Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “phenotypes”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 937 records · Page 52Linked to original sources
PubMed2000

Evaluating limited specificity of drug pumps reduced relative resistance in human MDR phenotypes.

In the parallel paper, we developed a property to characterize drug efflux pumps, i.e. the reduced relative resistance (RRR). Using this RRR, we here investigate whether the observed diversity in human multidrug resistance (MDR) phenotypes might be due to variable levels of P-glycoprotein encoded by MDR1. We analyzed resistance phenotypes of various human cell lines in which either one, or both, classical human multidrug resistance genes, MDR1 and MDR3, are overexpressed. In addition, RRR values were calculated for MDR phenotypes presented in the literature. The results suggest that more than a single mechanism is required to account for the observed phenotypic diversity of classical multidrug resistance. This diversity is only partly due to differences in plasma membrane permeabilities between cell line families. It is discussed whether the alternative MDR phenotypes might be MDR1 phenotypes modified by other factors that do not themselves cause MDR. The method we here apply may also be useful for other nonspecific enzymes or pumps.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2000

Phenotypic variation and antifungal susceptibility patterns of Candida albicans strains isolated from neutropenic patients.

The aim of this study was to investigate the relationship between phenotypes of Candida albicans strains isolated from clinical specimens and the susceptibility of the strains to three antifungal agents, fluconazole, amphotericin B and flucytosine. Oropharyngeal, gastrointestinal and urogenital tract specimens were collected from 122 neutropenic patients who had received no previous prophylactic treatment. Each of 122 C. albicans strains recovered was found to express one of the six phenotypes: smooth, fuzzy, irregular, star, ring and stipple. The mean minimum inhibitory concentrations (MICs) of fluconazole was consistently higher for C. albicans strains expressing the stipple phenotype. The mean MICs for the six phenotypes of C. albicans strains ranged between 1.22 and 7.94 micrograms ml-1 for fluconazole, 0.99 and 2.55 micrograms ml-1 for amphotericin B and 1.23 and 1.83 micrograms ml-1 for flucytosine. The antifungal susceptibility of the stipple phenotype requires attention, especially in patients who are clinically unresponsive to fluconazole chemotherapy or in cases of life-threatening C. albicans infections of immunocompromised hosts. Long-term use of fluconazole may explain the outcome of the resistant stipple phenotype.

Amphotericin B↗
PubMed2001

New approaches for validation of lethal phenotypes and genetic reversion in Helicobacter pylori.

BACKGROUND: Because of limited genetic tools for use in Helicobacter pylori, tests routinely applied in other bacteria for demonstrating a gene's role in viability and other phenotypes have not been applied to this organism. In a mutational study of putative response regulator genes, we aimed to develop such tools for H. pylori. MATERIALS AND METHODS: We attempted to mutate five response regulator genes by allelic exchange insertional mutagenesis. For genes that yielded no viable mutants, a second copy of the gene was inserted into the chromosome via a suicide vector, and it was seen if providing the second copy would permit the gene's disruption. For genes that yielded mutants with selectable phenotypes, a strategy was developed for reversion whereby an intact copy of the gene is introduced to the organism by transformation with PCR products. Following this procedure, revertants were selected by phenotypic tests then tested for genetic reversion. RESULTS: After failure to attain transformants upon attempted mutation of genes HP0166 and HP1365, we inserted a second copy of each gene within the H. pylori chromosome. In each case the second copy relieved the block of transformation. Mutation of genes HP0703 and HP1021 gave non-motile and small-colony phenotypes, respectively. Following transformation with PCR products containing intact copies of the genes, both phenotype and genotype had reverted following phenotypic selections. CONCLUSIONS: The methods used in this study provide new approaches for confirming suspected genotype/phenotype associations and should be widely applicable in the study of H. pylori.

Animals↗
PubMed2002

Isolation, characterization, and family study of DTI, a novel partial D phenotype affecting the fourth external loop of D polypeptides.

