bluuebunny/crossref_metadata_2025 huggingface dataset:
Global mRNA expression analysis in myosin II deficient strains of Saccharomyces cerevisiae reveals an impairment of cell integrity functions
Authors: Rodríguez-Quiñones José F , Irizarry Rafael A , Díaz-Blanco Nitza L , Rivera-Molina Félix E , Gómez-Garzón Diana , Rodríguez-Medina José R
Published: January 2008

Background

TheSaccharomyces cerevisiae MYO1gene encodes the myosin II heavy chain (Myo1p), a protein required for normal cytokinesis in budding yeast. Myo1p deficiency in yeast (myo1Δ) causes a cell separation defect characterized by the formation of attached cells, yet it also causes abnormal budding patterns, formation of enlarged and elongated cells, increased osmotic sensitivity, delocalized chitin deposition, increased chitin synthesis, and hypersensitivity to the chitin synthase III inhibitor Nikkomycin Z. To determine how differential expression of genes is related to these diverse cell wall phenotypes, we analyzed the global mRNA expression profile ofmyo1Δstrains.

Results

Global mRNA expression profiles ofmyo1Δstrains and their corresponding wild type controls were obtained by hybridization to yeast oligonucleotide microarrays. Results for selected genes were confirmed by real time RT-PCR. A total of 547 differentially expressed genes (p ≤ 0.01) were identified with 263 up regulated and 284 down regulated genes in themyo1Δstrains. Gene set enrichment analysis revealed the significant over-representation of genes in the protein biosynthesis and stress response categories. TheSLT2/MPK1gene was up regulated in the microarray, and amyo1Δslt2Δdouble mutant was non-viable. Overexpression of ribosomal protein genesRPL30andRPS31suppressed the hypersensitivity to Nikkomycin Z and increased the levels of phosphorylated Slt2p inmyo1Δstrains. Increased levels of phosphorylated Slt2p were also observed in wild type strains under these conditions.

Conclusion

Following this analysis of global mRNA expression in yeastmyo1Δstrains, we conclude that 547 genes were differentially regulated inmyo1Δstrains and that the stress response and protein biosynthesis gene categories were coordinately regulated in this mutant. TheSLT2/MPK1gene was confirmed to be essential formyo1Δstrain viability, supporting that the up regulated stress response genes are regulated by thePKC1cell integrity pathway. Suppression of Nikkomycin Z hypersensitivity together with Slt2p phosphorylation was caused by the overexpression of ribosomal protein genesRPL30andRPS31. These ribosomal protein mRNAs were down regulated in themyo1Δarrays, suggesting that down regulation of ribosomal biogenesis may affect cell integrity inmyo1Δstrains.
Development of a human mitochondrial oligonucleotide microarray (h-MitoArray) and gene expression analysis of fibroblast cell lines from 13 patients with isolated F1Fo ATP synthase deficiency
Authors: Čížková Alena , Stránecký Viktor , Ivánek Robert , Hartmannová Hana , Nosková Lenka , Piherová Lenka , Tesařová Markéta , Hansíková Hana , Honzík Tomáš , Zeman Jiří , Divina Petr , Potocká Andrea , Paul Jan , Sperl Wolfgang , Mayr Johannes A , Seneca Sara , Houštĕk Josef , Kmoch Stanislav
Published: January 2008

Background

To strengthen research and differential diagnostics of mitochondrial disorders, we constructed and validated an oligonucleotide microarray (h-MitoArray) allowing expression analysis of 1632 human genes involved in mitochondrial biology, cell cycle regulation, signal transduction and apoptosis. Using h-MitoArray we analyzed gene expression profiles in 9 control and 13 fibroblast cell lines from patients with F1FoATP synthase deficiency consisting of 2 patients with mt9205ΔTA microdeletion and a genetically heterogeneous group of 11 patients with not yet characterized nuclear defects. Analysing gene expression profiles, we attempted to classify patients into expected defect specific subgroups, and subsequently reveal group specific compensatory changes, identify potential phenotype causing pathways and define candidate disease causing genes.

Results

Molecular studies, in combination with unsupervised clustering methods, defined three subgroups of patient cell lines – M group with mtDNA mutation and N1 and N2 groups with nuclear defect. Comparison of expression profiles and functional annotation, gene enrichment and pathway analyses of differentially expressed genes revealed in the M group a transcription profile suggestive of synchronized suppression of mitochondrial biogenesis and G1/S arrest. The N1 group showed elevated expression of complex I and reduced expression of complexes III, V, and V-type ATP synthase subunit genes, reduced expression of genes involved in phosphorylation dependent signaling along MAPK, Jak-STAT, JNK, and p38 MAP kinase pathways, signs of activated apoptosis and oxidative stress resembling phenotype of premature senescent fibroblasts. No specific functionally meaningful changes, except of signs of activated apoptosis, were detected in the N2 group. Evaluation of individual gene expression profiles confirmed already knownATP6/ATP8defect in patients from the M group and indicated several candidate disease causing genes for nuclear defects.

Conclusion

Our analysis showed that deficiency in the ATP synthase protein complex amount is generally accompanied by only minor changes in expression of ATP synthase related genes. It also suggested that the site (mtDNA vs nuclear DNA) and the severity (ATP synthase content) of the underlying defect have diverse effects on cellular gene expression phenotypes, which warrants further investigation of cell cycle regulatory and signal transduction pathways in other OXPHOS disorders and related pharmacological models.
SNPExpress: integrated visualization of genome-wide genotypes, copy numbers and gene expression levels
Authors: Sanders Mathijs A , Verhaak Roel GW , Geertsma-Kleinekoort Wendy MC , Abbas Saman , Horsman Sebastiaan , van der Spek Peter J , Löwenberg Bob , Valk Peter JM
Published: January 2008

Background

Accurate analyses of comprehensive genome-wide SNP genotyping and gene expression data sets is challenging for many researchers. In fact, obtaining an integrated view of both large scale SNP genotyping and gene expression is currently complicated since only a limited number of appropriate software tools are available.

