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Recombination, Genetic

Genetic recombination is a fundamental biological process that involves the rearrangement of genetic material during meiosis or mitosis.
This process generates genetic diversity by creating new combinations of alleles, genes, and chromosomes.
Recombination is essential for sexual reproduction and plays a crucial role in evolutionary processes.
Researchers can leverage PubCompare.ai's AI-driven platform to enhance their genetic recombination studies, easily locating the best protocols from literature, pre-prints, and patents using intelligent comparisons.
This tool helps discover the most effective methods and products to advance research in this field, providing the power of AI-driven accuracy and efficiency.

Most cited protocols related to «Recombination, Genetic»

Of approximately 6.9 million SNPs in dbSNP release 122 approximately 4.7 million were selected for genotyping by Perlegen. 2.5 million SNPs were excluded because no assay could be designed and a further 350,000 were excluded for other reasons (see Methods). Perlegen performed genotyping using custom high-density oligonucleotide arrays as previously described15 (link). Additional genotype submissions are described in the text. QC filters were applied as previously described3 (link). Where multiple submissions met the QC criteria the submission with the lowest missing data rate was chosen for inclusion in the non-redundant filtered data set. Haplotypes were estimated from genotype data as described previously3 (link). Ancestral states at SNPs were inferred by parsimony by comparison to orthologous bases in the chimpanzee (panTro2) and rhesus macaque (rheMac2) assemblies. Recombination rates and the location of recombination hotspots were estimated as described previously3 (link). Additional details can be found in the Methods section and the Supplementary Information. The data described in this paper are in release 21 of the International HapMap Project.
Publication 2007
Biological Assay Genotype Haplotypes Macaca mulatta Oligonucleotide Arrays Pan troglodytes Recombination, Genetic Single Nucleotide Polymorphism
Targeting constructs were generated using a combined gene synthesis (GenScript Corp.) and molecular cloning approach. Briefly, to target the Rosa26 locus, a cassette containing the following components was constructed: FRT – LoxP – Stop codons – 3x SV40 polyA – LoxP – EYFP – WPRE – bGH polyA – AttB – PGK promoter – FRT – Neo – PGK polyA – AttP. For most targeting vectors, this cassette was cloned into a Rosa-CAG targeting vector3 (link), downstream of the CAG promoter and upstream of the 3′ arm, to generate the final EYFP targeting vector. Unique restriction sites flanking the EYFP gene were used to replace EYFP with alternative reporter genes. For the Ai2 vector, which lacks the WPRE, the CAG promoter was inserted between the first FRT and LoxP sites, and the cassette was cloned immediately downstream of the 5′ homology arm. The final targeting vectors contained 5′ and 3′ homology arms of 1.1 kb and 4.3 kb, as well as a PGK-DTA cassette for negative selection. Targeting constructs for knock-in Cre lines inserted into other gene loci were constructed in similar ways.
The targeting vectors were linearized and transfected into the 129/B6 F1 hybrid ES cell line G442 (link) using an Amaxa electroporator. G418-resistant ES clones were screened by Southern blot analysis of HindIII digested DNA, which was probed with a 1.1 kb genomic fragment from immediately upstream of the 5′ arm. We observed a recombination rate of about 25% for the four constructs. Positive ES clones were injected into C57BL/6J blastocysts to obtain chimeric mice following standard procedures. Both ES cell transfections and blastocyst injections were performed by the University of Washington Transgenic Resources Program. Due to the robustness of the G4 cells, high-percentage chimeras and high rates of germline transmission were routinely obtained. Chimeric mice were bred with either C57BL/6J mice to obtain germline transmission or various Cre-driver lines for direct characterization.
An Ai9 ES cell clone with strong germline transmission potency was used in subsequent transfections for the Flp-mediated exchange strategy outlined in Supplementary Figure 4 online. Ai9 ES cells were co-transfected using a Bio-Rad electroporator with 100 μg of pCAGGS-FLPe (Open Biosystems) and 40 μg of an incoming replacement vector. After 8 to 10 days of Hygromycin B selection, surviving colonies that also appeared green by fluorescence microscopy were picked and screened by PCR using primer sets designed to confirm a correct insertion of the incoming vector at the 5′ and 3′ FRT recombinase sites.
Publication 2009
Anabolism Animals, Transgenic antibiotic G 418 Blastocyst Cells Chimera Clone Cells Cloning Vectors Codon, Terminator Embryonic Stem Cells Genes Genes, Reporter Genetic Loci Genome Germ Cells Germ Line Hybrid Cells Hygromycin B Mice, Inbred C57BL Microscopy, Fluorescence Mus N-fluoresceinylphosphatidylethanolamine Oligonucleotide Primers Poly A Recombinase Recombination, Genetic Rosa Simian virus 40 Southern Blotting Transfection Transmission, Communicable Disease
Targeting constructs were generated using a combined gene synthesis (GenScript Corp.) and molecular cloning approach. Briefly, to target the Rosa26 locus, a cassette containing the following components was constructed: FRT – LoxP – Stop codons – 3x SV40 polyA – LoxP – EYFP – WPRE – bGH polyA – AttB – PGK promoter – FRT – Neo – PGK polyA – AttP. For most targeting vectors, this cassette was cloned into a Rosa-CAG targeting vector3 (link), downstream of the CAG promoter and upstream of the 3′ arm, to generate the final EYFP targeting vector. Unique restriction sites flanking the EYFP gene were used to replace EYFP with alternative reporter genes. For the Ai2 vector, which lacks the WPRE, the CAG promoter was inserted between the first FRT and LoxP sites, and the cassette was cloned immediately downstream of the 5′ homology arm. The final targeting vectors contained 5′ and 3′ homology arms of 1.1 kb and 4.3 kb, as well as a PGK-DTA cassette for negative selection. Targeting constructs for knock-in Cre lines inserted into other gene loci were constructed in similar ways.
