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PubMed2000

A CD2-based model of yeast alpha-agglutinin elucidates solution properties and binding characteristics.

We have previously shown that the Saccharomyces cerevisiae cell adhesion protein alpha-agglutinin has sequence characteristics of immunoglobulin-like proteins and have successfully modeled residues 200-325, based on the structure of immunoglobulin variable-type domains. Alignments matching residues 20-200 of alpha-agglutinin with domains I and II of members of the CD2/CD4 subfamily of the immunoglobulin superfamily showed > 80% conservation of key residues despite low sequence similarity overall. Three-dimensional models of two alpha-agglutinin domains constructed on the basis of these alignments were shown to conform to peptide mapping data and biophysical properties of alpha-agglutinin. In addition, the residue volume and surface accessibility characteristics of these models resembled those of the well-packed structures of related proteins. Residue-by-residue analysis showed that packing and accessibility anomalies were largely confined to glycosylated and protease-susceptible loop regions of the domains. Surface accessibility of hydrophobic residues was typical of proteins with extensive domain interactions, a finding compatible with the hydrodynamic properties of alpha -agglutinin and the hydrophobic nature of binding to its peptide ligand alpha-agglutinin. The procedures used to align the alpha-agglutinin sequence and test the quality of the model may be applicable to other proteins, especially those that resist crystallization because of extensive glycosylation.

Algorithms↗
PubMed2003

PCMA: fast and accurate multiple sequence alignment based on profile consistency.

UNLABELLED: PCMA (profile consistency multiple sequence alignment) is a progressive multiple sequence alignment program that combines two different alignment strategies. Highly similar sequences are aligned in a fast way as in ClustalW, forming pre-aligned groups. The T-Coffee strategy is applied to align the relatively divergent groups based on profile-profile comparison and consistency. The scoring function for local alignments of pre-aligned groups is based on a novel profile-profile comparison method that is a generalization of the PSI-BLAST approach to profile-sequence comparison. PCMA balances speed and accuracy in a flexible way and is suitable for aligning large numbers of sequences. AVAILABILITY: PCMA is freely available for non-commercial use. Pre-compiled versions for several platforms can be downloaded from ftp://iole.swmed.edu/pub/PCMA/.

Algorithms↗
PubMed1997

Assessment of pituitary microadenomas: comparison between 2D and 3D MR sequences.

The aim of this study was to compare the diagnostic value and image quality of two different T1-weighted MR sequences in the evaluation of PRL-secreting pituitary microadenomas. Twenty-four patients with a clinical diagnosis of pituitary microprolactinoma were prospectively examined with both a 2D SE and a 3D turbo-SE T1-weighted coronal sequence, before and after intravenous contrast medium administration. Evaluation of MR images was done only on postcontrast images and considered the number of slices in which the lesions were visible and image quality, which was evaluated by both a subjective score and objective parameters (signal-to-noise and contrast-to-noise ratios). Pituitary microprolactinomas are visible in a higher number of slices in 3D TSE sequences; the subjective scores for image quality and signal-to-noise ratios were similar in both 2D and 3D sequences; the contrast-to-noise ratio was always higher in 3D sequences. In patients with hyperprolactinemia, the authors recommend using coronal 3D TSE T1-weighted sequences for evaluation of the pituitary region. 2D SE T1-weighted sequences may be considered if a shorter examination time is required (i.e., for claustrophobic patients) and in assessment or follow-up of microadenomas when a larger size lesion is clinically suspected.

Adult↗
PubMedDate not supplied

Hepatic MR imaging: comparison of 2D and 3D gradient echo techniques.

