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PubMed2001

Computerized ST depression analysis improves prediction of all-cause and cardiovascular mortality: the strong heart study.

BACKGROUND: Nonspecific ST depression assessed by standard visual Minnesota coding (MC) has been demonstrated to predict risk. Although computer analysis has been applied to digital ECGs for MC, the prognostic value of computerized MC and computerized ST depression analyses have not been examined in relation to standard visual MC. METHODS: The predictive value of nonspecific ST depression as determined by visual and computerized MC codes 4.2 or 4.3 was compared with computer-measured ST depression >or= 50 microV in 2,127 American Indian participants in the first Strong Heart Study examination. Computerized MC and ST depression were determined using separate computerized-ECG analysis programs and visual MC was performed by an experienced ECG core laboratory. RESULTS: The prevalence of MC 4.2 or 4.3 by computer was higher than by visual analysis (6.4 vs 4.4%, P < 0.001). After mean follow-up of 3.7 +/- 0.9 years, there were 73 cardiovascular deaths and 227 deaths from all causes. In univariate Cox analyses, visual MC (relative risk [RR] 4.8, 95% confidence interval [CI] 2.6-9.1), computerized MC (RR 6.0, 95% CI 3.5-10.3), and computer-measured ST depression (RR 7.6, 95% CI 4.5-12.9) were all significant predictors of cardiovascular death. In separate multivariate Cox regression analyses that included age, sex, diabetes, HDL and LDL cholesterol, body mass index, systolic and diastolic blood pressure, microalbuminuria, smoking, and the presence of coronary heart disease, computerized MC (RR 3.0, 95% CI 1.6-5.6) and computer-measured ST depression (RR 3.1, 95% CI 1.7-5.7), but not visual MC, remained significant predictors of cardiovascular mortality. When both computerized MC and computer-measured ST depression were entered into the multivariate Cox regression, each variable provided independent risk stratification (RR 2.1, 95% CI 1.0-4.4, and RR 2.1, 95% CI 1.0-4.4, respectively). Similarly, computerized MC and computer-measured ST depression, but not visual MC, were independent predictors of all-cause mortality after controlling for standard risk factors. CONCLUSIONS: Computer analysis of the ECG, using computerized MC and computer-measured ST depression, provides independent and additive risk stratification for cardiovascular and all-cause mortality, and improves risk stratification compared with visual MC. These findings support the use of routine computer analysis of ST depression on the rest ECG for assessment of risk and suggest that computerized MC can replace visual MC for this purpose.

Aged↗
PubMed2003

[Mutation analysis of hMSH2 and hMLH1 genes in Chinese hereditary nonpolyposis colorectal cancer families].

OBJECTIVES: To determine the germ-line mutations of hMSH2 and hMLH1 genes in Chinese hereditary nonpolyposis colorectal cancer (HNPCC) families' probands or in patients fulfilling different clinical criteria or guidelines; to clarify the nature and distribution of the mutations; to evaluate the sensitivity of different clinical criteria in mutation prediction. METHODS: The entire coding regions (35 exons including exon-intron boundaries) of hMSH2 and hMLH1 genes were directly sequenced in 24 Amsterdam criteria (AC) probands, 15 Japanese criteria (JC) probands (except AC kindreds) and 19 Bethesda guidelines (BG) patients (except two former groups). All available affected and unaffected members from families of those with mutations were screened for mutation. RESULTS: In 16 unrelated families selected by the different clinical criteria, 17 germ-line mutations were found with 11 (64.7%) of hMLH1 and 6 (35.3%) of hMSH2. Two mutations were identified in one of the families. Among the 17 germ-line mutations, 12 had not been reported previously. A diversified mutation spectrum was found, but 6 hMLH1 mutations were found to be concentrated in the region encompassing exon 14, 15 and 16. There was a wide spectrum of mutation type including frame shift, nonsense, splice site mutation, in frame insertion or deletion and missense mutations. The mutation detection rate of hMSH2 and hMLH1 in the AC group was significantly higher than that in the JC group (12/24 vs. 3/15). On the other hand, a low mutation rate (1/19) was detected in 19 BG patients. The mutation cosegregated with disease. Besides, three different genotypes in tumors from probands of mutation-positive families were found. CONCLUSIONS: hMSH2 and hMLH1 mutations in Chinese HNPCC families show a wide spectrum. It seems that hMLH1 gene is involved more frequently than hMSH2 gene in Chinese HNPCC families. Different clinical criteria predict mutations with different sensitivities. The Amsterdam Criteria are most sensitive, while Japanese Criteria are highly practical and the Bethesda Guidelines are also practical to some extent. Gene mutations cosegregate with the disease phenotype. Carriers with no symptom in HNPCC families are most vulnerable groups, follow-ups are required for this group to get early diagnosis and to prevent the development of CRCs.

