bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenetic footprint of the plant clock system in angiosperms: evolutionary processes of Pseudo-Response Regulators
Authors: Takata Naoki , Saito Shigeru , Saito Claire Tanaka , Uemura Matsuo 
Published: May 2010

AbstractBackgroundPlant circadian clocks regulate many photoperiodic and diurnal responses that are conserved among plant species. The plant circadian clock system has been uncovered in the model plant,Arabidopsis thaliana, using genetics and systems biology approaches. However, it is still not clear how the clock system had been organized in the evolutionary history of plants. We recently revealed the molecular phylogeny ofLHY/CCA1genes, one of the essential components of the clock system. The aims of this study are to reconstruct the phylogenetic relationships of angiosperm clock-associatedPRRgenes, the partner of theLHY/CCA1genes, and to clarify the evolutionary history of the plant clock system in angiosperm lineages.ResultsIn the present study, to investigate the molecular phylogeny ofPRRgenes, we performed two approaches: reconstruction of phylogenetic trees and examination of syntenic relationships. Phylogenetic analyses revealed thatPRRgenes had diverged into three clades prior to the speciation of monocots and eudicots. Furthermore, copy numbers ofPRRgenes have been independently increased in monocots and eudicots as a result of ancient chromosomal duplication events.ConclusionsBased on the molecular phylogenies of bothPRRgenes andLHY/CCA1genes, we inferred the evolutionary process of the plant clock system in angiosperms. This scenario provides evolutionary information that a common ancestor of monocots and eudicots had retained the basic components required for reconstructing a clock system and that the plant circadian clock may have become a more elaborate mechanism after the speciation of monocots and eudicots because of the gene expansion that resulted from polyploidy events.
A toolkit for rapid gene mapping in the nematode Caenorhabditis briggsae
Authors: Koboldt Daniel C , Staisch Julia , Thillainathan Bavithra , Haines Karen , Baird Scott E , Chamberlin Helen M , Haag Eric S , Miller Raymond D , Gupta Bhagwati P 
Published: May 2010

Abstract

Background
The nematode C. briggsae serves as a useful model organism for comparative analysis of developmental and behavioral processes. The amenability of C. briggsae to genetic manipulations and the availability of its genome sequence have prompted researchers to study evolutionary changes in gene function and signaling pathways. These studies rely on the availability of forward genetic tools such as mutants and mapping markers.

Results
We have computationally identified more than 30,000 polymorphisms (SNPs and indels) in C. briggsae strains AF16 and HK104. These include 1,363 SNPs that change restriction enzyme recognition sites (snip-SNPs) and 638 indels that range between 7 bp and 2 kb. We established bulk segregant and single animal-based PCR assay conditions and used these to test 107 polymorphisms. A total of 75 polymorphisms, consisting of 14 snip-SNPs and 61 indels, were experimentally confirmed with an overall success rate of 83%. The utility of polymorphisms in genetic studies was demonstrated by successful mapping of 12 mutations, including 5 that were localized to sub-chromosomal regions. Our mapping experiments have also revealed one case of a misassembled contig on chromosome 3.

Conclusions
We report a comprehensive set of polymorphisms in C. briggsae wild-type strains and demonstrate their use in mapping mutations. We also show that molecular markers can be useful tools to improve the C. briggsae genome sequence assembly. Our polymorphism resource promises to accelerate genetic and functional studies of C. briggsae genes.
Epigenetic chromatin modifiers in barley: IV. The study of barley Polycomb group (PcG) genes during seed development and in response to external ABA
Authors: Kapazoglou Aliki , Tondelli Alessandro , Papaefthimiou Dimitra , Ampatzidou Helen , Francia Enrico , Stanca Michele A , Bladenopoulos Konstantinos , Tsaftaris Athanasios S 
Published: May 2010

Abstract

Background
Epigenetic phenomena have been associated with the regulation of active and silent chromatin states achieved by modifications of chromatin structure through DNA methylation, and histone post-translational modifications. The latter is accomplished, in part, through the action of PcG (Polycomb group) protein complexes which methylate nucleosomal histone tails at specific sites, ultimately leading to chromatin compaction and gene silencing. Different PcG complex variants operating during different developmental stages have been described in plants. In particular, the so-called FIE/MEA/FIS2 complex governs the expression of genes important in embryo and endosperm development in Arabidopsis. In our effort to understand the epigenetic mechanisms regulating seed development in barley (Hordeum vulgare), an agronomically important monocot plant cultivated for its endosperm, we set out to characterize the genes encoding barley PcG proteins.

