bluuebunny/crossref_metadata_2025 huggingface dataset:
Investigation of performance characteristics and water flooding in the cathode flow channel of a polymer electrolyte membrane fuel cell
Authors: Seo S H , Lee C S
Published: May 2011

This study was experimentally carried out to investigate the relationship between fuel-cell performance and the water flooding phenomena at the cathode, which is an important research area of water management in the polymer electrolyte membrane fuel cell. A transparent fuel cell was fabricated to observe the water flooding phenomenon in the cathode channel. Images of the flooding phenomena were obtained by digital and high-speed cameras under various operating conditions involving cell temperature, cathode flowrate, humidifying temperature, cathode backpressure, and oxygen concentration. At the same time, performance was measured at the potentiostatic mode. In this study, investigations for the effects of operating parameters on the water flooding phenomenon, as well as water droplet generation and removal in the cathode flow channel were made. As time elapsed, it was seen that small water droplets formed and then grew into larger water droplets, when the flooding phenomena occurred.

It was also observed that when the cell temperature increased the occurrence of flooding phenomena decreased due to evaporation, and performance was significantly improved. The water droplets in the cathode channel were found to be almost zero at high cathode flowrates, and the instances of the flooding phenomenon were decreased by evaporation as the humidified temperature was increased. On account of increasing cathode backpressure, the flooding phenomenon due to high partial pressure was reduced and as compared to air when oxygen was used as an oxidant, the water distribution was increased. Based on this experimental study, it is seen that the flooding phenomenon is closely related to fuel-cell performance.
Theoretical model for the hot-melt-drawn fabrication of optical fibre probes and analysis of fabrication parameters
Authors: Lin Z-C , Yang C-B , Lee K-P
Published: May 2011

Optical fibre probes made by manually operated hot-melt-drawn methods may have unreliable production quality. This can result in unreliable results during use of the probes. This article presents a theoretical model for the construction of optical fibre probes by a hot-melt-drawn method, intending to simulate the optical fibre melt-drawing process using the P-2000 Sutter melt-drawing installation, and investigates changes in length, radius, and geometric profile of the optical fibre. Using preset processing parameters, the study simulates the profile, size, and shape of an optical fibre probe, and the geometric shape and diameter of the probe tip.

Additionally, the article presents an analysis of fabrication parameters to determine which of the three processing parameters, probe diameter, melt-drawing rate, and hard-drawn value, is most significant in determining the length and profile of a simulation model probe.
Evolution of endogenous retroviruses in the Suidae: evidence for different viral subpopulations in African and Eurasian host species
Authors: Nascimento Fabrícia F , Gongora Jaime , Charleston Michael , Tristem Michael , Lowden Stewart , Moran Chris
Published: May 2011

Background

Porcine endogenous retroviruses (PERVs) represent remnants of an exogenous form that have become integrated in the domestic pig (Sus scrofa) genome. Although they are usually inactive, the capacity of γ1 ERVs to infect human cells in vitro has raised concerns about xenotransplantation because the viruses could cross the species barrier to humans. Here we have analyzed the evolution of γ1 ERVs in ten species of Suidae (suids, pigs and hogs) from Eurasia and Africa using DNA sequences for their coding domains (gag, pro/pol and env genes). For comparison with γ1 PERVs, we have also analysed γ2 ERVs which in domestic pigs are known to be inactive and do not pose a risk to xenotransplantation.

Results

Phylogenetic analysis using Bayesian inference showed that γ1 and γ2 ERVs have distinctive evolutionary histories. Firstly, two different viral lineages of γ1 ERVs were found and a coevolutionary analysis demonstrated that they correspond broadly to their host phylogeny, one of Eurasian and another of African species, and show no evidence of horizontal transmission. γ2 ERVs, however, show a bush-like evolution, suggesting a rapid viral radiation from a single common ancestor with no correspondence between host and viral evolutionary trees. Furthermore, though γ1 ERV env genes do not possess frequent stop codons, γ2 env genes do. To understand whether γ1 suid ERVs may be still replicating, we have also evaluated their likely mechanism of proliferation by statistically testing internal to terminal branches using nonsynonymous versus synonymous substitution ratios. Our results suggest that γ1 ERVs are increasing in copy number by reinfection, which requires the translocation of the virus from one cell to another.

Conclusions

Evidence of at least two viral subpopulations was observed in γ1 ERVs from Eurasian and African host species. These results should be taken into account in xenotransplantation since γ1 ERVs appear to be codiverging with their host and maintaining ongoing capacity to infect somatic and germ cells.
Microarray analysis and scale-free gene networks identify candidate regulators in drought-stressed roots of loblolly pine (P. taeda L.)
Authors: Lorenz W Walter , Alba Rob , Yu Yuan-Sheng , Bordeaux John M , Simões Marta , Dean Jeffrey FD
Published: May 2011

Background

Global transcriptional analysis of loblolly pine (Pinus taeda L.) is challenging due to limited molecular tools. PtGen2, a 26,496 feature cDNA microarray, was fabricated and used to assess drought-induced gene expression in loblolly pine propagule roots. Statistical analysis of differential expression and weighted gene correlation network analysis were used to identify drought-responsive genes and further characterize the molecular basis of drought tolerance in loblolly pine.