Results

We present SNPExpress, a software tool to accurately analyze Affymetrix and Illumina SNP genotype calls, copy numbers, polymorphic copy number variations (CNVs) and Affymetrix gene expression in a combinatorial and efficient way. In addition, SNPExpress allows concurrent interpretation of these items with Hidden-Markov Model (HMM) inferred Loss-of-Heterozygosity (LOH)- and copy number regions.

Conclusion

The combined analyses with the easily accessible software tool SNPExpress will not only facilitate the recognition of recurrent genetic lesions, but also the identification of critical pathogenic genes.
The surface protein Shr of Streptococcus pyogenes binds heme and transfers it to the streptococcal heme-binding protein Shp
Authors: Zhu Hui , Liu Mengyao , Lei Benfang
Published: January 2008

Background

The heme acquisition machinery in Streptococcus pyogenes is believed to consist of the surface proteins, Shr and Shp, and heme-specific ATP-binding cassette transporter HtsABC. Shp has been shown to rapidly transfer its heme to the lipoprotein component, HtsA, of HtsABC. The function of Shr and the heme source of Shp have not been established.

Results

The objective of this study was to determine whether Shr binds heme and is a heme source of Shp. To achieve the objective, recombinant Shr protein was prepared. The purified Shr displays a spectrum typical of hemoproteins, indicating that Shr binds heme and acquires heme from Escherichia coli hemoproteins in vivo. Spectral analysis of Shr and Shp isolated from a mixture of Shr and heme-free Shp (apoShp) indicates that Shr and apoShp lost and gained heme, respectively; whereas Shr did not efficiently lose its heme in incubation with apoHtsA under the identical conditions. These results suggest that Shr directly transfers its heme to Shp. In addition, the rates of heme transfer from human hemoglobin to apoShp are close to those of simple ferric heme dissociation from hemoglobin, suggesting that methemoglobin does not directly transfer its heme to apoShp.

Conclusion

We have demonstrated that recombinant Shr can acquire heme from E. coli hemoproteins in vivo and appears to directly transfer its heme to Shp and that Shp appears not to directly acquire heme from human methemoglobin. These results suggest the possibility that Shr is a source of heme for Shp and that the Shr-to-Shp heme transfer is a step of the heme acquisition process in S. pyogenes. Further characterization of the Shr/Shp/HtsA system would advance our understanding of the mechanism of heme acquisition in S. pyogenes.
Adenylate kinase-independent thiamine triphosphate accumulation under severe energy stress in Escherichia coli
Authors: Gigliobianco Tiziana , Lakaye Bernard , Makarchikov Alexander F , Wins Pierre , Bettendorff Lucien
Published: January 2008

Background

Thiamine triphosphate (ThTP) exists in most organisms and might play a role in cellular stress responses. In E. coli, ThTP is accumulated in response to amino acid starvation but the mechanism of its synthesis is still a matter of controversy. It has been suggested that ThTP is synthesized by an ATP-dependent specific thiamine diphosphate kinase. However, it is also known that vertebrate adenylate kinase 1 catalyzes ThTP synthesis at a very low rate and it has been postulated that this enzyme is responsible for ThTP synthesis in vivo.

Results

Here we show that bacterial, as vertebrate adenylate kinases are able to catalyze ThTP synthesis, but at a rate more than 106-fold lower than ATP synthesis. This activity is too low to explain the high rate of ThTP accumulation observed in E. coli during amino acid starvation. Moreover, bacteria from the heat-sensitive CV2 strain accumulate high amounts of ThTP (>50% of total thiamine) at 37°C despite complete inactivation of adenylate kinase and a subsequent drop in cellular ATP.

Conclusion

These results clearly demonstrate that adenylate kinase is not responsible for ThTP synthesis in vivo. Furthermore, they show that E. coli accumulate large amounts of ThTP under severe energy stress when ATP levels are very low, an observation not in favor of an ATP-dependent mechanisms for ThTP synthesis.
Diverse antidepressants increase CDP-diacylglycerol production and phosphatidylinositide resynthesis in depression-relevant regions of the rat brain
Authors: Tyeryar Kimberly R , Vongtau Habiba OU , Undieh Ashiwel S
Published: January 2008

Background

Major depression is a serious mood disorder affecting millions of adults and children worldwide. While the etiopathology of depression remains obscure, antidepressant medications increase synaptic levels of monoamine neurotransmitters in brain regions associated with the disease. Monoamine transmitters activate multiple signaling cascades some of which have been investigated as potential mediators of depression or antidepressant drug action. However, the diacylglycerol arm of phosphoinositide signaling cascades has not been systematically investigated, even though downstream targets of this cascade have been implicated in depression. With the ultimate goal of uncovering the primary postsynaptic actions that may initiate cellular antidepressive signaling, we have examined the antidepressant-induced production of CDP-diacylglycerol which is both a product of diacylglycerol phosphorylation and a precursor for the synthesis of physiologically critical glycerophospholipids such as the phosphatidylinositides. For this, drug effects on [3H]cytidine-labeled CDP-diacylglycerol and [3H]inositol-labeled phosphatidylinositides were measured in response to the tricyclics desipramine and imipramine, the selective serotonin reuptake inhibitors fluoxetine and paroxetine, the atypical antidepressants maprotiline and nomifensine, and several monoamine oxidase inhibitors.

