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PubMed1990

Simultaneous manipulation of propositional and analog codes in picture memory.

Revealing a picture as a whole or as momentarily displayed strips presumably manipulated the propositional coding of the picture. Analog manipulation employed superimposition of a grid pattern. Effectiveness of simultaneous manipulations was tested via recognition with three foil categories, each of which presumably tapped the analog or propositional codes mainly, or both of them in detection. While figural units' perspective reversals should presumably be detected via the analog code, their locational displacements should be detected via the propositional code. Foils with novel item substitution should be detected by both codes. On the basis of such presumptions about encoding and recognition manipulations, certain predictions were made for scan and grid effects in "reversal," "displacement," and "novelty" foil categories. Full confirmation of these predictions was then taken as evidence that both analog and propositional codes do exist. Once such evidence was established, other issues were tackled, showing that target detection involves the propositional code only, while foil detection involves both codes. Further, recognition hypermnesia, where performance improves with repeated testing, was obtained only when both codes were attenuated. Data suggested that subjects might be switching from analog to propositional codes when both codes were strong, thereby preventing hypermnesia.

Adult↗
PubMed2001

Complete scanning of the hereditary hemochromatosis gene (HFE) by use of denaturing HPLC.

BACKGROUND: Between 4% and 35% of hereditary hemochromatosis (HC) probands are C282Y or H63D heterozygotes or lack both of these two common HFE mutations, and 15 novel HFE mutations have been described recently. We evaluated denaturing HPLC (DHPLC) for screening of the whole HFE coding region and further defined whether HC probands with an incomplete HFE genotype carry uncommon mutations. METHODS: Analytical conditions for each coding exon were determined by a combination of computer melting profile predictions and experimental melting curves. To test accuracy for scanning the complete HFE coding region and optimize DHPLC running conditions, each melting domain was investigated with at least one mutation or one polymorphism as reference. We tested 100 DNA samples harboring the C282Y, H63D, or S65C mutations and 17 artificially created positive controls that carried either 1 of the 14 other known HFE mutations or 3 selected polymorphisms. RESULTS: Investigations on each of the coding exons 1, 2, 4, 5, and 6 could be performed at one analysis temperature. Coding exon 3 displayed a more complex melting profile and required two analysis temperatures. DHPLC detected all known HFE mutations as well as the three selected polymorphisms. CONCLUSIONS: DHPLC can be used to scan the HFE gene in HC probands in whom at least one chromosome lacks an assigned mutation.

Chromatography, High Pressure Liquid↗
PubMed2004

Accuracy of Medicare claims-based diagnosis of acute myocardial infarction: estimating positive predictive value on the basis of review of hospital records.

BACKGROUND: Many cardiovascular epidemiologic studies rely on diagnosis codes in health care claims databases. Despite important changes in the care and diagnosis of acute myocardial infarction (AMI), the validity of hospital discharge diagnosis codes for AMI in the US Medicare system has not been recently examined. Our objective was to examine the accuracy of International Classification of Diseases--ninth revision--Clinical Modifications (ICD-9-CM) discharge diagnosis codes and diagnosis-related groups (DRG) codes for AMI in a Medicare claims database. METHODS: We sampled hospitalization episodes from Medicare beneficiaries in Pennsylvania during 1999, 2000, or both. We used Medicare data to identify patients with hospitalizations containing indicators of AMI (ICD-9-CM diagnosis codes 410.X0 and 410.X1 or DRG codes 121, 122, and 123). Hospital records for these episodes were reviewed by trained abstractors using World Health Organization criteria for diagnosing AMI. We then calculated the positive predictive value of Medicare claims-based definitions of AMI. RESULTS: Of 2200 hospitalization episodes with Medicare diagnosis codes suggestive of AMI, 2022 hospital records (91.9%) were obtained. The positive predictive value for a primary Medicare claims-based definition was 94.1% (95% CI, 93.0%-95.2%). Positive predictive values for alternative claims-based definitions ranged slightly, with the definition including DRG codes and length-of-stay restrictions yielding the highest positive predictive value, 95.4% (95% CI, 94.3%-96.4%). Subjects with a history of myocardial infarction had a significantly lower positive predictive value than subjects without a history of myocardial infarction (88.1% vs 94.6%, P <.001). CONCLUSIONS: In this study, we observed high positive predictive values for a Medicare claims-based diagnosis of AMI and a diagnosis based on structured hospital record review.

Aged↗
PubMed1999

Directional coding of three-dimensional movements by the vestibular semicircular canals.

