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PubMed1989

Neuropsychological correlates of school achievement in young children: longitudinal findings with a construct valid perceptual processing instrument.

A form discrimination and a form copying test developed using constructs from basic research in form perception were administered to first-, second-, and third-grade children. Relationships between performance on these tests and achievement scores were investigated both concurrently and over a 2-year follow-up period. These analyses demonstrated the relevance of visual-perceptual factors to academic achievement at all grade levels. Additionally, the pattern of relationships obtained substantiated the existence of age trends in the relationship between perceptual processing factors and academic achievement as has been hypothesized in the child neuropsychology literature.

Achievement↗
PubMed2004

The Dnmt1 DNA-(cytosine-C5)-methyltransferase methylates DNA processively with high preference for hemimethylated target sites.

In the cell, Dnmt1 is the major enzyme in maintenance of the pattern of DNA methylation after DNA replication. Evidence suggests that the protein is located at the replication fork, where it could directly modify nascent DNA immediately after replication. To elucidate the potential mechanism of this process, we investigate the processivity of DNA methylation and accuracy of copying an existing pattern of methylation in this study using purified Dnmt1 and hemimethylated substrate DNA. We demonstrate that Dnmt1 methylates a hemimethylated 958-mer substrate in a highly processive reaction. Fully methylated and unmethylated CG sites do not inhibit processive methylation of the DNA. Extending previous work, we show that unmethylated sites embedded in a hemimethylated context are modified at an approximately 24-fold reduced rate, which demonstrates that the enzyme accurately copies existing patterns of methylation. Completely unmodified DNA is methylated even more slowly due to an allosteric activation of Dnmt1 by methylcytosine-containing DNA. Interestingly, Dnmt1 is not able to methylate hemimethylated CG sites on different strands of the DNA in a processive manner, indicating that Dnmt1 keeps its orientation with respect to the DNA while methylating the CG sites on one strand of the DNA.

Animals↗
PubMed2004

Interaction with capsid protein alters RNA structure and the pathway for in vitro assembly of cowpea chlorotic mottle virus.

Viruses use sophisticated mechanisms to allow the specific packaging of their genome over that of host nucleic acids. We examined the in vitro assembly of the Cowpea chlorotic mottle virus (CCMV) and observed that assembly with viral RNA follows two different mechanisms. Initially, CCMV capsid protein (CP) dimers bind RNA with low cooperativity and form virus-like particles of 90 CP dimers and one copy of RNA. Longer incubation reveals a different assembly path. At a stoichiometry of about ten CP dimers per RNA, the CP slowly folds the RNA into a compact structure that can be bound with high cooperativity by additional CP dimers. This folding process is exclusively a function of CP quaternary structure and is independent of RNA sequence. CP-induced folding is distinct from RNA folding that depends on base-pairing to stabilize tertiary structure. We hypothesize that specific encapsidation of viral RNA is a three-step process: specific binding by a few copies of CP, RNA folding, and then cooperative binding of CP to the "labeled" nucleoprotein complex. This mechanism, observed in a plant virus, may be applicable to other viruses that do not halt synthesis of host nucleic acid, including HIV.

Bromovirus↗
PubMed1980

Nitropyrenes: isolation, identificaton, and reduction of mutagenic impurities in carbon black and toners.

Extracts of selected xerographic toners and copies were found to be mutagenic in the Salmonella assay. The activity was independent of the xerographic hardware and process and was traced to nitropyrenes present as impurities in the carbon black, the toner colorant. Manufacturing process changes resulted in a substantial reduction of the nitropyrene content of the carbon black and thus in the mutagenicity of the corresponding toners. Nitropyrenes are potent frameshift mutagens, and possible mechanisms for their biological action are discussed.

Biotransformation↗
PubMed2006

The coaching schematic: validation through expert coach consensus.

Current research in coaching development infers that coaching is predominantly a decision-making process. The same and other research is not, however, informing the coaching development process due to a lack of a big picture approach. Consequently, there is a need for a model of coaching. In this paper, we offer such a model in the form of a schematic that reflects the coaching process from both a content and information-processing stance. To assess the validity of the schematic, 16 expert coaches were interviewed to elicit a complete description of their coaching process. The coaches were then shown a copy of the schematic and asked to comment on its design and content with respect to its accuracy in reflecting their coaching process. Following analysis of the interview, six general categories emerged: Roles, Goals, Typical Actions, Required Knowledge, Support for the Schematic, and Factors Influencing Development. The first four categories clearly displayed an implicit support for the schematic. Furthermore, all coaches offered explicit support for the schematic. Such strong support confirmed that the schematic was valid and could form the basis of focused interventions in coaching development.

