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PubMed1998

Immunization with purified natural and recombinant allergens induces mouse IgG1 antibodies that recognize similar epitopes as human IgE and inhibit the human IgE-allergen interaction and allergen-induced basophil degranulation.

Molecular characterization of allergens by recombinant DNA technology has made rapid progress in the recent few years. In the present study we immunized mice with aluminum hydroxide-adsorbed purified recombinant major timothy grass pollen allergens (rPhl p 1, rPhl p 2, rPhl p 5), dog albumin, a major animal dander allergen, and proteins with low (beta-lactoglobulin) or no (ribulose diphosphate carboxylase) allergenic potential in humans. Allergens that bind high levels of IgE in humans (Phl p 1, Phl p 5, dog albumin) induced high IgE and IgG1 levels in mice, whereas proteins with little or no allergenic activity in humans failed to induce significant IgE and IgG1 levels in mice. Continuous immunization for a period of 27 wk resulted in the production of mouse IgG1 Abs that recognized recombinant allergen fragments/epitopes defined by IgE Abs of allergic patients. As a consequence, allergen-specific mouse Abs strongly inhibited human IgE binding to the allergens and suppressed the allergen-induced histamine release from human basophils. In summary, our data indicate that 1) the allergenic potency of a protein may be related to its overall immunogenicity and 2) prolonged immunization with single purified recombinant allergens induces protective IgG Abs. The presented experimental in vivo/in vitro system allows the evaluation of Ag preparations (e.g., recombinant allergens) to be used for immunotherapy in humans.

Allergens↗
PubMed2004

Genomic portraits of the nervous system in health and disease.

As the human genome project moves toward its goal of sequencing the entire human genome, gene expression profiling by DNA microarray technology is being employed to rapidly screen genes for biological information. In this review, we will introduce DNA microarray technology, outline the basic experimental paradigms and data analysis methods, and then show with some examples how gene expression profiling can be applied to the study of the central nervous system in health and disease.

Algorithms↗
PubMed2000

Effective construction of DNA vaccines against variable influenza genes by homologous recombination.

We demonstrate the potential of cloning by homologous recombination as a rapid method to construct DNA molecules encoding newly developing hemagglutinins (HA) of influenza A virus. The variable parts of the HA genes were cloned into a basic construct containing the HA gene from an H3N2 strain. The recombinant DNAs thus created encode different variable domains with neutralising epitopes from four recently circulating influenza A H3 strains. The technology allows rapid production of DNA constructs for vaccines that can induce antibody and, particularly, cellular immune responses. These new constructs were also capable of conferring protection to challenge in mice. The technology may hence be a valuable tool for rapid adaptation of influenza vaccines to changes in the circulating influenza strains.

Amino Acid Substitution↗
PubMed2003

Evaluation of a modular strategy for the construction of novel polydactyl zinc finger DNA-binding proteins.

In previous studies, we have developed a technology for the rapid construction of novel DNA-binding proteins with the potential to recognize any unique site in a given genome. This technology relies on the modular assembly of modified zinc finger DNA-binding domains, each of which recognizes a three bp subsite of DNA. A complete set of 64 domains would provide comprehensive recognition of any desired DNA sequence, and new proteins could be assembled by any laboratory in a matter of hours. However, a critical parameter for this approach is the extent to which each domain functions as an independent, modular unit, without influence or dependence on its neighboring domains. We therefore examined the detailed binding behavior of several modularly assembled polydactyl zinc finger proteins. We first demonstrated that 80 modularly assembled 3-finger proteins can recognize their DNA target with very high specificity using a multitarget ELISA-based specificity assay. A more detailed analysis of DNA binding specificity for eight 3-finger proteins and two 6-finger proteins was performed using a target site selection assay. Results showed that the specificity of these proteins was as good or better than that of zinc finger proteins constructed using methods that allow for interdependency. In some cases, near perfect specificity was achieved. Complications due to target site overlap were found to be restricted to only one particular amino acid interaction (involving an aspartate in position 2 of the alpha-helix) that occurs in a minority of cases. As this is the first report of target site selection for designed, well characterized 6-finger proteins, unique insights are discussed concerning the relationship of protein length and specificity. These results have important implications for the design of proteins that can recognize extended DNA sequences, as well as provide insights into the general rules of recognition for naturally occurring zinc finger proteins.

DNA↗
PubMed2005

Accurate multiplex polony sequencing of an evolved bacterial genome.

