Abstract: Compositions and methods of identifying and characterizing potential gene editing on-target and off-target sites and/or edits in a nucleic acid are provided.

Abstract: Compositions and methods of identifying and characterizing potential gene editing on-target and off-target sites and/or edits in a nucleic acid are provided.

Abstract: Systems and methods for improving marker-trait associations and for improving trait introgression precision while reducing trait introgression time are disclosed. Genes responsible for recombination are edited to reduce function, and thus increase recombination rates. Increased recombination rates allow more precise quantification of marker-trait associations, and more precise and faster trait introgression. Methods and compositions useful for selecting an organism with a trait of interest are provided herein. Candidate organisms identified and/or selected by any of the methods described above are also of interest.

Abstract: Compositions and methods of identifying and characterizing potential gene editing on-target and off-target sites and/or edits in a nucleic acid are provided.

Abstract: Methods and compositions to genotype microspores and/or pollen grains are provided. Methods provided include using meiotically-related products to non-destructively determine the genotype of one of the meiotically-related products such that it can be further used. For example, methods to obtain a genotype of a microspore are provided. The methods include: isolating tetrads, separating the tetrads to obtain four tetrad microspores; genotyping three of the four tetrad microspores, and inferring the genotype of the fourth tetrad microspore. Methods are also provided for generating doubled haploid plants from the microspores that are selected for further analysis based on inferred genotypes. Viable genotyped pollen produced by these methods, as well as seed, cells, plants, germplasm, progeny, and plant parts derived therefrom are also provided.

Abstract: Methods and compositions to genotype microspores and/or pollen grains are provided. Methods provided include using meiotically-related products to non-destructively determine the genotype of one of the meiotically-related products such that it can be further used. For example, methods to obtain a genotype of a microspore are provided. The methods include: isolating tetrads, separating the tetrads to obtain four tetrad microspores; genotyping three of the four tetrad microspores, and inferring the genotype of the fourth tetrad microspore. Methods are also provided for generating doubled haploid plants from the microspores that are selected for further analysis based on inferred genotypes. Viable genotyped pollen produced by these methods, as well as seed, cells, plants, germplasm, progeny, and plant parts derived therefrom are also provided.

Abstract: The invention concerns the use of duplex oligonucleotides about 25 to 30 base pairs to introduce site specific genetic alterations in plant cells. The oligonucleotides can be delivered by mechanical (biolistic) systems or by electroporation of plant protoplasts. Thereafter plants having the genetic alteration can be generated form the altered cells. In specific embodiments the invention concerns the alteration in the gene that encode acid invertase, UDP-glucose pyrophosphorylase, polyphenol oxidase, O-methyl transferase, cinnamyl alcohol dehydrogenase, ACC synthase and ACC oxidase or etr-1 or homolog of etr-1, and plants having isolated point mutations in such genes.

Abstract: Disclosed are methods of identifying elements associated with a trait, such as a disease. The methods can comprise, for example, identifying the association of a relevant element (such as a genetic variant) with a relevant component phenotype (such as a disease symptom) of the trait, wherein the association of the relevant element with the relevant component phenotype identifies the relevant element as an element associated with the trait, wherein the relevant component phenotype is a component phenotype having a threshold value of severity, age of onset, specificity to the trait or disease, or a combination, wherein the relevant element is an element having a threshold value of importance of the element to homeostasis relevant to the trait, intensity of the perturbation of the element, duration of the effect of the element, or a combination. The disclosed methods are based on a model of how elements affect complex diseases.

Abstract: The invention concerns the use of duplex oligonucleotides about 25 to 30 base pairs to introduce site specific genetic alterations in plant cells. The oligonucleotides can be delivered by mechanical (biolistic) systems or by electroporation of plant protoplasts. Thereafter plants having the genetic alteration can be generated form the altered cells. In specific embodiments the invention concerns the alteration in the gene that encode acid invertase, UDP-glucose pyrophosphorylase, polyphenol oxidase, O-methyl transferase, cinnamyl alcohol dehydrogenase, ACC synthase and ACC oxidase or etr-1 or homolog of etr-1, and plants having isolated point mutations in such genes.

Abstract: The invention concerns the use of duplex oligonucleotides about 25 to 30 base pairs to introduce site specific genetic alterations in plant cells. The oligonucleotides can be delivered by mechanical (biolistic) systems or by electrpoporation of plant protoplasts. Thereafter plants having the genetic alteration can be generated from the altered cells. In specific embodiments the invention concerns alteration in the gene that encode acid invertase, UDP-glucose pyrophosphorylase, polyphenol oxidase, O-methyl transferase, cinnamyl alcohol dehydrogenase, ACC synthase and ACC oxidase or etr-1 or a homolog of etr-1, and plants having isolated point mutations in such genes.

Abstract: The invention relates to isolated nucleic acid molecules encoding MutS homologues (MSHs). Such MSH proteins are involved in DNA mismatch-repair processes in organisms. The invention provides isolated nucleic acid molecules comprising MSH2 nucleotide sequences which encode MSH2 proteins and MSH2 nucleotide sequences which encode dominant-negative MSH2 variants. Such MSH2 nucleotide sequences find use in altering mismatch repair, mutation rates and recombination frequencies in both eukaryotic and prokaryotic organisms. The invention also provides isolated nucleic acid molecules comprising MSH2 promoter nucleotide sequences. Such MSH2 promoter nucleotide sequences find use in regulating the expression of genes of interest in plants. Additionally provided are isolated proteins, transformed host cells, and transformed plants, tissues, cells and seeds thereof.

