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Results for “Automated phenotyping”

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PubMed2006

[Experimental study on cell adhesion characteristic between porous biphasic calcium phosphate nanocomposite and bone marrow mesenchymal stem cells in vitro].

OBJECTIVE: To study the adhesion characteristic in vitro between porous biphasic calcium phosphate (BCP) nanocomposite and bone marrow mesenchymal stem cells (MSCs) that have been induced and proliferated. METHODS: MSCs obtained from SD rat bone marrow were in vitro induced and proliferated. After their osteoblastic phenotype were demonstrated, MSCs were seeded onto prepared porous BCP nanocomposite (experiment group)and common porous hydroxyapatite (control group). Their adhesion situation was analyzed by scanning electron microscope. The initial optimal cell seeding density was investigated between new pattern porous BCP nanocomposite and MSCs by MTT automated colorimetric microassay method. RESULTS: The differentiation of MSCs to osteoblastic phenotype were demonstrated by the positive staining of mineralized node, alkaline phosphatase (ALP) and collagen type I, the most appropriate seeding density between them was 2 X 10(6)/ml. The maximal number which MSCs could adhere to porous BCP nanocomposite was 1.28 X 10(7)/cm3. CONCLUSION: MSCs can differentiate to osteoblastic phenotype. The MSCs were well adhered to porous BCP nanocomposite.

Animals↗

PubMed2006

Production of myeloid dendritic cells (DC) pulsed with tumor-specific idiotype protein for vaccination of patients with multiple myeloma.

BACKGROUND: Immunotherapy of cancer with DC vaccines has produced encouraging results in clinical trials. Antigen (Ag)-pulsed DC have elicited CD4+ and CD8+ T-cell immunity and tumor regression in humans. However, there is no standard method of DC production. The DC phenotype, number and Ag-loading process used in these studies have varied, making comparisons between trials difficult. METHODS: In the present report a reproducible method was developed for the production of a DC-based vaccine. Monocytes were enriched by adhesion from healthy donor apheresis products and cultured with growth factors for maturation into DC. The cells were loaded with the tumor Ag idiotype proteins from patients with multiple myeloma. DC culture and Ag loading were performed in an automated and closed system. The DC product was characterized for phenotype by flow cytometry and for function in Ag uptake and Ag presentation. RESULTS: These monocyte-derived DC expressed high levels of costimulatory molecules (CD80/86). Ag-pulsed DC functioned to induce allogeneic proliferative lymphocyte responses and Ag-specific cytotoxic T lymphocyte (CTL) responses. The DC viability, phenotype and function were well preserved following prolonged frozen storage. Aliquots from the product of a single DC preparation could be used for sequential vaccinations without batch to batch variability. DISCUSSION: Ag-pulsed DC can be reproducibly generated for clinical use. These standardized methods are now being employed for a clinical trial to evaluate idiotype-pulsed DC vaccine therapy following non-myeloablative transplant for the treatment of multiple myeloma.

Antigen Presentation↗

PubMed2001

[Methicillin-resistant Staphylococcus aureus (MRSA) in an intensive care unit: a one-year survey].

Methicillin-resistant Staphylococcus aureus (MRSA) is frequently isolated in nosocomial outbreaks. In our study, we analysed the occurrence of colonisation and infection in an Intensive Care Unit of our hospital during a 12-month period. We also evaluated the possibility of using automated ribotyping as a molecular method in order to type the isolates. Twice a week a nasal swab and a rectal swab were performed on all patients; from ventilator-assisted patients, a sputum culture was also taken. All the MRSA isolated were identified by using commonly phenotypic procedures and on all isolates susceptibility tests were performed. An automated ribotyping using EcoRI was also done. Out of 292 patients enrolled in the study, 205 were never colonised (group N); among the other 87 who were colonised by MRSA (29.8%), 40 patients (group A) were MRSA carriers at the time of admission, while 47 (group B) were colonised in the ICU. Twenty-seven patients (11 from group A, 15 from group B and 1 from group N) developed 31 infections due to MRSA. Patients from group A exhibited, as a rule, worse clinical conditions than those from the other two groups. For the former group, MRSA infection was frequently systemic (sepsis), while in group B pneumonia was the predominant infection. The prevalence of colonisations in our study was 30%, which is a value comparable to those presented by other authors in similar cases. MRSA colonisation is a necessary condition for subsequent infections in almost all cases, with an average lag of 7 days. Susceptibility tests were non-discriminating among the isolates: all the strains were susceptible to glycopeptides; nearly all of them were resistant to erythromycin, clindamycin, ciprofloxacin and gentamicin. Automated ribotyping allowed us to distinguish 12 different ribogroups, the most frequent of which was composed of 146 isolates. In our study, this molecular method was able to define a possible endemic clone that should be better investigated by using methods with a higher discriminatory power, such as RAPD or PFGE. The method that we employed is highly reliable, easy to perform and not time-consuming. In our opinion, it could be the method of choice in the first screening of high numbers of isolates.

