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Results for “phenotypic identification”

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At least 19 recordsLinked to original sources
PubMedDate not supplied

Immunofixation following electrophoresis or isoelectric focusing for identification and phenotyping of proteins.

Immunofixation following electrophoresis or isoelectric focusing has proven to be a powerful tool for the phenotyping of plasma proteins, the identification of proteins such as M-components and the study of conversion or breakdown products of proteins such as C3. One of the major advantages is the ability to compare, side by side, the mobilities of relatively low-concentration proteins. The technique is relatively simple, can be used with most types of gels and can be enhanced when necessary by the use of enzyme- or radiolabeled antibodies. The cost is competitive with other immunochemical procedures which are more tedious but which give less information.

Amniotic Fluid↗
PubMed1976

Bvr-1, a restriction locus of a type C RNA virus in the feline cellular genome: identification, location, and phenotypic characterization in cat X mouse somatic cell hybrids.

Somatic cell hybrids were constructed between BALB/c-RAG mouse cells and feline lymphoma cells by the hypoxanthine-aminopterin-thymidine selection scheme. RAG cells spontaneously produce an endogenous B-tropic type C virus. Cat-mouse hybrids preferentially segregate feline chromosomes and retain murine chromosomes-demonstrable by karyotypic and isozyme analyses. Despite the presence of the complete mouse genome, including the viral genome, virus production was diminished to 1-5% of the levels observed in RAG parents based upon particle-associated RNA-dependent DNA polymerase (reverse transcriptase) activity in the culture fluid. Thirty-seven hybrids made on four different occasions had suppressed virus levels, and no hybrids expressed parental virus levels. Reverse selection experiments on 6-thioguanine demonstrated that a restriction gene, tentatively named Bvr-1, was linked to the feline structural genes for hypoxanthine phosphoribosyltransferase (IMP:pyrophosphate phosphoribosyltransferase; EC 2.4.4.8) and glucose-6-phosphate dehydrogenase (D-glucose-6-phosphate: NADP+ 1-oxidoreductase; EC 1.1.1.49) in cats, probably on the X-chromosome. The genetic mode of action of Bvr-1 is trans dominant in restriction of murine leukemia virus. The restriction locus results in a block late in virus maturation but prior to release, since expression of antigens for viral structural proteins and matrue budding particles is apparent on surfaces of restriced hybrid cells but not in high-speed pellets from culture fluid of restricted cells.

Animals↗
PubMed1979

Improved identification of antitrypsin phenotypes through isoelectric focusing with dithioerythritol.

Isoelectric focusing has replaced acid starch-gel electrophoresis for the routine determination of antitrypsin phenotypes in recent years. We observed increased sharpness of antitrypsin bands and decreased background stain following the addition of DTE to serum before isoelectric ofcusing in polyacrylamide gels. DTE and DTT were the only sulfhydryl reducing agents which produced this effect. Electrophoretic mobility of antitrypsin bands was increased very slightly. Decreased background stain resulted from the precipitation of albumin. Precipitation (coagulation) of albumin was complete in serum after 60 min incubation at 37 degrees C at concentrations of 30 mM DTE or DTT. Optimal pH for denaturation was 7.6 to 8.8. Ionic concentrations reduced the strength of the coagulum at 2.5M sodium chloride but had little effect at lower concentrations. Marked temperature effects were noted. As a result of these studies, we recommend examination of native and reduced (30 mM DTE) serum on isoelectric focusing in polyacrylamide gel for all samples submitted for routine antitrypsin phenotype determinations. It also seems possible that the nontoxic DTE (DTT) precipitation of albumin could prove useful for studies of serum proteins other than alpha 1-antitrypsin.

Animals↗
PubMed1979

Family study on the kindred of an adenosine deaminase deficient child with severe combined immunodeficiency.

A study was performed on the family of a child with severe combined immunodeficiency and deficiency of the purine salvage pathway enzyme, adenosine deaminase (ADA). Sixteen relatives over three generations were studied. Erythrocyte ADA levels clearly indicated the heterozygous status of five members. A sixth member, whose erythrocyte ADA level of 48 nmol/hr/ml Hb was within two standard deviations (32) of the mean (76) was shown by ADA determination on platelets to be clearly heterozygous. Similarly, consideration of ADA data of either serum, platelets or lymphocytes only, would have failed to identify all heterozygotes. The survey shows that the identification of phenotype by the indirect means of enzyme level determination is enhanced by the simultaneous study of several tissues.

