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Germline mutation rates have been found to be higher in males than in females in many organisms, a likely consequence of cell division being more frequent in spermatogenesis than in oogenesis. If the majority of mutations are due to DNA replication error, the male-to-female mutation rate ratio (alpha(m)) is expected to be similar to the ratio of the number of germ line cell divisions in males and females (c), an assumption that can be tested with proper estimates of alpha(m) and c. Alpha(m) is usually estimated by comparing substitution rates in putatively neutral sequences on the sex chromosomes. However, substantial regional variation in substitution rates across chromosomes may bias estimates of alpha(m) based on the substitution rates of short sequences. To investigate regional substitution rate variation, we estimated sequence divergence in 16 gametologous introns located on the Z and W chromosomes of five bird species of the order Galliformes. Intron ends and potentially conserved blocks were excluded to reduce the effect of using sequences subject to negative selection. We found significant substitution rate variation within Z chromosome (G15 = 37.6, p = 0.0010) as well as within W chromosome introns (G15 = 44.0, p = 0.0001). This heterogeneity also affected the estimates of alpha(m), which varied significantly, from 1.53 to 3.51, among the introns (ANOVA: F(13,14) = 2.68, p = 0.04). Our results suggest the importance of using extensive data sets from several genomic regions to avoid the effects of regional mutation rate variation and to ensure accurate estimates of alpha(m).
J Mol Evol 2006 Feb
PMID:Substitution rate heterogeneity and the male mutation bias. 1647 85

TAK-778 has been shown to stimulate osteogenesis both in vitro and in vivo. However, the mechanism by which TAK-778 exerts its effects is still unclear. There is evidence that TAK-778 acts via estrogen-receptor (ER)-mediated signaling; this study therefore aimed to investigate the roles that ERalpha, ERbeta, and membrane ER play in the osteogenic effect of TAK-778. To this end, human bone marrow mesenchymal cells were cultured with TAK-778 in the presence of either ICI182,780 (ERalpha and ERbeta antagonist) or MPP (ERalpha antagonist) or PD98059 (an extracellular-regulated kinase inhibitor that acts on the membrane ER pathway). The following parameters were evaluated: cell proliferation, collagen content, alkaline phosphatase (ALP) activity and bone-like formation. Data were compared using ANOVA. The effect of TAK-778 on expression of ERalpha and ERbeta was investigated by immunolabeling. In order to investigate whether TAK-778 binds to ER, an ER binding assay was performed. Both immunolabeling and binding assays were conducted using cells from human alveolar bone. The osteogenic effect of TAK-778 was inhibited by ICI182,780 and MPP; however, it was not affected by PD98059. The expression of both ERalpha and ERbeta was not affected by TAK-778. The competition curve obtained from the binding assay using TAK-778 showed maximal displacement when 10(-5) M TAK-778 was used. This study's results show that TAK-778 enhances osteoblast differentiation through an ERalpha-dependent pathway by binding to this receptor and not by increasing the expression of ER.
Mol Cell Biochem 2006 Apr
PMID:Participation of estrogen receptors in the enhancement of osteoblast differentiation by TAK-778. 1647 74

Ovarian cancer is the fourth leading cause of gynecological cancer death among women in the United States. Early detection is a critical prerequisite to initiating effective cancer therapy. Gene microarray technology and proteomics have provided much of the biomarkers with potential use for diagnosis. However, more research is needed to fully understand disease onset and progression. To this end, we have performed microarray analysis with the goal of identifying molecular interaction networks defining tumor growth. Microarray analysis was performed on a limited set of ovarian tissues with various pathological diagnoses using Human Genome Focus Array (HGFA) for the detection of approximately 8500 human transcripts. Hierarchical clustering identified groups of ovarian tissues reflective of low malignant potential/early cancer onset and possible pre-cancerous stages involving small molecule, cytokine and/or hormone-dependent feed-back responses specific to the pelvic reproductive system and a priori initiated tumor suppression mechanisms. ANOVA followed by post hoc Scheffe confirmed our hypotheses. Moreover, we established a protein/protein interaction database associated with HGFA probe sets. This database was used to build and visualize molecular networks integrating small but significant changes in gene expression. In conclusion, we were able for the first time to delineate an intersecting genetic pattern linking ovarian tissues reflective of low potential malignancy/early cancer onset stages via long distance signaling between tissues of gynecological origin.
J Mol Biol 2006 Apr 21
PMID:Gene expression profiling of ovarian tissues for determination of molecular pathways reflective of tumorigenesis. 1650 37

