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Results for “Phenotype modeling”

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PubMed2003

Skin pigmentation, biogeographical ancestry and admixture mapping.

Ancestry informative markers (AIMs) are genetic loci showing alleles with large frequency differences between populations. AIMs can be used to estimate biogeographical ancestry at the level of the population, subgroup (e.g. cases and controls) and individual. Ancestry estimates at both the subgroup and individual level can be directly instructive regarding the genetics of the phenotypes that differ qualitatively or in frequency between populations. These estimates can provide a compelling foundation for the use of admixture mapping (AM) methods to identify the genes underlying these traits. We present details of a panel of 34 AIMs and demonstrate how such studies can proceed, by using skin pigmentation as a model phenotype. We have genotyped these markers in two population samples with primarily African ancestry, viz. African Americans from Washington D.C. and an African Caribbean sample from Britain, and in a sample of European Americans from Pennsylvania. In the two African population samples, we observed significant correlations between estimates of individual ancestry and skin pigmentation as measured by reflectometry (R(2)=0.21, P<0.0001 for the African-American sample and R(2)=0.16, P<0.0001 for the British African-Caribbean sample). These correlations confirm the validity of the ancestry estimates and also indicate the high level of population structure related to admixture, a level that characterizes these populations and that is detectable by using other tests to identify genetic structure. We have also applied two methods of admixture mapping to test for the effects of three candidate genes (TYR, OCA2, MC1R) on pigmentation. We show that TYR and OCA2 have measurable effects on skin pigmentation differences between the west African and west European parental populations. This work indicates that it is possible to estimate the individual ancestry of a person based on DNA analysis with a reasonable number of well-defined genetic markers. The implications and applications of ancestry estimates in biomedical research are discussed.

Africa↗

PubMed2006

Sympatric speciation under incompatibility selection.

The existing theory of sympatric speciation assumes that a local population splits into two species under one-dimensional disruptive selection, which favors both of the opposite extreme values of a quantitative trait. Here we model sympatric speciation under selection that favors high values of either of the two independently inherited traits, each required to efficiently consume one of the two available resources, but acts, because of a tradeoff, against those possessing high values of both traits. Such two-dimensional incompatibility selection is similar to that involved in allopatric speciation. Using a hypergeometric phenotypic model, we show that incompatibility selection readily leads to sympatric speciation. In contrast to disruptive selection, two distinct modes of sympatric speciation exist under incompatibility selection: under strong tradeoffs both of the new species are specialists, each consuming its own resource, but under moderate tradeoffs speciation may be asymmetric and involve the origin of a specialist and a generalist species. Also, incompatibility selection may lead to irreversible specialization: under strong tradeoffs, the population speciates if it consists mostly of unspecialized individuals, but remains undivided if most of the individuals are specialized to consume one of the resources. Incompatibility selection appears to be more realistic than disruptive selection, implying that incompatibility between individually adaptive alleles or trait states drives both allopatric and sympatric speciation.

Animals↗

PubMed1997

Initial genome scan of the NIMH genetics initiative bipolar pedigrees: chromosomes 4, 7, 9, 18, 19, 20, and 21q.

An initial genome scan was performed on 540 individuals from 97 families segregating bipolar disorder, collected through the National Institutes of Mental Health Genetics Initiative. We report here affected-sib-pair (ASP) data on 126 marker loci (approximately 68,000 genotypes) mapping to chromosomes 4, 7, 9, 18, 19, 20, and 21q, under three affection status models. Modest increases in identical-by-descent (IBD) allele sharing were found at the following loci: D4S2397 and D4S391 (P < 0.05) on 4p, D4S1647 (P < 0.05) on 4q, D7S1802 and D7S1869 (low P = 0.01) on 7p, D9S302 (P = 0.004) on 9q, and D20S604 on 20p and D20S173 on 20q (P < 0.05). In addition, five markers on 7q displayed increased IBD sharing (P = 0.046-0.002). Additional ASP analyses on chromosomes 18 and 21q marker data were performed using disease phenotype models defined previously. On chromosome 18, only D18S40 on 18p and D18S70 on 18q yielded a slight elevation in allele sharing (P = 0.02), implying that the reported linkages in these regions were not confirmed. On chromosome 21q, a cluster of markers within an approximately 9 cM interval: D21S1254, D21S65, D21S1440, and D21S1255 exhibited excess allele sharing (P = 0.041-0.008). Multilocus data on overlapping marker quartets, from D21S1265 to D21S1255, which were consistent with increased IBD sharing (P < 0.01, with a low of 0.0009), overlapped a broad interval of excess allele sharing reported previously, increasing support for a susceptibility locus for bipolar disorder on 21q.

