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At least 1,639 records · Page 91Linked to original sources
PubMed2000

Quantification of liver iron concentration with magnetic resonance imaging by combining T1-, T2-weighted spin echo sequences and a gradient echo sequence.

BACKGROUND: The aim of the study was to quantify hepatic iron by MRI for practical use. METHODS: In twenty-three patients with various degrees of iron overload, measurements were carried out with a 1.5 Tesla MR unit. A combination of pulse sequences (T1, T2 and gradient echo) enabled us to quantify smaller amounts of liver iron as accurately as larger amounts of liver iron. The gradient echo sequence provided us with a good correlation when detecting smaller amounts of iron in the liver where the T1 sequence provided a good correlation when larger amounts of iron were present. RESULTS: The combination of the three sequences showed a nice correlation (r=-0. 93, P<0.001) and provided us with an accurate estimate of the liver iron content (LIC). This correlation was achieved with a LIC from the lower range of normal up to LIC of 146 mmol/kg dry weight, which seems the highest measurable liver iron content for a 1.5 Tesla MRI. Measuring in the lower range makes it possible to decide whether further invasive diagnostic investigations by a liver biopsy are indicated. CONCLUSION: MRI is a useful tool to quantify iron overload non-invasively. In cases where a liver biopsy is hazardous MRI can easily be used to obtain reliable, quantitative information about the initial LIC. Quantification by MRI could also be used for follow up of the iron content during depletion treatment by phlebotomy or iron chelation. The stronger the magnet the more sensitive the detection of concentrations up to 150 mmol/kg is. A semi-quantitative judgement will only be possible with severe iron overload over 150 mmol/kg. If such an iron excess is found, a liver biopsy should be performed to exclude cirrhosis.

Adult↗
PubMed1997

Cross-linking and sequence specific alkylation of DNA by aziridinyl quinones. 2. Structure requirements for sequence selectivity.

The cytotoxicities and DNA sequence selectivity for guanine-N7 alkylation of 22 mono- and disubstituted 2,5-diaziridinyl-1,4-benzoquinones have been investigated. Several quinones produced patterns of alkylation following reduction with a selectivity for 5'-TGC-3' sequences. This sequence selectivity appeared to be dependent only on the presence of a hydrogen in position-6 of the quinone. A computer model, based on published crystallographic data, was used to explain this selectivity. The sequence selective quinones were generally more cytotoxic that the quinones which reacted randomly.

Alkylation↗
PubMed1999

Complete sequence and gene map of a human major histocompatibility complex. The MHC sequencing consortium.

Here we report the first complete sequence and gene map of a human major histocompatibility complex (MHC), a region on chromosome 6 which is essential to the immune system. When it was discovered over 50 years ago the region was thought to specify histocompatibility genes, but their nature has been resolved only in the last two decades. Although many of the 224 identified gene loci (128 predicted to be expressed) are still of unknown function, we estimate that about 40% of the expressed genes have immune system function. Over 50% of the MHC has been sequenced twice, in different haplotypes, giving insight into the extraordinary polymorphism and evolution of this region. Several genes, particularly of the MHC class II and III regions, can be traced by sequence similarity and synteny to over 700 million years ago, clearly predating the emergence of the adaptive immune system some 400 million years ago. The sequence is expected to be invaluable for the identification of many common disease loci. In the past, the search for these loci has been hampered by the complexity of high gene density and linkage disequilibrium.

Chromosome Mapping↗
PubMed2003

Fetal hydrocolpos leading to Pierre Robin sequence: an unreported effect of oligohydramnios sequence.

The presence of distal atretic vagina causing accumulation of fluid and mucus secretions in the proximal vaginal cavity resulted in fetal hydrocolpos. Obstructive uropathy developed gradually because of direct compression of hydrocolpos on bilateral lower ureters, resulting in oligohydramnios from decreased urine formation. Oligohydramnios inhibited normal mandibular development with resulting cleft palate and glossoptosis (Pierre Robin Sequence). The development of sequence of events in this case indicates Pierre Robin Sequence as another effect of Oligohydramnios Sequence arising out of deformational forces acting on cranio-facial structures.

Adult↗
PubMed1982

Cloned cDNA sequences of the hypoxanthine/guanine phosphoribosyltransferase gene from a mouse neuroblastoma cell line found to have amplified genomic sequences.

