Abstract: The present invention proivdes methods of identifying new carcinoma oncogenes or analyzing functions of known carcinoma oncogenes by transformation of RK3E cells. Also provided are methods of using nuclear localization of Krüppel-like factor 4 (KLF4, or termed Gut-Enriched Krüppel-Like Factor, GKLF) as a marker and prognostic factor for aggressive early-stage breast carcinoma.

Abstract: The present invention is directed to directly measure distribution in vivo and the frequency of generation in vivo of DNA strand breaks which induce cell death and mutations. The present inventors accomplished the present invention by providing a method for detecting a DNA strand break in a sample, which comprises a step of binding a PprA protein derived from Deinococcus radiodurans to a DNA strand break and a step of detecting the PprA protein which is bound to the DNA strand break; as well as by providing a kit for detecting a DNA strand break in a sample which comprises PprA proteins derived from Deinococcus radiodurans and a means for detecting a PprA protein which is bound to a DNA strand break.

Abstract: Disclosed are biomarkers, methods and assay kits for the identification of cancer patients who are predicted to benefit, or not to benefit, from the therapeutic administration of an epidermal growth factor receptor (EGFR) inhibitor. The biomarkers of the present invention include detection of EGFR and HER 2 gene amplification and polysomy, EGFR protein expression, EGFR mutations, phosphorylated Akt protein expression, and various combinations of such biomarkers, as well as the combination of these biomarkers with mutations in the tyrosine kinase domain of the EGFR gene. Increased EGFR gene copy number, increased HER2 gene copy number, increased EGFR, protein expression, activated AKT protein expression (phosphorylated AKT) and EGFR mutations are all associated with better outcome for cancer patients treated with EGFR inhibitors.

Abstract: A method and apparatus for preparing biological cell samples for intracellular analysis. The invention is based upon the recognition that many of the steps of the conventional methods for such sample preparation can be eliminated, leading to a process that readily lends itself to automation and the advantages associated therewith. The method of the invention comprises the steps of (a) cell-fixation, (b) permeabilization and (c) staining (or labeling) of intracellular molecules of interest by probes that are readily detectable by flow cytometric techniques, all without any intervening cell-washing (and re-suspension) steps. Rather, the single cell-washing step is effected after these three steps have been carried out. Preferably, the washing step is carried out by passing the fixed, permeabilized and stained cell sample through a semi-permeable membrane that serves to filter out (by transmission) interferants to waste while retaining the cells of interest.

Abstract: The invention provides a flow cytometric method for measuring dendritic cell function in whole blood, comprising: (a) contacting a whole blood sample with a dendritic cell activator; (b) adding to the sample a plurality of dendritic cell-distinguishing antibodies and at least one cytokine-specific antibody; and then (c) flow cytometrically assaying the sample for the binding of the cytokine-specific antibody by at least one distinguishable DC subset. Other assays are presented in which DC activation markers are assessed.

Abstract: The invention is related to diagnostic methods for detecting transmissible spongiform encephalopathies (TSEs) such as BSE and scrapie and related disease in humans. The invention provides use of guanidine thiocyanate (gdnSCN) or a functional equivalent thereof for treating at least one sample derived from a mammal, including humans for reducing the risk of scoring a false-positive test result in testing said sample for the presence of aberrant prion protein.

Abstract: A fixative for fixing biological materials contains a depot agent, preferably a polyamine and especially hexamethylenetetramine, which reacts chemically with positively charged ions, especially H+ from an acid, while forming a fixative, where the fixative is an aldehyde and especially formaldehyde, which in turn reacts chemically with the biological material to be fixed in order to fix it and is consumed in doing so. By adjusting the pH of a solution containing the depot agent, a chemical equilibrium reaction occurs between the depot agent, fixative and biological material, so that just as much fixative is continuously formed as can be immediately consumed by the biological material. With that, the fixative, and especially the hazardous formaldehyde, cannot escape. Thus, an externally formaldehyde-free fixative that at the same time has the excellent fixative properties of formaldehyde is created.

Abstract: This invention relates to an improved procedure for the multiparameter analysis of leukocyte subpopulations from peripheral blood, bone marrow or any body fluid containing blood nucleated cells, including the quantification of each subpopulation in terms of cells per microliter. The method uses a cocktail of at least four monoclonal antibodies labelled each with a different fluorescent tag, the measurement of at least two light scatter and four fluorescence emissions related parameters and at least one population of fluorescent beads to differentiate and enumerate between and among the different leukocyte subpopulations in the peripheral blood, the bone marrow or other body fluid.