Alleles↗

PubMed2006

Determining human immunodeficiency virus coreceptor use in a clinical setting: degree of correlation between two phenotypic assays and a bioinformatic model.

Two recombinant phenotypic assays for human immunodeficiency virus (HIV) coreceptor usage and an HIV envelope genotypic predictor were employed on a set of clinically derived HIV type 1 (HIV-1) samples in order to evaluate the concordance between measures. Previously genotyped HIV-1 samples derived from antiretroviral-naïve individuals were tested for coreceptor usage using two independent phenotyping methods. Phenotypes were determined by validated recombinant assays that incorporate either an approximately 2,500-bp ("Trofile" assay) or an approximately 900-bp (TRT assay) fragment of the HIV envelope gp120. Population-based HIV envelope V3 loop sequences ( approximately 105 bp) were derived by automated sequence analysis. Genotypic coreceptor predictions were performed using a support vector machine model trained on a separate genotype-Trofile phenotype data set. HIV coreceptor usage was obtained from both phenotypic assays for 74 samples, with an overall 85.1% concordance. There was no evidence of a difference in sensitivity between the two phenotypic assays. A bioinformatic algorithm based on a support vector machine using HIV V3 genotype data was able to achieve 86.5% and 79.7% concordance with the Trofile and TRT assays, respectively, approaching the degree of agreement between the two phenotype assays. In most cases, the phenotype assays and the bioinformatic approach gave similar results. However, in cases where there were differences in the tropism results, it was not clear which of the assays was "correct." X4 (CXCR4-using) minority species in clinically derived samples likely complicate the interpretation of both phenotypic and genotypic assessments of HIV tropism.

Computational Biology↗

PubMed1984

[Genetic analysis of the susceptibility to neurological manifestations in spinal osteochondrosis].

Complex genetic-mathematical analysis (component decomposition of the phenotype variance, segregation analysis, estimation of penetrance parameters) of 324 probands' families with neurologic manifestation of spinal osteochondrosis (3437 relatives of I-III degree) has been carried out is shown that the structure of liability to the disease studied is better approximated by semi-continuous phenotype model within the limits of which contribution of genetic factors reaches 80% (63-66% owing to autosomes and 14-17% owing to gonosomes) under considerable influence (20%) of environmental force (14% accidental and 6% systematic).

Age Factors↗

PubMed1998

Left-right development: mammalian phenotypes and conceptual models.

Consistent left-right asymmetry in a population requires a special kind of developmental specification. Models of this process must account for the complex phenotypes seen when left-right is abnormal. In some human and mouse mutations, there appears to be a randomisation of global situs to either solitus or inversus, whereas in the inv/inv mouse essentially all are inversus. However, in these and all additional examples there are frequently other anomalies, including symmetry (isomerism) and discordance between organs (heterotaxia). Current models invoke a molecular chiral referent as the source of the primary handed information. We describe a new two-gradient model which accommodates all defects of situs whilst leaving the primary asymmetry unaltered.

Animals↗

PubMedDate not supplied

Vernal keratoconjunctivitis: a model of 5q cytokine gene cluster disease.

Clinical studies of vernal keratoconjunctivitis (VKC) patients show that total IgE serum levels are increased even in the absence of IgE antibodies to common allergens. Activated eosinophils are also a constant feature of VKC at both the circulation (cytofluorimetry) and tissue (tear cytology and conjunctival scrapings) levels. Moreover, allergen challenge induces a prolonged inflammatory reaction with a prevalent participation of eosinophils, lymphocytes and possibly basophils. Immunohistochemical studies of VKC biopsies show a multicellular inflammatory infiltrate with prevalence of activated eosinophils, mast cells and CD4 lymphocytes in both epithelium and subepithelium. Mediator studies indicate that eosinophil products (eosinophil peroxidase, eosinophinal cationic protein and eosinophil-derived neurotoxin/eosinophil protein X) are increased in both serum and tears, where tryptase and interleukin (IL)-5 are also detectable in higher amounts than in controls. On the basis of these findings, we postulate that VKC can represent a phenotypic model of up-regulation of the cytokine gene cluster on chromosome 5q which through its products (IL-3, IL-4, IL-5 and granulocyte/macrophage-colony-stimulating factor) regulates Th2 prevalence, IgE production as well as mast cell and eosinophil growth and function in VKC.

Allergens↗

PubMed1993

Rat hepatocyte cultures and co-cultures in biotransformation studies of xenobiotics.

