Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Transformation efficiency”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 811 records · Page 45Linked to original sources
PubMed1997

Deoxyribonuclease treatment improves the homogeneity of single-stranded DNA preparations.

The isolation of single-stranded (ss) phagemid DNA using standard protocols often results in impure preparations, which contain undesirable quantities of chromosomal and/or double-stranded (ds) phagemid DNA. Here we report a simple and efficient method for elimination of virtually all dsDNA by incubation of phagemid viral particles with deoxyribonuclease I. In addition to analyzing the ratio of linear-to-circular topological forms of ssDNA after deoxyribonuclease I treatment, we verified that no decrease in transformation efficiency occurred and demonstrated that ssDNA molecules covered by capsid proteins remained intact following such treatment.

Bacteriophages↗
PubMed2005

Polyrigid and polyaffine transformations: a novel geometrical tool to deal with non-rigid deformations - application to the registration of histological slices.

We describe in this paper a novel kind of geometrical transformations, named polyrigid and polyaffine. These transformations efficiently code for locally rigid or affine deformations with a small number of intuitive parameters. They can describe compactly large rigid or affine movements, unlike most free-form deformation classes. Very flexible, this tool can be readily adapted to a large variety of situations, simply by tuning the number of rigid or affine components and the number of parameters describing their regions of influence. The displacement of each spatial position is defined by a continuous trajectory that follows a differential equation which averages the influence of each rigid or affine component. We show that the resulting transformations are diffeomorphisms, smooth with respect to their parameters. We devise a new and flexible numerical scheme to allow a trade-off between computational efficiency and closeness to the ideal diffeomorphism. Our algorithms are implemented within the Insight Toolkit, whose generic programming style offers rich facilities for prototyping. In this context, we derive an effective optimization strategy of the transformations which demonstrates that this new tool is highly suitable for inference. The whole framework is exemplified successfully with the registration of histological slices. This choice is challenging, because these data often present locally rigid deformations added during their acquisition, and can also present a loss of matter, which makes their registration even more difficult. Powerful and flexible, this new tool opens up large perspectives, in non-rigid 3D rigid registration as well as in shape statistics.

Algorithms↗
PubMed2000

Redox properties of iron-dithiocarbamates and their nitrosyl derivatives: implications for their use as traps of nitric oxide in biological systems.

While the Fe(2+)-dithiocarbamate complexes have been commonly used as NO traps to estimate NO production in biological systems, these complexes can undergo complex redox chemistry. Characterization of this redox chemistry is of critical importance for the use of this method as a quantitative assay of NO generation. We observe that the commonly used Fe(2+) complexes of N-methyl-D-glucamine dithiocarbamate (MGD) or diethyldithiocarbamate (DETC) are rapidly oxidized under aerobic conditions to form Fe(3+) complexes. Following exposure to NO, diamagnetic NO-Fe(3+) complexes are formed as demonstrated by the optical, electron paramagnetic resonance and gamma-resonance spectroscopy, chemiluminescence and electrochemical methods. Under anaerobic conditions the aqueous NO-Fe(3+)-MGD and lipid soluble NO-Fe(2+)-DETC complexes gradually self transform by reductive nitrosylation into paramagnetic NO-Fe(2+)-MGD complexes with yield of up to 50% and the balance is converted to Fe(3+)-MGD and nitrite. In dimethylsulfoxide this process is greatly accelerated. More efficient transformation of NO-Fe(3+)-MGD into NO-Fe(2+)-MGD (60-90% levels) was observed after addition of reducing equivalents such as ascorbate, hydroquinone or cysteine or with addition of excess Fe(2+)-MGD. With isotope labeling of the NO-Fe(3+)-MGD with (57)Fe, it was shown that these complexes donate NO to Fe(2+)-MGD. NO-Fe(3+)-MGD complexes were also formed by reversible oxidation of NO-Fe(2+)-MGD in air. The stability of NO-Fe(3+)-MGD and NO-Fe(2+)-MGD complexes increased with increasing the ratio of MGD to Fe. Thus, the iron-dithiocarbamate complexes and their NO derivatives exhibit complex redox chemistry that should be considered in their application for detection of NO in biological systems.

Dimethyl Sulfoxide↗
PubMed1996

Efficient homologous recombination in fast-growing and slow-growing mycobacteria.