Abstract: The present invention relates to a process for identifying a novel target for use for the development of therapeutic modalities and drugs effective against tuberculosis comprising testing M. tuberculosis devR mutant strain for virulence in guinea pigs.

Abstract: A system and methods for co-registering multi-channel images of a tissue micro array, comprising the steps of, providing a biological material on a substrate; applying one or more molecular probes, adapted to provide fluorescent molecular markers, to the biological material; obtaining a first digital image of the biological material and the fluorescent molecular markers; applying a morphological stain to the biological material; obtaining a second digital image of the biological material, computing information common to the first and second images; and co-registering the second image with the first image based on one or more registration metrics.

Abstract: A new method of cell fixation using a mild denaturing heat and the fixative PERMIFLOW™ or similar fixative that preserves cell morphology, light scatter profiles, nucleic acid content, cell surface epitopes and unmasks internal epitopes previously not available. The method can be combined with analysis of each of these parameters by flow cytometry and thus has application in drug screening and patient or tumor monitoring protocols.

Abstract: Systems and methods for providing dynamic mechanical loading and mechanical property assessment of tissue cultures in open dish cultures are provided. An actuator may be provided under a cell culture dish for driving the dish upward toward a fixed post member, thereby providing controlled compression of a tissue sample.

Abstract: The invention relates to a method of determining the binding site specificity of an analyte to a ligand having at least two different binding sites, which method comprises immobilizing the ligand to a solid support, mixing the analyte with a reversibly binding reference analyte which has a dissociation behaviour that differs significantly from that of the analyte, contacting the mixture with the ligand to determine dissociation characteristics for the mixture, and determining therefrom the binding site specificity of the analyte in relation to the reference analyte. The invention also relates to an analytical system for carrying out the method, and to a computer program, computer program product and computer system for performing the method.

Abstract: The present disclosure involves a method of preparing a cervical sample for medical examination in which a papanicolaou stained sample is additionally stained with a label targeted to one or more high risk cancer markers to allow for optical detection of the human papilloma virus. That optical detection can be combined with morphometric detection of abnormal cells, which may be improved by multispectral imaging using an acousto-optic tunable filter. Several variations of screening methods and an apparatus for performing the methods are disclosed.

Abstract: A method of staining bacteria comprises: working a polymethine dye on a sample in the presence of a substance capable of reducing nitrite ions to stain bacteria in the sample. A method of detecting bacteria comprises the following steps of: (1) working a polymethine dye on a sample by a method as described above to stain bacteria in the sample, (2) introducing the thus treated sample into a detecting part of a flow cytometer and irradiating cells of the stained bacteria one by one with light to measure scattered light and fluorescent light emitted from each of the cells; and (3) discriminating the bacteria from other components in accordance with an intensity of a scattered light signal and an intensity of a fluorescent light signal or a pulse width reflecting the length of particles to count the bacteria.

Abstract: Automated staining equipment that can mix reagents is used to spray a Romanowsky stain onto slide mounted specimens which are then briefly centrifuged. The centrifugation step removes excess stain leaving only a thin film. Depending on the time of the centrifugation step, most of the organic solvent and part of the water in the stain are evaporated by airflow through the equipment. This greatly accelerates the staining reaction and preserves water soluble structures such as the granules in basophilic leukocytes. For optimal performance, this staining procedure requires a thiazin-eosin stain with about 90% to about 40% organic solvent, such as methanol, and only about 10% to about 60% water. This is a unique staining reagent in Romanowsky staining.

Abstract: The present invention is generally directed towards a method, system, apparatus and/or kit for collecting samples of bodily fluids, and more specifically towards collection of supplies that enable a lay person to collect and analyze a semen sample for use at home for male fertility or in the animal husbandry arts. In one embodiment, the semen analysis method includes a sperm count or determination of sperm concentration or sperm density, and may include an evaluation of motility and/or morphology.