Long-term cultures of hepatocytes could represent a suitable in vitro model for biotransformation studies of xenobiotics. At present however, no ideal culture system can be proposed since, in all existing models, phenotypic changes occur, affecting selectively some components of phase I and/or phase II xenobiotic metabolism. From the authors' own results and recent studies of several other investigators, carried out on rat hepatocytes, it becomes clear that four groups of factors may affect biotransformation capacity: soluble medium factors, extracellular matrix components, cell-cell interactions and factors affecting replication. For the maintenance of liver-specific functions, it seems of utmost importance that the tridimensional shape of the hepatocytes is kept. Usually, phase II enzymatic activity is better kept than that of phase I. The cytochrome P450 dependent monoxygenases, in particular, are easily lost. Interesting is the observation that co-cultures of rat hepatocytes with rat liver epithelial cells exhibit higher and much better preserved phase I and phase II biotransformation than monocultures. Clearly, further research is needed to improve this promising in vitro model.

Animals↗

PubMed2006

Is prenatal smoking associated with a developmental pattern of conduct problems in young boys?

OBJECTIVE: Prenatal smoking is robustly associated with increased risk of conduct problems in offspring. Observational studies that provide detailed phenotypic description are critical for generating testable hypotheses about underlying processes through which the effects of prenatal smoking may operate. To this end, we use a developmental framework to examine the association of exposure with (1) oppositional defiant disorder and attention-deficit/hyperactivity disorder in young boys and (2) the pattern of delinquent behavior at adolescence. METHOD: Using diagnostic measures and repeated measures of delinquency, we compare exposed and nonexposed boys from the youngest cohort of the Pittsburgh Youth Study (N = 448). RESULTS: Exposed boys were significantly more likely to (1) develop oppositional defiant disorder and comorbid oppositional defiant disorder-attention-deficit/hyperactivity disorder but not attention-deficit/hyperactivity disorder alone and (2) to have an earlier onset of significant delinquent behavior. CONCLUSIONS: The early emergence and developmental coherence of exposure-related conduct problems is striking and is consistent with a behavioral teratological model. Phenotypically, exposure-related conduct problems appear to be characterized by socially resistant and impulsively aggressive behavior. Whether prenatal smoking plays an etiological role in or is a risk marker for the development of conduct problems, exposed offspring are at increased risk of an early-starter pathway to conduct problems.

Adolescent↗

PubMed1997

Pathogenesis of ectrodactyly in the Dactylaplasia mouse: aberrant cell death of the apical ectodermal ridge.

Dactylaplasia, or Dac, was recently mapped to the distal portion of mouse chromosome 19 and shown to be inherited as an autosomal semi-dominant trait characterized by missing central digital rays. The most common locus for human split hand split foot malformation, also typically characterized by missing central digital rays, is 10q25, a region of synteny to the Dac locus. The Dac mouse appears to be an ideal genotypic and phenotypic model for this human malformation syndrome. Several genes lie in this region of synteny, however, only Fibroblast Growth Factor 8, or Fgf-8, has been implicated to have a role in limb development. We demonstrate that the developmental mechanism underlying loss of central rays in Dac limbs is dramatic cell death of the apical ectodermal ridge, or AER. This cell death pattern is apparent in E10.5-11.5 Dac limb buds stained with the supravital dye Nile Blue Sulfate. We demonstrate that Fgf8 expression in wild type limbs colocalizes spatially and temporally with AER cell death in Dac limbs. Furthermore, in our mapping panel, there is an absence of recombinants between Fgf-8 and the Dac locus in 133 backcross progeny with a median linkage estimate of approximately 0.5 cM. Thus, our results demonstrate that cell death of the AER in Dac limbs silences the role of the AER as key regulator of limb outgrowth, and that Fgf-8 is a strong candidate for the cause of the Dac phenotype.

Animals↗

PubMed2006

Behavioral phenotyping of mouse models of neurodevelopmental disorders: relevant social behavior patterns across the life span.

Social responses are a key element for behavioral phenotyping of mouse models of neurodevelopmental disorders associated with social deficits. Here we describe selected behavioral responses that can be measured in developing and adult mice, with special emphasis on ultrasonic vocalizations, a behavioral response not yet systematically characterized in most of the genetic mouse models of social abnormalities. A recently developed task to measure social approach relevant to the first core symptom of autism is highlighted. We also focus on those developmental factors, including litter size, litter composition, and early social milieu, that are often underestimated when measuring adult social behavior in mouse models of neurodevelopmental disorders. We present a summary of available data concerning social behavioral responses in mice with targeted gene mutations. We conclude by suggesting that assessment of early behavioral traits, and corresponding relationships with adult behavioral profiles, could be a useful strategy to investigate mouse models of neurodevelopmental disorders associated with social deficits.