Although homologous recombination is a major mechanism for DNA rearrangement in most living organisms, it has been difficult to detect in slowly growing mycobacteria by a classical suicide vector approach. Among the possible reasons for this are the low levels of transformation efficiency, the relatively high levels of illegitimate recombination, and the peculiar nature of the recA gene in slowly growing mycobacteria. In this report, we present an efficient homologous recombination system for these organisms based on the use of replicative plasmids which facilitates the detection of rare recombination events, because the proportions of recombined molecules increase over time. Intraplasmid homologous recombination in Mycobacterium smegmatis and Mycobacterium bovis BCG was easily selected by the reconstitution of an interrupted kanamycin resistance gene. Chromosomal integration via homologous recombination was selected by the expression of the kanamycin resistance gene under the control of a chromosomal promoter that was not present in the plasmid before recombination. This technique was termed STORE (for selection technique of recombination events). All the clones selected by STORE had undergone homologous recombination, as evidenced by PCR analyses of the kanamycin-resistant clones. This technique should be applicable to all organisms for which homologous recombination has been difficult to achieve, provided the gene of interest is expressed.

Amino Acid Sequence↗
PubMed1996

Malignant transformation induced by cytokine genes: a comparison of the abilities of germline and mutated interleukin 3 genes to transform hematopoietic cells by transcriptional and posttranscriptional mechanisms.

The effects of inheritance of germline (gIL3) and rearranged interleukin 3 (rIL3) genes on the factor dependency and tumorigenicity of a hematopoietic cell line were compared. The rIL3 gene arose after intracisternal type A particle transposition into the 3' untranslated region (UTR). The rlL3 gene efficiently transformed cells. In contrast, factor-independent cell lines were recovered only rarely from gIL3-transfected cells, and they fell into two categories. One class inherited more than one copy of the transgene and expressed moderate levels of lL-3, whereas the other group received one copy and expressed lower amounts of lL-3. Tumorigenicity was associated with the quantity of lL-3 expression because cells from the first class were malignant, whereas those from the latter set were not. To determine which portions of the rIL3 gene were responsible for cell transformation, chimeric constructs were made containing exchanged sections of the gIL3 and rIL3 genes. The transforming region was mapped to the 3' end of the rIL3 gene, and no point mutations in the promoter region were detected. RNA gel shift assays indicated that the transposition eliminated the ability of proteins to bind the 3'UTR. These results demonstrate that the mutation of the IL-3 3'UTR by intracisternal type A particle transposition results in: (a) the inability of proteins to bind the 3'UTR; (b) prolonged mRNA half life; (c) constitutive IL-3 expression; (d) cytokine independence; and (e) tumorigenicity. Inheritance of a gIL3 gene was not normally sufficient to abrogate cytokine dependency; however, rare tumorigenic cells were isolated, implicating the importance that deregulated cytokine expression can have upon malignant transformation.

Animals↗
PubMed1987

Transforming and mitogenic effects of avian leukemia virus E26 on chicken hematopoietic cells and fibroblasts, respectively, correlate with level of expression of the provirus.

We have investigated the effect of E26, an avian leukemia retrovirus, on the growth properties of chicken embryo fibroblasts (CEFs). E26-infected CEFs were not transformed, according to several transformation parameters, but exhibited an activated growth in vitro. They started to grow without latency in serum-supplemented medium, maintained long-term growth in regular or low-serum medium, and could grow when seeded at low cell density in low-serum medium. We compared the integration and the level of expression of the proviral DNA in E26-infected CEFs and E26-transformed hematopoietic cells. An average of two provirus copies were found in each kind of cells. However, whereas high contents of both viral mRNA and E26-specific protein products were found in transformed hematopoietic cells, we detected only low amounts of viral mRNA and no E26 protein in infected CEFs. These data show that the level of expression of the E26 provirus is lower in CEFs than in hematopoietic cells. They suggest that transformation efficiency of the virus depends on its level of expression.

Animals↗
PubMed1988

myc protooncogene linked to retroviral promoter, but not to enhancer, transforms embryo cells.

