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Results for “reduced representation sequencing”

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PubMed2001

Functional MRI for presurgical planning: problems, artefacts, and solution strategies.

OBJECTIVES: Presurgical mapping of motor function is a widely used clinical application of functional (f) MRI, employing the blood oxygenation level dependent contrast. The aim of this study was to report on 3 years experience of 194 fMRI studies on the representation of motor function in 103 patients and to describe the problems and artefacts that were typically present. METHODS: An evaluation was carried out to determine whether the patients' age, type or location of the tumourous lesion, severity of the paresis, or the tasks used during the investigation have an effect on artefacts of fMRI studies and how these artefacts are best overcome. RESULTS: Functional MRI identified the motor regions in 85% of all investigated paradigms. In 11% of the investigated patients no information at all on functional localisation was obtained. A draining vein within the central sulcus was present in all patients that showed activation within the parenchyma of the precentral gyrus but also in three patients in whom no parenchymal activation was present. Head movement artefacts were the most frequent cause for fMRI failure, followed by low signal to noise ratio. Motion artefacts were correlated with the degree of paresis and with the functional task. Tasks involving more proximal muscles led to significantly more motion artefacts when compared with tasks that primarily involved distal muscles. Mean MR signal change during task performance was 2.5%. CONCLUSIONS: Most of the artefacts of functional MRI can be reliably detected and at least in part be reduced or eliminated with the help of mathematical algorithms, appropriate pulse sequences and tasks, and-probably most important-by evaluating the fMRI raw data-that is, the MR signal time courses.

Adolescent↗

PubMed2001

[Virtual rendering techniques in otologic imaging].

UNLABELLED: Virtual postprocessing techniques combine the advantages of condensing the large amounts of data provided by high-resolution (HR) cross-sectional imaging modalities with those of three-dimensional (3D) imaging. The techniques and indications for virtual representations in imaging of the middle ear (ME), internal ear (IE), and cerebellopontine angle (CPA) are presented together with practical examples. MATERIAL AND METHODS: HR data sets acquired by computed tomography (CT) and magnetic resonance imaging (MRI) in patients with ME, IE, and CPA pathologies were transferred to a workstation via an internal network to generate endo- or extraluminal 3D views by means of the volume rendering technique (VRT). The source data were acquired using scanners and imaging protocols with the highest resolution available at present: a multislice spiral CT (MSCT) with a slice thickness of 0.5 mm and a reconstruction increment of 0.2 mm and a 3D CISS sequence with a slice thickness of 0.5 mm for MRI. RESULTS: Virtual endoscopy was superior to cross-sectional images for assessing ME pathologies like dysplasia, postoperative changes, and destructive bone processes with extensive soft-tissue involvement; fibrous obliterations of the internal ear and labyrinthine dysplasia were depicted with a superior image quality on 3D renderings compared to conventional reconstruction techniques. Virtual endoscopy of the CPA and external acoustic meatus (EAM) was helpful in detecting and visualizing neurovascular conflicts and in assigning small intrameatal tumors to components of the acousticofacial bundle. A common feature of all applications was that the large numbers of source images could be reduced to a few 3D reconstructions for documentation and optimized communication of the findings between the radiologist and otologist. CONCLUSION: Virtual rendering makes an important contribution towards establishing, presenting, and documenting the findings when certain otologic pathologies have to be assessed. It can be used for routine imaging and allows for more efficient handling of the large amounts of imaging data generated by high-resolution cross-sectional imaging modalities.

Cerebellopontine Angle↗

PubMed2000

Synthesis and structures of bis(dithiolene)-tungsten(IV) complexes related to the active sites of tungstoenzymes.

