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Results for “Functional verification”

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At least 469 records · Page 26Linked to original sources
PubMed2005

Ferrite supports for isolation of DNA from complex samples and polymerase chain reaction amplification.

The influence of cobalt ferrite particles, with non-modified or modified surface, on the course of polymerase chain reaction (PCR) was investigated. DNA isolated from bacterial cells of Bifidobacterium bifidum was used in PCR evaluation of magnetic microspheres. The presence of cobalt ferrite particles inhibits PCR amplification. The effect is not dependent on the functional groups of the modifying reagents used (none, amino, carboxyl). Amplification was improved after the magnetic separation of magnetic particles. Proposed indirect method enabled verification of the suitability of designed particles for their application in PCR assays. Magnetic particles coated with alginic acid under high PEG and sodium chloride concentration were used for the isolation of PCR-ready bacterial DNA from various dairy products. DNA was isolated from crude bacterial cell lysates without phenol extraction of samples. Bifidobacterium and Lactobacillus DNAs were identified in dairy products using PCR.

Bifidobacterium↗
PubMed2005

Androgen receptor binding sites identified by a GREF_GATA model.

Changes in transcriptional regulation can be permissive for tumor progression by allowing for selective growth advantage of tumor cells. Tumor suppressors can effectively inhibit this process. The PMEPA1 gene, a potent inhibitor of prostate cancer cell growth is an androgen-regulated gene. We addressed the question of whether or not androgen receptor can directly bind to specific PMEPA1 promoter upstream sequences. To test this hypothesis we extended in silico prediction of androgen receptor binding sites by a modeling approach and verified the actual binding by in vivo chromatin immunoprecipitation assay. Promoter upstream sequences of highly androgen-inducible genes were examined from microarray data of prostate cancer cells for transcription factor binding sites (TFBSs). Results were analyzed to formulate a model for the description of specific androgen receptor binding site context in these sequences. In silico analysis and subsequent experimental verification of the selected sequences suggested that a model that combined a GREF and a GATA TFBS was sufficient for predicting a class of functional androgen receptor binding sites. The GREF matrix family represents androgen receptor, glucocorticoid receptor and progesterone receptor binding sites and the GATA matrix family represents GATA binding protein 1-6 binding sites. We assessed the regulatory sequences of the PMEPA1 gene by comparing our model-based GREF_GATA predictions to weight matrix-based predictions. Androgen receptor binding to predicted promoter upstream sequences of the PMEPA1 gene was confirmed by chromatin immunoprecipitation assay. Our results suggested that androgen receptor binding to cognate elements was consistent with the GREF_GATA model. In contrast, using only single GREF weight matrices resulted in additional matches, apparently false positives. Our findings indicate that complex models based on datasets selected by biological function can be superior predictors as they recognize TFBSs in their functional context.

Binding Sites↗
PubMed2003

Dynamic measurement of internal solid displacement in articular cartilage using ultrasound backscatter.

Mechanics of articular cartilage can be represented using poroelastic theories where fluid and solid displacements are viscously coupled to create a time-dependent spatially heterogeneous behavior. In recent models of this tissue, finite element methods have been used to predict tissue deformation as a function of time for adult articular cartilage bearing a characteristic depth-dependent structure and composition. However, current experimental methods are limited in providing verification of these predictions. The current study presents an apparatus for imaging the radial displacement profile of cartilage in unconfined compression using an ultrasound technique called elastography. We acquired ultrasound A-scans across the lateral diameter of full-thickness cartilage disks containing a thin layer of underlying bone, during axial compression. Elastography was then applied to correlate temporally sequential A-scans to estimate the solid radial displacement profile in articular cartilage while it undergoes compression and stress-relaxation. Both time-dependent and depth-dependent solid radial displacement profiles were obtained with a precision better than 0.2 micro The results generally agree with predictions of poroelastic models, demonstrating lateral expansion with an effective Poisson's ratio just after completion of the compression phase of the mechanical tests reaching values from 0.18 to 0.4 (depending on compression speed), followed by contraction to lower values. A more restricted movement was observed at both the articular surface and near to the subchondral bone than at regions midway between these two locations.

Animals↗
PubMedDate not supplied

Do individuals with autism process categories differently? The effect of typicality and development.