We describe a DNA sequencing technology in which a commonly available, inexpensive epifluorescence microscope is converted to rapid nonelectrophoretic DNA sequencing automation. We apply this technology to resequence an evolved strain of Escherichia coli at less than one error per million consensus bases. A cell-free, mate-paired library provided single DNA molecules that were amplified in parallel to 1-micrometer beads by emulsion polymerase chain reaction. Millions of beads were immobilized in a polyacrylamide gel and subjected to automated cycles of sequencing by ligation and four-color imaging. Cost per base was roughly one-ninth as much as that of conventional sequencing. Our protocols were implemented with off-the-shelf instrumentation and reagents.

Acrylic Resins↗
PubMed1994

Metabolic effects of insulin-like growth factor I in normal humans.

Since the development of recombinant DNA technology, there has been a rapid expansion of interest in the use of human insulin-like growth factor I (IGF-I) synthesized by recombinant DNA technology for the treatment of clinical disorders. This article reviews recent studies of the metabolic effects of recombinant human IGF-I in normal humans. These studies demonstrated that under euglycemic conditions, IGF-I had potent effects on glucose (hepatic and peripheral), lipid and amino acid metabolism that closely resemble those of insulin, despite a concomitant inhibitory effect on insulin secretion. Hypoglycemia produced by IGF-I infusions (free-fall study and glucose clamps) had a different effect on counterregulatory responses compared with insulin. The glucagon response was absent, growth hormone (GH) release was attenuated, while norepinephrine levels were increased. Suppression of glucagon release during hypoglycemia impaired glucose recovery. Paradoxically, awareness of hypoglycemia was enhanced with IGF-I, partly due to stimulation of sympathetic activity. Studies performed under hyperglycemic conditions showed that IGF-I inhibited glucose-stimulated insulin secretion, but that this inhibitory effect was partially overcome by increasing the hyperglycemic stimulus. Moreover, despite the decrease in insulin secretion, glucose disposal was accelerated by IGF-I. These observations imply that IGF-I might be effective in human diabetes. In particular, normalization of the decreased basal IGF-I levels, which are characteristic of poorly controlled patients with insulin-dependent diabetes mellitus (IDDM), in pubertal patients might lower glucagon and GH levels and improve cellular metabolism in muscle.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMed1992

The rationale for the use of growth hormone or insulin-like growth factor I in adult patients with renal failure.

Since the development of recombinant DNA technology, there has been a rapid expansion of research concerning the use of recombinant DNA synthesized human growth hormone (rhGH) for the treatment of clinical disorders. rhGH has been used to treat patients with acute catabolic stress caused by surgery, trauma and sepsis, children with chronic renal insufficiency and impaired growth, patients undergoing maintenance hemodialysis who are malnourished, and individuals on weight reduction diets. These studies indicate that rhGH enhances protein balance in acutely stressed patients and in malnourished maintenance hemodialysis patients, promotes catch-up growth in children with chronic renal failure, and may reduce protein wasting and enhance lipolysis in obese individuals on weight reduction diets. Experimental studies suggest that in addition to enhancing anabolism, rhGH may increase both immune function and the rate of wound healing. Many, but not all, of the effects of rhGH are mediated through insulin-like growth factor I (IGF-I). For example, the hyperglycemic and lipolytic effects of rhGH do not seem to be caused by IGF-I. Animal or human studies suggest that with severe malnutrition or severe sepsis, rhGH treatment may neither increase serum IGF-I levels nor promote anabolism. These observations provide a rationale for administering IGF-I as an anabolic hormone for severely malnourished or septic patients with renal failure. Further studies will be necessary to examine both the short-term and long-term potential benefits and adverse effects of rhGH or rhIGF-I treatment in these conditions.

Adult↗
PubMed2005

DNA drug design for cancer therapy.

DNA (antisense and other oligonucleotides) drug design represents a direct genetic approach for cancer treatment. Such an approach takes advantage of mechanisms that activate genes known to confer a growth advantage to neoplastic cells. The ability to block the expression of these genes allows exploration of normal growth regulation. Progress in DNA drug technology has been rapid, and the traditional antisense inhibition of gene expression is now viewed on a genomic scale. This global view has led to a new vision in antisense technology, the elimination of nonspecific and undesirable side effects, and ultimately the generation of more effective and less toxic nucleic acid medicines. Several antisense oligonucleotides are in clinical trials, are well tolerated, and are potentially active therapeutically. DNA drugs are promising molecular medicines for treating human cancer in the near future.

Animals↗
PubMed2003

p53-induced gene expression analysis.

