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PubMed1994

Nucleic acid probes for the food industry.

Recombinant DNA technology has revolutionised microbiological analysis by providing rapid and sensitive methods for the direct detection and identification of organisms. These advances have been most successfully applied to basic research and to clinical microbiology. Continued improvements in the techniques and in assay formats have now brought them to the stage where they could be useful on an industrial scale. The use of nucleic acid techniques for the identification of bacteria of importance to the food industry is discussed with emphasis on developments in practical applications.

Journal Article↗
PubMed1987

Application of DNA-based diagnosis to patient care: the example of hemophilia A.

DNA-based carrier testing and prenatal diagnosis are rapidly expanding medical applications of recombinant-DNA technology. The ultimate goal of DNA-based diagnosis is the determination of the causative mutation, but, in general, this is possible only for large deletions, insertions, or certain nonsense mutation that, in most diseases, involve only a few percent of affected families. If direct diagnosis of the carrier state or fetal disease state is not feasible, indirect diagnosis can be performed by following the segregation of linked polymorphisms through the family pedigree. For such indirect diagnosis, DNA from multiple family members must be analyzed. Although this procedure is highly accurate in many families, errors can potentially occur because of meiotic recombination, genetic heterogeneity, new mutations, and nonpaternity. In this review, a general introduction to DNA-based diagnosis of mendelian diseases is presented and the methods and strategy are outlined. The use of these techniques for the diagnosis of hemophilia A is then described to illustrate the principles of diagnosis and to highlight some of the complexities encountered. DNA-based diagnosis is in its infancy and has the potential to revolutionize preventive medicine.

DNA, Recombinant↗
PubMed1999

Molecular pathogenesis of human cytomegalovirus infection.

Despite progress in diagnosis and treatment of human cytomegalovirus (CMV) infection, we do not understand why, in hosts with comparable levels of immunosuppression, some CMV infections result in symptomatic CMV disease while others are limited to asymptomatic virus shedding with no discernible clinical consequences. CMV viral detection and quantification are useful for identifying those at highest risk, but do not consistently predict clinical outcome. Factors such as host genotype and immune response are active areas of research. However, the importance of CMV strain variability, recognized since 1976, is now receiving attention. Advances in technology that allow the rapid sequencing of viral DNA for purposes of strain characterization have fueled the renewed interest. The focus of this review will be to summarize our evolving knowledge of CMV strain variability and to document where possible a potential relationship to strain virulence. Studies with the UL55 (gB) envelope glycoprotein will be emphasized because of the ability to clearly identify naturally occurring variants, as well as the increasing number of reports that there are differences in biological activities that may contribute to virulence.

Cytomegalovirus↗
PubMed1998

Functional quantitative analysis of the genome in cultured human mesangial cells. Technical note.

For normal physiological function, each cell tightly regulates gene expression in a specific fashion so that critical proteins are synthesized in a well-coordinated manner. Therefore, it is very important to uncover which genes are expressed in specific cells. Recent technological advances combined with rapid large-scale DNA sequencing and computerized data processing have allowed us to investigate the expression levels of a variety of transcripts in the mesangial cells, a target of injury in many forms of glomerulonephritis. Utilizing a large scale sequencing of a 3'-directed cDNA library, which allows us to avoid variable cloning efficiencies reflecting the size of cDNA, we investigated expression profiles of various molecules in cultured human mesangial cells. Among the 1,193 sequenced clones, 688 (57.7%) appeared more than once (redundant sequence group), representing 203 different species. Thirty-nine of these appeared more than three times. The most abundant mRNA was that of fibronectin, which consisted of 3.9% of the total mRNA population. Except for mitochondrial or ribosomal genes, calcyclin came next (2.5%), followed by two cytoskeletal genes, gamma-actin gene and calpactin 1 light chain gene, in addition to an amyloid precursor protein homolog (0.7%). In conclusion, we performed a molecular biological quantification of transcripts in mesangial cells. Fibronectin was the most abundantly expressed, followed by calcyclin, gamma-actin, calpactin 1 light chain, and an amyloid precursor protein homolog. We also discovered some candidate genes specific for human mesangial cells. The expression profile of the transcripts serves as an important tool in understanding the biological properties of mesangial cells.

Actins↗
PubMed2001

A hierarchical unsupervised growing neural network for clustering gene expression patterns.