Adaptor Proteins, Signal Transducing↗
PubMed1992

Comoviruses and enteroviruses share a T cell epitope.

An in vitro murine T cell proliferation assay was used to determine whether an antigenic epitope(s) recognized by enterovirus-immune T cells is held in common between plant comoviruses and human enteroviruses. Splenocytes isolated from C3H/HeJ mice infected with coxsackievirus B3 (CVB3) proliferated in vitro not only against a variety of enterovirus (CVB2, CVB3, CVB6, CVA16, PV1) antigens, but against comovirus (CPMV, BPMV) antigens as well. Splenocytes from mice inoculated with bean pod mottle virus (BPMV) also proliferated in response to comoviral and enteroviral antigens in vitro. However, if the viral inocula were highly purified prior to inoculation, then the splenocyte response was generated only against the group used to inoculate, suggesting that the epitope shared between the comoviruses and the enteroviruses resided in the nonstructural region. B (nonstructural) and M (structural) genomic segments of CPMV were translated in rabbit reticulocyte lysates and used as in vitro antigens. Splenocytes from mice inoculated with live CVB3 proliferated in response to the B-RNA-encoded but not the M-RNA-encoded polypeptides, confirming the nonstructural coding region location of the common epitope. Comparison of predicted amino acid sequences in the nonstructural coding regions of the comoviruses and picornaviruses suggested a potentially immunogenic linear epitope in protein 2C. The consensus peptide LEEKGI was synthezized and shown to be immunogenic for both BPMV- and CVB3-immune splenocytes.

Amino Acid Sequence↗
PubMed2005

Validity of hospital discharge data for identifying infants with cardiac defects.

OBJECTIVE: To examine validity of the International Classification of Diseases, 9th Edition, Clinical Modification (ICD-9-CM) codes in discharge data for identifying infants with cardiac defects according to surveillance guidelines. STUDY DESIGN: Retrospective medical record review of infants born in 2001 at one hospital in Minneapolis, Minnesota. Infants were identified using ICD-9-CM codes from hospital discharge data, and keywords in medical records. RESULTS: Of 2,697 children, ICD-9-CM codes identified 66 infants coded with cardiac defects; physician review confirmed 24 had cardiac defects. Only 35 of 85 (41.2%) ICD-9-CM codes accurately reflected the cardiac defect diagnoses. Additional case finding located four infants with five cardiac defects. Sensitivity of ICD-9-CM codes for identifying these infants was 0.857, predictive value positive was 0.364. CONCLUSIONS: ICD-9-CM codes from hospital discharge data identified most infants with cardiac defects, but many were false positives. ICD-9-CM codes were inaccurate for specific cardiac defects.

Birth Certificates↗
PubMed1996

Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae.