Aged↗

PubMed1989

Quantitative studies on the D antigen of red cells with the Du phenotype.

Rh-positive red cells (RBCs) that fail to agglutinate with commercial anti-D reagents by the tube method are considered to have the Du phenotype. The quantities of D epitopes on such RBCs have been measured previously in one kindred. The authors report on the number of D epitopes on Du RBCs of 23 unrelated individuals, as calculated by Scatchard's analysis. Cell-bound anti-D was measured by an automated antiglobulin consumption technique. On the average, RBCs of the Rh phenotype CcDue had a mean of 1568 +/-1220 (n = 12) D epitopes per cell. The relatively large range of values in this group implies a heterogeneous genetic background. The lowest number of D epitopes, 285 per cell, was observed on the RBCs of one individual who was apparently homozygous for C. In this case, the D antigen was detected only by adsorption/elution tests. RBCs of the phenotype cDuEe had a mean of 775 +/- 378 epitopes per cell (n = 8), and those from two individuals with phenotype cDue had 2840 and 1560 D epitopes, respectively. Thus, on the average, RBCs with the Du phenotype bear about 10 to 20 times less D antigen than normal Rh-positive RBCs. It is suggested that the low D antigen density of Du red cells may account for their poor immunogenicity.

Coombs Test↗

PubMed2026

ClearDepthIAS enables automated high-throughput quantification of roots in soil-grown taproot crops.

Understanding root system architecture is critical for improving crop productivity and resilience, yet phenotyping root traits such as root growth angle and rooting depth remains technically challenging, especially at high throughput. Here, we present ClearDepthIAS, a high-throughput imaging and analysis platform that enables nondestructive, automated quantification of root architecture traits in taproot system crops. By capturing and stitching 360° images of roots growing along the transparent walls of pots and applying deep learning-based segmentation (ClearDepth-WRT), we measured wall root shallowness (WRS)-a proxy for root growth angle-with high precision. We demonstrated for the tap root systems of soybean and canola that the system accurately detects root tips, quantifies their vertical distribution, and extracts biologically meaningful traits such as root area, distribution indices, and growth angles. Validation experiments in canola and soybean demonstrated that WRS can correlate with root crown architecture in mature plants, both in greenhouse and field settings. Furthermore, WRS and root distribution indices derived from ClearDepthIAS are predictors of early root architecture and can be correlated with root biomass distribution across soil depths under field conditions; however, environmental interactions may influence these relationships and weaken or even negate such correlations, as observed when comparing field to field variation in root system architecture. Our system enables efficient phenotyping of genetically diverse populations, with medium to high trait heritability, supporting its utility for genome-wide association studies and breeding. ClearDepthIAS accelerates the development of root ideotypes for improved resource acquisition and carbon sequestration, offering a scalable tool for supporting climate-resilient agriculture.

Plant Roots↗

PubMed2006

Australian multicentre comparison of subtyping methods for the investigation of Campylobacter infection.

