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PubMed2002

Chromosome replication patterns in the hyperthermophilic euryarchaea Archaeoglobus fulgidus and Methanocaldococcus (Methanococcus) jannaschii.

We analysed chromosome replication patterns in the two hyperthermophilic euryarchaea Archaeoglobus fulgidus and Methanocaldococcus(Methanococcus) jannaschii by marker frequency analysis (MFA). For A. fulgidus, the central region of the chromosomal physical map displayed a higher relative abundance in gene dosage during exponential growth, with two continuous gradients to a region of lower abundance at the diametrically opposite side of the genome map. This suggests bidirectional replication of the A. fulgidus chromosome from a single origin. The organization of the putative replication origin region relative to the cdc6, mcm and DNA polymerase genes differed from that reported for Pyrococcus species. No single replication origin or termination regions could be identified for M. jannaschii, adding to the list of unusual properties of this organism. The organization of the A. fulgidus cell cycle was characterized by flow cytometry analysis of the samples from which genomic DNA was extracted for MFA. The relative lengths of the cell cycle periods were found to be similar to those of crenarchaea.

Archaeoglobus fulgidus↗
PubMed2003

High delta-like 1 expression in a subset of neuroblastoma cell lines corresponds to a differentiated chromaffin cell type.

The childhood tumour neuroblastoma originates from neural crest-derived progenitors of the sympathetic nervous system. By Serial Analysis of Gene Expression (SAGE), we previously identified the Drosophila Delta homologue Dlk1 as one of the genes most highly expressed in the neuroblastoma cell line SK-N-FI. The Delta-Notch pathway controls many differentiation steps in Drosophila and man. We analysed expression of 21 genes of this pathway in 21 neuroblastoma cell lines. Dlk1 expression was very high in 5 cell lines, while another subset expressed Notch3. The imprinting of Dlk1 was faithfully preserved in neuroblastomas. The single paternal allele can therefore produce over 0.5% of all cellular mRNAs. Dlk1 maps to 14q32, a region that exhibited LOH in 31/170 (18%) tumours. The random parental origin of the deleted alleles excluded Dlk1 as target of the LOH. In addition, Dlk1 was not amplified, rearranged or mutated in neuroblastoma cell lines and tumours. We therefore analysed whether high Dlk1 expression marks a specific differentiation stage of the sympatho-adrenal lineage. Many neuroblastomas arise in the adrenal medulla, which predominantly consists of chromaffin cells. Normal adrenal medulla exhibited equally high Dlk1 levels as the SK-N-FI cell line. Chromaffin cells in young children are marked by noradrenalin production, which is mediated by dopamine-beta-hydroxylase (DBH). DBH expression in the neuroblastoma cell lines almost perfectly corresponded to Dlk1 expression. Neuroblastoma cell lines with high Dlk1 expression are therefore arrested in a relatively late stage of chromaffin lineage differentiation, while Notch3 expression might correspond to earlier precursor stages or to an alternative developmental fate.

Adrenal Medulla↗
PubMed1993

A homozygous deletion within the carbonic anhydrase-like domain of the Ptprg gene in murine L-cells.

Protein tyrosine phosphatases, on purely theoretical grounds, were suggested as possible tumor suppressor genes, and receptor protein tyrosine phosphatase gamma (PTPRG) has been proposed, on the basis of its location at human chromosome region 3p14.2, specifically as a tumor suppressor gene for renal cell carcinoma. We have isolated murine genomic and complementary DNA clones for analysis and mapping of the murine Ptprg locus; interspecific backcross analysis showed that the Ptprg locus maps to the centromeric region of mouse chromosome 14. We also observed a homozygous, intragenic deletion in the Ptprg gene in all clonal derivatives of the original L-cell strain, a methylcholanthrene-treated mouse connective tissue cell line which produces sarcomas in syngeneic mice. The deletion begins in the second intron of the carbonic anhydrase-like domain of the Ptprg gene and ends in the fourth intron of the carbonic anhydrase-like domain. At the genomic level, perhaps several hundred kilobases of DNA are deleted; at the complementary DNA level the 400 base pairs comprising exons 2, 3, and 4 of the carbonic anhydrase-like domain are deleted. By reverse transcription polymerase chain reaction, an amplified fragment is produced from L-cell mRNA which is 400 base pairs shorter than the wild type gene product, suggesting that the deleted gene is transcribed and may produce a protein product. Thus, mouse L-cells have lost one Ptprg allele and sustained an intragenic deletion in the other; such allele loss and mutation frequently occur at tumor suppressor gene loci.