The targeting vectors were linearized and transfected into the 129/B6 F1 hybrid ES cell line G442 (link) using an Amaxa electroporator. G418-resistant ES clones were screened by Southern blot analysis of HindIII digested DNA, which was probed with a 1.1 kb genomic fragment from immediately upstream of the 5′ arm. We observed a recombination rate of about 25% for the four constructs. Positive ES clones were injected into C57BL/6J blastocysts to obtain chimeric mice following standard procedures. Both ES cell transfections and blastocyst injections were performed by the University of Washington Transgenic Resources Program. Due to the robustness of the G4 cells, high-percentage chimeras and high rates of germline transmission were routinely obtained. Chimeric mice were bred with either C57BL/6J mice to obtain germline transmission or various Cre-driver lines for direct characterization.
An Ai9 ES cell clone with strong germline transmission potency was used in subsequent transfections for the Flp-mediated exchange strategy outlined in Supplementary Figure 4 online. Ai9 ES cells were co-transfected using a Bio-Rad electroporator with 100 μg of pCAGGS-FLPe (Open Biosystems) and 40 μg of an incoming replacement vector. After 8 to 10 days of Hygromycin B selection, surviving colonies that also appeared green by fluorescence microscopy were picked and screened by PCR using primer sets designed to confirm a correct insertion of the incoming vector at the 5′ and 3′ FRT recombinase sites.
Publication 2009
Anabolism Animals, Transgenic antibiotic G 418 Blastocyst Cells Chimera Clone Cells Cloning Vectors Codon, Terminator Embryonic Stem Cells Genes Genes, Reporter Genetic Loci Genome Germ Cells Germ Line Hybrid Cells Hygromycin B Mice, Inbred C57BL Microscopy, Fluorescence Mus N-fluoresceinylphosphatidylethanolamine Oligonucleotide Primers Poly A Recombinase Recombination, Genetic Rosa Simian virus 40 Southern Blotting Transfection Transmission, Communicable Disease
Illumina short reads were obtained from Short Read Archive and capillary reads from TraceDB. Reads were aligned to the human reference genome with BWA26 . The consensus sequences were called by SAMtools27 and then divided into non-overlapping 100bp bins with a bin scored heterozygous if there is a heterozygote in the bin or being homozygous otherwise. The resultant bin sequences were taken as the input of the PSMC estimate. Coalescent simulation was done by ms28 and cosi21 . The simulated sequences were binned in the same way.
The free parameters in the discrete PSMC-HMM model are the scaled mutation rate, recombination rate and piecewise constant population sizes. The time interval each size parameter spans was manually chosen. The estimation-maximization iteration started from a constant-sized population history. The estimation step was done analytically; Powell’s direction set method is used for the maximization step. Parameter values stablized by the 20th iteration, and these were taken as the final estimate. All parameters are scaled to a constant that is further determined under the assumption of a neutral mutation rate 2.5×10−8.
Publication 2011
Capillaries Consensus Sequence Genome, Human Heterozygote Homozygote MS 28 Recombination, Genetic
HaploGrep 2 is a web application that communicates through a REST API with the web server. Thus, all computation intensive tasks are executed directly on the server. The haplogroup classification itself is based on pre-calculated phylogenetic weights that correspond to the occurrence per position in Phylotree and reflecting the mutational stability of a variant. In the updated classification algorithm, the weights are now scaled from 1 to 10 in a non-linear way (see Supplementary Table S1). Thus, the rare occurrences of variants in Phylotree will no longer influence the classification toward those haplogroups as much as in the previous version. Once the data is imported, the haplogroup classification is started automatically. Optimizations within the code led to a 20-fold speed-up compared to HaploGrep 1. By storing only the 50 highest ranked haplogroups per sample the memory consumption could be reduced significantly.
Furthermore, new dissimilarity metrics for the mtDNA haplogroup classification were introduced. In addition to the already implemented Kulczynski distance (1 (link)), the Jaccard index, the Hamming distance and the Kimura 2-parameter distance were included (24 ) (see Supplementary Table S2 and 3 for performance comparison). Further major improvements included a check for artificial recombination (25 (link)) and a check for systematic artefacts and for rare or potential phantom mutations (26 (link)). For detecting artificial recombination, we apply two different strategies: the first strategy, proposed by Kong et al. (27 (link)), counts the remaining variants that were not assigned to the resulting best haplogroup, and tests whether these variants could be assigned to another haplogroup. For this step, mutational hotspots are excluded (e.g. 315.1C or 16519). The second recombination strategy assumes prior knowledge about the specific placement of the fragments of the polymerase chain reaction products (amplicons). With this information in hand, a check comparing the profiles relative to the fragment ranges can be executed. The user-defined fragments are generated, and the profiles split accordingly. If the distance of both haplogroup fragments exceeds five phylogenetic nodes, the sample is listed as potentially contaminated.
Publication 2016
DNA, Mitochondrial Memory Mutation Polymerase Chain Reaction Recombination, Genetic

