The University of Texas System

Purdue Research Foundation

Harvard College

Iowa State University Research Foundation Inc.

Texas A&M University System

Research Development Foundation

Ambion, Inc.

Andrew D Ellington

Eric V Anslyn

Jagannath Swaminathan

Jimmy Gollihar

Ross Thyer

Edward M Marcotte

Sanchita Bhadra

Raghav Shroff

Jared Ellefson

Alexander Boulgakov

Edward Marcotte

Randy Allen Hughes

Bingling Li

Yu Sherry Jiang

Yan Du

Erik Hernandez

Helen Seifert

James L Bachman

Amber Johnson

George Georgiou

Babak Ziaie

Cagri Abdullah Savran

Robert Setterquist

Chun-Li Chang

Anumantha G Kanthasamy

Zhenwen Ding

Christopher John Gregg

George L Murphy

Daniel J Mandell

Venkata Naga Lakshmi Rekha Patchigolla

Sulay Jhaveri

Xin Ge

Jason Lavinder

Sai Reddy

Gregory Phillips

Peter Benjamin Stranges

Daniel Boutz

Cheulhee Jung

Manjula Rajendran

Ichiro Matsumura

Erhu Xiong

Elizabeth Gardner

Katy Kao

Michelle Byrom

Jon Laurent

Arti Pothukuchy

Nicholas Backes

Ahmed Abdalla

Austin Cole

Ted Chitai Chu

Amy Yan

Matthew Levy

Danny Boutz

Adam J Meyer

Daniel Garry

John N Milligan

Sheng Cai

Jimmy D Gollihar

Chi-Tai Chu

Methods of identifying a sequence of a polypeptide within a heterogenous mixture of polypeptides, the polypeptide being immobilized to a support and having at least one labeled amino acid residue. Methods involve detecting at least one signal or signal change from the immobilized polypeptide and subjecting the polypeptide to conditions sufficient to remove at least one amino acid residue from the polypeptide.

Single molecule peptide sequencing

Recombinant bacterial cells are provided that comprise a stable non-canonical amino acid translation pathway. In some aspects, the bacteria comprise nucleic acids encoding a non-canonical amino acid translation pathway (e.g., a tRNA for incorporation of a non-canonical amino acid, such selenocysteine); a marker polypeptide that includes the non-canonical amino acid. Recombinant tRNA and selection marker coding sequences are likewise provided.

Transgenic bacteria with expanded amino acid usage and nucleic acid molecules for use in the same

The present disclosure provides methods for molecular neighborhood detection of molecules, such as by iterative proximity ligation or split-and-pool methods for obtaining positional information.

Molecular neighborhood detection by oligonucleotides

Embodiments of the disclosure concern methods and compositions related to generation and/or use of proofreading reverse transcriptases, including those that are thermophilic or hyperthermophilic. The disclosure encompasses specific recombinant polymerases and their use. In some embodiments, the polymerases are utilized for RNA sequencing in the absence of generation of a cDNA intermediate.

Thermostable reverse transcriptase

Disclosed are methods for isothermal nucleic acid amplification and detection.

Strand displacement with loop-mediated isothermal amplification

Disclosed herein is a method of utilizing an enzyme in a nucleic acid manipulation process, the method comprising: a) transforming a microorganism with a non-native enzyme; b) inducing expression of the enzyme in the microorganism, thereby producing the non-native enzyme; c) adding the microorganism of step b) directly to a non-naturally occurring nucleic acid manipulation process, wherein the non-native enzyme is not purified from the microorganism prior to addition to the nucleic acid manipulation process; and carrying out the nucleic acid manipulation process using the enzyme. Importantly, this method can be carried out without the need to purify the enzyme from the cell producing it before it is used in the nucleic acid manipulation method. Also disclosed herein is a kit for carrying out a nucleic acid manipulation process, the kit comprising a) a microorganism expressing a non-native enzyme; b) nucleic acids of interest; and c) reagents for use in the nucleic acid manipulation process.

Methods and kits for using recombinant microorganisms as direct reagents in biological applications

Disclosed herein are methods and platforms using Receptor Compartmentalized Partnered Replication (CPR), in which the partner gene is a receptor, signal transduction pathway, or metabolic pathway that leads to the production of an effector molecule for the receptor or signal transduction pathway. The signal transduction pathway or receptor is coupled to the production of a thermostable polymerase. Emulsification of libraries of organisms with primers that can amplify the partner gene led to the selective amplification of those partner genes that were best able to produce the thermostable polymerase during thermal cycling of the emulsion.

Methods and platform for screening and selecting metabolites and their receptors

The present invention generally provides methods and compositions for the treatment of Parkinson's disease and depression and/or anxiety. The invention relates to recombinant microorganisms, particularly gut-colonizing probiotics, modified to produce L-DOPA.

L-DOPA microbiome therapy

A computer-implemented method of training a neural network to improve a characteristic of a protein comprises collecting a set of amino acid sequences from a database, compiling each amino acid sequence into a three-dimensional crystallographic structure of a folded protein, training a neural network with a subset of the three-dimensional crystallographic structures, identifying, with the neural network, a candidate residue to mutate in a target protein, and identifying, with the neural network, a predicted amino acid residue to substitute for the candidate residue, to produce a mutated protein, wherein the mutated protein demonstrates an improvement in a characteristic over the target protein. A system for improving a characteristic of a protein is also described. Improved blue fluorescent proteins generated using the system are also described.

System and method for increasing synthesized protein stability

Polypeptides that fold into biologies are stabilized by diselenide bonds between selenocysteine amino acids. Methods to produce such polypeptides in genomically recoded organisms (GRO) can be scaled up for industrial production. Since diselenides have the same geometric bond angles and torsions as disulfides, as well as very similar bond lengths, they can be substituted into polypeptides without disrupting the three dimensional structure of the polypeptides. Diselenides render the polypeptides resistant to reduction when they are exposed to blood serum or to reducing components of blood serum or to reducing components components within cells.

Production of seleno-biologics in genomically recoded organisms

Identifying proteins and peptides, and more specifically large-scale sequencing of single peptides in a mixture of diverse peptides at the single molecule level is an unmet challenge in the field of protein sequencing. Herein are methods for identifying amino acids in peptides, including peptides with unnatural amino acids. In one embodiment, the N-terminal amino acid is labeled with a first label and an internal amino acid is labeled with a second label. In some embodiments, the labels are fluorescent labels. In other embodiments, the internal amino acid is Lysine. In other embodiments, amino acids in peptides are identified based on the fluorescent signature for each peptide at the single molecule level.

Disclosed are compositions and methods for nucleic acid amplification and detection. Specifically, disclosed herein are compositions and methods that allow for amplification of nucleic acids at a wide variety of temperatures. This includes a polymerase which is thermostable at high temperatures, and a method of amplification that can be conducted at relatively low temperatures.

Methods and devices related to amplifying nucleic acid at a variety of temperatures

The disclosure concerns methods for identifying amino acids in peptides, including peptides including unnatural amino acids. Various aspects of the present disclosure provide compositions and methods for amino acid-type specific labeling, as well as methods for detecting the labels. Further disclosed herein are strategies for highly multiplexed, high-throughput peptide analysis.

Composition comprising purified recombinant selenoproteins, such an antibodies and enzymes, are provided. Method of producing such recombinant polypeptides and bacterial strains for the same are likewise provided.

Recombinant polypeptides comprising selenocysteine and method for producing the same

Growing community of inventors

Austin, TX, United States of America

Andrew D Ellington