Results

Multiple compounds from each antidepressant category significantly stimulated [3H]CDP-diacylglycerol accumulation in cerebrocortical, hippocampal, and striatal tissues, and also enhanced the resynthesis of inositol phospholipids. Conversely, various antipsychotics, anxiolytics, and non-antidepressant psychotropic agents failed to significantly induce CDP-diacylglycerol or phosphoinositide synthesis. Drug-induced CDP-diacylglycerol accumulation was independent of lithium and only partially dependent on phosphoinositide hydrolysis, thus indicating that antidepressants can mobilize CDP-diacylglycerol from additional pools lying outside of the inositol cycle. Further, unlike direct serotonergic, muscarinic, or α-adrenergic agonists that elicited comparable or lower effects on CDP-diacylglycerol versus inositol phosphates, the antidepressants dose-dependently induced significantly greater accumulations of CDP-diacylglycerol.

Conclusion

Chemically divergent antidepressant agents commonly and significantly enhanced the accumulation of CDP-diacylglycerol. The latter is not only a derived product of phosphoinositide hydrolysis but is also a crucial intermediate in the biosynthesis of several signaling substrates. Hence, altered CDP-diacylglycerol signaling might be implicated in the pathophysiology of depression or the mechanism of action of diverse antidepressant medications.
Sgt1, but not Rar1, is essential for the RB-mediated broad-spectrum resistance to potato late blight
Authors: Bhaskar Pudota B , Raasch John A , Kramer Lara C , Neumann Pavel , Wielgus Susan M , Austin-Phillips Sandra , Jiang Jiming
Published: January 2008

Background

Late blight is the most serious potato disease world-wide. The most effective and environmentally sound way for controlling late blight is to incorporate natural resistance into potato cultivars. Several late blight resistance genes have been cloned recently. However, there is almost no information available about the resistance pathways mediated by any of those genes.

Results

We previously cloned a late blight resistance gene, RB, from a diploid wild potato species Solanum bulbocastanum. Transgenic potato lines containing a single RB gene showed a rate-limiting resistance against all known races of Phytophthora infestans, the late blight pathogen. To better understand the RB-mediated resistance we silenced the potato Rar1 and Sgt1 genes that have been implicated in mediating disease resistance responses against various plant pathogens and pests. The Rar1 and Sgt1 genes of a RB-containing potato clone were silenced using a RNA interference (RNAi)-based approach. All of the silenced potato plants displayed phenotypically normal growth. The late blight resistance of the Rar1 and Sgt1 silenced lines were evaluated by a traditional greenhouse inoculation method and quantified using a GFP-tagged P. infestans strain. The resistance of the Rar1-silenced plants was not affected. However, silencing of the Sgt1 gene abolished the RB-mediated resistance.

Conclusion

Our study shows that silencing of the Sgt1 gene in potato does not result in lethality. However, the Sgt1 gene is essential for the RB-mediated late blight resistance. In contrast, the Rar1 gene is not required for RB-mediated resistance. These results provide additional evidence for the universal role of the Sgt1 gene in various R gene-mediated plant defense responses.
Duloxetine versus placebo for the treatment of women with stress predominant urinary incontinence in Taiwan: a double-blind, randomized, placebo-controlled trial
Authors: Lin Alex Tong-Long , Sun Mou-Jong , Tai Hui-Lung , Chuang Yao Chi , Huang Shih-Tsung , Wang Nick , Zhao Yan Daniel , Beyrer Julie , Wulster-Radcliffe Meghan , Levine Louise , Chang Curtis , Viktrup Lars
Published: January 2008

Background

This manuscript compares the efficacy and safety of duloxetine with placebo in Taiwanese women with SUI.

Methods

Taiwanese women with SUI were were randomly assigned to placebo (n = 61) or duloxetine 80 mg/day (n = 60) in this double-blind, 8-week, placebo-controlled study. Outcome variables included: incontinence episode frequency (IEF), Incontinence Quality of Life questionnaire (I-QOL) scores, and Patient Global Impression of Improvement rating (PGI-I).

Results

Decrease in IEF was significantly greater in duloxetine-treated than placebo-treated women (69.98% vs 42.56%, P < .001). No treatment differences in I-QOL scores were significant. There were significant differences in PGI-I rating. Treatment-emergent adverse events (TEAEs) were experienced by more duloxetine-treated than placebo-treated women (80.0% vs 44.3%; P < .001). Discontinuations due to adverse events were significantly greater for duloxetine-treated than placebo-treated women (26.7% vs 6.6%; P = .003).

Conclusion

Data provide evidence for the safety and efficacy of duloxetine for the treatment for Taiwanese women with SUI.

Trial Registration

ClinicalTrials.gov Identifier: NCT00475358
Characterization of two putative potassium channels in Plasmodium falciparum
Authors: Waller Karena L , McBride Sean M , Kim Kami , McDonald Thomas V
Published: January 2008

Background

Potassium channels are essential for cell survival and participate in the regulation of cell membrane potential and electrochemical gradients. During its lifecycle, Plasmodium falciparum parasites must successfully traverse widely diverse environmental milieus, in which K+ channel function is likely to be critical. Dramatically differing conditions will be presented to the parasite in the mosquito mid-gut, red blood cell (RBC) cytosol and the human circulatory system.

