Abstract: Markers of caloric restriction (CR) can be identified in a selected tissue by exposing an animal to CR conditions and selecting one or more genes differentially expressed in response to CR conditions in multiple subject groups. A candidate compound can be screened for likely ability to mimic the effects of CR when administered to an animal by comparing the tissue levels of expression products of the genes in animals treated with the candidate compound to those of animals subjected to CR.

Abstract: Focused libraries of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of antibody peptides, polypeptides or proteins and collectively display, display and express, or comprise at least a portion of the focused diversity of the family. The libraries have length and sequence diversities that mimic that found in native human antibodies.

Abstract: A compound synthesis method includes bonding a first compound to a substrate to form a first film. A second film is formed on the first film using an acid-transfer composition including (A) a polymer that includes a structural unit shown by a following formula (1) and a structural unit shown by a following formula (2), (B) a photoacid generator shown by a following formula (3), and (C) a sensitizer shown by a following formula (4). The second film is exposed to remove the protecting group from the first compound under an exposed area of the second film. An acid generated in the exposed area of the second film is transferred to the first film. The second film after being exposed is removed. A second compound is bonded to the first compound from which the protecting group has been removed.

Abstract: The present invention provides reagents and methods for breast cancer detection.

Abstract: Described herein are a group of 1,013 genes and 1 phenotypic variable are identified as candidate predictors that differentiated smokers (current or former) with or without COPD. The full predictor set can be reduced to a nine-gene classifier (IL6R, CCR2, PPP2CB, RASSF2, WTAP, DNTTIP2, GDAP1, LIPE, and RPL14) with similar performance. Also described herein is the use of the full predictor set and the reduced nine gene set in methods of diagnosing lung disease or an increased risk of developing lung disease, such as COPD, in a subject. Also described herein is the use of the full predictor set and the reduced nine gene set in methods of providing a prognosis for a subject with lung disease, such as COPD.

Abstract: Identified herein are different forms of bitter receptor genes that occur in different humans. These alleles are generated by numerous coding single nucleotide polymorphisms (cSNP's) that occur within the members of the T2R gene family. Some SNP's cause amino acid substitutions, while others introduce chain termination codons, rendering the allele non-functional. Differences in these genes are believed to have a large effect on those individuals' sense of bitter taste, such that these individuals perceive the taste of bitter substances differently than the rest of the population. The ability to assay this allelic information is useful in the development of flavorings and flavor enhancers, as it can be used to define large groups and populations who perceive bitter tastes differently. This in turn allows the taste preferences of these groups to be addressed at the molecular level for the first time.

Abstract: Methods and compositions involving molecular markers for the detection and characterization of cancer in a patient are provided.

Abstract: A plurality of probes are immobilized on a carrier for detecting food poisoning bacteria, the plurality of probes being selected, either alone or in combination, respectively from two or more groups among a first probe group for detecting Escherichia coli including probes that respectively have base sequences of SEQ ID NO: 1 to 6, and probes that respectively have base sequences complementary to the base sequences of SEQ ID NO: 1 to 6 (hereinafter referred to as “complementary probes”), a second probe group for detecting Listeria including probes that respectively have base sequences of SEQ ID NO: 7 to 13, and complementary probes, a third probe group for detecting Campylobacter including probes that respectively have base sequences of SEQ ID NO: 14 to 19, and complementary probes, a fourth probe group for detecting Vibrio parahaemolyticus including probes that respectively have base sequences of SEQ ID NO: 20 to 24, and complementary probes, a fifth probe group for detecting Staphylococcus aureus including p

Abstract: Methods are provided for evaluating an oocyte for fertilization and implantation. For example, methods are provided for determining whether an oocyte expresses, or does not express, one or more of a group of markers identified as differently expressed between chromosomally normal and chromosomally abnormal oocytes. Also provided, for example, are methods for determining whether a cumulus cell expresses, or does not express, one or more of a group of markers identified as differently expressed between cumulus cells associated with chromosomally normal oocytes and cumulus cells associated with chromosomally abnormal oocytes. Methods are provided for the detection of marker expression of differentially expressed genes at the RNA level, as well as at the protein level.

Abstract: The present invention concerns in vitro methods for predicting or monitoring whether a patient affected by a cancer is responsive to a treatment with a molecule of the taxoid family based on a resistance expression signature, kits for performing the methods, and methods for screening or identifying a compound suitable for improving the treatment of a cancer with a molecule of the taxoid family or for reducing the resistance development during the treatment of a cancer with the molecule of the taxoid family.

