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PubMed2003

[Polymorphism of six Alu-insertions in residents of Morocco: comparative study in Arab and Berber populations and residents of Casablanca].

Alu elements are the largest family of short tandem interspersed elements (SINEs) in human who have arisen to a copy number with an excess of 500,000 copies per haploid human genome and mobilize through an RNAse polymerase III derived transcript in a process termed "retroposition." Several features make Alu insertions a powerful tool used in population genetic studies: the polymorphic nature of many Alu insertions, the stability of an Alu insertion event and, furthermore, the ancestral state of an Alu insertion is known to be the absence (complete and exact) of the Alu element at a particular locus and the presence of an Alu insertion at the site that forward mutational change. Here we report on the distribution of six polymorphic Alu insertions in a general Moroccan population and in the Arab and Berber populations from Morocco and their relationships with other populations previously studied. Our results show that there is a small difference between Arabs and Berbers and that the Arab population was closer to African populations than Berber population which is closest to Europeans.

Alu Elements↗
PubMed1992

Expression of nuclear envelope lamins A and C in human myeloid leukemias.

The lamins are intermediate filament proteins that form a fibrous layer at the periphery of the nucleus. Experiments in cell-free systems have suggested that mammalian lamins A and C mediate an interaction between chromatin and the inner nuclear membrane that is essential for the reformation of the nucleus after mitosis. Other investigations, however, have suggested that lamins A and C are absent from myeloid cells and myeloid leukemia cell lines. To further investigate this apparent paradox, highly sensitive Western blotting techniques were utilized in the present study to examine the expression of lamins A and C in a series of human myeloid leukemia cell lines and in bone marrow samples from patients with acute nonlymphocytic leukemia (ANLL) and chronic myelogenous leukemia. Western blotting revealed that HL-60 progranulocytic leukemia cells contained an average of 0.1 x 10(6) copies of lamins A and C per cell compared to 0.5 x 10(6) copies of lamin B1 (the quantitatively prominent human B-type lamin) per cell. During the process of phorbol ester-induced maturation to macrophages, the mRNA for lamins A and C increased in abundance, with a concomitant 4-fold increase in the average cellular content of these polypeptides. To rule out the possibility that the low but detectable levels of lamins A and C observed in untreated HL-60 cells reflected incipient maturation, the content of lamins A and C was analyzed in ANLL cell lines that do not mature toward granulocytes or monocytes. Lamins A and C were readily detected in cell lines (KG1a, HEL, Mo-7e) derived from patients with a variety of subtypes of ANLL. Expression of lamins A and C was not limited to myeloid cell lines. These polypeptides were also detectable in marrow samples from 9 of 26 patients with ANLL including at least 1 patient from each of the 5 subtypes of ANLL examined. In contrast, only 1 of 12 marrow samples from patients with aggressive phase chronic myelogenous leukemia and chronic myelogenous leukemia in blast crisis contained readily detectable lamins A and C. The implications of these findings for current hypotheses regarding the functions of the lamin polypeptides are discussed.

Blast Crisis↗
PubMed1991

Yeast CAL1 is a structural and functional homologue to the DPR1 (RAM) gene involved in ras processing.

A 2.3-kilobase pair DNA fragment of the yeast CAL1 gene was cloned by complementation of the cal1-1 mutation, which causes a defect in nuclear division and bud formation (Ohya, Y., Ohsumi, Y., and Anraku, Y. (1984) Mol. & Gen. Genet. 193, 389-394). Nucleotide sequencing of this fragment revealed a single open reading frame (ORF) encoding a polypeptide of 376 amino acids. Comparative analysis of the predicted amino acid sequence has shown that the CAL1 product has similarity to two yeast proteins: the DPR1 (RAM) gene product that is involved in processing of ras protein at the farnesylation step, and the essential ORF2 protein whose structural gene has a head-to-head arrangement with PRP4, which is involved in mRNA processing. Functional homology between CAL1 and DPR1 has also been suggested from genetic evidence that multiple copies of the CAL1 gene suppress the growth defects of a dpr1 null mutant at high temperature. This suppression is Ca(2+)-dependent, since it was not observed in complete medium containing 200 microM CaCl2 but was apparent in medium containing 100 mM CaCl2. From sequence analysis of the cal1-1 mutation, together with the alignment of the three gene products, we have concluded that the conserved Gly328 in the C terminus is important for activity. We suggest that the CAL1 protein participates in a ras-like C-terminal modification of proteins involved in nuclear division and bud growth.