Results

Microarrays were used to interrogate root cDNA populations obtained from 12 genotype × treatment combinations (four genotypes, three watering regimes). Comparison of drought-stressed roots with roots from the control treatment identified 2445 genes displaying at least a 1.5-fold expression difference (false discovery rate = 0.01). Genes commonly associated with drought response in pine and other plant species, as well as a number of abiotic and biotic stress-related genes, were up-regulated in drought-stressed roots. Only 76 genes were identified as differentially expressed in drought-recovered roots, indicating that the transcript population can return to the pre-drought state within 48 hours. Gene correlation analysis predicts a scale-free network topology and identifies eleven co-expression modules that ranged in size from 34 to 938 members. Network topological parameters identified a number of central nodes (hubs) including those with significant homology (E-values ≤ 2 × 10-30) to 9-cis-epoxycarotenoid dioxygenase, zeatin O-glucosyltransferase, and ABA-responsive protein. Identified hubs also include genes that have been associated previously with osmotic stress, phytohormones, enzymes that detoxify reactive oxygen species, and several genes of unknown function.

Conclusion

PtGen2 was used to evaluate transcriptome responses in loblolly pine and was leveraged to identify 2445 differentially expressed genes responding to severe drought stress in roots. Many of the genes identified are known to be up-regulated in response to osmotic stress in pine and other plant species and encode proteins involved in both signal transduction and stress tolerance. Gene expression levels returned to control values within a 48-hour recovery period in all but 76 transcripts. Correlation network analysis indicates a scale-free network topology for the pine root transcriptome and identifies central nodes that may serve as drivers of drought-responsive transcriptome dynamics in the roots of loblolly pine.
A genome scan for quantitative trait loci affecting cyanogenic potential of cassava root in an outbred population
Authors: Whankaew Sukhuman , Poopear Supannee , Kanjanawattanawong Supanath , Tangphatsornruang Sithichoke , Boonseng Opas , Lightfoot David A , Triwitayakorn Kanokporn
Published: May 2011

Background

Cassava (Manihot esculenta Crantz) can produce cyanide, a toxic compound, without self-injury. That ability was called the cyanogenic potential (CN). This project aimed to identify quantitative trait loci (QTL) associated with the CN in an outbred population derived from 'Hanatee' × 'Huay Bong 60', two contrasting cultivars. CN was evaluated in 2008 and in 2009 at Rayong province, and in 2009 at Lop Buri province, Thailand. CN was measured using a picrate paper kit. QTL analysis affecting CN was performed with 303 SSR markers.

Results

The phenotypic values showed continuous variation with transgressive segregation events with more (115 ppm) and less CN (15 ppm) than either parent ('Hanatee' had 33 ppm and 'Huay Bong 60' had 95 ppm). The linkage map consisted of 303 SSR markers, on 27 linkage groups with a map that encompassed 1,328 cM. The average marker interval was 5.8 cM. Five QTL underlying CN were detected. CN08R1 from 2008 at Rayong, CN09R1 and CN09R2 from 2009 at Rayong, and CN09L1 and CN09L2 from 2009 at Lop Buri were mapped on linkage group 2, 5, 10 and 11, respectively. Among all the identified QTL, CN09R1 was the most significantly associated with the CN trait with LOD score 5.75 and explained the greatest percentage of phenotypic variation (%Expl.) of 26%.

Conclusions

Five new QTL affecting CN were successfully identified from 4 linkage groups. Discovery of these QTL can provide useful markers to assist in cassava breeding and studying genes affecting the trait.
Differential distribution of a SINE element in the Entamoeba histolytica and Entamoeba dispar genomes: Role of the LINE-encoded endonuclease
Authors: Kumari Vandana , Sharma Rahul , Yadav Vijay P , Gupta Abhishek K , Bhattacharya Alok , Bhattacharya Sudha
Published: May 2011

Background

Entamoeba histolytica and Entamoeba dispar are closely related protistan parasites but while E. histolytica can be invasive, E. dispar is completely non pathogenic. Transposable elements constitute a significant portion of the genome in these species; there being three families of LINEs and SINEs. These elements can profoundly influence the expression of neighboring genes. Thus their genomic location can have important phenotypic consequences. A genome-wide comparison of the location of these elements in the E. histolytica and E. dispar genomes has not been carried out. It is also not known whether the retrotransposition machinery works similarly in both species. The present study was undertaken to address these issues.

Results

Here we extracted all genomic occurrences of full-length copies of EhSINE1 in the E. histolytica genome and matched them with the homologous regions in E. dispar, and vice versa, wherever it was possible to establish synteny. We found that only about 20% of syntenic sites were occupied by SINE1 in both species. We checked whether the different genomic location in the two species was due to differences in the activity of the LINE-encoded endonuclease which is required for nicking the target site. We found that the endonucleases of both species were essentially very similar, both in their kinetic properties and in their substrate sequence specificity. Hence the differential distribution of SINEs in these species is not likely to be influenced by the endonuclease. Further we found that the physical properties of the DNA sequences adjoining the insertion sites were similar in both species.

