An Esrrb and Nanog Cell Fate Regulatory Module Controlled by Feed Forward Loop Interactions

Cell fate decisions during development are governed by multi-factorial regulatory mechanisms including chromatin remodeling, DNA methylation, binding of transcription factors to specific loci, RNA transcription and protein synthesis. However, the mechanisms by which such regulatory “dimensions” coordinate cell fate decisions are currently poorly understood. Here we quantified the multi-dimensional molecular changes that occur in mouse embryonic stem cells (mESCs) upon depletion of Estrogen related receptor beta (Esrrb), a key pluripotency regulator. Comparative analyses of expression changes subsequent to depletion of Esrrb or Nanog, indicated that a system of interlocked feed-forward loops involving both factors, plays a central part in regulating the timing of mESC fate decisions. Taken together, our meta-analyses support a hierarchical model in which pluripotency is maintained by an Oct4-Sox2 regulatory module, while the timing of differentiation is regulated by a Nanog-Esrrb module.

Activation of tumor suppressor protein PP2A inhibits KRAS-driven tumor growth

Targeted cancer therapies, which act on specific cancer-associated molecular targets, are predominantly inhibitors of oncogenic kinases. While these drugs have achieved some clinical success, the inactivation of kinase signaling via stimulation of endogenous phosphatases has received minimal attention as an alternative targeted approach. Here, we have demonstrated that activation of the tumor suppressor protein phosphatase 2A (PP2A), a negative regulator of multiple oncogenic signaling proteins, is a promising therapeutic approach for the treatment of cancers. Our group previously developed a series of orally bioavailable small molecule activators of PP2A, termed SMAPs. We now report that SMAP treatment inhibited the growth of KRAS-mutant lung cancers in mouse xenografts and transgenic models. Mechanistically, we found that SMAPs act by binding to the PP2A Aα scaffold subunit to drive conformational changes in PP2A. These results show that PP2A can be activated in cancer cells to inhibit proliferation. Our strategy of reactivating endogenous PP2A may be applicable to the treatment of other diseases and represents an advancement toward the development of small molecule activators of tumor suppressor proteins.

The behavioural homing response of adult chum salmon Oncorhynchus keta to amino-acid profiles

Adult chum salmon Oncorhynchus keta homing behaviour in a two-choice test tank (Y-maze) was monitored using a passive integrated transponder (PIT)-tag system in response to river-specific dissolved free amino-acid (DFAA) profiles and revealed that the majority of O. keta showed a preference for artificial natal-stream water and tended to stay in this maze arm for a longer period; natal-stream water was chosen over a nearby tributary's water, but not when the O. keta were presented with a non-tributary water. The results demonstrate the ability of O. keta to discriminate artificial stream waters containing natural levels of DFAA.

Skeletal Muscle Oxygenation Measured by EPR Oximetry Using a Highly Sensitive Polymer-Encapsulated Paramagnetic Sensor

We have incorporated LiNc-BuO, an oxygen-sensing paramagnetic material, in polydimethylsiloxane (PDMS), which is an oxygen-permeable, biocompatible, and stable polymer. We fabricated implantable and retrievable oxygen-sensing chips (40 % LiNc-BuO in PDMS) using a 20-G Teflon tubing to mold the chips into variable shapes and sizes for in vivo studies in rats. In vitro EPR measurements were used to test the chip's oxygen response. Oxygen induced linear and reproducible line broadening with increasing partial pressure (pO2). The oxygen response was similar to that of bare (unencapsulated) crystals and did not change significantly on sterilization by autoclaving. The chips were implanted in rat femoris muscle and EPR oximetry was performed repeatedly (weekly) for 12 weeks post-implantation. The measurements showed good reliability and reproducibility over the period of testing. These results demonstrated that the new formulation of OxyChip with 40 % LiNc-BuO will enable the applicability of EPR oximetry for long-term measurement of oxygen concentration in tissues and has the potential for clinical applications.

NetworkPainter: dynamic intracellular pathway animation in Cytobank

BACKGROUND

High-throughput technologies such as flow and mass cytometry have the potential to illuminate cellular networks. However, analyzing the data produced by these technologies is challenging. Visualization is needed to help researchers explore this data.

RESULTS

We developed a web-based software program, NetworkPainter, to enable researchers to analyze dynamic cytometry data in the context of pathway diagrams. NetworkPainter provides researchers a graphical interface to draw and "paint" pathway diagrams with experimental data, producing animated diagrams which display the activity of each network node at each time point.

CONCLUSION

NetworkPainter enables researchers to more fully explore multi-parameter, dynamical cytometry data.

Krüppel-like factor 6 regulates mitochondrial function in the kidney

Maintenance of mitochondrial structure and function is critical for preventing podocyte apoptosis and eventual glomerulosclerosis in the kidney; however, the transcription factors that regulate mitochondrial function in podocyte injury remain to be identified. Here, we identified Krüppel-like factor 6 (KLF6), a zinc finger domain transcription factor, as an essential regulator of mitochondrial function in podocyte apoptosis. We observed that podocyte-specific deletion of Klf6 increased the susceptibility of a resistant mouse strain to adriamycin-induced (ADR-induced) focal segmental glomerulosclerosis (FSGS). KLF6 expression was induced early in response to ADR in mice and cultured human podocytes, and prevented mitochondrial dysfunction and activation of intrinsic apoptotic pathways in these podocytes. Promoter analysis and chromatin immunoprecipitation studies revealed that putative KLF6 transcriptional binding sites are present in the promoter of the mitochondrial cytochrome c oxidase assembly gene (SCO2), which is critical for preventing cytochrome c release and activation of the intrinsic apoptotic pathway. Additionally, KLF6 expression was reduced in podocytes from HIV-1 transgenic mice as well as in renal biopsies from patients with HIV-associated nephropathy (HIVAN) and FSGS. Together, these findings indicate that KLF6-dependent regulation of the cytochrome c oxidase assembly gene is critical for maintaining mitochondrial function and preventing podocyte apoptosis.

LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures

For the Library of Integrated Network-based Cellular Signatures (LINCS) project many gene expression signatures using the L1000 technology have been produced. The L1000 technology is a cost-effective method to profile gene expression in large scale. LINCS Canvas Browser (LCB) is an interactive HTML5 web-based software application that facilitates querying, browsing and interrogating many of the currently available LINCS L1000 data. LCB implements two compacted layered canvases, one to visualize clustered L1000 expression data, and the other to display enrichment analysis results using 30 different gene set libraries. Clicking on an experimental condition highlights gene-sets enriched for the differentially expressed genes from the selected experiment. A search interface allows users to input gene lists and query them against over 100 000 conditions to find the top matching experiments. The tool integrates many resources for an unprecedented potential for new discoveries in systems biology and systems pharmacology. The LCB application is available at http://www.maayanlab.net/LINCS/LCB. Customized versions will be made part of the http://lincscloud.org and http://lincs.hms.harvard.edu websites.

The characteristic direction: a geometrical approach to identify differentially expressed genes

Background

Identifying differentially expressed genes (DEG) is a fundamental step in studies that perform genome wide expression profiling. Typically, DEG are identified by univariate approaches such as Significance Analysis of Microarrays (SAM) or Linear Models for Microarray Data (LIMMA) for processing cDNA microarrays, and differential gene expression analysis based on the negative binomial distribution (DESeq) or Empirical analysis of Digital Gene Expression data in R (edgeR) for RNA-seq profiling.

Results

Here we present a new geometrical multivariate approach to identify DEG called the Characteristic Direction. We demonstrate that the Characteristic Direction method is significantly more sensitive than existing methods for identifying DEG in the context of transcription factor (TF) and drug perturbation responses over a large number of microarray experiments. We also benchmarked the Characteristic Direction method using synthetic data, as well as RNA-Seq data. A large collection of microarray expression data from TF perturbations (73 experiments) and drug perturbations (130 experiments) extracted from the Gene Expression Omnibus (GEO), as well as an RNA-Seq study that profiled genome-wide gene expression and STAT3 DNA binding in two subtypes of diffuse large B-cell Lymphoma, were used for benchmarking the method using real data. ChIP-Seq data identifying DNA binding sites of the perturbed TFs, as well as known drug targets of the perturbing drugs, were used as prior knowledge silver-standard for validation. In all cases the Characteristic Direction DEG calling method outperformed other methods. We find that when drugs are applied to cells in various contexts, the proteins that interact with the drug-targets are differentially expressed and more of the corresponding genes are discovered by the Characteristic Direction method. In addition, we show that the Characteristic Direction conceptualization can be used to perform improved gene set enrichment analyses when compared with the gene-set enrichment analysis (GSEA) and the hypergeometric test.

Conclusions

The application of the Characteristic Direction method may shed new light on relevant biological mechanisms that would have remained undiscovered by the current state-of-the-art DEG methods. The method is freely accessible via various open source code implementations using four popular programming languages: R, Python, MATLAB and Mathematica, all available at: http://www.maayanlab.net/CD.

Knowledge and attitudes about hepatitis C virus (HCV) infection and its treatment in HCV mono-infected and HCV/HIV co-infected adults

Hepatitis C virus (HCV) treatment is rapidly changing but little is known about patients' attitudes and knowledge about HCV. This study used a cross-sectional survey to examine the relationship between HCV knowledge and attitudes towards HCV in patients with HCV mono-infection and HIV/HCV co-infection. Subsequently, an education intervention was developed with an abridged version of the cross-sectional survey administered before and after the education session to assess changes in knowledge and attitudes. 292 people participated in the cross-sectional survey, and 87 people participated in the education intervention. In the cross-sectional survey, the mean knowledge score regarding HCV was low (<50% of the total possible score). Mono-infected and co-infected individuals shared similar knowledge deficits and attitudes towards HCV despite having distinct demographic differences. Attitudes endorsed by patients included the following: 57% feared the consequences of HCV on their life, 37% felt HCV was not fatal, 27% did not believe they needed HCV medication, 21% felt ashamed of having HCV and 16% felt HCV treatment was not important. Attitudes that reflected indifference and shame towards HCV were associated with lower knowledge scores (HCV knowledge score of 15.1 vs. 17.5, P < 0.01 for indifference and 15.3 vs. 17.2 for shame, P = 0.02). The education intervention improved knowledge scores but did not modify the assessed attitudes. Intervention studies are needed to effectively change attitudes towards HCV infection and treatment.

ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells

High content studies that profile mouse and human embryonic stem cells (m/hESCs) using various genome-wide technologies such as transcriptomics and proteomics are constantly being published. However, efforts to integrate such data to obtain a global view of the molecular circuitry in m/hESCs are lagging behind. Here, we present an m/hESC-centered database called Embryonic Stem Cell Atlas from Pluripotency Evidence integrating data from many recent diverse high-throughput studies including chromatin immunoprecipitation followed by deep sequencing, genome-wide inhibitory RNA screens, gene expression microarrays or RNA-seq after knockdown (KD) or overexpression of critical factors, immunoprecipitation followed by mass spectrometry proteomics and phosphoproteomics. The database provides web-based interactive search and visualization tools that can be used to build subnetworks and to identify known and novel regulatory interactions across various regulatory layers. The web-interface also includes tools to predict the effects of combinatorial KDs by additive effects controlled by sliders, or through simulation software implemented in MATLAB. Overall, the Embryonic Stem Cell Atlas from Pluripotency Evidence database is a comprehensive resource for the stem cell systems biology community. Database URL: http://www.maayanlab.net/ESCAPE

Network2Canvas: network visualization on a canvas with enrichment analysis

MOTIVATION

Networks are vital to computational systems biology research, but visualizing them is a challenge. For networks larger than ∼100 nodes and ∼200 links, ball-and-stick diagrams fail to convey much information. To address this, we developed Network2Canvas (N2C), a web application that provides an alternative way to view networks. N2C visualizes networks by placing nodes on a square toroidal canvas. The network nodes are clustered on the canvas using simulated annealing to maximize local connections where a node's brightness is made proportional to its local fitness. The interactive canvas is implemented in HyperText Markup Language (HTML)5 with the JavaScript library Data-Driven Documents (D3). We applied N2C to visualize 30 canvases made from human and mouse gene-set libraries and 6 canvases made from the Food and Drug Administration (FDA)-approved drug-set libraries. Given lists of genes or drugs, enriched terms are highlighted on the canvases, and their degree of clustering is computed. Because N2C produces visual patterns of enriched terms on canvases, a trained eye can detect signatures instantly. In summary, N2C provides a new flexible method to visualize large networks and can be used to perform and visualize gene-set and drug-set enrichment analyses.