Cultured myometrial (M) and fibroid (F) smooth muscle cells (SMCs) have been widely used as a model for the study of F growth. The aim of this study was to compare gene expression profiles using microarrays between six paired M and F tissues from hysterectomy specimens, as well as cells isolated from the same tissues and cultured for up to three passages. A total of 2055 genes were differentially expressed by ANOVA between all experimental groups. Among them, 128 genes were found to be statistically different between M and F tissues. More than 1100 genes were significantly changed between tissues and cultured cells, with 648 genes common between both M and F cells at P0 and P3. Expression profiles of six genes including estrogen receptor-alpha (ERalpha) and progesterone receptor (PR) were also validated using real-time PCR. These data demonstrate that large changes occur in SMC gene expression in culture, reducing differences between M and F cells. They also show that ERalpha and PR levels are reduced in cells compared with whole tissue. These results indicate that although M and F cell cultures provide an important tool to study these tumours, in vitro studies must be carefully planned and evaluated to provide meaningful results.
Mol Hum Reprod 2006 Mar
PMID:In vitro culture significantly alters gene expression profiles and reduces differences between myometrial and fibroid smooth muscle cells. 1652 27

This study investigates the role of bone resorption in defining interdigitations characteristic of cranial suture waveform. Male mice from the CD-1 (ICR) background were analyzed at six age groups (n = 5 mice per group) in order to study the ontogenetic changes of osteoclast counts using tartrate-resistant acid phosphatase-stained histological sections of sagittal sutures. Additionally, the complexity of suture lines were measured ectocranially from the same age groups (n = 5 per group) using image capture and fractal geometry (ruler dimension method). The results suggest that osteoclast resorption is a contributor to suture patterning. Specifically, osteoclasts show the greatest activity along concave suture regions at 42 and 84 days (Kruskal-Wallis test statistic = 14.9; P < or = 0.01). This coincides with significant increases incrementally in suture complexity as measured with fractal dimension at 42 and 84 days of age (ANOVA F-statistic = 19.84; P < or = 0.001). In congruence with these data, mice given osteoclast-depleting injections of alendronate show a decrease in sagittal suture complexity. Data from this experiment indicate a positive relationship between suture complexity and osteoclast count (P < 0.01; r = 76%). Increases in suture complexity and osteoclast activity occur after peak rates of cranial width growth and coincide with weaning and the transition to a hard chow diet. These data demonstrate osteoclasts along the bone margin of the cranial suture and also indicate that sutures attain their complex shape at the same age when osteoclast number is highest along concave suture margins, underscoring the role of osteoclasts in generating the suture waveform pattern.
Anat Rec A Discov Mol Cell Evol Biol 2006 May
PMID:Role of the osteoclast in cranial suture waveform patterning. 1660 42

Two channel microarray data often contain systematic variations that can be minimized by data transformation prior to further analysis. The most commonly observed effects are revealed by viewing scatter plots of the logarithm of the ratio by the average logarithmic intensity of the two color channels (RI plots). In this paper we present a general model for signal intensity data with multiple error sources. We demonstrate how these sources of error influence the shape of an RI plot. We then compare some currently available transformation strategies in terms of their mechanism and performance on both simulated and real microarray data. A linlog transformation is proposed to stabilize the variance of the log ratios. We also propose a regional smoothing method to remove variation in log ratios due to spatial heterogeneity on the microarray surface. The discussed transformations represent an important initial step in microarray data analysis for both ratio-based and ANOVA methods.
Stat Appl Genet Mol Biol 2003
PMID:Transformations for cDNA microarray data. 1664 82

In the exploding field of gene expression techniques such as DNA microarrays, there are still few general probabilistic methods for analysis of variance. Linear models and ANOVA are heavily used tools in many other disciplines of scientific research. The usual F-statistic is unsatisfactory for microarray data, which explore many thousand genes in parallel, with few replicates. We present three potential one-way ANOVA statistics in a parametric statistical framework. The aim is to separate genes that are differently regulated across several treatment conditions from those with equal regulation. The statistics have different features and are evaluated using both real and simulated data. Our statistic B1 generally shows the best performance, and is extended for use in an algorithm that groups cell lines by equal expression levels for each gene. An extension is also outlined for more general ANOVA tests including several factors. The methods presented are implemented in the freely available statistical language R. They are available at http://www.math.uu.se/staff/pages/?uname=ingrid.
Stat Appl Genet Mol Biol 2005
PMID:Empirical bayes microarray ANOVA and grouping cell lines by equal expression levels. 1664 60

