Abstract: The invention encompasses methods for reducing the proportion of sperm cells with abnormal morphology, and unviable sperm cells, in a sperm cell population using flow-cytometric processing. The methods generally entail staining the sperm cells in the population; irradiating the sperm cells in the population; detecting fluorescence emitted by the sperm cells in the population in response to the step of irradiating; differentiating the sperm cells in the population based on orientation or viability; and then collecting a subpopulation of oriented or viable sperm cells.

Abstract: The invention includes a method of screening a biological sample for contamination by sequencing a first biological sample at a first depth to generate a first nucleotide sequence; determining map coordinates for one or more homozygous loci in the first nucleotide sequence; sequencing a second biological sample at a second depth to generate a second nucleotide sequence, wherein the second depth is lower than the first depth; determining loci in the second nucleotide sequence at the determined map coordinates; and comparing the one or more homozygous loci in the first nucleotide sequence with the determined loci in the second nucleotide sequence.

Abstract: The invention includes a method of identifying high genomic value, non-human mammalian embryos that would otherwise be disposed of or frozen based on their morphology. The method generally involves establishing a stem cell culture from the non-human mammalian embryo, which entails generating a population of embryos in vitro or in vivo, assessing the morphology of each of the embryos in the population, selecting a subpopulation of embryos for embryo transfer based on the morphological assessment, thereby establishing a group of selected embryos and a group of unselected embryos in the population, and establishing a stem cell culture from an embryo in the group of unselected embryos.

Abstract: The invention encompasses a method of estimating a distribution or a standard deviation of breeding values or predicted transmitting abilities of gametes from an individual using population-wide estimates of linkage disequilibrium for one or more genetic markers or genes, so as to more efficiently produce offspring having breeding values or predicted transmitting abilities that equal or exceed a desired breeding value or predicted transmitting ability.

Abstract: The invention encompasses methods for reducing the incidence of hemorrhagic heart disease in livestock.

Abstract: Embodiments of the present invention relate generally to processes, systems, and compositions useful in manipulating a ratio of viable X chromosome bearing sperm to viable Y chromosome bearing sperm in at least one sperm population and useful for preserving the resulting manipulated sperm population. In some embodiments a cryoprotectant may be incorporated into various medias used in manipulating the sperm sample, such as in a staining media, a sheath fluid, and a collection media.

Abstract: The invention consists of methods and compositions for detecting the presence or absence of a DNA aberration by analyzing fluorescence emission characteristics in sperm cells or sperm nuclei, which generally consists of entraining sperm cells or sperm nuclei stained with a DNA selective dye in sheath fluid; exposing the entrained sperm cells or sperm nuclei to electromagnetic radiation; determining a forward fluorescence characteristic and a side fluorescence characteristic of individual events associated with the exposed sperm cells or sperm nuclei; and gating the individual events based on the forward fluorescence characteristic and the side fluorescence characteristic with a criterion.

Abstract: A method of distinguishing between a first type of object and a second type of object in a fluid column by receiving output light from an objects in the fluid column, generating an electrical signal in response to the output light, and compensating for position dependence of the object in the fluid column.

Abstract: The invention encompasses methods of selecting an animal or plant, and producing progeny from the animal or plant, using segmented phased genotypes.

Abstract: A discrimination system with optics that collect output electromagnetic radiation from sperm cells within a measurement region, a split detector that generates an electrical signal responsive to the intensity of the collected electromagnetic radiation and which detects the position of sperm cells in the measurement region, and an analyzer for discriminating between X-chromosome bearing sperm and Y-chromosome bearing sperm in the measurement region.

Abstract: This disclosure relates to methods for sorting sperm cells in a microfluidic chip. In particular, various steps are incorporated to align and orienting sperm in flow channels, as well as, to determining sperm orientation and measure relative DNA content for analysis and/or sorting.

Abstract: The invention provides methods of flow-cytometrically processing sperm cells in which greater than 25% of sperm cells in the population to be processed have abnormal morphology.

Abstract: A method for magnetic cellular manipulation may include contacting a composition with a biological sample to form a mixture. The composition may include a plurality of particles. Each particle in the plurality of particles may include a magnetic substrate. The magnetic substrate may be characterized by a magnetic susceptibility greater than zero. The composition may also include a chargeable silicon-containing compound. The chargeable silicon-containing compound may coat at least a portion of the magnetic substrate. The biological sample may include cells and/or cellular structures. The method may also include applying a magnetic field to the mixture to manipulate the composition.

Abstract: An optical arrangement receives output light emanating from an object disposed within a fluid column that crosses an optical refraction boundary of the fluid column between the object and the optical arrangement. The optical arrangement modifies the output light such that the modified output light has an intensity that is more uniform than the output light.

Abstract: A discrimination system that forms a fluid column and interrogates objects within the fluid column with an excitation source. An optical arrangement collects output electromagnetic radiation emanating from the excited objects disposed within the fluid column and directs the output electromagnetic radiation to a detector. An analyzer reduces the positional dependency of the detected intensity by normalizing the value based on the position of each object.

Abstract: The invention provides serialized artificial insemination straws, as well as systems and methods for authentication of the serialized artificial insemination straws.

Abstract: Methods for processing and sorting sperm are disclosed. Portions of sperm sorting or staining processes may include standardizing sperm samples by adjusting the concentration of the sperm sample to a predetermined concentration and adjusting the pH of the sample to a predetermined value. Sperm may also be stained in a single staining buffer having a DNA selective dye and a quenching dye.

Abstract: This disclosure relates to methods for sorting sperm cells in a microfluidic chip. In particular, various steps are incorporated to align and orienting sperm in flow channels, as well as, to determining sperm orientation and measure relative DNA content for analysis and/or sorting.

Abstract: The invention includes a method of evaluating a bovine embryo by fertilizing an egg obtained from a first bovine heterozygote of a recessive lethal haplotype with sperm cells obtained from a second bovine heterozygote of the recessive lethal haplotype; producing the embryo from the fertilized egg, wherein the embryo is homozygous for the lethal haplotype; establishing a cell culture from the embryo; collecting a plurality of cultured cells; and obtaining omics data, comprising one or more features, from the plurality of cultured cells.

Abstract: The invention relates to methods of increasing genetic merit of swine by establishing a plurality of mating subtypes for a line of swine, and determining a percentage of progeny that are male for each of the mating subtypes, or a percentage of progeny that are female for each of the mating subtypes, that would result, relative to a control, in an increase in genetic merit in the line; the invention further relates to sorting a sperm cell sample from a male swine in one of the mating subtypes into one or more subpopulations of sperm cells, wherein a majority of sperm cells in a subpopulation of sperm cells bear X chromosomes or Y chromosomes, and inseminating one or more female swine in the one of the mating subtypes with the subpopulation of sperm cells to achieve the percentage of progeny that are male, or the percentage of progeny that are female, determined to increase genetic merit relative to the control.