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At least 1,279 records · Page 71Linked to original sources
PubMed2004

Gene amplification involves site-specific short homology-independent illegitimate recombination in Acinetobacter sp. strain ADP1.

A system for studying gene amplification in the bacterium Acinetobacter sp. strain ADP1 was used to isolate 105 spontaneous mutants. The method selects for the elevated expression of neighboring transcriptional units in a parent strain lacking its normal transcriptional activators. Gene amplification can compensate for the activator loss by increasing the copy number of seven weakly expressed genes. Mutant colonies arose from the parent strain at a frequency of 10(-8) within three weeks. All but one of these mutants carried tandem head-to-tail repeats of a chromosomal segment (amplicon). These amplicons varied in size from approximately 12-290 kb and ranged in copy number from 3 to more than 30. Gene amplification involved a two-step process in which duplications formed independently of recA. Illegitimate recombination fused normally distant chromosomal regions to create novel DNA duplication junctions. These junctions were isolated from amplification mutants using an assay that exploits Acinetobacter natural transformability. Sequence analysis of 72 junctions revealed little identity in the recombining regions. Furthermore, multiple independently isolated mutants contained identical junctions. Six different junctions, each found in two to six mutants, revealed that some recombination events are site-specific. Several recurring junctions were studied using PCR. In each case, the identical duplication present in the mutant was estimated to have occurred in as many as one in a million cells in populations of strains never exposed to selective conditions. These duplications appeared to form spontaneously by a novel type of short homology-independent, site-specific process. However, in the absence of recA, mutant colonies were not selected from parent cells containing these duplications. Thus, the second gene amplification step most likely depends on homologous recombination to increase amplicon copy number. These studies support the theory that gene amplification is a driving force in the evolution of functionally related gene clusters.

Acinetobacter↗
PubMed2002

Implementing the DICOM Grayscale Standard Display Function for mixed hard- and soft-copy operations.

The aim of this work was to implement the DICOM Grayscale Standard Display Function (GSDF) at all stages of image presentation for computed radiography (CR) and direct digital radiography (DR) modalities. Cathode-ray tubes (CRT) were calibrated according to vendor procedures. Printer look-up-tables (LUT) were measured. Custom LUTs were created and loaded. Fuji CR gradation processing parameters were adjusted to accommodate a GSDF printer LUT. Conformance to the GSDF for hard-copy and soft-copy displays was measured with DICOM Part 14 procedures. One system was intended to completely incorporate the GSDF, although the hard-copy result was correct. The CR systems required creation of custom GSDF printer LUTs, adjustment of gradation processing parameters, and/or calibration of CRT luminance response at the quality control station. The picture archiving and communication system workstations from one vendor required third-party software for calibration. Current implementations of DICOM GSDF by vendors may be inconsistent or nonexistent. Significant effort by in-house staff must be expended to properly incorporate the GSDF.

Data Display↗
PubMed1993

Hydra: a C-language environment for real-time DOS multitasking at the bedside.

Patient monitoring at the bedside is an inherently parallel job, best handled by multiple individual tasks running concurrently. Cost and diffusion considerations strongly favor the use of PC's at the bedside, but their most widespread operating system, DOS, is not built for multitasking. Hence, a software platform in C language has been prepared, allowing the intermediate programmer to easily write independent modules which will then run simultaneously without conflicts. Such a platform aims at allowing effortless sharing of data among concurrently running processes, while providing strong insulation between tasks, enough to allow multiple copies of any one task to run simultaneously unknown to each other. A cooperative, memory sharing multitasking paradigm has been chosen, which offers fine granularity of timeslicing and low execution overhead at the price of some loss in generality of design. Speed, data exchange capability and number of stackable windows are greater than with commercial packages like Windows or LabWindows. Dynamical reprioritization of tasks is built in, allowing the computerized monitor to focus its attention and resources on urgent tasks.

Algorithms↗
PubMed1982

The structure and expression of the preproenkephalin gene.

Enkephalins are pentapeptides with opioid activity which are found in a wide variety of tissues. Studies of enkephalin-containing peptides from the adrenal gland have established that the mature pentapeptides are derived by proteolytic processing of a precursor protein. We have shown that human adrenal medullary tumours contain mRNA which can be translated in vitro to yield a single major enkephalin precursor. The sequence of cloned cDNA shows that the preproenkephalin mRNA encodes four copies of met-enkephalin, two copies of met-enkephalin extended sequences and one copy of leu-enkephalin; each copy is flanked by paired basic amino acids which are presumably recognised by the processing protease. We have used the cloned human cDNA as a hybridisation probe to detect the corresponding mRNAs in rat adrenal gland and, in smaller amounts, in rat brain. We have been unable to detect in brain any other cross-hybridising mRNAs which might encode other putative precursor proteins.

