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At least 343 records · Page 19Linked to original sources
PubMed2003

Selection conflicts, gene expression, and codon usage trends in yeast.

Synonymous codon usage in yeast appears to be influenced by natural selection on gene expression, as well as regional variation in compositional bias. Because of the large number of potential targets of selection (i.e., most of the codons in the genome) and presumed small selection coefficients, codon usage is an excellent model for studying factors that limit the effectiveness of selection. We use factor analysis to identify major trends in codon usage for 5836 genes in Saccharomyces cerevisiae. The primary factor is strongly correlated with gene expression, consistent with the model that a subset of codons allows for more efficient translation. The secondary factor is very strongly correlated with third codon position GC content and probably reflects regional variation in compositional bias. We find that preferred codon usage decreases in the face of three potential limitations on the effectiveness of selection: reduced recombination rate, increased gene length, and reduced intergenic spacing. All three patterns are consistent with the Hill-Robertson effect (reduced effectiveness of selection among linked targets). A reduction in gene expression in closely spaced genes may also reflect selection conflicts due to antagonistic pleiotropy.

Codon↗
PubMed2004

Complete remission of hyperprolactinemia and erythrocytosis after hysterectomy for a uterine fibroid in a woman with a previous diagnosis of prolactin-secreting pituitary microadenoma.

A 44-year-old woman who had been suffering for 10 years from amenorrhea and hyperprolactinemia resistant to high doses of bromocriptine was hospitalized with erythrocytosis, normal serum erythropoietin (sEpo) levels, and hypertension. Erythrocytosis secondary to uterine myoma and a prolactin-secreting pituitary microadenoma were initially diagnosed. The hyperprolactinemia was bromocriptine resistant, despite gradual increase of the dosage to 30 mg/day. Both hyperprolactinemia and erythrocytosis unexpectedly regressed completely after the patient underwent hysterectomy for a uterine fibroid 9 months after the erythrocytosis was first disclosed. Given the well-known effects of prolactin on hematopoietic cells, we hypothesize that--in this very unusual case--the two main, apparently unrelated abnormalities (erythrocytosis with normal sEpo levels and hyperprolactinemia) may have been the clinical consequence of the functional redundancy and pleiotropy of the "pituitary" hormone prolactin, inappropriately secreted by a uterine fibroid for more than 10 years.

Adult↗
PubMed2006

Quantitative trait loci for body size components in mice.

Do body size components, such as weights of internal organs and long bone lengths, with different functions and different developmental histories also have different genetic architectures and pleiotropic patterns? We examine murine quantitative trait loci (QTL) for necropsy weight, four long bone lengths, and four organ weights in the LG/J x SM/J intercross. Differences between trait categories were found in number of QTL, dominance, and pleiotropic patterns. Ninety-seven QTLs for individual traits were identified: 52 for long bone lengths, 30 for organ weights, and 15 for necropsy weight. Results for long bones are typically more highly significant than for organs. Organ weights were more frequently over- or underdominant than long bone lengths or necropsy weight. The single-trait QTLs map to 35 pleiotropic loci. Long bones are much more frequently affected in groups while organs tend to be affected singly or in pairs. Organs and long bones are found at the same locus in only 11 cases, 8 of which also include necropsy weight. Our results suggest mainly separate genetic modules for organ weights and long bone lengths, with a few loci that affect overall body size. Antagonistic pleiotropy, in which a locus has opposite effects on different characteristics, is uncommon.

Animals↗
PubMed2026

Cross-tissue Mendelian randomization prioritizes RAB27B as a brain-derived candidate protein for postpartum depression.

