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Results for “Automated phenotyping”

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PubMed2005

Automated home cage observations as a tool to measure the effects of wheel running on cage floor locomotion.

This paper introduces automated observations in a modular home cage system as a tool to measure the effects of wheel running on the time distribution and daily organization of cage floor locomotor activity in female C57BL/6 mice. Mice (n = 16) were placed in the home cage system for 6 consecutive days. Fifty percent of the subjects had free access to a running wheel that was integrated in the home cage. Overall activity levels in terms of duration of movement were increased by wheel running, while time spent inside a sheltering box was decreased. Wheel running affected the hourly pattern of movement during the animals' active period of the day. Mice without a running wheel, in contrast to mice with a running wheel, showed a clear differentiation between novelty-induced and baseline levels of locomotion as reflected by a decrease after the first day of introduction to the home cage. The results are discussed in the light of the use of running wheels as a tool to measure general activity and as an object for environmental enrichment. Furthermore, the possibilities of using automated home cage observations for e.g. behavioural phenotyping are discussed.

Activity Cycles↗

PubMed2005

Automated tissue analysis--a bioinformatics perspective.

OBJECTIVES: Recent progress in automated tissue analysis (tissomics) provides reproducible phenotypical characterization of histological specimens. We introduce informatics tools to cluster and correlate quantitative tissue profiles with gene expression data. The great potential of synergies between tissue analysis and bioinformatics and its perspectives in medical research and computational diagnostics are discussed. METHODS: Key enablers in microscopic imaging and machine vision are reviewed to perform a high-throughput tissue analysis. Methodologies are described and results are demonstrated that support a combined analysis of tissue with gene expression profiles whereby the consideration of individual responses is key. RESULTS: Comprehensive histomorphometric profiles, extracted using machine vision, provide information regarding the components and heterogeneity of a tissue in a reproducible format amenable to data mining and analysis. Tissue quantitative information can be placed in synergetic context with bioinformatics data, such as gene expression profiles, for a more comprehensive stratification of individual responses. From a bioinformatics point of view tissue data are co-variants that support the identification of candidate genes relevant in tissue injury or disease. CONCLUSIONS: Progress in automated analytics enables the generation of quantitative data about tissue previously limited to visual histopathology. Such reproducible data sets can be statistically correlated and clustered throughout the continuum of bioinformatics. The combined approach supports a system-wide view of biology and has a potential to accelerate developments for a personalized computational diagnosis.

Automation↗

PubMed2005

Monoclonal T-cell dyscrasia of undetermined significance associated with recalcitrant erythroderma.

BACKGROUND: Erythroderma is a diffuse, inflammatory skin reaction that, in rare instances, is associated with hematologic malignancies such as cutaneous T-cell lymphoma (erythrodermic mycosis fungoides) or T-cell leukemia (Sezary syndrome or adult T-cell leukemia/lymphoma). OBSERVATIONS: We screened 30 patients with erythroderma (20 patients with erythroderma of known etiology and 10 patients with idiopathic erythroderma) for the presence of circulating monoclonal T-lymphocyte populations using T-cell receptor (TCR)-gamma gene-specific polymerase chain reaction and automated capillary DNA electrophoresis. Moreover, the phenotypic analysis of peripheral blood CD4+ lymphocytes was performed using the following surface markers: CD3, CD7, CD8, CD25, CD26, CD27, CD28, CD29, CD30, CD45RO, CD45RA, CD56, CD134, HLA-DR, TCRalphabeta, TCRgammadelta, and cutaneous lymphocyte antigen (CLA). In 5 patients with idiopathic erythroderma we detected T-cell clones in peripheral blood (in 1 case, associated with the presence of the same clone in the skin) and a 2-fold increase in the proportion of CD3+ CD4+ CD7- CD26- cells. Cell depletion studies indicated that the monoclonal T cells were present within the CD4+ CD7- cell population. Clinically, all patients had chronic, recalcitrant erythroderma but none developed any hematological malignancy during their lifetimes or fulfilled the criteria for cutaneous lymphoma or Sezary syndrome. CONCLUSIONS: A proportion of patients with chronic erythroderma present with the monoclonal expansion of CD4+ CD7- CD26- lymphocytes in their blood. This condition represents a probably benign T-cell dyscrasia, or one of very low malignancy. Alongside monoclonal gammapathy of undetermined significance (MGUS) and monoclonal (B-cell) lymphocytosis of undetermined significance (MLUS), we propose using monoclonal T-cell dyscrasia of undetermined significance (MTUS) to underline a conceptual similarity between this disorder and the more common types of lymphocytic dyscrasia.