Adrenal Gland Neoplasms↗
PubMed1986

Functional expression of rat cytochrome c in Saccharomyces cerevisiae.

To determine whether a mammalian cytochrome c could efficiently replace iso-1-cytochrome c, which is encoded by the yeast CYC1 gene, the coding sequence of RC9 (a nondefective processed gene from rat) was cloned in both single- and multiple-copy expression vectors under the direction of the yeast alcohol dehydrogenase 1 (ADC1) promoter. Upon transformation of a CYC1 deletion strain, the multiple-copy construct restored a wild-type growth rate on lactate medium; such growth normally requires derepressed amounts of iso-1-cytochrome c. These transformants expressed a level of hybrid ADC1/RC9 mRNA approximately 5- to 10-fold greater than the amount of message from the endogenous ADC1 gene and produced a steady-state level of rat cytochrome c equivalent to that of the wild-type yeast protein. A requirement for the vector was evidenced by its absence in all transformants that lost the lactate growth phenotype after propagation in nonselective medium. In contrast, the level of vector-specific message in single copy was equivalent to that of the endogenous ADC1 mRNA, but transformants exhibited no significant growth on lactate. Constructions having a small deletion or a mammalian intron within the rat cytochrome c coding region failed to support lactate-dependent growth, indicating that complementation depends upon proper translation of the correct rat coding sequence. Therefore, the rat polypeptide, when expressed at normal physiological levels, is recognized by the yeast machinery involved in the multiple steps required for the processing and transport of an active cytochrome c as well as its functional interaction with the respiratory apparatus.

Animals↗
PubMed2003

Mutations that are synthetically lethal with a gas1Delta allele cause defects in the cell wall of Saccharomyces cerevisiae.

The GAS1-related genes of fungi encode GPI-anchored proteins with beta-1,3-glucanosyltransferase activity. Loss of this activity results in defects in the assembly of the cell wall. We isolated mutants that show a synthetic defect when combined with a gas1Delta allele in Saccharomyces cerevisiae, and identified nine wild-type genes that rescue this defect. The indispensability of BIG1 and KRE6 for the viability of gas1Delta cells confirmed the important role of beta-1,6-glucan in cells that are defective in the processing of beta-1,3-glucan. The identification of the Wsc1p hypo-osmotic stress sensor and components of the PKC signal transduction pathway in our screen also confirmed that the cell wall integrity response attenuates the otherwise lethal gas1Delta defect. Unexpectedly, we found that the KEX2 gene is also required for the viability of the gas1Delta mutant. Kex2p is a Golgi/endosome-membrane-anchored protease that processes secretory preproteins. A cell wall defect was also found in the kex2Delta mutant, which was suppressible by multiple copies of the MKC7 or YAP3 gene, both of which encode other GPI-anchored proteases. Therefore, normal cell wall assembly requires proteolytic processing of secretory preproteins. Furthermore, the genes CSG2 and IPT1 were found to be required for normal growth of gas1Delta cells in the presence of 1 M sorbitol. This finding suggests that complex sphingolipids play a role in the hyper-osmotic response.

Cell Wall↗
PubMed2004

Adding to the ends: what makes telomerase processive and how important is it?

Telomerase is a cellular reverse transcriptase responsible for telomere maintenance in most organisms. It does so by adding telomere repeats onto pre-existing ends using an integral RNA component as template. Compared to "prototypical" reverse transcriptases, telomerase is unique in being able to repetitively copy a short templating RNA segment, thus adding multiple copies of the repeat to the DNA substrate following a single binding event. This uniquely processive property hints at the intricate conformational alterations that the enzyme must choreograph during its reaction cycles. Recent studies have identified distinct structural elements within both the RNA and protein components of telomerase that modulate enzyme processivity. Pharmacological and genetic analysis suggest that telomerase processivity is a significant determinant of telomere length. Because telomere maintenance and the lack thereof have been linked to tumor progression and aging, further investigation of telomerase processivity may lead to novel medical intervention strategies.

