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Results for “Phenotype similarity”

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At least 19 recordsLinked to original sources
PubMed1978

Role of murein lipoprotein in morphogenesis of the bacterial division septum: phenotypic similarity of lkyD and lpo mutants.

Phenotypes were compared in two different classes of mutants with defects in murein-lipoprotein (lkyD mutants of Salmonella typhimurium and an lpo mutant of Escherichia coli). Both mutations are associated with the same triad of phenotypic abnormalities, consisting of defective formation of the division septum, leakage of periplasmic proteins during growth, and increased sensitivity to several unrelated external toxic agents. The abnormality in septum formation consists of a defect in invagination of the outer membrane during formation of the nascent septum. The results suggest that formation of the murein-lipoprotein link plays an important role in differentiation of the division septum and perhaps also in maintaining the normal barrier function of the outer membrane.

Bacterial Proteins↗
PubMed1975

[Comparative frequency of phenotypical similarity between interfamilial and intrafamilial pairs of patients with generalized and focal epilepsy].

The correlation of the frequency of intra-paired phenotypical resemblance of intrafamilial (parents-children--46 pairs, sibses--26 pairs) and interfamilial (48 pairs) epilepsy according to the complex of constitutional and clinical features is studied. The intra-paired resemblance of the onset (homochronicity) and clinic (homotypia) of intrafamilial (even in different generations) epilepsy was discovered more often (41.3--85.5%) than interfamilial epilepsy (18.7--33.3%). The complete intra-paired phenotypical resemnlance is the most characteristic for generalized, than focal intrafamiliar epilepsy. The comparison of the frequency of intra-paired resemblance according to constitutional features and the medium influence showed that the phenotypical manifestation of the epileptical genotype depends on the complex constellation of hereditary and medium factors being subjected to considerable modification by exogenes. However the clear difference of the frequency of intra-paired clinical resemblance of intra- and interfamilial epilepsy in considerable degree was caused rather by consitutional pecularities than by exogenens influence and may testify to possible hereditary heterogeneity of epilepsy.

Adolescent↗
PubMed1977

Partial duplication 5q syndrome: phenotypic similarity in two sisters with identical karyotype (partial duplication 5q33 leads to 5qter and partial deficiency 8p23 leads to pter).

Two sisters with statomotor developmental retardation microcephaly, hydrocephalus internus and externus without signs of pressure, heart defect (ventricular septal defect), early pulmonary resistance and characteristic facial changes were found to have the same unbalanced karyotype with partial trisomy 5q3300 leads to 5qter and partial monosomy 8p2300 leads to 8pter, derived from a balanced reciprocal paternal translocation: 46,XY,t(5;8)(q3300;p2300). The older girl was tested for the erythrocyte enzyme glutathion reductase. She had normal values.

Abnormalities, Multiple↗
PubMed2025

Charting the phenotypic landscape of mitochondrial diseases through a systematic evaluation of pathogenic mitochondrial DNA and nuclear gene variants.

PURPOSE: Primary mitochondrial diseases (PMD) arise from variants in the mitochondrial or nuclear genomes. Phenotype-based recognition of specific PMD genotypes remains difficult, prolonging the diagnostic odyssey. We expanded the MitoPhen database to characterize phenotypic variation across PMD more systematically. METHODS: Individual-level data on mitochondrial DNA disorders, nuclear-encoded mitochondrial diseases, and single large-scale mitochondrial DNA deletions were manually curated with Human Phenotype Ontology (HPO) terms to produce MitoPhen v2. Principal-component analysis summarized system-level abnormalities; HPO-level enrichment and mean phenotype-similarity scores were then used to distinguish common PMD genotypes. RESULTS: MitoPhen v2 adds 3940 individuals to the original release, now encompassing 1597 publications, 10,626 individuals, and 117 genotypes. Among 7586 affected cases, 72,861 HPO terms were recorded. Principal-component analysis revealed 6 phenotype dimensions capturing most system-level variance. At the HPO level, we observed genotype-specific enrichments and identified 111 gene-phenotype links absent from the current HPO database. Using MT-TL1, single large-scale mitochondrial DNA deletions, and POLG as exemplars, phenotype-similarity scores reliably separated individuals with these genotypes from those without. CONCLUSION: MitoPhen v2 enabled systematic, genotype-aware analysis of heterogeneous PMD phenotypes and highlighted the diagnostic value of structured, individual-level data. Phenotype-similarity metrics from such data sets can refine variant interpretation in large rare-disease cohorts and provide a transferable framework for other phenotypically complex genetic disorders.

