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Results for “Automated phenotyping”

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At least 109 records · Page 6Linked to original sources

PubMed1983

Stability of the paraoxonase phenotyping ratio in collections of human sera with differing storage times.

Results from automated testing of 673 human sera, divided into four batches by duration of storage at -20 degrees C, indicated that paraoxon-hydrolysing activity, a, decreased with increased storage time. By contrast, the paraoxonase phenotyping ratio, c/b, a ratio designating enzyme activation by Na+ in the presence of Ca2+, was stable over a four year storage period.

Aryldialkylphosphatase↗

PubMed1996

Automated classification of human brain tumours by neural network analysis using in vivo 1H magnetic resonance spectroscopic metabolite phenotypes.

We present a novel method to integrate in vivo nuclear magnetic resonance spectroscopy (MRS) information into the clinical diagnosis of brain tumours. Water-suppressed 1H MRS data were collected from 33 patients with brain tumours and 28 healthy controls in vivo. The data were treated in the time domain for removal of residual water and a region from the frequency domain (from 3.4 to 0.3 p.p.m.) together with the unsuppressed water signal were used as inputs for artificial neural network (ANN) analysis. The ANN distinguished tumour and normal tissue in each case and was able to classify benign and malignant gliomas as well as other brain tumours to match histology in a clinically useful manner with an accuracy of 82%. Thus the present data indicate existence of tumour tissue-specific metabolite phenotypes that can be detected by in vivo 1H MRS. We believe that a user-independent ANN analysis may provide an alternative method for tumour classification in clinical practice.

Astrocytoma↗

PubMed2003

Automated measurement of Drosophila wings.

BACKGROUND: Many studies in evolutionary biology and genetics are limited by the rate at which phenotypic information can be acquired. The wings of Drosophila species are a favorable target for automated analysis because of the many interesting questions in evolution and development that can be addressed with them, and because of their simple structure. RESULTS: We have developed an automated image analysis system (WINGMACHINE) that measures the positions of all the veins and the edges of the wing blade of Drosophilid flies. A video image is obtained with the aid of a simple suction device that immobilizes the wing of a live fly. Low-level processing is used to find the major intersections of the veins. High-level processing then optimizes the fit of an a priori B-spline model of wing shape. WINGMACHINE allows the measurement of 1 wing per minute, including handling, imaging, analysis, and data editing. The repeatabilities of 12 vein intersections averaged 86% in a sample of flies of the same species and sex. Comparison of 2400 wings of 25 Drosophilid species shows that wing shape is quite conservative within the group, but that almost all taxa are diagnosably different from one another. Wing shape retains some phylogenetic structure, although some species have shapes very different from closely related species. The WINGMACHINE system facilitates artificial selection experiments on complex aspects of wing shape. We selected on an index which is a function of 14 separate measurements of each wing. After 14 generations, we achieved a 15 S.D. difference between up and down-selected treatments. CONCLUSION: WINGMACHINE enables rapid, highly repeatable measurements of wings in the family Drosophilidae. Our approach to image analysis may be applicable to a variety of biological objects that can be represented as a framework of connected lines.

Animals↗

PubMed1995

Immunological changes among workers occupationally exposed to styrene.

The functional status of the immune system was investigated in a group of 71 workers exposed to styrene and in 65 control subjects, recruited according to the same selection criteria and comparable as to sex, age, and confounding variables. Air and biological monitoring were used to characterize styrene exposure (median of the main urinary metabolites in the "next-morning" spot samples: 106 mg/g creatinine). Phenotypic analysis of peripheral blood lymphocytes (PBL) by automated flow cytometry revealed a reduced proportion of T lymphocyte subsets (CD3+, CD4+ and CD4+45+), with no changes in CD8+, and a higher proportion of B lymphocytes (CD19+) among styrene-exposed workers. The exposed workers showed a higher proportion of activation markers, namely DR and interleukin-2 receptors (CD25). Immunoglobulin subclasses were comparable in the two groups. An increased prevalence of abnormally low values was apparent for CD2+, CD3+, CD4+, CD4+45+ and CD11b subsets among workers exposed to styrene, whereas CD19+, DR+ and CD25+ showed an increased prevalence of abnormally high values. Natural killer-related phenotypes (CD56+, CD56+16+, and CD56+16-) were more expressed among styrene workers, with average increase of 30%. However, the frequency distribution of the lytic activity of natural killer cells against K-562 target cells was shifted towards lower values in the exposed workers as compared to control subjects. Dose-response relationships between indices of internal dose and prevalence of abnormal values were detectable for T lymphocyte subsets, NK phenotypes, and activation markers. These findings suggest that moderate exposure to styrene is associated with an altered distribution of lymphocyte subsets.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗

PubMed2001

Introduction of an automated service for the laboratory confirmation of meningococcal disease in Scotland.