Results
Four barley PcG gene homologues, named HvFIE, HvE(Z), HvSu(z)12a, and HvSu(z)12b were identified and structurally and phylogenetically characterized. The corresponding genes HvFIE, HvE(Z), HvSu(z)12a, and HvSu(z)12b were mapped onto barley chromosomes 7H, 4H, 2H and 5H, respectively. Expression analysis of the PcG genes revealed significant differences in gene expression among tissues and seed developmental stages and between barley cultivars with varying seed size. Furthermore, HvFIE and HvE(Z) gene expression was responsive to the abiotic stress-related hormone abscisic acid (ABA) known to be involved in seed maturation, dormancy and germination.

Conclusion
This study reports the first characterization of the PcG homologues, HvFIE, HvE(Z), HvSu(z)12a and HvSu(z)12b in barley. All genes co-localized with known chromosomal regions responsible for malting quality related traits, suggesting that they might be used for developing molecular markers to be applied in marker assisted selection. The PcG differential expression pattern in different tissues and seed developmental stages as well as in two barley cultivars with different seed size is suggestive of a role for these genes in barley seed development. HvFIE and HvE(Z) were also found to be induced by the plant hormone ABA implying an association with ABA-mediated processes during seed development, germination and stress response.
Large screening of CA-MRSA among Staphylococcus aureus colonizing healthy young children living in two areas (urban and rural) of Portugal
Authors: Tavares Débora A , Sá-Leão Raquel , Miragaia Maria , de Lencastre Hermínia 
Published: May 2010

Abstract

Background
The incidence of pediatric infections due to community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA), including children with no identifiable risk factors, has increased worldwide in the last decade. This suggests that healthy children may constitute a reservoir of MRSA in the community. In this study, nested within a larger one on nasopharyngeal ecology, we aimed to: (i) evaluate the prevalence of MRSA colonizing young children in Portugal; and (ii) compare results with those obtained in a study conducted a decade ago, when this prevalence was <0.5%.

Methods
In the years 2006, 2007, and 2009, nasopharyngeal samples were obtained from 2,100 children aged up to 6 years attending day-care centers. S. aureus were isolated by routine procedures and strains were tested for susceptibility against a panel of 12 antimicrobial agents. MRSA isolates were further characterized by SmaI-PFGE profiling, MLST, spa typing, SCCmec typing, and presence of virulence factors.

Results
Seventeen percent of the children carried S. aureus. Among the 365 isolates, non-susceptibility rates were 88% to penicillin, 14% to erythromycin, 6% to clindamycin, 2% to tetracycline, and <1% to oxacillin, rifampicin, ciprofloxacin, and SXT. Three MRSA strains were isolated. These had properties of CA-MRSA, such as low-level resistance to oxacillin and limited resistance to non-beta-lactams. Two CA-MRSA were related to USA700 (ST72-IV): one was ST72-IVc, spa type t148; the other was ST939-IVa (ST939 is a single locus variant (SLV) of ST72), spa type t324. The third strain was related to USA300 (ST8-IV) being characterized by ST931 (SLV of ST8)-VI, spa type t008. The three MRSA strains were PVL-negative, but all carried LukE-LukD leukocidin, hemolysins gamma, gamma variant and beta, and staphylococcal enterotoxin sel.

Conclusions
Our results, based on analysis of S. aureus isolated from nasopharyngeal samples, suggest that in Portugal the prevalence of CA-MRSA carriage in healthy young children remains extremely low favoring the exclusion of this group as a reservoir of such isolates.
POLG1 p.R722H mutation associated with multiple mtDNA deletions and a neurological phenotype
Authors: Komulainen Tuomas , Hinttala Reetta , Kärppä Mikko , Pajunen Leila , Finnilä Saara , Tuominen Hannu , Rantala Heikki , Hassinen Ilmo , Majamaa Kari , Uusimaa Johanna 
Published: May 2010

Abstract

Background
The c.2447G>A (p.R722H) mutation in the gene POLG1 of the catalytic subunit of human mitochondrial polymerase gamma has been previously found in a few occasions but its pathogenicity has remained uncertain. We set out to ascertain its contribution to neuromuscular disease.