Recent protein crystallographic results on tungsten enzymes and primary sequence relationships between certain molybdenum and tungsten enzymes provoke interest in the generalized bis(dithiolene) complexes [WIV(QR)(S2C2R'2)2]1- and [WVIO(QR)(S2C2R'2)2]1- (Q = O, S, Se) as minimal representations of enzyme sites. The existence and stability of W(IV) complexes have been explored by synthesis. Reaction of [W(CO)2(S2C2Me2)2] (1) with PhO- results in complete CO substitution to give [W(OPh)(S2C2Me2)2]1- (2). Reaction of 1 with PhQ- affords the monocarbonyls [W(CO)(QPh)(S2C2Me2)2]1- (Q = S (3), Se (5)). The use of sterically demanding 2,4,6-Pri3C6H2Q- also yields monocarbonyls, [W(CO)(QC6H2-2,4,6-Pri3)(S2C2Me2)2]1- (Q = S (4), Se (6)). The X-ray structures of square pyramidal 2 and trigonal prismatic 3-6 (with unidentate ligands cis) are described. The tendency to substitute one or both carbonyl ligands in 1 in the formation of [MIV(QAr)(S2C2Me2)2]1- and [MIV(CO)(QAr)(SeC2Me2)2]1- with M = Mo and W is related to the M-Q bond length and ligand steric demands. The results demonstrate a stronger binding of CO by W(IV) than Mo(IV), a behavior previously demonstrated by thermodynamic and kinetic features of zerovalent carbonyl complexes. Complexes 3-6 can be reversibly reduced to W(III) at approximately -1.5 V versus SCE. On the basis of the potential for 2(-2.07 V), monocarbonyl ligation stabilizes W(III) by approximately 500 mV. This work is part of a parallel investigation of the chemistry of bis(dithiolene)-molybdenum (Lim, B. S.; Donahue, J. P.; Holm, R. H. Inorg. Chem. 2000, 39, 263) and -tungsten complexes related to enzyme active sites.

Archaea↗

PubMed2004

Mechanism of chaperone function in small heat shock proteins: dissociation of the HSP27 oligomer is required for recognition and binding of destabilized T4 lysozyme.

Mammalian small heat shock proteins (sHSP) form polydisperse and dynamic oligomers that undergo equilibrium subunit exchange. Current models of their chaperone activity hypothesize that recognition and binding of protein non-native states involve changes in the oligomeric state. The equivalent thermodynamic representation is a set of three coupled equilibria that includes the sHSP oligomeric equilibrium, the substrate folding equilibrium, and the equilibrium binding between the sHSP and the substrate non-native states. To test this hypothesis and define the binding-competent oligomeric state of human Hsp27, we have perturbed the two former equilibria and quantitatively determined the consequences on binding. The substrate is a set of T4 lysozyme (T4L) mutants that bind under conditions that favor the folded state over the unfolded state by 10(2)-10(4)-fold. The concentration-dependent oligomer equilibrium of Hsp27 was perturbed by mutations that alter the relative stability of two major oligomeric states including phosphorylation-mimicking mutations that result in the dissociation to a small multimer over a wide range of concentrations. Correlation of binding isotherms with size exclusion chromatography analysis of the Hsp27 oligomer equilibrium demonstrates that the multimer is the binding-competent state. Binding occurs through two modes, each characterized by different affinity and number of binding sites, and results in T4L.Hsp27 complexes of different hydrodynamic properties. Mutants of the Hsp27 phosphorylation mimic that reverse the reduction in oligomer size also reduce the extent of T4L binding. Taken together, these results suggest a central role for the oligomeric equilibrium in regulating the chaperone activity of sHSP. The mutants identify sequence features important for modulating this equilibrium.

Bacteriophage T4↗

PubMed1998

MHC class II expression in double mutant mice lacking invariant chain and DM functions.