Animal Communication↗

PubMed2003

Genome scan of a second wave of NIMH genetics initiative bipolar pedigrees: chromosomes 2, 11, 13, 14, and X.

As part of the on-going NIMH Genetics Initiative on Bipolar Disorder, we have ascertained 153 multiplex bipolar pedigrees and genotyped them in two waves. We report here the genome scan results for chromosomes 2, 11, 13, 14, and X in the second wave of 56 families. A total of 354 individuals were genotyped and included in the current analyses, including 5 with schizoaffective/bipolar (SA/BP), 139 with bipolar I disorder (BPI), 41 with bipolar II disorder (BPII), and 43 with recurrent unipolar depression (RUP). Linkage analyses were carried out with multi-point parametric and non-parametric affected relative pair methods using three different definitions of the affected phenotype: (model 1) SA/BP and BPI; (model 2) SA/BP, BPI, and BPII; and (model 3) SA/BP, BPI, BPII, and RUP. The best findings were on 11p15.5 (NPL = 2.96, P = 0.002) and Xp11.3 (NPL = 2.19, P = 0.01). These findings did not reach conventional criteria for significance, but they were located near regions that have been identified in previous genetic studies of bipolar disorder. The relatively modest but consistent findings across studies may suggest that these loci harbor susceptibility genes of modest effect in a subset of families. Large samples such as that being collected by the NIMH Initiative will be necessary to examine the heterogeneity and identify these susceptibility genes.

Bipolar Disorder↗

PubMed2001

Perseverative behavior underlying attentional set-shifting deficits in rats chronically treated with the neurotoxin 3-nitropropionic acid.

Huntington's disease (HD) is generally considered a prototypic motor disorder, but cognitive deficits are also prominent features of the disease. Systemic administration of the mitochondrial toxin 3-nitropropionic acid (3NP) has been proposed to be a phenotypic model of HD in rats and nonhuman primates. In this study, we investigated the effect of 5 days continuous subcutaneous infusion of 3NP on motor and cognitive abilities in Lewis rats. Intoxicated animals developed a motor syndrome consisting of bradykinesia as well as gait abnormalities and dystonic hindlimbs. Results from learning tasks showed that these rats: (1) did not exhibit learning deficits per se in our discrimination task but showed impairments in inhibiting behavioral responses when a transfer of learning (to new stimuli) or a transfer of response (new position of the lever) was required; (2) showed a marked tendency to persevere in choosing the compartment they previously visited in a T maze, thus leading to a clear retardation in learning a reinforced alternation task; and (3) did not show any memory deficit when a delay was introduced. Six months later, histological analyses showed severe neurodegeneration within the lateral striatum accompanied by apparent cell loss in the ventral pallidum and entopedoncular nucleus. We suggest that the 3NP rat model of basal ganglia neurodegeneration may provide a useful model for studying certain fundamental aspects of the physiopathology of HD and for evaluating the functional efficacy of new therapeutic strategies.

Animals↗

PubMed1994

No evidence for linkage between familial hypertriglyceridemia and apolipoprotein B, apolipoprotein C-III or lipoprotein lipase genes.

Familial hypertriglyceridemia has been suggested to be an autosomal dominant condition with age-dependent penetrance, but so far the underlying defective gene has not been elucidated. We examined the possible role of three candidate gene loci by linkage analysis in six Finnish families with familial clustering of hypertriglyceridemia. The probands were initially recruited from a group of hyperlipidemic outpatients after measurement of serum triglyceride concentrations exceeding 2.00 mmol/l on two occasions. Altogether, 71 subjects were included in the linkage analyses. Bi- or multiallelic DNA polymorphisms were used as markers for the apolipoprotein B gene (chromosome 2), lipoprotein lipase gene (chromosome 8), and apolipoprotein A-I/C-III/A-IV gene cluster (chromosome 11). Linkage analysis was performed by applying two alternative phenotyping models, one adopting quantitative serum triglyceride concentrations and another using qualitative classification of the subjects into hypertriglyceridemic, normotriglyceridemic, and borderline hypertriglyceridemic groups. Using either approach, the cumulative lod scores of each of the three candidate genes in the six families were less than -2.0 at the recombination fraction 0.0. These results suggest that none of the candidate genes investigated is involved in familial clustering of hypertriglyceridemia in our study.

Adult↗

PubMed1984

Histochemical and immunohistochemical localization of hexokinase isoenzymes in normal rat liver.