Methods
Probands from two families with probable mitochondrial disease were examined clinically, muscle and buccal epithelial DNA were analyzed for mtDNA deletions, and the POLG1, POLG2, ANT1 and Twinkle genes were sequenced.

Results
An adult proband presented with progressive external ophthalmoplegia, sensorineural hearing impairment, diabetes mellitus, dysphagia, a limb myopathy and dementia. Brain MRI showed central and cortical atrophy, and 18F-deoxyglucose PET revealed reduced glucose uptake. Histochemical analysis of muscle disclosed ragged red fibers and cytochrome c oxidase-negative fibers. Electron microscopy showed subsarcolemmal aggregates of morphologically normal mitochondria. Multiple mtDNA deletions were found in the muscle, and sequencing of the POLG1 gene revealed a homozygous c.2447G>A (p.R722H) mutation. His two siblings were also homozygous with respect to the p.R722H mutation and presented with dementia and sensorineural hearing impairment. In another family the p.R722H mutation was found as compound heterozygosity with the common p.W748S mutation in two siblings with mental retardation, ptosis, epilepsy and psychiatric symptoms. The estimated carrier frequency of the p.R722H mutation was 1:135 in the Finnish population. No mutations in POLG2, ANT1 and Twinkle genes were found. Analysis of the POLG1 sequence by homology modeling supported the notion that the p.R722H mutation is pathogenic.

Conclusions
The recessive c.2447G>A (p.R722H) mutation in the linker region of the POLG1 gene is pathogenic for multiple mtDNA deletions in muscle and is associated with a late-onset neurological phenotype as a homozygous state. The onset of the disease can be earlier in compound heterozygotes.
Increased concentration of two different advanced glycation end-products detected by enzyme immunoassays with new monoclonal antibodies in sera of patients with rheumatoid arthritis
Authors: Vytášek Richard , Šedová Liliana , Vilím Vladimír 
Published: May 2010

AbstractBackgroundLevels of pentosidine (representative of advanced glycation end-products) in sera of patients with rheumatoid arthritis are increased when compared with sera of other diagnoses or healthy controls. These levels have been reported to correlate with clinical indices of rheumatoid arthritis activity and with laboratory markers of inflammation. The purpose of this study was to find out if these findings pertain to other advanced glycation end-products.MethodsWe have developed two immunoassays based on new monoclonal antibodies to advanced glycation end-products. Antibody 103-E3 reacts with an unidentified antigen, formed in the reaction of proteins with ribose, while antibody 8-C1 responds to Nε-(carboxyethyl)lysine. We have used these monoclonal antibodies to measure levels of advanced glycation end-products in sera of patients with rheumatoid arthritis, systemic lupus erythematosus, osteoarthritis, and healthy controls. We calculated the correlations between advanced glycation end-product levels in rheumatoid arthritis sera and the Disease Activity Score 28 (DAS28), age, disease duration, CRP, anti-CCP, rheumatoid factor and treatment with corticosteroids, respectively.ResultsLevels of both glycation products were significantly higher in sera of patients with rheumatoid arthritis when compared with sera of patients with systemic lupus erythematosus, osteoarthritis, or the healthy controls. Neither the level of Nε-(carboxyethyl)lysine nor the level of the 103-E3 antigen in rheumatoid arthritis sera correlated with the DAS28-scored rheumatoid arthritis activity. The levels of both antigens in rheumatoid arthritis sera did not correlate with age, gender, corticosteroid treatment, or levels of CRP, anti-CCP antibodies, and rheumatoid factor in sera.ConclusionsWe report highly specific increases in the levels of two advanced glycation end-products in sera of patients with rheumatoid arthritis. This increase could be explained neither by rheumatoid arthritis activity nor by inflammation. We propose a working hypothesis that presumes the existence of a link between advanced glycation end-product formation and induction of autoimmunity.
Social determinants of prescribed and non-prescribed medicine use
Authors: Daban Ferran , Pasarín M Isabel , Rodríguez-Sanz Maica , García-Altés Anna , Villalbí Joan R , Zara Corinne , Borrell Carme 
Published: May 2010

