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Results for “Phenotypic variability”

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PubMed1989

Expression of the surface properties of the fibrillar Streptococcus salivarius HB and its adhesion deficient mutants grown in continuous culture under glucose limitation.

Streptococcus salivarius HB and four adhesion deficient mutants, HB-7, HB-V5, HB-V51 and HB-B, were grown in continuous culture in a defined medium under glucose limitation over a range of growth rates from 0.1 to 1.1 h-1. The ability to coaggregate with Veillonella parvula V1 cells and the ability to adhere to buccal epithelial cells did not alter with increasing growth rate. Cell surface hydrophobicity decreased markedly with increasing growth rate for the non-fibrillar non-adhesive mutant HB-B but not for the other four strains which all carry different combinations of fibril classes. The thickness of the ruthenium red staining layer (RRL) also varied with growth rate for strain HB-B, ranging from 19.5 +/- 3.8 nm at high growth rate to a minimum of 12.3 +/- 4.8 nm at low growth rate. Low cell surface hydrophobicity correlated with a thicker RRL for strain HB-B. Strains HB-V5 and HB-7 also showed a significant increase in RRL thickness at high growth rates although to a lesser degree than HB-B. SDS-PAGE revealed a large number of protein bands common to all strains at all growth rates, with the major common protein occurring at 15.6 kDa. Protein bands at 70, 56, 40.5 and 39 kDa appeared stronger at high growth rates than at low. A protein band at 82 kDa showed strongly only at low growth rates. Therefore, adhesion and coaggregation are not phenotypically variable with increasing growth rate but RRL thickness, hydrophobicity and cell surface proteins may be phenotypically variable depending on the strain.

Bacterial Adhesion↗

PubMed2000

Exclusion of Htra2-beta1, an up-regulator of full-length SMN2 transcript, as a modifying gene for spinal muscular atrophy.

Spinal muscular atrophy (SMA) is a neurodegenerative disease caused by homozygous mutations of the survival motor neuron gene 1 (SMN1). In rare cases sibs with identical 5q13-homologs and identical SMN1 mutations can show variable phenotypes from unaffected to affected, suggesting the influence of modifying genes. SMN is part of an 800 kDa macromolecular complex that plays an essential role in snRNP biogenesis and pre-mRNA splicing. Due to a single nucleotide difference within SMN1 exon 7 that disrupts an exonic splicing enhancer (ESE), SMN2, a nearly identical copy of SMN1, predominantly expresses alternatively spliced transcripts lacking exon 7, whereas SMN1 mainly produces full-length transcripts. The SR-like trans-acting splicing factor Htra2-beta1 was shown to interact with this ESE and to restore full-length SMN2 expression in vivo in a concentration-dependent manner. Since Htra2-beta1 prevents skipping of exon 7 it is obvious to ask whether mutations within Htra2-beta1 are responsible for the intrafamilial variability of the SMA phenotype. We sequenced either RT-PCR products or genomic DNA covering the complete coding region of Htra2-beta1 as well as the putative promoter of 36 sibs belonging to 15 SMA families with discordant phenotypes but identical genotypes. Neither a mutation nor a polymorphism was found within Htra2-beta1. Additionally, we performed quantitative analysis of Htra2-beta isoforms from 26 sibs without identifying any significant difference between phenotypically discordant sibs. Based on these data, we suggest that the intrafamilial phenotypic variability in SMA families is not caused by polymorphic variants or transcription differences within Htra2-beta1.

Genetic Variation↗

PubMed2000

Proportion of cells with paternal 11p15 uniparental disomy correlates with organ enlargement in Wiedemann-beckwith syndrome.