Histochemical and immunohistochemical procedures have been used to examine the localization of three of the four hexokinase isoenzymes present in the liver of fed female Wistar rats. Distinctive distribution patterns were found for hexokinase type I and glucokinase but hexokinase type II was not detectable. Hexokinase type I was identified in sinusoidal cells and in bile duct epithelia, nerves and arteries in the portal triad. Glucokinase, the major isoenzyme, was confined to parenchymal cells where it was present in much higher amounts in perivenous compared with periportal hepatocytes. Staining within these two zones was not homogeneous and each had a mosaic appearance caused by the presence of a few hepatocytes containing little or no glucokinase amongst the majority of darkly stained cells in perivenous areas and a few darkly stained cells amongst the majority of unstained cells in periportal areas. Hence, hepatocytes in situ are a strikingly heterogeneous population of cells. Their metabolic status cannot be controlled simply by the differential supply of oxygen, substrates and hormones to different regions of the liver acini as proposed in the metabolic zonation model. Phenotypic differences may exist between cells within a given metabolic zone which influence their ability to respond to different environmental conditions.

Animals↗

PubMed2006

Impact of strain and D-amphetamine on impulsivity (delay discounting) in inbred mice.

RATIONALE: Many studies have shown that human drug abusers are more impulsive than nonusers, but the mechanisms underlying this difference are unknown. C57BL/6J (B6) and DBA/2J (D2) mouse strains differ in sensitivity to the associative effects and in self-administration of several drugs of abuse. OBJECTIVE: To determine whether these strains exhibit differences in impulsivity that might correspond to the differences in phenotypes related to drug seeking. METHODS: We examined impulsive choice in drug-naive B6 and D2 mice using a delay discounting protocol (adjusting amount procedure, J Exp Anal Behav 67:353-366, 1997). RESULTS: Contrary to our initial expectations, we observed greater delay discounting (higher impulsivity) in D2 rather than in B6 mice. For both strains, discounting was enhanced by 0.80 and 1.20 mg/kg (i.p.) D-amphetamine relative to saline. CONCLUSIONS: Data demonstrate the sensitivity of the procedure to strain differences and pharmacological manipulations. However, additional data are required to clarify the factors underlying this difference and how the delay discounting measure of impulsivity relates to phenotypic models of drug reinforcement and drug seeking.

Animals↗

PubMed2026

Functional role and regulatory network of miR-22-3p in chicken hepatic lipid metabolism.

Although microRNA-22-3p (miR-22-3p) is abundantly expressed in the avian liver, its epigenetic role in lipid homeostasis remains largely uncharacterized. To elucidate its in vivo function, 14-day-old female Qingyuan Partridge chickens were intravenously injected with lentiviral vectors to establish miR-22-3p overexpression and knockdown models. Phenotypic analysis demonstrated that miR-22-3p knockdown significantly elevated hepatic triglyceride (TG) levels (p < 0.05) and drove marked steatosis, whereas its overexpression reduced TG content. Transcriptome sequencing (RNA-Seq) revealed profound metabolic remodeling, identifying 23 core lipid-associated genes (e.g., ELOVL6, FADS2, ACSBG2, and PTGIS) heavily enriched in steroid biosynthesis, fatty acid metabolism, and elongation pathways. In conclusion, miR-22-3p functions as a bidirectional epigenetic rheostat that negatively regulates hepatic lipid deposition by orchestrating a multilayered polygenic network, providing novel molecular targets for mitigating avian metabolic disorders and optimizing production traits in indigenous poultry breeds.

Animals↗

PubMed2004

Identification of promoters bound by c-Jun/ATF2 during rapid large-scale gene activation following genotoxic stress.

The NH2-terminal Jun kinases (JNKs) function in diverse roles through phosphorylation and activation of AP-1 components including ATF2 and c-Jun. However, the genes that mediate these processes are poorly understood. A model phenotype characterized by rapid activation of Jun kinase and enhanced DNA repair following cisplatin treatment was examined using chromatin immunoprecipitation with antibodies against ATF2 and c-Jun or their phosphorylated forms and hybridization to promoter arrays. Following genotoxic stress, we identified 269 genes whose promoters are bound upon phosphorylation of ATF2 and c-Jun. Binding did not occur following treatment with transplatin or the JNK inhibitor SP600125 or JNK-specific siRNA. Of 89 known DNA repair genes represented on the array, 23 are specifically activated by cisplatin treatment within 3-6 hr. Thus, the genotoxic stress response occurs at least partly via activation of ATF2 and c-Jun, leading to large-scale coordinate gene expression dominated by genes of DNA repair.

Activating Transcription Factor 2↗