Abstract: A modular bidirectional optical amplification system includes a multiwavelength dual amplifier building block, a multiwavelength unidirectional booster amplifier BB, a unidirectional and a bidirectional Optical Service Channel (OSC) BB, an Intelligent Optical Terminal Accessway (IOTA) module, and an interleaved filter BB. The dual amplifier BB is available in a C-band version, an E-band version and a hybrid version, and provides unidirectional or bidirectional multichannel amplification. The booster amplifier is available in a C-band version, an E-band version and in a booster plus variant; one for the C-band and one for E-band. The unidirectional and bidirectional OSC BBs provide a means for OAM&P functionality to the optical network. The IOTA BB provides multiplexing and demultiplexing, and the filter BB provides separation of the signal into grid-1 and grid-2 channels.

Abstract: An in vivo or in vitro cell-free method for genetic repair of mutation in plastid genes has been found which consists of (1) reacting a plasmid which contains a specific mutation (point mutation or frameshift mutation) of interest, a chimeric RNA/DNA oligonucleotide or a modified single stranded oligonucleotide which is believed to contain the genetic code for correcting the plastid gene mutation, and a chloroplast extract taken from the plant of interest, and (2) determining the success of gene conversion using a genetic readout system. A cell-free assay is disclosed by which the enzymatic capacity of chloroplast extracts to direct gene repair such as corrections to both point mutations and frameshift mutations can be determined. This assay method also enables the mechanistic study of plastid gene repair and facilitates the direct comparison between plant nuclear and organelle DNA repair pathways.

Abstract: An accurate method for characterizing optical fiber using a modest enhancement to equipment that is already in place for other purposes within an optical transmission system is thereby disclosed. In particular, optical amplifier light sources already embedded in transmission equipment are used to provide accurate characterization information in addition to their conventional purpose. Therefore, the invention permits fiber characterization at little additional cost over the optical amplifier light sources already present in a system. Furthermore, the need of going out to the field, disconnecting the transmission equipment and performing the field measurements with separate test equipment is eliminated.

Abstract: The present invention provides isolated and purified genes which are differentially expressed during banana fruit development, and the protein products of these genes. The present invention further provides DNA regulatory elements which are differentially expressed during banana fruit development, chimeric genes comprising these DNA regulatory elements operably linked to heterologous DNA molecules, and plants transformed with said chimeric genes, providing for controlled expression of said heterologous DNA molecules during the development and ripening of the fruit of said plants, or in response to exogenous ethylene signals in said plants. The present invention also provides a method for expression of a heterologous protein in fruit comprising transforming fruiting plants with one or more chimeric genes according to the present invention, exposing said fruit to an endogenous or exogenous ethylene signal, and harvesting fruit containing said heterologous protein.

Abstract: The invention concerns the use of duplex oligonucleotides about 25 to 30 base pairs to introduce site specific genetic alterations in plant cells. The oligonucleotides can be delivered by mechanical (biolistic) systems or by electrpoporation of plant protoplasts. Thereafter plants having the genetic alteration can be generated from the altered cells. In specific embodiments the invention concerns alteration in the gene that encode acid invertase, UDP-glucose pyrophosphorylase, polyphenol oxidase, O-methyl transferase, cinnamyl alcohol dehydrogenase, ACC synthase and ACC oxidase or etr-1 or a homolog of etr-1, and plants having isolated point mutations in such genes.

Abstract: Methods and compositions are presented for the generation of targeted alterations in a plant genome using double-stranded homogeneous oligonucleotides containing a single type of nucleotide. These methods can be used to correct mutations, introduce mutations and/or alter gene activity in a plant cell. A cell-free assay system for monitoring genetic alteration using the oligonucleotides of the invention is also presented.

Abstract: A modular bidirectional optical amplification system includes a multiwavelength dual amplifier building block, a multiwavelength unidirectional booster amplifier BB, a unidirectional and a bidirectional Optical Service Channel (OSC) BB, an Intelligent Optical Terminal Accessway (IOTA) module, and an interleaved filter BB. The dual amplifier BB is available in a C-band version, an E-band version and a hybrid version, and provides unidirectional or bidirectional multichannel amplification. The booster amplifier is available in a C-band version, an E-band version and in a booster plus variant; one for the C-band and one for E-band. The unidirectional and bidirectional OSC BBs provide a means for OAM&P functionality to the optical network. The IOTA BB provides multiplexing and demultiplexing, and the filter BB provides separation of the signal into grid-1 and grid-2 channels.

Abstract: The invention relates to isolated nucleic acid molecules encoding MutS homologues (MSHs). Such MSH proteins are involved in DNA mismatch-repair processes in organisms. The invention provides isolated nucleic acid molecules comprising MSH2 nucleotide sequences which encode MSH2 proteins and MSH2 nucleotide sequences which encode dominant-negative MSH2 variants. Such MSH2 nucleotide sequences find use in altering mismatch repair, mutation rates and recombination frequencies in both eukaryotic and prokaryotic organisms. The invention also provides isolated nucleic acid molecules comprising MSH2 promoter nucleotide sequences. Such MSH2 promoter nucleotide sequences find use in regulating the expression of genes of interest in plants. Additionally provided are isolated proteins, transformed host cells, and transformed plants, tissues, cells and seeds thereof.

Abstract: The invention relates to isolated nucleic acid molecules encoding plant XRCC3 proteins. Such XRCC3 proteins are believed to be involved in homologous recombination and DNA-repair processes in organisms, particularly plants. The invention provides isolated nucleic acid molecules comprising XRCC3 nucleotide sequences which encode XRCC3 proteins and XRCC3 nucleotide sequences which encode dominant-negative XRCC3 variants. Such XRCC3 nucleotide sequences find use in altering DNA repair, mutation rates and recombination frequencies in both eukaryotic and prokaryotic organisms. Additionally provided are isolated proteins, transformed non-human host cells, and transformed plants, tissues, cells and seeds thereof.