MOTIVATION: We describe a new approach to the analysis of gene expression data coming from DNA array experiments, using an unsupervised neural network. DNA array technologies allow monitoring thousands of genes rapidly and efficiently. One of the interests of these studies is the search for correlated gene expression patterns, and this is usually achieved by clustering them. The Self-Organising Tree Algorithm, (SOTA) (Dopazo,J. and Carazo,J.M. (1997) J. Mol. Evol., 44, 226-233), is a neural network that grows adopting the topology of a binary tree. The result of the algorithm is a hierarchical cluster obtained with the accuracy and robustness of a neural network. RESULTS: SOTA clustering confers several advantages over classical hierarchical clustering methods. SOTA is a divisive method: the clustering process is performed from top to bottom, i.e. the highest hierarchical levels are resolved before going to the details of the lowest levels. The growing can be stopped at the desired hierarchical level. Moreover, a criterion to stop the growing of the tree, based on the approximate distribution of probability obtained by randomisation of the original data set, is provided. By means of this criterion, a statistical support for the definition of clusters is proposed. In addition, obtaining average gene expression patterns is a built-in feature of the algorithm. Different neurons defining the different hierarchical levels represent the averages of the gene expression patterns contained in the clusters. Since SOTA runtimes are approximately linear with the number of items to be classified, it is especially suitable for dealing with huge amounts of data. The method proposed is very general and applies to any data providing that they can be coded as a series of numbers and that a computable measure of similarity between data items can be used. AVAILABILITY: A server running the program can be found at: http://bioinfo.cnio.es/sotarray.

Algorithms↗
PubMedDate not supplied

Cytomegalovirus: where have we been and where are we going?

Nearly 30 years have elapsed since Rowe and Weller and their colleagues discovered human cytomegalovirus (CMV). Because of its complex structure, long replicative cycle, low yield in vitro, and highly species-specific cell-substrate requirement, the cellular and molecular biologic analyses of human CMV have been slow, but recombinant DNA and monoclonal antibody technologies are bringing about rapid changes. Because of the long period of latency and wide range of disease presentations, epidemiologic and medical insights have also come slowly. However, the clinical events that occur during iatrogenic immunosuppression (transplantation and cancer therapy) and as a result of immunocompromise due to human immunodeficiency virus infection are currently promoting our understanding of the epidemiology of CMV disease and the definition of its clinical spectrum. Rapid diagnostic methods, antiviral drugs, and vaccines for CMV are becoming available. We may not yet understand completely the impact of this agent on the nonimmunosuppressed or aspects of its pathogenesis: e.g., the immune functions controlling recrudescence and the possibility of increased disease severity in those with no detectable immune defect. With the availability of new approaches, other issues should be clarified, such as the functions of host and virus involved in the mechanism of persistence.

Acquired Immunodeficiency Syndrome↗
PubMed1990

Basic concepts and practical applications of recombinant DNA techniques in detection of human papillomavirus (HPV) infection. Review article.

Recent studies on the role of infectious agents in the pathogenesis of malignancy have demonstrated a strong association between HPV and several human benign and malignant epithelial neoplasms. There are 60 distinct types of HPV, of which HPV 16, 18, 31, 33, 35 and 39 have been associated with squamous cell neoplasia of the genital tract. Rapid progress in the field of recombinant DNA technology with the availability of specific probes has enabled the detection of HPV genomic sequences in characteristic HPV lesions. In addition, HPV sequences have been found in malignant squamous cell lesions, and even in normal tissues lacking the morphologic signs of HPV infection. Currently, hybridization analysis of the nucleic acid is the most reliable method for diagnosis of HPV infections, also permitting the genotyping of these viruses. A variety of hybridization procedures have been developed with different sensitivities and specificities. Despite the divergent technical modifications, however, all hybridization tests working according to the same basic principles. The double helix of DNA composed of two complementary polynucleotide chains can be opened by heating or by increasing pH. Cooling of the two strands allows reassociation. Labeled HPV DNA or RNA probe hybridizes with the complementary sequences allowing the detection of HPV sequences in the samples. Hybridization assays can be conducted under conditions in which virtually all HPVs will be detected, but not specifically typed (low stringency) or under conditions in which the type can be identified (high stringency). Widely divergent results have been reported both in prevalence of HPV infection and distribution of different HPV types in the genital tract. These discordant results have been explained on the basis of sampling effects, differences in histopathological diagnosis, geographical variations in HPV types and interlaboratory variation in HPV detection and typing techniques. In this review the various procedures for detecting HPV sequences by hybridization and related techniques are shortly described.

Blotting, Southern↗
PubMed2005

The clinical use of tumor makers in select cancers: are you confident enough to discuss them with your patients?

PURPOSE/OBJECTIVES: To review the clinical use of tumor markers in select cancers and highlight future directions in tumor marker development. DATA SOURCES: Guidelines from national and international societies, scientific literature, and Internet resources. DATA SYNTHESIS: Tumor markers are important tools in the management of cancer. Sequencing of the human genome has led to new tumor marker development in the fields of proteomics and DNA microarray technologies. CONCLUSIONS: Tumor marker technology is expanding rapidly; almost a dozen tumor markers currently are being used in the oncology arena, with many more in development. The use of tumor markers can be controversial, particularly because guidelines have not been established for all of the markers. IMPLICATIONS FOR NURSING: Oncology nurses need to be well versed in the use of tumor markers to educate and counsel patients with cancer.