To define conditions under which the chicken protooncogene p-myc is converted to a viral and possibly to a cellular transforming gene, we assayed transforming function of hybrid genes put together from cloned retroviral and p-myc elements and of p-myc genes isolated from spontaneous viral lymphomas. Transforming function was measured in quail embryo cells transfected with cloned myc genes. We found that only myc genes with a promoter of a retroviral long terminal repeat (LTR) located between the native p-myc promoter and the second p-myc exon have transforming function. Transforming efficiencies decreased with increasing lengths of unspliced sequences between the LTR and p-myc exon 2. p-myc DNAs with LTRs downstream of the coding region or upstream but in the opposite transcriptional orientation failed to transform embryo cells. Likewise, only those retroviral-p-myc combinations from chicken B-cell lymphomas with a LTR positioned as promoter upstream of p-myc exon 2 had transforming function. We conclude that substitution of a retroviral LTR for the promoter and for as yet poorly defined, untranscribed regulatory elements of p-myc is sufficient to convert chicken p-myc to a transforming gene. However, retroviral LTRs can only convert p-myc genes to embryo-cell-transforming genes from a limited number of positions, and not as position-independent enhancers. Further, we deduce that there are two classes of viral chicken B-cell lymphomas, those with and those without embryo-cell-transforming p-myc genes.

Animals↗
PubMed1989

A rapid and efficient procedure for transformation of intact Saccharomyces cerevisiae by electroporation.

A rapid and efficient procedure is described for transforming Saccharomyces cerevisiae using electroporation to render intact cells permeable to DNA. The technique uses relatively low voltages and is particularly sensitive to low concentrations of plasmid DNA. At the highest voltage used (400 volts), the frequency of transformation increased with the amount of plasmid DNA between 25 ng and 100 ng. At higher concentrations of DNA (1-1.5 micrograms) electroporation yielded one-third to one-half the number of transformants obtained with a standard lithium acetate pretreatment. Because this method requires neither pretreatment of cells nor addition of polyethylene glycol (PEG), it has several advantages over currently used transformation procedures.

Electric Stimulation↗
PubMed1999

Polarity of recombination in transformation of Streptococcus pneumoniae.

In transformation of Streptococcus pneumoniae DNA enters the cell as single-strand fragments and integrates into the chromosome by homologous recombination. Deletions and insertions of a few hundred base pairs frequently stop the recombination process of a donor strand. In this work we took advantage of such interruptions of recombination to compare the transformation efficiencies of the segments 5'- and 3'-ward from a deletion. The deletion was created in the center of a fragment of the ami locus, and sites around the deletion were labeled by a frameshift generating a restriction site. Heteroduplexes were constructed containing two restriction sites on one strand and two different ones on the complementary strand. ami+ bacteria were transformed with such heteroduplexes. ami- transformants were isolated and individually underwent amplification of the transformed ami region. We have obtained two kinds of amplification products: short when the deletion was integrated, long when recombination stops at the deletion. Each long fragment was tested by the four restriction enzymes to detect which strand and which side of the deletion had recombined. We found that 80% of the cuts were located 5' to the deletion, showing that, in vivo, the 5' side is strongly favored by recombination. Further results suggest that exchanges occurring from 5' to 3' relative to the donor strand are more efficient than in the opposite direction, thus accounting for the 5' preference.

DNA, Bacterial↗
PubMed2026

High-efficiency genome-editing, transgene evaluation, and antimicrobial efficacy testing using Citrus medica L. hairy roots.

Huanglongbing (HLB) disease, associated with the fastidious bacterium Candidatus Liberibacter asiaticus (CLas), has a significant impact on citrus production worldwide. Conventional biochemical and genetic evaluation studies to identify potential disease resistance strategies have been mainly hindered due to the inability to culture CLas in a defined medium and the general recalcitrance of Citrus cultivars (grapefruits and oranges) to Agrobacterium-mediated plant transformation. We previously demonstrated the utility of plant hairy roots to co-cultivate CLas. In this study, we developed a hairy root transformation system using citron (Citrus medica L.), which is highly amenable to Rhizobium-mediated hairy root transformation. The explant survival and hairy root transformation efficiencies were up to 100% and 73%, respectively, and transgenic roots can be attained in as little as 30-60 days. We demonstrate the utility of this citron-based hairy root transformation for rapid CRISPR/Cas9-mediated gene editing, transgene evaluation, and antimicrobial efficacy testing. The citron-based hairy root transformation system will significantly help the research community to speed-track the assessment of potential HLB disease resistance strategies.

Citrus↗
PubMed2006

Genetic improvement of the somatic embryogenesis and regeneration in soybean and transformation of the improved breeding lines.

