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At least 739 records · Page 41Linked to original sources
PubMed2001

Genetic modification and plant food allergens: risks and benefits.

Plant genetic engineering has the potential to both introduce new allergenic proteins into foods and remove established allergens. A number of allergenic plant proteins have been characterized, showing that many are related to proteins which have potentially valuable properties for use in nutritional enhancement, food processing and crop protection. It is therefore important to monitor the allergenic potential of proteins used for plant genetic engineering and major biotechnology companies have established systems for this. Current technology allows gene expression to be down-regulated using antisense or co-suppression and future developments may allow targeted gene mutation or gene replacement. However, the application of this technology may be limited at least in the short term by the presence of multiple allergens and their contribution to food processing or other properties. Furthermore, the long-term stability of these systems needs to be established as reversion could have serious consequences.

Allergens↗
PubMed2002

IL-7 surface-engineered lentiviral vectors promote survival and efficient gene transfer in resting primary T lymphocytes.

Important gene therapy target cells such as resting human T cells are refractory to transduction with lentiviral vectors. Completion of reverse transcription, nuclear import, and subsequent integration of the lentiviral genome occur in these cells only if they have been activated. In T-cell-based gene therapy trials performed to date, cells have been activated via their cognate antigen receptor. To couple activation with gene transfer, we previously generated lentiviral vectors displaying an anti-CD3 scFv fragment that allowed up to 48% transduction of freshly isolated T cells. However, transduction of highly purified resting T cells with these anti-CD3-displaying lentiviral vectors was inefficient and shifted the T cells from the naive to the memory phenotype. Here, we describe interleukin-7 (IL-7)-displaying HIV-1-derived vectors. Like recombinant IL-7, these modified particles could promote the survival of primary T cells placed in culture without inducing a naive-to-memory phenotypic switch. Furthermore, a single exposure to the IL-7-displaying vectors resulted in efficient gene transfer in both resting memory adult T cells and naive cord blood T cells. With adult naive T cells, preactivation with recombinant IL-7 was necessary for efficient gene transfer. Altogether, these results suggest that IL-7-displaying vectors could constitute interesting tools for T-cell-targeted gene therapy.

CD3 Complex↗
PubMed2006

Gene expression profiling of human articular cartilage grafts generated by tissue engineering.

Cartilage tissue engineering is applied clinically to cover and regenerate articular cartilage defects. In this study autologous human cartilage tissue engineering grafts based on bioresorbable polyglactin/polydioxanone scaffolds were analyzed on the broad molecular level. RNA from freshly isolated, primary and expanded adult articular chondrocytes and from three-dimensional cartilage grafts were used for gene expression profiling using oligonucleotide microarrays. The capacity of cartilage grafts to form cartilage matrix was evaluated after subcutaneous transplantation into nude mice. Gene expression profiling showed reproducibly the regulation of 905 genes and documented that chondrocytes undergo fundamental changes during cartilage tissue engineering regarding chondrocyte metabolism, growth, and differentiation. Three-dimensional assembly of expanded, dedifferentiated chondrocytes initiated the re-differentiation of cells that was accompanied by the reversal of the expression profile of multiple players of the transforming growth factor (TGF) signaling pathway including growth and differentiation factor-5 and inhibitor of differentiation-1 as well as by the induction of typical cartilage-related matrix genes such as type II collagen and cartilage oligomeric matrix protein. Cartilage grafts formed a cartilaginous matrix after transplantation into nude mice. Three-dimensional tissue culture of expanded articular chondrocytes initiates chondrocyte re-differentiation in vitro and leads to the maturation of cartilage grafts towards hyaline cartilage in vivo.

Base Sequence↗
PubMed2006

Characterization of human islet-like structures generated from pancreatic precursor cells in culture.

This study addresses the characterization of human islet-like structures generated from a newly discovered sparse population of precursor cells (Petropavlovskaia and Rosenberg, 2002) in the human pancreas. These cells may be progenitor cells capable of producing pancreatic cells suitable for the treatment of type 1 diabetes. The cells were cultured successfully in non-adherent stationary cultures and yielded, as an important first step, a 1.9-fold expansion in a serum-free medium developed specifically for this cell type. This expanded population grew as pancreatic cell aggregates, which were analyzed for islet-like characteristics. Specifically, through RT-PCR analyses and functionality assays, we show that cells within the population expressed all four of the endocrine hormone genes and proteins (insulin, glucagon, somatostatin, pancreatic polypeptide). As well, the expanded pancreatic precursor cell population exhibited glucose responsiveness although the produced cells appeared to be still primitive in nature.