Amino Acid Sequence↗
PubMed1988

Mapping large spontaneous deletion endpoints in the human HPRT gene.

In an attempt to understand the nature, frequency, and molecular origin of spontaneous mutations in human cells, we have analyzed 85 independent, spontaneous HPRT- human B-lymphoblast clones with particular emphasis on the determination and characterization of large structural alterations (i.e., deletions, insertions, duplications, etc.). Southern blot analysis using a full-length HPRT cDNA probe revealed that 39% (33/85) of these spontaneous mutants contained alterations affecting different regions of the gene. 12% (10/85) were total gene deletions, 25% (21/85) involved alterations with one or both endpoints intragenic to HPRT, and 2% (2/85) showed wild-type banding patterns with an additional hybridizing band. To further address the positional behavior of these alterations, the endpoints of the large deletions were mapped to specific exon/intron regions by hybridization of Southern blots with a series of HPRT exon-specific probes. This analysis revealed a disproportionate number of endpoints within the 3' portion of the gene. These findings are discussed in relation to the positional specificity of large alterations in human cells and the use of such an analysis for assessing the molecular mechanism(s) responsible for their production.

B-Lymphocytes↗
PubMed2002

Double minute chromosomes in acute myeloid leukemia and myelodysplastic syndrome: identification of new amplification regions by fluorescence in situ hybridization and spectral karyotyping.

Double minute chromosomes (dmin) are small chromatin bodies consisting of genes amplified in an extrachromosomal location. dmins are uncommon in hematologic malignancies; they are seen primarily in acute myeloid leukemia, with amplification of the MYC oncogene or, less frequently, the MLL transcription factor. Nine patients with hematologic malignancies with dmin were seen at the Roswell Park Cancer Institute between 1985 and 2000; eight had acute myeloid leukemia and one a myelodysplastic syndrome. Fluorescence in situ hybridization (FISH) demonstrated MYC amplification on dmin in four patients, but MLL amplification was not seen. Spectral karyotyping showed that the dmin derived from chromosome 11 in one patient and from chromosome 19 in two others without MYC or MLL amplification; derivation from these chromosomes was confirmed by FISH with chromosome paint probes. The dmin of chromosome 11 origin hybridized to a bacterial artificial chromosome (BAC) RP11-112M22 that maps to 11q24.3 and is predicted to contain ETS1 and other markers, including D11S11351 and D11S4091. The dmin of chromosome 19 origin in one patient hybridized to BACs RP11-46I12 and RP11-110J19; in the other patient, these clones did not hybridize with the dmin, but were found to be amplified on a marker chromosome that was derived from chromosome 19 in that patient's cells. These BACs have been mapped to 19q12-19q13.1 and 19q11-19q13.1, respectively, and are predicted to contain the markers D19S409 and D19S919 and the gene for ubiquinol-cytochrome C reductase, Rieske iron-sulfur polypeptide1 (UQCRFS1). dmin originating from chromosome 19 have not been reported previously in hematologic malignancies.

Adult↗
PubMed2002

TGF-beta induces cell death in the oligodendroglial cell line OLI-neu.

We have shown that TGF-beta plays an important role during the period of developmental cell death in the nervous system. Immunoneutralization of TGF-beta prevents ontogenetic neuron death in vivo. Like neurons, oligodendrocytes are generated in excess and eliminated by apoptosis. It has been shown that oligodendrocyte progenitors and newly formed oligodendrocytes are especially susceptible to apoptosis. We choose the oligodendrocyte precursor cell line OLI-neu to address the question if TGF-beta could play a role for the control of oligodendrocyte proliferation and cell death. Flow cytometric analysis revealed that OLI-neu cells arrested in the G1 phase of the cell cycle underwent apoptosis in response to TGF-beta. TUNEL assays, apoptosis ELISA, and caspase assays substantiated the finding that OLI-neu cells died after TGF-beta treatment. Cell death could be inhibited by application of pan-caspase or caspase 8 and 9 inhibitors, whereas the inhibition of calpain was unaffected. Furthermore, we found a reduction of bcl-X(L) at the protein as well as at the mRNA level, while p27 was upregulated. The Smad cascade was activated while TGF-beta reduced the activity of the p42/p44 MAP kinase pathway. Together, these data show that TGF-beta induced apoptotic cell death in cells of oligodendroglial origin, whereby the signaling cascade involved the downregulation of antiapoptotic signaling such as bcl-X(L) leading to the activation of caspases.