AbstractBackgroundThe aim of the present study was to describe the use of prescribed and non prescribed medicines in a non-institutionalised population older than 15 years of an urban area during the year 2000, in terms of age and gender, social class, employment status and type of Primary Health Care.MethodsCross-sectional study. Information came from the 2000 Barcelona Health Interview Survey. The indicators used were the prevalence of use of prescribed and non-prescribed medicines in the two weeks prior to the interview. Descriptive analyses, bivariate and multivariate logistic regression analyses were carried out.ResultsMore women than men took medicines (75.8%vs. 60% respectively). The prevalence of use of prescribed medicines increased with age while the prevalence of non-prescribed use decreased. These age differences are smaller among those with poor perceived health. In terms of social class, a higher percentage of men with good health in the more advantaged classes took non-prescribed medicines compared with disadvantaged classes (38.7% vs 31.8%). In contrast, among the group with poor health, more people from the more advantaged classes took prescribed medicines, compared with disadvantaged classes (51.4% vs 33.3%). A higher proportion of people who were either retired, unemployed or students, with good health, used prescribed medicines.ConclusionThis study shows that beside health needs, there are social determinants affecting medicine consumption in the city of Barcelona.
Differential chemosensitization of P-glycoprotein overexpressing K562/Adr cells by withaferin A and Siamois polyphenols
Authors: Suttana Wipob , Mankhetkorn Samlee , Poompimon Wilart , Palagani Ajay , Zhokhov Sergey , Gerlo Sarah , Haegeman Guy , Berghe Wim Vanden 
Published: May 2010

Abstract

Background
Multidrug resistance (MDR) is a major obstacle in cancer treatment and is often the result of overexpression of the drug efflux protein, P-glycoprotein (P-gp), as a consequence of hyperactivation of NFκB, AP1 and Nrf2 transcription factors. In addition to effluxing chemotherapeutic drugs, P-gp also plays a specific role in blocking caspase-dependent apoptotic pathways. One feature that cytotoxic treatments of cancer have in common is activation of the transcription factor NFκB, which regulates inflammation, cell survival and P-gp expression and suppresses the apoptotic potential of chemotherapeutic agents. As such, NFκB inhibitors may promote apoptosis in cancer cells and could be used to overcome resistance to chemotherapeutic agents.

Results
Although the natural withanolide withaferin A and polyphenol quercetin, show comparable inhibition of NFκB target genes (involved in inflammation, angiogenesis, cell cycle, metastasis, anti-apoptosis and multidrug resistance) in doxorubicin-sensitive K562 and -resistant K562/Adr cells, only withaferin A can overcome attenuated caspase activation and apoptosis in K562/Adr cells, whereas quercetin-dependent caspase activation and apoptosis is delayed only. Interestingly, although withaferin A and quercetin treatments both decrease intracellular protein levels of Bcl2, Bim and P-Bad, only withaferin A decreases protein levels of cytoskeletal tubulin, concomitantly with potent PARP cleavage, caspase 3 activation and apoptosis, at least in part via a direct thiol oxidation mechanism.

Conclusions
This demonstrates that different classes of natural NFκB inhibitors can show different chemosensitizing effects in P-gp overexpressing cancer cells with impaired caspase activation and attenuated apoptosis.
Use of cracked maize as a carrier for NDV4 vaccine in experimental vaccination of chickens
Authors: Olabode Atanda O , Ndako James A , Echeonwu Georgebest ON , Nwankiti Obinna O , Chukwuedo Anthony A 
Published: May 2010

Abstract
The suitability of V4 vaccine coated on cracked local grain (maize) and its husks and used for oral vaccination of chickens was assessed. Seventy-two (72) birds aged three (3) weeks and above were divided into six groups of twelve (12) birds per group. The birds were bled to determine their prevaccination HI antibody status while five different samples of cracked maize were coated with the V4 vaccine and fed to the chickens orally in each of the groups. All birds in the group including the controls were bled at 7, 14 and 21 days post vaccination to determine the presence and level of antibody response in each of the groups. Results obtained showed that prevaccination haemagglutination inhibition (HI) titre was less than two (log2) in 18% of the birds used in this experiment, however 14% of the birds had an HI titre of ≤ 4. The post vaccination antibody titre showed that birds vaccinated with vaccine coated maize gave a post vaccination HI antibody titre of between Log2(6-8). when the coated maize samples were soaked in water at room temperature and assessed after 24 hours, the treated maize parts gave >6.3 log10 EID50 and above while the untreated parts gave < 3.0 log10 EID50. The experiment showed that whole maize and husks, which were not treated, may contain agents which are virus inhibitory. Form this research the treated maize which was soaked and washed gave a higher geometric mean titre, hence tends to be good carriers of the virus (vaccine). It is therefore concluded from this work that processed cracked maize could be a good carrier of NDV4 vaccine. It is hereby recommended that only treated maize could be used as carrier for the V4 vaccine.
Genomics and proteomics approaches to the study of cancer-stroma interactions
Authors: Rodrigues-Lisoni Flávia C , Peitl Paulo , Vidotto Alessandra , Polachini Giovana M , Maniglia José V , Carmona-Raphe Juliana , Cunha Bianca R , Henrique Tiago , Souza Caique F , Teixeira Rodrigo AP , Fukuyama Erica E , Michaluart Pedro , de Carvalho Marcos B , Oliani Sonia M ,   Head and Neck Genome Project GENCAPO, Tajara Eloiza H 
Published: May 2010

