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PubMedDate not supplied

State-of-the-art techniques for lossless compression of 3D medical image sets.

This paper explains the basic principles of lossless two-dimensional (2D) and three-dimensional (3D) image coding at a high level of abstraction. It discusses also a new inter-frame technique for lossless video coding based on intra-frame prediction and inter-frame context modelling. The performance of this technique is compared to that of state-of-the-art 2D coders on CT and MRI data sets from the Visual Human Project. The results show that the inter-frame technique outperforms state-of-the-art intra-frame coders, i.e. Calic and JPEG-LS. The improvement in compression ratio is significant in the case of CT data but is rather small in the case of MRI data.

Algorithms↗

PubMed1999

Identification of the essential EPE1 gene involved in retention of secreted proteins on the cell surface of Saccharomyces cerevisiae cells.

Saccharomyces cerevisiae yeast cells secrete extracellularly low amounts of a few proteins. The reasons for retardation of secreted proteins on the cell surface remain obscure. We describe here a mutant able to export enhanced amount of proteins. Classical genetic methods, nucleic acids manipulations and cloning procedures were used to isolate and characterize the mutant and to clone and sequence the corresponding wild type gene. The isolated Saccharomyces cerevisiae mutant MW11, is temperature sensitive and exports on average twenty-fold more proteins at 37 degrees C than parental wild type strain (80 micrograms of proteins/1 x 10(8) mutant cells, SEM +/- 5, n22; versus 3 micrograms of proteins/1 x 10(8) parental cells, SEM +/- 1, n22). Protein overexport in the mutant requires a functional SEC1 pathway and is independent of cell lysis. Cloning and sequencing of the corresponding wild type gene identified an open reading frame of 786 bp coding for a hydrophilic protein with predicted molecular mass of 30 kDa and cytosolic localization. The newly identified gene, designated EPE1, is an essential gene. Its DNA and amino acids sequence showed no homology with other yeast genes and proteins. It is concluded that the function of unknown yet genes, such as EPE1 is needed for retention of secreted proteins on the surface of Saccharomyces cerevisiae cells.

Amino Acid Sequence↗

PubMed2000

Direct in situ measurements of labile inorganic and organically bound metal species in synthetic solutions and natural waters using diffusive gradients in thin films.

The emerging technique of DGT (diffusive gradients in thin films) is shown to be capable of performing new speciation measurements in situ in natural waters. In DGT, metals are bound to a resin layer after passing through a well-defined diffusion layer. Cd was measured in solutions containing glycine, EDTA, and fulvic (FA) and humic acids (HA) by atomic absorption spectroscopy (AAS), anodic stripping voltammetry (ASV), and DGT. DGT measured similar labile fractions to ASV, with detailed differences being consistent with a thicker diffusion layer allowing more dissociation of labile complexes and a slower diffusion of FA and HA complexes through the gel. When single measurements are made in complex solutions with DGT, precise quantification is impossible due to uncertainties concerning the distribution of species with different diffusion coefficients. A new procedure was proposed based on the advantage of DGT of being able to control the pore size of the diffusive gel layer. Small (inorganic) species diffuse freely through all gels but larger FA and HA (organic) complexes diffuse less freely in more constrained gels. When measurements were made on known solutions of Cu and FA or HA, it was possible to quantify the inorganic and organic species separately. They agreed well with predictions made using the WHAM speciation code. Multiple DGT units were also deployed in situ in a stream with high dissolved organic carbon (14.6 mg/L). The systematic differences between the devices with different gel compositions enabled determination, for the first time, of the in situ concentrations of both labile inorganic and organic species in natural water. A single DGT device with a constrained gel can be used to quantify inorganic species directly, providing absolute accuracy is not required. This ability of DGT to measure well-defined fractions of metals in situ using a simple device gives it considerable potential as a regulatory tool. A direct speciation measurement may be preferable to modeling approaches which require diverse input data that are difficult to determine.

Benzopyrans↗

PubMed2004

T7 RNA polymerase mediates fast promoter-independent extension of unstable nucleic acid complexes.

T7 RNA polymerase is a processive, DNA-dependent RNA polymerase that has a high specificity for its 17 base pair (bp) promoter. In addition to normal transcription, the enzyme can produce anomalous transcripts in the absence of a promoter. We report here the systematic characterization of the transient aspects of this promoter-independent process. Oligonucleotides that are able to form transient unimolecular loop structures closed by as little as one Watson-Crick base pair between the 3' terminal residue and an internal nucleotide proved to be viable substrates. A single nucleotide triphosphate assay system found that incorporation was encoded by the nucleotide 5' to the predicted transient base pair. When this coding nucleotide was identical to the internal nucleotide participating in the transient base pair, multiple nucleotide incorporations were observed and could only be explained by a continuous shifting and resetting of the transient base-pairing required for extension. This intermittent extension process can be quite efficient. Short DNA or RNA substrates were good substrates for the enzyme (affinities ranged from 2 to 43 microM) and were extended rapidly with apparent catalytic rates of up to 240 min(-1) being observed, only 2-fold slower than the rate of transcriptional initiation. Our data suggest a possible mechanism for this promoter-independent extension activity and may add to the understanding of viral RNA replicative strategies.