Most recents protocols related to «Recombination, Genetic»

Not available on PMC !

Example 18

Lines were raised and maintained following standard literature practice and in accordance with the Guide for the Care and Use of Laboratory Animals provided by the University of Southern California. Fish samples were part of a protocol approved by the IACUC (permit number: 12007 USC).

Transgenic FlipTrap Gt(desm-Citrine) ct122a/+ line is the result of previously reported screen, Tg(kdrl:eGFP)s843 line was provided by the Stainier lab (Max Planck Institute for Heart and Lung Research). The Tg(ubi:Zebrabow) line was a kind gift from Alex Schier. Controllable recombination of fluorophores was obtained by crossing homozygous Tg(ubi:Zebrabow) adults with a Tg(hsp70I:Cerulean-P2A-CreERT2) line. Embryos were raised in Egg Water (60 μg/ml of Instant Ocean and 75 μg/ml of CaSO4 in Milli-Q water) at 28.5° C. with addition of 0.003% (w/v) 1-phenyl-2-thiourea (PTU) around 18 hpf to reduce pigment formation.

Zebrafish samples with triple fluorescence were obtained by crossing Gt(desm-Citrine)ct122a/+ with Tg(kdrl:eGFP) fish followed by injection of 100 μg per embryo of mRNA encoding H2B-Cerulean at one cell stage as described in previous work29. Samples of Gt(desm-Citrine)ct122a/+;Tg(kdrl:eGFP); H2B-Cerulean were imaged with 458 nm laser to excite Cerulean, Citrine and eGFP and narrow 458-561 nm dichroic for separating excitation and fluorescence emission.

Patent 2024
Adult Animals, Laboratory Animals, Transgenic Cells Embryo Fishes Fluorescence Heart Homozygote Institutional Animal Care and Use Committees Lung Phenylthiourea Pigmentation Recombination, Genetic RNA, Messenger Zebrafish
Not available on PMC !