OBJECTIVE: Postpartum depression (PPD) is one of the most common and debilitating complications of childbirth, yet the candidate proteins linking genetic risk to disease remain poorly defined. Building on recent genome-wide association studies (GWAS), we sought to integrate cross-tissue proteogenomic data to identify candidate proteins for PPD and explore therapeutic opportunities. METHODS: We conducted two-sample Mendelian randomization (MR) using genome-wide significant cis-protein QTLs from brain (n = 608 proteins), cerebrospinal fluid (CSF; n = 214), and plasma (n = 612). PPD summary statistics were obtained from FinnGen R8 (13,657 cases, 236,178 controls) and replicated in an independent GWAS. Phenome-wide association (PheWAS) was used to assess pleiotropy. Potential therapeutic targets were evaluated through DSigDB drug repurposing, molecular docking, and molecular dynamics simulations. RESULTS: Among all proteins tested, RAB27B was the only brain-derived protein surpassing Bonferroni correction (OR = 1.60; 95% CI: 1.30-1.96; P = 6.6 × 10⁻⁶), whereas no significant proteins were identified in CSF or plasma. This association was replicated in an independent GWAS (OR = 1.27; 95% CI: 1.02-1.58; P = 0.037). PheWAS identified no pleiotropic associations at genome-wide significance. In silico drug repurposing identified pregnenolone as a candidate ligand with computationally predicted stable binding to RAB27B, providing a starting point for future experimental validation. CONCLUSION: This study provides the first cross-tissue proteogenomic evidence that RAB27B is a brain-derived, reproducible candidate protein genetically associated with PPD. By extending GWAS signals to functional protein-level mechanisms and therapeutic inference, our findings nominate RAB27B and pregnenolone as promising directions for postpartum psychiatric research.

Humans↗
PubMed2004

Global analysis of gene expression in mammalian kidney.

The past decade has seen the achievement of sequencing of human, rat and mouse genomes and the development of high-throughput methods for quantitative monitoring of gene expression. The aim of the beginning post-genomic era is to determine the function of all these genes, a challenge in which the community of physiologists should have a leading role. In this short review, we discuss the relevance, feasibility and impact of transcriptome analysis in renal physiology. Comparison of transcriptomes demonstrates that cell lines are poor physiological models, making it necessary to work on native kidney tissue. Palliating kidney heterogeneity therefore requires the development of methods for transcriptome analysis sensitive enough to be compatible with microdissected nephron segments. Axial comparison of transcriptomes along the human nephron unexpectedly points out that the segmentation of nephrons concerns not only genes involved in solute and water transport functions and their regulation, but also genes related to the control of cell division, differentiation and apoptosis. Comparison of transcriptome of a same nephron segment from mice under different pathophysiological conditions outlines the wide pleiotropy of kidney function regulations. Both types of comparative studies also identify yet unknown transcripts specifically expressed along the nephron or under pathophysiological conditions.

Animals↗
PubMed2001

Genetic analyses of correlated solids, flavor, and health-enhancing traits in onion (Allium cepa L.).

Onion possesses organosulfur compounds and carbohydrates that provide unique flavor and health-enhancing characteristics. Significant phenotypic correlations have been reported among soluble solids content (SSC), total dry matter, pungency, and onion-induced in vitro antiplatelet activity. A genetic map and segregating F3M families derived from a cross between two inbred populations were used to identify and estimate the effects of quantitative trait loci (QTLs) controlling these traits at 30 and 90 days postharvest. In vitro antiplatelet activities among different onion populations were consistent across six human blood donors. Most of the populations showed in vitro antiplatelet activities; however, for some donors, one of the parental lines and two F3M families had pro-aggregatory effects under our experimental conditions. SSC, dry matter, pungency, and in vitro antiplatelet activity showed significant positive phenotypic and genetic correlations. A chromosome region on linkage group E accounted for a significant amount of the phenotypic variation for all of these traits. The correlations among these traits may be due to linkage or pleiotropy of genes controlling solids content. Our results indicate that it will be difficult to develop onion populations with lower pungency and high in vitro antiplatelet activity; however, the strong genetic and phenotypic correlations between high in vitro antiplatelet activity and high SSC are beneficial for the health functionality of onion.

Adult↗
PubMed1997

Sex chromosomes and human growth. A dental approach.

Studies on tooth crown size and structure of individuals with various sex chromosome anomalies and their normal male and female relatives have demonstrated differential direct effects on growth of genes on the human X and Y chromosomes. The Y chromosome promotes growth of both tooth enamel and dentin, whereas the effect of the X chromosome on tooth growth seems to be restricted to enamel formation. Enamel growth is decisively influenced by cell secretory function and dentin growth by cell proliferation. It is suggested that these differential effects of the X and Y chromosomes on growth explain the expression of sexual dimorphism in various somatic features, such as the size, shape and number of teeth, and, under the assumption of genetic pleiotropy, torus mandibularis, statural growth, and sex ratio. Future questions concern, among other topics, the Y chromosome and the mineralization process, concentric control of enamel and dentin growth, and gene expression.

Dental Enamel↗
PubMed1998

Loss of heterozygosity in polycystic kidney disease with a missense mutation in the repeated region of PKD1.