Base Pairing↗

PubMed1999

Novel characteristics and regulation of a divergent cinnamate 4-hydroxylase (CYP73A15) from French bean: engineering expression in yeast.

cDNAs showing high sequence similarity (>70%) over large stretches to plant CYP73A orthologues from other species were isolated from a cDNA library derived from mRNAs expressed in elicitor-treated suspension-cultured cells. These clones appear to code for a full-length 1554 bp open reading frame with a 78 bp 5'-untranslated region and a 140 bp 3'-untranslated region. The open reading frame, determined by sequence similarity, codes for a protein with a predicted Mr of 59229 and a pI of 8.8. It contains the conserved cysteine haem-binding site found in all cytochrome P450s. The protein encoded by this cDNA diverges however from other CYP73As in its N- and C-terminus and in four domains internally, so that overall sequence similarity is in the range 58-66%. Many clones contained an identical intron, which may be associated with a novel regulatory mechanism. Sequence similarity is sufficient for it to be classified as CYP73A15, although it is the least similar member of this family classified so far. The cDNA was expressed in yeast. Successful expression of cinnamate 4-hydroxylase activity required removal of the intron. High-level expression also required modification of the N-terminus to that of CYP73A1. Yeast did not process the intron at all and the leader sequence for A15 was not as compatible as that of A1. The mRNA for CYP73A15 was shown to be rapidly induced by elicitor treatment of suspension-cultured cells of French bean but induction was more transient than that of phenylalanine ammonia-lyase (PAL). In contrast, induction in cells undergoing xylogenesis was much more coordinate with PAL. The cloned cDNA may represent a cinnamate 4-hydroxylase isoform, whose expression is more related to differentiation than the responses to stress in which the majority of CYP73As cloned so far are involved.

Amino Acid Sequence↗

PubMedDate not supplied

The precursor of Alzheimer's disease amyloid A4 protein resembles a cell-surface receptor.

Alzheimer's disease is characterized by a widespread functional disturbance of the human brain. Fibrillar amyloid proteins are deposited inside neurons as neurofibrillary tangles and extracellularly as amyloid plaque cores and in blood vessels. The major protein subunit (A4) of the amyloid fibril of tangles, plaques and blood vessel deposits is an insoluble, highly aggregating small polypeptide of relative molecular mass 4,500. The same polypeptide is also deposited in the brains of aged individuals with trisomy 21 (Down's syndrome). We have argued previously that the A4 protein is of neuronal origin and is the cleavage product of a larger precursor protein. To identify this precursor, we have now isolated and sequenced an apparently full-length complementary DNA clone coding for the A4 polypeptide. The predicted precursor consists of 695 residues and contains features characteristic of glycosylated cell-surface receptors. This sequence, together with the localization of its gene on chromosome 21, suggests that the cerebral amyloid deposited in Alzheimer's disease and aged Down's syndrome is caused by aberrant catabolism of a cell-surface receptor.

Alzheimer Disease↗

PubMed1995

The use of colour-coded and spectral Doppler ultrasound in the differentiation of benign and malignant breast lesions.

The aim of this study was to evaluate the role of colour-coded and spectral Doppler sonography to predict the benign or malignant nature of breast lesions. A total of 112 women with mammographically suspicious breast lesions were investigated prior to surgery. Thirty-nine breast carcinomas and 73 benign lesions were evaluated for the resistance index, pulsatility index and the flow velocity. A resistance index of > or = 0.70 was characteristic of malignant tumours with a sensitivity of 82% and a specificity of 81%. The positive predictive value was 70% and the negative predictive value 89%. Doppler sonography offers one possible method for further investigation of patients with mammographic abnormalities.

Adult↗

PubMed1993

3,400 new expressed sequence tags identify diversity of transcripts in human brain.

We present the results of the partial sequencing of over 3,400 expressed sequence tags (ESTs) from human brain cDNA clones, which increases the number of distinct genes expressed in the brain, that are represented by ESTs, to about 6,000. By choosing clones in an unbiased manner, it is possible to construct a profile of the transcriptional activity of the brain at different stages. Proteins that comprise the cytoskeleton are the most abundant; however, a large variety of regulatory proteins are also seen. About half of the ESTs predicted to contain a protein-coding region have no matches in the public peptide databases and may represent new gene families.

