bluuebunny/crossref_metadata_2025 huggingface dataset:
solQTL: a tool for QTL analysis, visualization and linking to genomes at SGN database
Authors: Tecle Isaak Y , Menda Naama , Buels Robert M , van der Knaap Esther , Mueller Lukas A
Published: October 2010

Background

A common approach to understanding the genetic basis of complex traits is through identification of associated quantitative trait loci (QTL). Fine mapping QTLs requires several generations of backcrosses and analysis of large populations, which is time-consuming and costly effort. Furthermore, as entire genomes are being sequenced and an increasing amount of genetic and expression data are being generated, a challenge remains: linking phenotypic variation to the underlying genomic variation. To identify candidate genes and understand the molecular basis underlying the phenotypic variation of traits, bioinformatic approaches are needed to exploit information such as genetic map, expression and whole genome sequence data of organisms in biological databases.

Description

The Sol Genomics Network (SGN, http://solgenomics.net) is a primary repository for phenotypic, genetic, genomic, expression and metabolic data for the Solanaceae family and other related Asterids species and houses a variety of bioinformatics tools. SGN has implemented a new approach to QTL data organization, storage, analysis, and cross-links with other relevant data in internal and external databases. The new QTL module, solQTL, http://solgenomics.net/qtl/, employs a user-friendly web interface for uploading raw phenotype and genotype data to the database, R/QTL mapping software for on-the-fly QTL analysis and algorithms for online visualization and cross-referencing of QTLs to relevant datasets and tools such as the SGN Comparative Map Viewer and Genome Browser. Here, we describe the development of the solQTL module and demonstrate its application.

Conclusions

solQTL allows Solanaceae researchers to upload raw genotype and phenotype data to SGN, perform QTL analysis and dynamically cross-link to relevant genetic, expression and genome annotations. Exploration and synthesis of the relevant data is expected to help facilitate identification of candidate genes underlying phenotypic variation and markers more closely linked to QTLs. solQTL is freely available on SGN and can be used in private or public mode.
High-throughput microarray technology in diagnostics of enterobacteria based on genome-wide probe selection and regression analysis
Authors: Friedrich Torben , Rahmann Sven , Weigel Wilfried , Rabsch Wolfgang , Fruth Angelika , Ron Eliora , Gunzer Florian , Dandekar Thomas , Hacker Jörg , Müller Tobias , Dobrindt Ulrich
Published: October 2010

Background

The Enterobacteriaceae comprise a large number of clinically relevant species with several individual subspecies. Overlapping virulence-associated gene pools and the high overall genome plasticity often interferes with correct enterobacterial strain typing and risk assessment. Array technology offers a fast, reproducible and standardisable means for bacterial typing and thus provides many advantages for bacterial diagnostics, risk assessment and surveillance. The development of highly discriminative broad-range microbial diagnostic microarrays remains a challenge, because of marked genome plasticity of many bacterial pathogens.

Results

We developed a DNA microarray for strain typing and detection of major antimicrobial resistance genes of clinically relevant enterobacteria. For this purpose, we applied a global genome-wide probe selection strategy on 32 available complete enterobacterial genomes combined with a regression model for pathogen classification. The discriminative power of the probe set was further tested in silico on 15 additional complete enterobacterial genome sequences. DNA microarrays based on the selected probes were used to type 92 clinical enterobacterial isolates. Phenotypic tests confirmed the array-based typing results and corroborate that the selected probes allowed correct typing and prediction of major antibiotic resistances of clinically relevant Enterobacteriaceae, including the subspecies level, e.g. the reliable distinction of different E. coli pathotypes.

Conclusions

Our results demonstrate that the global probe selection approach based on longest common factor statistics as well as the design of a DNA microarray with a restricted set of discriminative probes enables robust discrimination of different enterobacterial variants and represents a proof of concept that can be adopted for diagnostics of a wide range of microbial pathogens. Our approach circumvents misclassifications arising from the application of virulence markers, which are highly affected by horizontal gene transfer. Moreover, a broad range of pathogens have been covered by an efficient probe set size enabling the design of high-throughput diagnostics.
Polytomous diagnosis of ovarian tumors as benign, borderline, primary invasive or metastatic: development and validation of standard and kernel-based risk prediction models
Authors: Van Calster Ben , Valentin Lil , Van Holsbeke Caroline , Testa Antonia C , Bourne Tom , Van Huffel Sabine , Timmerman Dirk
Published: October 2010

Background

Hitherto, risk prediction models for preoperative ultrasound-based diagnosis of ovarian tumors were dichotomous (benign versus malignant). We develop and validate polytomous models (models that predict more than two events) to diagnose ovarian tumors as benign, borderline, primary invasive or metastatic invasive. The main focus is on how different types of models perform and compare.

Methods

A multi-center dataset containing 1066 women was used for model development and internal validation, whilst another multi-center dataset of 1938 women was used for temporal and external validation. Models were based on standard logistic regression and on penalized kernel-based algorithms (least squares support vector machines and kernel logistic regression). We used true polytomous models as well as combinations of dichotomous models based on the 'pairwise coupling' technique to produce polytomous risk estimates. Careful variable selection was performed, based largely on cross-validated c-index estimates. Model performance was assessed with the dichotomous c-index (i.e. the area under the ROC curve) and a polytomous extension, and with calibration graphs.

