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At least 721 records · Page 40Linked to original sources
PubMed1995

Characterization and mapping of the gene encoding mouse proteasome subunit DELTA (Lmp19).

The proteasome subunit DELTA is unusually closely related to the major histocompatibility complex (MHC)-linked proteasome subunit, LMP2. The sequence of a mouse cDNA for DELTA confirms that this 22,100 M(r) proteasome subunit is highly conserved across species. Sequence analysis of the mouse gene encoding DELTA, designated Lmp19, indicates that it consists of six exons and five introns, similar to the Lmp2 gene. The 5' upstream region lacks a TATA regulatory sequence, which is also absent from proteasome genes isolated from Drosophila. BXD recombinant inbred (RI) mice were used to map the potential chromosomal location of Lmp19, and revealed that the DELTA subunit has related sequences present on two different mouse chromosomes, chromosomes 1 and 11. Typing of 89 progeny from a C57BL/6J X Mus spretus DNA backcross panel (BSS) confirmed the chromosome 1 assignment. Southern hybridization with a polymerase chain reaction-generated Lmp19 intron 2-specific probe indicates that the Lmp19 genomic clone corresponds to the sequence on chromosome 11, and further suggests that the chromosome 1 copy represents a processed pseudogene (Lmp19-ps1).

Amino Acid Sequence↗
PubMed2005

Origin recognition and the chromosome cycle.

Prior to the initiation of DNA replication, chromosomes must establish a biochemical mark that permits the recruitment in S phase of the DNA replication machinery that copies DNA. The process of chromosome replication in eukaryotes also must be coordinated with segregation of the duplicated chromosomes to daughter cells during mitosis. Protein complexes that utilize ATP coordinate events at origins of DNA replication and later they participate in the initiation of DNA replication. In eukaryotes, some of these proteins also play a part in later processes that ensure accurate inheritance of chromosomes in mitosis, including spindle attachment of chromosomes, accurate duplication of centrosomes and cytokinesis. A perspective of how ATP-dependent proteins accomplish this task in eukaryotes is discussed.

Archaea↗
PubMed2005

Updating the 'crop circle'.

Comparative analyses unravel the relationships between genomes of related species. The most comprehensive comparative dataset obtained to date is from the grass family, which contains all of the major cereals. Early studies aimed to identify chromosomal regions that have remained conserved over long evolutionary time periods, but in recent years, researchers have focused more on the extent of colinearity at the DNA-sequence level. The latter studies have uncovered many small rearrangements that disturb colinearity in orthologous chromosome regions. In part, genomes derive their plasticity from genome- and gene-amplification processes. Duplicated gene copies are more likely to escape selective constraints and thus move to other regions of the genome, where they might acquire new functions or become deleted. These rearrangements will affect map applications. The most popular applications, especially since the complete rice genomic sequence has been available, are the use of comparative data in the generation of new markers to tag traits in other species and to identify candidate genes for these traits. The isolation of genes underlying orthologous traits is the first step in conducting comparative functional studies.

Base Sequence↗
PubMed1995

Consonant harmony as a compensatory mechanism in fluent aphasic speech.

This study addresses how fluent aphasics construct complete phonological representations, given the premise that their phonological speech errors result from faulty information about stored lexical representations. We explored whether consonant harmony, a common rule-governed process of feature copying, operates as a compensatory device for completing phonological representations in fluent aphasia. This was examined in a corpus of phonemic paraphasias (n = 543) produced by 8 fluent aphasics during picture naming. Consonant substitutions due to a single feature change (n = 143) were analyzed for the properties of consonant harmony predicted by the phonological principles embodied in a Universal Markedness version of Underspecification Theory (e.g., Chomsky and Halle, 1968). Results indicated that harmony constrained the feature substitution errors involving the feature class of voice (e.g., calendar-->/[symbol: see text]/), but not place of articulation (e.g., igloo-->/idlu/); substitutions due to an error in manner were rare. These findings were used to argue that for English-speaking fluent aphasics a consonant harmony rule for the feature voice is incorporated into a compensatory output mechanism that is used to complete faulty lexical-phonological representations.

Aged↗
PubMed1999

Abnormalities of imaged motor sequences in children with developmental coordination disorder.