Invariant (Ii) chain and DM functions are required at distinct stages during class II maturation to promote occupancy by diverse peptide ligands. The class II molecules expressed by mutant mouse strains lacking Ii chain or DM activities display discrete structural and functional abnormalities. The present report describes the cellular and biochemical characteristics of Ii-DM- doubly deficient mice. As for Ii chain mutants, their mature Aalphab Abetab dimers similarly exhibit reduced mobilities in SDS-PAGE, and in functional assays these molecules behave as if empty or occupied by an easily displaced peptide. Additionally, the present experiments demonstrate that the production of floppy Aalphab Abetab dimers is TAP independent. In comparison with Ii chain mutants, Ii-DM- doubly deficient cell populations exhibit increased peptide binding activities and consistently greater presentation abilities in T cell stimulation assays. These functional differences appear to reflect higher class II surface expression associated with their increased representation of B lymphocytes. We also observe defective B cell maturation in mice lacking Ii chain or DM expression, and interestingly, B cell development appears more severely compromised in Ii-DM- double mutants. These mutant mice lacking both Ii chain and DM activities should prove useful for analyzing nonconventional class II Ag presentation under normal physiological conditions in the intact animal.

ATP Binding Cassette Transporter, Subfamily B, Mem↗

PubMed2002

Multiple immuno-regulatory defects in type-1 diabetes.

Susceptibility to immune-mediated diabetes (IMD) in humans and NOD mice involves their inherently defective T cell immunoregulatory abilities. We have followed natural killer (NK) T cell numbers in patients with IMD, both by flow cytometry using mAbs to the characteristic junctions found in the T cell receptors of this cell subtype, and by semiquantitative RT-PCR for the corresponding transcripts. Both before and after clinical onset, the representation of these cells in patients' PBMCs is reduced. We also report low numbers of resting CD4(+) CD25(+) T cells in IMD patients, a subset of T cells shown to have important immunoregulatory functions in abrogating autoimmunities in 3-day thymectomized experimental mice. Whereas a biased Th1 to Th2 cytokine profile has been suggested to underlie the pathogenesis of IMD in both species, we found defective production of IFN-gamma in our patients after in vitro stimulation of their PBMCs by phorbol-myristate acetate and ionomycin and both IFN-gamma and IL-4 deficiencies in V(alpha)24(+) NK T-enriched cells. These data suggest that multiple immunoregulatory T (Treg) cell defects underlie islet cell autoimmunity leading to IMD in humans and that these lesions may be part of a broad T cell defect.

Adolescent↗

PubMed2003

Effect of the environment on genotypic diversity of Actinomyces naeslundii and Streptococcus oralis in the oral biofilm.

The genotypic diversity of Actinomyces naeslundii genospecies 2 (424 isolates) and Streptococcus oralis (446 isolates) strains isolated from two sound approximal sites in all subjects who were either caries active (seven subjects) or caries free (seven subjects) was investigated by using the repetitive extragenic palindromic PCR. The plaque from the caries-active subjects harbored significantly greater proportions of mutans streptococci and lactobacilli and a smaller proportion of A. naeslundii organisms than the plaque sampled from the caries-free subjects. These data confirmed that the sites of the two groups of subjects were subjected to different environmental stresses, probably determined by the prevailing or fluctuating acidic pH values. We tested the hypothesis that the microfloras of the sites subjected to greater stresses (the plaque samples from the caries-active subjects) would exhibit reduced genotypic diversity since the sites would be less favorable. We found that the diversity of A. naeslundii strains did not change (chi2 = 0.68; P = 0.41) although the proportional representation of A. naeslundii was significantly reduced (P < 0.05). Conversely, the diversity of the S. oralis strains increased (chi2 = 11.71; P = 0.0006) and the proportional representation of S. oralis did not change. We propose that under these environmental conditions the diversity and number of niches within the oral biofilm that could be exploited by S. oralis increased, resulting in the increased genotypic diversity of this species. Apparently, A. naeslundii was not able to exploit the new niches since the prevailing conditions within the niches may have been deleterious and not supportive of its proliferation. These results suggest that environmental stress may modify a biofilm such that the diversity of the niches is increased and that these niches may be successfully exploited by some, but not necessarily all, members of the microbial community.

Actinomyces↗

PubMed2005

Experimental design for three-color and four-color gene expression microarrays.

