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PubMedDate not supplied

Digital wavelet-encoded MRI: a new wavelet-encoding methodology.

A new digital wavelet-encoding method for MRI is described. The method differs from previously described wavelet-encoding approaches, because the point-spread function is made independent of the wavelet basis used. This has a significant practical advantage, because wavelet bases can now be considered that would otherwise be excluded due to the difficulty of precisely exciting wavelet-shaped RF profiles. The method has been implemented on a clinical MRI system, and human images are presented.

Brain↗

PubMed2006

Faster flow quantification using sensitivity encoding for velocity-encoded cine magnetic resonance imaging: in vitro and in vivo validation.

PURPOSE: To test the agreement between conventional and sensitivity-encoded (SENSE) velocity encoded cine (VEC) MRI in a flow phantom and in subjects with congenital and acquired heart disease. MATERIALS AND METHODS: Flow measurements were performed in a 1.5 T scanner using a segmented k-space VEC MRI sequence and then repeated with a SENSE factor of 2. The flow phantom used a piston pump to generate physiologic arterial waveforms (0.5-4.9 L/min). In the subjects, flow measurements were performed in the ascending aorta (N = 33) and/or the main pulmonary artery (N = 24). RESULTS: Utilization of SENSE reduced the scan time by 50%. In the phantom, measurements without and with SENSE agreed closely with a mean difference of 0.01 +/- 0.08 L/min or 0.12% +/- 3.8% (P = 0.68). In the subjects, measurements without and with SENSE also agreed closely with a mean difference of 0.08 +/- 0.36 L/min or 1.3% +/- 7.2% (P = 0.08). Compared with standard imaging, the use of SENSE reduced the signal-to-noise ratio (SNR) by 28% in the phantom (N = 10) and 27% in vivo (N = 22). CONCLUSION: VEC MRI flow measurements with a SENSE factor of 2 were twice as fast and agreed closely with the conventional technique in vitro and in vivo. VEC MRI with SENSE can be used for rapid and reliable quantification of blood flow.

Adolescent↗

PubMed1994

A 12.5 kb fragment of the yeast chromosome II contains two adjacent genes encoding ribosomal proteins and six putative new genes, one of which encodes a putative transcriptional factor.

The nucleotide sequence of a 12.5 kb fragment localized to the right arm of chromosome II of Saccharomyces cerevisiae has been determined. The sequence contains eight putative genes. Two of them are contiguous and represent two ribosomal protein genes: SUP46 and URP1. SUP46 is implicated in translation fidelity and encodes the ribosomal protein S13. URP1 is homologous to the rat ribosomal protein gene L21. The open reading frame (ORF) YBR1245 is similar in its N-terminal part to transcription factors like SRF and MCM1. The ORF YBR1308 shows homology with proteins of the AAA-family (ATPases Associated with diverse cellular Activities). Two genes are predicted to encode putative membrane proteins.

Amino Acid Sequence↗

PubMed2001

Phylogeny of Alariaceae, Laminariaceae, and Lessoniaceae (Phaeophyceae) based on plastid-encoded RuBisCo spacer and nuclear-encoded ITS sequence comparisons.

Concatenated sequences from the plastid-encoded RuBisCo spacer and nuclear-encoded rDNA ITS region of the Alariaceae, Laminariaceae, and Lessoniaceae as currently recognized were used to determine the phylogeny of kelps (Phaeophyceae). Our analyses indicate that all taxa in the Alariaceae, Laminariaceae, and Lessoniaceae form a monophyletic lineage (the Laminariales sensu stricto). The phylogenetic analyses show that the kelps form eight well-supported clades (represented by Egregia, Laminaria, Hedophyllum, Macrocystis, Alaria, Agarum, Ecklonia, and Lessonia) that conform to the tribes of the current morphological classification system of the "advanced" kelps. Our results suggest that the kelps should be classified into eight families rather than the three that are presently used. The interrelationships among the eight lineages were, however, unresolved in the phylogenetic analyses. In all trees, Egregia diverged first and is the sister to the other kelp taxa. Our phylogenetic analyses also indicate that Kjellmaniella and Laminaria do not form a monophyletic group. Taken together, the RuBisCo spacer and rDNA ITS prove useful for understanding the evolutionary history of the advanced kelps and provide a new framework for establishing the systematics of these commercially important brown algae.