Somatic embryos of soybean [Glycine max (L.) Merrill] have been used to generate transgenic plants by particle bombardment. The induction and proliferation of somatic embryos from immature cotyledons are dependent on the genotype of the cultivar. Whereas somatic embryogenesis and plant regeneration are inefficient in most cultivars, they are efficient in the cultivar Jack. We previously established a breeding line, QF2, by the integration of null mutations of each subunit of the major seed storage proteins glycinin and beta-conglycinin, but the embryogenic response of this line is insufficient to allow efficient transformation. We have now backcrossed QF2 to cultivar Jack in order to combine the null traits with competence for somatic embryogenesis. The backcrossed breeding lines selected on the basis of the absence of the major storage proteins exhibited an improved capacity for the induction and proliferation of somatic embryos compared with that of QF2. The induced somatic embryogenic tissue of these breeding lines was successfully used for the production of transgenic plants by particle bombardment. These results also indicate that somatic embryogenesis in soybean is genetically controlled and inherited in a manner independent of the null traits of the major seed storage proteins.

Antigens, Plant↗
PubMed2006

Characterization of LF9, an octoploid strawberry genotype selected for rapid regeneration and transformation.

Cultivated strawberry (Fragaria xananassa) is a valuable crop, yet the absence of a rapid, high-throughput transgenic system has precluded meaningful application of biotechnology and translation of information from plant models to this crop. A new octoploid strawberry genetic line Laboratory Festival #9 has been identified, selected solely for its rapid regeneration and efficient transformation. Direct organogenesis has been achieved from all tissues tested, with rapidly-growing shoot initials visible in as few as 13 days. The conditions for optimal shoot regeneration, transformant selection, root generation, and plant acclimatization are presented. The progression from explant to plant in soil can be achieved in about 60 days. The development of transformation protocols in this rapid-cycling genotype allows high-throughput studies of gene function in the octoploid strawberry genetic background.

Acclimatization↗
PubMed2006

Quality factor concept in piezoceramic transformer performance description.

A new general approach based on the quality factor concept to piezoceramic transformer (PT) performance description is proposed. The system's quality factor, material elastic anisotropy, and coupling factors of the input and output sections of an electrically excited and electrically loaded PT fully characterize its resonance and near-resonance behavior. The PT efficiency, transformation ratio, and input and output power were analytically analyzed and simulated as functions of the load and frequency for the simplest classical Langevin-type and Rosen-type PT designs. A new formulation of the electrical input impedance allows one to separate the power consumed by PT from the power transferred into the load. The system's PT quality factor takes into account losses in each PT "input-output-load" functional components. The loading process is changing PT input electrical impedance on the way that under loading the minimum series impedance is increasing and the maximum parallel impedance is decreasing coincidentally. The quality-factors ratio, between the states of fully loaded and nonloaded PT, is one of the best measures of PTs dynamic performance--practically, the lower the ratio is, the better PT efficiency. A simple and effective method for the loaded PT quality factor determination is proposed. As was found, a piezoceramic with low piezoelectric anisotropy is required to provide maximum PT efficiency and higher corresponding voltage gain. Limitations on the PT output voltage and power, caused by nonlinear effects in piezoceramics, were established.

Ceramics↗
PubMed1994

A simple and efficient system for targeting DNA to the am locus of Neurospora crassa.

We have developed a system of recipient strains and donor plasmids that allows targeting of DNA sequences to the am locus of Neurospora crassa. A recipient strain was constructed that contains the 3' two-thirds of the bacterial Hygromycin B (Hy) phosphotransferase-encoding gene (hph) in single copy downstream from the am structural gene encoding NADP-specific glutamate dehydrogenase. Plasmids have been constructed that contain am, but with the 5' end of hph downstream from am. Resistance to Hy can occur during transformation only if recombination occurs within the region of overlap of the hph sequences from the transforming DNA and of the chromosomal hph sequences. A lacZ alpha gene with a multiple cloning site has been inserted into the region between the am and hph sequences to facilitate subcloning into the targeting vector. Additionally, unique sites at the junctions of the vector and targeting DNA allow easy removal of vector sequences prior to transformation. A second recipient strain has been constructed that has had the am structural gene deleted. This strain may be used to provide a double selection for homologous integration. Additionally, this strain facilitates replacement of am with heterologous constructs, including constructs that drive transcription of am with different promoters. The insertion of hph downstream from am has no apparent effect on am expression, and the resistance segregates as a Mendelian factor in crosses. Transformation efficiency is reduced two to three orders of magnitude, but interestingly, nearly all of the resistant strains have only a single copy of the transforming DNA.

Chromosomes, Fungal↗
PubMed1996

Genetic transformation of cassava (Manihot esculenta Crantz).