Conclusions

Our data shows that the basic retrotransposition machinery is conserved in these sibling species. SINEs may indeed have occupied all of the insertion sites in the genome of the common ancestor of E. histolytica and E. dispar but these may have been subsequently lost from some locations. Alternatively, SINE expansion took place after the divergence of the two species. The absence of SINE1 in 80% of syntenic loci could affect the phenotype of the two species, including their pathogenic properties, which needs to be explored.
Retest reliability of measuring hip extensor muscle strength in different testing positions in young people with cerebral palsy
Authors: Dyball Kate M , Taylor Nicholas F , Dodd Karen J
Published: May 2011

Background

In young people with spastic diplegic cerebral palsy weakness of the hip extensor muscles are associated with limitations in activity. It is important that clinicians can reliably measure hip extensor muscle strength to monitor changes over time and the effects of any interventions. Previous research has demonstrated high reliability for measuring strength of all muscles of the lower limb, with the exception of the hip extensors. Therefore the aim of this study was to examine the retest reliability of measuring hip extensor strength in young people with cerebral palsy.

Methods

Using a test-retest reliability research design, 19 participants with spastic diplegic cerebral palsy (Gross Motor Function Classification System Levels II and III) (mean 19 y 2 mo [S D 2 y 5 mo]) attended two testing sessions held 12 weeks apart. Three trials with a hand-held dynamometer were taken at each testing session in supine, prone and standing. Retest reliability was calculated with Intraclass Correlation Coefficients (ICC(2,1)) and with units of measurement (kilograms) converted to a percentage strength change.

Results

ICC values ranged from .74 to .78 in supine, .75 to .80 in prone, and .73 to .75 in standing. To be 95% confident that real change had occurred, an individual's strength would need to increase 55 to 60% in supine, 86 to 102% in prone, and 102 to 105% in standing. To be 95% confident that real change had occurred across groups, strength would need to increase 4 to 8% in supine, 22 to 31% in prone, and 32% to 34% in standing. Higher ICC values were observed when three trials were used for testing.

Conclusions

The supine testing position was more reliable than the prone or standing testing positions. It is possible to measure hip extensor strength with sufficient reliability to be able monitor change within groups using the supine position provided three trials are used during testing. However, there is insufficient reliability to monitor changes in hip extensor strength in individuals with cerebral palsy unless they exhibit very large strength increases.
An association between Helicobacter pylori infection and cognitive function in children at early school age: a community-based study
Authors: Muhsen Khitam , Ornoy Asher , Akawi Ashraf , Alpert Gershon , Cohen Dani
Published: May 2011

Background

H. pylori infection has been linked to iron deficiency anemia, a risk factor of diminished cognitive development. The hypothesis on an association between H. pylori infection and cognitive function was examined in healthy children, independently of socioeconomic and nutritional factors.

Methods

A community-based study was conducted among 200 children aged 6-9 years, from different socioeconomic background. H. pylori infection was examined by an ELISA kit for detection of H. pylori antigen in stool samples. Cognitive function of the children was blindly assessed using Stanford-Benit test 5th edition, yielding IQ scores. Data on socioeconomic factors and nutritional covariates were collected through maternal interviews and from medical records. Multivariate linear regression analysis was performed to obtain adjusted beta coefficients.

Results

H. pylori infection was associated with lower IQ scores only in children from a relatively higher socioeconomic community; adjusted beta coefficient -6.1 (95% CI -11.4, -0.8) (P = 0.02) for full-scale IQ score, -6.0 (95% CI -11.1, -0.2) (P = 0.04) for non-verbal IQ score and -5.7 (95% CI -10.8, -0.6) (P = 0.02) for verbal IQ score, after controlling for potential confounders.

Conclusions

H. pylori infection might be negatively involved in cognitive development at early school age. Further studies in other populations with larger samples are needed to confirm this novel finding.
From planning to practice: building the national network for the surveillance of severe maternal morbidity
Authors: Haddad Samira M , Cecatti José G , Parpinelli Mary A , Souza João P , Costa Maria L , Sousa Maria H , Surita Fernanda G , Pinto e Silva João L , Pacagnella Rodolfo C , Camargo Rodrigo S , Bahamondes Maria V , Zotareli Vilma , Gurgel Lúcio T , Say Lale , Pattinson Robert C ,   National Network for the Surveillance of Severe Maternal Morbidity Group
Published: May 2011

Background

Improving maternal health is one of the Millennium Development Goals for 2015. Recently some progress has been achieved in reducing mortality. On the other hand, in developed regions, maternal death is a relatively rare event compared to the number of cases of morbidity; hence studying maternal morbidity has become more relevant. Electronic surveillance systems may improve research by facilitating complete data reporting and reducing the time required for data collection and analysis. Therefore the purpose of this study was to describe the methods used in elaborating and implementing the National Network for the Surveillance of Severe Maternal Morbidity in Brazil.

Methods

The project consisted of a multicenter, cross-sectional study for the surveillance of severe maternal morbidity including near-miss, in Brazil.

Results

Following the development of a conceptual framework, centers were selected for inclusion in the network, consensus meetings were held among the centers, an electronic data collection system was identified, specific software and hardware tools were developed, research material was prepared, and the implementation process was initiated and analyzed.