Decision Making↗
PubMed1990

Isochromosome 12p in non-seminoma cell lines: karyologic amplification of c-ki-ras2 without point-mutational activation.

We examined eight human germ cell cancer lines (GCCLs) for cytogenetic abnormalities and found an isochromosome 12p, i(12p), marker in all seven male nonseminoma GCCLs, but not in the single female teratocarcinoma cell line. Southern blot analysis of these cell lines showed increased copy number for c-ki-ras2, a gene located on 12p, in all the male GCCLs. The comparison of Southern blot analysis for a restriction fragment length polymorphism (RFLP) probe localized to 12p to a probe for int-1, which maps to 12q, indicates that the increased copy number for c-ki-ras2 is primarily from the greater numbers of 12p relative to 12q. Although Northern analysis revealed enhanced mRNA expression for c-ki-ras2 in the GCCLs with an i(12p), hybridization of specific end-labelled oligonucleotides to the polymerase chain reaction products of c-ki-ras2 codons 12, 13, or 61 did not identify c-ki-ras2 mutations of these codons in these cells. Thus, c-ki-ras2 activation through point mutation is an infrequent event in GCCLs. These data further suggest that increased 12p copy number is a common event in the transformation process leading to male germ cell cancer. We conclude that determination of 12p copy number by cytogenetic analysis or Southern blotting is useful in the diagnostic evaluation of human germ cell cancer.

Blotting, Southern↗
PubMed2006

Utilizing quantitative polymerase chain reaction to evaluate prostate stem cell antigen as a tumor marker in pancreatic cancer.

BACKGROUND: Real-time quantitative polymerase chain reaction (qPCR) may prove to be a sensitive technique by which to evaluate potential tumor markers in pancreatic cancer. METHODS: The prostate stem cell antigen (PSCA) gene was identified as a marker highly expressed in pancreatic adenocarcinoma and not normal pancreas. RNA from pancreatic and nonpancreatic cancer cell lines as well as tissue and blood from pancreatic cancer and control patients was reverse-transcribed and PSCA quantified by qPCR. RESULTS: Individual operator experience affects the results of qPCR, with significantly different copy numbers at experiment numbers 5, 15, and 40. Five of six pancreatic cell lines had PSCA/actin ratios 10-fold greater than nonpancreatic cancer lines. Mean PSCA expression in pancreatic tumor tissue was significantly higher (P < 0.05, Student's t-test) than in the tissue of benign pancreatic processes. The close correlation of PSCA/actin copy number with number of tumor cells in the blood was demonstrated by regression analysis (r = 0.768, P = 0.0001). PSCA copy number was significantly higher in the blood of patients with metastatic pancreatic cancer than in that of normal patients (P < 0.05, Student's t-test). CONCLUSIONS: Such trends suggest that PSCA may prove to be a valuable pancreatic cancer tumor marker. More generally, the technique of qPCR is shown to provide a sensitive method of evaluating markers in cancer patients.

Adenocarcinoma↗
PubMed1999

Fluorescent antibiotic resistance marker for tracking plastid transformation in higher plants.

Plastid transformation in higher plants is accomplished through a gradual process, during which all the 300-10,000 plastid genome copies are uniformly altered. Antibiotic resistance genes incorporated in the plastid genome facilitate maintenance of transplastomes during this process. Given the high number of plastid genome copies in a cell, transformation unavoidably yields chimeric tissues, which requires the identification of transplastomic cells in order to regenerate plants. In the chimeric tissue, however, antibiotic resistance is not cell autonomous: transplastomic and wild-type sectors both have a resistant phenotype because of phenotypic masking by the transgenic cells. We report a system of marker genes for plastid transformation, termed FLARE-S, which is obtained by translationally fusing aminoglycoside 3"-adenyltransferase with the Aequorea victoria green fluorescent protein. 3"-adenyltransferase (FLARE-S) confers resistance to both spectinomycin and streptomycin. The utility of FLARE-S is shown by tracking segregation of individual transformed and wild-type plastids in tobacco and rice plants after bombardment with FLARE-S vector DNA and selection for spectinomycin and streptomycin resistance, respectively. This method facilitates the extension of plastid transformation to nongreen plastids in embryogenic cells of cereal crops.

Chloroplasts↗
PubMed1996

Timing of differential amplification of macronucleus-destined sequences during macronuclear development in the hypotrichous ciliate Euplotes crassus.

