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Results for “Phenotype modeling”

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At least 55 records · Page 3Linked to original sources
PubMed1990

Coordinate occupancy of AP-1 sites in the vitamin D-responsive and CCAAT box elements by Fos-Jun in the osteocalcin gene: model for phenotype suppression of transcription.

Osteocalcin, a bone-specific protein and marker of the mature osteoblast, is expressed only in nonproliferating osteoblasts in a mineralizing extracellular matrix, while type I collagen is expressed in proliferating cells. The nuclear proteins encoded by the c-fos and c-jun protooncogenes are expressed during the proliferation period of osteoblast phenotype development. We present evidence that AP-1 (HeLa cell-activating protein 1) sites residing within two promoter elements of the osteocalcin gene bind the Fos-Jun protein complex: the osteocalcin box (OC box; nucleotides -99 to -76), which contains a CCAAT motif as a central element and influences tissue-specific basal levels of osteocalcin gene transcription, and the vitamin D-responsive element (VDRE; nucleotides -462 to -440), which mediates enhancement of osteocalcin gene transcription. Gel electrophoretic mobility-shift analysis demonstrated high AP-1 binding activity in proliferating osteoblasts and dramatic changes in this activity after the down-regulation of proliferation and the initiation of extracellular-matrix mineralization in primary cultures of normal diploid osteoblasts. Methylation interference analysis established at single nucleotide resolution that purified recombinant Fos and Jun proteins bind in a sequence-specific manner to the AP-1 sites within the VDRE and OC box. Similarly, an AP-1 motif within a putative VDRE of the alkaline phosphatase gene, which is also expressed after the completion of proliferation, binds the Fos-Jun complex. These results support a model in which coordinate occupancy of the AP-1 sites in the VDRE and OC box in proliferating osteoblasts may suppress both basal level and vitamin D-enhanced osteocalcin gene transcription as well as transcription of other genes associated with osteoblast differentiation--a phenomenon we describe as phenotype suppression. This model is further supported by binding of the Fos-Jun complex at an AP-1 site in the type alpha I collagen promoter that is contiguous with, but not overlapping, the VDRE. Such a sequence organization in the collagen VDRE motif is compatible with vitamin D modulation of collagen but not with osteocalcin and alkaline phosphatase expression in proliferating osteoblasts.

Animals↗
PubMed1992

Erythrocyte membrane transport of glutathione conjugates and oxidized glutathione in the Dubin-Johnson syndrome and in rats with hereditary hyperbilirubinemia.

The Dubin-Johnson syndrome is manifested by conjugated hyperbilirubinemia and pigment accumulation in hepatocellular lysosomes. The TR-rat model is a phenotypic model of the Dubin-Johnson syndrome and is characterized by defective ATP-dependent transport of a group of nonbile acid organic anions, including glutathione-S-conjugates and oxidized glutathione, across the bile canaliculus. Similar ATP-dependent transport mechanisms have been described in erythrocytes. Intact erythrocytes and inverted erythrocyte membrane vesicles from Dubin-Johnson patients, TR-rats and appropriate controls were studied with regard to ATP-dependent transport of dinitrophenyl glutathione and oxidized glutathione. No significant differences were observed, indicating that the erythrocyte and canalicular ATP-dependent transporters for these substrates are functionally and potentially genetically distinct.

Adenosine Triphosphate↗
PubMed2000

Variability in centred house-of-cards mutation models.

Convergence of variability in phenotypic models with balance between selection and mutation is analysed. The mutation assumed occurs with weak probability and brings down the evolutionary process built up by selection around the mean in the population. Gaussian approximations are used.

Biological Evolution↗
PubMed2026

Complementary vertebrate Wac models exhibit phenotypes relevant to DeSanto-Shinawi Syndrome.

Monogenic syndromes are associated with neurodevelopmental changes that result in cognitive impairments and neurobehavioral phenotypes, including autism and seizures. Limited studies and resources are available to make meaningful headway into the underlying molecular mechanisms that result in these symptoms. One such example is DeSanto-Shinawi Syndrome (DESSH), a rare disorder caused by pathogenic variants in the WAC gene. Individuals with DESSH syndrome exhibit a recognizable craniofacial gestalt, developmental delay/intellectual disability, neurobehavioral symptoms that include autism, ADHD, behavioral difficulties, and seizures. However, no thorough studies from a vertebrate model exist to understand how these changes occur. To overcome this, we developed both murine and zebrafish Wac/wac deletion mutants and studied whether their phenotypes recapitulate those described in individuals with DESSH syndrome. We first show that the two Wac models exhibit craniofacial and behavioral changes, reminiscent of abnormalities found in DESSH syndrome. In addition, each model revealed impacts on GABAergic neurons and further studies showed that the mouse mutants are susceptible to seizures, changes in brain volumes that are different between sexes and relevant behaviors. Finally, we uncovered transcriptional impacts of Wac loss-of-function in mice that will pave the way for future molecular studies into DESSH. These studies present two new vertebrate models that begin to uncover biological underpinnings of DESSH syndrome and elucidate the biology of Wac.