Biomarkers, Tumor↗
PubMed2005

[Pharmacogenetics: towards personalized medicine].

For 50 years, pharmacogenetics has been studying the genetic basis for variability in drug response between individual patients, both with respect to drug toxicity and drug efficacy. Following the completion of The Human Genome Project about three years ago, and the development of technologies allowing rapid identification of polymorphic alleles using DNA chips, pharmacogenetics would soon allow the introduction of personalized medicine. For most medical disciplines, this would allow pharmacotherapy according to each patient's individual genetic data. This would allow a reduction in the rates of adverse drug reactions, currently responsible by American and European estimates for about 6% of new admissions to internal medicine wards, and causing more morbidity annually than road accidents or breast cancer. The purpose of this review is to delineate the principles of pharmacogenetics, focusing on the aspects closest to implementation in the clinic: the polymorphism of liver CYP450 metabolic enzymes, mostly CYP2D6 and CYP2C19. We shall also review current efforts to better understand the scope of human genome diversity, and present several examples for variability in drug efficacy and genetic polymorphism of drug target genes. Education of health professionals in pharmacogenetics as part of their pharmacology curricula, and explaining its potential to the general public, would be indispensable for the success of personalized medicine.

Cytochrome P-450 Enzyme System↗
PubMed1988

Using the microbiology laboratory in the diagnosis of pneumonia.

Pneumonia/influenza is one of the top ten leading causes of mortality in the United States each year. The identification of the etiologic agent responsible for lower respiratory tract infection plays an important role in the proper management of this clinical problem. The specimens submitted for evaluation are obtained in diverse ways and include expectorated sputum, material from transtracheal and bronchoscopic procedures, pleural fluid and lung aspirates, and biopsy of actual lung tissue. Processing of material can include stained smears, aerobic and anaerobic cultures, and special processing techniques for fungal, viral, Pneumocystis carinii, Legionella, mycobacterial, and mycoplasma identification. Modifications of smear preparation techniques and application of the new DNA probe technology are providing the opportunity for rapid microbiologic testing of clinical specimens with increased sensitivity and specificity, often obviating the need for invasive diagnostic procedures. Laboratory methodology is continually undergoing technological change, and optimal care of the patient with pneumonia requires close cooperation between the attending physician and the clinical laboratory.

Bacteriological Techniques↗
PubMed1996

Chromosome microdissection: a brief overview.

Chromosome microdissection arose as a means of facilitating long range physical mapping of chromosome regions involved in either a genetic or malignant disorder. However, with the rapid development of improved techniques for mapping and sequencing the human genome, microdissection is considered by many investigators to be a cumbersome and time consuming procedure. Nonetheless, based on the impressive number of informative diagnostic DNA markers that are now available as a result of this technology, microdissection still must be considered one of the most rapid and direct methods available for generating new DNA markers from any chromosome region, irrespective of its sequence composition. In addition, it remains an important means to dissect DNA markers from any organism, eukaryotic and prokaryotic, and has resulted in generating disease associated DNA sequences from both human and animal genomes. Recently, microdissection of single cells has emerged as a viable alternative for isolating pure populations of specific cell types, especially tumor cells, which can then be studied without background contamination from any other cellular constituents. This overview will provide a glimpse into the present applications of the microdissection technology, as well as the importance this technology will have for future exploration into the human genome.

Animals↗
PubMed2003

The Corynebacterium glutamicum genome: features and impacts on biotechnological processes.

Corynebacterium glutamicum has played a principal role in the progress of the amino acid fermentation industry. The complete genome sequence of the representative wild-type strain of C. glutamicum, ATCC 13032, has been determined and analyzed to improve our understanding of the molecular biology and physiology of this organism, and to advance the development of more efficient production strains. Genome annotation has helped in elucidation of the gene repertoire defining a desired pathway, which is accelerating pathway engineering. Post genome technologies such as DNA arrays and proteomics are currently undergoing rapid development in C. glutamicum. Such progress has already exposed new regulatory networks and functions that had so far been unidentified in this microbe. The next goal of these studies is to integrate the fruits of genomics into strain development technology. A novel methodology that merges genomics with classical strain improvement has been developed and applied for the reconstruction of classically derived production strains. How can traditional fermentation benefit from the C. glutamicum genomic data? The path from genomics to biotechnological processes is presented.

Amino Acid Sequence↗
PubMed1999

Resequencing and mutational analysis using oligonucleotide microarrays.