The Scottish Meningococcus and Pneumococcus Reference Laboratory provides a national service for the laboratory confirmation of meningococcal and pneumococcal disease in Scotland. The main tests used for the laboratory confirmation of meningococcal disease are culture, the polymerase chain reaction (PCR), antibody testing, and more recently DNA sequencing. This paper describes the automation of PCR for the laboratory confirmation of meningococcal disease and the typing of meningococcal isolates using DNA sequencing. Both methods have been automated using a robotic liquid handler and automated DNA sequencer. These methods, along with standard culture phenotyping and antibody testing, provide Scotland with an excellent service for the confirmation of meningococcal disease.

Automation↗

PubMed1989

Sleuthing out bacterial identities.

Global phenotype analyses are now possible using a versatile redox chemistry that is readily automated with computerization and microplate technology.

Bacteria↗

PubMed2006

Automated imaging of C. elegans behavior.

Automated systems for recording and analyzing behavior have many applications for the study of neurobiology in Caenorhabditis elegans. In particular, machine-based approaches allow for precise quantitative definitions of behavioral phenotypes that have traditionally been subjectively described by individual observers. Automated systems also facilitate the analysis of behaviors that occur over long time scales or are difficult to detect by eye. Here we describe the detailed methodology for the use of one recently described automated tracking system for C. elegans. These protocols make it possible to measure a wide range of parameters related to the morphology, body posture, and locomotion patterns of individual wild-type and mutant nematodes.

Algorithms↗

PubMed2004

Caenorhabditis elegans MPP+ model of Parkinson's disease for high-throughput drug screenings.

The neurotoxin MPTP and its active metabolite MPP+ cause Parkinson's disease (PD)-like symptoms in vertebrates by selectively destroying dopaminergic neurons in the substantia nigra. MPTP/MPP+ models have been established in rodents to screen for pharmacologically active compounds. In addition to being costly and time consuming, these animal models are not suitable for large scale testings using compound libraries. We present a novel MPP+-based model for high-throughput screenings using the nematode Caenorhabditis elegans. Incubation of C. elegans with MPTP or its active metabolite MPP+ resulted in strong symptomatic defects including reduced mobility and increased lethality, and is correlated with a specific degeneration of the dopaminergic neurons. The phenotypic consequences of MPTP/MPP+ treatments were recorded using automated hardware and software for quantification. Incubation of C. elegans with a variety of pharmacologically active components used in PD treatment reduced the MPP+-induced defects. Our data suggest that the C. elegans MPTP/MPP+ model can be used for the quantitative evaluation of anti-PD drugs.

1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine↗

PubMed1996

Prion protein genotype and pathological phenotype studies in sporadic Creutzfeldt-Jakob disease.

A comparative semi-automated morphometric study was performed on the distribution of prion protein, spongiform change and astrocytosis in the brains of nine cases of sporadic Creutzfeldt-Jakob disease of differing genotype at the methionine-valine polymorphism at codon 129 of the prion protein gene. Custom-designed image analysis software was used to produce objective figures for each of the different pathological features throughout 13 different areas of the brain used for analysis. A significant positive correlation was observed between prion protein deposition and astrocytosis in all cases and no significant correlation was observed between spongiform change and prion protein deposition. Different patterns of pathology were found to relate to codon 129 genotype; valine homozygosity favoured the targeting of pathology to deep grey matter structures, while methionine homozygosity favoured cortical targeting of pathology. These results provide evidence that prion protein deposition is closely associated with an astrocytic reaction and suggest that codon 129 genotype may influence the pathological phenotype.

Aged↗

PubMed2005

High-throughput assay for small molecules that modulate zebrafish embryonic heart rate.