Methods

In silico sequence analyses identified two open-reading frames in the P. falciparum genome that are predicted to encode for proteins with high homology to K+ channels. To further analyse these putative channels, specific antisera were generated and used in immunoblot and immunofluorescence analyses of P. falciparum-infected RBCs. Recombinant genome methods in cultured P. falciparum were used to create genetic knock outs of each K+ channel gene to asses the importance of their expression.

Results

Immunoblot and IFA analyses confirmed the expression of the two putative P. falciparum K+ channels (PfK1 and PfK2). PfK1 is expressed in all asexual stage parasites, predominantly in late stages and localizes to the RBC membrane. Conversely, PfK2 is predominantly expressed in late schizont and merozoite stage parasites and remains primarily localized to the parasite. Repeated attempts to knockout PfK1 and PfK2 expression by targeted gene disruption proved unsuccessful despite evidence of recombinant gene integration, indicating that pfk1 and pfk2 are apparently refractory to genetic disruption.

Conclusion

Putative K+ channel proteins PfK1 and PfK2 are expressed in cultured P. falciparum parasites with differing spatial and temporal patterns. Eventual functional characterization of these channels may reveal future pharmacological targets.
DNMT3b overexpression contributes to a hypermethylator phenotype in human breast cancer cell lines
Authors: Roll J Devon , Rivenbark Ashley G , Jones Wendell D , Coleman William B
Published: January 2008

Background

DNA hypermethylation events and other epimutations occur in many neoplasms, producing gene expression changes that contribute to neoplastic transformation, tumorigenesis, and tumor behavior. Some human cancers exhibit a hypermethylator phenotype, characterized by concurrent DNA methylation-dependent silencing of multiple genes. To determine if a hypermethylation defect occurs in breast cancer, the expression profile and promoter methylation status of methylation-sensitive genes were evaluated among breast cancer cell lines.

Results

The relationship between gene expression (assessed by RT-PCR and quantitative real-time PCR), promoter methylation (assessed by methylation-specific PCR, bisulfite sequencing, and 5-aza-2'deoxycytidine treatment), and the DNA methyltransferase machinery (total DNMT activity and expression of DNMT1, DNMT3a, and DNMT3b proteins) were examined in 12 breast cancer cell lines. Unsupervised cluster analysis of the expression of 64 methylation-sensitive genes revealed two groups of cell lines that possess distinct methylation signatures: (i) hypermethylator cell lines, and (ii) low-frequency methylator cell lines. The hypermethylator cell lines are characterized by high rates of concurrent methylation of six genes (CDH1, CEACAM6, CST6, ESR1, LCN2, SCNN1A), whereas the low-frequency methylator cell lines do not methylate these genes. Hypermethylator cell lines coordinately overexpress total DNMT activity and DNMT3b protein levels compared to normal breast epithelial cells. In contrast, most low-frequency methylator cell lines possess DNMT activity and protein levels that are indistinguishable from normal. Microarray data mining identified a strong cluster of primary breast tumors that express the hypermethylation signature defined byCDH1,CEACAM6, CST6, ESR1, LCN2, andSCNN1A. This subset of breast cancers represents 18/88 (20%) tumors in the dataset analyzed, and 100% of these tumors were classified as basal-like, suggesting that the hypermethylator defect cosegregates with poor prognosis breast cancers.

Conclusion

These observations combine to strongly suggest that: (a) a subset of breast cancer cell lines express a hypermethylator phenotype, (b) the hypermethylation defect in these breast cancer cell lines is related to aberrant overexpression of DNMT activity, (c) overexpression of DNMT3b protein significantly contributes to the elevated DNMT activity observed in tumor cells expressing this phenotype, and (d) the six-gene hypermethylator signature characterized in breast cancer cell lines defines a distinct cluster of primary basal-like breast cancers.
Human endogenous retrovirus-FRD envelope protein (syncytin 2) expression in normal and trisomy 21-affected placenta
Authors: Malassiné André , Frendo Jean-Louis , Blaise Sandra , Handschuh Karen , Gerbaud Pascale , Tsatsaris Vassilis , Heidmann Thierry , Evain-Brion Danièle
Published: January 2008

Human trophoblast expresses two fusogenic retroviral envelope proteins, the widely studied syncytin 1, encoded by HERV-W and the recently characterized syncytin 2 encoded by HERV-FRD. Here we studied syncytin 2 in normal and Trisomy 21-affected placenta associated with abnormal trophoblast differentiation. Syncytin 2 immunolocalization was restricted throughout normal pregnancy to some villous cytotrophoblastic cells (CT). During the second trimester of pregnancy, syncytin 2 was immunolocalized in some cuboidal CT in T21 placentas, whereas in normal placentas it was observed in flat CT, extending into their cytoplasmic processes. In vitro, CT isolated from normal placenta fuse and differentiate into syncytiotrophoblast. At the same time, syncytin 2 transcript levels decreased significantly with syncytiotrophoblast formation. In contrast, CT isolated from T21-affected placentas fused and differentiated poorly and no variation in syncytin 2 transcript levels was observed. Syncytin 2 expression illustrates the abnormal trophoblast differentiation observed in placenta of fetal T21-affected pregnancies.
Primary monophasic synovial sarcoma presenting as a pulmonary mass: a case report
Authors: Mermigkis Charalampos M. , Kopanakis Antony , Patentalakis George , Polychronopoulos Vlassis , Patentalakis Michael
Published: January 2008

Introduction

Primary pulmonary synovial sarcoma is an extremely rare tumor with only few case reports in the literature.

