SEARCH · PubMed Health

Results for “Automated phenotyping”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 73 records · Page 4Linked to original sources

PubMed2026

Zebrafish as a versatile model in biomedical research, from disease modeling to regenerative medicine: a review.

Zebrafish are an effective animal model widely utilized in biomedical research. They are known for their rapid reproduction and substantial genetic similarity to humans. Their transparent embryos directly enable the visualization of developmental processes and disease progression. This makes zebrafish invaluable for studying a broad range of human diseases, including cancer, cardiovascular disorders, and neurodegenerative conditions. Compared with other vertebrate models, zebrafish offer several advantages, including ease of genome editing, cost-effective maintenance, and suitability for high-throughput drug screening. Recent advancements have expanded the use of zebrafish in disease modeling and regenerative medicine, providing deeper insights into the genetic and cellular mechanisms underlying human pathologies. Zebrafish provide a robust platform for evaluating the safety, efficacy, and regenerative potential of both natural and synthetic biomaterials, including hydroxyapatite, bioactive glass nanoparticles, and bioceramics. This capability facilitates the creation of artificial tissues that closely resemble native structures. Additionally, integrating artificial intelligence technologies has improved automated data analysis and phenotyping in zebrafish studies, enhancing both accuracy and throughput. This review highlights current applications of zebrafish in disease modeling, drug discovery, regenerative medicine, and biomaterial assessment, emphasizing their evolving role as a versatile preclinical platform supported by advanced genetic and computational tools.

Animals↗

PubMed1997

Study of the polymorphism of caprine milk caseins by capillary electrophoresis.

Polymorphism of caprine milk proteins was studied by capillary electrophoresis. Identification of casein (CN) fractions was effected by using isolated fractions from cation-exchange fast protein liquid chromatography. Genetic polymorphisms in caprine alpha s2-CN, alpha s1-CN, beta-CN and kappa-CN have been determined. kappa-CN A and B, beta-CN A and null, alpha s2-CN A, B and C, alpha s1-CN A, B, C and null, and other forms with intermediate and low alpha s1-CN content have been identified. The capillary electrophoresis method made it possible to analyse whole caprine milk using simple sample preparation and was rapid, automated and suitable for phenotyping studies. This method may also permit the quantitative study of different protein fractions.

Animals↗

PubMed2026

DeepPlaque: a scalable multimodal platform for Aβ pathology and cell analysis in Alzheimer's disease.

Histological analysis is essential for understanding disease pathology and the microenvironment, particularly in Alzheimer's disease (AD), characterized by beta-amyloid (Aβ) plaques that exist as diffuse, fibrillar, and core species, with distinct toxicity levels. However, accurate classification of Aβ plaque types in postmortem brain tissues and profiling of surrounding cells present significant challenges. To address these challenges, we developed "DeepPlaque", an integrated system featuring "PlaqueNet", a deep learning model for automated classification of Aβ plaque species from diverse imaging platforms. DeepPlaque includes automated workflows for cellular phenotyping and proteomic profiling through targeted laser microdissection. PlaqueNet achieves expert-level accuracy (AUC > 90%) in classifying the 3 major Aβ plaque species, supporting consistent and large-scale annotation. By integrating spatial cellular phenotyping with laser microdissection, DeepPlaque enables high-throughput proteomic analysis of Aβ plaque niches, revealing that microglia are more abundant around core and fibrillar Aβ plaques, with increased expression of apolipoprotein E and amyloid precursor protein in core Aβ plaques. This customizable platform enhances the molecular and cellular characterization of Aβ plaque-associated environments, providing critical insights into AD pathology.

Alzheimer Disease↗

PubMed1992

Immunocytometry and gene rearrangement analysis in the diagnosis of lymphoma in an idiopathic pleural effusion.

We report a patient with an idiopathic pleural effusion in whom the diagnosis of non-Hodgkin's lymphoma was established by immunocytometry of pleural fluid and confirmed by the detection of B-cell immunoglobulin gene rearrangement. Immunocytometry is a rapid, semi-automated laboratory method for phenotyping lymphoid cells by determining immunoglobulin and other cell surface antigen expression. This method defines the cell lineage (T or B cells) and the clonality (monoclonal or polyclonal) of a population of lymphocytes. The presence of a monoclonal population of lymphocytes can also be confirmed by recently developed molecular biologic techniques (e.g., Southern blotting) that provide the ability to detect rearrangements of the genes that encode either B-cell immunoglobulin proteins or T-cell antigen receptor proteins. To our knowledge, this case represents the first reported application of immunophenotypic and gene rearrangement analysis in a previously undiagnosed pleural effusion to establish the diagnosis of lymphoma. These relatively new laboratory methods may have a role in the evaluation of idiopathic lymphocytic pleural effusions.

