BILE SALT HYDROLASE PROBE AND METHOD OF MAKING AND USING THE SAME
The complex mixture of microbes in the gut (i.e. the gut microbiome) can have a major impact on host health, with effects ranging from altering nutrient absorption and creating chemical signals that modulate host physiology. A prominent example of microbiome-host interaction is chemical microbial modification of the host's bile acid pool. Certain microbes are capable of modulating the hydrophobicity of the bile acid pool through the activity of bile salt hydrolases. Bile salt hydrolases catalyze the hydrolysis of bile salts to free bile acids and amino acids. The result of BSH activity is a net change in the physicochemical properties of the bile acid pool, ultimately making it more hydrophobic, and therefore making fatty gut contents more prone to excretion. Increasing BSH activity is postulated to be an effective strategy for treating obesity and hypercholesterolemia. Currently, the bioassays for characterizing bile salt hydrolase activity are time-consuming or have poor sensitivity. We have invented a continuous fluorescence-based BSH assay that is easy to use and is compatible with gut microbiome samples. The chemistry of our assay is fundamentally different from other BSH assays. Because our assay provides a fluorescent readout in real time it is significantly easier to setup than other BSH assays, and has considerably higher sensitivity that assays that rely on detection of the amine product.
GENE-MATCHED ENRICHMENT AND POLYMERASE CHAIN REACTION FOR RAPID DETECTION OF MICROORGANISMS
A method for amplifying and detecting microorganisms, such as species of Listeria, is described. The method utilizes gene-matched enrichment media and PCR-based detection. The enrichment media is spent media produced using a modified microorganism containing a plurality of mutations in a selected gene such that the modified microorganism does not contain the PCR signature. Thus, PCR detects only the amplified microorganism of interest, not the modified microorganism. Exemplary methods and kits for amplification and detection of Listeria species are described
GENE TARGETS FOR IMPROVED ENZYME PRODUCTION IN FUNGI
Deletion of a putative sugar transporter, resulted in a doubling of the heterologous BG activity detected in culture supernatants. This could potentially allow for increased production of heterologous proteins by A. niger for industrial use. In addition, deletion of this putative sugar transporter resulted in increased glucoamylase production.
GENE TARGETS FOR IMPROVED ENZYME PRODUCTION IN FUNGI
Deletion of a putative sugar transporter, resulted in a doubling of the heterologous BG activity detected in culture supernatants. This could potentially allow for increased production of heterologous proteins by A. niger for industrial use. In addition, deletion of this putative sugar transporter resulted in increased glucoamylase production.
Peptide and Protein Biomarkers for Type 1 Diabetes Mellitus (iEdison Invention Report No. 0685901-11-0005.)
A method for identifying persons with increased risk of developing type 1 diabetes mellitus, or having type I diabetes mellitus, utilizing selected biomarkers described herein either alone or in combination. The present disclosure allows for broad based, reliable, screening of large population bases. Also provided are arrays and kits that can be used to perform such methods.
GENE-MATCHED ENRICHMENT AND POLYMERASE CHAIN REACTION FOR RAPID DETECTION OF MICROORGANISMS
A method for amplifying and detecting microorganisms, such as species of Listeria, is described. The method utilizes gene-matched enrichment media and PCR-based detection. The enrichment media is spent media produced using a modified microorganism containing a plurality of mutations in a selected gene such that the modified microorganism does not contain the PCR signature. Thus, PCR detects only the amplified microorganism of interest, not the modified microorganism. Exemplary methods and kits for amplification and detection of Listeria species are described
BILE SALT HYDROLASE PROBE AND METHOD OF MAKING AND USING THE SAME
The complex mixture of microbes in the gut (i.e. the gut microbiome) can have a major impact on host health, with effects ranging from altering nutrient absorption and creating chemical signals that modulate host physiology. A prominent example of microbiome-host interaction is chemical microbial modification of the host's bile acid pool. Certain microbes are capable of modulating the hydrophobicity of the bile acid pool through the activity of bile salt hydrolases. Bile salt hydrolases catalyze the hydrolysis of bile salts to free bile acids and amino acids. The result of BSH activity is a net change in the physicochemical properties of the bile acid pool, ultimately making it more hydrophobic, and therefore making fatty gut contents more prone to excretion. Increasing BSH activity is postulated to be an effective strategy for treating obesity and hypercholesterolemia. Currently, the bioassays for characterizing bile salt hydrolase activity are time-consuming or have poor sensitivity. We have invented a continuous fluorescence-based BSH assay that is easy to use and is compatible with gut microbiome samples. The chemistry of our assay is fundamentally different from other BSH assays. Because our assay provides a fluorescent readout in real time it is significantly easier to setup than other BSH assays, and has considerably higher sensitivity that assays that rely on detection of the amine product.
