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Results for “Donor DNA engineering”

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PubMed2005

MAGIC, an in vivo genetic method for the rapid construction of recombinant DNA molecules.

We describe a highly engineered in vivo cloning method, mating-assisted genetically integrated cloning (MAGIC), that facilitates the rapid construction of recombinant DNA molecules. MAGIC uses bacterial mating, in vivo site-specific endonuclease cleavage and homologous recombination to catalyze the transfer of a DNA fragment between a donor vector in one bacterial strain and a recipient plasmid in a separate bacterial strain. Recombination events are genetically selected and result in placement of the gene of interest under the control of new regulatory elements with high efficiency. MAGIC eliminates the need for restriction enzymes, DNA ligases, preparation of DNA and all in vitro manipulations required for subcloning and allows the rapid construction of multiple constructs with minimal effort. We show that MAGIC can generate constructs for expression in multiple organisms. As this new method requires only the simple mixing of bacterial strains, it represents a substantial advance in high-throughput recombinant DNA production that will save time, effort and expense in functional genomics studies.

Amino Acid Sequence↗

PubMedDate not supplied

[Genetic transformation of animals by the insertion of foreign genes into the zygotes].

A review of literature on genetic transformation of animal (mouse and Drosophila) germ cells by microinjection of the cloned genes into the pronuclei or into the early embryos. The fate of foreign genes and mechanisms of their integration into the recipient genome are considered in detail, as well as genetic consequences of the exogenic DNA insertion. Expression of the donor genes in transgenic animals is analyzed, its irregular and unusual pattern is noted in transgenic mice. An attempt has been undertaken not only to stress obvious advances in genetic transformation of animals, but also to outline unsolved problems related to inheritance of exogenous genes, insertion mutagenesis and irregular expression of the donor genes.

Animals↗

PubMed2002

A new method (GOREC) for directed mutagenesis and gene repair by homologous recombination.

Directed mutagenesis in mammalian cells has been the focus of intense research because of its promising application for gene correction and engineering. Both natural and modified oligonucleotides (ODN), RNA-DNA chimeric oligonucleotide (RDO) and small fragment DNA (SFHR), as well as vector DNA were used for promoting homologous replacement with varying success. It was recently shown that a triple helix-forming oligonucleotide (TFO) tethered to an oligonucleotide (donor DNA) can enhance mutagenesis by homologous recombination in cells. The basic idea is to accelerate homology search by oligonucleotide-directed triple helix formation in the vicinity of the target site for donor DNA. Here we describe a new method named GOREC (guided homologous recombination) which shares similar gene targeting, but has notable difference in the concept with the previous method. It is made of a homing device (TFO) and a donor DNA for effecting distinct functions. They are linked together by non-covalent or covalent interaction. This modular concept allows guidance of either an oligonucleotide (ODN, RDO) or a small DNA fragment to the target site for homologous replacement. Therefore, the triple helix site can be hundreds of base pairs away from the target site. An episomal assay for proof-of-principle study will be presented and discussed.

Animals↗

PubMed2004

[New horizons in heart transplantation].

Since its beginning in 1967 heart transplantations have become in 80s of the 20th century a routine treatment method of an advanced heart failure. In spite of the successes in transplantations a range of possible topics and research goals still has to be disclosed to improve quality of life and survival of patients. New horizons in heart transplantations can be summarised in following points: 1 Search of new more efficient immunosuppressives with less adverse effects. Classically a combination of Cyclosporin, Azathioprin, and corticoids have been used. Mycophenolate mofetil starts to be used in treatment instead of Azathioprin, Tacrolimus has been introduced as a drug for resistant rejections and also Rapamycin or Baziliximab are planned to be used in future. Use of Rapamycin seems desirable in patients suffering from nephropathy because it makes possible to lower doses of Cyclosporin or Tacrolimus or to stop taking them. 2 Diagnostics of rejection episodes without endomyocardial biopsy. From noninvasive methods echocardiography methods are looked for--tissue doppler imaging, densitometry, contrast echocardiography, strain and strain rate or assessing levels of some of the humoral agents: interleukin, cerebral natriuretic peptide or troponin T or direct assessment of donor DNA release in receptor's blood. 3 Earlier diagnostics of vasculopathy (here intravascular ultrasound is possible to use), particularly its pharmacology prevention. Statin treatment has been preventively introduced. 4 Xenotransplantation as a possible way of a heart replacement with an animal heart. Progresses in gene engineering lead to a development of transgenic animals, particularly pigs, with human proteins inserted in their genome and regulating activation of immune system. This way hyperacute rejection could be prevented. A range of unclear questions still remains in this area, particularly ethical ones and a risk of animal diseases transfer onto a human together with transplanted tissue. 5 Transplantation of cells from skeletal muscles (myoblasts) or marrow stem cells. 6 Development of apparatuses able to substitute heart function--total artificial heart. However, a range of questions is still unanswered in this area: a suitable material or source for long-term operation is needed to be found. Heart transplantation has become in last two decades a well-established treatment method of a serious heart failure. In spite of numerous difficulties it extends life of patients and improves its quality. Future will show whether we are able to replace it with other procedures.

