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PubMedDate not supplied

Morgane, a new LTR retrotransposon group, and its subfamilies in wheats.

Transposable elements are the main components of grass genomes, especially in Triticeae species. In a previous analysis, we identified a very short element, Morgane_CR626934-1; here we describe more precisely this unusual element. Morgane_CR626934-1 shows high sequence identity (until 98%) with ESTs belonging to other possible small elements, expressed under abiotic and biotic stress conditions. No putative functional polyprotein could be identified in all of these different Morgane-like sequences. Moreover, elements from the Morgane_CR626934-1 subfamily are found only in wheats and Agropyrum genomes and among these species, only Ae. tauschii and T. aestivum present a high copy number of these elements. They are highly conserved in wheat genomes (95.5%). Based on the uncommon characteristics of the described Morgane-like elements, we proposed to classify them in a new group within the Class I LTR retrotransposon, the Morgane group.

Base Sequence↗

PubMed1990

Detection of an IE responsive element(s) in the BamHI J fragment of human cytomegalovirus AD169.

The BamHI J fragment of human cytomegalovirus (HCMV) AD169 located at 0.815 to 0.855 map units in the unique short component of the genome was demonstrated to be responsive to the HCMV IE proteins by using a transient chloramphenicol acetyltransferase (cat) gene expression system. The BamHI J fragment was cloned into a cat gene expression plasmid and then cotransfected with a plasmid that expresses the immediate early (IE) genes of HCMV AD169 into the HCMV permissive cell line MRC-5. The results indicated that the BamHI J fragment enhanced cat gene expression 10-fold when the HCMV IE proteins were present. The BamHI J fragment was demonstrated to have properties of an inducible enhancer. In the presence of the HCMV IE proteins, it enhances cat gene expression when positioned in either orientation both upstream and downstream from the cat gene; it enhances transcription from the herpes simplex virus type 1 (HSV-1) thymidine kinase gene and the simian virus 40 (SV40) early gene promoters; and it requires a cis-positioned promoter for enhancer activity.

Base Sequence↗

PubMed1976

The effect of SV40 transformation on the chromosomal proteins of 3T3 mouse embryo fibroblasts.

The composition and metabolism of chromosomal proteins-histones and nonhistones chromosomal proteins-were examined in normal and SV40 transformed 3T3 mouse cells. Variations were observed, many of which were similar to those previously reported for normal and SV40 transformed W138 human diploid fibroblasts. The possible implications of these viral induced changes in the protein component of the genome for the phenotypic modifications which occur in transformed cells are discussed.

Aged↗

PubMed1983

Ultrastructural characteristics of in vitro parasite-lymphocyte behaviour in invasions with Theileria annulata and Theileria parva.

Host-parasite relationships have been studied by electron microscopy using glutaraldehyde-OsO4-fixed pellets of lymphoid cultures infected in vitro by Theileria annulata and T. parva. Intracellular presence of the parasite resulted in a progressive and marked lymphoblastoid transformation. The schizont stage periodically provoked the formation of, and adopted an intimate association with, cytoplasmic annulate lamellae in the interphase cell. Annulate lamellae developed from the outer nuclear membrane of the host cell by a delamination process and were taken into the cytoplasmic matrix of the schizont by phagotrophy through the cytostome. Schizont nuclei themselves were seen to divide at the prometaphase stage of host cell mitosis, the division being characterized by the development of intranuclear spindle microtubules anchored in spindle pole bodies. A hypothesis is propounded that Theileria parasites, consequent on interiorization, provoke the blastoid transformation and the formation of annulate lamellae through the influence of components of their genomic material on host cell deoxyribonucleic acid (DNA) and that the annulate lamellae represent a species of messenger ribonucleic acid (mRNA) and serve as a monitoring device for the schizont, facilitating the accurate timing of the host cell cyclical events.

Animals↗

PubMed1992

Isolation and mapping of 88 new RFLP markers on human chromosome 8.