This study examined the effect of exemplar typicality on reaction time and accuracy of categorization. High-functioning children (age 9-12), adolescents (age 13-16), and adults with autism (age 17-48) and matched controls were tested in a category verification procedure. All groups showed improved processing throughout the lifespan for typical and somewhat typical category exemplars. However, individuals with autism responded more slowly than matched controls to atypical exemplars at all ages. The results are discussed in terms of potential differences in the type of processing that may be required for categorizing typical and atypical category exemplars. Parallels are also drawn to the results of previous studies on face processing in individuals with autism.

Adolescent↗
PubMed2005

Preliminary evaluation of the performance of a new, highly sensitive commercial immunoassay for serum ferritin determination.

We evaluated the analytical performance of a new, commercial, fully automated immunoturbidimetric assay for the determination of ferritin [FER-Latex(X2)CN SEIKEN, Denka Seiken, Japan] in serum on the Olympus AU2700 analyzer. The new assay is a latex-enhanced turbidimetric immunoassay with an analysis time of 10 min. The linearity of the assay was confirmed up to 2505 pmol/L (R2=0.999). The detection limit and the functional sensitivity were both 4.5 pmol/L. The intra- and inter-assay imprecision (CV) at 67, 506, 2186 pmol/L was < 1.8% and < 2.5%, respectively. Verification of the traceability to a WHO standard (80/578) showed a recovery of 102.6% (target value 449 pmol/L). No hook effect was observed in samples containing up to 33,705 pmol/L. The assay showed good correlation with the Beckman Immage nephelometric system (r=0.999). Hemoglobin (< or = 9.8 g/L), total bilirubin (< or = 113 micromol/L), conjugated bilirubin (< or = 109 micromol/L) and rheumatoid factor (< or = 5.2x10(5) IU/L) did not interfere with the assay. The reference interval (2.5-97.5 percentile) was 72-521 pmol/L for men and 27-267 pmol/L for women. The reference interval in patients with anemia, malignant tumors and hemochromatosis was 5.6-52, 130-2436 and 1465-2903 pmol/L, respectively. On the basis of the receiver operating characteristic curve, the 90% sensitivity cut-off value to distinguish between patients with and without iron deficiency was 40 pmol/L. The new latex turbidimetric procedure for ferritin assay is an attractive alternative that avoids the need for dedicated instrumentation.

Adult↗
PubMedDate not supplied

Tumor suppressor genes (TSG).

In the last two decades the field of tumor suppressor genes (TSG) has developed from a novel epidemiology-based concept into one of the pillars of cancer research. New TSG are being discovered and although at a painstakingly slower pace, their functions are also being unravelled. These breakthroughs have not only brought about immediate benefits to clinical medicine such as genetic predictive testing for familial cancer syndromes, but have also introduced new strategies against cancer including early intervention, prevention and promising anti-cancer drugs. Despite that, we are still far from fully understanding the functional complexity of TSG with each discovery leading to even more queries. New developments that challenge the paradigm of TSG have also surfaced warranting verification and there is still a lack of consensual criteria and systematic cataloging for TSG. With the advent of high throughput sequencing and powerful bio-informatics, it is expected that the field of TSG will be expanding at an even faster pace. This review is to give a summary of the history, new concepts and recent advancements in the field of TSG in the hope that some of these concepts and works can be evaluated, expanded or even challenged.

Cell Transformation, Neoplastic↗
PubMed1994

[CT and MR imaging in stereotaxic neurosurgery].

The combination of CT and MR examinations indicates a specific approach to the treatment of brain mass lesions. CT guided stereotaxy is sufficient for well demarcated tumors, haemorrhages and abscesses. MR guided stereotaxy is necessary to be performed in invasively growing brain tumors where explicit histological verification and localisation must be ascertained. In addition it is necessary to take into account the image deformation due to the stereotactic ring. In functional neurosurgery the MR examination visualises the anatomical structures which are needed for the ascertainment of coordinate systems landmarks in coordinate system. (Fig. 1, Tab. 1, Ref. 5.).

Aged↗
PubMed2006

ABCdb: an online resource for ABC transporter repertories from sequenced archaeal and bacterial genomes.

The ATP-binding cassette (ABC) transporters are one of the major classes of active transporters. They are widespread in archaea, bacteria, and eukaryota, indicating that they have arisen early in evolution. They are involved in many essential physiological processes, but the majority import or export a wide variety of compounds across cellular membranes. These systems share a common architecture composed of four (exporters) or five (importers) domains. To identify and reconstruct functional ABC transporters encoded by archaeal and bacterial genomes, we have developed a bioinformatic strategy. Cross-reference to the transport classification system is used to predict the type of compound transported. A high quality of annotation is achieved by manual verification of the predictions. However, in order to face the rapid increase in the number of published genomes, we also include analyses of genomes issuing directly from the automated strategy. Querying the database (http://www-abcdb.biotoul.fr) allows to easily retrieve ABC transporter repertories and related data. Additional query tools have been developed for the analysis of the ABC family from both functional and evolutionary perspectives.