BACKGROUND: To compare fat-suppressed three-dimensional gradient echo (3D-GRE) and two-dimensional gradient echo (2D-GRE) techniques for hepatic magnetic resonance imaging. METHODS: For 107 patients with suspected focal hepatic lesions, unenhanced 2D-GRE multislice in-phase and opposed-phase images and 3D-GRE images were obtained. Two radiologists independently and in random order reviewed the images. Quantitative analysis compared contrast-to-noise ratio (C/N) of liver masses and of the liver to spleen and signal-to-noise ratio (S/N) of the liver. Subjective grading of lesion conspicuity, confidence for lesion detection, artifacts, and overall image quality were also evaluated. RESULTS: Conspicuity and confidence for focal lesions was statistically significantly higher on 3D-GRE than on 2D-GRE images. Liver-to-spleen C/N was higher on 3D-GRE images than on in-phase and opposed-phase 2D-GRE images (p < 0.01). Liver S/N was higher on in-phase 2D-GRE images than on 3D-GRE and opposed-phase 2D-GRE images (p < 0.001). Lesion-to-liver C/N was higher on 3D-GRE images than on 2D-GRE images for nonsolid lesions (p < 0.05), but there was no significant difference for solid lesions. Motion and pulsation artifacts were significantly fewer on 3D-GRE images, but graininess and shading were significantly higher. Overall image quality was not significantly different for the three sequences. CONCLUSION: Fat-suppressed 3D-GRE sequences can afford comparable or better image quality than 2D-GRE images and may have the potential to detect more focal hepatic lesions.

Adult↗
PubMed2002

Fetal magnetic resonance imaging: indications, technique, anatomical considerations and a review of fetal abnormalities.

Fetal MR imaging often poses a diagnostic challenge for the radiologist. Both fetal anatomy and pathology differ decidedly from pediatric and adult MR imaging. While ultrasound remains the method of choice for screening examinations of the fetus, MR imaging is playing an increasingly important role in the detection and classification of malformations not diagnosable by ultrasonography alone. Recently, advances in fast single-shot MR sequences have allowed high-resolution, high-quality imaging of the moving fetus. Preferable sequences to be applied are a true fast imaging steady precession (true-FISP) or a half-Fourier acquired single-shot turbo spin-echo (HASTE) sequence. Premedication is generally no longer required. In all fetal MR imaging, every aspect of fetal anatomy has to be scrutinized. Subsequently, any abnormalities need to be described and classified. A close collaboration with the referring obstetrician is of paramount importance.

Brain↗
PubMed2005

Parasite genomes.

The availability of genome sequences and the associated transcriptome and proteome mapping projects has revolutionised research in the field of parasitology. As more parasite species are sequenced, comparative and phylogenetic comparisons are improving the quality of gene prediction and annotation. Genome sequences of parasites are also providing important data sets for understanding parasite biology and identifying new vaccine candidates and drug targets. We review some of the preliminary conclusions from examination of parasite genome sequences and discuss some of the bioinformatics approaches taken in this analysis.

Animals↗
PubMed1997

Protein sequence-structure compatibility criteria in terms of statistical hypothesis testing.

The assignment of query protein sequences to probable folds in a threading approach is based on the statistical analysis (learning) of structural properties of amino acids in known protein structures. We formalize the recognition problem in terms of mathematical statistics, namely statistical hypothesis testing. Our general formulation leads to various mathematical forms of a decision rule function for evaluation of the quality of a sequence-structure fit. Three criteria were derived according to a likelihood ratio approach. Two of them have new functional forms while the third happens to coincide with the mean force potential function previously derived under the additional assumption of the Boltzmann law. New decision rule functions employ (i) the Parzen estimator of a probability density and (ii) the newly introduced non-parametric statistic with known asymptotic distribution. We compared criteria efficiency by a 'structure seeks sequence' search for three highly populated template folds through a query library of non-homologous sequences of proteins with known 3D structure using residue accessibility as an environmental variable. Various criteria reflect different underlying statistical propositions and thus often recognize diverse correct sequence-structure matches. On the other hand, if an amino acid sequence is recognized as compatible with a template by each of three decision rules it appears that one can make a more reliable inference of sequence-structure relationship since almost all false positives obtained by the three criteria differ.

Algorithms↗
PubMed2003

[Quality rating of MR-cholangiopancreatography with oral application of iron oxide particles].