Example 2

A 30× genome coverage of both Xi19 and Robigus was generated. Bio-informatic mapping of the gDNA reads to the IWGSCWGAV02_2BS_scaffold14096, IWGSCWGAV02_2BS_scaffold11627 and the BAC sequence confirmed large structural differences in the region, which explain the observed lack of recombination. Essentially, there were no gDNA-seq reads from Xi19 that mapped onto the BAC sequence of Renan (FIG. 3). Similarly, none of the gDNA-seq reads from Robigus mapped onto scaffold11627 portion located in the interval. This indicates that the gene content of the corresponding genomic regions in susceptible and resistant plants is very divergent and this was probably caused by a local chromosomal rearrangement. Similar structural rearrangements between the Chinese Spring reference genome sequence and the region containing the Fusarium head blight resistance gene (Fhb1) have recently been published (Schweiger et al, 2016).

Patent 2024
Chinese Chromosomes Fusarium Gene Rearrangement Genes Genome Head Plants Recombination, Genetic

Example 95

After testing the different strategies for HDR gene editing, the lead CRISPR-Cas9/DNA donor combinations will be re-assessed in primary human hepatocytes for efficiency of deletion, recombination, and off-target specificity. Cas9 mRNA or RNP will be formulated into lipid nanoparticles for delivery, sgRNAs will be formulated into nanoparticles or delivered as AAV, and donor DNA will be formulated into nanoparticles or delivered as AAV.

Patent 2024
Clustered Regularly Interspaced Short Palindromic Repeats Deletion Mutation Hepatocyte Homo sapiens Lipid Nanoparticles Obstetric Delivery Recombination, Genetic RNA, Messenger Tissue Donors

Example 1

This example describes the generation of a marker-free B. subtilis strain expressing allulose epimerase. Briefly, in a first step, a B. subtilis strain was transformed with a cassette encoding the BMCGD1 epimerase and including an antibiotic resistance marker. This cassette recombined into the Bacillus chromosome and knocked out 8 kb of DNA, including a large sporulation gene cluster and the lysine biosynthesis gene lysA. In a second step, a second cassette was recombined into the B. subtilis chromosome, restoring the lysA gene and removing DNA encoding the antibiotic resistance. E. coli strain 39 A10 from the Keio collection was used to passage plasmid DNA prior to transformation of B. subtilis. The relevant phenotype is a deficiency in the DNA methylase HsdM in an otherwise wild-type K-12 strain of E. coli.

In detail, a cassette of 5120 bp (SEQ ID NO:1; synthetic DNA from IDT, Coralville, Iowa) was synthesized and cloned into a standard ampicillin resistant pIDT vector. The synthetic piece encoded 700 bp upstream of lysA on the B. subtilis chromosome, the antibiotic marker cat (651 bp), the DNA-binding protein lad (1083 bp), and the allulose epimerase (894 bp), and included 700 bp of homology in dacF. This vector was transformed into E. coli strain 39 A10 (Baba et al., 2006), and plasmid DNA was prepared and transformed into B. subtilis strains 1A751 and 1A976.

Transformants were selected on LB supplemented with chloramphenicol. The replicon for pIDT is functional in E. coli but does not work in Gram positive bacteria such as B. subtilis. The colonies that arose therefore represented an integration event into the chromosome. In strain 1A751, the colony morphology on the plates was used to distinguish between single and double recombination events. The double recombination event would knock out genes required for sporulation, whereas the single recombination would not. After three days on LB plates, colonies capable of sporulation were brown and opaque; sporulation-deficient colonies were more translucent.

B. subtilis strain 1A976 with the allulose epimerase cassette is auxotrophic for histidine and lysine and can achieve very high transformation efficiency upon xylose induction. A 1925 bp synthetic DNA (SEQ ID NO:2) was amplified by primers (SEQ ID NO:3, SEQ ID NO:4) and Taq polymerase (Promega). This PCR product encoded the lysA gene that was deleted by the dropping in the epimerase cassette and 500 bp of homology to lad. A successful double recombination event of this DNA should result in colonies that are prototrophic for lysine and sensitive to chloramphenicol; i.e., the entire cat gene should be lost.

Transformants were selected on Davis minimal media supplemented with histidine. Colonies that arose were characterized by PCR and streaking onto LB with and without chloramphenicol. Strains that amplified the introduced DNA and that were chloramphenicol sensitive were further characterized, and their chromosomal DNA was extracted.

Strain 1A751 containing the chloramphenicol resistant allulose was transformed with this chromosomal DNA and selected on Davis minimal media supplemented with histidine. Transformants were streaked onto LB with and without chloramphenicol and characterized enzymatically as described below.