A morphologically descriptive mathematical model was developed to study the role of labyrinthine geometry in determining sensitivities of each semicircular canal to angular motion stimuli in three-dimensional (3D) space. For this, equations describing viscous flow of the endolymph and poro-elastic response of the cupulae were coupled together and solved within a 3D reconstructed geometry. Results predict the existence of prime rotational directions about which the labyrinth resolves 3D angular movements into separate vectorial components. The components are predicted to be transmitted to the brain separately, one coded by each canal nerve. Prime directions predicted by the model are non-orthogonal, distinct from the anatomical canal planes, and distinct from the directions of rotation which elicit maximal responses of individual canal nerves. They occur for each canal along the intersection of the two null planes defined by its sister canals. Hence, rotation about a prime direction excites only one canal nerve. This contrasts the situation for rotations about anatomical canal planes, or about maximal response directions, where the model predicts activation of multiple canal nerves. The prime directions are sensitive to labyrinthine morphology and, hence, are predicted to vary between species and, to a lesser extent, vary between individual animals. Prime directions were estimated in the present work using a mathematical model, but could be determined experimentally based on the directional sensitivities of individual canal nerves. The model also predicts the existence of dominant eigenmodes and time constants associated with rotation in each of the prime directions. Results may have implications regarding the central representation of angular head movements in space as well as the neuronal mappings between three-canal afferent inputs and motor outputs.

Head Movements↗
PubMed2003

Clinical and molecular analysis of Grebe acromesomelic dysplasia in an Omani family.

Grebe syndrome is a rare autosomal recessive acromesomelic dysplasia. The syndrome was studied clinically, radiographically, and genetically in an Omani family with four affected children. The affected persons had normal axial skeletons, severely shortened, and deformed limbs with severity increasing in a proximo-distal gradient, and subluxated joints. The humeri and femora were hypoplastic with distal malformations. The radii/ulnae were shortened and deformed whereas carpal bones were invariably rudimentary or absent. The tibiae appeared rudimentary; fibulae were absent in two children, and some tarsal and metatarsal bones were absent. The proximal and middle phalanges were absent while the distal phalanges were present. The father and mother had short first metacarpal and middle phalynx of the fifth finger and hallux valgus respectively. Transition A1137G and deletion delG1144 mutations in the gene encoding the cartilage-derived morphogenetic protein-1 (CDMP-1) were identified in this family. The A1137G is a silent mutation coding for lysine, whereas the delG1144 predicts a frameshift mutation resulting in a presumable loss of the CDMP-1 biologically active carboxy-terminal domain. The affected siblings were homozygous for the delG1144 mutation while parents were heterozygous.

Abnormalities, Multiple↗
PubMed2006

Prioritizing regions of candidate genes for efficient mutation screening.

The availability of the complete sequence of the human genome has dramatically facilitated the search for disease-causing sequence variations. In fact, the rate-limiting step has shifted from the discovery and characterization of candidate genes to the actual screening of human populations and the subsequent interpretation of observed variations. In this study we tested the hypothesis that some segments of candidate genes are more likely than others to contain disease-causing variations and that these segments can be predicted bioinformatically. A bioinformatic technique, prioritization of annotated regions (PAR), was developed to predict the likelihood that a specific coding region of a gene will harbor a disease-causing mutation based on conserved protein functional domains and protein secondary structures. This method was evaluated by using it to analyze 710 genes that collectively harbor 4,498 previously identified mutations. Nearly 50% of the genes were recognized as disease-associated after screening only 9% of the complete coding sequence. The PAR technique identified 90% of the genes as containing at least one mutation, with less than 40% of the screening resources that traditional approaches would require. These results suggest that prioritization strategies such as PAR can accelerate disease-gene identification through more efficient use of screening resources.

Computational Biology↗
PubMed2006

Autonomous cytoplasmic linear plasmid pPac1-1 of Pichia acaciae: molecular structure and expression studies.