Animals↗
PubMed1982

A regulatory upstream promoter element in the Drosophila hsp 70 heat-shock gene.

Deletion mutants of the Drosophila hsp 70 heat-shock gene have been assayed in COS cells using a vector that contains an SV40 replication origin. COS cells are SV40-transformed monkey cells that support high-level replication of the vector. S1 mapping of transcripts shows that the hsp 70 gene is heat-inducible in these cells, whereas the herpes virus thymidine kinase gene is not. Residues -10 to -66 of the hsp 70 gene are apparently sufficient for heat-inducible promotion, and residues between -47 and -66 are necessary. This region upstream of the TATA box contains sequence features common to other heat-shock genes. Expression of the hsp 70 gene can be forced at low temperature by SV40 sequences that include the 72 bp repeat, but only if these are present on the 5' side of the gene. It seems that the upstream element of the hsp 70 promoter is analogous to that of other promoters, but is only functional in heat-shocked cells.

Animals↗
PubMed1987

A detailed mapping of dopamine D-2 receptors in rat central nervous system by autoradiography with [125I]iodosulpride.

The benzamide derivative [125I]iodosulpride was used to generate light microscopic autoradiograms on sections of rat brain and spinal cord. Sites specifically labelled by [125I]iodosulpride over a low background correspond to dopamine D-2 receptors as shown by their pharmacology established by densitometric analysis of 11 typical areas from autoradiograms generated in the presence of five dopamine-competing agents. An atlas of D-2 receptors was established using 1 horizontal, 6 sagittal and 30 frontal sections, the latter serially prepared at 0.5-1 mm intervals. Labelled areas were identified by comparison with corresponding, classically stained sections. When their density, rated according to an arbitrary scale, was then compared to that previously reported for dopamine innervation, evaluated from distributional maps of dopamine histofluorescence or tyrosine hydroxylase immunoreactivity, three situations were found. In areas corresponding to cells of origin and established projection fields of the mesostriatal, mesolimbocortical, diencephalospinal and periglomerular systems the density of D-2 receptors generally paralleled that of dopamine innervation. D-2 receptors in substantia nigra (pars compacta or reticulata) and ventral tegmental area were strongly reduced after injections of the neurotoxin 6-hydroxydopamine into the medial forebrain bundle, suggesting their major localization on dendrites and perikarya of dopamine neurons. Most other described dopamine cell group areas also contained D-2 receptors. In contrast many areas without established dopamine innervation contained D-2 receptors, sometimes in high density. This was the case for large areas of the cerebral cortex (layers I-III and V-VI) outside the established projection fields of the mesocortical system, the cerebellum (moleculare layer and dense patches within lobule 9), the hippocampal formation (lacunosum moleculare layer), several septal, thalamic and hypothalamic nuclei, large tectal areas, numerous brainstem areas (including cranial nerve nuclei), etc. This situation might correspond to areas with minor and still undetected dopamine innervation or to a localization of D-2 receptors on cells (or cell parts) not receiving dopamine inputs. Finally several well-established dopaminergic areas did not reveal any D-2 receptor labelling. This was particularly the case in the hypothalamus (areas of origin or termination of the tuberohypophyseal and incertohypothalamic dopamine systems) but also in the hippocampal formation (alveus, fimbria, hilus dentate gyrus), amygdaloid complex (anterior, basolateral, medial nuclei).(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2003

Dissecting Arabidopsis lateral root development.