BACKGROUND: The Rh system is the most polymorphic of the blood group systems and is of major importance in transfusion medicine. The partial D phenotypes lack one or more of the D epitopes. These variants appear to have arisen through hybrid RhD-CE-D or by spontaneous point mutations in RhD. The serologic findings and the molecular characterization of a novel partial D phenotype, termed DTI, are presented here. STUDY DESIGN AND METHODS: RBCs from the DTI proband and RBCs from individuals with other partial D phenotypes were tested with MoAbs against 16 D epi- topes, according to the recommendations of the 4th ISBT Workshop on MoAbs (Rh Section 1A). A full-length cDNA encoding DTI and introns 4 and 5 of RhD were isolated and analyzed by DNA sequencing. A family study of the DTI allele was carried out using PCR-RFLP and long-range PCR methods. RESULTS: Analysis of RBCs from the proband revealed that the DTI phenotype lacks epitopes D1, D2.1 (partial), D2.2, D5, D6 (partial), and D8. The DTI polypeptide exhibits seven amino acid substitutions in the D polypeptide: F223V, A226P, E233Q, V238M, V245L, G263R, and K267M. The genomic organization of DTI showed that the replacement of RhD with RhCE was located in intron 4, and the replacement of RhCE with RhD was located in intron 5. Family studies revealed that the DTI allele was inherited maternally, whereas the RhD- allele was inherited paternally in the proband. CONCLUSION: The serologic data provide the first molecular characterization of DTI, a previously unknown partial D phenotype. This phenotype affected the D polypeptide within the fourth external loop, resulting in a new RhD-CE (entire exon 5)-D hybrid gene. It is worth noting that P226, encoded by exon 5, is derived from E of RhCE in the DTI polypeptide. Family studies demonstrated that DTI was associated with a cDTIE haplotype.

Alleles↗
PubMed1999

Rapid phenotyping of HPA-1a using either diabody-based hemagglutination or recombinant IgG1-based assays.

BACKGROUND: The HPA-1 system is carried on the beta3 integrin. HPA-1a (Zw(a), Pl(A1)) is immunogenic in an HPA-1b homozygote (HPA-1b1b). In pregnancy, 1 of 365 women forms anti-HPA-1a, which causes severe thrombocytopenia in 1 in 1100 neonates. Identification of women at risk of forming anti-HPA-1a and the screening of donors to obtain HPA-1a-negative platelets for therapy need reliable, low-cost, automated assays. STUDY DESIGN AND METHODS: A diabody with dual specificity for HPA-1a x D and an IgG1 anti-HPA-1a have been constructed by the use of the genes encoding the first anti-HPA-1a fragment. With these reagents, two complementary HPA-1a phenotyping assays have been developed. RESULTS: This diabody was used in a simple hemagglutination technique to perform HPA-1a phenotyping on soluble glycoprotein IIb/IIIa from EDTA plasma samples. Over 1000 unselected donors have been correctly HPA-1a-phenotyped by use of the diabody. The human recombinant IgG1 anti-HPA-1a was produced in a rat myeloma cell line and was fluorescein labeled for use in a whole-blood flow cytometric HPA-1a phenotyping assay. This IgG1 anti-HPA-1a shows a clear differential between HPA-1a-positive and HPA-1a-negative platelets at nM antibody concentrations. CONCLUSIONS: The two recombinant reagents described are highly suitable for screening and confirmatory HPA-1a phenotyping. They permit rapid determination of the HPA-1a phenotype and are amenable to automation.

Antigens, CD↗
PubMed2002

Influence of deficient alpha1-anti-trypsin phenotypes on clinical characteristics and severity of asthma in adults.

Severe alpha1-anti-trypsin (AAT) deficiency implies a high risk of pulmonary emphysema development. The possible relationship between partial deficiencies of this enzyme and bronchial asthma remains controversial. The objective of this study was to ascertain the distribution of AAT phenotypes in a non-selected asthmatic patient population. Across-sectional study on a sample of 111 patients with asthma was carried out. Demographic and clinical variables were collected with serum IgE concentrations, plasma eosinophil number and serum AAT concentrations determined, together with the Pi phenotype. Asthma was mild in 36 (32.4%) patients, moderate in 45 (40.5%) and severe in 30 (27%). No differences were observed in eosinophil count or serum IgE or AAT concentrations among patients with different degrees of severity. Twenty-two (19.8%) asthmatics with deficient phenotypes for AAT were identified, distributed equally in all severity stages of the disease. No significant differences were found in clinical and functional characteristics, or in asthma morbidity between PiMM and PiMS patients or the heterozygote group (PiMS and PiMZ). Eosinophil count and IgE concentrations did not differ significantly between asthmatics with normal phenotype and heterozygotes. In conclusion, the distribution of AAT phenotypes in asthmatic patients did not differ from that found in the general population. Heterozygote phenotypes for the deficiency do not appear to confer greater severity or different clinical expression of asthma in adults.