Amino Acid Sequence↗

PubMed2025

Chromosome-level genome assembly of Qihe gibel carp.

Qihe gibel carp (Carassius gibelio var. Qihe) is a local population of natural gynogenetic amphitriploid (AAABBB) Carassius gibelio, and has high nutritional and economic value. In this study, we assemble a high-quality chromosome-level genome of Qihe gibel carp through DNBSEQ, PacBio HiFi, and Hi-C sequencing data. The resulting assembly consisted of 350 contigs with the full length of 1.607 Gb and 96.21% (1.515 Gb) of the assembled genome was successfully anchored to 50 chromosomes, with a contig N50 of 28.97 Mb and a scaffold N50 of 29.84 Mb. Repeated sequences accounting for 43.72% (732.494 Mb) of the total were also identified, and gene prediction revealed 46,131 protein-coding genes with an annotation ratio of 96.48%. Furthermore, Benchmarking Universal Single-Copy Orthologue (BUSCO) analysis demonstrated that the genome assembly achieved high completeness, with a score of 97.66%. This high-quality chromosome-level genome lays the foundation for molecular biology research as well as molecular breeding and evolutionary studies of Qihe gibel carp in the future.

Animals↗

PubMed2001

Purification, characterization, and cDNA cloning of a novel soluble saxitoxin and tetrodotoxin binding protein from plasma of the puffer fish, Fugu pardalis.

Some species of puffer fish have been reported to possess both of tetrodotoxin and saxitoxin, which share one binding site on sodium channels. We purified a novel soluble glycoprotein that binds to these toxins from plasma of the puffer fish, Fugu pardalis, and named puffer fish saxitoxin and tetrodotoxin binding protein (PSTBP). PSTBP possessed a binding capacity of 10.6 +/- 0.97 nmol x mg(-1) protein and a K(d) of 14.6 +/- 0.33 nm for [(3)H]saxitoxin in equilibrium binding assays. [(3)H]Saxitoxin (10 nm) binding to PSTBPs was half-inhibited by the presence of tetrodotoxin and saxitoxin at 12 microm and 8.5 nm, respectively. From the results of gel filtration chromatography (200 kDa) and SDS/PAGE (104 kDa), PSTBP was suggested to consist of noncovalently linked dimers of a single subunit. PSTBP was completely deglycosylated by glycopeptidase F, producing a single band at 42 kDa. Two highly homologous cDNAs to each other coding PSTBP (PSTBP1 and PSTBP2, the predicted amino-acid identity 93%), were obtained from a cDNA library of F. pardalis liver. These proteins consisted to two tandemly repeated homologous domains. The predicted amino-acid sequences of PSTBP1 and 2 were not homologous to that of saxiphilin, a reported saxitoxin binding protein, or sodium channels, but their N-terminus sequences were homologous to that of the reported tetrodotoxin binding protein from plasma of Fugu niphobles, which has not been fully characterized. The partially homologous cDNA sequences to PSTBP1 and 2 were also found in expressed sequence tag clones of nontoxic flounders liver. Presumably, PSTBP is involved in accumulation and/or excretion of toxins in puffer fish.

Amino Acid Sequence↗

PubMed1998

Cloning and characterization of an adenosine kinase from Physcomitrella involved in cytokinin metabolism.

Adenosine kinase (adk) from the moss Physcomitrella patens (Hedw.) B.S.G. was cloned from a cDNA library by functional complementation of an Escherichia coli purine auxotrophic strain. The length of the entire cDNA clone was 1175 bp with an open reading frame coding for a protein with a predicted molecular weight of 37.3 kDa. Southern analysis indicated the presence of a single adenosine kinase gene within the Physcomitrella genome. The deduced amino acid sequence had a 52% identity with the human adenosine kinase. The transfer of phosphate from ATP to adenosine resulting in AMP, as well as the phosphorylation of the cytokinin, isopentenyladenosine, to isopentenyladenosine monophosphate, was shown by in vitro enzyme assays using crude extracts from E. coli mutants expressing the adk cDNA clone and from Physcomitrella chloronemal tissue. Results from in vivo feeding of chloronemal tissue with tritiated isopentenyladenosine suggest that adenosine kinase plays an important role in the conversion of cytokinins towards their nucleotides in Physcomitrella.

Adenosine Kinase↗

PubMed2000

BRCA1 and BRCA2 mutations in ovarian cancer: Covariation with specific cytogenetic features.