Recent studies in the model plant Arabidopsis provide new insight into the regulation of root architecture, a key determinant of nutrient- and water-use efficiency in crops. Lateral root (LR) primordia originate from a subset of pericycle founder cells. Sophisticated mass-spectroscopy-based techniques have been used to map the sites of biosynthesis of auxin and its distribution in Arabidopsis seedlings, highlighting the importance of the phytohormone during LR initiation and emergence. Key components of the cell cycle and signal-transduction pathway(s) that promote and attenuate auxin-dependent LR initiation have recently been identified. Additional signals, such as abscisic acid and nitrate, also regulate LR emergence, raising intriguing questions about the cross-talk between their transduction pathways.

Arabidopsis↗
PubMed1979

Patterns of mobilization of the Proteus mirabilis chromosome by R plasmids.

R plasmids R40a, Rip69, R447b, R769 belonging to incompatibility groups A-C, M, N, V, respectively, were investigated for chromosomal mobilizing ability in Proteus mirabilis. Plasmids R40a, Rip69 and R447b mediated polarized transfer of markers in a clockwise direction from origins near tyr-1, metF and ser-2, respectively, on the linkage map. The recovery frequency per donor cell of proximal markers approached 1 x 10(-4) for these three plasmids and the efficiency of chromosomal transfer was higher than that of the previously studied plasmid D. The plasmid-guided chromosomal trajectories overlap and it was possible to complement results obtained with plasmid D to assemble a time-of-entry chromosomal map and directly establish the circularity of the linkage group. The map comprises a length of 93 min in terms of transfer time. Plasmid R769 had a different pattern of chromosome transfer. This plasmid produced recombinants for all markers at frequencies of about 4 x 10(-6) per donor. It effected multiple and more or less simultaneous entry of markers and produced recombination over lengths of chromosome rarely corresponding to more than 10 min on the linkage map.

Chromosome Mapping↗
PubMed1993

Bacillus subtilis alkA gene encoding inducible 3-methyladenine DNA glycosylase is adjacent to the ada operon.

In Bacillus subtilis, the adaptive response to DNA alkylation depends on the ada operon, which consists of the adaA and adaB genes, which encode methylphosphotriester DNA methyltransferase (AdaA protein) and O6-methylguanine DNA methyltransferase (AdaB protein), respectively. A structural gene (alkA) that encodes 3-methyladenine DNA glycosylase was found upstream of the ada operon, but in the opposite orientation. This cluster of genes was mapped at about 235 kb from the SfiI recognition site near the origin of replication in the physical map of the B. subtilis chromosome. Disruption of the alkA gene sensitized cells to N-propyl-N'-nitro-N-nitrosoguanidine, while its overproduction rendered cells highly resistant to N-propyl-N'-nitro-N-nitrosoguanidine, indicating that lethal DNA damage produced by bulky alkylating agents was effectively counteracted by AlkA glycosylase. Transcription of the alkA gene was induced by treating adaA+ cells with methylating agents concurrent with transcription of the ada operon. This was accomplished by using methylated AdaA protein bound to a 30-bp segment in the middle of the 100-bp sequence between the transcriptional start sites of the alkA gene and ada operon. Thus, in this organism, the adaptive response to DNA alkylation is achieved by autologous activation of a divergent regulon composed of the genes for a DNA glycosylase and two species of DNA alkyltransferase.

Alkylating Agents↗
PubMed1988

Pacemaker development in embryonic rat heart cultured in oculo.

Conditions that cause pacemaker formation in the developing heart are poorly understood. Embryonic rat myocardium grafted into the anterior eye chamber of an adult rat provides a promising model system in which to study pacemaker development. Electrophysiologic mapping with two microelectrodes showed that each embryonic heart graft developed a primary pacemaker within the region of contact with the host iris. These single, primary pacemakers were found in the centers of graft-iris junctions both in grafts that originally contained the natural pacemaker (e.g. right atria and whole hearts) and in grafts that excluded the sinoatrial pacemaker region (i.e. ventricles and left atrial appendages). Pacemaker action potentials were recorded in the region identified by mapping as the origin of the impulse in 11 of 11 grafts. Action potentials recorded from surrounding working cells were similar to adult rat heart cells in maximum diastolic potential, overshoot, amplitude, and duration. In contrast, maximum upstroke velocity was consistently slower in grafts than in adult hearts. Beating of grafts slowed or stopped within 3 days after transplantation but resumed by 10-14 days at rates similar to those observed before dissection (265 +/- 12), a pattern consistent with development of a new pacemaker in oculo. The graft-iris junction is the site of blood vessel and nerve ingrowth into the graft and it is a region of contact between differentiated embryonic myocardial cells and nonmyocardial (iris epithelial) cells. The roles of these three factors (vascularization, innervation, and surface contact) in establishing the pacemaker were examined using embryonic heart cultured both in the anterior eye chamber and in vitro.