Aged↗

PubMed1999

Line probe assay for rapid detection of mutations in the rpoB gene of Mycobacterium tuberculosis.

Detection of mutations in the rpoB gene of Mycobacterium tuberculosis has been reported to be an accurate predictor of rifampin resistance. DNA sequence analysis and screening methods such as single-strand conformation polymorphism analysis and dideoxy fingerprinting are labor-intensive, expensive, or yield results that may prove difficult to interpret. We evaluated the accuracy of a commercial line probe assay for rapid identification and characterization of mutations in the rpoB gene in 72 isolates of M. tuberculosis, including 50 rifampin-resistant and 22 rifampin-susceptible strains. Ten distinct rpoB mutations were identified. Concordances with automated sequencing results and phenotypic rifampin susceptibility testing results were 99% and 93%, respectively. The results demonstrate the line probe assay to be a rapid (as short as 1 day) and informative tool for the early detection and characterization of rpoB mutations associated with rifampin resistance in a clinical laboratory setting.

Antibiotics, Antitubercular↗

PubMed1996

Automated HPLC screening of newborns for sickle cell anemia and other hemoglobinopathies.

Automated HPLC is used to test dried blood-spot specimens from newborns for hemoglobins (Hb) F, A, S, C, E, and D. We present the method and report on its performance determined during >4 years of testing 2.5 x 10(6) newborns. The method features automated derivation of presumptive phenotypes; quantitative quality control and proficiency testing; throughput of one specimen per minute; small sample volume; hemoglobin concentrations quantified with an interlaboratory CV of 14-18%; retention times with interlaboratory CV of <2% and matching, within +/- 0.03 min, of laboratories and reagent lots; control of peak resolution; 0.5% detection limit for Hb S and C, and 1.0% for Hb F, A, E, and D; few interferences; and negligible background and carryover. Shortcomings of the method are the absence of microplate barcode identification and the need for manually pipetting the sample eluate into the microplate.

Anemia, Sickle Cell↗

PubMed2004

High-throughput phenotypic profiling of gene-environment interactions by quantitative growth curve analysis in Saccharomyces cerevisiae.

Cell-based assays are widely used in high-throughput screening to determine the effects of toxicants and drugs on their biological targets. To enable a functional genomics modeling of gene-environment interactions, quantitative assays are required both for gene expression and for the phenotypic responses to environmental challenge. To address this need, we describe an automated high-throughput methodology that provides phenotypic profiling of the cellular responses to environmental stress in Saccharomyces cerevisiae. Standardized assay conditions enable the use of a single metric value to quantify yeast microculture growth curves. This assay format allows precise control of both genetic and environmental determinants of the cellular responses to oxidative stress, a common mechanism of environmental insult. These yeast-cell-based assays are validated with hydrogen peroxide, a simple direct-acting oxidant. Phenotypic profiling of the oxidative stress response of a yap1 mutant strain demonstrates the mechanistic analysis of genetic susceptibility to oxidative stress. As a proof of concept for analysis of more complex gene-environment interactions, we describe a combinatorial assay design for phenotypic profiling of the cellular responses to tert-butyl hydroperoxide, a complex oxidant that is actively metabolized by its target cells. Thus, the yeast microculture assay format supports comprehensive applications in toxicogenomics.

Environment↗

PubMed1995

Fluorescence-based DNA fingerprinting elucidates nosocomial transmission of phenotypically variable Pseudomonas aeruginosa in intensive care units.

