Chemistry: molecular biology and microbiology – Micro-organism – tissue cell culture or enzyme using process... – Recombinant dna technique included in method of making a...
Reexamination Certificate
2000-01-31
2002-11-12
Park, Hankyel T. (Department: 1648)
Chemistry: molecular biology and microbiology
Micro-organism, tissue cell culture or enzyme using process...
Recombinant dna technique included in method of making a...
C530S350000, C536S023200
Reexamination Certificate
active
06479258
ABSTRACT:
CONTENTS
1. GENERAL
1.1. Field of the Invention
1.2. Background
1.3. Summary of the Invention
1.4. Brief Description of the Drawings
2. DETAILED DESCRIPTION OF THE INVENTION
2.1. Definitions
2.2. General Considerations & Formats for Recombination
2.3. Vectors Used in Genetic Vaccination
2.3.1. Viral Vectors
2.3.1.1. Adenoviruses
2.3.1.2. Adeno-Associated Virus (AAV)
2.3.1.3. Papilloma Virus
2.3.1.4. Retroviruses
2.3.2. Non-Viral Genetic Vaccine Vectors
2.4. Multicomponent Genetic Vaccines
2.4.1. Vector “AR”, Designed to Provide Optimal Antigen Release
2.4.2. Vector Components “CTL-DC”, “CTL-LC” and “CTL-MM”I Designed for Optimal Production of CTLs
2.4.3. Vectors “M” Designed for Optimal Release of Immune Modulators
2.4.4. Vectors “CK”, Designed to Direct Release of Chemokines
2.4.5. Other Vectors
2.5. Screening Methods
2.5.1. Screening for Vector Longevity or Translocation to Desired Tissue
2.5.1.1. Selection for Expression of Cell Surface-Localized Antigen
2.5.1.2. Selection for Expression of Secreted Antigen/Cytokine/Chemokine
2.5.2. Flow Cytometry
2.5.3. Additional In Vitro Screening Methods
2.5.4. Antigen Library Immunization
2.5.5. Screening for Optimal Induction of Protective Immunity
2.5.6. Screening of Genetic Vaccine Vectors that Activate Human Antigen-Specific Lymphocyte Responses
2.5.7. SCID-Human Skin Model for Vaccination Studies
2.5.8. Mouse Model for Studying the Efficiency of Genetic Vaccines in Transfecting Human Muscle Cells and Inducing Human Immune Responses in Vivo
2.5.9. Screening for Improved Delivery of Vaccines
2.5.10. Enhanced Entry of Genetic Vaccine Vectors into Cells
2.6. Optimization of Genetic Vaccine Components
2.6.1. Episomal Vector Maintenance
2.6.2. Evolution of Optimized Promoters for Expression of an Antigen
2.6.2.1. Constitutive Promoters
2.6.2.2. Cell-Specific Promoters
2.6.2.3. Inducible Promoters
2.6.3. Evolution of Binding Polypeptides that Enhance Specificity and Efficiency of Genetic Vaccines
2.6.4. Evolution of Bacteriophage Vectors
2.6.4.1. Evolution of Efficient Delivery of Bacteilgpliage Vehicles by Inhalation or Oral Delive
2.6.4.2. Evolution of Bacteriophage Vehicles for Efficient Homing to APCs
2.6.4.3. Evolution of Bacteriophage for Invasion of APCs
2.6.5. Evolution of Improved Immunomodulatory Sequences
2.6.5.1. Immunostimulatory DNA Sequences
2.6.5.2. Cytokines, Chemokines, and Accessory Molecules
2.6.5.3. Agonists or Antogonists of Cellular Receptors
2.6.5.4. Costimulatory Molecules Capable of Inhibiting or Enhancing Activation, Differentiation, or Anergy of Antigen-Specific T Cells
2.6.6. Evolution of Genetic Vaccine Vectors for Increased VAccination Efficacy and Ease of Vaccination
2.6.6.1. Topical Application of Genetic Vaccine Vectors
2.6.6.2. Enhanced Ability to Escape Host Immune System
2.6.6.3. Enhanced Antiviral Activity
2.6.6.4. Evolution of Vectors Having Increased Copy Number in Production Cells
2.7. Optimization of Transport and Presentation of Antigens
2.7.1. Proteasomes
2.7.2. Antigen Transport
2.7.3. Cytotoxic T-Cell Inducing Sequences and Immunogenic Agonist Sequences
2.8. Genetic Vaccine Pharmaceutical Compositions and Methods of Administration
2.9. Uses of Genetic Vaccines
2.9.1. Infectious Diseases
2.9.1.1. Bacterial Pathogens and Toxins
2.9.1.2. Viral Pathogens
2.9.2. Inflammatory and Autoimmune Diseases
2.9.3. Allergy and Asthma
2.9.4. Cancer
2.9.5. Parasites
2.9.6. Contraception
2.10. Malarial Antigens and Vaccines
2.10.1. Malarial Polypeptides
2.10.2. Malarial Nucleic Acids and Cells Capable of Expressing Same
2.10.3. Antibodies
2.10.4. Methods of Use
2.10.4.1. Diagnostic Applications
2.10.4.2. Screening Applications
2.10.4.3. Therapeutic and Prophylactic Applications
2.11. Directed Evolution Methods
2.11.1. Saturation Mutagenesis
2.11.2. Chimerizations
2.11.2.1. “Shuffling”
2.11.2.2. Exonuclease-Mediated Reassembly