To obtain new RFLP markers for construction of a high-resolution map of human chromosome 8, a cosmid library was constructed from a somatic hybrid cell that contained chromosome 8 as the only human component in mouse genomic background. Eighty-eight new RFLP markers were isolated and characterized, and 71 of them were sublocalized to chromosomal bands by fluorescent in situ hybridization (FISH). Of these, 36 were localized to the short arm, 34 to the long arm, and 1 to the centromeric region. Five markers defined VNTR loci. This work represents the first extensive isolation and physical mapping of RFLP markers on human chromosome 8. These new markers will serve as useful resources for linkage mapping of loci for inherited diseases and for efforts to identify a putative tumor suppressor gene(s) on chromosome 8.

Autoradiography↗

PubMed2006

Transposable elements as a significant source of transcription regulating signals.

Transposable elements (TEs) are major components of eukaryotic genomes, contributing about 50% to the size of mammalian genomes. TEs serve as recombination hot spots and may acquire specific cellular functions, such as controlling protein translation and gene transcription. The latter is the subject of the analysis presented. We scanned TE sequences located in promoter regions of all annotated genes in the human genome for their content in potential transcription regulating signals. All investigated signals are likely to be over-represented in at least one TE class, which shows that TEs have an important potential to contribute to pre-transcriptional gene regulation, especially by moving transcriptional signals within the genome and thus potentially leading to new gene expression patterns. We also found that some TE classes are more likely than others to carry transcription regulating signals, which can explain why they have different retention rates in regions neighboring genes.

Base Sequence↗

PubMed2006

Expression of a novel gene, MafB, in Dupuytren's disease.

PURPOSE: Dupuytren's disease (DD) is characterized by fibroblastic proliferation of the palmar fascia, often leading to flexion contracture in the hand. Although there is a strong genetic component the genome-wide expression of novel genes is not known. The purpose of this study was to use DNA microarray technology to identify upregulated genes in DD. METHODS: Human tissue samples were harvested from 3 patient sources: DD cord tissue (n = 20), normal-appearing adjacent control fascia (n = 15), and palmar fascia from patients having carpal tunnel release (n = 15). DNA microarray analysis was performed on amplified sample RNA. Novel genes were compared with known gene functions. A candidate gene of interest was studied further by using immunohistochemistry on DD tissue samples and controls. RESULTS: Several novel genes not described previously in the study of DD were upregulated significantly, including MafB, collagen type V, alpha-2 (COL5A2), collagen type VIII, alpha-1 (COL8A1), contactin I (CNTN1), and leucine-rich repeat containing 17 (LRRC17). These upregulated genes were compared with their known gene-expression profiles in other tissues and their purported functions. MafB was found to be of particular interest because of its prominent role in tissue development and cellular differentiation. MafB immunohistochemistry showed positive staining in 50% of the DD specimens but complete absence of MafB in all control tissues (adjacent control fascia, carpal tunnel fascia). Co-localization experiments with MafB and alpha-smooth muscle actin showed staining properties in similar regions but these 2 proteins were not confined solely to the same cells. CONCLUSIONS: Microarray analysis of DD tissue has identified significant upregulated gene expression of MafB. MafB protein also is found in Dupuytren's cords but not in control fascia. Co-localization data suggest that the association of MafB with DD is not related exclusively to myofibroblast proliferation. Because of its role in fibroblastic transformation in other models MafB and its relationship to the pathogenesis of DD deserves further study.

Actins↗

PubMed2004

Large-scale expression screening by automated whole-mount in situ hybridization.

Gene expression profiling is an important component of functional genomics. We present a time and cost efficient high-throughput whole-mount in situ technique to perform a large-scale gene expression analysis in medaka fish (Oryzias latipes) embryos. Medaka is a model system ideally suited for the study of molecular genetics of vertebrate development. Random cDNA clones from an arrayed stage 20 medaka plasmid library were analyzed by whole-mount in situ hybridization on embryos of three representative stages of medaka development. cDNA inserts were colony PCR amplified in a 384-format. The PCR products were used to generate over 2000 antisense RNA digoxigenin probes in a high-throughput process. Whole-mount in situ hybridization was carried out in a robot and a broad range of expression patterns was observed. Partial cDNA sequences and expression patterns were documented with BLAST results, cluster analysis, images and descriptions, respectively; collectively this information was entered into a web-based database, "MEPD" (http://www.embl-heidelberg.de/mepd/), that is publicly accessible.

