bluuebunny/crossref_metadata_2025_split huggingface dataset:
The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction
Authors: Manning Jonathan R , Jefferson Emily R , Barton Geoffrey J 
Published: January 2008

Abstract

Background
Amino acids responsible for structure, core function or specificity may be inferred from multiple protein sequence alignments where a limited set of residue types are tolerated. The rise in available protein sequences continues to increase the power of techniques based on this principle.

Results
A new algorithm, SMERFS, for predicting protein functional sites from multiple sequences alignments was compared to 14 conservation measures and to the MINER algorithm. Validation was performed on an automatically generated dataset of 1457 families derived from the protein interactions database SNAPPI-DB, and a smaller manually curated set of 148 families. The best performing measure overall was Williamson property entropy, with ROC
0.1 scores of 0.0087 and 0.0114 for domain and small molecule contact prediction, respectively. The Lancet method performed worse than random on protein-protein interaction site prediction (ROC
0.1 score of 0.0008). The SMERFS algorithm gave similar accuracy to the phylogenetic tree-based MINER algorithm but was superior to Williamson in prediction of non-catalytic transient complex interfaces. SMERFS predicts sites that are significantly more solvent accessible compared to Williamson.

Conclusion

Williamson property entropy is the the best performing of 14 conservation measures examined. The difference in performance of SMERFS relative to Williamson in manually defined complexes was dependent on complex type. The best choice of analysis method is therefore dependent on the system of interest. Additional computation employed by Miner in calculation of phylogenetic trees did not produce improved results over SMERFS. SMERFS performance was improved by use of windows over alignment columns, illustrating the necessity of considering the local environment of positions when assessing their functional significance.
MyoD- and nerve-dependent maintenance of MyoDexpression in mature muscle fibres acts through the DRR/PRR element
Authors: Chargé Sophie B , Brack Andrew S , Bayol Stéphanie A , Hughes Simon M 
Published: January 2008

Abstract

Background
MyoD is a transcription factor implicated in the regulation of adult muscle gene expression. Distinguishing the expression of MyoD in satellite myoblasts and muscle fibres has proved difficult in vivo leading to controversy over the significance of MyoD expression within adult innervated muscle fibres. Here we employ the MD6.0-lacZ transgenic mouse, in which the 6 kb proximal enhancer/promoter (DRR/PRR) of MyoD drives lacZ, to show that MyoD is present and transcriptionally active in many adult muscle fibres.

Results
In culture, MD6.0-lacZ expresses in myotubes but not myogenic cells, unlike endogenous MyoD. Reporter expression in vivo is in muscle fibre nuclei and is reduced in MyoD null mice. The MD6.0-lacZ reporter is down-regulated both in adult muscle fibres by denervation or muscle disuse and in cultured myotubes by inhibition of activity. Activity induces and represses MyoD through the DRR and PRR, respectively. During the postnatal period, accumulation of β-galactosidase correlates with maturation of innervation. Strikingly, endogenous MyoD expression is up-regulated in fibres by complete denervation, arguing for a separate activity-dependent suppression of MyoD requiring regulatory elements outside the DRR/PRR.

Conclusion
The data show that MyoD regulation is more complex than previously supposed. Two factors, MyoD protein itself and fibre activity are required for essentially all expression of the 6 kb proximal enhancer/promoter (DRR/PRR) of MyoD in adult fibres. We propose that modulation of MyoD positive feedback by electrical activity determines the set point of MyoD expression in innervated fibres through the DRR/PRR element.
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

AbstractBackgroundTheSaccharomyces 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.ResultsGlobal 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.ConclusionFollowing 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

AbstractBackgroundTo 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.ResultsMolecular 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.ConclusionOur 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

AbstractBackgroundAccurate 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.ResultsWe 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.ConclusionThe 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

Abstract

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

Abstract

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

Abstract

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

Abstract

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

Abstract

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

Abstract

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.