Animals↗
PubMed2000

Allelic association is increased by correlation of effective family size.

In a previous study, we showed that the observation of high frequencies of certain inherited disorders in the population of Saguenay Lac Saint Jean (SLSJ) in Quebec can be explained in terms of the variance and the auto-correlation of effective family size (EFS) across generations. Correlated EFS, across generations, allows alleles introduced as a single copy to reach very high frequencies in about 12 generations. Here, we investigate the impact of this same demographic process on allelic association between a disease locus and closely linked neutral markers. We model the fate of a disease allele, introduced as a single copy, and of its surrounding haplotype. We show that the auto-correlation of EFS across generations increases the expected proportion of individuals who carry the ancestral haplotype in the present generation. Thus, the length of a shared haplotype is longer, making this population useful for coarse mapping. But this autocorrelation decreases the estimated value; thus ignoring the auto-correlation in EFS leads to an underestimate of the recombination rate. This result is of importance, since socio-demographic processes such as auto-correlation of EFS across generations have been described in other human populations.

Alleles↗
PubMed1996

Multifactor cis-dominant negative regulation of IL-2 gene expression in anergized T cells.

The molecular mechanism underlying IL-2 transcriptional blockade in anergic T cell clones is not fully understood. To examine whether an active negative regulatory process occurs, we created a reporter construct containing as an enhancer four copies of the NF-AT site and one copy of the octamer site (4X NF-AT-Oct). This construct was only slightly reduced (1.3-fold) in its expression when stimulated under anergic conditions, while a whole mouse IL-2 enhancer construct showed a reduction of 4.3-fold. Addition of the -176 to -96 sequence to the 4X NF-AT-Oct construct did not impart the ability to be affected by anergy, but addition of the -236 to -96 sequence did, demonstrating that anergy is an active inhibitory process and that more than the presence of the -150 AP-1 binding site (-152 to -147) is required to mediate the effect. Mutational studies of the -236 to -96 sequence indicated that the presence of both the -130 AP-1-like site (-187 to -181) and the -150 proximal AP-1 site were necessary to observe anergy. Because the -180 site is not required for trans-activation, it was possible to confirm by mutation in the normal mouse IL-2 enhancer that this site is absolutely essential for anergy induction. The simplest model to explain these results is that anergy is mediated by a complex of multiple transcription factors that exert a cis-acting dominant negative regulatory effect on the trans-activation of the IL-2 gene.

Animals↗
PubMed2001

Development of a real-time PCR procedure including an internal control for the measurement of HCMV viral load.

Human cytomegalovirus (HCMV) infections are frequent in immuno-compromised patients. The recent development of real-time PCR procedures that allow the rapid quantification of genome load will be helpful for accurate monitoring of these infections. Two extraction procedures were evaluated using 30 blood samples that were processed pure and diluted (1/10). Repeatability and reproducibility of the quantitative PCR procedure using an internal control for amplification were analysed, and its sensitivity compared to a qualitative PCR procedure using 50 HCMV culture positive blood samples. The real-time PCR and qualitative PCR procedures were positive in 46 and 48 of the samples tested, respectively. Discrepancies were observed for samples with a low viral load. The sensitivity of the real-time PCR procedure was evaluated at 500 HCMV DNA copies per ml of sera. The use of an internal control concomitantly processed during the HCMV quantification did not alter the sensitivity of the procedure, and was relevant for the detection of putative PCR inhibitors that may interfere with the amplification process. This procedure was used to measure genome load in two bone marrow transplant patients with HCMV disease, confirming that this new PCR procedure should be used widely for diagnosing and monitoring HCMV infections in transplant patients.

Bone Marrow Transplantation↗
PubMed2000

Multiple homing pathways used by yeast mitochondrial group II introns.