Animals↗

PubMed2004

Animal models of type I allergy using recombinant allergens.

Various animal models including guinea pigs, monkeys, dogs, rats, and mice have been established in an attempt to provide insights into the complex immunological and pathophysiological mechanisms of human type I allergic diseases. The detailed knowledge of the murine genome, the various components of the murine immune system, and the generation of engineered mice has made the murine system the most attractive among all animal models. The availability of multitude technologies and reagents to characterize and manipulate immunological pathways and mediators adds to the outstanding opportunities to assess the pathology of allergic diseases and to develop novel therapeutic strategies in mice. Numerous sensitization protocols with food and aero-allergens are used to establish an allergic/asthma-like phenotype in mice. Requirements for an appropriate murine model include a close resemblance to the pathology of the disease in humans, the objective measurement of the physiologic parameters, as well as reliability and reproducibility of the experimental data. With respect to reproducible experimental conditions, it has been recognized that extract preparations from natural allergen sources can vary in their allergen-content and -composition. This might influence the degree of sensitization or the outcome of treatment strategies in dependence of the applied extract preparation. The use of recombinant allergens in experimental in vivo and in vitro systems can overcome these problems. Another aspect, that has become obvious from the experimental studies, is that allergens can differ in their immunogenicity as well as in their capacity to act as tolerogens. Therefore, it seems important that the efficacy of the different allergen-molecules to act as therapeutic agents is individually examined. In this review, examples of animal models are described, in which recombinant allergens have been used for sensitization and/or treatment of allergic responses and how they have been used to enhance our understanding of the pathology of allergic diseases.

Allergens↗

PubMed2003

Commercialization of animal biotechnology.

Commercialization of animal biotechnology is a wide-ranging topic for discussion. In this paper, we will attempt to review embryo transfer (ET) and related technologies that relate to food-producing mammals. A brief review of the history of advances in biotechnology will provide a glimpse to present and future applications. Commercialization of animal biotechnology is presently taking two pathways. The first application involves the use of animals for biomedical purposes. Very few companies have developed all of the core competencies and intellectual properties to complete the bridge from lab bench to product. The second pathway of application is for the production of animals used for food. Artificial insemination (AI), embryo transfer, in vitro fertilization (IVF), cloning, transgenics, and genomics all are components of the toolbox for present and future applications. Individually, these are powerful tools capable of providing significant improvements in productivity. Combinations of these technologies coupled with information systems and data analysis, will provide even more significant change in the next decade. Any strategies for the commercial application of animal biotechnology must include a careful review of regulatory and social concerns. Careful review of industry infrastructure is also important. Our colleagues in plant biotechnology have helped highlight some of these pitfalls and provide us with a retrospective review. In summary, today we have core competencies that provide a wealth of opportunities for the members of this society, commercial companies, producers, and the general population. Successful commercialization will benefit all of the above stakeholders.

Animals↗

PubMed2001

Coronavirus derived expression systems.

Both helper dependent expression systems, based on two components, and single genomes constructed by targeted recombination, or by using infectious cDNA clones, have been developed. The sequences that regulate transcription have been characterized mainly using helper dependent expression systems and it will now be possible to validate them using single genomes. The genome of coronaviruses has been engineered by modification of the infectious cDNA leading to an efficient (>20 microg ml(-1)) and stable (>20 passages) expression of the foreign gene. The possibility of engineering the tissue and species tropism to target expression to different organs and animal species, including humans, increases the potential of coronaviruses as vectors. Thus, coronaviruses are promising virus vectors for vaccine development and, possibly, for gene therapy.

