbgtfvs3stvk4ewfy

Quality Sample Collection, Handling, and Preservation for an Effective Microbial Forensics Program

B. Budowle, S. E. Schutzer, J. P. Burans, D. J. Beecher, T. A. Cebula, R. Chakraborty, W. T. Cobb, J. Fletcher, M. L. Hale, R. B. Harris, M. A. Heitkamp, F. P. Keller (+8 others)
2006 Applied and Environmental Microbiology  
types of effective signatures, and minimizing the impact of potential inhibitors.  ...  These discussions should include the best methods for the collection and handling of evidence, collection of specimens to assess the level of contamination in order to guide public health (or agricultural  ... 
doi:10.1128/aem.01165-06 pmid:17021190 pmcid:PMC1610269 fatcat:fsqtq7kpnnagbmollwhve3cq7i

PlasmidHawk improves lab of origin prediction of engineered plasmids using sequence alignment

Qi Wang, Bryce Kille, Tian Rui Liu, R. A. Leo Elworth, Todd J. Treangen
2021 Nature Communications  
In addition, PlasmidHawk can precisely single out the signature sub-sequences that are responsible for the lab-of-origin detection.  ...  A recent study employed machine learning to identify the lab-of-origin of DNA sequences to help mitigate some of these concerns.  ...  to being used for bioforensics.  ... 
doi:10.1038/s41467-021-21180-w pmid:33637701 fatcat:bwcxe2zsbffe3orpbl2r5b54au

A simplified strategy for sensitive detection of Rose rosette virus compatible with three RT-PCR chemistries

Shefali Dobhal, Jennifer D. Olson, Mohammad Arif, Johnny A. Garcia Suarez, Francisco M. Ochoa-Corona
2016 Journal of Virological Methods  
A primer set (RRV2F/2R) was designed from 38 consensus sequences of the nucleocapsid protein gene p3 located in the RNA 3 region of RRV. 39 The specificity of primer set RRV2F/2R was validated in silico  ...  Thirty rose samples from 8 different states of 43 the United States were tested using the developed methods.  ...  The preliminary specificity of the primer set was assessed in-silico using BLASTn 152 (Altschul et al., 1990).  ... 
doi:10.1016/j.jviromet.2016.01.013 pmid:26850142 fatcat:5tr5wjkfonbfrhpofdtyocnlyq

GeMInA, Genomic Metadata for Infectious Agents, a geospatial surveillance pathogen database

L. M. Schriml, C. Arze, S. Nadendla, A. Ganapathy, V. Felix, A. Mahurkar, K. Phillippy, A. Gussman, S. Angiuoli, E. Ghedin, O. White, N. Hall
2009 Nucleic Acids Research  
the breadth of hosts and diseases known for these pathogens, to identify the extent of outbreak locations, and to identify unique genomic regions with the DNA Signature Insignia Detection Tool.  ...  The Gemina database will provide a greater understanding of the interactions of viral and bacterial pathogens with their hosts and infectious diseases through in-depth literature text-mining, integrated  ...  ACKNOWLEDGEMENTS The authors thank Matthew Davenport for his continue guidance and support of the Gemina project.  ... 
doi:10.1093/nar/gkp832 pmid:19850722 pmcid:PMC2808878 fatcat:y4pap3wjqbaazhacqwrpu2k754

Detection of Diverse New Francisella-Like Bacteria in Environmental Samples

S. M. Barns, C. C. Grow, R. T. Okinaka, P. Keim, C. R. Kuske
2005 Applied and Environmental Microbiology  
This is the first report of the detection of Francisella-related species in soil samples by DNA-based methods.  ...  Cloning and sequencing of PCR products indicated the presence of a wide variety of Francisella-related species.  ...  polymorphism (SNP) signatures.  ... 
doi:10.1128/aem.71.9.5494-5500.2005 pmid:16151142 pmcid:PMC1214603 fatcat:3g3oe7l75fey5ho4qaffzbanqa

Microbial forensics for natural and intentional incidents of infectious disease involving animals

S A McEwen, T M Wilson, D A Ashford, E D Heegaard, B Kournikakis
2006 Rev Sci Tech Off Int Epizoot  
Existing capacities for the detection and reporting of epidemic and even endemic diseases should be an international priority for the prevention of catastrophic losses in animal and potentially in human  ...  The veterinary community needs to be more aware of the legal requirements related to forensic investigations so that veterinarians will be prepared to handle evidence properly within their own fields.  ...  E. coli O157:H7) by pulsedfield gel electrophoresis (PFGE) (29 Quality assurance Quality assurance is an important aspect of forensic examinations, and the recent emergence of the field of microbial  ... 
pmid:16796058 fatcat:a7hhyp5kb5h63k6ojecz52mnya