The chronometry of real and imagined movements was investigated in a group of children with developmental coordination disorder (DCD) and a group of matched controls. The visually-guided pointing task was used to investigate the speed for accuracy trade-offs that occur as target size is varied for both real and imagined performance. In the control group, the speed for accuracy trade-off for both real and imagined performance conformed to Fitts' law. In the DCD group only real movements conformed to Fitts' law. This pattern of performance suggests that children with DCD have an impairment in the ability to generate internal representations of volitional movements. This may reflect part of a general impairment in the processing of efference copy in DCD.

Analysis of Variance↗
PubMed2002

Isolation and characterization of annexin 2 pseudogene in Rattus norvegicus.

Annexin 2 is a calcium-regulated, phospholipid-binding protein present in endothelial cells, macrophages and some tumor cells. Annexin 2 is a substrate for a variety of protein kinases, and plays roles in the regulation of endocytosis, exocytosis and thrombolysis. We have determined the nucleotide sequence of a rat genomic DNA fragment that hybridized to a rat annexin 2 DNA complementary to RNA (cDNA) probe. Sequence analysis revealed that it was an intronless rat annexin 2, consisting of a start-to-stop-codon-length copy of the processed transcript. This pseudogene contained 33 point mutations and two deletion sites in the coding region as compared with the cDNA, and thus displayed typical features of a retroposon. Transitions were more frequent than transversions, and the most frequent type of mutation was G to A transition. We isolated a phage clone that contained a functional rat annexin 2 genomic fragment including coding exons 3 and 4. Polymerase chain reaction and subsequent sequence analysis revealed an intron of approximately 4 kbp at the same site as in humans and mice. Whereas the annexin 2 gene or its cDNA homologues have been detected in various species from Xenopus to humans, its pseudogene has been reported only in humans. In the present study, we demonstrated the presence of an annexin 2 pseudogene in rats.

Animals↗
PubMed2003

Structure and enzymatic properties of a stable complex of the human REV1 and REV7 proteins.

With yeast Saccharomyces cerevisiae, results from a variety of genetic and biochemical investigations have demonstrated that the REV genes play a major role in induction of mutations through replication processes that directly copy the damaged DNA template during DNA replication. However, in higher eucaryotes functions of homologues are poorly understood and appear somewhat different from the yeast case. It has been suggested that human REV1 interacts with human REV7, this being specific to higher eucaryotes. Here we show that purified human REV1 and REV7 proteins form a heterodimer in solution, which is stable through intensive purification steps. Results from biochemical analysis of the transferase reactions of the REV1-REV7 complex demonstrated, in contrast to the case of yeast Rev3 whose polymerase activity is stimulated by assembly with yeast Rev7, that human REV7 did not influence the stability, substrate specificity, or kinetic parameters of the transferase reactions of REV1 protein. The possible role of human REV7 is discussed.

Carrier Proteins↗
PubMed1998

Building health plan databases to risk adjust outcomes and payments.

OBJECTIVES: To highlight the types and sources of data on medical risk and outcomes routinely collected by managed care organizations over time; to summarize the quality and consistency of these data; and to describe some of the difficulties that arise in collecting, pooling, and using these data. DESIGN: Synthesis of the experiences of two risk-adjustment modeling projects in assembling large volumes of demographic, diagnostic, and expense data from several health maintenance organizations (HMOs) over multiple years. SETTING: Six large HMOs from the Northwest, North Central, and Northeast regions of the USA. INTERVENTIONS: Health plans were approached to participate in a risk-adjustment study, presented with an extensive variable-by-variable data request, and, if willing to participate, asked to specify a desired process for extracting, copying, and transferring selected variables to the study site for purposes of research. Depending on local circumstances, three different approaches were used: (i) health plan staff obtained the data and organized them into the requested study format; (ii) study staff were provided access to health plan data systems to perform the extractions directly; and (iii) health plans hired contract programmers to perform the extractions under the direction of the study team. Key measures of risk and cost were extracted and merged into analysis files. MAIN OUTCOME MEASURES: Complete and consistent eligibility maps, demographic information, inpatient and outpatient diagnoses, and total health plan expense for each enrollee. RESULTS: We have been successful in collecting and integrating complete utilization, morbidity, demographic, and cost data on total memberships of five large HMOs as well as a subset from a sixth HMO, all for multiple years. CONCLUSION: While HMOs vary greatly in the quality and comprehensiveness of their data systems, these attributes have been improving across the board over time. Automated health plan data systems represent potentially valuable sources of data on health risks and outcomes and can be used to benchmark disease management programs and risk adjust capitation payments and medical outcomes.

