Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.

The completion of the Arabidopsis thaliana genome sequence allows a comparative analysis of transcriptional regulators across the three eukaryotic kingdoms. Arabidopsis dedicates over 5% of its genome to code for more than 1500 transcription factors, about 45% of which are from families specific to plants. Arabidopsis transcription factors that belong to families common to all eukaryotes do not share significant similarity with those of the other kingdoms beyond the conserved DNA binding domains, many of which have been arranged in combinations specific to each lineage. The genome-wide comparison reveals the evolutionary generation of diversity in the regulation of transcription.

EMAAS: an extensible grid-based rich internet application for microarray data analysis and management.

BACKGROUND: Microarray experimentation requires the application of complex analysis methods as well as the use of non-trivial computer technologies to manage the resultant large data sets. This, together with the proliferation of tools and techniques for microarray data analysis, makes it very challenging for a laboratory scientist to keep up-to-date with the latest developments in this field. Our aim was to develop a distributed e-support system for microarray data analysis and management. RESULTS: EMAAS (Extensible MicroArray Analysis System) is a multi-user rich internet application (RIA) providing simple, robust access to up-to-date resources for microarray data storage and analysis, combined with integrated tools to optimise real time user support and training. The system leverages the power of distributed computing to perform microarray analyses, and provides seamless access to resources located at various remote facilities. The EMAAS framework allows users to import microarray data from several sources to an underlying database, to pre-process, quality assess and analyse the data, to perform functional analyses, and to track data analysis steps, all through a single easy to use web portal. This interface offers distance support to users both in the form of video tutorials and via live screen feeds using the web conferencing tool EVO. A number of analysis packages, including R-Bioconductor and Affymetrix Power Tools have been integrated on the server side and are available programmatically through the Postgres-PLR library or on grid compute clusters. Integrated distributed resources include the functional annotation tool DAVID, GeneCards and the microarray data repositories GEO, CELSIUS and MiMiR. EMAAS currently supports analysis of Affymetrix 3' and Exon expression arrays, and the system is extensible to cater for other microarray and transcriptomic platforms. CONCLUSION: EMAAS enables users to track and perform microarray data management and analysis tasks through a single easy-to-use web application. The system architecture is flexible and scalable to allow new array types, analysis algorithms and tools to be added with relative ease and to cope with large increases in data volume.

Hormonal characteristics of the human menstrual cycle throughout reproductive life.

The changes in serum levels of luteinizing hormone (LH), follicle-stimulating hormone (FHS), estradiol, and progesterone that occur both early and late in reproductive life were characterized and compared with findings in young, normal women and in patients with certain menstrual disorders. A total of 50 complete menstrual cycles in 37 were examined. Five distinct patterns of hormonal regulation were found, three of which are reported here: (a) A long follicular phase and delayed follicular maturation in young women with long, unpredictable intermenstrual intervals from menarche; (b) a short follicular phase with increasing age and in short cycles in perimenopausal women; and (c) true anovulatory vaginal bleeding in long cycles in perimenopausal women. The short cycles before and during the menopausal transition were found to have lower E2 levels and high FSH concentrations throughout, while LH remained in the normal range. During long cycles in perimenopausal women, concentrations of LH and FSH were in the menopausal range. However, follicular maturation was observed months after high levels of gonadotropins were attained. These studies permit the characterization of the menstrual history of the normal woman in terms of the hormonal changes that occur and provide a basis for the definition of several disorders of follicular maturation.

Proinsulin-like component of circulating insulin in the basal state and in patients and hamsters with islet cell tumors.