Results

For all models, between 9 and 11 predictors were selected. Internal validation was successful with polytomous c-indexes between 0.64 and 0.69. For the best model dichotomous c-indexes were between 0.73 (primary invasive vs metastatic) and 0.96 (borderline vs metastatic). On temporal and external validation, overall discrimination performance was good with polytomous c-indexes between 0.57 and 0.64. However, discrimination between primary and metastatic invasive tumors decreased to near random levels. Standard logistic regression performed well in comparison with advanced algorithms, and combining dichotomous models performed well in comparison with true polytomous models. The best model was a combination of dichotomous logistic regression models. This model is available online.

Conclusions

We have developed models that successfully discriminate between benign, borderline, and invasive ovarian tumors. Methodologically, the combination of dichotomous models was an interesting approach to tackle the polytomous problem. Standard logistic regression models were not outperformed by regularized kernel-based alternatives, a finding to which the careful variable selection procedure will have contributed. The random discrimination between primary and metastatic invasive tumors on temporal/external validation demonstrated once more the necessity of validation studies.
The non-syndromic familial thoracic aortic aneurysms and dissections maps to 15q21 locus
Authors: Keramati Ali R , Sadeghpour Anita , Farahani Maryam M , Chandok Gurangad , Mani Arya
Published: October 2010

Background

Thoracic aortic aneurysms and dissections (TAAD) is a critical condition that often goes undiagnosed with fatal consequences. While majority of the cases are sporadic, more than 20% are inherited as a single gene disorder. The most common familial TAA is Marfan syndrome (MFS), which is primarily caused by mutations in fibrillin-1 (FBN1) gene. Patients with FBN1 mutations are at higher risk for dissection compared to other patients with similar size aneurysms.

Methods

Fifteen family members were genotyped using Affymetrix-10K genechips. A genome-wide association study was carried out using an autosomal dominant model of inheritance with incomplete penetrance. Mutation screening of all exons and exon-intron boundaries of FBN1 gene which reside near the peak Lod score was carried out by direct sequencing.

Results

The index case presented with agonizing substernal pain and was found to have TAAD by transthoracic echocardiogram. The family history was significant for 3 first degree relatives with TAA. Nine additional family members were diagnosed with TAA by echocardiography examinations. The affected individuals had no syndromic features. A genome-wide analysis of linkage mapped the disease gene to a single locus on chromosome 15q21 with a peak Lod score of 3.6 at fibrillin-1 (FBN1) gene locus (odds ratio > 4000:1 in favour of linkage), strongly suggesting that FBN1 is the causative gene. No mutation was identified within the exons and exon-intron boundaries of FBN1 gene that segregated with the disease. Haplotype analysis identified additional mutation carriers who had previously unknown status due to borderline dilation of the ascending aorta.

Conclusions

A familial non-syndromic TAAD is strongly associated with the FBN1 gene locus and has a malignant disease course often seen in MFS patients. This finding indicates the importance of obtaining detailed family history and echocardiographic screening of extended relatives of patients with non-syndromic TAAD to improve the outcome. In addition, association of non-syndromic TAAD with the Marfan disease gene locus poses the question whether secondary prevention strategies employed for Marfan syndrome patients should be applied to all patients with familial TAAD.
Spontaneous preterm labor is associated with an increase in the proinflammatory signal transducer TLR4 receptor on maternal blood monocytes
Authors: Pawelczyk Edyta , Nowicki Bogdan J , Izban Michael G , Pratap Siddharth , Sashti Nupur A , Sanderson Maureen , Nowicki Stella
Published: October 2010

Background

Localized inflammation and increased expression of TLR4 receptors within the uterus has been implicated in the pathogenesis of preterm labor. It remains unclear whether intrauterine inflammatory responses activate the maternal peripheral circulatory system. Therefore we determined whether increased TLR4 expression is present in the peripheral maternal white blood cells of women with spontaneous preterm labor.

Methods

This is a cross-sectional study of 41 preterm labor cases and 41 non-preterm controls. For each case and control sample, RNA was purified from white blood cells and TLR4 mRNA pool size was evaluated by quantitative PCR. Protein expression levels were determined by flow cytometry. Statistical evaluation using multiple linear regressions was used to determine any significant differences between the cases and controls. The purpose was to determine association prevalence of TLR4 levels and preterm labor.

Results

Adjusted mean TLR4 mRNA levels of 0.788 ± 0.037 (standard error) for preterm labor and 0.348 ± 0.038 for the corresponding pregnant control women were statistically significantly different (P = 0.002). Using the lower 95% confidence interval of the mean expression level in PTL subjects (0.7) as a cutoff value for elevated TLR4 mRNA levels, 25/41 (60.9%) of PTL patients expressed elevated TLR4 mRNA as compared to 0/41 (0%) in control subjects. The TLR4 receptor levels in the granulocyte fraction of white blood cells from preterm labor and pregnant controls were similar. However, TLR4+/CD14+monocytes were 2.3 times more frequent (70% vs. 30%) and TLR4 also had a 2.6-fold higher density (750 vs. 280 molecules per cell) in preterm labor women compared with pregnant controls. There was no difference in the levels of TLR4 in patients at term.

Conclusions

Patients with preterm labor exhibited elevated levels of CD14+ maternal blood monocytes each bearing enhanced expression of TLR4, indicating that the peripheral circulatory system is activated in patients with preterm labor. Elevated leukocyte TLR4 levels may be a useful biomarker associated with preterm labor.
Intranasal vaccination with messenger RNA as a new approach in gene therapy: Use against tuberculosis
Authors: Lorenzi Julio CC , Trombone Ana PF , Rocha Carolina D , Almeida Luciana P , Lousada Ricardo L , Malardo Thiago , Fontoura Isabela C , Rossetti Renata AM , Gembre Ana F , Silva Aristóbolo M , Silva Celio L , Coelho-Castelo Arlete AM
Published: October 2010

Background

mRNAs are highly versatile, non-toxic molecules that are easy to produce and store, which can allow transient protein expression in all cell types. The safety aspects of mRNA-based treatments in gene therapy make this molecule one of the most promising active components of therapeutic or prophylactic methods. The use of mRNA as strategy for the stimulation of the immune system has been used mainly in current strategies for the cancer treatment but until now no one tested this molecule as vaccine for infectious disease.

