T-DNA structure in transgenic tobacco plants with multiple independent integration sites

Summary Transgenic tobacco plants were produced by inoculation of leaf disks withAgrobacterium tumefaciens harboring a disarmed binary vector containing soybean leghemoglobin Lbc3 and glycinin G2 genes. Physical and genetic characterization of these plants indicated that one to six copies of DNA from the vector were transferred and maintained in the plant genome. Approximately 30% of the copies transferred were found to be incomplete or rearranged and in some cases joined as inverted repeats. The transferred DNA was found at multiple genetic loci in five of the six cases examined. In one plant, kanamycin-resistance traits were at four independent chromosomal positions, although two were genetically linked at about 3 centimorgans. Thus,Agrobacterium-mediated DNA transfer to plants has some characteristics in common with “natural” systems in animals, such as retroviral or P-element derived systems, some characteristics in common with “artificial” systems, such as microinjection, electroporation, or calcium phosphate coprecipitation techniques, and some novel characteristics.     

The structures of integration sites in transgenic rice

Extensive genomic sequencing and sequence motif analysis have been conducted over the integration sites of two transgenic rice plants, #478 and #559, carrying the luciferase gene and/or hygromycin phosphotransferase gene. The transgenes reside in a region with inverted structure and a large duplication of rice genome over 2 kb. Integration was found at the AT-rich region and/or at the repetitive sequence region, including a SAR-like structure, retrotransposon and telomere repeats. The presence of a patch of sequence homology between plasmid and target DNA, and a small region of duplication involving the target DNA around the recombination site, implicated illegitimate recombination in the process of gene integration. Massive rearrangement of genomic DNA including deletion or translocation was also observed at the integration site and the flanking region of the transgene. The recognition sites of DNA topoisomerases I or II were observed in the rearranged sequences. Since only three junctions of transgenic rice were implicated in the illegitimate recombination and extensive rearrangement of the rice genome, rice protoplasts may be active in this process.     

Molecular characterization of T-DNA integration sites in transgenic birch

The integration and structure of a transgene locus can have profound effects on the level and stability of transgene expression. We screened 28 transgenic birch (Betula platyphylla Suk.) lines transformed with an insect-resistance gene (bgt) using Agrobacterium tumefaciens. Among the transgenic plants, the copy number of transgene varied from one to four. A rearrangement or partial deletion had occurred in the process of T-DNA integration. T-DNA repeat formation, detected by reverse primer PCR, was found among randomly screened transgenic lines. Sequencing of the junctions between the T-DNA inserts revealed deletions of 19–589 bp and an additional 45 bp filler DNA sequence was inserted between the T-DNA repeats at one junction. Micro-homologous sequences (1–6 bp) were observed in the junctions between the T-DNA inserts. Using SiteFinding-PCR, a relatively high percentage of AT value was found for the flanking regions. Deletion of the right border repeat was observed in 12/18 of the T-DNA/plant junctions analyzed. The number of nucleotides deleted varied from 3 to 712. Deletions of 17–89 bp were observed in all left T-DNA/plant junctions analyzed. A vector backbone DNA sequence in the transgene loci was also detected using primer pairs outside the left and right T-DNA borders. Approximately 89.3% of the lines contained some vector backbone DNA. These observations revealed that it is important to check the specificity of the integration. A mechanism of T-DNA transport and integration is proposed for this long-lived tree species.     

Analysis of integration sites of T-DNA insertions in transgenic tobacco plants

DNA fragments containing T-DNA/plant DNA junctions isolated from 17 transgenic tobacco plants were amplified using inverse PCR. Analysis of the nucleotide sequences of 34 cloned DNA fragments revealed 100% homology with vector sequences outside T-DNA in 10 cases. Nine nucleotide sequences had homology with the repeats in the tobacco genome. The percentage of homology varied from 70 to 90%, with the identified repeats belonging to different types. In most clones no homology was revealed with the GENEBANK sequences. Alignment of the sequences truncated during the integration of the left and the right borders of the T-DNA insertions demonstrated significant clusterization (10 bp region) of truncation sites for the left border. Five sequences had identical truncation sites (+23 T) that showed the perferable use of this nucleotide. The AT content varied from 51 to 72% which was close to the total percentage of AT pairs in the tobacco genome.     