Databases, Factual↗
PubMedDate not supplied

Rapid three-dimensional angiography with undersampled MR imaging.

Techniques for subtraction angiography with magnetic resonance imaging have been extended from two to three dimensions, and a novel method that reduces the expected data acquisition time by at least an order of magnitude is presented. Electrocardiogram-gated three-dimensional (3D) images are acquired by Fourier transform technique, and flow contrast is obtained by subtracting pairs of images acquired at different points in the cardiac cycle. The vascular tree is shown in 3D perspective by means of a surface detection and a 3D display program. Isotropic 3D angiography requires determining the disposition of the blood vessels in a matrix of cubical voxels. Using orthodox Fourier transform technique, for an image matrix with 256 voxels to the edge, a data acquisition with 256 X 256 = 65 K phase-encodings would be needed. If gated, this would require approximately 1 day. In this study we abbreviate the data acquisition by doing only 1/64 of the usual set of phase-encoding gradient pulses. Spatial resolution is undiminished, but aliasing or "wraparound" results in each of the two phase-encoded coordinates of the 3D image. This aliasing is rectified in a two stage process. First, 64 copies of the undersampled 3D arteriogram are juxtaposed in a two-dimensional grid pattern. This assembles many copies of the complete vascular tree. Because they occupy only a small fraction of ambient volume, these copies are unlikely to overlap or collide with one another. Second, a single copy of the vascular tree is isolated by a surface detection program that takes advantage of the fact that the vascular tree is topologically connected. Studies of the abdominal aorta are presented.

Blood Vessels↗
PubMed2002

Computational detection and location of transcription start sites in mammalian genomic DNA.

Transcription, the process whereby RNA copies are made from sections of the DNA genome, is directed by promoter regions. These define the transcription start site, and also the set of cellular conditions under which the promoter is active. At least in more complex species, it appears to be common for genes to have several different transcription start sites, which may be active under different conditions. Eukaryotic promoters are complex and fairly diffuse structures, which have proven hard to detect in silico. We show that a novel hybrid machine-learning method is able to build useful models of promoters for >50% of human transcription start sites. We estimate specificity to be >70%, and demonstrate good positional accuracy. Based on the structure of our learned models, we conclude that a signal resembling the well known TATA box, together with flanking regions of C-G enrichment, are the most important sequence-based signals marking sites of transcriptional initiation at a large class of typical promoters.

Animals↗
PubMed2006

Simultaneous detection of pathogens in clinical samples from patients with community-acquired pneumonia by real-time PCR with pathogen-specific molecular beacon probes.

In this study, real-time PCR with pathogen-specific molecular beacons (MB) and primers was evaluated for prediction of community-acquired pneumonia (CAP) causative agents, detecting six main CAP agents, Streptococcus pneumoniae, Haemophilus influenzae, Mycoplasma pneumoniae, Chlamydophila pneumoniae, Legionella pneumophila, and Streptococcus pyogenes, simultaneously. The PCR assay was evaluated for fresh clinical specimens from infants and children (n = 389) and from adults (n = 40). The MB probes and primers are both pathogen specific, namely, the lytA gene for S. pneumoniae, the mip gene for L. pneumophila, and 16S rRNA genes for the remaining four organisms. DNA extraction of clinical specimens was performed with a commercially available EXTRAGEN II kit, and amplification was performed with Stratagene Mx3000P. The limit of detection for these pathogens ranged from 2 copies to 18 copies. The whole process from DNA extraction to the analysis was finished in less than 2 h. The obtained sensitivity and specificity of this real-time PCR study relative to those of conventional cultures were as follows: 96.2% and 93.2% for S. pneumoniae, 95.8% and 95.4% for H. influenzae, 100% and 100% for S. pyogenes, and 100% and 95.4% for M. pneumoniae, respectively. The sensitivity and specificity for M. pneumoniae relative to those of a serologic assay were 90.2% and 97.9%, respectively. In six clinical samples of C. pneumoniae, the real-time PCR gave positive predictable values, and in those cases, elevation of the titer value was also observed. In conclusion, we demonstrated that a real-time PCR assay with pathogen-specific MB is useful in identifying CAP causative agents rapidly and in examining the clinical course of empirical chemotherapy in a timely manner, supporting conventional culture methods.