Cloned cDNA sequences of the murine hypoxanthine/guanine phosphoribosyltransferase (HPRT; EC 2.4.2.8) gene have been isolated by using a mouse neuroblastoma cell line containing increased levels of a variant HPRT protein. We have used these sequences as probes to demonstrate that protein overproduction in this cell line is a consequence of at least a 20-fold increase in HPRT mRNA levels resulting from approximately 50-fold amplification of HPRT genomic sequences. The largest cDNA insert so far characterized represents about 70% of the HPRT mRNA sequence. This cDNA is shown to possess regions of homology with mRNA and DNA from Chinese hamster, baboon, and human, thus facilitating detailed analysis of this locus in these four species.

Animals↗
PubMed1986

Dinoflagellate 17S rRNA sequence inferred from the gene sequence: Evolutionary implications.

We present the complete sequence of the nuclear-encoded small-ribosomal-subunit RNA inferred from the cloned gene sequence of the dinoflagellate Prorocentrum micans. The dinoflagellate 17S rRNA sequence of 1798 nucleotides is contained in a family of 200 tandemly repeated genes per haploid genome. A tentative model of the secondary structure of P. micans 17S rRNA is presented. This sequence is compared with the small-ribosomal-subunit rRNA of Xenopus laevis (Animalia), Saccharomyces cerevisiae (Fungi), Zea mays (Planta), Dictyostelium discoideum (Protoctista), and Halobacterium volcanii (Monera). Although the secondary structure of the dinoflagellate 17S rRNA presents most of the eukaryotic characteristics, it contains sufficient archaeobacterial-like structural features to reinforce the view that dinoflagellates branch off very early from the eukaryotic lineage.

Journal Article↗
PubMed1988

In vivo "photofootprint" changes at sequences between the yeast GAL1 upstream activating sequence and "TATA" element require activated GAL4 protein but not a functional TATA element.

Transcription of the yeast GAL1 and GAL10 genes is induced by growth on galactose. Using the technique of photofootprinting in vivo, we previously documented equivalent transcription-dependent footprints within the putative "TATA" elements of both genes. To explore the functional significance of these observations, we created a 3-base-pair substitution mutation within the GAL1 promoter TATA element, which disrupted the ATATAA consensus sequence but left intact the photomodification targets. The mutation reduced galactose-induced RNA levels by a factor of 100. The mutant promoter no longer displayed the characteristic TATA sequence footprint, supporting the hypothesis that transcription activation involves the binding of a TATA box factor. We also observed a collection of transcription-correlated alterations in the modification pattern at sites between the UASG and the GAL1 TATA element, within sequences that are not required for inducible transcription. These patterns, characteristic of the induced wild-type GAL1 gene, were still galactose inducible with the TATA mutant GAl1 promoter, despite the low level of transcription from this promoter. We conclude that the GAL4-dependent protein/DNA structure responsible for the altered pattern within nonessential sequences is therefore not strictly coupled to an active TATA element or to high levels of expression. Nonetheless, the patterns probably reflect a stable protein-dependent structure that accompanies assembly of the transcription initiation complex.

DNA, Fungal↗
PubMed1992

Binding of sequence-specific proteins to the adenosine- plus uridine-rich sequences of the murine granulocyte/macrophage colony-stimulating factor mRNA.

Adenosine+uridine (AU)-rich sequences in the 3' untranslated region (3'UTR) of the mRNA of many cytokines and oncogenes play an important role in mediating RNA degradation. Among the cytokines containing such AU-rich sequences in their 3'UTR is the hematopoietic growth factor granulocyte/macrophage colony-stimulating factor (GM-CSF). GM-CSF gene expression in T cells is regulated by modulation of mRNA half-life. Transfection studies using murine EL-4 thymoma cells have demonstrated that degradation depends on the presence of specific elements in the 3'UTR, including the AU-rich sequences. A number of AU-binding factors have recently been discovered, suggesting that specific regulation may occur through specific protein-mRNA interaction(s). We present evidence from gel-shift analyses and label-transfer experiments that murine cells contain proteins that bind specifically to AU-rich sequences. Three major proteins of 33, 39.5, and 42 kDa are detected. Phorbol ester treatment of cells does not alter the abundance or apparent binding affinity of the proteins. The 33-kDa protein is present in the cytoplasm of murine and human cells, whereas the 39.5- and 42-kDa proteins are present in murine extracts only. Constitutively expressed AU-binding proteins of the type that we describe may function by directing mRNA degradation in the absence of a stimulus to the contrary.