ATP-Binding Cassette Transporters↗
PubMed1991

Quantifying hepatic function in the presence of liver disease with phenazone (antipyrine) and its metabolites.

The disposition of phenazone (antipyrine), a low extraction compound with low protein binding, is known to be altered in the presence of various types of hepatic dysfunction. As such, its pharmacokinetics may be useful in the objective characterisation of altered liver function. Understanding the known effects of various liver disease states upon the disposition of this probe may provide insight into future applications. This article provides a review of background information about normal plasma phenazone pharmacokinetics, urinary metabolite disposition and tabulations of reported total body clearances of the drug in the presence of cirrhosis, fatty liver, hepatitis and cholestasis in humans. An estimate is made of the sensitivity and specificity of phenazone testing for the verification of the presence of cirrhosis based on this compiled literature.

Antipyrine↗
PubMed2002

Follicular administration of a cyclooxygenase inhibitor can prevent oocyte release without alteration of normal luteal function in rhesus monkeys.

BACKGROUND: Prostaglandins (PG), produced by the follicle just before ovulation, appear to act locally to promote follicle rupture and oocyte release. METHODS: To determine whether administration of PG synthesis inhibitor directly into the primate follicle would prevent ovulatory events, serum estradiol was used to predict the day of the ovulatory LH surge in rhesus monkeys. On the day before or the day of the LH surge, vehicle (n = 9), the PG synthesis inhibitor indomethacin (10(-6) or 10(-5) mol/l final concentration; n = 8), or 10(-5) mol/l indomethacin + 1 micro g/ml PGE(2) (n = 3) was injected into the follicular fluid of the pre-ovulatory follicle. In some animals, luteal phase estrogen and progesterone were measured in daily serum samples. Other animals were ovariectomized 3 days after follicle injection; ovaries were examined for verification of follicle rupture and oocyte release. RESULTS: Follicle injection of indomethacin [10(-6) mol/l (n = 4) or 10(-5) (n = 4) mol/l final concentration] or vehicle (n = 6) did not alter luteal function. Examination of serial sections of removed ovaries confirmed follicle rupture and the absence of oocytes in vehicle-injected follicles (n = 3). Trapped oocytes were observed in 4/8 indomethacin-injected follicles, though several ovaries with trapped oocytes had experienced follicle rupture. Oocytes were not detected in the ruptured, luteinizing follicles from indomethacin + PGE(2)-injected monkeys (n = 3). CONCLUSIONS: Follicular administration of indomethacin can prevent oocyte release without inhibition of follicle rupture or disruption of subsequent luteal function. The ability of PGE(2) to prevent indomethacin-induced ovulatory failure suggests a critical role for locally produced PGE(2) in the process of oocyte release in primates.

Animals↗
PubMed2006

Point defect concentrations in metastable Fe-C alloys.

Point defect species and concentrations in metastable Fe-C alloys are determined using density functional theory and a constrained free-energy functional. Carbon interstitials dominate unless iron vacancies are in significant excess, whereas excess carbon causes greatly enhanced vacancy concentration. Our predictions are amenable to experimental verification; they provide a baseline for rationalizing complex microstructures known in hardened and tempered steels, and by extension other technological materials created by or subjected to extreme environments.

Journal Article↗
PubMed1989

Initial clinical experience with a rate responsive pacemaker.

Prism-CLR is a new single chamber unipolar pace, bipolar or unipolar sense, rate responsive pacemaker that utilizes a closed-loop system based on the analysis of the evoked potential for rate adjustment. It also has an automatic output regulation feature for capture verification and threshold search. Five patients in whom this pacemaker was implanted exhibited an appropriate rate increase with exercise and psychological stress. Automatic output regulation functioned appropriately in three of five patients. Preliminary data suggest that Prism-ClR is an effective pacemaker for patients who may benefit from rate responsive pacing. The automatic output regulation recognition algorithm may need modification in some patients.

Aged↗
PubMed2002

Functional analysis of self-injurious behavior in an adult with Lesch-Nyhan syndrome.