The change in copy numbers of macronucleus-destined gene sequences was followed in anlagen DNA during postconjugational development in Euplotes crassus. As noted earlier, copy numbers increase during the polytene stage. During this replication process major differential amplification of different genes is not observed. Instead it is only achieved during or shortly after the fragmentation of the polytene chromosomes. This process is not totally synchronous with respect to different genes. Highly amplified genes are excised earlier than genes with a low final macronuclear copy number. Unexpectedly, the pattern of processing of the newly added oversized telomeres also appears to correlate with the degree of gene amplification. These observations are discussed in terms of a limited replication period after polytene chromosome fragmentation leading to preferential amplification of early excised genes.

Animals↗
PubMed2001

Williams syndrome and deficiency in visuospatial recognition.

This study aimed to assess the visuospatial abilities of five children with Williams syndrome (four males aged 9 years 3 months, 7 years 11 months, 8 years 1 month, and 10 years 8 months respectively, and one female aged 6 years 3 months). First, the children's visuospatial abilities were examined by asking them to copy a figure. Second, their cognitive processing abilities were assessed using the Japanese Kaufman Assessment Battery for Children. This test was used because it is an objective one, standardized in Japan, and is a measure of fluid ability including spatial localization. Participants scored significantly low on the spatial memory subtest indicating that there was a deficit in spatial localization. Children's performance in line copying tasks improved when the dots were in colour. Results suggest a deficit in the dorsal stream of visual cognition, with a relatively preserved ventral stream.

Child↗
PubMed1998

Intracellular RNA cleavage by the hairpin ribozyme.

Studies involving ribozyme-directed inactivation of targeted RNA molecules have met with mixed success, making clear the importance of methods to measure and optimize ribozyme activity within cells. The interpretation of biochemical assays for determining ribozyme activity in the cellular environment have been complicated by recent results indicating that hammerhead and hairpin ribozymes can cleave RNA following cellular lysis. Here, we report the results of experiments in which the catalytic activity of hairpin ribozymes is monitored following expression in mammalian cells, and in which post-lysis cleavage is rigorously excluded through a series of biochemical and genetic controls. Following transient transfection, self-processing transcripts containing active and inactive hairpin ribozymes together with cleavable and non-cleavable substrates were generated within the cytoplasm of mouse OST7-1 cells using T7 RNA polymerase. Unprocessed RNA and products ofintracellular cleavage were detected and analyzed using a primer-extension assay. Ribozyme-containing transcripts accumulated to a level of 4 x 10(4) copies per cell, and self-processing proceeded to an extent of >75% within cells. Cellular RNA processing was blocked by mutations within the ribozyme (G8A, G21U) or substrate (DeltaA-1) that, in vitro , eliminate cleavage without affecting substrate binding. In addition to self-processing activity, trans -cleavage reactions were supported by the ribozyme-containing product of the self-processing reaction, and by the ribozyme linked to the non-cleavable substrate analog. Ribozyme activity was present in extracts of cells expressing constructs with active ribozyme domains. These results provide direct biochemical evidence for the catalytic activity of the hairpin ribozyme in a cellular environment, and indicate that self-processing ribozyme transcripts may be well suited for cellular RNA-inactivation experiments.

Animals↗
PubMed2001

[Data protection--an obstacle for prospective studies? Solutions exemplified by a cohort study].

Prospective studies require the storage of the participants' personal data for follow-up. This demands special precautions for the protection of these data. Additional to the informed consent of the participant which enables the researchers to collect the prospective study data, the participant's right of informal self-determination should be protected. In the EPIC (European Prospective Investigation into Cancer and Nutrition) Potsdam study, therefore, an internal trustee was established that collects follow-up information from participants, physicians, clinics, health offices, tumour and population registries with the aim to obtain valid information on vital status and diseases of the participants. The internal trustee is a spatial and organizational separated working group. The isolated electronic data processing network, the alarm system which controls the rooms of the working group, the access control for employees are special security arrangements. During follow-up the individual identification number of the study data base is replaced by a specific identification number solely for the follow-up. Further, unique identification numbers are allocated to every single action and every single document such as inquiry forms which are sent to physicians, health offices, or population registries, that allow anonymous mailing and processing of the collected information. On copies of important documents, the name is erased and replaced by a specific record number. The inquiry forms for the physicians, for instance, contain the name of the participant at the head which has to be cut off before returning the form to the internal trustee. The identification number is also printed as bar code on each document facilitating its processing with technical aids such as scanners. If checkbacks are necessary, only certain work group members are able to reconnect the document number with the name. Depending on the task, the computer programmes confine automatically the details presented to the assistant. All arrangements to protect personal data do not interfere with research interests; on the contrary they lead to an efficient work routine and guarantee follow-up according to international rules.