1-Methyl-3-isobutylxanthine↗
PubMed2003

Engineering of technetium-99m-binding artificial receptors for imaging gene expression.

BACKGROUND: Optimization of gene therapy protocols requires accurate and non-invasive quantification of vector delivery and gene expression. To facilitate non-invasive imaging of gene expression, we have genetically engineered 'artificial receptors', i.e. membrane proteins that bind (99m)Tc-oxotechnetate ((99m)TcOT) via transchelation from a complex with glucoheptonate. The latter is a component of a widely used clinical imaging kit. METHODS: The engineered marker proteins were designed as type I and II membrane proteins and consisted of (1) an (99m)TcOT-binding domain, metallothionein (MT), and (2) a membrane-anchoring domain. Engineered constructs were used for transfection of COS-1 and 293 cells; the expression of mRNA was verified by RT-PCR. RESULTS: Immunofluorescent analysis, cell fractionation and immunoblotting revealed expression of marker proteins on plasma membrane. Transfection of cells resulted in strong positive staining of plasma membrane with anti-His-tag antibodies. Scintigraphic imaging in vitro confirmed the ability of transfected cells to bind (99m)TcOT. The fraction of bound radioactivity reached a peak (3.53%) when 0.93 MBq (99m)TcOT was added to transfected COS-1 cells. The experiment-to-control signal ratio was equal to 32 at the same added dose. CONCLUSIONS: (1) Both types of engineered 'artificial receptors' were expressed on the surface of eukaryotic cells; (2) marker proteins were functional in binding (99m)TcOT; and (3) type II membrane proteins were more efficient in binding (99m)TcOT than type I proteins. We anticipate that the developed approach could be useful for 'tagging' transfected cells with (99m)TcOT enabling imaging of tracking in vivo transduced cells or cell therapies.

Cell Membrane↗
PubMed1997

Reverse transcriptase. The use of cloned Moloney murine leukemia virus reverse transcriptase to synthesize DNA from RNA.

Reverse transcriptase (RT) is the key enzyme required for conversion of RNA to DNA. Cloning of Moloney murine leukemia virus (MMLV) RT has enable engineering an RT that lacks endogenous RNase H activity. RT catalyzes cDNA synthesis more efficiently in the absence of RNase H. We describe here a number of properties of MMLV RT and RNase H-minus MMLV RT not summarized in a single location elsewhere, providing a basis for best use of these enzymes in cDNA synthesis. In addition, general guidelines and detailed protocols are provided for use of MMLV RTs in one tube double-stranded cDNA synthesis, in [32P]cDNA synthesis, and in RT-PCR and long RT-PCR.

DNA, Complementary↗
PubMed2005

Inhibition of CYP2E1 catalytic activity in vitro by S-adenosyl-L-methionine.

The objective of this work was to evaluate the possible in vitro interactions of S-adenosyl-l-methionine (SAM) and its metabolites S-(5'-Adenosyl)-l-homocysteine (SAH), 5'-Deoxy-5'-(methylthio)adenosine (MTA) and methionine with cytochrome P450 enzymes, in particular CYP2E1. SAM (but not SAH, MTA or methionine) produced a type II binding spectrum with liver microsomal cytochrome P450 from rats treated with acetone or isoniazid to induce CYP2E1. Binding was less effective for control microsomes. SAM did not alter the carbon monoxide binding spectrum of P450, nor denature P450 to P420, nor inhibit the activity of NADPH-P450 reductase. However, SAM inhibited the catalytic activity of CYP2E1 with typical substrates such as p-nitrophenol, ethanol, and dimethylnitrosamine, with an IC(50) around 1.5-5mM. SAM was a non-competitive inhibitor of CYP2E1 catalytic activity and its inhibitory actions could not be mimicked by methionine, SAH or MTA. However, SAM did not inhibit the oxidation of ethanol to alpha-hydroxyethyl radical, an assay for hydroxyl radical generation. In microsomes engineered to express individual human P450s, SAM produced a type II binding spectrum with CYP2E1-, but not with CYP3A4-expressing microsomes, and SAM was a weaker inhibitor against the metabolism of a specific CYP3A4 substrate than a specific CYP2E1 substrate. SAM also inhibited CYP2E1 catalytic activity in intact HepG2 cells engineered to express CYP2E1. These results suggest that SAM interacts with cytochrome P450s, especially CYP2E1, and inhibits the catalytic activity of CYP2E1 in a reversible and non competitive manner. However, SAM is a weak inhibitor of CYP2E1. Since the K(i) for SAM inhibition of CYP2E1 activity is relatively high, inhibition of CYP2E1 activity is not likely to play a major role in the ability of SAM to protect against the hepatotoxicity produced by toxins requiring metabolic activation by CYP2E1 such as acetaminophen, ethanol, carbon tetrachloride, thioacetamide and carcinogens.