Graft Rejection↗

PubMed1993

Conjugal gene transfer to aquatic bacteria detected by the generation of a new phenotype.

An experimental approach based on the assembly of genes of a catabolic pathway was used to detect transconjugants in aquatic communities. Resistance to phenylmercury acetate was established in transconjugants when wide-host-range conjugal plasmids containing merB, the gene encoding organomercurial lyase, were transferred to strains from aquatic communities that had been acclimated to inorganic mercury and thus enriched for populations containing merA, the gene encoding mercuric reductase (T. Barkay, Appl. Environ. Microbiol. 53:2725-2732, 1987). Conjugation was confirmed by using the plasmids' encoded antibiotic resistance patterns and by hybridization with a eukaryotic gene. Three merB-conjugal plasmids, belonging to incompatibility groups W (pGTE16), P1 (pGTE26), and N (pGTE25), were prepared. Transfers by filter matings of pGTE16 and pGTE26 from Pseudomonas aeruginosa PA01 to indigenous strains were at efficiencies of 4.5 x 10 and 4.8 x 10 transconjugant per potential recipient, respectively. These efficiencies were from 1 to 2 orders of magnitude below those observed for intraspecies matings with genetically marked recipients. The third plasmid, pGTE25, was not stably maintained in P. aeruginosa donors, and its transfer from Escherichia coli donors was below the level of detection. Characterized transconjugant strains were shown to be Pseudomonas spp. Potential applications of the described experimental approach in the creation of bacterial populations with new catabolic capabilities in hazardous waste sites and in the detection of transfer of recombinant DNA from engineered microorganisms to indigenous bacteria are discussed.

Journal Article↗

PubMed2006

Living autologous heart valves engineered from human prenatally harvested progenitors.

BACKGROUND: Heart valve tissue engineering is a promising strategy to overcome the lack of autologous growing replacements, particularly for the repair of congenital malformations. Here, we present a novel concept using human prenatal progenitor cells as new and exclusive cell source to generate autologous implants ready for use at birth. METHODS AND RESULTS: Human fetal mesenchymal progenitors were isolated from routinely sampled prenatal chorionic villus specimens and expanded in vitro. A portion was cryopreserved. After phenotyping and genotyping, cells were seeded onto synthetic biodegradable leaflet scaffolds (n=12) and conditioned in a bioreactor. After 21 days, leaflets were endothelialized with umbilical cord blood-derived endothelial progenitor cells and conditioned for additional 7 days. Resulting tissues were analyzed by histology, immunohistochemistry, biochemistry (amounts of extracellular matrix, DNA), mechanical testing, and scanning electron microscopy (SEM) and were compared with native neonatal heart valve leaflets. Fresh and cryopreserved cells showed comparable myofibroblast-like phenotypes. Genotyping confirmed their fetal origin. Neo-tissues exhibited organization, cell phenotypes, extracellular matrix production, and DNA content comparable to their native counterparts. Leaflet surfaces were covered with functional endothelia. SEM showed cellular distribution throughout the polymer and smooth surfaces. Mechanical profiles approximated those of native heart valves. CONCLUSIONS: Prenatal fetal progenitors obtained from routine chorionic villus sampling were successfully used as an exclusive, new cell source for the engineering of living heart valve leaflets. This concept may enable autologous replacements with growth potential ready for use at birth. Combined with the use of cell banking technology, this approach may be applied also for postnatal applications.

Absorbable Implants↗

PubMed2012

The nontoxic cell cycle modulator indirubin augments transduction of adeno-associated viral vectors and zinc-finger nuclease-mediated gene targeting.