Abstract: The present invention provides a linker preferably used when constructing an mRNA/cDNA-puromycin-protein conjugate used in an in vitro virus method, and an mRNA/cDNA-puromycin-protein conjugate constructed using that linker. More specifically, the present invention provides a linker for ligating mRNA and puromycin or a puromycin-like compound to construct an mRNA/cDNA-puromycin-protein conjugate, the linker comprising a single-stranded RNA as a main backbone, and having, in this main backbone, a solid phase binding site for binding an mRNA-puromycin-protein conjugate to a solid phase site, and a pair of cleavage sites provided at locations surrounding the solid phase binding site; an mRNA-puromycin-protein conjugate constructed using this linker; an mRNA bead or an mRNA chip comprising this conjugate; a protein chip produced from this mRNA chip; and a diagnostic kit using the mRNA bead or the mRNA chip.

Abstract: Biomarkers, kits, and diagnostic and treatment methods for idiopathic pulmonary fibrosis are provided.

Abstract: Methods for prognosis and diagnosis of dysplasia and cancer are disclosed. In particular, the invention relates to the use of the biomarker PERP, a desmosome protein involved in cell adhesion and apoptosis, for aiding diagnosis, prognosis, and treatment of dysplasia and cancer.

Abstract: The invention relates to a method for generating a gene mosaic by somatic in vivo recombination, comprising: e) in a single step procedure (vii) transforming a cell with at least one gene A having a sequence homology of less than 99.5% to another gene to be recombined that is an integral part of the cell genome or presented in the framework of a genetic construct, (viii) recombining said genes, (ix) generating a gene mosaic of the genes at an integration site of a target genome, wherein said at least one gene A has a single flanking target sequence either at the 5? end or 3? end anchoring to the 5? or 3? end of said integration site, and f) selecting clones comprising the gene mosaic, as well as a method of producing a diversity of gene mosaics and gene assembly.

Abstract: A method for predicting the sensitivity of tumor cells to an anthracycline-based chemotherapy includes determining the differential expression level of a MYBL2 gene in tumors cells. A polynucleotide library is useful to predict the sensitivity of tumor cells to an anthracycline-based chemotherapy and includes a pool of polynucleotide sequences or subsequences thereof wherein the sequences or subsequences correspond substantially to any of the polynucleotide sequences SEQ ID No: 308, SEQ ID No: 309 and/or SEQ ID No: 310 or the complements thereof.

Abstract: The present invention relates to a method for assessing the endometrium receptivity of a patient, comprising a step consisting of measuring the expression level of eleven genes in an endometrial biopsy sample obtained from said patient wherein said genes are MFAP5, ANGPTL1, PROK1, NLF2, LAMB3, BCL2L10, CD68, TRPC4, SORCS1, FST and KRT80.

Abstract: Libraries of nucleic acids encoding chimeric binding polypeptides based on plant scaffold polypeptide sequences. Also described are methods for generating the libraries.

Abstract: Focused libraries of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of antibody peptides, polypeptides or proteins and collectively display, display and express, or comprise at least a portion of the focused diversity of the family. The libraries have length and sequence diversities that mimic that found in native human antibodies.

Abstract: The invention provides methods and compositions for attaching oligonucleotide tags to polynucleotides for the purpose of carrying out analytical assays in parallel and for decoding the oligonucleotide tags of polynucleotides selected in such assays. Words, or subunits, of oligonucleotide tags index submixtures in successively more complex sets of submixtures (referred to herein as “tiers” of submixtures) that a polynucleotide goes through while successive words are added to a growing tag. By identifying each word of an oligonucleotide tag, a series of submixtures is identified including the first submixture that contains only a single polynucleotide, thereby providing the identity of the selected polynucleotide. The analysis of the words of an oligonucleotide tag can be carried out in parallel, e.g.

Abstract: The invention relates to amino acid residues within an immunoglobulin light chain amino acid sequence (VL) which stabilize the monomeric state of the immunoglobulin single variable domain. In particular, but not exclusively, the invention describes a number of mutations that stabilize the monomeric state of DPK9 framework V? domain antibodies.

Abstract: Focused aptamer libraries are constructed in accordance with a proteome (i.e., complex mixture of native biomolecules). The libraries may be screened to identify one or more candidate aptamers with desired biological activities other than specific binding to a target. Aptamers which are selected or derivatives thereof may be used for those specific activities in biological systems. Any combination of deconvoluting a focused library (functional profiling), increasing frequencies of particular aptamers in a focused library (Laser SELEX), and decreasing frequencies of particular aptamers in a focused library (DeSELEX) may be performed prior to assaying biological activity.

