vissE: a versatile tool to identify and visualise higher-order molecular phenotypes from functional enrichment analysis

Functional analysis of high throughput experiments using pathway analysis is now ubiquitous. Though powerful, these methods often produce thousands of redundant results owing to knowledgebase redundancies upstream. This scale of results hinders extensive exploration by biologists and can lead to investigator biases due to previous knowledge and expectations. To address this issue, we present vissE, a flexible network-based analysis and visualisation tool that organises information into semantic categories and provides various visualisation modules to characterise them with respect to the underlying data, thus providing a comprehensive view of the biological system. We demonstrate vissE's versatility by applying it to three different technologies: bulk, single-cell and spatial transcriptomics. Applying vissE to a factor analysis of a breast cancer spatial transcriptomic data, we identified stromal phenotypes that support tumour dissemination. Its adaptability allows vissE to enhance all existing gene-set enrichment and pathway analysis workflows, empowering biologists during molecular discovery.

Basonuclin-2 regulates extracellular matrix production and degradation

Epithelial-mesenchymal transition is essential for tissue patterning and organization. It involves both regulation of cell motility and alterations in the composition and organization of the ECM-a complex environment of proteoglycans and fibrous proteins essential for tissue homeostasis, signaling in response to chemical and biomechanical stimuli, and is often dysregulated under conditions such as cancer, fibrosis, and chronic wounds. Here, we demonstrate that basonuclin-2 (BNC2), a mesenchymal-expressed gene, that is, strongly associated with cancer and developmental defects across genome-wide association studies, is a novel regulator of ECM composition and degradation. We find that at endogenous levels, BNC2 controls the expression of specific collagens, matrix metalloproteases, and other matrisomal components in breast cancer cells, and in fibroblasts that are primarily responsible for the production and processing of the ECM within the tumour microenvironment. In so doing, BNC2 modulates the motile and invasive properties of cancers, which likely explains the association of high BNC2 expression with increasing cancer grade and poor patient prognosis.

Single-cell RNA sequencing captures patient-level heterogeneity and associated molecular phenotypes in breast cancer pleural effusions

BACKGROUND

Malignant pleural effusions (MPEs) are a common complication of advanced cancers, particularly those adjacent to the pleura, such as lung and breast cancer. The pathophysiology of MPE formation remains poorly understood, and although MPEs are routinely used for the diagnosis of breast cancer patients, their composition and biology are poorly understood. It is difficult to distinguish invading malignant cells from resident mesothelial cells and to identify the directionality of interactions between these populations in the pleura. There is a need to characterize the phenotypic diversity of breast cancer cell populations in the pleural microenvironment, and investigate how this varies across patients.

METHODS

Here, we used single-cell RNA-sequencing to study the heterogeneity of 10 MPEs from seven metastatic breast cancer patients, including three Miltenyi-enriched samples using a negative selection approach. This dataset of almost 65 000 cells was analysed using integrative approaches to compare heterogeneous cell populations and phenotypes.

RESULTS

We identified substantial inter-patient heterogeneity in the composition of cell types (including malignant, mesothelial and immune cell populations), in expression of subtype-specific gene signatures and in copy number aberration patterns, that captured variability across breast cancer cell populations. Within individual MPEs, we distinguished mesothelial cell populations from malignant cells using key markers, the presence of breast cancer subtype expression patterns and copy number aberration patterns. We also identified pleural mesothelial cells expressing a cancer-associated fibroblast-like transcriptomic program that may support cancer growth.

CONCLUSIONS

Our dataset presents the first unbiased assessment of breast cancer-associated MPEs at a single cell resolution, providing the community with a valuable resource for the study of MPEs. Our work highlights the molecular and cellular diversity captured in MPEs and motivates the potential use of these clinically relevant biopsies in the development of targeted therapeutics for patients with advanced breast cancer.

The site of breast cancer metastases dictates their clonal composition and reversible transcriptomic profile

Intratumoral heterogeneity is a driver of breast cancer progression, but the nature of the clonal interactive network involved in this process remains unclear. Here, we optimized the use of optical barcoding to visualize and characterize 31 cancer subclones in vivo. By mapping the clonal composition of thousands of metastases in two clinically relevant sites, the lungs and liver, we found that metastases were highly polyclonal in lungs but not in the liver. Furthermore, the transcriptome of the subclones varied according to their metastatic niche. We also identified a reversible niche-driven signature that was conserved in lung and liver metastases collected during patient autopsies. Among this signature, we found that the tumor necrosis factor-α pathway was up-regulated in lung compared to liver metastases, and inhibition of this pathway affected metastasis diversity. These results highlight that the cellular and molecular heterogeneity observed in metastases is largely dictated by the tumor microenvironment.

Measuring and Modelling the Epithelial- Mesenchymal Hybrid State in Cancer: Clinical Implications

The epithelial-mesenchymal (E/M) hybrid state has emerged as an important mediator of elements of cancer progression, facilitated by epithelial mesenchymal plasticity (EMP). We review here evidence for the presence, prognostic significance, and therapeutic potential of the E/M hybrid state in carcinoma. We further assess modelling predictions and validation studies to demonstrate stabilised E/M hybrid states along the spectrum of EMP, as well as computational approaches for characterising and quantifying EMP phenotypes, with particular attention to the emerging realm of single-cell approaches through RNA sequencing and protein-based techniques.