The entire genome of the bacterium Mycoplasma pneumoniae M129 has been sequenced. It has a size of 816,394 base pairs with an average G+C content of 40.0 mol%. We predict 677 open reading frames (ORFs) and 39 genes coding for various RNA species. Of the predicted ORFs, 75.9% showed significant similarity to genes/proteins of other organisms while only 9.9% did not reveal any significant similarity to gene sequences in databases. This permitted us tentatively to assign a functional classification to a large number of ORFs and to deduce the biochemical and physiological properties of this bacterium. The reduction of the genome size of M. pneumoniae during its reductive evolution from ancestral bacteria can be explained by the loss of complete anabolic (e.g. no amino acid synthesis) and metabolic pathways. Therefore, M. pneumoniae depends in nature on an obligate parasitic lifestyle which requires the provision of exogenous essential metabolites. All the major classes of cellular processes and metabolic pathways are briefly described. For a number of activities/functions present in M. pneumoniae according to experimental evidence, the corresponding genes could not be identified by similarity search. For instance we failed to identify genes/proteins involved in motility, chemotaxis and management of oxidative stress.

Base Sequence↗
PubMed1996

Cloning and expression of the canine interferon-beta gene.

We isolated the canine interferon-beta (IFN-beta) gene from dog liver chromosomal DNA by the polymerase chain reaction (PCR). The coding region encodes a predicted protein of 197 amino acids, consisting of a signal sequence of 32 amino acids and a mature IFN-beta of 165 amino acids. In the IFN-beta sequence, there are five potential N-glycosylation sites and four cysteine residues. Canine IFN-beta has 44% and 60% amino acid sequence homology with murine and human IFN-beta, respectively, whereas it has only 28% homology with canine IFN-alpha. The canine IFN-beta gene was expressed in insect cells under the control of the polyhedrin promoter in a recombinant baculovirus. After infecting Sf21 cells with the recombinant baculovirus, IFN activity was detected in the culture medium, indicating that it is secreted from the cells. This activity was stable from pH 2 to 12 for 18 h at 4 degrees C. Southern blot analysis indicated that the gene for canine IFN-beta is a single gene in the dog haploid chromosome.

Amino Acid Sequence↗
PubMed1994

Expression, functional analysis, and in situ hybridization of a cloned rat kidney collecting duct water channel.

The cloning and expression of an apical membrane water channel from rat kidney collecting duct (WCH-CD) homologous to a 28-kDa integral membrane protein (CHIP28) was reported recently (K. Fushimi, S. Uchida, Y. Hara, Y. Hirata, F. Marumo, and S. Sasaki. Nature Lond. 361: 549-552, 1993). We obtained an approximately 1.8-kilobase clone from a rat kidney lambda gt10 cDNA library by a polymerase chain reaction cloning method; whereas the coding sequence (814 base pairs, predicted protein size 29 kDa) was identical to that reported, we identified an in-frame ATG codon at base pair -123 predicting a protein size of 33 kDa. On Northern blots probed by cDNAs corresponding to the WCH-CD coding sequence (base pairs +1 to +814) or 5'-untranslated sequence (-403 to -16), a single band at 1.9 kilobases was observed in kidney medulla greater than in cortex but not in other tissues; mRNA expression was increased strongly by dehydration. Translation and oocyte expression studies were performed to identify the translation start site. The short (base pairs +1 to +814) and long (base pairs -123 to +814) cDNAs were subcloned in vector pSP64 containing the 5'-untranslated Xenopus globin sequence upstream to the ATGs; a 30-base pair c-myc sequence was engineered at the COOH- terminal for antibody recognition.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1995

Characterization of placenta accreta using transvaginal sonography and color Doppler imaging.

The safe use of transvaginal sonography in patients with placenta previa has been confirmed, and has revolutionized precise placental localization. The aim of our study was to evaluate the efficacy of transvaginal sonography and color-coded blood flow in the prediction of placenta accreta. Twenty-one patients with persistent placenta previa were scanned using transvaginal sonography and color-coded flow. Suspicion for placenta accreta consisted of total placenta previa at term with several placental lacunae exhibiting marked or turbulent blood flow, as seen with color Doppler transvaginal sonography from within the placenta, extending into the surrounding tissues. Five of the patients exhibited sonographic placental patterns suspicious for placenta accreta and one patient exhibited placental and cervical blood flow described as lacunar. Five Cesarean hysterectomies were performed for placenta accreta. Every placenta accreta was correctly diagnosed sonographically by the use of color flow studies. One patient with suspicion of placenta accreta delivered at another institution, a Cesarean hysterectomy was performed, and the pathology was confirmed. The one placenta previa exhibiting turbulent lacunar flow in the cervical area only was not confirmed to be an accreta at Cesarean section, although hemostasis was difficult at the placental bed. The remaining 15 patients with placenta previa and who on sonography were not suspicious for placenta accreta underwent uncomplicated Cesarean section. Transvaginal sonography and color Doppler imaging improve the diagnostic accuracy in the prediction of placenta accreta in patients with persistent placenta previa. A pattern of turbulent blood flow extending from the placenta into the surrounding tissues should alert the physician to the possibility of placenta accreta.