DNA fingerprinting based on automated laser fluorescence analysis of randomly amplified polymorphic DNA (RAPD-ALFA) is a rapid and convenient technique for detecting clonal relatedness of bacterial isolates of nosocomial concern. During an outbreak of Pseudomonas aeruginosa among five patients in a medical intensive care unit, transmission was not suspected because of the phenotypic variability of the initial isolates. However, DNA fingerprinting by RAPD-ALFA and macrorestriction analysis identified a single genotype (strain A) for isolates from three patients and another genotype (strain B) for isolates from the remaining two patients. Strain A isolates displayed three phenotypes defined by different antibiotypes and distinct colony appearance. Retrospective analysis of DNA fingerprints demonstrated that strain A had been transmitted to the index patient one year previously in a different intensive care unit. The study demonstrates that genetic typing approaches are warranted should epidemiological relatedness be identified between phenotypically variant pathogens. Automated laser fluorescence analysis of PCR fingerprints may facilitate routine screening of bacterial isolates for in-house epidemiological surveillance. Antibiograms are an unsuitable approach for the typing of Pseudomonas aeruginosa.

Adult↗

PubMed1994

Monoclonal antibodies to high-incidence Kell epitopes: characterization and application in automated screening of donor samples.

Monoclonal antibodies, LM313/706 and LM357/828, recognize high-frequency epitopes which are absent on red cells of Ko phenotype. Both antibodies have proved suitable for automated screening of blood donor samples, with 5 ml of each culture supernatant sufficient to screen 3,000 donor samples. In a screen of 45,545 samples, LM313/706 revealed 11 samples (1:3686) of Kp(a+b-) phenotype. Thirty-seven samples of K+k- phenotype were identified in 15,235 samples screened with LM357/828 antibody (0.24%). The epitope recognized by LM313/706 was inactivated by 2 mM DTT suggesting a possible association with the Jsa/Jsb antigen structure. The expression of the k-like epitope detected by LM357/828 antibody was found to be influenced by pH change.

Antibodies, Monoclonal↗

PubMed2004

Terminological mapping for high throughput comparative biology of phenotypes.

Comparative biological studies have led to remarkable biomedical discoveries. While genomic science and technologies are advancing rapidly, our ability to precisely specify a phenotype and compare it to related phenotypes of other organisms remains challenging. This study has examined the systematic use of terminology and knowledge based technologies to enable high-throughput comparative phenomics. More specifically, we measured the accuracy of a multi-strategy automated classification method to bridge the phenotype gap between a phenotypic terminology (MGD: Phenoslim) and a broad-coverage clinical terminology (SNOMED CT). Furthermore, we qualitatively evaluate the additional emerging properties of the combined terminological network for comparative biology and discovery science. According to the gold standard (n = 100), the accuracies (precision / recall) of the composite automated methods were 67% / 97% (mapping for identical concepts) and 85% / 98% (classification). Quantitatively, only 2% of the phenotypic concepts were missing from the clinical terminology, however, qualitatively the gap was larger: conceptual scope, granularity and subtle yet significant, homonymy problems were observed. These results suggest that, as observed in other domains, additional strategies are required for combining terminologies.

Animals↗

PubMed2005

CRYGD gene analysis in a family with autosomal dominant congenital cataract: evidence for molecular homogeneity and intrafamilial clinical heterogeneity in aculeiform cataract.

PURPOSE: To present a previously unreported four generation affected Mexican pedigree with congenital hereditary aculeiform cataract caused by a mutation in the gammaD-crystallin (CRYGD) gene. METHODS: A four generation family with 14 available members of whom 8 were affected was analyzed. Interventions included complete ophthalmological examination, cataract phenotype characterization, PCR amplification, and automated DNA sequencing of the 2 exons and exon/intron junctions of the CRYGD gene. RESULTS: A heterozygous missense mutation consisting of a G to A transition at nucleotide position 411 in exon 2 that predicts an Arg to His replacement in residue 58 (R58H) of the CRYGD protein was demonstrated. Intrafamilial clinical heterogeneity was observed as one affected member exhibited a coral-like cataract. CONCLUSIONS: The R58H mutation described in this Mexican family is identical to that demonstrated previously in three unrelated families with aculeiform cataract, suggesting that this type of cataract has a specific molecular basis represented by the Arg to His change at residue 58 of CRYGD. However, intrafamilial clinical heterogeneity associated with this mutation can occur as evidenced by the identification of a subject in this family exhibiting a coral-like cataract, a phenotype classically distinguished from aculeiform cataract. To our knowledge, this is the first example of phenotypic heterogeneity associated with the Arg 58 His CRYGD mutation.

Cataract↗

PubMed2006

Expanding the mutational spectrum in TGFBI-linked corneal dystrophies: Identification of a novel and unusual mutation (Val113Ile) in a family with granular dystrophy.