AVAILABILITY

N2C is freely available at http://www.maayanlab.net/N2C and is open source.

CONTACT

avi.maayan@mssm.edu

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

BACKGROUND

System-wide profiling of genes and proteins in mammalian cells produce lists of differentially expressed genes/proteins that need to be further analyzed for their collective functions in order to extract new knowledge. Once unbiased lists of genes or proteins are generated from such experiments, these lists are used as input for computing enrichment with existing lists created from prior knowledge organized into gene-set libraries. While many enrichment analysis tools and gene-set libraries databases have been developed, there is still room for improvement.

RESULTS

Here, we present Enrichr, an integrative web-based and mobile software application that includes new gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to display enrichment results using the JavaScript library, Data Driven Documents (D3). The software can also be embedded into any tool that performs gene list analysis. We applied Enrichr to analyze nine cancer cell lines by comparing their enrichment signatures to the enrichment signatures of matched normal tissues. We observed a common pattern of up regulation of the polycomb group PRC2 and enrichment for the histone mark H3K27me3 in many cancer cell lines, as well as alterations in Toll-like receptor and interlukin signaling in K562 cells when compared with normal myeloid CD33+ cells. Such analyses provide global visualization of critical differences between normal tissues and cancer cell lines but can be applied to many other scenarios.

CONCLUSIONS

Enrichr is an easy to use intuitive enrichment analysis web-based tool providing various types of visualization summaries of collective functions of gene lists. Enrichr is open source and freely available online at: http://amp.pharm.mssm.edu/Enrichr.

Renoprotective effect of combined inhibition of angiotensin-converting enzyme and histone deacetylase

The Connectivity Map database contains microarray signatures of gene expression derived from approximately 6000 experiments that examined the effects of approximately 1300 single drugs on several human cancer cell lines. We used these data to prioritize pairs of drugs expected to reverse the changes in gene expression observed in the kidneys of a mouse model of HIV-associated nephropathy (Tg26 mice). We predicted that the combination of an angiotensin-converting enzyme (ACE) inhibitor and a histone deacetylase inhibitor would maximally reverse the disease-associated expression of genes in the kidneys of these mice. Testing the combination of these inhibitors in Tg26 mice revealed an additive renoprotective effect, as suggested by reduction of proteinuria, improvement of renal function, and attenuation of kidney injury. Furthermore, we observed the predicted treatment-associated changes in the expression of selected genes and pathway components. In summary, these data suggest that the combination of an ACE inhibitor and a histone deacetylase inhibitor could have therapeutic potential for various kidney diseases. In addition, this study provides proof-of-concept that drug-induced expression signatures have potential use in predicting the effects of combination drug therapy.

Prenatal exposure to MDMA alters noradrenergic neurodevelopment in the rat

3,4-methylenedioxymethamphetamine (MDMA; ecstasy) binds with high affinity to the norepinephrine transporter (NET), making the noradrenergic system a potential target during fetal exposure. Recent data indicate that adult rats that had been prenatally exposed to MDMA display persistent deficits in working memory and attention; behaviors consistent with abnormal noradrenergic signaling in the forebrain. The present study was designed to investigate whether prenatal exposure to MDMA from embryonic days 14-20 affects the structure and/or function of the noradrenergic system of the rat on postnatal day 21. Offspring that were prenatally exposed to MDMA exhibited an increase in noradrenergic fiber density in the prelimbic region of the prefrontal cortex and the CA1 region of the hippocampus that was not accompanied by an increase in the number of noradrenergic neurons in the locus coeruleus. Direct tissue autoradiography using tritiated nisoxetine demonstrated that while NET binding was not altered in the prelimbic cortex, the dentate gyrus, or the locus coeruleus, it was increased in the CA1, CA2, and CA3 regions of the hippocampus. Basal levels of norepinephrine were increased in the prefrontal cortex and the nucleus accumbens of MDMA-exposed rats, as compared to saline-treated controls. These findings indicate that prenatal exposure to MDMA results in structural changes in the noradrenergic system as well as functional alterations in NE neurotransmission in structures that are critical in attentional processing.

Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers

MOTIVATION

Genome-wide mRNA profiling provides a snapshot of the global state of cells under different conditions. However, mRNA levels do not provide direct understanding of upstream regulatory mechanisms. Here, we present a new approach called Expression2Kinases (X2K) to identify upstream regulators likely responsible for observed patterns in genome-wide gene expression. By integrating chromatin immuno-precipitation (ChIP)-seq/chip and position weight matrices (PWMs) data, protein-protein interactions and kinase-substrate phosphorylation reactions, we can better identify regulatory mechanisms upstream of genome-wide differences in gene expression. We validated X2K by applying it to recover drug targets of food and drug administration (FDA)-approved drugs from drug perturbations followed by mRNA expression profiling; to map the regulatory landscape of 44 stem cells and their differentiating progeny; to profile upstream regulatory mechanisms of 327 breast cancer tumors; and to detect pathways from profiled hepatic stellate cells and hippocampal neurons. The X2K approach can advance our understanding of cell signaling and unravel drugs mechanisms of action.

AVAILABILITY

The software and source code are freely available at: http://www.maayanlab.net/X2K.

