Recombination, Genetic
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»
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
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.
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.
Most recents protocols related to «Recombination, Genetic»
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.
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 (
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.
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.
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.
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More about "Recombination, Genetic"
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.