Animals↗
PubMed1994

[A model of phenotypic plasticity: the hypothalamo-posthypophyseal neurons].

In neurons, which are post-mitotic cells, a structural and biochemical plasticity occurs, namely for the mediators. The magnocellular hypothalamic neurons innervating the neural lobe are a favourable model for the study of the dynamic aspects of neuropeptides expression. In fact, they synthetize these peptides in large amounts, as a function of the physiological or experimental conditions. In addition to the major neuropeptides, oxytocin (OT) and vasopressin (VP) which are contained in control rats within different neuronal populations, immunocytochemistry and in situ hybridization used alone or in combination in the same preparations have revealed other neuropeptides and corresponding mRNAs respectively. These multiple labellings demonstrate that after osmotic stimulation or during lactation some neurons are able to synthetize OT and VP simultaneously, together with galanin and even tyrosine hydroxylase (but not catecholamines). Similarly, hypophysectomy or transection of the pituitary stalk differentially modify the contents in mRNA coding for VP, OT and galanin. These results have also been described in other neuronal types such as spinal ganglia sensory neurons, suggesting possible mechanisms at different levels of genetic expression: transcription, translation, post-translational events and possibly interneuronal exchanges of mRNA. The in vivo regulation of this neurochemical plasticity probably involves the innervation of these neurons and perhaps the colocalized peptides themselves. In fact, galanin selectively inhibits the expression of VP but not that of OT. Functional implications of the neuronal phenotypic plasticity in the adaptation of the nervous system to the changing physiological conditions are discussed, together with its possible implications in pathology and therapeutics.

Humans↗
PubMed2004

Modelling neuroinflammatory phenotypes in vivo.

Inflammation of the central nervous system is an important but poorly understood part of neurological disease. After acute brain injury or infection there is a complex inflammatory response that involves activation of microglia and astrocytes and increased production of cytokines, chemokines, acute phase proteins, and complement factors. Antibodies and T lymphocytes may be involved in the response as well. In neurodegenerative disease, where injury is more subtle but consistent, the inflammatory response is continuous. The purpose of this prolonged response is unclear, but it is likely that some of its components are beneficial and others are harmful. Animal models of neurological disease can be used to dissect the specific role of individual mediators of the inflammatory response and assess their potential benefit. To illustrate this approach, we discuss how mutant mice expressing different levels of the cytokine transforming growth factor beta-1 (TGF-beta1), a major modulator of inflammation, produce important neuroinflammatory phenotypes. We then demonstrate how crosses of TGF-beta1 mutant mice with mouse models of Alzheimer's disease (AD) produced important new information on the role of inflammation in AD and on the expression of different neuropathological phenotypes that characterize this disease.

Journal Article↗
PubMed2025

Complimentary vertebrate Wac models exhibit phenotypes relevant to DeSanto-Shinawi Syndrome.

Monogenic syndromes are associated with neurodevelopmental changes that result in cognitive impairments, neurobehavioral phenotypes including autism and seizures. Limited studies and resources are available to make meaningful headway into the underlying molecular mechanisms that result in these symptoms. One such example is DeSanto-Shinawi Syndrome (DESSH), a rare disorder caused by pathogenic variants in the WAC gene. Individuals with DESSH syndrome exhibit a recognizable craniofacial gestalt, developmental delay/intellectual disability, neurobehavioral symptoms that include autism, ADHD, behavioral difficulties and seizures. However, no thorough studies from a vertebrate model exist to understand how these changes occur. To overcome this, we developed both murine and zebrafish Wac/wac deletion mutants and studied whether their phenotypes recapitulate those described in individuals with DESSH syndrome. We first show that the two Wac models exhibit craniofacial and behavioral changes, reminiscent of abnormalities found in DESSH syndrome. In addition, each model revealed impacts to GABAergic neurons and further studies showed that the mouse mutants are susceptible to seizures, changes in brain volumes that are different between sexes and relevant behaviors. Finally, we uncovered transcriptional impacts of Wac loss of function in mice that will pave the way for future molecular studies into DESSH. These studies present two new animals that begin to uncover some biological underpinnings of DESSH syndrome and elucidate the biology of Wac.