Amino Acid Sequence↗
PubMed1987

History and recent developments in xeroradiography of the breast.

The article deals in very broad terms with the development of xeroradiography. The imaging process is a by-product of the search by Chester Carlson for a method to copy documents. The early experimental work was done at Battelle Memorial Institute, Columbus, Ohio. Clinical trials followed the fabrication of a machine by the Xerox Corporation. The machine as we know it today was introduced to the market in 1970-1971.

Female↗
PubMed1995

Direct sample polymerase chain reaction for the detection of Mycoplasma pneumoniae: a simple system for clinical application.

A semi-nested polymerase chain reaction system with primers derived from the P1 adhesin gene of Mycoplasma pneumoniae was evaluated for sensitivity and specificity for detection of M. pneumoniae. The method used target DNA within samples of M. pneumoniae broth cultures and clinical material, without a formal extraction process. The sensitivity for detection of DNA was found to be to a level of one copy per sample and was specific to M. pneumoniae only, discriminating from the other human mycoplasma and ureaplasma species tested. The system offers the opportunity for a simple and highly specific laboratory method for diagnosis which may be compared to currently available serological methods, and may provide another method of studying mycoplasma-induced pathology.

Base Sequence↗
PubMed1996

Spatial arrangement of intra-nucleolar rDNA chromatin in amplified Xenopus oocyte nucleoli: structural changes precede the onset of rDNA transcription.

Amphibian oocyte nucleoli are a particular suited object for research on nucleolar chromatin organization. By selective rDNA amplification each pachytene oocyte nucleus accumulates 30 pg of extrachromosomal rDNA, this amount corresponds to 2 million rDNA copies. Following the selective amplification stage, the amplified gene copies are finally distributed within more than thousand extrachromosomal nucleoli per individual oocyte nucleus. The aim of the present study was first to obtain a precise documentation of the fate of amplified rDNA during early Xenopus oogenesis until the final functional integration of these copies into individual oocyte nucleoli, and, second, a close correlation of the structural data with determination of rDNA transcription rates by S1 transcript analysis for the subsequent stages of oocyte differentiation. In order to investigate the structural complexity of the intranuclear rDNA translocation process in detail, a confocal laser scan microscope (CLSM) was used, equipped with an external UV-laser. This instrumentation unambiguously allowed (i) the detection of small clusters of rDNA copies and (ii) the precise spatial documentation of the intranuclear position of rDNA clusters in relation to the protein-free pre-nucleolar protein bodies, a specific characteristic of late pachytene/early diplotene amphibian oocyte nuclei. Our results indicate that the major rDNA translocation processes, e.g. the association of rDNA clusters with pre-nucleolar protein bodies, the formation of ribbon-like pre-nucleolar units sensu Van Gansen and Schramm (J. Cell Sci. 10: 339-367, 1972), and, finally, the translocation of fused rDNA units into the interior of pre-nucleolar protein bodies, occur--for the most part--in absence of massive rDNA transcription. As shown by the S1 transcript analysis, the onset of massive rDNA transcription starts concomitantly with an unraveling of the densely packed rDNA clusters into finely dispersed rDNA units, which were shown by CLSM analysis to be distributed throughout the entire nucleolar volume.

Animals↗
PubMed2001

Emerging links between hypermutation of antibody genes and DNA polymerases.

Substantial antibody variability is created when nucleotide substitutions are introduced into immunoglobulin variable genes by a controlled process of hypermutation. Evidence points to a mechanism involving DNA repair events at sites of targeted breaks. In vertebrate cells, there are many recently identified DNA polymerases that inaccurately copy templates. Some of these are candidates for enzymes that introduce base changes during hypermutation. Recent research has focused on possible roles for DNA polymerases zeta (POLZ), eta (POLH), iota (POLI), and mu (POLM) in the process.