Extensive transcriptional responses are co-ordinated by microRNAs as revealed by Exon-Intron Split Analysis (EISA)

Epithelial-mesenchymal transition (EMT) has been a subject of intense scrutiny as it facilitates metastasis and alters drug sensitivity. Although EMT-regulatory roles for numerous miRNAs and transcription factors are known, their functions can be difficult to disentangle, in part due to the difficulty in identifying direct miRNA targets from complex datasets and in deciding how to incorporate 'indirect' miRNA effects that may, or may not, represent biologically relevant information. To better understand how miRNAs exert effects throughout the transcriptome during EMT, we employed Exon-Intron Split Analysis (EISA), a bioinformatic technique that separates transcriptional and post-transcriptional effects through the separate analysis of RNA-Seq reads mapping to exons and introns. We find that in response to the manipulation of miRNAs, a major effect on gene expression is transcriptional. We also find extensive co-ordination of transcriptional and post-transcriptional regulatory mechanisms during both EMT and mesenchymal to epithelial transition (MET) in response to TGF-β or miR-200c respectively. The prominent transcriptional influence of miRNAs was also observed in other datasets where miRNA levels were perturbed. This work cautions against a narrow approach that is limited to the analysis of direct targets, and demonstrates the utility of EISA to examine complex regulatory networks involving both transcriptional and post-transcriptional mechanisms.

CBED contrast in the lower order Laue zone

Contrast in a systematic arrangement of lower order Laue zone (LOLZ) beams is reported and analysed using a Bloch wave description. Observations are reported for hexagonal barium ruthenium zirconate (Ba4Ru3ZrO12) and barium ruthenium titanate (Ba3Ti2RuO9), both near the c-axis orientation. The specific scattering dynamics invoked by this diffraction geometry may have novel uses in the exploration of crystallographic parameters.

Energetics of nanocrystalline TiO2

The energetics of the TiO(2) polymorphs (rutile, anatase, and brookite) were studied by high temperature oxide melt drop solution calorimetry. Relative to bulk rutile, bulk brookite is 0.71 +/- 0.38 kJ/mol (6) and bulk anatase is 2.61 +/- 0.41 kJ/mol higher in enthalpy. The surface enthalpies of rutile, brookite, and anatase are 2.2 +/- 0.2 J/m(2), 1.0 +/- 0.2 J/m(2), and 0.4 +/- 0.1 J/m(2), respectively. The closely balanced energetics directly confirm the crossover in stability of nanophase polymorphs inferred by Zhang and Banfield (7). An amorphous sample with surface area of 34,600 m(2)/mol is 24.25 +/- 0.88 kJ/mol higher in enthalpy than bulk rutile.

The human mineralocorticoid receptor gene promoter: its structure and expression

The structure and expression of a clone containing the promoter region, all of exon 1, and part of the first intron of the human mineralocorticoid receptor (hMR) gene is presented. The clone has three sets of CAAT and TATA elements, one located at the very 5'-end of the clone, one located just 5'- to the start of transcription, and one set located in intron A, approximately 300 bp into the intron. The major start of transcription site by primer extension analysis and ribonuclease protection assays is located 26 bp downstream of a TATA-like box (TTTAA) and 90 and 143 bp downstream, respectively, of two CCAAT boxes. Putative cis-transcription factor binding sites are as follows: two potential AP1 sites, one potential AP2 site, two ATF/CREB sites, six potential GC boxes or SP1 sites, one potential perfect half-palindromic estrogen response element, and three potential PEA3 sites. Therefore, the hMR promoter region contains elements characteristic of both regulated genes and "housekeeping" genes. CAT assays of overlapping deletions of the promoter region demonstrated tissue-specific regulation in human neuroepithelioma (SK-N-MC-IXC) and non-neuronal, peripheral choriocarcinoma cell lines (JEG-3).

Solid state NMR characterisation of crystalline Na2O-ZrO2-SiO2 phases

The NMR interactions of crystalline phases in the system Na2O-ZrO2-SiO2 have been studied by a combination of static and magic angle spinning NMR methods for the first time. A full multinuclear (17O, 23Na, 29Si and 91Zr) approach has been employed that allows the phases to be clearly identified. NMR interactions such as 29Si isotropic chemical shift correlate with the known structural units present. For 23Na the the different sites can often be distinguished on the basis of differing quadrupolar interactions.

17O magic-angle spinning nuclear magnetic resonance of CaCO3

The first 17O magic-angle spinning nuclear magnetic resonance (MAS-NMR) from a carbonate ion in an inorganic compound is reported. The 17O MAS centreband of CaCO3 can be simulated with parameters CQ = 6.97 MHz, eta approximately 1 and an isotropic chemical shift of 204 ppm.

Structural characterisation of Na2ZrO3

A combination of X-ray and electron diffraction, electron microscopy and solid-state nuclear magnetic resonance (NMR) has been used to elucidate the structure and the ordering of Na2ZrO3. The diffraction data confirm a monoclinic crystal structure. A sample prepared by a conventional solid-state reaction of the components is shown by both X-ray diffraction and electron microscope imaging to have an extremely high concentration of planar defects associated with stacking disorder of the planes along the c-axis. The incidence of these defects is significantly reduced in a sample recrystallised from a bismuth oxide flux. NMR indicates that the local coordinations are well defined in both samples but with some sharpening of the spectra from the recrystallised sample indicative of the increase of long-range order. The 23Na magic angle spinning (MAS) NMR spectra clearly show three distinct sites with widely differing quadrupolar interaction parameters that can be related to the known site symmetries. Two distinct oxygen resonances are observed in the MAS NMR spectrum from an 17O-enriched sample while the static 91Zr NMR spectrum can be simulated with one set of interaction parameters.