Abstract: The invention relates to novel marker sequences for Alzheimer's disease, in particular Alzheimer's dementia, and their diagnostic use including a screening method in order to identify potential drugs for the treatment/prophylaxis of Alzheimer's disease by means of the said novel marker sequences. Moreover, the invention relates to a diagnostic device comprising said novel marker sequences for diagnosing Alzheimer's disease, particularly a protein array (chip) and its use hereto.

Abstract: The invention relates to a procedure for linking cognate pairs of VH and VL encoding sequences from a population of cells enriched in particular surface antigen markers. The linking procedure involves a multiplex molecular amplification procedure capable of linking nucleotide sequences of interest in connection with the amplification, in particular polymerase chain reaction (multiplex PCR). The method is particularly advantageous for the generation of cognate pair libraries as well as combinatorial libraries of variable region encoding sequences from immunoglobulins. The invention also relates to methods for generation of chimeric human/non-human antibodies and expression libraries generated by such methods.

Abstract: The invention relates to a method of producing an oligonucleotide library comprising a plurality of oligonucleotides, each oligonucleotide in the library having at least one predetermined position, a randomization codon selected from a defined group of codons, the codons within the defined group coding for different amino acids. Vector, host cells containing such libraries and kits for the production of such libraries are also provided.

Abstract: Antigen-specific immunoglobulin V-regions are identified from a library of nucleic acids amplified using polymerase chain reaction using leader sequence-specific forward primers. The use of leader sequence primers allows all V-region sequences to be amplified (including those with extensive 5? end mutations) without loss of the original 5? V gene segment sequence. A second V-region library is made using a larger than conventional set of 5? V-region primers. The sequence errors introduced into the amplification products by this method are corrected using sequence information obtained in the products amplified by the V-region primers to screen the library created using the leader sequence primers. Amino acid sequence information from fragments of donor immunoglobulins can be used to assist in the identification of nucleic acids encoding the heavy and light chains of donor antibodies as well as to design primers to amplify such nucleic acids.

Abstract: The present invention refers to novel hetero-multimeric proteins obtained from modified ubiquitin capable of binding the extradomain B of fibronectin (ED-B) with high affinity. Furthermore, the invention refers to fusion proteins comprising said recombinant protein fused to a pharmaceutically and/or diagnostically active component. The invention is further directed to the use of said proteins in medical treatment methods.

Abstract: Mutations of the epidermal growth factor receptor (EGFr), of phosphatidylinositol 3?-kinase (“PI3K”), and of B-Raf are described. Methods of treating tumors containing mutated EGFr with human monoclonal antibodies against EGFr are described. Methods and kits for ascertaining the presence of one or more mutant EGFr, mutant PI3K, and/or mutant B-Raf in a sample and for treating disorders or conditions related to the presence of mutant EGFr, mutant PI3K, and/or mutant B-Raf are also described. Methods of treating tumors containing mutant EGFr, mutant PI3K, and/or mutant B-Raf are also described.

Abstract: A method is described to identify secreted proteins identified with stages of malignancy of cancer. The proteins are initially identified by trapping them with a fluorescent protein containing vector that can insert in any gene. The secreted proteins are initially identified by their fluorescence. Secreted proteins identifying tumors with specific degrees of malignancy are isolated to determine if they can serve as markers of cancer progression.

Abstract: The invention relates to a procedure for linking cognate pairs of VH and VL encoding sequences from a population of cells enriched in particular surface antigen markers. The linking procedure involves a multiplex molecular amplification procedure capable of linking nucleotide sequences of interest in connection with the amplification, in particular polymerase chain reaction (multiplex PCR). The method is particularly advantageous for the generation of cognate pair libraries as well as combinatorial libraries of variable region encoding sequences from immunoglobulins. The invention also relates to methods for generation of chimeric human/non-human antibodies and expression libraries generated by such methods.