Humans↗
PubMed2026

Phenotypic and transcriptomic characterization of biallelic RNU2-2 developmental and epileptic encephalopathy.

OBJECTIVE: A significant proportion of individuals with suspected genetic developmental and epileptic encephalopathies (DEEs) remain unsolved following whole genome sequencing (WGS). Here we describe biallelic RNU2-2 variants causing a recently reported, severe, recessive DEE. METHODS: We screened individuals who have received WGS analyses at the Genomic Medicine Centre Karolinska for Rare Diseases for biallelic RNU2-2 variants. Deep phenotyping was performed through reviewing entire medical histories and phenotypic traits were transcribed to their corresponding Human Phenotype Ontology (HPO) term. HPO terms were used to generate pairwise phenotypic similarity scores and assess for significantly shared phenotype enrichment in the RNU2-2 sub-cohort. RNA sequencing analyses were performed in fibroblast and blood tissues to compare splicing events between RNU2-2 individuals and two independent control groups. RESULTS: We identified 14 individuals from nine families with 12 ultra-rare biallelic RNU2-2 variants clustering in the conserved 5' domains. Genotype data from 13 of 14 individuals has been reported previously as part of a larger cohort. All individuals presented with a highly concordant, severe DEE, characterized by severe to profound intellectual disability, inability to walk or communicate, hyperkinesia, and refractory seizures. Infantile spasms and tonic seizures were the predominant seizure types and a Lennox-Gastaut syndrome-like phenotype was common. These individuals had a significantly similar phenotypic signature when compared with 703 individuals with complex pediatric epilepsies (two-sided Monte Carlo permutation test, p = .005). RNA sequencing analyses showed aberrant splicing, with the most pronounced effects in fibroblast tissues in mutually exclusive exon and alternate 3' splice-site events, which were not detectable in blood. SIGNIFICANCE: We present deep phenotyping data and transcriptomic analyses that provide support for rare, 5' clustering biallelic RNU2-2 variants causing this novel, severe DEE. We propose an RNA sequencing methodology on fibroblast tissue for future validation of RNU2-2 variants.

autosomal recessive disease↗
PubMed1979

New markers for Eubacterium lentum.

Of 37 strains of Eubacterium lentum and phenotypically similar organisms, 26 (70%) synthesized a corticoid 21-dehydroxylase and/or a 3 alpha-hydroxysteroid dehydrogenase. It appeared that the corticoid 3 alpha-hydroxysteroid dehydrogenase was identical to the bile acid 3 alpha-hydroxysteroid dehydrogenase. Steroid-metabolizing enzymes were found both in E. lentum and in phenotypically similar organisms. E. lentum is characterized by nitrate reduction and enhanced growth in the presence of arginine. Many phenotypically similar organisms possess either one or the other of the two markers. In contrast, using the steroid-metabolizing enzymes as markers, a "steroid-active" and a "steroid-inactive" group were established with minimal overlapping of metabolic characteristics. Synthesis of the steroid enzymes was positively correlated with production of gas from H2O2 and formation of H2S. A simple method for the detection of corticoid 21-dehydroxylase and 3 alpha-hydroxysteroid dehydrogenase, one or both of which were present in 92% of the steroid-active group, is described.

3-Hydroxysteroid Dehydrogenases↗
PubMed1979

Comparative studies of wild-type and cold-mutant (temperature-sensitive) influenza viruses: independent segregation of temperature-sensitivity of virus replication from temperature-sensitivity of virion transcriptase activity during recombination of mutant A/Ann Arbor/6/60 with wild-type H3N2 strains.

