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PubMed2004

Essential motifs in the 3' untranslated region required for retrotransposition and the precise start of reverse transcription in non-long-terminal-repeat retrotransposon SART1.

Non-long-terminal-repeat (non-LTR) retrotransposons amplify their copies by reverse transcribing mRNA from the 3' end, but the initial processes of reverse transcription are still unclear. We have shown that a telomere-specific non-LTR retrotransposon of the silkworm, SART1, requires the 3' untranslated region (3' UTR) for retrotransposition. With an in vivo retrotransposition assay, we identified several novel motifs within the 3' UTR involved in precise and efficient reverse transcription. Of 461 nucleotides (nt) of the 3' UTR, the central region, from nt 163 to nt 295, was essential for SART1 retrotransposition. Of five putative stem-loops formed in RNA for the SART1 3' UTR, the second stem-loop (nt 159 to 221) is included in this region. Loss of the 3' region (nt 296 to 461) in the 3' UTR and the poly(A) tract resulted in decreased and inaccurate reverse transcription, which starts mostly from several telomeric repeat-like GGUU sequences just downstream of the second stem-loop. These results suggest that short telomeric repeat-like sequences in the 3' UTR anneal to the bottom strand of (TTAGG)(n) repeats. We also demonstrated that the mRNA for green fluorescent protein (GFP) could be retrotransposed into telomeric repeats when the GFP coding region is fused with the SART1 3' UTR and SART1 open reading frame proteins are supplied in trans.

3' Untranslated Regions↗
PubMed1991

Rheumatoid factors isolated from patients with autoimmune disorders are derived from germline genes distinct from those encoding the Wa, Po, and Bla cross-reactive idiotypes.

To better understand the structural basis for rheumatoid factor activity, the nucleotide sequence of the light chain variable regions of nine human monospecific IgM rheumatoid factors were analyzed. Rheumatoid factors were isolated from three patients with rheumatoid arthritis, a patient with systemic lupus erythematosus, and a normal individual. The VL gene segments used by these rheumatoid factors are not as restricted as previous work on mixed cryoglobulin rheumatoid factors had suggested. Each of the different VK families is represented and there are two examples where a V lambda gene segment is used. Molecules with structures similar to those of the Wa and Po CRI, characteristic of mixed cryoglobulin rheumatoid factors, are not common among these rheumatoid factors isolated from patients with rheumatoid arthritis. While there are clear examples of rheumatoid factors that are direct copies of germline genes, most of the sequence data suggest that the processes of antigenic selection and somatic mutation contribute significantly to the generation of monospecific rheumatoid factors in patients with autoimmune disease.

Autoimmune Diseases↗
PubMed1996

Glanzmann thrombasthenia. Cooperation between sequence variants in cis during splice site selection.

Glanzmann thrombasthenia (GT), an autosomal recessive bleeding disorder, results from abnormalities in the platelet fibrinogen receptor, GP(IIb)-IIIa (integrin alpha(IIb)beta3). A patient with GT was identified as homozygous for a G-->A mutation 6 bp upstream of the GP(IIIa) exon 9 splice donor site. Patient platelet GP(IIIa) transcripts lacked exon 9 despite normal DNA sequence in all of the cis-acting sequences known to regulate splice site selection. In vitro analysis of transcripts generated from mini-gene constructs demonstrated that exon skipping occurred only when the G-->A mutation was cis to a polymorphism 116 bp upstream, providing precedence that two sequence variations in the same exon which do not alter consensus splice sites and do not generate missense or nonsense mutations, can affect splice site selection. The mutant transcript resulted from utilization of a cryptic splice acceptor site and returned the open reading frame. These data support the hypothesis that pre-mRNA secondary structure and allelic sequence variants can influence splicing and provide new insight into the regulated control of RNA processing. In addition, haplotype analysis suggested that the patient has two identical copies of chromosome 17. Markers studied on three other chromosomes suggested this finding was not due to consanguinity. The restricted phenotype in this patient may provide information regarding the expression of potentially imprinted genes on chromosome 17.

Adult↗
PubMed2005

Identification of insertion sequence from a gamma-hexachlorocyclohexane degrading bacterium, Sphingomonas paucimobilis UT26.