3T3 Cells↗
PubMed1996

Apolipoprotein B sequence requirements for hepatic very low density lipoprotein assembly. Evidence that hydrophobic sequences within apolipoprotein B48 mediate lipid recruitment.

We studied the structural requirements of apolipoprotein (apo) B for assembly of very low density lipoproteins (VLDL) using rat hepatoma McA-RH7777 cells expressing human apoB (h-apoB). Recombinant h-apoB48, like endogenous rat apoB48 (r-apoB48), was secreted as VLDL in addition to high density lipoproteins (HDL) by transfected cells, indicating that the N-terminal 48% of apoB contains sequences sufficient for VLDL assembly. Truncation of the C terminus of h-apo-B48 to -B42 or -B37 had little effect on the ability of apoB to assemble VLDL, whereas truncation to -B34 or -B29 markedly diminished or abolished VLDL formation. None of the truncations affected the integration of apoB into HDL. To determine whether the ability to assemble VLDL is governed by apoB length or by sequences beyond apoB29, we created chimeric proteins that contained human apoA-I and a segment derived from between the C-terminal 29 and 34%, 34 and 37%, or 37 and 42% of apoB100. The resulting chimeras, namely AI/B29-34, AI/B34-37, and AI/B37-42, were secreted by the transfected cells as lipoproteins with buoyant density (d < 1.006 g/ml), electrophoretic mobility (pre-beta), and size characteristics of human plasma VLDL. The chimeras could assemble discrete VLDL particles devoid of endogenous r-apoB100, and could actively recruit triglycerides and phospholipids into the lipoproteins. However, these chimeras were secreted inefficiently. Pulse-chase analysis showed that less than 5% of the newly synthesized AI/B proteins were secreted, and more than 70% was degraded intracellularly. Degradation of the chimeras could be blocked by the cysteine protease inhibitor N-acetyl-leucyl-leucyl-norleucinal, but the treatment did not enhance their secretion. Protease protection analysis of microsomes isolated from transfected cells indicated that >65% of AI/B chimeras (compared with <25% of r-apoB100) were inaccessible to exogenous trypsin. These data suggest that the recruitment of large quantities of triglycerides during VLDL formation is not governed simply by apoB length, but is mediated by short hydrophobic sequences ranging from 152 to 237 amino acids (3-5%) of apoB. The existence of multiple such hydrophobic sequences within apoB48 may facilitate efficient assembly of hepatic VLDL particles.

Animals↗
PubMed1997

COL1A1 transgene expression in stably transfected osteoblastic cells. Relative contributions of first intron, 3'-flanking sequences, and sequences derived from the body of the human COL1A1 minigene.

Collagen reporter gene constructs have be used to identify cell-specific sequences needed for transcriptional activation. The elements required for endogenous levels of COL1A1 expression, however, have not been elucidated. The human COL1A1 minigene is expressed at high levels and likely harbors sequence elements required for endogenous levels of activity. Using stably transfected osteoblastic Py1a cells, we studied a series of constructs (pOBColCAT) designed to characterize further the elements required for high level of expression. pOBColCAT, which contains the COL1A1 first intron, was expressed at 50-100-fold higher levels than ColCAT 3.6, which lacks the first intron. This difference is best explained by improved mRNA processing rather than a transcriptional effect. Furthermore, variation in activity observed with the intron deletion constructs is best explained by altered mRNA splicing. Two major regions of the human COL1A1 minigene, the 3'-flanking sequences and the minigene body, were introduced into pOBColCAT to assess both transcriptional enhancing activity and the effect on mRNA stability. Analysis of the minigene body, which includes the first five exons and introns fused with the terminal six introns and exons, revealed an orientation-independent 5-fold increase in CAT activity. In contrast the 3'-flanking sequences gave rise to a modest 61% increase in CAT activity. Neither region increased the mRNA half-life of the parent construct, suggesting that CAT-specific mRNA instability elements may serve as dominant negative regulators of stability. This study suggests that other sites within the body of the COL1A1 minigene are important for high expression, e.g. during periods of rapid extracellular matrix production.

Animals↗
PubMed2000

Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro.