Adenosine Deaminase↗
PubMed2025

Tumor-immune partitioning and clustering algorithm for identifying tumor-immune cell spatial interaction signatures within the tumor microenvironment.

BACKGROUND: Growing evidence supports the importance of characterizing the organizational patterns of various cellular constituents in the tumor microenvironment in precision oncology. Most existing data on immune cell infiltrates in tumors, which are based on immune cell counts or nearest neighbor-type analyses, have failed to fully capture the cellular organization and heterogeneity. METHODS: We introduce a computational algorithm, termed Tumor-Immune Partitioning and Clustering (TIPC), that jointly measures immune cell partitioning between tumor epithelial and stromal areas and immune cell clustering versus dispersion. As proof-of-principle, we applied TIPC to a prospective cohort incident tumor biobank containing 931 colorectal carcinoma cases. TIPC identified tumor subtypes with unique spatial patterns between tumor cells and T lymphocytes linked to certain molecular pathologic and prognostic features. T lymphocyte identification and phenotyping were achieved using multiplexed (multispectral) immunofluorescence. In a separate hepatocellular carcinoma cohort, we replaced the stromal component with specific immune cell types-CXCR3+CD68+ or CD8+-to profile their spatial relationships with CXCL9+CD68+ cells. RESULTS: Six unsupervised TIPC subtypes based on T lymphocyte distribution patterns were identified, comprising two cold and four hot subtypes. Three of the four hot subtypes were associated with significantly longer colorectal cancer (CRC)-specific survival compared to a reference cold subtype. Our analysis showed that variations in T-cell densities among the TIPC subtypes did not strictly correlate with prognostic benefits, underscoring the prognostic significance of immune cell spatial patterns. Additionally, TIPC revealed two spatially distinct and cell density-specific subtypes among microsatellite instability-high colorectal cancers, indicating its potential to upgrade tumor subtyping. TIPC was also applied to additional immune cell types, eosinophils and neutrophils, identified using morphology and supervised machine learning; here two tumor subtypes with similarly low densities, namely 'cold, tumor-rich' and 'cold, stroma-rich', exhibited differential prognostic associations. Lastly, we validated our methods and results using The Cancer Genome Atlas colon and rectal adenocarcinoma data (n = 570). Moreover, applying TIPC to hepatocellular carcinoma cases (n = 27) highlighted critical cell interactions like CXCL9-CXCR3 and CXCL9-CD8. CONCLUSIONS: Unsupervised discoveries of microgeometric tissue organizational patterns and novel tumor subtypes using the TIPC algorithm can deepen our understanding of the tumor immune microenvironment and likely inform precision cancer immunotherapy.

Humans↗
PubMed2026

[Genetic diversity analysis of Forsythia suspensa germplasm resources in Shanxi based on phenotypic traits and SNP molecular markers].

This study aimed to clarify the degree of fruit phenotypic variation and the characteristics of genetic diversity, population structure, and genetic differentiation of Forsythia suspensa resources in Shanxi, providing an important basis for germplasm conservation and breeding of superior varieties. A total of 46 F. suspensa fruits were collected, and 12 agronomic traits were measured and analyzed. The population genetic structure and genetic diversity of F. suspensa germplasm were evaluated using simplified genome sequencing technology. For the five quality traits of the 46 fruits, the Shannon-Wiener index ranged from 0.631 to 1.074, and the Simpson index ranged from 0.379 to 0.560. The seven quantitative traits exhibited abundant genetic variation, with coefficients of variation ranging from 9.764%(fruit shape index) to 45.494%(forsythin content). Principal component analysis reduced the 12 phenotypic traits to four factors, with a cumulative variance contribution of 74.547%. Sequencing data showed mean Q20 and Q30 values of 98.13% and 94.33%, respectively, with an average GC content of 35.95%. After filtering, a total of 12 347 327 high-quality single nucleotide polymorphism(SNP) loci were obtained. Based on these high-quality SNPs, principal component analysis, population structure analysis, and phylogenetic tree construction were carried out. The 46 germplasm resources were divided into four groups; however, grouping showed little relationship with geographic origin, and intermixing occurred among regions. Mantel test revealed a significant but weak positive correlation between phenotypic and genetic distances(r=0.159, P=0.001). At the molecular level, the four groups exhibited moderate genetic diversity overall, and the genetic differentiation index among populations ranged from 0.027 to 0.084, indicating low to moderate differentiation. The rich genetic diversity of the main phenotypic traits provides a solid material basis for screening superior germplasm and genetic breeding of F. suspensa.