MOTIVATION: Three-color microarrays, compared with two-color microarrays, can increase design efficiency and power to detect differential expression without additional samples and arrays. Furthermore, three-color microarray technology is currently available at a reasonable cost. Despite the potential advantages, clear guidelines for designing and analyzing three-color experiments do not exist. RESULTS: We propose a three- and a four-color cyclic design (loop) and a complementary graphical representation to help design experiments that are balanced, efficient and robust to hybridization failures. In theory, three-color loop designs are more efficient than two-color loop designs. Experiments using both two- and three-color platforms were performed in parallel and their outputs were analyzed using linear mixed model analysis in R/MAANOVA. These results demonstrate that three-color experiments using the same number of samples (and fewer arrays) will perform as efficiently as two-color experiments. The improved efficiency of the design is somewhat offset by a reduced dynamic range and increased variability in the three-color experimental system. This result suggests that, with minor technological improvements, three-color microarrays using loop designs could detect differential expression more efficiently than two-color loop designs. AVAILABILITY: http://www.jax.org/staff/churchill/labsite/software SUPPLEMENTARY INFORMATION: Multicolor cyclic design construction methods and examples along with additional results of the experiment are provided at http://www.jax.org/staff/churchill/labsite/pubs/yong.

Algorithms↗

PubMed2005

Enhanced recognition of protein transmembrane domains with prediction-based structural profiles.

MOTIVATION: Membrane domain prediction has recently been re-evaluated by several groups, suggesting that the accuracy of existing methods is still rather limited. In this work, we revisit this problem and propose novel methods for prediction of alpha-helical as well as beta-sheet transmembrane (TM) domains. The new approach is based on a compact representation of an amino acid residue and its environment, which consists of predicted solvent accessibility and secondary structure of each amino acid. A recently introduced method for solvent accessibility prediction trained on a set of soluble proteins is used here to indicate segments of residues that are predicted not to be accessible to water and, therefore, may be 'buried' in the membrane. While evolutionary profiles in the form of a multiple alignment are used to derive these simple 'structural profiles', they are not used explicitly for the membrane domain prediction and the overall number of parameters in the model is significantly reduced. This offers the possibility of a more reliable estimation of the free parameters in the model with a limited number of experimentally resolved membrane protein structures. RESULTS: Using cross-validated training on available sets of structurally resolved and non-redundant alpha and beta membrane proteins, we demonstrate that membrane domain prediction methods based on such a compact representation outperform approaches that utilize explicitly evolutionary profiles and multiple alignments. Moreover, using an external evaluation by the TMH Benchmark server we show that our final prediction protocol for the TM helix prediction is competitive with the state-of-the-art methods, achieving per-residue accuracy of approximately 89% and per-segment accuracy of approximately 80% on the set of high resolution structures used by the TMH Benchmark server. At the same time the observed rates of confusion with signal peptides and globular proteins are the lowest among the tested methods. The new method is available online at http://minnou.cchmc.org.

Algorithms↗

PubMed2025

A vision of how low-coverage sequence data should contribute to genetic evaluation in the future.

Low-coverage sequencing refers to sequencing DNA of individuals to a low depth of coverage (e.g., 0.5X) and imputing that sequence to a genomic sequence based on reference haplotypes from individuals sequenced to a high depth of coverage (e.g., ≥10X). It has been proposed as an alternative to genotyping by Single-nucleotide polymorphisms (SNP) arrays. At least one commercial product based on it is available for agricultural species. Concerns limiting adoption in its current form are: 1) the cost of storing the huge volume of data it generates and 2) whether that additional data will result in improved accuracy of genetic evaluation. This work envisions future implementation of low-coverage sequencing to reduce storage costs and enhance genetic evaluations by leveraging the additional information in the full sequence of the pangenome to account for more genetic variation. We propose addressing the storage issue by representing genomic sequence of an individual in a pair of haplotype arrays with each element pointing to an enumerated haplotype of the sequence within one of approximately 50,000 defined genome segments. Assuming 60 million genomic variants, the infrastructure required to translate the identifier of any enumerated haplotype into its genomic sequence would require less than 10 gigabytes of binary storage. Each haplotype array element would require 2 bytes, so the marginal binary storage required to represent the genomic sequence of an individual would be about 200 kilobytes (KB), similar to the genotypes from a SNP array with 200,000 markers. This assumes no pedigree and no ambiguity of the imputation, though the latter is unrealistic. Strategies to minimize, and when necessary, to manage and efficiently represent ambiguity are proposed. The genomic sequence of an individual could be stored in about 1 KB (binary) if both parents have unambiguous sequences stored as described above. The proposed system for representing the pangenome includes algorithms for read mapping and imputation intended to leverage all known genetic variation in the target population. It is also designed to use sequencing reads generated for imputing the genomic sequence of new individuals to identify unrecognized mutations, crossovers, and structural variants, thus continuously improving the genome representation, especially if widespread use of low-coverage sequencing in livestock industries is realized. This could make improved genetic merit and management of livestock feasible without computational burden.