Induced reciprocal translocation in transgenic mice near sites of transgene integration

Transgenic mice (JCP₀ #18), heterozygous for an insertion of approximately 50 copies of the rat peripheral myelin (P₀) protein cDNA, displayed a pattern of reduced litter size that suggested a chromosome rearrangement. Chromosome banding studies of fetal cells disclosed the presence of an apparently balanced translocation between a Chromosome (Chr) 1 and 14 with breakpoints at bands 1H3 and 14C3. In situ hybridization of biotin-labeled P₀ rat cDNA probe to chromosome spreads and detection of specific signal with fluorescein isothiocyanate-conjugated avidin revealed a strong signal on the 1¹⁴ translocation chromosome at the site of the breakpoint. A weaker signal was present near the breakpoint on the 14¹ derivative chromosome. These results suggest an etiologic relationship between the insertion of the transgene and the origin of the translocation. To further elucidate possible mechanisms, we first mapped the endogenous P₀ gene (gene symbol Mpp). As previously reported (You et al., Genomics 9: 751, 1991), we found that Mpp is located on Chr 1 in the region of the translocation breakpoint in JCP₀ mice. Subsequently, we have carried out pulsed-field gel and standard Southern analyses with P₀ gene probes, but found no evidence for a direct involvement of the endogenous P₀ gene in the process that generated the balanced reciprocal translocation. Thus, we favor the hypothesis that, during repair of DNA strand breakage—possibly induced by the microinjection procedure—the transgene copies were ligated to broken ends of Chrs 1 and 14. According to convention, this translocation is designated T(1;14) 1Po. Homozygotes are phenotypically normal and breed well; they will be useful for genetic and physical mapping of Chrs 1 and 14.     

Privacy-preserving integration of multiple institutional data for single-cell type identification with scPrivacy

The rapid accumulation of large-scale single-cell RNA-seq datasets from multiple institutions presents remarkable opportunities for automatically cell annotations through integrative analyses. However, the privacy issue has existed but being ignored, since we are limited to access and utilize all the reference datasets distributed in different institutions globally due to the prohibited data transmission across institutions by data regulation laws. To this end, we present scPrivacy, which is the...     

Identification of plasmid and Bacillus subtilis chromosomal recombination sites used for pE194 integration.

The plasmid pE194 (3.7 kilobases) is capable of integrating into the genome of the bacterial host Bacillus subtilis in the absence of the major homology-dependent RecE recombination system. Multiple recombination sites have been identified on both the B. subtilis chromosome and pE194 (J. Hofemeister, M. Israeli-Reches, and D. Dubnau, Mol. Gen. Genet. 189:58-68, 1983). The B. subtilis chromosomal recombination sites were recovered by genetic cloning, and these sites were studied by nucleotide sequence analysis. Recombination had occurred between regions of short nucleotide homology (6 to 14 base pairs) as indicated by comparison of the plasmid and the host chromosome recombination sites with the crossover sites of the integration products. Recombination between the homologous sequences of the plasmid and the B. subtilis genome produced an integrated pE194 molecule which was bounded by direct repeats of the short homology. These results suggest a recombination model involving a conservative, reciprocal strand exchange between the two recombination sites. A preferred plasmid recombination site was found to occur within a 70-base-pair region which contains a GC-rich dyad symmetry element. Five of seven pE194-integrated strains analyzed had been produced by recombination at different locations within this 70-base-pair interval, located between positions 860 and 930 in pE194. On the basis of these data, mechanisms are discussed to explain the recombinational integration of pE194.     

Spatial integration characteristics in motion detection and direction identification

Spatial integration characteristics were assessed with drifting gratings for both detection and direction-identification contrast thresholds. Thresholds were measured while stimulus width, length or both were varied. It was found that: (1) the shape of the size/sensitivity functions changes with spatial, but not with temporal, frequency; (2) direction-identification thresholds diverge from the detection thresholds below 1 cycle but can be reliably measured for stimulus widths as small as 0.1275 cycles; (3) the integration characteristics are slightly anisotropic for the identification but not for the detection process, and (4) the two-dimensional spatial integration cannot be directly predicted from its one-dimensional characteristics. Width/sensitivity detection functions are well fitted by predictions of Wilson and Bergen's four-channel model. Predictions from a temporal covariance model provide a poor fit to the identification data. It is argued that classes of detection and direction-identification models must involve identical nonlinearities prior to their respective thresholds. It is concluded that the hypothesis according to which both performances are determined by the same spatial integration stage cannot be rejected.     