We have carried out a human cDNA sequencing project to accumulate information regarding the coding sequences of unidentified human genes. As an extension of the preceding reports, we herein present the entire sequences of 150 cDNA clones of unknown human genes, named KIAA1294 to KIAA1443, from two sets of size-fractionated human adult and fetal brain cDNA libraries. The average sizes of the inserts and corresponding open reading frames of cDNA clones analyzed here reached 4.8 kb and 2.7 kb (910 amino acid residues), respectively. From sequence similarities and protein motifs, 73 predicted gene products were functionally annotated and 97% of them were classified into the following four functional categories: cell signaling/communication, nucleic acid management, cell structure/motility and protein management. Additionally, the chromosomal loci of the genes were assigned by using human-rodent hybrid panels for those genes whose mapping data were not available in the public databases. The expression profiles of the genes were also studied in 10 human tissues, 8 brain regions, spinal cord, fetal brain and fetal liver by reverse transcription-coupled polymerase chain reaction, products of which were quantified by enzyme-linked immunosorbent assay.

Adult↗
PubMed2000

Prediction of the coding sequences of unidentified human genes. XIX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro.

As an extension of our human cDNA project for accumulating sequence information on the coding sequences of unidentified genes, we here present the entire sequences of 100 cDNA clones of unidentified genes, named KIAA1673-KIAA1772, from three sets of size-fractionated cDNA libraries derived from human adult whole brain, hippocampus, and fetal whole brain. The average sizes of the inserts and corresponding open reading frames of cDNA clones analyzed here were 4.9 kb and 2.7 kb (corresponding to 895 amino acid residues), respectively. By computer-assisted analysis of the deduced amino acid sequences, 44 predicted gene products were classified into five functional categories of proteins relating to cell signaling/communication, nucleic acid management, cell structure/motility, protein management, and metabolism. Furthermore, the expression profiles of the genes were also studied in 10 human tissues, 8 brain regions, spinal cord, fetal brain and fetal liver by reverse-transcription-coupled polymerase chain reaction, the products of which were quantified by enzyme-linked immunosorbent assay.

Amino Acids↗
PubMed2000

SELEX_DB: an activated database on selected randomized DNA/RNA sequences addressed to genomic sequence annotation.

SELEX_DB is a novel curated database on selected randomized DNA/RNA sequences designed for accumulation of experimental data on functional site sequences obtained by using SELEX and SELEX-like technologies from the pools of random sequences. This database also contains the programs for DNA/RNA functional site recognition within arbitrary nucleotide sequences. The first release of SELEX_DB has been installed under SRS and is available through the WWW at http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/

DNA↗
PubMedDate not supplied

Breath-held MR cholangiopancreatography with half-averaged single shot hybrid rapid acquisition with relaxation enhancement sequence: comparison of fast GRE and SE sequences.

PURPOSE: Our goal was to determine whether half-averaged single shot hybrid rapid acquisition with relaxation enhancement (single shot hybrid RARE) sequence can improve image quality, duct conspicuity, signal intensity ratio (SIR), and contrast-to-noise ratio (CNR) of MR cholangiopancreatography (MRCP) by comparing it with two other MRCP sequences: fast SE (FSE) and contrast-enhanced Fourier-acquired steady-state technique (CE-FAST). METHOD: MRCP with three sequences was obtained in 46 people (10 volunteers, 36 patients with pancreatobiliary disease). Overall image quality and duct conspicuity were graded. SIR and CNR were also measured. RESULTS: Overall image quality was graded excellent or good in all 46 patients (100%) with single shot hybrid RARE, in 38 of 46 (83%) with FSE, and in 5 of 46 (11%) with CE-FAST. Duct conspicuity was the best in single shot hybrid RARE statistically. SIR was the highest in FSE, while CNR was highest statistically in single shot hybrid RARE of three sequences. CONCLUSION: Single shot hybrid RARE can provide consistently higher quality MRCP than FSE and CE-FAST because sequential images by single shot hybrid RARE minimize respiratory, bowel, and cardiac motion artifacts.

Adolescent↗
PubMed2002

Structural characterization of a new crystal form of the four-way Holliday junction formed by the DNA sequence d(CCGGTACCGG)2: sequence versus lattice?