Tn5-derived mutants of the gamma-hexachlorocyclohexane-degrading bacterium Sphingomonas paucimobilis UT26 were genetically characterized, and an endogenous insertion sequence (IS) which belongs to the IS1380 family was identified. The IS, named ISsp1, existed as multi copies in UT26, and its transposition appeared to be activated during the process of Tn5-mutagenesis. It was found that transposon mutagenesis can cause endogenous mutations.

DNA Transposable Elements↗
PubMed1998

Property instantiation in conceptual combination.

In four experiments, I examined how a property in one concept is transferred to a second concept during conceptual combination. The results suggest that people instantiate properties: that is, they use a specific representation of a property in the modifier concept to construct a new version of that property that is specific to the combination. If people are instantiating properties, then the modifier property should match its counterpart in the combination to the extent that the modifier and head noun are similar. This observation leads to a variety of predictions (supported by the experiments) about interpretations of similar and dissimilar combinations and about plausibility, preference, and similarity judgments associated with such interpretations. The results argue against an alternative view of transfer that posits that, in general, abstract representations of properties are copied from one concept to another. In this paper, I describe various processing accounts of instantiation and discuss the implications of the instantiation view for theories of metaphor, conceptual combination, and induction.

Adult↗
PubMed2005

Variability in cytologic-histologic correlation practices and implications for patient safety.

CONTEXT: The Clinical Laboratory Improvement Amendments of 1988 require that laboratories perform cytologic-histologic correlation, although the optimal methods and the value of performing correlation have not been determined. OBJECTIVE: To determine the similarities and differences in how laboratories perform cytologic-histologic correlation. DESIGN: One hundred sixty-two American laboratories were sent a letter requesting copies of the materials they used in the cytologic-histologic correlation process. The returned materials were classified into the categories of forms, logs, and tally sheets. A checklist (derived from the College of American Pathologists Laboratory Accreditation Cytopathology Checklist) was developed to classify the "minimum expected" (15) and "additional" data points that laboratories collected when they performed a correlation. PARTICIPANTS: American pathology laboratories. MAIN OUTCOME MEASURES: Measures were percentage of laboratories that recorded minimum expected and additional data points and the frequency with which specific minimum expected data points were recorded. RESULTS: The response frequency was 32.1%, and a total of 84 cytologic-histologic correlation materials were obtained. The only minimum expected variables recorded on forms or logs by more than 50% of laboratories were cytology case number, sign-out cytology diagnosis, surgical pathology case number, and sign-out surgical pathology diagnosis. Nine (17.3%) laboratories did not record data on forms, logs, or tally sheets. The mean number of minimum expected and additional variables recorded on forms was 6.5 and 8.7, respectively. CONCLUSIONS: Laboratories record data from the cytologic-histologic correlation process in a number of ways, indicating the lack of standardization of the data collection process.

Accreditation↗
PubMed2000

Which retinal and extra-retinal information is crucial for circular vection?

In contradistinction to conventional wisdom, we propose that retinal image slip of a visual scene (optokinetic pattern, OP) does not constitute the only crucial input for visually induced percepts of self-motion (vection). Instead, the hypothesis is investigated that there are three input factors: 1) OP retinal image slip, 2) motion of the ocular orbital shadows across the retinae, and 3) smooth pursuit eye movements (efference copy). To test this hypothesis, we visually induced percepts of sinusoidal rotatory self-motion (circular vection, CV) in the absence of vestibular stimulation. Subjects were presented with three concurrent stimuli: a large visual OP, a fixation point to be pursued with the eyes (both projected in superposition on a semi-circular screen), and a dark window frame placed close to the eyes to create artificial visual field boundaries that simulate ocular orbital rim boundary shadows, but which could be moved across the retinae independent from eye movements. In different combinations these stimuli were independently moved or kept stationary. When moved together (horizontally and sinusoidally around the subject's head), they did so in precise temporal synchrony at 0.05 Hz. The results show that the occurrence of CV requires retinal slip of the OP and/or relative motion between the orbital boundary shadows and the OP. On the other hand, CV does not develop when the two retinal slip signals equal each other (no relative motion) and concur with pursuit eye movements (as it is the case, e.g., when we follow with the eyes the motion of a target on a stationary visual scene). The findings were formalized in terms of a simulation model. In the model two signals coding relative motion between OP and head are fused and fed into the mechanism for CV, a visuo-oculomotor one, derived from OP retinal slip and eye movement efference copy, and a purely visual signal of relative motion between the orbital rims (head) and the OP. The latter signal is also used, together with a version of the oculomotor efference copy, for a mechanism that suppresses CV at a later stage of processing in conditions in which the retinal slip signals are self-generated by smooth pursuit eye movements.