Cell Nucleus↗

PubMed1992

Isolation and characterization of a gene encoding a chlorophyll a/b-binding protein from mustard and the targeting of the encoded protein to the thylakoid membrane of pea chloroplasts in vitro.

Three independent clones carrying a mustard gene coding for the chlorophyll a/b-binding protein were isolated by screening a genomic library of mustard with a heterologous cDNA probe from pea. All of them encode the same CAB gene, which, as shown by sequence analysis and comparison with published CAB sequences, belongs to the family of type I PSII CAB genes, encoding a precursor protein of 266 amino acids. Several conserved sequence motifs are observed in the 5' and 3' non-coding region of the gene. The putative transcription start site could be localized to 60 bp upstream of SA-CAB1 initiator codon by S1 mapping. Plasmids were constructed which allow in vitro transcription and translation of the whole chlorophyll a/b-binding protein and of truncated species which lack increasing portions of the C-terminus. Whereas the in vitro import into pea chloroplasts is not affected by these C-terminal deletions, targeting to the thylakoid membrane is abolished by the removal of the C-terminal helical domain. Accordingly, the 54 amino acids which contain the C-terminal membrane-spanning helix and flanking regions is an essential component of the thylakoid targeting signal.

Amino Acid Sequence↗

PubMed1993

Co-expression of an Erwinia chrysanthemi pectate lyase-encoding gene (pelE) and an E. carotovora polygalacturonase-encoding gene (peh1) in Saccharomyces cerevisiae.

A pectate lyase (PL)-encoding gene (pelE) from Erwinia chrysanthemi and a polygalacturonase (PG)-encoding gene (peh1) from E. carotovora were each inserted between a novel yeast expression-secretion cassette and a yeast gene terminator, and cloned separately into a yeast-centromeric shuttle vector (YCp50), generating recombinant plasmids pAMS12 and pAMS13. Transcription initiation signals present in the expression-secretion cassette were derived from the yeast alcohol dehydrogenase gene promoter (ADC1P), whereas the transcription termination signals were derived from the yeast tryptophan synthase gene terminator (TRP5T). Secretion of PL and PG was directed by the signal sequence of the yeast mating pheromone alpha-factor (MF alpha 1s). A pectinase cassette comprising ADC1P-MF alpha 1s-pelE-TRP5T and ADC1P-MF alpha 1s-peh1-TRP5T was subcloned into YCp50, generating plasmid pAMS14. Subsequently, the dominant selectable Geneticin G418-resistance (GtR) marker, APH1, inserted between the yeast uridine diphosphoglucose 4-epimerase gene promoter (GAL10P) and yeast orotidine-5'-phosphate carboxylase gene terminator (URA3T), was cloned into pAMS14, resulting in plasmid pAMS15. Plasmids pAMS12, pAMS13 and pAMS14 were transformed into a laboratory strain of Saccharomyces cerevisiae, whereas pAMS15 was stably introduced into two commercial wine yeast strains. DNA-DNA and DNA-RNA hybridization analyses revealed the presence of these plasmids, and the pelE and peh1 transcripts in the yeast transformants, respectively. A polypectate agarose assay indicated the extracellular production of biologically active PL and PG by the S. cerevisiae transformants and confirmed that co-expression of the pelE and peh1 genes synergistically enhanced pectate degradation.

Bacterial Proteins↗

PubMed1989

Isolation and expression of a cDNA clone encoding HLA-Cw6: unique characteristics of HLA-C encoded gene products.

