Scarab Genomics, LLC

Wisconsin Alumni Research Foundation

Dnastar, Inc.

Other

Dnstar, Inc.

Campbell, John W.

Frederick R Blattner

Gyorgy Posfai

Guy Plunkett

John Walter Campbell

David A Frisch

Robert E Novy

Hyunsic Choi

Eric A Steffen

Charles Landry

Nicole T Perna

John Brandon

Schuyler F Baldwin

Daniel A Nash

Jeremy D Glasner

Valerie Burland

Christopher D Herring

Richard D Nelson

Francesco Cerrina

Roland D Green

Michael Richard Sussman

Sangeet Singh-Gasson

Balint Csorgo

John L Schroeder

Terrance M Henker

Rod Welch

Timothy J Durfee

Kenneth C Dullea

Daniel Warren Van Der Weide

Sun Chang Kim

Jun Hyoung Lee

Tim Durfee

Luther E Lindler

Susan C Straley

Robert D Perry

Madalina Miskoski

George F Mayhew

Gregory V Plano

Jose A Sanchez

Debra J Rose

Christopher R Blattner

Jacqueline D Fetherston

Steven J Darnell

Nian Shi

Buffy Stahl

Carolyn F Allex

Jude W Shavlik

Michael Waterman

Donna L Daniels

Matthew R Larson

Amanda E Mitchell

Cristopher R Blattner

Trevor Twose

Charles F Landry

Guy D Plunkett

Twose Trevor

Roland Green

György Posfai

Trevor Martin Twose

Provided herein arehost strains with improved capacity for producing recombinant proteins.

Reduced genomelacking toxin-antitoxin genes

Provided herein are methods for the improved production of periplasmic-targeted recombinant proteins inhost strains. Also provided arehost strains with improved capacity for producing recombinant proteins.

Methods and compositions for improved expression of recombinant proteins

Systems and methods to automatically de novo assemble a set of unordered read sequences into one or more, larger nucleotide sequences are presented. The method involves first creating two identical sets of the reads, dividing each read in both sets into smaller sorted mer sequences and then comparing the mers for each read in set 1 to the mers from each read in set 2 to exhaustively identify overlapping segments. Overlap information is used to construct a modified assembly string graph, traversal of which produces a sorted string graph layout file consisting of all the reads ordered left to right including their approximate starting offset position. The sorted string graph layout file is then processed by a novel multiple sequence alignment system that uses mer matches between all the overlapping reads at a given position to place matching individual bases from each read into columns from which an overall consensus sequence is determined.

Systems and methods for de novo assembly of nucleotide sequence reads using a modified string graph

The present invention relates to the use of redox agents for purification of the CRM 197 variant of diphtheria toxin. The invention further relates to multi-step purification of CRM 197 from bacterial fermentates.

Purification of CRM 197 from bacteria

Methods and compositions for long term continuous flow fermentation using a two vessel continuous culture fermentation apparatus are described.

Materials and methods for extended continuous flow fermentation of reduced genome bacteria

The present invention is an accelerated conformational sampling method for predicting target peptide and protein structures comprising a process of determining energy minimized synthetic templates using a simple system for modeling individual molecular bonds within the subject peptide or protein. Use of these synthetic templates greatly reduces the computational resources necessary for optimally determining structural features of the target peptide or protein. The present invention also provides methods for rapid and efficient analysis of the effect of mutations on target peptides and proteins.

Protein structure prediction system

Systems and methods automatically identify a set of read sequences in one or more larger nucleotide sequences within a set of comparing sequences as a template. The sequences of each set are divided into smaller mer sequences and sorted to arrange the mer sequences in order, and the sets of mers originating from the read sequence set and the comparing sequence set are compared pairwise to determine matching regions between the sequences of the read sequence set and the sequences of the comparing set. The sorting of the sequence sets prior to the pairwise comparison reduces the amount of volatile memory required to assemble the read sequence set and also reduces the overall time to identify matches of the read sequence set in one or more larger nucleotide sequence databases.

Systems and methods for identifying nucleotide sequence matches

A two-vessel continuous flow system in conjunction with low mutation reduced genome bacterial strains provides a platform for long term extended fermentations. Such systems require modification of standard fermentation devices such as probes, pumps and monitoring systems as well as improved procedures for feed delivery, culture monitoring and product harvesting methods. An optimized two-vessel system for producing large quantities of fermentation products from small volume, long duration continuous fermentations represents a significant improvement over existing fermentation strategies. Methods and compositions for long term continuous flow fermentation using a two vessel continuous culture fermentation apparatus are described.

Rediced genome or native K12 strainbacteria comprising expression vectors encoding a recombinant CRM197 protein and their use in the production of CRM 197 is provided. The CRM 197 protein may be fused to a signal sequence that directs the expressed CRM197 protein to the periplasm of thehost.

Enhanced production of recombinant CRM197 in

Reduced genome bacteria with improved genetic stability are provided. Also provided are methods of producing polypeptides using the reduced genome bacteria with improved genetic stability.

Reduced genome bacteria with improved genetic stability

bacteria comprising genetic modifications to enhance fermentability and production of protein and nucleic acids are provided.

Bacteria with improved metabolic capacity

Systems and methods automatically assemble a set of read sequences into one or more larger nucleotide sequences using a set of comparing sequences as a template. The sequences of each set are divided into smaller mer sequences and sorted to arrange the mer sequences in order, and the sets of mers originating from the read sequence set and the comparing sequence set are compared pairwise to determine matching regions between the sequences of the read sequence set and the sequences of the comparing set. The sorting of the sequence sets prior to the pairwise comparison reduces the amount of volatile memory required to assemble the read sequence set and also reduces the overall time to assemble the read sequence set into one or more larger nucleotide sequences.

System for assembling a derived nucleotide sequence

Reduced genome strains ofMGl 655 are described. In various embodiments, the strains have one or more of equal or improved growth rate, transformation efficiency, protein expression, DNA production, DNA yield and/or DNA quality compared to the parental strain and commercially available strains.

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The present invention relates to novel strains of microorganisms with oxygen-regulated metabolism. The microorganisms have higher growth rates and are more efficient than parental strains. The microorganisms may be used to produce a variety of products of interests, such as recombinant proteins, nucleic acids, such as DNA, amino acids, and chemicals.

Oxygen-regulated microorganisms

Growing community of inventors

Madison, WI, United States of America

Frederick R Blattner