Forsythia↗
PubMed1979

Pi phenotypes of alpha1-antitrypsin in Southern England: identification of M subtypes and implications for genetic studies.

Phenotypes of alpha1-antitrypsin (A1AT) were determined by isoelectric focusing in blood samples from 926 healthy Caucasians living in South-West England. Three subtypes of the most common allele product (M), designated M1, M2, and M3, were identified. Routine determination of these subtypes should considerably amplify the usefulness of the A1AT polymorphism in population genetics and, in view of the possible association of clinical disorders with heterozygous deficient M phenotypes, may enhance the value of Pi determinations in clinical genetics.

Alleles↗
PubMed1977

Liver replacement for alpha1-antitrypsin deficiency.

A 16-year-old girl with advanced cirrhosis and severe alpha 1-antitrypsin deficiency of the homozygous Pi ZZ phenotype was treated by orthotopic liver transplantation. After replacement of the liver with a homograft from a donor with the normal Pi MM phenotype, the alpha 1-antitrypsin concentration in the recipient's serum rose to normal; it had the Pi MM phenotype. Two and a third years later, chronic rejection necessitated retransplantation. Insertion of a homograft from a heterozygous Pi MZ donor was followed by the identification of that phenotype in the recipient's serum. Neither liver graft developed the alpha 1-antitrypsin glycoprotein deposits seen with the deficiency state. These observations confirm that this hepatic-based inborn error of metabolism is metabolically cured by liver replacement.

Adolescent↗
PubMed1979

Identification of TL+ thymocytes with different Lyt phenotypes.

The surface antigenic phenotype of BALB/c thymocytes has been analyzed by sequential cytotoxic treatment with Lyt-1.2, Lyt-2.2 and TL.2 antisera plus complement. Two new minor subpopulations with TL+Lyt-1+2- and TL+Lyt-1-2+ phenotypes have been identified providing direct evidence for the heterogeneity of the Lyt phenotype among the TL-positive supopulation of thymocytes. This finding suggests that differentiation pathways of Lyt subsets of T cells are more complex than originally proposed and that commitment to separate lines of differentiation may occur already at the level of immature, cortical thymocytes.

Animals↗
PubMed2026

Identification of a putative RocS homolog through phenotypic profiling of uncharacterized essential genes in Streptococcus mutans.

Genome-wide viability catalogs produced by transposon sequencing (Tn-seq) and CRISPR interference (CRISPRi) have successfully mapped the essential genome of Streptococcus mutans . In this study, we combined predictive bioinformatics, conditional CRISPRi transcriptional silencing, transmission electron microscopy, transcriptomics, and genetic suppressor screens to investigate nine poorly characterized essential genes in S. mutans . From this screen, phenotypic and genetic analyses identified SMU_393 as a functional homolog of the pneumococcal chromosome segregation factor, RocS. Depletion of SMU_393 resulted in abnormal cell widening, hypersensitivity to DNA damage, and a significant subpopulation of anucleate cells. These phenotypes were bypassed by a spontaneous surface-exposed missense mutation ( dnaA Q197E ) within the AAA+ ATPase domain of the replication initiator. Together, this study refines annotations within the S. mutans essential genome and provides genetic insights into streptococcal chromosome segregation and cell cycle control.

Journal Article↗
PubMed1977

Genetic heterogeneity within the chondroitinsulphaturias.

The approach, identification of clinical phenotype followed by lysosomal enzyme assays in cell culture, used in the classification of the genetic mucopolysaccharidoses I-VI has been applied to the chondroitinsulphaturias. There was evidence of heterogeneity in the first 9 patients reported.