The HLA-C encoded gene products display several characteristics which distinguish them from HLA-A and -B. The HLA-C antigens are poorly expressed on the cell surface, they display multiple proteins with different isoelectric points, and alloimmunization to HLA-C antigens is less common. To investigate whether the multiple products result from differential splicing of HLA-C gene transcripts, we have isolated a full-length cDNA clone encoding the Cw6 antigen. Class I antigens produced by the cDNA clone in transfected cells were of the same relative mass as those observed in the parental cells when analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Isoelectric focusing (IEF) gel analysis of the cDNA translated products in transfectants revealed multiple IEF bands. All IEF bands detected in the transfectants were also found in the parental cells, indicating that the multiplicity of the C-locus products was not due to differential splicing of HLA-C gene transcripts, but was probably due to post-translational modification. Comparison of the sequences of C-locus alleles with those of A and B alleles did not show any apparent sequences which would generate multiple IEF bands. Comparison of the coding regions for seven HLA-C alleles and one HLA-C-related class I gene with available data for 15 HLA-A and 20 HLA-B alleles demonstrated several unique features for the HLA-C locus. Six sites in the extra cellular domains, three in a1 and three in a3, were unique. While the cytoplasmic (CP) domain of HLA-A and -B are almost identical, the CP of HLA-C alleles is unique. Similar unique features of HLA-C are also observed in the transmembrane domain, resulting in locus-specific residues between positions 295 and 300. The present study has ruled out differential mRNA splicing as a mechanism for the multiplicity of Cw6 antigens and demonstrated unique HLA-C locus sequences.

Amino Acid Sequence↗

PubMed1989

Nucleotide sequences of cDNA clones encoding the entire precursor polypeptide for subunit VI and of the plastome-encoded gene for subunit VII of the photosystem I reaction center from spinach.

Recombinant phage which encode the entire precursor polypeptide for subunit VI of the photosystem I reaction center have been selected from a lambda gt11 cDNA expression library made from polyadenylated RNA of spinach seedlings. The sequence predicts a precursor polypeptide of 144 amino acids (Mr = 15.3 kDa), a mature protein of 95 residues (Mr = 10.4 kDa) that lacks methionine, histidine and cysteine, and a transit peptide of 49 residues (Mr = 4.9 kDa). The corresponding gene(s) is (are) designated psaH. The gene for subunit VII, psaC, has been located in the small single-copy region of the spinach plastid chromosome using a synthetic oligonucleotide and a heterologous hybridization probe. It is part of a polycistronic transcription unit that is constitutively expressed and processed. Putative processing products include a monocistronic RNA for psaC. The polypeptide chain of 18 (deduced) amino acids is highly conserved and strikingly resembles bacterial-type ferredoxins. It harbours cysteine residues that appear to be involved in the ligation of the two 4Fe4S centres A and B in photosystem I. None of the two subunits appears to be membrane-spanning, and subunit VI, as subunit VII, is located at the reducing (stromal) side of the reaction center. All available information on the major subunits of photosystem I from spinach has been combined into a (revised) topographic model. Evidence that the innermost - plastome-encoded - core of photosystem I represents an old bacterial heritage in present day chloroplasts is discussed.

Amino Acid Sequence↗

PubMed1989

Responses against antigens encoded by the H-3 histocompatibility locus: antigens stimulating class I MHC- and class II MHC-restricted T cells are encoded by separate genes.