Journal Article↗
PubMed1999

Targeted inactivation of the type VII collagen gene (Col7a1) in mice results in severe blistering phenotype: a model for recessive dystrophic epidermolysis bullosa.

Dystrophic forms of epidermolysis bullosa (DEB) are associated with mutations in the type VII collagen gene (Col7a1) which encodes the major component of anchoring fibrils. To develop a DEB animal model, type VII collagen deficient mice were generated by targeted homologous recombination. The targeting vector replaced exons 46-69 of Col7a1 with the neomycin-resistance gene, in reverse transcriptional orientation, resulting in elimination of most of the collagenous domain 1. Col7a1 heterozygous (+/-) mice were phenotypically normal. Mating of Col7a1 +/- mice revealed that Col7a1 null (-/-) mice, which were born with extensive cutaneous blistering, died during the first two weeks of life probably due to complications arising from the blistering. Transmission electron microscopy revealed subepidermal blistering below the lamina densa and absence of anchoring fibrils. Immunohistochemical staining with anti-human type VII collagen antibody stained the dermal-epidermal junction in control mice, but did not stain the skin of Col7a1 null mice. Collectively, the DEB mice recapitulate the clinical, genetic, immunohistochemical and ultrastructural characteristics of recessive DEB in humans. These mice provide an animal model to study the pathomechanisms of DEB and serve as a system to test therapeutic approaches, including gene replacement, towards the cure of this devastating skin disease.

Animals↗
PubMed2026

Bridging the gap between genomic, phenotypic, and modeling data in picophytoplankton-virus interactions.

We present a comprehensive synthesis of recent developments in methodological approaches to combine experimental and genomic studies of picophytoplankton-virus interactions. This synthesis will not only enhance our understanding of these relationships but also stimulate new hypotheses for the interpretation of metagenomic data and enrich current modeling efforts. Marine picophytoplankton are significant primary producers despite their low contribution to biomass. Pan-oceanic metagenomic studies have revealed an astounding genetic diversity within these communities and the astronomical abundance of viruses that infect them. Despite recent advances in understanding the genetic and genomic diversity of picophytoplankton and viruses, the interpretation of these data relies heavily on ecological and physiological insights. Specifically, our understanding of the mechanisms and dynamics governing host-virus interactions is limited because the current wealth of sequence data has not yet been matched with corresponding life-history traits. Linking phenotypes to genotypes in picophytoplankton-virus systems is also essential for accurately modeling their interactions and their impact on the global carbon cycle. Ultimately, the synergy of the three domains allows for a mechanistic interpretation of environmental data.

Chlorophyta↗
PubMed1995

Linkage analysis between manic-depressive illness and markers on the long arm of chromosome 11.

The long arm of chromosome 11 is one of the most interesting regions in the search for major genes involved in the etiology of manic-depressive illness. Several candidate genes have been identified, including the gene encoding the dopamine D2 receptor, the M1 muscarinic receptor, and porfobillinogen deaminase. Furthermore, different families with co-segregation of psychiatric illness and structural chromosome abnormalities involving regions 11q21, 11q22.3, and 11q25 have been reported. Using narrow as well as broad phenotypic models, conservative genetic parameters, models with dominant or recessive modes of inheritance, and various methods to reduce misclassification, the present study did not find evidence for a major gene causing manic-depressive illness on the long arm of chromosome 11. In the broader phenotypic models multi-point analyses excluded at least 11q14 to 11q23.3, approximately 60 cM, even in one large family. Assuming homogeneity close linkage to DRD2 was excluded for all dominant models, and also in the affecteds-only analyses in the large family alone.

Biomarkers↗
PubMedDate not supplied

[Fluctuating asymmetry as a marker of phenotypic adaptiveness (modelled on the neurological manifestations of lumbar osteochondrosis].

Analysis of palm ridge count a-b was carried out in 217 males having neurological expressions of lumbar osteochondrosis and 300 control persons. Higher indices of fluctuating asymmetry have been recorded in the group of patients thus suggesting a low stability of development. It was proposed that fluctuating asymmetry can mark phenotypes weakly adapted to postnatal environmental effects.

Adaptation, Physiological↗
PubMed1999

Cancer risk in ATM heterozygotes: a model of phenotypic and mechanistic differences between missense and truncating mutations.