Cohort Studies↗
PubMed1989

Loss of bovine papillomavirus DNA replication control in growth-arrested transformed cells.

The bovine papillomavirus type 1 (BPV-1) genome replicates as a plasmid within the nuclei of BPV-1-transformed murine C127 cells at a constant multiple copy number, and spontaneous amplification of the viral DNA is rarely observed. We report here that a mutant BPV-1 plasmid within a contact-inhibited C127 cell line replicated as a stable multicopy plasmid in exponentially growing cells but amplified to a high level in confluent cell culture. In situ hybridization analysis revealed that most of the mutant viral DNA amplification occurred in a minor subpopulation of cells within the culture. These consisted of giant nondividing cells with greatly enlarged nuclei, a cell form which was specifically induced in stationary-phase cultures. These observations indicated that expression of a viral DNA replication factor was cell growth stage specific. Consistent with this hypothesis, considerable amplification of wild-type BPV-1 DNA associated with characteristic giant cell formation was observed in typical wild-type virus-transformed C127 cultures following a period of growth arrest achieved by serum deprivation. Further observations indicated that induction of the giant-cell phenotype was dependent on BPV-1 gene expression and implicated a viral E1 replication factor in this process. Moreover, heterogeneity in virus genome copy numbers within the giant-cell population suggested a complex regulation of induction of DNA synthesis in these cells. It appears that this process represents a mechanism employed by the virus to ensure maximal viral DNA synthesis within a growth-arrested cell. Fundamental questions concerning the integration of the virus-cell control circuitry in proliferating and resting cells are discussed.

Animals↗
PubMed2000

Loss of heterozygosity at the Ink4a/Arf locus facilitates Abelson virus transformation of pre-B cells.

In many tumor systems, analysis of cells for loss of heterozygosity (LOH) has helped to clarify the role of tumor suppressor genes in oncogenesis. Two important tumor suppressor genes, p53 and the Ink4a/Arf locus, play central roles in the multistep process of Abelson murine leukemia virus (Ab-MLV) transformation. p53 and the p53 regulatory protein, p19Arf, are required for the apoptotic crisis that characterizes the progression of primary transformed pre-B cells to fully malignant cell lines. To search for other tumor suppressor genes which may be involved in the Ab-MLV transformation process, we used endogenous proviral markers and simple-sequence length polymorphism analysis to screen Abelson virus-transformed pre-B cells for evidence of LOH. Our survey reinforces the role of the p53-p19 regulatory pathway in transformation; 6 of 58 cell lines tested had lost sequences on mouse chromosome 4, including the Ink4a/Arf locus. Consistent with this pattern, a high frequency of primary pre-B-cell transformants derived from Ink4a/Arf +/- mice became established cell lines. In addition, half of them retained the single copy of the locus when the transformation process was complete. These data demonstrate that a single copy of the Ink4a/Arf locus is not sufficient to fully mediate the effects of these genes on transformation.

Abelson murine leukemia virus↗
PubMed1984

Human metallothionein MT-I and MT-II processed genes.

Two intronless pseudogenes, corresponding to the human metallothionein MT-I and MT-II processed genes, have been isolated from a human genomic library. MT-I processed gene has accumulated a number of mutations including a nonsense mutation giving rise to a termination codon at amino acid position 21, and a single base deletion at amino acid position 47 causing a shift in the reading frame. MT-II processed gene is a full-length perfect copy of its corresponding mRNA except for a few mutations. Most of the mutations in MT-II processed gene are silent except that the amino acid glycine (GGT) at position 10 is changed to serine (AGT) due to a transition. Both MT-I and MT-II processed genes possess poly(A) sequences of 21 and 17 nucleotides, respectively, 3' to the consensus AATAAA sequence. While these genes are quite similar in their sequences at the 3'-untranslated region, they show less than 50% homology in the 5'-untranslated sequences. Two direct repeats of 16 and 18 nucleotides in length define the limits of the MT-I and MT-II processed genes, respectively, and have been confirmed by S1 nuclease mapping analysis. In both MT-I and MT-II processed genes these direct repeats towards the 5' end of the gene start with an AhaIII (TTTAAA) restriction site. Our studies suggest that these direct repeats are the results of the insertion site duplication.

Amino Acid Sequence↗
PubMed2000

Requirements for the dGTP-dependent repeat addition processivity of recombinant Tetrahymena telomerase.

