Abstract: Provided herein are methods and systems to selectively deplete a biological sample of host compartments and/or host nucleic acid while enriching the sample microbial compartments and/or related microbial nucleic acid. In addition, provided herein are compositions, methods and systems related to said host depletion and microbial enrichment methods and systems.

Abstract: Provided herein are methods for making a freeze-cast material having a internal structure, the methods comprising steps of: determining the internal structure of the material, the internal structure having a plurality of pores, wherein: each of the plurality of pores has directionality; and the step of determining comprises: selecting a temperature gradient and a freezing front velocity to obtain the determined internal structure based on the selected temperature gradient and the selected freezing front velocity; directionally freezing a liquid formulation to form a frozen solid, the step of directionally freezing comprising: controlling the temperature gradient and the freezing front velocity to match the selected temperature gradient and the selected freezing front velocity during directionally freezing; wherein the liquid formulation comprises at least one solvent and at least one dispersed species; and subliming the at least one solvent out of the frozen solid to form the material.

Abstract: Methods, systems and related compositions are provided to perform single-cell marking of a nucleic acid and/or protein in a sample based on in-cell or in-organelle barcoding of nucleic acid and/or protein complexes of the cell or organelle; the methods and systems herein described are configured to provide in-cell or in-organelle single-cell marked nucleic acid and/or protein complexes comprising a single-cell, cell-specific, or a single-cell organelle-specific marker.

Abstract: Methods and systems and related compositions for separating through a solid matrix a mixture comprising a nucleic acid in a concentration of 1 ?M or less, together with a target compound having a water solubility equal to or greater than 0.001 g per 100 mL, which can be used for managing fluid flow, biochemical reactions and purification of the nucleic acid or other target analytes. The method comprises contacting the solid matrix with a target compound removing agent having a water solubility equal to or less than 0.05 g per 100 mL at 25° C. at 1 atm pressure with water having a solubility in the removing agent of less than 10 g per 100 mL at 25° C. at 1 atm pressure, the contacting performed to remove the target compound from the solid matrix.

Abstract: The present invention provides microfluidic technology enabling rapid and economical manipulation of reactions on the femtoliter to microliter scale.

Abstract: Provided herein is an antibiotic susceptibility test and related compositions, methods and systems based on detection of a nucleic acid from a target microorganism in a sample in the presence or absence of a lysis treatment of the sample.

Abstract: Provided herein are methods for making a freeze-cast material having a internal structure, the methods comprising steps of: determining the internal structure of the material, the internal structure having a plurality of pores, wherein: each of the plurality of pores has directionality; and the step of determining comprises: selecting a temperature gradient and a freezing front velocity to obtain the determined internal structure based on the selected temperature gradient and the selected freezing front velocity; directionally freezing a liquid formulation to form a frozen solid, the step of directionally freezing comprising: controlling the temperature gradient and the freezing front velocity to match the selected temperature gradient and the selected freezing front velocity during directionally freezing; wherein the liquid formulation comprises at least one solvent and at least one dispersed species; and subliming the at least one solvent out of the frozen solid to form the material.

Abstract: Provided herein are methods and systems for absolute quantification of a target 16S rRNA and/or of a target prokaryotic taxon, based on amplifying and sequencing a same 16S rRNA recognition segment in which target 16S rRNA conserved regions flank 16S rRNA variable regions, conserved and variable among a plurality of sample 16S rRNAs and/or of a sample prokaryotic taxon of higher taxonomic rank with respect to the target taxon. In the methods and systems, absolute abundance of the a plurality of sample 16S rRNAs and/or of the sample prokaryotic taxon detected by the amplifying, is multiplied by the relative abundance of the target 16S rRNA and/or of a target prokaryotic taxon detected by the sequencing to provide the absolute quantification in accordance with method and systems of the disclosure.

Abstract: The present invention relates to assays, including amplification assays, conducted in the presence of modulators. These assays can be used to detect the presence of particular nucleic acid sequences. In particular, these assays can allow for genotyping or other genetic analysis.

Abstract: Provided herein are RNA markers and compositions, methods and systems for the related identification and/or uses in methods for detection of antibiotic susceptibility and resistance in a microorganism, and in particular in N. gonorrhoeae.

Abstract: Provided herein are devices and methods that enable co-incubation of microorganisms. Also provided are methods of making such devices for co-incubation of microorganisms, and various applications of such devices.

Abstract: Methods, systems and related compositions are provided to perform single-cell marking of a nucleic acid and/or protein in a sample based on in-cell or in-organelle barcoding of nucleic acid and/or protein complexes of the cell or organelle; the methods and systems herein described are configured to provide in-cell or in-organelle single-cell marked nucleic acid and/or protein complexes comprising a single-cell, cell-specific, or a single-cell organelle-specific marker.

Abstract: Disclosed herein are methods and devices for rapid assessment of whether a microorganism present in a sample is susceptible or resistant to a treatment.

Abstract: The present invention provides microfabricated substrates and methods of conducting reactions within these substrates. The reactions occur in plugs transported in the flow of a carrier-fluid.

Abstract: Provided herein is an antibiotic susceptibility and related compositions, methods and systems based on nucleic acid detection based on detected intracellular and extracellular nucleic acid from a same sample, which allows determination of antibiotic susceptibility of microorganisms as well as the diagnosis and/or treatment of related infections in individuals.

Abstract: The present invention relates to assays, including amplification assays, conducted in the presence of modulators. These assays can be used to detect the presence of particular nucleic acid sequences. In particular, these assays can allow for genotyping or other genetic analysis.

Abstract: Provided herein are methods and systems for absolute quantification of a target 16S rRNA and/or of a target prokaryotic taxon, based on amplifying and sequencing a same 16S rRNA recognition segment in which target 16S rRNA conserved regions flank 16S rRNA variable regions, conserved and variable among a plurality of sample 16S rRNAs and/or of a sample prokaryotic taxon of higher taxonomic rank with respect to the target taxon. In the methods and systems, absolute abundance of the a plurality of sample 16S rRNAs and/or of the sample prokaryotic taxon detected by the amplifying, is multiplied by the relative abundance of the target 16S rRNA and/or of a target prokaryotic taxon detected by the sequencing to provide the absolute quantification in accordance with method and systems of the disclosure.

Abstract: The present invention provides microfabricated substrates and methods of conducting reactions within these substrates. The reactions occur in plugs transported in the flow of a carrier-fluid.

Abstract: The present invention provides microfabricated substrates and methods of conducting reactions within these substrates. The reactions occur in plugs transported in the flow of a carrier-fluid.

Abstract: Provided herein are methods for making a freeze-cast material having a internal structure, the methods comprising steps of: determining the internal structure of the material, the internal structure having a plurality of pores, wherein: each of the plurality of pores has directionality; and the step of determining comprises: selecting a temperature gradient and a freezing front velocity to obtain the determined internal structure based on the selected temperature gradient and the selected freezing front velocity; directionally freezing a liquid formulation to form a frozen solid, the step of directionally freezing comprising: controlling the temperature gradient and the freezing front velocity to match the selected temperature gradient and the selected freezing front velocity during directionally freezing; wherein the liquid formulation comprises at least one solvent and at least one dispersed species; and subliming the at least one solvent out of the frozen solid to form the material.