Abstract

Background
The development and progression of cancer depend on its genetic characteristics as well as on the interactions with its microenvironment. Understanding these interactions may contribute to diagnostic and prognostic evaluations and to the development of new cancer therapies. Aiming to investigate potential mechanisms by which the tumor microenvironment might contribute to a cancer phenotype, we evaluated soluble paracrine factors produced by stromal and neoplastic cells which may influence proliferation and gene and protein expression.

Methods
The study was carried out on the epithelial cancer cell line (Hep-2) and fibroblasts isolated from a primary oral cancer. We combined a conditioned-medium technique with subtraction hybridization approach, quantitative PCR and proteomics, in order to evaluate gene and protein expression influenced by soluble paracrine factors produced by stromal and neoplastic cells.

Results
We observed that conditioned medium from fibroblast cultures (FCM) inhibited proliferation and induced apoptosis in Hep-2 cells. In neoplastic cells, 41 genes and 5 proteins exhibited changes in expression levels in response to FCM and, in fibroblasts, 17 genes and 2 proteins showed down-regulation in response to conditioned medium from Hep-2 cells (HCM). Nine genes were selected and the expression results of 6 down-regulated genes (ARID4A, CALR, GNB2L1, RNF10, SQSTM1, USP9X) were validated by real time PCR.

Conclusions
A significant and common denominator in the results was the potential induction of signaling changes associated with immune or inflammatory response in the absence of a specific protein.
Estrogen Alone in Postmenopausal Women and Breast Cancer Detection by Means of Mammography and Breast Biopsy
Authors: Chlebowski Rowan T. , Anderson Garnet , Manson JoAnn E. , Pettinger Mary , Yasmeen Shagufta , Lane Dorothy , Langer Robert D. , Hubbell F. Allan , McTiernan Anne , Hendrix Susan , Schenken Robert , Stefanick Marcia L. 
Published: May 2010

PurposeAs the influence of estrogen alone on breast cancer detection is not established, we examined this issue in the Women's Health Initiative trial, which randomly assigned 10,739 postmenopausal women with prior hysterectomy to conjugated equine estrogen (CEE; 0.625 mg/d) or placebo.MethodsScreening mammography and breast exams were performed at baseline and annually. Breast biopsies were based on clinical findings. Effects of CEE alone on breast cancer detection were determined by using receiver operating characteristic (ROC) analyses of mammogram performance.ResultsAfter a 7.1-year mean follow-up, fewer invasive breast cancers were diagnosed in the CEE than in the placebo group, but the difference was not statistically significant. Use of CEE alone increased mammograms with short-interval follow-up recommendations (cumulative, 39.2% v 29.6.3%; P < .001) but not abnormal mammograms (ie, those suggestive of or highly suggestive of malignancy; cumulative, 7.3% v 7.0%; P = .41). Breast biopsies were more frequent in the CEE group (cumulative, 12.5% v 10.7%; P = .004) and less commonly diagnosed as cancer (8.9% v 15.8%, respectively, with positive biopsies; P = .04). Mammographic breast cancer detection in the CEE group was significantly compromised only in the early years of use.ConclusionCEE alone use for 5 years results in approximately one in 11 and one in 50 women having otherwise avoidable mammograms with short-interval follow-up recommendations or breast biopsies, respectively. Although the breast biopsies on CEE were less commonly diagnosed as cancer, breast cancer detection was not substantially compromised. These findings differ from estrogen-plus-progestin use, for which significantly increased abnormal mammograms and a compromise in breast cancer detection are seen.