The genome organization of the linear DNA-element pPac1-1 from Pichia acaciae was determined. It turned out to be the smallest autonomous cytoplasmic yeast plasmid known so far, consisting of only 12 646 bp, carrying the shortest terminal inverted repeats yet found (138 bp). As for other cytoplasmic linear yeast plasmids, it is characterized by a strikingly high A + T content (75.35%). Ten putative genes (open reading frames, ORFs) reside on the element, leaving only 2.9% of the sequence outside a coding region. Highest similarities of the predicted proteins were obtained for proteins encoded by the three hitherto known autonomous cytoplasmic linear yeast plasmids. Amino acid sequences correspond to predicted polypeptides encoded by ORFs 2-11 of the linear plasmids pGKL2 of Kluyveromyces lactis, pSKL of Saccharomyces kluyveri and pPE1B of Pichia etchellsii. As for the latter, ORF1 existing on the two other plasmids is lacking on pPac1-1. Consistent with cytoplasmic localization, a cytoplasmic promoter termed upstream conserved sequence (UCS) is located in front of each reading frame. RT-PCR transcript analyses for ORFs 8, 9 and 11 proved expression of such genes but functions could not be attributed. The genome organization of pPac1-1 and other autonomous linear elements was found to be almost congruent, irrespective of the accompanying smaller elements, which may or may not encode their own element-specific DNA polymerases.

Amino Acid Sequence↗
PubMed2002

Cloning and characterization of WMSU1, a Williopsis saturnus var. mrakii gene encoding a new yeast SUN protein involved in the cell wall structure.

SUN proteins of Saccharomyces cerevisiae have been defined on the basis of high homologies in their C-terminal domain. Recently, two of these four proteins were shown to be involved in cell wall morphogenesis (Mouassite et al., 2000a). In the present study, we have isolated WMSU1 (Accession No. AF418983), a new SUN-related gene, from W. saturnus var. mrakii MUCL 41968. Sequencing of the gene revealed an open reading frame coding for 402 amino acids. The predicted amino acid sequence of WMSU1 is closely related to the S. cerevisiae SUN proteins and to other yeast proteins involved in cell wall metabolism. WMSU1 is proposed to encode a cell wall protein since its predicted product contains a signal sequence, a Kex2p cleavage site and a serine/threonine-rich N-terminal domain. Southern blot analysis of the W. saturnus var. mrakii MUCL 41968 genome using the highly conserved domain of WMSU1 as a probe suggested that the isolated gene belongs to a multigenic family. Expression of WMSU1 in E. coli led to a 45 kDa protein, which appeared to be toxic to this host. Scanning electron microscopy analysis of a recombinant S. cerevisiae producing Wmsu1p showed that this strain exhibited an altered cell wall, thus pointing to a probable role of this protein in the cell wall structure.

Amino Acid Sequence↗
PubMed2001

Cloning and expression of a putative common cytokine receptor gamma chain (gammaC) gene in rainbow trout (Oncorhynchus mykiss).

A full length cDNA of a putative common cytokine receptor gamma chain (gammaC) gene of rainbow trout (Oncorhynchus mykiss) has been cloned and sequenced. The contiguous cDNA contained 2291 nucleotides, consisting of an ORF of 1029 bp, with a 72 bp 5' UTR and a 1190 bp 3' UTR. The coding region showed 44-46% identity to mammalian gammaC genes. The ORF translated into a 343 amino acid protein, with some 28-30% amino acid identity to the coding region of mammalian sequences. A predicted signal peptide and transmembrane domain were identified, giving a 206 amino acid extracellular domain and a 98 amino acid intracellular domain in the trout molecule. Five potential glycosylation sites were present in the extracellular domain, as were six conserved cysteine residues and the W-S-X-W-S motif typical of haemopoietin receptors. One of the most interesting differences between the trout and mammalian sequences was the lack of tyrosines in the trout intracellular domain. RT-PCR studies revealed a wide tissue distribution of gammaC expression, with detectable transcript in blood, spleen, gill, kidney, brain and liver. Low levels of gammaC transcript were detectable in unstimulated macrophage cultures and expression was increased by stimulation of the cells with recombinant trout interleukin-1beta (IL-1beta) or LPS. Similarly, in the RTG cell line which exhibited even lower level constitutive expression, stimulation with IL-1beta increased gammaC transcript levels but LPS had no effect.

Amino Acid Sequence↗
PubMed1994

Structure of the mouse arylsulfatase A gene and cDNA.

The murine arylsulfatase A (ARSA) gene and cDNA have been cloned and sequenced. The gene is 3.8 kb long and contains eight exons. All intron/exon splice junctions conform to the GT/AG consensus sequence. The genomic structure is similar to that of the human gene. One major RNA species of 3.2 kb is transcribed. This RNA species has a 5' untranslated region of 638 nucleotides and terminates in a region around nucleotide 700 downstream of the termination codon. In addition, a rare mRNA species terminating at a polyadenylation signal 135 nucleotides downstream of the termination codon has been found. A larger transcript of 4 kb can be detected in liver. The size difference is due to initiation of transcription 5' of the cap site of the 3.2-kb mRNA species. The entire ARSA cDNA has been cloned by PCR from reverse-transcribed RNA. The coding sequence has 1518 nucleotides and predicts a protein of 506 amino acids. The nucleotide as well as the amino acid sequence is highly conserved among humans and mice.