The proinsulin-like component comprised approximately 20% of total circulating basal immunoreactive insulin in 15 patients without islet cell tumors. 15 min after oral glucose, the concentration of the proinsulin-like component was unchanged and its percentage of the total immunoreactive insulin decreased with the acute release of the insulin component. By 2 hr after oral glucose, the concentration of the proinsulin-like component increased and the insulin component concentration decreased so that the percentage of the proinsulin-like component was essentially the same as in the basal state. In five patients with islet cell tumors and fasting hypoglycemia, basal proinsulin-like component ranged from 26 to 79% of the total immunoreactive insulin. While basal proinsulin-like component was higher in the islet cell tumor patients, the fluctuations after stimulation were qualitatively similar to the nontumor patients. Acute stimulation with glucose, tolbutamide, leucine, and streptozotocin mainly released the insulin component resulting in a fall in the per cent proinsulin-like component with a subsequent increase in percentage of this component as the total insulin concentration returns towards basal levels. Three islet-cell tumor patients with less than 46% proinsulin-like component had favorable therapeutic responses to diazoxide whereas one patient with over 80% proinsulin-like component was completely refractory. Syrian hamsters bearing islet cell tumors provided an excellent model for islet cell tumors in man. These animals have a high proportion of a proinsulin-like component in plasma; stimulation of tumor slices in vitro with tolbutamide and glucagon releases mainly the insulin component similar to the observations in man. These studies suggest that the mechanisms regulating the release of the proinsulin-like and of the insulin components are different.

Circulating insulin: th proinsulin-like properties of "big" insulin in patients withou islet cell tumors.

When plasma is filtered on Sephadex G-50, insulin immunoreactivity is recovered in two peaks. "Big" insulin, the higher molecular weight component, and "little" insulin, the lower molecular weight component, have elution volumes that correspond to those of proinsulin-(125)I and insulin-(125)I respectively. When plasma was extracted with acid ethanol and filtered in 1.0 M acetic acid, the patterns and proportions of "big" and "little" insulin were indistinguishable from those obtained by filtration of whole plasma in neutral buffer. When "big" insulin was isolated from plasma and mixed with a tracer of porcine proinsulin-(125)I, trypsin converted the "big" insulin immunoreactivity to the gel filtration pattern of "little" insulin in the same way that it converted the proinsulin radioactivity. More than 90% of both "big" insulin and proinsulin were converted at optimal trypsin concentrations. Our present guinea pig anti-insulin serum failed to distinguish "big" from "little" but a porcine proinsulin anti-serum, under appropriate conditions of assay, reacted strongly with "big" insulin but not at all with "little." When tested on isolated fat cells, "little" insulin had the same bioactivity as porcine insulin, whereas "big" insulin had the same low activity as porcine proinsulin. These studies suggest that "big" insulin represents either single-chain proinsulin and/or a proinsulin intermediate that has similar low bioactivity.

Endocrine consequences of continuous antiestrogen therapy with tamoxifen in premenopausal women.

Daily administration of estrogen antagonists to premenopausal women has been incorporated into the adjuvant treatment of breast cancer. We have studied the changes in reproductive hormones, pituitary responses to hypothalamic-releasing hormones, and endometrial histology during treatment with the antiestrogen tamoxifen in five healthy, premenopausal women. These studies were carried out during one menstrual cycle before and during two cycles of antiestrogen treatment. All subjects continued to have regular menses with biphasic basal body temperature records. During treatment, estradiol (E2) levels were increased but followed the usual pattern reflecting follicular maturation and corpus luteum formation. The mean E2 concentration at the midcycle peak and during the luteal phase was twice that observed during the non-treatment cycle. By contrast, the concentrations and secretory patterns of luteinizing hormone and follicle-stimulating hormone were not greatly changed, and the gonadotropin responses to gonadotropin-releasing hormone were not suppressed. Endometrial biopsies obtained during the follicular phase of control and tamoxifen treatment cycles showed no differences whereas biopsies obtained during the luteal phase of tamoxifen cycles uniformly showed a lack of changes attributed to progesterone action with no progression of histologic changes beyond those expected on day 7-8 of the luteal phase. These observations are consistent with maturation of multiple ovarian follicles, a surprising finding considering the normal gonadotropin concentrations. The retarded development of the endometrium in the presence of supranormal serum E2 and progesterone concentrations is a morphologic demonstration of the antiprogestational effect of antiestrogens. The lack of gonadotropin suppression in the presence of hyperestrogenemia suggests a major antiestrogen action on the hypothalmus and pituitary gland.