The purpose of this work was to study the genetic basis of histocompatibility antigens encoded by the mouse minor histocompatibility (H) locus H-3. Both class I major histocompatibility complex (MHC)-restricted cytotoxic T lymphocytes (CTL) and class II MHC-restricted helper T cells (TH) specific for antigens encoded by genes within the H-3 locus were isolated and analyzed. Typing a number of mouse strains for expression of antigens recognized by these TH and CTL suggested that there was a different strain distribution pattern of expression of the antigens recognized by TH compared with those recognized by CTL. Separation of the genes whose products stimulate TH from those whose products stimulate CTL was suggested by: (1) analysis of the strain B10.FS(92NX)/Grf that has undergone recombination within the H-3 region; (2) genetic segregation studies of (B10.UW-H-3b/Sn x C57BL/10Sn)F2 mice; and (3) F1 complementation studies in which CTL specific for products of the TH-defined gene(s) could not be detected, even in the absence of immune responses to products of the CTL-defined genes. Taken together, these data suggest that in addition to two genes (B2m and Cd-1) within the H-3 region whose products typically stimulate class I MHC-restricted CTL, there is at least one additional gene whose product selectively stimulates class II MHC-restricted TH. This new gene is located telomeric from the CTL-defined genes and between the loci we and un on chromosome 2. These data demonstrate a novel degree of complexity of the H-3 "locus" and suggest selective presentation of minor H gene products in the context of class I or class II MHC proteins.

Animals↗

PubMed1998

The Acinetobacter calcoaceticus NCIB8250 mop operon mRNA is differentially degraded, resulting in a higher level of the 3' CatA-encoding segment than of the 5' phenolhydroxylase-encoding portion.

The 7.5-kb polycistronic mop mRNA is differentially degraded in Acinetobacter calcoaceticus. The 4.9-kb 5' portion of the transcript contains the genes mopKLMNOP, encoding the multi-component phenol hydroxylase, and its 5' end decays three times faster than the 2.3-kb 3' portion encoding catechol 1,2-dioxygenase (catA). Larger amounts of the catA mRNA than the mopKLMNOP mRNA are present in the cells as a result of this processing. The site for endonucleolytic cleavage is located in the intercistronic region between mopP and catA, and contains a potential stem-loop structure and a putative RNase E cleavage site. Decay of the mop mRNA in Escherichia coli depends on RNase E. Thus, we propose that an RNase E-like activity is also present in A. calcoaceticus. Expression of MopN, one polypeptide of the multi-component phenol hydroxylase, interferes with growth of A. calcoaceticus. Thus, harmful expression of MopN may be reduced by rapid decay of its mRNA, indicating that mRNA processing contributes to differential gene expression in the large mop operon of A. calcoaceticus NCIB8250.

Acinetobacter calcoaceticus↗

PubMed2000

Genes encoding human killer-cell Ig-like receptors with D1 and D2 extracellular domains all contain untranslated pseudoexons encoding a third Ig-like domain.

Human killer-cell immunoglobulin-like receptors (KIR) show three types of organization of their extracellular domains: D0-D1-D2 in KIR3D, D1-D2 in the majority of KIR2D, and D0-D2 in KIR2DL4 and the novel KIR2DL5. The gene for a KIR2DL3 variant, which has a D1-D2 structure, has been shown previously to have a nonexpressed region (pseudoexon 3) that is paralogous to the exon encoding the D0 domain of other KIR. This pseudoexon is not expressed because it is skipped during splicing of pre-mRNA. In this study, we demonstrate that all eight genes encoding human KIR with D1-D2 configuration (KIR2DL1-KIR2DL3, KIR2DS1-KIR2DS5) have similarly untranslated pseudoexons. Whereas the pseudoexons of four of these KIR genes bear nonsense mutations and/or altered splicing sites, the pseudoexons in the other four KIR genes have no major structural abnormalities, indicating that other mechanisms are responsible for inactivation of their exons 3. A comparison of the sequences on pseudoexons 3 with the paralogous expressed exons suggests that an exonic splicing enhancer may be necessary for the expression of exon 3 in KIR genes.

Adult↗

PubMed2003

Cloning and characterization of katA, encoding the major monofunctional catalase from Xanthomonas campestris pv. phaseoli and characterization of the encoded catalase KatA.