CONTACT

avi.maayan@mssm.edu

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

No association between T102C polymorphism of serotonin-2A receptor gene and clinical phenotypes of Chinese schizophrenic patients

Serotonin dysfunction has been implicated in the pathogenesis of schizophrenia. Previous studies have shown an association between the T102C polymorphism of the 5HT2a receptor gene and schizophrenia. However, negative findings have also been reported. One possible explanation for such discrepancy is disease heterogeneity due to the current limitations in the diagnosis of schizophrenia. We conducted a case-control study of the T102C polymorphism with detailed characterisation of the clinical phenotypes to investigate the possible association with schizophrenia not only at the diagnostic level, but also with reference to other clinical phenotypes potentially related to serotonin dysfunction. Four hundred and seventy-one biologically unrelated schizophrenic patients and 523 unrelated healthy controls of Han Chinese descent in Hong Kong were compared for genotypes and allele frequencies of the T102C polymorphism by PCR amplification and restriction analysis. No evidence of association was detected at the diagnostic level and various clinical phenotypes. However, we found a trend association with small effect size between genotype 102T/102C and patients with better verbal fluency and less motor co-ordination soft neurological signs. There is a need for future large-scale studies on the possible associations between genetic polymorphisms and neurocognitive function impairments in schizophrenia.

[N-[dimethyl(eta5-2,3,4,6-tetramethylindenyl)silyl]cyclobutylamido-kappaN](eta4-1,4-diphenyl-1,3-buta-diene)titanium(II)

The titanium metal center in the title compound, [Ti(C19H27NSi)(C16H14)], is coordinated in a distorted tetrahedral geometry by a eta5-indenyl ligand, a dimethylsilyl-bridged N-cyclobutylamido ligand and an s-cis-eta4-1,4-diphenyl-1,3-butadiene ligand in a 'prone' pi-fashion, revealing a formal divalent Ti center.

Neurological signs and sustained attention impairment in schizophrenia

Both neurological signs and attention impairments are often found in schizophrenia. This study addresses the extent to which neurological signs are related to sustained attention impairment. We assessed subgroups of neurological signs using the standardised Cambridge Neurological Inventory (CNI). Sustained attention was measured using a monotone counting paradigm. After taking into consideration potential confounds such as age, education level and duration of illness, we explored the correlation between sustained attention and groups of neurological signs, as well as with individual signs. We found that "motor coordination" and "disinhibition" signs were significantly related to sustained attention. The correlation with "sensory integration" just failed to reach significance after correction for multiple comparison. "Dyskinesia", "catatonia", "pyramidal" and "extrapyramidal" subgroups were unrelated to sustained attention. The results support the notion of heterogeneity and diversity in neurological signs (even among soft neurological signs) and argue against the use of a single global measure to embrace all soft neurological signs in schizophrenia.

Early degenerative changes in transgenic mice expressing mutant huntingtin involve dendritic abnormalities but no impairment of mitochondrial energy production

Mitochondrial defects, which occur in the brain of late-stage Huntington's disease (HD) patients, have been proposed to underlie the selective neuronal loss in the disease. To shed light on the possible role of mitochondrial energy impairment in the early phases of HD pathophysiology, we carried out Golgi impregnation and quantitative histochemical/biochemical studies in HD full-length cDNA transgenic mice that were symptomatic but had not developed to a stage in which neuronal loss could be documented. Golgi staining showed morphologic abnormalities that included a significant decrease in the number of dendritic spines and a thickening of proximal dendrites in striatal and cortical neurons. In contrast, measurements of mitochondrial electron transport Complexes I-IV did not reveal changes in the striatum and cerebral cortex in these mice. Examination of the neostriatum and cerebral cortex in human presymptomatic and pathological Grade 1 HD cases also showed no change in the activity of mitochondrial Complexes I-IV. These data suggest that dendritic alterations precede irreversible cell loss in HD, and that mitochondrial energy impairment is a consequence, rather than a cause, of early neuropathological changes.

Hypoxia activates a platelet-derived growth factor receptor/phosphatidylinositol 3-kinase/Akt pathway that results in glycogen synthase kinase-3 inactivation

Hypoxia initiates numerous intracellular signaling pathways important in regulating cell proliferation, differentiation, and death. In this study, we investigated the pathway that hypoxia uses to activate Akt and inactivate glycogen synthase kinase-3 (GSK-3), two proteins the functions of which are important in cell survival and energy metabolism. Severe hypoxia (0.01% oxygen) initiated a signaling cascade by inducing the tyrosine phosphorylation of the platelet-derived growth factor (PDGF) receptor within 1 h of treatment and increasing receptor association with the p85 subunit of phosphatidylinositol 3-kinase (PI 3-K). Hypoxia-induced signaling also resulted in PI 3-K-dependent phosphorylation of Akt on Ser-473, a modification of Akt that is important for its activation. This activation of Akt by hypoxia was substantially diminished in cells that possessed mutations in their PDGF receptor-PI 3-K interaction domain. In addition, Akt activation by hypoxia was resistant to treatment with the growth factor receptor poison suramin but was sensitive to treatment with the PI 3-K inhibitor wortmannin. Activation of Akt by hypoxia resulted in the phosphorylation of GSK-3alpha and GSK-3beta at Ser-9 and Ser-21, two well-documented Akt phosphorylation sites, respectively, that are inactivating modifications of each GSK-3 isoform. In support of the phosphorylation data, GSK-3 activity was significantly reduced under hypoxia. In conclusion, we propose that hypoxia activates a growth factor receptor/PI 3-K/Akt cascade that leads to GSK-3 inactivation, a pathway that can impact cell survival, proliferation, and metabolism.