DIRECT DETERMINATION OF ANTIBODY CHAIN PAIRING
I have developed a tandem mass spectrometry (MS/MS) based approach for the direct determination of antibody heavy and light chain pairing. This approach eliminates the need for costly and invasive genomics approaches (e.g. B cell sequencing and hybridoma) for determining heavy and light chain pairing during therapeutic antibody discovery. IgG antibodies are composed of two copies of a light chain and two copies of a heavy chain covalently linked by intermolecular disulfide bonds. I have demonstrated that ultraviolet photodissociation (UVPD) and electron capture dissociation (ECD) can efficiently cleave the intermolecular disulfide bonds that bind the heavy and light chains together. This yields a MS/MS spectrum that contains the mass of the intact antibody or Fab fragment, intact mass of the light chain, intact mass of the heavy chain or Fd subunit, and product ions that provide confirmation of the (complementarity determining regions) CDR sequences. This information provides unambiguous confirmation of heavy and light chain pairing. These are completely unprecedented results and will have significant impact on therapeutic antibody discovery as well as quality control during production of antibody therapeutics.
PROSTATE CANCER-ASSOCIATED SECRETED PROTEINS (NIH iEdison No. 0685901-16-0007)
Methods are provided for treating a subject with prostate cancer and/or diagnosing a subject at risk for prostate cancer, which can include measuring increased expression of at least two prostate cancer-related molecules in a sample obtained from a subject, including the prostate cancer-related molecules AGR2, AGR3, CRISP3, CCL3, CEACAM5, CEACAM6, IL24, MMP9, CXCL14, CD90, POSTN, and SFRP4. The methods can include administering at therapy to a subject with prostate cancer. Methods are provided for treating a subject with intermediate- or high-risk prostate cancer, which can include measuring increased expression of MMP9 in a sample obtained from a subject compared to a control representing expression of MMP9 expected in a sample from a subject who has low-risk prostate cancer.
CONTROLLED SYNTHESIS OF HIERARCHICALLY-STRUCTURED HYBRID MATERIALS THROUGH PEPTOID ENGINEERING
In nature, specific biomolecules interacting with mineral precurors are responsible for the precise production of nanostructured inorganic materials that exhibit complex morphologies and superior performance. Despite advances in developing biomimetic approaches, the design rules for creating sequence-defined molecules that lead to the synthesis of inorganic nanomaterials with predictable complex morphologies are unknown. To address this challenge, this patent application highlights a new peptoid-based biomimetic approach for controlled synthesis of hierarchically-structured metallic nanomaterials. Though the detailed investigation of some peptoid-controlled gold nanomaterial formation processes by engineering peptoid sequences and investigating the resulting particle formation mechanisms, we develop a rule of thumb for designing peptoids that predictively enabled the morphological evolution from spherical to coral-shaped nanoparticles. These individual coral-shaped gold nanoparticles exhibit a plasmonic enhancement as high as 105 fold. This research presented in this patent application significantly advances our ultimate vision of predictive bio-inspired materials synthesis using sequence-defined synthetic molecules that mimic proteins and peptides.