The yeast mitochondrial DNA group II introns aI1 and aI2 are retroelements that insert site specifically into intronless alleles by a process called homing. Here, we used patterns of flanking marker coconversion in crosses with wild-type and mutant aI2 introns to distinguish three coexisting homing pathways: two that were reverse transcriptase (RT) dependent (retrohoming) and one that was RT independent. All three pathways are initiated by cleavage of the recipient DNA target site by the intron-encoded endonuclease, with the sense strand cleaved by partial or complete reverse splicing, and the antisense strand cleaved by the intron-encoded protein. The major retrohoming pathway in standard crosses leads to insertion of the intron with unidirectional coconversion of upstream exon sequences. This pattern of coconversion suggests that the major retrohoming pathway is initiated by target DNA-primed reverse transcription of the reverse-spliced intron RNA and completed by double-strand break repair (DSBR) recombination with the donor allele. The RT-independent pathway leads to insertion of the intron with bidirectional coconversion and presumably occurs by a conventional DSBR recombination mechanism initiated by cleavage of the recipient DNA target site by the intron-encoded endonuclease, as for group I intron homing. Finally, some mutant DNA target sites shift up to 43% of retrohoming to another pathway not previously detected for aI2 in which there is no coconversion of flanking exon sequences. This new pathway presumably involves synthesis of a full-length cDNA copy of the inserted intron RNA, with completion by a repair process independent of homologous recombination, as found for the Lactococcus lactis Ll.LtrB intron. Our results show that group II intron mobility can occur by multiple pathways, the ratios of which depend on the characteristics of both the intron and the DNA target site. This remarkable flexibility enables group II introns to use different recombination and repair enzymes in different host cells.

Base Sequence↗
PubMed1989

Cytogenetic analysis of amplification and deamplification of UMP synthase genes in Chinese hamster cells.

Chinese hamster lung cells selected for resistance to pyrazofurin and 6-azauridine contain amplified UMP synthase genes. With selection in 5-fluorouracil, cells that have lost the amplified gene copies can be isolated. Reselection of deamplified cells in pyrazofurin and 6-azauridine results in reamplification of the UMP synthase genes. We have used chromosomal banding and in situ hybridization techniques to characterize this cyclic process of amplification and deamplification. Homogeneously staining regions (HSRs) were observed in cells containing amplified copies of the UMP synthase gene but not in cells in which the amplified UMP synthase genes had been lost. After reselection in pyrazofurin and 6-azauridine, abnormally banded regions (ABRs) were observed. Both HSRs and ABRs were located at a single site on the distal regions of a small acrocentric autosome, and both were shown to contain the amplified genes. The majority of 5-fluorouracil-selected cells showed residual marker acrocentric chromosomes of various sizes, suggesting excision of portions of the HSR or ABR as the mechanism of deamplification. The acrocentrics carrying the amplified genes resulted from rearrangements involving chromosome 4, site of the endogenous gene. This reversible selection system provides a unique model for investigating gene amplification and deamplification in association with chromosomal rearrangements and the relationship of G-banding to underlying DNA structure.

Animals↗
PubMed2004

Lonely in Paris: when one gene copy isn't enough.

Circulating platelets are continually replenished by fragmentation of terminally differentiated megakaryocytes. Processes disrupted in inherited thrombocytopenias frequently shed light on normal thrombopoietic mechanisms. An especially rare condition called Paris-Trousseau syndrome (PTS) seems to occur by virtue of hemizygous loss of the FLI1 transcription factor gene. Provocative new data suggest that FLI1 shows monoallelic expression during a brief window in megakaryocyte differentiation, which thus explains the dominant inheritance pattern of PTS despite the presence of one normal FLI1 allele.

Cell Differentiation↗
PubMed1997

Impaired recognition of disgust in Huntington's disease gene carriers.

Face processing and facial expression recognition were investigated in the earliest stages of Huntington's disease, by studying 40 people who presented for genetic testing. Twenty-three of these 'at risk' individuals turned out not to carry the gene for Huntington's disease (the AR- group). Seventeen were found to be gene carriers (the AR+ group); 15 from genetic testing, and two who showed signs of early stages of Huntington's disease. A number of standard tasks were used to provide background information, including recognition memory for words, picture naming, verbal fluency, and figure copying; none revealed significant differences between the AR+ and AR- groups. Face processing abilities were investigated using tests of identification of familiar (famous) faces, unfamiliar face matching, recognition memory for faces, and recognition of facial expressions of emotion. No statistically significant differences between the AR+ and AR- groups were found for any of these tests, but the AR+ group showed a borderline overall impairment in recognizing facial expressions of emotion (0.05 < P < 0.1). When recognition of each of the six basic emotions used was examined separately, only disgust was found to be significantly impaired. This highly selective deficit in the recognition of disgust was confirmed in the subgroup of 15 individuals shown by genetic testing to be Huntington's gene carriers; it was therefore found in people who were free from clinical symptoms and did not perform significantly more poorly than non-carriers on any of the background tests, on any of the other face processing tasks, and even for recognition of any other basic emotion. This points strongly to the importance of the basal ganglia in the emotion of disgust.