Researchers in the p53 field have successfully used many high-throughput screening technologies to analyze and characterize p53-induced gene expression. This chapter will focus on one such technology, the Affymetrix GeneChip. DNA-Chip technology has grown rapidly over the last several years. The ability to hybridize RNA from a sample to thousands to tens of thousands of known and unknown cDNAs spotted on a microarray chip has led to the explosion of information ranging from macro-global expression pattern changes to micro-gene-specific expression changes. The relative ease of making a nonradioactive probe from either total RNA or mRNA to be hybridized to a GeneChip makes microarray technology highly attractive.

Animals↗
PubMed2005

A human ImmunoChip cDNA microarray provides a comprehensive tool to study immune responses.

DNA microarray technology has developed rapidly in recent years and has become an essential tool, providing novel approaches to biomedical research. In this paper, we describe a self-designed ImmunoChip cDNA array for immunological research. With a comprehensive selection of genes of interest, we can focus on key signalling pathways and molecular mechanisms at relatively low cost compared to commercial platforms which are usually targeted at global screening of gene expression. To validate the efficiency of the ImmunoChip, we studied T helper cell polarization to functionally distinct subsets (Th1 and Th2). We also developed a tool for quality control of cDNA microarrays that assesses the technical quality of an ImmunoChip. The information produced with the quality control tool is shown to be valuable for extracting correct information from cDNA microarrays. Gene expression measurements with ImmunoChip are in agreement with the results obtained using oligonucleotide microarrays and with published quantitative RT-PCR data. The ImmunoChip provides reliable measurements and gives new insights into various aspects of human immune responses.

DNA, Complementary↗
PubMed1985

Nucleic acid probes in diagnosis of viral diseases of man. Brief review.

With the recent, rapid advances in recombinant DNA technology, it has become possible to consider the use of nucleic acid probes in diagnosis of human viral diseases. Several examples are discussed which employ techniques of dot blot hybridization, sandwich hybridization and in situ hybridization. Typing of viral strains using restriction endonuclease digestion as an epidemiological tool is considered. Finally, the present limitations of molecular hybridization are discussed, and future developments including the production of non-radioactively labeled probes, are assessed.

Cytomegalovirus↗
PubMed1996

[Basic principles of gene therapy].

The rapid development of recombinant DNA technology and our enhanced understanding of the genetic basis of human disease has facilitated the development of new molecular therapeutic modalities, termed gene therapy. Gene therapy involves the transfer of functional genes into somatic cells and their expression in target tissues in order to replace absent genes, correct defective genes, or induce antitumoral activity in the tumor-bearing host. Currently, an increasing number of gene therapy strategies are being investigated in experimental and clinical trials. Despite substantial progress, a number of technical and logistical hurdles must still be overcome before gene therapy can be safety and effectively applied in the human patient. Since gene therapy involves complex cell processing and can be time consuming and costly, simplifications or even alternative approaches will be necessary in order to establish this therapy as suitable for clinical use. This report reviews various gene therapy strategies and gene delivery techniques currently under clinical or experimental investigation. Special emphasis is given to cytokine gene therapy using gene-modified tumor vaccines for cancer treatment.

Cancer Vaccines↗
PubMed1992

Genetic engineering of beta-lactam antibiotic biosynthetic pathways in filamentous fungi.

Recombinant DNA technology has facilitated a rapid increase in our knowledge of beta-lactam antibiotic biosynthesis. Using the tools of this technology, beta-lactam biosynthetic genes and proteins have been characterized at the molecular level, cephalosporin-C production has been improved, new beta-lactams produced, and novel beta-lactam biosynthetic pathways have been constructed.

Anti-Bacterial Agents↗
PubMed1989

Assessment of immunity.

An approach to the assessment of the immune system primarily from the vantage point of the general physician is presented, indicating the clinical situations where analysis is most likely to yield informative results. Preliminary screening by the primary physician is discussed, followed by a brief description of measures which are employed in referral centers. A definitive diagnosis should be possible in nearly all cases. With the rapid advances in recombinant DNA technology and bone marrow transplantation, a cure can be expected for most patients, particularly if the diagnosis is made early.

Child↗
PubMed1999

Analysis of gene expression data using self-organizing maps.

DNA microarray technologies together with rapidly increasing genomic sequence information is leading to an explosion in available gene expression data. Currently there is a great need for efficient methods to analyze and visualize these massive data sets. A self-organizing map (SOM) is an unsupervised neural network learning algorithm which has been successfully used for the analysis and organization of large data files. We have here applied the SOM algorithm to analyze published data of yeast gene expression and show that SOM is an excellent tool for the analysis and visualization of gene expression profiles.