Conclusion

The conceptual framework developed for this network was based on the experience acquired in various studies carried out in the area over recent years and encompasses maternal and perinatal health. It is innovative especially in the context of a developing country. The implementation of the project represents the first step towards this planned management. The system online elaborated for this surveillance network may be used in further studies in reproductive and perinatal health.
Using spatial analysis to demonstrate the heterogeneity of the cardiovascular drug-prescribing pattern in Taiwan
Authors: Cheng Ching-Lan , Chen Yi-Chi , Liu Tzu-Ming , Kao Yang Yea-Huei
Published: May 2011

Background

Geographic Information Systems (GIS) combined with spatial analytical methods could be helpful in examining patterns of drug use. Little attention has been paid to geographic variation of cardiovascular prescription use in Taiwan. The main objective was to use local spatial association statistics to test whether or not the cardiovascular medication-prescribing pattern is homogenous across 352 townships in Taiwan.

Methods

The statistical methods used were the global measures of Moran'sIand Local Indicators of Spatial Association (LISA). While Moran'sIprovides information on the overall spatial distribution of the data, LISA provides information on types of spatial association at the local level. LISA statistics can also be used to identify influential locations in spatial association analysis. The major classes of prescription cardiovascular drugs were taken from Taiwan's National Health Insurance Research Database (NHIRD), which has a coverage rate of over 97%. The dosage of each prescription was converted into defined daily doses to measure the consumption of each class of drugs. Data were analyzed with ArcGIS and GeoDa at the township level.

Results

The LISA statistics showed an unusual use of cardiovascular medications in the southern townships with high local variation. Patterns of drug use also showed more low-low spatial clusters (cold spots) than high-high spatial clusters (hot spots), and those low-low associations were clustered in the rural areas.

Conclusions

The cardiovascular drug prescribing patterns were heterogeneous across Taiwan. In particular, a clear pattern of north-south disparity exists. Such spatial clustering helps prioritize the target areas that require better education concerning drug use.
The effects of disruption of phosphoglucose isomerase gene on carbon utilisation and cellulase production in Trichoderma reesei Rut-C30
Authors: Carmen Limón M , Pakula Tiina , Saloheimo Markku , Penttilä Merja
Published: May 2011

Background

Cellulase and hemicellulase genes in the fungus Trichoderma reesei are repressed by glucose and induced by lactose. Regulation of the cellulase genes is mediated by the repressor CRE1 and the activator XYR1. T. reesei strain Rut-C30 is a hypercellulolytic mutant, obtained from the natural strain QM6a, that has a truncated version of the catabolite repressor gene, cre1. It has been previously shown that bacterial mutants lacking phosphoglucose isomerase (PGI) produce more nucleotide precursors and amino acids. PGI catalyzes the second step of glycolysis, the formation of fructose-6-P from glucose-6-P.

Results

We deleted the gene pgi1, encoding PGI, in the T. reesei strain Rut-C30 and we introduced the cre1 gene in a Δpgi1 mutant. Both Δpgi1 and cre1

+
Δpgi1 mutants showed a pellet-like and growth as well as morphological alterations compared with Rut-C30. None of the mutants grew in media with fructose, galactose, xylose, glycerol or lactose but they grew in media with glucose, with fructose and glucose, with galactose and fructose or with lactose and fructose. No growth was observed in media with xylose and glucose. On glucose, Δpgi1 and cre1

+
Δpgi1 mutants showed higher cellulase activity than Rut-C30 and QM6a, respectively. But in media with lactose, none of the mutants improved the production of the reference strains. The increase in the activity did not correlate with the expression of mRNA of the xylanase regulator gene, xyr1. Δpgi1 mutants were also affected in the extracellular β-galactosidase activity. Levels of mRNA of the glucose 6-phosphate dehydrogenase did not increase in Δpgi1 during growth on glucose.

Conclusions

The ability to grow in media with glucose as the sole carbon source indicated that Trichoderma Δpgi1 mutants were able to use the pentose phosphate pathway. But, they did not increase the expression of gpdh. Morphological characteristics were the result of the pgi1 deletion. Deletion of pgi1 in Rut-C30 increased cellulase production, but only under repressing conditions. This increase resulted partly from the deletion itself and partly from a genetic interaction with the cre1-1 mutation. The lower cellulase activity of these mutants in media with lactose could be attributed to a reduced ability to hydrolyse this sugar but not to an effect on the expression of xyr1.
Decreased expression of BRCA1 in SK-BR-3 cells is the result of aberrant activation of the GABP Beta promoter by an NRF-1-containing complex
Authors: Thompson Crista , MacDonald Gwen , Mueller Christopher R
Published: May 2011

Background

BRCA1 has recently been identified as a potential regulator of mammary stem/progenitor cell differentiation, and this function may explain the high prevalence of breast cancer in BRCA1 mutation carriers, as well as the downregulation of BRCA1 in a large proportion of sporadic breast cancers. That is, loss of BRCA1 function results in blocked differentiation with expansion of the mammary stem/progenitor cells. Because BRCA1 also maintains genomic integrity, its loss could produce a pool of genetically unstable stem/progenitor cells that are prime targets for further transforming events. Thus, elucidating the regulatory mechanisms of BRCA1 expression is important to our understanding of normal and malignant breast differentiation.

Results

Loss of BRCA1 expression in the ErbB2-amplified SK-BR-3 cell line was found to be the result of loss of activity of the ets transcription factor GABP, a previously characterized regulator of BRCA1 transcription. The expression of the non-DNA binding GABPβ subunit was shown to be deficient, while the DNA binding subunit, GABPα was rendered unstable by the absence of GABPβ. Deletion analysis of the GABPβ proximal promoter identified a potential NRF-1 binding site as being critical for expression. Supershift analysis, the binding of recombinant protein and chromatin immunoprecipitation confirmed the role of NRF-1 in regulating the expression of GABPβ. The siRNA knockdown of NRF-1 resulted in decreased GABPβ and BRCA1 expression in MCF-7 cells indicating that they form a transcriptional network. NRF-1 levels and activity did not differ between SK-BR-3 and MCF-7 cells, however the NRF-1 containing complex on the GABPβ promoter differed between the two lines and appears to be the result of altered coactivator binding.