Animals↗
PubMed1989

Cooperative interaction of Agrobacterium VirE2 protein with single-stranded DNA: implications for the T-DNA transfer process.

Induction of Agrobacterium tumefaciens vir gene expression by wounded plant cells results in production of a free transferable single-stranded (ss) copy of T-DNA, the T-strand. One of the Vir proteins, the VirE2 polypeptide, is a ssDNA-binding protein. In the present work, interaction of nopaline-specific VirE2 protein (Mr 69,000) with ssDNA was studied by using nitrocellulose filter binding, gel retardation, and electron microscopy techniques. The VirE2 protein was found to bind to ssDNA molecules with strong cooperativity, forming VirE2-ssDNA complexes with a binding site of 28-30 nucleotides. The VirE2-ssDNA complexes are stable at high salt concentrations and resistant to exonucleolytic activity. When examined under the electron microscope, the VirE2 protein converted collapsed free ssDNA molecules into unfolded and extended structures. The structure and properties of VirE2-ssDNA complexes predict possible functions in Agrobacterium virulence to (i) protect the T-strands from cellular nucleases and (ii) facilitate transfer of the T-strands through bacterial membranes possibly by specific interaction with putative membrane pores formed in plant-induced Agrobacterium cells.

Bacterial Proteins↗
PubMed2002

Interhemispheric cooperation for familiar but not unfamiliar face processing.

Evidence for interhemispheric cooperation during language processing has been demonstrated for words, but not for meaningless pseudowords. Specifically, responses were found to be faster and more accurate when identical copies of a word were presented bilaterally to both hemispheres, relative to unilateral single presentations. This bilateral advantage for words seems to be a robust effect in normals. The present study addressed the question of whether the bilateral advantage is restricted to lexical material or whether it is a more global phenomenon occurring for meaningful material in general. Thirty healthy participants performed a familiarity decision in which one copy of familiar and unfamiliar faces was presented tachistoscopically to the right visual hemifield (RVF), the left visual hemifield (LVF) or simultaneously to both visual hemifields (bilateral condition, BVF). We obtained a highly significant familiarity by visual field interaction(P < 0.006) showing that only for familiar faces, a bilateral advantage was obtained. Unfamiliar face processing did not yield a bilateral advantage. We conclude that interhemispheric cooperation only occurs for meaningful material for which cortical representations can be assumed.

Adult↗
PubMed1999

Cognitive processing of drawing abilities.

This critical review examines constructional apraxia from a cognitive neuropsychological perspective. To our knowledge, van Sommers (1989) is the only researcher to present a global cognitive model of drawing abilities. He organizes it into two hierarchical systems: Marr's model of visual perception and a graphic production system. The latter comprises four hierarchically organized components: depiction decisions, production strategy, contingent planning, and articulatory and economic constraints. Van Sommers' model will be discussed in light of other models and on the basis of empirical neuropsychological studies (Farah, 1984; Kosslyn & Koenig, 1992; Roncato, Sartori, Masterson, & Rumiati, 1987; van Sommers, 1989). We find that: (1) the Kosslyn and Koenig visual perception model describes more accurately the perceptual components underlying copying than the visual perception system of van Sommers' drawing model, (2) Van Sommers' arguments in favor of a depiction processing as opposed to visual imagery are not convincing, (3) Van Sommers' assumption that a production strategy is a component is unclear, and (4) articulatory and economic constraints are not cognitive components, but constraints imposed during action programming. This literature review leads to a discussion of future research topics and the specificity of constructional apraxia.

Apraxias↗
PubMed2005

Effects of degenerate oligonucleotide-primed polymerase chain reaction amplification and labeling methods on the sensitivity and specificity of metaphase- and array-based comparative genomic hybridization.

Degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR) is often applied to small amounts of DNA from microdissected tissues in the analyses of chromosomal copy number with comparative genomic hybridization (CGH). The sensitivity and specificity in CGH analyses largely depend on the unbiased amplification and labeling of probe DNA, and the sensitivity and specificity should be high enough to detect one-copy changes in aneuploid cancer cells when accurate assessment of chromosomal instability is needed. The present study was designed to assess the effects of DOP-PCR and labeling method on the sensitivity of metaphase- and array-based CGHs in the detection of one-copy changes in near-tetraploid Kato-III cells. By focusing on several chromosomes whose absolute copy numbers were determined by FISH, we first compared the green-to-red ratio profiles of metaphase- and array-based CGH to the absolute copy numbers using the DNA diluted with varying proportions of lymphocyte DNA, with and without prior DOP-PCR amplification, and found that the amplification process scarcely affected the sensitivity but gave slightly lower specificity. Second, we compared random priming (RP) labeling with nick translation (NT) labeling and found that the RP labeling gave fewer false-positive gains and fewer false-negative losses in the detection of one-copy changes. In array CGH, locus-by-locus concordance between the DNAs with and without DOP-PCR amplification was high (nearly 100%) in the gain of three copies or more and the loss of two copies or more. This suggests that we could pinpoint the candidate genes within large-shift losses-gains that are detected with array CGH in microdissected tissues.

Cell Line, Tumor↗
PubMed2006

Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice.

Retrotransposons are the main components of eukaryotic genomes, representing up to 80% of some large plant genomes. These mobile elements transpose via a "copy and paste" mechanism, thus increasing their copy number while active. Their accumulation is now accepted as the main factor of genome size increase in higher eukaryotes, besides polyploidy. However, the dynamics of this process are poorly understood. In this study, we show that Oryza australiensis, a wild relative of the Asian cultivated rice O. sativa, has undergone recent bursts of three LTR-retrotransposon families. This genome has accumulated more than 90,000 retrotransposon copies during the last three million years, leading to a rapid twofold increase of its size. In addition, phenetic analyses of these retrotransposons clearly confirm that the genomic bursts occurred posterior to the radiation of the species. This provides direct evidence of retrotransposon-mediated variation of genome size within a plant genus.

Base Sequence↗
PubMed2002

Loss of RecA function affects the ability of Escherichia coli to maintain recombinant plasmids containing a Ter site.

In the Escherichia coli chromosome, DNA replication forks arrested by a Tus-Ter complex or by DNA damage are reinitiated through pathways that involve RecA and numerous other recombination functions. To examine the role of recombination in the processing of replication forks arrested by a Tus-Ter complex, the requirements for recombination-associated gene products were assessed in cells carrying Ter plasmids, i.e., plasmids that contain a Ter site oriented to block DNA replication. Of the E. coli recombination functions tested, only loss of recA conferred an observable phenotype on cells containing a Ter plasmid, which was inefficient transformation and reduced ability to maintain a Ter plasmid when Tus was expressed. Given the current understanding of replication reinitiation, the simplest explanation for the restriction of Ter plasmid maintenance was a reduced ability to restart plasmid replication in a recA tus(+) background. However, we were unable to detect a difference in the efficiency of replication arrest by Tus in recA-proficient and recA-deficient cells, which suggests that the inability to restart arrested replication forks is not the cause of the restriction on growth, but is due to an additional function provided by RecA. Other explanations for restriction of Ter plasmid maintenance were examined, including plasmid multimerization, plasmid rearrangements, and copy number differences. The most likely cause of the restriction on Ter plasmid maintenance was a reduced copy number in recA cells that was detected when the copy number was measured in relation to an external control. Possibly, loss of RecA function leads to improper processing of replication forks arrested at a Ter site, leading to the generation of degradation-prone substrates.

DNA Replication↗
PubMed2003

On the safety of a new generation of DSM Aspergillus niger enzyme production strains.