"Genetic mosaicism" describes the presence of two or more populations of cells within a single individual that differ in their genomic constitution. Although the occurrence of asymmetric overgrowth in Wiedemann-Beckwith syndrome (WBS) suggests that mosaicism has some role in the WBS phenotype, no direct evidence for this has been published. WBS is a congenital overgrowth syndrome with variable phenotype linked to the imprinted gene cluster on chromosome region 11p15. We have performed a molecular survey of multiple organs and tissues in a case of WBS with a high degree of mosaic paternal 11p15 uniparental disomy (UPD). The organs most severely affected were those with the highest percentage of cells with UPD. In particular there was a striking difference in the degree of mosaicism for 11p15 UPD between the extremely enlarged left adrenal and non-enlarged right adrenal gland. This result indicates that the proportion of paternal 11p15 UPD cells correlates with the tissue phenotype of WBS. Our results suggest that high proportions of abnormal cells result from a combination of stochastic events and cell selection. Mosaicism may explain the variable phenotypes including hemihyperplasia and predisposition to childhood cancers in WBS patients.

Adrenal Glands↗

PubMed2005

Androgen receptor CAGn repeat length influences phenotype of 47,XXY (Klinefelter) syndrome.

CONTEXT: Klinefelter syndrome (KS; 47,XXY karyotype and variants) is characterized by tall stature and testicular failure, with marked variation in severity of the phenotype. Previous studies have proposed that genetic factors including mosaicism, parental origin of the supernumerary X-chromosome, skewed X inactivation, and androgen receptor (AR) polyglutamine repeat length may contribute to phenotypic variability in KS. OBJECTIVE: The objective of this study was to investigate the roles of these genetic factors in the variability of the KS phenotype. DESIGN: This was a cross-sectional study. SETTING: The study was performed at a pediatric endocrinology referral clinic. PATIENTS: Thirty-five KS boys and men, aged 0.1-39 yr, were studied. INTERVENTIONS: There were no interventions. MAIN OUTCOME MEASURES: Auxological measurements, biological indices of testicular function, and clinical assessment of muscle tone were the main outcome measures. Genetic studies included karyotyping to detect mosaicism, genotyping of microsatellite markers to determine parental origin of the supernumerary X-chromosome, and genotyping and methylation studies to measure AR polyglutamine (AR CAGn) repeat length and X inactivation ratio. RESULTS: The only genetic factor that significantly influenced the KS phenotype was the AR CAGn repeat length, which was inversely correlated with penile length, a biological indicator of early androgen action. Mosaicism, imprinting, and skewed X inactivation did not account for the variability of the KS phenotype. CONCLUSIONS: Normal genetic variation in the AR coding sequence may be clinically significant in the setting of early testicular failure and subnormal circulating testosterone levels, as occur in KS.

Adolescent↗

PubMed1996

COL3A1 mutations cause variable clinical phenotypes including acrogeria and vascular rupture.

We have recently analysed by histological, protein and molecular DNA techniques 23 mutations of the collagen III gene (COL3A1), most of which cause premature arterial fragility, thin skin and variants of vascular Ehlers-Danlos syndrome. There were 14 glycine substitutions between residues 637 and 1021, eight exon skips between exons 7 and 45 and one small inframe deletion. The glycine substitutions produce a gradient of increasingly abnormal clinical phenotypes from exons 36 to 49 while the clinical severity of exon skips is much more variable. Each mutation is private for the affected family or individual concerned having the potential for early prenatal diagnosis and prevention.

Adolescent↗

PubMedDate not supplied

Warning: the use of heterogeneous mice may seriously damage your research.

Genetically heterogeneous (GH) mice and rats continue to be widely used in research even though the case for using isogenic strains has been argued repeatedly. The paper by Miller et al. in this issue appears to be the only one in the last 22 to attempt a scientific justification for the continued use of (a limited subset of) GH stocks. However, although they are to be commended for bravery, they fail to make their case. GH stocks represent poor material for controlled studies because genetic heterogeneity normally leads to phenotypic variability and a decline in experimental sensitivity. To counter this argument, Miller et al. claim that phenotypic variability may actually be smaller in GH animals than in their isogenic parents. Were this so (e.g., all mice being short lived, small, and aggressive), it is difficult to see how the use of such a stock could increase the generality of research results based on it, as claimed by Miller et al. Isogenic strains are a vital, proven, and powerful resource for biomedical research, and should be used in preference to GH stocks by all scientists who use laboratory rodents.