Animals↗

PubMed2006

Ab initio modelling of the structure and redox behaviour of copper(I) bound to a His-His model peptide: relevance to the beta-amyloid peptide of Alzheimer's disease.

A contributing factor to the pathology of Alzheimer's disease is the generation of reactive oxygen species, most probably a consequence of the beta-amyloid (Abeta) peptide coordinating copper ions. Experimental and theoretical results indicate that His13 and His14 are the two most firmly established ligands in the coordination sphere of Cu(II) bound to Abeta. Abeta1-42 is known to reduce Cu(II) to Cu(I). The Abeta-Cu(II) complex has been shown to catalytically generate H(2)O(2) from reducing agents and O(2). Cu(II) in the presence of Abeta has been reported to have a formal reduction potential of +0.72-0.77 V (vs. the standard hydrogen electrode). Quantum chemical calculations using the B3LYP hybrid density functional method with the 6-31G(d) basis set were performed to model the reduction of previously studied Cu(II) complexes representing the His13-His14 portion of Abeta (Raffa et al. in J. Biol. Inorg. Chem. 10:887-902, 2005). The effects of solvation were accommodated using the CPCM method. The most stable complex between Cu(I) and the model compound, 3-(5-imidazolyl)propionylhistamine (1) involves tricoordinated Cu(I) in a distorted-T geometry, with the Npi of both imidazoles as well as the oxygen of the backbone carbonyl bound to copper. This model would be the most likely representation of a Cu(I) binding site for a His-His peptide in aqueous solution. A variety of possible redox processes are discussed.

Alzheimer Disease↗

PubMed2001

Rapid changes in hepatitis C virus quasispecies produced by a single dose of IFN-alpha in chronically infected patients.

The effects of a single dose of 3 international megaunits of interferon-alpha2b (IFN-alpha2b) on hepatitis C virus (HCV) load and quasispecies were examined 24 h after administration in 12 previously untreated, chronically infected patients. All patients had viremia loads appreciably reduced relative to baseline values, thus confirming that the viral load is rapidly affected by IFN-alpha2b. Five patients also exhibited changes in plasma HCV quasispecies composition that were clearly evident by single-strand conformation polymorphism, analysis, thus indicating that one dose of IFN-alpha2b may suffice to produce rapid perturbations in the genetic heterogeneity of circulating HCV. Prior to IFN-alpha2b administration, 3 patients exhibited viral quasispecies differences between plasma and peripheral blood mononuclear cells (PBMC). Interestingly, in 2 such patients, the viral quasispecies found in the 24-h plasma resembled that in the pre-IFN PBMC. The latter finding raises the possibility that in these patients, the differences in quasispecies composition between pre-IFN and post-IFN plasma resulted from increased representation of lymphoid tissue-originated variants in the latter sample, possibly because of poor sensitivity to IFN-alpha2b of HCV replication in the lymphoid compartment.

Base Sequence↗

PubMed2004

Protein modeling and structure prediction with a reduced representation.