Consumers safety of enzyme preparations is determined by three variables: the producing organism, the raw materials used in the production, and the production process itself. The latter one is embedded in current Good Manufacturing Practice (cGMP) and Hazard Analysis of Critical Control Points (HACCP); therefore the safety focus can be directed to raw materials and the producing organism. In this paper, we describe the use of novel genetically modified strains of Aspergillus niger-made by a design and build strategy-from a lineage of classically improved strains with a history of safe use in enzyme production. The specifics of the host strain allow for integration and over-expression of any gene of interest at a targeted integration site implying that the rest of the host genome is not affected by this integration. Furthermore due to the fact that the newly integrated gene copies are put under the genetic regulation of the host's own glucoamylase promoter, the recipe of the production process of any new production strain can be kept constant with respect to the raw materials composition. Consequently the safety of a new enzyme product from these novel genetically modified strains is determined by the background of the production organism. The use of a strain with a history of safe use and targeted integration according to the concept described above has consequences for the safety studies on the final product. If a known enzymatic activity is over-expressed the safety of a new enzyme preparation is covered by the results of the safety studies performed for other strains from this specific Aspergillus niger strain lineage. In this paper an overview is given on the available toxicity tests with these strains. We conclude that for new enzyme products produced with strains from this lineage using the design and build technology no new sub-acute/chronic oral toxicity studies are needed. This also has the benefit that no longer test animals are needed to demonstrate the safety of products produced by these strains.

Animals↗
PubMed2003

The breakpoint region of the most common isochromosome, i(17q), in human neoplasia is characterized by a complex genomic architecture with large, palindromic, low-copy repeats.

Although a great deal of information has accumulated regarding the mechanisms underlying constitutional DNA rearrangements associated with inherited disorders, virtually nothing is known about the molecular processes involved in acquired neoplasia-associated chromosomal rearrangements. Isochromosome 17q, or "i(17q)," is one of the most common structural abnormalities observed in human neoplasms. We previously identified a breakpoint cluster region for i(17q) formation in 17p11.2 and hypothesized that genome architectural features could be responsible for this clustering. To address this hypothesis, we precisely mapped the i(17q) breakpoints in 11 patients with different hematologic malignancies and determined the genomic structure of the involved region. Our results reveal a complex genomic architecture in the i(17q) breakpoint cluster region, characterized by large ( approximately 38-49-kb), palindromic, low-copy repeats, strongly suggesting that somatic rearrangements are not random events but rather reflect susceptibilities due to the genomic structure.

Blast Crisis↗
PubMed2005

The ins and outs of HIV replication.

The life cycle of HIV-1 involves a series of steps necessary for the successful infection of human target cells. First the RNA genome enters the cytoplasm after the fusion of the viral membrane and that of the target cell. The RNA genome is then converted to DNA form through the process of reverse transcription. The DNA genome is then integrated into the host cell DNA. Next, viral proteins and more copies of the viral genome are produced. These components assemble to form new virions that are then able to propagate. The cellular proteins involved in HIV-1 entry have been known for more than a decade now and the study of the cellular and viral components involved in HIV-1 entry has led to the development of many therapeutic strategies and drugs designed to block viral replication. Recently, there have been significant advances in the understanding of HIV-1 assembly as a consequence of the identification of the cellular factors that mediate this process. This review will provide a basic outline of the current understanding of HIV-1 entry and exit.

Animals↗
PubMed1984

The cohesive population genetics of molecular drive.

The long-term population genetics of multigene families is influenced by several biased and unbiased mechanisms of nonreciprocal exchanges (gene conversion, unequal exchanges, transposition) between member genes, often distributed on several chromosomes. These mechanisms cause fluctuations in the copy number of variant genes in an individual and lead to a gradual replacement of an original family of n genes (A) in N number of individuals by a variant gene (a). The process for spreading a variant gene through a family and through a population is called molecular drive. Consideration of the known slow rates of nonreciprocal exchanges predicts that the population variance in the copy number of gene a per individual is small at any given generation during molecular drive. Genotypes at a given generation are expected only to range over a small section of all possible genotypes from one extreme (n number of A) to the other (n number of a). A theory is developed for estimating the size of the population variance by using the concept of identity coefficients. In particular, the variance in the course of spreading of a single mutant gene of a multigene family was investigated in detail, and the theory of identity coefficients at the state of steady decay of genetic variability proved to be useful. Monte Carlo simulations and numerical analysis based on realistic rates of exchange in families of known size reveal the correctness of the theoretical prediction and also assess the effect of bias in turnover. The population dynamics of molecular drive in gradually increasing the mean copy number of a variant gene without the generation of a large variance (population cohesion) is of significance regarding potential interactions between natural selection and molecular drive.

Biological Evolution↗