Child, Preschool↗
PubMed1997

Placement of tRNA primer on the primer-binding site requires pol gene expression in avian but not murine retroviruses.

In an early step in the retroviral infectious process, reverse transcriptase copies the genomic RNA of the virus into complementary minus-strand DNA. The primer for this synthetic event is a molecule of cellular tRNA, which is annealed by its 3' 18 nucleotides to a region of the genomic RNA termed the primer-binding site (PBS); the sequence of the PBS and hence the identity of the tRNA depend upon the retrovirus species. In addition to the primer tRNA, retrovirus particles contain a substantial number of other tRNA molecules. The latter tRNA population is enriched for the tRNA species which serves as primer for the virus. While there is considerable evidence that the enrichment for the primer species can be attributed to the pol gene product, nothing is known regarding mechanisms of annealing the primer to the PBS. We have analyzed pol- mutants of avian leukosis virus (ALV) and murine leukemia virus (MuLV) for the presence of primer at the PBS in virion genomic RNA. Remarkably, the results were different for the two viruses: the PBS was substantially occupied by primer in MuLV but not in ALV. Previous data indicates that the Pol-dependent enrichment of the primer within the virion is much greater in ALV than in MuLV. We therefore propose that the absence of primer at the PBS in pol- ALV is due to the deficiency of the primer species within the particle. The results suggest that, at least in MuLV, the tRNA is unwound by either the Gag protein or a cellular protein for annealing to the PBS. Further, the C-terminal 17 amino acids of Gag are unnecessary for this function in MuLV.

Animals↗
PubMed2005

Identification and characterization of critical cis-acting sequences within the yeast Ty1 retrotransposon.

The yeast long terminal repeat (LTR) retrotransposon Ty1, like retroviruses, encodes a terminally redundant RNA, which is packaged into virus-like particles (VLPs) and is converted to a DNA copy by the process of reverse transcription. Mutations predicted to interfere with the priming events during reverse transcription and hence inhibit replication are known to dramatically decrease transposition of Ty1. However, additional cis-acting sequences responsible for Ty1 replication and RNA dimerization and packaging have remained elusive. Here we describe a modular mini-Ty1 element encoding the minimal sequence that can be retrotransposed by the Ty1 proteins, supplied in trans by a helper construct. Using a mutagenic screening strategy, we recovered transposition-deficient modular mini-Ty1-HIS3 elements with mutations in sequences required in cis for Ty1 replication and integration. Two distinct clusters of mutations mapped near the 5'-end of the Ty1 RNA. The clusters define a GAGGAGA sequence at the extreme 5'-end of the Ty1 transcript and a complementary downstream UCUCCUC sequence, 264 nt into the RNA. Disruption of the reverse complementarity of these two sequences decreased transposition and restoration of complementarity rescued transposition to wild-type levels. Ty1 cDNA was reduced in cells expressing RNAs with mutations in either of these short sequences, despite nearly normal levels of Ty1 RNA and VLPs. Our results suggest that the intramolecular interaction between the 5'-GAGGAGA and UCUCCUC sequences stabilizes an RNA structure required for efficient initiation of reverse transcription.

Base Sequence↗
PubMed2006

[Anisotropic bone remodeling model with mechanostat].

At present, the numerical model of bone remodeling is inadequate to copy the physiological process of bone remodeling. According to the physiological mechanism of bone remodeling and the anisotropy of bone mechanics properties, an anisotropic bone modeling model with mechanostat was developed, and then was applied to a study on the remodeling evolution of 2D squareplate model. Good results were obtained. The model can be used in the study of implant, osteoporosis and other bone diseases.

Anisotropy↗
PubMed1990

How does the cell count the number of ectopic copies of a gene in the premeiotic inactivation process acting in Ascobolus immersus?

