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At least 451 records · Page 25Linked to original sources
PubMed2000

Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning.

The primary neuroendocrine interface, hypothalamus and pituitary, together with adrenals, constitute the major axis responsible for the maintenance of homeostasis and the response to the perturbations in the environment. The gene expression profiling in the human hypothalamus-pituitary-adrenal axis was catalogued by generating a large amount of expressed sequence tags (ESTs), followed by bioinformatics analysis (http://www.chgc.sh.cn/ database). Totally, 25,973 sequences of good quality were obtained from 31,130 clones (83.4%) from cDNA libraries of the hypothalamus, pituitary, and adrenal glands. After eliminating 5,347 sequences corresponding to repetitive elements and mtDNA, 20,626 ESTs could be assembled into 9, 175 clusters (3,979, 3,074, and 4,116 clusters in hypothalamus, pituitary, and adrenal glands, respectively) when overlapping ESTs were integrated. Of these clusters, 2,777 (30.3%) corresponded to known genes, 4,165 (44.8%) to dbESTs, and 2,233 (24.3%) to novel ESTs. The gene expression profiles reflected well the functional characteristics of the three levels in the hypothalamus-pituitary-adrenal axis, because most of the 20 genes with highest expression showed statistical difference in terms of tissue distribution, including a group of tissue-specific functional markers. Meanwhile, some findings were made with regard to the physiology of the axis, and 200 full-length cDNAs of novel genes were cloned and sequenced. All of these data may contribute to the understanding of the neuroendocrine regulation of human life.

Alternative Splicing↗
PubMed2005

Efficacy of spectral presaturation of inversion recovery in evaluating delayed myocardial enhancement.

OBJECTIVE: Delayed myocardial enhancement is caused by a variety of cardiovascular diseases. The extent of the enhanced area has been examined by the inversion recovery (IR) method, whereby at the inversion time (TI), normal myocardium shows a low signal intensity. In this sequence, as pericardial fat shows a very high intensity, a delayed enhancement just below the pericardium may be indistinct. To improve the accuracy of delayed myocardial enhancement, we employed the spectral presaturation of inversion recovery (SPIR) method. MATERIALS AND METHODS: Thirty-five patients with symptoms of cardiovascular disease aged between 36 and 80 years old (mean age, 62 years old) were investigated. Thirty were men and five were women. Inversion recovery and SPIR images were obtained 25 min after initial administration of a gadolinium-based contrast material. Each TI, when the signal intensity of the normal myocardium was null, was determined by images obtained at serial different TIs. A radiologist and a cardiologist examined each image by a consensus reading. The extent of myocardial enhancement was described as none, subendocardial, transmural and a random pattern in each case. Images were ranked over three levels and were based on whether myocardial enhancement could be easily detected or whether the contour of the myocardium was visualized precisely. Student's t-test was conducted to compare the quality of two sequences in all patients and in 22 patients who showed delayed myocardial enhancement. RESULTS: The imaging quality in evaluating delayed myocardial enhancement in all patients was superior with IR compared with SPIR, although it was not statistically significant. The imaging quality in the patients with delayed myocardial enhancement was similar between SPIR and IR. SPIR was superior to the IR sequence in two of the four patients who exhibited transmural enhancement. CONCLUSION: SPIR exhibited equivalent image quality to IR in evaluating delayed myocardial enhancement. As it has the potential advantage in patients with rich adipose tissue surrounding the myocardium, it can be an alternative sequence to evaluate myocardial viability.

Adult↗
PubMed2004

Optimization of Gd-DTPA-enhanced balanced turbo field echo sequence in abdominal imaging: clinical application.

