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At least 865 records · Page 48Linked to original sources
PubMed2003

A neural network approach to evaluate fold recognition results.

Fold recognition techniques assist the exploration of protein structures, and web-based servers are part of the standard set of tools used in the analysis of biochemical problems. Despite their success, current methods are only able to predict the correct fold in a relatively small number of cases. We propose an approach that improves the selection of correct folds from among the results of two methods implemented as web servers (SAMT99 and 3DPSSM). Our approach is based on the training of a system of neural networks with models generated by the servers and a set of associated characteristics such as the quality of the sequence-structure alignment, distribution of sequence features (sequence-conserved positions and apolar residues), and compactness of the resulting models. Our results show that it is possible to detect adequate folds to model 80% of the sequences with a high level of confidence. The improvements achieved by taking into account sequence characteristics open the door to future improvements by directly including such factors in the step of model generation. This approach has been implemented as an automatic system LIBELLULA, available as a public web server at http://www.pdg.cnb.uam.es/servers/libellula.html.

Internet↗
PubMed1993

Recognition of errors in three-dimensional structures of proteins.

A major problem in the determination of the three-dimensional structure of proteins concerns the quality of the structural models obtained from the interpretation of experimental data. New developments in X-ray crystallography and nuclear magnetic resonance spectroscopy have accelerated the process of structure determination and the biological community is confronted with a steadily increasing number of experimentally determined protein folds. However, in the recent past several experimentally determined protein structures have been proven to contain major errors, indicating that in some cases the interpretation of experimental data is difficult and may yield incorrect models. Such problems can be avoided when computational methods are employed which complement experimental structure determinations. A prerequisite of such computational tools is that they are independent of the parameters obtained from a particular experiment. In addition such techniques are able to support and accelerate experimental structure determinations. Here we present techniques based on knowledge based mean fields which can be used to judge the quality of protein folds. The methods can be used to identify misfolded structures as well as faulty parts of structural models. The techniques are even applicable in cases where only the C alpha trace of a protein conformation is available. The capabilities of the technique are demonstrated using correct and incorrect protein folds.

Models, Molecular↗
PubMed2001

Two isoforms of trimming glucosidase II exist in mammalian tissues and cell lines but not in yeast and insect cells.

We previously cloned glucosidase II and provided in vivo evidence for its involvement in protein folding quality control. DNA-sequencing of different clones demonstrated the existence of two isoforms of glucosidase II which differed by 66 nucleotides due to alternative splicing. The existence of two enzyme isoforms in various organs of pig and rat as well as human, bovine, rat, and mouse cell lines could be demonstrated by RT-PCR and Western blotting. Furthermore, the two isoforms of glucosidase II could be detected in embryonic and postnatal rat kidney and liver. In yeast, Saccharomyces cerevisiae, and in insects, Drosophila S2 cells, only one isoforms of the enzyme was detectable. The ubiquitous occurrence of the two glucosidase II isoforms in mammalian tissues and cell lines might be indicative of a special function of each isoform.

Animals↗
PubMed1998

An adiabatic multiple spin-echo pulse sequence: removal of systematic errors due to pulse imperfections and off-resonance effects.

Application of AFP (adiabatic fast passage) pulses for removal of systematic errors associated with multiple spin-echo sequences is demonstrated. The adiabatic fast passage pulses facilitate minimization of cumulative pulse errors for all three components of magnetization. It is also shown that off-resonance effects present in conventional CPMG sequences which degrade image quality in magnetic resonance imaging and introduce systematic errors in measured T2 relaxation time peak amplitudes can be suppressed by introduction of AFP pulses without any degradation of overall signal intensity. The technique has been tested on the 15N spin-spin relaxation time measurements of a 110 amino acid domain of the F-actin cross-linking protein.

Actins↗
PubMed2005

Vertebral shape: automatic measurement with dynamically sequenced active appearance models.

The shape and appearance of vertebrae on lateral dual x-ray absorptiometry (DXA) scans were statistically modelled. The spine was modelled by a sequence of overlapping triplets of vertebrae, using Active Appearance Models (AAMs). To automate vertebral morphometry, the sequence of trained models was matched to previously unseen scans. The dataset includes a significant number of pathologies. A new dynamic ordering algorithm was assessed for the model fitting sequence, using the best quality of fit achieved by multiple sub-model candidates. The accuracy of the search was improved by dynamically imposing the best quality candidate first. The results confirm the feasibility of substantially automating vertebral morphometry measurements even with fractures or noisy images.

Algorithms↗
PubMedDate not supplied

Magnetic resonance imaging of the intrauterine fetal genitourinary tract: normal anatomy and pathology.

