Abstract: A method for concentrating viruses includes applying a magnetic force to a mixture containing: sugar chain-immobilized magnetic metal nano-particles each having a structure in which a sugar chain-immobilized metal nano-particle is bound to a first magnetic nano-particle; second magnetic particles with mean particle size larger than that of the sugar chain-immobilized magnetic metal nano-particles; and a specimen. Each sugar chain-immobilized metal nano-particle has a structure where a ligand-conjugate is bound to a metal nano-particle via sulfur atoms. The ligand-conjugate has a structure where a linker compound's amino group is connected to a sugar chain having a reducing terminal. The linker compound includes, in molecules thereof, an amino group, sulfur atoms, and a hydrocarbon chain having carbon-nitrogen bonds.

Abstract: Methods of characterizing a test subject's risk of having or developing cardiovascular disease are provided. The methods include using an analytic device to determine levels of choline-related trimethylamine-containing compounds such as trimethylamine N-oxide, choline, or betaine in a biological sample obtained from the subject and comparing the levels of the choline-related trimethylamine-containing compound in the subject's biological sample to a control value. The test subject's risk of having cardiovascular disease is then characterized as higher if the levels of the choline-related trimethylamine-containing compound are higher than the control value. Also provided are methods of identifying a subject at risk of experiencing a complication of atherosclerotic cardiovascular disease, and methods of evaluating the efficacy of a cardiovascular therapeutic agent in a subject with cardiovascular disease using levels of choline-related trimethylamine-containing compounds.

Abstract: The invention is related to a method and test kits for quantitative determination of polynucleotide amounts present in a sample. The test kit comprises organized pools with polynucleotide probes having distinct sizes and optionally provided with tracer tags or primer tags. The probes are allowed to hybridize with affinity tagged analyte polynucleotides from the sample. The result is hybrids, which can be recovered on a separation aiding tool provided with the pair of the affinity tag. After the quantitative release of the probes, the probes are either directly recorded, or if primer tagged, they are amplified and optionally provided with a tracer tag before recording. The invention provides a sensitive and quantitative determination of the amount polynucleotides present in a cell or tissue sample and allows a quantitative assessment of variations in the amounts of polynucleotides as a response to inherent changes or due to external stimuli.

Abstract: The present invention relates to biological substance-immobilized fibers wherein a biological substance is immobilized on a fiber, fibers retaining a biological substance-immobilized gel, and fiber alignments having bundles of the above-described fibers and slices of the same.

Abstract: The present invention is related to nucleic acid sequences that can be used in the field of virus diagnostics, more specifically the diagnosis of infections with the AIDS causing Human Immuno-deficiency Virus (HIV). With the present invention nucleotide sequences are provided that can be used as primers and probes in the amplification and detection of HIV-1 nucleic acid. The oligonucleotide sequences provided with the present invention are located in the LTR part of the HIV viral genome. It has been found that, by using the sequences of the present invention in methods for the amplification and detection of nucleic acid a sensitive and specific detection of HIV-1 can be obtained. The benefit of the sequences of the present invention primarily resides in the fact that, with the aid of primers and probes comprising the sequences according to the invention the nucleic acid of all presently known subtypes of HIV-1 can be detected with high accuracy and sensitivity.

Abstract: A method of analyzing genetic markers includes binding a set of probes to a segment of single stranded nucleic acids. The segment of single stranded nucleic acids includes a repeat region formed of at least two of a repeat unit. The repeat unit can include at least two nucleic acids. The set of probes includes a first probe complementary to the repeat unit. The method can further include directing the segment through a nanopore device and measuring a signal through the nanopore device. The signal can be indicative of the number of repeat units.

Abstract: Methods, compositions and articles of manufacture for assaying a sample for a target polynucleotide are provided. A sample suspected of containing the target polynucleotide is contacted with a polycationic multichromophore and a sensor PBP that can bind to the target polynucleotide. The sensor PBP comprises a signaling chromophore to absorb energy from the excited multichromophore and emit light in the presence of the target polynucleotide. The methods can be used in multiplex form. Kits comprising reagents for performing such methods are also provided.

Abstract: Adeno-associated virus 7 sequences, vectors containing same, and methods of use are provided.

Abstract: One embodiment of the present invention provides for a method of determining if a sputum sample contains dysplastic or carcinomic cells by obtaining a sputum sample containing cells. The sputum sample is labeled with TCPP to stain cells suspected to be dysplastic or carcinomic. The labeled sputum sample is excited with an excitation wavelength of light of about 475 nm+/?30 nm and emission at about 560 nm+/?30 nm is detected from cells identified to be macrophages. An imager focuses on the plasma membrane of one or more cells suspected to be dysplastic or carcinomic and emission at about 655 nm+/?30 nm, if present, is detected for TCPP labeled cells of the sputum sample after focusing on the plasma membrane of the cells of the sputum sample. Photon flux for each pixel of a sensor is measured to obtain a value for the imaged cell. The measured value is scored to determine if a cell is cancerous or dysplastic.

Abstract: A method comprises loading a sample portion into a sample chamber which comprises means for minimizing diffusion of the sample portion, subjecting the sample portion to an amplification step, and determining whether the sample portion contains at least one molecule of a target nucleic acid. If the sample portion contains a single molecule of the target nucleic acid, the sample portion would attain a detectable concentration of the target nucleic acid after a single round of amplification. Also, a microfluidic device comprising a sample portion and a sample chamber comprising means for minimizing diffusion of the sample portion. Also, a microfluidic device comprising a sample chamber and an amplification targeting reagent positioned in the first sample chamber.