Differential mineralocorticoid (type 1) and glucocorticoid (type 2) receptor expression in Lewis and Fischer rats

Lewis (LEW/N) and Fischer (F344/N) rats represent two extremes of the spectrum of corticosterone responses to stressful stimuli, from the chronical hyporesponsiveness of LEW/N to the chronical hyperresponsiveness of F344/N. It might be expected that the amount of mineralocorticoid receptor (MR) and glucocorticoid receptor (GR) binding, and the levels of their corresponding mRNAs in various tissues in LEW/N and F344/N rats might reflect the overall integrated levels of corticosterone to which these receptors have been exposed. We have found that while the binding affinity (Kd) of MR and GR varies between tissues, there was no strain difference in any tissue. Receptor binding number (Bmax), however, varied not only between tissues, but also between strains. MR Bmax in the hippocampus and pituitary was lower in LEW/N than in F344/N, whereas the GR Bmax in the LEW/N thymus was greater than that found in F344/N rats. The hippocampal levels of MR mRNAs in Adx LEW/N and F344/N rats were in good agreement with, and paralleled, the functional levels of these receptors as determined by binding assays. On the other hand, the number of hippocampal GR binding sites and the level of GR nRNA while similar were not identical in the two strains: the hippocampal GR Bmax did not differ between strains, while the hippocampal GR mRNA level was slightly, but significantly, lower in Adx LEW/N compared to F344/N rats.

Schizophrenic deficits: neuroleptics and the prefrontal cortex

Modern techniques have been applied to brain modeling, based on recent approaches in the artificial intelligence field that use brain-like "connectionistic" computational architectures. The model proposed by Cohen and Servan-Schreiber uses a gain parameter which they identify with dopamine function. They apply their model to neuroleptically treated schizophrenia patients who show improved task performance which they link to increased dopamine function and increased gain in the prefrontal cortex. However, evidence indicates that antipsychotic medications block dopamine (especially D2) receptors, decreasing mesolimbic and mesocortical dopamine function. If therapeutic dosages of neuroleptics diminish dopamine function, this would decrease gain in context modules needed for adequate task performance. Schizophrenia patients would perform more poorly by further reducing gain in their already compromised context modules. The current investigators suggest three possible ways to resolve this difficulty, to explain why normals perform more poorly when taking neuroleptics, although acute schizophrenia patients' performance may be enhanced in several areas. Evidence would suggest that multiple processes occur simultaneously in neuroleptically treated patients with some processes counterbalancing others.

Effects of the glucocorticoid antagonist RU 486 on pituitary-adrenal function in patients with anorexia nervosa and healthy volunteers: enhancement of plasma ACTH and cortisol secretion in underweight patients

To further explore whether the hypercortisolism of anorexia nervosa reflects an alteration in the set point for corticotropin-releasing hormone (CRH) secretion or is a manifestation of glucocorticoid resistance, we examined plasma ACTH and cortisol responses to the competitive glucocorticoid antagonist RU 486 (10 mg/kg, p.o. at 8.00 h) versus placebo (PBO) in 7 healthy female volunteers and 8 patients with DSM-III-R anorexia nervosa, all of whom were studied while underweight [64.3 +/- 2.1% average body weight (ABW), mean +/- SE] and 5 of whom were restudied longitudinally following refeeding (> or = 85% ABW, mean 87.4 +/- 0.4% ABW). Blood samples were obtained from 16.00 to 16.30 h and from 4.00 to 8.00 h following dosing. Underweight anorexics were significantly hypercortisolemic by 24 h urinary free cortisol excretion compared with controls (239 +/- 37 vs. 119 +/- 12 nmol/day, p < 0.01). Both controls and underweight anorexics had robust early morning (4.00-8.00 h) plasma cortisol responses to RU 486 (465 +/- 61 and 719 +/- 49 nmol/l) compared with PBO (370 +/- 52 and 451 +/- 31 nmol/l; p < 0.02 and p < 0.01, respectively). The underweight anorexics showed a significant mean early morning plasma ACTH response to RU compared with placebo (3.28 +/- 0.63 vs. 2.01 +/- 0.24 pmol/l, p < 0.05), while the controls showed a trend toward an increase in mean plasma ACTH after RU (3.11 +/- 0.36 pmol/l) compared with PBO (2.31 +/- 0.41 pmol/l, p < 0.13); plasma ACTH means were greater on the RU day than the placebo day at 20 of 25 sampling points (p < 0.001). However, the increment in ACTH on the RU day compared to the placebo day was greater in the underweight anorexics at the first 20 of 25 consecutive time points of the early morning sampling period (p < 0.001). Moreover, underweight anorexics showed a significant plasma ACTH and cortisol response to RU 486 at 16.00-16.30 h (8-8.5 h following administration), while the controls showed no significant response of plasma ACTH or cortisol at this time. When restudied following weight recovery, anorexic patients showed reductions in 24-hour urinary free cortisol excretion (to 191 +/- 40 nmol/day) which were no longer significantly elevated compared with control values.(ABSTRACT TRUNCATED AT 400 WORDS)