PURPOSE: To compare image quality in magnetic resonance cholangiopancreatography (MRCP) performed with and without oral application of Lösferron (ferrous gluconate, Lilly Pharma, Hamburg). MATERIALS AND METHODS: A prospective study compares MRCPs performed on 52 patients with a 1.5 T clinical whole body scanner using a standard body coil. After randomization, patients ingested either 0.5 l of Lösferron (n = 27, group 1) or no oral contrast agent (n = 25, group 2) prior to the examination. 7 RARE (40 to 20 degrees) sequences were obtained, followed by selected 3 mm HASTE (T 2 -weighted with fat suppression) sequences. After blinding, image quality was rated by two radiologists using a scale of 1 (not discernible) to 5 (very well discernible). The following sections of the biliary ductal system were evaluated: left and right hepatic duct, extrahepatic bile duct and intrapancreatic bile duct. The pancreatic duct was evaluated by its location: head, body and tail of the pancreas. A Wilcoxon-Mann-Whitney test was used to determine significant differences (p < 0.05) between sampled ductal segments. Correction for multiple testing was applied. RESULTS: The oral application of Lösferron was well tolerated by all patients, and all sequences could be acquired and evaluated in all 52 patients. For the different sections of the biliary system, the mean ratings with and without Lösferron were, respectively, 3.28 and 3.36 for the left hepatic duct, 3.26 and 3.33 for the right hepatic duct, 3.46 and 4.0 for the extrahepatic bile duct, and 2.8 and 3.48 for the intrapancreatic bile duct. The corresponding ratings for the pancreatic duct were 2.8 and 3.24 for the pancreatic head, 2.84 and 3.38 for the pancreatic body, and 2.68 and 3.22 for the pancreatic tail. The differences with and without contrast agent were not statistically significant. Interobserver variability was between 0.37 for the pancreatic duct in the tail of the pancreas and 0.66 for the right hepatic duct. CONCLUSION: Despite the trend toward a better rating of the image quality for all sections of the pancreaticobiliary ductal system with Lösferron, a significant difference was not found in any ductal section after correction for multiple testing. Thus, we believe that the ingestion of Lösferron is not absolutely required prior MRCP.

Administration, Oral↗
PubMed2004

Array-A-Lizer: a serial DNA microarray quality analyzer.

BACKGROUND: The proliferate nature of DNA microarray results have made it necessary to implement a uniform and quick quality control of experimental results to ensure the consistency of data across multiple experiments prior to actual data analysis. RESULTS: Array-A-Lizer is a small and convenient stand-alone tool providing the necessary initial analysis of hybridization quality of an unlimited number of microarray experiments. The experiments are analyzed for even hybridization across the slide and between fluorescent dyes in two-color experiments in spotted DNA microarrays. CONCLUSIONS: Array-A-Lizer allows the expedient determination of the quality of multiple DNA microarray experiments allowing for a rapid initial screening of results before progressing to further data analysis. Array-A-Lizer is directed towards speed and ease-of-use allowing both the expert and non-expert microarray researcher to rapidly assess the quality of multiple microarray hybridizations. Array-A-Lizer is available from the Internet as both source code and as a binary installation package.

Computer Graphics↗
PubMed2003

Systematic analysis of the ABO gene diversity within exons 6 and 7 by PCR screening reveals new ABO alleles.

BACKGROUND: Mutations critical for ABO blood group phenotypes have predominantly been found in exons 6 and 7 of the ABO gene, both of which encode the catalytic domain of ABO glycosyltransferase. To design rapid and reliable ABO genotyping assays, a profound knowledge of the prevalent alleles is required and a reliable sequence database needs to be established. STUDY DESIGN AND METHODS: A PCR screening system was established consisting of 102 different PCRs, each specific for a single nucleotide (nt) variation. The primer mixes were developed to walk from the 5' to the 3' end of exons 6 and 7 of the ABO gene to screen for nt mutations at 50 known polymorphic sites. A total of 109 unrelated individuals with common and rare ABO characteristics were screened. All blood samples in which the PCR results were inconclusive or inconsistent with the ABO phenotypes were subjected to sequence analysis of exons 6 and 7. RESULTS: The results of PCR screening were conclusive and consistent with the ABO phenotypes in 90 cases. In the remaining 19 cases, PCR screening revealed unusual allele combinations or amplification results that were incompatible with known ABO allele combinations or subgroups predicted by serologic analysis. In these 19 cases, sequencing revealed new ABO alleles (one ABO*Ael allele, one ABO*B(A) allele and two ABO*O alleles) in two individuals with common and seven individuals with variant ABO phenotypes. CONCLUSION: This PCR screening strategy is an effective tool for obtaining deeper insight into the ABO gene diversity and diversification and may be useful to increase the quality of the ABO sequence database.