To increase the facility and throughput of scoring phenotypic traits in embryonic zebrafish, we developed an automated micro-well assay for heart rate using automated fluorescence microscopy of transgenic embryos expressing green fluorescent protein in myocardium. The assay measures heart rates efficiently and accurately over a large linear dynamic range, and it rapidly characterizes dose dependence and kinetics of small molecule-induced changes in heart rate. This is the first high-throughput micro-well assay for organ function in an intact vertebrate.

Animals↗

PubMed2005

Phage display tools for blood typing.

Current technologies used in blood banks for blood group antigen typing and other pretransfusion tests are extraordinarily labor-intensive, prone to human error, and an order of magnitude more expensive per test than those in other clinical laboratories. With a growing shortage of skilled medical technologists, dwindling supplies of human plasma-derived phenotyping reagents, and an inherent difficulty in fully automating agglutination-based methodologies, the ability to perform rapid and accurate pretransfusion testing in a cost-effective manner has become a significant challenge. This paper reviews the latest advances in the use of phage display technologies to address these issues through the development of inexpensive and renewable blood bank testing reagents that are amenable to high-throughput, automatable assay systems.

Blood Grouping and Crossmatching↗

PubMed2004

Identification and phenotypic characterization of the cell-division protein CdpA.

Analysis of the automated computer annotation of the early draft phase genome of Lactobacillus acidophilus NCFM revealed the previously discovered S-layer gene slpA and an additional partial ORF with weak similarities to S-layer proteins. The entire gene was sequenced to reveal a 1799-bp gene coding for 599 amino acids with a calculated molecular mass of 64.8 kDa. No transcription or translation signals could be determined in close proximity to the 5'-region. However, a strong putative terminator with a free energy of -16.84 kcal/mol was identified directly downstream of the gene. A PSI-Blast analysis showed similarities to members of S-layer proteins, cell-wall associated proteinases and hexosyl-transferases. Calculation of an unrooted phylogenetic tree with other examples of S-layer proteins and proteinases placed the deduced protein separately from both groups. A derivative of L. acidophilus NCFM was constructed by targeted integration into the gene. SDS-PAGE analysis of non-covalently linked proteins of the cell wall of the mutant, compared to the wild type, revealed the loss of a cell-surface protein. Phenotypic analyses of the mutant revealed significant changes in cell morphology, altered responses to various environmental stresses, and lowered cell adhesion. Based on the in silico and functional analyses, we ascertained that this protein plays a role in cell-wall processing during the growth and cell-cell separation and designated the gene as cell-division protein, cdpA.

Bacterial Adhesion↗

PubMed2006

Compound classification using image-based cellular phenotypes.

Compounds with similar target specificities and modes of inhibition cause similar cellular phenotypes. Based on this observation, we hypothesized that we could quantitatively classify compounds with diverse mechanisms of action using cellular phenotypes and identify compounds with unintended cellular activities within a chemical series. We have developed Cytometrix technologies, a highly automated image-based system capable of quantifying, clustering, and classifying changes in cellular phenotypes for this purpose. Using this system, 45 out of 51 known compounds were accurately classified into 12 distinct mechanisms of action. We also demonstrate microtubule-binding activity in one of seven related cytochalasin actin poisons. This technology can be used for a variety of drug discovery applications, including high-throughput primary screening of chemical and siRNA libraries and as a secondary assay to detect unintended activities and toxicities.

Actins↗

PubMed2007

A new strategy based on recombinant viruses as a tool for assessing drug susceptibility of human immunodeficiency virus type 1.

The emergence of drug-resistant variants during antiretroviral therapy is a serious obstacle to sustained suppression of the human immunodeficiency virus type 1 (HIV-1). For that reason, resistance assays are essential to guide clinicians in the selection of optimal treatment regimens. Genotypic assays are less expensive and results are available faster than phenotypic assays. However, in heavily experienced patients with multiple treatment failures interpretation of complex mutation patterns remains difficult, and in these cases phenotypic assays are recommended. This report describes a novel recombinant virus assay where protease (PR) and reverse transcriptase (RT) sequences derived from the plasma isolated from patients are introduced into the back-bone of an HIV molecular clone that expresses Renilla luciferase protein in the place of nef gene. All drug resistance profiles analyzed correlate with previously reported data and showed high reproducibility. This assay, in addition to a fast (completed in 10 days), precise, reproducible and automated method, presents several advantages as compared to other phenotypic assays. The system described below allows the generation of recombinant viruses with multiples cycles of replication carrying a reporter gene in their genomes. These features increase the sensitivity of the test, an important aspect to be considered in the evaluation of less fit viral isolates. In conclusion, the assay permits the quantitation of the level of resistance of clinical HIV-1 isolates to PR and RT inhibitors.