Repeated genes, artificially introduced in Ascobolus immersus by integrative transformation, are frequently inactivated during the sexual phase. Inactivation is observed in about 50% of meioses if duplicated genes are at ectopic chromosomal locations, and in 90% of meioses if genes are tandemly repeated. Inactivation is associated with extensive methylation of the cytosine residues of the duplicated sequences and is induced in the still haploid nuclei of the dikaryotic cell which will undergo karyogamy and subsequent meiosis. Only repeated sequences become methylated. This raises the intriguing question of how the premeiotic inactivation machinery is informed that a nucleus contains multiple copies of a gene. By using in crosses recombinant strains of A. immersus in which either one, two or three genetically independent copies of the exogenous amdS gene from Aspergillus nidulans had been introduced, we could follow the premeiotic inactivation of each one of the ectopic amdS copies. This led us to propose that a prerequisite for inactivation is a premeiotic pairing of repeated sequences and that each copy can undergo successive cycles of pairing. In fact, once methylated, a copy can pair with a still unmethylated copy, so that an uneven number of copies can be subject to inactivation.

Ascomycota↗
PubMed1995

Promotion of V(D)J recombinational accessibility by the intronic E kappa element: role of the kappa B motif.

The accessibility of a chromosomally integrated TCR beta minilocus recombination substrate in a V(D)J recombinase-inducible cell line (HDR37) depends on incorporation of transcriptional enhancer elements such as the Ig kappa light chain intronic enhancer (E kappa). The E kappa element contains several functional motifs including the kappa B motif, which binds the NF-kappa B transcription factor. To assess molecular mechanisms by which E kappa promotes V(D)J recombinational accessibility, we compared the abilities of the wild-type E kappa, a corresponding E kappa sequence with a mutant kappa B motif (E kappa-kappa B-) and a kappa B motif dimer (kappa B2) to function in the context of the TCR beta minilocus/HDR37 system. The E kappa-containing minilocus underwent demethylation, transcription and V(D)J recombination, independently of copy number of integration site. Transfectants containing low copy numbers (one or two) of the E kappa-kappa B(-)-containing minilocus, like enhancerless or kappa B2-containing miniloci at any copy number, were inactive with respect to all three processes. In contrast, high-copy-number integrants of the E kappa-kappa B- substrates showed an integration-site dependent activation of all three processes. Together these data show that the kappa B motif plays a critical role in the ability of E kappa to confer V(D)J recombinational accessibility, but that it is not sufficient to mediate this process by itself.

Animals↗
PubMed2006

Iterative gene prediction and pseudogene removal improves genome annotation.

Correct gene prediction is impaired by the presence of processed pseudogenes: nonfunctional, intronless copies of real genes found elsewhere in the genome. Gene prediction programs frequently mistake processed pseudogenes for real genes or exons, leading to biologically irrelevant gene predictions. While methods exist to identify processed pseudogenes in genomes, no attempt has been made to integrate pseudogene removal with gene prediction, or even to provide a freestanding tool that identifies such erroneous gene predictions. We have created PPFINDER (for Processed Pseudogene finder), a program that integrates several methods of processed pseudogene finding in mammalian gene annotations. We used PPFINDER to remove pseudogenes from N-SCAN gene predictions, and show that gene prediction improves substantially when gene prediction and pseudogene masking are interleaved. In addition, we used PPFINDER with gene predictions as a parent database, eliminating the need for libraries of known genes. This allows us to run the gene prediction/PPFINDER procedure on newly sequenced genomes for which few genes are known.

Animals↗
PubMed1988

Translational control by antisense RNA in control of plasmid replication.

Control of replication of plasmids involves two processes: measurement of the copy number of the plasmid and adjustment of the replication frequency accordingly. For both these processes IncFII plasmids use an antisense RNA (CopA RNA) that forms a duplex with the upstream region (CopT) of the mRNA of the rate-limiting RepA protein. The kinetics of duplex formation was measured in vitro for the wild type and for a cop mutant plasmid; the mutant showed a reduction in the second-order rate constant for the formation of the RNA duplex and a similar increase in copy number. Hence, the kinetics of duplex formation and the concentration of CopA RNA determines the copy number of the plasmid.

Base Sequence↗