PURPOSE: We performed MRI examinations of patients in order to confirm the enhancement effect of the balanced turbo field echo (bTFE) sequence with centric view ordering and SPIR (SPIR-centric-bTFE) as mentioned in the prior paper, and to evaluate the actual image quality of this sequence. MATERIALS AND METHODS: The upper abdomens of 30 patients with various abdominal disorders were examined with the SPIR-centric-bTFE sequence before and after Gd-DTPA administration. To assess the enhancement effect of Gd-DTPA, ROI measurements were taken in the aorta, superior mesenteric artery, portal vein, liver and bile juice in the common bile duct in each patient both in pre- and postcontrast images. Visual evaluations were also carried out in order to depict the peripheral vessels in the peritoneal fat and the apparent brightness of the soft-tissue organs. RESULTS: In all patients, the signal of the arteries after Gd-DTPA administration increased by about 50% compared with precontrast images. On the other hand, the veins and the liver showed a signal gain of less than 20% in postcontrast images. Consequently, only the signal of the arteries appeared enhanced in the postcontrast images. The visual evaluation revealed that postcontrast SPIR-centric-bTFE acquisition can depict the thin vessels clearly and the abdominal soft-tissue organs brightly. CONCLUSION: The balanced turbo field echo sequence with centric view ordering and SPIR after Gd-DTPA injection was considered the most appropriate protocol when this sequence was employed for abdominal imaging.

Blood Flow Velocity↗
PubMedDate not supplied

MR cholangiopancreatography: comparison of images obtained with 1.0 and 1.5 Tesla units.

OBJECTIVE: To compare the image quality and visualization obtained in MR cholangiopancreatography (MRCP) using different high-field strength (1.0 vs. 1.5 Tesla) MR units and to assess the effect of field strength on MRCP. MATERIALS AND METHODS: This study population included 10 healthy volunteers and 37 patients suspected of having pancreatobiliary diseases. MRCP images were obtained using two MR units with different high-field strengths (1.0 and 1.5 Tesla), with half-Fourier acquisition single-shot turbo spin-echo (HASTE) and rapid acquisition by relaxation enhancement (RARE) sequences. The image quality and visualization of each portion of the pancreatobiliary system were graded and recorded using a four-point scale. Additionally, the signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) were measured. RESULTS: The SNR and CNR in HASTE sequences acquired with the 1.5 Tesla (T) unit were significantly higher than those acquired with the 1.0 T unit (p=0.001). In qualitative analysis, there were no statistically significant differences in image quality or visualization of the ducts in either HASTE or RARE sequences between 1.0 T and 1.5 T. CONCLUSION: Our study showed that visual image quality provided by MRCP was equivalent at 1.0 and 1.5 T.

Adult↗
PubMedDate not supplied

Safety and optimum concentration of a manganese chloride-based oral MR contrast agent.

To determine the safety of a manganese chloride-based oral magnetic resonance (MR) contrast agent and the ideal concentration of the agent for marking in three different anatomic sites (stomach, middle of the small bowel, and ileocecal region), six healthy volunteers were evaluated before and after administration of 900 mL of three different concentrations of the contrast agent. Images were evaluated subjectively and objectively. No adverse events were noted. There was a minimal rise in manganese blood levels at 6 hours after administration, with a return to baseline at 24 hours. The imaging data demonstrated good-to-excellent bowel marking on T1-weighted images at all three concentrations. However, on T2-weighted images, the 40 mg Mn+2/L concentration provided improved hypointense bowel marking relative to the 20 mg/L concentration. Little difference was seen between the 40 and 60 mg/L concentrations. Fast T1- and T2-weighted sequences provided superior image quality to that of conventional spin-echo sequences.

Administration, Oral↗
PubMed2003

A thermostable alpha-arabinofuranosidase from xylanolytic Bacillus pumilus: purification and characterisation.

Bacillus pumilus PS213 secretes an alpha-L-arabinofuranosidase (AF) when grown in the presence of arabinogalactan or oat meal. The enzyme has been purified to homogeneity and characterised. Its molecular mass, as determined by gel filtration, is 220 kDa, while sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) showed a single band of approximately 60 kDa. According to the result of the mass spectrometry analysis showing a molecular mass of 56 kDa, the enzyme should be a homotetramer. The isoelectric point was found to be 5.2, the enzyme activity was optimal at 55 degrees C and pH 7.0. The enzyme retained 80% of its activity after 2 h at 65 degrees C and lost 50% of activity at 75 degrees C after 135 min. The Michaelis constant K(m) and V(max) for p-nitrophenylarabinofuranoside at 37 degrees C were 1.7 mM and 52.9 U mg(-1), respectively. N-terminal sequence analysis and internal peptide fragments showed homology with glycosyl hydrolases of family 51.

Amino Acid Sequence↗
PubMed2000

Resolution of allelic and non-allelic variants of histone H1 by cation-exchange-hydrophilic-interaction chromatography.