A three-phase functional analysis was conducted to discover controlling variables of self-injury in a 28-year-old individual with Lesch-Nyhan syndrome. Experimental verification followed information-gathering and interpretive phases. Self-injurious responses were blocked to prevent harm to the participant; therefore, responses measured were precursors to self-injury. A multielement experimental design included four assessment conditions: social attention contingent on precursory behavior, attention contingent on behavior incompatible with precursory behavior, continuous attention and minimal attention. Highest rates of precursory behavior occurred during continuous attention and when incompatible behavior was reinforced. Social attention appeared to act as a discriminative stimulus for self-injurious behavior in this participant.

Adult↗
PubMed1985

Fetal sonography and neonatal scintigraphy of a choledochal cyst.

A choledochal cyst, observed by ultrasound at 27 wk gestation and diagnosed at 36 wk gestation, was confirmed postpartum by [99mTc]DISIDA cholescintogram. Cystic dilatation of the common bile duct was proven by surgical excision and histological verification. Ultrasonography provides in utero diagnosis of choledochal cyst, often vital for successful management. Technetium-99m DISIDA imaging is a valuable companion for defining function of the cyst.

Adolescent↗
PubMed2000

The effect of sarcomere shortening velocity on force generation, analysis, and verification of models for crossbridge dynamics.

The study tests the hypothesis that the transition rate (G) of the cardiac cross-bridge (XB) from the strong force generating state to the weak state is a linear function of the sarcomere shortening velocity (V(SL)). Force (F) was measured with a strain gauge in six trabeculae from the rat right ventricle in K-H solution [(Ca]0 = 1.5 mM, 25 degrees C). Sarcomere length (SL) was measured with laser diffraction techniques. Twitch F at constant SL and the F response to shortening at constant V(SL) (0-8 microm/s; deltaSL 50-100 nm) were measured at varied times during the twitch. The F response to shortening consisted of an initial fast exponential decline (tau = 2 ms), followed by a slow decrease of F. The instantaneous difference (deltaF) between the isometric F (F(M)) and F during the slow phase depended on the duration of shortening (deltat), the instantaneous F(M) and V(SL). deltaF = G1 x F(M) x deltat x V(SL) x (1 -V(SL)/V(MAX)), where V(MAX) is the unloaded V(SL) and G1 was 6.15+/-2.12 microm(-1) (mean +/- s.d.; n=6). DeltaF/F(M) was independent of the time onset of shortening. The linear interrelation between deltaF and V(SL) is consistent with the suggested feedback, whereby XB kinetics depends on V(SL). This feedback provides a more universal description of the interrelation between shortening and force, as well as the observed linear relation between energy consumption and the mechanical energy output.

Animals↗
PubMedDate not supplied

[Experimental verification of a mathematical model of plasma protein and erythrocyte regeneration after blood loss].

The regeneration process after 40% bleeding is mathematically regular. Albumin, hemoglobin and red cells regeneration is expressed by the fraction-linear function. This law is true for albumin resotration only immediately after blood loss. Red cells and hemoglobin recovery begins only 3 days after acute bleeding, when albumin concentration rises by 90% of the normal level. Mathematical regularity of albumin regeneration was destroyed after the liver denervation or spleenectomy.

Animals↗
PubMed2002

[Molecular cloning, characterization, chromosomal assignment, genomic organization and verification of SFRS12(SRrp508), a novel member of human SR protein superfamily and a human homolog of rat SRrp86].