Adult↗
PubMed2002

Influence of mutation type and location on phenotype in 123 patients with Rett syndrome.

Rett syndrome (RTT) is a neurodevelopmental disorder that almost exclusively affects girls. It is caused by mutations in the MECP2 gene that encodes the methyl-CpG-binding protein 2 (MeCP2). In this study we correlated mutation type and location with the severity of the phenotype in 123 girls with RTT. The ability to sit, walk, speak, hand function, head growth, occurrence of epilepsy and a combined severity score were assessed in all girls at 5 years of age and then statistically correlated with the results of the molecular genetic tests. We found that patients who carry either missense mutations or deletions located within the hotspot for deletions, an area between the base pairs (bp) 1030 and 1207 of the MECP2 gene, present with a milder phenotype than other patients. We correlated the location of the mutations with the phenotype and found that all mutations that lead to either a complete or partial truncation of the region coding for the nuclear localisation signal (NLS) are associated with a more severe phenotype than other truncating mutations (p = 0.001). We did not find a significant difference between the patients with mutations in the methyl-CpG-binding domain (MBD) and those with mutations in the transcriptional repression domain (TRD). We conclude that mutation type and location correlate with the phenotype in Rett syndrome. All mutations that impair the nuclear localisation signal (NLS) are associated with more severe phenotypes.

Binding Sites↗
PubMed2004

Development of a cancer DNA phenotype prior to tumor formation.

Using the carcinogen 3-methylcholanthrene (MCA), we demonstrate with Fourier transform-infrared spectroscopy that a cancer DNA phenotype is produced well in advance of palpable tumors. We further demonstrate that the administration of cyclophosphamide markedly inhibits the development of the cancer phenotype and concomitantly delays tumor formation. MCA, injected into the hind legs of mice, produced a variety of significant structural changes in the nucleotide bases and phosphodiester-deoxyribose backbone, as reflected in a substantial (34%) difference between the mean DNA spectra of the control and the MCA-injected mice. Strikingly, 57 days before the mean appearance of tumors, we could not distinguish the DNA structure of the histologically normal tissues of the MCA-injected mice from the DNA structure of the tumor tissues. This finding indicates the early development of a cancer phenotype. Confirmatory evidence was obtained when tissues from a group of mice injected with both MCA and cyclophosphamide did not manifest the cancer phenotype, and their mean DNA structure closely resembled that of the control mice. Accordingly, we propose that the cancer DNA phenotype, as evinced by Fourier transform-infrared spectroscopy, is a promising early indicator of tumor formation, and we postulate that agents capable of inhibiting this phenotype may delay or prevent carcinogenesis.

Animals↗
PubMed2000

Induced defenses in response to an invading crab predator: an explanation of historical and geographic phenotypic change.

The expression of defensive morphologies in prey often is correlated with predator abundance or diversity over a range of temporal and spatial scales. These patterns are assumed to reflect natural selection via differential predation on genetically determined, fixed phenotypes. Phenotypic variation, however, also can reflect within-generation developmental responses to environmental cues (phenotypic plasticity). For example, water-borne effluents from predators can induce the production of defensive morphologies in many prey taxa. This phenomenon, however, has been examined only on narrow scales. Here, we demonstrate adaptive phenotypic plasticity in prey from geographically separated populations that were reared in the presence of an introduced predator. Marine snails exposed to predatory crab effluent in the field increased shell thickness rapidly compared with controls. Induced changes were comparable to (i) historical transitions in thickness previously attributed to selection by the invading predator and (ii) present-day clinal variation predicted from water temperature differences. Thus, predator-induced phenotypic plasticity may explain broad-scale geographic and temporal phenotypic variation. If inducible defenses are heritable, then selection on the reaction norm may influence coevolution between predator and prey. Trade-offs may explain why inducible rather than constitutive defenses have evolved in several gastropod species.