We analyzed 37 primary invasive carcinomas for BRCA1 and BRCA2 mutations by screening the entire coding regions of both genes. Seven predicted truncating mutations (four in BRCA1 and three in BRCA2) and one novel BRCA1 missense variant (S1542C) were identified (8/37, 22%). Two of the BRCA1 mutations were somatic changes, whereas the remaining three BRCA1 changes and all mutations of BRCA2 were found to be of germline origin. All eight BRCA-positive tumors were serous or seropapillary carcinomas (8/27 serous tumors, 30%), and all but one were poorly differentiated. The correlation between tumor karyotype and BRCA status showed that clonal chromosomal aberrations were present in all BRCA-positive tumors (8/8) compared with 20 of 29 BRCA-negative ones. The most consistently affected region in BRCA-positive tumors was the long arm of chromosome 6; alterations within this arm with a breakpoint in band 6q21 were seen in four of five BRCA1-positive and in two of three BRCA2-positive tumors, but only in four of 20 karyotypically abnormal tumors without BRCA mutations, suggesting that the genetic pathways of tumor progression differ in the two groups. The high frequency of germline BRCA mutations detected in this pilot study (16% of 37 invasive carcinomas) points to the need for more extended analyses of population-based series of patients to determine the true contribution of these predisposing genes to the overall incidence of ovarian cancer in this population.

Journal Article↗

PubMed2006

Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis.

The developing science called structural genomics has focused to date mainly on high-throughput expression of individual proteins, followed by their purification and structure determination. In contrast, the term structural biology is used to denote the determination of structures, often complexes of several macromolecules, that illuminate aspects of biological function. Here we bridge structural genomics to structural biology with a procedure for determining protein complexes of previously unknown function from any organism with a sequenced genome. From computational genomic analysis, we identify functionally linked proteins and verify their interaction in vitro by coexpression/copurification. We illustrate this procedure by the structural determination of a previously unknown complex between a PE and PPE protein from the Mycobacterium tuberculosis genome, members of protein families that constitute approximately 10% of the coding capacity of this genome. The predicted complex was readily expressed, purified, and crystallized, although we had previously failed in expressing individual PE and PPE proteins on their own. The reason for the failure is clear from the structure, which shows that the PE and PPE proteins mate along an extended apolar interface to form a four-alpha-helical bundle, where two of the alpha-helices are contributed by the PE protein and two by the PPE protein. Our entire procedure for the identification, characterization, and structural determination of protein complexes can be scaled to a genome-wide level.

Bacterial Proteins↗

PubMed1984

Structural relationships among genes that control development: sequence homology between the Antennapedia, Ultrabithorax, and fushi tarazu loci of Drosophila.

Genes that regulate the development of the fruit fly Drosophila melanogaster exist as tightly linked clusters in at least two cases. These clusters, the bithorax complex (BX-C) and the Antennapedia complex (ANT-C), both contain multiple homoeotic loci: mutations in each locus cause a transformation of one part of the fly into another. Several repetitive DNA sequences, including at least one transposon, were mapped in the ANT-C. DNA from the 3' exon of Antennapedia (Antp), a homoeotic locus in the ANT-C, hybridized weakly to DNA from the 3' exon of Ultrabithorax (Ubx), a homoeotic locus in the BX-C. DNA from each of these 3' exons also hybridized weakly to DNA from the fushi tarazu locus of the ANT-C. The fushi tarazu (ftz) locus controls the number and differentiation of segments in the developing embryo. Sequence analysis of the cross-hybridizing DNA from the three loci revealed the conservation of predicted amino acid sequences derived from coding parts of the genes. This suggests that two homoeotic loci and a "segment-deficient" locus encode protein products with partially shared structures and that the three loci may be evolutionarily and functionally related.

Amino Acid Sequence↗

PubMed1995

Characterization of FP21, a cytosolic glycoprotein from Dictyostelium.

FP21 is a glycoprotein which, when tracked by radioactivity in its fucosyl moiety, was previously detected in the cytosol of Dictyostelium cells after cell fractionation. This compartmentalization is confirmed by SDS-polyacrylamide gel electrophoresis/Western blotting of cell fractions using three different antibodies. Although a substantial fraction of FP21 is also detected in the particulate fraction using these new antibodies, particulate FP21 is released by disrupting protein-protein interactions, but not membrane disruption. Since purified FP21 is susceptible to aggregation, and purified nuclei do not contain FP21, particulate FP21 is also part of the cytosol. Additional compositional and structural information provides strong evidence that FP21 does not at any time traverse the rough endoplasmic reticulum. First, cDNAs spanning the entire coding region of the FP21 gene predict no hydrophobic motifs expected to promote membrane insertion, but do predict an NH2-terminal coiled coil domain which could explain aggregation. Second, monosaccharide composition analysis of the predominant glycoform of FP21 yields 2 mol of galactose, 1 mol of xylose, and 1 mol of fucose/mol of polypeptide; FP21 from a fucosylation-defective mutant contains 1 additional mol of xylose in place of fucose. Thus the N-glycosylation sequon present in FP21 is not utilized by oligosaccharyl transferase, which resides in the rough endoplasmic reticulum. These findings indicate that nascent FP21 remains in the cytosol after synthesis and is therefore glycosylated by unusual cytosolic xylosyl-, galactosyl-, and fucosyltransferases.