Abstract: The present invention is directed to the preparation and use of a collection of antibody heavy chain complementarity determining region 3 (HCDR3) members, where diversity of the collection is a function of the length of the HCDR3 members. The diversity of the collection of HCDR3 regions substantially represents the natural amino acid distribution of HCDR3 in the human repertoire. This natural amino acid distribution can be represented by biasing the complete random distribution of amino acids, accordingly, in the HCDR3 encoding DNA sequence by using trinucleotide mutagenesis (TRIM) technology. A collection of HCDR3 members of the invention each can be comprised within a variable region of an antibody (or fragment thereof) to form a library of synthetic antibodies or antibody fragments. The invention also provides nucleic acid molecules encoding such diverse collection and methods of making and using the same.

Abstract: The present invention concerns the identification of individuals that have triple negative breast cancer and/or identification of an appropriate treatment therefor. In certain cases, the identification includes determining the expression levels of a multitude of genes.

Abstract: The invention relates to the use of an inhibitor of one of the following polypeptides, wherein the polypeptide is represented by the following sequences selected from the following group SEQ ID NO:1-32, each of the polypeptide being preferably as identified in claim 1 as a medicament, preferably for preventing, delaying and/or treating metastasis in a cancer patient. The invention also relates to a diagnostic portfolio comprising or consisting of isolated nucleic acid sequences, their complement or portions thereof, of a combination of genes selected from the groups consisting of genes represented by the following sequences SEQ ID NO:1-32 or SEQ ID NO:1-169.

Abstract: Focused libraries of vectors or genetic packages that display, display and express, or comprise a member of a diverse family of antibody peptides, polypeptides or proteins and collectively display, display and express, or comprise at least a portion of the focused diversity of the family. The libraries have length and sequence diversities that mimic that found in native human antibodies.

Abstract: Methods to improve the tropism or other features of a virus are disclosed. Such methods can be used to prepare, e.g., DNA or plasmid libraries of variants of a gene encoding a viral capsid or envelope protein having a randomly inserted restriction site, libraries of viral clones with such variant genes with a randomly inserted restriction site or polypeptide sequence targeting a receptor expressed by a specific type of mammalian cells. Described are also methods to prepare mosaic viruses, i.e., viral particles wherein copies of one or more capsid or envelope proteins originate from different sources. These methods can be used to prepare mosaic viruses of a specific mixture of wild-type and mutant proteins, or of different types of mutant proteins.

Abstract: Methods for improving antibodies by a variety of DNA diversification and selection procedures are provided. Improvements include increases in affinity, alterations in specificity and effector function, as well as reduced antigenicity, e.g. humanization. Libraries of recombinant antibody sequences are provided, as are cells expressing members of such libraries. Novel phage display vectors are provided. Methods for the coevolution of an antibody and its cognate antigen are provided. Coevolution is used to evolve HIV envelope proteins with increased antigenicity and broadly neutralizing antibodies that interact therewith. Methods of improving antibodies for use in the detection of biological warfare agents are provided.

Abstract: Compositions and methods for the diagnosis, treatment and prevention of prostate cancer, as well as for treatment selection.

Abstract: The present invention provides a method for identifying a modulator or mediator of a biological activity, which activity includes antigenicity and or immunogenicity, said method comprising the step of: (i) producing a gene fragment expression library derived from defined nucleotide sequence fragments; and (ii) assaying the expression library for at least an amino acid sequence derived from step (i) for a biological activity wherein that activity is different from any activity the amino acid sequence may have in its native environment.

Abstract: In alternative embodiments, the invention provides phosphatidylinositol-specific phospholipase C (PI-PLC) enzymes, nucleic acids encoding them, antibodies that bind specifically to them, and methods for making and using them. Industrial methods and products comprising use of these phospholipases are also provided. In certain embodiments, provided herein are methods for hydration of non hydratable phospholipids (NHPs) within a lipid matrix. The methods enable migration of NHPs to an oil-water interface thereby allowing the NHPs to be reacted and/or removed from the lipids. In certain embodiments, provided is a method for removing NHPs, hydratable phospholipids, and lecithins from vegetable oils to produce a degummed oil or fat product that can be used for food production and/or non-food applications. In certain embodiments, provided herein are methods for hydration of NHPs followed by enzymatic treatment and removal of various phospholipids and lecithins.

Abstract: Herein is described a bacterial microcompartment catalog comprising a total of 634 gene sequences encoding bacterial microcompartments, the proteins of each can be inserted into a host organism and if needed, expressed using an inducible expression system. Disclosed are at least 32 types of gene clusters which provide microcompartments having metabolizing or other enzyme activity. The expression of these microcompartments can be used to provide or enhance an organism's carbon fixation and/or sequestration activity or biomass production or, generally speaking additional or enhanced metabolic activities to an organism.