RNA 1 (see end of Summary) of a cold-adapted and temperature-sensitive (ts) influenza virus mutant A/Ann Arbor/6/60 has a different mobility from RNA 1 of wild-type (wt) A/Ann Arbor/6/60 when subjected to electrophoresis through acrylamide/agarose gels in the absence of denaturing agents. Detection of this lesion in RNA 1 of the mutant virus was dependent on the temperature of the gel during electrophoresis. Because RNA 1 is believed to code for a protein involved in virus-specific RNA synthesis we compared phenotypes of virion transcriptases in the wt and mutant viruses. The enzyme of the mutant virus was found to be about 40% less active at 40 degrees C than the enzyme of the wt virus when related to their activities at 31 degrees C. Two cold-adapted ts recombinants which derive their RNA 1 from the mutant A/Ann Arbor/6/60 have virion transcriptases with a phenotype similar to that of their mutant parent. Three different cold-adapted ts recombinants, however, which also derive their RNA 1 from the mutant A/Ann Arbor/6/60, have virion transcriptases with a phenotype similar to that of wt virus. We conclude, therefore, that the conditional-lethal ts property of A/Ann Arbor/6/60 mutant and its recombinants is independent of the phenotypic marker observed for the A/Ann Arbor/6/60 mutant virion transcriptase, and that the lesion in RNA 1 of the mutant may also be unrelated to the observed difference between virion transcriptases of the mutant and wt A/Ann Arbor/6/60 viruses. The phenotypes of the virion transcriptases in recombinants did, however, correlate with the derivation of their RNA 2. This suggests that the increased temperature-sensitivity of virion transcriptase of the A/Ann Arbor/6/60 mutant is caused by either (1) a lesion (not necessarily conditionally lethal) that occurred in its RNA 2 during the course of cold-adaptation, or (2) a lesion in another gene whose product is a component of the virion transcriptase complex, but which lesion is only expressed phenotypically when there is a synergistic interaction in the transcriptase complex with the product of A/Ann Arbor/6/60 rna 2.

Cold Temperature↗
PubMed1979

Bile salt 3 alpha- and 12 alpha-hydroxysteroid dehydrogenases from Eubacterium lentum and related organisms.

Thirty-two strains of Eubacterium lentum and phenotypically similar anaerobic gram-positive bacilli were screened for intracellular bile salt 3alpha- and 12alpha-hydroxysteroid dehydrogenase (HSDHase) activities. These organisms were categorized into four groups: (A) those containing 12alpha-HSDHase only (10 strains), (B) those containing 3alpha- and 12alpha-HSDHase (13 strains), (C) those containing 3alpha-HSDHase only (2 strains), and (D) those devoid of any measurable HSDHase activity (7 strains). Of the respective four groups, 9/10, 13/13, 0/2, and 0/7 were like the neotype strain of E. lentum (ATCC 25559) in that they produced H(2)S in a triple sugar iron agar butt, reduced nitrate to nitrite, and weakly decomposed hydrogen peroxide. The other strains were variable for nitrate reduction and activity on hydrogen peroxide, but all the organisms in the first three categories (with one exception) were H(2)S producers (triple sugar iron agar butt) and all (with one exception) were designated E. lentum, whereas the organisms of category B were non-H(2)S producers (triple sugar iron agar butt). Five of these seven were not stimulated by arginine and are designated "phenotypically similar organisms." Thin-layer chromatography of extracted spent bacterial medium of four representative strains from each group grown in the presence of cholate revealed the presence of (A) 12-oxo product, (B) 12-oxo and 3-oxo products, (C) 3-oxo product, and (D) the absence of any of these products. The 12alpha-HSDHase of category B organisms was unstable unless 10(-3) M dithioerythritol was added to the buffer. With the exception of 3 out of 32 strains, there was a positive correlation between the production of measurable amounts of 12alpha-HSDHase and H(2)S production. Growth curves and the effect of arginine on growth and the production of 3alpha- and 12alpha-HSDHase were examined in representative strains of categories A, B, and C. Both enzymes were shown to bind onto a nicotinamide adenine dinucleotide-Sepharose column and could be eluted by high-ionic-strength buffer, resulting in approximately 25-fold and 18-fold purification, respectively. Molecular weight estimations by Sephadex G-200 gave values of 205,000 and 125,000 for the 3alpha- and 12alpha-HSDHase, respectively. Purified 12alpha-HSDHase was investigated with respect to pH requirement, substrate specificity, and enzyme kinetics.

3-Hydroxysteroid Dehydrogenases↗
PubMed1978

Segregation of an insertional chromosome rearrangement in 3 generations.

