Shoreline Biome, LLC

Qiagen Gmbh

Alere San Diego, Inc.

Mark Driscoll

Thomas Jarvie

Roger S Lasken

Frank B Dean

Osama A Alsmadi

A Fawad Faruqi

Seiyu Hosono

Linhua Fang

Stephen F Kingsmore

Velizar T Tchernev

Michele Wisniewski

Serguei J Lejnine

Wanmin Song

Disclosed are methods for lysis of cells that combine three lysis steps&#x2014;(1) heat, (2) detergent and (3) base&#x2014;into a single step and that can be completed in a short period of time, e.g., a few minutes. The methods combine a normally incompatible detergent and base lysis, allow for simplified removal of detergent after lysis, and importantly, limits damage to DNA, such as shearing, that typically results from separate application of conventional lysis methods, yielding improved quality and quantities of genomic DNA (gDNA).

Methods for cell lysis and preparation of high molecular weight DNA from modified cells

Disclosed are methods for screening biological samples for the presence unknown microbes, such as bacteria and archaea or unknown eukaryotes using rRNA gene sequences or other highly conserved genetic regions, across multiple biological samples using a unique sequence tag (barcode) corresponding to the sample. The screening process tracks the unknown microbe or eukaryote in a diluted sample where the DNA has been prepared using whole genome amplification. The whole genome of the unknown microbe or eukaryote is then sequenced and assembled.

High throughput method for identification and sequencing of unknown microbial and eukaryotic genomes from complex mixtures

Disclosed are methods for lysis of cells, such as bacteria present in microbiomes, that combine three lysis steps&#x2014;(1) heat, (2) detergent and (3) base&#x2014;into a single step and that can be completed in a short period of time, e.g., a few minutes. The methods combine a normally incompatible detergent and base lysis, allows for simplified removal of detergent after lysis, and importantly, yields improved quantities of genomic DNA (gDNA) from difficult to lyse bacteria.

Combined lysis protocol for comprehensive cell lysis

Biomarkers for sepsis and resulting mortality can be detected by assaying blood samples. Changes in the concentration of the biomarkers can be used to indicate sepsis, risk of sepsis, progression of sepsis, remission from sepsis, and risk of mortality. Changes can be evaluated relative to data sets, natural or synthetic or semisynthetic control samples, or patient samples collected at different time points. Some biomarkers' concentrations are elevated during disease and some are depressed. These are termed informative biomarkers. Some biomarkers are diagnostic in combination with others. Individual biomarkers may be weighted when used in combinations. Biomarkers can be assessed in individual, isolated or assays, in parallel assays, or in single-pot assays.

Biomarkers for sepsis

Disclosed are compositions and a method for amplification of nucleic acid sequences of interest. The disclosed method generally involves replication of a target sequence such that, during replication, the replicated strands are displaced from the target sequence by strand displacement replication of another replicated strand. In one form of the disclosed method, the target sample is not subjected to denaturing conditions. It was discovered that the target nucleic acids, genomic DNA, for example, need not be denatured for efficient multiple displacement amplification. The primers used can be hexamer primers. The primers can also each contain at least one modified nucleotide such that the primers are nuclease resistant. The primers can also each contain at least one modified nucleotide such that the melting temperature of the primer is altered relative to a primer of the same sequence without the modified nucleotide(s). The DNA polymerase can be &#x3c6;29 DNA polymerase.

Amplification of denatured and stabilized nucleic acids

Multiple displacement amplification

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Wallingford, CT, United States of America

Mark Driscoll