We have identified and characterized a novel human serine-arginine-rich (SR) splicing regulatory protein 508 (SRrp508) gene that is related to other members of the growing SR superfamily, but only homologous to rat (Rattus norvegicus) serine-arginine-rich splicing regulatory protein 86 (SRrp86) gene. The full-length cDNA of 3811 bp for human SRrp508 was cloned through a blast search of public databases following the identification of a cDNA contig of 658 bp obtained by EST assembly with full robotization in supercomputer in large-scale. Structurally, human SRrp508 encodes a polypeptide of 508 amino acids, which contains a single amino-terminal RNA recognition motif (RRM) and two carboxy-terminal domains rich in serine-arginine dipeptides that are highly conserved among other members of the SR superfamily. The conserved SR and RRM domains emphasize the biological importance of this gene. The SRrp508 gene, which contains 12 exons ranging from 0.096 to 2.093 kb and 11 introns ranging from 0.14 to 5.153 kb, is mapped to the human cytogenetic region 5q11.2-q12.1 using the bioinformatic analysis, and it does not link to any other genes. Furthermore, we have experimentally cloned and sequenced a cDNA fragment of 1680 bp containing the full-length ORF of 1527 bp in this novel human gene by RT-PCR from the single-stranded human pancreas cDNA library (Clontech), which is fully identical with that of the in silico cloning determined by the nucleotide sequencing. Thus, we in silico cloned his gene with GenBank accession number of AF459094 identified solely by bioinformatic analysis of the nucleotide and protein. This novel gene has promotors, TATA-box, several stop codons in the upstream of ORF, and PolyA signal in the downstream of ORF. Based on the above results, it can be concluded that we have obtained a complete novel human gene. The gene sequence exhibits good overall homology to that of rat SRrp86 gene, with 84% and 86% identity over the full-length nucleotide and protein, respectively, and with 96% and 86% identity over the serine-rich domain (RS) or arginine-rich domain (RA), respectively. The full-length sequence exhibits little overall homology to any other known protein at either the nucleotide or the amino acid level. The other two most closely related proteins, with 34% and 35% identity over the full-length protein, respectively, or with 51% and 54% identity over the full-length nucleotide of ORF, respectively, are drosophila serine-arginine-rich protein 54 (SRp54) and human arginine-rich nuclear protein 54 (p54). When comparisons are restricted to the RS or RA domains, the percent identity increased for both SRp54 and p54 are 44% and 54% or 38% and 43%, respectively. These results well demonstrate that only the novel human protein of 508 amino acids cloned is the human homolog of rat SRrp86, thus correcting the standpoint made by Barnard and Patton (Barnard DC, Patton JG. Identification and Characterization of a Novel Serine-Arginine-Rich Splicing Regulatory Protein. Molecular and Cellular Biology, 2000, 20(9): 3049-3057) that human arginine-rich nuclear protein 54 (p54) is the human homolog of the rat SRrp86, and suggesting that human SRrp508 is a new member of this growing superfamily of SR proteins. SRrp508 has an extensive expression profile, and may be a transcriptional factor. On the basis of its sequence and functional properties, we have named this protein SRrp508 for SR-related splicing regulatory protein of 508 amino acids. In summary, by combining bioinformatic analysis with experimental verification, we have successfully cloned the human cDNA homolog of rat SRrp86, which is verified by a series of theoretical and experimental evidence. The HGNC has just given SRrp508 gene entry the nomenclature information containing APPROVED SYMBOL: SFRS12; NAME: splicing factor, arginine/serine-rich 12; and ALIAS: DKFZp564B176, SRrp86. We have cloned this gene for near one year with no person landing the GenBank for registering the same gene. Our newly-established technique line will be helpful in discovering much more novel human genes.

Amino Acid Sequence↗
PubMed2006

Differential expression of TGFbeta-stimulated clone 22 in normal prostate and prostate cancer.

The transforming growth factor-beta (TGFbeta) superfamily and its downstream effector genes are key regulators of epithelial homeostasis. Altered expression of these genes may be associated with malignant transformation of the prostate gland. The cDNA array analysis of differential expression of the TGFbeta superfamily and functionally related genes between patient-matched noncancerous prostate (NP) and prostate cancer (PC) bulk tissue specimens highlighted two genes, namely TGFbeta-stimulated clone-22 (TSC-22) and Id4. Verification of their mRNA expression by real-time PCR in patient-matched NP and PC bulk tissue, in laser-captured pure epithelial and cancer cells and in NP and PC cell lines confirmed TSC-22 underexpression, but not Id4 overexpression, in PC and in human PC cell lines. Immunohistochemical analysis showed that TSC-22 protein expression in NP is restricted to the basal cells and colocalizes with the basal cell marker cytokeratin 5. In contrast, all matched PC samples lack TSC-22 immunoreactivity. Likewise, PC cell lines do not show detectable TSC-22 protein expression as shown by immunoblotting. TSC-22 should be considered as a novel basal cell marker, potentially useful for studying lineage determination within the epithelial compartment of the prostate. Conversely, lack of TSC-22 seems to be a hallmark of malignant transformation of the prostate epithelium. Accordingly, TSC-22 immunohistochemistry may prove to be a diagnostic tool for discriminating benign lesions from malignant ones of the prostate. The suggested tumour suppressor function of TSC-22 warrants further investigation on its role in prostate carcinogenesis and on the TSC-22 pathway as a candidate therapeutic target in PC.

Aged↗