Parameters that regulate or affect the cell cycle or the DNA repair choice between non-homologous end-joining and homology-directed repair (HDR) are excellent targets to enhance therapeutic gene targeting. Here, we have evaluated the impact of five cell-cycle modulating drugs on targeted genome engineering mediated by DNA double-strand break (DSB)-inducing nucleases, such as zinc-finger nucleases (ZFNs). For a side-by-side comparison, we have established four reporter cell lines by integrating a mutated EGFP gene into either three transformed human cell lines or primary umbilical cord-derived mesenchymal stromal cells (UC-MSCs). After treatment with different cytostatic drugs, cells were transduced with adeno-associated virus (AAV) vectors that encode a nuclease or a repair donor to rescue EGFP expression through DSB-induced HDR. We show that transient cell-cycle arrest increased AAV transduction and AAV-mediated HDR up to six-fold in human cell lines and ten-fold in UC-MSCs, respectively. Targeted gene correction was observed in up to 34% of transduced cells. Both the absolute and the relative gene-targeting frequencies were dependent on the cell type, the cytostatic drug, the vector dose, and the nuclease. Treatment of cells with the cyclin-dependent kinase inhibitor indirubin-3'-monoxime was especially promising as this compound combined high stimulatory effects with minimal cytotoxicity. In conclusion, indirubin-3'-monoxime significantly improved AAV transduction and the efficiency of AAV/ZFN-mediated gene targeting and may thus represent a promising compound to enhance DSB-mediated genome engineering in human stem cells, such as UC-MSCs, which hold great promise for future clinical applications.

Blotting, Western↗

PubMed1993

In vivo transfer of pR68.45 from Pseudomonas aeruginosa into indigenous soil bacteria.

The release of genetically engineered organisms (GEMs) into the environment could result in novel gene sequences becoming transferred to, and established in, the indigenous soil biota. The potential for recombination in nonsterile soil is difficult to determine due to problems isolating transconjugants of indigenous microbes, while concurrently suppressing introduced donors. We have developed a system that allows us to detect the transfer of the plasmid R68.45 from Pseudomonas aeruginosa strain PA025 into the indigenous soil bacterial population. Transconjugants were selected by plating on minimal media containing antibiotics and were verified by DNA-DNA hybridization. The observed maximum transfer frequency was approximately 10(-6). Fatty acid analysis of transconjugants showed that intergeneric transfer was occurring between the introduced organism and genetically dissimilar species.

Conjugation, Genetic↗

PubMed2003

A new method for rapidly generating gene-targeting vectors by engineering BACs through homologous recombination in bacteria.

Generating knockout mice is still an expensive and highly time-consuming process. Target construct generation, the first labor-intensive step in this process, requires the manipulation of large fragments of DNA and numerous, and often cumbersome, cloning steps. Here we show the development of a rapid approach for generating targeting constructs that capitalizes on efficient homologous recombination between linear DNA fragments and circular plasmids in Escherichia coli ("recombineering"), the availability of bacterial artificial chromosomes (BACs), and the accessibility of the sequence of the mouse genome. Employing recombineering, we demonstrate with only 1-2 template plasmids, short homologies (40-50bp) between donor and target DNA, and one subcloning step that we can efficiently manipulate BACs in situ to generate a complicated targeting vector. This procedure avoids the need to construct or screen genomic libraries and permits the generation of most standard, conditional, or knock-in targeting vectors, often within two weeks.

Animals↗

PubMed1996

Doing the conjugative two-step: evidence of recipient autonomy in retrotransfer.

Bidirectional exchange of genetic information, called retrotransfer, during bouts of bacterial conjugation has drawn the interest of those concerned with the risk of releasing genetically engineered microbes, the fluidity of genes among species, and the mechanism of DNA transport between cells. The phenomenon has generated two models in explanation, both of which yield highly testable predictions. The first model, called the one-step, predicts that the flow of genes from recipient bacteria to donor bacteria is mechanistically distinct from, but dependent on, conjugation between donors and recipients. The second model, called the two-step, predicts that the same genetic requirements and mechanistic constraints apply to the process of gene flow from recipients to donors as for gene flow from donors to recipients. The requirement for expression of at least 10 plasmid-encoded genes in recipients, sensitivity of the reverse flow (recipient to donor) to restriction of DNA transferring from the donor, and the requirement of an additional 30-90 min for DNA to flow from recipients back to donors are predictions of the two-step model and directly refute the one-step model. Retrotransfer of genes to donors during conjugation remains genetically and physically indistinguishable from two successive rounds of conjugation between neighbors.

Conjugation, Genetic↗

PubMed2004

Fluorescence resonance energy transfer-based detection of analytes using antiidiotypic affinity protein pairs.