Conclusions

Both NRF-1 and GABP have been linked to the regulation of nuclear-encoded mitochondrial proteins, and the results of this study suggest their expression is coordinated by NRF-1's activation of the GABPβ promoter. Their linkage to BRCA1, a potential breast stem cell regulator, implies a connection between the induction of mitochondrial metabolism and breast differentiation.
Understanding client satisfaction with a health insurance scheme in Nigeria: factors and enrollees experiences
Authors: Mohammed Shafiu , Sambo Mohammad N , Dong Hengjin
Published: May 2011

Background

Health insurance schemes have been widely introduced during this last decade in many African countries, which have strived for improvements in health service provision and the promotion of health care utilization. Client satisfaction with health service provision during the implementation of health insurance schemes has often been neglected since numerous activities take place concurrently. The satisfaction of enrollees and its influencing factors have been providing evidence which have assisted in policy and decision making. Our objective is to determine the enrollee's satisfaction with health service provision under a health insurance scheme and the factors which influence the satisfaction.

Methods

This retrospective, cross-sectional survey took place between May and September 2008. Two hundred and eighty (280) enrollees insured for more than one year in Zaria-Nigeria were recruited using two stage sampling. Enrollee's satisfaction was categorized into more satisfied and less satisfied based on positive responses obtained. Satisfaction, general knowledge and awareness of contribution were each aggregated and assessed as composite measure. Logistic regression analysis was used to analyze factors that influenced the satisfaction of enrollees.

Results

A high satisfaction rate with the health insurance scheme was observed (42.1%). Marital status (p < .05), general knowledge (p < .001) and awareness of contributions (p < .05) positively influenced clients' satisfaction. Length of employment, salary income, hospital visits and duration of enrolment slightly influenced satisfaction.

Conclusions

This study highlighted the potential effects of general health insurance knowledge and awareness of contributions by end-users (beneficiaries) of such new program on client satisfaction which have significant importance. The findings provided evidence which have assisted the amendment and re-prioritization of the medium term strategic plan of operations for the scheme. Future planning efforts could consider the client satisfaction and the factors which influenced it regularly.
Response to combination therapy of HCV 3a infected Pakistani patients and the role of NS5A protein
Authors: Ali Ijaz , Khan Sanaullah , Attaullah Sobia , Khan Shahid Niaz , Khan Jabbar , Siraj Sami , Iqbal Aqib , Swati Zahoor A , Idrees Muhammad
Published: May 2011

Background

Hepatitis C virus (HCV) genotype 3a is known to show comparatively better response to combination therapy than genotype 1 and 4. Mutations within NS5A gene of HCV have earlier been implicated with response to interferon (IFN) therapies in chronic HCV patients among various populations. As response to therapy are available in different populations because of the ethnic and viral factors and there was no study available on the phenomenon of resistivity to IFN.

Results

Chronic HCV 3a infected Pakistani patients were kept on IFN-α and ribavirin therapy for six months. NS5A gene of HCV was amplified and sequenced in the case of all the patients prior to therapy and the sequences were analysed for mutations. Out of the total 27 patients, 20 (74.07%) were observed with sustained virological response (SVR), 4 (14.81%) patients were non responder (NR) while 3 (11.11%) patients exhibited in end of treatment response (ETR). Three (3/20) (15%) SVR patients and two (2/3) ETR patients had mutations (ranging from I-V amino acids) within the NS5A ISDR regions. While the rest of the SVR patients (85%) and the NR had no mutations at ISDR region when compared with HCV K3a ISDR.

Conclusions

Mutations within the NS5A gene of HCV 3a genotype may not influence the outcome of combination therapy in Pakistani populations.
Exploring the metabolic network of the epidemic pathogen Burkholderia cenocepacia J2315 via genome-scale reconstruction
Authors: Fang Kechi , Zhao Hansheng , Sun Changyue , Lam Carolyn MC , Chang Suhua , Zhang Kunlin , Panda Gurudutta , Godinho Miguel , Martins dos Santos Vítor AP , Wang Jing
Published: May 2011

Background

Burkholderia cenocepacia is a threatening nosocomial epidemic pathogen in patients with cystic fibrosis (CF) or a compromised immune system. Its high level of antibiotic resistance is an increasing concern in treatments against its infection. Strain B. cenocepacia J2315 is the most infectious isolate from CF patients. There is a strong demand to reconstruct a genome-scale metabolic network of B. cenocepacia J2315 to systematically analyze its metabolic capabilities and its virulence traits, and to search for potential clinical therapy targets.