Results

We produce messenger RNA of Hsp65 protein from Mycobacterium leprae and show that vaccination of mice with a single dose of 10 μg of naked mRNA-Hsp65 through intranasal route was able to induce protection against subsequent challenge with virulent strain of Mycobacterium tuberculosis. Moreover it was shown that this immunization was associated with specific production of IL-10 and TNF-alpha in spleen. In order to determine if antigen presenting cells (APCs) present in the lung are capable of capture the mRNA, labeled mRNA-Hsp65 was administered by intranasal route and lung APCs were analyzed by flow cytometry. These experiments showed that after 30 minutes until 8 hours the populations of CD11c+, CD11b+ and CD19+ cells were able to capture the mRNA. We also demonstrated in vitro that mRNA-Hsp65 leads nitric oxide (NO) production through Toll-like receptor 7 (TLR7).

Conclusions

Taken together, our results showed a novel and efficient strategy to control experimental tuberculosis, besides opening novel perspectives for the use of mRNA in vaccines against infectious diseases and clarifying the mechanisms involved in the disease protection we noticed as well.
Diet-induced obesity in zebrafish shares common pathophysiological pathways with mammalian obesity
Authors: Oka Takehiko , Nishimura Yuhei , Zang Liqing , Hirano Minoru , Shimada Yasuhito , Wang Zhipeng , Umemoto Noriko , Kuroyanagi Junya , Nishimura Norihiro , Tanaka Toshio
Published: October 2010

Background

Obesity is a multifactorial disorder influenced by genetic and environmental factors. Animal models of obesity are required to help us understand the signaling pathways underlying this condition. Zebrafish possess many structural and functional similarities with humans and have been used to model various human diseases, including a genetic model of obesity. The purpose of this study was to establish a zebrafish model of diet-induced obesity (DIO).

Results

Zebrafish were assigned into two dietary groups. One group of zebrafish was overfed with Artemia (60 mg dry weight/day/fish), a living prey consisting of a relatively high amount of fat. The other group of zebrafish was fed with Artemia sufficient to meet their energy requirements (5 mg dry weight/day/fish). Zebrafish were fed under these dietary protocols for 8 weeks. The zebrafish overfed with Artemia exhibited increased body mass index, which was calculated by dividing the body weight by the square of the body length, hypertriglyceridemia and hepatosteatosis, unlike the control zebrafish. Calorie restriction for 2 weeks was applied to zebrafish after the 8-week overfeeding period. The increased body weight and plasma triglyceride level were improved by calorie restriction. We also performed comparative transcriptome analysis of visceral adipose tissue from DIO zebrafish, DIO rats, DIO mice and obese humans. This analysis revealed that obese zebrafish and mammals share common pathophysiological pathways related to the coagulation cascade and lipid metabolism. Furthermore, several regulators were identified in zebrafish and mammals, including APOH, IL-6 and IL-1β in the coagulation cascade, and SREBF1, PPARα/γ, NR1H3 and LEP in lipid metabolism.

Conclusion

We established a zebrafish model of DIO that shared common pathophysiological pathways with mammalian obesity. The DIO zebrafish can be used to identify putative pharmacological targets and to test novel drugs for the treatment of human obesity.
Prognostic significance of Oct4 and Sox2 expression in hypopharyngeal squamous cell carcinoma
Authors: Ge Nan , Lin Huan-Xin , Xiao Xiang-Sheng , Guo Ling , Xu Hui-Min , Wang Xin , Jin Ting , Cai Xiu-Yu , Liang Yi , Hu Wei-Han , Kang Tiebang
Published: October 2010

Background

Oct4 and Sox2 are two major transcription factors related to the stem cell self-renewal and differentiation. The aim of this study was to examine the association between Oct4 and Sox2 expression levels with both the clinicopathological characteristics and prognoses of patients with hypopharyngeal squamous cell carcinoma.

Method

Tumor tissue samples from 85 patients with hypopharyngeal squamous cell carcinoma were collected, and the clinical follow-up data of these patients were recorded, and expression status of Oct4 and Sox2 were examined in these tissue samples by immunohistochemistry (IHC).

Results

Oct4 expression was found to be an independent predictive factor for overall survival (p = 0.004) in patients with hypopharyngeal squamous cell carcinoma and was independently related to loco-regional control (p = 0.001). Although Sox2 expression status showed no significant association with overall survival (p = 0.166), disease-free survival (p = 0.680) or loco-regional control (p = 0.383), when using a subgroup analysis, the subgroup with both high Oct4 and Sox2 expression had the best prognosis (p = 0.000). Sox2 expression could be a potential prognostic predictor for patients with hypopharyngeal squamous cell carcinoma. Simultaneous analyses of Oct4 and Sox2 expression could be more effective in evaluating the prognoses of patients with hypopharyngeal squamous cell carcinoma.

