System and method for modulating a cell mediated immune response

• US 20060095211A1
• Filed: 08/26/2005
• Published: 05/04/2006
• Est. Priority Date: 08/24/2004
• Status: Abandoned Application

• Current Assignee: Searete LLC (Intellectual Ventures LLC)
• Original Assignee: Searete LLC (Intellectual Ventures LLC)
• Inventors: Ishikawa, Muriel Y., Myhrvold, Nathan P., Wood, Lowell L. Jr., Jung, Edward K.Y., Wilson, Richa
• Application Number:
  US11/213,325
• Publication Number:
  US 20060095211A1
• Time in Patent Office: Days
• US Class Current: 702/19
• CPC Class Codes: A61K 39/00 Medicinal preparations containing antigens or antibodies materials for immunoassay G01N33/53
• CPC Class Codes: G16B 10/00 ICT specially adapted for evolutionary bioinformatics, e.g. phylogenetic tree construction or analysis
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 20/30 Detection of binding sites or motifs
• CPC Class Codes: G16B 20/50 Mutagenesis
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 40/30 Unsupervised data analysis
• CPC Class Codes: G16B 5/00 ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16H 50/70 for mining of medical data, e.g. analysing previous cases of other patients
• CPC Class Codes: G16H 70/20 relating to practices or guidelines
• CPC Class Codes: G16H 70/40 relating to drugs, e.g. their side effects or intended usage
• CPC Class Codes: Y02A 50/30 Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change
• CPC Class Codes: Y02A 90/10 Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Abstract

The present application relates, in general, to a system and/or method related to detection and/or treatment.

Claims

1. A method, comprising:

presenting one or more computable epitopes of at least one agent;

predicting one or more computable pattern changes in the one or more computable epitopes of the at least one agent; and

designating the one or more computable epitopes including at least one pattern change for modulating at least a part of the at least one agent.

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75. A system, comprising:

circuitry for presenting one or more computable epitopes of at least one agent;

circuitry for predicting one or more computable pattern changes in the one or more computable epitopes of the at least one agent; and

circuitry for designating the one or more computable epitopes including at least one pattern change for modulating at least a part of the at least one agent.

78. The system of claim 75, wherein the circuitry for presenting one or more computable epitopes of at least one agent further comprises:

circuitry for presenting one or more computable epitopes of at least three amino acids.

79. The system of claim 75, wherein the circuitry for presenting one or more computable epitopes of at least one agent further comprises:

circuitry for presenting one or more computable epitopes of at least nine nucleotides.

80. The system of claim 75, wherein the circuitry for presenting one or more computable epitopes of at least one agent further comprises:

circuitry for presenting one or more computable epitopes of a target antigen.

82. The system of claim 75, wherein the circuitry for presenting one or more computable epitopes of at least one agent further comprises:

circuitry for presenting at least a portion of at least one of a living agent, a quasi-living agent, or a non-living agent.

85. The system of claim 75, wherein the circuitry for presenting one or more computable epitopes of at least one agent further comprises:

circuitry for presenting one or more computable epitopes displayed by the agent.

87. The system of claim 75, wherein the circuitry for presenting one or more computable epitopes of at least one agent further comprises:

circuitry for presenting one or more substantially linear computable epitopes.

88. The system of claim 75, wherein the circuitry for presenting one or more computable epitopes of at least one agent further comprises:

circuitry for presenting one or more substantially non-linear computable epitopes.

90. The system of claim 75, wherein the circuitry for presenting one or more computable epitopes of at least one agent further comprises:

circuitry for presenting a set of one or more computable epitopes of the at least one agent wherein the set includes one or more computable epitopes having a substantially similar functional sequence match with at least a portion of (a) the at least one agent or (b) a host.

91. The system of claim 75, wherein the circuitry for presenting one or more computable epitopes of at least one agent further comprises:

circuitry for presenting a set of one or more computable epitopes of the at least one agent wherein the set includes one or more computable epitopes having a substantially similar structural match with at least a portion of (a) the at least one agent or (b) a host.

93. The system of claim 75, wherein the circuitry for presenting one or more computable epitopes of at least one agent further comprises:

circuitry for presenting a set of one or more computable epitopes of the at least one agent wherein the set includes one or more computable epitopes having a substantially similar functional effect as at least a portion of (a) the at least one agent or (b) a host.

95. The system of claim 75, wherein the circuitry for predicting one or more computable pattern changes in the one or more computable epitopes of the at least one agent further comprises:

circuitry for predicting one or more computable pattern changes in the one or more computable epitopes associated with the transmission of the at least one agent.

97. The system of claim 75, wherein the circuitry for predicting one or more computable pattern changes in the one or more computable epitopes of the at least one agent further comprises:

circuitry for predicting at least one of a computable epitopic shift or a computable epitopic drift.