Evidence for the Source of the 2001 Attack Anthrax

Martin E. Hugh-Jones
2013 Journal of Bioterrorism & Biodefense  
of the anthrax attacks.  ...  Avoidance of governmentsponsored, classified research may account for some of the limitations of the investigation. ' *  ...  The "unwashed" preparation had a titer of 9×10 11 cfu/g, an indication of its high quality (compare to the titer of the pristine Daschle sample, 2.1×10 12 , which had been determined at USAMRIID just after  ... 
doi:10.4172/2157-2526.s3-008 fatcat:f6trar53uvhdlhksrdyp2jpv34

The Microbe: The Basics of Structure, Morphology, and Physiology as They Relate to Microbial Characterization and Attribution [chapter]

Joany Jackman
2011 Chemical and Physical Signatures for Microbial Forensics  
In contrast, the newer molecular methods often seek to expand the classification of microbes not only as a means to organize microbial phylogeny but also to differentiate signatures between microbes identifi  ...  Thus, the focus was to describe the common features which discriminated closely related groups of organisms.  ...  These methods and the associated quality systems are described in more detail in Chap. 9 (Wilson, this volume).  ... 
doi:10.1007/978-1-60327-219-3_2 fatcat:hqz5btddtbcz7l6yyavtgsbwiy

Genome characterisation of the genus Francisella reveals insight into similar evolutionary paths in pathogens of mammals and fish

Andreas Sjödin, Kerstin Svensson, Caroline Öhrman, Jon Ahlinder, Petter Lindgren, Samuel Duodu, Anders Johansson, Duncan J Colquhoun, Pär Larsson, Mats Forsman
2012 BMC Genomics  
Only limited data were available for other members of the Francisella genus, including F. philomiragia, an opportunistic pathogen of humans, F. noatunensis, a serious pathogen of farmed fish, and other  ...  The observed genome to genome variation in gene content and IS elements of different species supports the view that similar evolutionary paths of host adaptation developed independently in F. tularensis  ...  Department of Homeland Security and the Swedish Civil Contingencies Agency pursuant to the Agreement between the Government of the United States of America and the Government of the Kingdom of Sweden on  ... 
doi:10.1186/1471-2164-13-268 pmid:22727144 pmcid:PMC3485624 fatcat:5ts6ixwiqbfwbfpigdsta43px4

Plant Pathogen Forensics: Capabilities, Needs, and Recommendations

J. Fletcher, C. Bender, B. Budowle, W. T. Cobb, S. E. Gold, C. A. Ishimaru, D. Luster, U. Melcher, R. Murch, H. Scherm, R. C. Seem, J. L. Sherwood (+2 others)
2006 Microbiology and Molecular Biology Reviews  
Sampling Methods, Sample Size, and Quality On-site disease assessment. Initial assessment of the disease in the field should be done prior to any disturbance of the site.  ...  A comprehensive microbial forensics program, part of the NBACC mission, is addressed by the National Bioforensic Analysis Center.  ... 
doi:10.1128/mmbr.00022-05 pmid:16760310 pmcid:PMC1489535 fatcat:5qsmhwbipjfm7cqp3rpdqjhziu

Array of Synthetic Oligonucleotides to Generate Unique Multi-Target Artificial Positive Controls and Molecular Probe-Based Discrimination of Liposcelis Species

Mohammad Arif, George Opit, Abigail Mendoza-Yerbafría, Shefali Dobhal, Zhihong Li, Zuzana Kučerová, Francisco M. Ochoa-Corona, Baochuan Lin
2015 PLoS ONE  
The development of multiplex endpoint PCR and multiplex TaqMan qPCR will greatly facilitate psocid identification and their management. The use of APCs will streamline and standardize PCR assays.  ...  APC will also provide the opportunity to have all positive controls in a single tube, which reduces maintenance cost and labor, but increases the accuracy and reliability of the assays.  ...  Mockford, who confirmed the identity of the psocid species used in the study and provided Lepinotus inquilinus and Lepinotus patruelis.  ... 
doi:10.1371/journal.pone.0129810 pmid:26086728 pmcid:PMC4472718 fatcat:j732mztk4nh73gzfo76sws5spe
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