PIP: Administration of antiestrogen has recently been incorporated into the management of breast cancer. To explore the endocrine consequences of this therapy 5 healthy premenopausal volunteers were observed and treated with daily administration of the antiestrogen Tamoxifen. During the treatment period all subjects continued to have regular menses and basal body temperature; estradiol (E2) levels increased but followed a regular pattern, and its concentration at midcycle and during the luteal phase were twice as high as during nontreatment. On the other hand, concentrations of LH and of ESH were not greatly changed. In the presence of higher concentrations of E2 and of progesterone the endometrium showed a retarded development, thus demonstrating the antiprogestational effect of Tamoxifen. The lack of gonadotropin suppression also suggests a major antiestrogen action on the hypotalamus and pituitary glands.

Cyclic ovarian function and breast cancer.

We postulated previously that systematic differences in menstrual cycle length and/or variability might be used as indicators of underlying hormonal abnormalities that could help explain the endocrine biology of some breast cancer risk factors. In the present study, we prospectively and retrospectively analyzed menstrual cycle patterns in breast cancer cases and controls in two populations. No significant differences were found. This and previous studies emphasize that contemporary women have a long reproductive experience characterized by uninterrupted, regular menses, which is a condition of maximum ovulation potential and which contributes to estrogen stimulation over time.

Menstrual cycle patterns and breast cancer risk factors.

Using a data set of women who longitudinally recorded menstrual and reproductive events, we examined menstrual cycle characteristics in relationship to early and late menarche, early and late menopause, and deferred parity, three variables epidemiologically related to breast cancer incidence. Women with late onset of menarche had longer and more variable cycles in the 10 years after menarche than did those with early onset. Women with late onset of menopause had longer and more variable cycles in the premenopausal interval than did those with early onset. Cumulative fertility in women after marriage did not differ according to cycle length and variance. Late menopause may be a breast cancer risk factor due to relative estrogen excess and progesterone lack as reflected in longer, more varied cycle patterns. Observed cycle differences between women with early and late menarche await further study of the endocrine physiology of the menstrual cycle in those groups.

A consensus map for loblolly pine (Pinus taeda L.). I. Construction and integration of individual linkage maps from two outbred three-generation pedigrees.

A consensus map for loblolly pine (Pinus taeda L.) was constructed from the integration of linkage data from two unrelated three-generation outbred pedigrees. The progeny segregation data from restriction fragment length polymorphism, random amplified polymorphic DNA, and isozyme genetic markers from each pedigree were recoded to reflect the two independent populations of parental meioses, and genetic maps were constructed to represent each parent. The rate of meiotic recombination was significantly greater for males than females, as was the average estimate of genome length for males (1983.7 cM [Kosambi mapping function (K)]) and females [1339.5 cM(K)]. The integration of individual maps allows for the synthesis of genetic information from independent sources onto a single consensus map and facilitates the consolidation of linkage groups to represent the chromosomes n = 12 of loblolly pine. The resulting consensus map consists of 357 unique molecular markers and covers approximately 1300 cM(K).

Identification of quantitative trait loci influencing wood specific gravity in an outbred pedigree of loblolly pine.

We report the identification of quantitative trait loci (QTL) influencing wood specific gravity (WSG) in an outbred pedigree of loblolly pine (Pinus taeda L.). QTL mapping in an outcrossing species is complicated by the presence of multiple alleles (> 2) at QTL and marker loci. Multiple alleles at QTL allow the examination of interaction among alleles at QTL (deviation from additive gene action). Restriction fragment length polymorphism (RFLP) marker genotypes and wood specific gravity phenotypes were determined for 177 progeny. Two RFLP linkage maps were constructed, representing maternal and paternal parent gamete segregations as inferred from diploid progeny RFLP genotypes. RFLP loci segregating for multiple alleles were vital for aligning the two maps. Each RFLP locus was assayed for cosegregation with WSG QTL using analysis of variance (ANOVA). Five regions of the genome contained one or more RFLP loci showing differences in mean WSG at or below the P = 0.05 level for progeny as grouped by RFLP genotype. One region contained a marker locus (S6a) whose QTL-associated effects were highly significant (P > 0.0002). Marker S6a segregated for multiple alleles, a prerequisite for determining the number of alleles segregating at the linked QTL and analyzing the interactions among QTL alleles. The QTL associated with marker S6a appeared to be segregating for multiple alleles which interacted with each other and with environments. No evidence for digenic epistasis was found among the five QTL.