The first cloning and characterization of the gene katA, encoding the major catalase (KatA), from Xanthomonas is reported. A reverse genetic approach using a synthesized katA-specific DNA probe to screen a X. campestris pv. phaseoli genomic library was employed. A positively hybridizing clone designated pKat29 that contained a full-length katA was isolated. Analysis of the nucleotide sequence revealed an open reading frame of 1,521 bp encoding a 507-amino acid protein with a theoretical molecular mass of 56 kDa. The deduced amino acid sequence of KatA revealed 84% and 78% identity to CatF of Pseudomonas syringae and KatB of P. aeruginosa, respectively. Phylogenetic analysis places Xanthomonas katA in the clade I group of bacterial catalases. Unexpectedly, expression of katA in a heterologous Escherichia coli host resulted in a temperature-sensitive expression. The KatA enzyme was purified from an overproducing mutant of X. campestris and was characterized. It has apparent K(m) and V(max) values of 75 m M [H(2)O(2)] and 2.55 x 10(5) micromol H(2)O(2) micromol heme(-1) s(-1), respectively. The enzyme is highly sensitive to 3-amino-1,2,4-triazole and NaN(3), has a narrower optimal pH range than other catalases, and is more sensitive to heat inactivation.

Catalase↗

PubMed1999

Genetic interactions between a null allele of the RIT1 gene encoding an initiator tRNA-specific modification enzyme and genes encoding translation factors in Saccharomyces cerevisiae.

The Saccharomyces cerevisiae gene RIT1 encodes a phospho-ribosyl transferase that exclusively modifies the initiator tRNA (tRNAMet(i)) by the addition of a 2'-O-ribosyl phosphate group to Adenosine 64. As a result, tRNAMet(i) is prevented from participating in the elongation steps of protein synthesis. We previously showed that the modification is not essential for the function of tRNAMet(i) in the initiation of translation, since rit1 null strains are viable and show no obvious growth defects. Here, we demonstrate that yeast strains in which a rit1 null allele is combined with mutations in any of the genes for the three subunits of eukaryotic initiation factor-2 (eIF-2), or with disruption alleles of two of the four initiator methionine tRNA (IMT) genes, show synergistic growth defects. A multicopy plasmid carrying an IMT gene can alleviate these defects. On the other hand, introduction of a high-copy-number plasmid carrying the TEF2 gene, which encodes the eukaryotic elongation factor 1alpha (eEF-1alpha), into rit1 null strains with two intact IMT genes had the opposite effect, indicating that increased levels of eEF-1alpha are deleterious to these strains, presumably due to sequestration of the unmodified met-tRNAMet(i) for elongation. Thus, under conditions in which the components of the ternary met-tRNAMet(i):GTP:eIF-2 complex become limiting or are functionally impaired, the presence of the 2'-O-ribosyl phosphate modification in tRNAMet(i) is important for the provision of adequate amounts of tRNAMet(i) for formation of this ternary complex.

Alleles↗

PubMed1991

The autocatalytic protease p29 encoded by a hypovirulence-associated virus of the chestnut blight fungus resembles the potyvirus-encoded protease HC-Pro.

Gene expression by a viral-like double-stranded RNA genetic element associated with reduced virulence (hypovirulence) of the chestnut blight fungus was recently shown to involve an autoproteolytic event which resulted in the release of an encoded protease, designated p29, from a polyprotein during translation. Mutational analysis of p29, described in this report, revealed that residues Cys-162 and His-215 are essential for autocatalytic cleavage. The results were also consistent with previous predictions that cleavage occurs between Gly-248 and Gly-249. Interestingly, p29 bears a striking resemblance to the potyvirus-encoded protease HC-Pro. Both proteases autocatalytically cleave at glycine dipeptides. In addition, there is a significant degree of similarity in the amino acid sequences flanking the essential Cys and His residues of the two proteases and in the spacing of these residues from their respective cleavage sites.

Amino Acid Sequence↗

PubMed2005

Encoding during the attentional lapse: accuracy of encoding during the semantic sustained attention to response task.