Coronavirus↗

PubMed2000

The eukaryotic-like Ser/Thr protein kinases of Mycobacterium tuberculosis.

In bacteria, extracellular signals are generally transduced into cellular responses via a two-component system. However, genome sequence data have now revealed the presence of 'eukaryotic-like' protein kinases and phosphatases. Mycobacterium tuberculosis appears to be unique among bacteria in that its genome contains 11 members of a newly identified protein kinase family. These M. tuberculosis eukaryotic-like protein kinases could be key regulators of metabolic processes, including transcription, cell development and interactions with host cells.

Amino Acid Sequence↗

PubMed2002

The SREBP pathway in Drosophila: regulation by palmitate, not sterols.

In mammals, synthesis of cholesterol and unsaturated fatty acids is controlled by SREBPs, a family of membrane-bound transcription factors. Here, we show that the Drosophila genome encodes all components of the SREBP pathway, including a single SREBP (dSREBP), SREBP cleavage-activating protein (dSCAP), and the two proteases that process SREBP at sites 1 and 2 to release the nuclear fragment. In cultured Drosophila S2 cells, dSREBP is processed at sites 1 and 2, and the liberated fragment increases mRNAs encoding enzymes of fatty acid biosynthesis, but not sterol or isoprenoid biosynthesis. Processing requires dSCAP, but is not inhibited by sterols as in mammals. Instead, dSREBP processing is blocked by palmitic acid. These findings suggest that the ancestral SREBP pathway functions to maintain membrane integrity rather than to control cholesterol homeostasis.

Animals↗

PubMed2005

The genetic epidemiology of human primary osteoarthritis: current status.

Osteoarthritis (OA) is a common disease characterised by the degeneration of the cartilage of synovial joints such as the hip and knee. In the past ten years a large number of twin-pair, sibling-risk and segregation studies have been conducted on the disease, and these have revealed a major genetic component that is transmitted in a nonmendelian manner. OA therefore fits best into the complex, multifactorial class of common diseases. With a genetic component established, genome-wide linkage scans were performed, and these uncovered several genomic intervals likely to harbour OA susceptibility. In the past few years these intervals have started to yield genes containing OA-associated variants. This is therefore a very exciting period in the molecular genetic analysis of this common disease. The genes that have so far been implicated in susceptibility include the interleukin 1 gene (IL1) cluster at chromosome 2q11.2-q13, the matrilin 3 gene (MATN3) at 2p24.1, the IL-4 receptor alpha-chain gene (IL4R) at 16p12.1, the secreted frizzled-related protein 3 gene (FRZB) at 2q32.1, the metalloproteinase gene ADAM12 at 10q26.2 and, most recently, the asporin gene (ASPN) at 9q22.31. The evidence for involvement of these genes in OA is more compelling for some than others, with the IL1 and ASPN associations being the most convincing to date. It is imperative that the veracity of each of the associations be tested by genotyping additional cohorts and that their global relevance be assessed by genotyping OA cohorts from different ethnic backgrounds. The gene products of IL1, IL4R, FRZB and ASPN regulate cartilage chondrocyte differentiation and survival, and their effects on the chondrocyte are potentially amenable to therapeutic intervention. The latest genetics is therefore providing new insights for the development of novel OA treatments.

Cell Differentiation↗

PubMed2004

Phospholipid scramblase 1 is imported into the nucleus by a receptor-mediated pathway and interacts with DNA.