Adaptation, Physiological↗
PubMed2002

Dynamics of bacterial phenotype selection in a colonized host.

The population dynamics of Helicobacter pylori during colonization in an infected animal host provide a quantifiable experimental model of in vivo microbial phenotype evolution. Phenotype variability in H. pylori populations can be typed as polymorphic expression of Lewis antigens on their cell surfaces. The high mutational frequency of H. pylori for Lewis expression provides substrate for differential selection by the host. Experimental challenge and successful colonization of mice and gerbils allows tracking of H. pylori phenotype variability from the initial inoculation to the ultimate establishment of a quasispecies. Colonization data provide a quantitative experimental model of phenotype evolution in a relatively large population (>10(4) individuals) over a relatively long evolutionary time scale (>10(3) generations). A mathematical model is developed to interpret the data in terms of the dynamic processes occurring during colonization. The mathematical model distinguishes the roles of selection and mutation; quantifies the effects of initial phenotype diversity, mutational frequency, and selective advantage; and applies generally to phenotype evolution in biological populations.

Animals↗
PubMed2005

Genetic interactions between [PSI+] and nonstop mRNA decay affect phenotypic variation.

Yeast strains can reversibly interconvert between [PSI+] and [psi-] states. The [PSI+] state is caused by a prion form of the translation termination factor eRF3. The [PSI+] state causes read-through at stop codons and can lead to phenotypic variation, although the molecular mechanisms causing those phenotypic changes remain unknown. We identify an interaction between [PSI+]-induced phenotypic variation and defects in nonstop mRNA decay. Nonstop mRNA decay is triggered when a ribosome reaches the 3' end of the transcript. In contrast, we observed little interaction between [PSI+]-induced phenotypic variation and defects in nonsense-mediated decay, which lead to suppression of premature stop codons. These results suggest that at least some of the phenotypic effects of [PSI+] may be due to read-through of "normal" stop codons, thereby producing extended proteins. Moreover, these observations suggest that nonstop mRNA decay may limit [PSI+]-induced phenotypic variation. Such a process would allow periodic sampling of the 3' UTR, which can diverge rapidly, for novel and beneficial protein extensions.

Blotting, Northern↗
PubMed2003

Subadult experience influences adult mate choice in an arthropod: exposed female wolf spiders prefer males of a familiar phenotype.

Current sexual selection theory proposes several potential mechanisms driving the evolution of female mating preferences, few of which involve social interactions. Although vertebrate examples of socially influenced mating preferences do exist, the invertebrate examples are virtually nonexistent. Here I demonstrate that the mating preferences of female wolf spiders can be acquired through exposure as subadults to unrelated, sexually active adult males. I first conducted exposure trials during which subadult females of the wolf spider Schizocosa uetzi were allowed to interact with mature males of an experimentally manipulated phenotype (either black or brown forelegs). After maturation, these previously exposed females were paired with a male of either a familiar or unfamiliar manipulated phenotype for mate-choice trials. Subadult females that were exposed to directed courtship by mature males of a particular morphological phenotype were subsequently more likely to mate with a male of a familiar phenotype as adults. Furthermore, females that were exposed as subadults were more likely, as adults, to cannibalize a courting male with an unfamiliar phenotype. Unexposed females did not distinguish between phenotypes in either mate choice or cannibalism frequency. These results suggest a previously uncharacterized mechanism influencing the origin of female mating preferences and ultimately the evolution of male traits: subadult experience. This study also stresses the potential importance of learning and memory on adult mate choice in an arthropod.

Animals↗
PubMed2001

Functional significance of concomitant inactivation of hMLH1 and hMSH6 in tumor cells of the microsatellite mutator phenotype.