ABO Blood-Group System↗
PubMedDate not supplied

Technical aspects on magnetic resonance imaging of the spine at 1.5 tesla.

Technical aspects on surface coil magnetic resonance imaging of the spine using a superconducting system with a field strength of 1.5 tesla are described. By using a flat surface coil instead of the body coil the image quality was markedly improved and the signal-to-noise ratio (S/N) was increased approximately 2.6 times. Small voxels resulted in low S/N. The best image quality was achieved with a slice thickness of 5 mm, a field of view of 20 to 24 cm and a matrix of 256 X 256. Interleaved slices provided superior image quality compared with contiguous slices at the expense of acquisition time. For sagittal images the phase encoding gradient should be in the cranio-caudal direction to minimize motion artifacts. To obtain T1 and T2 images of high quality, spin echo pulse sequences with TR 600/TE 20 ms and TR 2000/TE 40 to 80 ms are useful.

Epidural Space↗
PubMed2026

A safety-centric perspective on innovation and risk in the use of artificial intelligence in genomics.

Adopting a safety-centric approach, this article explores how generative artificial intelligence (AI), and more specifically, foundation models for biological sequences, can exacerbate data quality issues, technical biases, and dual-use potential, particularly in critical applications such as clinical genetics, precision medicine, and pathogen engineering. This work centres on how misuse risks emerge throughout the innovation pipeline and how these intersect with the growing accessibility of generative genomic models. Particular attention is given to dual-use governance and infrastructure hardening in sequence analysis workflows. The work aims to provide scientists, regulators, and policymakers with a toolkit to discuss beneficial innovation in genomic AI while maintaining robust safeguards against harm and misuse.

Genomics↗
PubMed1994

Complete DNA sequence of yeast chromosome II.

In the framework of the EU genome-sequencing programmes, the complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome II (807 188 bp) has been determined. At present, this is the largest eukaryotic chromosome entirely sequenced. A total of 410 open reading frames (ORFs) were identified, covering 72% of the sequence. Similarity searches revealed that 124 ORFs (30%) correspond to genes of known function, 51 ORFs (12.5%) appear to be homologues of genes whose functions are known, 52 others (12.5%) have homologues the functions of which are not well defined and another 33 of the novel putative genes (8%) exhibit a degree of similarity which is insufficient to confidently assign function. Of the genes on chromosome II, 37-45% are thus of unpredicted function. Among the novel putative genes, we found several that are related to genes that perform differentiated functions in multicellular organisms of are involved in malignancy. In addition to a compact arrangement of potential protein coding sequences, the analysis of this chromosome confirmed general chromosome patterns but also revealed particular novel features of chromosomal organization. Alternating regional variations in average base composition correlate with variations in local gene density along chromosome II, as observed in chromosomes XI and III. We propose that functional ARS elements are preferably located in the AT-rich regions that have a spacing of approximately 110 kb. Similarly, the 13 tRNA genes and the three Ty elements of chromosome II are found in AT-rich regions. In chromosome II, the distribution of coding sequences between the two strands is biased, with a ratio of 1.3:1. An interesting aspect regarding the evolution of the eukaryotic genome is the finding that chromosome II has a high degree of internal genetic redundancy, amounting to 16% of the coding capacity.

Base Composition↗
PubMed2003

A novel MALDI LIFT-TOF/TOF mass spectrometer for proteomics.

A new matrix-assisted laser-desorption/ionization time-of-flight/time-of-flight mass spectrometer with the novel "LIFT" technique (MALDI LIFT-TOF/TOF MS) is described. This instrument provides high sensitivity (attomole range) for peptide mass fingerprints (PMF). It is also possible to analyze fragment ions generated by any one of three different modes of dissociation: laser-induced dissociation (LID) and high-energy collision-induced dissociation (CID) as real MS/MS techniques and in-source decay in the reflector mode of the mass analyzer (reISD) as a pseudo-MS/MS technique. Fully automated operation including spot picking from 2D gels, in-gel digestion, sample preparation on MALDI plates with hydrophilic/hydrophobic spot profiles and spectrum acquisition/processing lead to an identification rate of 66% after the PMF was obtained. The workflow control software subsequently triggered automated acquisition of multiple MS/MS spectra. This information, combined with the PMF increased the identification rate to 77%, thus providing data that allowed protein modifications and sequence errors in the protein sequence database to be detected. The quality of the MS/MS data allowed for automated de novo sequencing and protein identification based on homology searching.

