Analysis of the nucleotide sequence of chromosome VI from Saccharomyces cerevisiae.

The complete nucleotide sequence of Saccharomyces cerevisiae chromosome VI (270 kb) has revealed that it contains 129 predicted or known genes (300 bp or longer). Thirty-seven (28%) of which have been identified previously. Among the 92 novel genes, 39 are highly homologous to previously identified genes. Local sequence motifs were compared to active ARS regions and inactive loci with perfect ARS core sequences to examine the relationship between these motifs and ARS activity. Additional ARS sequences were predominantly observed in 3' flanking sequences of active ARS loci.

Identification of the coding region of Saccharomyces cerevisiae chromosome VI using the computer program GenMark.

We searched the nucleotide sequence of budding yeast Saccharomyces cerevisiae chromosome VI (270 kb) for candidate coding regions, using the computer program GenMark. One hundred and twenty-nine putative genes were identified, which is almost the same as the number of ORFs on this chromosome. Nineteen new putative genes were identified through the GenMark analysis. Most large ORFs were also correctly identified (87% of the predicted putative genes identified by the GenMark (110 of 127) matched the reported ORFs). The new coding regions were mostly small but they were distinguished from the more than 2000 ORFs identified by Genetyx. GenMark did not predict 17 ORFs that were over 300 bp long. As these ORFs include known genes, their sequence context may differ somewhat from that of typical yeast genes. These analyses revealed the high potential of GenMark to identify putative genes from numerous short ORFs and will produce information on the likelihood of their being actual genes.

Cloning and characterization of novel gene, DCRR1, expressed from Down's syndrome critical region of human chromosome 21q22.2.

The new gene, DCRR1, from the proximal part of the Down's syndrome critical region (DCR) was identified by the GRAIL analysis of the 97-kb nucleotide sequence of two P1 DNAs and the cDNA for DCRR1 gene was cloned. A 7.36-kb cDNA encodes the imcompleted open reading frame composed of 1941 amino acid residues (220.2 kDa). The deduced amino acid sequence contains the conserved domain for protein phosphatases at the N-terminus. The domain encoding the rod-like tail of a myosin heavy chain was also found near the C-terminal region besides the signature for an actin binding protein, profilin, suggesting its possible role as a microtuble-associated protein. Two different sizes (7.9 and 9.0 kb) of mRNAs were detected in the poly(A)+ RNA from abundant tissues by the Northern analysis. The smaller transcript was only transcribed at a high level in the testis. The imbalance of the DCRR1 gene dosage may contibute to the pathogenesis of Down's syndrome.

[How to determine the prophylactic effect on postoperative infections].

With the cooperation of 13 medical institutions in the Tokyo area, the methods to determine the prophylactic effect on postoperative infections in gynecological surgery were evaluated. Two hundred and ninety-nine patients were enrolled for the study of postoperative infections, febrile morbidity and fever index following abdominal (275) and vaginal (24) hysterectomies. Prophylactic cefotiam (CTM) of 1 gram was intravenously administered twice a day postoperatively for 3 to 5 days. The rates of postoperative infections were 5.1% (14/275) in abdominal hysterectomy and 4.2% (1/24) in vaginal hysterectomy. The febrile morbidity (57.1% = 8/14) and fever index (52.3 +/- 41.1 degree hours) in the infection group were approximately about 4 times higher than those (12.3% = 32/261, and 15.6 +/- 13.7 degree hours, respectively) in the non-infection group. No significant differences were observed in age, body weight, height of patients, period of operation and blood loss between these 2 groups. These data suggested that febrile morbidity and fever index were able to indicate the prophylactic effect of antibiotics on patients undergoing abdominal and vaginal hysterectomies.

[Relapse of acute monocytic leukemia present with skin and tracheal involvement].

A 34 year-old female was admitted because of anemia and leukopenia. Her bone marrow contained abundant blastic cells, which were histochemically positive for peroxidase and alpha-naphthyl butyrate esterase, but negative for ASD chloroacetate esterase. She was diagnosed as acute monocytic leukemia (FAB, M5a). Complete remission was achieved after the administration of BHAC, daunorubicin, 6MP and prednisolone, and she was discharged after consolidation therapies. But shortly later, she noticed hoarseness and erythematous nodules on her breast and abdomen. Though the examinations of peripheral blood and bone marrow did not show any abnormality, hoarseness rapidly worsened and she complained of dyspnea. X-ray and CT scan demonstrated narrowing of the trachea under the cricoid cartilage, and trans-tracheal biopsy revealed leukemic involvement. In addition, erythematous skin lesion showed the infiltration of leukemic cells by biopsy. Although radiation and chemotherapy was initiated, she died of pneumonia. We tried to discuss the laryngo-tracheal and skin involvement of acute monocytic leukemia as early symptoms of relapse.

Detection of Mycoplasma fermentans DNA from lymph nodes of acquired immunodeficiency syndrome patients.