Results

We reconstructed the genome-scale metabolic network of B. cenocepacia J2315. An iterative reconstruction process led to the establishment of a robust model, i KF1028, which accounts for 1,028 genes, 859 internal reactions, and 834 metabolites. The model i KF1028 captures important metabolic capabilities of B. cenocepacia J2315 with a particular focus on the biosyntheses of key metabolic virulence factors to assist in understanding the mechanism of disease infection and identifying potential drug targets. The model was tested through BIOLOG assays. Based on the model, the genome annotation of B. cenocepacia J2315 was refined and 24 genes were properly re-annotated. Gene and enzyme essentiality were analyzed to provide further insights into the genome function and architecture. A total of 45 essential enzymes were identified as potential therapeutic targets.

Conclusions

As the first genome-scale metabolic network of B. cenocepacia J2315, i KF1028 allows a systematic study of the metabolic properties of B. cenocepacia and its key metabolic virulence factors affecting the CF community. The model can be used as a discovery tool to design novel drugs against diseases caused by this notorious pathogen.
Copy number polymorphisms and anticancer pharmacogenomics
Authors: Gamazon Eric R , Huang R Stephanie , Dolan M Eileen , Cox Nancy J
Published: May 2011

Background

Recent studies have investigated the contribution of copy number variants (CNVs) to disease susceptibility in a multitude of complex disorders, including systemic lupus erythematosus, Crohn's disease, and various neurodevelopmental disorders. Relatively few CNV studies, however, have been conducted on pharmacologic phenotypes even though these structural variants are likely to play an important role. We developed a genome-wide method to identify CNVs that contribute to heterogeneity in drug response, focusing on drugs that are widely used in anticancer treatment regimens.

Results

We conducted a comprehensive genome-wide study of CNVs from population-scale array-based and sequencing-based surveys by analyzing their effect on cellular sensitivity to platinating agents and topoisomerase II inhibitors. We identified extensive CNV regions associated with cellular sensitivity to functionally diverse chemotherapeutics, supporting the hypothesis that variation in copy number contributes to variation in drug response. Interestingly, although single nucleotide polymorphisms (SNPs) tag some of the CNVs associated with drug sensitivity, several of the most significant CNV-drug associations are independent of SNPs; consequently, they represent genetic variations that have not been previously interrogated by SNP studies of pharmacologic phenotypes.

Conclusions

Our findings demonstrate that pharmacogenomic studies may greatly benefit from the study of CNVs as expression quantitative trait loci, thus contributing broadly to our understanding of the complex traits genetics of CNVs. We also extend our PACdb resource, a database that makes available to the scientific community relationships between genetic variation, gene expression, and sensitivity to various drugs in cell-based models.
This issue of GEOPHYSICS
Authors: Grechka Vladimir
Published: May 2011

In this article, the Editor of Geophysics provides an overview of all technical articles in this issue of the journal.
Loss of keratins 8 and 18 leads to alterations in α6β4-integrin-mediated signalling and decreased neoplastic progression in an oral-tumour-derived cell line
Authors: Alam Hunain , Kundu Samrat T. , Dalal Sorab N. , Vaidya Milind M.
Published: May 2011

Keratins 8 and 18 (K8 and K18) are predominantly expressed in simple epithelial tissues and perform both mechanical and regulatory functions. Aberrant expression of K8 and K18 is associated with neoplastic progression and invasion in squamous cell carcinomas (SCCs). To understand the molecular basis by which K8 promotes neoplastic progression in oral SCC (OSCC), K8 expression was inhibited in AW13516 cells. The K8-knockdown clones showed a significant reduction in tumorigenic potential, which was accompanied by a reduction in cell motility, cell invasion, decreased fascin levels, alterations in the organization of the actin cytoskeleton and changes in cell shape. Furthermore, K8 knockdown led to a decrease in α6β4 integrin levels and α6β4-integrin-dependent signalling events, which have been reported to play an important role in neoplastic progression in epithelial tissues. Therefore, modulation of α6β4 integrin signalling might be one of the mechanisms by which K8 and K18 promote malignant transformation and/or progression in OSCCs.
Cadherins at cell-autonomous membrane contacts control macropinocytosis
Authors: Sabatini Peter J. B. , Zhang Ming , Silverman-Gavrila Rosalind V. , Bendeck Michelle P.
Published: May 2011

Cadherins aggregate and stabilize cell–cell junctions through interactions with adjacent cells. In addition, N-cadherin and E-cadherin concentrate at free edges or at the lamellipodia of migrating cells and are found within large vesicles called macropinosomes, which develop from membrane ruffles. The binding properties of cadherins have not previously been associated with the localization of cadherins at membrane ruffles; however, we report that the dorsal, ventral and lateral membrane contacts that occur as a result of the overlap of membrane ruffles aggregate N-cadherin, and that both N-cadherin and E-cadherin promote macropinosome closure and fluid-phase uptake in macropinosomes. These data reveal a previously unsuspected function for cadherin-mediated cell–cell adhesion molecules in the closure of cell-autonomous membrane contacts at membrane ruffles, resulting in macropinocytosis.
Interplay between N-WASP and CK2 optimizes clathrin-mediated endocytosis of EGFR
Authors: Galovic Magda , Xu Dalu , Areces Liliana Beatriz , van der Kammen Rob , Innocenti Metello
Published: May 2011