The antidepressants fluoxetine, idazoxan and phenelzine alter corticotropin-releasing hormone and tyrosine hydroxylase mRNA levels in rat brain: therapeutic implications

Various classes of antidepressant drugs with distinct pharmacologic actions are differentially effective in the treatment of classic melancholic depression--characterized by pathological hyperarousal and atypical depression--associated with lethargy, hypersomnia, and hyperphagia. All antidepressant agents exert their therapeutic efficacy only after prolonged administration. In situ hybridization histochemistry was used to examine in rats the effects of short-term (2 weeks) and long-term (8 weeks) administration of 3 different classes of activating antidepressant drugs which tend to be preferentially effective in treating atypical depressions, on the expression of central nervous system genes thought to be dysregulated in major depression. Daily administration (5 mg/kg, i.p.) of the selective 5-hydroxytryptophan (5-HT) reuptake inhibitor fluoxetine, the selective alpha 2-adrenergic receptor antagonist idazoxan, and the nonspecific monoamine oxidase A and B inhibitor phenelzine increased tyrosine hydroxylase mRNA levels by 70-150% in the locus coeruleus after 2 weeks of drug and by 71-115% after 8 weeks. The 3 drugs decreased corticotropin-releasing hormone mRNA levels by 30-48% in the paraventricular nucleus of the hypothalamus. The decreases occurred at 8 weeks but not at 2 weeks. No consistent change in steroid hormone receptor mRNA levels was seen in the hippocampus with the 3 drugs, but fluoxetine and idazoxan increased the level of mineralocorticoid receptor (MR) and glucocorticoid receptor (GR) mRNA, respectively, after 8 weeks of drug administration. Proopiomelanocortin (POMC) mRNA levels in the anterior pituitary and plasma adrenocorticotropic-hormone (ACTH) levels were not altered after 2 or 8 weeks of drug treatment.(ABSTRACT TRUNCATED AT 250 WORDS)

Intrahippocampal colchicine alters hypothalamic corticotropin-releasing hormone and hippocampal steroid receptor mRNA in rat brain

The hippocampus appears to be an important modulator of the negative feedback effects of glucocorticoids on the hypothalamic-pituitary-adrenal axis. It is not known if hippocampal subfields CA1-4 or the dentate gyrus differentially alter gene expression of corticotropin-releasing hormone (CRH) in the paraventricular nucleus (PVN) of the hypothalamus. We, therefore, examined the effects of selective destruction of dentate gyrus granule cells, which send excitatory glutaminergic inputs to subfields CA4, CA3 and CA2, on CRH expression in the PVN. To determine the possible involvement of steroid receptors in the regulation of CRH expression, we examined the effects of intrahippocampal colchicine on gene expression of the mineralocorticoid (MR; type I) and glucocorticoid (GR; type II) receptors in hippocampal CA fields and dentate gyrus. Colchicine produced a selective loss of dentate gyrus granule cells without affecting pyramidal cells in CA1-4 as early as 1 day after injection; granule cells were completely destroyed after 3 days. CRH mRNA levels were reduced by 38-48% in the PVN 2-14 days after colchicine. MR mRNA levels were decreased in dorsal and ventral CA fields 1-7 days after colchicine. GR mRNA levels were relatively unchanged, showing a slight decrease only in dorsal CA fields on days 2-7. Unexpectedly, CRH was transiently expressed in dorsal and ventral CA fields 1-3 days after colchicine. In the same time period, mRNA levels of inositol 1,4,5-trisphosphate kinase were decreased, suggesting that increases in neural metabolic activity, indicated by this marker, are not responsible for the transient CRH effect. The results suggest that the dentate gyrus is important for maintenance of steroid hormone receptor mRNA levels in the hippocampus and CRH expression in the hypothalamic PVN, and that CRH gene expression is differentially regulated in the hypothalamus and hippocampus.

Arthritis-susceptible Lewis rats fail to emerge from the stress hyporesponsive period

Susceptibility to streptococcal cell wall (SCW)-induced arthritis in 4- to 6-week-old Lewis (LEW/N) rats is associated with blunted glucocorticoid production secondary to a profound defect in inflammatory mediator-induced hypothalamic corticotropin-releasing hormone (CRH) biosynthesis and secretion. The relative SCW arthritis resistance in histocompatible Fischer (F344/N) rats, on the other hand, is associated with robust hypothalamic-pituitary-adrenal (HPA) axis responses to inflammatory mediators. In this study, we investigated HPA axis responses to SCW during the postnatal developmental period in LEW/N and F344/N rats. We found that SCW-induced plasma corticosterone (CORT) responses do not significantly increase during development in LEW/N, while such responses clearly appear at postnatal day 14 in F344/N and outbred Harlan-Sprague-Dawley (HSD) rats. Additionally, LEW/N rats fail to exhibit the normal ontogenic increase in CRH mRNA levels in the paraventricular nucleus (PVN), whereas their SCW-induced PVN CRH mRNA responses are blunted compared to F344/N at postnatal day 14. Taken together, these results suggest that LEW/N rats fail to emerge completely from their stress hyporesponsive period. This may account for the lack of stress responsiveness in young adult LEW/N rats, and consequently, for their susceptibility to SCW-induced arthritis and other inflammatory diseases.