Biopsy samples from seven patients with acquired immunodeficiency syndrome were screened for Mycoplasma fermentans, M. pneumoniae and M. genitalium infection by the polymerase chain reaction. M. fermentans DNA was detected in four patients. Various tissues were evaluated and the mycoplasma were mainly detected from lymph nodes. Moreover, mycoplasma genus-specific DNA was isolated from peripheral blood mononuclear cells of asymptomatic human immunodeficiency virus(HIV)-infected individuals (two of 31 HIV-infected individuals). These data suggest that mycoplasma infection in AIDS patients is not uncommon.

Expression profiles of transcripts from 126 open reading frames in the entire chromosome VI of Saccharomyces cerevisiae by systematic northern analyses.

Chromosome VI of Saccharomyces cerevisiae contains 126 open reading frames (ORFs), and the functions of proteins encoded by 80 ORFs are still unknown. In this report, we have systematically examined the expression profiles of all 126 ORFs on chromosome VI under five kinds of growth conditions by quantitative Northern hybridization. A series of Northern analyses and reverse transcription polymerase chain reactions have revealed that more than 64 novel ORFs are transcribed. Two ORFs (YFL059w and YFR011c) are specifically expressed in the presence of galactose. Two ORFs (YFL012w and YFR032c) are specifically transcribed in sporulation. Six ORFs (YFL049w, YFL035c, YFL010c, YFR006w, YFR010w and YFR017c) are abundantly expressed in many growth conditions.

Sequencing of an 18.8 kb fragment from Saccharomyces cerevisiae chromosome VI.

The nucleotide sequence of lambda phage clone 4121, which contains the 18.8 kb fragment of Saccharomyces cerevisiae chromosome VI left arm, was determined. This sequence had seven open reading frames (ORFs), four of which were identical to known genes (ACT1, YPT1, TUB2 and RPO41). Another three ORFs (4121orfR003, 4121orfR004 and 4121orfRN001) were highly homologous to FET3 multi-copper oxidase, glucose transport protein, and hypothetical protein of YIL106w on chromosome IX, respectively. 4121orfRN01 is suggested to contain an intron.

Analysis of a 36.2 kb DNA sequence including the right telomere of chromosome VI from Saccharomyces cerevisiae.

The nucleotide sequence of a 36.2-kb distal region containing the right telomere of chromosome VI was determined. Both strands of DNA cloned into cosmid clone 9965 and plasmid clone pEL174P2 were sequenced with an average redundancy of 7.9 per base pair, by both dye primer and dye terminator cycle sequencing methods. The G+C content of the sequence was found to be 37.9%. Eighteen open reading frames (ORFs) longer than 100 amino acids were detected. Four of these ORFs (9965orfR017, 9965orfF016, 9965orfR009 and 9965orfF003) were found to encode previously identified genes (YMR31, PRE4, NIN1 and HXK1, respectively). Six ORFs (9965orfR013, 9965orfF018, 9965orfF006, 9965orfR014, 9965orfF013 and 9965orfR020) were found to be homologous to hypothetical 121.4-kDa protein in the BCK 5' region, Bacillus subtilis DnaJ protein, hypothetical Trp-Asp repeats containing protein in DBP3-MRPL27, putative mitochondrial carrier YBR291C protein, Salmonella typhimurium nicotinate-nucleotide pyrophosphorylase, and Escherichia coli cystathionine beta-lyase, respectively. The putative proteins encoded by 9965orfF018, 9965orfR014 and 9965orfR020 were found to be, respectively, a new member of the family of DnaJ-like proteins, the mitochondrial carrier protein and cystathionine lyase.

Fifteen open reading frames in a 30.8 kb region of the right arm of chromosome VI from Saccharomyces cerevisiae.

The nucleotide sequence of cosmid clone 9765, which contains 30.8 kb of the right arm of chromosome VI, was determined. Both strands were sequenced, with an average redundancy of 8.17 per base pair by both dye primer and dye terminator cycle sequencing methods. The G+C content of the sequence was found to be 40.3%. Fifteen open reading frames (ORFs) greater than 100 amino acids and one tRNA-Tyr gene (SUP6) were detected. Seven of the ORFs were found to encode previously identified genes (HIS2, CDC14, MET10, SMC2, QCR6, PH04 and CDC26). One ORF, 9765orfF010, was found to encode a new member of the Snf2/Rad54 helicase family. Three ORFs (9765orfR002, 9765orfR011 and 9765orfR013) were found to be homologous with Schizosaccharomyces pombe polyadenylate binding protein, Escherichia coli hypothetical 38.1-kDa protein in the BCR 5' region, and transcription regulatory protein Swi3, respectively.

Sequencing of a 23 kb fragment from Saccharomyces cerevisiae chromosome VI.

Plasmid clone gapB and lambda phage clone 4682, which contain fragments of Saccharomyces cerevisiae chromosome VI, were analysed. A 23 kb sequence was determined and ten open reading frames (ORFs) were revealed. Among them, five ORFs were identical to five yeast genes (SEC4, MSH4, SPB4, DEG1 and NIC96), two were identical to transposable elements (TYA and TYB), one (gapBorfF003) was highly homologous to a yeast expressed sequence tag, and another (4682orfF002) was predicted to be a nuclear protein. Sequence data have been submitted to DDBJ/EMBL/GenBank data library under Accession Number D44604 (clone gapB) and D44600 (clone 4682), respectively.