A mixed-mode high-performance liquid chromatography (HPLC) method that resolves the six known non-allelic variants of chicken erythrocyte histone H1 is described. Common, but previously unknown, allelic variants of H1 that comigrate in polyacrylamide gel electrophoresis are also resolved. The resolution of H1 variants achieved by this method should be useful in determining the functional significance of H1 sequence heterogeneity and in analyses of post-translational modification of H1. Furthermore, the principles behind the separation should be applicable to analyses of polymorphism in other proteins.

Acetonitriles↗
PubMed2002

Microarray databases: standards and ontologies.

A single microarray can provide information on the expression of tens of thousands of genes. The amount of information generated by a microarray-based experiment is sufficiently large that no single study can be expected to mine each nugget of scientific information. As a consequence, the scale and complexity of microarray experiments require that computer software programs do much of the data processing, storage, visualization, analysis and transfer. The adoption of common standards and ontologies for the management and sharing of microarray data is essential and will provide immediate benefit to the research community.

Database Management Systems↗
PubMed2002

Empirical determination of effective gap penalties for sequence comparison.

MOTIVATION: No general theory guides the selection of gap penalties for local sequence alignment. We empirically determined the most effective gap penalties for protein sequence similarity searches with substitution matrices over a range of target evolutionary distances from 20 to 200 Point Accepted Mutations (PAMs). RESULTS: We embedded real and simulated homologs of protein sequences into a database and searched the database to determine the gap penalties that produced the best statistical significance for the distant homologs. The most effective penalty for the first residue in a gap (q+r) changes as a function of evolutionary distance, while the gap extension penalty for additional residues (r) does not. For these data, the optimal gap penalties for a given matrix scaled in 1/3 bit units (e.g. BLOSUM50, PAM200) are q=25-0.1 * (target PAM distance), r=5. Our results provide an empirical basis for selection of gap penalties and demonstrate how optimal gap penalties behave as a function of the target evolutionary distance of the substitution matrix. These gap penalties can improve expectation values by at least one order of magnitude when searching with short sequences, and improve the alignment of proteins containing short sequences repeated in tandem.

Amino Acid Sequence↗
PubMed2003

Evolutionary algorithms for finding optimal gene sets in microarray prediction.

MOTIVATION: Microarray data has been shown recently to be efficacious in distinguishing closely related cell types that often appear in different forms of cancer, but is not yet practical clinically. However, the data might be used to construct a minimal set of marker genes that could then be used clinically by making antibody assays to diagnose a specific type of cancer. Here a replication algorithm is used for this purpose. It evolves an ensemble of predictors, all using different combinations of genes to generate a set of optimal predictors. RESULTS: We apply this method to the leukemia data of the Whitehead/MIT group that attempts to differentially diagnose two kinds of leukemia, and also to data of Khan et al. to distinguish four different kinds of childhood cancers. In the latter case we were able to reduce the number of genes needed from 96 to less than 15, while at the same time being able to classify all of their test data perfectly. We also apply this method to two other cases, Diffuse large B-cell lymphoma data (Shipp et al., 2002), and data of Ramaswamy et al. on multiclass diagnosis of 14 common tumor types. AVAILABILITY: http://stravinsky.ucsc.edu/josh/gesses/.

Algorithms↗
PubMed2003

Microarray standard data set and figures of merit for comparing data processing methods and experiment designs.

MOTIVATION: There is a very large and growing level of effort toward improving the platforms, experiment designs, and data analysis methods for microarray expression profiling. Along with a growing richness in the approaches there is a growing confusion among most scientists as to how to make objective comparisons and choices between them for different applications. There is a need for a standard framework for the microarray community to compare and improve analytical and statistical methods. RESULTS: We report on a microarray data set comprising 204 in-situ synthesized oligonucleotide arrays, each hybridized with two-color cDNA samples derived from 20 different human tissues and cell lines. Design of the approximately 24 000 60mer oligonucleotides that report approximately 2500 known genes on the arrays, and design of the hybridization experiments, were carried out in a way that supports the performance assessment of alternative data processing approaches and of alternative experiment and array designs. We also propose standard figures of merit for success in detecting individual differential expression changes or expression levels, and for detecting similarities and differences in expression patterns across genes and experiments. We expect this data set and the proposed figures of merit will provide a standard framework for much of the microarray community to compare and improve many analytical and statistical methods relevant to microarray data analysis, including image processing, normalization, error modeling, combining of multiple reporters per gene, use of replicate experiments, and sample referencing schemes in measurements based on expression change. AVAILABILITY/SUPPLEMENTARY INFORMATION: Expression data and supplementary information are available at http://www.rii.com/publications/2003/HE_SDS.htm

Base Sequence↗
PubMed2005

Homology-extended sequence alignment.