Animals↗
PubMed2006

Absolute quantification of gene expression in biomaterials research using real-time PCR.

One major measurement of tissue-engineered constructs efficacy and performance is determining expression levels of genes of interest at the molecular level. This measurement is commonly carried out with reverse transcription-polymerase chain reaction (RT-PCR). In this study, we described a novel method in achieving absolute quantification of gene expression using real-time PCR (aqPCR). This novel method did not require molecular cloning steps to prepare the standards for quantification comparison. Standards were linear double-stranded DNA molecules instead of the typical gene-in-plasmid format. aqPCR could also be used to give relative quantification comparisons between samples simply by dividing the copy numbers readings of the gene of interest with that of the normalization gene. RNA was extracted from monolayer and from polycaprolactone scaffold cultures and assayed for beta-actin and osteocalcin genes. We compared our aqPCR method with end-point PCR since end-point PCR is still a common means of measuring gene expression in the biomaterials field. This study showed that aqPCR was a better method to quantify gene expression than end-point PCR. With our described linear DNA standards method, we were able to obtain not only relative quantification of osteocalcin and beta-actin expression level but also actual copy numbers of osteocalcin and beta-actin for the monolayer culture and to be 1.34 x 10(4) and 1.45 x 10(7) copies, respectively and for the scaffold cultures to be 772 and 2.83 x 10(5) copies, respectively per starting total RNA mass of 10 ng. The standards curves made from these linear DNA standards showed good linearity (R(2)=0.9964 and 0.9902 for osteocalcin and beta-actin standards graphs), ranged from 10 to 10(9) copies and of comparable accuracy to current absolute quantification real-time PCR methods (which used plasmid standards obtained through molecular cloning methods). Our method might be a viable and more user-friendly alternative to current absolute quantification real-time PCR protocols.

Biocompatible Materials↗
PubMed2005

Creating small-molecule-dependent switches to modulate biological functions.

Biological small-molecule-dependent switches sense external chemical signals and transduce them into appropriate internal signals and cellular responses. Artificial molecular switches that control the function of any protein of interest using a small molecule are powerful tools for studying biology because they enable cellular responses to be controlled by inputs chosen by researcher. Furthermore, these switches can combine the generality of genetic regulation with the reversibility and temporal control afforded by small molecules. Three approaches to creating molecular switches include altering a natural switch to recognize new exogenous ligands, engineering novel allosteric responses to ligand binding, or enforcing protein localization with chemical dimerizers. Here, we discuss the development of small-molecule-dependent switches that control in a general fashion transcriptional activation, translational initiation, and protein activity posttranslationally.

Base Sequence↗
PubMed2005

Ploidy changes associated with disruption of two adjacent genes on Leishmania major chromosome 1.

Leishmania major Friedlin (LmjF) is a kinetoplastid protozoan whose genomic sequence has been recently elucidated. About 60% of the identified genes do not have a known function, and many are trypanosomatid-specific. Here we characterise two adjacent genes from LmjF chromosome 1 (chr1): LmjF01.0750, which encodes a predicted protein with a serine/threonine protein kinase motif and LmjF01.0760, which encodes a product with no similarity to other known proteins. Orthologues of both genes are present in Trypanosoma cruzi, but neither occur in Trypanosoma brucei. We have mapped polyadenylation and spliced-leader acceptor sites for both genes, and show that they differ between Leishmania species. Attempts to generate null mutants of LmjF01.0750 by homologous recombination were unsuccessful and led to the apparent triploidy of the entire genome, suggesting that it is an essential gene. Interestingly, at least two copies of LmjF01.0750 are required for cell survival. Further evidence of genome plasticity in Leishmania was provided by changes in chr1 copy number that occurred during in vitro growth of wild-type LmjF promastigotes and following replacement of a single copy of LmjF01.0760.