Long-term antidepressant administration alters corticotropin-releasing hormone, tyrosine hydroxylase, and mineralocorticoid receptor gene expression in rat brain. Therapeutic implications

Imipramine is the prototypic tricyclic antidepressant utilized in the treatment of major depression and exerts its therapeutic efficacy only after prolonged administration. We report a study of the effects of short-term (2 wk) and long-term (8 wk) administration of imipramine on the expression of central nervous system genes among those thought to be dysregulated in imipramine-responsive major depression. As assessed by in situ hybridization, 8 wk of daily imipramine treatment (5 mg/kg, i.p.) in rats decreased corticotropin-releasing hormone (CRH) mRNA levels by 37% in the paraventricular nucleus (PVN) of the hypothalamus and decreased tyrosine hydroxylase (TH) mRNA levels by 40% in the locus coeruleus (LC). These changes were associated with a 70% increase in mRNA levels of the hippocampal mineralocorticoid receptor (MR, type I) that is thought to play an important role in mediating the negative feedback effects of low levels of steroids on the hypothalamic-pituitary-adrenal (HPA) axis. Imipramine also decreased proopiomelanocortin (POMC) mRNA levels by 38% and glucocorticoid receptor (GR, type II) mRNA levels by 51% in the anterior pituitary. With the exception of a 20% decrease in TH mRNA in the LC after 2 wk of imipramine administration, none of these changes in gene expression were evident as a consequence of short-term administration of the drug. In the light of data that major depression is associated with an activation of brain CRH and LC-NE systems, the time-dependent effect of long-term imipramine administration on decreasing the gene expression of CRH in the hypothalamus and TH in the LC may be relevant to the therapeutic efficacy of this agent in depression.

Cerebrospinal fluid immunoreactive corticotropin-releasing hormone and adrenocorticotropin secretion in Cushing's disease and major depression: potential clinical implications

To explore whether possible differences in central nervous system neuromodulators contribute to the differential presentation of affective symptomatology in Cushing's disease and major depression, we examined the levels of immunoreactive CRH and ACTH in the cerebrospinal fluid (CSF) of 11 patients with Cushing's disease, a patient with ectopic ACTH secretion, 34 patients with major depression, and 60 healthy subjects. We elected to measure these peptides not only because both are classically involved in pituitary-adrenal regulation, but also because their primarily arousal-producing and anorexigenic behavioral effects in experimental animals suggest that they may play a role in the symptom complex of depressive syndromes. We also explored whether the CSF levels of these peptides were more helpful in determining the often difficult differential diagnosis between major depression and Cushing's disease than the plasma ACTH response to ovine CRH, a currently used but somewhat insensitive laboratory means of distinguishing these disorders. CSF levels of immunoreactive CRH and ACTH were significantly lower in Cushing's disease patients [21.9 +/- 2.7 and 15.4 +/- 1.8 pg/mL, (mean +/- SEM), respectively] compared to patients with major depression [38.4 +/- 2.3 pg/mL (P less than 0.01) and 24.5 +/- 1.6 pg/mL (P less than 0.01), respectively] and controls [38.4 +/- 1.6 pg/mL (P less than 0.001) and 26.3 +/- 1.1 pg/mL (P less than 0.001), respectively]. The coexistence of high plasma ACTH and low CSF ACTH in Cushing's disease yielded a CSF/plasma ACTH ratio consistently less than that in depressed patients, with only 2 of 31 subjects comprising both groups showing values that overlapped. In contrast, 9 of the combined patients showed ACTH responses to ovine CRH that overlapped. These data suggest that differences in centrally directed CRH secretion may account for the differential presentation of the dysphoric syndromes seen in major depression and Cushing's disease. Hence, the classic form of major depression (melancholia), is often associated with evidence of pathological hyperarousal, such as intense anxiety, sleeplessness, and anorexia, while that of Cushing's disease is associated with evidence of pathological hyperarousal, including hyperphagia, fatigue, and inertia. Moreover, measurement of the CSF/plasma ACTH ratio may serve as a clinically useful adjunct to the ovine CRH stimulation test and other laboratory measures in determining the differential diagnosis between major depression and Cushing's disease.

Optimization of cRNA probe in situ hybridization methodology for localization of glucocorticoid receptor mRNA in rat brain: a detailed protocol

1. We have described a general ribonucleotide probe in situ hybridization methodology for localization of mRNA in frozen, unfixed tissue sections of brain. 2. The most important steps in obtaining consistent and reproducible autoradiographs with ribonucleotide probes were tissue acetylation and application of the radiolabeled probe to tissue sections under unsealed, glass coverslips. 3. Variability of the hybridization signal in tissue sections has been minimized to achieve a high degree of reproducibility within a given experiment as determined by densitometric analysis of rat glucocorticoid and mineralocorticoid receptor mRNA hybridization autoradiographs. 4. Tissue quality has been optimized for high-resolution anatomical localization of mRNA species by nuclear track emulsion. 5. The protocol is amenable to rapid, batchwise processing of tissue samples.