Cells, Cultured↗
PubMed2026

Identification of candidate genes and regulatory mechanisms for thick shank phenotype of Dong Tao chickens.

The Dong Tao Chicken has garnered widespread attention owing to its hallmark trait of remarkably thick shanks. However, the genetic mechanisms and molecular basis underlying this unique phenotype remain largely elusive to date. We carried out crossbreeding trials, performed genome-wide association study (GWAS), and completed transcriptome sequencing of leg tissues. Crossbreeding experiments confirmed that the thick-leg trait of Dong Tao chickens is polygenically controlled. Furthermore, GWAS analysis on the F₂ segregating population screened NAKIN3 as a key candidate gene associated with this trait. Transcriptomic results indicated that tarsometatarsal skin acts as the primary tissue regulating shank circumference growth. Moreover, ACTB was recognized as a core gene driving dermal thickening of the tarsometatarsus. By interacting with IRF family members, TLR4, SOS1, IFNG, STAT family members, EGF and other molecules, ACTB participates in multiple Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways including the Toll-like receptor signaling pathway and cytokine-cytokine receptor interaction pathway to coordinately modulate dermal thickening in the tarsometatarsal skin of Dong Tao chickens. This study identifies key loci and genes governing shank development, offering theoretical basis and genetic resources for dissecting molecular mechanisms and selective breeding of Dong Tao chickens. Nevertheless, these preliminary findings need to be further verified by expanding the experimental population and sample size, together with additional independent validation experiments.

Dong Tao chicken↗
PubMed2025

Pervasive fitness trade-offs revealed by rapid adaptation to shifting population densities in large experimental populations of Drosophila melanogaster.

Trade-offs are an inherent feature of organismal biology that are expected play a fundamental role in the evolution of natural populations. Efforts to quantify trade-offs are largely confined to phenotypic measurements and the identification of negative genetic-correlations among fitness-relevant traits. Here, we use time-series genomic data collected during experimental evolution in large, genetically diverse populations of Drosophila melanogaster to directly measure the manifestation of trade-offs in response to fluctuating selection on ecological timescales. Specifically, we first conducted a lab-based selection experiment to quantify a genome-wide signal of antagonistic pleiotropy elicited in response to shifting population densities and associated with reproduction and stress tolerance selection. In doing so, we identified a putative role of two cosmopolitan inversions in these trade-offs. We then conducted an independent experiment to show that a simple manipulation of increasing population density under controlled lab-based conditions identified loci that are relevant to selection during population expansion and collapse in a complex, semi-natural setting. In concert, our results reveal how adaptation in complex, natural environments can be coarse-grained in such a manner to drive repeatable and predictable patterns of genomic variation, and further add credence to models positing a role of generic fitness trade-offs in the maintenance of variation in natural populations.

Drosophila melanogaster↗
PubMed1975

[Transferrin variants: significance and identification in paternity cases (author's transl)].

Transferrin phenotypes were determined in 3380 sera of unrelated persons of the western region of Germany with 97.60 percent for TfC and 2.40 percent for Tf variants. Identification was achieved by immunochemical means or through autoradiography. Relative mobilities in some variants were measured using Tf B2C (0.7) as reference. Application of Tf variants is demonstrated in paternity cases.

Clostridium perfringens↗
PubMed2026

An oral tyrosine challenge test for functional phenotyping of microbiota-derived phenyl sulfate production.

Phenyl sulfate (PS), a gut microbiota-derived metabolite implicated in the pathogenesis of diabetic kidney disease, is generated through microbial conversion of dietary tyrosine to phenol, followed by hepatic sulfation via SULT1A1. We developed an oral tyrosine challenge test (OTyCT) to phenotype individual PS-producing capacity. Forty-eight healthy adults underwent a standardized tyrosine load with serial plasma PS levels measured over 48 h using LC-MS. OTyCT revealed substantial interindividual variability of PS production independent of baseline PS levels, highlighting marked heterogeneity in host-microbiome metabolic interactions. Sixteen participants in the highest tertile of the incremental area under the curve of PS were defined as high-PS producers. High PS producers exhibited distinct gut microbial signatures despite comparable abundances of known phenol-biosynthetic genes and host SULT1A1 genotypes. These findings suggest that susceptibility to PS-related complications may vary according to gut microbial profiles, supporting OTyCT as a practical tool for metabolic phenotyping and microbiome-informed precision nutrition. Clinical Trial registry name and registration number: Identification of P-Cresyl Sulfate Producer Phenotype by Oral Tyrosine Challenge Test: Interactions Among Diet, Gut Microbiota, and Host Genome, NCT04204174.