Animals↗
PubMed2005

Analysis of polarity in the expression from a multifactorial bidirectional promoter designed for high-level expression of transgenes in plants.

A synthetic bidirectional expression module was constructed by placing a computationally designed minimal promoter sequence on the 5' and 3' sides of a transcription activation module. The activation of transcription from the unidirectional and bidirectional promoters constructed from the same sequence elements was evaluated by using the reporter genes gusA and gfp. The analysis based on transient and stable transformation of tobacco showed that the artificially designed multifactorial activation module activated transcription simultaneously to comparable levels in both the directions. The transcription activation module responded to elicitors like salicylic acid, NaCl and IAA in the forward as well as reverse directions. The concentration of the elicitor required for highest gene activation was similar for the two directions in case of the three activators. The kinetics of time of induction was similar in the two directions for salicylic acid and NaCl. In the case of IAA, the transcription activation was faster in the reverse direction. The results show that constitutive and chemically inducible bidirectional promoters can be deployed for predictable simultaneous regulation of two genes for genetic engineering in plants.

Factor Analysis, Statistical↗
PubMed1998

The etiology of obesity: relative contribution of metabolic factors, diet, and physical activity.

Three major factors modulate body weight: metabolic factors, diet, and physical activity, each influenced by genetic traits. Despite recent advances in these areas, the prevalence of obesity in Westernized societies has increased. In contrast to monogenic animal models and rare human genetic syndromes, predisposition to common forms of obesity is probably influenced by numerous susceptibility genes, accounting for variations in energy requirements, fuel utilization, muscle metabolic characteristics, and taste preferences. Although recent increases in obesity prevalence cannot be explained by changes in the gene pool, previously "silent" genetic variants may now play important permissive roles in modern societies. Available data suggest that variations in resting energy expenditure, thermic effect of food, and fuel utilization exist but, by themselves, are unlikely to explain the onset of obesity. Regarding diet, the best available trend survey data indicate that fat and energy intake have fallen, in this and other Westernized countries. Diverging trends of decreasing energy intake and increasing body weight suggest that reduced physical activity may be the most important current factor explaining the rising prevalence of obesity. Subsistence in modern societies requires extreme adaptations in previously useful energy-conserving diet and exercise behaviors. Recognizing the difficulties in sustaining energy-restricted diets in the presence of fast foods and social feasts, the current trend toward increasing body weight is not likely to be reversed solely through recommendations for further reductions in energy intake. In all likelihood, activity levels will have to increase in response to an environment engineered to be more physically demanding.

Appetite↗
PubMed2006

Wettability changes induced by biochemical surface reactions.

We report the use of proteins, lipids, and enzymes for the preparation of surfaces with reversible wettability changes, in particular, surfaces capable of switching from hydrophobic to hydrophilic and back. We demonstrate that these reactions can be used for engineering capillary systems with gating properties.

Adsorption↗
PubMed1997

In vitro scanning saturation mutagenesis of an antibody binding pocket.

We have combined PCR mutagenesis with in vitro transcription/translation and ELISA for the rapid generation and characterization of antibody mutants. The PCR products are used directly as the template for the in vitro transcription/translation reactions and because no cloning steps are required, the in vitro saturation mutagenesis of one residue can be completed in duplicate within a week by a single investigator. In vitro scanning saturation mutagenesis was used to analyze the role and plasticity of six key contact residues (H:Tyr-33, H:Asn-35, H:Tyr-50, H:Trp-100, L:Val-94, and L:Pro-96) in the binding pocket of a single chain Fv antibody derived from the 26-10 monoclonal antibody. A total of 114 mutant antibodies were produced; all 19 substitutions at each of the 6 chosen positions. The mutants were analyzed for binding to digoxin, digitoxin, digoxigenin, and ouabain resulting in the generation of a comprehensive data base of 456 relative affinity values. Excellent agreement between the relative affinity values obtained with in vitro synthesized mutant antibodies and equilibrium affinity data obtained with previously reported purified mutant monoclonal antibodies was observed. Approximately 75% of the single amino acid mutants exhibited significant binding to one or more of the digoxin analogs. Mutations that alter and, in some cases, reverse specificity for the different digoxin analogs were identified. In vitro scanning saturation mutagenesis represents a new tool for protein structure-function and engineering studies and can be interfaced with laboratory automation so that an even higher throughput of protein mutants can be constructed and analyzed.