Loss of heterozygosity (LOH) is a molecular phenomenon that denotes the loss of one of the two alleles at a specific locus. It is frequently associated with tumour suppressor genes in various cancers and also with hyperproliferative disorders, although not exclusively. Interestingly, in conditions where there is an inherited germline mutation, the lost allele is always the functional one, thereby rendering a phenotypically dominant disease of recessive character at the cellular level. A disease more recently shown to be associated with LOH is polycystic kidney disease type 1, a systemic disorder characterized by significant pleiotropy. The main pathology is from renal cyst formation that eventually leads to end-stage renal failure during adult life. We describe the identification of a missense mutation in the repeated part of the PKD1 gene, exon 31, that substitutes valine for methionine. The mutation, M3375V, cosegregates with the disease phenotype in a large Cypriot family. During transplantation of one patient, one of the polycystic kidneys was removed and DNA was isolated from cystic epithelial cells. In 3 of 17 cysts examined with intragenic and flanking polymorphic markers on chromosome 16 we detected LOH, since the wild-type allele was lost, thereby rendering the affected kidneys of mosaic character. The degree of LOH was extensive and varied among the three cysts, supporting the multiplicity of expression of the phenomenon on different occasions. No LOH was detected for other selected loci examined. Our work further supports the hypothesis that the rate-limiting step in cyst formation may be the occurrence of a second somatic hit, although other factors may be also involved. The high frequency of mutations at this locus may, to a great extent, explain the variability in phenotype observed among patients in the same families, and the relatively high frequency of the disease worldwide.

Adult↗
PubMed2003

Covariance of preference and performance on normal and novel hosts in a locally monophagous and locally polyphagous butterfly population.

Covariance between preference and performance was quantified for Papilio glaucus strains derived from a locally monophagous Florida population and a locally polyphagous Ohio population. I used two-choice assays to assess relative host preferences of mothers for plant species that represent reciprocal normal and novel hosts for each population (i.e., Liriodendron tulipifera and Magnolia virginiana) and a split-brood design to quantify relative performance of their progeny on each host. Covariance between preference and proxies of performance was detected independently within each population, which is a level of genetic structure at which such covariance has rarely been documented. These results support the hypothesis that preference-performance covariance can exist in populations that have no obvious internal host-associated structure. In the Ohio strain, all proxies of performance (larval duration, pupal mass, relative growth rate, and survival) were significantly correlated with relative preference for the normal host, L. tulipifera. In the Florida strain, however, only pupal mass was correlated with maternal preference, and this correlation was not in the direction expected. Progeny that attained the heaviest mass were derived from mothers that preferred L. tulipifera, the locally rare host. The nature of the preference-performance links was not in the manner predicted by conventional optimal oviposition theory, whereby host-associated tradeoffs have been considered an implicit element. Relative performance was congruent across hosts, regardless of whether mothers preferred L. tulipifera, M. virginiana, or neither host. After considering possible genetic and nongenetic explanations that could account for preference-performance covariance in P. glaucus, I conclude that this covariance has a genetic basis. Likely, multiple genetic control mechanisms (e.g., pleiotropy and co-adaptation) integrate at the level of different trait combinations and/or a particular trait combination to generate observed patterns.

Adaptation, Physiological↗
PubMedDate not supplied

Seckel-like syndrome in three siblings.

Seckel syndrome has been described as the prototype of the primordial bird-headed type of dwarfism. Since Seckel originally defined the disorder, less than 60 cases have been reported. In addition to the characteristic craniofacial dysmorphism and skeletal defects, abnormalities have been described in the cardiovascular, hematopoietic, endocrine, and central nervous systems. This pleiotropy has implied genetic heterogeneity and prompted reviews of previously reported cases of Seckel syndrome. As a result, the characteristic diagnostic features of Seckel syndrome have been highly debated. Although deletions in chromosome 2q have been described, to date, no genetic defect has been defined. We report three cases of Seckel-like syndrome in siblings from nonconsanguinous Caucasian parents. In addition to the typical Seckel phenotypic features, all three cases were characterized by severe hydrocephalus. We review the literature and propose that there is a spectrum of Seckel conditions that share some common key features, but also demonstrate a wide range of phenotypic features.

Abnormalities, Multiple↗
PubMed2026

Shared genetic architecture and cellular convergence between female reproductive disorders and pulmonary function: a genome-wide cross-trait analysis.