Abstract: Methods and kits for used as an internal or external control in rare cell analysis are disclosed. A plurality of fluorescently distinct sets of cells is used to define a range to assess the isolation of rare target cells from a sample. Thus, a known number of cells, expressing the surface and intracellular antigens present in the targeted rare cells, are stabilized and modified in such a way that they can be discriminated from the targeted rare cells. In addition, these cells are separated into at least two sets based upon the number. These sets are detectably distinct from each other and provide an upper and lower indication of the detection ability of the rare cell assay.

Abstract: A method for the identification of human foetal cell nuclei is provided wherein the method involves subjecting chromosomes of cell nuclei to exonucleolytic digestion by an enzyme so as to remove end regions of each chromosome; and detecting the presence of a DNA sequence remaining in foetal DNA but absent from maternal DNA as a result of the digestion process. Once identified, the foetal DNA can be subject to diagnosis for example to detect chromosomal abnormalities.

Abstract: A method for diagnosing the presence in an animal of an infection due to a microorganism in which a test sample obtained from the animal is exposed to a population of the microorganism and the presence of binding of the microorganism by an antibody in the test sample is determined.

Abstract: A rapid tissue processing method and apparatus including the steps of fixation, dehydration, clearing, and impregnation. The preferred method is performed in a processing unit that employs alternating microwave and ohmic energy to heat the process solution and tissue sample. In one embodiment, the method employs environmentally friendly green chemicals to effectuate the processing.

Abstract: A rapid tissue processing method and apparatus including the steps of fixation, dehydration, clearing, and impregnation. The preferred method is performed in a processing unit that employs alternating microwave and ohmic energy to heat the process solution and tissue sample. In one embodiment, the method employs environmentally friendly green chemicals to effectuate the processing.

Abstract: The present invention relates to blood products, and more particularly to compositions comprising a modified hemoglobin in plasma.

Abstract: The present invention relates to DNA sequences from regions of copy number change on chromosome 20. The sequences can be used in hybridization methods for the identification of chromosomal abnormalities associated with various diseases.

Abstract: Methods of fixing and processing tissue and samples on a membrane by using ultrasound radiation as a part of the method are presented. Ultrasound of a frequency in the range of 0.1-50 MHz is used and the sample or tissue receives 0.1-200 W/cm2 of ultrasound intensity. The use of ultrasound allows much shorter times in the methods. Also presented are apparati comprising transducers of one or of multiple heads for producing the ultrasound radiation and further comprising a central processing unit and optionally comprising one or more sensors. Sensors can include those to measure and monitor ultrasound and temperature. This monitoring system allows one to achieve accurate and optimum tissue fixation and processing without overfixation and tissue damage. The system also allows the performance of antigen-antibody reactions or nucleic acid hybridizations to be completed in a very short time while being highly specific and with a very low or no background.

Abstract: An automated in situ heat induced antigen recovery and staining method and apparatus for treating a plurality of microscope slides. The process of heat induced antigen recovery and the process of staining the biological sample on the microscope slide are conducted in the same apparatus, wherein the microscope slides do not need to by physically removed from one apparatus to another. Each treatment step occurs within the same reaction compartment. The reaction conditions of each reaction compartment for treating a slide can preferably be controlled independently, including the individualized application of reagents to each slide and the individualized treatment of each slide. The reagents are preferably held in a reagent dispensing strip similar to a “blister pack”.

Abstract: The present invention concerns the methods and compositions for preparing a tissue section or biological sample, particularly to preserve RNA in the section or sample, by not exposing or contacting the sample or section to a solution that is composed of mostly water. Tissue sections can be fixed, stained, and dehydrated for subsequent manipulation, including laser capture microdissection (LCM) for further analysis using methods and/or compositions of the invention.

Abstract: It is intended to provide a method for fluorescently staining a tissue accurately and clearly by convenient procedures and a staining agent used in this method. The present invention provides a method for fluorescently staining a tissue, comprising treating a tissue with a solution comprising fluorescein or a salt thereof and then fluorescently observing the treated portion under an acidic condition of lower than pH 7.

Abstract: A reagent system is provided for substantially lysing red blood cells in a whole blood sample prior to leukocyte analysis, which system includes a first reagent for substantially lysing the red blood cells in the whole blood sample, and a second reagent for quenching the activity of the first reagent. The first reagent is formulated to include an autoclaved saponin compound and an acid selected from the group consisting of a halogenated carboxylic acid, a phosphoric acid and a combination thereof. The second reagent includes a base and has a pH value of about 8 to 12. Also provided is a method of lysing the red blood cells and stabilizing white blood cells present in a sample of whole blood.