Stroop interference and facilitation effects in first-episode schizophrenic patients

In the Stroop test, interference occurs in naming the print color of a word when the word is itself the name of another color. Facilitation occurs when the word is the same as the print color. Previous studies on selective attention in schizophrenia using the Stroop interference effects have yielded contradicting results. Constraints included limited sample size and the recruitment of medicated chronic patients. We studied the Stroop interference and facilitation effects in a relatively large sample of first-episode schizophrenic patients (n=56), a substantial proportion of whom were medication-naïve (n=30) at the time of initial testing. We have also carried out longitudinal follow-up assessments when patients reached a clinically stable state, as well as 4months after recovery from the episode. We found that the Stroop interference effect was not increased in first-episode schizophrenic patients, whether medication-naïve or not. This effect did not change over the follow-up period. In addition, we detected an increase in Stroop facilitation effect in medicated schizophrenic patients, but only in the initial assessment soon after they had received medication. After sustained treatment, the increase in facilitation was normalized. These observations supported previous findings of a normal Stroop interference effect amongst schizophrenic patients. The increased facilitation effect for patients in their early phase of treatment (but not later) may represent an acute effect of anti-psychotic medication. Its nature and significance require further investigation.

Insight changes in acute psychotic episodes: a prospective study of Hong Kong Chinese patients

Insight impairment occurs commonly in psychotic disorders (including mood episodes with psychotic symptoms). The aim of the present study is to measure changes of insight over the course of a psychotic episode and to investigate its relationships with symptoms and neurocognitive functions, as well as psychosocial factors. Insight was assessed at weekly intervals in 80 consecutive inpatients presenting with a psychotic episode by using a Chinese translation of the Scale to Assess Unawareness of Mental Disorder (SUMD). The relationships between insight change and other variables were explored. Modest but significant changes in insight were found in both directions with clinical resolution of psychotic symptoms. In particular, insight "declined" as symptoms improved in a number of patients. In addition, changes in insight score correlated with changes in Wisconsin Card Sorting Test (WCST) performance. More changes in insight (in either direction) tended to occur in younger patients. These results indicated that adequate control of psychotic symptoms and improvement in neuropsychological functioning might be associated with better insight recovery.

University students' attitudes towards mental patients and psychiatric treatment

BACKGROUND

Public attitudes towards mental patients and psychiatric treatment are mostly unfavorable. Mental patients tend to conceal their illness or selectively disclose their treatment histories to someone they trust.

AIMS

To examine the university students' attitudes towards different information regarding a person labeled as mentally ill.

METHODS

We designed seven descriptions of a mentally ill person of varying past and current treatment histories and randomly assigned 308 university undergraduates to read one of the descriptions. Subjects rated their willingness to interact with the hypothetical case using a 19-item social distance scale.

RESULTS

Greater social distance was associated with non-medical field of study, no previous contact with the mentally ill and female gender. Subjects without previous contact with mentally ill individuals kept greater distance from a discharged mental patient receiving psychiatric care than a mental patient who did not require medications nor psychiatric follow-up. In contrast, respondents who had previous contact with the mentally ill were more willing to interact with a discharged mental patient receiving psychiatric care comparing with a person labeled as mentally ill alone and a mental patient who had never been admitted to hospital.

CONCLUSIONS

Implications of our findings in clinical management and designing stigma-reducing programme are discussed.

B2 bradykinin receptor immunoreactivity in rat brain

Bradykinin has long been known to exist in the central nervous system and has been hypothesized to mediate specific functions. Despite an increasing understanding of the functions of bradykinin, little is known about the cell types expressing the bradykinin receptor within the brain. The present investigation employed a monoclonal antibody directed against the 15-amino-acid portion of the C-terminal of the human bradykinin B2 receptor to establish the cellular distribution of bradykinin B2 receptor immunoreactivity in the rat brain. Bradykinin B2 receptor immunoreactivity was ubiquitously and selectively observed in neurons, including those within the olfactory bulb, cerebral cortex, hippocampus, basal forebrain, basal ganglia, thalamus, hypothalamus, cerebellum, and brainstem nuclei. Bradykinin B2 receptor immunoreactivity was also present in the circumventricular organs including choroid plexus, subfornical organ, median eminence, and area postrema. Double-labeling experiments colocalizing the bradykinin B2 receptor with the neuronal marker NeuN or the astrocytic marker glial fibrillary acidic protein revealed that virtually 100% of the bradykinin B2 receptor-immunoreactive positive cells were neurons. The widespread distribution of bradykinin B2 receptor immunoreactivity in neuronal compartments suggests a greater than previously appreciated role for this peptide in neuronal function.

Progressive deterioration of soft neurological signs in chronic schizophrenic patients

OBJECTIVE

Neurological signs are found to be increased in schizophrenia in cross-sectional studies. Whether they progress with time is an important issue in addressing the course of the illness.

METHOD

The current study investigated different groups of neurological signs in 43 stable chronic schizophrenic patients over a 3-year period using an operationalized instrument.

RESULTS

While symptoms and medication have remained largely unchanged in the 3-year period, significant increase in soft neurological signs (SNS) ('motor coordination', 'sensory integration' and 'disinhibition') has been observed. This contrasted with the stability of 'pyramidal', 'extrapyramidal', 'dyskinesia' and 'catatonia' signs. The increase in SNS appears not to be related to age, illness duration, symptoms or medication.

CONCLUSION

This finding suggests that SNS represent a marker sensitive to a possible late deterioration process in the course of a schizophrenic illness.