Journal Article↗
PubMed2024

Genetic and Microbial Analysis of Invasiveness for Escherichia coli Strains Associated With Inflammatory Bowel Disease.

BACKGROUND & AIMS: The adherent-invasive Escherichia coli (AIEC) pathotype is implicated in inflammatory bowel disease (IBD) pathogenesis. AIEC strains are currently defined by phenotypic measurement of their pathogenicity, including invasion of epithelial cells. This broad definition, combined with the genetic diversity of AIEC across patients with IBD, has complicated the identification of virulence determinants. We sought to quantify the invasion phenotype of clinical isolates from patients with IBD and identify the genetic basis for their invasion into epithelial cells. METHODS: A pangenome with core and accessory genes (genotype) was assembled using whole genome sequencing of 168 E coli samples isolated from 13 patients with IBD. A modified assay for invasion of epithelial cells (phenotype) was established with consideration of antibiotic resistance phenotypes. Isolate genotype was correlated to invasiveness phenotype to identify genetic factors that cosegregate with invasion. RESULTS: Pangenome-wide comparisons of E coli clinical isolates identified accessory genes that can cosegregate with invasion phenotype. These correlations found the acquisition of antibiotic resistance genes in clinical isolates compromised the traditional gentamicin protection assays used to quantify invasion. Therefore, an alternate assay, based on amikacin resistance, identified genes cosegregating with invasion. These genes encode an arylsulfatase, a glycoside hydrolase, and genetic islands carrying propanediol utilization and sulfoquinovose metabolism pathways. CONCLUSIONS: This study highlights the importance of incorporating antibiotic resistance screening for invasion assays used in AIEC identification. Accurately screened invasion phenotypes identified accessory genome elements among E coli IBD isolates that correlate with their ability to invade epithelial cells. These results help explain why single genetic markers for the AIEC phylotype are challenging to identify.

Humans↗
PubMed2026

Integrating Next-Generation Sequencing into von Willebrand Disease Diagnostics: Insights from the PCM-EVW-ES Multicenter Project.

Von Willebrand disease (VWD) is the most common inherited bleeding disorder, caused by quantitative or qualitative defects in von Willebrand factor (VWF). Diagnosis is challenging and requires integrating bleeding history, VWF antigen and activity measurements, FVIII assays, and specialized phenotyping. Genetic testing is increasingly recognized as a key component. Here, we review current concepts in VWD diagnostics and highlight the Spanish Clinical and Molecular Profile of von Willebrand Disease (PCM-EVW-ES) project as a model for genomics-enabled precision medicine. PCM-EVW-ES is a multicenter initiative involving 48 hospitals, centralized phenotypic testing, and next-generation sequencing of the VWF coding region, enabling definitive classification in 730 individuals with VWD to date. Harmonized recruitment criteria and standardized workflows improve subtype assignment, uncover complex genotypes, refine genotype-phenotype correlations, and facilitate the identification of asymptomatic carriers. The PCM-EVW-ES variant spectrum highlights recurrent disease-causing variants in Spain and underscores the value of coordinated national registries for variant curation. Building on these data, we propose a diagnostic algorithm in which bleeding assessment and first-line VWF/FVIII assays, combined with, early VWF molecular testing increases diagnostic accuracy and guides targeted second-line investigations to confirm and refine VWD subtype classification. We also outline persisting challenges, including the interpretation of variants of uncertain significance and patients without identifiable pathogenic VWF variants, and future directions integrating third-generation sequencing, expanded gene panels, functional studies, and artificial-intelligence-driven multiomic approaches. Together, these advances illustrate how robust multicenter studies can bridge the gap between complex diagnostics and clinical practice in VWD.

Humans↗