Adult↗

PubMedDate not supplied

Attempts to use the HPRT-assay as an automated short-term monitor for an acute exposure to mutagens.

Attempts have been made to use the hypoxanthine-guanine-phospho-ribosyl-transferase-assay as a method for automated screening of agent-induced phenotypic variants of human peripheral lymphocytes reflecting 6-thioguanine resistance and assumed to indicate genotoxic action. Different protocols of the hypoxanthine-guanine-phospho-ribosyl-transferase-system were used in this study in order to investigate whether the system can be a candidate for a short-term test for a rapid and reliable identification of biological systems exposed to agents. The current protocols were based on: 1) fluoresceinated monoclonal antibodies against bromodeoxyuridine-DNA for labelling of 6-thioguanine-resistant human lymphocytes and direct flow-cytometric enumeration of bromodeoxyuridine-positive events and: 2) indirect flow-cytometric enrichment of 6-thioguanine-resistant cells labelled with 3H-thymidine followed by autoradiographic enumeration of positive events. Both the direct and the indirect enumeration method yielded similar results down to the range 10(-4) with respect to frequency of variants. For the less time-consuming direct enumeration method the resolution was limited due to non-specific binding of the antibody and false positives. It was, nevertheless, sufficient to score variants induced in vitro with the mutagens EMS, MMC and TT in the same range as e.g. that of cancer patients during and after chemotherapy or radiotherapy, or that of psoriasis patients during the after PUVA (8-methoxypsoralen and long range UV light)-therapy. We conclude that the direct enumeration protocol can be used for a rapid screening of so called outliers, but a more sensitive test, such as the more time-consuming enrichment protocol based on autoradiography, must be used in order to score variants in the range 10(-5)-10(-6).

Autoradiography↗

PubMed2004

Lack of correlation between phenotypic techniques and PCR-based genotypic methods for identification of Enterococcus spp.

A total of 123 genetically-unrelated strains of Enterococcus spp. strains (51 Enterococcus faecalis, 57 Enterococcus faecium, 10 Enterococcus gallinarum, and 5 Enterococcus casseliflavus) were phenotypically identified by biochemical profiles and by using an automated method. The strains were also analyzed by a PCR assay to assess the accuracy of the phenotypically-based methods for identification of Enterococcus spp. With this aim, a PCR assay using different cell targets, which allows simultaneous detection of glycopeptide-resistant genotypes as well as identification to the species level by means of different gene targets, was used as the gold standard method. All 51 strains of E. faecalis were correctly identified, whereas 48 of 57 strains (84.2%) of E. faecium, were correctly identified. All of the strains of E. gallinarum and 3 out of 5 strains of E. casseliflavus were also correctly identified. The overall results showed that it is possible to identify Enterococcus spp. at the molecular level in less than 30 hours, compared with the 48-96 hours required for the phenotypically-based methods. The excellent accuracy of the PCR assay in identifying these species, particularly E. faecium, must also be emphasized. These findings may have implications for the routine clinical identification of enterococci species.

Bacterial Typing Techniques↗

PubMed1997

Linkage of bipolar affective disorder to chromosome 18 markers in a new pedigree series.

Several groups have reported evidence suggesting linkage of bipolar affective disorder (BPAD) to chromosome 18. We have reported data from 28 pedigrees that showed linkage to marker loci on 18p and to loci 40 cM distant on 18q. Most of the linkage evidence derived from families with affected phenotypes in only the paternal lineage and from marker alleles transmitted on the paternal chromosome. We now report results from a series of 30 new pedigrees (259 individuals) genotyped for 13 polymorphic markers spanning chromosome 18. Subjects were interviewed by a psychiatrist and were diagnosed by highly reliable methods. Genotypes were generated with automated technology and were scored blind to phenotype. Affected sib pairs showed excess allele sharing at the 18q markers D18S541 and D18S38. A parent-of-origin effect was observed, but it was not consistently paternal. No robust evidence of linkage was detected for markers elsewhere on chromosome 18. Multipoint nonparametric linkage analysis in the new sample combined with the original sample of families supports linkage on chromosome 18q, but the susceptibility gene is not well localized.