In order to identify subtyping methods able to contribute to the surveillance or investigation of Australian Campylobacter infection, six genotypic and three phenotypic subtyping methods were evaluated on a collection of 84 clinical isolates collected over a 30-month period from one region in Australia. The aim was to compare the logistics of various subtyping methods and examine their ability to assist in finding outbreaks or common sources of sporadic infection. The genotypic subtyping methods used were sequencing of the short variable region of the flaA gene, two methods using restriction fragment length polymorphism (RFLP) of the flaA gene using either DdeI or EcoRI with PstI, automated ribotyping, pulsed field gel electrophoresis and multilocus sequence typing. The phenotypic methods employed included Laboratory of Enteric Pathogens serotyping, Lior biotyping and antibiotic resistotyping. The level of agreement between subtyping results was determined. Phenotypic methods showed little agreement whereas genotypic typing methods showed a high level of agreement. Using the premise that five of the six genotypic typing methods were in agreement 15 genotypic groupings were identified. Sequencing of the short variable region of the flaA gene, RFLP of the flaA gene or automated ribotyping in conjunction with multilocus sequence typing best identified genotypic groupings. An alternative combination of RFLP of the flaA gene followed by ribotyping was equally satisfactory. RFLP of the flaA gene appeared to be suitable as a preliminary typing method based on ease of operation, equipment availability and cost.

Australia↗

PubMed1996

Evaluation of an expert system linked to a rapid antibiotic susceptibility testing system for the detection of beta-lactam resistance phenotypes.

Interpretive reading of antibiotic disc agar diffusion tests indicates the resistance mechanisms, if any, expressed by a bacterium. An expert system for determining resistance mechanisms using rapid automated antibiotic susceptibility tests has been developed. The beta-lactam susceptibility of each of 300 strains of clinically significant species of enterobacteria, displaying natural and acquired resistance mechanisms, was determined by disc agar diffusion and by a rapid automated method of susceptibility testing associated with an expert system. For every strain, the conclusion of the expert analysis of the automated test was compared with the commonly accepted interpretation of disc agar diffusion tests. Of the 300 strains studied, 275 were similarly interpreted (91.7% agreement). The susceptible and naturally beta-lactam-resistant phenotypes (wild phenotypes) were equally recognized by both methods. Similarly, the results of the two methods concurred for most of the acquired resistance phenotypes. However, for 25 strains (8.3%) the results diverged. The expert system proposed an erroneous phenotype (5 strains), several phenotypes including the correct one (17 strains), or no phenotype (1 strain). For 2 strains the natural resistance mechanism was not detected at first by the automated method but was subsequently deduced by the expert analysis according to bacterial identification. These results demonstrate that satisfactory interpretive reading of automated antibiotic susceptibility tests is possible in 4 to 5 hours but requires careful selection of the antibiotics tested as phenotypic markers.

Anti-Bacterial Agents↗

PubMed2003

Rapid testing for nitrate reductase activity of Mycobacterium tuberculosis grown in an automated culture system.

In order to reduce the time to detection of nitrate reductase activity, which is arguably the most widely used phenotypic trait to differentiate between Mycobacterium tuberculosis, Mycobacterium bovis and Mycobacterium bovis BCG, the following study was conducted using cultures grown in an automated system. Automated culture systems, which are typically based on liquid medium, have greatly reduced the time-to-recovery of mycobacteria. Yet subsequent testing of isolates for nitrate reductase activity may take several weeks, because culture on solid media is required. Presented here is a procedure to obtain a final result within 24 h for nitrate reductase activity of cultures grown in an automated culture system. Using this procedure, Mycobacterium tuberculosis was rapidly differentiated from Mycobacterium bovis and Mycobacterium bovis BCG.

Antigens, Bacterial↗

PubMed2004

Exploration of essential gene functions via titratable promoter alleles.

Nearly 20% of yeast genes are required for viability, hindering genetic analysis with knockouts. We created promoter-shutoff strains for over two-thirds of all essential yeast genes and subjected them to morphological analysis, size profiling, drug sensitivity screening, and microarray expression profiling. We then used this compendium of data to ask which phenotypic features characterized different functional classes and used these to infer potential functions for uncharacterized genes. We identified genes involved in ribosome biogenesis (HAS1, URB1, and URB2), protein secretion (SEC39), mitochondrial import (MIM1), and tRNA charging (GSN1). In addition, apparent negative feedback transcriptional regulation of both ribosome biogenesis and the proteasome was observed. We furthermore show that these strains are compatible with automated genetic analysis. This study underscores the importance of analyzing mutant phenotypes and provides a resource to complement the yeast knockout collection.