Corticotropin-releasing hormone: from endocrinology to psychobiology

Corticotropin-releasing hormone (CRH) is a brain neuropeptide which coordinates the endocrine, autonomic and behavioral responses to stress. We review the abnormal response to exogenous CRH in various psychiatric syndromes, including major depression and anorexia nervosa. We also contrast pituitary responses to CRH in patients with depression versus Cushing's disease. We hypothesize that CRH may play a role in the pathogenesis of various psychiatric syndromes which are characterized during their course by the symptom of depression.

Coordinate developmental regulation of high and low molecular weight mRNAs for rat insulin-like growth factor II

Insulin-like growth factor II (IGF-II) is a mitogenic polypeptide that is thought to play a role in fetal growth and development. To study the hormonal and developmental regulation of IGF-II gene expression, we have isolated a cDNA clone for rat IGF-II (rIGF-II) from a 12S [1.2-kilobase-pair (kbp)] fraction of mRNA from a rat liver cell line (BRL-3A) that directs the cell-free synthesis of pre-pro-rIGF-II. In the present study, the rIGF-II probe was used to determine the size of IGF-II RNA. Surprisingly, in BRL-3A cells and in neonatal liver, the probe hybridized under stringent conditions 10-20 times more strongly to a larger (4 kbp) RNA than to 1.2-kbp RNA. The 4-kbp RNA is almost exclusively cytoplasmic and is colinear with a 551-base fragment of the rIGF-II cDNA insert containing coding and 3' noncoding regions. The 4-kbp and 1.2-kbp RNA species are regulated coordinately with developmental age, being high in liver from neonatal rats but not detectable in liver from older animals, suggesting that both IGF-II mRNA species arise from a single primary transcript by alternative RNA processing. Although oligodeoxynucleotide hybridization and S1 nuclease protection experiments suggest that the 4-kbp RNA contains an intact protein-coding region, fractions enriched in 4-kbp RNA do not direct the translation of pre-pro-rIGF-II in vitro. This may indicate that the 4-kbp RNA specifies an altered protein product that has not yet been recognized, or alternatively that it contains a normal protein-coding region but requires further RNA processing to be activated for translation.

Experimental Determination of the Imaging Properties of a 200 kV Electron Microscope

Optical transforms from a through focal series of images of amorphous films of Ge were used to measure the spatial frequencies of maximum and minimum phase contrast of a specific 200 kV lEOL electron microscope. This information was used to determine precise values for the spherical aberration coefficient and defect of focus. Under the appropriate conditions of lens excitation the spherical aberration coefficient was found to be as low as 0�94 mm. Other image defects revealed with great precision were associated with astigmatism, beam divergence and specimen drift in the microscope stage. Quantitative examples illustrating these effects are discussed.

Isolation of a cDNA clone encoding rat insulin-like growth factor-II precursor

Insulin-like growth factor-I (IGF-I) and IGF-II are mitogenic polypeptides of relative molecular mass (Mr) approximately 7,500 isolated from human plasma each containing four peptide domains in a single chain and identical at more than 60% of their amino acid loci. The B- and A-domains of the IGFs are approximately 40% identical to the B- and A-chains of human insulin. IGF-I and IGF-II have similar in vitro biological activities and receptor reactivity, but are immunologically distinct. IGF-I appears to mediate the effects of growth hormone on cartilage to promote skeletal growth whereas IGF-II may have a special role in fetal development and in the central nervous system. To investigate the in vivo role of IGF-II, we have studied IGF-II biosynthesis in the BRL-3A rat liver cell line. BRL-3A cells synthesize and secrete a 7,484 Mr protein 93% identical to human IGF-II and representing rat IGF-II (rIGF-II). Rat IGF-II is synthesized as a approximately 22,000 Mr prepro-rIGF-II (ref. 12) from 12 S poly(A)+mRNA. In addition, approximately 20,000 Mr pro-rIGF-II has been identified in lysates of biosynthetically labelled intact BRL-3A cells. We report here the isolation of an almost complete cDNA clone for rIGF-II. Our results indicate that pro-rIGF-II is synthesized as a 156 amino acid peptide precursor (17,619 Mr) containing mature rIGF-II 1-67 at its amino-terminus and an 89-residue carboxy-terminal peptide extension.

Association of adhesive, invasive, and virulent phenotypes of Salmonella typhimurium with autonomous 60-megadalton plasmids

The plasmid DNA content of six invasive and adhesive strains of Salmonella typhimurium was determined, and all six strains (CR8500 [S850], CR6600 [TML], W118, NY, PR, and S2204) were found to harbor at least one plasmid equivalent in size to the 60-megadalton plasmid ("cryptic" plasmid), pSLT, which is normally resident in S. typhimurium strain LT2. The role of such 60-megadalton plasmids in the adhesive and invasive properties of strain CR6600, a commonly encountered salmonella pathogen that produces type 1 fimbriae, and strain CR8500, a representative FIRN biotype which does not produce type 1 fimbriae, was studied further by obtaining derivatives of these strains that no longer harbored an autonomous 60-megadalton plasmid. Strains CR6260 and CR6190 and strains CR8100 and CR8353, which were "cured" derivatives of strains CR6600 and CR8500, respectively, were significantly less adhesive and invasive in the HeLa cell test. A 53.5-megadalton colicin plasmid harbored by strain CR6600 did not detectably influence these properties. Additionally, strain CR6260 was avirulent, and strain CR8100 was 1,000 to 10,000-fold less virulent for orally infected mice as compared with their respective parental strains. Significantly, the virulence of strain CR8100 correlated with tissue colonization by bacteria that exhibited autonomous copies of a 60-megadalton plasmid. We propose that this plasmid exists in both autonomous and integrated states and that the in vivo environment selects for bacteria with autonomous plasmid copies which can express the virulent phenotype, thus enabling such strains to survive the defense mechanisms of the host.