Conclusion

Oct4 expression is an independent predictive factor for patients with hypopharyngeal squamous cell carcinoma, suggesting that Oct4 expression may be a useful indicator for predicting the prognosis of hypopharyngeal squamous cell carcinoma.
Cytomorphometric changes in the dorsal raphe neurons after rapid eye movement sleep deprivation are mediated by noradrenalin in rats
Authors: Ranjan Amit , Biswas Sudipta , Mallick Birendra N.
Published: October 2010

Objectives

This study was carried out to investigate the effect of rapid eye movement sleep (REMS) deprivation (REMSD) on the cytomorphology of the dorsal raphe (DR) neurons and to evaluate the possible role of REMSD-induced increased noradrenalin (NA) in mediating such effects.

Methods

Rats were REMS deprived by the flowerpot method; free moving normal home cage rats, large platform and post REMS-deprived recovered rats were used as controls. Further, to evaluate if the effects were induced by NA, separate sets of experimental rats were treated (i.p.) with α1-adrenoceptor antagonist, prazosin (PRZ). Histomorphometric analysis of DR neurons in stained brain sections were performed in experimental and control rats; neurons in inferior colliculus (IC) served as anatomical control.

Results

The mean size of DR neurons was larger in REMSD group compared to controls, whereas, neurons in the recovered group of rats did not significantly differ than those in the control animals. Further, mean cell size in the post-REMSD PRZ-treated animals was comparable to those in the control groups. IC neurons were not affected by REMSD.

Conclusions

REMS loss has been reported to impair several physiological, behavioral and cellular processes. The mean size of the DR neurons was larger in the REMS deprived group of rats than those in the control groups; however, in the REMS deprived and prazosin treated rats the size was comparable to the normal rats. These results showed that REMSD induced increase in DR neuronal size was mediated by NA acting on α1-adrenoceptor. The findings suggest that the sizes of DR neurons are sensitive to REMSD, which if not compensated could lead to neurodegeneration and associated disorders including memory loss and Alzheimer's disease.
Immortalized, premalignant epithelial cell populations contain long-lived, label-retaining cells that asymmetrically divide and retain their template DNA
Authors: Bussard Karen M , Boulanger Corinne A , Kittrell Frances S , Behbod Fariba , Medina Daniel , Smith Gilbert H
Published: October 2010

Introduction

During selective segregation of DNA, a cell asymmetrically divides and retains its template DNA. Asymmetric division yields daughter cells whose genome reflects that of the parents, simultaneously protecting the parental cell from genetic errors that may occur during DNA replication. We hypothesized that long-lived epithelial cells are present in immortal, premalignant cell populations, undergo asymmetric division, retain their template DNA strands, and cycle both during allometric growth and during pregnancy.

Methods

The glands of 3-week-old immune-competent Balb/C female mice were used intact or cleared of host epithelium and implanted with ductal-limited, lobule-limited, or alveolar-ductal progenitor cells derived from COMMA-D1 pre-malignant epithelial cells. 5-Bromo-2-deoxyuridine (5-BrdU) was administered to identify those cells that retain their template DNA. Nulliparous mice were then either injected with [3H]-thymidine (3H-TdR) to distinguish 5-BrdU label-retaining cells that enter the cell cycle and euthanized, or mated, injected with 3H-TdR, and euthanized at various days after coitus. Sections were stained for estrogen receptor-α (ER-α) or progesterone receptor (PR) with immunohistochemistry. Cells labeled with both 5-BrdU and 3H-TdR were indicative of label-retaining epithelial cells (LRECs).

Results

Cells that retained a 5-BrdU label and cells labeled with [3H]-thymidine were found in all mice and were typically detected along the branching epithelium of mature mouse mammary glands. Cells containing double-labeled nuclei (LRECs) were found in the intact mammary glands of both pregnant and nulliparous mice, and in mammary glands implanted with premalignant cells. Double-labeled cells (3H-TdR/5-BrdU) represent a small portion of cells in the mammary gland that cycle and retain their template DNA (5-BrdU). Some label-retaining cells were also ER-α or PR positive. LRECs distributed their second label (3H-TdR) to daughter cells, and this effect persisted during pregnancy. LRECs, and small focal hyperplasia, were found in all immortalized premalignant mammary-implant groups.

Conclusions

The results indicate that a subpopulation of long-lived, label-retaining epithelial cells (LRECs) is present in immortal premalignant cell populations. These LRECs persist during pregnancy, retain their original DNA, and a small percentage express ER-α and PR. We speculate that LRECs in premalignant hyperplasia represent the long-lived (memory) cells that maintain these populations indefinitely.
Energetic Metabolism and Human Sperm Motility: Impact of CB1 Receptor Activation
Authors: Barbonetti A. , Vassallo M. R. C. , Fortunato D. , Francavilla S. , Maccarrone M. , Francavilla F.
Published: October 2010