Analysis of transgene integration sites in transgenic pigs by fluorescence in situ hybridization

The production of pigs transgenic for human decay accelerating factor (hDAF) as potential donors for clinical organ xenotransplantation was reported several years ago. For this purpose it is required that high levels of hDAF are expressed at relevant sites in transplantable organs. Currently, homozygous lines have been produced as well as lines from crosses between heterozygous animals from different founder lines, termed jigsaw pigs. The purpose of the jigsaw crosses is to combine the desirable hDAF protein expression patterns found in different founder lines. Initial selection of the jigsaw pigs is based on the inheritance of the hDAF integration sites from both lines. Litters with potential homozygous transgenics and jigsaw transgenics were analysed by fluorescence in situ hybridization (FISH) and slot blot analysis. Results show that both slot blot analysis and FISH are suitable to distinguish between pigs that are heterozygous and homozygous for hDAF. However, FISH has the advantage of producing results more rapidly. For the identification of jigsaw pigs FISH analysis was required since slot blot analysis lacked the required accuracy. On basis of these results, FISH analysis was made part of the routine screening programme for hDAF transgenic pigs     

The detection of transgenic animals using a polymerase chain reaction in situ

The technique for detecting both foreign and host specific DNA sequences inside nuclei and chromosomes of single cells of transgenic mice with the help of polymerase chain reaction (PCR) in situ is described. The mouse preimplantation and postimplantation embryonic and adult cells were studied. The methodology is described in detail with particular attention to the optimization of composition of reaction mixture, kind of fixation and preliminary denaturation of target DNA. The reaction takes only several hours and needs no sophisticated equipment.     

Probability models and the applicability of statistical procedures in the identification of chromosomal fragile sites

Summary. Böhm et al. (1995, Human Genetics 95 , 249–256) introduced a statistical model (named FSM–fragile site model) specifically designed for the identification of fragile sites from chromosomal breakage data. In response to claims to the contrary (Hou et al., 1999, Human Genetics 104 , 350–355; Hou et al., 2001, Biometrics 57 , 435–440), we show how the FSM model is correctly modified for application under the assumption that the probability of random breakage is proportional to chromosomal band length and how the purportedly alternative procedures proposed by Hou, Chang, and Tai (1999, 2001) are variations of the correctly modified FSM algorithm. With the exception of the test statistic employed, the procedure described by Hou et al. (1999) is shown to be functionally identical to the correctly modified FSM and the application of an incorrectly modified FSM is shown to invalidate all of the comparisons of FSM to the alternatives proposed by Hou et al. (1999, 2001). Last, we discuss the statistical implications of the methodological variations proposed by Hou et al. (2001) and emphasize the logical and statistical necessity for fragile site identifications to be based on data from single individuals.     

Cloning, characterization, and multiple chromosomal integration of a Bacillus alkaline protease gene

Extracellular Bacillus proteases are used as additives in detergent powders. We identified a Bacillus strain that produces a protease with an extremely alkaline pH optimum; this protease is suitable for use in modern alkaline detergent powders. The alkalophilic strain Bacillus alcalophilus PB92 gene encoding this high-alkaline serine protease was cloned and characterized. Sequence analysis revealed an open reading frame of 380 amino acids composed of a signal peptide (27 amino acids), a prosequence (84 amino acids), and a mature protein of 269 amino acids. Amino acid comparison with other serine proteases shows good homology with protease YaB, which is also produced by an alkalophilic Bacillus strain. Both show moderate homology with subtilisins but show some remarkable differences from subtilisins produced by neutrophilic bacilli. The prosequence of PB92 protease has no significant homology with prosequences of subtilisins. The abundance of negatively charged residues in the prosequences of PB92 protease is especially remarkable. The cloned gene was used to increase the production level of the protease. For this purpose the strategy of gene amplification in the original alkalophilic Bacillus strain was chosen. When introduced on a multicopy plasmid, the recombinant strain was unstable; under production conditions, plasmid segregation occurred. More stable ways of gene amplification were obtained by chromosomal integration. This was achieved by (i) homologous recombination, resulting in a strain with two tandemly arranged genes, and (ii) illegitimate recombination, resulting in a strain with a second copy of the protease gene on a locus not adjacent to the originally present gene. Both strains showed increased production and were more stable than the plasmid-containing strain. Absolute stability was only found when nontandem duplication occurred. This method of gene amplification circumvents stability problems often encountered in gene amplification in Bacillus species when plasmids or tandemly arranged genes in the chromosome are used.     