Increased hexose transport in Chinese hamster ovary cells resistant to 3-O-methyl-D-glucose

3-O-Methyl-D-glucose-resistant mutants were selected from Chinese hamster ovary cells after mutagenesis with ethyl methanesulfonate. A mutant, MegR24, was isolated which was significantly more resistant than the parent to 3-O-methylglucose. Uptake of 50 microM D-glucose by metabolizing MegR24 cells was 2- to 3-fold higher than the parental cells in the absence or presence of 100 mM 3-O-methylglucose. A study of transport of D-[3H]glucose in ATP-depleted cells indicated an apparent Km for D-glucose transport that was 3-fold lower for the mutant (2.7 +/- 0.3 mM) than for the parent (8.9 +/- 1.0 mM). The apparent Km for transport of 3-O-methylglucose by the mutant (10.9 +/- 2.4 mM) was almost 2-fold lower than that of the parent (21.4 +/- 4.7 mM). The Vmax values for transport of D-glucose or 3-O-methylglucose by the mutant and parental cell lines were not significantly different. The MegR24 mutant also exhibited enhanced countertransport of D-[3H]glucose following preloading of ATP-depleted cells with 100 mM 3-O-methylglucose. Simple diffusion of hexoses as measured by L-glucose uptake was not altered in the mutant. These results suggest that the MegR24 hexose carrier has an increased affinity for transport of hexoses and that the resistance to the cytotoxic effects of 3-O-methylglucose exhibited by MegR24 is due to its ability to transport D-glucose 2- to 3-fold more efficiently than the parental strain.

Transcription termination factor rho from wild type and rho-111 strains of Salmonella typhimurium

Transcription termination factor rho was purified to near homogeneity from the wild type and temperature-sensitive rho-111 mutant strains of Salmonella typhimurium. Each protein had identical physical properties with respect to native and subunit molecular weight, elution from ion-exchange columns, and poly(C)-dependent ATPase specific activity at 30 degrees C. The mutant protein exhibited a thermolabile poly(C)-dependent ATPase activity. The transcription termination and nascent RNA-dependent ATPase activities associated with the purified wild type S. typhimurium rho protein were not present in the mutant protein. Binding studies demonstrated that the stability of the rho-111:poly(C) complex was significantly more sensitive to ionic strength and temperature than that of the rho +: poly(C) complex. This result suggests that the altered activities of the mutant protein are due to its decreased ability to participate in a specific interaction with RNA which is insensitive to ionic strength. The rho-111 mutation resulted in a 20- to 30-fold elevation in the level of the mutant protein, indicating that rho biosynthesis in S. typhimurium is autogenously regulated. Therefore, defective molecular interactions between the mutant rho protein and RNA might account for the absence of transcription termination in vitro, and the polarity suppressor phenotype and defective autogenous regulation of rho biosynthesis in vivo.

Genetic analysis of a temperature-sensitive Salmonella typhimurium rho mutant with an altered rho-associated polycytidylate-dependent adenosine triphosphatase activity

A conditional-lethal rho mutant of Salmonella typhimurium LT2 has been isolated. The mutation was selected as a suppressor of the polarity of an insertion sequence (IS)2-induced mutation (gal3) carried on an F' plasmid. In addition to suppression of IS2-induced polarity, the rho-111 mutation suppressed nonsense and frameshift polarity. The rho-associated polycytidylic acid-dependent adenosine triphosphatase activity in the mutant strain was elevated 15-fold above that in the parental strain, and the mutant rho protein was thermally unstable. A temperature-resistant revertant of the mutant strain did not suppress polarity and contained normal levels of polycytidylic acid-dependent adenosine triphosphatase, suggesting that the phenotype of the rho-111-bearing strain is the consequence of a single mutation. The rho-111 mutation was located on the S. typhimurium linkage map midway between the ilv and cya loci by phage P22 cotransduction studies. F' plasmid maintenance was not impaired in the mutant strain, and the mutation was recessive to the wild-type allele. The rho-111 mutation did not alter in vivo expression of either the tryptophan or histidine operons.

Physical characterization of a plasmid cointegrate containing an F'his gnd element and the Salmonella typhimurium LT2 cryptic plasmid

A recombinant plasmid (pAS19) isolated from a derivative of Salmonella typhimurium LT2, containing the strain LT2 cryptic plasmid and an F'his gnd element, has been physically characterized. The pAS19 plasmid contour length equals the sum of the contour lengths of the cryptic plasmid and F'his gnd element. Deoxyribonucleic acid (DNA)-DNA hybridization experiments demonstrated that whereas the pAS19 plasmid exhibits extensive DNA homology with both the cryptic plasmid and the F'his gnd element, there is little DNA homology between these latter two plasmids. The DNA fragmentation pattern of the pAS19 plasmid produced by the restriction endonuclease R-EcoRI is consistent with that expected for a composite plasmid cointegrate containing most, if not all, of the DNA sequences present in its two component plasmids.