PURPOSE: To report the clinical and molecular study of a family with an autosomal dominant stromal granular dystrophy of the cornea caused by a novel and unusual TGFBI gene mutation. METHODS: A complete ophthalmological examination, corneal dystrophy phenotype characterization, PCR amplification, and automated nucleotidic sequencing of exons 4, 11,12, 13, and 14 of the TGFBI gene was carried out on the family. DNA from 40 unrelated ethnically matched healthy individuals were analyzed as controls. RESULTS: Corneal dystrophy in two sisters was characterized by multiple grayish-white lesions located in the anterior and mid-stroma. Numerous small sized non-coalescent opacities were observed in the peripheral cornea while fewer larger lesions were apparent towards the central part of the cornea. A heterozygous missense mutation, consisting of a G to A transition at nucleotide position 384 in TGFBI exon 4 that predicts a valine (GTT) to isoleucine (ATT) replacement in residue 113 (Val113Ile) of the TGFBI protein was identified. CONCLUSIONS: This is the most 5' located mutation detected so far in subjects with TGFBI-linked corneal dystrophy. Valine 113 is strictly conserved in TGFBI from several species and we suggest that the phenotype observed in these patients is related to the unusual location of the mutation. Our results expand the mutational spectrum in the group of TGFBI-linked corneal dystrophies.

Adenine↗

PubMed2006

Systematic profiling of cellular phenotypes with spotted cell microarrays reveals mating-pheromone response genes.

We have developed spotted cell microarrays for measuring cellular phenotypes on a large scale. Collections of cells are printed, stained for subcellular features, then imaged via automated, high-throughput microscopy, allowing systematic phenotypic characterization. We used this technology to identify genes involved in the response of yeast to mating pheromone. Besides morphology assays, cell microarrays should be valuable for high-throughput in situ hybridization and immunoassays, enabling new classes of genetic assays based on cell imaging.

Gene Expression Profiling↗

PubMed2005

Sensitive detection using microfluidics technology of single cell PCR products from high and low abundance IgH VDJ templates in multiple myeloma.

Human cancer is inherently heterogeneous, so the ability to monitor individual cancer cells at every clinic visit would be a valuable tool. This work describes the first step towards developing handheld and automated devices for molecular and phenotypic analysis of cancer cells. Here, we show that use of capillary electrophoresis to detect PCR product amplified from either transcripts (high abundance template) or genomic DNA (low abundance template) encoding clonotypic immunoglobulin heavy chain VDJ of plasma cells from patients with multiple myeloma. High abundance IgH VDJ transcripts amplified in conventional systems or by capillary electrophoresis through channels on microfluidic chips or, alternatively, PCR product amplified from individual myeloma plasma cells in a single stage RT-PCR reaction was readily detectable on microfluidic chips. For low abundance templates, a nested PCR strategy was needed to detect PCR product by any method. Using microfluidic chips, PCR products amplified from genomic IgH VDJ DNA were detected in six out of eight plasma cells. Comparison of the ABI3100 and the microfluidic chip indicates that approximately 20 times more sample is injected into the ABI 3100 capillary than for the microfluidics chip. Overall, for high and low abundance template in individual cells, the microfluidic separation/detection system is at least as sensitive as the ABI 3100. In the future, integrated microfluidic platforms that incorporate both PCR cycling and product detection on the same chip are likely to exceed conventional systems in sensitivity and speed of genetic analysis by RT-PCR or PCR.

DNA, Neoplasm↗

PubMed1999

Application of molecular methods for detection and transmission analysis of mycobacterium tuberculosis drug resistance in patients attending a reference hospital in Italy.

A molecular analysis of drug-resistant isolates of Mycobacterium tuberculosis was done in a population with a high prevalence of human immunodeficiency virus infection. Seventy-one consecutive isolates were tested for genotypic resistance to isoniazid, rifampicin, streptomycin, and ethambutol by polymerase chain reaction-single strand conformation polymorphism analysis and automated sequencing of target regions. Phenotypic and genotypic resistance to isoniazid, rifampicin, streptomycin, and ethambutol were detected in 23.4%, 11.2%, 7%, and 5.6% of isolates and in 87%, 88%, 40%, and 100% of resistant isolates, respectively. Specificity was 100% for all target regions. When rpoB, katG, and ahpC mutation analysis were combined, 86% of resistant isolates to any drug were identified. No mutations in inhA were found in isoniazid-resistant isolates. Molecular detection of drug resistance, particularly for isoniazid and rifampicin, may represent a sensitive and very specific technique. The strategy of selecting rpoB, katG, and ahpC to quickly identify most resistant isolates, with a relevant saving of resources, is warranted.