Amino Acid Sequence↗
PubMed2002

Elucidation of factors responsible for enhanced thermal stability of proteins: a structural genomics based study.

Understanding the molecular basis for the enhanced stability of proteins from thermophiles has been hindered by a lack of structural data for homologous pairs of proteins from thermophiles and mesophiles. To overcome this difficulty, complete genome sequences from 9 thermophilic and 21 mesophilic bacterial genomes were aligned with protein sequences with known structures from the protein data bank. Sequences with high homology to proteins with known structures were chosen for further analysis. High quality models of these chosen sequences were obtained using homology modeling. The current study is based on a data set of models of 900 mesophilic and 300 thermophilic protein single chains and also includes 178 templates of known structure. Structural comparisons of models of homologous proteins allowed several factors responsible for enhanced thermostability to be identified. Several statistically significant, specific amino acid substitutions that occur going from mesophiles to thermophiles are identified. Most of these are at solvent-exposed sites. Salt bridges occur significantly more often in thermophiles. The additional salt bridges in thermophiles are almost exclusively in solvent-exposed regions, and 35% are in the same element of secondary structure. Helices in thermophiles are stabilized by intrahelical salt bridges and by an increase in negative charge at the N-terminus. There is an approximate decrease of 1% in the overall loop content and a corresponding increase in helical content in thermophiles. Previously overlooked cation-pi interactions, estimated to be twice as strong as ion-pairs, are significantly enriched in thermophiles. At buried sites, statistically significant hydrophobic amino acid substitutions are typically consistent with decreased side chain conformational entropy.

Archaeal Proteins↗
PubMed2003

Isolation and characterization of a phytase with improved properties from Citrobacter braakii.

Citrobacter braakii YH-15 produced an intracellular phytase which was purified 12800 fold to homogeneity with the specific activity of 3457 units mg(-1), which is 1.9 times higher than E. coli phytase previously recorded as having the highest specific activity. Its molecular weight was 47 kDa by SDS-PAGE gel. Enzyme activity was optimal at pH 4 and at 50 degrees C. The Km value for sodium phytate was 0.46 mM with a Vmax 6027 U mg(-1). The phytase was resistant to proteases such as trypsin, pepsin, papain, pancreatin, and elastase.

6-Phytase↗
PubMed2002

Finding motifs in the twilight zone.

MOTIVATION: Gene activity is often affected by binding transcription factors to short fragments in DNA sequences called motifs. Identification of subtle regulatory motifs in a DNA sequence is a difficult pattern recognition problem. In this paper we design a new motif finding algorithm that can detect very subtle motifs. RESULTS: We introduce the notion of a multiprofile and use it for finding subtle motifs in DNA sequences. Multiprofiles generalize the notion of a profile and allow one to detect subtle patterns that escape detection by the standard profiles. Our MULTIPROFILER algorithm outperforms other leading motif finding algorithms in a number of synthetic models. Moreover, it can be shown that in some previously studied motif models, MULTIPROFILER is capable of pushing the performance envelope to its theoretical limits. AVAILABILITY: http://www-cse.ucsd.edu/groups/bioinformatics/software.html

Algorithms↗
PubMed2006

Movie and video scale-time equalization application to flicker reduction.

Image flicker is a general film effect, which can be observed in videos as well as in old films, and consists of fast variations of the frame contrast and brightness. Reducing flicker of a sequence improves its visual quality and can be an essential first treatment before ulterior manipulations. This paper presents an axiomatic analysis of the problem, which leads to a global and fast method of "de-flicker," based on the scale-space theory. The stability of this process, called scale-time equalization, is ensured by the scale-time framework. Results on different sequences are given and show great visual improvement.

Algorithms↗