A new method for specific detection of proteins based on fluorescence resonance energy transfer (FRET) using affinity proteins (affibodies) derived from combinatorial engineering of Staphylococcal protein A has been developed. Antiidiotypic affibody pairs were used in a homogeneous competitive binding assay, where the idiotypic, target-specific affibody was labeled with fluorescein and the antiidiotypic affibody was labeled with tetramethylrhodamine. Intermolecular FRET between the two fluorescent probes was observed in the antiidiotypic affibody complex, but upon addition of target protein the antiidiotypic affibody was displaced, which was monitored by a shift in the relative emission of the donor and acceptor fluorophores. The feasibility of the system was demonstrated by the detection of IgA and Taq DNA polymerase with high specificity, using two different antiidiotypic affibody pairs. Detection of Taq DNA polymerase in 25% human plasma was successfully carried out, demonstrating that the method can be used for analysis of proteins in samples of complex composition.

Binding Sites↗

PubMed1995

Engineering of fibroblast growth factor: alteration of receptor binding specificity.

A five-residue loop structure in basic fibroblast growth factor (FGF-2) which extends from amino acid residue 118 to residue 122 was replaced, by cassette mutagenesis, with the corresponding seven-residue loop structure from the structural homologue acidic fibroblast growth factor (FGF-1) or the corresponding five-residue loop from interleukin-1 beta to give FGF-2LA and FGF-2LI, respectively. The mutants were expressed in Escherichia coli and purified to homogeneity, and their heparin and receptor binding and biological properties were examined. The ability of FGF-2LA to induce endothelial cell proliferation was the same as that of FGF-2. Affinities of the mutants to heparin and to cells that express FGF receptor-1 (FGFR-1) were identical to those of the wild-type protein. The role of the loop structure in FGF-1 and FGF-2 was elucidated by using soluble FGF receptor systems, which display distinct ligand binding specificities. Thus, FGF-2LA bound, with the same affinity as FGF-1 and FGF-2, to FGFR-1 and FGFR-2, whereas only FGF-1 and the FGF-1 loop-containing mutant, FGF-2LA, bound to the keratinocyte growth factor receptor. A change in receptor binding specificity was not observed with the FGF-2LI engineered mutant. That the binding specificity of FGF-2 was dramatically altered by transfer of a loop structure from FGF-1 to resemble the binding profile of the donor protein provides strong evidence that this motif is a receptor binding specificity determinant of fibroblast growth factors.

3T3 Cells↗

PubMed2003

A genome-based functional screening approach to vaccine development that combines in vitro assays and DNA immunization.

A two-step screening strategy was developed to identify strong immunogenic polypeptides with putative vaccine and/or adjuvant activity. In the first step, a mycobacterial genomic DNA library was screened in vitro to identify plasmids encoding polypeptides that stimulate splenocytes from mycobacteria-immunized mice and T cells from PPD-positive healthy donors to produce interferon-gamma. In the second step, plasmids were selected for their ability to induce protective immunity in a mouse model of tuberculosis following DNA immunization. The potential of this approach is illustrated by the identification of a panel of immunogenic polypeptides that may be used to engineer a new generation of vaccines.

Adjuvants, Immunologic↗

PubMed2006

Dispersion of the RmInt1 group II intron in the Sinorhizobium meliloti genome upon acquisition by conjugative transfer.

RmInt1 is a self-splicing and mobile group II intron initially identified in the bacterium Sinorhizobium meliloti, which encodes a reverse transcriptase-maturase (Intron Encoded Protein, IEP) lacking the C-terminal DNA binding (D) and DNA endonuclease domains (En). RmInt1 invades cognate intronless homing sites (ISRm2011-2) by a mechanism known as retrohoming. This work describes how the RmInt1 intron spreads in the S.meliloti genome upon acquisition by conjugation. This process was revealed by using the wild-type intron RmInt1 and engineered intron-donor constructs based on ribozyme coding sequence (DeltaORF)-derivatives with higher homing efficiency than the wild-type intron. The data demonstrate that RmInt1 propagates into the S.meliloti genome primarily by retrohoming with a strand bias related to replication of the chromosome and symbiotic megaplasmids. Moreover, we show that when expressed in trans from a separate plasmid, the IEP is able to mobilize genomic DeltaORF ribozymes that afterward displayed wild-type levels of retrohoming. Our results contribute to get further understanding of how group II introns spread into bacterial genomes in nature.

Bacterial Proteins↗

PubMed2006

Hydrodynamic compression of young and adult rat osteoblast-like cells on titanium fiber mesh.