Animals↗

PubMed2006

Intronic breakpoint definition and transcription analysis in DMD/BMD patients with deletion/duplication at the 5' mutation hot spot of the dystrophin gene.

Dystrophin mutations occurring at the 5' end of the gene frequently behave as exceptions to the "frame rule," their clinical severity being variable and often not related to the perturbation of the translation reading frame. The molecular mechanisms underlying the phenotypic variability of 5' dystrophin mutations have not been fully clarified. We have characterized the genomic breakpoints within introns 2, 6 and 7 and identified the splicing profiles in a cohort of DMD/BMD patients with deletion of dystrophin exons 3-7, 3-6 and duplication of exons 2-4. Our findings indicate that the occurrence of intronic cryptic promoter as well as corrective splicing events are unlikely to play a role in exons 3-7 deleted patients phenotypic variability. Our data suggest that re-initiation of translation could represent a major mechanism responsible for the production of a residual dystrophin in some patients with exons 3-7 deletion. Furthermore, we observed that the out-of-frame exon 2a is almost constantly spliced into a proportion of the dystrophin transcripts in the analysed patients. In the exons 2-4 duplicated DMD patient, producing both in-frame and out-of-frame transcripts, this splicing behaviour might represent a critical factor contributing to the severe phenotype. In conclusion, we suggest that multiple mechanisms may have a role in modulating the outcome of 5' dystrophin mutations, including recoding mechanisms and unusual splicing choices.

5' Flanking Region↗

PubMed2000

Replication error phenotype, clinicopathological variables, and patient outcome in Dukes' B stage II (T3,N0,M0) colorectal cancer.

AIMS: To examine the relation between the replication error (RER) phenotype and other genetic events, clinical features, and long term survival in patients with Dukes' B stage II (T3,N0,M0) colorectal cancer. METHODS: RER phenotype was investigated in 159 patients by PCR amplification of microsatellite marker loci on chromosomes 5q, 17p, 17q, and 18q from tumour DNA extracted from archival tissue. Data on activating c-Ki-ras mutations were available from a previous study. Immunohistochemical detection of p53 and c-erbB-2 expression was performed on paraffin wax embedded tissue. RESULTS: Of 159 colorectal cancers studied, 22 (14%) were RER+ while 137 (86%) were RER- for two or more loci. RER+ tumours were more commonly located in the right colon, tended to be larger than RER- tumours, and were more often poorly differentiated than RER- cancers. No significant associations were seen between RER status and the presence of a mutant c-Ki-ras gene, or between RER status and p53, c-erbB-2, or c-myc gene expression. Univariate survival analysis showed that outcome was similar in RER+ and RER- cases. Multivariate survival analysis showed that the relative risk of death for patients with RER+ cancers was 0.95 that of patients with RER- cancers. CONCLUSIONS: The results suggest that, while the RER phenotype may be associated with some differences in tumour pathology (site, size, differentiation), it is not associated with the genetic alterations studied or with significant differences in long term survival.

Aged↗

PubMed2004

mdclust--exploratory microarray analysis by multidimensional clustering.

MOTIVATION: Unsupervised clustering of microarray data may detect potentially important, but not obvious characteristics of samples, for instance subgroups of diagnoses with distinct gene profiles or systematic errors in experimentation. RESULTS: Multidimensional clustering (mdclust) is a method, which identifies sets of sample clusters and associated genes. It applies iteratively two-means clustering and score-based gene selection. For any phenotype variable best matching sets of clusters can be selected. This provides a method to identify gene-phenotype associations, suited even for settings with a large number of phenotype variables. An optional model based discriminant step may reduce further the number of selected genes.

Cluster Analysis↗

PubMed2006

Striosomes and mood dysfunction in Huntington's disease.