Binding Sites, Antibody↗
PubMed2004

Genetic engineering of onco/lentivirus hybrids results in formation of infectious but not of replication-competent viruses.

To achieve specific gene transfer into human CD4(+) cells, murine leukaemia virus (MLV)-based pseudotype vector particles were generated employing Env variants derived from human or simian immunodeficiency virus (HIV-1 or SIVagm). Here, we describe the generation of full-length onco/lentivirus hybrid genomes comprising components of MLV and HIV-1 or SIVagm, respectively, to assess the possibility of replication-competent hybrid virus formation. The env reading frame of an infectious molecular clone of MLV was replaced with the analogous coding regions of HIV-1 or SIVagm encompassing the env gene and accessory genes. Resulting MLV/HIV-1 or MLV/SIVagm hybrid genomes were transfected into 293T cells. Expression of viral proteins and budding of retroviral particles was shown by specific immunostaining and electron microscopy. The viral particles mediated CD4- and co-receptor-specific infection of human cells as demonstrated by PCR and immunostaining in the respective target cells. However, no productive infection resulting in the generation of infectious virus was detected in these cells. Thus, these onco/lentivirus hybrids, although able to initiate single-round infection, were not replication competent. Thus, MLV-based pseudotype vectors carrying Env variants of HIV-1 or SIVagm are not prone to form replication-competent retroviruses, suggesting a favourable safety profile for MLV-based CD4-specific pseudotype vectors.

Base Sequence↗
PubMed2006

Average entropy dissipation in irreversible mesoscopic processes.

The Clausius inequality is rectified to obtain expressions for the entropy produced as the result of irreversible work and/or heat exchanges. These are combined with the Jarzynski equality and its generalizations to explicitly relate mean (as opposed to transient) entropy dissipation to experimental or simulation observables. The results are extended to nonisothermal processes which begin and end at nonequilibrium steady states, leading to a new exact expression and positive lower bound for the resulting average entropy dissipation. The Carnot engine emerges as a limiting case of a family of irreversible processes arising from an interface between materials at different temperatures, whose mapping onto reversible and irreversible molecular extension experiments is discussed.

Journal Article↗
PubMed1999

A rapid novel method for the extraction of RNA from wild-type and genetically modified kanamycin resistant mycobacteria.

RNA extraction from mycobacteria can be a difficult and time consuming process due to their unique mycolic acid cell wall composition and the short half life of RNA. Rapid cell wall disruption is essential to isolate intact high quality RNA. Genetically modified Mycobacteria smegmatis resistant to kanamycin demonstrate an altered cell wall composition which impairs the quality of RNA obtained from these mycobacteria. In this report we describe a method of RNA extraction using the detergent Catrimox-14 resulting in high yields of pure, undegraded RNA in less than 1 h. Yields of 25-30 microg RNA per 1x10(9) cells were consistently obtained from both wild-type and genetically modified M. smegmatis. The integrity of this RNA is demonstrated by gel electrophoresis, Northern blot and cDNA analysis.

Blotting, Northern↗
PubMed1995

Vascular permeability factor expression influences tumor angiogenesis in human melanoma lines xenografted to nude mice.

We studied the expression of the angiogenic factor vascular permeability factor) (VPF, also called vascular endothelial growth factor), in human melanoma cells in vitro and in vivo. Melanoma lines that develop tumors with a low metastatic potential in nude mice were found to have low expression levels of VPF in vitro, and the VPF expression levels in melanoma lines that yield highly metastatic xenografts were high. However, in vivo the correlation between VPF mRNA levels and the frequency of metastasis was lost; in all xenografts equally high levels of VPF mRNA were found, independent of the parental cell line. Hence, in vivo VPF gene expression was upregulated in the low expressing lines. The external factor responsible for this induction may be hypoxia, given that we found that low oxygen tension caused a (reversible) increase in the VPF mRNA levels in otherwise low expressing melanoma lines in vitro. A melanoma line with an inducible VPF expression was engineered into a line with a constitutive VPF expression. In the xenografts from this line a change in the vascular architecture was seen, indicating that the pattern or the level of VPF expression is important for tumor angiogenesis in melanoma xenografts.

Alternative Splicing↗