Abstract: A method of producing antibodies comprising the step of encoding a peptide sequence from a Domain I perlecan splice variant, wherein the peptide sequence is used to produce anti-peptide antibodies.

Abstract: Cell based assays are used to assess the hepatotoxicity of a stimulus. Imaging technologies are used to analyze the effects of a stimulus on hepatocytes. Image analysis may characterize the stimulus on the basis of whether it is hepatotoxic, and if so what type of pathology is exhibited; e.g., apoptosis, necrosis, cholestasis, and/or steatosis.

Abstract: The present invention is directed to a cleaning system and methods for cleaning tissue embedding molds. The cleaning system includes a cleaning vessel that holds a cleaning solution. The tissue processing molds are supported by a basket receptacle which is placed inside the cleaning vessel. Cleaning solution is supplied to the cleaning vessel through a supply line. Additional fluids are stored in a reservoir and may be mixed with the cleaning solution in the supply line. Cleaning solution drains from the cleaning vessel through a drain line. A controller controls the opening and closing of valves and the activation or deactivation of a heat source to operate a wash cycle, a rinse cycle, and a dry cycle.

Abstract: The present invention provides methods and compositions for the diagnosis and treatment of cancer, including cancers involving the NOTCH pathway. In particular, the present invention provides methods and compositions for the diagnosis of mucoepidermoid carcinoma, the most common malignant salivary gland tumor. The present invention further provides methods and compositions for the diagnosis of other tumors associated with the t(11;19)(q14–21;12–13) translocation.

Abstract: The invention provides methods for the detection of prion diseases, such as scrapie of sheep, bovine spongiform encephalopathy of cattle, Creutzfeld-Jacob disease of man, whereby aberrant proteins or prion proteins are detected in tissues which can be sampled from live animals.

Abstract: An animal, e.g., transgenic mouse, in which the MSH5 gene is misexpressed. The animal is useful for screening treatments for a number of conditions. Methods for identifying contraceptive agents are also described.

Abstract: The present invention is directed to a composition and method for regulating the adhesion of cells and biomolecules to hydrophobic surfaces and hydrophobic coated surfaces. The composition is a biomolecule conjugated end-group activated polymer (EGAP). The biomolecule conjugated EGAP can be put to numerous uses including cell adhesion, cell growth, cell sorting, and other biological assays.

Abstract: This invention relates to methods for reducing background fluorescence in cell detection and measurement systems. In accordance with one aspect of the invention, cell-impermeant chemical agents are used to modify the fluorescent probes that reside outside the cells to be detected. The chemical agents can chemically modify one or more functional groups in the probes, thereby reducing or eliminating the fluorescence of the probes. In accordance with another aspect of the invention, Acid Black 48 is used to reduce background fluorescence produced by fluorescent probes such as SYTO 62.

Abstract: A fluorescent label compound of formula where Z is a reactive group that can be used for covalent coupling of the fluorescent label compound to other molecule. Either the fluorophore is a dipyrrometheneboron difluoride dye and Y is a water-solubilizing moiety, or Y is —CH2CH2SO3? X+ where X+ is a cation. The use of the compounds in bianalytical assays and cytological or histological staining methods, and a method for increasing the hydrophilicity of fluorescent compounds, are also disclosed.

Abstract: Method and kits are provided for the detection and diagnosis of metastatic disease. More particularly, the methods and kits employ compounds that can detect EphA2, a specific epithelial cell tyrosine kinase that is overexpressed in metastatic tumor cells. In one embodiment the compound is an antibody capable of binding to an epitope of EphA2.

Abstract: Embodiments of the invention provide methods for evaluating the accuracy of a molecular model properties model (or predictions generated using a molecular properties model). The accuracy of a molecular properties model may be evaluated using three general approaches, (i) by using the same data set to both train the model and to estimate the accuracy of the model, (ii) by using distinct data sets to train and subsequently test a model, and (iii) by using multiple models (or sets of predictions).