Age-related decreases in GTP-cyclohydrolase-I immunoreactive neurons in the monkey and human substantia nigra

Guanosine triphosphate cyclohydrolase I (GTPCHI) is a critical enzyme in catecholamine function and is rate limiting for the synthesis of the catecholamine co-factor tetrahydrobiopterin. The present study assessed the distribution of GTPCHI immunoreactivity (-ir) within the monkey and human ventral midbrain and determined whether its expression is altered as a function of age. Light and confocal microscopic analyses revealed that young monkeys and humans displayed GTPCHI-ir within melanin-containing and tyrosine-hydroxylase-ir neurons in primate substantia nigra. Stereological counts revealed that there was a 67.4% reduction in GTPCHI-ir neuronal number, a 63.5% reduction in GTPCHI-ir neuronal density, and a 37.6% reduction in neuronal volume in aged monkeys relative to young cohorts. Similar age-related changes were seen in humans, in whom there were significant reductions in the number of GTPCHI-ir nigral neurons in middle age (58.4%) and aged (81.5%) cases relative to young cohorts. The density of GTPCHI-ir neurons within the nigra was similarly reduced in middle-aged (63.0%) and aged (81.8%) cases. In contrast to monkeys, aged humans did not display shrinkage in the volume of GTPCHI-ir nigral neurons. The presence of numerous melanin-positive, but GTPCHI-ir immunonegative, neurons in the aged monkey and human nigra indicates that these decreases represent an age-related phenotypic downregulation of this enzyme and not a loss of neurons per se. These data indicate that there is a dramatic decrease in GTPCHI-ir in nonhuman primates and humans as a function of age and that loss of this enzyme may be partly responsible for the age-related decrease in dopaminergic tone within nigrostriatal systems.

Neurodegeneration prevented by lentiviral vector delivery of GDNF in primate models of Parkinson's disease

Lentiviral delivery of glial cell line-derived neurotrophic factor (lenti-GDNF) was tested for its trophic effects upon degenerating nigrostriatal neurons in nonhuman primate models of Parkinson's disease (PD). We injected lenti-GDNF into the striatum and substantia nigra of nonlesioned aged rhesus monkeys or young adult rhesus monkeys treated 1 week prior with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). Extensive GDNF expression with anterograde and retrograde transport was seen in all animals. In aged monkeys, lenti-GDNF augmented dopaminergic function. In MPTP-treated monkeys, lenti-GDNF reversed functional deficits and completely prevented nigrostriatal degeneration. Additionally, lenti-GDNF injections to intact rhesus monkeys revealed long-term gene expression (8 months). In MPTP-treated monkeys, lenti-GDNF treatment reversed motor deficits in a hand-reach task. These data indicate that GDNF delivery using a lentiviral vector system can prevent nigrostriatal degeneration and induce regeneration in primate models of PD and might be a viable therapeutic strategy for PD patients.

The complete sequence of the mucosal pathogen Ureaplasma urealyticum

The comparison of the genomes of two very closely related human mucosal pathogens, Mycoplasma genitalium and Mycoplasma pneumoniae, has helped define the essential functions of a self-replicating minimal cell, as well as what constitutes a mycoplasma. Here we report the complete sequence of a more distant phylogenetic relative of those bacteria, Ureaplasma urealyticum (parvum biovar), which is also a mucosal pathogen of humans. It is the third mycoplasma to be sequenced, and has the smallest sequenced prokaryotic genome except for M. genitalium. Although the U. urealyticum genome is similar to the two sequenced mycoplasma genomes, features make this organism unique among mycoplasmas and all bacteria. Almost all ATP synthesis is the result of urea hydrolysis, which generates an energy-producing electrochemical gradient. Some highly conserved eubacterial enzymes appear not to be encoded by U. urealyticum, including the cell-division protein FtsZ, chaperonins GroES and GroEL, and ribonucleoside-diphosphate reductase. U. urealyticum has six closely related iron transporters, which apparently arose through gene duplication, suggesting that it has a kind of respiration system not present in other small genome bacteria The genome is only 25.5% G+C in nucleotide content, and the G+C content of individual genes may predict how essential those genes are to ureaplasma survival.

Pramipexole attenuates the dopaminergic cell loss induced by intraventricular 6-hydroxydopamine

The D3 preferring dopamine agonist pramipexole has been shown to attenuate the cell loss induced by levodopa in vitro. Pramipexole was herein evaluated in the 6-hydroxydopamine lesion model to determine its in vivo effect. Rats were treated with pramipexole or saline before and after an intracerebroventricular 6-hydroxydopamine injection. In the preliminary study, 6-hydroxydopamine produced a 68% reduction in striatal dopamine and a 62% loss in tyrosine hydroxylase immunoreactive (THir) cell counts in the substantia nigra. Pramipexole treated animals exhibited a 29% and a 27% reduction in striatal dopamine and THir cell counts, respectively. THir cell counts and striatal dopamine were significantly correlated. In the stereological study, 6-hydroxydopamine reduced THir cell counts by 47% in saline treated animals and 26% in pramipexole treated animals. These data demonstrate that pramipexole attenuates the biochemical and THir cell changes normally produced by 6-hydroxydopamine consistent with its neuroprotective actions in vitro.

PLAC1, an Xq26 gene with placenta-specific expression

A novel human X-linked gene shows placenta-specific expression and has been named PLAC1. The gene maps 65 kb telomeric to HPRT at Xq26 and has been completely sequenced at the cDNA and genomic levels. The mouse orthologue Plac1 maps to the syntenically equivalent region of the mouse X chromosome. In situ hybridization studies with the antisense mRNA during mouse embryogenesis detect Plac1 expression from 7.5 dpc (days postcoitum) to 14.5 dpc in ectoplacental cone, giant cells, and labyrinthine trophoblasts. The putative human and murine PLAC1 proteins are 60% identical and 77% homologous. Both include a signal peptide and a peptide sequence also found in an interaction domain of the ZP3 (zona pellucida 3) protein. These results make PLAC1 a marker for placental development, with a possible role in the establishment of the mother-fetus interface.