2.11.2.3. Non-Stochastic Ligation Reassembly
2.11.2.4. End-Selection
2.11.3. Additional Screening Methods
3. LITERATURE CITED
GENERAL
1.1. Field of the Invention
This invention pertains to the field of genetic vaccines. Specifically, the invention provides multi-component genetic vaccines that contain components that are optimized for a particular vaccination goal. In a particular aspect this invention provides methods for improving the efficacy of genetic vaccines by providing materials that facilitate targeting of a genetic vaccine to a particular tissue or cell type of interest.
This invention also pertains to the field of modulation of immune responses such as those induced by genetic vaccines and also pertains to the field of methods for developing immunogens that can induce efficient immune responses against a broad range of antigens.
Thus, the present invention also relates generally to novel proteins, and fragments thereof, as well as nucleic acids which encode these proteins, and methods of making and using these proteins in diagnostic, prophylactic and therapeutic applications. In a particular exemplification, the present invention relates to proteins from the Plasmodium falciparum erythrocyte membrane protein 1 (“PfEMP1”) gene family and fragments thereof which are derived from malaria parasitized erythrocytes. In particular, these proteins are derived from the erythrocyte membrane protein of Plasmodium falciparum parasitized erythrocytes, also termed “PfEMP1”. The present invention also provides nucleic acids encoding these proteins, which proteins and nucleic acids are associated with the pathology of malaria infections, and which may be used as vaccines or other prophylactic treatments for the prevention of malaria infections, and/or in diagnosing and treating the symptoms of patients who suffer from malaria and associated diseases.
This invention also relates to the field of protein engineering. Specifically, this invention relates to a directed evolution method for preparing a polynucleotide encoding a polypeptide. More specifically, this invention relates to a method of using mutagenesis to generate a novel polynucleotide encoding a novel polypeptide, which novel polypeptide is itself an improved biological molecule &/or contributes to the generation of another improved biological molecule. More specifically still, this invention relates to a method of performing both non-stochastic polynucleotide chimerization and non-stochastic site-directed point mutagenesis.
Thus, in one aspect, this invention relates to a method of generating a progeny set of chimeric polynucleotide(s) by means that are synthetic and non-stochastic, and where the design of the progeny polynucleotide(s) is derived by analysis of a parental set of polynucleotides &/or of the polypeptides correspondingly encoded by the parental polynucleotides. In another aspect this invention relates to a method of performing site-directed mutagenesis using means that are exhaustive, systematic, and non-stochastic.
Furthermore this invention relates to a step of selecting from among a generated set of progeny molecules a subset comprised of particularly desirable species, including by a process termed end-selection, which subset may then be screened further. This invention also relates to the step of screening a set of polynucleotides for the production of a polypeptide &/or of another expressed biological molecule having a useful property.
Novel biological molecules whose manufacture is taught by this invention include genes, gene pathways, and any molecules whose expression is affected thereby, including directly encoded polypetides &/or any molecules affected by such polypeptides. Said novel biological molecules include those that contain a carbohydrate, a lipid, a nucleic acid, &/or a protein component, and specific but non-limiting examples of these include antibiotics, antibodies, enzymes, and steroidal and non-steroidal hormones.
In a particular non-limiting aspect, the present invention relates to enzymes, particularly to thermostable enzymes, and to their generation by directed evolution. More particularly, the present invention relates to thermostable enzymes which are stable at high temperatures and which h
Diversa Corporation
Gray Cary Ware & Freidenrich LLP
Haile Lisa A.
Park Hankyel T.
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