Abstract: Whether or not a sample of skin or of a skin equivalent contains such amount of a papillary fibroblast population as to be considered a normal skin is determined by labelling said skin or skin equivalent with at least one antibody specific for papillary fibroblasts and evaluating the extent of such labelling as a marker for skin or skin equivalent quality.

Abstract: A method for treating a biological sample with a Papanicolaou staining process is provided. The method comprises incorporating a detergent treatment into the staining process at any of various steps. The method has been found to advantageously reduce the number of artifacts produced during Papanicolaou staining. Also provided is a sample stained by such a process.

Abstract: The present invention relates generally to a method and compound for sensing the presence of anionic phospholipids, especially phosphatidylserine, on the surface of vesicles and cells.

Abstract: A method and apparatus for physically separating polypeptide constituents of a sample fluid by (a) providing a sample fluid comprising a mixture of polypeptides of differing physical and/or chemical properties; (b) contacting the fluid with at least two individual polymer matrix units, each polymer matrix unit preferentially accepting a different set of polypeptides on the basis of one or more physical and/or chemical properties; and (c) extracting the set of polypeptides from each polymer matrix unit.

Abstract: The present invention describes methods and cassettes for cell-based toxin detection and organ localization. The cassettes includes an array containing cells and a matrix of openings or depressions, wherein each region of the substrate enclosed by the opening or depression in the matrix forms a domain individually addressable by microfluidic channels in the device.

Abstract: The present invention provides a method for the staining of fungi and microsporidia for observation with a light microscope based upon the presence of chitin in the composition of these organisms. With the method of the present invention a sample to be analyzed is treated with a solution of Ponceau S and Stains-all dye. The sample is then selectively decolorized and rinsed. The resulting sample is examined with a light microscope, or photographed for a permanent record, to identify the presence of a variety of microorganisms, to include fungi and microsporidia.

Abstract: High affinity monoclonal antibodies for recognizing estrogen receptor (clone SP1) with immunohistochemistry and methods for creating such an antibody are disclosed. The lagomorph derived ER antibody provides a significant advantage over the currently available mouse ER antibodies in that there is no need for target retrieval when performing immunohistochemistry. Furthermore, the very low background when the lagomorph derived ER antibody is used in immunohistochemistry is also impressive. The immunohistochemistry comparative study with about fifty clinical specimens showed that the new ER (clone SP1) antibody had favorable results when compared to mouse monoclonal ER antibodies (clone 1D5). The lagomorph derived ER antibody may prove of great value in the assessment of ER status in human breast cancer. Humanized versions of the ER antibody may also provide therapeutic benefits.

Abstract: A pharmaceutical preparation useful for treating a skin or mucous membrane lesion is provided. The pharmaceutical preparation including, as active ingredients, a therapeutically effective amount of trichloroacetic acid and hydrochloric acid, or trichloroacetic acid and formic acid or all three of these acids and optionally a crosslinking/fixating/preserving agent. Additional preparations are also described.

Abstract: The invention relates to a method for detecting an infection of a mammal with an acid-resistant microorganism comprising the following steps: (a) provision of an immunochromatographic test with a sample application area for the application of a stool sample of the mammal with an antigen and application of the stool sample, (b) incubation of the stool sample using (i) a first receptor under conditions permitting a complex formation of the antigen from the acid resistant microorganism with the receptor; or (ii) at least two different first receptors under conditions permitting a complex formation of the antigen from the acid-resistant microorganism with the at least two first receptors and wherein the first receptor according to (i) or the first receptors according to (ii) specifically bind(s) an antigen which shows, at least with some mammals, a structure after passage through the intestine that corresponds to the native structure or the structure against which a mammal produces antibodies against after being

Abstract: Genetic modification or selection of avians requires that large numbers of birds be genetically analyzed for sequences of interest. Typically, DNA is extracted on an individual basis from samples taken from the birds. Current methods of DNA extraction extract the DNA from blood or other tissues using tedious and time-consuming procedures. The present invention provides a high throughput screening assay for detecting a genetic sequence in multiple samples. The assay further provides a DNA extraction method that allows DNA to be extracted rapidly from multiple avian samples, such as red blood cells. The extraction method is extremely reliable and does not require that each sample be quantitated post-extraction. The extracted DNA can be used for a variety of genetic assays, including a high throughput screening assay to identify insertion of a transgene. The present invention is particularly useful for extracting DNA from nucleated RBCs.