Abstract: The invention provides methods and compositions relating to cells having altered functions, and the nucleic acids that impart those functions. Altered cellular function arises from in vivo directed recombination of genetic elements to yield a recombined nucleic acid. These methods and compositions may utilize altered host cells having altered recombination enzyme profiles and/or altered recombination sites. The invention involves in some aspects methods for assembling nucleic acid molecules, such as genomic DNA. Aspects of the invention also provide kits, compositions, devices, and systems for generating novel recombined nucleic acids and cells having altered cell function.

Abstract: A system and method for aiding in the design of molecular constructs is provided. A feature set associated with a molecular building block in a construct may be determined, wherein the feature set may comprise data indicative of third party rights that restrict use of the molecular segment or the lack of such rights. The method may include steps of defining a molecular structure for use in the construct; searching a database including a plurality of molecular structures and a plurality of rights, each right of the plurality of rights associated with each of the plurality of molecular structures; and displaying rights associated with the defined molecular structures in response to the search of said database.

Abstract: Certain aspects of the present invention provide methods for assembling nucleic acid molecules. Some embodiments involve analyzing nucleic acid sequences and determining appropriate assembly strategies based on the presence or absence of sequence features that are known or predicted to interfere with extension-based and/or ligation-based assembly techniques. Aspects of the invention also provide kits, compositions, devices, and systems for assembling synthetic nucleic acids using polymerase-based techniques, ligase-based techniques, or combinations thereof.

Abstract: Aspects of the invention provide compositions and methods for displaying engineered polypeptides on a cell surface. According to aspects of the invention, immobilized polypeptides can be screened to identify one or more variants having one or more functional or structural properties of interest. Aspects of the invention provide composition and methods for producing engineered protein or protein variants having a functional or a structural property of interest.

Abstract: Aspects of the invention relate to the design and synthesis of nucleic acid libraries containing non-random mutations or variants. Aspects of the invention provide methods for assembling libraries containing high densities of predetermined variant sequences. Certain embodiments relate to the design and synthesis of nucleic acid libraries that express a predetermined polypeptide from a library of nucleic acids having silent sequence variants. Certain embodiments relate to the design and synthesis of nucleic acid libraries that express predetermined RNA variants that encode the same polypeptide sequence.

Abstract: Aspects of the invention relate to the design and synthesis of nucleic acid libraries. Certain embodiments relate to the design and synthesis of nucleic acid libraries that express polypeptides. In some embodiments, the invention provides methods for analyzing polypeptide sequences and identifying those that may confer undesirable properties in vivo (e.g., poor solubility, high immunogenicity, low stability, etc.). In some embodiments, the invention provides methods for synthesizing a library of nucleic acids having predetermined sequences (e.g., a library of nucleic acids that encode polypeptides having related sequences with predetermined sequence variations).

Abstract: The present invention provides recombination based methods for assembling nucleic acids. In certain aspects the present invention provides hierarchical assembly methods for producing genome sized polynucleotide constructs. The methods may be used for assembling large polynucleotide constructs, for synthesizing synthetic genomes, or for introducing a plurality of nucleotide changes throughout the genome of an organism. In another aspect, the invention provides cells having increased genomic stability. For example, cells comprising alterations in at least a substantial portion of the transposons in the genome are provided.

Abstract: An isolated chemokine is disclosed. The isolated chemokine is expressed preferentially in breast tissue or can be detected in breast milk. It includes from about 100 to about 132 amino acids, has a deduced molecular weight of from about 10 to about 16 kDa, and has a deduced isoionic point of from about pH 10.1 to about pH 10.7. Antibodies and binding portions thereof recognizing the subject chemokine and peptides which include the antigenic portions of the subject chemokines are described. DNA molecules which encode the subject chemokines as well as nucleic acid molecules which, under stringent conditions, hybridize to nucleic acid molecules encoding the subject chemokines or to a complement thereof are also disclosed.

Abstract: An isolated chemokine is disclosed. The isolated chemokine is expressed preferentially in breast tissue or can be detected in breast milk. It includes from about 100 to about 132 amino acids, has a deduced molecular weight of from about 10 to about 16 kDa, and has a deduced isoionic point of from about pH 10.1 to about pH 10.7. Antibodies and binding portions thereof recognizing the subject chemokine and peptides which include the antigenic portions of the subject chemokines are described. DNA molecules which encode the subject chemokines as well as nucleic acid molecules which, under stringent conditions, hybridize to nucleic acid molecules encoding the subject chemokines or to a complement thereof are also disclosed.