Drug Resistance, Microbial↗

PubMed1994

Composition and diversity of intestinal coliform flora influence bacterial translocation in rats after hemorrhagic stress.

Coliform bacteria are the most frequently reported bacteria to translocate after hemorrhage. We investigated the correlation between composition and diversity of the cecal coliform flora and the degree of translocation in a rat model of hemorrhagic stress. Two groups of nine rats each were bled to 60 and 50 mm Hg mean arterial blood pressure, respectively. A sham-operated group without bleeding (n = 9) and a noninstrumented group (n = 6) served as controls. From each rat, 40 coliform isolates from the cecum and up to 16 from positive mesenteric lymph node (MLN) cultures were tested with an automated biochemical fingerprinting method. The phenotypic diversity of coliforms in each cecal sample was calculated as Simpson's diversity index (DI), and similarities between bacterial types in different samples were calculated as population similarity coefficients. Three rats in the sham-operated group and seven in each of the bled groups showed bacterial translocation. Of the different biochemical phenotypes (BPTs) found in the cecum of bled rats (mean, 6.5 BPTs), only a few were detected in MLNs (mean, 1.9 BPTs per MLN), with Escherichia coli being the dominant species. The translocating E. coli strains were mainly of two BPTs. Rats showing no translocation either did not carry these strains or had a high diversity of coliforms in the cecum. Furthermore, translocation of these coliform types was independent of their proportion in the cecum. In bled rats, the diversity of coliforms (mean DI, 0.53) was significantly higher than that in control groups (mean DI, 0.30; P = 0.004), suggesting that hemorrhage stimulates an increase in diversity of cecal coliforms. Rats with similar coliform flora and subjected to the same treatment showed similar patterns of translocation. Our results suggest that the composition of the coliform flora is an important factor in translocation and that certain coliform strains have the ability to translocate and survive in MLNs more easily than others.

Animals↗

PubMed2006

PROPHECY--a yeast phenome database, update 2006.

Connecting genotype to phenotype is fundamental in biomedical research and in our understanding of disease. Phenomics--the large-scale quantitative phenotypic analysis of genotypes on a genome-wide scale--connects automated data generation with the development of novel tools for phenotype data integration, mining and visualization. Our yeast phenomics database PROPHECY is available at http://prophecy.lundberg.gu.se. Via phenotyping of 984 heterozygous diploids for all essential genes the genotypes analysed and presented in PROPHECY have been extended and now include all genes in the yeast genome. Further, phenotypic data from gene overexpression of 574 membrane spanning proteins has recently been included. To facilitate the interpretation of quantitative phenotypic data we have developed a new phenotype display option, the Comparative Growth Curve Display, where growth curve differences for a large number of mutants compared with the wild type are easily revealed. In addition, PROPHECY now offers a more informative and intuitive first-sight display of its phenotypic data via its new summary page. We have also extended the arsenal of data analysis tools to include dynamic visualization of phenotypes along individual chromosomes. PROPHECY is an initiative to enhance the growing field of phenome bioinformatics.

Chromosomes, Fungal↗

PubMed2004

Identification of the emerging pathogen Vibrio vulnificus biotype 3 by commercially available phenotypic methods.

Identification of the emerging pathogen Vibrio vulnificus biotype 3 has become a challenge for clinical laboratories in the last few years. In this study, the abilities of five commercial systems to identify this new species have been evaluated for the first time, using a unique collection of strains. Fifty-one well-documented wild strains of V. vulnificus biotype 3 were processed using API 20 NE, GNI+ Vitek 1 cards, ID-GNB Vitek 2 cards, Neg Combo 20 Microscan panels, and NMIC/ID-5 BD Phoenix panels. The numbers of strains identified as V. vulnificus by ID-GNB, NMIC/ID-5, and GNI+ were 50 (98.0%), 46 (90.2%), and 7 (13.7%), respectively. Neg Combo 20 Microscan panels and API 20 NE were unable to identify any of the strains of this emerging pathogen to the species level and mostly misidentifies them as other species of the Vibrionaceae family. Data on the phenotypic pattern of V. vulnificus biotype 3 when processed in all five systems as presented here could help clinical laboratories in identifying this new pathogen.

Automation↗