Patent 2024
Ampicillin Anabolism Antibiotic Resistance, Microbial Antibiotics Bacillus Bacillus subtilis Chloramphenicol Chromosomes Cloning Vectors DNA, A-Form DNA-Binding Proteins Epimerases Escherichia coli Gene Clusters Gene Knockout Techniques Genes Gram-Positive Bacteria Histidine Lysine Methyltransferase Oligonucleotide Primers Phenotype Plasmids psicose Recombination, Genetic Replicon Strains Taq Polymerase Xylose

Example 4

In total, 23,400 lines were screened from crosses segregating for Sm1 with ten SNP markers distributed across the Sm1 locus in order to search for extra recombinants within this region. In total, 576 putative recombinants were identified and these, plus their parental lines, were also genotyped with two Real-Time PCR markers developed from RGA 1 and RGA 2 (Table 1B) and 46 markers that included 24 SNPs from within the interval and 22 markers tightly flanking the region. The results showed that no recombination events were found between the two RGA genes and no recombinant plants were found within the small 0.067 cM region identified in the Xi19 x Robigus bi-parental mapping population. The lack of recombination within the region is due to the absence of any sequence homology between resistant and susceptible lines. Moreover, all the lines that carried the two Robigus RGA genes shared the Robigus haplotype based on the 24 markers within the target interval suggesting a single origin and a common ancestor for the Sm1 resistance locus.

Amongst the 576 lines, a sub-panel of 113 diverse lines was selected for phenotypic analysis. This sub-panel contained many recombinant plants arising from different genetic origins in order to validate any potential diagnostic SNP markers. All the recombinant plants and their parental lines were sown and genotyped in summer 2014. The presence of the two RGA genes was always shown to be 100% diagnostic for the presence of Sm1. From these 24 markers within the interval, five were found to be correlated with the presence and absence of the two RGAs (Table 1A), which makes them ideal for marker-assisted selection of the Sm1 gene.

Patent 2024
A 113 Diagnosis Genes Genetic Markers Haplotypes Parent Phenotype Plants Real-Time Polymerase Chain Reaction Recombination, Genetic

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The PENTR/D-TOPO vector is a plasmid designed for direct cloning of PCR products. It features a pUC origin of replication and a kanamycin resistance gene for selection in E. coli. The vector includes TOPO cloning sites that facilitate the direct insertion of PCR products without the need for restriction enzyme digestion or ligation.
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The Gateway LR Clonase II Enzyme Mix is a laboratory reagent used for performing recombination-based cloning. It catalyzes the in vitro recombination between an entry clone and a destination vector to generate an expression clone.
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LR clonase is a laboratory reagent used in molecular biology for the recombination of DNA sequences. It catalyzes the integration of DNA fragments into an expression vector during the process of gene cloning. The core function of LR clonase is to facilitate the site-specific recombination of DNA sequences.
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More about "Recombination, Genetic"

Genetic recombination is a fundamental biological process that involves the rearrangement of genetic material during meiosis or mitosis.
This process generates genetic diversity by creating new combinations of alleles, genes, and chromosomes.
Recombination is essential for sexual reproduction and plays a crucial role in evolutionary processes.
Researchers can leverage AI-driven platforms like PubCompare.ai to enhance their genetic recombination studies.
These tools help easily locate the best protocols from literature, pre-prints, and patents using intelligent comparisons.
This allows researchers to discover the most effective methods and products to advance their work in this field, providing the power of AI-driven accuracy and efficiency.
Some key subtopics and related terms to consider in genetic recombination research include: - Tamoxifen and 4-hydroxytamoxifen: Selective estrogen receptor modulators (SERMs) that can be used to induce recombination in certain cell types. - Lipofectamine 2000: A transfection reagent commonly used to introduce genetic material, including recombination-inducing constructs, into cells. - PENTR/D-TOPO and Gateway recombination: Molecular cloning techniques that leverage recombination-based systems to quickly and efficiently generate expression vectors. - Gateway LR Clonase II Enzyme Mix and LR clonase: Enzymes used in the Gateway recombination process to facilitate the transfer of DNA sequences between entry and destination vectors. - Corn oil: A common vehicle used to deliver compounds like tamoxifen in recombination-based experiments.
By incorporating these related topics and terms, researchers can optimize their content for search engines and provide a comprehensive, informative resource for those interested in advancing genetic recombination studies.