Medicaments in the form of therapeutic molecules including inflammatory modulators are designed and selected. A target site is on Interleukin 13 (IL-13) in which a glycosaminoglycan (GAG) molecule or polyanionic glycoconjugate or anionic polysaccharide modulates IL-13 activity or function. The target site can include amino acids located in the AB loops and/or helix D of human IL-13 or its homolog or derivative. The IL-13 target site is used to design a medicament for modulating physiological processes. Therapeutic and prophylactic compositions can include the designed medicaments.

The disclosure provides a general method for the production of protein variants with a reduced aggregation propensity without affecting the thermodynamic stability of the variant with respect to the wild-type protein.

Methods and compositions related to the selective, specific disruption of multiple ligand-receptor signaling interactions, such as ligand-receptor interactions implicated in disease, are disclosed. These interactions may involve multiple cytokines in a single receptor family or multiple ligand receptor interactions from at least two distinct ligand-receptor families. The compositions may comprise polypeptides having composite sequences that comprise sequence fragments of two or more ligand binding sites. The methods and compositions may involve sequence fragments of two or more ligand binding sites that are arranged to conserve the secondary structure of each of the ligands from which the sequence fragments were taken.

The present invention relates to novel short interfering RNA (siRNA) molecules that are multi-targeted. More specifically, the present invention relates to siRNA molecules that target two or more sequences. In one embodiment, multi-targeting siRNA molecules are designed to incorporate features of siRNA molecules and features of micro-RNA (miRNA) molecules. In another embodiment, multi-targeting siRNA molecules are designed so that each strand is directed to separate targets.

A method for selectively obtaining a natural variant of an enzyme having activity includes (1) a step of detecting an ORF sequence of a protein having enzyme activity from a genome database including base sequences of metagenomic DNA of environmental microbiota; (2) a step of obtaining at least one PCR clone including the ORF sequence having a full length, a partial sequence of the ORF sequence, or a base sequence encoding an amino acid sequence which is formed by deletion, substitution, or addition of at least one amino acid residue in an amino acid sequence encoded by the ORF sequence, by performing PCR cloning on at least one metagenomic DNA of the environmental microbiota by using a primer designed based on the ORF sequence; (3) a step of determining a base sequence and an amino acid sequence which is encoded by the base sequence for each PCR clone obtained in the step (2); and (4) a step of selecting a natural variant of an enzyme having activity by measuring enzyme activity of proteins encoded by each PCR clone obtained in the step (2).

In alternative embodiments the invention provides libraries of compounds, or drugs or drug candidates, manufactured and selected for having a desired property such as a biological or a chemical activity, and methods for making and using them. In one embodiment, the invention provides methods for identifying desirable compounds from very large compound sets using a compound fragment as the query. In alternative embodiments, the invention provides methods of making compounds, and libraries of compounds, using a feasible reaction growth scheme.

Disclosed are methods and tools for rapidly aligning reads to a reference sequence. These methods and tools employ Bloom filters or similar set membership testers to perform the alignment. The reads may be short sequences of nucleic acids or other biological molecules and the reference sequences may be sequences of genomes, chromosomes, etc. The Bloom filters include a collection of hash functions, a bit array, and associated logic for applying reads to the filter. Each filter, and there may be multiple of these used in a particular application, is used to determine whether an applied read is present in a reference sequence. Each Bloom filter is associated with a single reference sequence such as the sequence of a particular chromosome. In one example, chromosomal abundance is determined by aligning reads from a sequencer to multiple chromosomes, each having an associated Bloom filter or other set membership tester.

Described are techniques for determining population structure from identity-by-descent (IBD) of individuals. The techniques may be used to predict that an individual belongs to zero, one or more of a number of communities identified within an IBD network. Additional data may be used to annotate the communities with birth location, surname, and ethnicity information. In turn, these data may be used to provide to an individual a prediction of membership to zero, one or more communities, accompanied by a summary of the information annotated to those communities.

The invention describes a method for identifying T-cell activating neo-epitopes from all genetically altered proteins. The mutated proteins contribute to neo-epitopes after they are proteolytically degraded within antigen presenting cells, such as dendritic cells and macrophages.

A fluid identification system comprising a plurality of particles, each particle encapsulating therein at least one tracer material having an identifiable DNA, the at least one tracer material being encapsulated by an encapsulation material, wherein the particles are adapted to retain the at least one tracer material in an encapsulated form after exposure of the particles to a temperature of at least 75? C. and/or a pressure of at least 1000 psi (6.9?10.sup.6 N/m.sup.2).