Abstract: The present disclosure relates to processes for producing hydrocarbon fuels from lignocellulosic biomass. A process may include introducing biomass to a pretreatment system, and a first separation system forming a pentose-rich stream and a pentose-lean stream. The pentose-lean stream may be introduced to a hydrolysis system forming a hydrolysate and the hydrolysate introduced to a second separation system forming a hexose-rich stream and a lignin stream. Additionally, at least one of the pentose-rich stream or the hexose-rich stream may be introduced to a bioreactor containing microorganisms configured to produce hydrocarbon fuels. Additionally, the present disclosure also relates to systems for the production of hydrocarbon fuels. A system may include a pretreatment system, a first separation system, a hydrolysis system, a second separation system, and one or more bioreactors.

Abstract: A method for identifying in situ presence of a hydrocarbon reservoir or of a pipeline leakage is disclosed. The method can include obtaining a sample from an area of interest, such as a sediment sample or water column sample near a hydrocarbon seep or near an offshore pipeline; analyzing the sample to detect nucleic acid, protein or metabolite signatures that are indicative of cold-shock response; identifying the relative abundance of the cold-shock signatures present in the sample in comparison to the surrounding environment.

Abstract: The present disclosure relates to processes for producing hydrocarbon fuels from lignocellulosic biomass. A process may include introducing biomass to a pretreatment system, and a first separation system forming a pentose-rich stream and a pentose-lean stream. The pentose-lean stream may be introduced to a hydrolysis system forming a hydrolysate and the hydrolysate introduced to a second separation system forming a hexose-rich stream and a lignin stream. Additionally, at least one of the pentose-rich stream or the hexose-rich stream may be introduced to a bioreactor containing microorganisms configured to produce hydrocarbon fuels. Additionally, the present disclosure also relates to systems for the production of hydrocarbon fuels. A system may include a pretreatment system, a first separation system, a hydrolysis system, a second separation system, and one or more bioreactors.

Abstract: The present disclosure relates to a porous liquid or a porous liquid enzyme that includes a high surface area solid and a liquid film substantially covering the high surface area solid. The porous liquid or porous liquid enzyme may be contacted with a fluid that is immiscible with the liquid film such that a liquid-fluid interface is formed. The liquid film may facilitate mass transfer of a substance or substrate across the liquid-fluid interface. The present disclosure also provides methods of performing liquid-based extractions and enzymatic reactions utilizing the porous liquid or porous liquid enzyme of the present disclosure.

Abstract: The present disclosure relates to methods and systems for converting biomass comprising lignocellulosic material into biofuels and biochemicals that contribute to reduction of greenhouse gas emissions. In particular, the present disclosure relates to methods and systems for the removal or reduction of impurities during lignocellulosic biomass processing to enhance biorefinery production of biofuels and biochemicals.

Abstract: The present disclosure relates to processes for producing hydrocarbon fuels from lignocellulosic biomass. A process may include introducing biomass to a pretreatment system forming a pretreatment effluent and introducing the pretreatment effluent to a hydrolysis system forming a hydrolysate. The hydrolysate may be introduced to a lignin separation system to form a sugar-rich stream and a lignin-rich stream. The sugar-rich stream may be introduced to a purification system comprising at least one toxin converting microorganism or subcellular material to form a purified sugar-rich stream, and the purified sugar-rich stream and one or more sugar converting microorganisms are introduced to a bioreactor configured to produce hydrocarbon fuels. Additionally, the present disclosure also related to systems for production of hydrocarbon fuels including, a pretreatment system, a hydrolysis system, a lignin separation system, a purification system, and at least one bioreactor.

Abstract: The present disclosure relates to processes for producing hydrocarbon fuels from lignocellulosic biomass. A process may include introducing biomass to a pretreatment system, and a first separation system forming a pentose-rich stream and a pentose-lean stream. The pentose-lean stream may be introduced to a hydrolysis system forming a hydrolysate and the hydrolysate introduced to a second separation system forming a hexose-rich stream and a lignin stream. Additionally, at least one of the pentose-rich stream or the hexose-rich stream may be introduced to a bioreactor containing microorganisms configured to produce hydrocarbon fuels. Additionally, the present disclosure also relates to systems for the production of hydrocarbon fuels. A system may include a pretreatment system, a first separation system, a hydrolysis system, a second separation system, and one or more bioreactors.

Abstract: The present disclosure relates to methods and systems for converting biomass into biofuels and biochemicals. In particular, the present disclosure relates to methods and systems for converting biomass comprising lignocellulosic material into biofuels and biochemicals, such as those comprising fatty acid esters, that contribute to reduction of greenhouse gas emissions.