We present a profile-profile multiple alignment strategy that uses database searching to collect homologues for each sequence in a given set, in order to enrich their available evolutionary information for the alignment. For each of the alignment sequences, the putative homologous sequences that score above a pre-defined threshold are incorporated into a position-specific pre-alignment profile. The enriched position-specific profile is used for standard progressive alignment, thereby more accurately describing the characteristic features of the given sequence set. We show that owing to the incorporation of the pre-alignment information into a standard progressive multiple alignment routine, the alignment quality between distant sequences increases significantly and outperforms state-of-the-art methods, such as T-COFFEE and MUSCLE. We also show that although entirely sequence-based, our novel strategy is better at aligning distant sequences when compared with a recent contact-based alignment method. Therefore, our pre-alignment profile strategy should be advantageous for applications that rely on high alignment accuracy such as local structure prediction, comparative modelling and threading.

Algorithms↗
PubMedDate not supplied

[Heterogeneity and homologies of the repeating and unique DNA of dragonflies (Odonata, Insecta)].

A relative content of unique and reiterated nucleotide sequences in DNA of eleven dragonfly species was estimated. The degree of intra- and intergenomic divergence of these DNA sequences was determined by means of DNA-DNA hybridization. Species from different genera share 40-45% of the repetitive sequences and those from different families--from 11 to 20% only. Data on the thermostability of homo- and heteroduplexes suggest that new families of the repetitive sequences have arisen repeatedly during dragonflies evolution. The quality of homologous unique sequences in the DNA compared (20-97%) correlates with the taxonomic relationships of species. Phylogenesis of some dragonfly families is discussed in view of the results obtained.

Animals↗
PubMed2025

Assembling genomes of non-model plants: A case study with evolutionary insights from Ranunculus (Ranunculaceae).

Whereas genome sequencing and assembly technologies are improving, cost can still be prohibitive for plant species with large, complex genomes. As a consequence, genomics work on some taxa in evolutionarily pivotal positions in the vascular plant tree of life has been hampered. The species-rich genus Ranunculus (Ranunculaceae) is an important angiosperm group for the study of polyploidy, apomixis, and reticulate evolution. However, neither mitochondrial nor high-quality nuclear genome sequences are available. This limits phylogenomic, functional, and taxonomic analyses thus far. Here, we tested Illumina short-read, Oxford Nanopore Technology (ONT) and PacBio (HiFi) long-read, and hybrid-read assembly strategies. We sequenced the diploid progenitor species R. cassubicifolius (R. auricomus species complex) and selected the best assemblies in terms of completeness, contiguity, and quality scores. We first assembled the plastome (156 kbp, 85 genes) and mitogenome (1.18 Mbp, 40 genes) sequences using Illumina and Illumina-PacBio-hybrid strategies, respectively. We also present an updated plastome and the first mitogenome phylogeny of Ranunculaceae, including studies of gene loss (e.g., infA, ycf15, or rps) with evolutionary implications. For the nuclear genome sequence, we favored a PacBio-based assembly polished three times with filtered short reads and subsequently scaffolded into eight pseudochromosomes by chromatin conformation data (Hi-C). We obtained a haploid genome sequence of 2.69 Gbp, with 94.1% complete BUSCO genes found and 35 482 annotated genes, and inferred ancient gene duplications compared to existing Ranunculales genomes. The genomic information presented here will enable advanced evolutionary-functional analyses for the species complex, but also for the genus and beyond Ranunculaceae.

Ranunculus↗
PubMed1998

[The influence of several factors on automated DNA sequencing].