Baltimore↗

PubMedDate not supplied

Alpha-1 antitrypsin protease inhibitor typing in immobilized pH gradients.

Alpha-1 antitrypsin deficiency is a cause of liver disease in neonates and emphysema in adults. Protein phenotypes are identified by isoelectric focusing using polyacrylamide gels. The Pharmacia Phastsystem was utilized for electrophoresis in miniature gels to identify heterozygotes for the deficiency. Protein phenotypes were identified by isoelectric focusing in a fixed pH gradient from 4.3 to 5 using the Pharmacia Phastsystem for automated electrophoresis and staining of gels. The gradient is formed with Immobilines to create gels of dimensions 50 x 43 x 0.5 mm. The processing time for 16 specimens is one hour and 45 minutes. This method is a rapid, automated method for the analysis of alpha-1 antitrypsin phenotypes and for establishing the diagnosis of a genetic deficiency of this protein.

Genetic Carrier Screening↗

PubMed2000

Ability of the VITEK 2 advanced expert system To identify beta-lactam phenotypes in isolates of Enterobacteriaceae and Pseudomonas aeruginosa.

The Advanced Expert System (AES) was used in conjunction with the VITEK 2 automated antimicrobial susceptibility test system to ascertain the beta-lactam phenotypes of 196 isolates of the family Enterobacteriaceae and the species Pseudomonas aeruginosa. These isolates represented a panel of strains that had been collected from laboratories worldwide and whose beta-lactam phenotypes had been characterized by biochemical and molecular techniques. The antimicrobial susceptibility of each isolate was determined with the VITEK 2 instrument, and the results were analyzed with the AES to ascertain the beta-lactam phenotype. The results were then compared to the beta-lactam resistance mechanism determined by biochemical and molecular techniques. Overall, the AES was able to ascertain a beta-lactam phenotype for 183 of the 196 (93.4%) isolates tested. For 111 of these 183 (60.7%) isolates, the correct beta-lactam phenotype was identified definitively in a single choice by the AES, while for an additional 46 isolates (25.1%), the AES identified the correct beta-lactam phenotype provisionally within two or more choices. For the remaining 26 isolates (14.2%), the beta-lactam phenotype identified by the AES was incorrect. However, for a number of these isolates, the error was due to remediable problems. These results suggest that the AES is capable of accurate identification of the beta-lactam phenotypes of gram-negative isolates and that certain modifications can improve its performance even further.

Enterobacteriaceae↗

PubMed2026

SNPannotator: automated functional annotation of genetic variants and linked proxies.

SUMMARY: Genome-wide association studies (GWASs) have identified thousands of genetic variants associated with complex traits and diseases. However, explaining the mechanisms underlying phenotypic variation remains challenging. Here, we introduce SNPannotator, an automated post-GWAS analysis software package designed to streamline the interpretation of GWAS findings. Our pipeline implements a multi-step process that identifies proxy variants in high linkage disequilibrium (LD) with associated lead variants, then queries comprehensive resources (including Ensembl, the GTEx Portal, the eQTL Catalog, and STRING DB) for genomic position, deleteriousness, regulatory annotations, clinical significance, trait associations, expression (eQTLs) and splicing quantitative trait loci (sQTLs), and functional enrichment analyses and compiles the results into user-friendly reports. This package is implemented in the R programming language and includes auxiliary functions for variant lookup and LD exploration. SNPannotator provides a practical framework for efficiently deriving biologically meaningful insights from GWAS data and for assisting researchers in prioritizing candidate variants for functional validation. AVAILABILITY AND IMPLEMENTATION: The SNPannotator package is available from the Comprehensive R Archive Network (CRAN) at https://cran.r-project.org/web/packages/SNPannotator. The development version and tutorial is available on GitHub (https://github.com/omicslaboratory/SNPannotator). The online version of the package is available at https://omicslab.org/snpannotator.

Software↗

PubMed2005

Integrating cytomics and proteomics.