Genetic engineering can be used to complement traditional breeding methods in crop plant improvement. Transfer of genes from heterologous species provides the means of selectively introducing new traits into crop plants and expanding the gene pool beyond what has been available to traditional breeding systems. The prerequisites for genetic engineering are efficient transformation and tissue culture systems that allow selection and regeneration of transgenic plants. Cassava, an integral plant for food security in developing countries, has until now been recalcitrant to transformation approaches. We report here a method for regenerating stably transformed cassava plants after cocultivation with Agrobacterium tumefaciens, which opens cassava for future improvement via biotechnology.

Agrobacterium tumefaciens↗
PubMed2001

A transformation system for the biocontrol yeast, Candida oleophila, based on hygromycin B resistance.

Lithium acetate transformation and electroporation were applied to the biocontrol yeast, Candida oleophila. The hygromycin B resistance gene, flanked by the phosphoglycerate kinase promoter and terminator of Candida tropicalis, served as the genetic selection marker. The transformation efficiency of electroporation was almost 400 times more efficient than that of the lithium acetate method. While incorporation of DNA, flanked by a sequence endogenous to C. oleophila, transpired apparently by homologous recombination, the integration of DNA (that did not contain C. oleophila DNA) occurred at random. Whereas transformants were observed with a linear segment of the plasmid, none were detected with the undigested plasmid. This system provides both a tool for the molecular analysis of the biocontrol mechanism of C. oleophila and a means of tagging C. oleophila for field studies.

Anti-Bacterial Agents↗
PubMed2002

Harvesting cells under anchorage-independent cell transformation conditions for biochemical analyses.

Most molecular biology and biochemical analyses use cultured cells grown in anchorage-dependent monolayer conditions. The standard oncogenic transformation assay for cell lines is usually performed in soft agar rather than in monolayers because of the higher transformation efficiency of cells in soft agar. However, cells suspended in soft agar cannot be readily recovered for studying inducible biochemical and molecular events. We developed an over-agar assay that enables us to study tumor promoter-induced cell transformation and the associated biochemical or molecular events under anchorage-independent conditions.

Agar↗
PubMed1994

Functional complementation of the adenovirus E1B 19-kilodalton protein with Bcl-2 in the inhibition of apoptosis in infected cells.

Expression of the adenovirus E1A oncogene induces apoptosis which impedes both the transformation of primary rodent cells and productive adenovirus infection of human cells. Coexpression of E1A with the E1B 19,000-molecular-weight protein (19K protein) or the Bcl-2 protein, both of which have antiapoptotic activity, is necessary for efficient transformation. Induction of apoptosis by E1A in rodent cells is mediated by the p53 tumor suppressor gene, and both the E1B 19K protein and the Bcl-2 protein can overcome this p53-dependent apoptosis. The functional similarity between Bcl-2 and the E1B 19K protein suggested that they may act by similar mechanisms and that Bcl-2 may complement the requirement for E1B 19K expression during productive infection. Infection of human HeLa cells with E1B 19K loss-of-function mutant adenovirus produces apoptosis characterized by enhanced cytopathic effects (cyt phenotype) and degradation of host cell chromosomal DNA and viral DNA (deg phenotype). Failure to inhibit apoptosis results in premature host cell death, which impairs virus yield. HeLa cells express extremely low levels of p53 because of expression of human papillomavirus E6 protein. Levels of p53 were substantially increased by E1A expression during adenovirus infection. Therefore, E1A may induce apoptosis by overriding the E6-induced degradation of p53 and promoting p53 accumulation. Stable Bcl-2 overexpression in HeLa cells infected with the E1B 19K- mutant adenovirus blocked the induction of the cyt and deg phenotypes. Expression of Bcl-2 in HeLa cells also conferred resistance to apoptosis mediated by tumor necrosis factor alpha and Fas antigen, which is also an established function of the E1B 19K protein. A comparison of the amino acid sequences of Bcl-2 family members and that of the E1B 19K protein indicated that there was limited amino acid sequence homology between the central conserved domains of E1B 19K and Bcl-2. This domain of the E1B 19K protein is important in transformation and regulation of apoptosis, as determined by mutational analysis. The limited sequence homology and functional equivalency provided further evidence that the Bcl-2 and E1B 19K proteins may possess related mechanisms of action and that the E1B 19K protein may be the adenovirus equivalent of the cellular Bcl-2 protein.

Adenovirus E1A Proteins↗