OBJECTIVE: To investigate the influence of several factors on isothermal automated DNA sequencing. METHODS: The effects of DNA purity and DNA concentration, as well as the quality of water used during sequencing on automated DNA sequencing results were retrospectively analyzed. RESULTS: When the DNA was not pure enough, the nucleotide curve showed lower ratio of signal to noise, or compression would occur, leading to difficulty in correctly judging the nucleotides; the readable length of nucleotides was shorter when low concentration of DNA was used; when the quality of water used in sequencing reaction and polyacrylamide gel solution was not high enough, the peaks of nucleotides became wider and flatter, or double peaks would occur, resulting in unreadable sequences. CONCLUSION: DNA purity and concentration as well as quality of water used in sequencing reaction and polyacrylamide gel solution had apparent influence on isothermal automated DNA sequencing. This suggests that high purity of DNA and high quality of water should be used in isothermal automated DNA sequencing; if longer DNA sequence needs to be obtained, DNA concentration should not be too low.

DNA↗
PubMed2006

DNA sequencing and multiplex STR analysis on plastic microfluidic devices.

The ability of plastic microfluidic devices with separation channel lengths of 6, 10 or 18 cm to perform high-quality and high-performance ssDNA analysis was evaluated. Specifically, four-color DNA sequencing separation of a terminator sequencing standard using replaceable, urea-denaturing linear polyacrylamide (LPA) solution as a sieving matrix, yielded read lengths of 410 bases in 15 min with base calling accuracy of 99.2% on a 6-cm device, and 640 bases in 35 min with accuracy of 98.0% on a 18-cm device. A two-color sizing analysis of four-locus (CSF1PO, TPOX, TH01, vWA) short tandem repeats (STRs) allelic ladder on a 10-cm device indicated a mean SD of +/- 0.08 base pairs (bp) between runs, and single bp resolution of spiked TH01 allele 9.3 (198 bp) from TH01 allele 10 (199 bp) of the CTTv ladder with R = 0.81. A four-color multiplex sizing analysis of three different AmpFlSTR allelic ladders consisting of nine loci (D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820) and gender alleles (Amelogenin) on a 10-cm device had a mean SD of +/- 0.15 bp between runs for sizing three loci, i.e., FGA, D18S51 and D3S818; alleles differing by 2 bp in size were resolved with resolutions close to baseline. This work demonstrates that plastic microfluidic devices are capable of quality sequencing and STR sizing comparable to that of glass devices of similar separation lengths.

DNA, Single-Stranded↗
PubMed2006

Methodological improvements of pyrosequencing technology.

Pyrosequencing technology is a rather novel DNA sequencing method based on the sequencing-by-synthesis principle. This bioluminometric, real-time DNA sequencing technique employs a cascade of four enzymatic reactions producing sequence peak signals. The method has been proven highly suitable for single nucleotide polymorphism analysis and sequencing of short stretches of DNA. Although the pyrosequencing procedure is relatively straightforward, users may face challenges due to varying parameters in PCR and sequencing primer design, sample preparation and nucleotide dispensation; such challenges are labor and cost intensive. In this study, these issues have been addressed to increase signal quality and assure sequence accuracy.

Base Sequence↗
PubMed2005

Structure and architecture of the maize genome.

Maize (Zea mays or corn) plays many varied and important roles in society. It is not only an important experimental model plant, but also a major livestock feed crop and a significant source of industrial products such as sweeteners and ethanol. In this study we report the systematic analysis of contiguous sequences of the maize genome. We selected 100 random regions averaging 144 kb in size, representing about 0.6% of the genome, and generated a high-quality dataset for sequence analysis. This sampling contains 330 annotated genes, 91% of which are supported by expressed sequence tag data from maize and other cereal species. Genes averaged 4 kb in size with five exons, although the largest was over 59 kb with 31 exons. Gene density varied over a wide range from 0.5 to 10.7 genes per 100 kb and genes did not appear to cluster significantly. The total repetitive element content we observed (66%) was slightly higher than previous whole-genome estimates (58%-63%) and consisted almost exclusively of retroelements. The vast majority of genes can be aligned to at least one sequence read derived from gene-enrichment procedures, but only about 30% are fully covered. Our results indicate that much of the increase in genome size of maize relative to rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana) is attributable to an increase in number of both repetitive elements and genes.

Base Composition↗