Although ultrasonography (US) remains the most widely used diagnostic imaging modality for routine evaluation of the fetus, magnetic resonance (MR) imaging has become an invaluable complement to US in all cases in which additional information is desirable. While the ability of US to detect fetal abnormalities is limited in cases such as maternal obesity, oligohydramnios, and in certain fetal positions, MR using fast and ultrafast pulse sequences enables high-quality fetal images to be acquired regardless of the mother's physical condition or fetal position. Fetal genitourinary disorders are the most common intrauterine abnormalities detected by US, accounting for approximately 30% of all antenatally detected anomalies. Although they usually occur in isolation, these defects can form part of more complex syndromes or chromosomopathies, and MR is indicated to rule out associated abnormalities. In some severe genitourinary disorders, there is a severe deficit of amniotic fluid; these cases are associated with other fetal anomalies such as pulmonary hypoplasia and very poor prognosis. In other cases, the amniotic fluid is not compromised, yet the further detection, localization, and characterization of prenatal disorders will have an impact on postnatal follow-up. This article reviews the role of fetal MR in urogenital tract disorders.

Female↗
PubMed2002

The GEDNAP (German DNA profiling group) blind trial concept.

This paper presents a review of the organisation and background of blind trial systems in general and in particular the system developed in Münster originally for the German Society of Forensic Medicine. This system, known as GEDNAP (German DNA profiling group), has now evolved into a multinational DNA blind trial open to all laboratories involved in paternity and forensic DNA testing.

DNA↗
PubMed2000

Random changes of amino acid residues with expected frequency by saturated point mutagenesis.

The yeast transcriptional activator protein, Gcn4p from Saccharomyces cerevisiae binds to the specific sequence in the promoters of many amino acid biosynthetic genes for general control. A new random saturation mutagenesis method was developed to isolate Gcn4p derivatives with only one or two mutations in the DNA binding domain without using radioactive isotope. This will be used to identify the amino acids of Gcn4p involved in protein-protein interactions. Saturation mutagenesis in the DNA binding domain of Gcn4p was performed using spiked degenerate oligonucleotides containing randomized codon bases designed specifically for only one or two base changes in the mutagenized area. These oligonucleotides were synthesized to have two flanking restriction enzyme sites for cloning to the appropriate vector. The 3' ends were mutually primed after hybridization via the palindromic sequences of the restriction enzyme sites. These molecules were then converted to double stranded DNA upon treatment with DNA polymerase. Here, a library collection of 100,680 in an altered Gcn4p pool was generated by cloning a mixed-base oligonucleotide in the place of the sequence coding for the DNA binding domains. The quality of the library was examined by DNA sequencing and found to be in good agreement with the expected statistical values. Calculated mutation frequency was 66% of mutant nucleotide rate and actual sequencing data revealed 68% mutant nucleotide rates from the sequenced library. Thus, among 21 mutants, 16 had one point mutations and 5 had two point mutations. This approach appears to be an effective and general tool for creating proteins with one or two amino acid change(s) in their molecules.

Binding Sites↗
PubMed2005

Artefacts in magnetic resonance imaging caused by dental material.

A common problem in computer tomography (CT) based imaging of the oral cavity is artefacts caused by dental restorations. The aim of this study was to investigate whether magnetic resonance imaging (MRI) of the oral cavity would be less affected than CT by artefacts caused by typical dental restorative alloys. In order to assess the extent of artefact generation, corresponding MRI scans of the same anatomic region with and without dental metal restorations were matched using a stereotactic frame. MRI imaging of the oral and maxillofacial region could be performed without reduction of the image quality by metallic dental restorations made from titanium, gold or amalgam. Dental restorations made from titanium, gold or amalgam did not reduce the image quality of the MRI sequence used in imaging of the oral and maxillofacial region for dental implant planning. In this respect MRI is superior to CT in implant planning.

Animals↗
PubMed1994

Radiosurgical treatment planning of brain metastases based on a fast, three-dimensional MR imaging technique.