Variable phenotype is common in neurological disorders with single-gene inheritance patterns. In Huntington's disease, mood and cognitive symptoms are variably co-expressed with motor symptoms. There is also variable degeneration of neurons in the two major neurochemical compartments of the striatum, the striosomes and the extrastriosomal matrix. To determine whether the phenotypic variability in Huntington's disease is related to this compartmental organization, we carried out a double-blind study in which we used GABA(A) receptor immunohistochemistry to analyse the status of striosomes and matrix in the brains of 35 Huntington's disease cases and 13 control cases, and collected detailed data on the clinical symptomatology expressed by the patients from family members and records. We report here a significant association between pronounced mood dysfunction in Huntington's disease patients and differential loss of the GABA(A) receptor marker in striosomes of the striatum. This association held for both clinical onset and end-stage assessments of symptoms. The cases with accentuated striosome abnormality further exhibited later onset age, lower disease grade and lower CAG repeat length in the HD gene. We found no independent association, however, between CAG repeat length or age of onset and mood dysfunction. We suggest that variation in clinical symptomatology in Huntington's disease is associated with variation in the relative abnormality of GABA(A) receptor expression in the striosome and matrix compartments of the striatum, and that striosome-related circuits may modulate mood functioning.

Adult↗

PubMed2004

A missense mutation in GUCY2D acts as a genetic modifier in RPE65-related Leber Congenital Amaurosis.

Leber congenital amaurosis (LCA) is a clinically and genetically heterogeneous severe retinal dystrophy presenting in infancy. To explain the phenotypical variability observed in two affected siblings of a consanguineous pedigree diagnosed with LCA and establish a genotype-phenotype correlation, we screened GUCY2D, RPE65, CRX, AIPL1, and RPGRIP1 for mutations. The more severely affected sibling carried a heterozygous missense mutation in the GUCY2D gene (Ile539Val), which did not segregate with the disease phenotype. Subsequently, a homozygous nonsense mutation (Glu102STOP) in the RPE65 gene was identified in both affected siblings, thus identifying the causative gene. This data provides evidence for the presence of genetic modulation in LCA. It appears that the heterozygous GUCY2D mutation further disrupts the already compromised photoreceptor function resulting in more severe retinal dysfunction in the older sibling. We suggest that the unusual phenotypic variability in these two siblings with LCA is caused by the modifying effect of a heterozygous GUCY2D mutation observed against the disease background of a homozygous RPE65 mutation.

Adult↗

PubMed2026

Novel splice-site and recurrent p.Arg729* CNKSR2 variants in ESES/CSWS: insights into sex-dependent expression.

PURPOSE: Pathogenic variants in CNKSR2 (Xp22.12) cause an X-linked neurodevelopmental disorder with intellectual disability, language impairment, and a distinctive epilepsy phenotype, including encephalopathy with status epilepticus during slow-wave sleep (ESES/CSWS). Hemizygous males are typically severely affected, whereas symptomatic females remain rare and incompletely characterized. We describe two unrelated patients with de novo CNKSR2 variants to expand the mutational and sex-dependent phenotypic spectrum of this disorder. METHODS: Both patients underwent clinical, electroencephalographic, and neuroimaging evaluation. CNKSR2 variants were identified by whole exome sequencing with parental segregation, and the splice-site variant was assessed in silico (SpliceAI, MaxEntScan, Human Splicing Finder). RESULTS: Patient 1, a 17-year-old female, harbored a novel canonical splice-site variant (c.64+1G>A) in the N-terminal region and presented with a relatively mild phenotype. In silico analysis supported abolition of the canonical donor splice site. Patient 2, an 8-year-old male, carried a de novo nonsense variant (c.2185C>T, p.Arg729*) and exhibited drug-resistant ESES, autism, and severe language impairment. p.Arg729* had previously been reported in one independent male. Our case represents its second independent occurrence, a CGA>TGA transition at a CpG dinucleotide consistent with a mutational hotspot. CONCLUSION: Together, these cases expand the mutational spectrum and provide further evidence for sex-dependent phenotypic variability in CNKSR2-related epilepsy. Our observations support the hypothesis that X-chromosome inactivation may contribute to phenotypic variability in females, although XCI was not assessed here, and support inclusion of CNKSR2 in epilepsy gene panels regardless of sex.