Adult↗
PubMed1992

Gene and pseudogene of the mouse cation-dependent mannose 6-phosphate receptor. Genomic organization, expression, and chromosomal localization.

The cation-dependent mannose 6-phosphate receptor (CD-MPR) is one of the two transmembrane proteins involved in transport of lysosomal enzymes. We have cloned the mouse CD-MPR gene and also a very unusual processed-type CD-MPR pseudogene. They are both present at one copy per haploid genome and map to chromosomes 6 and 3, respectively. Comparison of the complete 10-kilobase (kb) sequence of the functional gene with the cDNA indicates that it contains seven exons. Exon 1 encodes the 5'-untranslated region of the mRNA, the others (exons 2-7) encode the luminal, transmembrane, and cytoplasmic domains of the CD-MPR. Exon 7 also contains a 1.2-kb-long 3'-untranslated region of the mRNA. A unique transcription-initiation site was determined by primer extension of mouse liver mRNA. The promoter elements in the 5' upstream region of this site resemble those contained in genes constitutively transcribed. However, Northern blot analysis demonstrates that the CD-MPR is variably expressed in adult mouse tissues and during mouse development. The pseudogene, which is flanked by direct repeats, is almost colinear with the cDNA indicating that it presumably arose by reverse transcription of an mRNA. However, the pseudogene differs from the cDNA. It contains at its 5' end, an additional 340-nucleotide (nt) sequence homologous to the promoter region of the functional gene. This sequence exhibits some promoter activity in vitro. Furthermore, a 24-nt insertion interrupts the region homologous to the 5'-noncoding region of the cDNA. In the functional gene, this 24-nt sequence occurs between exon 1 and 2, where it is flanked by typical consensus sequences of exon/intron boundaries. Therefore, it may represent an additional exon of the functional gene. These two features of the pseudogene suggest that expression of the CD-MPR gene may be regulated by use of different promoters and/or alternative splicing.

Amino Acid Sequence↗
PubMed2004

[Cause for maintaining high instability at the yellow gene in Drosophila melanogaster lines, isolated during the "mode for mutation" period in Uman populations].

Mobile genetic elements are responsible for most spontaneous mutations in Drosophila melenogaster. The discovered in the 1980s phenomenon of frequent change of the wild-type yellow phenotype for a mutant one, and vice-versa, in strains of Drosophila melanogaster isolated from the Uman' natural population can be, according to our data, explained by repeated inversions and reinversions of the gene regulatory region located between the two copies of the hobo transport. However, most molecular genetic events accompanying the process can occur without the phenotype change. After several generations, the strains, remaining phenotypically unchanged, can possess different molecular genetic properties with respect to yellow. Using genetically homogenous or isogenic strains for the genetic analysis or for production of the new plant cultivars or animal breeds, geneticists and breeders often face the problem of stability of the strains. In the present study, the mechanism underlying the generation of instability at the yellow locus of D. melanogaster determined by the hobo-induced genome instability is described.

Animals↗
PubMed1991

[The spontaneous aneuploidy of the embryonic fibroblasts in C3H/He and CBA/Ca mouse strains occurring during their neoplastic evolution].

Karyological analysis of 6 cell lines with distinct tumorigenic properties of mouse strains C3H/He and CBA/Ca has been carried out using differential chromosome staining. All the cell lines are characterized by a decreased number of copies of normal chromosome 7, the increased number of normal copies of chromosome 10 being specific of the cell lines with intermediate tumorigenicity. Cell lines with maximum tumorigenicity differed from all other lines by the increased number of copies of chromosome 5 and by the decreased number of copies of chromosome 6. A wide independent variability was observed in the number of chromosomes and of several types of abnormal chromosomes throughout the neoplastic evolution of cells, to begin from the early immortal passages. But the proportion of normal chromosomes per cell in the studied lines revealed relatively stable values. The potential phenotypical heterogenicity of the lines with maximum tumorigenicity, expressed in their clonal progeny, was associated with the instability in the number of chromosome 15 copies in cells of these lines. It is concluded that multiple genetic events are required in the spontaneous neoplastic evolution of fibroblasts, and only specific traits of the karyotypic instability, associated with the variability of the number of copies of specific chromosomes, may constitute the genetic basis for the above process.