The interstitial deletion of a segment of chromosome 13, 13q21 leads to 13q22, and its inversion and insertion into the long arm of chromosome 3 at breakpoint q12, was found to segregate in 3 generations of a family. Segregation of this 3 break rearrangement gave rise to individuals monosomic, trisomic, or balanced for the involved segment. Monosomy for 13q21 leads to 13q22 was associated with mental retardation, expressive aphasia, microcephaly, hand abnormalities, and short stature. Partially trisomic individuals had normal mentality, extremely high arched palate, and mild dysmorphic features. There was no evidence for retinoblastoma in the individuals examined. The balanced carriers were normal. Comparison of monosomic individuals with one previous report of a similar deletion reveals marked phenotypic similarities.

Adult↗
PubMed1977

Plasma corticosterone concentrations in diabetic (db) mice.

Plasma corticosterone concentrations in diabetic (db) mice maintained on two different inbred backgrounds were found to be elevated significantly when compared to normal controls. These data are similar to that reported with the phenotypically similar obese (ob) mouse. These results suggest that the hyperadrenolcorticism is not related to the primary gene action of either gene but rather is a consequence of the development of the obesity-diabetes syndromes.

Animals↗
PubMed1975

Trisomy 22. Two new cases and delineation of the phenotype.

Two unrelated children, not affected with Down's syndrome, with strikingly similar phenotypes and an extra G-like chromosome are presented. Quinacrine and trypsin-Giemsa banding identified the extra chromosome as No. 22. The phenotype of these patients and the review of 15 additional similar cases from the literature permit a definition of the cardinal features of trisomy 22; mental and growth retardation, microcephaly and craniofacial asymmetry, strabismus, beaked and prominent nose, long philtrum, cleft palate, micrognathia, large low set ears with preauricular tags and/or pits, long slender fingers, congenital heart disease, inguinal hernia, and hip dislocation.

Abnormalities, Multiple↗
PubMed1978

Positive and negative geotaxis: sex-linked traits in Drosophila pseudoobscura.

Using a Hirsch classification maze, selection was made for positive and negative geotactic behaviors in three different strains of Drosophila pseudoobscura. Hybridization studies were then carried out with flies from the diverged strains. The geotactic scores of the parents and F1 flies indicate that both negative and positive geotactic behaviors in these strains are strongly influenced by genes in the X chromosome. Additional hybridization studies using flies from strains with similar phenotypes suggest that the diverged strains contain similar alleles and the number of loci in the X chromosomes responsible for these types of behavior is limited. The loci may be highly organized in the X chromosome.

Animals↗
PubMed2026

Genomic evidence that Shouchella miscanthi (Shin et al. 2020) Joshi et al. 2022 is a later heterotypic synonym of Shouchella hunanensis (Patel and Gupta 2020) Joshi et al. 2022.

Shouchella hunanensis DSM 23008T and Shouchella miscanthi AK13T were originally described from forest soil and the rhizosphere of Miscanthus sacchariflorus, respectively. The two strains share closely similar phenotypic properties, and their 16S rRNA gene sequences show 99.5% similarity. Phylogenetic analysis of all 16S rRNA gene copies revealed copy-dependent placements, whereas the phylogenomic analysis placed the two type strains and three additional genomes in a strongly supported, short-branched cluster. Eight 16S rRNA gene copies were identified in each genome, with detectable intragenomic heterogeneity, particularly in AK13ᵀ. Pairwise average nt identity among the two type-strain genomes and three additional publicly available genomes ranged from 99.0% to 99.3%, clearly above the accepted species boundary. The digital DNA-DNA hybridization value between strains S. hunanensis DSM 23008T and S. miscanthi AK13T was 92.5%. On the basis of the combined phylogenetic, genomic and phenotypic evidence, S. miscanthi (Shin et al. 2020) Joshi et al. 2022 is proposed as a later heterotypic synonym of S. hunanensis (Patel and Gupta 2020) Joshi et al. 2022.

Phylogeny↗
PubMed1979

Two mutations which affect the barrier function of the Escherichia coli K-12 outer membrane.