Abstract: The present invention relates generally to the field of molecular biology. More particularly, it concerns methods and compositions for detecting, evaluating, and/or mapping 5-hydroxymethyl-modified cytosine bases within a nucleic acid molecule.

Abstract: The present invention is related to nucleic acid sequences that can be used in the field of virus diagnostics, more specifically the diagnosis of infections with the AIDS causing Human Immuno-deficiency Virus (HIV). With the present invention nucleotide sequences are provided that can be used as primers and probes in the amplification and detection of HIV-1 nucleic acid. The oligonucleotide sequences provided with the present invention are located in the LTR part of the HIV viral genome. It has been found that, by using the sequences of the present invention in methods for the amplification and detection of nucleic acid a sensitive and specific detection of HIV-1 can be obtained. The benefit of the sequences of the present invention primarily resides in the fact that, with the aid of primers and probes comprising the sequences according to the invention the nucleic acid of all presently known subtypes of HIV-1 can be detected with high accuracy and sensitivity.

Abstract: Von Willebrand's Factor (VWF) is produced using an expression vector that includes: 1) a DNA sequence encoding a functional VWF protein; and 2) regulatory DNA capable of effecting expression of that DNA sequence in a host cell transformed with the vector. Restriction fragment length polymorphisms (RFLP's) associated with the VWF gene are identified and used in a probe for determining the source of a VWF gene in a DNA sample. The gene for VWF is localized to the short arm of human chromosome 12 (12p).

Abstract: A method comprising subjecting one or more sample portion(s) to a single amplification step, thereby amplifying a single molecule in the sample portion to a detectable level, and, in some embodiments, then determining whether the sample portion contains at least one molecule of the target nucleic acid. In some embodiments, the sample portion is in a porous sample structure, or in a sample chamber which comprises means for minimizing diffusion of the sample portion, or in a sample chamber which is inside a microcapillary device, or in a sample retaining means.

Abstract: A method for detecting and isolating AAV sequences in a sample of DNA obtained from tissue or cells is provided, which sample contains DNA and proviral AAV. The method involves subjecting the sample containing DNA to amplification via polymerase chain reaction (PCR) using a first set of primers which specifically amplify a first AAV region. The first AAV region is characterized by having at least 250 nucleotides of AAV capsid nucleic acid sequence, a variable sequence flanked by a sequence of at least 18 nucleotides at the 5? end of the first AAV region and a sequence of at least 18 nucleotides at the 3? end of the first AAV region. Each of the 5? and 3? at least 18 nucleotides is the same over at least 9 consecutive nucleotides relative to corresponding sequences in an alignment of at least two AAV serotypes. Each of the sets of primers consist of a 5? primer and a 3? primer. The method is further useful for identifying AAV sequences in the sample by the presence of amplified proviral AAV sequences.

Abstract: The present invention relates to a device for interfacing nanofluidic and microfluidic components suitable for use in performing high throughput macromolecular analysis. Diffraction gradient lithography (DGL) is used to form a gradient interface between a microfluidic area and a nanofluidic area. The gradient interface area reduces the local entropic barrier to nanochannels formed in the nanofluidic area. In one embodiment, the gradient interface area is formed of lateral spatial gradient structures for narrowing the cross section of a value from the micron to the nanometer length scale. In another embodiment, the gradient interface area is formed of a vertical sloped gradient structure. Additionally, the gradient structure can provide both a lateral and vertical gradient.

Abstract: A rapid, safe method for predicting sepsis, or a condition similar to sepsis, in a mammal is disclosed, which comprises the following steps: I) isolating RNA from a biological sample of a mammal; ii) labeling the isolated RNA of step I) with a detectable marker; iii) hybridizing the labeled isolated RNA of step ii) with at least one DNA of genes Seq.-ID 1 to Seq.-ID 6705 (Table 1), which is spotted onto a microarray and which is a sepsis-specific gene or gene fragment, under the reaction conditions for hybridizations; iv) quantitatively recording labeling signals of the hybridized RNA of step iii) in an expression profile; v) comparing the expression profile of step iv) with a control sample with respect to a stronger or weaker expression of genes or gene fragments which are specific for sepsis; and vi) combining the expression profile of step v) with protein- and metabolite patterns of the biological sample.

Abstract: A method comprising subjecting one or more sample portion(s) to a single amplification step, thereby amplifying a single molecule in the sample portion to a detectable level, and, in some embodiments, then determining whether the sample portion contains at least one molecule of the target nucleic acid. In some embodiments, the sample portion is in a porous sample structure, or in a sample chamber which comprises means for minimizing diffusion of the sample portion, or in a sample chamber which is inside a microcapillary device, or in a sample retaining means.

Abstract: The present invention provides nucleic acid compositions or ladders which may be used as standards for estimating the size (in base pairs) and or mass of nucleic acid molecules of unknown size and/or mass. The invention also relates to methods for producing such compositions or ladders, ladders or compositions produced by such methods, and to methods for estimating the size and/or mass of nucleic acid molecules by comparison to these nucleic acid sizing ladders.

Abstract: Described herein are methods for detecting conformational changes in bioentities.