An experiment investigated the relationship between the ability to encode verbal stimuli during an attentional lapse. The task employed a variation on the sustained attention to response task (SART, Robertson, Manly, Andrade, Baddeley, & Yiend, 1997) which involved the detection of an infrequent target against a background of words. As a manipulation, participants were either instructed to encode the stimuli or were merely exposed to the stimuli. Retrieval was measured using process dissociation. Irrespective of the instructions given to the participants during the task, participants were more likely to retrieve information on the basis of recollection after an error was made than before, whilst the likelihood of retrieving information on the basis of familiarity remained invariant over the same period. The implications of this result for methods of investigating subjective experience are discussed.

Adult↗

PubMed2004

Determination of species-specific sequences of superoxide dismutase A encoding gene sodA and chaperonin 60 encoding gene cpn60 for identification and phylogenetic analysis of Streptococcus phocae.

Species-specific PCR tests, based on the manganese-dependent superoxide dismutase A encoding gene (sodA) and the chaperonin 60 encoding gene (cpn60), were developed for the identification of Streptococcus phocae, a bacterial pathogen of seals. The selection of both oligonucleotide primer pairs was performed after amplification and sequencing of internal parts of both genes using universal oligonucleotide primers. The sequence studies of both genes additionally confirmed that S. phocae could taxonomically be classified to the pyogenic group of the genus Streptococcus.

Animals↗

PubMed2003

Nuclear exopolyphosphatase of Saccharomyces cerevisiae is not encoded by the PPX1 gene encoding the major yeast exopolyphosphatase.

Intact nuclei from a parental strain CRY and a PPX1-mutant CRX of Saccharomyces cerevisiae were isolated and found to be essentially free of cytoplasmic, mitochondrial and vacuolar marker enzymes. The protein-to-DNA ratios of the nuclei were 22 and 30 for CRY and CRX nuclei, respectively. An exopolyphosphatase (exopolyPase) with molecular mass of approximately 57 kDa and a pyrophosphatase (PPase) of approximately 41 kDa were detected in the parental strain CRY. Inactivation of PPX1 encoding a major exopolyPase (PPX1) in S. cerevisiae did not result in considerable changes in the content and properties of nuclear exopolyPase as compared to the parental strain of S. cerevisiae. Consequently, the nuclear exopolyPase was not encoded by PPX1. In the CRX strain, the exopolyPase was stimulated by bivalent metal cations. Co2+, the best activator, stimulated it by approximately 2.5-fold. The exopolyPase activity was nearly the same with polyphosphate (polyP) chain lengths ranging from 3 to 208 orthophosphate when measured with Mg2+. With Co 2+, the exopolyPase activity increased along with the increase in polymerization degree of the substrate.

Acid Anhydride Hydrolases↗

PubMed1989

Characterization of the gene encoding mouse serum amyloid P component. Comparison with genes encoding other pentraxins.

A CBA/J-strain mouse serum amyloid P component (SAP) genomic clone was isolated and analysed. The clone contains the entire SAP gene and specifies a primary transcript of 1065 nucleotide residues. This comprises a first exon of 206 nucleotide residues containing the mRNA 5'-untranslated region and sequence encoding the pre-SAP leader peptide and the first two amino acid residues of mature SAP separated by a single 110-base intron from a 749-nucleotide-residue second exon containing sequence encoding the bulk of the mature SAP and specifying the mRNA 3'-untranslated region. The overall organization is similar to that of the human SAP gene, and the coding region and intron sequences are highly conserved. The SAP RNA cap site was defined by primer extension analysis of polyadenylated acute-phase liver RNA. The 5'-region of the mouse SAP gene contains modified CAAT and TATA promoter elements preceded by a putative hepatocyte-nuclear-factor-1-recognition site; these structures are in a region that is highly homologous to the corresponding region of the human SAP gene. Comparisons of the mouse SAP gene structure and derived amino acid sequence with those of other mammalian pentraxins were made.

Acute-Phase Proteins↗