Case presentation

A healthy 67-year-old woman was admitted for investigation of a pulmonary mass found on a routine X-ray. She had a history of breast cancer diagnosed and treated 13 years previously with left mastectomy followed by adjuvant endocrine therapy. No progression of the disease was reported. Thoracic computer tomography disclosed a soft-tissue mass in the lower lobe of the left lung arising in the vicinity of the pleura. No abnormal lymph nodes were noted. Further work-up for metastases was negative. Subsequently, the lower lobe of the left lung was removed and the diagnosis was a monophasic synovial sarcoma.

Conclusion

The diagnosis of monophasic primary pulmonary synovial sarcoma requires clinical, imaging and immunohistochemical investigation to exclude alternative primary sources. The treatment of choice is excision (lobectomy or pneumonectomy), which in most of cases is helpful for diagnosis. The prognosis is usually poor.
CD47 associates with alpha 5 integrin and regulates responses of human articular chondrocytes to mechanical stimulation in an in vitromodel
Authors: Orazizadeh Mahmoud , Lee Herng Sheng , Groenendijk Bianca , Sadler S Jane Millward , Wright Malcolm O , Lindberg Frederik P , Salter Donald M
Published: January 2008

Background

Recent studies provide evidence of roles for integrins in mechanical signalling in bone and cartilage. Integrin signalling is modulated by various mechanisms, including interaction with other transmembrane proteins. We aimed to identify whether one such protein, integrin-associated protein (CD47/IAP), is expressed by chondrocytes and whether it may regulate integrin-dependent mechanotransduction.

Methods

Chondrocytes, isolated from macroscopically normal and osteoarthritic articular cartilage of human knee joints, were studied in a resting state or following mechanical stimulation at 0.33 Hz. CD47/IAP expression and associations were confirmed by immunohistology, reverse transcription-polymerase chain reaction, Western blotting, and immunoprecipitation. Roles in mechanotransduction were studied by assessing effects of function-blocking antibodies on a range of electrophysiological, cellular, and molecular responses of primary chondrocytes and responses of CD47/IAP-null cell lines transfected with CD47/IAP.

Results

Human articular chondrocytes were shown to express CD47/IAP, predominantly the type 2 isoform. Immunoprecipitation showed association of CD47/IAP with α5 integrin and thrombospondin but not SIRPα (signal-regulatory protein-alpha). The function-blocking anti-CD47/IAP antibody Bric 126 inhibited changes in membrane potential, tyrosine phosphorylation, and elevation of relative levels of aggrecan mRNA induced by mechanical stimulation, whereas in the presence of B6H12, an antibody that has partial agonist activity, a membrane depolarisation rather than a membrane hyperpolarisation response was induced by mechanical stimulation. CD47-null cell lines did not show changes in cell membrane potential following mechanical stimulation. Changes in cell membrane potential following mechanical stimulation were seen when CD47-null cells were transfected with CD47/IAP expression vectors but were not seen following mechanical stimulation of cells transfected with vectors for the extracellular immunoglobulin variable (IgV) domain of CD47/IAP in the absence of the transmembrane and intracellular domains.

Conclusion

CD47/IAP is necessary for chondrocyte mechanotransduction. Through interactions with α5β1 integrin and thrombospondin, CD47/IAP may modulate chondrocyte responses to mechanical signals.
Three-dimensional and thermal surface imaging produces reliable measures of joint shape and temperature: a potential tool for quantifying arthritis
Authors: Spalding Steven J , Kwoh C Kent , Boudreau Robert , Enama Joseph , Lunich Julie , Huber Daniel , Denes Louis , Hirsch Raphael
Published: January 2008

Introduction

The assessment of joints with active arthritis is a core component of widely used outcome measures. However, substantial variability exists within and across examiners in assessment of these active joint counts. Swelling and temperature changes, two qualities estimated during active joint counts, are amenable to quantification using noncontact digital imaging technologies. We sought to explore the ability of three dimensional (3D) and thermal imaging to reliably measure joint shape and temperature.

Methods

A Minolta 910 Vivid non-contact 3D laser scanner and a Meditherm med2000 Pro Infrared camera were used to create digital representations of wrist and metacarpalphalangeal (MCP) joints. Specialized software generated 3 quantitative measures for each joint region: 1) Volume; 2) Surface Distribution Index (SDI), a marker of joint shape representing the standard deviation of vertical distances from points on the skin surface to a fixed reference plane; 3) Heat Distribution Index (HDI), representing the standard error of temperatures. Seven wrists and 6 MCP regions from 5 subjects with arthritis were used to develop and validate 3D image acquisition and processing techniques. HDI values from 18 wrist and 9 MCP regions were obtained from 17 patients with active arthritis and compared to data from 10 wrist and MCP regions from 5 controls. Standard deviation (SD), coefficient of variation (CV), and intraclass correlation coefficients (ICC) were calculated for each quantitative measure to establish their reliability. CVs for volume and SDI were <1.3% and ICCs were greater than 0.99.

Results

Thermal measures were less reliable than 3D measures. However, significant differences were observed between control and arthritis HDI values. Two case studies of arthritic joints demonstrated quantifiable changes in swelling and temperature corresponding with changes in symptoms and physical exam findings.