Amino Acid Sequence↗

PubMed1999

Purification of the spliced leader ribonucleoprotein particle from Leptomonas collosoma revealed the existence of an Sm protein in trypanosomes. Cloning the SmE homologue.

Trans-splicing in trypanosomes involves the addition of a common spliced leader (SL) sequence, which is derived from a small RNA, the SL RNA, to all mRNA precursors. The SL RNA is present in the cell in the form of a ribonucleoprotein, the SL RNP. Using conventional chromatography and affinity selection with 2'-O-methylated RNA oligonucleotides at high ionic strength, five proteins of 70, 16, 13, 12, and 8 kDa were co-selected with the SL RNA from Leptomonas collosoma, representing the SL RNP core particle. Under conditions of lower ionic strength, additional proteins of 28 and 20 kDa were revealed. On the basis of peptide sequences, the gene coding for a protein with a predicted molecular weight of 11.9 kDa was cloned and identified as homologue of the cis-spliceosomal SmE. The protein carries the Sm motifs 1 and 2 characteristic of Sm antigens that bind to all known cis-spliceosomal uridylic acid-rich small nuclear RNAs (U snRNAs), suggesting the existence of Sm proteins in trypanosomes. This finding is of special interest because trypanosome snRNPs are the only snRNPs examined to date that are not recognized by anti-Sm antibodies. Because of the early divergence of trypanosomes from the eukaryotic lineage, the trypanosome SmE protein represents one of the primordial Sm proteins in nature.

Amino Acid Sequence↗

PubMed2006

PSF, LSF and S/P in mammography: GEANT4 validation.

The main goal of this study was to validate the predictions of GEANT4, a Monte Carlo code originally developed for high-energy physics, for low-energy (10-40 keV) photon transmission and scattering through matter similar to biological tissue. We compared GEANT4 calculations with existing phantom data relevant for the mammographic imaging technique. This work showed that scattered-to-primary ratio data can be simulated using GEANT4 with a deviation smaller than 5%. At the same time, we encountered a limitation in the small-angle region description by the code, which is important for point- and line-spread function calculations. The comparison with forward angle data showed that the GEANT4 models, known as "G4 Low Energy" and "G4 Penelope", describe the measurements for X-ray beams typically used in mammography better than 10% for angles above 10 degrees, and that "G4 Low Energy" is preferable to "G4 Penelope ". The results confirm the possible use of GEANT4 for the optimization of applications based on low-energy photon transmission and scattering.

Female↗

PubMed1998

Bassoon, a novel zinc-finger CAG/glutamine-repeat protein selectively localized at the active zone of presynaptic nerve terminals.

The molecular architecture of the cytomatrix of presynaptic nerve terminals is poorly understood. Here we show that Bassoon, a novel protein of >400,000 Mr, is a new component of the presynaptic cytoskeleton. The murine bassoon gene maps to chromosome 9F. A comparison with the corresponding rat cDNA identified 10 exons within its protein-coding region. The Bassoon protein is predicted to contain two double-zinc fingers, several coiled-coil domains, and a stretch of polyglutamines (24 and 11 residues in rat and mouse, respectively). In some human proteins, e.g., Huntingtin, abnormal amplification of such poly-glutamine regions causes late-onset neurodegeneration. Bassoon is highly enriched in synaptic protein preparations. In cultured hippocampal neurons, Bassoon colocalizes with the synaptic vesicle protein synaptophysin and Piccolo, a presynaptic cytomatrix component. At the ultrastructural level, Bassoon is detected in axon terminals of hippocampal neurons where it is highly concentrated in the vicinity of the active zone. Immunogold labeling of synaptosomes revealed that Bassoon is associated with material interspersed between clear synaptic vesicles, and biochemical studies suggest a tight association with cytoskeletal structures. These data indicate that Bassoon is a strong candidate to be involved in cytomatrix organization at the site of neurotransmitter release.

Amino Acid Sequence↗