Publications

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Characterization of Pathogens in Clinical Specimens via Suppression of Host Background for Efficient Second Generation Sequencing Analyses

Branda, Steven B.; Jebrail, Mais J.; Van De Vreugde, James L.; Langevin, Stanley A.; Bent, Zachary B.; Curtis, Deanna J.; Lane, Pamela L.; Carson, Bryan C.; La Bauve, Elisa L.; Patel, Kamlesh P.; Ricken, James B.; Schoeniger, Joseph S.; Solberg, Owen D.; Williams, Kelly P.; Misra, Milind; Powell, Amy J.; Pattengale, Nicholas D.; May, Elebeoba E.; Lane, Todd L.; Lindner, Duane L.; Young, Malin M.; VanderNoot, Victoria A.; Thaitrong, Numrin T.; Bartsch, Michael B.; Renzi, Ronald F.; Tran-Gyamfi, Mary B.; Meagher, Robert M.

Abstract not provided.

Copy of Automated Molecular Biology Platform Enabling Rapid & Efficient SGS Analysis of Pathogens in Clinical Samples

Branda, Steven B.; Jebrail, Mais J.; Van De Vreugde, James L.; Langevin, Stanley A.; Bent, Zachary B.; Curtis, Deanna J.; Lane, Pamela L.; Carson, Bryan C.; La Bauve, Elisa L.; Patel, Kamlesh P.; Ricken, James B.; Schoeniger, Joseph S.; Solberg, Owen D.; Williams, Kelly P.; Misra, Milind; Powell, Amy J.; Pattengale, Nicholas D.; May, Elebeoba E.; Lane, Todd L.; Lindner, Duane L.; Young, Malin M.; VanderNoot, Victoria A.; Thaitrong, Numrin T.; Bartsch, Michael B.; Renzi, Ronald F.; Tran-Gyamfi, Mary B.; Meagher, Robert M.

Abstract not provided.

Automated Molecular Biology Platform Enabling Rapid & Efficient SGS Analysis of Pathogens in Clinical Samples

Branda, Steven B.; Jebrail, Mais J.; Van De Vreugde, James L.; Langevin, Stanley A.; Bent, Zachary B.; Curtis, Deanna J.; Lane, Pamela L.; Carson, Bryan C.; La Bauve, Elisa L.; Patel, Kamlesh P.; Ricken, James B.; Schoeniger, Joseph S.; Solberg, Owen D.; Williams, Kelly P.; Misra, Milind; Powell, Amy J.; Pattengale, Nicholas D.; May, Elebeoba E.; Lane, Todd L.; Lindner, Duane L.; Young, Malin M.; VanderNoot, Victoria A.; Thaitrong, Numrin T.; Bartsch, Michael B.; Renzi, Ronald F.; Tran-Gyamfi, Mary B.; Meagher, Robert M.

Abstract not provided.

Host suppression and bioinformatics for sequence-based characterization of unknown pathogens

Misra, Milind; Patel, Kamlesh P.; Kaiser, Julia N.; Meagher, Robert M.; Branda, Steven B.; Schoeniger, Joseph S.

Bioweapons and emerging infectious diseases pose formidable and growing threats to our national security. Rapid advances in biotechnology and the increasing efficiency of global transportation networks virtually guarantee that the United States will face potentially devastating infectious disease outbreaks caused by novel ('unknown') pathogens either intentionally or accidentally introduced into the population. Unfortunately, our nation's biodefense and public health infrastructure is primarily designed to handle previously characterized ('known') pathogens. While modern DNA assays can identify known pathogens quickly, identifying unknown pathogens currently depends upon slow, classical microbiological methods of isolation and culture that can take weeks to produce actionable information. In many scenarios that delay would be costly, in terms of casualties and economic damage; indeed, it can mean the difference between a manageable public health incident and a full-blown epidemic. To close this gap in our nation's biodefense capability, we will develop, validate, and optimize a system to extract nucleic acids from unknown pathogens present in clinical samples drawn from infected patients. This system will extract nucleic acids from a clinical sample, amplify pathogen and specific host response nucleic acid sequences. These sequences will then be suitable for ultra-high-throughput sequencing (UHTS) carried out by a third party. The data generated from UHTS will then be processed through a new data assimilation and Bioinformatic analysis pipeline that will allow us to characterize an unknown pathogen in hours to days instead of weeks to months. Our methods will require no a priori knowledge of the pathogen, and no isolation or culturing; therefore it will circumvent many of the major roadblocks confronting a clinical microbiologist or virologist when presented with an unknown or engineered pathogen.

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Macro-meso-microsystems integration in LTCC : LDRD report

Rohde, Steven B.; Okandan, Murat O.; Pfeifer, Kent B.; De Smet, Dennis J.; Patel, Kamlesh P.; Ho, Clifford K.; Nordquist, Christopher N.; Walker, Charles A.; Rohrer, Brandon R.; Buerger, Stephen B.; Wroblewski, Brian W.

Low Temperature Cofired Ceramic (LTCC) has proven to be an enabling medium for microsystem technologies, because of its desirable electrical, physical, and chemical properties coupled with its capability for rapid prototyping and scalable manufacturing of components. LTCC is viewed as an extension of hybrid microcircuits, and in that function it enables development, testing, and deployment of silicon microsystems. However, its versatility has allowed it to succeed as a microsystem medium in its own right, with applications in non-microelectronic meso-scale devices and in a range of sensor devices. Applications include silicon microfluidic ''chip-and-wire'' systems and fluid grid array (FGA)/microfluidic multichip modules using embedded channels in LTCC, and cofired electro-mechanical systems with moving parts. Both the microfluidic and mechanical system applications are enabled by sacrificial volume materials (SVM), which serve to create and maintain cavities and separation gaps during the lamination and cofiring process. SVMs consisting of thermally fugitive or partially inert materials are easily incorporated. Recognizing the premium on devices that are cofired rather than assembled, we report on functional-as-released and functional-as-fired moving parts. Additional applications for cofired transparent windows, some as small as an optical fiber, are also described. The applications described help pave the way for widespread application of LTCC to biomedical, control, analysis, characterization, and radio frequency (RF) functions for macro-meso-microsystems.

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8 Results
8 Results