Analysis of secondary,integration sites for IS117 in Streptomyces lividans and their role in the generation of chromosomal deletions

IS117, the 2.6 kb mini-circle of Streptomyces coelicolor A3(2), is a transposable element previously shown to be integrated into two distant sites in the chromosome. When introduced into S. lividans, IS117 integrates into one preferred chromosomal site, but when this site was artificially deleted, IS117 integrated into many secondary sites. Nucleotide sequence analysis of several secondary integration sites revealed varying degrees of similarity with the preferred site, but no consensus sequence. Nevertheless, sites more similar to the preferred site tended to be occupied more often than those that are less similar. Insertion of IS117 into secondary sites in the chromosome of S. lividans sometimes mediated chromosomal rearrangements. It was shown that some strains containing IS117 integrated into secondary sites had suffered deletions of chromosomal DNA. Deletions were adjacent to the inserted element and were at least several kilobases long. The proposed model implicates homologous recombination between IS117 copies integrated into two different secondary sites in the same chromosome as a cause of the deletions.     

Production of transgenic pigs mediated by pseudotyped lentivirus and sperm

Sperm-mediated gene transfer can be a very efficient method to produce transgenic pigs, however, the results from different laboratories had not been widely repeated. Genomic integration of transgene by injection of pseudotyped lentivirus to the perivitelline space has been proved to be a reliable route to generate transgenic animals. To test whether transgene in the lentivirus can be delivered by sperm, we studied incubation of pseudotyped lentiviruses and sperm before insemination. After incubation with pig spermatozoa, 62±3 lentiviral particles were detected per 100 sperm cells using quantitative real-time RT-PCR. The association of lentivirus with sperm was further confirmed by electron microscopy. The sperm incubated with lentiviral particles were artificially inseminated into pigs. Of the 59 piglets born from inseminated 5 sows, 6 piglets (10.17%) carried the transgene based on the PCR identification. Foreign gene and EGFP was successfully detected in ear tissue biopsies from two PCR-positive pigs, revealed via in situ hybridization and immunohistochemistry. Offspring of one PCR-positive boar with normal sows showed PCR-positive. Two PCR-positive founders and offsprings of PCR-positive boar were further identified by Southern-blot analysis, out of which the two founders and two offsprings were positive in Southern blotting, strongly indicating integration of foreign gene into genome. The results indicate that incubation of sperm with pseudotyped lentiviruses can incorporated with sperm-mediated gene transfer to produce transgenic pigs with improved efficiency.     

Piecing together the timetable for visual transduction with transgenic animals

Transgenic mice bearing null or functional mutations are being used to define the roles of specific elements in phototransduction and also to time the molecular interactions. Genetic manipulation of the collision frequency between rhodopsin and transducin molecules identified this parameter as rate-limiting for the photoresponse onset. Genetic interference with rhodopsin phosphorylation and arrestin binding, transducin shut-off and calcium feedback has revealed their respective roles in shaping the response waveform. The timetable for all of these molecular events determines the amplitude, kinetics and reproducibility of the photoresponse.     

Antibody manufacture in transgenic animals and comparisons with other systems

Various forms of recombinant monoclonal antibodies are being used increasingly, mainly for therapeutic purposes. The isolation and engineering of the corresponding genes is becoming less of a bottleneck in the process; however, the production of recombinant antibodies is itself a limiting factor and a shortage is expected in the coming years. Milk from transgenic animals appears to be one of the most attractive sources of recombinant antibodies. None of the production systems presently implemented (CHO cells, insect cells infected by baculovirus, or transgenic animals and plants) has yet been optimized. This review describes the advantages of using milk for antibody production in comparison with the other systems.