Aneuploidy↗
PubMed1994

A system for analysis of sleep and nocturnal activity in craniomandibular muscles.

A system was developed for continuous, full-night, polysomnographic recording of sleep using manual sleep scoring and automatic electromyographic analysis of craniomandibular muscle activity. In the sleep laboratory, data are stored on tape with hard copy on paper followed by off-line, computer-controlled digital processing. Muscle activity is described by the Amplitude Probability Distribution Function and by parameters of time and intensity. Sleep and electromyographic data are available graphically on screen, and the results are presented in tables and graphics after statistical treatment. The system was developed to provide a differentiated, detailed analysis of sleep and nocturnal muscle activity in the craniomandibular system that is suitable for comparing groups of individuals, effects of treatments, and physical load of muscles. Applications of the system are demonstrated.

Adult↗
PubMed1993

Unmodified pancreatic islet allograft rejection results in the preferential expression of certain T cell activation transcripts.

Polymerase chain reaction-assisted reverse transcription was used to study the temporal course of rejection in unmodified recipients of murine pancreatic islet cell allografts (DBA/2-->B6AF1) by using syngeneic tissues as controls. The histologic appearance of the grafts was analyzed in parallel. Preproinsulin and constant region of the TCR-beta chain transcripts were studied as markers of graft integrity and infiltrating T cell mass, respectively. The participation of certain cytokines and CTL were analyzed by the detection of IL-2, IFN-gamma, IL-4, and CTL-specific serine protease (granzyme B) transcripts. The time-related disappearance of intragraft preproinsulin transcripts correlated with graft destruction, whereas the intensity of intragraft TCR-beta chain transcript levels correlated with the magnitude of mononuclear leukocyte infiltration in allografts. In unmodified allografts, the magnitude of IL-2 and IFN-gamma intragraft mRNA levels correlated with the intense mononuclear leukocyte infiltrate found on histologic examination at day 8. Only after stable IL-2 gene transcription on day 8 does evidence of graft destruction become apparent, indicating that IL-2 gene activation is closely related to and probably required for expression of alloimmune cytopathic processes. In contrast, IL-4 transcripts were absent or detected in low copy number throughout this time course. Intragraft expression of granzyme B mRNA, a CTL-specific transcript, peaked from day 8 to day 12 in allografts compared with syngeneic grafts or normal tissue. In syngeneic grafts IL-2 and/or IL-4 mRNA was essentially not detected. Although IFN-gamma and granzyme B transcripts were detected in syngeneic grafts, after 4 days the levels of detected transcripts were far less than those noted in allografts. In vivo detection of intragraft IL-2 transcripts in the relative absence of detectable IL-4 transcripts strongly suggests IL-2-dependent immune effector mechanisms are associated with, and perhaps responsible, for allograft rejection. Apparently IL-4-dependent effector mechanisms are not necessary for allograft rejection.

Animals↗
PubMed1995

Extraction, preparation, and presentation of patient classification-data for the benefit of management overviews.

In the Free University Hospital, the nursing staff enters data daily into the computerized patient classification system. The computer calculates and gives a retrospective overview of the patient workload per day and per nursing unit. The present system does not comply with the information needs of the middle and higher management. This is due to differences in the manner of working on the various nursing units. For these reasons, the patient classification data was extracted from the central HIS database and copied to a PC environment. Here, the data was further ordered and processed to produce overviews for the nursing management. This was done by developing a user friendly interface with the spreadsheet program QuattroPro.

Data Display↗
PubMed1996

[Dry view laser imager--a new economical photothermal imaging method].

The production of hard copies is currently achieved by means of laser imagers and wet film processing in systems attached either directly in or to the laser imager or in a darkroom. Variations in image quality resulting from a not always optimal wet film development are frequent. A newly developed thermographic film developer for laser films without liquid powdered chemicals, on the other hand, is environmentally preferable and reducing operating costs. The completely dry developing process provides permanent image documentation meeting the quality and safety requirements of RöV and BAK. One of the currently available systems of this type, the DryView Laser Imager is inexpensive and easy to install. The selective connection principle of the DryView Laser Imager can be expanded as required and accepts digital and/or analog interfaces with all imaging systems (CT, MR, DR, US, NM) from the various manufactures.