Abstract: An isolated chemokine is disclosed. The isolated chemokine is expressed preferentially in breast tissue or can be detected in breast milk. It includes from about 100 to about 132 amino acids, has a deduced molecular weight of from about 10 to about 16 kDa, and has a deduced isoionic point of from about pH 10.1 to about pH 10.7. Antibodies and binding portions thereof recognizing the subject chemokine and peptides which include the antigenic portions of the subject chemokines are described. DNA molecules which encode the subject chemokines as well as nucleic acid molecules which, under stringent conditions, hybridize to nucleic acid molecules encoding the subject chemokines or to a complement thereof are also disclosed.

Abstract: The invention relates to compositions of matter capable of serving as residues for specific binding of third strands to double-stranded complementary nucleic acids of any base-pair sequence.

Abstract: An isolated chemokine is disclosed. The isolated chemokine is expressed preferentially in breast tissue or can be detected in breast milk. It includes from about 100 to about 132 amino acids, has a deduced molecular weight of from about 10 to about 16 kDa, and has a deduced isoionic point of from about pH 10.1 to about pH 10.7. Antibodies and binding portions thereof recognizing the subject chemokine and peptides which include the antigenic portions of the subject chemokines are described. DNA molecules which encode the subject chemokines as well as nucleic acid molecules which, under stringent conditions, hybridize to nucleic acid molecules encoding the subject chemokines or to a complement thereof are also disclosed.

Abstract: An isolated chemokine is disclosed. The isolated chemokine is expressed preferentially in breast tissue or can be detected in breast milk. It includes from about 100 to about 132 amino acids, has a deduced molecular weight of from about 10 to about 16 kDa, and has a deduced isoionic point of from about pH 10.1 to about pH 10.7. Antibodies and binding portions thereof recognizing the subject chemokine and peptides which include the antigenic portions of the subject chemokines are described. DNA molecules which encode the subject chemokines as well as nucleic acid molecules which, under stringent conditions, hybridize to nucleic acid molecules encoding the subject chemokines or to a complement thereof are also disclosed.

Abstract: Disclosed are methods and compositions for stimulating cellular nitric oxide (NO) synthesis, cyclic guanosine monophosphate levels (cGMP), and protein kinase G (PKG) activity for purposes of treating diseases mediated by deficiencies in the NO/cGMP/PKG signal transduction pathway, by administration of various compounds including alcohols, diols and/or triols and their analogues.

Abstract: Methods, compositions and kits for effecting homologous recombination are described. In one aspect, the method utilizes two introduced DNAs: (1) a mutagen-linked single-stranded oligonucleotide capable of specifically binding to double-stranded DNA to form a triple-stranded helix, and (2) a donor DNA fragment capable of undergoing homologous recombination with DNA targeted by the oligonucleotide.

Abstract: Transforming growth factor .beta. (TGF-.beta.) is produced in relatively large quantities and at a relatively high purity by fermentation in a perfusion microcarrier reactor. Conditioned media from the reactor is first treated to provide the active form of TGF-.beta. and subsequently purified by cation exchange chromatography followed by hydrophobic interaction chromatography. Optionally, nucleic acids complexed with the TGF-.beta. may be removed while the protein is bound to the cation exchange resin.

Abstract: Methods for recovering t-PA from a liquid medium are disclosed. The methods comprise contacting a liquid medium with at least one substrate capable of effecting a separation of intact t-PA from degraded t-PA thereafter recovering the intact t-PA free from other unrelated protein. The present invention also provides compounds produced by this method, compounds comprising intact one-chain t-PA and pharmaceutical compositions containing them and methods for using such compositions.

Abstract: T. Cruzi polypeptide antigens that react with serum from chagasic individuals and does not cross-react with serum from uninfected individuals or individuals infected with related parasites such as Leishmania is described. The DNA from T. Cruzi culture trypomastigotes and epimastigotes coding for antigenic material having a molecular weight of 70 kd is identified, sequenced, and inserted into a cloning vector, which, in turn, is inserted into a host cell line. The expressed polypeptide is immunologically reactive with sera from Chagas' disease infect patients. The cloned gene for the 70 kd polypeptide is expressed and purified and a diagnostic test for Chagas' disease comprising the synthesized polypeptide is described.

Abstract: Methods for detecting fibrin or fibrin clots in a host suspected of producing fibrin by: introducing labeled tissue plasminogen activator or a binding site fragment derived therefrom into the host's bloodstream and assaying for the presence of concentrations of labeled tissue plasminogen activator in said host. Also provided are kits for practicing the invention.