Abstract: Described herein are compositions and methods for combinatorial metabolic pathway optimization.

Abstract: Disclosed are molecular diagnostic compositions and methods for predicting brain metastasis of breast cancer, as well as methods for drug repositioning to identify existing and new therapeutics for use in developing individualized, patient-specific treatment regimens for improving diagnoses and patient outcomes in individuals at risk for brain metastasis of breast cancer.

Abstract: A method and device is disclosed for increasing droplet and micro-well reactor densities per unit area for microfluidic platforms. The device and method use controlled Height to Droplet Diameter Ratios (HDR) of the collection region which can produce different crystalline packing formations. HDR ratios above unity and less than about 2.65 are used to create a variety of three-dimensional packing schemes with increased density over conventional single layer hexagonal packing.

Abstract: Compounds and methods for controlling the surface properties are described. Compounds of the invention can form radicals upon exposure to irradiation, which can then react with nearby molecules to alter the surface properties of various substrates. The invention can provide surfaces that are resistant to dewetting, surfaces that have immobilized molecules such as carbohydrates and polymers immobilized, and surfaces that have metals deposited on the surface. The invention can be utilized in a wide range of application, such as sensors, microreactors, microarrays, electroless deposition of metals, and the like.

Abstract: Provided is a method and system for screening chemical compounds or compositions, wherein replicating entities are introduced into the yolk of an (un)fertilized egg or embryo. The method may be extended to elucidate the mechanism-of-action of functional chemical compounds or compositions in the same method and system. The method and system may also be employed for identifying marker genes, marker proteins or marker metabolites.

Abstract: The present invention provides polypeptides that contain one or more PDZ loop-variants and are useful in the detection of pathogens and disease-associated molecules. The polypeptides of the invention are also useful in the diagnosis, treatment, and prevention of diseases. Also provided are methods of preparing polypeptides of the invention.

Abstract: Compositions and methods are provided for selection and enrichment of a target gene from a library of polynucleotide sequences such as might be formed from a genome or by random mutagenesis of a genetic sequence. The selection and enrichment occurs in aqueous droplets formed in an emulsion that compartmentalize individual polynucleotides from the library or a plurality of polynucleotides that may include polynucleotides not derived from the library, transcription and translation reagents and optionally additional chemical and enzyme reagents. The selection and enrichment method utilizes a polynucleotide adaptor which when ligated to the polynucleotide fragment enables amplification to occur in the presence of an adaptor specific primer.

Abstract: Described herein are RNA-protein fusion production methods which involve a high salt post-translational incubation step.

Abstract: The present invention makes known an array of nucleotidic sequences for rapidly and simultaneously identifying the presence of certain genes that codify proteins with relevant activities in biotechnology present in a microbiological sample, and the method with which this array is used in the identification of the above mentioned genes. Specifically speaking, genes that codify for proteins relevant in the biofilm formation, in CO2 fixation, in energetic metabolism, for chemiotaxis and mobility, in iron oxidizing, in nitrogen metabolism, in sulfur assimilation, and in oxidation/reduction of sulphide compounds, are identified. This array of nucleotidic sequences is presented as a useful tool in biotechnology whenever evaluating the quality of a microbiological community is required.

Abstract: Plasma samples of ovarian and breast cancer patients were used to search for markers of cancer, using two-dimensional gel electrophoresis and MALDI TOF mass spectrometry. Truncated forms of cytosolic serine hydroxymethyl transferase (cSHMT), T-box transcription factor 3 (Tbx3) and utrophin were aberrantly expressed in samples from cancer patients, as compared to samples from noncancer cases. Aberrant expression of proteins was validated by immunoblotting of plasma samples with specific antibodies to cSHMT, Tbx3 and utrophin. A cohort of 79 breast and 39 ovarian cancer patients, and 31 individuals who were either healthy or had noncancerous conditions was studied. We observed increased expression of truncated cSHMT, Tbx3 and utrophin in plasma samples obtained from patients at early stages of disease. The results indicate that cSHMT, Tbx3, utrophin and truncated forms thereof can be used as components of multiparameter monitoring of ovarian and breast cancer.

Abstract: GB1 peptidic libraries and methods of screening the same for specific binding to a target protein are provided. Libraries of polynucleotides that encode GB1 peptidic compounds are provided. These libraries find use in a variety of applications in which specific binding to target molecules, e.g., target proteins is desired. Also provided are methods of screening the libraries for binding to a target.