Systems biology along with what is now classified as cytomics provides an excellent opportunity for cytometry to become integrated into studies where identification of functional proteins in complex cellular mixtures is desired. The combination of cell sorting with rapid protein-profiling platforms offers an automated and rapid technique for greater clarity, accuracy, and efficiency in identification of protein expression differences in mixed cell populations. The integration of cell sorting to purify cell populations opens up a new area for proteomic analysis. This article outlines an approach in which well defined cell analysis and separation tools are integrated into the proteomic programs within a core laboratory. In addition we introduce the concepts of flow cytometry sorting to demonstrate the importance of being able to use flow cytometry as a cell separation technology to identify and collect purified cell populations. Data demonstrating the speed and versatility of this combination of flow cytometry-based cell separation and protein separation and subsequent analysis, examples of protein maps from purified sorted cells, and an analysis of the overall procedure will be shown. It is clear that the power of cell sorting to separate heterogeneous populations of cells using specific phenotypic characteristics increases the power of rapid automated protein separation technologies.

Animals↗

PubMed1991

Biochemical fingerprinting of water coliform bacteria, a new method for measuring phenotypic diversity and for comparing different bacterial populations.

A simple, automated microplate system for biochemical characterization of water isolates can be used to obtain fingerprints of the bacterial flora from various water samples. Mathematical models for calculating the diversities and similarities between bacterial populations are described for such fingerprints. The diversity may give information on whether an indigenous or allochthonous flora is present, and the similarities between bacterial populations, as calculated by using a population similarity coefficient (Sp), may indicate contaminations between different water samples. The system was demonstrated on coliform bacterial populations from various water samples, with or without suspected intercontamination. For unrelated water samples, the Sps were close to 0, whereas repeated samples of the same source showed Sps of 0.64 to 0.74. The Sp values from several water samples were also clustered to form a dendrogram, thus indicating the relative similarities between the bacterial populations to confirm suspected common sources of pollution.

Bacterial Typing Techniques↗

PubMed2004

Dissecting complex behaviours in the post-genomic era.

Identifying gene functions in behaviours has so far relied mainly on achievements in the field of molecular genetics. Further progress can be made by developing new approaches that allow refinement of behavioural phenotypes. The current availability of several thousand different mutant mice challenges behavioural neuroscientists to extend their views and methodologies, to dissect complex behaviours into behavioural phenotypes, and subsequently to define gene-behavioural phenotype relationships. Here, we plead for multi-day automated behavioural observations in carefully designed environments.

Animals↗

PubMed1990

Selective cloning of hybridoma cells for enhanced immunoglobulin production using flow cytometric cell sorting and automated laser nephelometry.

Techniques for selective cloning of murine hybridoma cells by flow cytometric cell sorting and use of automated laser nephelometry to determine the resultant clones' immunoglobulin secretion levels are described. Using a commercially available attachment to a fluorescence-activated cell sorter, individual hybridoma cells were successfully distributed into microtiter wells in an automated manner based on their forward angle light scatter properties and their reaction to fluorescein-conjugated anti-mouse-IgG. The techniques were used to estimate successfully the frequency of immunoglobulin-secreting cells in established cultures. In addition, heterogeneity of cell surface immunoglobulin expression was observed and utilized as a criterion for flow sorting of new hybridoma variants. In these studies, clones derived from high (anti-IgG) intensity sorting regions yielded cultures with enhanced immunoglobulin secretion levels, as determined by automated laser nephelometry. Furthermore, the surface immunoglobulin phenotype of the derived clones was conserved in subsequent progeny. Finally, it was established that inclusion of propidium iodide in the hybridoma cell sorting mixtures improved cloning efficiency by facilitating enhanced discrimination and elimination of nonviable cells. Our results indicate that flow cytometric-assisted single cell deposition provides positive attributes of several traditional hybridoma cloning techniques and, in addition, furnishes a tool for steering the cloning process toward selection of enhanced immunoglobulin producing cultures.

Animals↗

PubMed2003

Quantification of single nucleotide polymorphisms by automated DNA sequencing.

Single nucleotide polymorphisms (SNPs) are linked to phenotypes associated with diseases and drug responses. Many techniques are now available to identify and quantify such SNPs in DNA or RNA pools, although the information on the latter is limited. The majority of these methodologies require prior knowledge of target sequences, normally obtained through DNA sequencing. Direct quantitation of SNPs from DNA sequencing raw data will save time and money for large amount sample analysis. A high throughput DNA sequencing assay, in combination with a SNP quantitative algorithm, was developed for the quantitation of a SNP present in HCV RNA sequences. For a side-by-side comparison, a Pyrosequencing assay was also developed. Quantitation performance was evaluated for both methods. The direct DNA sequencing quantitation method was shown to be more linear, accurate, sensitive, and reproducible than the Pyrosequencing method for the quantitation of the SNP present in HCV RNA molecules.