Phospholipid scramblase 1 (PLSCR1) is a multiply palmitoylated, Ca(2+)-binding, endofacial plasma membrane protein originally identified by its capacity to accelerate transbilayer movement of membrane phospholipids. We recently reported that when palmitoylation of PLSCR1 does not occur, it is localized to the nucleus rather than the plasma membrane. Nuclear localization of PLSCR1 was also observed upon induction of its de novo synthesis by cytokines such as interferon alpha that activate the PLSCR1 gene. Despite its capacity to enter the nucleus, its sequence does not predict a nuclear localization signal. To gain insight into the mechanism and potential significance of nuclear PLSCR1, we investigated the conditions required for its import and retention in the nucleus. We show that nuclear localization of PLSCR1 is dependent on cytosolic factors and energy. Furthermore, we show that PLSCR1 is specifically transported into the nucleus by the importin alpha/beta import pathway, and binds directly and with high affinity to importin alpha. Analysis of deletion mutants suggested that the NLS of PLSCR1 is between residues 242 and 290 and, furthermore, that a peptide within this region encompassing residues (257)GKISKHWTGI(266) is sufficient for nuclear import when conjugated to BSA. In addition, in intact cells, mutation of positively charged amino acids within this putative NLS in the full-length protein completely blocked its entry into the nucleus, consistent with its role in targeting PLSCR1 to the nucleus. Release of PLSCR1 from the nucleus was only observed after treatment of cells with both detergent and an elevated NaCl concentration, or following DNase treatment of the nucleus, suggesting ionic interactions of PLSCR1 with a nuclear component bound to genomic DNA or directly with genomic DNA. Purified PLSCR1 was also found to bind directly to a genomic DNA-cellulose conjugate, and its elution from DNA also required an elevated NaCl concentration. These data support a mechanism of receptor-mediated nuclear import of PLSCR1 and suggest a potential nuclear function for this plasma membrane protein.

Active Transport, Cell Nucleus↗

PubMed2006

Chemometrical characterization of four italian rice varieties based on genetic and chemical analyses.

This paper describes a method for achieving qualitative identification of four rice varieties from two different Italian regions. To estimate the presence of genetic diversity among the four rice varieties, we used polymerase chain reaction-randomly amplified polymorphic DNA (PCR-RAPD) markers, and to elucidate whether a relationship exists between the ground and the specific characteristics of the product, we studied proximate composition, fatty acid composition, mineral content, and total antioxidant capacity. Using principal component analysis on genomic and compositional data, we were able to classify rice samples according to their variety and their district of production. This work also examined the discrimination ability of different parameters. It was found that genomic data give the best discrimination based on varieties, indicating that RAPD assays could be useful in discriminating among closely related species, while compositional analyses do not depend on the genetic characters only but are related to the production area.

Antioxidants↗

PubMed2000

Ty1-copia-retrotransposon behavior in a polyploid cotton.

Retrotransposons constitute a ubiquitous and dynamic component of plant genomes. Intragenomic and intergenomic comparisons of related genomes offer potential insights into retrotransposon behavior and genomic effects. Here, we have used fluorescent in-situ hybridization to determine the chromosomal distributions of a Ty1-copia-like retrotransposon in the cotton AD-genome tetraploid Gossypium hirsutum and closely related putative A- and D-genome diploid ancestors. Retrotransposon clone A108 hybridized to all G. hirsutum chromosomes, approximately equal in intensity in the A- and D-subgenomes. Similar results were obtained by hybridization of A108 to the A-genome diploid G. arboreum, whereas no signal was detected on chromosomes of the D-genome diploid G. raimondii. The significance and potential causes of these observations are discussed.

Gossypium↗

PubMed2002

Repeated DNA sequences in the microbat species Miniopterus schreibersi (Vespertilionidae; Chiroptera).

Repetitive DNA sequences represent a substantial component of eukaryotic genomes. These sequences have been described and characterized in many mammalian species. However, little information about repetitive DNA sequences is available in bat species. Here we describe an EcoRI family of repetitive DNA sequences present in the species Miniopterus schreibersi. These repetitive sequences are 57.85%, A-T rich, organized in tandem, and with a monomer unit length of 904 bp. Methylation analysis using the isoesquizomer pair MspI and HpaII indicates that the cytosines present in the sequences CCGG are partially methylated. Furthermore, Southern blot analysis demonstrated that these DNA sequences are absent in the genomes of four related microbat species and suggest that it could be specific to the M. schreibersi genome.

Animals↗