Abstract: The inventors have modified the amino acid sequence of a maltogenic alpha-amylase to obtain variants with improved properties, based on the three-dimensional structure of the maltogenic alpha-amylase Novamyl. The variants have altered physicochemical properties., e.g. an altered pH optimum, improved thermostability, increased specific activity, an altered cleavage pattern or an increased ability to reduce retrogradation of starch or staling of bread.

Abstract: The invention relates to the analysis of interactions of substances or materials with surfaces or interfaces made from amphiphilic materials and in particular partition coefficients and/or binding constants are determined. For this purpose use is made of a carrier material, which is so coated with amphiphilic molecules in the so-called fluid phase that the lateral diffusion of the amphiphilic molecules is substantially unimpeded. The invention also relates to a kit suitable for such analyses, and to a process for analyzing these interactions in column chromatography, particularly high pressure or performance liquid chromatography.

Abstract: A method for obtaining a nucleotide sequence that is indicative of the sequence of a target polynucleotide molecule T. The method makes use of hybridization data obtained by incubating T with nucleotide probes. A score is assigned to each of a plurality of candidate nucleotide sequences based upon the hybridization data and upon at least one reference nucleotide sequence. A candidate nucleotide sequence in then selected having an essentially maximal score.

Abstract: One embodiment of the present invention provides methods for detecting known blocks of functionally aligned protein sequences in a test nucleic acid sequence, e.g., in an uncharacterized EST. The method can include the following steps. A) Reverse translate the set of protein sequences to a set of functionally aligned nucleic acid sequences using codon-usage tables and create a profile from the set of functionally aligned nucleic acid sequences. B) Construct a first indicator function for the profile. The first indicator function corresponds to adenine. The first indicator function allows the value at a given position to be continuous between 0 and 1 as a function of the percentage presence of adenine at a particular position. C) Construct a second indicator function for the test nucleic acid sequence. The second indicator function also corresponds to adenine. D) Compute the Fourier transform of each of the indicator functions. E) Complex conjugate the Fourier transform of the second indicator function.

Abstract: The present invention determines properties of combinatorial library products from features of library building blocks. At least one feature is determined for each building block of a combinatorial library having a plurality of products. A training subset of products is selected from the products, and at least one property is determined for each product of the training subset. A building block set is identified for each product of the training subset, and an input features vector is formed from the features of the identified building blocks for each product of the training subset. A supervised machine learning approach is used to infer a mapping function that transforms the input features vector for each product of the training subset to the corresponding at least one property for each product of the training subset. After the mapping function is inferred, it is used for determining properties of other products of the library from their corresponding input features vectors.

Abstract: The invention provides a method of determining an amino acid sequence of a parent polypeptide. The method consists of: (a) obtaining mass spectra of two or more differentially labeled polypeptide fragments of a parent polypeptide; (b) assigning a mass and a weighting characteristic to two or more paired signals having a difference in mass corresponding to an integer value of said differential label, the weighting characteristic combining properties of each signal within said paired signals; (c) selecting from the mass spectra a paired signal having the assigned mass and a weighting characteristic distinguishable from non-peptide signals, the assigned mass indicating the mass of a polypeptide fragment within the spectra; (d) determining the difference in mass of the polypeptide fragments; (e) assigning the mass differences a satisfying amino acid name, and (f) orienting the assigned amino acid names. Also provided is a method of determining the amino acid sequence of a polypeptide.

Abstract: A method and system for chromatogram analysis is disclosed. An aspect of the invention is a method for reducing each chromatogram to a data set that can be compared to another such data set, producing a comparison result that indicates the similarity or dissimilarity of the two chromatograms. The present invention provides a system and method that can be used to identify DNA sequence variations through chromatogram analysis. The present invention also provides a user interface to display results of chromatogram analysis, which quickly and efficiently illustrates which samples are dissimilar or similar to reference chromatograms.

Abstract: The invention concerns the geNo.mic sequence and cDNA sequences of the PCTA-1 gene. The invention also concerns biallelic markers of the PCTA-1 gene and the association established between these markers and prostate cancer. The invention provides means to determine the predisposition of individuals to prostate cancer as well as means for the diagNo.sis of prostate cancer and for the progNo.sis/detection of an eventual treatment response to agents acting against prostate cancer.

Abstract: A system for acquiring knowledge from cellular information. The system has a database comprising a database management module (“DBMS”). The system also has a variety of modules, including a population module coupled to the DBMS for categorizing and storing a plurality of features (e.g., cell size, distance between cells, cell population, cell type) from an image acquisition device into the database. The system has a translation module coupled to the DBMS for defining a descriptor from a set of selected features from the plurality of features. In a specific embodiment, the descriptor is for a known or unknown compound, e.g., drug. A prediction module is coupled to the DBMS for selecting one of a plurality of a descriptors from known and unknown compounds from the database based upon a selected descriptor from a selected compound. The selected compound may be one that is useful for treatment of human beings or the like.

Abstract: The present invention concerns a method for the quantification of a target nucleic acid in a sample comprising the following steps: (i) determination of the amplification efficiency of the target nucleic acid under defined amplification conditions, (ii) amplification of the target nucleic acid contained in the sample under the same defined reaction conditions, (iii) measuring the amplification in real-time, (iv) quantification of the original amount of target nucleic acid in the sample by correction of the original amount derived from step (iii) with the aid of the determined amplification efficiency. The efficiency correction of PCR reactions according to the invention for the quantification of nucleic acids can be used for absolute quantification with the aid of an external or internal standard as well as for relative quantification compared to the expression of housekeeping genes.

Abstract: A method for continuously determining a parameter (D, Cbin, K, Kt/V) indicative of an extracorporeal blood treatment includes flowing patient's blood and a treatment liquid flow on opposite sides of a semipermeable membrane. The treatment liquid has a characteristic (Cd) associated with the effectiveness of the treatment flow through the exchanger. A succession of variations are caused in the characteristic (Cd) upstream of the exchanger, and a plurality of values (Cdin1 . . . Cdinj . . . Cdinp) of the characteristic (Cd) upstream of the exchanger are continuously stored in memory. Similarly, plurality of values (Cdout1 . . . Cdoutj . . . Cdoutp) adopted by the characteristic (Cd) downstream of the exchanger are continuously stored in memory. From the stored values, the effectiveness of the treatment is calculated using a mathematical model.

Abstract: Methods and compositions for determining the three dimensional structure of a particle are provided. In the subject methods, a plurality of images of the identically heavy atom labeled particles of interest is obtained. Each of the images in the plurality is obtained by rigidly attaching at least four heavy atom clusters to the particle of interest and imaging the particle in an electron microscope. The three-dimensional structure of the particle is then derived from the plurality of images of the labeled particle. This derivation step preferably includes an alignment step in which the orientation of the images is determined using the heavy atom cluster projections. In preferred embodiments, the heavy atom clusters serve to reveal particle homogeneity, particle location, particle orientation, image artifacts, and image parameters required for computational image restoration. The subject methods are particularly suited for use in determining the three dimensional structure of biological particles, e.g.