Algorithms↗

PubMed2000

Absence of association between genetic variation in the promoter of the microsomal triglyceride transfer protein gene and plasma lipoproteins in the Framingham Offspring Study.

Microsomal triglyceride transfer protein (MTP) is a lipid transfer protein that is required for the assembly and secretion of very low density lipoproteins (VLDL) by the liver and chylomicrons by the intestine. The common G-493T polymorphism of the MTP promoter has been shown to be associated with decreased plasma LDL-cholesterol and ApoB content of VLDL. The purpose of the present study was, therefore, to investigate the association of this mutation with variations in lipid and apoprotein levels, lipoprotein subclass profiles and coronary heart disease (CHD) risk in a population-based sample of 1226 male and 1284 female Framingham Offspring participants. In men and women, no significant association was found between the G-493T MTP polymorphism and variations of plasma levels of total cholesterol, LDL-cholesterol, apoprotein B, HDL-cholesterol, apoprotein AI and triglycerides. In order to further investigate potential relationships with variations of lipoprotein phenotypes, lipoprotein subclass profiles were measured using automated nuclear magnetic resonance (NMR) spectroscopy. Each NMR profile yielded information on lipid mass of VLDL, LDL, and HDL subclasses. In both genders, there was no significant association between the G-493T polymorphism and variability of lipoprotein subclass distributions or lipoprotein particle size. Furthermore, no significant association was found between the polymorphism of the MTP promoter and prevalence or the age of onset of CHD. Thus, our results suggest that the G-493T mutation in the MTP promoter is unlikely to have significant implications for cardiovascular disease in men and women.

Adult↗

PubMed2005

Dysgonomonas capnocytophagoides bacteraemia in a neutropenic patient treated for acute myeloid leukaemia.

Dysgonomonas capnocytophagoides, formerly known as CDC group DF-3, is an opportunistic pathogen associated with diarrhoea and very rarely bacteraemia. We report a case of D. capnocytophagoides found in blood cultures from a severely neutropenic patient treated for acute myeloid leukaemia. The isolate was found resistant to penicillin, cephalosporins, meropenem, aminoglycosides and ciprofloxacin, and susceptible to ampicillin, tetracycline, chloramphenicol, clindamycin and trimethoprim-sulphamethoxazole. It was identified using conventional phenotypic testing but remained unidentified by the automated identification system (Vitek-2) as this system did not contain DF-3 or D. capnocytophagoides in its database.

Acute Disease↗

PubMed2001

PCR screening for common weak D types shows different distributions in three Central European populations.

BACKGROUND: DNA sequencing showed RHD mutations for all weak D phenotypes investigated in a study from Southwestern Germany. Molecular classification of weak D offers a more reliable basis than serotyping and is relevant for optimal D transfusion strategies. STUDY DESIGN AND METHODS: Sequence-specific primers were designed to detect weak D types 1 to 5 and the partial D phenotype HMi in a modular set for conventional PCR analysis. Alternatively, all reactions were multiplexed into a single tube, and the products were identified after automated capillary electrophoresis by their size and fluorescence. Weak D phenotype samples from 436 donors in the Tyrol (Austria) and Northern Germany were investigated by PCR. RESULTS: More than 90 percent of the weak D types identified by PCR represented type 1, 2, or 3. The distribution among the common types varied between the Tyrol and Northern Germany (p<0.0001). Three new RHD alleles were identified. CONCLUSION: A PCR method of detecting the common weak D types was validated. This PCR system introduces a simple and rapid tool for routine DNA typing of weak D samples. The results confirmed that all weak D phenotype samples identified by current serologic criteria carry altered D proteins.

Alleles↗

PubMed2005

EMPReSS: European mouse phenotyping resource for standardized screens.

UNLABELLED: Standardized phenotyping protocols are essential for the characterization of phenotypes so that results are comparable between different laboratories and phenotypic data can be related to ontological descriptions in an automated manner. We describe a web-based resource for the visualization, searching and downloading of standard operating procedures and other documents, the European Mouse Phenotyping Resource for Standardized Screens-EMPReSS. AVAILABILITY: Direct access: http://www.empress.har.mrc.ac.uk CONTACT: e.green@har.mrc.ac.uk.

Animals↗