Blood Flow Velocity↗
PubMed2003

Computer software to find genes in plant genomic DNA.

Gene finding is the most important phase of genome annotation. Eukaryotic genomes contain thousands of protein coding genes, and computational gene prediction would rapidly increase the pace of experimental confirmation of expressed genes at the bench. The purpose of this chapter is to discuss the use of different computer programs that identify protein-coding genes in large genomic sequences. We describe most commonly used gene prediction programs that are available on the World Wide Web and demonstrate the use of some of these programs by an example. We provide a list of these programs along with their. Web uniform resource locators (URLs) and suggest guidelines for successful gene finding.

Arabidopsis↗
PubMed2001

Rice genomics: current status of genome sequencing.

Since its establishment in 1991, the Rice Genome Research Program (RGP) has produced some basic tools for rice genome analysis, including a cDNA catalogue, a genetic linkage map and a yeast artificial chromosome (YAC)-based physical map. For the further development of rice genomics, RGP launched in 1998 an international collaborative project on rice genome sequencing. A P1-derived artificial chromosome (PAC)-based, sequence-ready physical map has been constructed using the PCR markers from cDNA sequences (expressed sequence tag [EST] markers). Selected PAC clones with 100-150 kb inserts from chromosomes 1 and 6 have been subjected to shotgun sequencing. The assembled genomic sequences, after predicting the gene-coding region, have been published both through a public database and through our website. As of January 2000, 1.9 Mb from 13 PAC clones were published. Future prospects for understanding rice genomic information at the nucleotide level are discussed.

DNA, Plant↗
PubMed1991

Variant cDNAs encoding proteins similar to the alpha subunit of chicken CapZ.

Chicken adult muscle and liver cDNA libraries were screened with a cDNA, alpha 1, previously isolated from a chicken embryo library by screening with antibodies against the alpha subunit of chicken CapZ. cDNAs with a new coding region, called alpha 2, were found in addition to ones with the alpha 1 coding region. alpha 2 predicts a protein sequence that matches exactly the N-terminal sequence of 5 peptides prepared from CapZ alpha purified from chicken muscle, while the protein sequence predicted by alpha 1 matches the peptides well, but not exactly. The predicted protein sequences of alpha 1 and alpha 2 are very similar to each other, and they are similar to those of the alpha subunit of capping protein from Dictyostelium [Hartmann et al., J. Biol. Chem. 163:5254-5254, 1989] and an actin-binding protein from Xenopus [Ankenbauer et al., Nature 342:822-824, 1989]. Other conserved features of the predicted primary and secondary structures are noted. Chicken alpha 1 and alpha 2 are transcribed in all of 7 adult chicken muscle and non-muscle tissues in comparable amounts by Northern analysis. alpha 2 has four poly(A)+RNA transcripts, one of which is rare in liver. alpha 1 has two transcripts. alpha 1 and alpha 2 are encoded by different single-copy genes by Southern analysis of chicken genomic DNA.

Actin Depolymerizing Factors↗
PubMed2003

Dlx1, Dlx2, Pax6, Brn3b, and Chx10 homeobox gene expression defines the retinal ganglion and inner nuclear layers of the developing and adult mouse retina.

