USA As Represented by Secretary of the Navy

Baochuan Lin

David A Stenger

Joel M Schnur

Brandy J White

Anthony P Malanoski

Frances S Ligler

James B Delehanty

Brian Melde

Zheng Wang

Marie J Archer

Clark J Tibbetts

Gary J Vora

Robb K Rowley

Donald Seto

Jennifer Johnson

Dzung C Thach

Elizabeth A Walter

Russell P Kruzelock

Eric H Hanson

Kate M Blaney

Brian K Agan

Mesoporous sorbents are effective for storing and transporting nucleic acids. In particular, two ethane-bridged silica sorbents with amine functionalities are particularly effective and capable of binding nucleic acids for storage.

Sorbents for the extraction and stabilization of nucleic acids

Sorbents for extraction and stabilization of nucleic acids

The present invention relates to pathogen detection and identification by use of DNA resequencing microarrays. The present invention also provides resequencing microarray chips for differential diagnosis and serotyping of pathogens present in a biological sample. The present invention further provides methods of detecting the presence and identity of pathogens present in a biological sample.

Re-sequencing pathogen microarray

A method of attaching a phosphorous dendrimer onto magnetic microparticles by taking magnetic microparticles in a water-based solution, then performing a solvent exchange, then suspending the microparticles in a phosphorous dendrimer solution and shaking, then washing the microparticles with an organic solvent, and then washing the microparticles with a transition solvent. The solvent exchange is done by washing the microparticles with a first concentration of a transition solvent, then washing the microparticles with a second concentration of the transition solvent where the second concentration is greater than the first concentration, then washing the microparticles with an organic solvent, then washing the microparticles with the transition solvent, then washing the microparticles with the organic solvent, and then suspending the microparticles in the transition solvent. Also disclosed is the related phosphorous dendrimer made by this method.

Large scale preparation method for functionalizing the surface of magnetic microparticles with an inorganic phosphorous dendrimer

A method of: providing a solid surface having a dendrimer molecule bound thereto and a single-stranded probe nucleic acid immobilized to the dendrimer; contacting the solid surface with a sample suspected or known to contain a double-stranded complimentary target nucleic acid; denaturing the target nucleic acids at thermal conditions and in a salt concentration sufficient to denature the target nucleic acids to produce denatured nucleic acids; and cooling the sample to allow hybridization of the denatured nucleic acids to the probe nucleic acids. An article having: one or more paramagnetic microbeads; a dendrimer molecule bound to the beads; and a probe nucleic acid immobilized to the dendrimer.

Solid phase for capture of nucleic acids

A composition having proanthocyanidin compounds having an average degree of polymerization of at least about 6. A method of administering to an immunosuppressed patient or a patient diagnosed with sepsis or septic shock a composition having a proanthocyanidin. A method of administering to a patient diagnosed with a gram negative bacterial infection a composition having proanthocyanidin compounds having an average degree of polymerization of at least about 6.

Binding interaction of proanthocyanidins with bacteria and bacterial components

A composition having: a proanthocyanidin; and a macromolecule, an assembly of macromolecules, a semi-solid, or a solid surface to which the proanthocyanidin is immobilized.

Applications of the binding interaction of proanthocyanidins with bacteria and bacterial components

A method of: submitting reference sequences to a taxonomic database to produce taxonomic results; and reporting a taxonomic identification based on the taxonomic results. The reference sequences are the output of genetic database queries that return a score for each reference sequence. A method for processing a biological sequence obtained from an assay by: converting base calls located in a predetermined list of positions within the biological sequence to N; and determining the ratio of single nucleotide polymorphisms in the biological sequence relative to a reference sequence. Each entry in the predetermined list of positions represents the capability of a substance hybridizing to a microarray used to generate the biological sequence. The substance is not the nucleic acid of a target pathogen.

Computer-implemented biological sequence identifier system and method

A PCR method involving: providing a biological sample suspected of containing one or more pathogen nucleic acids; adding a plurality of PCR primers corresponding to genes found in the pathogens; and performing a polymerase chain reaction on the sample to amplify a subset of the nucleic acids that correspond to the genes. The primers include at least one primer pair for each pathogen, and the primers contain a tail sequence that is not homologous any pathogen DNA or to any background DNA in the sample. The concentration of at least one primer in the polymerase chain reaction is no more than about 100 nM.

Multiplexed polymerase chain reaction for genetic sequence analysis

A computer-implemented method as follows. Providing a list of target sequences associated with one or more organisms. Providing a list of candidate prototype sequences suspected of hybridizing to one or more of the target sequences. Generating a collection of probes corresponding to each candidate prototype sequence, each collection of probes having a set of probes for every subsequence. The sets consist of the corresponding subsequence and every variation of the corresponding subsequence formed by varying a center nucleotide of the corresponding subsequence. Generating a set of fragments corresponding to each target sequence. Calculating the binding free energy of each fragment with a perfect complimentary sequence of the fragment. Determining which extended fragments are perfect matches to any of the probes. Assembling a base call sequence corresponding to each candidate prototype sequence.

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Bethesda, MD, United States of America

Baochuan Lin