The failure to find an increased frequency of ATM mutations in large cancer cohorts, especially breast cancer, is contrary to what was anticipated based on the increased cancer susceptibility of obligate ATM heterozygotes from families with ataxia-telangiectasia (A-T). We hypothesize that this paradox might be resolved if two types of ATM heterozygotes exist and the phenotypes differ, i.e., those with truncating types of mutations (ATM(trunc)), that make no protein, and those with missense types of mutations (ATM(mis)), that make reduced amounts of defective protein. The phenotype of ATM(trunc/trunc) mutations is the A-T syndrome; the phenotype of ATM(mis/mis) mutations, judging from the few homozygous patients that have been documented, appears to include some neurological features and cancer susceptibility but not the A-T syndrome. Evidence is reviewed which suggests that ATM(mis/wt) mutations are technically more difficult to detect than ATM(trunc/wt) mutations. Despite this, most large cancer cohort studies have identified mainly missense mutations and few truncating mutations. This model would require a paradigm shift for cancer risk analyses, to recognize the existence of different allele frequencies for the two types of A-T heterozygotes.

Ataxia Telangiectasia↗
PubMed2000

An EM algorithm for obtaining maximum likelihood estimates in the multi-phenotype variance components linkage model.

In recent years variance components models have been developed for localising genes that contribute to human quantitative variation. In typical applications one assumes a multivariate normal model for phenotypes and estimates model parameters by maximum likelihood. For the joint analysis of several correlated phenotypes, however, finding the maximum likelihood estimates for an appropriate multivariate normal model can be a difficult computational task due to complex constraints among the model parameters. We propose an algorithm for computing maximum likelihood estimates in a multi-phenotype variance components linkage model that readily accommodates these parameter constraints. Data simulated for Genetic Analysis Workshop 10 are used to demonstrate the potential increase in power to detect linkage that can be obtained if correlated phenotypes are analysed jointly rather than individually.

Algorithms↗
PubMed2001

Multistep renal carcinogenesis as gene expression disease in tumor suppressor TSC2 gene mutant model--genotype, phenotype and environment.

Cancer is an inheritable disorder of somatic cells. Environment and heredity both operate in the origins of human cancer. These environmental and genetic determinants of cancer can be classified into four groups designated "Oncodemes" [1]. Oncodeme 1 is the irreducible "background" level of cancer due to spontaneous mutagenesis. Oncodeme 2 is "environmentally induced" cancer, whose causative agents are chemical carcinogens, radiation and viruses. Oncodeme 3 is basically "environmentally induced" cancer, but there are genetically determined differences among persons, e.g. the activation or inactivation of carcinogenes. Most human cancers are believed to belong to Oncodemes 2 and/or 3 (about 80%), for which the probability of the occurrence of the initial carcinogenic step(s) is increased, although the number of steps is not decreased. Oncodeme 1 would contain the approximately 20% that would remain if "environmentally induced" cancers (Oncodeme 2 and/or 3) were prevented. Lastly, Oncodeme 4 is "hereditary" cancer. Hereditary cancers could prove valuable in elucidating carcinogenesis, even though only a small proportion of cancers belong to this group. Here, we present a unique animal model of Oncodeme 4 for the study of problems in carcinogenesis; e.g. cell stage and tissue/cell-type-specific tumorigenesis, multistep carcinogenesis, species-specific differences in tumorigenesis, modifier gene(s) in renal carcinogenesis and cancer prevention.

Animals↗
PubMed2006

Statistical epistasis is a generic feature of gene regulatory networks.

Functional dependencies between genes are a defining characteristic of gene networks underlying quantitative traits. However, recent studies show that the proportion of the genetic variation that can be attributed to statistical epistasis varies from almost zero to very high. It is thus of fundamental as well as instrumental importance to better understand whether different functional dependency patterns among polymorphic genes give rise to distinct statistical interaction patterns or not. Here we address this issue by combining a quantitative genetic model approach with genotype-phenotype models capable of translating allelic variation and regulatory principles into phenotypic variation at the level of gene expression. We show that gene regulatory networks with and without feedback motifs can exhibit a wide range of possible statistical genetic architectures with regard to both type of effect explaining phenotypic variance and number of apparent loci underlying the observed phenotypic effect. Although all motifs are capable of harboring significant interactions, positive feedback gives rise to higher amounts and more types of statistical epistasis. The results also suggest that the inclusion of statistical interaction terms in genetic models will increase the chance to detect additional QTL as well as functional dependencies between genetic loci over a broad range of regulatory regimes. This article illustrates how statistical genetic methods can fruitfully be combined with nonlinear systems dynamics to elucidate biological issues beyond reach of each methodology in isolation.

Epistasis, Genetic↗