It has been reported that the endocannabinoid anandamide (AEA) exerts an adverse effect on human sperm motility, which has been ascribed to inhibition of mitochondrial activity. This seems to be at variance with evidence suggesting a major role of glycolysis in supplying ATP for sperm motility; furthermore, the role of AEA-binding receptors in mediating mitochondrial inhibition has not yet been explored. In this study, human sperm exposure to Met-AEA (methanandamide, nonhydrolyzable analog of AEA) in the micromolar range significantly decreased mitochondrial transmembrane potential (ΔΨm), similarly to rotenone, mitochondrial complex I inhibitor. The effect of Met-AEA (1 μm) was prevented by SR141716, CB1 cannabinoid receptor antagonist, but not by SR144528, CB2 antagonist, nor by iodoresiniferatoxin, vanilloid receptor antagonist. The effect of Met-AEA did not involve activation of caspase-9 or caspase-3 and was reverted by washing. In the presence of glucose, sperm exposure either to Met-AEA up to 1 μm or to rotenone for up to 18 h did not affect sperm motility. At higher doses Met-AEA produced a CB1-independent poisoning of spermatozoa, reducing their viability. Under glycolysis blockage, 1 μm Met-AEA, similarly to rotenone, dramatically abolished sperm motility, an effect that was prevented by SR1 and reverted by washing. In conclusion, CB1 activation induced a nonapoptotic decrease of ΔΨm, the detrimental reflection on sperm motility of which could be revealed only under glycolysis blockage, unless very high doses of Met-AEA, producing CB1-independent sperm toxicity, were used. The effects of CB1 activation reported here contribute to elucidate the relationship between energetic metabolism and human sperm motility.
Pregnane X Receptor as a Therapeutic Target to Inhibit Androgen Activity
Authors: Zhang Bin , Cheng Qiuqiong , Ou Zhimin , Lee Jung Hoon , Xu Meishu , Kochhar Upasana , Ren Songrong , Huang Min , Pflug Beth R. , Xie Wen
Published: October 2010

The androgen-androgen receptor signaling pathway plays an important role in the pathogenesis of prostate cancer. Accordingly, androgen deprivation has been the most effective endocrine therapy for hormone-dependent prostate cancer. Here, we report a novel pregnane X receptor (PXR)-mediated and metabolism-based mechanism to reduce androgenic tone. PXR is a nuclear receptor previously known as a xenobiotic receptor regulating the expression of drug metabolizing enzymes and transporters. We showed that genetic (using a PXR transgene) or pharmacological (using a PXR agonist) activation of PXR lowered androgenic activity and inhibited androgen-dependent prostate regeneration in castrated male mice that received daily injections of testosterone propionate by inducing the expression of cytochrome P450 (CYP)3As and hydroxysteroid sulfotransferase (SULT)2A1, which are enzymes important for the metabolic deactivation of androgens. In human prostate cancer cells, treatment with the PXR agonist rifampicin (RIF) inhibited androgen-dependent proliferation of LAPC-4 cells but had little effect on the growth of the androgen-independent isogenic LA99 cells. Down-regulation of PXR or SULT2A1 in LAPC-4 cells by short hairpin RNA or small interfering RNA abolished the RIF effect, indicating that the inhibitory effect of RIF on androgens was PXR and SULT2A1 dependent. In summary, we have uncovered a novel function of PXR in androgen homeostasis. PXR may represent a novel therapeutic target to lower androgen activity and may aid in the treatment and prevention of hormone-dependent prostate cancer.
Abnormal Epithelial Cell Polarity and Ectopic Epidermal Growth Factor Receptor (EGFR) Expression Induced in Emx2 KO Embryonic Gonads
Authors: Kusaka Masatomo , Katoh-Fukui Yuko , Ogawa Hidesato , Miyabayashi Kanako , Baba Takashi , Shima Yuichi , Sugiyama Noriyuki , Sugimoto Yukihiko , Okuno Yasushi , Kodama Ryuji , Iizuka-Kogo Akiko , Senda Takao , Sasaoka Toshikuni , Kitamura Kunio , Aizawa Shinichi , Morohashi Ken-ichirou
Published: October 2010

The gonadal primordium first emerges as a thickening of the embryonic coelomic epithelium, which has been thought to migrate mediodorsally to form the primitive gonad. However, the early gonadal development remains poorly understood. Mice lacking the paired-like homeobox gene Emx2 display gonadal dysgenesis. Interestingly, the knockout (KO) embryonic gonads develop an unusual surface accompanied by aberrant tight junction assembly. Morphological and in vitro cell fate mapping studies showed an apparent decrease in the number of the gonadal epithelial cells migrated to mesenchymal compartment in the KO, suggesting that polarized cell division and subsequent cell migration are affected. Microarray analyses of the epithelial cells revealed significant up-regulation of Egfr in the KO, indicating that Emx2 suppresses Egfr gene expression. This genetic correlation between the two genes was reproduced with cultured M15 cells derived from mesonephric epithelial cells. Epidermal growth factor receptor signaling was recently shown to regulate tight junction assembly through sarcoma viral oncogene homolog tyrosine phosphorylation. We show through Emx2 KO analyses that sarcoma viral oncogene homolog tyrosine phosphorylation, epidermal growth factor receptor tyrosine phosphorylation, and Egfr expression are up-regulated in the embryonic gonad. Our results strongly suggest that Emx2 is required for regulation of tight junction assembly and allowing migration of the gonadal epithelia to the mesenchyme, which are possibly mediated by suppression of Egfr expression.
The Metabolic Phenotype of Prader-Willi Syndrome (PWS) in Childhood: Heightened Insulin Sensitivity Relative to Body Mass Index
Authors: Haqq Andrea M. , Muehlbauer Michael J. , Newgard Christopher B. , Grambow Steven , Freemark Michael
Published: October 2010

Context: Insulin sensitivity is higher in patients with Prader-Willi syndrome (PWS) than in body mass index-matched obese controls (OCs). Factors contributing to the heightened insulin sensitivity of PWS remain obscure. We compared the fasting levels of various hormones, cytokines, lipids, and liver function tests in 14 PWS patients and 14 OCs with those in 14 age- and gender-matched lean children (LC). We hypothesized that metabolic profiles of children with PWS are comparable with those of LC, but different from those of OCs.