Conclusion

3D and thermal imaging provide reliable measures of joint volume, shape, and thermal patterns. Further refinement may lead to the use of these technologies to improve the assessment of disease activity in arthritis.
The role of diacylglyceride generation by phospholipase D and phosphatidic acid phosphatase in the activation of 5-lipoxygenase in polymorphonuclear leukocytes
Authors: Albert Dana , Pergola Carlo , Koeberle Andreas , Dodt Gabriele , Steinhilber Dieter , Werz Oliver
Published: January 2008

Diacylglycerides (DAGs) such as 1-oleoyl-2-acetyl-sn-glycerol (OAG) stimulate 5-lipoxygenase (5-LO) enzyme activity and function as agonists for human polymorphonuclear leukocytes (PMNL) to induce 5-LO product synthesis. Here, we addressed the role of endogenous DAG generation in agonist-induced 5-LO activation in human PMNL. Preincubation of PMNL with the phospholipase D (PLD) inhibitor 1-butanol potently suppressed 5-LO product synthesis induced by the Ca2+ ionophore A23187 or thapsigargin (TG) and blocked A23187-evoked translocation of 5-LO from the cytosol to the nuclear membrane, analyzed by subcellular fractionation as well as by indirect immunofluorescence microscopy. Tertiary-butanol, a rather poor inhibitor of PLD, caused only moderate suppression of 5-LO and hardly inhibited 5-LO translocation. Interestingly, 1-butanol failed to inhibit 5-LO product formation when PMNL were stimulated with OAG (30 μM). Moreover, coincubation of A23187- or TG-stimulated PMNL with OAG reversed inhibition of 5-LO product formation by 1-butanol in a concentration-dependent manner (EC50, ∼1 μM) and also restored 5-LO translocation. In addition, inhibition of phosphatidic acid phosphatase (PA-P) by propranolol or bromoenol lactone caused suppression of 5-LO product formation and of translocation, which could be reversed by addition of exogenous OAG. Together, our data suggest that in agonist-stimulated PMNL, the endogenous formation of DAGs via the PLD/PA-P pathway determines 5-LO activation.
LGD-5552, an Antiinflammatory Glucocorticoid Receptor Ligand with Reduced Side Effects, in Vivo
Authors: López Francisco J. , Ardecky Robert J. , Bebo Bruce , Benbatoul Khalid , De Grandpre Louise , Liu Sha , Leibowitz Mark D. , Marschke Keith , Rosen Jon , Rungta Deepa , Viveros Humberto O. , Yen Wan-Ching , Zhi Lin , Negro-Vilar Andrés , Miner Jeffrey N.
Published: January 2008

Treatment of inflammation is often accomplished through the use of glucocorticoids. However, their use is limited by side effects. We have examined the activity of a novel glucocorticoid receptor ligand that binds the receptor efficiently and strongly represses inflammatory gene expression. This compound has potent antiinflammatory activity in vivo and represses the transcription of the inflammatory cytokine monocyte chemoattractant protein-1 and induces the antiinflammatory cytokine IL-10. The compound demonstrates differential gene regulation, compared with commonly prescribed glucocorticoids, effectively inducing some genes and repressing others in a manner different from the glucocorticoid prednisolone. The separation between the antiinflammatory effects of LGD-5552 and the side effects commonly associated with glucocorticoid treatment suggest that this molecule differs significantly from prednisolone and other steroids and may provide a safer therapeutic window for inflammatory conditions now commonly treated with steroidal glucocorticoids.
Progestin-Regulated Luminal Cell and Myoepithelial Cell-Specific Responses in Mammary Organoid Culture
Authors: Haslam Sandra Z. , Drolet Alexis , Smith Kyle , Tan May , Aupperlee Mark
Published: January 2008

Normal mammary gland development requires the coordinated proliferation and morphogenesis of both mammary luminal epithelial cells (LECs) and myoepithelial cells (MECs). Cell proliferation in cultured mammary organoids containing both LECs and MECs is not increased by progestin (R5020) or 17β-estradiol (E2) alone or R5020+E2 but is increased by E2-regulated, mammary stroma-derived Hepatocyte growth factor (HGF) and further increased by HGF+R5020. We investigated the effects of HGF and/or R5020 on morphology and LEC- and MEC-specific in vitro proliferation in organoids. HGF-induced tubulogenesis was initiated and carried out by LECs starting with cellular extensions, followed by the formation of chains and cords, and culminating in tubule formation. MECs did not appear to have an active role in this process. Whereas HGF by itself caused maximal proliferation of LECs, HGF+R5020 produced a synergistic and specific increase in MEC proliferation. Because only LECs expressed progesterone receptors (PRs), we investigated the role of receptor activator of nuclear factor-κB ligand (RANKL), a progestin-induced paracrine factor, in mediating increased MEC proliferation. Quantitative RT-PCR showed that RANKL mRNA was induced by R5020 or HGF+R5020 and RANKL protein colocalized with PRs in LECs. The increased proliferation of MECs in response to HGF+R5020 could be blocked by neutralizing antibody to RANKL and reproduced by treatment with HGF plus exogenous RANKL in place of R5020. Neither R5020, nor exogenously administered RANKL increased proliferation of LECs. These results led us to conclude that RANKL, induced by progestin in PR-positive cells, is secreted and interacts with HGF to specifically increase proliferation of PR-negative MECs.
Implication of the Endocannabinoid System in the Locomotor Hyperactivity Associated with Congenital Hypothyroidism
Authors: Asúa Teresa , Bilbao Ainhoa , Gorriti Miguel Angel , Lopez-Moreno Jose Antonio , del Mar Álvarez Maria , Navarro Miguel , Rodríguez de Fonseca Fernando , Perez-Castillo Ana , Santos Angel
Published: January 2008