Female reproductive disorders (FRDs), including polycystic ovary syndrome, endometriosis, uterine leiomyomata, and infertility, have been epidemiologically associated with impaired pulmonary function. However, it remains unclear whether this cross-organ link reflects shared genetic etiology and, if so, which cellular mechanisms mediate it. We performed a systematic genome-wide cross-trait analysis of three FRDs and lung function traits (FEV₁, FVC, FEV₁/FVC) using GWAS summary statistics from individuals of European ancestry, integrating genetic correlation, bidirectional causal inference, pleiotropy mapping, and single-cell enrichment analyses. We identified significant negative genetic correlations between FRDs and lung volume traits, most prominently for FVC (rg range: - 0.077 to - 0.178). Bidirectional causal analyses indicated that FRDs have a detrimental effect on lung volume, with higher FRD genetic liability associated with reduced lung volume. Cross-trait meta-analysis identified 17 pleiotropic variants across 11 loci, with the 19q13.2 (LTBP4) and 12q13.13 (HOXC6/HOXC9) loci showing strong evidence of shared causal variants. Critically, single-cell analyses revealed that shared genetic risk converged on mesenchymal lineages across organs, specifically alveolar adventitial fibroblasts in the lung and stromal/smooth muscle cells in the endometrium. Transcriptome-wide analyses further nominated the estrogen-responsive gene RERG as a convergent gene linking these conditions with lung function. Our study revealed a shared genetic architecture between female reproductive disorders and lung function traits, providing a basis for further mechanistic investigations and potential clinical evaluation. Furthermore, our findings suggest that shared fibroproliferative and hormone-responsive pathways may offer insights into the biological mechanisms underlying these conditions.

Female↗
PubMed2006

Exercise participation and self-rated health: do common genes explain the association?

The purpose of this study is to investigate whether there is an association between exercise participation and self-rated health and whether this association can be explained by common genes and/or common environmental influences. In a sample of 5,140 Dutch adult twins and their non-twin siblings from 2,831 families, exercise participation (sedentaries, light or moderate, vigorous exercisers) and self-rated health were assessed by survey. To investigate the etiology of the association, bivariate genetic models using structural equation modeling were applied to the data. The correlation between exercise participation and self-rated health is significant but modest (r = 0.20). Exercise participation and self-rated health are both heritable (around 50% of the variance of both phenotypes is explained by genetic factors). The genetic factors influencing exercise participation and self-rated health partially overlap (r = 0.36) and this overlap fully explains their phenotypic correlation. We conclude that the association between exercise and self-rated health can be explained by genes predisposing to both exercise participation and self-rated health. These genes may directly influence both phenotypes (pleiotropy). Alternatively, genes that affect exercise or self-rated health may indirectly influence the other phenotype through a causal relationship. We propose that identification of the genes that cause differences in exercise behavior will help resolve the issue of causality.

Adolescent↗
PubMed2005

Sex differences in recombination and mapping adaptations.

Since the raw material of marker based mapping is recombination, understanding how and why recombination rates evolve, and how we can use variation in these rates will ultimately help to improve map resolution. For example, using this variation could help in discriminating between linkage and pleiotropy when QTL for several traits co-locate. It might also be used to improve QTL mapping algorithms. The goals of this chapter are: (1) to highlight differences in recombination rates between the sexes, (2) describe why we might expect these differences, and (3) explore how sex difference in recombination can be used to improve resolution in QTL mapping.

Animals↗
PubMed2005

Epistasis and genotype-environment interaction for quantitative trait loci affecting flowering time in Arabidopsis thaliana.

A major goal of evolutionary biology is to understand the genetic architecture of the complex quantitative traits that may lead to adaptations in natural populations. Of particular relevance is the evaluation of the frequency and magnitude of epistasis (gene-gene and gene-environment interaction) as it plays a controversial role in models of adaptation within and among populations. Here, we explore the genetic basis of flowering time in Arabidopsis thaliana using a series of quantitative trait loci (QTL) mapping experiments with two recombinant inbred line (RIL) mapping populations [Columbia (Col) x Landsberg erecta (Ler), Ler x Cape Verde Islands (Cvi)]. We focus on the response of RILs to a series of environmental conditions including drought stress, leaf damage, and apical damage. These data were explicitly evaluated for the presence of epistasis using Bayesian based multiple-QTL genome scans. Overall, we mapped fourteen QTL affecting flowering time. We detected two significant QTL-QTL interactions and several QTL-environment interactions for flowering time in the Ler x Cvi population. QTL-environment interactions were due to environmentally induced changes in the magnitude of QTL effects and their interactions across environments--we did not detect antagonistic pleiotropy. We found no evidence for QTL interactions in the Ler x Col population. We evaluate these results in the context of several other studies of flowering time in Arabidopsis thaliana and adaptive evolution in natural populations.