Alleles↗

PubMedDate not supplied

Automated analysis of mature red blood cells and reticulocytes in SS and SC disease.

Phenotypic expression of sickle cell disease (SCD) is highly variable. We investigated red blood cells (RBCs) and reticulocytes using a laser light scattering method (ADVIA120, Bayer Diagnostics, Tarrytown, NY) in a series of patients with either sickle cell anemia (SS) or compound SC heterozygosity (SC), both groups with or without alpha thalassemia. Results were compared with those of a series of patients without hematological disease. Known data were consistently confirmed, namely heterogeneity in cell volume and hemoglobin (Hb) concentration, as well as the premature exit of "stress" reticulocytes from the bone marrow, mostly in SS patients. Specific changes were observed during maturation, including decreases in macrocytic and hypodense cells. Simultaneous viewing of the indices of the different RBC populations provided information on erythropoietic maturation by a rapid, reproducible, and cost-effective method.

Anemia, Sickle Cell↗

PubMed1983

[Automation of immunohematologic testing activities at French blood transfusion centers].

In May 1982, a questionnaire was sent to all of the 170 French Blood Transfusion Services (BTS), on behalf of the French Society of Blood Transfusion. The purpose was to determine the types of automated equipment used for immunohematological controls, the way in which they are used and the result of automation and computerization in daily laboratory operations. We received 135 replies (80%). A generalized conclusion can be drawn from the collected information. 50% of the respondents are neither automated nor computerized. 30% are both automated and computerized. 10% are automated but not computerized and 8% are not automated but are computerized. In the field of automated serology there is an increased tendency to complete the ABO/Rh testing by Cc D Ee and Kell phenotyping. The use of computers allows the current test determination to be compared with previous donation data. However, no fully automated equipment, which can conduct antibody screening, exists, cost effectively, in small or average BTS. In France, there has been a significant increase in automation between 1970 and 1980 but only the most important BTS have carried out automation at the same time as computerization. The smaller BTS have usually become automated without becoming computerized. In 1978, Codabar was first used. This has been one of the principal advances of the last 10 years, allowing all the users of automation to start moving towards complete computerization. This advance was assisted by the use of prepackaged software. This questionnaire also determined that the current emphasis is now to computerize administrative and management activities before laboratory activities. This survey has been conducted during a turning point of the automation of French BTS. It shows that they are, on the whole, satisfied with their automation. As far as the safety and the efficiency of the service are concerned, it is only fair to consider that the main purposes of the automation have been achieved. But in terms of cost, and serological accuracy for antibody screening, a new generation of automated equipment should appear to satisfy the users in the nineties.

ABO Blood-Group System↗

PubMed2002

Weightlessness affects cytoskeleton of rat utricular hair cells during maturation in vitro.

The aim of this study was to investigate whether an altered gravitational environment affected the phenotype of vestibular hair cells during maturation. We developed, using an automated incubator, a 3D culture of utricles from newborn rats. These cultures were subjected to weightlessness for 1 or 3 days, and then compared with control cultures developed in natural and induced 1G gravity. Immunocytochemistry for alpha-tubulin and calretinin revealed disorganisation of the microtubules and a loss of hair cell shape in cells subjected to weightlessness during maturation. We conclude that the lack of gravitational strain affected cytoskeletal dynamics, resulting in loss of the specific morphological phenotype of the cells.

Animals↗

PubMed2003

Characterization of clinical isolates of Enterobacteriaceae from Italy by the BD Phoenix extended-spectrum beta-lactamase detection method.