Results: Leptin levels were comparable in PWS patients and OCs, suggesting comparable degrees of adiposity. Glucose levels were comparable among groups. However, fasting insulin concentrations and homeostasis model assessment insulin resistance index were lower in PWS patients than in OCs (P < 0.05) and similar to LC. Moreover, high-density lipoprotein levels were lower and triglycerides higher in OCs (P < 0.05) but not PWS patients. Total adiponectin, high-molecular-weight (HMW) adiponectin and the HMW to total adiponectin ratio were higher in PWS patients (P < 0.05) than in OCs and similar to LC. High-sensitivity C-reactive protein and IL-6 levels were higher in OCs than in PWS patients or LC (P < 0.05). Nevertheless, PAI-1 levels were elevated in both OC and PWS patients. There were no group differences in glucagon-like peptide-1, macrophage chemoattractant protein-1, TNFα, IL-2, IL-8, IL-10, IL-12p40, IL-18, resistin, total or low-density lipoprotein cholesterol, aspartate aminotransferase, or alanine aminotransferase.

Conclusions: The heightened insulin sensitivity of PWS patients relative to OCs is associated with higher levels of adiponectin and lower levels of high-sensitivity C-reactive protein and IL-6. Future studies will determine whether PWS children are protected from obesity comorbidities such as type 2 diabetes, hyperlipidemia, and nonalcoholic fatty liver disease.
Interferon Tau Regulates PGF2α Release from the Ovine Endometrial Epithelial Cells via Activation of Novel JAK/EGFR/ERK/EGR-1 Pathways
Authors: Banu Sakhila K. , Lee JeHoon , Stephen Sam D. , Nithy Thamizh K. , Arosh Joe A.
Published: October 2010

In ruminants, pulsatile release of prostaglandin F2α (PGF2α) from the endometrium is transported to the ovary and induces luteolysis thereby allowing new estrous cycle. Interferon tau (IFNT), a type 1 IFN secreted by the trophoblast cells of the developing conceptus, acts on endometrial luminal epithelial (LE) cells and inhibits pulsatile release of PGF2α and establishes pregnancy. One of the unknown mechanisms is that endometrial pulsatile release of PGF2α is inhibited whereas basal release of PGF2α is increased in pregnant compared with nonpregnant sheep. We have recently found that pulsatile release of PGF2α from the endometrium is regulated by prostaglandin transporter (PGT)-mediated mechanisms. We hypothesize that modulation in the endometrial pulsatile vs. basal release of PGF2α likely requires PGT-mediated selective transport, and IFNT interacts with PGT protein and modulates pulsatile vs. basal release of PGF2α. The new findings of the present study are: 1) IFNT activates novel JAK-SRC kinase-EGFR-RAS-RAF-ERK1/2-early growth response (EGR)-1 signaling module in LE cells; 2) IFNT increases interactions between PGT and ERK1/2 or EGR-1 proteins and alters phosphorylation of PGT protein; 3) IFNT precludes action of protein kinase C and Ca2+ on PGT function; and 4) IFNT inhibits 80% PGT-mediated but not 20% simple diffusion-mediated release of PGF2α from the endometrial LE cells through this novel signaling module. The results of the present study provide important new insights on IFNT signaling and molecular control of PGT-mediated release of PGF2α and unravel the underlying mechanisms responsible for the increased basal release of PGF2α at the time of establishment of pregnancy in ruminants.
Syndecan-1 couples the insulin-like growth factor-1 receptor to inside-out integrin activation
Authors: Beauvais DeannaLee M. , Rapraeger Alan C.
Published: October 2010

Syndecan-1 (Sdc1) engages and activates the αvβ3 (and/or αvβ5) integrin when clustered in human carcinoma and endothelial cells. Although the engagement is extracellular, the activation mechanism is cytoplasmic. This talin-dependent, inside-out signaling pathway is activated downstream of the insulin-like growth factor-1 receptor (IGF1R), whose kinase activity is triggered by Sdc1 clustering. In vitro binding assays using purified receptors suggest that association of the Sdc1 ectodomain with the integrin provides a ‘docking face’ for IGF1R. IGF1R docking and activation of the associated integrin is blocked by synstatin (SSTN92–119), a peptide derived from the integrin engagement site in Sdc1. IGF1R colocalizes with αvβ3 integrin and Sdc1 in focal contacts, but fails to associate with or activate the integrin in cells either lacking Sdc1 or expressing Sdc1Δ67–121, a mutant that is unable to form the Sdc1–integrin–IGF1R ternary complex. Integrin activation is also blocked by IGF1R inhibitors or by silencing IGF1R or talin expression with small-interfering RNAs (siRNAs). In both cases, expression of the constitutively active talin F23 head domain rescues integrin activation. We recently reported that SSTN92–119 blocks angiogenesis and impairs tumor growth in mice, therefore this Sdc1-mediated integrin regulatory mechanism might be a crucial regulator of disease processes known to rely on these integrins, including tumor cell metastasis and tumor-induced angiogenesis.
Efficient Capping of Growing Gold Nanoparticles by Porphyrin Having Two Disulfide Straps over One Face
Authors: Hitomi Yutaka , Ohyama Junya , Higuchi Yasuhiro , Aoki Kazuki , Shishido Tetsuya , Funabiki Takuzo , Kodera Masahito , Tanaka Tsunehiro
Published: October 2010