Protein modeling could be done on various levels of structural details, from simplified lattice or continuous representations, through high resolution reduced models, employing the united atom representation, to all-atom models of the molecular mechanics. Here I describe a new high resolution reduced model, its force field and applications in the structural proteomics. The model uses a lattice representation with 800 possible orientations of the virtual alpha carbon-alpha carbon bonds. The sampling scheme of the conformational space employs the Replica Exchange Monte Carlo method. Knowledge-based potentials of the force field include: generic protein-like conformational biases, statistical potentials for the short-range conformational propensities, a model of the main chain hydrogen bonds and context-dependent statistical potentials describing the side group interactions. The model is more accurate than the previously designed lattice models and in many applications it is complementary and competitive in respect to the all-atom techniques. The test applications include: the ab initio structure prediction, multitemplate comparative modeling and structure prediction based on sparse experimental data. Especially, the new approach to comparative modeling could be a valuable tool of the structural proteomics. It is shown that the new approach goes beyond the range of applicability of the traditional methods of the protein comparative modeling.

Amino Acid Sequence↗

PubMed1997

Information and viewpoint dependence in face recognition.

How we recognize faces despite rotations in depth is of great interest to psychologists, computer scientists and neurophysiologists because of the accuracy of human performance despite the intrinsic difficulty of the task. Three experiments are reported here which used three-dimensional facial surface representations to investigate the effects of rotations in depth on a face recognition task. Experiment 1, using "shape only" representations, showed that all the views used (full-face, three-quarter and profile) were equally well recognized when all had been learned. Performance was better when the same views were presented in an animated sequence rather than at random, suggesting that structure-from-motion provides useful information for recognition. When stimuli were presented inverted, performance was worse and there were differences in the recognizability of views, demonstrating that the familiarity of upright faces affects generalization across views. Experiments 2 and 3 investigated generalization from single views and found performance to be dependent on learned view. In both experiments, generalization from learned full-face fell off with increasing angle of rotation. With shape only stimuli, three-quarter views generalized well to each other, even when inverted but for profiles generalization was equally bad to all unlearned views. This difference may be explained because of the particular relationship of the profile to the axis of symmetry. In Experiment 3, addition of information about superficial properties including color and texture facilitated performance, but patterns of generalization remained substantially the same, emphasizing the importance of underlying shape information. However, generalization from the three-quarter view became viewpoint invariant and there was some evidence for better generalization between profiles. The results are interpreted as showing that three-dimensional shape information is fundamental for recognition across rotations in depth although superficial information may also be used to reduce viewpoint dependence.

Adult↗

PubMed2002

Multiple sources of sodium starch glycolate, NF: evaluation of functional equivalence and development of standard performance tests.

Sodium starch glycolate is a commonly used super-disintegrant employed to promote rapid disintegration and dissolution of IR solid dosage forms. It is manufactured by chemical modification of starch, i.e., carboxymethylation to enhance hydrophilicity and cross-linking to reduce solubility. It has been reported in the literature that the source of starch, particle size, amount of sodium chloride (reaction by-product), viscosity, degree of substitution and cross-linking affect the functionality of sodium starch glycolate. Compendial assays provide an accurate representation of the chemical quality of an excipient, but they are not useful in describing the physical properties associated with the excipients. Physical characterization of sodium starch glycolate, NF revealed differences in particle size, surface area, porosity, surface morphology, and viscosity between two of the three sources examined. An automated liquid uptake test (in neutral and acidic medium) demonstrated similar initial rates of uptake, however, the extent of liquid uptake differed for the disintegrant powders examined. Settling volume was also observed to be different for the disintegrant from two sources. Lowering the pH of the medium reduced the rate and extent of liquid uptake and the settling volume in all instances. The extent of liquid uptake and settling volume was observed to be higher for the smaller sieve fractions in either medium, Although differences were also observed in the axial and radial disintegration force measurements of the pure disintegrant compacts, disintegration and dissolution of a model drug (hydrochlorothiazide) from either the soluble or insoluble core did not reveal any significant differences between the multiple sources.

Absorption↗

PubMed2001

Ribosomal protein L5 has a highly twisted concave surface and flexible arms responsible for rRNA binding.