Gonadotropin response to LH-RH in anorexia nervosa.

The gonadotropin-ovary axis of patients with anorexia nervosa was assessed with the aim of distinguishing between an intrinsically hypophysial deficiency and pituitary malfunction secondary to hypothalamic impairment. The most consistent endocrine abnormality was low serum luteinizing and follicle stimulating hormone (LH and FSH) levels associated with depressed serum estradiol levels. Gonadotropin levels responded to luteinizing hormone-releasing hormone (LH-RH), thus indicating a primarily hypothalamic dysfunction. The increase in serum FSH was at least as great as that of LH. The LH levels were additionally depressed and their increase after LH-RH injection somewhat blunted by three-day treatment with ethinyl estradiol.

Circadian analysis of plasma cortisol levels before and after dexamethasone administration in depressed patients.

Pituitary-adrenal regulation in healthy subjects and in depressed patients is very dynamic. Interpretation of results of the 1-mg dexamethasone suppression test has usually depended on the result of a single blood cortisol level measurement obtained in the morning or afternoon. We analyzed circulating cortisol concentrations by obtaining blood samples at 20-minute intervals for 24 hours before and after dexamethasone administration in depressed patients. The results illustrate the variability in patterns of escape from the effects of dexamethasone among depressed patients; they also indicate the influence of the sampling time on the test results and thus on the relationship of the test result to various clinical classifications. Finally, these results provide the basis for understanding the consequences of alternative sampling strategies.

Hypothalamic-pituitary-adrenal axis activity in depressive illness. Its relationship to classification.

Serum cortisol response to the 1-mg overnight dexamethasone suppression test was studied in 221 depressed patients and 109 nondepressed psychiatric controls. Nonsuppression distinguished patients with primary unipolar depression (65/146) from patients with secondary unipolar depression (0/42) and nondepressed controls (0/109). Furthermore, nonsuppression distinguished the three familial subtypes of primary unipolar depressive illness: familial pure depressive disease (FPDD; 38/50 patients), sporadic depressive disease (SDD; 24/55 patients), and depression spectrum disease (3/41 patients). Moderate elevations in baseline serum cortisol levels were found in FPDD, SDD, and bipolar depression. Medication did not affect the results. The data suggest that the depressive syndrome is composed of separate illnesses, each of which has a distinctive pattern of hypothalamic-pituitary-adrenal axis activity during the depressed state as well as a specific clinical and familial psychiatric history.

Pituitary-adrenal axis rhythm disturbances in psychiatric depression.

We studied disturbances in the circadian pattern of plasma corticotropin and cortisol concentrations in 25 depressed patients (eight dexamethasone suppression test [DST] nonsuppressors and 17 suppressors) and 21 normal control subjects. Blood samples were drawn every 20 minutes for 24 hours before the administration of dexamethasone, and for a second 24 hours after the administration of 1 mg of dexamethasone. The corticotropin and cortisol level rhythms were examined using three different statistical methods. Nonsuppressors averaged greater elevations in plasma cortisol and corticotropin levels than did subjects in the other two groups, both before and after administration of the dexamethasone. The cortisol levels of the suppressors were virtually identical to those of the control subjects. However, the suppressors had significant elevations of corticotropin levels compared with normal control subjects, especially on the day before taking dexamethasone. Before taking dexamethasone, the depressed patients reached a daily nadir of cortisol concentration approximately two hours earlier than did the normal control subjects. The DST nonsuppressors also exhibited a blunting in the expected circadian rhythm of the corticotropin level.

Differentiation of depressive subtypes by insulin insensitivity in the recovered phase.

The glucose response to a standard insulin tolerance test (ITT) has been reported to be blunted in the acute phase of heterogeneous depressive disorders and to be normal in the recovered phase. We studied the glucose response to ITT in the recovered phase depression in patients who had previously been subclassified according to familial and clinical characteristics. All patients with depressive spectrum disease had an adequate glucose response to the ITT, whereas only 40% of patients with familial pure depressive disease and 56% of patients with bipolar illness had an adequate hypoglycemic response. There was also a trend toward a decrease in insulin sensitivity in patients who had been nonsuppressors to dexamethasone when depressed. These findings suggest that the glucose response to ITT may be a useful tool in differentiating among the heterogeneous depressive disorders.