Abstract: Provided are methods for diagnosing, monitoring and mitigating microbiologically influenced corrosion (MIC). The methods employ steps to determine the nature and concentration of biological signatures, formed through metabolism of microorganisms, and correlating the biological signatures with MIC. Based on such analyses, appropriate MIC mitigation strategies may be implemented so as to efficiently target MIC at sites of interest. The methods advantageously allow selection of appropriate MIC mitigation treatments that correspond to the level of severity of the MIC and based on historical data correlating particular biological signatures with particular MIC risk.

Abstract: The present disclosure relates to a porous liquid or a porous liquid enzyme that includes a high surface area solid and a liquid film substantially covering the high surface area solid. The porous liquid or porous liquid enzyme may be contacted with a fluid that is immiscible with the liquid film such that a liquid-fluid interface is formed. The liquid film may facilitate mass transfer of a substance or substrate across the liquid-fluid interface. The present disclosure also provides methods of performing liquid-based extractions and enzymatic reactions utilizing the porous liquid or porous liquid enzyme of the present disclosure.

Abstract: Methods and systems for differential expression analysis of ribonucleic acid sequencing (RNA-Seq) data, and in particular to an automated workflow for differential expression analysis of RNA-Seq data. More particularly, an automated workflow for differential expression analysis of RNA-Seq data permitting analysis of pairs of any number of RNA-Seq reads subjected to multiple experimental conditions and tested in replicate.

Abstract: A method including: obtaining a field sample; extracting DNA from the field sample and identifying a marker gene; amplifying and sequencing the marker gene; identifying a genetic makeup of the marker gene; identifying a potential compound associated with the genetic makeup; and identifying a gene associated with the potential compound and associating that gene with a metabolite.

Abstract: A method for identifying in situ presence of a hydrocarbon reservoir or of a pipeline leakage is disclosed. The method can include obtaining a sample from an area of interest, such as a sediment sample or water column sample near a hydrocarbon seep or near an offshore pipeline; analyzing the sample to detect nucleic acid, protein or metabolite signatures that are indicative of cold-shock response; identifying the relative abundance of the cold-shock signatures present in the sample in comparison to the surrounding environment.

Abstract: The present disclosure describes methods for detecting, monitoring, and modulating (e.g., promoting, enhancing, sustaining, maintaining, reducing, mitigating or eliminating of) biofilm formation, as well as mitigating or eliminating Microbial Influenced Corrosion (MIC) of a metal surface. The method of monitoring includes: providing a test sample; detecting at least one of a prophage gene, a prophage gene expression, a prophage gene transcript, a prophage protein, a prophage metabolite, a prophage intermediate, or a combination thereof, wherein the existence, amount or level of prophage gene expression, a prophage gene transcript, a prophage protein, a prophage metabolite, a prophage intermediate, or a combination thereof relative to a control is indicative of biofilm presence, formation or the state of the biofilm in a sample. The present disclosure also describes a composition for modulating biofilm formation, maintenance, mitigation, reduction, and elimination.

Abstract: Provided is a multi-phase process for conditionally treating MIC by evaluating whether MIC-correlating conditions exist, the degree of MIC, if present, and then applying a concomitant MIC-mitigating treatment which is adjusted in its degree of aggressiveness in proportion to MIC severity. The disclosed methodology allows, in part, for the continuous or periodic monitoring and assessment of MIC risk in petroleum-based equipment (e.g., pipeline) and the administering of a treatment that corresponds to the level of severity of the MIC resulting in a more fine-tuned, localized, and cost-effective treatment.

Abstract: Provided is a multi-phase process for conditionally treating MIC by evaluating whether MIC-correlating conditions exist, the degree of MIC, if present, and then applying a concomitant MIC-mitigating treatment which is adjusted in its degree of aggressiveness in proportion to MIC severity. The disclosed methodology allows, in part, for the continuous or periodic monitoring and assessment of MIC risk in petroleum-based equipment (e.g., pipeline) and the administering of a treatment that corresponds to the level of severity of the MIC resulting in a more fine-tuned, localized, and cost-effective treatment.

Abstract: Provided are methods for mitigating or eliminating Microbial Influenced Corrosion of a metal surface including contacting the metal surface with an effective amount of a liquid composition comprising indole or a functionally equivalent analog or derivative thereof. Also provided are methods for reducing the formation or activity of a corrosion-associated biofilm on a metal surface including contacting the metal surface with an effective amount of a liquid composition including indole or a functionally equivalent analog or derivative thereof.