A fast, three-dimensional (3D) sequence for magnetic resonance (MR) imaging of the brain and its application in radiosurgical treatment planning of brain metastases is reported. The measuring sequence (MPRAGE) requires magnetization-prepared 180 degrees inversion pulses followed by rapid low angle excitation pulses and gradient-echoes for image generation. The resulting T1-weighted MPRAGE images were compared with two-dimensional (2D) T1-weighted spin-echo (SE) images after administration of 0.1 mmol/kg b.w. Gd-DTPA in 10 patients with known brain metastases. Original or multiplanar reformatted images obtained from a 128 partition data set of the 3D MPRAGE sequence offered comparable diagnostic quality to that of 2D SE imaging. Gd-DTPA enhancement and lesion targeting was similar in most of the patients in SE as well as MPRAGE imaging. During imaging and therapy the patient's head was fixed in a stereotactic localization system which is usable at the MR and the linear accelerator installations. The dose calculation of the radiosurgery planning was based on 3D MR imaging data assuming a homogenous attenuation value inside the head which was sufficient for an accurate dose calculation since tissue inhomogeneities do not significantly influence the shape of the relative dose distribution especially for radiosurgery of the brain. Under this circumstance the dose calculation can be based only on the 3D geometric conformation of the patient's head. A simple algorithm for treatment planning can be used if the MR data are free of geometric distortion.(ABSTRACT TRUNCATED AT 250 WORDS)

Brain↗
PubMed2006

A catalog for transcripts in the venom gland of the Agkistrodon acutus: identification of the toxins potentially involved in coagulopathy.

Agkistrodon acutus is a special agkistrodon halys, only distributed in Southern China, with a few exceptions in Vietnam. It is a cherished element used in traditional Chinese medicine. In order to produce a global panorama of gene expression in the Agkistrodon acutus venom gland, a non-normalized cDNA library was constructed, and 8696 high quality 5' end expressed sequenced tags (ESTs) were sequenced and analyzed. The initial sequences were assembled into 2855 clusters. Of these clusters, only 45.60% clusters matched known sequence and 54.40% had no match to any known sequence in GenBank. Except for putative cellular proteins (1184 clusters), the remaining 118 clusters (40.16% of all ESTs) corresponded to sequences associated with diverse toxin function. According to expression abundance, the major toxin components were metalloproteinases (32.08%) and C-type lectin (5.22%), and other components including bradykinin-potentiating peptide (0.90%), serine proteases (0.51%), nucleotidase and nuclease (0.41%), phospholipase A2 (0.30%), disintegrin (0.05%), cytokine-like molecules (0.06%), and other proteins (0.63%). The majority of these components are thought to be responsible for coagulopathy after A. acutus bites. We have therefore generated a comprehensive catalog of the A. acutus venom gland described so far. Gene expression from the very specialized secretory tissue, especially for those involved in coagulopathy, can be surveyed and provide important information in finding novel toxins.

Agkistrodon↗
PubMed2004

Microarray gene expression profiling during the segmentation phase of zebrafish development.

We analyzed 15,512 unique transcripts from wild-type Danio rerio using a long oligonucleotide microarray containing >16,000 65-mers probes. Total RNA was isolated from staged embryos at 2 h intervals over a 24-h period. On average, at any given time point, 27% of the probe set detected corresponding transcripts in embryonic RNA. There were two predominant patterns in the nearly 4000 genes that changed expression in at least one time point during the first 24 hpf. At 12 hpf, we detected 420 up-regulated and 386 down-regulated genes. By 24 hpf, the number of up- and down-regulated genes had increased to 954 and 766, respectively. While the majority of these genes maintained their new level of expression for the duration of the time course, we identified five genes with phasic regulation over the 24-h time course. Two of these genes, germ cell nuclear factor and mesogenin, have been identified as being expressed during gastrulation (5 1/4 to 10 h postfertilization) and subsequently repressed. A cluster containing 36 distinct ribosomal proteins was up-regulated at 12 h, indicating a capability for de novo protein synthesis during and after this stage. Twenty-three muscle-specific genes were up-regulated late during the initial 24 hpf, corresponding to the development and differentiation of the somites.

Animals↗
PubMed2006

Molecular characterization of the developmental gene in eyes: through data-mining on integrated transcriptome databases.

OBJECTIVES: Our aim was to utilize publicly available and proprietary sources to discover candidate genes important for ocular development. DESIGN AND METHODS: The collated information on our 5092 non-redundant clusters was grouped and functional annotation was conducted using gene ontology (FatiGO) for categorizing them with respect to molecular function. The web-based viewer technological platform (H-InvDB) was employed for transcription analyses of in-house high quality fetal eye Expressed Sequence Tags (ESTs). Eye-specific ESTs were also analyzed across species by using EMBEST. RESULTS: According to adult eye cDNA libraries, nucleic acid binding and cell structure/cytoskeletal protein genes were the most abundant among the ESTs of fetal eyes. Using cDNA assembly in H-InvDB, 20 (80%) of the 25 most commonly expressed genes in the human eye are also expressed in extraocular tissues. The crystalline gamma S gene is highly expressed in the eye, but not in other tissues. We used EMBEST to compare human fetal eye and octopus eye ESTs and the expression similarity was low (1.6%). This indicated that our fetal eye library contains genes necessary for the developmental process and biological function of the eye, which may not be expressed in the fully developed octopus eyes. The human fetal eye cDNA library also contained highly abundant eye tissue genes, including alphaA-crystallin, eukaryotic translation elongation factor 1 alpha 1 (EEF1A1), bestrophin (VMD2), cystatin C, and transforming growth factor, beta-induced (BIGH3). CONCLUSIONS: Our annotated EST set provides a valuable resource for gene discovery and functional genomic analysis. This display will help to appreciate the strengths and weaknesses of the different technological platforms, so that in future studies the maximum amount of beneficial information can be derived from the appropriate use of each method.