Distal-less homeobox genes are expressed in the developing forebrain. We assessed Dlx gene expression in the developing and adult mouse retina. Dlx1 and Dlx2 are detected in retinal neuroprogenitors by embryonic day (E) 12.5 (Eisenstat et al. [1999] J. Comp. Neurol. 217-237). At E13.5, the expression of four homeodomain proteins, DLX2, BRN3b, PAX6, and CHX10, define distinct yet overlapping domains in the retinal neuroepithelium. By postnatal day (P) 0, DLX2 is expressed in the neuroblastic layer and the ganglion cell layer (GCL) consisting of ganglion and displaced amacrine cells. DLX1 expression resembles DLX2 to P0 but decreases postnatally. In the adult, DLX2 is localized to ganglion, amacrine, and horizontal cells as determined by coexpression with retinal cell-specific markers. There is coincident expression of DLX2 with gamma-aminobutyric acid (GABA), glutamic acid decarboxylase (GAD)65, and GAD67 in the inner nuclear layer (INL) and GCL. In the adult, DLX2 is coexpressed with BRN3b in ganglion cells; PAX6 in amacrine, horizontal, and ganglion cells; and Chx10 in some bipolar cells. We predict that a combinatorial code of these homeobox genes and others specify retinal cell fate. Our results support a possible role for Dlx1 and Dlx2 in inner retinal development and in the terminal differentiation and/or maintenance of INL interneurons and ganglion cells in the adult. The correlation of DLX2 with GABA expression in the mouse retina closely mirrors the relationship of DLX2 to GABAergic neuronal differentiation in the embryonic forebrain, including neocortex, olfactory bulb and hippocampus, signifying a conservation of function of Dlx genes in the developing central nervous system.

Amacrine Cells↗
PubMed2004

A new complex rearrangement involving the ETV6, LOC115548, and MN1 genes in a case of acute myeloid leukemia.

A new complex rearrangement involving chromosome bands 5q13, 12p13, 22q11, and 3q12 was identified and characterized in a patient with acute myeloid leukemia. Fluorescence in situ hybridization showed the involvement of the ETV6 gene in 12p13. ETV6 primers were specifically designed for 3'- and 5'-RACE-PCR experiments, which led to the identification of the other two rearranged genes. The derivative chromosome 5 harbored a fusion of the ETV6 sequence with that of the LOC115548 gene. The two genes were placed in opposite orientation and did not encode a fusion protein. On the derivative chromosome 12, ETV6 was fused to the MN1 gene on chromosome 22. Also in this case, the insertion, within the MN1 sequence, of a portion of chromosome 3 prevented the formation of a fusion protein. Finally, the derivative chromosome 22 contained the 3' portions of both LOC115548 and MN1, and no fusion transcript with coding potential could be predicted. In conclusion, all chromosome breakpoints led to the truncation of the three involved genes in the absence of predicted fusion proteins. This study lends further support to the hypothesis that gene disruption resulting in either loss of function or haploinsufficiency may be relevant in acute myeloid leukemia pathogenesis.

Adolescent↗
PubMed1992

Isolation of cDNA clones encoding rat glial fibrillary acidic protein: expression in astrocytes and in Schwann cells.

Glial fibrillary acidic protein (GFAP) expressed by astrocytes in the central nervous system (CNS) has been extensively characterized but the molecular identity of related molecules in the peripheral nervous system (PNS) remains unclear. To examine possible structural differences between CNS and PNS GFAP, we have isolated cDNA clones for rat GFAP from both cultured astrocyte and Schwann cell libraries. Nucleotide sequence analysis indicated that the PNS and CNS GFAP clones contained identical coding regions, with a predicted protein product of 430 amino acids. However, the 5'-untranslated region of clone rGFA15, isolated from the Schwann cell library, was longer than that predicted for brain-derived GFAP mRNA. Primer extension analysis of RNA isolated from the RT4-D6 Schwann cell line indicated that the start site for PNS GFAP mRNA lies 169 bases upstream from that used in the CNS. In addition, tryptic peptide mapping of GFAP prepared from cultured astrocytes and Schwann cells revealed one major peptide fragment present in CNS GFAP but absent from PNS GFAP. These results suggest structural differences between GFAP in these two cell types, at both the nucleic acid and protein level, and are consistent with previous observations of immunochemical differences existing between CNS and PNS GFAP.