Opposing effects of hypoxia on expression of the angiogenic inhibitor thrombospondin 1 and the angiogenic inducer vascular endothelial growth factor

Tumor angiogenesis, the development of new blood vessels during malignant progression, is a regulated process that has both genetic and physiological controls. Physiologically, angiogenesis is stimulated by decreases in tissue oxygenation (i.e., hypoxia). We investigated the effect of hypoxia on the expression of two angiogenic factors reported to be genetically regulated by the p53 tumor suppressor gene: (a) the angiogenic inhibitor thrombospondin 1 (TSP-1); and (b) the angiogenic inducer vascular endothelial growth factor (VEGF). Analysis of rodent cells that differ in their p53 genotype (p53+/+ or p53-/-) indicated that in vitro exposure to hypoxia simultaneously suppressed TSP-1 and induced VEGF expression, regardless of the p53 genotype. On transformation of these cells with E1A and oncogenic H-ras, the basal level of TSP-1 expression was strongly diminished, whereas that of VEGF could still be induced by hypoxia. Consistent with these in vitro findings, sections of tumors derived from the transformed p53+/+ and p53-/- cells showed that VEGF protein overlapped with regions of hypoxia, whereas TSP-1 protein was below the limits of detection in tumor tissue. Using a panel of normal/immortalized and transformed human cells, it was found that the ability of hypoxia to inhibit TSP-1 expression depends on the cell type and/or the degree of transformation. In contrast, VEGF expression was induced by hypoxia in all of the human cell types examined. Together, these findings suggest that hypoxic and oncogenic signals could interact in the tumor microenvironment to inhibit TSP-1 and induce VEGF expression, promoting the switch to the angiogenic phenotype.

[Property of compliance and change of structural components in anastomosed artery]

OBJECTIVE

To explore the relationship between the properties of compliance and the change of structure of components in anastomosed arteries.

METHODS

The arterial pressure and diameter of femoral arteries of dogs were measured in vivo before and after arterial anastomosis in different time intervals to deduce the arterial compliance. The anastomosed arteries were removed and evaluated through light microscopic examination and various staining methods, the relative contents of elastin, collagen and smooth muscles were measured through image analysis system.

RESULTS

The compliance of arteries was gradually decreased after anastomosis with peak-time on the 14th day. The content of elastin at different time had no significant difference, while the content of collagen increased gradually, the ratio of them was increased.

CONCLUSION

The property of compliance of anastomosed arteries is closely related to the contents of the structural components.

Cystic fibrosis transmembrane conductance regulator has an altered structure when its maturation is inhibited

Inefficient maturation and trafficking to the cell surface of the cystic fibrosis transmembrane conductance regulator (CFTR) is the primary cause of cystic fibrosis. CFTR protein that fails to mature accumulates as an immature core-glycosylated protein and is rapidly degraded. To determine how the structures of mature and immature CFTR are different, we compared the properties of CFTR that had been expressed in the presence or absence of the proteasome inhibitor, MG-132 (carbobenzoxy-L-leucyl-L-leucyl-L-leucinal). Transient expression of wild-type CFTR in the presence of submicromolar concentrations of MG-132 blocks maturation of the protein. We found that expression of CFTR in the presence of MG-132 trapped the protein in a trypsin-sensitive conformation. In addition, the structure of the carboxyl-terminus of immature and mature CFTR differed as histidine-tagged mature CFTR was preferentially recovered by metal-chelate chromatography. No chloride channel activity was detected when membranes containing immature CFTR were fused with planar lipid bilayers. These results show that expression of CFTR in the presence of MG-132 traps the protein in an altered conformation that may be inactive.

Verbal fluency in schizophrenia: reduction in semantic store

OBJECTIVE

This is a study of the word production of patients with schizophrenia using a semantic verbal fluency task to address the unresolved issue of retrieval or storage impairment.

METHOD

Twenty-one patients with schizophrenia and 11 matched healthy subjects performed a semantic verbal fluency task on 'food', 'animal' and 'transport' categories in Cantonese for 3 minutes each on five separate trials.

RESULTS

Patients generated significantly fewer numbers of words compared with control on each trial. The estimated lexicon size of the patients was significantly smaller than that of the equivalent group. The amount of shared words and variable words generated in all five trials were reduced in the patient group.

CONCLUSIONS

Our results suggest that poor verbal fluency in patients with schizophrenia may partly be attributable to reduction in semantic store. The importance of temporal lobe involvement on verbal fluency deficits needs to be emphasised as an integral part of the neurobiological basis of schizophrenia research.

Anatomical study on arteries of fasciae in the forearm fasciocutaneous flap

The arteries of the forearm flap were studied systematically and quantitatively to determine the survival mechanism of fasciocutaneous flaps and provide morphological basis for clinical application. Fourteen forearms from fresh adult cadavers were investigated by methods of dissection under operating and biological microscopes, tissue clearing, tissue sectioning, and image analysis. There were four arterial types in the forearm flaps in which the intermuscular space cutaneous artery was predominant in number. Both intermuscular space cutaneous arteries and intermuscular septal cutaneous arteries anastomosed by branches as arterial chains along the intermuscular spaces and septa where the stem arteries ran through. Arteries of each type gave off epi- and subfascial branches to the deep fascia, and the former were greater in number and larger in diameter. In the same way, the vascular network was thicker in the epifascial level than that in the subfascial level. The percentage of the area of blood vessels in deep fascia (Aa%) was larger than that of the superficial fascia. In the forearm, the deep fascial vasculature is the main pathway through which the fasciocutaneous flap gains its blood supply, and the epifascial vascular network is especially important. It would be better to select the fascial pedicle where the arterial chain exists.

Evolution of the X-specific block embedded in the human Xq21.3/Yp11.1 homology region

The region Xq21.3/Yp11.1 represents the largest segment of homology between the sex chromosomes in humans, though no recombination occurs in male meiosis. It presumably arose as a transposition from the X to the Y chromosome; the present-day organization in the latter chromosome indicates a paracentric inversion that disrupted its continuity. Moreover, an X-specific block (defined by the marker DXS214) is embedded in the region. Previously, no hypotheses about the length, origin, or evolution of this X-specific segment have been proposed. Here we report on the refinement of the size and the sequence of the distal boundary of the X-specific block. Furthermore, we have tracked by FISH experiments the evolution of this region in primates. This further clarifies the multistep mechanism of origin for the XY homology region, by demonstrating that the X-specific block was deleted from the Y chromosome after the initial transfer from the X chromosome.