Evidence for a composite state of an F'his, gnd element and a cryptic plasmid in a derivative of Salmonella typhimurium LT2

A method designed to select mutants constitutive for expression of the histidine operon has been applied to a Salmonella typhimurium LT2 strain containing an F'his,gnd element and a cryptic plasmid. One of the mutants isolated, strain AA0019, has not only increased levels of histidinol phosphate phosphatase (hisB), but also increased levels of gluconate-6-phosphate dehydrogenase (gnd). Ultracentrifugation studies of extrachromosomal deoxyribonucleic acid (DNA) isolated from strain AA0019 revealed the presence of a single species of covalently closed circular (CCC) DNA that sedimented more rapidly through neutral and alkaline sucrose gradients than any of its possible plasmid precursors. From neutral sucrose gradients, sedimentation coefficients of 130, 100, and 86S were derived, corresponding to the CCC DNA of the large plasmid in strain AA0019, the F'his,gnd element and the cryptic LT2 plasmid, respectively. An Escherichia coli plasmid-free strain that upon mating had received the large 130S plasmid also contained 86S and 100S CCC DNA components. A histidine-requiring derivative of strain AA0019 obtained after acridine orange treatment retained the cryptic plasmid DNA. Apparently, the large plasmid in strain AA0019 consists of the F'his,gnd element and the cryptic LT2 plasmid of the parental strain.

Bromine nuclear quadrupole resonance in zinc bromide and in lead bromide

Nuclear quadrupole resonances of 79Br and 81Br have been observed in both ZnBr2 and PbBr2 at 77, 195 and 298 K. For ZnBr2 three closely spaced lines at 81.425, 83.100 and 84.137 MHz (81Br, 77 K) of relative intensities 1 : 2 : 1 are in accord with three non-equivalent lattice sites of space group I41/acd. For PbBr2 two lines observed at 20.669 and 27.824 MHz (81Br, 77 K), consistent with space group P bnm, have been assigned to their respective lattice sites on the basis of point-charge model calculations.

Isolation and characterization of a mutant of Salmonella typhimurium deficient in a major deoxyribonucleic acid polymerase activity

A mutant of Salmonella typhimurium strain LT2 that is deficient in a major deoxyribonucleic acid (DNA) polymerase activity has been isolated and characterized. This mutant resembles the pol mutants of E. coli in that it has low DNA polymerase activity and it is sensitive to methyl methane sulfonate as well as ultraviolet irradiation. Revertants selected for methyl methane sulfonate resistance are no longer sensitive to ultraviolet irradiation and contain normal DNA polymerase levels. No direct role in replication can be ascribed to this polymerase activity since cells grow well in its absence. In addition, the LT2 plasmid has been shown to exist in the mutant strain.

An arsenic-75 nuclear quadrupole resonance study of α and β As4S3

The nuclear quadrupole resonance frequencies of 75As in the α and β forms of As4S3 have been measured at 77, 195, and 293 K. The frequencies at 77 K were: α phase 64.87 65.94 79.56 MHz β phase 65.42 67.16 79.65 MHz An analysis is presented in terms of Townes-Dailey theory and of the temperature dependence in terms of Bayer-Brown theory. The differences in frequencies of the α and β forms were attributed to the effect of electrostatic field gradients, estimated by lattice sums. Allowance must be made for the thermal expansion of the lattice to obtain a consistent interpretation.

The far-infrared spectra of arsenic chalcogenides

The far-infrared spectra of AsS, As2S3, As4Se3, and As2Se3 are reported for the range 15-400 cm-1. For As4S3 molecules, of symmetry C3v, strong bands at 370 cm-1 and 340 cm-1 arise from symmetric As-S stretching frequencies of symmetry class A1 and a strong band at 176 cm-1 arises from a S-4s-S bending mode of degenerate class E. For As2Se3, bands in the region 90-130 cm-1 are identified as Se-As-Se bending modes and bands between 200 and 280 cm-1 are due to As-Se stretching modes.

Procedure for identifying nonsense mutations

A method has been devised for the rapid identification of nonsense mutations (UAG, UAA, UGA codons) in Salmonella. The mutations to be tested are reverted, and the revertants are replica-printed onto lactose plates spread with lawns of tester strains. These tester strains contain F' lac episomes with nonsense mutations in the episomal Z gene. The revertants are infected with the episome from the tester strain lawn. Because S. typhimurium is unable to ferment lactose, only those revertants which have nonsense suppressors are able to grow on lactose. If colonies appear on the lactose plate, it may be concluded that the original strain carries a nonsense mutation, since nonsense suppressors suppress the mutant phenotype.

Mössbauer effect in the system Ca2Fe2O5-Ca2FeAlO5

Mossbauer spectra were measured on Ca2Fe2O5, Ca2Fe1.5Al0.5O5, Ca2FeAlO5, and Ca2Fe0.67Al1.33O5 at temperatures from 95�K to above the Neel points. The Mossbauer spectrum of Ca2Fe2O5 below its Neel point shows lines which were assigned to tetrahedral and octahedral site ferric ions on the basis of the observed isomer shifts and hyperfine splittings. The Mossbauer spectra of the aluminium-substituted calcium ferrites give unequivocal evidence that the aluminium goes preferentially into tetrahedral sites. A four-sublattice magnetic structure is suggested for Ca2Fe2O5.