Cost-Benefit Analysis↗
PubMed1998

Single gene complementation of the hPMS2 defect in HEC-1-A endometrial carcinoma cells.

Results from the analysis of human tumor cell lines with mutations in DNA mismatch repair genes have contributed to the understanding of the functions of these gene products in DNA mismatch repair, microsatellite instability, cell cycle checkpoint control, transcription-coupled nucleotide excision repair, and resistance to cytotoxic agents. However, complementation of human DNA mismatch repair defects by introduction of a single cloned gene or cDNA, which would serve to directly prove or disprove their involvement in these processes, has not been accomplished. Here, we introduce a wild-type copy of the hPMS2 cDNA by stable transfection into the PMS2 mutant HEC-1-A cell line. HEC-1-A cells expressing wild-type hPMS2 exhibit increased microsatellite stability, have a reduced mutation rate at the endogenous hypoxanthine phosphoribosyltransferase locus and extracts from these cells are able to perform strand-specific mismatch repair. These results demonstrate that the hPMS2 gene is integral to the maintenance of genome stability.

Adenosine Triphosphatases↗
PubMed1995

Evaluation of digital mammography in diagnosis of breast cancer.

Mammography has been digitized in all cases at our hospital. Digital mammography (MMG) of our hospital and its diagnostic accuracy were described in this report. Fuji Computed Radiography (FCR; Fuji Medical Systems, Tokyo, Japan) imaging plate was used and imaging data were processed with FCR 7000 or FCR 9000. Each image was output to a single hard copy. Sampling pitches for reading and output were 0.1 mm. The rate of breast cancer diagnosis by digital MMG was 67%, 95%, 94%, and 100% for unpalpable tumor, tumor less than phi 2 cm, tumor of phi 2 to 5 cm, and tumor greater than phi 5 cm, respectively, being 94% overall. Digital MMG enables us to establish goal-oriented image-processing conditions. The use of digital MMG, which provides an excellent diagnostic rate similar to that of screen-film MMG, is expected to became wide-spread in the near future.

Breast Neoplasms↗
PubMed1996

Reversion in Chinese hamster lines amplified at the AMPD2 locus: spontaneous and benzamide-stimulated gradual loss of amplified alleles of marker genes.

The HC47 and HC474 cell lines of Chinese hamster fibroblasts resist coformycin through the intrachromosomal amplification of the AMP deaminase 2 (AMPD2) gene. Due to the coamplification of a mu glutathione S-transferase (GST) gene, these mutant lines are more sensitive than GMA32 wild-type parental cells to buthionine sulfoximine (BSO), an inhibitor of glutathione biosynthesis. This property was exploited to select revertants of amplification from HC474 cells. Reversion in that line is frequently a gradual process that does not involve extrachromosomal intermediates. The terminal products of this process are commonly cells with a complete deletion of the amplified allele of marker genes and are therefore haploid for these loci on the homologous chromosome. Exposing HC474 cells to benzamide (BA), an inhibitor of polyADP-ribosylation, increased the recovery of revertants to an extent allowing the detection of reverting cells without BSO selection. This effect of BA was used to isolate revertant cells from the HC47 line that is extremely stable and to demonstrate that the mechanism of gradual reversion also occurs in this line. The gradual deletion of amplified copies within the chromosomes suggests that breakage-fusion-bridge (BFB) cycles drive this process.

AMP Deaminase↗
PubMed2005

Array comparative genomic hybridization and its applications in cancer.

Alteration in DNA copy number is one of the many ways in which gene expression and function may be modified. Some variations are found among normal individuals, others occur in the course of normal processes in some species and still others participate in causing various disease states. For example, many defects in human development are due to gains and losses of chromosomes and chromosomal segments that occur before or shortly after fertilization, and DNA dosage-alteration changes occurring in somatic cells are frequent contributors to cancer. Detecting these aberrations and interpreting them in the context of broader knowledge facilitates the identification of crucial genes and pathways involved in biological processes and disease. Over the past several years, array comparative genomic hybridization has proven its value for analyzing DNA copy-number variations. Here, we discuss the state of the art of array comparative genomic hybridization and its applications in cancer, emphasizing general concepts rather than specific results.

Gene Dosage↗