Adult↗
PubMed2002

The P1 plasmid in action: time-lapse photomicroscopy reveals some unexpected aspects of plasmid partition.

The prophage of bacteriophage P1 is a low copy number plasmid in Escherichia coli and is segregated to daughter cells by an active partition system. The dynamics of the partition process have now been successfully followed by time-lapse photomicroscopy. The process appears to be fundamentally different from that previously inferred from statistical analysis of fixed cells. A focus containing several plasmid copies is captured at the cell center. Immediately before cell division, the copies eject bi-directionally along the long axis of the cell. Cell division traps one or more plasmid copies in each daughter cell. These copies are free to move, associate, and disassociate. Later, they are captured to the new cell center to re-start the cycle. Studies with mutants suggest that the ability to segregate accurately at a very late stage in the cell cycle is dependent on a novel ability of the plasmid to control cell division. Should segregation be delayed, cell division is also delayed until segregation is successfully completed.

Bacteriophage P1↗
PubMed1998

Stability of human immunodeficiency virus RNA in blood specimens as measured by a commercial PCR-based assay.

We investigated the effects of conditions often encountered during handling, transit, and storage of blood specimens on the quantity of detectable human immunodeficiency virus (HIV) RNA in plasma. HIV RNA copy numbers were measured with a commercially available assay (the Amplicor HIV-1 Monitor test kit). Variables examined were the time to processing of blood and plasma, the holding temperature of blood and plasma prior to processing, the effect of freezing and thawing of plasma, and the use of different anticoagulants. The relationship between the HIV RNA copy number and the HIV isolation rate by peripheral blood mononuclear cell (PBMC) coculture was also examined. We found that RNA copy numbers were maintained to within 0.5 log10 (approximately threefold) in blood and plasma samples held at room temperature or 4 degrees C for up to 3 days and remained stable despite (limited) freezing and thawing of the plasma. HIV RNA copy numbers were also maintained after long-term storage of plasma at -70 degrees C. The ability to isolate HIV from PBMCs was directly proportional to the HIV RNA copy number.

Adolescent↗
PubMed1989

Alternative processing of mRNAs encoding mammalian chromosomal high-mobility-group proteins HMG-I and HMG-Y.

The high-mobility-group protein HMG-I is a well-characterized nonhistone chromosomal protein that is preferentially expressed in rapidly dividing cells, binds to A. T-rich regions of DNA in vitro, and has been localized to particular regions of mammalian metaphase chromosomes. We isolated eight cDNA clones encoding HMG-I and its isoform HMG-Y from a human Raji cell cDNA library and detected blocks of nucleotide sequence rearrangements in the 5'-untranslated regions of these clones. In addition to this leader sequence variation, five of the eight cDNA clones had either a 33- or 36-base-pair in-frame deletion in their open reading frame (ORF); we found that this shortened ORF encodes the HMG-Y protein isoform. We present evidence that the 5'-untranslated-region and ORF heterogeneity of the cDNA clones is the result of alternative processing of RNA transcripts from a single functional gene. Several additional but probably nonfunctional HMG-I or HMG-Y gene copies exist in the human genome; we isolated and partially sequenced one of these pseudogenes and found that it is a processed HMG-Y retropseudogene.

Amino Acid Sequence↗
PubMed1989

Identification of a T4 gene required for bacteriophage mRNA processing.

A ribonucleolytic activity that cleaves within the Shine/Dalgarno sequences of the bacteriophage T4 motA and ORF2 mRNAs was recently described. We have identified additional sites of processing within several other ribosome binding sites, including two sites in the polycistronic frd transcript. Deletion mutants (farP) that overproduce the product of frd are defective in this mRNA processing. The mutants were used to identify processing events dependent on the T4 activity including attack at nuclease-sensitive sites within the coding sequences of some genes and within the intercistronic region 5' of gene 43. All known processing sites lie within similar sequences. Another mutant in mRNA processing carries a point mutation in one of the open reading frames (orf61.9) removed by the farP deletions. Introduction of a cloned copy of this open reading frame into a unique site in the chromosome of farP phage is sufficient to restore mRNA processing capability. The open reading frame probably encodes the T4 regB protein.

Base Sequence↗