Oligonucleotide microarray (DNA chip)-based hybridization analysis is a promising new technology which potentially allows rapid and cost-effective screens for all possible mutations and sequence variations in genomic DNA. Here, I review current strategies and uses for DNA chip-based resequencing and mutational analysis, the underlying principles of experimental designs, and future efforts to improve the sensitivity and specificity of chip-based assays.

Animals↗
PubMed1996

[High-throughput of DNA sequencing by automated machines].

I describe recent advance of DNA sequencing technology including automated machines. The human genome project, particularly large-scale DNA sequencing, forces us to handle numbers of samples simultaneously and rapidly. This lead us to develop new technologies. I herein introduce current progress of sequencing technologies and automated machines.

Human Genome Project↗
PubMed2005

Specific antitumor immune response induced by a novel DNA vaccine composed of multiple CTL and T helper cell epitopes of prostate cancer associated antigens.

The loss of immunogenic epitopes by tumors has urged the development of vaccines against multiple epitopes. Recombinant DNA technologies have opened the possibility to develop multiepitope vaccines in a relatively rapid and efficient way. In this study, several DNA fragments encoding multiple cytotoxic T lymphocyte (CTL) and T helper (Th) cell epitopes were selected from human prostate-specific membrane antigen (hPSM), mouse prostatic acid phosphatase (mPAP), and human prostate-specific antigen (hPSA), These DNA fragments were ligated together to form a novel fusion gene, termed 3P gene. The 3P gene and human IgG Fc gene were inserted into pcDNA3.1 to construct a DNA vaccine designated psig-3P-Fc. Vaccination with psig-3P-Fc by gene gun inoculation induced strong antitumor response in a mouse tumor model, which significantly inhibited tumor growth and prolonged survival time of the tumor-bearing mice. In vitro, when lymphocytes were stimulated by psig-3P-Fc-transfected autologous peripheral blood mononuclear cells (PBMC), CTLs were induced which could specifically kill hPSM-, hPAP-, or hPSA-expressing tumor cells. These observations provide a new vaccine strategy for cancer therapy through concomitant enhancement of antigen specific CD4(+) helper and CD8(+) cytotoxic T-cell responses against tumors.

Animals↗
PubMed1995

Ordered restriction endonuclease maps of yeast artificial chromosomes created by optical mapping on surfaces.

We have developed a surface mounting technology for the rapid construction of ordered restriction maps from individual DNA molecules. Optical restriction maps constructed from yeast artificial chromosome DNA molecules mounted on specially derivatized glass surfaces are accurate and reproducible, and the technology is amenable to automation. The mounting procedures described here should also be useful for fluorescence in situ hybridization studies. We believe these improvements to optical mapping will further stimulate the development of nonelectrophoretic approaches to genome analysis.

Automation↗
PubMed2002

Rapid detection of herpes simplex virus DNA in genital ulcers by real-time PCR using SYBR green I dye as the detection signal.

We have evaluated a real-time PCR procedure based on the LightCycler technology for rapid detection of herpes simplex virus (HSV) in genital lesions. Two sets of primers, corresponding to the thymidine kinase and DNA polymerase regions, were used for the amplification reactions in separate capillaries containing the SYBR Green I dye as detection signal. In 28 of 118 samples (24%), HSV was isolated by conventional cell culture. All cell culture-positive samples were also positive by real-time PCR. Six additional cell culture-negative samples were positive by PCR with both sets of primers. Total processing time was less than 3 h. Real-time PCR using SYBR Green I as detection signal is a sensitive procedure for the rapid diagnosis of HSV in genital lesions.

Benzothiazoles↗
PubMed2001

Defined flanking spacers and enhanced proteolysis is essential for eradication of established tumors by an epitope string DNA vaccine.

Loss of immunogenic epitopes by tumors has urged the development of vaccines against multiple epitopes. Recombinant DNA technologies have opened the possibility to develop multiepitope vaccines in a relatively rapid and efficient way. We have constructed four naked DNA-based multiepitope vaccines, containing CTL, Th cell, and B cell epitopes of the human papillomavirus type 16. Here we show that gene gun-mediated vaccination with an epitope-based DNA vaccine protects 100% of the vaccinated mice against a lethal tumor challenge. The addition of spacers between the epitopes was crucial for the epitope-induced tumor protection, as the same DNA construct without spacers was significantly less effective and only protected 50% of the mice. When tested for therapeutic potential, only the epitope construct with defined spacers significantly reduced the size of established tumors, but failed to induce tumor regression. Only after targeting the vaccine-encoded protein to the protein degradation pathway by linking it to ubiquitin, the vaccine-induced T cell-mediated eradication of 100% of 7-day established tumors in mice. The finding that defined flanking sequences around epitopes and protein targeting dramatically increased the efficacy of epitope string DNA vaccines against established tumors will be of importance for the further development of multiepitope DNA vaccines toward clinical application.

Adjuvants, Immunologic↗