Abstract: Provided herein are E. coli host strains with improved capacity for producing recombinant proteins.

Abstract: Provided herein are E. coli host strains with improved capacity for producing recombinant proteins.

Abstract: Provided herein are methods for the improved production of periplasmic-targeted recombinant proteins in E. coli host strains. Also provided are E. coli host strains with improved capacity for producing recombinant proteins.

Abstract: 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.

Abstract: 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.

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

Abstract: 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.

Abstract: 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.

Abstract: 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.

Abstract: Provided herein are methods for the improved production of periplasmic-targeted recombinant proteins in E. coli host strains. Also provided are E. coli host strains with improved capacity for producing recombinant proteins.

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

Abstract: 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.

Abstract: 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.

Abstract: Rediced genome or native K12 strain E. coli bacteria 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 the E. coli host.

Abstract: 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.

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

Abstract: 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.

Abstract: 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.

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

Abstract: 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.