Animals↗
PubMed2005

Evaluating the forensic informativeness of mtDNA haplogroup H sub-typing on a Eurasian scale.

The impact of phylogeographic information on mtDNA forensics has been limited to the quality control of published sequences and databases. In this work we use the information already available on Eurasian mtDNA phylogeography to guide the choice of coding-region SNPs for haplogroup H. This sub-typing is particularly important in forensics since, even when sequencing both HVRI and HVRII, the discriminating power is low in some Eurasian populations. We show that a small set (eight) of coding-region SNPs resolves a substantial proportion of the identical haplotypes, as defined by control-region variation alone. Moreover, this SNP set, while substantially increasing the discriminating efficiency in most Eurasian populations by roughly equal amounts, discloses population-specific profiles.

Asia↗
PubMed2005

Optimising two-dye microarray designs for estimating associations with a quantitative trait.

We discuss how the samples should be arranged in two-dye microarray studies when the objective is to investigate associations between gene expression and quantitative traits measured on each sample. Because there is typically large between array variation, information about the association will come from the differences in traits and expression measurements between the two values hybridised to the two dyes on the same array. It is shown that within-slide correlation of trait values should be minimised. The arrangement of samples for which this occurs will depend on the trait values in question, and is a computationally demanding problem. An alternative is to minimise the rank correlation. We discuss this and related issues for different combinations of numbers of samples and arrays. Data analysis, including estimation of the variance components, is also described.

Algorithms↗
PubMed2005

Robotic spotting of cDNA and oligonucleotide microarrays.

DNA microarrays are a uniquely efficient method for simultaneously assessing the expression levels of thousands of genes. Owing to their flexibility and value, mechanically spotted microarrays remain the most popular platform. Here, we review recent technological advances with a focus on spotted arrays. Robotic spotting still poses numerous technical challenges. To reduce artefacts, many laboratories have recently investigated ways of improving the spotting process. We compare alternative options and discuss implications for next-generation systems. Together with modern approaches to data analysis, such developments bring greatly improved reliability to individual microarray experiments. Advancing towards the ultimate goal of delivering calibrated, truly quantitative gene-expression measurements on a genomic scale, microarray technology remains at the forefront of post-genomic systems biology.

DNA Probes↗
PubMed2004

High intensity focused ultrasound ablation of kidney guided by MRI.

The effectiveness of magnetic resonance imaging (MRI) to monitor therapeutic protocols of high-intensity focused ultrasound (HIFU), in freshly excised pig kidney cortex is investigated. For high quality imaging, the pulse sequence fast spin echo (FSE) T1- and T2-weighted, and proton density were evaluated. For fast imaging, the pulse sequence T1-weighted fast spoiled gradient (FSPGR) was used. The main goal was to evaluate the MRI detection of large lesions (bigger than 1 cm x 1 cm x 1 cm) that is achieved by moving the transducer in a predetermined pattern. The contrast between lesion and kidney tissue is excellent with either T1-weighted or T2-weighted FSE. With T1-weighted FSE, the best contrast is observed for recovery time (TR) between 200 ms and 400 ms. With T2-weighted FSE best contrast can be achieved for echo time (TE) between 16 and 32 ms. T2-weighted FSE was proven as the best pulse sequence to detect cavitational activity. This advantage is attributed to the significant difference in signal intensity between air spaces and necrotic tissue. Air spaces appear brighter than thermal lesions. Therefore, for therapeutic protocols created using cavitational mode, T2-weighted FSE may be the optimum pulse sequence to use. The proton density pulse sequence does not provide any advantage over the T1- and T2-weighted pulse sequences. Using T1-weighted FSPGR, acquisition time as low as 5 s could be achieved. Good contrast and signal-to-noise ratio (SNR) are achieved with TR = 100 ms and flip angle between 75 to 90 degrees. The above techniques were very successful in detecting large lesion volumes.

Animals↗