Production of extended-spectrum beta-lactamases (ESBLs) is an important mechanism of beta-lactam resistance in Enterobacteriaceae: Identification of ESBLs based on phenotypic tests is the strategy most commonly used in clinical microbiology laboratories. The Phoenix ESBL test (BD Diagnostic Systems, Sparks, Md.) is a recently developed automated system for detection of ESBL-producing gram-negative bacteria. An algorithm based on phenotypic responses to a panel of cephalosporins (ceftazidime plus clavulanic acid, ceftazidime, cefotaxime plus clavulanic acid, cefpodoxime, and ceftriaxone plus clavulanic acid) was used to test 510 clinical isolates of Escherichia coli, Klebsiella pneumoniae, Klebsiella oxytoca, Proteus mirabilis, Providencia stuartii, Morganella morganii, Enterobacter aerogenes, Enterobacter cloacae, Serratia marcescens, Citrobacter freundii, and Citrobacter koseri. Of these isolates, 319 were identified as ESBL producers, and the remaining 191 were identified as non-ESBL producers based on the results of current phenotypic tests. Combined use of isoelectric focusing, PCR, and/or DNA sequencing demonstrated that 288 isolates possessed bla(TEM-1)- and/or bla(SHV-1)-derived genes, and 28 had a bla(CTX-M) gene. Among the 191 non-ESBL-producing isolates, 77 isolates produced an AmpC-type enzyme, 110 isolates possessed TEM-1, TEM-2, or SHV-1 beta-lactamases, and the remaining four isolates (all K. oxytoca strains) hyperproduced K1 chromosomal beta-lactamase. The Phoenix ESBL test system gave positive results for all the 319 ESBL-producing isolates and also for two of the four K1-hyperproducing isolates of K. oxytoca. Compared with the phenotypic tests and molecular analyses, the Phoenix system displayed 100% sensitivity and 98.9% specificity. These findings suggest that the Phoenix ESBL test can be a rapid and reliable method for laboratory detection of ESBL resistance in gram-negative bacteria.

Algorithms↗

PubMed2003

SEE locomotor behavior test discriminates C57BL/6J and DBA/2J mouse inbred strains across laboratories and protocol conditions.

Conventional tests of behavioral phenotyping frequently have difficulties differentiating certain genotypes and replicating these differences across laboratories and protocol conditions. This study explores the hypothesis that automated tests can be designed to quantify ethologically relevant behavior patterns that more readily characterize heritable and replicable phenotypes. It used SEE (Strategy for the Exploration of Exploration) to phenotype the locomotor behavior of the C57BL/6 and DBA/2 mouse inbred strains across 3 laboratories. The 2 genotypes differed in 15 different measures of behavior, none of which had a significant genotype-laboratory interaction. Within the same laboratory, most of these differences were replicated in additional experiments despite the test photoperiod phase being changed and saline being injected. Results suggest that well-designed tests may considerably enhance replicability across laboratories.

Animals↗

PubMed2026

Accelerating natural product discovery, characterization and engineering by biofoundries.

Covering: From early developments to the presentNatural product (NP) discovery is increasingly constrained by low-throughput screening, repeated rediscovery, and challenges in scaling genome mining-guided validation workflows. This highlight examines how automated biofoundries are accelerating NP discovery, characterization, and engineering through integrated design-build-test-learn (DBTL) cycles. We discuss recent advances in phenotype-first and genome-first discovery strategies enabled by robotics, high-throughput pathway reconstitution, and automated screening platforms. We further highlight emerging technologies, including cell-free biosynthesis, automated culturomics, programmable chassis engineering, and AI-assisted workflow orchestration, that may enable increasingly autonomous biofoundries for scalable exploration of NP chemical space and therapeutic discovery.

Journal Article↗

PubMed1995

Analysis of RET protooncogene point mutations distinguishes heritable from nonheritable medullary thyroid carcinomas.