Living bone cells are responsive to mechanical loading. Consequently, numerous in vitro models have been developed to examine the application of loading to cells. However, not all systems are suitable for the fibrous and porous three-dimensional materials, which are preferable for tissue repair purposes, or for the production of tissue engineering scaffolds. For three-dimensional applications, mechanical loading of cells with either fluid flow systems or hydrodynamic pressure systems has to be considered. Here, we aimed to evaluate the response of osteoblast-like cells to hydrodynamic compression, while growing in a three-dimensional titanium fiber mesh scaffolding material. For this purpose, a custom hydrodynamic compression chamber was built. Bone marrow cells were obtained from the femora of young (12-day-old) or old (1-year-old) rats, and precultured in the presence of dexamethasone and beta-glycerophosphate to achieve an osteoblast-like phenotype. Subsequently, cells were seeded onto the titanium mesh scaffolds, and subjected to hydrodynamic pressure, alternating between 0.3 to 5.0 MPa at 1 Hz, at 15-min intervals for a total of 60 min per day for up to 3 days. After pressurization, cell viability was checked. Afterward, DNA levels, alkaline phosphatase (ALP) activity, and extracellular calcium content were measured. Finally, all specimens were observed with scanning electron microscopy. Cell viability studies showed that the applied pressure was not harmful to the cells. Furthermore, we found that cells were able to detect the compression forces, because we did see evident effects on the cell numbers of the cells derived from old animals. However, there were no other changes in the cells under pressure. Finally, it was also noticeable that cells from old animals did not express ALP activity, but did show similar calcified extracellular matrix formation to the cells from young animals. In conclusion, the difference in DNA levels as reaction toward pressure, and the difference in ALP levels, suggest that the osteogenic properties of bone marrow-derived osteoblast-like cells are different with respect to the age of the donor.

Aging↗

PubMed1992

Bioethics as a new human rights emphasis in European research policy.

Although issues of morals and ethics remain largely a national matter, the European Community (EC) and the Council of Europe have taken an increasing interest in identifying and harmonizing the often conflicting policies of the European countries on bioethical matters. This article examines the role these organizations are playing and identifies some of the initiatives that have been taken in specific areas.

Abortion, Induced↗

PubMed1997

Genetic manipulation of anaerobic cellulolytic bacteria.

Transposon Tn1545 was introduced into the chromosome of the ruminal cellulolytic bacterium Eubacterium cellulosolvens. This was achieved by conjugal transfer of the transposon from Clostridium beijerinckii at a frequency of about 1 per 10(4) recipient cells. Transconjugants of E. cellulosolvens were resistant to both tetracycline and erythromycin. E. cellulosolvens could also serve as a donor for conjugal transfer of Tn1545 back into C. beijerinckii.

Animals↗

PubMed2006

Aminotryptophan-containing barstar: structure--function tradeoff in protein design and engineering with an expanded genetic code.

The indole ring of the canonical amino acid tryptophan (Trp) possesses distinguished features, such as sterical bulk, hydrophobicity and the nitrogen atom which is capable of acting as a hydrogen bond donor. The introduction of an amino group into the indole moiety of Trp yields the structural analogs 4-aminotryptophan ((4-NH(2))Trp) and 5-aminotryptophan ((5-NH(2))Trp). Their hydrophobicity and spectral properties are substantially different when compared to those of Trp. They resemble the purine bases of DNA and share their capacity for pH-sensitive intramolecular charge transfer. The Trp --> aminotryptophan substitution in proteins during ribosomal translation is expected to result in related protein variants that acquire these features. These expectations have been fulfilled by incorporating (4-NH(2))Trp and (5-NH(2))Trp into barstar, an intracellular inhibitor of the ribonuclease barnase from Bacillus amyloliquefaciens. The crystal structure of (4-NH(2))Trp-barstar is similar to that of the parent protein, whereas its spectral and thermodynamic behavior is found to be remarkably different. The T(m) value of (4-NH(2))Trp- and (5-NH(2))Trp-barstar is lowered by about 20 degrees Celsius, and they exhibit a strongly reduced unfolding cooperativity and substantial loss of free energy in folding. Furthermore, folding kinetic study of (4-NH(2))Trp-barstar revealed that the denatured state is even preferred over native one. The combination of structural and thermodynamic analyses clearly shows how structures of substituted barstar display a typical structure-function tradeoff: the acquirement of unique pH-sensitive charge transfer as a novel function is achieved at the expense of protein stability. These findings provide a new insight into the evolution of the amino acid repertoire of the universal genetic code and highlight possible problems regarding protein engineering and design by using an expanded genetic code.

Bacterial Proteins↗