Amino Acid Sequence↗
PubMed1997

cDNA cloning, expression analysis, and chromosomal localization of a gene with high homology to wheat eIF-(iso)4F and mammalian eIF-4G.

A novel mammalian gene, Eif4g2, with a high degree of homology to the p82 subunit of the wheat germ eukaryotic translation initiation factor eIF-(iso)4F and mammalian eIF-4G has been isolated. Zoo blot analysis indicates that Eif4g2 is a single-copy gene that is highly conserved among vertebrates. Northern blot analysis shows that Eif4g2 is ubiquitously expressed at high levels in all human and mouse tissues examined. The 3810-nucleotide Eif4g2 cDNA contains a 907-amino-acid open reading frame that codes for a polypeptide with a predicted molecular mass of 102 kDa. The Eif4g2 polypeptide exhibits an overall similarity to wheat p82 of 52%. A 248-amino-acid segment at the amino-terminal end of both peptides exhibits 63% similarity and contains conserved potential RNA binding domains and a phosphorylation site. The Eif4g2 polypeptide contains multiple potential N-linked glycosylation sites as well as protein kinase C and casein kinase II phosphorylation sites. Southern blot analysis of DNA from interspecific backcross mice shows that Eif4g2 is localized to distal mouse chromosome 7 in a region syntenic with human chromosome 11p15.

Amino Acid Sequence↗
PubMed1997

Cloning of GPR37, a gene located on chromosome 7 encoding a putative G-protein-coupled peptide receptor, from a human frontal brain EST library.

A cDNA sequence encoding a putative peptide-specific G-protein-coupled receptor (GPR37) was isolated from a set of human brain frontal lobe expressed sequence tags. The GPR37 cDNA predicts a single open reading frame coding for a 613-amino-acid protein with seven hydrophobic transmembrane domains. The GPR37 genomic sequence was mapped to chromosome 7q31, and it was isolated upon screening of a chromosome 7-specific genomic library. The GPR37 gene spans more than 25 kb and contains two exons and a single intron which interrupts the GPR37 cDNA within the sequence encoding the presumed third transmembrane domain. Northern blot analysis with GPR37 probes revealed a main 3.8-kb mRNA and a less abundant 8-kb mRNA, both expressed in human brain tissues, particularly in corpus callosum, medulla, putamen, and caudate nucleus. The lowest level of expression was detected in cerebellum. The 3.8-kb mRNA is also less abundantly expressed in liver and placenta. Although the ligand for the putative GPR37 receptor has not been identified, its deduced amino acid sequence shows a high degree of homology (approximately 40% in the transmembrane regions) with most mammalian peptide-specific G-protein-coupled receptors and particularly with the human endothelin-B, bombesin-BB1, and bombesin-BB2 receptors.

Adult↗
PubMed1999

Mutational analysis of the PMS2 gene in sporadic endometrial cancers with microsatellite instability.

OBJECTIVE: Approximately 20% of endometrial tumors have a defect in DNA mismatch repair and exhibit microsatellite instability (MSI). We assessed the role of the PMS2 DNA mismatch repair gene in MSI-positive sporadic endometrial tumors. METHODS: We examined 40 sporadic endometrial tumor specimens with MSI. All 15 exons of the PMS2 gene were investigated for sequence alterations by single-strand conformational variant analysis. RESULTS: Twelve polymorphisms were identified, 8 of which were in the coding sequence. Four specimens revealed mutations in intronic sequences that are not predicted to affect the PMS2 mRNA. No mutations were detected within the coding region of the PMS2 gene. CONCLUSION: We conclude that structural mutations in the PMS2 gene are not responsible for defective DNA mismatch repair in sporadic endometrial cancers with MSI. The identification of single nucleotide polymorphisms in the PMS2 locus may aid in the mapping and characterization of genetic diseases.

Adenosine Triphosphatases↗
PubMed1997

KpnAI, a new type I restriction-modification system in Klebsiella pneumoniae.

The KpnAI restriction-modification (R-M) system has been identified in Klebsiella pneumoniae strain M5a1. The restriction gene of KpnAI was first cloned into pBR322 using an r-m+ M5a1 derivative and phage SBS for screening. Subsequently, an adjacent DNA fragment showing modification activity was cloned into pUC19. A total of 7.2 kb DNA sequencing data revealed three open reading frames, corresponding to hsdR, hsdM and hsdS genes of type I R-M systems. The predicted hsdR, hsdM and hsdS-coded peptides shared 95%, 98% and 44% identity, respectively, with the corresponding peptides of the recently identified StySBLI system, a prototype of the type ID family. This high homology suggests that KpnAI is also a member of the type ID family. The KpnAI system seems to be the first type I system identified in Klebsiella species.