Action Potentials↗
PubMed2026

The TRIM-cancer paradox: BCG as a programmable vaccine platform and a mechanistic probe for rational immunotherapy design.

BCG, a first-generation live vaccine, is being reconsidered as an immunological platform. Interest in its heterologous protection intensified during the pandemic. However, large-scale clinical trials revealed inconsistencies in the efficacy of native BCG. This review argues that BCG's main value lies in its potential as a modifiable vector platform and in its ability to reveal tractable molecular pathways for therapeutic design. This review summarizes the molecular basis of BCG-induced trained immunity (TRIM), focusing on PRR-driven signaling, metabolic rewiring, and epigenetic remodeling in innate immune cells and hematopoietic progenitors. It also maps their convergence with pathways that sustain pro-tumorigenic inflammation. The original conceptual paradigm of the "TRIM-Cancer Paradox" is presented. This paradigm posits that the same innate immune circuits that mediate protective heterologous responses can drive tumor-promoting inflammation and immune escape under conditions of chronic dysregulation. Recombinant BCG (rBCG) is further analyzed as a strategy to rationally amplify or redirect these circuits, the current clinical landscape of BCG-based interventions across various diseases and oncological malignancies is highlighted, and specific molecular nodes that could be exploited to increase the precision, efficacy, and safety of rBCG-based therapies are identified. Overall, this review proposes BCG a programmable immunological platform and to use the TRIM-Cancer Paradox as a novel design principle for next-generation rBCG platforms that transcend traditional vaccinology and cancer immunotherapy applications.

Humans↗
PubMed1978

Origin of DNA replication in papovavirus chromatin is recognized by endogenous endonuclease.

Isolated simian virus 40 (SV40) and polyoma nucleoprotein complexes contain endonuclease that, under in vitro conditions, converts part (up to 30%) of the covalently closed superhelical DNA to full-length linear rods. The positions of the cleavage sites within the genomes of SV40 and polyoma were determined by digestion with various single-cut restriction endonucleases and subsequent agarose gel electrophoresis of the cleavage products. Both SV40 and polyoma covalently closed superhelical DNA were cleaved open at their respective origins of DNA replication (+/- 75 base pairs). The full-length linear DNA rods whose ends map adjacent to the origin of DNA replication could also be isolated by sodium dodecyl sulfate/phenol extraction both from SV40-infected permissive cells and from purified SV40 virions. These data reveal the presence of a unique structure of the papovavirus chromatin close to the initiation site of DNA replication.

Chromatin↗
PubMed2006

The history of the HSV amplicon: from naturally occurring defective genomes to engineered amplicon vectors.

We have derived the HSV amplicon vector in 1981/1982 after elaborate experience with "defective viruses", arising spontaneously in viral stocks propagated at high multiplicities of infection (m.o.i.). The defective viruses were found to contain large concatemeric genomes with repeat units of limited complexity. We employed cloned defective genome repeats to generate the "amplicon" vectors, which in the presence of helper virus replicate to produce packaged large concatemeric genomes, transmissible to uninfected cells. The cloned amplicons were then employed to fine map and analyze the signals essential for amplicon propagation: (i) A DNA replication origin, producing concatemeric genomes by rolling circle replication. Three DNA replication origins were identified in the HSV genome. (ii) Signals termed pac-1 and pac-2, directing a measuring function for coordinate cleavage of the concatemeric genomes and their packaging as full-size (150 kb) genomes. Using amplicons, foreign genes of large sizes could be linked to less than 1 kb of the cis-acting HSV DNA sequences and become amplified in packaged defective genomes, transmissible to new cells. The transgenes are expressed efficiently, due to sequence reiterations. Large quantities of vectors can be produced in vitro. The amplicons are attractive vectors for use as non-integrating gene delivery vectors. The packaging signals pac-1 and pac-2 are well conserved in different herpesviruses and amplicons with a DNA replication origin and cleavage and packaging signals have been produced in additional herpesviruses. Depending on amplicon-host cell combination, the vectors can be employed with and without mutated helper virus(es) to obtain high gene expression, and desired effect on the target cell. In the absence of helper virus, the defective virus produced is limited for spread in the targeted cells. We expect that new vectors employing state of the art transgenes, will be developed to generate amplicon based concatemeric defective viruses capable of efficient expression of these genes.