Clathrin-mediated endocytosis (CME) involves spatially and temporally restricted molecular dynamics, to which protein kinases and actin contribute. However, whether and how these two elements merge to properly execute CME remains unknown. Here, we show that neural Wiskott–Aldrich syndrome protein (N-WASP) and casein kinase 2 (CK2) form a complex and localize to clathrin-coated vesicles. N-WASP binds to and is phosphorylated by CK2, thereby reducing the kinase activity of CK2. By contrast, N-WASP-promoted actin polymerization is decreased upon both phosphorylation and binding of CK2. Knockdown of CK2 and N-WASP, either alone or in combination, causes a similar inhibition in the initial rate of CME of epidermal growth factor receptor (EGFR) and its accumulation at the plasma membrane. Increased levels of EGFR at the cell surface can only be efficiently rescued by reconstituting the N-WASP–CK2 complex with either wild-type or phosphorylation-mimicking N-WASP and wild-type CK2. Notably, perturbation of N-WASP–CK2 complex function showed that N-WASP controls the presence of F-actin at clathrin-coated structures. In summary, the N-WASP–CK2 complex integrates in a single circuit different activities contributing to CME.
From bouncy legs to poisoned arrows: elastic movements in invertebrates
Authors: Patek S. N. , Dudek D. M. , Rosario M. V.
Published: May 2011

Elastic mechanisms in the invertebrates are fantastically diverse, yet much of this diversity can be captured by examining just a few fundamental physical principles. Our goals for this commentary are threefold. First, we aim to synthesize and simplify the fundamental principles underlying elastic mechanisms and show how different configurations of basic building blocks can be used for different functions. Second, we compare single rapid movements and rhythmic movements across six invertebrate examples – ranging from poisonous cnidarians to high-jumping froghoppers – and identify remarkable functional properties arising from their underlying elastic systems. Finally, we look to the future of this field and find two prime areas for exciting new discoveries – the evolutionary dynamics of elastic mechanisms and biomimicry of invertebrate elastic materials and mechanics.
Experimentally reduced corticosterone release promotes early breeding in black-legged kittiwakes
Authors: Goutte Aurélie , Clément-Chastel Céline , Moe Børge , Bech Claus , Gabrielsen Geir Wing , Chastel Olivier
Published: May 2011

Breeding at the right time is important for successful reproduction. In birds, stressful environmental conditions are known to delay the timing of breeding but the underlying mechanisms are poorly understood. The stress hormone corticosterone appears to be a good candidate for mediating egg-laying date according to early environmental conditions and physiological state. By experimentally reducing the release of corticosterone in black-legged kittiwakes during the pre-laying period, we tested whether egg-laying date was mechanistically linked to corticosterone levels. Male and female kittiwakes were implanted with a low dose of exogenous corticosterone to inhibit endogenous corticosterone production. According to our predictions, the experimental reduction of corticosterone release was paralleled by a significant advancement of egg laying in females (around 4 days earlier). In addition, females with experimentally reduced corticosterone release gained mass during the pre-laying period compared with controls. Ultimately, the advancement of egg laying in females with experimentally reduced corticosterone levels was associated with an enhanced breeding success. This effect was strongly sex specific. In corticosterone-treated male kittiwakes, egg-laying date and reproductive success were not affected, but breeding probability was lower than in controls. This corticosterone treatment did not influence immediate clutch size, or return rate and breeding decision the following year. Our results support the hypothesis that corticosterone secretion during the pre-laying period mediates the timing of breeding in this long-lived seabird, possibly through the dynamics of energy reserves.
The influence of PKA treatment on the Ca2+ activation of force generation by trout cardiac muscle
Authors: Gillis Todd E. , Klaiman Jordan M.
Published: May 2011

β-Adrenergic stimulation of the mammalian heart increases heart rate, the strength of contraction as well as the kinetics of force generation and relaxation. These effects are due to the phosphorylation of select membrane and thin filament proteins by cAMP-activated protein kinase (PKA). At the level of the sarcomere, it is typically the phosphorylation of cardiac myosin binding protein C (cMyBP-C) and cardiac troponin I (cTnI) that is responsible for the change in the kinetics of contraction and relaxation. Trout cTnI (ScTnI) lacks two critical PKA targets within the N-terminus of the protein that, when phosphorylated in mammalian cTnI, cause a reduction in myofilament Ca2+ affinity. To determine what role the contractile element plays in the response of the trout heart to β-adrenergic stimulation, we characterized the influence of PKA treatment on the Ca2+ activation of skinned preparations dissected from ventricular trabeculae. In these experiments, isometric force generation and the rate of force development were measured over a range of Ca2+ concentrations. The results demonstrate that PKA treatment does not influence the Ca2+ sensitivity of force generation but it decreases maximum force generation by 25% and the rate of force re-development at maximal activation by 46%. Analysis of the trabeculae preparations for phosphoproteins revealed that PKA treatment phosphorylated myosin light chain 2 but not cTnI or cMyBP-C. These results indicate that the function of the trout cardiac contractile element is altered by PKA phosphorylation but in a manner different from that in mammalian heart.
Energetically optimal stride frequency in running: the effects of incline and decline
Authors: Snyder Kristine L. , Farley Claire T.
Published: May 2011