Humans↗

PubMed1986

Intrafamilial variability of popliteal pterygium syndrome: a family description.

Popliteal pterygium syndrome is one of the autosomal dominant limb pterygium syndromes. It has incomplete penetrance and extreme phenotypic variability that leads to difficulty in diagnosis. A case is presented to emphasize the variable phenotype of this disorder. The absence of pterygia in the family members led to the misdiagnosis of van der Woude's syndrome. However, the presence of a pyramidal fold of skin over the nail of the hallux in family members suggested the diagnosis of popliteal pterygium syndrome. It is concluded that the presence of this distinctive nail abnormality in infants with cleft lip, cleft palate or both suggests the diagnosis of the popliteal pterygium syndrome.

Abnormalities, Multiple↗

PubMed2006

Genetic modifiers of muscular dystrophy: implications for therapy.

The genetic understanding of the muscular dystrophies has advanced considerably in the last two decades. Over 25 different individual genes are now known to produce muscular dystrophy, and many different "private" mutations have been described for each individual muscular dystrophy gene. For the more common forms of muscular dystrophy, phenotypic variability can be explained by precise mutations. However, for many genetic mutations, the presence of the identical mutation is associated with marked phenotypic range that affects muscle function as well as cardiac function. The explanation for phenotype variability in the muscular dystrophies is only now being explored. The availability of genetically engineered animal models has allowed the generation of single mutations on the background of highly inbred strain. Phenotypic variation that is altered by genetic background argues for the presence of genetic modifier loci that can ameliorate or enhance aspects of the dystrophic phenotype. A number of individual genes have been implicated as modifiers of muscular dystrophy by studies in genetically engineered mouse models of muscular dystrophy. The value of these genes and products is that the pathways identified through these experiments may be exploited for therapy.

Animals↗

PubMed1993

Somatic cell mosaicism: another source of phenotypic heterogeneity in nuclear families with osteogenesis imperfecta.

Mutations in the genes coding for the pro alpha 1 and pro alpha 2 chains of type I procollagen have been found in many patients with osteogenesis imperfecta (OI), a heritable disorder of connective tissue. The severity of the disease varies between families and even among members of the same family. This phenotypic variability covers a spectrum extending from very mild forms that cannot be easily detected to perinatally lethal forms. One explanation for this phenotypic variability is the nature of the mutation in the type I procollagen genes. Another explanation is mosaicism. Here we report on 2 families with propositi who have OI, whereas their mothers had a milder form of the disease. In one family, the molecular defect was previously shown to be a substitution of alpha 1(904) by cysteine [Constantinou et al., 1990]. The biochemical phenotype was characterized by significant post-translational overmodification of the mutated type 1 collagen molecules which also had a 3-4 degrees C decrease in their thermal unfolding. Also, secretion of the procollagen into the culture media was delayed. In the second family, the proposita's muscle fibroblasts synthesized and secreted type I procollagen molecules that were highly over-modified along the entire length of their triple-helical domain. Cells from the mother also synthesized normal and over-modified protein, although the amount of over-modified protein was less than that synthesized by her daughter's cells. The exact molecular defect has not yet been defined.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗

PubMed2002

Social variables affect phenotype in the neuroma model of neuropathic pain.