Hypoxic microenvironment within an embryo induces apoptosis and is essential for proper morphological development

Recent studies have suggested the importance of hypoxia-inducible transcription factors in development, yet the questions of whether hypoxia actually exists in a developing embryo in vivo and, if so, what role it plays in development remain unanswered. In this study, we directly demonstrate that regions of hypoxia, most prominently the hindbrain, otic vesicle, and first branchial arch, exist in a gestational day (GD) 11 rat embryo grown in utero. We also show that varying the oxygen environment of an embryo affects its morphological development. Rat embryos which were grown at 45% oxygen from GD 9-11 showed gross morphological abnormalities, including defective cranial neural tube closure, incomplete otic vesicle invagination, and abnormal somite formation and embryo turning. These embryos, in addition, exhibited reduced cell death. On the other hand, embryos which were grown at 5% oxygen during the same period were stunted in overall growth, yet morphologically normal, and displayed prominent areas of apoptosis. In this study, we propose that embryonic development, like tumor development, requires two different but interactive sets of signals. One set exists in the genetic program for development; the other set arises from changes in the microenvironment of the embryo. Therefore, it is the interplay between these two sets of cues that drives normal embryonic development. The requirement for hypoxia to activate apoptotic cell death is but one example of such interactions.

Clinicopathological findings following intraventricular glial-derived neurotrophic factor treatment in a patient with Parkinson's disease

As part of a safety and tolerability study, a 65-year-old man with Parkinson's disease (PD) received monthly intracerebroventricular injections of glial-derived neurotrophic factor (GDNF). His parkinsonism continued to worsen following intracerebroventricular GDNF treatment. Side effects included nausea, loss of appetite, tingling, L'hermitte's sign, intermittent hallucinations, depression, and inappropriate sexual conduct. There was no evidence of significant regeneration of nigrostriatal neurons or intraparenchymal diffusion of the intracerebroventricular GDNF to relevant brain regions. Alternative GDNF delivery systems should be explored.

Entorhinal cortex beta-amyloid load in individuals with mild cognitive impairment

The deposition of beta-amyloid within the entorhinal cortex (EC) may play a key role in the development of mild cognitive impairment (MCI) in the elderly. To examine the relationship of beta-amyloid deposition to MCI, EC tissue immunostained for this protein was quantitated from a cohort of aged Catholic religious clergy with a clinical diagnosis of MCI and compared to those with no cognitive impairment (NCI) and Alzheimer's disease (AD). beta-amyloid staining was seen in 12 of the 20 NCI, in 10 of 12 MCI, and in all 12 AD cases within the EC. beta-amyloid immunoreactivity displayed two patterns within the EC: (1) a crescent-shaped band within layers 3-4 or (2) bilaminar staining mainly within layers 2-3 and 5-6. Ten cases failed to display any detectable beta-amyloid imunoreactivity. Despite the heterogeneity of beta-amyloid loads within the clinical groups, decomposing an analysis of variance revealed a significant difference across groups in mean beta-amyloid load within the EC based upon a linear trend analysis. Multiple comparisons testing revealed that NCI individuals had a significantly lower mean beta-amyloid load (1.32) than AD individuals (4.55). The MCI individuals had a mean intermediate (2.60) load between NCI and AD, but not statistically distinguishable from the mean for either NCI or AD. Spearman rank correlation showed a trend for decreasing MMSE with increasing amyloid load that failed to reach statistical significance. Since many NCI cases displayed beta-amyloid loads equal to or greater than that seen in some MCI and some AD cases, it is mostly likely that deposition of this protein is not the sole pathogenic event underlying cognitive impairment in the elderly.

Cortical ablation induces a spreading calcium-dependent, secondary pathogenesis which can be reduced by inhibiting calpain

Many forms of acute brain injury are associated with a secondary, glutamate- and calcium-dependent cascade which greatly exacerbates the final damage. The calcium-dependent protease, calpain, has been implicated as an important variable in this pathogenic process. The present studies tested (i) if similar secondary degeneration occurs following surgical ablation of a discrete area within rat visual cortex, (ii) if activation of calpain contributes to the secondary degeneration by spreading into areas adjacent to the ablation, and (iii) if blocking calpain's proteolytic effects reduces the secondary degeneration attendant to the lesion. Antibodies selective for a protein fragment specifically generated by calpain were used to map areas in which the protease had been activated. Labeling was present 5 min after surgery in a narrow zone surrounding the ablated region. The volume of the immunopositive staining increased twofold within 24 h and fivefold by 48 h, at which time it was equivalent in size to the original lesion. This staining pattern significantly decreased in size at 5 days postsurgery. Application of calpain inhibitors to the ablation site immediately after surgery reduced the spread of calpain activation by approximately 80%. Following cortical ablation, the volume of the lateral geniculate nucleus ipsilateral to the cortical ablation shrank by 46 +/- 3% in control rats but only by 31 +/- 5% in animals given the calpain inhibitors. These results establish that (i) a secondary degenerative cascade is unleashed following discrete cortical surgery which expands into brain areas clearly outside the initial perturbation site, (ii) the gradual expansion of calpain activation contributes to the underlying secondary pathology, and (iii) blocking calpain activity substantially reduces atrophy in areas anatomically connected, but physically distal to the damaged zone. The possible utility of topical applications of calpain inhibitors, or analogously acting drugs, in minimizing the secondary effects of brain surgery is discussed.

Sequencing multimegabase-template DNA with BigDye terminator chemistry

Using the recently introduced BigDye terminators, large-template DNA can be directly sequenced with custom primers on automated instruments. Cycle sequencing conditions are presented to sequence DNA samples isolated from a number of microbial genomes including 750-kb Ureaplasma urealyticum, 1.2-Mb Mycoplasma fermentans, 2.3-Mb Streptococcus pneumoniae, and 4.6-Mb Escherichia coli. Average read lengths of >700 bp from unique primer annealing sites are often sufficient to fill final gaps in microbial genome sequencing projects without additional manipulations of template DNA. The technique can also be applied to sequence-targeted regions, thereby bypassing tedious subcloning steps.