BACKGROUND: The distinction of sporadic from inherited medullary thyroid carcinomas (MTCs) is of clinical importance because of the differences in prognosis, and the need for family screening for genetic counseling required in the latter. Germline mutations in the RET protooncogene are associated with multiple endocrine neoplasia (MEN) type 2A, familial medullary thyroid carcinoma (FMTC), and MEN type 2B. Somatic point mutations in the same gene have been identified in a subset of sporadically occurring medullary thyroid carcinomas. METHODS: A nonisotopic polymerase chain reaction-(PCR) based single strand conformation polymorphism (SSCP) analysis and heteroduplex gel electrophoresis method was used to screen DNA extracted from 32 formaldehyde fixed and paraffin embedded MTC specimens and normal tissue or blood of the same patient for point mutations in RET exons 10, 11, and 16. Point mutations were identified by nonisotopic cycle sequencing of PCR-products using an automated DNA-sequencer. Results were compared with the disease phenotype, clinical findings, and follow-up. RESULTS: Six different missense germline mutations were identified at cysteine residues 618, 630, and 634 of the cysteine-rich extracellular RET domain encoded by exons 10 and 11 in all patients with FMTC and MEN 2A. The frequency of mutations at codon 634 was higher in patients with MEN 2A than with FMTC and a 634 Cys-->Arg mutation was associated with parathyroid disease in three patients. A germline Met-->Thr point mutation at codon 918 of the RET tyrosine kinase domain was identified in all three patients with MEN 2B. Two patients with clinically sporadic MTCs and negative family history exhibited a RET germline mutation at codon 634, indicating the presence of an nonpredicted inherited MTC. Furthermore, one patient had a 618 Cys-->Ser mutation in the tumor and nontumorous thyroid DNA but not in blood DNA, indicating a mosaic mutation affecting thyroid tissue but not blood cells. Tumor specific (somatic) Met-->Thr point mutations at codon 918 were identified in 5 of 13 sporadic MTCs. The remaining eight sporadic MTCs lacked mutations in all three RET exons tested. CONCLUSIONS: This study demonstrates that (1) the molecular methods are not only suitable to identify asymptomatic individuals at risk for MEN 2A, FMTC, and MEN 2B but also to distinguish heritable from nonheritable MTCs using archival tissue specimens, and (2) that more MTCs than clinically expected are heritable, indicating the need for genetic analysis of all patients with MTC.

Adult↗

PubMed2001

Integrating molecular medicine with functional proteomics: realities and expectations.

We analyze key proteomic issues and cutting-edge technologies that will spearhead inroads into functional interpretations of human diseases and their therapeutic rectification, following the availability of the predicted human proteome. We contrast the distinctions between high quality data that are low throughput, (e.g., 3-D proteomic reconstructions in embryogenic and nervous system contexts, and multigenerational transgenic studies), versus automated data harvesting that is more distant from human disease phenotypes and currently fulfills a diagnostic role, (e.g., molecular portraits of human diseases via transcriptomic analyses). We examine the extent to which these approaches impinge upon a realistic understanding of human diseases, namely how close they come to revealing the causal events involved in the initiation of disease. While tissue sources from human embryogenesis, foetal development and the brain remain the absolute priority, the pragmatic approaches utilize judicious data integration from selected proteomic studies of model organisms. The role of genome-wide disease-related screens, "humanized" transgenic analyses, multigenerational gene interference methods, and analyses of post-translational modifications in epigenetic contexts from Drosophila will be crucial, since these avenues are far too slow and transgenically cumbersome in mammals. Finally, the implementation of multi compartment electrolyzers (MCE) and multi photon detection (MPD) systems will be pivotal for the proteomic profiling of human tissue samples.

Animals↗

PubMed2002

G6PDdb, an integrated database of glucose-6-phosphate dehydrogenase (G6PD) mutations.

G6PDdb (http://www.rubic.rdg.ac.uk/g6pd/ or http://www.bioinf.org.uk/g6pd/) is a newly created web-accessible locus-specific mutation database for the human Glucose-6-phosphate dehydrogenase (G6PD) gene. The relational database integrates up-to-date mutational and structural data from various databanks (GenBank, Protein Data Bank, etc.) with biochemically characterized variants and their associated phenotypes obtained from published literature and the Favism website. An automated analysis of the mutations likely to have a significant impact on the structure of the protein has been performed using a recently developed procedure. The database may be queried online and the full results of the analysis of the structural impact of mutations are available. The web page provides a form for submitting additional mutation data and is linked to resources such as the Favism website, OMIM, HGMD, HGVBASE, and the PDB. This database provides insights into the molecular aspects and clinical significance of G6PD deficiency for researchers and clinicians and the web page functions as a knowledge base relevant to the understanding of G6PD deficiency and its management.

Databases, Genetic↗