When the degree of genetic determination of a trait (i.e. its heritability) is high, one tends to presume that environmental factors will not modify its expression by much. Contrary to this expectation, we show here in rats that a psychosocial-behavioral variable, the identity of cagemates, can largely over-ride genetic predisposition to pain behavior. We used selection-line rats that consistently show high (HA) or low (LA) pain phenotype (autotomy) in the neuroma model of neuropathic pain. Normally, HA animals show autotomy after nerve injury while LA animals do not. However, when caged together with HA rats, LA rats showed high levels of autotomy. This occurred even when the individual HA cagemates were familiar preoperatively, and it did not depend on the actual performance of autotomy by the HA rats. Indeed, cage bedding soiled by HA rats was sufficient to induce a modest level of autotomy in LA animals. Chemical cues associated with HA rats, perhaps in combination with behavioral characteristics, are apparently able to induce pain phenotype despite the powerful protection otherwise rendered by the LA genotype. Social factors must be considered in behavior-related research on rodents that have undergone genetic modification. More generally, the overwhelming influence that psychosocial-behavioral variables have on pain perception, and on pain behavior, in humans may have evolutionary roots deeper than has previously been appreciated.

Animals↗

PubMed2000

Molecular mapping of QTLs conferring stay-green in grain sorghum (Sorghum bicolor L. Moench).

Drought resistance is of enormous importance in crop production. The identification of genetic factors involved in plant response to drought stress provides a strong foundation for improving drought tolerance. Stay-green is a drought resistance trait in sorghum (Sorghum bicolor L. Moench) that gives plants resistance to premature senescence under severe soil moisture stress during the post-flowering stage. The objective of this study was to map quantitative trait loci (QTLs) that control the stay-green and chlorophyll content in sorghum. By using a restriction fragment length polymorphism (RFLP) map, developed from a recombinant inbred line (RIL) population, we identified four stay-green QTLs, located on three linkage groups. The QTLs (Stg1 and Stg2) are on linkage group A, with the other two, Stg3 and Stg4, on linkage groups D and J, respectively. Two stay-green QTLs, Stg1 and Stg2, explaining 13-20% and 20-30% of the phenotypic variability, respectively, were consistently identified in all trials at different locations in two years. Three QTLs for chlorophyll content (Chl1, Chl2, and Chl3), explaining 25-30% of the phenotypic variability were also identified under post-flowering drought stress. All coincided with the three stay-green QTL regions (Stg1, Stg2, and Stg3) accounting for 46% of the phenotypic variation. The Stg1 and Stg2 regions also contain the genes for key photosynthetic enzymes, heat shock proteins, and an abscisic acid (ABA) responsive gene. Such spatial arrangement shows that linkage group A is important for drought- and heat-stress tolerance and yield production in sorghum. High-resolution mapping and cloning of the consistent stay-green QTLs may help to develop drought-resistant hybrids and to understand the mechanism of drought-induced senescence in plants.

Adaptation, Physiological↗

PubMed2006

Polymorphisms in the interleukin-10 gene and relation to phenotype in patients with ulcerative colitis.

BACKGROUND AND OBJECTIVES: Interleukin-10 (IL-10) has a key role in regulating mucosal inflammation in inflammatory bowel disease. In our population of Spanish ulcerative colitis (UC) patients, we have previously demonstrated that two polymorphisms (IL-10.G14 microsatellite allele and homozygous for the -1082G allele (guanine at position -1082)) in the IL-10 gene were susceptibility markers for disease. No data exist regarding the relationship of these IL-10 polymorphisms with phenotypic subpopulations in UC. Therefore, this study sought to examine the contribution of IL-10 polymorphisms to phenotypical variability in UC. MATERIAL AND METHODS: A cohort of 215 Spanish unrelated patients with UC recruited in a single center was studied. All patients were rigorously phenotyped and followed for at least 3 years (mean time: 11.8 years). The clinical phenotype was established before genotyping. Genotyping was performed using polymerase chain reaction (PCR) assays. RESULTS: Patients with UC included 129 (60%) men and 89 (40%) women. Mean age at diagnosis was 38 years, with a range of 8-83. Disease extent included 127 (59.1%) left-side patients and 88 (40.9%) extensive patients. Neither UC phenotype variable was associated with the presence of susceptibility polymorphisms (10G14 microsatellite and -1082G allele). CONCLUSIONS: In Madrid's Spanish population of UC patients, the carrying of the ILG14 microsatellite or -1082G polymorphism in the IL-10 gene was not associated with phenotype of disease.

Adolescent↗