Ribosomal protein L5 is a 5S rRNA binding protein in the large subunit and plays an essential role in the promotion of a particular conformation of 5S rRNA. The crystal structure of the ribosomal protein L5 from Bacillus stearothermophilus has been determined at 1.8 A resolution. The molecule consists of a five-stranded antiparallel beta-sheet and four alpha-helices, which fold in a way that is topologically similar to the ribonucleoprotein (RNP) domain. The molecular shape and electrostatic representation suggest that the concave surface and loop regions are involved in 5S rRNA binding. To identify amino acid residues responsible for 5S rRNA binding, we made use of Ala-scanning mutagenesis of evolutionarily conserved amino acids occurring in the beta-strands and loop regions. The mutations of Asn37 at the beta1-strand and Gln63 at the loop between helix 2 and beta3-strand as well as that of Phe77 at the tip of the loop structure between the beta2- and beta3-strands caused a significant reduction in 5S rRNA binding. In addition, the mutations of Thr90 on the beta3-strand and Ile141 and Asp144 at the loop between beta4- and beta5-strands moderately reduced the 5S rRNA-binding affinity. Comparison of these results with the more recently analyzed structure of the 50S subunit from Haloarcula marismortui suggests that there are significant differences in the structure at N- and C-terminal regions and probably in the 5S rRNA binding.

Amino Acid Sequence↗

PubMed2006

Maximum common subgraph: some upper bound and lower bound results.

BACKGROUND: Structure matching plays an important part in understanding the functional role of biological structures. Bioinformatics assists in this effort by reformulating this process into a problem of finding a maximum common subgraph between graphical representations of these structures. Among the many different variants of the maximum common subgraph problem, the maximum common induced subgraph of two graphs is of special interest. RESULTS: Based on current research in the area of parameterized computation, we derive a new lower bound for the exact algorithms of the maximum common induced subgraph of two graphs which is the best currently known. Then we investigate the upper bound and design techniques for approaching this problem, specifically, reducing it to one of finding a maximum clique in the product graph of the two given graphs. Considering the upper bound result, the derived lower bound result is asymptotically tight. CONCLUSION: Parameterized computation is a viable approach with great potential for investigating many applications within bioinformatics, such as the maximum common subgraph problem studied in this paper. With an improved hardness result and the proposed approaches in this paper, future research can be focused on further exploration of efficient approaches for different variants of this problem within the constraints imposed by real applications.

Algorithms↗

PubMed2003

Genetic evaluation of localized prostate cancer in a cohort of forty patients: gain of distal 8q discriminates between progressors and nonprogressors.

Over-representation of sequences on chromosome 7 and 8 have been reported to be associated with aggressive behavior of prostate cancer. In this study we have performed a molecular cytogenetic survey by comparative genomic hybridization of a cohort of 40 prostate cancer patients, consisting of 20 progressors and 20 nonprogressors, after radical surgery for localized adenocarcinoma. Progression was defined as a biochemical relapse, ie, an elevation in prostate-specific antigen level in the serum. The mean follow-up after prostatectomy for the progressor group was 10.6 years, for the nonprogressor group, 9.1 years. Using comparative genomic hybridization, we found that progressors harbored on average more aberrations than nonprogressors. Gains were especially more prominent among progressors (p < 0.05), whereas a statistical trend was detected for losses (p = 0.10). As a consequence we examined all chromosome arms separately. The frequencies of loss for areas known to be frequently deleted in prostate cancer, such as 6q, 8p, or 13q, were not different between the two groups. A tendency was observed for more frequent gain on 3q in the progressor group (p = 0.09). However, gain of 8q (minimal overlapping region at 8q24-qter) was significantly more frequent in the progressor group (p = 0.04). This biomarker retained its significance when adjusted for the factors age, tumor grade, tumor stage, resection margin status, and preoperative prostate-specific antigen level. In conclusion we have created a map of genetic changes in progressive and nonprogressive prostatic carcinomas. Importantly, the presence of gain of distal 8q markedly reduced the progression-free survival, suggesting a clinical role for 8q gain in assessing the malignant potential of localized prostatic adenocarcinoma.

Aged↗