Algorithms↗
PubMed2003

Discriminating two classes of toxicants through expression analysis of HepG2 cells with DNA arrays.

Microarray technology provides a rapid and cost-effective method to associate specific cellular responses with unique gene expression patterns. If characteristic expression patterns of a small number of genes could be associated with drug toxicity, this association may be used for toxicity prediction, and thereby to reduce the need for traditional toxicity testing. To test this hypothesis, we have designed an array composed of 92 known human genes of toxicological interest (including seven housekeeping genes) and eight bacterial controls. HepG2 cells were treated with either ethanol or one of two quinone containing anticancer drugs, mitomycin C or doxorubicin. RNA was isolated from treated and untreated cells, differentially labeled with fluorescent dyes, and then hybridized to the array. Our results show that the expression patterns induced by ethanol and the anticancer drugs are different. Both of the anticancer drugs, but not ethanol had a differential effect on the regulation of several genes, including CYP4F2/3, CYP3A3, TNFRSF6 and CHES1, demonstrating that the two drugs might function through a similar mechanism, which differs from that of ethanol. These results suggest that microarray-based expression analysis may offer a rapid and efficient means for assessing drug toxicity.

Antineoplastic Agents↗
PubMed2003

Cross-platform comparison and visualisation of gene expression data using co-inertia analysis.

BACKGROUND: Rapid development of DNA microarray technology has resulted in different laboratories adopting numerous different protocols and technological platforms, which has severely impacted on the comparability of array data. Current cross-platform comparison of microarray gene expression data are usually based on cross-referencing the annotation of each gene transcript represented on the arrays, extracting a list of genes common to all arrays and comparing expression data of this gene subset. Unfortunately, filtering of genes to a subset represented across all arrays often excludes many thousands of genes, because different subsets of genes from the genome are represented on different arrays. We wish to describe the application of a powerful yet simple method for cross-platform comparison of gene expression data. Co-inertia analysis (CIA) is a multivariate method that identifies trends or co-relationships in multiple datasets which contain the same samples. CIA simultaneously finds ordinations (dimension reduction diagrams) from the datasets that are most similar. It does this by finding successive axes from the two datasets with maximum covariance. CIA can be applied to datasets where the number of variables (genes) far exceeds the number of samples (arrays) such is the case with microarray analyses. RESULTS: We illustrate the power of CIA for cross-platform analysis of gene expression data by using it to identify the main common relationships in expression profiles on a panel of 60 tumour cell lines from the National Cancer Institute (NCI) which have been subjected to microarray studies using both Affymetrix and spotted cDNA array technology. The co-ordinates of the CIA projections of the cell lines from each dataset are graphed in a bi-plot and are connected by a line, the length of which indicates the divergence between the two datasets. Thus, CIA provides graphical representation of consensus and divergence between the gene expression profiles from different microarray platforms. Secondly, the genes that define the main trends in the analysis can be easily identified. CONCLUSIONS: CIA is a robust, efficient approach to coupling of gene expression datasets. CIA provides simple graphical representations of the results making it a particularly attractive method for the identification of relationships between large datasets.

Breast Neoplasms↗
PubMed2001

Cancer gene therapy by adenovirus-mediated gene transfer.

Cancer arises as a direct result of genetic mutations. It therefore stands to reason that cancer should be well suited for the correction through gene therapy. Recent advances in the understanding of the molecular pathogenesis of cancer and the rapid development of recombinant DNA technology have made cancer gene therapy feasible in the clinical setting. The current efforts for cancer gene therapy mainly focus on immunogene therapy, chemogene therapy, restoration of tumor suppressor gene function, and oncolytic virus therapy. Central to all these therapies is the development of efficient vectors for gene delivery--this remains a work in progress. These vectors can be classified as viral and non-viral vectors. This paper will concentrate on viral vectors because of their practical advantages over non-viral vectors. Of the viral vectors, by far the most important are the human adenoviruses as is reflected by the enormous data and literature accumulated by studies relating to animal tumor models and clinical trials. In this review, we examine the recent progress in adenovirus-mediated cancer gene therapy with regard to cytokine gene, tumor suppressor gene, chemogene, and oncolytic adenovirus. We also discuss the current limitations of the adenoviral vector system and how they may be circumvented in future developments relating to targeted gene delivery.

Adenoviridae↗