Two genetically distinct classes of novobiocin-supersensitive mutants were isolated from Escherichia coli K-12. One class, given the phenotypic name NbsA, lies at 10 min on the E. coli chromosome. The order of the genes in this region, based on transductional analyses, is proC NbsA plsA purE. The second, NbsB, lies at 80 min. The order of the genes in this region, based on transduction analyses, is xyl cysE NbsB pyrE. Both classes of mutants show increased sensitivity to hydrophobic drugs but are different: NbsA cells tend to be more sensitive to cationic agents, whereas NbsB cells show the opposite tendency. The sole detectable biochemical alteration in NbsA strain is greater than 90% reduction in the phosphate content of the lipid A region of the lipopolysaccharide. The NbsB mutation results in lipopolysaccharide that contains primarily the stereoisomer D-glycero-D-mannoheptose, rather than L-glycero-D-mannoheptose, and which contains very little of the distal sugars. Since NbsA strains have apparently normal outer membrane proteins and total cellular phospholipids, changes solely in lipopolysaccharide can increase permeability to certain hydrophobic antibiotics. Complementation studies indicate that the NbsA marker is probably allelic with acrA. In addition, the NbsB marker is genetically and phenotypically similar to the rfaD locus of Salmonella typhimurium. For this reason, the phenotypic designations NbsA and NbsB have been changed to the genotypic designations acrA and rfaD, respectively.

Cell Membrane↗
PubMed1976

A molecular analysis of transductional marker rescue involving P-group plasmids in Pseudomonas aeruginosa.

The molecular properties of the P-group plasmids R26, R527 and R18-18- (a carbenicillin-sensitive derivative of R18) have been compared with those of RP1. R18-18 and RPI have a MW about 38 X 10(6) daltons, and R26 and R527 of 52 X 10(6) daltons (determined from contour lengths). All three plasmids have a bouyant density similar to that of RPI (1.719 g/cm3, 60% GN. From their molecular and phenotypic similarities, these plasmids probably represent two pairs of identical or closely similar elements. Resistant bacteria are not recovered following F116L-mediated transduction of R26 (or R527), and this correlates with the plasmids' larger size (phage genome=40 X 10(6) daltons). Fragments of R26 are, however, transduced and their resistance determinants may be "rescued" by recombination if the recipient harbours R1818. Such events are accompanied by an increase in the size of the recipient plasmid from 38 X 10(6) to 52 X 10(6) daltons following inheritance of the resistance determinants Sm Su Gm Hg, but not Cb. Thus, Sm Su Gm Hg are encoded in a DNA segment of MW about 14 X 10(6) daltons which apparently has no homologous region on R18-18. Since a piece of DNA of this MW also corresponds to the difference in size between R26 and R18-18, it is possible that the former is derived from an RPI-like element which has acquired these additional resistance determinants.

Carbenicillin↗
PubMed1979

The distorted shell method for clustering for syndrome classification.

Syndrome classification may be described as the arrangement of individuals into groups on the basis of their phenotypic resemblance. This paper describes how phenotypic resemblance may be quantified and demonstrates a numerical method called distorted shell clustering, which isolates groups of phenotypically similar individuals representing syndromes. This new method takes into consideration apparent biological properties of syndromes. It allows for overlapping phenotypes between syndromes, and differing character association and variability within syndromes. This method is compared to four other clustering methods by using suspects for a syndrome of known etiology (Down syndrome). The numerical results based on the phenotype then can be compared with the actual diagnosis. Only the distorted shell method classifies patients, without error, into two major clusters: the Down and the non-Down, while maintaining a high level of efficiency.

Disease↗
PubMed2026

Mapping convergent regulators of melanoma drug resistance by PerturbFate.

High-throughput genomic studies have uncovered associations between diverse genetic alterations and disease phenotypes. However, elucidating how perturbations in functionally disparate genes give rise to convergent cellular states remains challenging. Here we present PerturbFate, a high-throughput, cost-effective, combinatorial-indexing single-cell platform that enables systematic interrogation of massively parallel CRISPR interference1 perturbations across the full spectrum of gene regulation, from chromatin remodelling and nascent transcription to steady-state transcriptomic phenotypes. Using PerturbFate, we profiled more than 300,000 cultured melanoma cells to characterize multimodal phenotypic and gene regulatory responses to perturbations in more than 140 vemurafenib resistance-associated genes. We uncovered a shared dedifferentiated cell state marked by convergent cooperative transcription factor activities across diverse genetic perturbations. We further dissected phenotypic responses to perturbations in Mediator complex components, linking module-specific biochemical properties to convergent transcriptional activations. We identified common regulatory nodes that drive similar phenotypic outcomes across distinct genetic perturbations. We also delineated how perturbations in functionally unrelated genes reshape cell state. Thus, PerturbFate establishes a versatile platform for identifying key molecular regulators by anchoring multimodal regulatory dynamics to disease-relevant phenotypes.

Humans↗