Genetic or epigenetic inactivation of one of the DNA mismatch repair (MMR) genes in tumor precursor cells causes a profound mutator phenotype, known as the microsatellite mutator phenotype (MMP). This mutator phenotype induces mutations not only in cancer genes that drive tumorigenesis but also in other DNA repair genes. The functional significance of these successive DNA repair gene mutations, however, has not been substantiated. Here we show that the concomitant inactivation of two DNA MMR genes (hMLH1 and hMSH6) increases the mutator phenotype. We isolated cell clones of the SW48 MMP-positive cell line with either active or inactive hMSH6. All of these clones lacked expression of hMLH1 because of promoter hypermethylation. Compared with inactivation of hMLH1 alone, the additional inactivation of hMSH6 produced a higher mutation rate and a different spectrum of mutations in the endogenous hprt gene. These results confirm our model that the mutator phenotype can increase during tumorigenesis by the consecutive inactivation of different members of the DNA MMR system. Thus, a stronger mutator phenotype accelerates the accumulation of mutations in target cancer genes, which, in turn, speeds up tumor progression. The results of this study also have significant impact on our understanding of the mechanism of DNA MMR.

Base Sequence↗
PubMed1992

Differential regulation of T helper phenotype development by interleukins 4 and 10 in an alpha beta T-cell-receptor transgenic system.

To address the mechanisms controlling T helper (Th) phenotype development, we used DO10, a transgenic mouse line that expresses the alpha beta T-cell receptor from an ovalbumin-reactive T hybridoma, as a source of naive T cells that can be stimulated in vitro with ovalbumin peptide presented by defined antigen-presenting cells (APCs). We have examined the role of cytokines and APCs in the regulation of Th phenotype development. Interleukin 4 (IL-4) directs development toward the Th2 phenotype, stimulating IL-4 and silencing IL-2 and interferon gamma production in developing T cells. Splenic APCs direct development toward the Th1 phenotype when endogenous IL-10 is neutralized with anti-IL-10 antibody. The splenic APCs mediating these effects are probably macrophages or dendritic cells and not B cells, since IL-10 is incapable of affecting Th phenotype development when the B-cell hybridoma TA3 is used as the APC. These results suggest that early regulation of IL-4 and IL-10 in a developing immune response and the identity of the initiating APCs are critical in determining the Th phenotype of the developing T cells.

Animals↗
PubMed1996

A modular misexpression screen in Drosophila detecting tissue-specific phenotypes.

Genetic screens in Drosophila have lead to the discovery of many genes important for patterning and signal transduction in diverse organisms. Traditionally, the phenotypic effects of loss-of-function mutations are analyzed. As an alternative way to link genes and function, I have developed a versatile misexpression screen in Drosophila, the first such screen in higher eukaryotes. The screen identifies genes that, when over- or misexpressed in a pattern of interest, give a specific phenotype or modulate an existing mutant phenotype. It is based on Gal4 transactivation of a mobile enhancer and promoter that "targets" random endogenous genes for expression. The modular design of the screen allows directed expression in any temporal or spatial pattern. When activated in the developing eye, 4% of target inserts gave dominant phenotypes. One insertion was in the gene encoding Ras GTPase-activating protein; its overexpression phenotype was strongly enhanced by a mutation in Ras1. Thus, biologically relevant phenotypes and genetic interactions are identified using this method. The screen is a powerful new tool for developmental genetics; similar approaches can also be developed for other organisms.

Animals↗
PubMed1996

Sensitivity to inhibition by beta-chemokines correlates with biological phenotypes of primary HIV-1 isolates.

Primary HIV-1 isolates were evaluated for their sensitivity to inhibition by beta-chemokines RANTES (regulated upon activation, normal T-cell expressed and secreted), macrophage inflammatory protein 1 alpha (MIP-1 alpha), and MIP-1 beta. Virus isolates of both nonsyncytium-inducing (NSI) and syncytium-inducing (SI) biological phenotypes recovered from patients at various stages of HIV-1 infection were assessed, and the results indicated that only the isolates with the NSI phenotype were substantially inhibited by the beta-chemokines. More important to note, these data demonstrate that resistance to inhibition by beta-chemokines RANTES, MIP-1 alpha, and MIP-1 beta is not restricted to T cell line-adapted SI isolates but is also a consistent property among primary SI isolates. Analysis of isolates obtained sequentially from infected individuals in whom viruses shifted from NSI to SI phenotype during clinical progression exhibited a parallel loss of sensitivity to beta-chemokines. Loss of virus sensitivity to inhibition by beta-chemokines RANTES, MIP-1 alpha, and MIP-1 beta was furthermore associated with changes in the third variable (V3) region amino acid residues previously described to correlate with a shift of virus phenotype from NSI to SI. Of interest, an intermediate V3 genotype correlated with a partial inhibition by the beta-chemokines. In addition, we also identified viruses sensitive to RANTES, MIP-1 alpha, and MIP-1 beta of NSI phenotype that were isolated from individuals with AIDS manifestations, indicating that loss of sensitivity to beta-chemokine inhibition and shift in viral phenotype are not necessarily prerequisites for the pathogenesis of HIV-1 infection.