Base Sequence↗
PubMed1994

Physical mapping of the uterine leiomyoma t(12;14)(q13-15;q24.1) breakpoint on chromosome 14 between SPTB and D14S77.

Uterine leiomyoma is the most common tumor of smooth muscle cell origin and is often associated with the recurrent balanced translocation t(12;14)(q13-15;q24). As an initial step toward finding the gene or genes that are interrupted by the translocation breakpoint, a somatic cell hybrid carrying the derivative 14 as the single t(12;14) translocated chromosome was constructed from a leiomyoma cell line with this translocation. Sequence tagged sites (STS) whose locations on the genetic map of chromosome 14 were known were used to map the breakpoint in the translocated chromosomes. The results of this analysis place the translocation breakpoint on the long arm of chromosome 14 between the proximal marker SPTB and the distal marker D14S77, narrowing the chromosomal translocation breakpoint to a region of approximately 7 cM. The identification of flanking markers on chromosome 14 lays the foundation for efforts to clone the breakpoint and to identify the genes involved in the formation of leiomyoma.

Animals↗
PubMed1994

Members of the novel WC1 gene family are differentially expressed on subsets of bovine CD4-CD8- gamma delta T lymphocytes.

CD4-CD8- gamma delta T cells of ruminants uniquely express a 220-kDa surface Ag recognized by several mAbs clustered as WC1. We recently reported the isolation of a cDNA clone encoding a WC1 Ag. Southern blotting suggested that the bovine genome contains multiple sequences highly related to the isolated WC1 cDNA. Here, we demonstrate that some of the clustered WC1 mAbs stain predominantly nonoverlapping subsets of bovine CD4-CD8- gamma delta T cells. By the isolation of two additional cDNA clones encoding molecules highly related to the original WC1 Ag, we provide a molecular basis for this phenomenon. Cells transfected with cDNAs encoding individual WC1 Ags are differentially recognized by various WC1 mAbs. Thus, expression of members of the WC1 gene family divides bovine CD4-CD8- gamma delta T cells into phenotypical subsets. Field inversion gel electrophoresis revealed that all WC1 genes map to a single, large (> 1 Mbp) Notl fragment. Although the function of WC1 remains unknown, it likely involves interaction with ligands that originate from a similarly complex genetic system.

Amino Acid Sequence↗
PubMed2000

A novel human multiple myeloma-derived cell line, NCU-MM-1, carrying t(2;11)(q11;q23) and t(8;22)(q24;q11) chromosomal translocations with overexpression of c-Myc protein.

A novel cell line, designated as NCU-MM-1, was established from a 66-year-old female patient with multiple myeloma (MM) that had shown rapid progression from solitary plasmacytoma to plasma cell leukemia. Interestingly, cytogenetic analysis including fluorescence in situ hybridization analysis disclosed that this cell line carried 2 kinds of chromosomal translocations involving immunoglobulin light chain (IgL) gene loci without the presence of 14q32 translocations (14q+). The Ig lambda locus juxtaposed to the c-MYC locus at 8q24 on the derivative (8) chromosome and a concomitant overexpression of the c-Myc protein was observed. On the derivative (11) chromosome, the Ig kappa locus was also fused to the chromosome 11q23 locus, which is known to be a nonrandom translocation breakpoint in mature B-cell malignancies. The NCU-MM-1 cell line may thus be useful not only for the identification of the responsible proto-oncogene(s) mapped to 11q23, deregulated by the Ig kappa enhancer sequences, but also for clarification of the molecular origin of MM lacking 14q+ chromosomes because IgL rearrangements can physiologically begin to occur in the pre-B-cell stage.

Aged↗