99. The system of claim 75, wherein the circuitry for predicting one or more computable pattern changes in the one or more computable epitopes of the at least one agent further comprises:

circuitry for predicting one or more computable pattern changes in the one or more computable epitopes associated with the transmission of the agent.

100. The system of claim 75, wherein the circuitry for predicting one or more computable pattern changes in the one or more computable epitopes of the at least one agent further comprises:

circuitry for predicting one or more computable pattern changes in the one or more computable epitopes associated with the transmission of the agent from a host.

102. The system of claim 75, wherein the circuitry for predicting one or more computable pattern changes in the one or more computable epitopes of the at least one agent further comprises:

circuitry for predicting one or more computable pattern changes including at least one point mutation, gene rearrangement, silent mutation, reassortment, domain swapping, or genetic mixing.

103. The system of claim 75, wherein the circuitry for predicting one or more computable pattern changes in the one or more computable epitopes of the at least one agent further comprises:

circuitry for predicting one or more computable pattern changes associated with a predicted course of an immune response.

104. The system of claim 75, wherein the circuitry for predicting one or more computable pattern changes in the one or more computable epitopes of the at least one agent further comprises:

circuitry for predicting one or more computable pattern changes associated with at least a part of a progression of an immune response.

105. The system of claim 75, wherein the circuitry for predicting one or more computable pattern changes in the one or more computable epitopes of the at least one agent further comprises:

circuitry for predicting one or more nucleotide changes in the one or more computable epitopes.

106. The system of claim 75, wherein the circuitry for predicting one or more computable pattern changes in the one or more computable epitopes of the at least one agent further comprises:

circuitry for predicting one or more amino acid changes in the one or more computable epitopes.

110. The system of claim 75, wherein the circuitry for predicting one or more computable pattern changes in the one or more computable epitopes of the at least one agent further comprises:

circuitry for predicting one or more computable pattern changes in response to a user input or a robotic input.

114. The system of claim 75, wherein the circuitry for designating the one or more computable epitopes including at least one pattern change for modulating at least a part of the at least one agent further comprises:

circuitry for designating one or more computable epitopes for binding at least one beta chain variable region of at least one T-cell.

116. The system of claim 75, wherein the circuitry for designating the one or more computable epitopes including at least one pattern change for modulating at least a part of the at least one agent further comprises:

circuitry for designating one or more computable epitopes for eliciting an antigen associated T-cell response.

121. The system of claim 75, further comprising:

circuitry for designating one or more computable epitopes for modulating a predicted host response.

122. The system of claim 75, further comprising:

circuitry for designating at least one immune response component for (a) modulating at least one of at least a portion of the at least one agent or for (b) modulating the predicted one or more computable pattern changes.

129. The system of claim 122, wherein the circuitry for designating at least one immune response component for (a) modulating at least one of at least a portion of the at least one agent or for (b) modulating the predicted one or more computable pattern changes further comprises:

circuitry for designating at least one immune response component specific for at least one computable epitope.

132. The system of claim 122, wherein the circuitry for designating at least one immune response component for (a) modulating at least one of at least a portion of the at least one agent or for (b) modulating the predicted one or more computable pattern changes further comprises:

circuitry for designating at least one modulator of at least one of (a) an epitopic shift or (b) an epitopic drift predicted in the at least one agent.

137. The system of claim 75, further comprising:

circuitry for designating a route of delivery for the one or more computable epitopes.

140. The system of claim 75, further comprising:

circuitry for including data from one or more databases for influencing at least one of said presenting, said predicting, or said designating.

142. The system of claim 140, wherein the circuitry for including data from one or more databases for influencing at least one of said presenting, said predicting or said designating further comprises:

circuitry for including data from at least one of a human database or a host database.

143. The system of claim 140, wherein the circuitry for including data from one or more databases for influencing at least one of said presenting, said predicting or said designating further comprises:

circuitry for including data from a pathogen database.

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135. The system of claim 134, wherein the circuitry for designating at least one interfering nucleic acid further comprises:

circuitry for designating one or more ribonucleotides.

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149. A system, comprising:

means for presenting one or more computable epitopes of at least one agent;

means for predicting one or more computable pattern changes in the one or more computable epitopes of the at least one agent; and

means for designating the one or more computable epitopes including at least one pattern change for modulating at least a part of the at least one agent.

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151. A program product, comprising:

at least one signal bearing medium including at least one of

one or more instructions for presenting one or more computable epitopes of at least one agent,

one or more instructions for predicting one or more computable pattern changes in the one or more computable epitopes of the at least one agent, and

one or more instructions for designating the one or more computable epitopes including at least one pattern change for modulating at least a part of the at least one agent.

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176. A system related to an immune response, comprising:

circuitry for specifying an agent; and

circuitry for presenting one or more epitopes of the specified agent.

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