Arabidopsis↗
PubMed1990

Marfan syndrome in China: a collective review of 564 cases among 98 families.

This is a collective review of 564 patients with Marfan syndrome among 98 pedigrees reported from 18 provinces and cities in China over a 37-year period from 1951 to 1987. A positive family history of Marfan syndrome was found in 74.3% of the patients: the mode of inheritance was dominant in 73.8% and recessive in 0.5%. Sporadic cases occurred in 25.7%. A screening of 29,067 children found five children with Marfan syndrome, giving a prevalence of 17.2 per 100,000 of the population, a gene frequency of 8.61 per 100,000 genes, and a penetrance of 71.69%. Pleiotropy was clear in these cases: arachnodactyly in 77%, ectopia lentis in 86.8%, and dilated aortic root in 80.1%. Chromosome examination showed no regular aberrations except in a family of five in whom a giant-satellited chromosome 14 was found in three afflicted members but not in the two unaffected relatives. The high prevalence of aortic root dilation in Marfan syndrome makes echocardiography the most useful and practical means of diagnosis. Close follow-up and regular echocardiographic evaluation are indicated not only in patients with Marfan syndrome but also in their families, for both diagnostic and therapeutic purposes.

Adolescent↗
PubMed1988

Altered plasma membrane ultrastructure in multidrug-resistant cells.

Multidrug resistance is mediated by P-glycoprotein, an integral plasma membrane component which is thought to function as a drug export pump. This model can explain drug resistance, but fails to account for the broader pleiotropy of the multidrug resistance phenotype. We report here a freeze-fracture study revealing increases in the densities of protoplasmic face intramembrane particles in multidrug-resistant Chinese hamster ovary (CHO) and human leukemic cells. The intramembrane particle density in a CHO cell revertant which had lost the characteristics of the multidrug resistance phenotype was indistinguishable from that of the drug-sensitive parental cell line. This demonstration of a global multidrug resistance-linked change in plasma membrane architecture may have significant implications for understanding the variety of concurrent membrane-related changes which are not easily explained by the current model for multidrug resistance.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed1980

An E. coli gene product required for lambda site-specific recombination.

We report characteristics of himA mutations of E. coli, selected for their inability to support the site-specific recombination reaction involved in the formation of lysogens by bacteriophage lambda. The himA allele lies at minute 38 on the chromosome. Three noncomplementing and closely linked mutations define the himA locus; one is a nonsense mutation which shows that the gene product is a protein. HimA mutations reduce both lambda integrative and excisive site-specific recombination. Since dominance tests demonstrate that himA mutations are recessive, it is probable that the himA protein is either a necessary component for site-specific recombination or, alternatively, regulates the expression of such a function. HimA mutations exhibit pleiotropic effects. They reduce integration of phages that have different attachment specificities from lambda and inhibit the growth of phage mu. In addition, himA mutations reduce precise excision of integrated phage mu as well as Tn elements. This pleiotropy suggests that the role of himA protein is nonspecific. Since all of the processes affected by himA mutations ultimately rely on protein-DNA interactions, we suggest that himA protein may act in an auxillary manner to facilitate these interactions.

Bacterial Proteins↗
PubMed1989

CD23: a multi-functional receptor/lymphokine?

With the demonstration of identity between CD23 and the low affinity IgE Fc receptor (Fc epsilon RII), two previously separate avenues of immunological research have converged into one. Particularly in its guise as 'Blast-2' antigen, evidence has been mounting to implicate CD23 as an important molecule in B-cell growth regulation. It might seem pertinent, however, to question a role for an apparently isotype-specific immunoglobulin (Ig) receptor in general B-cell processes. In this article, John Gordon and colleagues attempt to reconcile the two, currently diverse, schools of thought regarding the primary function of CD23 and to provide a structural model that accounts for the biological pleiotropy observed.

Antigens, Differentiation, B-Lymphocyte↗