Acquired Immunodeficiency Syndrome↗
PubMed2003

The conserved and non-conserved regions of Rpb4 are involved in multiple phenotypes in Saccharomyces cerevisiae.

Rpb4, the fourth largest subunit of RNA polymerase II in Saccharomyces cerevisiae, is required for many phenotypes, including growth at high and low temperatures, sporulation, pseudohyphal growth, activated transcription of a subset of genes, and efficient carbon and energy metabolism. We have used deletion analysis to delineate the domains of the protein involved in these multiple phenotypes. The scRpb4 protein is conserved at the N and C termini but possesses certain non-conserved regions in the central portion. Our deletion analysis and molecular modeling results show that the N- and C-terminal conserved regions of Rpb4 are involved in interaction with Rpb7, the Rpb4 interacting partner in the RNA polymerase II. We further show that the conserved N terminus is required for efficient activated transcription from the INO1 promoter but not the GAL10- or the HSE-containing promoters. The N terminus is not required for any of the stress responses tested: growth at high temperatures, sporulation, and pseudohyphal growth. The conserved C-terminal 23 amino acids are not required for the role of Rpb4 in the pseudohyphal growth phenotype but might play a role in other stress responses and activated transcription. From the deletion analysis of the non-conserved regions, we report that they influence phenotypes involving both the N and C termini (interaction with Rpb7 and transcription from the INO1 promoter) but not any of the stress-responsive phenotypes tested suggesting that they might be involved in maintaining the two conserved domains in an appropriate conformation for interaction with Rpb7 and other proteins. Taken together, our results allow us to assign phenotype-specific roles for the different conserved and non-conserved regions of Rpb4.

Amino Acid Sequence↗
PubMed2004

Calcium restriction allows cAMP activation of the B-Raf/ERK pathway, switching cells to a cAMP-dependent growth-stimulated phenotype.

cAMP can be either mitogenic or anti-mitogenic, depending on the cell type. We demonstrated previously that cAMP inhibited the proliferation of normal renal epithelial cells and stimulated the proliferation of cells derived from the cysts of polycystic kidney disease (PKD) patients. The protein products of the genes causing PKD, polycystin-1 and polycystin-2, are thought to regulate intracellular calcium levels, suggesting that abnormal polycystin function may affect calcium signaling and thus cause a switch to the cAMP growth-stimulated phenotype. To test this hypothesis, we disrupted intracellular calcium mobilization by treating immortalized mouse M-1 collecting duct cells and primary cultures of human kidney epithelial cells with calcium channel blockers and by lowering extracellular calcium with EGTA. Calcium restriction for 3-5 h converted both cell types from a normal cAMP growth-inhibited phenotype to an abnormal cAMP growth-stimulated phenotype, characteristic of PKD. In M-1 cells, we showed that calcium restriction was associated with an elevation in B-Raf protein levels and cAMP-stimulated, Ras-dependent activation of B-Raf and ERK. Moreover, the activity of Akt, a negative regulator of B-Raf, was decreased by calcium restriction. Inhibition of Akt or phosphatidylinositol 3-kinase also allowed cAMP-dependent activation of B-Raf and ERK in normal calcium. These results suggest that calcium restriction causes an inhibition of the phosphatidylinositol 3-kinase/Akt pathway, which relieves the inhibition of B-Raf to allow the cAMP growth-stimulated phenotypic switch. Finally, M-1 cells stably overexpressing an inducible polycystin-1 C-terminal cytosolic tail construct were shown to exhibit a cAMP growth-stimulated phenotype involving B-Raf and ERK activation, which was reversed by the calcium ionophore A23187. We conclude that disruption of calcium mobilization in cells that are normally growth-inhibited by cAMP can derepress the B-Raf/ERK pathway, thus converting these cells to a phenotype that is growth-stimulated by cAMP.

Animals↗