Two types of tetrathiolated surface passivants were synthesized in order to explore the effect of S-functional groups (disulfide vs. S-thioester) to control the size of gold nanoparticles prepared by a simple one-pot reduction of tetrachloroaurate with sodium tetrahydroborate. Both the passivants have four thiolated arms in the same direction perpendicular to a porphyrin plane, and produced small porphyrin-coated gold nanoparticles 2 to 4 nm in size by one-pot reduction of AuIII ions at S/Au from 1 to 16. The constancy in particle size at S/Au ratio less than 4 was greater with use of tetradentate disulfide passivant compared with use of tetradentate S-thioester ligand, which should be attributed to faster adsorption of disulfide groups with gold than that of S-thioester groups. The results described here suggest that passivants having multivalent disulfide bonds should be promising candidates for constructing monolayer-protected gold nanoparticles of well-defined size.
Potential of Phosphate Ion Removal Using an Al3+-Cross-linked Chitosan-g-Poly(Acrylic Acid)/Vermiculite Ionic Hybrid
Authors: Zheng Yian , Wang Aiqin
Published: October 2010

In this study, a composite, chitosan- g-poly(acrylic acid)/ vermiculite, was prepared by aqueous dispersion polymerization using chitosan as the stabilizer, acrylic acid as the monomer and vermiculite as the inorganic additive. It was then cross-linked with common divalent or trivalent cations to obtain adsorbents with a higher affinity for phosphate ions. Factors influencing the adsorption capacity were investigated, the results indicating that the trivalent ion cross-linked hybrid exhibited a potential for the removal of phosphate ions and that a lower concentration of cross-linking agent could achieve the complete cross-linking of carboxylate groups within the composite. The adsorption of phosphate ions onto the developed adsorbent was pH-dependent, with a lower pH yielding a higher adsorption capacity. The Langmuir and Freundlich models were used to describe the adsorption data; the maximum adsorption capacity of 22.64 mg/g was comparable with that reported for other adsorbents. Desorption studies showed that the adsorbed phosphate ions were relatively difficult to remove from the hybrid material.
Bentonite as an Alternative Adsorbent for the Purification of Styrene Monomer: Adsorption Kinetics, Equilibrium and Process Design
Authors: Ovejero Gabriel , Romero M. Dolores , Díaz Ismael , Mestanza María , Díez Eduardo
Published: October 2010

Some problems have been reported regarding the purification of styrene monomer by adsorption onto alumina beds, making this process both difficult and expensive. A study of the adsorption equilibrium and kinetics of t-butylcatechol (TBC) and water onto an alternative adsorbent, bentonite, is presented herein. Experimental equilibrium and kinetic measurements onto silica gel and commercial alumina are also included in order to compare the equilibrium capacities and adsorption rates. In addition, process design and economic evaluation of the adsorption process using bentonite as an adsorbent are also included.
Removal of Copper(II) Ions from Aqueous Solution Using Sphingomonas Paucimobolis Biomass
Authors: Wang Xue Song , Huang Li Ping , Li Yuan , Chen Jing
Published: October 2010

Sphingomonas paucimobilis biomass has been successfully utilized to degrade several persistent organic pollutants (POPs). However, few studies have been conducted using it to remove heavy metal ions from aqueous solutions. In the present study, the biosorption of copper(II) ions was investigated using non-living Sphingomonas paucimobilis biomass isolated from activated sludge, as obtained from the Lianyungang Dapu sewage treatment plant in China. The effects of several parameters including solution pH, contact time and ionic strength on the Cu(II) ion uptake were studied. The biomass was characterized by scanning electron microscopy/X-ray energy dispersive spectroscopy (SEM–EDS) and Fourier-transform infrared spectrometry (FT-IR). The applicability of the Langmuir and Freundlich models was tested. The correlation coefficients (R2) of both models were greater than 0.9. The maximum adsorption capacities were found to be 50.1 mg/g for Cu(II) ions at 20 °C. The adsorption process was rapid and followed pseudo-second-order kinetics. Optimum adsorption was achieved at pH 5. The adsorption was also found to be dependent on the NaCl concentration employed. The Sphingomonas paucimobilis biomass could serve as an adsorbent for the removal of Cu(II) ions from industrial effluents.
An Integrated 3D Geodatabase for Palladio's Work
Authors: Apollonio Fabrizio I. , Corsi Cristiana , Gaiani Marco , Baldissini Simone
Published: October 2010

The paper presents a novel digital 3D GIS web-based system entirely founded on Google Earth, built to offer a deep insight into Palladio's opera for restitution of its architectural surveys, reconstruction for historical reasons, analysis for structural and other options, and assembly and presentation of all certified Palladian documentation. The development of the application follows the philosophy of visual computing and it is based on an architectural knowledge representation. The information system is conceived as a typical Rich Internet Application and it is based on the digitalization of the complete Palladian corpus documentation implemented by the Centro Internazionale di Studi di Architettura Andrea Palladio (CISAAP). The 3D geodatabase system is, actually, in use at the Centro as the Palladian information system for researchers and in two expositions at Barbaran da Porto Palace in Vicenza, and at Villa Poiana at Poiana Maggiore, where is widely used by tourists for virtual visits to Palladian buildings.
Parametric Documenting of Built Heritage: 3D Virtual Reconstruction of Architectural Details
Authors: Chevrier Christine , Charbonneau Nathalie , Grussenmeyer Pierre , Perrin Jean-Pierre
Published: October 2010