Telomerase is a reverse transcriptase responsible for adding simple sequence repeats to chromosome 3'-ends. The template for telomeric repeat synthesis is carried within the RNA component of the telomerase ribonucleoprotein complex. Telomerases can copy their internal templates with repeat addition processivity, reusing the same template multiple times in the extension of a single primer. For some telomerases, optimal repeat addition processivity requires high micromolar dGTP concentrations, a much higher dGTP concentration than required for processive nucleotide addition within a repeat. We have investigated the requirements for dGTP-dependent repeat addition processivity using recombinant Tetrahymena telomerase. By altering the template sequence, we show that repeat addition processivity retains the same dGTP-dependence even if dGTP is not the first nucleotide incorporated in the second repeat. Furthermore, no dNTP other than dGTP can stimulate repeat addition processivity, even if it is the first nucleotide incorporated in the second repeat. Using structural variants of dGTP, we demonstrate that the stimulation of repeat addition processivity is specific for dGTP base and sugar constituents but requires only a single phosphate group. However, all nucleotides that stimulate repeat addition processivity also inhibit or compete with dGTP incorporation into product DNA. By assaying telomerase complexes reconstituted with a variety of altered templates, we find that repeat addition processivity has an unanticipated template or product sequence specificity. Finally, we show that a novel, nascent product DNA binding site establishes dGTP-dependent repeat addition processivity.

Animals↗
PubMed2004

Control elements within the PWS/AS imprinting box and their function in the imprinting process.

A cluster of imprinted genes on human chromosome 15q11-q13 (the PWS/AS domain) and its ortholog on mouse chromosome 7c is believed to be regulated by an imprinting control center. Although minideletions in this region in Angelman syndrome (AS) and Prader-Willi syndrome (PWS) patients revealed that two elements, shortest deletion regions of overlap in AS families and PWS families (AS-SRO and PWS-SRO), respectively, constitute the IC, the molecular mechanism that governs this regional control remains obscure. To understand how this imprinting center works, a mouse model was sought. The striking similarity between the human and mouse sequences allowed the generation of a minitransgene (AS-SMP) composed of AS-SRO and the Snrpn minimal promoter (SMP) the mouse ortholog of PWS-SRO. This minitransgene carries out, in a highly reliable and reproducible manner, all steps of the imprinting process. In an attempt to decipher the molecular mechanism of the imprinting process, we generated and tested for imprinting five minitransgenes based on AS-SMP, in which various parts of the 160 bp SMP were deleted. These experiments revealed a set of five cis elements that carry out the various steps of the imprinting process. This set includes: (i). two copies of a de novo methylation signal (DNS) that establish the maternal imprint during oogenesis; (ii). an allele discrimination signal that establishes the paternal imprint; and (iii). two elements that act together to maintain the paternal imprint. Two functionally redundant sets of the five elements were found on the respective endogenous mouse sequence explaining the previously published contradictory results of targeted deletion experiments. Together with the fact that all five elements bind specific proteins that are presumably the factors acting in trans in the imprinting process, our observations set the stage for a comprehensive study of the molecular mechanism involved in the control of the imprinting process.

Alleles↗
PubMed2001

Genomic organization of the murine G protein beta subunit genes and related processed pseudogenes.

The functional significance of heterotrimeric guanine nucleotide binding protein (G protein) for the many physiological processes including the molecular mechanisms of drug addiction have been described. In investigating the changes of mRNA expression after acute psychostimulant administration, we previously identified a cDNA encoding a G protein beta1 subunit (Gbeta1) that was increased up to four-fold in certain brain regions after administration of psychostimulants. The mouse Gbeta1 gene (the mouse genetic symbol, GNB1) was mapped to chromosome 4, but little was known of its genetic features. To characterize the GNB1 gene further, we have cloned and analyzed the genomic structures of the mouse GNBI gene and its homologous sequences. The GNBI gene spans at least 50 kb, and consists of 12 exons and 11 introns. The exon/intron boundaries were determined and found to follow the GT/AG rule. Exons 3-11 encode the Gbeta1 protein, and the exon 2 is an alternative, resulting in putative two splicing variants. Although intron 11 is additional for GNBI compared with GNB2 and GNB3, the intron positions within the protein coding region of GNB1, GNB2 and GNB3 are identical, suggesting that GNB1 should have diverged from the ancestral gene family earlier than the genes for GNB2 and GNB3. We also found the 5'-truncated processed pseudogenes with 71-89% similarities to GNBI mRNA sequence, suggesting that the truncated cDNA copies, which have been reverse-transcribed from a processed mRNA for GNB1, might have been integrated into several new locations in the mouse genome.

Animals↗