The American Women's Health Initiative study published in July 2002 caused considerable concern among hormone replacement therapy (HRT) users and prescribers in many countries. This study is an exploratory research comparing the genome-wide expression profile in whole-blood samples according to HRT use. Within the Norwegian Women and Cancer study, 100 postmenopausal women (50 HRT users and 50 non-HRT users) born between 1943 and 1949 with normal to high body mass index and no other medication use were selected. After total RNA extraction, amplification, and labeling, the samples were hybridized together with a common reference (Universal human reference RNA, Stratagen) to Agilent Human 1A oligoarrays (G4110b, Agilent Technologies) containing 20,173 unique genes. Differentially expressed genes were used to build a classifier using the nearest shrunken centroid method (PAM). Then, we tested the significant changes in single genes by different methods like t test, Significance Analysis of Microarrays, and Bayesian ANOVA analysis. Results did not reveal any distinct gene list which predicted accurately HRT exposure (error rate, 0.40). Classifier performance slightly improved (error rate, 0.26) including only women who were using continuous combined HRT treatment. According to the small amplitude of expression alterations observed in whole blood, more quantitative technique and larger sample sizes will be needed to be able to investigate whether significant single genes are differentially expressed in HRT versus non-HRT users. Taken cautiously, significant enrichments in biological process of genes with small changes after HRT use were observed (e.g., receptor and transporter activities, immune response, frizzled signaling pathway, actin filament organization, and glycogen metabolism).
Mol Cancer Ther 2006 Apr
PMID:Gene expression profiling of whole-blood samples from women exposed to hormone replacement therapy. 1664 56

Pericryptal fibroblasts (PFs), a class of myofibroblasts, have strongly been implicated in the regulation of villous structure because of their location close to crypts and their ability to secrete cytokines affecting intestinal epithelial cell proliferation and differentiation. Recently, mast cells (MCs) have also been involved in the homeostasis of villous architecture. As myofibroblasts arise in a wide variety of settings concurrently with a local increase in the number of tissue MCs, we calculated in this study the density of both PF and distinct pericryptal MC phenotypes in the mucosa of human duodenum showing normal, defective, or atrophic villous profiles. In addition, we evaluated the statistical association between PF-MC densities and each pattern of villous architecture. Finally, we correlated the density of PF with the density of pericryptal MC phenotypes. For this purpose, samples taken by endoscopy from 30 patients complaining of inflammatory bowel disorders were studied by immunohistochemistry. The densities of alpha-smooth muscle actin-positive PFs as well as tryptase-, chymase-, and c-kit-positive MCs were determined in the crypt lamina propria. Villous architecture was found to be significantly associated with the number of PFs and tryptase-, chymase-, c-kit-positive MCs in the lamina propria (ANOVA group effect P < 0.001). High density of both PFs and MCs was found in intestinal samples with normal villous morphology while lower densities were associated with defective or atrophic villous profiles (Tukey's test for multiple comparison P < 0.001). In addition, a significant correlation was found between PF density and the density of each pericryptal MC phenotype (vs. tryptase-positive MCs, r = 0.913; vs. chymase-positive MC, r = 0.905; vs. c-kit-positive MC, r = 0.927; P < 0.001 in all cases). This study provides morphological support for an important cooperation between PFs and MCs in maintaining normal villous architecture.
Anat Rec A Discov Mol Cell Evol Biol 2006 Jun
PMID:Number of pericryptal fibroblasts correlates with density of distinct mast cell phenotypes in the crypt lamina propria of human duodenum: implications for the homeostasis of villous architecture. 1665 53

A substantial increase in NADH production, arising from accelerated glycolysis, occurs in cardiac hypertrophy and this raises the question of how the NADH is oxidised. We have addressed this problem by reconstructing appropriate mitochondrial shuttles in vitro, using mitochondria from the left ventricles of both normotensive and spontaneously hypertensive rats at 5 and 24 weeks of age as model systems for left ventricle hypertrophy and hypertrophy/hypertension respectively. We found that most NADH oxidation occurs via a novel malate/oxaloacetate shuttle, the activity of which increases with time and with the progression of hypertrophy and development of hypertension as judged by statistical ANOVA analysis. In contrast, alpha-glycerol-phosphate and the malate/aspartate shuttles were shown to make only a minor contribution to NADH oxidation in a manner essentially independent of age and progression of hypertrophy/hypertension. The rate of malate transport in exchange with oxaloacetate proved to limit the rate of NADH oxidation via this malate/oxaloacetate shuttle.
Int J Mol Med 2006 Jul
PMID:Mitochondria from the left heart ventricles of both normotensive and spontaneously hypertensive rats oxidize externally added NADH mostly via a novel malate/oxaloacetate shuttle as reconstructed in vitro. 1678 70


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