Cloning, Molecular↗
PubMed1996

Neutralizing epitope on penetration protein of vaccinia virus.

The monoclonal antibody 2D5 neutralized vaccinia virus by preventing penetration of the virus and reacting with VP23-29K. The conformation of the VP23-29K was maintained by a disulfide bond(s), and the 2D5mAb reacted stronger with the nonreduced 23-kDa form than with the reduced 29-kDa form. We selected several escape mutants. Sequences of the A17L genes, which were thought to encode the VP23-29K, did not show cognate mutation. Genomic DNA of a 2D5mAb-resistant mutant (M4) was cleaved with HindIII, and all the fragments were introduced into parental IHD-J strain vaccinia virus by transfection. Only the L fragment produced a 2D5mAb-resistant virus. Dissection of the L fragment and subsequent transfection revealed that the L1R gene induced the 2D5mAb-resistant virus. The 2D5mAb-resistant mutants showed a consensus G to A conversion at nucleotide 101 of their LIRs which would replace asparatic acid 35 with asparagine. Ishibashi-111 strain mousepox virus spontaneously resistant to 2D5mAb also had the same sequence at this region. Moreover, the VP23-29K was myristoylated as predicted by the L1R gene. The coding gene of the VP23-29K was L1R.

Amino Acid Sequence↗
PubMed1998

Sequence analysis of the nucleocapsid protein gene of the porcine reproductive and respiratory syndrome virus Taiwan MD-001 strain.

The 3'-portion of the genome from a Taiwan isolate of porcine reproductive and respiratory syndrome (PRRS) virus, strain MD-001, was cloned and sequenced. The resultant 549 nucleotides contained an open reading frame with a coding capacity of 123 amino acids (predicted Mr 13,600). The predicted protein corresponds to the nucleocapsid protein, the gene product of ORF7. Comparative sequence analysis of several known PRRSV strains indicated that this protein showed the highest degree of amino acid similarity to the US VR2332 and the Canadian IAF-Exp91 strains (92.7%) and the least to the Dutch Lelystad strain (56.5%). The phylogenic trees constructed on the basis of the known PRRSV nucleotide sequences indicated that MD-001 strain belongs to the North American strain cluster and that it is distinct from the European virus.

Amino Acid Sequence↗
PubMed1989

Isolation, sequence and transcription of the gene encoding the photosystem II chlorophyll-binding protein, CP-47, in the cyanobacterium Anabaena 7120.

The psbB gene from the cyanobacterium Anabaena 7120 was cloned and its nucleotide sequence determined. This gene codes for the photosystem II chlorophyll-binding protein CP-47. We identified an open reading frame of 1527 bases that can code for a polypeptide with a predicted molecular weight of 56,254. Expression of the psbB gene in Anabaena 7120 results in two transcripts that begin 302 or 238 bp upstream of the open reading frame and both end 288 bp downstream following a 21 bp inverted repeat. We also show that the levels of these psbB gene transcripts as well as those of the glnA, rbcLS, and psbA genes, in RNA prepared from whole filaments, remain constant during heterocyst differentiation.

Amino Acid Sequence↗
PubMed1991

Hypoxanthine-guanine phosphoribosyltransferase deficiency: analysis of HPRT mutations by direct sequencing and allele-specific amplification.

The Lesch-Nyhan syndrome is a severe X chromosome-linked human disease caused by a virtual absence of hypoxanthine-guanine phosphoribosyltransferase (HPRT) activity. A partial deficiency in the activity of this enzyme can result in gouty arthritis. To determine the genetic basis for reduction or loss of enzyme activity, we have amplified and sequenced the coding region of HPRT cDNA from four patients: one with Lesch-Nyhan syndrome (HPRTPerth) and three with partial deficiencies of HPRT activity, which have been designated HPRTUrangan, HPRTSwan and HPRTToowong. In all four patients, the only mutation identified was a single base substitution in exons 2 or 3 of the coding region, which in each case predicts a single amino acid substitution in the translated protein. Each base change was confirmed by allele-specific amplification of the patient's genomic DNA. It is interesting to note that the mutation found for HPRTPerth is identical to that reported for HPRTFlint. It appears that the two mutations are de novo events.

Alleles↗