Alterations in motor functions are well-characterized features observed in humans and experimental animals subjected to thyroid hormone dysfunctions during development. Here we show that congenitally hypothyroid rats display hyperactivity in the adult life. This phenotype was associated with a decreased content of cannabinoid receptor type 1 (CB1) mRNA in the striatum and a reduction in the number of binding sites in both striatum and projection areas. These findings suggest that hyperactivity may be the consequence of a thyroid hormone deficiency-induced removal of the endocannabinoid tone, normally acting as a brake for hyperactivity at the basal ganglia. In agreement with the decrease in CB1 receptor gene expression, a lower cannabinoid response, measured by biochemical, genetic and behavioral parameters, was observed in the hypothyroid animals. Finally, both CB1 receptor gene expression and the biochemical and behavioral dysfunctions found in the hypothyroid animals were improved after a thyroid hormone replacement treatment. Thus, the present study suggests that impairment in the endocannabinoid system can underlay the hyperactive phenotype associated with hypothyroidism.
Lack of Hexose-6-Phosphate Dehydrogenase Impairs Lipid Mobilization from Mouse Adipose Tissue
Authors: Bujalska Iwona J. , Hewitt Kylie N. , Hauton David , Lavery Gareth G. , Tomlinson Jeremy W. , Walker Elizabeth A. , Stewart Paul M.
Published: January 2008

In adipose tissue, glucocorticoids regulate lipogenesis and lipolysis. Hexose-6-phosphate dehydrogenase (H6PDH) is an enzyme located in the endoplasmic reticulum that provides a cofactor for the enzyme 11β-hydroxysteroid dehydrogenase type 1 (11β-HSD1), regulating the set point of its activity and allowing for tissue-specific activation of glucocorticoids. The aim of this study was to examine the adipose tissue biology of the H6PDH null (H6PDH/KO) mouse. Real-time PCR analysis confirmed similar mRNA levels of 11β-HSD1 and glucocorticoid receptor-α in wild-type (WT) and H6PDH/KO mice in liver and gonadal fat depots. Microsomal 11β-HSD1 protein levels shown by Western blot analysis corresponded well with mRNA expression in gonadal fat of WT and H6PDH/KO mice. Despite this, the enzyme directionality in these tissues changed from predominately oxoreductase in WT to exclusively dehydrogenase activity in the H6PDH/KO mice. In the fed state, H6PDH/KO mice had reduced adipose tissue mass, but histological examination revealed no difference in average adipocyte size between genotypes. mRNA expression levels of the key lipogenic enzymes, acetyl CoA carboxylase, adiponutrin, and stearoyl-coenzyme A desaturase-2, were decreased in H6PDH/KO mice, indicative of impaired lipogenesis. In addition, lipolysis rates were also impaired in the H6PDH/KO as determined by lack of mobilization of fat and no change in serum free fatty acid concentrations upon fasting. In conclusion, in the absence of H6PDH, the set point of 11β-HSD1 enzyme activity is switched from predominantly oxoreductase to dehydrogenase activity in adipose tissue; as a consequence, this leads to impairment of fat storage and mobilization.
The Thyrotropin Receptor Hinge Region Is Not Simply a Scaffold for the Leucine-Rich Domain but Contributes to Ligand Binding and Signal Transduction
Authors: Mizutori Yumiko , Chen Chun-Rong , McLachlan Sandra M. , Rapoport Basil
Published: January 2008

The glycoprotein hormone receptor hinge region connects the leucine-rich and transmembrane domains. The prevalent concept is that the hinge does not play a significant role in ligand binding and signal transduction. Portions of the hinge are redundant and can be deleted by mutagenesis or are absent in certain species. A minimal hinge will be more amenable to future investigation of its structure and function. We, therefore, combined and progressively extended previous deletions (Δ) in the TSH receptor (TSHR) hinge region (residues 277–418). TSHRΔ287–366, Δ287–371, Δ287–376, and Δ287–384 progressively lost their response to TSH stimulation of cAMP generation in intact cells, consistent with a progressive loss of TSH binding. The longest deletion (TSHRΔ287–384), reducing the hinge region from 141 to 43 amino acids, totally lost both functions. Surprisingly, however, with deletions extending from residues 371–384, constitutive (ligand-independent) activity increased severalfold, reversing the suppressive (inverse agonist) effect of the TSHR extracellular domain. TSHR-activating point mutations I486F and I568T in the first and second extracellular loops (especially the former) had reduced activity on a background of TSHRΔ287–371. In summary, our data support the concept that the TSHR hinge contributes significantly to ligand binding affinity and signal transduction. Residues within the hinge, particularly between positions 371–384, appear involved in ectodomain inverse agonist activity. In addition, the hinge is necessary for functionality of activating mutations in the first and second extracellular loops. Rather than being an inert linker between the leucine-rich and transmembrane domains, the TSHR hinge is a signaling-specificity domain.
Nuclear Hormone Receptors for Heme: REV-ERBα and REV-ERBβ Are Ligand-Regulated Components of the Mammalian Clock
Authors: Burris Thomas P.
Published: January 2008

The nuclear hormone receptors (NHRs), REV-ERBα and REV-ERBβ, regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. These two receptors lack the activation function-2 region that is associated with the ability of NHRs to recruit coactivators and activate target gene transcription. These NHRs have been characterized as constitutive repressors of transcription due to their lack of an identified ligand and their strong ability to recruit the corepressor, nuclear receptor corepressor. Recently, the porphyrin heme was demonstrated to function as a ligand for both REV-ERBs. Heme binds directly to the ligand-binding domain and regulates the ability of these NHRs to recruit nuclear receptor corepressor to target gene promoters. This review focuses on the physiological roles that these two receptors play and the implications of heme functioning as their ligand. The prospect that these NHRs, now known to be regulated by small molecule ligands, may be targets for development of drugs for treatment of diseases associated with aberrant circadian rhythms including metabolic and psychiatric disorders as well as cancer is also addressed.
Mutation from guanine to adenine in 25S rRNA at the position equivalent to E. coli A2058 does not confer erythromycin sensitivity in Sacchromyces cerevisae
Authors: Bommakanti Ananth S. , Lindahl Lasse , Zengel Janice M.
Published: January 2008