DNA-strand exchange is a vital step in the recombination process, of which a key intermediate is the four-way DNA Holliday junction formed transiently in most living organisms. Here, the single-crystal structure at a resolution of 2.35 A of such a DNA junction formed by d(CCGGTACCGG)(2), which has crystallized in a more highly symmetrical packing mode to that previously observed for the same sequence, is presented. In this case, the structure is isomorphous to the mismatch sequence d(CCGGGACCGG)(2), which reveals the roles of both lattice and DNA sequence in determining the junction geometry. The helices cross at the larger angle of 43.0 degrees (the previously observed angle for this sequence was 41.4 degrees) as a right-handed X. No metal cations were observed; the crystals were grown in the presence of only group I counter-cations.

Base Pair Mismatch↗
PubMed2005

Utility of three dimension fast asymmetric spin-echo (3D-FASE) sequences in MR sialographic sequences: model and volunteer studies.

OBJECTIVES: To evaluate the utility of 3D-FASE for the visualization of salivary gland ducts for use in MR sialographic sequences. METHODS: We compared MR sialographic images and virtual endoscopic views from 3D-FASE with those from three kinds of sequences described by previous reports in a 3D parotid gland duct model and volunteer. The four sequences were two-dimension fast spin-echo (2D-FSE), three-dimension fast spin-echo (3D-FSE), two-dimension fast asymmetric spin-echo (2D-FASE), and three-dimension fast asymmetric spin-echo (3D-FASE). RESULTS: In the 3D parotid gland duct model, image visibility on visual score was clearest with 3D-FSE, followed by 3D-FASE (P = 0.028). In the volunteers, the visualization of images improved in the following order: 3D-FASE > 3D-FSE > 2D-FSE > 2D-FASE. CONCLUSIONS: The technique of 3D-FASE sequencing is more suitable and useful for MR sialography with an appropriate acquisition time.

Adolescent↗
PubMed2004

Ambiguous allele combinations in HLA Class I and Class II sequence-based typing: when precise nucleotide sequencing leads to imprecise allele identification.

Sequence-based typing (SBT) is one of the most comprehensive methods utilized for HLA typing. However, one of the inherent problems with this typing method is the interpretation of ambiguous allele combinations which occur when two or more different allele combinations produce identical sequences. The purpose of this study is to investigate the probability of this occurrence. We performed HLA-A,-B SBT for Exons 2 and 3 on 676 donors. Samples were analyzed with a capillary sequencer. The racial distribution of the donors was as follows: 615-Caucasian, 13-Asian, 23-African American, 17-Hispanic and 8-Unknown. 672 donors were analyzed for HLA-A locus ambiguities and 666 donors were analyzed for HLA-B locus ambiguities. At the HLA-A locus a total of 548 total ambiguous allele combinations were identified (548/1344 = 41%). Most (278/548 = 51%) of these ambiguities were due to the fact that Exon 4 analysis was not performed. At the HLA-B locus 322 total ambiguous allele combinations were found (322/1332 = 24%). The HLA-B*07/08/15/27/35/44 antigens, common in Caucasians, produced a large portion of the ambiguities (279/322 = 87%). A large portion of HLA-A and B ambiguous allele combinations can be addressed by utilizing a group-specific primary amplification approach to produce an unambiguous homozygous sequence. Therefore, although the prevalence of ambiguous allele combinations is high, if the resolution of these ambiguities is clinically warranted, methods exist to compensate for this problem.

Journal Article↗
PubMed2006

Taxonomic reliability of DNA sequences in public sequence databases: a fungal perspective.

BACKGROUND: DNA sequences are increasingly seen as one of the primary information sources for species identification in many organism groups. Such approaches, popularly known as barcoding, are underpinned by the assumption that the reference databases used for comparison are sufficiently complete and feature correctly and informatively annotated entries. METHODOLOGY/PRINCIPAL FINDINGS: The present study uses a large set of fungal DNA sequences from the inclusive International Nucleotide Sequence Database to show that the taxon sampling of fungi is far from complete, that about 20% of the entries may be incorrectly identified to species level, and that the majority of entries lack descriptive and up-to-date annotations. CONCLUSIONS: The problems with taxonomic reliability and insufficient annotations in public DNA repositories form a tangible obstacle to sequence-based species identification, and it is manifest that the greatest challenges to biological barcoding will be of taxonomical, rather than technical, nature.

DNA, Fungal↗