At a given running speed, humans strongly prefer to use a stride frequency near their ‘optimal’ stride frequency that minimizes metabolic cost. Although there is no definitive explanation for why an optimal stride frequency exists, elastic energy usage has been implicated. Because the possibility for elastic energy storage and return may be impaired on slopes, we investigated whether and how the optimal stride frequency changes during uphill and downhill running. Presuming a smaller role of elastic energy, we hypothesized that altering stride frequency would change metabolic cost less during uphill and downhill running than during level running. To test this hypothesis, we collected force and metabolic data as nine male subjects ran at 2.8 m s–1 on the level, 3 deg uphill and 3 deg downhill. Stride frequency was systematically varied above and below preferred stride frequency (PSF ±8% and ±15%). Ground reaction force data were used to calculate potential, kinetic and total mechanical energy, and to calculate the theoretical maximum possible and estimated actual elastic energy storage and return. Contrary to our hypothesis, we found that neither the overall relationship between metabolic cost and stride frequency nor the energetically optimal stride frequency changed substantially with slope. However, estimated actual elastic energy storage as a percentage of total positive power increased with increasing stride frequency on all slopes, indicating that muscle power decreases with increasing stride frequency. Combined with the increased cost of force production and internal work with increasing stride frequency, this leads to an intermediate optimal stride frequency and overall U-shaped curve.
Involvement of redox- and phosphorylation-dependent pathways in osmotic adaptation in sperm cells of euryhaline tilapia
Authors: Morita Masaya , Nakajima Ayako , Takemura Akihiro , Okuno Makoto
Published: May 2011

Sperm cells involved in fertilisation must tolerate hypo-osmotic and hyper-osmotic environments. Euryhaline tilapia (Oreochromis mossambicus) can acclimatise to and reproduce in freshwater and seawater because its sperm are able to adapt to these differing osmotic environments. In this study, we found that the dephosphorylation of sperm proteins in O. mossambicus correlated with the activation of flagellar motility when sperm were exposed to hypotonic or hypertonic conditions, and that differences in phosphorylation may reflect adaptations to a given osmotic environment. Of the sperm proteins that were dephosphorylated, the phosphorylation pattern of an 18 kDa protein, identified as the superoxide anion scavenger Cu/Zn superoxide dismutase (Cu/Zn SOD), was different in freshwater- and seawater-acclimatised tilapia sperm. Cu/Zn SOD was distributed from the sperm head to the flagellum. Additionally, differences were observed between freshwater and seawater tilapia in the nitration of tyrosine residues (which might be mediated by SOD) in sperm flagellar proteins in response to osmotic shock. These results demonstrate that reactive-oxygen-species-dependent mechanisms contribute to both osmotic tolerance and the activation of flagellar motility.
Circumferential spicule growth by pericellular silica deposition in the hexactinellid sponge Monorhaphis chuni
Authors: Wang Xiaohong , Wiens Matthias , Schröder Heinz C. , Jochum Klaus P. , Schloßmacher Ute , Götz Hermann , Duschner Heinz , Müller Werner E. G.
Published: May 2011

The giant basal spicule of the hexactinellid sponge Monorhaphis chuni represents the longest natural siliceous structure on Earth. This spicule is composed of concentrically arranged lamellae that are approximately 10 μm thick. In the present study, we investigated the formation of outer lamellae on a cellular level using microscopic and spectroscopic techniques. It is shown that the formation of an outermost lamella begins with the association of cell clusters with the surface of the thickening and/or growing spicule. The cells release silica for controlled formation of a lamella. The pericellular (silica) material fuses to a delimited and textured layer of silica with depressions approximately 20–30 μm in diameter. The newly formed layer initially displays 40 μm wide, well-structured banded ribbons and only attains its plain surface in a final step. The chemical composition in the depressions was studied using energy dispersive X-ray spectroscopy and by staining with Texas Red. The data suggest that those depressions are the nests for the silica-forming cells and that silica formation starts with a direct association of silica-forming cells with the outer surface of the spicule, where they remain and initiate the development of the next lamellae.
Extraction of Cu(II) Based on Tube Radial Distribution of Ternary Mixed Carrier Solvent in Microchannels
Authors: Jinno Naoya , Hashimoto Masahiko , Tsukagoshi Kazuhiko
Published: May 2011

The extraction of Cu(II) as a model was examined based on tube radial distribution of a ternary mixed carrier solution of water–acetonitrile–ethyl acetate (2:3:1 volume ratio) in a microchannel in a microchip. A microchip incorporating microchannels in which one wide channel was separated into three narrow channels was designed and manufactured. When the ternary carrier solution was fed into the wide channel under laminar flow conditions, the carrier solvent molecules were radially distributed in the channel, generating inner (organic solvent-rich major) and outer (water-rich minor) phases. The Cu(II) dissolved in the carrier solution was distributed between the inner and outer phases due to its hydrophilic nature and then collected through the three narrow channels. The concentrations of Cu(II) in the two side narrow channels were greater than that in the center narrow channel through extraction.
Synthesis and Characterization of a Novel Ruthenium Complex Bearing a Curcumin Derivative Ligand and Its Application to Dye-sensitized Solar Cells
Authors: Ozawa Hironobu , Kawaguchi Hiroki , Okuyama Yu , Arakawa Hironori
Published: May 2011

A novel ruthenium complex bearing a bisdemethoxycurcumin, which is a natural dye exhibiting a strong absorption around 410 nm, as a ligand has been synthesized and characterized for application to dye-sensitized solar cells (DSCs). The DSC with this sensitizer showed about 55% incident photon-to-current conversion efficiency at the wavelength region between 450 and 600 nm, and 5.76% conversion efficiency under AM 1.5 (100 mW cm−2) irradiation.