The macrolide erythromycin binds to the large subunit of the prokaryotic ribosome near the peptidyltransferase center (PTC) and inhibits elongation of new peptide chains beyond a few amino acids. Nucleotides A2058 and A2059 (E. coli numbering) in 23S rRNA play a crucial role in the binding of erythromycin, and mutation of nucleotide A2058 confers erythromycin resistance in both Gram-positive and Gram-negative bacteria. There are high levels of sequence and structural similarity in the PTC of prokaryotic and eukaryotic ribosomes. However, eukaryotic ribosomes are resistant to erythromycin and the presence of a G at the position equivalent to E. coli nucleotide A2058 is believed to be the reason. To test this hypothesis, we introduced a G to A mutation at this position of the yeast Saccharomyces cerevisiae 25S rRNA and analyzed sensitivity toward erythromycin. Neither growth studies nor erythromycin binding assays on mutated yeast ribosomes indicated any erythromycin sensitivity in mutated yeast strains. These results suggest that the identity of nucleotide 2058 is not the only determinant responsible for the difference in erythromycin sensitivity between yeast and prokaryotes.
Inverse problems of plane wave scattering by 1D inhomogeneous layers
Authors: Alekseev A. S. , Megrabov A. G.
Published: January 2008

Inverse problems of the plane waves scattering of inclined incidence of the SH type by an inhomogeneous half-space (in particular, by a transition layer) or by an inhomogeneous layer with a free boundary are considered. The characteristics of an inhomogeneous elastic medium, i.e., the wave propagation velocity ν(z) and the density ρ(z), are functions of depth z and should be determined in the inverse problems. The following are considered: the inverse problems with data for a fixed angle of incidence θ0 of a plane wave (the angle between the vector of the normal to the plane wave front and z-axis) when the shape φ0(ξ, θ0) of an incident wave is known; the inverse problems with data for a family of angles θ0 both for known and unknown shapes of the incident wave. The functions φ0(ξ, θ0) and φ1(ξ, θ0) (the shapes of incident and reflected waves), the functions φ0(ξ, θ0) and u(H, ξ, θ0) (the shapes of the incident wave and the free boundary oscillation field), only the function u(H, ξ, θ0) (in the inverse problem with the unknown function φ0(ξ, θ0)), or other data are given as data corresponding to any fixed value of θ0. Possible application areas of the inverse problems under consideration are specified.

This paper is essentially a review. A new result presented here has been obtained for inverse problems with the data {φ0(ξ, θ0), φ1(ξ, θ0} or {φ(ξ, θ0), u(H, ξ, θ0)} for a set of angles θ0. The results [Mathematical Problems of Geophysics, V. 5, P. 2. Computer Center of Siberian Branch of USSR Academy of Sciences, Novosibirsk, 1974, 78–107] (the uniqueness theorem, the solution method) are extended to the case when the limiting point θ0 of this set is zero. Also, a new explicit formula (formula (5.3) from Section 5), which makes it possible to find the functions ν(z) and ρ(z) using the data of these inverse problems for θ0 = 0, has been obtained.
Tikhonov regularization of nonlinear ill-posed equations under general source condition
Authors: Mahale Pallavi , Nair M. Thamban
Published: January 2008

Tikhonov regularization is one of the widely used procedures for the regularization of nonlinear as well as linear ill-posed problems. The error analysis carried out in most of the works that appeared in last few years on Tikhonov regularization of nonlinear ill-posed problems are under Hölder type source conditions on the unknown solution which is known to be applicable only for mildly ill-posed problems. In this paper we consider Tikhonov regularization of nonlinear ill-posed problems and derive order optimal error estimate under a general source condition together with an a posteriori parameter rule proposed by Scherzer et al., which is applicable for severely ill-posed problems as well.
On approximation of inverse problem for abstract parabolic differential equations in Banach spaces
Authors: Prilepko A. , Piskarev S. , Shaw S.-Y.
Published: January 2008

The paper is devoted to the approximation of a control element for an abstract parabolic equation. The presentation is given for general approximation schemes, which includes finite element methods, finite difference schemes, projection methods. We apply an iteration-approximation method for the investigation of inverse problems for parabolic equations.
Tikhonov regularization with nondifferentiable stabilizing functionals
Authors: Vasin V. V. , Korotkii M. A.
Published: January 2008

Tikhonov regularization with a stabilizer being the sum of total variation and the norm of space L
p[a; b] (1 < p ≤ ∞) is considered. For one-dimensional case we prove that, along with the convergence of regularized solutions, in L
p we have uniform convergence over intervals where the solution to be found is continuous. Results of numerical experiments on reconstruction of model solutions, differing in smoothness, of the one-dimensional first-kind Fredholm integral equation are reported.
The Review on Sustainability of National Building Standard Design in China
Authors: Gang Liu
Published: January 2008

There are more than 40 billion square metres of buildings in China and the number is forecasted to grow by 1.6∼1.9 billion square metres year over year by 2020. China has been facing serious energy and environmental challenges to address sustainable development. The National Building Standard Design (NBSD) is a set of standard drawings, compiled according to Chinese building standards and codes by the Ministry of Construction (MOC), including construction details, building components, selection and installation of equipment, etc. The NBSD has been tested by real projects and market feedback. It’s crucial to implement it to increase the efficiency of the construction process. The paper describes the historical development of NBSD and the contribution to sustainable development in China’s construction sector. The paper also introduces the effects and new trends of standard designs on sustainability in China.