Synthesis, characterization, and water oxidation by a molecular chromophore-catalyst assembly prepared by atomic layer deposition. The "mummy" strategy.

A new strategy for preparing spatially-controlled, multi-component films consisting of molecular light absorbing chromophores and water oxidation catalysts on high surface area, mesoporous metal oxide surfaces is described. Atomic layer deposition (ALD) is used to embed a surface-bound chromophore in a thin layer of inert Al2O3, followed by catalyst binding to the new oxide surface. In a final step, catalyst surface-binding is stabilized by a subsequent ALD overlayer of Al2O3. The ALD assembly procedure bypasses synthetic difficulties arising from the preparation of phosphonic acid derivatized, covalently-linked assemblies. An ALD mummy-based assembly has been used to demonstrate photoelectrochemical dehydrogenation of hydroquinone. Electrocatalytic water oxidation at pH 8.8 is observed over a 2 hour electrolysis period and light-assisted water oxidation over a 6 hour photolysis period with O2 detected with a generator-collector electrode configuration.

Sympathectomy, which induces membranous bone remodeling, has no effect on endochondral long bone remodeling in vivo.

Sympathectomy has been shown to induce resorption within the membranous middle ear bone of gerbils. It is unknown whether sympathectomy exerts a similar effect on endochondral long bone. In the present study, guanethidine sulfate (GS) and 6-hydroxydopamine (HDA) were administered to gerbils to induce sympathectomy. One week later, samples of middle ear bulla bone and radial long bone were harvested and assessed for osteoclastic activity. Histomorphometric analysis showed both pharmacologic sympathectomy with GS and chemical sympathectomy with HDA significantly increased the osteoclast counts and osteoclast surfaces of bulla bone samples but not radial long bone samples, respectively. In contrast, HDA but not GS increased the osteoclast profile area of both long bone and membranous bone samples when compared with vehicle-treated controls. Sympathectomy, induced both chemically and pharmacologically, thus has been shown to increase resorption in membranous bone but not endochondral long bone in the gerbilline model.

Regulation of lactogenic hormone binding in rat liver by steroid hormones.

We have measured the effects of testosterone propionate, medroxy-progesterone acetate and cortisol on the binding of ovine [125I]iodoprolactin to 100,000 X g particulate fractions from liver of normal and estrogen-treated female rats. In untreated animals 6.7 +/- 1.1% (SD) of the radioactivity added to 0.5 mg of membrane protein was specifically bound to the hormone receptor. Specific binding was significantly (P less than .05) decreased after 7 daily doses of testosterone (1.0 mg) to 2.8 +/- 1.4%, medroxyprogesterone (0.25 mg) to 2.7 +/- 0.2% and cortisol (5.0 mg) to 3.1 +/- 1.3%. The serum prolactin concentration, 4.2 +/- 3.4 ng/ml in normal animals, was not affected by the hormone treatment. Ethinyl estradiol, 10 mug/day for 7 days, increasing the binding of [125I]iodo-prolactin to 16.6 +/- 6.0% and increased serum prolactin to 50.6 +/- 11.5 ng/ml. Simultaneous administration of testosterone, medroxyprogesterone or cortisol with estradiol did not diminish the estradiol-induced increase in serum prolactin, but completely prevented the increase in prolactin binding. Testosterone or cortisol given to animals pretreated with estradiol suppressed prolactin binding from 16.4 +/- 4.2% to less than 2.5% after 48-72 h. Parellel results were obtained with 125I labeled human growth hormone whereas 125I labeled-insulin binding was not affected by these treatments. Scatchard analysis showed that the decrease in lactogenic hormone binding was due to a reduced concentration of receptors with no significant change in affinity. Since serum levels of prolactin were not changed, we conclude that treatment with testosterone, medroxyprogesterone, and cortisol decreased lactogenic hormone binding by a direct action on the liver.