This paper examines 3D modelling of architectural elements with the help of parametric components. Such components may be useful within the framework of projects dealing with virtual 3D reconstruction of heritage monuments. Architectural components of the built heritage often have complex geometry. We studied the various geometrical shapes of a given architectural element, representative of a specific period and place. This study allowed us to identify the parameters and to implement parametric objects (in Maya Environment [1]). We also developed a Graphical User Interface (GUI) to answer the user's needs while generating the 3D model representing the architectural element. Within this GUI, the user is able to make adjustments with the help of laser point clouds from laserscanning, 2D plans or photographs. We exemplify our method with a case study dealing with openings and lintels. The corpus under study consists of elements of the built heritage of Montreal (Canada) and Nancy (France).
The Chair Back Experiment: Hierarchical Temporal Memory and the Evolution of Artificial Intelligence in Architecture
Authors: Jacobus Frank , McCormack Jay , Hartung Josh
Published: October 2010

Computational synthesis tools that automatically generate solutions to design problems are not widely used in architectural practice despite many years of research. This deficiency can be attributed, in part, to the difficulty of constructing robust building specific databases. New advances in artificial intelligence such as Hierarchical Temporal Memory (HTM) have the potential to make the construction of these databases more realistic in the near future. Based on an emerging theory of human neurological function, HTMs excel at ambiguous pattern recognition. This paper includes a first experiment using HTMs for learning and recognizing patterns in the form of visual style characteristics in three distinct chair back types. Results from the experiment indicate that HTMs develop a similar storage of quality to humans and are therefore a promising option for capturing multi-modal information in future design automation efforts.
Loop and stem dynamics during RNA hairpin folding and unfolding
Authors: Sarkar Krishnarjun , Nguyen Duc A. , Gruebele Martin
Published: October 2010

2-Aminopurine (2AP) is a fluorescent adenine analog that probes mainly base stacking in nucleic acids. We labeled the loop or the stem of the RNA hairpin gacUACGguc with 2AP to study folding thermodynamics and kinetics at both loci. Thermal melts and fast laser temperature jumps detected by 2AP fluorescence monitored the stability and folding/unfolding kinetics. The observed thermodynamic and kinetic traces of the stem and loop mutants, though strikingly different at a first glance, can be fitted to the same free-energy landscape. The differences between the two probe locations arise because base stacking decreases upon unfolding in the stem, whereas it increases in the loop. We conclude that 2AP is a conservative adenine substitution for mapping out the contributions of different RNA structural elements to the overall folding process. Molecular dynamics (MD) totaling 0.6 μsec were performed to look at the conformations populated by the RNA at different temperatures. The combined experimental data, and MD simulations lead us to propose a minimal four-state free-energy landscape for the RNA hairpin. Analysis of this landscape shows that a sequential folding model is a good approximation for the full folding dynamics. The frayed state formed initially from the native state is a heterogeneous ensemble of structures whose stem is frayed either from the end or from the loop.
Serum-stable RNA aptamers to urokinase-type plasminogen activator blocking receptor binding
Authors: Dupont Daniel Miotto , Madsen Jeppe Buur , Hartmann Roland Karl , Tavitian Bertrand , Ducongé Frédéric , Kjems Jørgen , Andreasen Peter André
Published: October 2010

The serine proteinase urokinase-type plasminogen activator (uPA) is widely recognized as a potential target for anticancer therapy. Its association with cell surfaces through the uPA receptor (uPAR) is central to its function and plays an important role in cancer invasion and metastasis. In the current study, we used systematic evolution of ligands by exponential enrichment (SELEX) to select serum-stable 2′-fluoro-pyrimidine-modified RNA aptamers specifically targeting human uPA and blocking the interaction to its receptor at low nanomolar concentrations. In agreement with the inhibitory function of the aptamers, binding was found to be dependent on the presence of the growth factor domain of uPA, which mediates uPAR binding. One of the most potent uPA aptamers, upanap-12, was analyzed in more detail and could be reduced significantly in size without severe loss of its inhibitory activity. Finally, we show that the uPA-scavenging effect of the aptamers can reduce uPAR-dependent endocytosis of the uPA–PAI-1 complex and cell-surface associated plasminogen activation in cell culture experiments. uPA-scavenging 2′-fluoro-pyrimidine-modified RNA aptamers represent a novel promising principle for interfering with the pathological functions of the uPA system.
A novel Nop5–sRNA interaction that is required for efficient archaeal box C/D sRNP formation
Authors: Ghalei Homa , Hsiao He-Hsuan , Urlaub Henning , Wahl Markus C. , Watkins Nicholas J.
Published: October 2010

Archaeal and eukaryotic box C/D RNPs catalyze the 2′-O-methylation of ribosomal RNA, a modification that is essential for the correct folding and function of the ribosome. Each archaeal RNP contains three core proteins—L7Ae, Nop5, and fibrillarin (methyltransferase)—and a box C/D sRNA. Base-pairing between the sRNA guide region and the rRNA directs target site selection with the C/D and related C′/D′ motifs functioning as protein binding sites. Recent structural analysis of in vitro assembled archaeal complexes has produced two divergent models of box C/D sRNP structure. In one model, the complex is proposed to be monomeric, while the other suggests a dimeric sRNP. The position of the RNA in the RNP is significantly different in each model. We have used UV-cross-linking to characterize protein–RNA contacts in the in vitro assembled Pyrococcus furiosus box C/D sRNP. The P. furiosus sRNP components assemble into complexes that are the expected size of di-sRNPs. Analysis of UV-induced protein–RNA cross-links revealed a novel interaction between the ALFR motif, in the Nop domain of Nop5, and the guide/spacer regions of the sRNA. We show that the ALFR motif and the spacer sequence adjacent to box C or C′ are important for box C/D sRNP assembly in vitro. These data therefore reveal new RNA–protein contacts in the box C/D sRNP and suggest a role for Nop5 in substrate binding and/or release.