Animals↗

PubMed2003

Classical mitochondrial phenotypes without mtDNA mutations: the possible role of nuclear genes.

The authors analyzed the total mitochondrial (mt) genome in 15 patients with classic mitochondrial phenotypes. Novel somatic mtDNA mutations in two patients with chronic progressive external ophthalmoplegia were identified. Total automated mtDNA genome analysis did not reveal other pathogenic mtDNA mutations. The authors conclude that classic mitochondrial phenotypes, including those with adult onset, may occur in the absence of mtDNA mutations. Nuclear gene mutations may be the cause.

Cell Nucleus↗

PubMed2004

Molecular epidemiology of selected multidrug-resistant bacteria: a global report from the SENTRY Antimicrobial Surveillance Program.

The SENTRY Antimicrobial Surveillance Program was initiated in 1997 as a global network for the longitudinal tracking of antimicrobial resistance and has incorporated a molecular typing protocol to detect and monitor emerging resistances in participant medical centers. Isolates with similar resistance profiles and patient demographics that were temporally related or those exhibiting emerging resistance phenotypes were routinely compared. Isolates were initially analyzed using the automated Riboprinter Microbial Characterization System (Qualicon, Inc., Wilmington, DE). Isolates with identical ribotype patterns were further characterized by pulsed field gel electrophoresis. During 2001, a total of 647 bacterial isolates were processed using this typing protocol; 36% were Staphylococcus aureus with multidrug-resistant, mupirocin- or quinupristin/dalfopristin-resistant phenotypes. Five ribotypes were predominant in this species with some occurring on more than one continent (184.5), whereas others were restricted to a single geographic region (893.2). Among S. aureus, 51 clusters demonstrating dissemination among patients were identified (31 medical centers). Twenty-three outbreaks/clusters were found among Enterobacteriaceae producing either extended-spectrum beta-lactamases or demonstrating resistance to fluoroquinolones. Carbapenem-resistant Pseudomonas aeruginosa and Acinetobacter spp. strains were also analyzed, some of which produced metallo-beta-lactamase enzymes. Clusters of carbapenem-resistant Acinetobacter were identified in Argentina and Israel, whereas metallo-beta-lactamase-producing P. aeruginosa epidemic strains were observed in Italy (three sites) and Brazil. The coupling of molecular epidemiologic investigations with global surveillance such as the SENTRY program adds significant value to participating medical centers and has proven to be effective in tracking changing trends and distribution of resistance genotypes both locally and globally.

Anti-Bacterial Agents↗

PubMed1998

MELAS: a new disease associated mitochondrial DNA mutation and evidence for further genetic heterogeneity.

OBJECTIVES: To define the molecular genetic basis of the MELAS phenotype in five patients without any known mutation of mitochondrial DNA. METHODS: Systematic automated mitochondrial DNA sequencing of all mitochondrial transfer RNA and cytochrome c oxidase genes was undertaken in five patients who had the MELAS phenotype. RESULTS: A novel heteroplasmic mitochondrial DNA mutation was identified in the transfer RNA gene for phenylalanine in one case (patient 3). This mutation was not detected in the patient's blood or in her mother's blood. No pathogenic mutations were identified in the other four patients. CONCLUSIONS: This is the first point mutation in the transfer RNA gene for phenylalanine to be associated with MELAS. The absence of mutations in the remaining four patients suggests that there is further genetic heterogeneity associated with this mitochondrial phenotype.

Adult↗

PubMed2006

CellProfiler: image analysis software for identifying and quantifying cell phenotypes.

Biologists can now prepare and image thousands of samples per day using automation, enabling chemical screens and functional genomics (for example, using RNA interference). Here we describe the first free, open-source system designed for flexible, high-throughput cell image analysis, CellProfiler. CellProfiler can address a variety of biological questions quantitatively, including standard assays (for example, cell count, size, per-cell protein levels) and complex morphological assays (for example, cell/organelle shape or subcellular patterns of DNA or protein staining).

Dose-Response Relationship, Drug↗