Amino Acid Sequence↗
PubMed1994

Cloning and characterization of a sulphite-resistance gene of Saccharomyces cerevisiae.

In this paper we describe the cloning and sequencing of the gene (SUL1) responsible for sulphite resistance in a Saccharomyces cerevisiae mutant (Casalone et al., 1992). The deduced amino acid sequence predicted that the gene codes for a zinc-finger protein with five fingers. Comparison of wild-type and mutant gene sequences demonstrated that the mutation event was a transversion from C to G; as a consequence of the mutation a histidine substituted an aspartic acid, affecting directly the fourth finger structure. The SUL1 gene sequence corresponds to that of FZF1 gene (Breitwieser et al., 1993) to which no function was attributed.

Amino Acid Sequence↗
PubMed1997

Human XPMC2H: cDNA cloning, mapping to 9q34, genomic structure, and evaluation as TSC1.

XPMC2 is a Xenopus gene identified on the basis of its ability to correct a mitotic defect in fission yeast. Here we report the identification of cDNA clones for human XPMC2H, its mapping to the tuberous sclerosis gene TSC1 region on 9q34, determination of genomic structure, and identification of several coding region polymorphisms. The predicted protein has strong sequence similarity to the Xenopus gene. Through SSCP and heteroduplex analysis of genomic DNA, we found two intragenic polymorphisms but no evidence for significant mutations in patients with tuberous sclerosis in this gene.

Chromosome Mapping↗
PubMed1998

Identification of novel genes encoding transcription elongation factor TFIIS (TCEA) in vertebrates: conservation of three distinct TFIIS isoforms in frog, mouse, and human.

We report the characterization of cDNA clones that define a new, third isoform of the transcription elongation factor TFIIS in Xenopus, mouse, and human. In Xenopus the mRNA of this isoform, termed TFIIS.h, shows tissue-restricted expression, frequently contains unspliced introns, and is characterized by three near-perfect 150-bp repeats at the 5'-terminus. Although we were unable to isolate full-length cDNAs, it is clear that these repeats contain an open reading frame encoding a region of TFIIS.h that is much more complex than in other isoforms. Identification of ESTs encoding TFIIS.h in mouse and human followed by the sequencing of cognate cDNA clones enabled the complete TFIIS.h coding region to be predicted. The conserved N- and C-terminal domains of mammalian TFIIS.h (TCEA3) are separated by a linker region that is more variable in sequence and that is also 50 amino acids longer than in other isoforms. The repetitive region of Xenopus TFIIS.h apparently corresponds to an even more extended linker. Phylogenetic analysis of TFIIS sequences demonstrates the ancient origins of the three vertebrate isoforms, although they appeared functionally equivalent in in vitro RNA cleavage assays.

Amino Acid Sequence↗
PubMed1996

Cloning of candidate autoantigen carboxypeptidase H from a human islet library: sequence identity with human brain CPH.

A number of proteins, many of them enzymes, i.e. glutamic acid decarboxylase (GAD), carboxypeptidase H, 37-40 K tyrosine phosphatase (ICA512, IA2/IA2 beta), have been proposed as islet autoantigens involved in the pathogenesis of IDDM. Until recently, progress in their characterization has been impeded by the inaccessibility of the human pancreas, resulting in many of them being cloned from animal or non-islet sources. Carboxypeptidase H, one of these enzymes, has been cloned and sequenced from human brain and from rat islets but not from human islets. In this study, we describe the production of a human islet cDNA library and the cloning of islet CPH from it. Since CPH clones were also detected in a human thyroid library, we have sequenced CPH from these two endocrine tissue libraries and compared them to the known brain sequence. The sequences from islets and thyroid were identical and differed from brain only in the absence of a second ATG in the predicted 5'non-coding region. Northern blot analysis revealed the presence of an identical 2.5 kb transcript in human islets, thyroid and brain. The confirmation of the existence of a single isoform of CPH expressed in brain and endocrine tissues simplifies future experiments to elucidate the role of CPH as autoantigen.

Animals↗